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  1. Fossil Gulch Wind Park | Open Energy Information

    Open Energy Info (EERE)

    Gulch Wind Park Jump to: navigation, search Name Fossil Gulch Wind Park Facility Fossil Gulch Wind Park Sector Wind energy Facility Type Commercial Scale Wind Facility Status In...

  2. DOE - Office of Legacy Management -- Estes Gulch Disposal Cell...

    Office of Legacy Management (LM)

    Estes Gulch Disposal Cell - 010 FUSRAP Considered Sites Site: Estes Gulch Disposal Cell (010) Designated Name: Alternate Name: Location: Evaluation Year: Site Operations: Site ...

  3. hare-98.pdf

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Diurnal Variability of Turbulent Fluxes in the Equatorial Pacific J. E. Hare Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder, Colorado C. W. Fairall NOAA-Environmental Technology Laboratory Boulder, Colorado Introduction During March and April of 1996, scientists from 13 national research institutions participated in the Combined Sensor Program (CSP) experiment. This program is a collaborative effort of the U.S. Department of Energy (DOE) and the

  4. HARE: Final Report

    SciTech Connect (OSTI)

    Mckie, Jim

    2012-01-09

    This report documents the results of work done over a 6 year period under the FAST-OS programs. The first effort was called Right-Weight Kernels, (RWK) and was concerned with improving measurements of OS noise so it could be treated quantitatively; and evaluating the use of two operating systems, Linux and Plan 9, on HPC systems and determining how these operating systems needed to be extended or changed for HPC, while still retaining their general-purpose nature. The second program, HARE, explored the creation of alternative runtime models, building on RWK. All of the HARE work was done on Plan 9. The HARE researchers were mindful of the very good Linux and LWK work being done at other labs and saw no need to recreate it. Even given this limited funding, the two efforts had outsized impact: _ Helped Cray decide to use Linux, instead of a custom kernel, and provided the tools needed to make Linux perform well _ Created a successor operating system to Plan 9, NIX, which has been taken in by Bell Labs for further development _ Created a standard system measurement tool, Fixed Time Quantum or FTQ, which is widely used for measuring operating systems impact on applications _ Spurred the use of the 9p protocol in several organizations, including IBM _ Built software in use at many companies, including IBM, Cray, and Google _ Spurred the creation of alternative runtimes for use on HPC systems _ Demonstrated that, with proper modifications, a general purpose operating systems can provide communications up to 3 times as effective as user-level libraries Open source was a key part of this work. The code developed for this project is in wide use and available at many places. The core Blue Gene code is available at https://bitbucket.org/ericvh/hare. We describe details of these impacts in the following sections. The rest of this report is organized as follows: First, we describe commercial impact; next, we describe the FTQ benchmark and its impact in more detail; operating

  5. DOE - Office of Legacy Management -- Estes Gulch Disposal Cell - 010

    Office of Legacy Management (LM)

    Estes Gulch Disposal Cell - 010 FUSRAP Considered Sites Site: Estes Gulch Disposal Cell (010) Remediated; managed by DOE LM. More information at http://www.lm.doe.gov/Rifle/Disposal/Sites.aspx Designated Name: Not Designated under FUSRAP Alternate Name: Rifle, CO, Disposal Site Location: Rifle, Colorado Evaluation Year: Not considered for FUSRAP - in another program Site Operations: Uranium mill tailings disposal Site Disposition: Remediated under UMTRCA Title I Radioactive Materials Handled:

  6. AmeriFlux US-Wkg Walnut Gulch Kendall Grasslands

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Scott, Russell [United States Department of Agriculture

    2016-01-01

    This is the AmeriFlux version of the carbon flux data for the site US-Wkg Walnut Gulch Kendall Grasslands. Site Description - This site is located in a small, intensively-studied, experimental watershed within USDA-ARS's Walnut Gulch Experimental Watershed. Eddy covariance measurements of energy, water and CO2 fluxes began in the spring of 2004, though meteorological (including Bowen ratio) and hydrological measurements are available much further back.

  7. Floodplain and Wetlands Assessment for Construction of a Second Full Service Access Road over Lena Gulch

    Broader source: Energy.gov [DOE]

    Floodplain and Wetlands Assessment for Construction of a Second Full Service Access Road over Lena Gulch from South Golden Road to the National Renewable Energy Laboratory’s South Table Mountain Complex, Golden, Colorado.

  8. Geologic map and coal resources of the Easton Gulch Quadrangle, Moffat County, Colorado

    SciTech Connect (OSTI)

    Reheis, M.C.

    1981-01-01

    This map of the Easton Gulch Quadrangle, Moffat County, Colorado is color coded to show the location of different age geologic formations. Various thickness coal bed are indicated as are abandoned coal mines or prospects, US Geologic Survey (USGS) test holes, abandoned oil and gas test holes, and USGS Mesozoic fossil localities. Various depth coal beds and other types of geologic structures are indicated on the cross-section geologic map. (BLM)

  9. Preliminary assessment report for Waiawa Gulch, Installation 15080, Pearl City, Oahu, Hawaii. Installation Restoration Program

    SciTech Connect (OSTI)

    Not Available

    1993-08-01

    This report presents the results of the preliminary assessment (PA) conducted by Argonne National Laboratory at the Hawaii Army National Guard (HIARNG) property near Pearl City, Oahu, Hawaii. Preliminary assessments of federal facilities are being conducted to compile the information necessary for completing preremedial activities and to provide a basis for establishing corrective actions in response to releases of hazardous substances. The principal objective of the PA is to characterize the site accurately and determine the need for further action by examining site activities, quantities of hazardous substances present, and potential pathways by which contamination could affect public health and the environment. This PA satisfies, for the Waiawa Gulch property, phase I of the Department of Defense Installation Restoration Program (IRP).

  10. Environmental assessment for the granting of US Navy easements near Pearl Harbor and Waikele Gulch Oahu, Hawaii to Hawaiian Electric Company, Inc. Final report

    SciTech Connect (OSTI)

    Luersen, P.; Wiley, M.; Hart, J.; Kanehiro, C.; Soloway, M.

    1994-09-23

    This document was prepared pursuant to the National Environmental Policy Act (NEPA: and Navy regulations (OPNAVINST 5090.1B)). The document addresses environmental impacts from the proposed granting of three easements to the Hawaiian Electric Company, Inc. (HECO) for the use of Navy property near Waikele Gulch, Pearl City and the Waiau Power Plant. HECO`s proposed Waiau-CIP, Part 2, Project requires installation, operation, and maintenance of steel transmission line poles and associated equipment on three Navy parcels crossed by the 7.8 mile project. Health risks from exposure to the electric and magnetic fields of 138-kV transmission lines are discussed.

  11. Wild Rose Geothermal Area | Open Energy Information

    Open Energy Info (EERE)

    Wild Rose Geothermal Area Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Wild Rose Geothermal Area Contents 1 Area Overview 2 History and Infrastructure 3 Regulatory...

  12. WILD PIG ATTACKS ON HUMANS

    SciTech Connect (OSTI)

    Mayer, J.

    2013-04-12

    Attacks on humans by wild pigs (Sus scrofa) have been documented since ancient times. However, studies characterizing these incidents are lacking. In an effort to better understand this phenomenon, information was collected from 412 wild pig attacks on humans. Similar to studies of large predator attacks on humans, data came from a variety of sources. The various attacks compiled occurred in seven zoogeographic realms. Most attacks occurred within the species native range, and specifically in rural areas. The occurrence was highest during the winter months and daylight hours. Most happened under non-hunting circumstances and appeared to be unprovoked. Wounded animals were the chief cause of these attacks in hunting situations. The animals involved were typically solitary, male and large in size. The fate of the wild pigs involved in these attacks varied depending upon the circumstances, however, most escaped uninjured. Most human victims were adult males traveling on foot and alone. The most frequent outcome for these victims was physical contact/mauling. The severity of resulting injuries ranged from minor to fatal. Most of the mauled victims had injuries to only one part of their bodies, with legs/feet being the most frequent body part injured. Injuries were primarily in the form of lacerations and punctures. Fatalities were typically due to blood loss. In some cases, serious infections or toxemia resulted from the injuries. Other species (i.e., pets and livestock) were also accompanying some of the humans during these attacks. The fates of these animals varied from escaping uninjured to being killed. Frequency data on both non-hunting and hunting incidents of wild pig attacks on humans at the Savannah River Site, South Carolina, showed quantitatively that such incidents are rare.

  13. NREL: Wind-Wildlife Impacts Literature Database (WILD) Home Page

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NREL - National Renewable Energy Laboratory Wind-Wildlife Impacts Literature Database (WILD) Wind Research WILD WILD Browse By Reset All Geography Africa (45) Apply Africa filter...

  14. Hog wild | Y-12 National Security Complex

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Hog wild Hog wild Posted: May 7, 2014 - 5:28pm | Y-12 Report | Volume 10, Issue 2 | 2014 Tennessee inventor Jake Gish, winner of the third annual Y-12 Innovation Competition, has it out for feral hogs, and with good reason. Originally found across much of Europe and Asia, the beasts, which are the size of small bears, have wreaked havoc on humans since at least the Middle Ages. The wild boars have since expanded their territory and in the past few decades have become increasingly prevalent - and

  15. Interagency Wild and Scenic Rivers Coordinating Council's WSRA...

    Open Energy Info (EERE)

    to use the flowcharts created by the Interagency Wild and Scenic Rivers Coordinating Council. Author The Interagency Wild and Scenic Rivers Coordinating Council Published The...

  16. Wild Horse Wind Power Project | Open Energy Information

    Open Energy Info (EERE)

    Wind Power Project Jump to: navigation, search Name Wild Horse Wind Power Project Facility Wild Horse Wind Power Project Sector Wind energy Facility Type Commercial Scale Wind...

  17. Chemical analysis of Wild-2 samples returned by Stardust (Conference...

    Office of Scientific and Technical Information (OSTI)

    Conference: Chemical analysis of Wild-2 samples returned by Stardust Citation Details In-Document Search Title: Chemical analysis of Wild-2 samples returned by Stardust Authors: ...

  18. Wild Horse II Wind Farm | Open Energy Information

    Open Energy Info (EERE)

    II Wind Farm Jump to: navigation, search Name Wild Horse II Wind Farm Facility Wild Horse II Sector Wind energy Facility Type Commercial Scale Wind Facility Status In Service Owner...

  19. Wild and Scenic Rivers Act (1968) | Department of Energy

    Office of Environmental Management (EM)

    Wild and Scenic Rivers Act (1968) The National Wild and Scenic Rivers System was created by Congress in 1968 (Public Law 90-542; 16 U.S.C. 1271 et seq.) to preserve certain rivers ...

  20. DOE - NNSA/NFO -- Photo Library Wild Flowers

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Wild Flowers NNSA/NFO Language Options U.S. DOE/NNSA - Nevada Field Office Photo Library - Wild Flowers Wild flowers such as Cane Spring suncup and White bearpoppy are included among the 750 varieties of plants located on the Nevada National Security Site. Instructions: Click the photograph THUMBNAIL to view the photograph details Thumbnail Category http://www.nv.doe.gov/library/photos/thumbs/CaneSpringsuncup.jpg Wild Flowers http://www.nv.doe.gov/library/photos/thumbs/Clokeys.jpg Wild Flowers

  1. Wild and Scenic Rivers Act | Open Energy Information

    Open Energy Info (EERE)

    as wild, scenic, or recreational. These classifications necessitate differing levels of environmental protection under the Act. Published NA Year Signed or Took Effect 1968...

  2. Technical Report of the Wild and Scenic Rivers Coordinating Council...

    Open Energy Info (EERE)

    search OpenEI Reference LibraryAdd to library PermittingRegulatory Guidance - GuideHandbook: Technical Report of the Wild and Scenic Rivers Coordinating...

  3. V-143: Fresh Java issues being exploited in the wild

    Broader source: Energy.gov [DOE]

    Java issues are being exploited in the wild by exploit kits, with Cool and Redkit specifically being known to use these bugs, and others likely to follow shortly.

  4. The antitrust wild card and electricity restructuring

    SciTech Connect (OSTI)

    Adelberg, A.W.; Ongman, J.W.

    1997-03-01

    If competitive policy issues in electricity restructuring are not addressed soon--preferably in federal legislation--it`s likely that someone will use the antitrust wild card to achieve its ends. Experience teaches that this may not be the best way to make public policy. As the electric utility industry restructures, it is widely assumed that Congress, the state legislatures, and regulators will set the ground rules for the restructured markets. Experience to date would seem to confirm this view: California`s restructuring legislation, FERC`s Order 888, and the restructuring proceedings in numerous states are all examples. And yet, there remains another player whose role could be equally important: The federal judiciary. While court decisions under the antitrust laws have had little influence to date on the industry`s direction, there is reason to believe that their role could increase dramatically. Certainly this is the history of other industries that have undergone similar transformations. The authors expect that forces at work in the electric utility industry could lead to antitrust actions playing a far greater role in the industry`s future than most observers currently expect. The electric utility industry has already experienced a close brush with the potential for antitrust rulings to unravel critical elements of regulatory policy on restructuring. The DC Circuit`s now famous (or infamous) dicta in the Cajun Electric Power case illustrated how a simple antitrust principle--the prohibition on so-called tying arrangements--could defeat the FERC`s policy with respect to utilities` recovery of billions of dollars of stranded costs. The FERC rebutted that dicta in its remand decisions and elsewhere, and it appears that the issue in now moot in the Cajun litigation itself. But the tying arrangement argument is far from dead.

  5. WILD PIGS: BIOLOGY, DAMAGE, CONTROL TECHINQUES AND MANAGEMENT

    SciTech Connect (OSTI)

    Mayer, John; Brisbin, I. Lehr

    2009-12-31

    The existence of problems with wild pigs (Sus scrofa) is nothing new to the Western Hemisphere. Damage by these introduced animals was reported as far back as 1505 by the early Spanish colonies in the Caribbean, where wild pigs were killing the colonists cattle. Droves of these animals also ravaged cultivated crops of maize and sugarcane on islands in the West Indies during this same time period. These wild pigs reportedly were very aggressive and often attacked Spanish soldiers hunting rebellious Indians or escaped slaves on these islands, especially when these animals were cornered. The documentation of such impacts by introduced populations of this species in the United States has subsequently increased in recent years, and continued up through the present (Towne and Wentworth. 1950, Wood and Barrett 1979, Mayer and Brisbin 1991, Dickson et al. 2001). In spite of a fairly constant history in this country since the early 1900s, wild pigs have had a dramatic recent increase in both distribution and numbers in the United States. Between 1989 and 2009, the number of states reporting the presence of introduced wild pigs went from 19 up to as many as 44. This increase, in part natural, but largely manmade, has caused an increased workload and cost for land and resource managers in areas where these new populations are found. This is the direct result of the damage that these introduced animals do. The cost of both these impacts and control efforts has been estimated to exceed a billion dollars annually (Pimentel 2007). The complexity of this problem has been further complicated by the widespread appeal and economic potential of these animals as a big game species (Tisdell 1982, Degner 1989). Wild pigs are a controversial problem that is not going away and will likely only get worse with time. Not only do they cause damage, but wild pigs are also survivors. They reproduce at a rate faster than any other mammal of comparable size, native or introduced; they can eat just

  6. Wind-Wildlife Impacts Literature Database (WILD)(Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2015-01-01

    The Wind-Wildlife Impacts Literature Database (WILD), developed and maintained by the National Wind Technology Center (NWTC) at the National Renewable Energy Laboratory (NREL), is comprised of over 1,000 citations pertaining to the effects of land-based wind, offshore wind, marine and hydrokinetic, power lines, and communication and television towers on wildlife.

  7. COLLOQUIUM: A Wild Solution for Climate Change | Princeton Plasma Physics

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Lab 15, 2015, 2:00pm to 3:30pm Colloquia MBG Auditorium COLLOQUIUM: A Wild Solution for Climate Change Professor Thomas E. Lovejoy George Mason University Presentation: PDF icon WC15APR2015_TELovejoy.pdf The impacts of climate change on biodiversity and nature is increasingly prevalent. Projected ahead climate change has increasingly greater impacts beyond what the Climate Convention refers to as allowing systems to adapt naturally. The presentation will examine the two degree target for

  8. Wind-Wildlife Impacts Literature Database (WILD)(Fact Sheet), NREL (National Renewable Energy Laboratory)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Wind-Wildlife Impacts Literature Database (WILD) What is WILD? The Wind-Wildlife Impacts Literature Database (WILD), developed and main- tained by the National Wind Technology Center (NWTC) at the National Renewable Energy Laboratory (NREL), is comprised of over 1,000 citations pertaining to the effects of land-based wind, offshore wind, marine and hydrokinetic power systems, power lines, and communication and television towers on wildlife. For the wind energy sector, WILD serves as an

  9. Transgenic crops get a test in the wild

    SciTech Connect (OSTI)

    Cherfas, J.

    1991-02-22

    A novel British research program called PROSAMO - Planned Release of Selected and Modified Organisms - has just produced its first batch of results on the ecological behavior of a genetically manipulated variety of oil seed rape (known to Americans as canola). As expected, the preliminary data indicate that these plants do not outgrow their competitors in the wild, nor is there any evidence that they pass on their foreign genes to other species. PROSAMO is moving on to test other crops with other foreign genes. If these results are as reassuring, scientists around the world will have solid evidence with which to soothe fears.

  10. Wild Horse 69-kV transmission line environmental assessment

    SciTech Connect (OSTI)

    1996-12-01

    Hill County Electric Cooperative Inc. (Hill County) proposes to construct and operate a 69-kV transmission line from its North Gildford Substation in Montana north to the Canadian border. A vicinity project area map is enclosed as a figure. TransCanada Power Corporation (TCP), a Canadian power-marketing company, will own and construct the connecting 69-kV line from the international border to Express Pipeline`s pump station at Wild Horse, Alberta. This Environmental Assessment is prepared for the Department of Energy (DOE) as lead federal agency to comply with the requirements of the National Environmental Policy Act (NEPA), as part of DOE`s review and approval process of the applications filed by Hill County for a DOE Presidential Permit and License to Export Electricity to a foreign country. The purpose of the proposed line is to supply electric energy to a crude oil pump station in Canada, owned by Express Pipeline Ltd. (Express). The pipeline would transport Canadian-produced oil from Hardisty, Alberta, Canada, to Caster, Wyoming. The Express Pipeline is scheduled to be constructed in 1996--97 and will supply crude oil to refineries in Wyoming and the midwest.

  11. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes Print Wednesday, 30 May 2007 00:00 NASA's $200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81P/Wild 2. Four ALS beamlines and the researchers using them were among the hundreds of scientists and dozens of experimental techniques in facilities around the world that contributed to the preliminary examination

  12. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Wild 2 Viewed by ALS Microscopes Print NASA's 200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81PWild...

  13. WAC - 232-12-064 Live Wildlife-Taking from the wild | Open Energy...

    Open Energy Info (EERE)

    32-12-064 Live Wildlife-Taking from the wild Jump to: navigation, search OpenEI Reference LibraryAdd to library Legal Document- RegulationRegulation: WAC - 232-12-064 Live...

  14. Title 36 CFR 297 Wild and Scenic Rivers | Open Energy Information

    Open Energy Info (EERE)

    Abstract Section 7 of the Wild and Scenic Rivers Act provides for the protection of the free-flowing, scenic, and natural values of rivers designated as components or potential...

  15. Title 36 C.F.R. 297 Wild and Scenic Rivers | Open Energy Information

    Open Energy Info (EERE)

    Abstract Section 7 of the Wild and Scenic Rivers Act provides for the protection of the free-flowing, scenic, and natural values of rivers designated as components or potential...

  16. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes Print NASA's $200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81P/Wild 2. Four ALS beamlines and the researchers using them were among the hundreds of scientists and dozens of experimental techniques in facilities around the world that contributed to the preliminary examination of the first samples. Adding to recent advances in cometary science showing the

  17. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes Print NASA's $200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81P/Wild 2. Four ALS beamlines and the researchers using them were among the hundreds of scientists and dozens of experimental techniques in facilities around the world that contributed to the preliminary examination of the first samples. Adding to recent advances in cometary science showing the

  18. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes Print NASA's $200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81P/Wild 2. Four ALS beamlines and the researchers using them were among the hundreds of scientists and dozens of experimental techniques in facilities around the world that contributed to the preliminary examination of the first samples. Adding to recent advances in cometary science showing the

  19. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes Print NASA's $200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81P/Wild 2. Four ALS beamlines and the researchers using them were among the hundreds of scientists and dozens of experimental techniques in facilities around the world that contributed to the preliminary examination of the first samples. Adding to recent advances in cometary science showing the

  20. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes Print NASA's $200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81P/Wild 2. Four ALS beamlines and the researchers using them were among the hundreds of scientists and dozens of experimental techniques in facilities around the world that contributed to the preliminary examination of the first samples. Adding to recent advances in cometary science showing the

  1. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes Print NASA's $200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81P/Wild 2. Four ALS beamlines and the researchers using them were among the hundreds of scientists and dozens of experimental techniques in facilities around the world that contributed to the preliminary examination of the first samples. Adding to recent advances in cometary science showing the

  2. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes Print NASA's $200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81P/Wild 2. Four ALS beamlines and the researchers using them were among the hundreds of scientists and dozens of experimental techniques in facilities around the world that contributed to the preliminary examination of the first samples. Adding to recent advances in cometary science showing the

  3. Stability of Iowa mutant and wild type Aβ-peptide aggregates

    SciTech Connect (OSTI)

    Alred, Erik J.; Scheele, Emily G.; Berhanu, Workalemahu M.; Hansmann, Ulrich H. E.

    2014-11-07

    Recent experiments indicate a connection between the structure of amyloid aggregates and their cytotoxicity as related to neurodegenerative diseases. Of particular interest is the Iowa Mutant, which causes early-onset of Alzheimer's disease. While wild-type Amyloid β-peptides form only parallel beta-sheet aggregates, the mutant also forms meta-stable antiparallel beta sheets. Since these structural variations may cause the difference in the pathological effects of the two Aβ-peptides, we have studied in silico the relative stability of the wild type and Iowa mutant in both parallel and antiparallel forms. We compare regular molecular dynamics simulations with such where the viscosity of the samples is reduced, which, we show, leads to higher sampling efficiency. By analyzing and comparing these four sets of all-atom molecular dynamics simulations, we probe the role of the various factors that could lead to the structural differences. Our analysis indicates that the parallel forms of both wild type and Iowa mutant aggregates are stable, while the antiparallel aggregates are meta-stable for the Iowa mutant and not stable for the wild type. The differences result from the direct alignment of hydrophobic interactions in the in-register parallel oligomers, making them more stable than the antiparallel aggregates. The slightly higher thermodynamic stability of the Iowa mutant fibril-like oligomers in its parallel organization over that in antiparallel form is supported by previous experimental measurements showing slow inter-conversion of antiparallel aggregates into parallel ones. Knowledge of the mechanism that selects between parallel and antiparallel conformations and determines their relative stability may open new avenues for the development of therapies targeting familial forms of early-onset Alzheimer's disease.

  4. Ecological interactions between hatchery summer steelhead and wild Oncorhynchus mykiss in the Willamette River basin, 2014

    SciTech Connect (OSTI)

    Harnish, Ryan A.; Green, Ethan D.; Vernon, Christopher R.; Mcmichael, Geoffrey A.

    2014-12-23

    The purpose of this study was to determine the extent to which juvenile hatchery summer steelhead and wild winter steelhead overlap in space and time, to evaluate the extent of residualism among hatchery summer steelhead in the South Santiam River, and to evaluate the potential for negative ecological interactions among hatchery summer steelhead and wild winter steelhead. Because it is not possible to visually discern juvenile winter steelhead from resident rainbow trout, we treated all adipose-intact juvenile O. mykiss as one group that represented juvenile wild winter steelhead. The 2014 study objectives were to 1) estimate the proportion of hatchery summer steelhead that residualized in the South Santiam River in 2014, 2) determine the extent to which hatchery and naturally produced O. mykiss overlapped in space and time in the South Santiam River, and 3) characterize the behavioral interactions between hatchery-origin juvenile summer steelhead and naturally produced O. mykiss. We used a combination of radio telemetry and direct observations (i.e., snorkeling) to determine the potential for negative interactions between hatchery summer and wild winter steelhead juveniles in the South Santiam River. Data collected from these two independent methods indicated that a significant portion of the hatchery summer steelhead released as smolts did not rapidly emigrate from the South Santiam River in 2014. Of the 164 radio-tagged steelhead that volitionally left the hatchery, only 66 (40.2%) were detected outside of the South Santiam River. Forty-four (26.8% of 164) of the radio-tagged hatchery summer steelhead successfully emigrated to Willamette Falls. Thus, the last known location of the majority of the tagged fish (98 of 164 = 59.8%) was in the South Santiam River. Thirty-three of the tagged hatchery steelhead were detected in the South Santiam River during mobile-tracking surveys. Of those, 21 were found to be alive in the South Santiam River over three months after

  5. Wood-Producing Sunflower? Mining Genetic Diversity in Desert-Dwelling Wild Species (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Knapp, Steve

    2011-04-26

    Steve Knapp from Monsanto on "Wood-Producing Sunflower? Mining Genetic Diversity in Desert-Dwelling Wild Species" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  6. Studies Concerning the Accumulation of Minerals and Heavy Metals in Fruiting Bodies of Wild Mushrooms

    SciTech Connect (OSTI)

    Stihi, Claudia; Radulescu, Cristiana; Gheboianu, Anca; Bancuta, Iulian; Popescu, Ion V.; Busuioc, Gabriela

    2011-10-03

    The minerals and heavy metals play an important role in the metabolic processes, during the growth and development of mushrooms, when they are available in appreciable concentration. In this work the concentrations of Cr, Mn, Fe, Ni, Cu, Zn, Se, Cd and Pb were analyzed using the Flame Atomic Absorption spectrometry (FAAS) together with Energy Dispersive X-ray Fluorescence spectrometry (EDXRF) in 3 wild mushrooms species and their growing substrate, collected from various forestry fields in Dambovita County, Romania. The analyzed mushrooms were: Amanita phalloides, Amanita rubescens and Armillariella mellea. The accumulation coefficients were calculated to assess the mobility of minerals and heavy metals from substrate to mushrooms [1].

  7. Science on Saturday: The Wild and Wacky World of Epigenetics | Princeton

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Plasma Physics Lab 6, 2016, 9:30am Science On Saturday PPPL, MBG Auditorium Science on Saturday: The Wild and Wacky World of Epigenetics Professor Shirley Tilghman Princeton University Abstract: PDF icon 02 Tilghman.pdf LIVE STREAMING LINK: https://mediacentral.princeton.edu/id/1_wdp1m3et Tweet us your questions @PPPLSciEd and/or #scionsat Science_on_Saturday16Jan2016_STilghman Contact Information Coordinator(s): Ms. Deedee Ortiz-Arias dortiz@pppl.gov Host(s): Dr. Andrew Zwicker

  8. Fukushima derived radiocesium in subsistence-consumed northern fur seal and wild celery

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ruedig, Elizabeth; Duncan, Colleen; Dickerson, Bobette; Williams, Michael; Gelatt, Thomas; Bell, Justin; Johnson, Thomas E.

    2015-11-28

    In July 2014, our investigative team traveled to St. Paul Island, Alaska to measure concentrations of radiocesium in wild-caught food products, primarily northern fur seal (Callorhinus ursinus). The 2011 Fukushima Daiichi Nuclear Power Plant accident released radiocesium into the atmosphere and into the western Pacific Ocean; other investigators have detected Fukushima-derived radionuclides in a variety of marine products harvested off the western coast of North America. We tested two subsistence-consumed food products from St. Paul Island, Alaska for Fukushima-derived radionuclides: 54 northern fur seal, and nine putchki (wild celery, Angelica lucida) plants. Individual northern fur seal samples were below minimummore » detectable activity concentrations of 137Cs and 134Cs, but when composited, northern fur seal tissues tested positive for trace quantities of both isotopes. Radiocesium was detected at an activity concentration of 37.2 mBq 134Cs kg-1 f.w. (95% CI: 35.9–38.5) and 141.2 mBq 137Cs kg-1f.w. (95% CI: 135.5–146.8). The measured isotopic ratio, decay-corrected to the date of harvest, was 0.26 (95% CI: 0.25–0.28). The Fukushima nuclear accident released 134Cs and 137Cs in roughly equal quantities, but by the date of harvest in July 2014, this ratio was 0.2774, indicating that this population of seals has been exposed to small quantities of Fukushima-derived radiocesium. Activity concentrations of both 134Cs and 137Cs in putchki were below detection limits, even for composited samples. Northern fur seal is known to migrate between coastal Alaska and Japan and the trace 134Cs in northern fur seal tissue suggests that the population under study had been minimally exposed Fukushima-derived radionuclides. Despite this inference, the radionuclide quantities detected are small and no impact is expected as a result of the measured radiation exposure, either in northern fur seal or human populations consuming this species.« less

  9. Fukushima derived radiocesium in subsistence-consumed northern fur seal and wild celery

    SciTech Connect (OSTI)

    Ruedig, Elizabeth; Duncan, Colleen; Dickerson, Bobette; Williams, Michael; Gelatt, Thomas; Bell, Justin; Johnson, Thomas E.

    2015-11-28

    In July 2014, our investigative team traveled to St. Paul Island, Alaska to measure concentrations of radiocesium in wild-caught food products, primarily northern fur seal (Callorhinus ursinus). The 2011 Fukushima Daiichi Nuclear Power Plant accident released radiocesium into the atmosphere and into the western Pacific Ocean; other investigators have detected Fukushima-derived radionuclides in a variety of marine products harvested off the western coast of North America. We tested two subsistence-consumed food products from St. Paul Island, Alaska for Fukushima-derived radionuclides: 54 northern fur seal, and nine putchki (wild celery, Angelica lucida) plants. Individual northern fur seal samples were below minimum detectable activity concentrations of 137Cs and 134Cs, but when composited, northern fur seal tissues tested positive for trace quantities of both isotopes. Radiocesium was detected at an activity concentration of 37.2 mBq 134Cs kg-1 f.w. (95% CI: 35.9–38.5) and 141.2 mBq 137Cs kg-1f.w. (95% CI: 135.5–146.8). The measured isotopic ratio, decay-corrected to the date of harvest, was 0.26 (95% CI: 0.25–0.28). The Fukushima nuclear accident released 134Cs and 137Cs in roughly equal quantities, but by the date of harvest in July 2014, this ratio was 0.2774, indicating that this population of seals has been exposed to small quantities of Fukushima-derived radiocesium. Activity concentrations of both 134Cs and 137Cs in putchki were below detection limits, even for composited samples. Northern fur seal is known to migrate between coastal Alaska and Japan and the trace 134Cs in northern fur seal tissue suggests that the population under study had been minimally exposed Fukushima-derived radionuclides. Despite this inference, the radionuclide quantities detected are small and no impact is expected as a result of the measured radiation

  10. Digital Mapping and Environmental Characterization of National Wild and Scenic River Systems

    SciTech Connect (OSTI)

    McManamay, Ryan A; Bosnall, Peter; Hetrick, Shelaine L; Smith, Brennan T

    2013-09-01

    Spatially accurate geospatial information is required to support decision-making regarding sustainable future hydropower development. Under a memorandum of understanding among several federal agencies, a pilot study was conducted to map a subset of National Wild and Scenic Rivers (WSRs) at a higher resolution and provide a consistent methodology for mapping WSRs across the United States and across agency jurisdictions. A subset of rivers (segments falling under the jurisdiction of the National Park Service) were mapped at a high resolution using the National Hydrography Dataset (NHD). The spatial extent and representation of river segments mapped at NHD scale were compared with the prevailing geospatial coverage mapped at a coarser scale. Accurately digitized river segments were linked to environmental attribution datasets housed within the Oak Ridge National Laboratory s National Hydropower Asset Assessment Program database to characterize the environmental context of WSR segments. The results suggest that both the spatial scale of hydrography datasets and the adherence to written policy descriptions are critical to accurately mapping WSRs. The environmental characterization provided information to deduce generalized trends in either the uniqueness or the commonness of environmental variables associated with WSRs. Although WSRs occur in a wide range of human-modified landscapes, environmental data layers suggest that they provide habitats important to terrestrial and aquatic organisms and recreation important to humans. Ultimately, the research findings herein suggest that there is a need for accurate, consistent, mapping of the National WSRs across the agencies responsible for administering each river. Geospatial applications examining potential landscape and energy development require accurate sources of information, such as data layers that portray realistic spatial representations.

  11. The Origin of Refractory Minerals in Comet 81P/Wild 2

    SciTech Connect (OSTI)

    Chi, M; Ishii, H A; Simon, S B; Bradley, J P; Dai, Z R; Joswiak, D J; Browning, N D; Matrajt, G

    2008-11-20

    Refractory Ti-bearing minerals in the calcium-, aluminium-rich inclusion (CAI) Inti, recovered from the comet 81P/Wild 2 sample, were examined using analytical (scanning) transmission electron microscopy (STEM) methods including imaging, nanodiffraction, energy dispersive spectroscopy (EDX) and electron energy loss spectroscopy (EELS). Inti fassaite (Ca(Mg,Ti,Al)(Si,Al){sub 2}O{sub 6}) was found to have a Ti{sup 3+}/Ti{sup 4+} ratio of 2.0 {+-} 0.2, consistent with fassaite in other solar system CAIs. The oxygen fugacity (log f{sub O{sub 2}}) of formation estimated from this ratio, assuming equilibration among phases at 1509K, is -19.4 {+-} 1.3. This value is near the canonical solar nebula value (-18.1 {+-} 0.3) and in close agreement with that reported for fassaite-bearing Allende CAIs (-19.8 {+-} 0.9) by other researchers using the same assumptions. Nanocrystals of osbornite (Ti(V)N), 2-40 nm in diameter, are embedded as inclusions within anorthite, spinel and diopside in Inti. Vanadium is heterogeneously distributed within some osbornite crystals. Compositions range from pure TiN to Ti{sub 0.36}V{sub 0.64}N. The possible presence of oxide and carbide in solid solution with the osbornite was evaluated. The osbornite may contain O but does not contain C. The presence of osbornite, likely a refractory early condensate, together with the other refractory minerals in Inti, indicates that the parent comet contains solids that condensed closer to the proto-sun than the distance at which the parent comet itself accreted. The estimated oxygen fugacity and the reported isotopic and chemical compositions are consistent with Inti originating in the inner solar system as opposed to it being a surviving CAI from an extrasolar source. These results provide insight for evaluating the validity of models of radial mass transport dynamics in the early solar system. The oxidation environments inferred for the Inti mineral assemblage are inconsistent with an X-wind formation

  12. A Refractory Inclusion Returned by Stardust from Comet 81P/Wild 2

    SciTech Connect (OSTI)

    Simon, S B; Joswiak, D J; Ishii, H A; Bradley, J P; Chi, M; Grossman, L; Al?on, J; Brownlee, D E; Fallon, S; Hutcheon, I D; Matrajt, G; McKeegan, K D

    2008-05-20

    Among the samples returned from comet 81P/Wild 2 by the Stardust spacecraft is a suite of particles from one impact track (Track 25) that are Ca-, Al-rich and FeO-free. We studied three particles from this track that range in size from 5.3 x 3.2 {micro}m to 15 x 10 {micro}m. Scanning and transmission electron microscopy show that they consist of very fine-grained (from {approx}0.5 to {approx}2 {micro}m) Al-rich, Ti-bearing and Ti-free clinopyroxene, Mg-Al spinel, anorthite, perovskite, and osbornite (TiN). In addition to these phases, the terminal particle, named 'Inti', also contains melilite. All of these phases, with the exception of osbornite, are common in refractory inclusions and are predicted to condense at high temperature from a gas of solar composition. Osbornite, though very rare, has also been found in meteoritic refractory inclusions, and could have formed in a region of the nebula where carbon became enriched relative to oxygen compared to solar composition. Compositions of Ti-pyroxene in Inti are similar, but not identical, to those of fassaite from Allende inclusions. Electron energy loss spectroscopy shows that Ti-rich pyroxene in Inti has Ti{sup 3+}/Ti{sup 4+} within the range of typical meteoritic fassaite, consistent with formation under reducing conditions comparable to those of a system of solar composition. Inti is {sup 16}O-rich, with {delta}{sup 18}O {approx} {delta}{sup 17}O {approx} 40{per_thousand}, like unaltered phases in refractory inclusions and refractory IDPs. With grain sizes, mineralogy, mineral chemistry, and an oxygen isotopic composition like those of refractory inclusions, we conclude that Inti is a refractory inclusion that formed in the inner solar nebula. Identification of a particle that formed in the inner Solar System among the comet samples demonstrates that there was transport of materials from the inner to the outer nebula, probably either in a bipolar outflow or by turbulence.

  13. Comparison of the oxidation state of Fe in comet 81P/Wild 2 and chondritic-porous interplanetary dust particles

    SciTech Connect (OSTI)

    Ogliore, Ryan C.; Butterworth, Anna L.; Fakra, Sirine C.; Gainsforth, Zack; Marcus, Matthew A.; Westphal, Andrew J.

    2010-07-16

    The fragile structure of chondritic-porous interplanetary dust particles (CP-IDPs) and their minimal parent-body alteration have led researchers to believe these particles originate in comets rather than asteroids where aqueous and thermal alterations have occurred. The solar elemental abundances and atmospheric entry speed of CP-IDPs also suggest a cometary origin. With the return of the Stardust samples from Jupiter-family comet 81P/Wild 2, this hypothesis can be tested. We have measured the Fe oxidation state of 15 CP-IDPs and 194 Stardust fragments using a synchrotron-based x-ray microprobe. We analyzed {approx}300 ng of Wild 2 material - three orders of magnitude more material than other analyses comparing Wild 2 and CP-IDPs. The Fe oxidation state of these two samples of material are > 2{sigma} different: the CP-IDPs are more oxidized than the Wild 2 grains. We conclude that comet Wild 2 contains material that formed at a lower oxygen fugacity than the parent-body, or parent bodies, of CP-IDPs. If all Jupiter-family comets are similar, they do not appear to be consistent with the origin of CP-IDPs. However, comets that formed from a different mix of nebular material and are more oxidized than Wild 2 could be the source of CP-IDPs.

  14. Hood River Steelhead Genetics Study; Relative Reproductive Success of Hatchery and Wild Steelhead in the Hood River, Final Report 2002-2003.

    SciTech Connect (OSTI)

    Blouin, Michael

    2003-05-01

    There is a considerable interest in using hatcheries to speed the recovery of wild populations. The Bonneville Power Administration (BPA), under the authority of the Northwest Power Planning Act, is currently funding several hatchery programs in the Columbia Basin as off-site mitigation for impacts to salmon and steelhead caused by the Columbia River federal hydropower system. One such project is located on the Hood River, an Oregon tributary of the Columbia. These hatchery programs cost the region millions of dollars. However, whether such programs actually improve the status of wild fish remains untested. The goal of this project was to evaluate the effectiveness of the Hood River hatchery program as required by the Northwest Power Planning Council Fish and Wildlife Program, by the Oregon Plan for Coastal Salmonids, by NMFS ESA Section 4(d) rulings, and by the Oregon Department of Fish and Wildlife (ODFW) Wild Fish Management Policy (OAR 635-07-525 through 529) and the ODFW Hatchery Fish Gene Resource Management Policy (OAR 635-07-540 through 541). The Hood River supports two populations of steelhead, a summer run and a winter run. They spawn only above the Powerdale Dam, which is a complete barrier to all salmonids. Since 1991 every adult passed above the dam has been measured, cataloged and sampled for scales. Therefore, we have a DNA sample from every adult steelhead that went over the dam to potentially spawn in the Hood River from 1991 to the present. Similar numbers of hatchery and wild fish have been passed above the dam during the last decade. During the 1990's 'old' domesticated hatchery stocks of each run (multiple generations in the hatchery, out-of-basin origin; hereafter H{sub old}) were phased out, and conservation hatchery programs were started for the purpose of supplementing the two wild populations (hereafter 'new' hatchery stocks, H{sub new}). These samples gave us the unprecedented ability to estimate, via microsatellite-based pedigree

  15. Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2

    SciTech Connect (OSTI)

    Brown, Steven D; Lamed, Raphael; Morag, Ely; Borovok, Ilya; Shoham, Yuval; Klingeman, Dawn Marie; Johnson, Courtney M; Yang, Zamin; Land, Miriam L; Utturkar, Sagar M; Keller, Martin; Bayer, Edward A

    2012-01-01

    Clostridium thermocellum wild-type strain YS is an anaerobic, thermophilic, cellulolytic bacterium capable of directly converting cellulosic substrates into ethanol. Strain YS and a derived cellulose adhesion-defective mutant strain AD2 played pivotal roles in describing the original cellulosome concept. We present their draft genome sequences.

  16. Category:Energy Generation Facilities | Open Energy Information

    Open Energy Info (EERE)

    " title"Fossil Gulch Wind Park">Fossil Gulch Wind Park","title":"Fossil Gulch Wind Park","link":null,"lat":42.814261,"lon":-114.996665,"alt":0,"address":""...

  17. Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    McIlwain, Sean J.; Peris, Davis; Sardi, Maria; Moskvin, Oleg V.; Zhan, Fujie; Myers, Kevin S.; Riley, Nicholas M.; Buzzell, Alyssa; Parreiras, Lucas S.; Ong, Irene M.; et al

    2016-04-20

    The genome sequences of more than 100 strains of the yeast Saccharomyces cerevisiae have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of S. cerevisiae derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assemblymore » approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any S. cerevisiae strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. Lastly, the Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.« less

  18. Recovering the Elemental Composition of Comet Wild 2 Dust in Five Stardust Impact Tracks and Terminal Particles in Aerogel

    SciTech Connect (OSTI)

    Ishii, H A; Brennan, S; Bradley, J P; Luening, K; Ignatyev, K; Pianetta, P

    2007-01-04

    The elemental (non-volatile) composition of five Stardust impact tracks and terminal particles left from capture of Comet 81P/Wild 2 dust were mapped in a synchrotron x-ray scanning microprobe with full fluorescence spectra at each pixel. Because aerogel includes background levels of several elements of interest, we employ a novel 'dual threshold' approach to discriminate against background contaminants: an upper threshold, above which a spectrum contains cometary material plus aerogel and a lower threshold below which it contains only aerogel. The difference between normalized cometary-plus-background and background-only spectra is attributable to cometary material. The few spectra in between are discarded since misallocation is detrimental: cometary material incorrectly placed in the background spectrum is later subtracted from the cometary spectrum, doubling the loss of reportable cometary material. This approach improves precision of composition quantification. We present the refined whole impact track and terminal particle elemental abundances for the five impact tracks. One track shows mass increases in Cr and Mn (1.4x), Cu, As and K (2x), Zn (4x) and total mass (13%) by dual thresholds compared to a single threshold. Major elements Fe and Ni are not significantly affected. The additional Cr arises from cometary material containing little Fe. We exclude Au intermixed with cometary material because it is found to be a localized surface contaminant carried by comet dust into an impact track. The dual threshold technique can be used in other situations where elements of interest in a small sample embedded in a matrix are also present in the matrix itself.

  19. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gaczynska, Maria; Karpowicz, Przemyslaw; Stuart, Christine E.; Norton, Malgorzata G.; Teckman, Jeffrey H.; Marszal, Ewa; Osmulski, Pawel A.

    2016-03-23

    α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemicalmore » data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found inWT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo

  20. Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.; Irwin, Brian J.; Beasley, James C.

    2016-05-25

    Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow

  1. Transportation as a Means of Increasing Wild Juvenile Salmon Survival : Recovery Issues for Threatened and Endangered Snake River Salmon : Technical Report 4 of 11.

    SciTech Connect (OSTI)

    Park, Donn L.

    1993-06-01

    Smolt transportation on the Snake and Columbia Rivers has been under nearly continuous study for 25 years. Most controversy surrounds transport of spring/summer chinook, so most analyses and discussion are devoted to that species. Sockeye migrate at the same time as spring/summer chinook as do the earliest of the fall chinook. Therefore, action taken o spring/summer chinook will also affect sockeye and fall chinook. Many factors influenced transportation study results including population structure change -- the shift from nearly all wild fish to nearly all hatchery fish; new dams; the number of turbines at Snake River dams alone increased from 3 in 1968 to 24 by 1979; installation of juvenile fish pass facilities; and calamitous natural events such as the 1977 drought. All the above had negative effects on the survival of wild fish in general and on transport test results specifically, except that when smolts were transported from the upper dam their survival was not influenced by new or existing structures downstream from the transport site.

  2. Crystal Structures of Wild-type and Mutant Methicillin-resistant Staphylococcus aureus Dihydrofolate Reductase Reveal an Alternative Conformation of NADPH that may be Linked to Trimethoprim Resistance

    SciTech Connect (OSTI)

    Frey, K.; Liu, J; Lombardo, M; Bolstad, D; Wright, D; Anderson, A

    2009-01-01

    Both hospital- and community-acquired Staphylococcus aureus infections have become major health concerns in terms of morbidity, suffering and cost. Trimethoprim-sulfamethoxazole (TMP-SMZ) is an alternative treatment for methicillin-resistant S. aureus (MRSA) infections. However, TMP-resistant strains have arisen with point mutations in dihydrofolate reductase (DHFR), the target for TMP. A single point mutation, F98Y, has been shown biochemically to confer the majority of this resistance to TMP. Using a structure-based approach, we have designed a series of novel propargyl-linked DHFR inhibitors that are active against several trimethoprim-resistant enzymes. We screened this series against wild-type and mutant (F98Y) S. aureus DHFR and found that several are active against both enzymes and specifically that the meta-biphenyl class of these inhibitors is the most potent. In order to understand the structural basis of this potency, we determined eight high-resolution crystal structures: four each of the wild-type and mutant DHFR enzymes bound to various propargyl-linked DHFR inhibitors. In addition to explaining the structure-activity relationships, several of the structures reveal a novel conformation for the cofactor, NADPH. In this new conformation that is predominantly associated with the mutant enzyme, the nicotinamide ring is displaced from its conserved location and three water molecules complete a network of hydrogen bonds between the nicotinamide ring and the protein. In this new position, NADPH has reduced interactions with the inhibitor. An equilibrium between the two conformations of NADPH, implied by their occupancies in the eight crystal structures, is influenced both by the ligand and the F98Y mutation. The mutation induced equilibrium between two NADPH-binding conformations may contribute to decrease TMP binding and thus may be responsible for TMP resistance.

  3. Infrared Spectroscopy of Wild 2 Particle Hypervelocity Tracks in Stardust Aerogel: Evidence for the presence of Volatile Organics in Comet Dust

    SciTech Connect (OSTI)

    Bajt, S; Sandford, S A; Flynn, G J; Matrajt, G; Snead, C J; Westphal, A J; Bradley, J P

    2007-08-28

    Infrared spectroscopy maps of some tracks, made by cometary dust from 81P/Wild 2 impacting Stardust aerogel, reveal an interesting distribution of volatile organic material. Out of six examined tracks three show presence of volatile organic components possibly injected into the aerogel during particle impacts. When particle tracks contained excess volatile organic material, they were found to be -CH{sub 2}-rich. Off-normal particle tracks could indicate impacts by lower velocity particles that could have bounced off the Whipple shield, therefore carry off some contamination from it. However, this theory is not supported by data that show excess organic-rich material in normal and off-normal particle tracks. It is clear that the population of cometary particles impacting the Stardust aerogel collectors also include grains that contained little or none of this volatile organic component. This observation is consistent with the highly heterogeneous nature of the collected grains, as seen by a multitude of other analytical techniques. We propose that at least some of the volatile organic material might be of cometary origin based on supporting data shown in this paper. However, we also acknowledge the presence of carbon (primarily as -CH{sub 3}) in the original aerogel, which complicates interpretation of these results.

  4. Metabolic Engineering of Light and Dark Biochemical Pathways in Wild-Type and Mutant Strains of Synechocystis PCC 6803 for Maximal, 24-Hour Production of Hydrogen Gas

    SciTech Connect (OSTI)

    Ely, Roger L.; Chaplen, Frank W.R.

    2014-03-11

    This project used the cyanobacterial species Synechocystis PCC 6803 to pursue two lines of inquiry, with each line addressing one of the two main factors affecting hydrogen (H2) production in Synechocystis PCC 6803: NADPH availability and O2 sensitivity. H2 production in Synechocystis PCC 6803 requires a very high NADPH:NADP+ ratio, that is, the NADP pool must be highly reduced, which can be problematic because several metabolic pathways potentially can act to raise or lower NADPH levels. Also, though the [NiFe]-hydrogenase in PCC 6803 is constitutively expressed, it is reversibly inactivated at very low O2 concentrations. Largely because of this O2 sensitivity and the requirement for high NADPH levels, a major portion of overall H2 production occurs under anoxic conditions in the dark, supported by breakdown of glycogen or other organic substrates accumulated during photosynthesis. Also, other factors, such as N or S limitation, pH changes, presence of other substances, or deletion of particular respiratory components, can affect light or dark H2 production. Therefore, in the first line of inquiry, under a number of culture conditions with wild type (WT) Synechocystis PCC 6803 cells and a mutant with impaired type I NADPH-dehydrogenase (NDH-1) function, we used H2 production profiling and metabolic flux analysis, with and without specific inhibitors, to examine systematically the pathways involved in light and dark H2 production. Results from this work provided rational bases for metabolic engineering to maximize photobiological H2 production on a 24-hour basis. In the second line of inquiry, we used site-directed mutagenesis to create mutants with hydrogenase enzymes exhibiting greater O2 tolerance. The research addressed the following four tasks: 1. Evaluate the effects of various culture conditions (N, S, or P limitation; light/dark; pH; exogenous organic carbon) on H2 production profiles of WT cells and an NDH-1 mutant; 2. Conduct metabolic flux analyses for

  5. Evaluation of the 1998 Predictions of the Run-Timing of Wild Migrant Yearling Chinook and Water Quality at Multiple Locations on the Snake and Columbia Rivers using CRiSP/RealTime, 1998 Technical Report.

    SciTech Connect (OSTI)

    Beer, W. Nicholas; Hayes, Joshua A.; Shaw, Pamela

    1999-07-21

    Since 1988, wild salmon have been PIT-tagged through monitoring and research programs conducted by the Columbia River fisheries agencies and Tribes. Workers at the University of Washington have used detection data at Lower Granite Dam to generate predictions of arrival distributions for various stocks at the dam. The prediction tool is known as RealTime. In 1996, RealTime predictions were linked to a downstream migration model, CRiSP.1. The composite model, known as CRiSP/RealTime, predicts the arrival distribution and fraction transported at downriver locations.

  6. Interpretation of Wild 2 Dust Fine Structure: Comparison of Stardust Aluminium Foil Craters to the Three-Dimensional Shape of Experimental Impacts by Artificial Aggregate Particles and Meteorite Powders

    SciTech Connect (OSTI)

    Kearsley, A T; Burchell, M J; Price, M C; Graham, G A; Wozniakiewicz, P J; Cole, M J; Foster, N J; Teslich, N

    2009-12-10

    New experimental results show that Stardust crater morphology is consistent with interpretation of many larger Wild 2 dust grains being aggregates, albeit most of low porosity and therefore relatively high density. The majority of large Stardust grains (i.e. those carrying most of the cometary dust mass) probably had density of 2.4 g cm{sup -3} (similar to soda-lime glass used in earlier calibration experiments) or greater, and porosity of 25% or less, akin to consolidated carbonaceous chondrite meteorites, and much lower than the 80% suggested for fractal dust aggregates. Although better size calibration is required for interpretation of the very smallest impacting grains, we suggest that aggregates could have dense components dominated by {micro}m-scale and smaller sub-grains. If porosity of the Wild 2 nucleus is high, with similar bulk density to other comets, much of the pore-space may be at a scale of tens of micrometers, between coarser, denser grains. Successful demonstration of aggregate projectile impacts in the laboratory now opens the possibility of experiments to further constrain the conditions for creation of bulbous (Type C) tracks in aerogel, which we have observed in recent shots. We are also using mixed mineral aggregates to document differential survival of pristine composition and crystalline structure in diverse fine-grained components of aggregate cometary dust analogues, impacted onto both foil and aerogel under Stardust encounter conditions.

  7. Monitoring and Evaluation of Smolt Migration in the Columbia Basin : Volume XV : Evaluation of the 2007 Predictions of the Run-Timing of Wild and Hatchery-Reared Salmon and Steelhead Smolts to Rock Island, Lower Granite, McNary, John Day, and Bonneville Dams using Program RealTime.

    SciTech Connect (OSTI)

    Griswold, Jim; Townsend, Richard L.; Skalski, John R.

    2008-12-01

    Program RealTime provided monitoring and forecasting of the 2007 inseason outmigrations via the internet for 26 PIT-tagged stocks of wild ESU Chinook salmon and steelhead to Lower Granite and/or McNary dams, one PIT-tagged hatchery-reared ESU of sockeye salmon to Lower Granite Dam, one PIT-tagged wild stock of sockeye salmon to McNary Dam, and 20 passage-indexed runs-at-large, five each to Rock Island, McNary, John Day, and Bonneville dams. Nineteen stocks are of wild yearling Chinook salmon which were captured, PIT-tagged, and released at sites above Lower Granite Dam in 2007 and have at least one year's historical migration data previous to the 2007 migration. These stocks originate in 19 tributaries of the Salmon, Grande Ronde and Clearwater Rivers, all tributaries to the Snake River, and are subsequently detected through tag identification and monitored at Lower Granite Dam. Seven wild PIT-tagged runs-at-large of Snake or Upper Columbia River ESU salmon and steelhead were monitored at McNary Dam. Three wild PIT-tagged runs-at-large were monitored at Lower Granite Dam, consisting of the yearling and subyearling Chinook salmon and the steelhead runs. The hatchery-reared PIT-tagged sockeye salmon stock from Redfish Lake was monitored outmigrating through Lower Granite Dam. Passage-indexed stocks (stocks monitored by FPC passage indices) included combined wild and hatchery runs-at-large of subyearling and yearling Chinook, coho, and sockeye salmon, and steelhead forecasted to Rock Island, McNary, John Day, and Bonneville dams.

  8. Insulin-Like Growth Factor-Type 1 Receptor Inhibitor NVP-AEW541 Enhances Radiosensitivity of PTEN Wild-Type but Not PTEN-Deficient Human Prostate Cancer Cells

    SciTech Connect (OSTI)

    Isebaert, Sofie F.; Swinnen, Johannes V.; McBride, William H.; Haustermans, Karin M.

    2011-09-01

    Purpose: During the past decade, many clinical trials with both monoclonal antibodies and small molecules that target the insulin-like growth factor-type 1 receptor (IGF-1R) have been launched. Despite the important role of IGF-1R signaling in radioresistance, studies of such agents in combination with radiotherapy are lagging behind. Therefore, the aim of this study was to investigate the effect of the small molecule IGF-1R kinase inhibitor NVP-AEW541 on the intrinsic radioresistance of prostate cancer cells. Methods and Materials: The effect of NVP-AEW541 on cell proliferation, cell viability, IGF-1R signaling, radiosensitivity, cell cycle distribution, and double strand break repair was determined in three human prostate cancer cell lines (PC3, DU145, 22Rv1). Moreover, the importance of the PTEN pathway status was explored by means of transfection experiments with constitutively active Akt or inactive kinase-dead Akt. Results: NVP-AEW541 inhibited cell proliferation and decreased cell viability in a time-and dose-dependent manner in all three cell lines. Radiosensitization was observed in the PTEN wild-type cell lines DU145 and 22Rv1 but not in the PTEN-deficient PC3 cell line. NVP-AEW541-induced radiosensitization coincided with downregulation of phospho-Akt levels and high levels of residual double strand breaks. The importance of PTEN status in the radiosensitization effect was confirmed by transfection experiments with constitutively active Akt or inactive kinase-dead Akt. Conclusions: NVP-AEW541 enhances the effect of ionizing radiation in PTEN wild-type, but not in PTEN-deficient, prostate cancer cells. Proper patient selection based on the PTEN status of the tumor will be critical to the achievement of optimal results in clinical trials in which the combination of radiotherapy and this IGF-1R inhibitor is being explored.

  9. Monitoring and Evaluation of Smolt Migration in the Columbia Basin, Volume XIV; Evaluation of 2006 Prediction of the Run-Timing of Wild and Hatchery-Reared Salmon and Steelhead at Rock Island, Lower Granite, McNary, John Day and Bonneville Dams using Program Real Time, Technical Report 2006.

    SciTech Connect (OSTI)

    Griswold, Jim

    2007-01-01

    Program RealTime provided monitoring and forecasting of the 2006 inseason outmigrations via the internet for 32 PIT-tagged stocks of wild ESU chinook salmon and steelhead to Lower Granite and/or McNary dams, one PIT-tagged hatchery-reared ESU of sockeye salmon to Lower Granite Dam, and 20 passage-indexed runs-at-large, five each to Rock Island, McNary, John Day, and Bonneville Dams. Twenty-four stocks are of wild yearling chinook salmon which were captured, PIT-tagged, and released at sites above Lower Granite Dam in 2006, and have at least one year's historical migration data previous to the 2006 migration. These stocks originate in drainages of the Salmon, Grande Ronde and Clearwater Rivers, all tributaries to the Snake River, and are subsequently detected through the tag identification and monitored at Lower Granite Dam. In addition, seven wild PIT-tagged runs-at-large of Snake or Upper Columbia River ESU salmon and steelhead were monitored at McNary Dam. Three wild PIT-tagged runs-at-large were monitored at Lower Granite Dam, consisting of the yearling and subyearling chinook salmon and the steelhead trout runs. The hatchery-reared PIT-tagged sockeye salmon stock from Redfish Lake was monitored outmigrating through Lower Granite Dam. Passage-indexed stocks (stocks monitored by FPC passage indices) included combined wild and hatchery runs-at-large of subyearling and yearling chinook, coho, and sockeye salmon, and steelhead trout forecasted to Rock Island, McNary, John Day, and Bonneville Dams.

  10. Rocky Mountain Basins Produced Water Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Historical records for produced water data were collected from multiple sources, including Amoco, British Petroleum, Anadarko Petroleum Corporation, United States Geological Survey (USGS), Wyoming Oil and Gas Commission (WOGC), Denver Earth Resources Library (DERL), Bill Barrett Corporation, Stone Energy, and other operators. In addition, 86 new samples were collected during the summers of 2003 and 2004 from the following areas: Waltman-Cave Gulch, Pinedale, Tablerock and Wild Rose. Samples were tested for standard seven component "Stiff analyses", and strontium and oxygen isotopes. 16,035 analyses were winnowed to 8028 unique records for 3276 wells after a data screening process was completed. [Copied from the Readme document in the zipped file available at http://www.netl.doe.gov/technologies/oil-gas/Software/database.html] Save the Zipped file to your PC. When opened, it will contain four versions of the database: ACCESS, EXCEL, DBF, and CSV formats. The information consists of detailed water analyses from basins in the Rocky Mountain region.

  11. Wild and Scenic Rivers | Open Energy Information

    Open Energy Info (EERE)

    Scenic Rivers Jump to: navigation, search Retrieved from "http:en.openei.orgwindex.php?titleWildandScenicRivers&oldid612228" Feedback Contact needs updating Image...

  12. Wild Fire Computer Model Helps Firefighters

    ScienceCinema (OSTI)

    Canfield, Jesse

    2014-06-02

    A high-tech computer model called HIGRAD/FIRETEC, the cornerstone of a collaborative effort between U.S. Forest Service Rocky Mountain Research Station and Los Alamos National Laboratory, provides insights that are essential for front-line fire fighters. The science team is looking into levels of bark beetle-induced conditions that lead to drastic changes in fire behavior and how variable or erratic the behavior is likely to be.

  13. Proposed Wild Horse Pass Substation Option

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    LAK E C ITY, U T PAN EL 2 ELEC TR IC ITY D ISTR IBU TION AN D EN D -U SE: H OW D O W E MAN AGE C H ALLEN GES AN D OPPOR TU N ITIES? AP R I L 2 5 , 2 0 1 6 Gila River Indian ...

  14. Stop Codon Reassignment in the Wild

    SciTech Connect (OSTI)

    Ivanova, Natalia; Schwientek, Patrick; Tripp, H. James; Rinke, Christian; Pati, Amrita; Huntemann, Marcel; Visel, Axel; Woyke, Tanja; Kyrpides, Nikos; Rubin, Edward

    2014-03-21

    Since the discovery of the genetic code and protein translation mechanisms (1), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages (2-3). Given the apparent ubiquity of the canonical genetic code, the design of genomically recoded organisms with non-canonical codes has been suggested as a means to prevent horizontal gene transfer between laboratory and environmental organisms (4). It is also predicted that genomically recoded organisms are immune to infection by viruses, under the assumption that phages and their hosts must share a common genetic code (5). This paradigm is supported by the observation of increased resistance of genomically recoded bacteria to phages with a canonical code (4). Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and non-canonical codon usage represents an absolute barrier to phage infection and genetic exchange between organisms. Our knowledge of the diversity of genetic codes and their use by viruses and their hosts is primarily derived from the analysis of cultivated organisms. Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages (6). These initial findings suggest that large scale systematic studies of uncultivated microorganisms and viruses may reveal the extent and modes of divergence from the canonical genetic code operating in nature. To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber, TGA opal, and TAA ochre codons in assembled metagenomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of phage sequences

  15. Manufacturing Demonstration Facilities Workshop Agenda, March...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Manufacturing Demonstration Facilities Workshop Marriott Springhill Suites O'Hare - ... mechanics of the Manufacturing Demonstration Facility (MDF) concept and the ...

  16. First Direct Evidence of Dirac Fermions in Graphite

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of finite effective mass and defect-induced localized states. Goodbye Silicon Valley, Hello Graphite Gulch? Why are scientists suddenly interested in graphite? It is, after all,...

  17. Floodplain and Wetlands Assessment for Construction of a Second...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Floodplain and Wetlands Assessment for Construction of a Second Full Service Access Road over Lena Gulch Floodplain and Wetlands Assessment for Construction of a Second Full ...

  18. 1 Advisory, Consultative, Deliberative, Draft SANDIA REPORT

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... for Wind (CREW) Program Update 11 5 Data Sources The transition of the CREW Program to ... Windy GulchAll Turbine Group Potential Energy Production Turbine XXX SUSPENDED ...

  19. Remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Rifle, Colorado: Final report

    SciTech Connect (OSTI)

    Not Available

    1992-02-01

    This volume contains Appendix F, bid schedule and specifications for remedial action on three sites: Old Rifle processing site; New Rifle processing site and Estes Gulch disposal site.

  20. Remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Rifle, Colorado: Final report. Volume 3, Appendix F, Final design, specifications, and drawings

    SciTech Connect (OSTI)

    Not Available

    1992-02-01

    This volume contains Appendix F, bid schedule and specifications for remedial action on three sites: Old Rifle processing site; New Rifle processing site and Estes Gulch disposal site.

  1. Nevada Site Office News News Media Contact: For Immediate...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    GRITTY GULCH FIRE CONTAINED AT THE NEVADA NATIONAL SECURITY SITE North Las Vegas - Current information on the wildfire at the Nevada National Security Site (NNSS): NEW ...

  2. EV Everywhere Challenge Battery Workshop

    Broader source: Energy.gov [DOE]

    Backsplash for the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree O'Hare, Chicago, IL.

  3. EV Everywhere Grand Challenge- Battery Status and Cost Reduction Prospects

    Office of Energy Efficiency and Renewable Energy (EERE)

    Presentation given by technology manager David Howell at the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree O'Hare, Chicago, IL.

  4. EV Everywhere Batteries Workshop- Beyond Lithium Ion Breakout Session Report

    Office of Energy Efficiency and Renewable Energy (EERE)

    Breakout session presentation for the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree O'Hare, Chicago, IL.

  5. EV Everywhere EV Everywhere Grand Challenge- Electric Drive (Power Electronics and Electric Machines) Workshop Agenda

    Broader source: Energy.gov [DOE]

    Agenda for the EV Everywhere Grand Challenge - Electric Drive Workshop on July 24, 2012 at the Doubletree O'Hare, Chicago, IL

  6. Dosage compensation can buffer copy-number variation in wild...

    Office of Scientific and Technical Information (OSTI)

    Publisher: eLife Sciences Publications, Ltd. Sponsoring Org: USDOE Country of Publication: United States Language: English Word Cloud More Like This Free Publicly Accessible Full ...

  7. Taming the Wild World of Management, Performance and Communication - 13459

    SciTech Connect (OSTI)

    Ford, Laurie

    2013-07-01

    Management has evolved a long way from its original meaning of 'governing a horse'. The industrial revolution fostered 'scientific management'; 1930's Hawthorne studies discovered that people's social interactions could alter productivity; and the dawn of the computer age in the post-war 1950's brought general systems theory into management thinking. Today, mobile wireless connectivity aims to transform ever-changing networks of players, mandates, and markets into something that can be 'managed'. So why is there no clear and simple recipe for how to practice management? We talk about financial management, safety management, and operations management, but surely the 'management' part of those endeavors will share the same set of practices. Instead, we are still arguing for 'management' to include everything from developing people to negotiating contracts. A manager's job may include many things, but one of them, the job of management, needs to be nailed down. Three standard practices for managing in a network are developed: (a) support the dialogues that connect people vital to accomplishing a goal or objective; (b) develop and sustain the scoreboards that serve as a road-map to reach the goal; and (c) control the feedback to 'govern the horse'. These three practices are useful for more than reaching goals, as they also support coordinating across boundaries and running productive meetings. The dialogues for productive relationships, scoreboards for goals and deliverables, and feedback for performance together constitute a recipe for managing in a networked world. (authors)

  8. Department of Energy Seeks Public Comment on Designation of Energy...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    MT Holiday Inn 22 North Last Chance Gulch Helena, MT 59601 November 1, 2005 Boise, ID Harrison Plaza Suite Hotel 409 S. Cole Road Boise, ID 83709 November 1, 2005 Sacramento, CA ...

  9. ARM - Logistics

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... Silver Gulch 2195 Old Steese Highway (great beer selection) Reservations: 907.452.2739 Turtle Club 10-Mile Old Steese Highway (great prime rib) Reservations: 907.457.3883 Zach's ...

  10. David Turner! NERSC User Services Group NERSC Data Management

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Data Management --- 1 --- September 10, 2013 Overview * File S ystem R eview, D ata S haring, D ata T ransfer - David T urner * GlobusOnline D emo - Shreyas C holia * HPSS - Lisa G ...

  11. EV Everywhere Workshop: Electric Motors and Critical Materials Breakout Group Report

    Broader source: Energy.gov [DOE]

    Presentation given at the EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL.

  12. A Look at MEMS Applications | GE Global Research

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    this video on www.youtube.com, or enable JavaScript if it is disabled in your browser. hare This Article Click to email this to a friend (Opens in new window) Share on Facebook...

  13. ARM - Publications: Science Team Meeting Documents

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    on the TOGA-COARE Bulk Algorithm for Computing the Air-Sea Fluxes Fairall, C.W., and Hare, J.E., National Oceanic and Atmospheric Administration- Environmental Technology...

  14. EV Everywhere Battery Workshop: Preliminary Target-Setting Framework

    Broader source: Energy.gov [DOE]

    Presentation given by Vehicle Technologies Office analyst Jacob Ward at the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree O'Hare, Chicago, IL.

  15. EV Everywhere Electric Drive Workshop: Preliminary Target-Setting Framework

    Broader source: Energy.gov [DOE]

    Presentation given by Vehicle Technologies Office analyst Jake Ward at the EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL.

  16. EV Everywhere Grand Challenge - Battery Status and Cost Reduction...

    Broader source: Energy.gov (indexed) [DOE]

    Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree O'Hare, Chicago, IL. 5howellb.pdf (1.24 MB) More Documents & Publications PHEV Battery Cost Assessment ...

  17. This list does not imply DOE endorsement of the individuals or...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Jeff jeff.hare@cascadeenergy.com 801-770-4332 UT Hash IV, Robert bhash@airsystemsales.com 615-373-0039 TN Hunter, Bill bhunter@aircleantech.com 206-860-4930 WA J Jackson, ...

  18. Traction Drive Systems Breakout

    Broader source: Energy.gov [DOE]

    Presentation given at the EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL.

  19. EV Everywhere Workshop: Traction Drive Systems Breakout Group Report

    Broader source: Energy.gov [DOE]

    Presentation given at the EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL.

  20. EV Everywhere Grand Challenge Introduction for Electric Drive Workshop

    Broader source: Energy.gov [DOE]

    Presentation given by EERE Assistant Secretary David Danielson at the EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL.

  1. Electric Motors and Critical Materials

    Broader source: Energy.gov [DOE]

    Presentation given at the EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL.

  2. Shreyas Cholia! Data and Analytics Services, NERSC

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Design Patterns in Web Gateways for Scientific Data --- 1 --- Joint F acili+es U ser F ... --- 2 --- Overview * Mo+va+on * PaDerns - Web D ata S haring - End---to---End F rameworks ...

  3. BR UFF BIG PINEY WILD ROSE BLU E GAP BR UFF UNIT WAMSUT TER

    U.S. Energy Information Administration (EIA) Indexed Site

    Authors: Sam Limerick (1), Lucy Luo (1), Gary Long (2), David Morehouse (2), Jack Perrin (1), Steve Jackson (1) and Robert King (2) (1) Z, Inc., (2) Energy Information ...

  4. Selective progressive response of soil microbial community to wild oat roots

    SciTech Connect (OSTI)

    DeAngelis, K.M.; Brodie, E.L.; DeSantis, T.Z.; Andersen, G.L.; Lindow, S.E.; Firestone, M.K.

    2008-10-01

    Roots moving through soil enact physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. Use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies previously reported compositional changes, including increases in chitinase and protease specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change in 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA T-RFLP analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared to bulk soil, but then increased in older root zones. Quantitative PCR revealed {beta}-Proteobacteria and Actinobacteria present at about 10{sup 8} copies of 16S rRNA genes g{sup -1} soil, with Nitrospira having about 10{sup 5} copies g{sup -1} soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in function in progressively more mature rhizosphere zones.

  5. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    this tangle, the picture that emerged is of cometary particles containing primarily silicate materials formed within the Solar System, including some grains born in the high...

  6. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    them contributed to many of the findings that are shedding new light on how the Solar System was formed. The Stardust results show that the mixing of materials throughout the...

  7. BR UFF BIG PINEY WILD ROSE BLU E GAP BR UFF UNIT WAMSUT TER

    U.S. Energy Information Administration (EIA) Indexed Site

    BIG PINEY TIP TOP BIR D CANYON SWAN FONTEN ELL E LABARGE HOGSBACK CHIMNEY BUT TE BIG PINEY AREA TIP TOP UNI T LINCOLN ROAD BLU E FOREST DEER HILL FOGART Y CREEK GREEN RIVER BEND ...

  8. BR UFF BIG PINEY WILD ROSE BLU E GAP BR UFF UNIT WAMSUT TER

    U.S. Energy Information Administration (EIA) Indexed Site

    BIG PINEY TIP TOP BIR D CANYON SWAN FONTEN ELL E LABARGE HOGSBACK CHIMNEY BUT TE BIG PINEY AREA TIP TOP UNI T LINCOLN ROAD BLU E FOREST SWAN DEER HILL FOGART Y CREEK GREEN RIVER ...

  9. Protein expression, characterization and activity comparisons of wild type and mutant DUSP5 proteins

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Nayak, Jaladhi; Gastonguay, Adam J.; Talipov, Marat R.; Vakeel, Padmanabhan; Span, Elise A.; Kalous, Kelsey S.; Kutty, Raman G.; Jensen, Davin R.; Pokkuluri, Phani Raj; Sem, Daniel S.; et al

    2014-12-18

    Background: The mitogen-activated protein kinases (MAPKs) pathway is critical for cellular signaling, and proteins such as phosphatases that regulate this pathway are important for normal tissue development. Based on our previous work on dual specificity phosphatase-5 (DUSP5), and its role in embryonic vascular development and disease, we hypothesized that mutations in DUSP5 will affect its function. Results: In this study, we tested this hypothesis by generating full-length glutathione-S-transferase-tagged DUSP5 and serine 147 proline mutant (S147P) proteins from bacteria. Light scattering analysis, circular dichroism, enzymatic assays and molecular modeling approaches have been performed to extensively characterize the protein form and function.more » We demonstrate that both proteins are active and, interestingly, the S147P protein is hypoactive as compared to the DUSP5 WT protein in two distinct biochemical substrate assays. Furthermore, due to the novel positioning of the S147P mutation, we utilize computational modeling to reconstruct full-length DUSP5 and S147P to predict a possible mechanism for the reduced activity of S147P. Conclusion: Taken together, this is the first evidence of the generation and characterization of an active, full-length, mutant DUSP5 protein which will facilitate future structure-function and drug development-based studies.« less

  10. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Stardust mission returned to Earth thousands of tiny particles snagged from the coma of comet 81PWild 2. Four ALS beamlines and the researchers using them were among the...

  11. BR UFF BIG PINEY WILD ROSE BLU E GAP BR UFF UNIT WAMSUT TER

    U.S. Energy Information Administration (EIA) Indexed Site

    Gas Reserve Class No 2001 gas reserves 0.1 - 10 MMCF 10.1 - 100 MMCF 100.1 - 1,000 MMCF 1,000.1 - 10,000 MMCF 10,000.1 - 100,000 MMCF > 100,000 MMCF Basin Outline ID The mapped oil and gas field boundary outlines were created by the Reserves and Production Division, Office of Oil and Gas, Energy Information Administration pursuant to studies required by Section 604 of the Energy Policy and Conservation Act Amendments of 2000 (P.L. 106-469). The boundaries are not informed by subsurface

  12. Particles from Comet 81P/Wild 2 Viewed by ALS Microscopes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Particles from Comet 81PWild 2 Viewed by ALS Microscopes Print NASA's 200-million, seven-year-long Stardust mission returned to Earth thousands of tiny particles snagged from the...

  13. Comet 81P/Wild 2 Under a Microscope (Journal Article) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Comet 81PWild 2 Under a Microscope Citation Details In-Document Search Title: Comet ... Publication Date: 2007-01-16 OSTI Identifier: 897746 Report Number(s): ...

  14. BR UFF BIG PINEY WILD ROSE BLU E GAP BR UFF UNIT WAMSUT TER

    U.S. Energy Information Administration (EIA) Indexed Site

    (1) and Robert King (2) (1) Z, Inc., (2) Energy Information Administration BIG PINEY TIP ... LINCOLN ROAD BLU E FOREST DEER HILL FOGART Y CREEK GREEN RIVER BEND DRY PINEY SWAN S ...

  15. BR UFF BIG PINEY WILD ROSE BLU E GAP BR UFF UNIT WAMSUT TER

    U.S. Energy Information Administration (EIA) Indexed Site

    (1) and Robert King (2) (1) Z, Inc., (2) Energy Information Administration BIG PINEY TIP ... BLU E FOREST SWAN DEER HILL FOGART Y CREEK GREEN RIVER BEND DRY PINEY SWAN S HOGSBACK AREA ...

  16. Ankit Bhagatwala! NERSC User Services Group! New User Training!

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Ankit Bhagatwala! NERSC User Services Group! ! New User Training! March 21, 2016 Computing Environment Node Types * Login nodes - Shared w ith o ther u sers - Code c ompila3on, j ob p repara3on a nd s ubmission * Compute n odes - Not s hared ( except s hared q ueue o n C ori) * Service nodes - File s ystem a ccess ( lustre), d ata m ovement ( HPSS), network c onnec3ons t o o utside w orld, e tc. - Not a ccessed d irectly --- 2 --- Login Node Configuration * Edison - Twelve n odes * 16 c ores, 2

  17. Radiation-induced DNA damage and the relative biological effectiveness of 18F-FDG in wild-type mice

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Taylor, Kristina; Lemon, Jennifer A.; Boreham, Douglas R.

    2014-05-28

    Clinically, the most commonly used positron emission tomography (PET) radiotracer is the glucose analog 2-[18F] fluoro-2-deoxy-d-glucose (18F-FDG), however little research has been conducted on the biological effects of 18F-FDG injections. The induction and repair of DNA damage and the relative biological effectiveness (RBE) of radiation from 18F-FDG relative to 662 keV γ-rays were investigated. The study also assessed whether low-dose radiation exposure from 18F-FDG was capable of inducing an adaptive response. DNA damage to the bone marrow erythroblast population was measured using micronucleus formation and lymphocyte γH2A.X levels. To test the RBE of 18F-FDG, mice were injected with a rangemore » of activities of 18F-FDG (0–14.80 MBq) or irradiated with Cs-137 γ-rays (0–100 mGy). The adaptive response was investigated 24 h after the 18F-FDG injection by 1 Gy in vivo challenge doses for micronucleated reticulocyte (MN-RET) formation or 1, 2 and 4 Gy in vitro challenges doses for γH2A.X formation. A significant increase in MN-RET formation above controls occurred following injection activities of 3.70, 7.40 or 14.80 MBq (P < 0.001) which correspond to bone marrow doses of ~35, 75 and 150 mGy, respectively. Per unit dose, the Cs-137 radiation exposure induced significantly more damage than the 18F-FDG injections (RBE = 0.79 ± 0.04). A 20% reduction in γH2A.X fluorescence was observed in mice injected with a prior adapting low dose of 14.80 MBq 18F-FDG relative to controls (P < 0.019). A 0.74 MBq 18F-FDG injection, which gives mice a dose approximately equal to a typical human PET scan, did not cause a significant increase in DNA damage nor did it generate an adaptive response. Typical 18F-FDG injection activities used in small animal imaging (14.80 MBq) resulted in a decrease in DNA damage, as measured by γH2A.X formation, below spontaneous levels observed in control mice. Lastly, the 18F-FDG RBE was <1.0, indicating that the mixed radiation quality and/or low dose rate from PET scans is less damaging than equivalent doses of gamma radiation.« less

  18. Fujifilm_NERSC_StorageOutlook.pptx

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    - Workload c an s aturate s ystem a nd c ause i ssues f or s hared u sers - Beam l ine o r e nd s taon w ork s chedule d rives b andwidth n eeds --- 6 --- Addressing large...

  19. Oct_2015_IM_Response_to_Public_Comments.xlsx

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    e nrollment a nd p rior t o a ny S EM a ctivity, u tilities w ill r eceive a " user n ame" a nd "password" t o a ccess t he s ecure o nline E SI S ecure F ile S hare (...

  20. EV Everywhere Framing Workshop - Report Out & Lessons Learned | Department

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of Energy - Report Out & Lessons Learned EV Everywhere Framing Workshop - Report Out & Lessons Learned Presentation given at the EV Everywhere Grand Challenge : Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL. 2_davis_ed.pdf (589.87 KB) More Documents & Publications EV Everywhere Framing Workshop

  1. EV Everywhere Framing Workshop Report Out & Lessons Learned | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Energy Report Out & Lessons Learned EV Everywhere Framing Workshop Report Out & Lessons Learned Presentation given at the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree O'Hare, Chicago, IL. 3_davis_b.pdf (588.37 KB) More Documents & Publications EV Everywhere Framing Workshop -

  2. Richard Gerber! NERSC User Services NUG Teleconference

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... 4 --- Fair Share Scheduling Experiment on Edison * What a re c urrent u sage g oals? - DARPA M ission P artners: 2 5% - Each D OE O ffice g ets a s hare o f t he r emaining 7 5% b ...

  3. BPA-2013-01256-FOIA Request

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    M1C1-Ti SSQcJTES, RC. AttojrneyN at.Law RECEIVED BY tWA FOIA OFFICE TillS DATE - 1143 DUE DATE: OF COUNS 6L 0014 5. KATES bATneonow4b. WA RuTh P HARING IL&Tri5w fri. HC'RDCZIcO Ws...

  4. Utilization of ash from municipal solid waste combustion

    SciTech Connect (OSTI)

    Jones, C.; Hahn, J.; Magee, B.; Yuen, N.; Sandefur, K.; Tom, J.; Yap, C.

    1999-09-01

    This ash study investigated the beneficial use of municipal waste combustion combined ash from the H-POWER facility in Oahu. These uses were grouped into intermediate cover for final closure of the Waipahu landfill, daily cover at the Waimanalo Gulch Landfill, and partial replacement for aggregate in asphalt for road paving. All proposed uses examine combined fly and bottom ash from a modern waste-to-energy facility that meets requirements of the Clean Air Act Amendments for Maximum Achievable Control Technology.

  5. Remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Rifle, Colorado

    SciTech Connect (OSTI)

    Not Available

    1992-02-01

    This appendix assesses the present conditions and data gathered about the two inactive uranium mill tailings sites near Rifle, Colorado, and the designated disposal site six miles north of Rifle in the area of Estes Gulch. It consolidates available engineering, radiological, geotechnical, hydrological, meteorological, and other information pertinent to the design of the Remedial Action Plan (RAP). The data characterize conditions at the mill, tailings, and disposal site so that the Remedial Action Contractor (RAC) may complete final designs for the remedial actions.

  6. Remedial action plan and site design for stabilization of the inactive uranium mill tailings sites at Rifle, Colorado. Volume 2, Appendices D and E: Final report

    SciTech Connect (OSTI)

    Not Available

    1992-02-01

    This appendix assesses the present conditions and data gathered about the two inactive uranium mill tailings sites near Rifle, Colorado, and the designated disposal site six miles north of Rifle in the area of Estes Gulch. It consolidates available engineering, radiological, geotechnical, hydrological, meteorological, and other information pertinent to the design of the Remedial Action Plan (RAP). The data characterize conditions at the mill, tailings, and disposal site so that the Remedial Action Contractor (RAC) may complete final designs for the remedial actions.

  7. Nevada Site Office News News Media Contact: For Immediate Release:

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    3, 2011 702-630-0120 (afterhours) 2:39:15 PM (PST) 702-683-0601 (afterhours) ***UPDATE*** CREWS FIGHTING WILDFIRE AT THE NEVADA NATIONAL SECURITY SITE North Las Vegas - Current information on the wildfire at the Nevada National Security Site (NNSS): NEW INFORMATION * Fire named Gritty Gulch Fire * Approximately 29 acres burned * Bureau of Land Management is conducting slurry air drops to surround the fire * The fire does not appear to be advancing PREVIOUS INFORMATION * Located in a remote area

  8. Significant Increase in Hydrogen Photoproduction Rates and Yields by Wild-Type Algae is Detected at High Photobioreactor Gas Phase Volume (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-07-01

    This NREL Hydrogen and Fuel Cell Technical Highlight describes how hydrogen photoproduction activity in algal cultures can be improved dramatically by increasing the gas-phase to liquid-phase volume ratio of the photobioreactor. NREL, in partnership with subcontractors from the Institute of Basic Biological Problems in Pushchino, Russia, demonstrated that the hydrogen photoproduction rate in algal cultures always decreases exponentially with increasing hydrogen partial pressure above the culture. The inhibitory effect of high hydrogen concentrations in the photobioreactor gas phase on hydrogen photoproduction by algae is significant and comparable to the effect observed with some anaerobic bacteria.

  9. Radiation-induced DNA damage and the relative biological effectiveness of 18F-FDG in wild-type mice

    SciTech Connect (OSTI)

    Taylor, Kristina; Lemon, Jennifer A.; Boreham, Douglas R.

    2014-05-28

    Clinically, the most commonly used positron emission tomography (PET) radiotracer is the glucose analog 2-[18F] fluoro-2-deoxy-d-glucose (18F-FDG), however little research has been conducted on the biological effects of 18F-FDG injections. The induction and repair of DNA damage and the relative biological effectiveness (RBE) of radiation from 18F-FDG relative to 662 keV γ-rays were investigated. The study also assessed whether low-dose radiation exposure from 18F-FDG was capable of inducing an adaptive response. DNA damage to the bone marrow erythroblast population was measured using micronucleus formation and lymphocyte γH2A.X levels. To test the RBE of 18F-FDG, mice were injected with a range of activities of 18F-FDG (0–14.80 MBq) or irradiated with Cs-137 γ-rays (0–100 mGy). The adaptive response was investigated 24 h after the 18F-FDG injection by 1 Gy in vivo challenge doses for micronucleated reticulocyte (MN-RET) formation or 1, 2 and 4 Gy in vitro challenges doses for γH2A.X formation. A significant increase in MN-RET formation above controls occurred following injection activities of 3.70, 7.40 or 14.80 MBq (P < 0.001) which correspond to bone marrow doses of ~35, 75 and 150 mGy, respectively. Per unit dose, the Cs-137 radiation exposure induced significantly more damage than the 18F-FDG injections (RBE = 0.79 ± 0.04). A 20% reduction in γH2A.X fluorescence was observed in mice injected with a prior adapting low dose of 14.80 MBq 18F-FDG relative to controls (P < 0.019). A 0.74 MBq 18F-FDG injection, which gives mice a dose approximately equal to a typical human PET scan, did not cause a significant increase in DNA damage nor did it generate an adaptive response. Typical 18F-FDG injection activities used in small animal imaging (14.80 MBq) resulted in a decrease in DNA damage, as measured by γH2A.X formation, below spontaneous levels observed in control mice. Lastly, the 18F-FDG RBE was <1.0, indicating that the mixed radiation quality and/or low dose rate from PET scans is less damaging than equivalent doses of gamma radiation.

  10. NERSC User Services Group Hybrid MPI/ OpenMP Programming

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    He! NERSC User Services Group Hybrid MPI/ OpenMP Programming --- 1 --- NUG 2 013, F ebruary 1 5, 2 013 Outline * Architecture T rend * Brief R eview o f O penMP B asics * Benefits o f H ybrid M PI/OpenMP * Hybrid M PI/OpenMP P rogramming M odel * Hybrid M PI/OpenMP I ssues * Compile a nd R un h ybrid M PI/OpenMP a t N ERSC Common Architectures * Shared M emory A rchitecture - Mul'ple C PUs s hare g lobal m emory, c ould h ave l ocal c ache - Uniform M emory A ccess ( UMA) - Typical S hared M

  11. Yun (Helen) He, NERSC!

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NERSC! Mar 23, 2015 OpenMP Basics and MPI/OpenMP Scaling --- 1 --- Outline * Introduc)ons t o O penMP * Features i n O penMP 3 .1 * What's n ew i n O penMP 4 .0 * Adding O penMP t o y our c ode u sing C ray R eveal * Hybrid M PI/OpenMP S caling --- 2 --- Introductions to OpenMP --- 3 --- Common Architectures * Shared M emory A rchitecture - Mul)ple C PUs s hare g lobal m emory, c ould h ave l ocal c ache - Uniform M emory A ccess ( UMA) - Typical S hared M emory P rogramming M odel: O penMP,

  12. Lisa Gerhardt! NERSC User Services Group! NUG Training!

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    February 23, 2015 Data Management at NERSC Where Do I Put My Data? --- 2 --- * Overview o f N ERSC fi le s ystems - Local v s. G lobal - Permanent v s. P urged - Personal v s. S hared * HPSS A rchive S ystem - What i s i t a nd h ow t o u se i t * Data S haring NERSC File Systems --- 3 --- The compute and storage systems 2015 Produc=on C lusters Carver, P DSF, J GI, MatComp, Planck /global/ scratch 4 PB /project 5 PB /home 250 TB 70 P B s tored, 2 40 P B capacity, 4 0 y ears o f community d ata

  13. CCM_NUG20120202.pptx

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Hopper c ompute n odes r un _ ______ A. L ight v ersion o f O pera9ng S ystem B. S tandard ( full) L inux O pera9ng S ystem * Hopper c ompute n odes d on't s upport _ _____ A. D ynamic s hared l ibraries B. s sh C. B oth A a nd B Hopper q uiz * Hopper c ompute n odes r un _ ______ A. L ight v ersion o f O pera9ng S ystem B. S tandard ( full) L inux O pera9ng S ystem * Hopper c ompute n odes d on't s upport _ _____ A. D ynamic s hared l ibraries B. s sh C. B oth A a nd B Hopper q uiz A B This t

  14. Research Highlight

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Modification of the Atmospheric Boundary Layer by a Small Island: Observations from Nauru Submitter: Long, C. N., NOAA Global Monitoring Division/CIRES Area of Research: Cloud Distributions/Characterizations Working Group(s): Radiative Processes Journal Reference: Matthews, S., J. M. Hacker, J. Cole, J. Hare, C. N. Long, and R. M. Reynolds, (2007): Modification of the atmospheric boundary layer by a small island: observations from Nauru, MWR, Vol. 135, No. 3, pages 891–905. Figure 1.

  15. Electric Vehicle Safety Training for Emergency Responders | Department of

    Broader source: Energy.gov (indexed) [DOE]

    Presentation given at the EV Everywhere Grand Challenge … Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL. 7b_electric_motors-and_critical_materials_ed.pdf (154.22 KB) More Documents & Publications EV Everywhere Workshop: Power Electronics and Thermal Management Breakout Session Report EV Everywhere Workshop: Electric Motors and Critical Materials Breakout Group Report EV Everywhere - Charge to Breakout Sessions

  16. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Surface Energy Budget Measurements from Nauru99 C. W. Fairall, J. E. Hare, A. A. Grachev, and A. B. White National Oceanic and Atmospheric Administration Environmental Technology Laboratory Boulder, Colorado Introduction The National Oceanic and Atmospheric Administration (NOAA) research vessel (R/V) Ronald H. Brown conducted a series of measurements in transit to and in the vicinity of the U.S. Department of Energy (DOE) Cloud and Radiation Testbed (CART) site on Nauru in June-July 1999 as part

  17. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Examination of Island Effects on Near-Surface Bulk Meteorology and Air-Sea Fluxes from the Nauru99 Field Program C. W. Fairall and M. J. Post National Oceanic and Atmospheric Administration Environmental Technology Laboratory Boulder, Colorado J. E. Hare, A. B. White, and A. A. Grachev Cooperative Institute for Research in Environmental Sciences University of Colorado and National Oceanic and Atmospheric Administration Environmental Technology Laboratory Boulder, Colorado Introduction The

  18. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Nauru99 Ship and Buoy Intercomparison J. E. Hare and A. A. Grachev Cooperative Institute for Research in Environmental Sciences, University of Colorado National Oceanic and Atmospheric Administration, Environmental Technology Laboratory Boulder, Colorado C. W. Fairall and M. J. Post National Oceanic and Atmospheric Administration Environmental Technology Laboratory Boulder, Colorado R. M. Reynolds and S. Smith Brookhaven National Laboratory Brookhaven, New York H. Ishida Kobe University of

  19. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Turbulent Surface Flux Measurements from Nauru99 C. W. Fairall, J. E. Hare, and A. A. Grachev National Oceanic and Atmospheric Administration Environmental Technology Laboratory Boulder, Colorado Introduction The National Oceanic and Atmospheric Administration (NOAA) Research Vessel (R/V) Ronald H. Brown conducted a series of measurements in transit to and in the vicinity of the U.S. Department of Energy (DOE) Cloud and Radiation Testbed (CART) site on Nauru in June-July 1999 as part of a joint

  20. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Observation of 4-5 Day Meridional Wind and Surface Stress Oscillations During Nauru99 A. A. Grachev and J. E. Hare University of Colorado Cooperative Institute for Research in Environmental Sciences National Oceanic and Atmospheric Administration Environmental Technology Laboratory Boulder, Colorado C. W. Fairall National Oceanic and Atmospheric Administration Environmental Technology Laboratory Boulder, Colorado Introduction The existence of the easterly wave disturbances in the Tropical

  1. Blue Gene/Q: Sequoia and Mira | Argonne Leadership Computing Facility

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Blue Gene/Q: Sequoia and Mira Authors: Bill Allcock, Anna Maria Bailey, Ray Bair, Charles Bacon, Ramesh Balakrishnan, Adam Bertsch, Barna Bihari, Brian Carnes, Dong Chen, George Chiu, Richard Coffey, Susan Coghlan, Paul Coteus, Kim Cupps, Erik W. Draeger, Thomas W. Fox, Larry Fried, Mark Gary, Jim Glosli, Thomas Gooding, John Gunnels, John Gyllenhaal, Jeff Hammond, Ruud Haring, Philip Heidelberger, Mark Hereld, Todd Inglett, K.H. Kim, Kalyan Kumaran, Steve Langer, Amith Mamidala, Rose McCallen,

  2. EVMS Training Snippet: 1.1 DOE Order 413.3B EVM Requirements | Department

    Office of Environmental Management (EM)

    Report | Department of Energy Batteries Workshop - Beyond Lithium Ion Breakout Session Report EV Everywhere Batteries Workshop - Beyond Lithium Ion Breakout Session Report Breakout session presentation for the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree OHare, Chicago, IL. report_out-beyond_lithium_ion_b.pdf (138.93 KB) More Documents & Publications EV Everywhere Batteries Workshop - Next Generation Lithium Ion Batteries Breakout Session

  3. EV Everywhere Batteries Workshop - Materials Processing and Manufacturing

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Breakout Session Report | Department of Energy Materials Processing and Manufacturing Breakout Session Report EV Everywhere Batteries Workshop - Materials Processing and Manufacturing Breakout Session Report Breakout session presentation for the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree OHare, Chicago, IL. report_out-manufacturing_b.pdf (117.4 KB) More Documents & Publications EV Everywhere Batteries Workshop - Next Generation Lithium Ion

  4. EV Everywhere Batteries Workshop - Next Generation Lithium Ion Batteries

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Breakout Session Report | Department of Energy Next Generation Lithium Ion Batteries Breakout Session Report EV Everywhere Batteries Workshop - Next Generation Lithium Ion Batteries Breakout Session Report Breakout session presentation for the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree OHare, Chicago, IL. report_out-next-generation_li-ion_b.pdf (136.48 KB) More Documents & Publications EV Everywhere Batteries Workshop - Beyond Lithium Ion

  5. EV Everywhere Batteries Workshop - Pack Design and Optimization Breakout

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Session Report | Department of Energy Pack Design and Optimization Breakout Session Report EV Everywhere Batteries Workshop - Pack Design and Optimization Breakout Session Report Breakout session presentation for the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree OHare, Chicago, IL. report_out-pack_design_b.pdf (141.92 KB) More Documents & Publications EV Everywhere Batteries Workshop - Beyond Lithium Ion Breakout Session Report EV Everywhere

  6. EV Everywhere Battery Workshop Introduction | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Workshop Introduction EV Everywhere Battery Workshop Introduction Presentation given at the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree O'Hare, Chicago, IL. 1_sandalow_b.pdf (3.21 MB) More Documents & Publications EV Everywhere Framing Workshop Overview EV Everywhere Consumer Acceptance and Charging Infrastructure Workshop Introduction Battery and Electric Drive Awardee List from American Recovery and Reinvestment Act funding

  7. EV Everywhere Battery Workshop: Setting the Stage for the EV Everywhere

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Grand Challenge | Department of Energy Setting the Stage for the EV Everywhere Grand Challenge EV Everywhere Battery Workshop: Setting the Stage for the EV Everywhere Grand Challenge Presentation given at the EV Everywhere Grand Challenge: Battery Workshop by EERE Assistant Secretary David Danielson on July 26, 2012 at the Doubletree O'Hare, Chicago, Illinois. 2 Danielson EV Everywhere Battery presentation [Read-Only].pdf (408.26 KB) More Documents & Publications EV Everywhere Grand

  8. EV Everywhere Grand Challenge - Battery Workshop Agenda | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Energy Agenda EV Everywhere Grand Challenge - Battery Workshop Agenda Agenda for the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree O'Hare, Chicago, IL. agenda_b.pdf (196.97 KB) More Documents & Publications EV Everywhere Grand Challenge - Charge to the Breakout Groups EV Everywhere Grand Challenge Introduction for Electric Drive Workshop EV Everywhere Grand Challenge Kick-Off

  9. EV Everywhere Grand Challenge - Battery Workshop attendees list |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy attendees list EV Everywhere Grand Challenge - Battery Workshop attendees list Attendance list for the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree OHare, Chicago, IL. companies_in_attendance_b.pdf (149.45 KB) More Documents & Publications EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric Machines) Workshop EV Everywhere Grand Challenge Overview EV Everywhere Grand Challenge Introduction for

  10. EV Everywhere Grand Challenge - Charge to the Breakout Groups | Department

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of Energy Charge to the Breakout Groups EV Everywhere Grand Challenge - Charge to the Breakout Groups Presentation given at the EV Everywhere Grand Challenge: Battery Workshop on July 26, 2012 held at the Doubletree OHare, Chicago, IL. 7_howell_b.pdf (796.65 KB) More Documents & Publications EV Everywhere - Charge to Breakout Sessions EV Everywhere Grand Challenge - Battery Workshop Agenda EV Everywhere EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric

  11. EV Everywhere Grand Challenge - Electric Drive (Power Electronics and

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Electric Machines) Workshop | Department of Energy - Electric Drive (Power Electronics and Electric Machines) Workshop EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric Machines) Workshop List of companies in attendance at the Electric Drive Workshop held on July 24, 2012 at the Doubletree O'Hare, Chicago, IL companies_in_attendance_ed.pdf (145.65 KB) More Documents & Publications EV Everywhere Grand Challenge Introduction for Electric Drive Workshop EV

  12. EV Everywhere Workshop: Power Electronics and Thermal Management Breakout

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Session Report | Department of Energy Power Electronics and Thermal Management Breakout Session Report EV Everywhere Workshop: Power Electronics and Thermal Management Breakout Session Report Presentation given at the EV Everywhere Grand Challenge … Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL. 9b_traction_drive_systems_ed.pdf (122.88 KB) More Documents & Publications EV Everywhere Batteries Workshop -

  13. QA Corporate Board Meeting - June 2010 | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    June 2010 QA Corporate Board Meeting - June 2010 7th EM Quality Assurance Corporate Board Meeting Meeting Location: Marriott Chicago O'Hare, 8535 West Higgins Road, Chicago, IL 60631 Room: TBD Draft Agenda for June 9, 2010 Documents Available for Download Meeting and Presentation Materials (6.16 MB) Meeting Minutes (173.99 KB) More Documents & Publications 2010 Quality Assurance Improvement Project Plan 2012 Quality Assurance Improvement Project Plan QA Corporate Board Meeting - September

  14. Fermilab | Visit Fermilab | Transportation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Transportation Transportation to and from Chicago O'Hare Airport or Midway Airport is available by limousine, taxi or car rental. Transportation to and from the Geneva local commuter Metra train station on the Union Pacific West line is available by taxi or Pace Call-n-Ride. Car rental All of the usual rental companies (such as Hertz, Avis, Budget and National) are located at the airports. Limousine service Reservations for limousine service should be made in advance when possible. West Suburban

  15. Table 2. Ten largest plants by generation capacity, 2014

    U.S. Energy Information Administration (EIA) Indexed Site

    Idaho" ,"Plant","Primary energy source","Operating company","Net summer capacity (MW)" 1,"Brownlee","Hydroelectric","Idaho Power Co",744 2,"Dworshak","Hydroelectric","USACE Northwestern Division",400 3,"Langley Gulch Power Plant","Natural gas","Idaho Power Co",299.7 4,"Evander Andrews Power Complex","Natural gas","Idaho Power

  16. Remedial action plan and site conceptual design for stabilization of the inactive uranium mill tailings sites at Rifle, Colorado. Appendix D, Final report

    SciTech Connect (OSTI)

    1992-02-01

    This appendix assesses the present conditions and data gathered about the two designated inactive uranium mill tailings sites near Rifle, Colorado, and the proposed disposal site six miles north of Rifle in the area of Estes Gulch. It consolidates available engineering, radiological, geotechnical, hydrological, meteorological, and other information pertinent to the design of the Remedial Action Plan (RAP). The data characterize conditions at the mill, tailings, and disposal site so that the Remedial Action Contractor (RAC) may complete final designs for the remedial actions.

  17. Microsoft Word - GUN 2005 CR.doc

    Office of Legacy Management (LM)

    Gunnison, Colorado Page 8-1 8.0 Gunnison, Colorado, Disposal Site 8.1 Compliance Summary The Gunnison Disposal Site, inspected on June 21, 2005, was in excellent condition. Six perimeter sign and the entrance sign were missing and bullets had damaged several others. All former erosion areas were stable. Areas reseeded in 2004 along the former Chance Gulch haul road require further monitoring, and therefore, the BLM right-of-way permit is still active. Revegetation of reseeded areas on Tenderfoot

  18. Nevada Site Office News News Media Contact: For Immediate Release:

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4, 2011 11:56:36 AM (PST) ***UPDATE*** GRITTY GULCH FIRE CONTAINED AT THE NEVADA NATIONAL SECURITY SITE North Las Vegas - Current information on the wildfire at the Nevada National Security Site (NNSS): NEW INFORMATION * The fire is 100 percent contained * Bureau of Land Management completed 24 slurry air drops during the duration of the fire * Approximately 29 acres burned PREVIOUS INFORMATION * Located in a remote area (Area 19) of the 1,360-square-mile site * Fire most likely started from

  19. Significance of cyclic Pennsylvanian-Permian coral/algal buildups Snaky Canyon

    SciTech Connect (OSTI)

    Canter, K.L. ); Isaacson, P.E. )

    1991-02-01

    Five cyclic algal, hydrozoan, and coral buildups occur within a thick sequence of Pennsylvanian-Permian (Virgilian through Wolfcampain) carbonates in south-central Idaho. The Juniper Gulch Member of the Snaky Canyon Formation, as described by Skipp and coworkers, is approximately 600 m thick and contains four depositional facies, including: (1) open circulation outer( ) platform, (2) hydrozoan and phylloid algal mound-dominated carbonate buildup, (3) backmound, restricted platform/lagoon, and (4) restricted inner platform facies. Several microlithofacies, including lime mud-rich bafflestone, diversely fossiliferous packstone and grainstone, bryozoan lime floatstone, and phylloid algal and hydrozoan (Palaeoaplysina) lime bindstone are described within the phylloid algal mounds. Successional faunal assemblage stages are recognized within the buildups. Colonial rugose corals comprise a stabilization stage. When the algal communities of the diversification stage reached wave base, because of their rapid upward growth, cross-bedded oolitic grainstone and occasional cross-bedded dolomite shoals developed. Supratidal to high intertidal platform sedimentation is represented by dolomitic Palaeoaplysina bindstone, algal mat bindstone, and vuggy dolomite. Five vertical sequences of buildup development, each terminate by intertidal, supratidal, or erosional events, are seen in the Juniper Gulch Member in the North Howe stratigraphic section of the southern Lost River Range. The carbonate platform was constructed within a depositional basin that includes an eroded highland to the west, and a mixed siliciclastic-carbonate inner platform with craton uplifts to the east.

  20. Scott French! NERSC User Services Group! New User Training!

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    French! NERSC User Services Group! ! New User Training! August 13, 2015 Computing Environment Node Types * Login nodes - Shared w ith o ther u sers - Code c ompila3on, j ob p repara3on a nd s ubmission * MOM n odes ( Cray m achines) - Shared w ith o ther u sers - Where b atch s cript e xecutes - Will g o a way w hen w e t ransi3on t o S LURM * Compute n odes - Not s hared ( except s erial q ueues) --- 2 --- Login Node Configuration * Edison - Twelve n odes * 16 c ores, 2 .0 G Hz I ntel S andy B

  1. MLM-462 Contract Number AT-33-l-GtiN-53 MOUND LABORATCRY Operatsd By

    Office of Legacy Management (LM)

    This Doeumr;t Consists of 116 ?zges This is COPY of i.3 k MLM-462 Contract Number AT-33-l-GtiN-53 MOUND LABORATCRY Operatsd By MONSAmOC~ALGoMPANY MIAMISBURG, OHIO REPORT NO. 3 OF STIEUING CaW'M'B FOR DISPUSAL CF UNITS 111 AND IV (Completion Report for Disposal of UrLt IV, Runnymeade Road sr,d Dixon live. Dayton, Ohlo) . Date: April 17, 1950 Prepared By: -36L254- F. L. Halbach Chairnan., St33ricg Gcicmittes 1ssue.d: DISTRIHJTION copy 1. - Dr. Carroll A. Hochwalt copy 2. - Dr. M. M. Haring copy 3.

  2. Electric Drive Transportation Association Conference | Department of Energy

    Broader source: Energy.gov (indexed) [DOE]

    Presentation given at the EV Everywhere Grand Challenge - Electric Drive (Power Electronics and Electric Machines) Workshop on July 24, 2012 held at the Doubletree O'Hare, Chicago, IL. 4_rogers_ed.pdf (1.3 MB) More Documents & Publications Power Electronics and Thermal Management Breakout Session Advanced Power Electronics and Electric Motors (APEEM) R&D Program Overview Advanced Power Electronics and Electric Motors (APEEM) R&D Program Overview

    Test Drive 1 of 5 Test Drive Deputy

  3. 04-Environment-Turner.pdf

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Computing Environment Node Types * Login nodes - Shared - Job p repara,on a nd s ubmission * MOM n odes - Shared - Where b atch s cript e xecutes * Parallel j ob l auncher - Hopper/Edison: a prun - Carver: m pirun * Compute n odes - Not s hared * Except s erial q ueue --- 2 --- Login Nodes * Edison - Twelve n odes * 16 c ores, 2 .0GHz I ntel S andy B ridge * 512GB * Hopper - Eight n odes * 16 c ores, 2 .4GHz A MD O pteron - Four nodes * 32 c ores, 2 .0GHz A MD O pteron - 128GB * Carver - Four

  4. 06-DataManagement-Gerhardt.pdf

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    New User Training! July 15, 2014 Data Management at NERSC Where Do I Put My Data? --- 2 --- * Overview o f N ERSC fi le s ystems - Local v s. G lobal - Permanent v s. P urged * HPSS A rchive S ystem - What i s i t a nd h ow t o u se i t * Data S haring NERSC File Systems --- 3 --- The compute and storage systems 2014 Produc<on C lusters Carver, P DSF, J GI, MatComp, Planck /global/ scratch 4 PB /project 5 PB /home 250 TB 65 PB stored, 240 PB capacity, 4 0 y ears o f community d ata HPSS 16 x

  5. 08-2-SharingDataWeb-Cholia.pptx

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NERSC User Training, Aug 2015! Sharing Data at NERSC Sharing Data Internally --- 2 --- The /project directory * Your p roject w ill h ave a s hared p roject d irectory at /global/project/projectdirs/<dirname> * Shared group permissions for your project repo * h=ps://www.nersc.gov/users/storage---and---file--- systems/sharing---data/ --- 3 --- Give/take * Give a fi le t o a u ser: - give --- u < recipient---username> < file---or---directory> - This s ends i s i nto a h olding a

  6. E

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    E nergy S ciences N etwork: Overview a nd I mpact NERSC U sers G roup 2 016 Berkeley, CA March 2 1, 2 016 Kate P etersen M ace Energy S ciences N etwork ( ESnet) Science E ngagement E ngineer Lawrence B erkeley N aNonal L aboratory Overview Impact 2 ESnet is a dedicated m ission n etwork e ngineered to accelerate a broad range of science outcomes. We d o t his b y o ffering u nique c apabiliNes, a nd opNmizing t he n etwork f or d ata a cquisiNon, d ata placement, d ata s haring, d ata m

  7. David Turner! NERSC User Services Group!

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Computing Environment Node Types * Login nodes - Shared - Job p repara,on a nd s ubmission * MOM n odes - Shared - Where b atch s cript e xecutes * Parallel j ob l auncher - Hopper/Edison: a prun - Carver: m pirun * Compute n odes - Not s hared * Except s erial q ueue --- 2 --- Login Nodes * Edison - Six n odes * 16 c ores, 2 .0GHz I ntel S andy B ridge * 512GB * Hopper - Eight n odes * 16 c ores, 2 .4GHz A MD O pteron - Four n odes * 32 c ores, 2 .0GHz A MD O pteron - 128GB * Carver - Four n

  8. David Turner! NERSC User Services Group! NUG New User Training!

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Computing Environment Node Types * Login nodes - Shared - Job p repara,on a nd s ubmission * MOM n odes - Shared - Where b atch s cript e xecutes * Parallel j ob l auncher - Hopper/Edison: a prun - Carver: m pirun * Compute n odes - Not s hared * Except s erial q ueue --- 2 --- Login Nodes * Edison - Twelve n odes * 16 c ores, 2 .0 G Hz I ntel S andy B ridge, 5 12 G B * Hopper - Eight n odes * 16 c ores, 2 .4 G Hz A MD O pteron, 1 28GB - Four n odes * 32 c ores, 2 .0 G Hz A MD O pteron, 1 28GB *

  9. David Turner! NERSC User Services Group! New User Training!

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Computing Environment Node Types * Login nodes - Shared - Job p repara,on a nd s ubmission * MOM n odes - Shared - Where b atch s cript e xecutes * Parallel j ob l auncher - Hopper/Edison: a prun - Carver: m pirun * Compute n odes - Not s hared * Except s erial q ueue --- 2 --- Login Nodes * Edison - Twelve n odes * 16 c ores, 2 .0 G Hz I ntel S andy B ridge, 5 12 G B * Hopper - Eight n odes * 16 c ores, 2 .4 G Hz A MD O pteron, 1 28GB - Four n odes * 32 c ores, 2 .0 G Hz A MD O pteron, 1 28GB *

  10. Microsoft Word - Document11

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    S cheinker Can s tudying i nfinite d imensional s pace h elp u s i mprove h ealthcare? Abstract: Could a hotel with a guest in each room give a new guest her own room without asking a nyone t o l eave o r s hare r ooms? C ould a s urgeon w ith a p erfect s calpel c ut a pea into 5 pieces and reassemble them into a sphere the size of the sun? Could the dough lying in a pizza pan be pushed out of the middle to form a ring of crust without being ripped? In our world, the answer to each of these

  11. CMN

    Office of Legacy Management (LM)

    sl CMN - t%1UB SECRET Copy 15 MI.-396 L a SCIOTO LABORATORY MARION, OHIO ~S5_ Ct-Jt4 0 This Document Consists of 57 Pages This is Copy / o rf 23A ~S~~g.^a^~T CAMLM-396 !eo T /xY/ 'INITIALS i Contract Number AT-33-1-CEN-53 RHTG # I 1- BOX ry scIOTr LABORATORY C Operated By MONSANTO CHEMICAL COMPANY MARION, OHIO Er M. M. Haring ,u Laboratory Director rq - -- r - Er OUTLINE FOR "COLD STAND-BY" OPERATION OF SCIOTO LABORATORY * (Limited Operation and Maintenance) CAUTION This document

  12. Microwave digestion techniques in the sequential extraction of calcium, iron, chromium, manganese, lead, and zinc in sediments

    SciTech Connect (OSTI)

    Mahan, K.I.; Foderaro, T.A.; Garza, T.L.; Martinez, R.M.; Maroney, G.A.; Trivisonno, M.R.; Willging, E.M.

    1987-04-01

    The sequential extraction scheme of Tessier partitions metals in sediments into exchangeable, carbonate bound iron-manganese oxide bound, organic bound, and residual binding fractions. Extraction rate experiments using conventional and microwave heating showed that microwave heating produces results comparable to the conventional procedure. Sequential microwave extraction procedures were established from the results of the extraction rate experiments. Recoveries of total metals from NBS SRM 1645 ranged from 76% to 120% for the conventional procedure and 62% to 120% for the microwave procedure. Recoveries of total metals using the microwave and conventional techniques were reasonably comparable except for iron (62% by microwave vs. 76% by conventional). Substitution of an aqua regia/HF extraction for total/residual metals results in essentially complete recovery of metals. Precision obtained from 31 replicate samples of the California Gulch, Colorado, sediment yielded about an average 11% relative standard deviation excluding the exchangeable fraction which was more variable.

  13. Microsoft Word - appxa

    Office of Legacy Management (LM)

    GS05: Woman Creek at West Fenceline A.1.4 GS08: South Walnut Creek at Pond B-5 Outlet A.1.5 GS10: South Walnut Creek at B-1 Bypass A.1.6 GS11: North Walnut Creek at Pond A-4 Outlet A.1.7 GS12: North Walnut Creek at Pond A-3 Outlet A.1.8 GS13: North Walnut Creek Above Pond A-1 A.1.9 GS31: Woman Creek at Pond C-2 Outlet A.1.10 GS33: No Name Gulch at Walnut Creek A.1.11 GS51: Ditch South of Former 903 Pad A.1.12 GS59: Woman Creek Upstream of Antelope Springs Confluence A.1.13 B5INFLOW: South Walnut

  14. Gas-and water-saturated conditions in the Piceance Basin, Western Colorado: Implications for fractured reservoir detection in a gas-centered coal basin

    SciTech Connect (OSTI)

    Hoak, T.E.; Decker, A.D.

    1995-10-01

    Mesaverde Group reservoirs in the Piceance Basin, Western Colorado contain a large reservoir base. Attempts to exploit this resource base are stymied by low permeability reservoir conditions. The presence of abundant natural fracture systems throughout this basin, however, does permit economic production. Substantial production is associated with fractured reservoirs in Divide Creek, Piceance Creek, Wolf Creek, White River Dome, Plateau, Shire Gulch, Grand Valley, Parachute and Rulison fields. Successful Piceance Basin gas production requires detailed information about fracture networks and subsurface gas and water distribution in an overall gas-centered basin geometry. Assessment of these three parameters requires an integrated basin analysis incorporating conventional subsurface geology, seismic data, remote sensing imagery analysis, and an analysis of regional tectonics. To delineate the gas-centered basin geometry in the Piceance Basin, a regional cross-section spanning the basin was constructed using hydrocarbon and gamma radiation logs. The resultant hybrid logs were used for stratigraphic correlations in addition to outlining the trans-basin gas-saturated conditions. The magnitude of both pressure gradients (paludal and marine intervals) is greater than can be generated by a hydrodynamic model. To investigate the relationships between structure and production, detailed mapping of the basin (top of the Iles Formation) was used to define subtle subsurface structures that control fractured reservoir development. The most productive fields in the basin possess fractured reservoirs. Detailed studies in the Grand Valley-Parachute-Rulison and Shire Gulch-Plateau fields indicate that zones of maximum structural flexure on kilometer-scale structural features are directly related to areas of enhanced production.

  15. Richard Gerber! NERSC Senior Science Advisor! User Services Group Lead

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    User Services Group Lead NUG Webinar January 2014 --- 1 --- January 9 , 2 014 Agenda * Edison C onfigura6on f or A Y 2 014 * Alloca6on Y ear R ollover I ssues * Project D irectories p er P roject * NUG 2 014 U ser G roup M ee6ng * Automa6c I /O P rofiling f or Y our C ode * Give / T ake U 6lity f or S haring F iles * NUG Q ueue C ommiRee U pdate * User Survey Needs Your Input * Open D iscussion --- 2 --- Edison Update --- 3 --- Jeff B roughton NERSC D eputy f or O pera6ons Systems D epartment H

  16. H

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    H ybrid M PI/OpenMP, UPC, a nd C AF a t N ERSC Yun ( Helen) H e a nd W oo---Sun Y ang NERSC U ser G roup M eeFng February 2 , 2 012 2 Outline * Architecture T rend * Benefits o f H ybrid M PI/OpenMP * Hybrid M PI/OpenMP P rogramming M odel * Hybrid M PI/OpenMP I ssues * Compile a nd R un h ybrid M PI/OpenMP * Using U PC a nd C AF o n H opper 3 Common A rchitectures * Shared M emory A rchitecture - MulFple C PUs s hare g lobal m emory, c ould h ave l ocal c ache - Uniform M emory A ccess ( UMA) -

  17. Shreyas Cholia! Data and Analytics Services, NERSC How To Share

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    How To Share Data With Your Collaborators --- 1 --- Joint F acili+es U ser F orum o n D ata---Intensive Compu+ng, O akland, J une 1 8, 2 014 Overview * Introduc+on * Data S haring o ver H TTP * APIs * High P erformance D ata A ccess * Data M anagement S ystems * We'll t ry t o d o a f ew l ive d emos a long t he w ay --- 2 --- Introduction --- 3 --- Data Islands * Data i s s +ll h eavily s iloed a nd i naccessible. * Data s its o n a m achine s omewhere, a nd y ou g ive people l ocal a ccounts t

  18. Title 16 U.S.C. 1278(a) Restrictions on Water Resources Projects...

    Open Energy Info (EERE)

    under the Federal Power Act on or directly affecting any river which is designated as a component of the national wild and scenic rivers system under the Wild and Scenic Rivers...

  19. Stock Assessment of Columbia River Anadromous Salmonids : Final Report, Volume II, Steelhead Stock Summaries, Stock Transfer Guidelines, Information Needs.

    SciTech Connect (OSTI)

    Howell, Philip J.

    1985-07-01

    This report presents brief descriptions of wild and hatchery-raised steelhead trout stocks in the Columbia River Basin. (ACR)

  20. Advocate- Issue 47- July 2012

    Broader source: Energy.gov [DOE]

    Here are some of the topics from this issue: Wild West Tour, EM SSAB Chairs’ Meeting, and Reservation Updates.

  1. Delineation of Piceance Basin basement structures using multiple source data: Implications for fractured reservoir exploration

    SciTech Connect (OSTI)

    Hoak, T.E.; Klawitter, A.L.

    1995-10-01

    Fractured production trends in Piceance Basin Cretaceous-age Mesaverde Group gas reservoirs are controlled by subsurface structures. Because many of the subsurface structures are controlled by basement fault trends, a new interpretation of basement structure was performed using an integrated interpretation of Landsat Thematic Mapper (TM), side-looking airborne radar (SLAR), high altitude, false color aerial photography, gas and water production data, high-resolution aeromagnetic data, subsurface geologic information, and surficial fracture maps. This new interpretation demonstrates the importance of basement structures on the nucleation and development of overlying structures and associated natural fractures in the hydrocarbon-bearing section. Grand Valley, Parachute, Rulison, Plateau, Shire Gulch, White River Dome, Divide Creek and Wolf Creek fields all produce gas from fractured tight gas sand and coal reservoirs within the Mesaverde Group. Tectonic fracturing involving basement structures is responsible for development of permeability allowing economic production from the reservoirs. In this context, the significance of detecting natural fractures using the intergrated fracture detection technique is critical to developing tight gas resources. Integration of data from widely-available, relatively inexpensive sources such as high-resolution aeromagnetics, remote sensing imagery analysis and regional geologic syntheses provide diagnostic data sets to incorporate into an overall methodology for targeting fractured reservoirs. The ultimate application of this methodology is the development and calibration of a potent exploration tool to predict subsurface fractured reservoirs, and target areas for exploration drilling, and infill and step-out development programs.

  2. Late glacial aridity in southern Rocky Mountains

    SciTech Connect (OSTI)

    Davis, O.K.; Pitblado, B.L.

    1995-09-01

    While the slopes of the present-day Colorado Rocky Mountains are characterized by large stands of subalpine and montane conifers, the Rockies of the late glacial looked dramatically different. Specifically, pollen records suggest that during the late glacial, Artemisia and Gramineae predominated throughout the mountains of Colorado. At some point between 11,000 and 10,000 B.P., however, both Artemisia and grasses underwent a dramatic decline, which can be identified in virtually every pollen diagram produced for Colorado mountain sites, including Como Lake (Sangre de Cristo Mountains), Copley Lake and Splains; Gulch (near Crested Butte), Molas Lake (San Juan Mountains), and Redrock Lake (Boulder County). Moreover, the same pattern seems to hold for pollen spectra derived for areas adjacent to Colorado, including at sites in the Chuska Mountains of New Mexico and in eastern Wyoming. The implications of this consistent finding are compelling. The closest modem analogues to the Artemisia- and Gramineae-dominated late-glacial Colorado Rockies are found in the relatively arid northern Great Basin, which suggests that annual precipitation was much lower in the late-glacial southern Rocky Mountains than it was throughout the Holocene.

  3. Using Experience to Train the Next Generation of Workers | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Energy Using Experience to Train the Next Generation of Workers Using Experience to Train the Next Generation of Workers July 5, 2011 - 1:46pm Addthis Bob Wilds working at a winding machine. | Photo Courtesy of Waukesha Electric Systems Bob Wilds working at a winding machine. | Photo Courtesy of Waukesha Electric Systems Lindsey Geisler Lindsey Geisler Public Affairs Specialist, Office of Public Affairs Bob Wilds has worked at Waukesha Electric Systems for the last 12 years as a coil winder.

  4. Retractable barrier strip

    DOE Patents [OSTI]

    Marts, Donna J.; Barker, Stacey G.; Wowczuk, Andrew; Vellenoweth, Thomas E.

    2002-01-01

    A portable barrier strip having retractable tire-puncture spikes for puncturing a vehicle tire. The tire-puncture spikes have an armed position for puncturing a tire and a retracted position for not puncturing a tire. The strip comprises a plurality of barrier blocks having the tire-puncture spikes removably disposed in a shaft that is rotatably disposed in each barrier block. The plurality of barrier blocks hare hingedly interconnected by complementary hinges integrally formed into the side of each barrier block which allow the strip to be rolled for easy storage and retrieval, but which prevent irregular or back bending of the strip. The shafts of adjacent barrier blocks are pivotally interconnected via a double hinged universal joint to accommodate irregularities in a roadway surface and to transmit torsional motion of the shaft from block to block. A single flexshaft cable is connected to the shaft of an end block to allow a user to selectively cause the shafts of a plurality of adjacently connected barrier blocks to rotate the tire-puncture spikes to the armed position for puncturing a vehicle tire, and to the retracted position for not puncturing the tire. The flexshaft is provided with a resiliently biased retracting mechanism, and a release latch for allowing the spikes to be quickly retracted after the intended vehicle tire is punctured.

  5. The ADVANCE project: Insights and achievments

    SciTech Connect (OSTI)

    1996-12-31

    ADVANCE [Advanced Driver and Vehicle Advisory Navigation ConcEpt] was a public/private partnership conceived and developed by four founding parties. The founding parties include the Federal Highway Administration (FHWA), the Illinois Department of Transportation (IDOT), the University of Illinois at Chicago and Northwestern University operating together under the auspices of the Illinois Universities Transportation Research Consortium (IUTRC), and Motorola, Inc. The major responsibilities of each party are fully described in the Project agreement. Subsequently, these four were joined on the Steering Committee by the American Automobile Association (AAA). This unique blending of public sector, private sector and university interests, augmented by more than two dozen other private sector participants, provided a strong set of resources for ADVANCE. The ADVANCE test area covered over 300 square miles including portions of the City of Chicago and 40 northwest suburban communities. The Project encompasses the high growth areas adjacent to O`Hare International Airport, the Schaumburg/Hoffman Estates office and retail complexes, and the Lake-Cook Road development corridor. It also includes major sports and entertainment complexes such as the Arlington International Racecourse and the Rosemont Horizon. The population in the area is more than 750,000. The Insights and Perspectives Compendium is intended to provide useful information to project managers, system developers, and system integrators of future similar ITS implementations. It is intended for those that are technically interested in the ADVANCE Project and have a basic understanding of the project.

  6. The ADVANCE project: Formal evaluation of the targeted deployment. Volume 3

    SciTech Connect (OSTI)

    1997-01-01

    ADVANCE [Advanced Driver and Vehicle Advisory Navigation ConcEpt] was a public/private partnership conceived and developed by four founding parties. The founding parties include the Federal Highway Administration (FHWA), the Illinois Department of Transportation (IDOT), the University of Illinois at Chicago and Northwestern University operating together under the auspices of the Illinois Universities Transportation Research Consortium (IUTRC), and Motorola, Inc. The major responsibilities of each party are fully described in the Project agreement. Subsequently, these four were joined on the Steering Committee by the American Automobile Association (AAA). This unique blending of public sector, private sector and university interests, augmented by more than two dozen other private sector participants, provided a strong set of resources for ADVANCE. The ADVANCE test area covered over 300 square miles including portions of the City of Chicago and 40 northwest suburban communities. The Project encompasses the high growth areas adjacent to O`Hare International Airport, the Schaumbura/Hoffman Estates office and retail complexes, and the Lake-Cook Road development corridor. It also includes major sports and entertainment complexes such as the Arlington International Racecourse and the Rosemont Horizon. The population in the area is more than 750,000. This volume provides a summary of the insights and achievements made as a result of this field test, and selected appendices containing more detailed information.

  7. SREL Reprint #3203

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Science, Amherst, Massachusetts, USA 4Bulmer and Associates, Auckland, New Zealand Abstract: In 1957, Troughton described the wild dog of New Guinea, naming it Canis hallstromi. ...

  8. RAPID/Roadmap/12-ID-a | Open Energy Information

    Open Energy Info (EERE)

    Contact Us State Biological Resource Considerations (12-ID-a) The Idaho Department of Fish & Game preserves wildlife against any direct take, including wild animals, birds, and...

  9. Structure of the DUF2233 Domain in Bacteria and the Stuttering...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    importance of most of these conserved residues as judged by comparison with the activity of wild-type UCE and its influence on trafficking to the Golgi. Similar...

  10. Beasley Lab | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Aging an anesthetized bobcat Wildlife studies in the Chernobyl exclusion zone Chernobyl wolf Amanda attaching satellite transmitter to a vulture Anesthetizing a wild pig ...

  11. SREL Reprint #3246

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    We artificially incubated wood duck (Aix sponsa) eggs at three temperature regimes (low, 35.0; ... ducklings from each temperature treatment were placed with wild foster mothers ...

  12. Social behavior and the microbiome (Journal Article) | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    Social behavior and the microbiome Prev Next Title: Social behavior and the microbiome Social interactions influence the communities of microbes that live in wild baboons. ...

  13. RAPID/Roadmap/20-FD-b | Open Energy Information

    Open Energy Info (EERE)

    on one of the following: Indian lands; Wilderness areas; Wild and scenic rivers; Wetlands; Units of the National Park System, National Refuges, or National Fish Hatcheries;...

  14. RAPID/Roadmap/7-FD-f | Open Energy Information

    Open Energy Info (EERE)

    on one of the following: Indian lands; Wilderness areas; Wild and scenic rivers; Wetlands; Units of the National Park System, National Refuges, or National Fish Hatcheries;...

  15. Fifteenmile Basin Habitat Enhancement Project: Annual Report...

    Office of Scientific and Technical Information (OSTI)

    wild winter steelhead in the Fifteenmile Creek Basin under the Columbia River Basin Fish and Wildlife Program. The project is funded by through the Bonneville Power...

  16. Appliance Rebates: Frequently Asked Questions | Department of...

    Energy Savers [EERE]

    Spikes Former Communicator at DOE's National Renewable Energy Laboratory The appliance rebate program has been wildly successful in many states. So successful, in fact, that people...

  17. ckm4195.tmp

    Office of Scientific and Technical Information (OSTI)

    ... Threshold effects concentration Threshold effect level U.S. Fish and Wildlife Service . ... Protection Agency (EPA), U.S. Fish and Wild- life Service (USFWS), ...

  18. Derivative-free optimization for parameter estimation in computational...

    Office of Scientific and Technical Information (OSTI)

    nuclear physics Citation Details In-Document Search Title: Derivative-free optimization for parameter estimation in computational nuclear physics Authors: Wild, S ; ...

  19. Once nearly extinct, Idaho sockeye regaining fitness advantage

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    in the wild once more. A newly published analysis by the Idaho Department of Fish and Game and the Northwest Fisheries Science Center shows endangered Snake River...

  20. Technical Sessions S. Lovejoy, A. Davis, Y. Tessier Physics Department

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    C. Gautier, D. Lavallee Earth Space Research Group University of California Santa Barbara, ... and wild statistics which require an infinite number of exponents to characterize. ...

  1. Blue light photoreceptors and methods of using the same

    DOE Patents [OSTI]

    Cashmore, Anthony Robert; Ahmad, Margaret; Lin, Chentao

    1998-01-01

    The invention features a substantially pure preparation of a nucleic acid encoding a HY4 or a HY4-related gene. The invention further features transgenic plants encoding a HY4 gene having a shorter stem than substantially homozygous wild type nontransgenic plants; and, transgenic plants comprising complementary HY4 sequences having a longer stem than substantially homozygous wild type nontransgenic plants.

  2. Streaked x-ray spectrometer having a discrete selection of Bragg geometries for Omega

    SciTech Connect (OSTI)

    Millecchia, M.; Regan, S. P.; Bahr, R. E.; Romanofsky, M.; Sorce, C.

    2012-10-15

    The streaked x-ray spectrometer (SXS) is used with streak cameras [D. H. Kalantar, P. M. Bell, R. L. Costa, B. A. Hammel, O. L. Landen, T. J. Orzechowski, J. D. Hares, and A. K. L. Dymoke-Bradshaw, in 22nd International Congress on High-Speed Photography and Photonics, edited by D. L. Paisley and A. M. Frank (SPIE, Bellingham, WA, 1997), Vol. 2869, p. 680] positioned with a ten-inch manipulator on OMEGA [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)] and OMEGA EP [L. J. Waxer et al., Presented at CLEO/QELS 2008, San Jose, CA, 4-9 May 2008 (Paper JThB1)] for time-resolved, x-ray spectroscopy of laser-produced plasmas in the 1.4- to 20-keV photon-energy range. These experiments require measuring a portion of this photon-energy range to monitor a particular emission or absorption feature of interest. The SXS relies on a pinned mechanical reference system to create a discrete set of Bragg reflection geometries for a variety of crystals. A wide selection of spectral windows is achieved accurately and efficiently using this technique. It replaces the previous spectrometer designs that had a continuous Bragg angle adjustment and required a tedious alignment calibration procedure. The number of spectral windows needed for the SXS was determined by studying the spectral ranges selected by OMEGA users over the last decade. These selections are easily configured in the SXS using one of the 25 discrete Bragg reflection geometries and one of the six types of Bragg crystals, including two curved crystals.

  3. CYP2E1-dependent elevation of serum cholesterol, triglycerides, and hepatic bile acids by isoniazid

    SciTech Connect (OSTI)

    Cheng, Jie; Krausz, Kristopher W.; Li, Feng; Ma, Xiaochao; Gonzalez, Frank J.

    2013-01-15

    Isoniazid is the first-line medication in the prevention and treatment of tuberculosis. Isoniazid is known to have a biphasic effect on the inhibitioninduction of CYP2E1 and is also considered to be involved in isoniazid-induced hepatotoxicity. However, the full extent and mechanism of involvement of CYP2E1 in isoniazid-induced hepatotoxicity remain to be thoroughly investigated. In the current study, isoniazid was administered to wild-type and Cyp2e1-null mice to investigate the potential toxicity of isoniazid in vivo. The results revealed that isoniazid caused no hepatotoxicity in wild-type and Cyp2e1-null mice, but produced elevated serum cholesterol and triglycerides, and hepatic bile acids in wild-type mice, as well as decreased abundance of free fatty acids in wild-type mice and not in Cyp2e1-null mice. Metabolomic analysis demonstrated that production of isoniazid metabolites was elevated in wild-type mice along with a higher abundance of bile acids, bile acid metabolites, carnitine and carnitine derivatives; these were not observed in Cyp2e1-null mice. In addition, the enzymes responsible for bile acid synthesis were decreased and proteins involved in bile acid transport were significantly increased in wild-type mice. Lastly, treatment of targeted isoniazid metabolites to wild-type mice led to similar changes in cholesterol, triglycerides and free fatty acids. These findings suggest that while CYP2E1 is not involved in isoniazid-induced hepatotoxicity, while an isoniazid metabolite might play a role in isoniazid-induced cholestasis through enhancement of bile acid accumulation and mitochondria ?-oxidation. -- Highlights: ? Isoniazid metabolites were elevated only in wild-type mice. ? Isoniazid caused no hepatotoxicity in wild-type and Cyp2e1-null mice. ? Isoniazid elevated serum cholesterol and triglycerides, and hepatic bile acids. ? Bile acid transporters were significantly decreased in isoniazid-treated mice.

  4. Idaho Habitat/Natural Production Monitoring Part I, 1994 Annual Report.

    SciTech Connect (OSTI)

    Hall-Griswold, Judy A.; Leitzinger, Eric J.; Petrosky, C.E. (Idaho Department of Fish and Game, Boise, ID

    1995-11-01

    A total of 333 stream sections were sampled in 1994 to monitor in chinook salmon and steelhead trout parr populations in Idaho. Percent carry capacity and density estimates were summarized by different classes of fish: wild A-run steelhead trout, wild B-run steelhead trout, natural A-run steelhead trout, natural B-run steelhead trout, wild spring and summer chinook salmon. These data were also summarized by cells and subbasins as defined in Idaho Department of Fish and Game`s 1992-1996 Anadromous Fish Management Plan.

  5. Distribution of Clokey's Eggvetch

    SciTech Connect (OSTI)

    David C. Anderson

    1998-12-01

    The Environment, Safety and Health Division of the U.S. Department of Energy, Nevada Operations Office implements the Ecological Monitoring and Compliance Program on the Nevada Test Site (NTS). This program ensures compliance with applicable environmental laws and regulations, delineates and describes NTS ecosystems, and provides ecological information for predicting and evaluating potential impacts of proposed projects on those ecosystems. Over the last several decades, has taken an active role in providing information on the tatus of plant species proposed for protection under the Endangered Species Act(ESA). One such species is Clokey's eggvetch (Astragalus oophorus var. clokeyanus), which is a candidate species under the listing guidelines of the ESA. Surveys for this species were conducted on the NTS in 1996, 1997, and 1998. Field surveys focused on potential habitat for this species in the southern Belted range and expanded to other areas with similar habitat. Over 30 survey day s were completed; five survey days in 1996, 25 survey days in 1997, and three survey days in 1998. Clokey's eggvetch was located at several sites in the southern Belted Range. It was found through much of the northern section of Kawich Canyon, one site at the head of Gritty Gulch, and a rather extensive location in Lambs Canyon. It was also located further south at Captain Jack Springs in the Eleana Range, in much of Falcon Canyon and around Echo Peak on Pahute Mesa, and was also found in the Timber and Shoshone Mountains. Overall, the locations of Clokey's eggvetch on the NTS appears to form a distinct bridge between populations of the species located further north in the Belted and Kawich Ranges and the population located in the Spring Mountains. Clokey's eggvetch was commonly found along washes and small draws, and typically in sandy loam soils with a covering of light tuffaceous rock. It occurs primarily above 1830 meters (6000 feet) in association with single-leaf pinyon (Pinus

  6. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... with a "wild" annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. ...

  7. Search for: All records | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    ... with a "wild" annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. ...

  8. BPA-2014-01120-FOIA Request

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Our Wild Salmon is a 501(c)(3) tax-exempt non-profit organization of more than 50 sport fishing, commercial fishing, and conservation organizations - local, regional, and...

  9. DOE/EIS-0005-FS-2

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... Indian Affairs; Bureau of Land Management; Fish and Wildlife Service; and Geological ... The U . S . Fish and Wildli fe Service and several state agenc ies al so manage land in ...

  10. RAPID/Roadmap/12-WA-a | Open Energy Information

    Open Energy Info (EERE)

    take wildlife from the wild without permission from the Washington State Department of Fish and Wildlife (WDFW). The WDFW issues Live Wildlife Taking Permits under WAC 232-12-064....

  11. DOE - NNSA/NFO -- Plants and Animals

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Plants & Animals NNSANFO Language Options U.S. DOENNSA - Nevada Field Office Click to subscribe to NNSS News Plants and Animals Wild Horses at the NNSS Because of its physical ...

  12. President Obama's Visit to Alaska: Closing Thoughts | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Guard cutters and the edges of ice fields, I've had the opportunity to see some wild and beautiful things in Alaska - and I've enjoyed sharing them with the rest of the country. ...

  13. Beasley Lab | Savannah River Ecology Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AND DISEASE DYNAMICS OF WILD PIGS ON THE SAVANNAH RIVER SITE SREL Collaborators: Jim ... At the Savannah River Site alone between 30 and 40 pigs are struck by vehicles each year, ...

  14. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Lamarque, J F (3) Szopa, S (3) Wild, O (3) Atherton, C (2) Bergmann, D. (2) Cameron-Smith, P (2) Cameron-Smith, Philip (2) Cuvelier, C (2) Dalsoren, S. (2) Save Results Save this ...

  15. SREL Reprint #3331

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    deer and wild boar within the Chernobyl exclusion zone are similar to those in four (uncontaminated) nature reserves in the region and wolf abundance is more than 7 times higher. ...

  16. Coal keeps the home fires burning, at a price

    SciTech Connect (OSTI)

    O'Connell, J.

    2007-11-15

    The wild ride of 2007 thermal and coking coal and freight prices does not show any signs of abating as 2008 nears, leaving consumers coping with historic high costs, except in the US. 3 figs.

  17. Mar_13Times.indd

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... Y-12 Employees' Soci- ety sport event, employees participated in outside-of-work activities: "Wild and Woolly Games Staged in Plant Loop," The Y-12 Bulletin, June 3, 1947, pg. 4. ...

  18. http://frwebgate.access.gpo.gov/cgi-bin/usc.cgi?ACTION=RETRIEVE

    National Nuclear Security Administration (NNSA)

    Congressional findings and declaration of policy Congress finds and declares that wild free-roaming horses and burros are living symbols of the historic and pioneer spirit of the...

  19. BPA-2015-01485-FCorrespondence

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    FREEDOM OF INFORMATION ACT PROGRAM In reply refer to: FOIA BPA-2015-01485-F Arlene Montgomery Friends of the Wild Swan PO Box 103 Bigfork, MT 59911 Ms. Montgomery: The Department...

  20. Fermilab Today | Tip of the Week Archive

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Sept. 28, 2015 Actions to avoid Sept. 21, 2015 Clean, green restrooms Sept. 14, 2015 Influenza 2015-16 Aug. 31, 2015 Our children depend on our safe driving Aug. 24, 2015 Wild...

  1. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three...

  2. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents,...

  3. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... By the year 2500, there are complete recoveries of the globally averaged surface air ... Source-Receptor Relationships for Ozone Pollution Fiore, A M ; Dentener, F J ; Wild, O ; ...

  4. November 12, 2010

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Cafs November 12, 2010 November 12, 2010 Print Friday, 12 November 2010 00:00 christine beavers Having a ball in the wild world of fullerenes Christine Beavers, Beamline 11.3.1 ...

  5. DOI-BLM-NV-C010-2013-0037-DNA | Open Energy Information

    Open Energy Info (EERE)

    37-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2013-0037-DNA DNA at Gabbs Valley Geothermal Area for GeothermalWell Field, DNA for Wild Rose Unit...

  6. Spotlights Archive | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    hosted a Northern Saw-Whet Owl banding demonstration by master bander, Tim Tolford. Bird banding is a technique used to study wild birds by attaching a tag to their leg to...

  7. 2013-02 "Review Material Disposal Areas at LANL in Addition to...

    Broader source: Energy.gov (indexed) [DOE]

    2 is to ensure that the appropriate level of review has been given to MDAs other than MDA G at LANL that may be at similar risk in the event of wild fires. Rec 2013-02 - March 20,...

  8. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    ... K. ; Ishikawa, Tetsuya ; La Trobe) ; RIKEN) ; ESRF) June 2016 , Advances in X-Ray Optics;SPIE;129-139 Chemical analysis of Wild-2 samples returned by Stardust Flynn, G.J. ; ...

  9. 180C

    Office of Environmental Management (EM)

    Fragua Council of State Governments-ERC Conrad Smith P. Edwards R. Pinney M. Mulhare C. Richardson M. Vyenielo W. Sherman C. Smith C. Smith E. Wilds C. Smith W. Sherman J. ...

  10. Form:Reference | Open Energy Information

    Open Energy Info (EERE)

    The reference title should match the book title. e.g.- Where the Wild Things Are Book Review Used when citing a review of a book. The reference title should include "Review of the...

  11. User Data Forum Presentations

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    M02: The Future of Data and Scientific Workflow June 16, 2014 | Author(s): Michael Wilde, ... MB M03: The Future of Large Scale Visual Data Analysis June 16, 2014 | Author(s): E. Wes ...

  12. User Data Forum Presentations

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Presentations User Data Forum Presentations Sort by: Default | Name | Date (low-high) | ... M02: The Future of Data and Scientific Workflow June 16, 2014 | Author(s): Michael Wilde, ...

  13. Search for: All records | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua ... associated with a "wild" annual grass, Avena fatua, which is commonly a dominant plant ...

  14. Worksheet

    U.S. Energy Information Administration (EIA) Indexed Site

    ... "VT","Chittenden",7601,"Green Mountain Power Corp",3737,"Essex Junction ... "WA","Kittitas",15500,"Puget Sound Energy Inc",56322,"Wild Horse",22,"WHS1",0.5,0.5...

  15. Cellobiohydrolase I enzymes

    DOE Patents [OSTI]

    Adney, William S; Himmel, Michael E; Decker, Stephen R; Knoshaug, Eric P; Nimlos, Mark R; Crowley, Michael F; Jeoh, Tina

    2014-01-28

    Provided herein is an isolated Cel7A polypeptide comprising mutations in the catalytic domain of the polypeptide relative to the catalytic domain of a wild type Cel7A polypeptide, wherein the mutations reduce N-linked glycosylation of the isolated polypeptide relative to the wild type polypeptide. Also provided herein is an isolated Cel7A polypeptide comprising increased O-linked glycosylation of the linker domain relative to a linker domain of a wild type Cel7A polypeptide. The increased O-linked glycosylation is a result of the addition of and/or substitution of one or more serine and/or threonine residues to the linker domain relative to the linker domain of the wild type polypeptide. In some embodiments, the isolated Cel7A polypeptide comprising mutations in the catalytic domain of the polypeptide relative to the catalytic domain of a wild type Cel7A polypeptide further comprises increased O-linked glycosylation of the linker domain relative to a linker domain of a wild type Cel7A polypeptide. The mutations in the catalytic domain reduce N-linked glycosylation of the isolated polypeptide relative to the wild type polypeptide. The addition of and/or substitution of one or more serine and/or threonine residues to the linker domain relative to the linker domain of the wild type polypeptide increases O-linked glycosylation of the isolated polypeptide. Further provided are compositions comprising such polypeptides and nucleic acids encoding such polypeptides. Still further provided are methods for making such polypeptides.

  16. Mutant HNF-1{alpha} and mutant HNF-1{beta} identified in MODY3 and MODY5 downregulate DPP-IV gene expression in Caco-2 cells

    SciTech Connect (OSTI)

    Gu Ning [Laboratory of Metabolism, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto (Japan); Laboratory of Neurochemistry, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto (Japan); Adachi, Tetsuya [Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto (Japan); Matsunaga, Tetsuro [Laboratory of Metabolism, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto (Japan); Takeda, Jun [Department of Endocrinology Diabetes and Rheumatology, Graduate School of Medicine, Gifu University School of Medicine, Gifu (Japan); Tsujimoto, Gozoh [Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto (Japan); Ishihara, Akihiko [Laboratory of Neurochemistry, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto (Japan); Yasuda, Koichiro [Laboratory of Metabolism, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto (Japan); Diabetic Center, Tsunashimakai-Kosei Hospital, Himeji (Japan); Tsuda, Kinsuke [Laboratory of Metabolism, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto (Japan)]. E-mail: jinkan@tom.life.h.kyoto-u.ac.jp

    2006-08-04

    Dipeptidylpeptidase IV (DPP-IV) is a well-documented drug target for the treatment of type 2 diabetes. Hepatocyte nuclear factors (HNF)-1{alpha} and HNF-1{beta}, known as the causal genes of MODY3 and MODY5, respectively, have been reported to be involved in regulation of DPP-IV gene expression. But, it is not completely clear (i) that they play roles in regulation of DPP-IV gene expression, and (ii) whether DPP-IV gene activity is changed by mutant HNF-1{alpha} and mutant HNF-1{beta} in MODY3 and MODY5. To explore these questions, we investigated transactivation effects of wild HNF-1{alpha} and 13 mutant HNF-1{alpha}, as well as wild HNF-1{beta} and 2 mutant HNF-1{beta}, on DPP-IV promoter luciferase gene in Caco-2 cells by means of a transient experiment. Both wild HNF-1{alpha} and wild HNF-1{beta} significantly transactivated DPP-IV promoter, but mutant HNF-1{alpha} and mutant HNF-1{beta} exhibited low transactivation activity. Moreover, to study whether mutant HNF-1{alpha} and mutant HNF-1{beta} change endogenous DPP-IV enzyme activity, we produced four stable cell lines from Caco-2 cells, in which wild HNF-1{alpha} or wild HNF-1{beta}, or else respective dominant-negative mutant HNF-1{alpha}T539fsdelC or dominant-negative mutant HNF-1{beta}R177X, was stably expressed. We found that DPP-IV gene expression and enzyme activity were significantly increased in wild HNF-1{alpha} cells and wild HNF-1{beta} cells, whereas they decreased in HNF-1{alpha}T539fsdelC cells and HNF-1{beta}R177X cells, compared with DPP-IV gene expression and enzyme activity in Caco-2 cells. These results suggest that both wild HNF-1{alpha} and wild HNF-1{beta} have a stimulatory effect on DPP-IV gene expression, but that mutant HNF-1{alpha} and mutant HNF-1{beta} attenuate the stimulatory effect.

  17. Arsenic (+ 3 oxidation state) methyltransferase genotype affects steady-state distribution and clearance of arsenic in arsenate-treated mice

    SciTech Connect (OSTI)

    Hughes, Michael F.; Edwards, Brenda C.; Herbin-Davis, Karen M.; Saunders, Jesse; Styblo, Miroslav; Thomas, David J.

    2010-12-15

    Arsenic (+ 3 oxidation state) methyltransferase (As3mt) catalyzes formation of mono-, di-, and tri-methylated metabolites of inorganic arsenic. Distribution and retention of arsenic were compared in adult female As3mt knockout mice and wild-type C57BL/6 mice using a regimen in which mice received daily oral doses of 0.5 mg of arsenic as arsenate per kilogram of body weight. Regardless of genotype, arsenic body burdens attained steady state after 10 daily doses. At steady state, arsenic body burdens in As3mt knockout mice were 16 to 20 times greater than in wild-type mice. During the post dosing clearance period, arsenic body burdens declined in As3mt knockout mice to {approx} 35% and in wild-type mice to {approx} 10% of steady-state levels. Urinary concentration of arsenic was significantly lower in As3mt knockout mice than in wild-type mice. At steady state, As3mt knockout mice had significantly higher fractions of the body burden of arsenic in liver, kidney, and urinary bladder than did wild-type mice. These organs and lung had significantly higher arsenic concentrations than did corresponding organs from wild-type mice. Inorganic arsenic was the predominant species in tissues of As3mt knockout mice; tissues from wild-type mice contained mixtures of inorganic arsenic and its methylated metabolites. Diminished capacity for arsenic methylation in As3mt knockout mice prolongs retention of inorganic arsenic in tissues and affects whole body clearance of arsenic. Altered retention and tissue tropism of arsenic in As3mt knockout mice could affect the toxic or carcinogenic effects associated with exposure to this metalloid or its methylated metabolites.

  18. WILDFIRE IGNITION RESISTANCE ESTIMATOR WIZARD SOFTWARE DEVELOPMENT REPORT

    SciTech Connect (OSTI)

    Phillips, M.; Robinson, C.; Gupta, N.; Werth, D.

    2012-10-10

    This report describes the development of a software tool, entitled “WildFire Ignition Resistance Estimator Wizard” (WildFIRE Wizard, Version 2.10). This software was developed within the Wildfire Ignition Resistant Home Design (WIRHD) program, sponsored by the U. S. Department of Homeland Security, Science and Technology Directorate, Infrastructure Protection & Disaster Management Division. WildFIRE Wizard is a tool that enables homeowners to take preventive actions that will reduce their home’s vulnerability to wildfire ignition sources (i.e., embers, radiant heat, and direct flame impingement) well in advance of a wildfire event. This report describes the development of the software, its operation, its technical basis and calculations, and steps taken to verify its performance.

  19. Divinyl ether synthase gene, and protein and uses thereof

    DOE Patents [OSTI]

    Howe, Gregg A.; Itoh, Aya

    2006-12-26

    The present invention relates to divinyl ether synthase genes, proteins, and methods of their use. The present invention encompasses both native and recombinant wild-type forms of the synthase, as well as mutants and variant forms, some of which possess altered characteristics relative to the wild-type synthase. The present invention also relates to methods of using divinyl ether synthase genes and proteins, including in their expression in transgenic organisms and in the production of divinyl ether fatty acids, and to methods of suing divinyl ether fatty acids, including in the protection of plants from pathogens.

  20. CONSEQUENCES OF ALTERING RUBISCO REGULATION

    SciTech Connect (OSTI)

    Salvucci, Michael

    2013-12-31

    Research examined the thermal stability and propensity for aggregation of wild type and the C- and N-terminally modified forms of activase to determine if loss of activity under heat stress is dependent on protein aggregation. The results showed that 1) loss of activity at high temperature is independent of aggregation; 2) activase with both C- and N-terminal S-Tags are more susceptible to aggregation than wild type activase, 3) aggregation is highly dependent on the concentration of Mg2+ and 4) the ATP analog, ATPgammaS, protects against both thermal inactivation and aggregation.

  1. Divinyl ether synthase gene and protein, and uses thereof

    SciTech Connect (OSTI)

    Howe, Gregg A.; Itoh, Aya

    2011-09-13

    The present invention relates to divinyl ether synthase genes, proteins, and methods of their use. The present invention encompasses both native and recombinant wild-type forms of the synthase, as well as mutants and variant forms, some of which possess altered characteristics relative to the wild-type synthase. The present invention also relates to methods of using divinyl ether synthase genes and proteins, including in their expression in transgenic organisms and in the production of divinyl ether fatty acids, and to methods of suing divinyl ether fatty acids, including in the protection of plants from pathogens.

  2. Regioselective alkane hydroxylation with a mutant AlkB enzyme

    SciTech Connect (OSTI)

    Koch, Daniel J.; Arnold, Frances H.

    2012-11-13

    AlkB from Pseudomonas putida was engineered using in-vivo directed evolution to hydroxylate small chain alkanes. Mutant AlkB-BMO1 hydroxylates propane and butane at the terminal carbon at a rate greater than the wild-type to form 1-propanol and 1-butanol, respectively. Mutant AlkB-BMO2 similarly hydroxylates propane and butane at the terminal carbon at a rate greater than the wild-type to form 1-propanol and 1-butanol, respectively. These biocatalysts are highly active for small chain alkane substrates and their regioselectivity is retained in whole-cell biotransformations.

  3. Development of ethanol tolerance in Clostridium thermocellum: effect of growth temperature

    SciTech Connect (OSTI)

    Herrero, A.A.; Gomez, R.F.

    1980-09-01

    The growth of Clostridium thermocellum ATCC 27405 and of C9, an ethanol-resistant mutant of this strain, at different ethanol concentrations and temperatures was characterized. The wild-type strain showed a higer energy of activation for growth than the ethanol-tolerant derivative. The optimum growth temperature of the wild type decreased as the concentration of the ethanol challenge increased, whereas the optimum growth temperature for C9 remained constant. The results are discussed in terms of what is known about the effects of ethanol and temperature on membrane composition and fluidity.

  4. Using weeds to fight wastes

    SciTech Connect (OSTI)

    1992-10-01

    Researchers at Los Alamos National Laboratory and New Mexico State University have discovered that jimson weed and wild tomato plants can remove the toxic wastes in wastewater associated with the production of trinitrotoluene (TNT). According to Wolfgang F. Mueller of New Mexico State, tissue-cultured cells of jimson weed rapidly absorb and break down toxic and carcinogenic elements in {open_quotes}pink water,{close_quotes} a by-product of the manufacture of TNT. Mueller and his colleagues have found similar results with the wild tomato plant.

  5. EA-1895: Lolo Creek Permanent Weir Construction near town of Weippe, Clearwater County, Idaho

    Broader source: Energy.gov [DOE]

    DOE’s Bonneville Power Administration was preparing this EA to evaluate the potential environmental impacts of replacing an existing seasonal fish weir with a permanent weir, which would have been used to monitor federally-listed Snake River steelhead and collect spring Chinook salmon adults to support ongoing supplementation programs in the watershed. The Bureau of Land Management, a cooperating agency, preliminarily determined Lolo Creek to be suitable for Congressional designation into the Wild and Scenic River System. The EA included a Wild and Scenic River Section 7 analysis. This project was canceled.

  6. Structure of adenovirus bound to cellular receptor car

    DOE Patents [OSTI]

    Freimuth, Paul I.

    2007-01-02

    Disclosed is a mutant CAR-DI-binding adenovirus which has a genome comprising one or more mutations in sequences which encode the fiber protein knob domain wherein the mutation causes the encoded viral particle to have a significantly weakened binding affinity for CAR-DI relative to wild-type adenovirus. Such mutations may be in sequences which encode either the AB loop, or the HI loop of the fiber protein knob domain. Specific residues and mutations are described. Also disclosed is a method for generating a mutant adenovirus which is characterized by a receptor binding affinity or specificity which differs substantially from wild type.

  7. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents, have only a limited ability to infect humans. However, with continued outbreaks of the virus in poultry and wild birds, the potential for the emergence of a human-adapted H5 virus, either by reassortment (the mixing of genetic material from similar viruses) or mutation, is seen as a major threat to public

  8. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents, have only a limited ability to infect humans. However, with continued outbreaks of the virus in poultry and wild birds, the potential for the emergence of a human-adapted H5 virus, either by reassortment (the mixing of genetic material from similar viruses) or mutation, is seen as a major threat to public

  9. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents, have only a limited ability to infect humans. However, with continued outbreaks of the virus in poultry and wild birds, the potential for the emergence of a human-adapted H5 virus, either by reassortment (the mixing of genetic material from similar viruses) or mutation, is seen as a major threat to public

  10. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Structure and Receptor Specificity of an Avian Flu Antigen Structure and Receptor Specificity of an Avian Flu Antigen Print Wednesday, 25 July 2007 00:00 To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents, have only a limited ability to infect humans. However, with continued outbreaks of the virus in poultry and wild birds, the potential for the emergence of a human-adapted H5 virus, either by reassortment (the mixing of

  11. Structure and Receptor Specificity of an Avian Flu Antigen

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Receptor Specificity of an Avian Flu Antigen Print To date, the H5N1 avian influenza viruses, which are currently circulating in domestic and wild birds on three continents, have only a limited ability to infect humans. However, with continued outbreaks of the virus in poultry and wild birds, the potential for the emergence of a human-adapted H5 virus, either by reassortment (the mixing of genetic material from similar viruses) or mutation, is seen as a major threat to public health

  12. Keep in mind, that with formality, often comes more of a standing presence of a committee within DOE-it gets into DOE's system and becomes a budget line item as well

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ICEIWG May 29, 2013 WILD HORSE PASS HOTEL & CASINO 5040 Wild Horse Pass Blvd., Chandler, AZ AGENDA CONFERENCE ROOM: ACACIA CD WEDNESDAY, MAY 29, 2013 8:00-9:00am REGISTRATION & BREAKFAST ** Continental breakfast will be provided on-site. ** 9:00-11:00am WELCOME & INTRODUCTIONS Opening Prayer by ICEIWG Tribal Representative Tracey A. LeBeau, Director, U.S. DOE Office of Indian Energy (IE) & DOE ICEIWG Co-Chair Jim Manion, Warm Springs Delegate & Tribal ICEIWG Co-Chair Pilar

  13. Nez Perce Tribal Hatchery Project, Operations and Maintenance and Planning and Design, 2001 Annual Report.

    SciTech Connect (OSTI)

    Larson, Roy Edward; Walker, Grant W.; Penney, Aaron K.

    2006-03-01

    Table 5). Purchases are itemized in Appendix D and E. FishPro, Inc. assisted tribal staff with equipment purchases. The unspent contract balances will be carried forward to the ensuing year to complete equipment purchases essential to hatchery operations. The NPTH activities focused on completion of the Northwest Power Planning Council Step-3 decision that authorized hatchery construction. Construction began in July 2000. It is anticipated to continue through October 2002. At the end of 2001, the hatchery facilities were approximately 70% completed and the budget approximately 90% expended. The following facilities are either completed or in final stages of construction: (1) NPTH Central Hatchery facility at Site 1705, and (2) North Lapwai Valley satellite, and (3) Sweetwater Springs satellite, and (4) Yoosa-Camp satellite, and (5) Newsome Creek satellite, and (6) Lukes Gulch satellite, and (7) Cedar Flats satellite.

  14. The Future of Scientific Workflow

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    W ilde wilde@anl.gov Argonne N a5onal L aboratory and T he U niversity o f C hicago Collaborators in this vision of workflow Timothy A rmstrong, U niversity o f C hicago Jus8n W ...

  15. Swift Parallel Scripting:

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Data Analytics at Extreme Scale Michael W ilde wilde@anl.gov h2p:swi7---lang.org ... S . K atz, K etan M aheshwari, Michael W ilde, J usOn W ozniak, Y angxinye Y ang ...

  16. Stock Assessment of Columbia River Anadromous Salmonids : Final Report, Volume I, Chinook, Coho, Chum and Sockeye Salmon Summaries.

    SciTech Connect (OSTI)

    Howell, Philip J.

    1986-07-01

    The purpose was to identify and characterize the wild and hatchery stocks of salmon and steelhead in the Columbia River Basin on the basis of currently available information. This report provides a comprehensive compilation of data on the status and life histories of Columbia Basin salmonid stocks.

  17. Idaho Habitat/Natural Production Monitoring Part I, 1995 Annual Report.

    SciTech Connect (OSTI)

    Hall-Griswold, J.A.; Petrosky, C.E.

    1996-12-01

    The Idaho Department of Fish and Game (IDFG) has been monitoring trends in juvenile spring and summer chinook salmon, Oncorhynchus tshawytscha, and steelhead trout, O. mykiss, populations in the Salmon, Clearwater, and lower Snake River drainages for the past 12 years. This work is the result of a program to protect, mitigate, and enhance fish and wildlife affected by the development and operation of hydroelectric power plants on the Columbia River. Project 91-73, Idaho Natural Production Monitoring, consists of two subprojects: General Monitoring and Intensive Monitoring. This report updates and summarizes data through 1995 for the General Parr Monitoring (GPM) database to document status and trends of classes of wild and natural chinook salmon and steelhead trout populations. A total of 281 stream sections were sampled in 1995 to monitor trends in spring and summer chinook salmon Oncorhynchus tshawytscha and steelhead trout O. mykiss parr populations in Idaho. Percent carrying capacity and density estimates were summarized for 1985--1995 by different classes of fish: wild A-run steelhead trout, wild B-run steelhead trout, natural A-run steelhead trout, natural B-run steelhead trout, wild spring and summer chinook salmon, and natural spring and summer chinook salmon. The 1995 data were also summarized by subbasins as defined in Idaho Department of Fish and Game`s 1992--1996 Anadromous Fish Management Plan.

  18. Technical Basis Agreement Document for UGTA CAU 99 RM/SM

    National Nuclear Security Administration (NNSA)

    D.L. Finnegan, J.L. Thompson, C.M. Miller, P.L. Baca, L.F. Olivas, C.G. Geoffrion, D.K. Smith, W. Goishi, B.K. Esser, J.W. Meadows, N. Namboodiri, J.F. Wild. 2001. Nevada Test Site...

  19. Microsoft Word - APP VI, Rev 3 _03-19-20

    National Nuclear Security Administration (NNSA)

    ... Bowen, S.M., D.L. Finnegan, J.L. Thompson, C.M. Miller, P.L. Baca, L.F. Olivas, C.G. Geoffrion, D.K. Smith, W. Goishi, B.K. Esser, J.W. Meadows, N. Namboodiri, and J.F. Wild. 2001. ...

  20. Deficiency in Homologous Recombination Renders Mammalian Cells More Sensitive to Proton Versus Photon Irradiation

    SciTech Connect (OSTI)

    Grosse, Nicole; Fontana, Andrea O. [Laboratory for Molecular Radiobiology, University Hospital Zurich, Zurich (Switzerland); Hug, Eugen B.; Lomax, Antony; Coray, Adolf [Center for Proton Therapy, Paul Scherrer Institute, Villigen (Switzerland); Augsburger, Marc [Laboratory for Molecular Radiobiology, University Hospital Zurich, Zurich (Switzerland); Paganetti, Harald [Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts (United States); Sartori, Alessandro A. [Institute of Molecular Cancer Research, University of Zurich, Zurich (Switzerland); Pruschy, Martin, E-mail: martin.pruschy@usz.ch [Laboratory for Molecular Radiobiology, University Hospital Zurich, Zurich (Switzerland)

    2014-01-01

    Purpose: To investigate the impact of the 2 major DNA repair machineries on cellular survival in response to irradiation with the 2 types of ionizing radiation. Methods and Materials: The DNA repair and cell survival endpoints in wild-type, homologous recombination (HR)-deficient, and nonhomologous end-joining-deficient cells were analyzed after irradiation with clinically relevant, low-linear energy transfer (LET) protons and 200-keV photons. Results: All cell lines were more sensitive to proton irradiation compared with photon irradiation, despite no differences in the induction of DNA breaks. Interestingly, HR-deficient cells and wild-type cells with small interfering RNA-down-regulated Rad51 were markedly hypersensitive to proton irradiation, resulting in an increased relative biological effectiveness in comparison with the relative biological effectiveness determined in wild-type cells. In contrast, lack of nonhomologous end-joining did not result in hypersensitivity toward proton irradiation. Repair kinetics of DNA damage in wild-type cells were equal after both types of irradiation, although proton irradiation resulted in more lethal chromosomal aberrations. Finally, repair kinetics in HR-deficient cells were significantly delayed after proton irradiation, with elevated amounts of residual ?H2AX foci after irradiation. Conclusion: Our data indicate a differential quality of DNA damage by proton versus photon irradiation, with a specific requirement for homologous recombination for DNA repair and enhanced cell survival. This has potential relevance for clinical stratification of patients carrying mutations in the DNA damage response pathways.

  1. 1998 - 07 | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    7 Jul 1998 Thu, 1998-07-02 00:00 Scientists Taking Laser on Wild Ride; Physicists Stretch Beam's Capabilities (Richmond Times Dispatch) Wed, 1998-07-01 00:00 Researchers Break Power Record for FEL (Opto Electronic News

  2. Survival Estimates for the Passage of Spring-Migrating Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2008.

    SciTech Connect (OSTI)

    Faulkner, James R.; Smith, Steven G.; Muir, William D.

    2009-06-23

    In 2008, the National Marine Fisheries Service completed the sixteenth year of a study to estimate survival and travel time of juvenile salmonids Oncorhynchus spp. passing through dams and reservoirs on the Snake and Columbia Rivers. All estimates were derived from detections of fish tagged with passive integrated transponder (PIT) tags. We PIT tagged and released a total of 18,565 hatchery steelhead O. mykiss, 15,991 wild steelhead, and 9,714 wild yearling Chinook salmon O. tshawytscha at Lower Granite Dam in the Snake River. In addition, we utilized fish PIT tagged by other agencies at traps and hatcheries upstream from the hydropower system and at sites within the hydropower system in both the Snake and Columbia Rivers. These included 122,061 yearling Chinook salmon tagged at Lower Granite Dam for evaluation of latent mortality related to passage through Snake River dams. PIT-tagged smolts were detected at interrogation facilities at Lower Granite, Little Goose, Lower Monumental, Ice Harbor, McNary, John Day, and Bonneville Dams and in the PIT-tag detector trawl operated in the Columbia River estuary. Survival estimates were calculated using a statistical model for tag-recapture data from single release groups (the single-release model). Primary research objectives in 2008 were to: (1) estimate reach survival and travel time in the Snake and Columbia Rivers throughout the migration period of yearling Chinook salmon and steelhead, (2) evaluate relationships between survival estimates and migration conditions, and (3) evaluate the survival estimation models under prevailing conditions. This report provides reach survival and travel time estimates for 2008 for PIT-tagged yearling Chinook salmon (hatchery and wild), hatchery sockeye salmon O. nerka, hatchery coho salmon O. kisutch, and steelhead (hatchery and wild) in the Snake and Columbia Rivers. Additional details on the methodology and statistical models used are provided in previous reports cited here. Survival

  3. CARBON SEQUESTRATION IN RECLAIMED MINED SOILS OF OHIO

    SciTech Connect (OSTI)

    M.K. Shukla; R. Lal

    2004-10-01

    This research project is aimed at assessing the soil organic carbon (SOC) sequestration potential of reclaimed minesoils (RMS). The experimental sites, owned and maintained by the American Electrical Power, are located in Guernsey, Morgan, Noble, and Muskingum Counties of Ohio. These sites, characterized by age chronosequences, were reclaimed with and without topsoil application and are under continuous grass or forest cover. During this quarter, water infiltration tests were performed on the soil surface in the experimental sites. Soil samples were analyzed for the soil carbon and nitrogen contents, texture, water stable aggregation, and mean weight and geometric mean diameter of aggregates. This report presents the results from two sites reclaimed during 1978 and managed under grass (Wilds) and forest (Cumberland) cover, respectively. The trees were planted in 1982 in the Cumberland site. The analyses of data on soil bulk density ({rho}{sub b}), SOC and total nitrogen (TN) concentrations and stocks were presented in the third quarter report. This report presents the data on infiltration rates, volume of transport and storage pores, available water capacity (AWC) of soil, particle size distribution, and soil inorganic carbon (SIC) and coal carbon contents. The SIC content ranged from 0.04 to 1.68% in Cumberland tree site and 0.01 to 0.65% in the Wilds. The coal content assumed to be the carbon content after oven drying the sample at 350 C varied between 0.04 and 3.18% for Cumberland and 0.06 and 3.49% for Wilds. The sand, silt and clay contents showed moderate to low variability (CV < 0.16) for 0-15 and 15-30 cm depths. The volume of transmission (VTP) and storage pores (VSP) also showed moderate to high variability (CV ranged from 0.22 to 0.39 for Wilds and 0.17 to 0.36 for Cumberland). The CV for SIC was high (0.7) in Cumberland whereas that for coal content was high (0.4) in the Wilds. The steady state infiltration rates (i{sub c}) also showed high variability

  4. The role of intrahepatic CD3 +/CD4 −/CD8 − double negative T (DN T) cells in enhanced acetaminophen toxicity

    SciTech Connect (OSTI)

    Getachew, Yonas; Cusimano, Frank A.; James, Laura P.; Thiele, Dwain L.

    2014-10-15

    The role of the immune system, specifically NK, NKT and CD3 cells, in acetaminophen (APAP) induced liver injury remains inconsistently defined. In the present study, wild type (C57BL/6J) mice and granzyme B deficient (GrB −/−) mice were treated with acetaminophen to assess the role of the immune system in acute liver injury. Doses of acetaminophen that induced sub lethal liver injury in wild type mice unexpectedly produced fatal hepatotoxicity in granzyme B deficient (GrB −/−) mice. Analysis revealed that GrB −/− mice had an increased population of intrahepatic CD3 (+), CD4 (−), and CD8 (−) lymphocytes expressing the CD69 activation marker and Fas ligand. Depletion of these cells in the GrB −/− and wild type mice made them less susceptible to APAP injury, while depletion of NK1.1 (+) cells or both CD4 (+) and CD8 (+) T cells failed to provide the same hepatoprotection. Transfer of the GrB −/− IHLs further exacerbated liver injury and increased mortality in wild type mice but not in LRP/LPR mice, lacking fas expression. Conclusions: Acetaminophen toxicity is enhanced by the presence of activated, FasL expressing intrahepatic CD3 (+), CD4 (−), CD8 (−), NK1.1 (−) T cells. Depletion of these cells from GrB −/− mice and wild type mice greatly reduces mortality and improves the course of liver injury recovery. - Highlights: • Intrahepatic lymphocytes (IHLs) from GrB −/− mice harbor activated DNT cells. • IHLs from GrB −/− mice exhibit enhanced Fas ligand expression. • Acetaminophen toxicity is enhanced by activated, FasL expressing DNT cells.

  5. Proteomics and transcriptomics analyses of Arabidopsis floral buds uncover important functions of ARABIDOPSIS SKP1-LIKE1

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lu, Dihong; Ni, Weimin; Stanley, Bruce A.; Ma, Hong

    2016-03-03

    The ARABIDOPSIS SKP1-LIKE1 (ASK1) protein functions as a subunit of SKP1-CUL1-F-box (SCF) E3 ubiquitin ligases. Previous genetic studies showed that ASK1 plays important roles in Arabidopsis flower development and male meiosis. However, the molecular impact of ASK1-containing SCF E3 ubiquitin ligases (ASK1-E3s) on the floral proteome and transcriptome is unknown. Here we identified proteins that are potentially regulated by ASK1-E3s by comparing floral bud proteomes of wild-type and the ask1 mutant plants. More than 200 proteins were detected in the ask1 mutant but not in wild-type and >300 were detected at higher levels in the ask1 mutant than in wild-type,more » but their RNA levels were not significantly different between wild-type and ask1 floral buds as shown by transcriptomics analysis, suggesting that they are likely regulated at the protein level by ASK1-E3s. Integrated analyses of floral proteomics and transcriptomics of ask1 and wild-type uncovered several potential aspects of ASK1-E3 functions, including regulation of transcription regulators, kinases, peptidases, and ribosomal proteins, with implications on possible mechanisms of ASK1-E3 functions in floral development. In conclusion, our results suggested that ASK1-E3s play important roles in Arabidopsis protein degradation during flower development. This study opens up new possibilities for further functional studies of these candidate E3 substrates.« less

  6. The Role of the Tetraheme Cytochrome c3 in Desulfovibrio vulgaris Hildenborough Metabolism

    SciTech Connect (OSTI)

    Semkiw, Elizabeth; Zane, Grant; Wall, Judy

    2010-05-17

    The role of tetraheme cytochrome c3 (CycA) in the metabolism of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was investigated by deletion of the cycA gene using a marker-exchange deletion strategy. A highly abundant periplasmic cytochrome, CycA has the important function of transferring electrons from periplasmic hydrogenases (Hyd, Hyn, Hys) to transmembrane complexes which transport the electrons to the cytoplasm where sulfate is reduced. Previous studies have indicated that during its interaction with periplasmic hydrogenases, CycA is also involved in the reduction of toxic metals. Growth of the cycA mutant strain on lactate as the electron donor and sulfate as the terminal electron acceptor showed that, despite its abundance, CycA is not essential for DvH growth. However, the rate of growth of the mutant strain was significantly lower, and the extent of growth less, than rates and extents of growth of the wild type and complement strains on lactate/sulfate medium. This indicates that a portion of the electrons generated from cytoplasmic lactate oxidation are transported by CycA for energy production, possibly in a hydrogen cycling mechanism employed to generate ATP. Failure of the mutant strain to grow on either formate or H2, with sulfate or sulfite as electron acceptors, further indicated that CycA may be the only redox partner of periplasmic hydrogenases. The cycA mutant strain also did not grow as well as either the wild type or complement strains on medium supplemented with pyruvate/sulfate. Final growth on pyruvate/sulfate was comparable, but the mutant grew more slowly than the wild type and complement strains. Interestingly, the mutant grew better than the wild type or complement strains on pyruvate alone, possibly due to the release of H2 and/or CO2 in concentrations which may be somewhat inhibitory to wild type growth.

  7. Evidence that an internal carbonic anhydrase is present in 5% CO/sub 2/-grown and air-grown Chlamydomonas. [Chlamydomonas reinhardtii

    SciTech Connect (OSTI)

    Moroney, J.V.; Togasaki, R.K.; Husic, H.D.; Tolbert, N.E.

    1987-07-01

    Inorganic carbon (C/sub i/) uptake was measured in wild-type cells of Chlamydomonas reinhardtii, and in cia-3, a mutant strain of C. reinhardtii that cannot grow with air levels of CO/sub 2/. Both air-grown cells, that have a CO/sub 2/ concentrating system, and 5% CO/sub 2/-grown cells that do not have this system, were used. When the external pH was 5.1 or 7.3, air-grown, wild-type cells accumulated inorganic carbon (C/sub i/) and this accumulation was enhanced when the permeant carbonic anhydrase inhibitor, ethoxyzolamide, was added. When the external pH was 5.1, 5% CO/sub 2/-grown cells also accumulated some C/sub i/, although not as much as air-grown cells and this accumulation was stimulated by the addition of ethoxyzolamide. At the same time, ethoxyzolamide inhibited CO/sub 2/ fixation by high CO/sub 2/-grown, wild-type cells at both pH 5.1 and 7.3. These observations imply that 5% CO/sub 2/-grown, wild-type cells, have a physiologically important internal carbonic anhydrase, although the major carbonic anhydrase located in the periplasmic space is only present in air-grown cells. Inorganic carbon uptake by cia-3 cells supported this conclusion. This mutant strain, which is thought to lack an internal carbonic anhydrase, was unaffected by ethoxyzolamide at pH 5.1. Other physiological characteristics of cia-3 resemble those of wild-type cells that have been treated with ethoxyzolamide. It is concluded that an internal carbonic anhydrase is under different regulatory control than the periplasmic carbonic anhydrase.

  8. Fungal-specific transcription factor AbPf2 activates pathogenicity in Alternaria brassicicola

    SciTech Connect (OSTI)

    Cho, Yangrae; Ohm, Robin A.; Grigoriev, Igor V.; Srivastava, Akhil

    2012-12-03

    Alternaria brassicicola is a successful saprophyte and necrotrophic plant pathogen. To identify molecular determinants of pathogenicity, we created non-pathogenic mutants of a transcription factor-encoding gene, AbPf2. The frequency and timing of germination and appressorium formation on host plants were similar between the non-pathogenic abpf2 mutants and wild-type A. brassicicola. The mutants were also similar in vitro to wild-type A. brassicicola in terms of vegetative growth, conidium production, and responses to a phytoalexin, reactive oxygen species and osmolites. The hyphae of the mutants grew slowly but did not cause disease symptoms on the surface of host plants. Transcripts of the AbPf2 gene increased exponentially soon after wild-type conidia contacted their host plants . A small amount of AbPf2 protein, as monitored using GFP fusions, was present in young, mature conidia. The protein level decreased during saprophytic growth, but increased and was located primarily in fungal nuclei during pathogenesis. Levels of the proteins and transcripts sharply decreased following colonization of host tissues beyond the initial infection site. When expression of the transcription factor was induced in the wild-type during early pathogenesis, 106 fungal genes were also induced in the wild-type but not in the abpf2 mutants. Notably, 33 of the 106 genes encoded secreted proteins, including eight putative effector proteins. Plants inoculated with abpf2 mutants expressed higher levels of genes associated with photosynthesis, the pentose phosphate pathway and primary metabolism, but lower levels of defense-related genes. Our results suggest that AbPf2 is an important regulator of pathogenesis, but does not affect other cellular processes in A. brassicicola.

  9. Smolt Monitoring at the Head of Lower Granite Reservoir and Lower Granite Dam, 2005 Annual Report.

    SciTech Connect (OSTI)

    Buettner, Edwin W.; Putnam, Scott A.

    2009-02-18

    This project monitored the daily passage of Chinook salmon Oncorhynchus tshawytscha, steelhead trout O. mykiss, and sockeye salmon O. nerka smolts during the 2005 spring out-migration at migrant traps on the Snake River and Salmon River. In 2005 fish management agencies released significant numbers of hatchery Chinook salmon and steelhead trout above Lower Granite Dam that were not marked with a fin clip or coded-wire tag. Generally, the age-1 and older fish were distinguishable from wild fish by the occurrence of fin erosion. Age-0 Chinook salmon are more difficult to distinguish between wild and non-adclipped hatchery fish and therefore classified as unknown rearing. The total annual hatchery spring/summer Chinook salmon catch at the Snake River trap was 0.34 times greater in 2005 than in 2004. The wild spring/summer Chinook catch was 0.34 times less than the previous year. Hatchery steelhead trout catch was 0.67 times less than in 2004. Wild steelhead trout catch was 0.72 times less than the previous year. The Snake River trap collected 1,152 age-0 Chinook salmon of unknown rearing. During 2005, the Snake River trap captured 219 hatchery and 44 wild/natural sockeye salmon and 110 coho salmon O. kisutch of unknown rearing. Differences in trap catch between years are due to fluctuations not only in smolt production, but also differences in trap efficiency and duration of trap operation associated with flow. Trap operations began on March 6 and were terminated on June 3. The trap was out of operation for a total of one day due to heavy debris. FPC requested that the trap be restarted on June 15 through June 22 to collect and PIT tag age-0 Chinook salmon. Hatchery Chinook salmon catch at the Salmon River trap was 1.06 times greater and wild Chinook salmon catch was 1.26 times greater than in 2004. The hatchery steelhead trout collection in 2005 was 1.41 times greater and wild steelhead trout collection was 1.27 times greater than the previous year. Trap operations

  10. Smolt Monitoring at the Head of Lower Granite Reservoir and Lower Granite Dam, 2002 Annual Report.

    SciTech Connect (OSTI)

    Buettner, Edwin W.; Putnam, Scott A.

    2009-02-18

    This project monitored the daily passage of Chinook salmon Oncorhynchus tshawytscha, steelhead trout O. mykiss, and sockeye salmon smolts O. nerka during the 2002 spring out-migration at migrant traps on the Snake River and Salmon River. In 2002 fish management agencies released significant numbers of hatchery Chinook salmon and steelhead trout above Lower Granite Dam that were not marked with a fin clip or coded-wire tag. Generally, these fish were distinguishable from wild fish by the occurrence of fin erosion. Total annual hatchery Chinook salmon catch at the Snake River trap was 11.4 times greater in 2002 than in 2001. The wild Chinook catch was 15.5 times greater than the previous year. Hatchery steelhead trout catch was 2.9 times greater than in 2001. Wild steelhead trout catch was 2.8 times greater than the previous year. The Snake River trap collected 3,996 age-0 Chinook salmon of unknown rearing. During 2002, the Snake River trap captured 69 hatchery and 235 wild/natural sockeye salmon and 114 hatchery coho salmon O. kisutch. Differences in trap catch between years are due to fluctuations not only in smolt production, but also differences in trap efficiency and duration of trap operation associated with flow. The significant increase in catch in 2002 was due to a 3.1 fold increase in hatchery Chinook production and a more normal spring runoff. Trap operations began on March 10 and were terminated on June 7. The trap was out of operation for a total of four days due to mechanical failure or debris. Hatchery Chinook salmon catch at the Salmon River trap was 4.2 times greater and wild Chinook salmon catch was 2.4 times greater than in 2001. The hatchery steelhead trout collection in 2002 was 81% of the 2001 numbers. Wild steelhead trout collection in 2002 was 81% of the previous year's catch. Trap operations began on March 10 and were terminated on May 29 due to high flows. The trap was out of operation for four days due to high flow or debris. The increase

  11. Smolt Monitoring at the Head of Lower Granite Reservoir and Lower Granite Dam, 2004 Annual Report.

    SciTech Connect (OSTI)

    Buettner, Edwin W.; Putnam, Scott A.

    2009-02-18

    This project monitored the daily passage of Chinook salmon Oncorhynchus tshawytscha, steelhead trout O. mykiss, and sockeye salmon O. nerka smolts during the 2004 spring out-migration at migrant traps on the Snake River and Salmon River. In 2004 fish management agencies released significant numbers of hatchery Chinook salmon and steelhead trout above Lower Granite Dam that were not marked with a fin clip or coded-wire tag. Generally, these fish were distinguishable from wild fish by the occurrence of fin erosion. Total annual hatchery Chinook salmon catch at the Snake River trap was 1.1 times greater in 2004 than in 2003. The wild Chinook catch was 1.1 times greater than the previous year. Hatchery steelhead trout catch was 1.2 times greater than in 2003. Wild steelhead trout catch was 1.6 times greater than the previous year. The Snake River trap collected 978 age-0 Chinook salmon of unknown rearing. During 2004, the Snake River trap captured 23 hatchery and 18 wild/natural sockeye salmon and 60 coho salmon O. kisutch of unknown rearing. Differences in trap catch between years are due to fluctuations not only in smolt production, but also differences in trap efficiency and duration of trap operation associated with flow. Trap operations began on March 7 and were terminated on June 4. The trap was out of operation for a total of zero days due to mechanical failure or debris. Hatchery Chinook salmon catch at the Salmon River trap was 10.8% less and wild Chinook salmon catch was 19.0% less than in 2003. The hatchery steelhead trout collection in 2004 was 20.0% less and wild steelhead trout collection was 22.3% less than the previous year. Trap operations began on March 7 and were terminated on May 28 due to high flows. There were two days when the trap was taken out of service because wild Chinook catch was very low, hatchery Chinook catch was very high, and the weekly quota of PIT tagged hatchery Chinook had been met. Travel time (d) and migration rate (km

  12. Designing a highly active soluble PQQ-glucose dehydrogenase for efficient glucose biosensors and biofuel cells

    SciTech Connect (OSTI)

    Durand, Fabien; Stines-Chaumeil, Claire; Flexer, Victoria; Andre, Isabelle; CNRS, UMR5504, F-31400 Toulouse; INRA, UMR 792 Ingenierie des Systemes Biologiques et des Procedes, F-31400 Toulouse ; Mano, Nicolas

    2010-11-26

    Research highlights: {yields} A new mutant of PQQ-GDH designed for glucose biosensors application. {yields} First mutant of PQQ-GDH with higher activity for D-glucose than the Wild type. {yields} Position N428 is a key point to increase the enzyme activity. {yields} Molecular modeling shows that the N428 C mutant displays a better interaction for PQQ than the WT. -- Abstract: We report for the first time a soluble PQQ-glucose dehydrogenase that is twice more active than the wild type for glucose oxidation and was obtained by combining site directed mutagenesis, modelling and steady-state kinetics. The observed enhancement is attributed to a better interaction between the cofactor and the enzyme leading to a better electron transfer. Electrochemical experiments also demonstrate the superiority of the new mutant for glucose oxidation and make it a promising enzyme for the development of high-performance glucose biosensors and biofuel cells.

  13. Prestack mid-value filtering

    SciTech Connect (OSTI)

    Changlian, X. )

    1992-01-01

    This paper describes mid-value filtering, a specific nonlinear smoothing filtering, and widely used in graphic processing, etc. Mid-value filtering before stack of seismic data can remove wild value (inconceivable particular big value) and improve signal-noise ratio. In view of big data volume before stack, computation efficiency of mid-value filtering is critical to its feasibility. The algorithm used here is sufficiently based on the properties of mid-value filtering, so that the computation efficiency is greatly improved. It is experimentally shown that prestack mid-value filtering can quite well eliminate wild value, abnormal traces as well as surface waves, and raise signal-noise ratio. After lateral low frequency noises are removed by high pass filtering, mid-value filtering works better.

  14. Cellulose fermentation by an asporogenous mutant and an ethanol-tolerant mutant of Clostridium thermocellum

    SciTech Connect (OSTI)

    Tailliez, P.; Girard, H.; Longin, R.; Beguin, P.; Millet, J. )

    1989-01-01

    Two mutants of Clostridium thermocellum were isolated after UV light mutagenesis. Mutant A1, selected as asporogenous, exhibited a fermentation pattern similar to that of the wild type. However, at pH 6.5, the mutant degraded 12% more cellulose than did the wild type, leading to enhanced ethanol production. Mutant 647, selected as ethanol tolerant, was able to grow in medium containing 4% ethanol. During the early stage of the exponential growth phase, ethanol was produced as the main product, up to a concentration of about 9 g/liter. After 3 days of culture, 48.3 g (89% of the initial amount) of degraded cellulose per liter was fermented into 12.7 g of ethanol per liter.

  15. Complex history of admixture during citrus domestication revealed by genome analysis

    SciTech Connect (OSTI)

    Wu, G. Albert; Prochnik, Simon; Jenkins, Jerry; Salse, Jerome; Hellsten, Uffe; Murat, Florent; Perrier, Xavier; Ruiz, Manuel; Scalabrin, Simone; Terol, Javier; Takita, Marco Auré lio,; Labadie, Karine; Poulain, Julie; Couloux, Arnaud; Jabbari, Kamel; Cattonaro, Federica; Fabbro, Cristian Del; Pinosio, Sara; Zuccolo, Andrea; Chapman, Jarrod; Grimwood, Jane; Tadeo, Francisco; Estornell, Leandro H.; Mu?oz-Sanz, Juan V.; Ibanez, Victoria; Herrero-Ortega, Amparo; Aleza, Pablo; Pé rez, Juliá n Pé rez,; Ramon, Daniel; Brunel, Dominique; Luro, Francois; Chen, Chunxian; Farmerie, William G.; Desany, Brian; Kodira, Chinnappa; Mohiuddin, Mohammed; Harkins, Tim; Fredrikson, Karin; Burns, Paul; Lomsadze, Alexandre; Borodovsky, Mark; Reforgiato, Giuseppe; Freitas-Astua, Juliana; Quetier, Francis; Navarro, Luis; Roose, Mikeal; Wincker, Patrick; Schmutz, Jeremy; Morgante, Michele; Machado, Marcos Antonio; Talon, Manuel; Jaillon, Olivier; Ollitrault, Patrick; Gmitter, Frederick; Rokhsar, Daniel

    2014-06-30

    Although Citrus is the most globally significant tree fruit, its domestication history is poorly understood. Cultivated citrus types are believed to comprise selections from and/or hybrids of several wild progenitor species, but the identities of these progenitors, and their contribution to modern cultivars, remain controversial. Here we report the genomes of a collection of mandarins, pummelos, and oranges, including a high quality reference sequence from a haploid Clementine mandarin. By comparative genome analysis we show that these cultivated types can be derived from two progenitor species. Cultivated pummelos represent selections from a single progenitor species C. maxima. Unexpectedly, however, we find that cultivated mandarins are introgressions of C. maxima into a distinct second population that we identify with the ancestral wild mandarin species C. reticulata. Sweet and sour oranges are found to be interspecific hybrids. Sweet orange, the most widely cultivated citrus, arose as the offspring of previously admixed individuals. In contrast, sour (or Seville) orange is an F1 hybrid of pure C. maxima and C. reticulata parents, implying that wild mandarins were part of the early breeding germplasm. Surprisingly, we also find that a wild Chinese mandarin from Mangshan, China shows substantial sequence divergence from C. reticulata and appears to represent a distinct taxon. Understanding the relationships and phylogeny of cultivated citrus through genome analysis will clarify taxonomic relationships and enable previously inconceivable opportunities for sequence-directed genetic improvement. Citrus are widely consumed worldwide as juice or fresh fruit, providing important sources of vitamin C and other health-promoting compounds. Global production in 2012 exceeded 86 million metric tons, with an estimated value of US$9 billion (http://www.fas.usda.gov/psdonline/circulars/citrus.pdf). The very narrow genetic diversity of cultivated citrus makes it highly

  16. NERSCbench_NUG_final.ppt

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Science Driven System Architectures (and a few words about benchmarking) John Shalf NERSC Users Group Meeting Princeton Plasma Physics Laboratory June 2006 Office of Science U.S. Department of Energy Overview  Overview of the SSP for procurement benchmarks  Recent Benchmarking Activities  Workload Characterization  Wild Ideas Office of Science U.S. Department of Energy NERSC Mission  Support large scale computational science that cannot be done elsewhere  Support wide variety

  17. NREL: Wind Research - Wind and Water Power Fact Sheets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Wind and Water Power Fact Sheets The capabilities for research at the National Wind Technology Center (NWTC) are numerous. Below you will find fact sheets about the many facilities and capabilities at the NWTC, including field testing research, modeling and simulation, and the Wind-Wildlife Impacts Literature Database. Fact Sheet Cover 35 Years of Innovation: Leading the Way to a Clean Energy Future Fact Sheet Cover Wind-Wildlife Impacts Literature Database (WILD) Fact Sheet Cover NREL Software

  18. Research Highlight

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Significant Decadal Brightening over the Continental United States Download a printable PDF Submitter: Long, C. N., NOAA Global Monitoring Division/CIRES Dutton, E. G., NOAA/OAR/ESRL Augustine, J., National Oceanic and Atmospheric Administration Wiscombe, W. J., Brookhaven National Laboratory Wild, M., Institute for Atmospheric and Climate Science - ETH Zurich McFarlane, S. A., U.S. Department of Energy Flynn, C. J., Pacific Northwest National Laboratory Area of Research: Radiation Processes

  19. Research Highlight

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Global Dimming and Brightening: an Update Beyond 2000 Download a printable PDF Submitter: Long, C. N., NOAA Global Monitoring Division/CIRES Wild, M., Institute for Atmospheric and Climate Science - ETH Zurich Truessel, B., Institute for Atmospheric and Climate Science - ETH Zurich Ohmura, A., Swiss Federal Institute of Technology Koenig-Langlo, G., Alfred Wegener Institute Dutton, E. G., NOAA/OAR/ESRL Tsvetkov, A. V., World Radiation Data Centre Area of Research: Radiation Processes Working

  20. Research Highlight

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Earth Lightens Up Submitter: Long, C. N., NOAA Global Monitoring Division/CIRES Area of Research: Radiation Processes Working Group(s): Radiative Processes Journal Reference: Wild, M., H. Gilgen, A. Roesch, A. Ohmura, C. N. Long, E. G. Dutton, B. Forgan, A. Kallis, V. Russak, and A. Tsvetkov, (2005): From dimming to brightening: Decadal changes in solar radiation at the Earth's surface, Science, 308, Issue 5723, 847-850, [DOI:10.1126/science.1103215] Global distribution of surface observation

  1. Jessica Mulhern | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Jessica Mulhern Albert Einstein Distinguished Educator Fellowship (AEF) Program Einstein Fellowship Home Eligibility Benefits Obligations How to Apply Key Dates Frequently Asked Questions Fellows Central Current Fellows Alumni Fellows Official AEF Logos Contact WDTS Home Current Fellows Jessica Mulhern Print Text Size: A A A FeedbackShare Page Jessica Mulhern Fellowship Placement: U.S. House of Representatives Hometown: Wall, NJ Jessica Mulhern taught high school biology at Wilde Lake High

  2. SREL Reprint #3364

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 Blood and plasma biochemistry reference intervals for wild juvenile American alligators (Alligator mississippiensis) Matthew T. Hamilton1,2, Caitlin A. Kupar1,2, Meghan D. Kelley3, John W. Finger Jr.1,3, and Tracey D. Tuberville1 1Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, South Carolina 29802, USA 2Warnell School of Forestry and Natural Resources, University of Georgia, 180 E Green Street, Athens, Georgia 30602, USA 3Department of Biological Sciences, Auburn

  3. Leveraging Tribal Renewable Resources to Support Military Energy Goals |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Leveraging Tribal Renewable Resources to Support Military Energy Goals Leveraging Tribal Renewable Resources to Support Military Energy Goals May 30-31, 2013 Image of a speaker at the forum. Chandler, Arizona Wild Horse Pass Hotel and Casino The Office of Indian Energy Tribal Leader Energy Forum on "Leveraging Tribal Renewable Resources to Support Military Energy Goals" was held May 30-31, 2013, in Chandler, Arizona. The forum provided information for western

  4. Projects | Argonne Leadership Computing Facility

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Projects bgclang Compiler Hal Finkel Cobalt Scheduler Bill Allcock, Paul Rich, Brian Toonen, Tom Uram GLEAN: Scalable In Situ Analysis and I/O Acceleration on Leadership Computing Systems Michael E. Papka, Venkat Vishwanath, Mark Hereld, Preeti Malakar, Joe Insley, Silvio Rizzi, Tom Uram Petrel: Data Management and Sharing Pilot Ian Foster, Michael E. Papka, Bill Allcock, Ben Allen, Rachana Ananthakrishnan, Lukasz Lacinski The Swift Parallel Scripting Language for ALCF Systems Michael Wilde,

  5. Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

    SciTech Connect (OSTI)

    Tringe, Susannah

    2012-01-01

    Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

  6. 'Comic Book Physics' examined at Jefferson Lab's March 25 Science Series

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    event | Jefferson Lab 'Comic Book Physics' examined at Jefferson Lab's March 25 Science Series event Comic book physics Even superheroes must obey the laws of physics - or do they? Artwork: Kim Dylla 'Comic Book Physics' examined at Jefferson Lab's March 25 Science Series event February 26, 2003 The wild, wacky world of 'Comic Book Physics' will be investigated by guest speaker Jim Kakalios, from the University of Minnesota, at Jefferson Lab's Spring Science Series event, set for Tuesday,

  7. Plants & Animals

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Plants & Animals Plants & Animals Plant and animal monitoring is performed to determine whether Laboratory operations are impacting human health via the food chain. February 2, 2015 A rabbit on LANL land. A rabbit on Los Alamos National Laboratory land. Contact Environmental Communication & Public Involvement P.O. Box 1663 MS M996 Los Alamos, NM 87545 (505) 667-0216 Email We sample many plants and animals, including wild and domestic crops, game animals, fish, and food products from

  8. U-054: Security Advisory for Adobe Reader and Acrobat

    Broader source: Energy.gov [DOE]

    This U3D memory corruption vulnerability (CVE-2011-2462) could cause a crash and potentially allow an attacker to take control of the affected system. There are reports that the vulnerability is being actively exploited in the wild in limited, targeted attacks against Adobe Reader 9.x on Windows. Adobe Reader X Protected Mode and Acrobat X Protected View mitigations would prevent an exploit of this kind from executing.

  9. Wall-associated kinase-like polypeptide mediates nutritional status perception and response

    DOE Patents [OSTI]

    Yang, Zhenbiao; Karr, Stephen

    2014-02-11

    The disclosure relates to methods for modulating plant growth and organogenesis using dominant-negative receptor-like kinases. The disclosure further provides a method for increasing plant yield relative to corresponding wild type plants comprising modulating the expression in a plant of a nucleic acid encoding a Wall-Associated Kinase-like 14 polypeptide or a homolog thereof, and selecting for plants having increased yield or growth on a nutrient deficient substrate.

  10. Hanford For Students and Kids - Hanford Site

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Hanford For Students and Kids Hanford For Students and Kids Hanford Fun Facts Classroom Projects Famous People of Hanford Hanford For Students and Kids Email Email Page | Print Print Page | Text Increase Font Size Decrease Font Size The Hanford Nuclear Reservation is a pretty amazing place. Located in the present-day southeast corner of Washington State, the area where Hanford sits has a history that actually began thousands of years ago when wild animals roamed free and Indians were the only

  11. Mercury Strategic Plan Outfall 200 Mercury Treatment Facility

    Office of Environmental Management (EM)

    The Menominee Nation once occupied 9.5 million acres of land * The present Menominee Reservation was established in 1854 with 234,000 acres. * The Menominee hunted, fished and harvested wild rice on their reservation. MTE Menominee Tribal Enterprises The Menominee Nation * The Menominee retained their island of timber & community by dint of their own tenacity, federal protection and fortuitous circumstance. MTE Menominee Tribal Enterprises The Menominee Nation * 95% of the reservation

  12. Transcription Factor Amr1 Induces Melanin Biosynthesis and Suppresses Virulence in Alternaria brassicicola

    SciTech Connect (OSTI)

    Cho, Yangrae; Srivastava, Akhil; Ohm, Robin A.; Lawrence, Christopher B.; Wang, Koon-Hui; Grigoriev, Igor V.; Marahatta, Sharadchandra P.

    2012-05-01

    Alternaria brassicicola is a successful saprophyte and necrotrophic plant pathogen. Several A. brassicicola genes have been characterized as affecting pathogenesis of Brassica species. To study regulatory mechanisms of pathogenesis, we mined 421 genes in silico encoding putative transcription factors in a machine-annotated, draft genome sequence of A. brassicicola. In this study, targeted gene disruption mutants for 117 of the transcription factor genes were produced and screened. Three of these genes were associated with pathogenesis. Disruption mutants of one gene (AbPacC) were nonpathogenic and another gene (AbVf8) caused lesions less than half the diameter of wild-type lesions. Unexpectedly, mutants of the third gene, Amr1, caused lesions with a two-fold larger diameter than the wild type and complementation mutants. Amr1 is a homolog of Cmr1, a transcription factor that regulates melanin biosynthesis in several fungi. We created gene deletion mutants of ?amr1 and characterized their phenotypes. The ?amr1 mutants used pectin as a carbon source more efficiently than the wild type, were melanin-deficient, and more sensitive to UV light and glucanase digestion. The AMR1 protein was localized in the nuclei of hyphae and in highly melanized conidia during the late stage of plant pathogenesis. RNA-seq analysis revealed that three genes in the melanin biosynthesis pathway, along with the deleted Amr1 gene, were expressed at low levels in the mutants. In contrast, many hydrolytic enzyme-coding genes were expressed at higher levels in the mutants than in the wild type during pathogenesis. The results of this study suggested that a gene important for survival in nature negatively affected virulence, probably by a less efficient use of plant cell-wall materials. We speculate that the functions of the Amr1 gene are important to the success of A. brassicicola as a competitive saprophyte and plant parasite.

  13. Modified Yeast Ferments Biomass Xylose - Energy Innovation Portal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Ferments Biomass Xylose Great Lakes Bioenergy Research Center Contact GLBRC About This Technology Technology Marketing Summary Producing biofuel on a useful scale requires efficient fermentation of cellulosic plant material. The sugars glucose and xylose are the most abundant carbohydrates found in hemicellulose. The yeast most commonly utilized for industrial fermentation - Saccharomyces cerevisiae - can ferment glucose but not xylose. By studying the genomes of wild strains of yeast capable of

  14. Seeking New Approaches to Investigate Domestication Events | Stanford

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Synchrotron Radiation Lightsource Seeking New Approaches to Investigate Domestication Events Monday, October 29, 2012 - 3:30am SSRL Bldg. 137, Rm. 322 Krish Seetah, Stanford University, Department of Anthropology and Zooarcheology Laboratory The domestication of wild animal species has underpinned some of the most fundamental developments in human history. The inclusion of a range of fauna into the human menagerie has altered the way we feed and transport ourselves, not to mention how we

  15. Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

    ScienceCinema (OSTI)

    Tringe, Susannah

    2013-05-29

    Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

  16. hagan-99.PDF

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Compact Spectral Radiometer for In Situ Solar Flux Measurements D. E. Hagan, M. Foote, J.-F. Blavier, L. Wild, and E. Jones Jet Propulsion Laboratory California Institute of Technology Pasadena, California Introduction We describe here the breadboard version of a lightweight, compact radiometer, which uses microthermopile detectors for hemispheric measurements of broadband and spectral downwelling solar irradiance. The instrument has undergone initial operability tests, and some limited field

  17. Antonella Amore | Bioenergy | NREL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Antonella Amore Postdoctoral Researcher Antonella.Amore@nrel.gov | 303-275-4399 Research Interests Second generation bioethanol production Lignocellulose conversion into high-added-value products Development and study of new ligninases, cellulases, and hemicellulases, from both fungi and bacteria Recombinant heterologous expression of wild-type and mutant (random mutants/site-directed mutants) (hemi)cellulolytic enzymes Study of the structure-function relationships in (hemi)cellulolytic enzymes

  18. Quickstart Resume Template

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    JAMES C. BEASLEY Savannah River Ecology Lab Phone: (803) 725-5113 P.O. Drawer E Fax: (803) 725-3309 Aiken, SC 29802 Email: beasley@srel.uga.edu RESEARCH INTERESTS Spatial ecology and population dynamics of carnivores, effects of anthropogenic stressors on wildlife, wild pig ecology and management, human-wildlife conflicts, wildlife disease ecology, scavenging ecology EDUCATION: Ph.D., Wildlife Ecology, Purdue University 2010 Advisor: Dr. Olin Rhodes, Jr. M.S., Wildlife Ecology, Purdue University

  19. Slide 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Stacy Charboneau June 2015 2 Safety and Health HAMMER Wild land fire in 200 West Area * Hanford Fire Danger "Very High" * CHPRC and site contractors implementing summer safety campaigns (heat safety) * Mission Support Alliance injury rate lowest in four years * Washington Closure Hanford reached 5.5 million safe hours (without an injury resulting in a lost work day) 3 4 2015 300 Area Progress 300 Area Cleanup * Completed remediation of the 309 Test Reactor below- grade structure. All

  20. ALSNews Vol. 276

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    6 Print Contents Particles from Comet 81P/Wild 2 viewed by ALS microscopes Nature and origin of the cuprate pseudogap In Memoriam: Gary Krebs Director's update at all-hands meeting First light for ultrafast Beamline 6.0.1 COSMIC/MAESTRO reviewers enthusiastic Users' Meeting, October 4-6 General user proposals submission deadline ALS Fellowship Program: doctoral deadline and new postdoctoral fellowship News Links Carbon joins the magnetic club 'Racetrack' memory could gallop past the hard disk

  1. ALSNews Vol. 276

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    6 Print Contents Particles from Comet 81P/Wild 2 viewed by ALS microscopes Nature and origin of the cuprate pseudogap In Memoriam: Gary Krebs Director's update at all-hands meeting First light for ultrafast Beamline 6.0.1 COSMIC/MAESTRO reviewers enthusiastic Users' Meeting, October 4-6 General user proposals submission deadline ALS Fellowship Program: doctoral deadline and new postdoctoral fellowship News Links Carbon joins the magnetic club 'Racetrack' memory could gallop past the hard disk

  2. Hellsgate Winter Range : Wildlife Mitigation Project. Preliminary Environmental Assessment.

    SciTech Connect (OSTI)

    United States. Bonneville Power Administration.

    1995-01-01

    The Bonneville Power Administration proposes funding the Hellsgate Winter Range Wildlife Mitigation Project in cooperation with the Colville Convederated Tribes and Bureau of Indian Affairs. This Preliminary Environmental Assessment examines the potential environmental effects of acquiring and managing property for wildlife and wildlife habitat within a large project area. The Propose action is intended to meet the need for mitigation of wildlife and wild life habitat that was adversely affected by the construction of Grand Coulee and Chief Joseph Dams and their reservoirs.

  3. Survival Estimates for the Passage of Spring-Migrating Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2005-2006 Annual Report.

    SciTech Connect (OSTI)

    Smith, Steven G.; Muir, William D.; Marsh, Douglas M.

    2006-05-01

    In 2005, the National Marine Fisheries Service and the University of Washington completed the thirteenth year of a study to estimate survival and travel time of juvenile salmonids Oncorhynchus spp. passing through dams and reservoirs on the Snake and Columbia Rivers. All estimates were derived from detections of fish tagged with passive integrated transponder tags (PIT tags). We PIT tagged and released a total of 18,439 hatchery steelhead, 5,315 wild steelhead, and 6,964 wild yearling Chinook salmon at Lower Granite Dam in the Snake River. In addition, we utilized fish PIT tagged by other agencies at traps and hatcheries upstream from the hydropower system and at sites within the hydropower system in both the Snake and Columbia Rivers. PIT-tagged smolts were detected at interrogation facilities at Lower Granite, Little Goose, Lower Monumental, Ice Harbor, McNary, John Day, and Bonneville Dams and in the PIT-tag detector trawl operated in the Columbia River estuary. Survival estimates were calculated using a statistical model for tag-recapture data from single release groups (the ''single-release model''). Primary research objectives in 2005 were: (1) Estimate reach survival and travel time in the Snake and Columbia Rivers throughout the migration period of yearling Chinook salmon O. tshawytscha and steelhead O. mykiss. (2) Evaluate relationships between survival estimates and migration conditions. (3) Evaluate the survival estimation models under prevailing conditions. This report provides reach survival and travel time estimates for 2005 for PIT-tagged yearling Chinook salmon (hatchery and wild), hatchery sockeye salmon O. nerka, hatchery coho salmon O. kisutch, and steelhead (hatchery and wild) in the Snake and Columbia Rivers. Additional details on the methodology and statistical models used are provided in previous reports cited here.

  4. INDIAN COUNTRY ENERGY AND INFRASTRUCTURE WORKING GROUP ICEIWG

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of 8 INDIAN COUNTRY ENERGY AND INFRASTRUCTURE WORKING GROUP ICEIWG May 29, 2013 Wild Horse Pass Hotel and Casino Chandler, Arizona MEETING OVERVIEW The U.S. Department of Energy Office (DOE) of Indian Energy (IE) hosted an Indian Country Energy and Infrastructure Working Group (ICEIWG) Meeting on Wednesday, May 29, 2013 in Chandler, Arizona. IE welcomed reappointed and new members to ICEIWG. The ICEIWG meeting was held prior to the seventh Tribal Leader Forum on "Leveraging Tribal Renewable

  5. Identification of a Xylogalacturonan Xylosyltransferase Involved in Pectin Biosynthesis in Arabidopsis

    SciTech Connect (OSTI)

    Pauly, Markus; Sorensen, Susanne Oxenboll; Harholt, Jesper; Geshi, Naomi; Sakuragi, Yumiko; Moller, Isabel; Zandleven, Joris; Bernal, Adriana J.; Jensen, Niels Bjerg; Sorensen, Charlotte; Jensen, Jacob K.; Beldman, Gerrit; Willats, William G.T.; Scheller, Henrik

    2009-08-19

    Xylogalacturonan (XGA) is a class of pectic polysaccharide found in plant cell walls. The Arabidopsis thaliana locus At5g33290 encodes a predicted Type II membrane protein, and insertion mutants of the At5g33290 locus had decreased cell wall xylose. Immunological studies, enzymatic extraction of polysaccharides, monosaccharide linkage analysis, and oligosaccharide mass profiling were employed to identify the affected cell wall polymer. Pectic XGA was reduced to much lower levels in mutant than in wild-type leaves, indicating a role of At5g33290 in XGA biosynthesis. The mutated gene was designated xylogalacturonan deficient1 (xgd1). Transformation of the xgd1-1 mutant with the wild-type gene restored XGA to wild-type levels. XGD1 protein heterologously expressed in Nicotiana benthamiana catalyzed the transfer of xylose from UDP-xylose onto oligogalacturonides and endogenous acceptors. The products formed could be hydrolyzed with an XGA-specific hydrolase. These results confirm that the XGD1 protein is a XGA xylosyltransferase. The protein was shown by expression of a fluorescent fusion protein in N. benthamiana to be localized in the Golgi vesicles as expected for a glycosyltransferase involved in pectin biosynthesis.

  6. Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Nafisi, Majse; Stranne, Maria; Fimognari, Lorenzo; Atwell, Susanna; Martens, Helle J.; Pedas, Pai R.; Hansen, Sara F.; Nawrath, Christiane; Scheller, Henrik V.; Kliebenstein, Daniel J.; et al

    2015-07-22

    Here we report that the epidermis on leaves protects plants from pathogen invasion and provides a waterproof barrier. It consists of a layer of cells that is surrounded by thick cell walls, which are partially impregnated by highly hydrophobic cuticular components. We show that the Arabidopsis T-DNA insertion mutants of REDUCED WALL ACETYLATION 2 (rwa2), previously identified as having reduced O-acetylation of both pectins and hemicelluloses, exhibit pleiotrophic phenotype on the leaf surface. The cuticle layer appeared diffused and was significantly thicker and underneath cell wall layer was interspersed with electron-dense deposits. A large number of trichomes were collapsed andmore » surface permeability of the leaves was enhanced in rwa2 as compared to the wild type. A massive reprogramming of the transcriptome was observed in rwa2 as compared to the wild type, including a coordinated up-regulation of genes involved in responses to abiotic stress, particularly detoxification of reactive oxygen species and defense against microbial pathogens (e.g., lipid transfer proteins, peroxidases). In accordance, peroxidase activities were found to be elevated in rwa2 as compared to the wild type. These results indicate that cell wall acetylation is essential for maintaining the structural integrity of leaf epidermis, and that reduction of cell wall acetylation leads to global stress responses in Arabidopsis.« less

  7. Metabonomic Profiling of TASTPM Transgenic Alzheimer's Disease Mouse Model

    SciTech Connect (OSTI)

    Hu, Zeping; Browne, Edward R.; Liu, Tao; Angel, Thomas E.; Ho, Paul C.; Chun Yong Chan, Eric

    2012-12-07

    Identification of molecular mechanisms underlying early stage Alzheimer’s disease (AD) is important for the development of new therapies against and diagnosis of AD. In this study, non-targeted metabotyping of TASTPM transgenic AD mice was performed. The metabolic profiles of both brain and plasma of TASTPM mice were characterized using gas chromatography-mass spectrometry and compared to those of wild type C57BL/6J mice. TASTPM mice were metabolically distinct compared to wild type mice (Q28 Y = 0.587 and 0.766 for PLS-DA models derived from brain and plasma, respectively). A number of metabolites were found to be perturbed in TASTPM mice in both brain (D11 fructose, L-valine, L-serine, L-threonine, zymosterol) and plasma (D-glucose, D12 galactose, linoleic acid, arachidonic acid, palmitic acid and D-gluconic acid). In addition, enzyme immunoassay confirmed that selected endogenous steroids were significantly perturbed in brain (androstenedione and 17-OH-progesterone) and plasma (cortisol and testosterone) of TASTPM mice. Ingenuity pathway analysis revealed that perturbations related to amino acid metabolism (brain), steroid biosynthesis (brain), linoleic acid metabolism (plasma) and energy metabolism (plasma) accounted for the differentiation of TASTPM and wild-type

  8. Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses

    SciTech Connect (OSTI)

    Nafisi, Majse; Stranne, Maria; Fimognari, Lorenzo; Atwell, Susanna; Martens, Helle J.; Pedas, Pai R.; Hansen, Sara F.; Nawrath, Christiane; Scheller, Henrik V.; Kliebenstein, Daniel J.; Sakuragi, Yumiko

    2015-07-22

    Here we report that the epidermis on leaves protects plants from pathogen invasion and provides a waterproof barrier. It consists of a layer of cells that is surrounded by thick cell walls, which are partially impregnated by highly hydrophobic cuticular components. We show that the Arabidopsis T-DNA insertion mutants of REDUCED WALL ACETYLATION 2 (rwa2), previously identified as having reduced O-acetylation of both pectins and hemicelluloses, exhibit pleiotrophic phenotype on the leaf surface. The cuticle layer appeared diffused and was significantly thicker and underneath cell wall layer was interspersed with electron-dense deposits. A large number of trichomes were collapsed and surface permeability of the leaves was enhanced in rwa2 as compared to the wild type. A massive reprogramming of the transcriptome was observed in rwa2 as compared to the wild type, including a coordinated up-regulation of genes involved in responses to abiotic stress, particularly detoxification of reactive oxygen species and defense against microbial pathogens (e.g., lipid transfer proteins, peroxidases). In accordance, peroxidase activities were found to be elevated in rwa2 as compared to the wild type. These results indicate that cell wall acetylation is essential for maintaining the structural integrity of leaf epidermis, and that reduction of cell wall acetylation leads to global stress responses in Arabidopsis.

  9. Thermodynamics imprinting reveals differential binding of metals to {alpha}-synuclein: Relevance to parkinson's disease

    SciTech Connect (OSTI)

    Bharathi; Rao, K.S.J. . E-mail: kjr5n@yahoo.co.in

    2007-07-20

    The aggregation of {alpha}-synuclein is a hallmark feature of Parkinson's disease (PD) and other synucleinopathies. Metals are the significant etiological factors in PD, and their interaction with {alpha}-synuclein affect dramatically the kinetics of fibrillation in vitro and are proposed to play an important and potential neurodegenerative role in vivo. In the present study, we investigated the stoichiometry of binding of copper [Cu (II)] and iron [Fe (III)] with {alpha}-synuclein (wild recombinant type and A30P, A53T, E46K mutant forms) using isothermal titration calorimetry (ITC). {alpha}-Synuclein monomer (wild and mutant forms) titrated by Cu (II), showed two binding sites, with an apparent K {sub B} of 10{sup 5} M and 10{sup 4} M, respectively. But, {alpha}-synuclein (wild type and mutant forms) titrated with Fe (III) revealed a K {sub B} of 10{sup 5} M with single binding site. The present investigation uncovers the detailed binding propensities between metals and {alpha}-synuclein and has biological implications in PD.

  10. Spatial and Functional Relationships Among Pol V-Associated loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome

    SciTech Connect (OSTI)

    Wierzbicki, A. T.; Cocklin, Ross; Mayampurath, Anoop; Lister, Ryan; Rowley, M. J.; Gregory, Brian D.; Ecker, Joseph R.; Tang, Haixu; Pikaard, Craig S.

    2012-08-15

    Multisubunit RNA polymerases IV and V (Pols IV and V) mediate RNA-directed DNA methylation and transcriptional silencing of retrotransposons and heterochromatic repeats in plants. We identified genomic sites of Pol V occupancy in parallel with siRNA deep sequencing and methylcytosine mapping, comparing wild-type plants with mutants defective for Pol IV, Pol V, or both Pols IV and V. Approximately 60% of Pol V-associated regions encompass regions of 24-nucleotide (nt) siRNA complementarity and cytosine methylation, consistent with cytosine methylation being guided by base-pairing of Pol IV-dependent siRNAs with Pol V transcripts. However, 27% of Pol V peaks do not overlap sites of 24-nt siRNA biogenesis or cytosine methylation, indicating that Pol V alone does not specify sites of cytosine methylation. Surprisingly, the number of methylated CHH motifs, a hallmark of RNA-directed de novo methylation, is similar in wild-type plants and Pol IV or Pol V mutants. In the mutants, methylation is lost at 50%-60% of the CHH sites that are methylated in the wild type but is gained at new CHH positions, primarily in pericentromeric regions. These results indicate that Pol IV and Pol V are not required for cytosine methyltransferase activity but shape the epigenome by guiding CHH methylation to specific genomic sites.

  11. Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum

    SciTech Connect (OSTI)

    Lynd, Lee R; Shao, Xiongjun; Raman, Babu; Mielenz, Jonathan R; Brown, Steven D; Guss, Adam M; Zhu, Mingjun

    2011-01-01

    Clostridium thermocellum is a model microorganism for converting cellulosic biomass into fuels and chemicals via consolidated bioprocessing. One of the challenges for industrial application of this organism is its low ethanol tolerance, typically 1 2% (w/v) in wild-type strains. In this study, we report the development and characterization of mutant C. thermocellum strains that can grow in the presence of high ethanol concentrations. Starting from a single colony, wild-type C. thermocellum ATCC 27405 was sub-cultured and adapted for growth in up to 50 g/L ethanol using either cellobiose or crystalline cellulose as the growth substrate. Both the adapted strains retained their ability to grow on either substrate and displayed a higher growth rate and biomass yield than the wild-type strain in the absence of ethanol. With added ethanol in the media, the mutant strains displayed an inverse correlation between ethanol concentration and growth rate or biomass yield. Genome sequencing revealed six common mutations in the two ethanol-tolerant strains including an alcohol dehydrogenase gene and genes involved in arginine/pyrimidine biosynthetic pathway. The potential role of these mutations in ethanol tolerance phenotype is discussed.

  12. Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum

    SciTech Connect (OSTI)

    Shao, Xiongjun; Raman, Babu; Zhu, Mingjun; Mielenz, Jonathan R; Brown, Steven D; Guss, Adam M; Lynd, Lee R

    2011-01-01

    Clostridium thermocellum is a model microorganism for converting cellulosic biomass into fuels and chemicals via consolidated bioprocessing. One of the challenges for industrial application of this organism is its low ethanol tolerance, typically 1-2% (w/v) in wild-type strains. In this study, we report the development and characterization of mutant C. thermocellum strains that can grow in the presence of high ethanol concentrations. Starting from a single colony, wild-type C. thermocellum ATCC 27405 was sub-cultured and adapted for growth in up to 50 g/L ethanol using either cellobiose or crystalline cellulose as the growth substrate. Both the adapted strains retained their ability to grow on either substrate and displayed a higher growth rate and biomass yield than the wild-type strain in the absence of ethanol. With added ethanol in the media, the mutant strains displayed an inverse correlation between ethanol concentration and growth rate or biomass yield. Genome sequencing revealed six common mutations in the two ethanol-tolerant strains including an alcohol dehydrogenase gene and genes involved in arginine/pyrimidine biosynthetic pathway. The potential role of these mutations in ethanol tolerance phenotype is discussed.

  13. Resistance to collagen-induced arthritis in SHPS-1 mutant mice

    SciTech Connect (OSTI)

    Okuzawa, Chie; Kaneko, Yoriaki; Murata, Yoji; Miyake, Astuko; Saito, Yasuyuki; Okajo, Jun; Tomizawa, Takeshi; Kaneko, Yuka; Okazawa, Hideki; Ohnishi, Hiroshi; Matozaki, Takashi Nojima, Yoshihisa

    2008-07-04

    SHPS-1 is a transmembrane protein that binds the protein tyrosine phosphatases SHP-1 and SHP-2 through its cytoplasmic region and is abundantly expressed on dendritic cells and macrophages. Here we show that mice expressing a mutant form of SHPS-1 fail to develop type-II collagen (CII)-induced arthritis (CIA), a model for rheumatoid arthritis in humans. Histological examinations of the arthritic paws from immunized wild-type mice revealed that cartilage was destroyed in association with marked mononuclear cell infiltration, while only mild cell infiltration was observed in immunized SHPS-1 mutant mice. Consistently, the serum levels of both IgG and IgG2a specific to CII and of IL-1{beta} in immunized SHPS-1 mutant mice were markedly reduced compared with those apparent for wild-type mice. The CII-induced proliferation of, and production of cytokines by, T cells from immunized SHPS-1 mutant mice were reduced compared to wild-type cells. These results suggest that SHPS-1 is essential for development of CIA.

  14. Hood River and Pelton Ladder Evaluation Studies, 2008 Annual Report : October 2007 - September 2008.

    SciTech Connect (OSTI)

    Reagan, Robert E.; Olsen, Erik A.

    2009-09-28

    This report summarizes the life history and production data collected in the Hood River subbasin during FY 2008. Included is a summary of jack and adult life history data collected at the Powerdale Dam trap on seventeen complete run years of winter steelhead, spring and fall chinook salmon, and coho salmon, and on fifteen complete run years of summer steelhead. Also included are summaries of (1) the hatchery winter steelhead broodstock collection program; (2) hatchery production releases in the Hood River subbasin; (3) subbasin wild summer and winter steelhead smolt production, (4) numbers of hatchery summer and winter steelhead smolts leaving the subbasin; (5) smolt migration timing past Bonneville Dam, (6) wild and hatchery steelhead smolt-to-adult survival rates; (7) wild summer and winter steelhead egg to smolt survival rates; and (8) streamflow at selected locations in the Hood River subbasin. Data will be used in part to (1) evaluate the HRPP relative to its impact on indigenous populations of resident and anadromous salmonids (see Ardren Draft), (2) evaluate the HRPP's progress towards achieving the biological fish objectives defined in the Hood River Subbasin Plan (Coccoli 2004) and the Revised Master Plan for the Hood River Production Program (HDR|FishPro, ODFW, and CTWSRO 2008), (3) refine spawner escapement objectives to more accurately reflect subbasin carrying capacity, and (4) refine estimates of subbasin smolt production capacity to more accurately reflect current and potential subbasin carrying capacity.

  15. TYLCV-Is movement in planta does not require V2 protein

    SciTech Connect (OSTI)

    Hak, Hagit; Levy, Yael; Chandran, Sam A.; Belausov, Eduard; Loyter, Abraham; Lapidot, Moshe; Gafni, Yedidya

    2015-03-15

    Tomato yellow leaf curl virus (TYLCV), a major tomato pathogen causing extensive crop losses, is a whitefly-transmitted geminivirus. V2 mutants of TYLCV-Is and related viruses tend to induce symptomless infection with attenuated viral DNA levels, while accumulating close to wild-type DNA levels in protoplasts, suggesting V2 as a movement protein. The discovery of plant-silencing mechanisms and viral silencing suppressors, V2 included, led us to reconsider V2's involvement in viral movement. We studied two mutant versions of the virus, one impaired in V2 silencing-suppression activity, and another carrying a non-translatable V2. While both mutant viruses spread in the infected plant to newly emerged leaves at the same rate as the wild-type virus, their DNA-accumulation levels were tenfold lower than in the wild-type virus. Thus, we suggest that the setback in virus proliferation, previously ascribed to a movement impediment, is due to lack of silencing-suppression activity. - Highlights: • TYLCV-Is V2 protein is localized in distinct microbodies throughout the cell cytoplasm, around the nucleus and in association with cytoplasmic strands but is not associated with the plasmodesmata. • Disruption of RNA-silencing suppression activity of TYLCV-Is V2 protein causes low titer of the virus in the infected plants. • The movement of TYLCV-Is in planta does not require a functional V2 protein.

  16. Smolt Monitoring at the Head of Lower Granite Reservoir and Lower Granite Dam, 2003 Annual Report.

    SciTech Connect (OSTI)

    Buettner, Edwin W.; Putnam, Scott A.

    2009-02-18

    This project monitored the daily passage of Chinook salmon Oncorhynchus tshawytscha, steelhead trout O. mykiss, and sockeye salmon O. nerka smolts during the 2003 spring out-migration at migrant traps on the Snake River and Salmon River. In 2003 fish management agencies released significant numbers of hatchery Chinook salmon and steelhead trout above Lower Granite Dam that were not marked with a fin clip or coded-wire tag. Generally, these fish were distinguishable from wild fish by the occurrence of fin erosion. Total annual hatchery Chinook salmon catch at the Snake River trap was 2.1 times less in 2003 than in 2002. The wild Chinook catch was 1.1 times less than the previous year. Hatchery steelhead trout catch was 1.7 times less than in 2002. Wild steelhead trout catch was 2.1 times less than the previous year. The Snake River trap collected 579 age-0 Chinook salmon of unknown rearing. During 2003, the Snake River trap captured five hatchery and 13 wild/natural sockeye salmon and 36 coho salmon O. kisutch of unknown rearing. Differences in trap catch between years are due to fluctuations not only in smolt production, but also differences in trap efficiency and duration of trap operation associated with flow. The significant differences in catch between 2003 and the previous year were due mainly to low flows during much of the trapping season and then very high flows at the end of the season, which terminated the trapping season 12 days earlier than in 2002. Trap operations began on March 9 and were terminated on May 27. The trap was out of operation for a total of zero days due to mechanical failure or debris. Hatchery Chinook salmon catch at the Salmon River trap was 16.8% less and wild Chinook salmon catch was 1.7 times greater than in 2002. The hatchery steelhead trout collection in 2003 was 5.6% less than in 2002. Wild steelhead trout collection was 19.2% less than the previous year. Trap operations began on March 9 and were terminated on May 24 due to high

  17. Transgenic Plants Lower the Costs of Cellulosic Biofuels (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2011-11-01

    A new transgenic maize was observed to be less recalcitrant than wild-type biomass, as manifested through lower severity requirements to achieve comparable levels of conversion. Expression of a single gene derived from bacteria in plants has resulted in transgenic plants that are easier and cheaper to convert into biofuels. Part of the high production cost of cellulosic biofuels is the relatively poor accessibility of substrates to enzymes due to the strong associations between plant cell wall components. This biomass recalcitrance makes costly thermochemical pretreatment necessary. Scientists at the National Renewable Energy Laboratory (NREL) have created transgenic maize expressing an active glycosyl hydrolase enzyme, E1 endoglucanase, originally isolated from a thermophilic bacterium, Acidothermus cellulolyticus. This engineered feedstock was observed to be less recalcitrant than wild-type biomass when subjected to reduced severity pretreatments and post-pretreatment enzymatic hydrolysis. This reduction in recalcitrance was manifested through lower severity requirements to achieve comparable levels of conversion of wild-type biomass. The improvements observed are significant enough to positively affect the economics of the conversion process through decreased capital construction costs and decreased degradation products and inhibitor formation.

  18. Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity

    SciTech Connect (OSTI)

    Joshi, Rakesh; Ho, Kwok Ki; Tenney, Kristen; Chen, Jui-Hui; Golden, Barbara L.; Gimble, Frederick S.

    2013-09-18

    Elucidating how homing endonucleases undergo changes in recognition site specificity will facilitate efforts to engineer proteins for gene therapy applications. I-SceI is a monomeric homing endonuclease that recognizes and cleaves within an 18-bp target. It tolerates limited degeneracy in its target sequence, including substitution of a C:G{sub +4} base pair for the wild-type A:T{sub +4} base pair. Libraries encoding randomized amino acids at I-SceI residue positions that contact or are proximal to A:T{sub +4} were used in conjunction with a bacterial one-hybrid system to select I-SceI derivatives that bind to recognition sites containing either the A:T{sub +4} or the C:G{sub +4} base pairs. As expected, isolates encoding wild-type residues at the randomized positions were selected using either target sequence. All I-SceI proteins isolated using the C:G{sub +4} recognition site included small side-chain substitutions at G100 and either contained (K86R/G100T, K86R/G100S and K86R/G100C) or lacked (G100A, G100T) a K86R substitution. Interestingly, the binding affinities of the selected variants for the wild-type A:T{sub +4} target are 4- to 11-fold lower than that of wild-type I-SceI, whereas those for the C:G{sub +4} target are similar. The increased specificity of the mutant proteins is also evident in binding experiments in vivo. These differences in binding affinities account for the observed -36-fold difference in target preference between the K86R/G100T and wild-type proteins in DNA cleavage assays. An X-ray crystal structure of the K86R/G100T mutant protein bound to a DNA duplex containing the C:G{sub +4} substitution suggests how sequence specificity of a homing enzyme can increase. This biochemical and structural analysis defines one pathway by which site specificity is augmented for a homing endonuclease.

  19. The prevalence of the pre-existing hepatitis C viral variants and the evolution of drug resistance in patients treated with the NS3-4a serine protease inhibitor telaprevir

    SciTech Connect (OSTI)

    Rong, Libin; Ribeiro, Ruy M; Perelson, Alan S

    2008-01-01

    Telaprevir (VX-950), a novel hepatitis C virus (HCV) NS3-4A serine protease inhibitor, has demonstrated substantial antiviral activity in patients infected with HCV genotype 1. Some patients experience viral breakthrough, which has been shown to be associated with emergence of telaprevir-resistant HCV variants during treatment. The exact mechanisms underlying the rapid selection of drug resistant viral variants during dosing are not fully understood. In this paper, we develop a two-strain model to study the pre-treatment prevalence of the mutant virus and derive an analytical solution of the mutant frequency after administration of the protease inhibitor. Our analysis suggests that the rapid increase of the mutant frequency during therapy is not due to mutant growth but rather due to the rapid and profound loss of wild-type virus, which uncovers the pre-existing mutant variants. We examine the effects of backward mutation and hepatocyte proliferation on the pre-existence of the mutant virus and the competition between wild-type and drug resistant virus during therapy. We then extend the simple model to a general model with multiple viral strains. Mutations during therapy do not play a significant role in the dynamics of various viral strains, although they are capable of generating low levels of HCV variants that would otherwise be completely suppressed because of fitness disadvantages. Hepatocyte proliferation may not affect the pretreatment frequency of mutant variants, but is able to influence the quasispecies dynamics during therapy. It is the relative fitness of each mutant strain compared with wild-type that determines which strain(s) will dominate the virus population. The study provides a theoretical framework for exploring the prevalence of pre-existing mutant variants and the evolution of drug resistance during treatment with other protease inhibitors or HCV polymerase inhibitors.

  20. Down-regulation of gibberellic acid in poplar has negligible effects on host-plant suitability and insect pest response

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Buhl, Christine; Strauss, Steven H.; Lindroth, Richard L.

    2015-01-06

    Abstract Endogenous levels and signaling of gibberellin plant hormones such as gibberellic acid (GA) have been genetically down-regulated to create semi-dwarf varieties of poplar. The potential benefits of semi-dwarf stature include reduced risk of wind damage, improved stress tolerance, and improved wood quality. Despite these benefits, modification of growth traits may have consequences for non-target traits that confer defense against insect herbivores. According to the growth-differentiation balance hypothesis, reductions in growth may shift allocation of carbon from growth to chemical resistance traits, thereby altering plant defense. To date, host-plant suitability and pest response have not been comprehensively evaluated in GAmore » down-regulated plants. We quantified chemical resistance and nitrogen (an index of protein) in GA down-regulated and wild-type poplar (Populus alba × P. tremula) genotypes. We also evaluated performance of both generalist (Lymantria dispar) and specialist (Chrysomela scripta) insect pests reared on these genotypes. Our evaluation of resistance traits in four GA down-regulated genotypes revealed increased phenolic glycosides in one modified genotype and reduced lignin in two modified genotypes relative to the non-transgenic wild type. Nitrogen levels did not vary significantly among the experimental genotypes. Generalists reared on the four GA down-regulated genotypes exhibited reduced performance on only one modified genotype relative to the wild type. Specialists, however, performed similarly across all genotypes. Results from this study indicate that although some non-target traits varied among GA down-regulated genotypes, the differences in poplar pest susceptibility were modest and highly genotype-specific.« less

  1. Development of a Markerless Genetic Exchange System in Desulfovibrio vulgaris Hildenborough and Its Use in Generating a Strain with Increased Transformation Efficiency

    SciTech Connect (OSTI)

    Keller, Kimberly L.; Bender, Kelly S.; Wall, Judy D.

    2009-07-21

    In recent years, the genetic manipulation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough has seen enormous progress. In spite of this progress, the current marker exchange deletion method does not allow for easy selection of multiple sequential gene deletions in a single strain because of the limited number of selectable markers available in D. vulgaris. To broaden the repertoire of genetic tools for manipulation, an in-frame, markerless deletion system has been developed. The counterselectable marker that makes this deletion system possible is the pyrimidine salvage enzyme, uracil phosphoribosyltransferase, encoded by upp. In wild-type D. vulgaris, growth was shown to be inhibited by the toxic pyrimidine analog 5-fluorouracil (5-FU); whereas, a mutant bearing a deletion of the upp gene was resistant to 5-FU. When a plasmid containing the wild-type upp gene expressed constitutively from the aph(3')-II promoter (promoter for the kanamycin resistance gene in Tn5) was introduced into the upp deletion strain, sensitivity to 5-FU was restored. This observation allowed us to develop a two-step integration and excision strategy for the deletion of genes of interest. Since this inframe deletion strategy does not retain an antibiotic cassette, multiple deletions can be generated in a single strain without the accumulation of genes conferring antibiotic resistances. We used this strategy to generate a deletion strain lacking the endonuclease (hsdR, DVU1703) of a type I restriction-modification system, that we designated JW7035. The transformation efficiency of the JW7035 strain was found to be 100 to 1000 times greater than that of the wild-type strain when stable plasmids were introduced via electroporation.

  2. Down-regulation of gibberellic acid in poplar has negligible effects on host-plant suitability and insect pest response

    SciTech Connect (OSTI)

    Buhl, Christine; Strauss, Steven H.; Lindroth, Richard L.

    2015-01-06

    Abstract Endogenous levels and signaling of gibberellin plant hormones such as gibberellic acid (GA) have been genetically down-regulated to create semi-dwarf varieties of poplar. The potential benefits of semi-dwarf stature include reduced risk of wind damage, improved stress tolerance, and improved wood quality. Despite these benefits, modification of growth traits may have consequences for non-target traits that confer defense against insect herbivores. According to the growth-differentiation balance hypothesis, reductions in growth may shift allocation of carbon from growth to chemical resistance traits, thereby altering plant defense. To date, host-plant suitability and pest response have not been comprehensively evaluated in GA down-regulated plants. We quantified chemical resistance and nitrogen (an index of protein) in GA down-regulated and wild-type poplar (Populus alba × P. tremula) genotypes. We also evaluated performance of both generalist (Lymantria dispar) and specialist (Chrysomela scripta) insect pests reared on these genotypes. Our evaluation of resistance traits in four GA down-regulated genotypes revealed increased phenolic glycosides in one modified genotype and reduced lignin in two modified genotypes relative to the non-transgenic wild type. Nitrogen levels did not vary significantly among the experimental genotypes. Generalists reared on the four GA down-regulated genotypes exhibited reduced performance on only one modified genotype relative to the wild type. Specialists, however, performed similarly across all genotypes. Results from this study indicate that although some non-target traits varied among GA down-regulated genotypes, the differences in poplar pest susceptibility were modest and highly genotype-specific.

  3. Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Papanek, Beth A.; Biswas, Ranjita; Rydzak, Thomas; Guss, Adam M.

    2015-09-12

    Clostridium thermocellum has the natural ability to convert cellulose to ethanol, making it a promising candidate for consolidated bioprocessing (CBP) of cellulosic biomass to biofuels. To further improve its CBP capabilities, we study a mutant strain of C. thermocellum that was constructed (strain AG553; C. thermocellum Δhpt ΔhydG Δldh Δpfl Δpta-ack) to increase flux to ethanol by removing side product formation. Strain AG553 showed a two- to threefold increase in ethanol yield relative to the wild type on all substrates tested. On defined medium, strain AG553 exceeded 70% of theoretical ethanol yield on lower loadings of the model crystalline cellulosemore » Avicel, effectively eliminating formate, acetate, and lactate production and reducing H2 production by fivefold. On 5 g/L Avicel, strain AG553 reached an ethanol yield of 63.5% of the theoretical maximum compared with 19.9% by the wild type, and it showed similar yields on pretreated switchgrass and poplar. The elimination of organic acid production suggested that the strain might be capable of growth under higher substrate loadings in the absence of pH control. Final ethanol titer peaked at 73.4 mM in mutant AG553 on 20 g/L Avicel, at which point the pH decreased to a level that does not allow growth of C. thermocellum, likely due to CO2 accumulation. In comparison, the maximum titer of wild type C. thermocellum was 14.1 mM ethanol on 10 g/L Avicel. In conclusion, with the elimination of the metabolic pathways to all traditional fermentation products other than ethanol, AG553 is the best ethanol-yielding CBP strain to date and will serve as a platform strain for further metabolic engineering for the bioconversion of lignocellulosic biomass.« less

  4. A semisynthetic strategy leads to alteration of the backbone amidate ligand in the NiSOD active site

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Campeciño, Julius O.; Dudycz, Lech W.; Tumelty, David; Berg, Volker; Cabelli, Diane E.; Maroney, Michael J.

    2015-07-01

    Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, NΔ5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategymore » that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ~1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ~11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. 14N-hyperfine is observed on gz« less

  5. A semisynthetic strategy leads to alteration of the backbone amidate ligand in the NiSOD active site

    SciTech Connect (OSTI)

    Campeciño, Julius O.; Dudycz, Lech W.; Tumelty, David; Berg, Volker; Cabelli, Diane E.; Maroney, Michael J.

    2015-07-01

    Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, NΔ5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategy that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ~1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ~11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. 14N-hyperfine is observed on gz

  6. KSR1 is a functional protein kinase capable of serine autophosphorylation and direct phosphorylation of MEK1

    SciTech Connect (OSTI)

    Goettel, Jeremy A.; Liang, Dongchun; Hilliard, Valda C.; Edelblum, Karen L.; Broadus, Matthew R.; Gould, Kathleen L.; Howard Hughes Medical Institute, Vanderbilt University School of Medicine, Nashville, TN 37232 ; Hanks, Steven K.; Polk, D. Brent

    2011-02-15

    The extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) pathway is a highly conserved signaling pathway that regulates diverse cellular processes including differentiation, proliferation, and survival. Kinase suppressor of Ras-1 (KSR1) binds each of the three ERK cascade components to facilitate pathway activation. Even though KSR1 contains a C-terminal kinase domain, evidence supporting the catalytic function of KSR1 remains controversial. In this study, we produced recombinant wild-type or kinase-inactive (D683A/D700A) KSR1 proteins in Escherichia coli to test the hypothesis that KSR1 is a functional protein kinase. Recombinant wild-type KSR1, but not recombinant kinase-inactive KSR1, underwent autophosphorylation on serine residue(s), phosphorylated myelin basic protein (MBP) as a generic substrate, and phosphorylated recombinant kinase-inactive MAPK/ERK kinase-1 (MEK1). Furthermore, FLAG immunoprecipitates from KSR1{sup -/-} colon epithelial cells stably expressing FLAG-tagged wild-type KSR1 (+KSR1), but not vector (+vector) or FLAG-tagged kinase-inactive KSR1 (+D683A/D700A), were able to phosphorylate kinase-inactive MEK1. Since TNF activates the ERK pathway in colon epithelial cells, we tested the biological effects of KSR1 in the survival response downstream of TNF. We found that +vector and +D683A/D700A cells underwent apoptosis when treated with TNF, whereas +KSR1 cells were resistant. However, +KSR1 cells were sensitized to TNF-induced cell loss in the absence of MEK kinase activity. These data provide clear evidence that KSR1 is a functional protein kinase, MEK1 is an in vitro substrate of KSR1, and the catalytic activities of both proteins are required for eliciting cell survival responses downstream of TNF.

  7. A semisynthetic strategy leads to alteration of the backbone amidate ligand in the NiSOD active site

    SciTech Connect (OSTI)

    Campecio, Julius O.; Dudycz, Lech W.; Tumelty, David; Berg, Volker; Cabelli, Diane E.; Maroney, Michael J.

    2015-07-01

    Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, N?5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategy that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ~1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ~11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. 14N-hyperfine is observed on gz

  8. The Phenazine 2-Hydroxy-Phenazine-1-Carboxylic Acid Promotes Extracellular DNA Release and Has Broad Transcriptomic Consequences in Pseudomonas chlororaphis 30–84

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wang, Dongping; Yu, Jun Myoung; Dorosky, Robert J.; Pierson, Leland S.; Pierson, Elizabeth A.

    2016-01-26

    Enhanced production of 2-hydroxy-phenazine-1-carboxylic acid (2-OH-PCA) by the biological control strain Pseudomonas chlororaphis 30–84 derivative 30-84O* was shown previously to promote cell adhesion and alter the three-dimensional structure of surfaceattached biofilms compared to the wild type. The current study demonstrates that production of 2-OH-PCA promotes the release of extracellular DNA, which is correlated with the production of structured biofilm matrix. Moreover, the essential role of the extracellular DNA in maintaining the mass and structure of the 30–84 biofilm matrix is demonstrated. To better understand the role of different phenazines in biofilm matrix production and gene expression, transcriptomic analyses were conductedmore » comparing gene expression patterns of populations of wild type, 30-84O* and a derivative of 30–84 producing only PCA (30-84PCA) to a phenazine defective mutant (30-84ZN) when grown in static cultures. RNA-Seq analyses identified a group of 802 genes that were differentially expressed by the phenazine producing derivatives compared to 30-84ZN, including 240 genes shared by the two 2-OH-PCA producing derivatives, the wild type and 30-84O*. A gene cluster encoding a bacteriophage- derived pyocin and its lysis cassette was upregulated in 2-OH-PCA producing derivatives. A holin encoded in this gene cluster was found to contribute to the release of eDNA in 30–84 biofilm matrices, demonstrating that the influence of 2-OH-PCA on eDNA production is due in part to cell autolysis as a result of pyocin production and release. The results expand the current understanding of the functions different phenazines play in the survival of bacteria in biofilm-forming communities.« less

  9. Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations

    SciTech Connect (OSTI)

    Li, Yongchao; Tschaplinski, Timothy J; Engle, Nancy L; Hamilton, Choo Yieng; Rodriguez, Jr., Miguel; Liao, James C; Schadt, Christopher Warren; Guss, Adam M; Yang, Yunfeng; Graham, David E

    2012-01-01

    Background: The model bacterium Clostridium cellulolyticum efficiently hydrolyzes crystalline cellulose and hemicellulose, using cellulosomes to degrade lignocellulosic biomass. Although it imports and ferments both pentose and hexose sugars to produce a mixture of ethanol, acetate, lactate, H2 and CO2, the proportion of ethanol is low, which impedes its use in consolidated bioprocessing for biofuels. Therefore genetic engineering will likely be required to improve the ethanol yield. Random mutagenesis, plasmid transformation, and heterologous expression systems have previously been developed for C. cellulolyticum, but targeted mutagenesis has not been reported for this organism. Results: The first targeted gene inactivation system was developed for C. cellulolyticum, based on a mobile group II intron originating from the Lactococcus lactis L1.LtrB intron. This markerless mutagenesis system was used to disrupt both the paralogous L-lactate dehydrogenase (Ccel_2485; ldh) and L-malate dehydrogenase (Ccel_0137; mdh) genes, distinguishing the overlapping substrate specificities of these enzymes. Both mutations were then combined in a single strain. This double mutant produced 8.5-times more ethanol than wild-type cells growing on crystalline cellulose. Ethanol constituted 93% of the major fermentation products (by molarity), corresponding to a molar ratio of ethanol to organic acids of 15, versus 0.18 in wild-type cells. During growth on acid-pretreated switchgrass, the double mutant also produced four-times as much ethanol as wild-type cells. Detailed metabolomic analyses identified increased flux through the oxidative branch of the mutant s TCA pathway. Conclusions: The efficient intron-based gene inactivation system produced the first gene-targeted mutations in C. cellulolyticum. As a key component of the genetic toolbox for this bacterium, markerless targeted mutagenesis enables functional genomic research in C. cellulolyticum and rapid genetic engineering to

  10. Viruses in laboratory-reared cactus moth, Cactoblastis cactorum (Lepidoptera: Pyralidae)

    SciTech Connect (OSTI)

    Marti, O.G.; Myers, R.E.; Carpenter, J.E.; Styer, E.L.

    2007-03-15

    The cactus moth, Cactoblastis cactorum (Lepidoptera: Pyralidae: Phycitinae), is a non-native species threatening a variety of native cacti, particularly endangered species of Opuntia (Zimmerman et al. 2001), on the coast of the Gulf of Mexico. Cactoblastis cactorum populations have expanded from Florida northward along the Atlantic coast as far as Charleston, SC, and westward along the Gulf of Mexico to Dauphin Island, south of Mobile, AL. It is feared that further movement to the west will allow C. cactorum to enter the US desert Southwest and Mexico, particularly the latter. Numerous cactus species, especially those of the genera Opuntia and Nopalea, are native to the U.S. and Mexico. Local economies based on agricultural and horticultural uses of cacti could be devastated by C. cactorum (Vigueras and Portillo 2001). A bi-national control program between the US and Mexico is being developed, utilizing the sterile insect technique (SIT). In the SIT program, newly emerged moths are irradiated with a {sup 60}Co source and released to mate with wild individuals. The radiation dose completely sterilizes the females and partially sterilizes the males. When irradiated males mate with wild females, the F1 progeny of these matings are sterile. In order for the SIT program to succeed, large numbers of moths must be reared from egg to adult on artificial diet in a quarantined rearing facility (Carpenter et al. 2001). Irradiated insects must then be released in large numbers at the leading edge of the invasive population and at times which coincide with the presence of wild individuals available for mating. Mortality from disease in the rearing colony disrupts the SIT program by reducing the numbers of insects available for release.

  11. Chief Joseph Kokanee Enhancement Project : Confederated Tribes of the Colville Reservaton 1997 Annual Report.

    SciTech Connect (OSTI)

    LeCaire, Richard

    1998-01-01

    In the early 1980's the Confederated Tribes of the Colville Reservation, the Spokane Tribe of Indians and the Washington Dept. of Fish and Wildlife developed a management plan for Lake Roosevelt on the restoration and enhancement of kokanee salmon populations using hatchery out plants and the restoration of natural spawning runs. The plan was incorporated into the Northwest Power Planning Council (NPPC) in their 1987 Columbia Basin Fish and Wildlife program as partial mitigation for hydropower caused fish losses resulting from the construction of Grand Coulee Dam. The Chief Joseph Kokanee Enhancement Project, as part of a basin wide effort, is evaluating the status of the natural production kokanee in streams tributary to Lakes Roosevelt and Rufus Woods and is examining entrainment through Grand Coulee Dam. The goal of this project is the protection and enhancement of the natural production kokanee in these two lakes. The project is currently collecting data under four phases or parts. Since 1991, Lake Whatcom Washington origin kokanee have been planted in considerable numbers into the waters of Lake Roosevelt. A natural production kokanee fishery has persisted in the lake since the early 1970's(Cash, 1995), (Scholz, 1991). Historical information alludes to wild Kokanee production in the San Poil River, Nespelem River, Big Sheep Creek, Ora-Pa-Ken Creek, Deep Creek and Onion Creeks. The genetic makeup of the fish within the fishery is unknown, as is their contribution to the fishery. The level of influence by the hatchery out planted stock on wild fish stocks is unknown as well. Project outcomes will indicate the genetic fitness for inclusion of natural production kokanee stocks into current Bonneville Power Administration funded hatchery programs. Other findings may determine contribution/interaction of/between wild/hatchery kokanee stocks found in the waters of Lake Franklin D. Roosevelt.

  12. Crystal Structure of a Super Leucine Zipper an Extended Two-Stranded Super Long Coiled Coil

    SciTech Connect (OSTI)

    J Diao

    2011-12-31

    Coiled coil is a ubiquitous structural motif in proteins, with two to seven alpha helices coiled together like the strands of a rope, and coiled coil folding and assembly is not completely understood. A GCN4 leucine zipper mutant with four mutations of K3A, D7A, Y17W, and H18N has been designed, and the crystal structure has been determined at 1.6 {angstrom} resolution. The peptide monomer shows a helix trunk with short curved N- and C-termini. In the crystal, two monomers cross in 35{sup o} and form an X-shaped dimer, and each X-shaped dimer is welded into the next one through sticky hydrophobic ends, thus forming an extended two-stranded, parallel, super long coiled coil rather than a discrete, two-helix coiled coil of the wild-type GCN4 leucine zipper. Leucine residues appear at every seventh position in the super long coiled coil, suggesting that it is an extended super leucine zipper. Compared to the wild-type leucine zipper, the N-terminus of the mutant has a dramatic conformational change and the C-terminus has one more residue Glu 32 determined. The mutant X-shaped dimer has a large crossing angle of 35{sup o} instead of 18{sup o} in the wild-type dimer. The results show a novel assembly mode and oligomeric state of coiled coil, and demonstrate that mutations may affect folding and assembly of the overall coiled coil. Analysis of the formation mechanism of the super long coiled coil may help understand and design self-assembling protein fibers.

  13. Flight Path 60R - GEANIE Collaborators

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Target 4 Flight Path 60R Collaborators LANL: M. Devlin, N. Fotiades, R. O Nelson, A. Couture, M.S. Boswell, D.R. Mayo, F. Merrill, S. Mosby, J. M. O'Donnell, R. Rundberg, S, Stange, S. Vogel, C. Wilde CEA DAM/DIF: G. Belier, T. Granier, T. Ethvignot LLNL: C. Y. Wu, A. Chyzh, J. Becker, E, Kwan, J. Escher, J, Burke, N. Scielzo, R. Hatarik U.S. Army Research Laboratory: J. Carroll, M. Litz Indiana University: T. Johnson, J. Albert, L. Kaufman, S. Dougherty Rutgers University: J. Cizewski, B.

  14. Manipulation Of Lignin Biosynthesis To Maximize Ethanol Production From Populus Feedstocks

    SciTech Connect (OSTI)

    Dr. Clint Chapple; Dr. Rick Lindroth; Dr. Burce Dien; Dr. Glen Stanosz; Dr. Alex Wiedenhoeft; Dr. Fu Zhao; Dr. Duane Wegener; Dr. Janice Kelly; Dr. Leigh Raymond; Dr. Wallace Tyner

    2012-05-15

    Our research focuses on transgenic strategies for modifying lignification to improve biomass quality, without leading to deleterious effects on plant performance. In order to accomplish this objective, we designed molecular strategies and selected appropriate transgenes for manipulating the expression of lignification-associated genes; we generated poplar engineered for altered lignin content and/or monomer composition, and field-tested them for fitness; we analyzed the impact of these transgenic strategies on metabolism in general and lignin biosynthesis in particular; and evaluated the ease with which cell wall deconstruction can be accomplished using both chemical and enzymatic means using wild-type and high syringyl poplar.

  15. Environmental profile of Paraguay

    SciTech Connect (OSTI)

    Not Available

    1985-12-01

    The social, cultural, physical, and economic dimensions of Paraguay's environment are analyzed to identify main environmental features and problems and to recommend specific actions. The environmental profile presents an overview of Paraguay's ethno-historic and anthropological background, present-day society, and the impact of pollution. Descriptions are presented of: the legal and institutional aspects of environmental policy; the structure and performance of the economy, with focus on the primary and energy sectors; physical resources (climate, geological, mineral, soil, and water resources); and biological resources (vegetation, wild animal life, protected areas, and fish resources).

  16. Pacific Lamprey Research and Restoration : Annual Report 1997.

    SciTech Connect (OSTI)

    Jackson, Aaron D.; Hatch, Douglas R.; Close, David A.

    1998-08-05

    The once abundant stocks of Pacific lamprey (Lampetra tridentata) above Bonneville Dam are currently depressed (Close et al. 1995). It is likely that many of the same factors that led to the decline of wild stocks of Columbia River Pacific salmon and steelhead have impacted Pacific lamprey populations as well. The Pacific Lamprey Research and Restoration Project, funded by Bonneville Power Administration, is a cooperative effort between the Confederated Tribes of the Umatilla Indian Reservation, the Columbia River Inter-Tribal Fish Commission, and Oregon State University with the goal to increase Pacific lamprey stocks above Bonneville Dam.

  17. Papua New Guinea: Tough course

    SciTech Connect (OSTI)

    Fritz, M.

    1991-11-01

    This paper describes the problems that seismic crews face in Papua New Guinea. The complex geologic conditions which often entail karstified carbonate rocks which are overlying folded sedimentary and igneous rocks, cause severe problems with data collection and interpretation. Secondly, the rugged topography and dense rain forest vegetation along with the wild animals and diseases create inaccessible or undesirable work areas. However, these conditions can be overcome and this paper briefly describes how one exploration company uses local natives to assist in development of reliable seismic surveys.

  18. Los Alamos National Laboratory

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    In 1914, Detroit businessman Ashley Pond constructed a log cabin on the Pajarito Plateau in north-central New Mexico. The one-room structure served as the office for the Pajarito Club, a guest ranch for well-heeled city folk looking for a little Wild West adventure. Although the Pajarito Club was short-lived (it disbanded in 1916), Pond remained in the area and went on to found the Los Alamos Ranch School in 1917. The elite prep school offered classical education and rigorous outdoor activity

  19. Role of Nrf2 in preventing ethanol-induced oxidative stress and lipid accumulation

    SciTech Connect (OSTI)

    Wu, Kai Connie; Liu, Jie; Klaassen, Curtis D.

    2012-08-01

    Oxidative stress and lipid accumulation play important roles in alcohol-induced liver injury. Previous reports showed that, in livers of nuclear factor erythroid 2-related factor 2 (Nrf2)-activated mice, genes involved in antioxidant defense are induced, whereas genes involved in lipid biosynthesis are suppressed. To investigate the role of Nrf2 in ethanol-induced hepatic alterations, Nrf2-null mice, wild-type mice, kelch-like ECH-associated protein 1-knockdown (Keap1-KD) mice with enhanced Nrf2, and Keap1-hepatocyte knockout (Keap1-HKO) mice with maximum Nrf2 activation, were treated with ethanol (5 g/kg, po). Blood and liver samples were collected 6 h thereafter. Ethanol increased alanine aminotransferase and lactate dehydrogenase activities as well as thiobarbituric acid reactive substances in serum of Nrf2-null and wild-type mice, but not in Nrf2-enhanced mice. After ethanol administration, mitochondrial glutathione concentrations decreased markedly in Nrf2-null mice but not in Nrf2-enhanced mice. H{sub 2}DCFDA staining of primary hepatocytes isolated from the four genotypes of mice indicates that oxidative stress was higher in Nrf2-null cells, and lower in Nrf2-enhanced cells than in wild-type cells. Ethanol increased serum triglycerides and hepatic free fatty acids in Nrf2-null mice, and these increases were blunted in Nrf2-enhanced mice. In addition, the basal mRNA and nuclear protein levels of sterol regulatory element-binding protein 1(Srebp-1) were decreased with graded Nrf2 activation. Ethanol further induced Srebp-1 mRNA in Nrf2-null mice but not in Nrf2-enhanced mice. In conclusion, Nrf2 activation prevented alcohol-induced oxidative stress and accumulation of free fatty acids in liver by increasing genes involved in antioxidant defense and decreasing genes involved in lipogenesis. -- Highlights: ► Ethanol depleted mitochondrial GSH in Nrf2-null mice but not in Keap1-KD mice. ► Ethanol increased ROS in hepatocytes isolated from Nrf2-null and wild

  20. T-600: Security Advisory for Adobe Flash Player, Adobe Reader and Acrobat

    Broader source: Energy.gov [DOE]

    This vulnerability (CVE-2011-0611) could cause a crash and potentially allow an attacker to take control of the affected system. There are reports that this vulnerability is being exploited in the wild in targeted attacks via a Flash (.swf) file embedded in a Microsoft Word (.doc) file delivered as an email attachment, targeting the Windows platform. At this time, Adobe is not aware of any attacks via PDF targeting Adobe Reader and Acrobat. Adobe Reader X Protected Mode mitigations would prevent an exploit of this kind from executing.

  1. Kuwaiti oil sector shows more signs of recovery

    SciTech Connect (OSTI)

    Not Available

    1992-04-06

    This paper reports that Kuwait's oil sector continues to show signs of recovery from the Persian Gulf war. On Mar. 23 Kuwait Petroleum Co. (KPC) loaded the country's first shipment of liquefied petroleum gas for export since the Iraqi invasion in August 1990. In addition, the first shipment of Kuwaiti crude recovered from giant oil lakes formed by hundreds of wild wells sabotaged in the war was to arrive by tanker in Naples, Italy, late last month. The tanker is carrying 210,000 bbl of crude. However, the project to clean up the lakes and recover more oil, undertaken by Bechtel Corp. with Kuwait Oil Co. (KOC), has reached a stand still.

  2. Role of Arginine 293 and Glutamine 288 in Communication between Catalytic and Allosteric Sites in Yeast Ribonucleotide Reductase

    SciTech Connect (OSTI)

    Ahmad, Md. Faiz; Kaushal, Prem Singh; Wan, Qun; Wijerathna, Sanath R.; An, Xiuxiang; Huang, Mingxia; Dealwis, Chris Godfrey

    2012-11-01

    Ribonucleotide reductases (RRs) catalyze the rate-limiting step of de novo deoxynucleotide (dNTP) synthesis. Eukaryotic RRs consist of two proteins, RR1 ({alpha}) that contains the catalytic site and RR2 ({beta}) that houses a diferric-tyrosyl radical essential for ribonucleoside diphosphate reduction. Biochemical analysis has been combined with isothermal titration calorimetry (ITC), X-ray crystallography and yeast genetics to elucidate the roles of two loop 2 mutations R293A and Q288A in Saccharomyces cerevisiae RR1 (ScRR1). These mutations, R293A and Q288A, cause lethality and severe S phase defects, respectively, in cells that use ScRR1 as the sole source of RR1 activity. Compared to the wild-type enzyme activity, R293A and Q288A mutants show 4% and 15%, respectively, for ADP reduction, whereas they are 20% and 23%, respectively, for CDP reduction. ITC data showed that R293A ScRR1 is unable to bind ADP and binds CDP with 2-fold lower affinity compared to wild-type ScRR1. With the Q288A ScRR1 mutant, there is a 6-fold loss of affinity for ADP binding and a 2-fold loss of affinity for CDP compared to the wild type. X-ray structures of R293A ScRR1 complexed with dGTP and AMPPNP-CDP [AMPPNP, adenosine 5-({beta},{gamma}-imido)triphosphate tetralithium salt] reveal that ADP is not bound at the catalytic site, and CDP binds farther from the catalytic site compared to wild type. Our in vivo functional analyses demonstrated that R293A cannot support mitotic growth, whereas Q288A can, albeit with a severe S phase defect. Taken together, our structure, activity, ITC and in vivo data reveal that the arginine 293 and glutamine 288 residues of ScRR1 are crucial in facilitating ADP and CDP substrate selection.

  3. Electron-microscopic study on the structure of indirect flight muscles in pupae of Drosophila melanogaster muscle mutant

    SciTech Connect (OSTI)

    Generalova, M.V.; Kryukova, M.E.; Myasnyankina, E.N.

    1994-11-01

    We have analyzed the ultrastructure of indirect flight muscles in Drosophila pupae heterozygous for the mutation Mhc{sup M66}, which is a cold-sensitive allele of locus Mhc (Myosin heavy chain). We found that initially the differentiation of the muscle fiber in the mutant does not differ from that of the wild type. The first visible changes (loss of individual myosin protofibrils) appear in myofibrils reaching a certain size. Disintegration of contractile machinery progresses with the increase in the size of myofibrils. We discuss possible mechanisms of triggering and progression of these destructive processes during ontogenesis. 26 refs., 2 figs.

  4. Comparative Survival [Rate] Study (CSS); Design and Analysis, 2002 Technical Report.

    SciTech Connect (OSTI)

    Bouwes, Nick; Petrosky, Charlie; Schaller, Howard

    2002-04-01

    Fisheries agencies and tribes have developed a multi-year program, the Comparative Survival Study (CSS), to obtain information to be used in monitoring and evaluating the impacts of the mitigation measures and actions (e.g., flow augmentation, spill, and transportation) under NMFS' Biological Opinion to recover listed stocks. Through 2001, the CSS has utilized PIT tagged yearling hatchery chinook that were tagged specifically for the CSS and PIT tagged wild chinook from all available marking efforts in the Snake River basin above Lower Granite Dam. We selected hatchery programs that would allow the opportunity to mark sufficient numbers of smolts to give enough returning adult fish that statistically rigorous smolt-to-adult survival rates could be computed. Since the CSS inception, hatchery fish that have consistently been used include spring/summer chinook tagged at McCall, Rapid River, Dworshak, and Lookingglass (Imnaha stock) hatcheries. The CSS has also included a group of spring chinook from Carson Hatchery in the lower Columbia River for planned upstream/downstream comparison. The wild stocks included chinook PIT tagged as parr (summer/fall tagging season) and smolts (spring tagging season) in each major tributary above Lower Granite Dam. Future years will see the CSS add wild and hatchery steelhead in the Snake River basin, hatchery steelhead in the Mid-Columbia River basin, hatchery yearling chinook in the Mid-Columbia River basin, and wild chinook in John Day River in the lower Columbia River. Each PIT (passive integrated transponder) tag has a unique code. The tags are glass encapsulated, 11 mm in length, and implanted into the fish's underbelly by a syringe. All attempts are made to make the PIT tagged fish as representative of their untagged cohorts as possible. At trapping sites, sampling and tagging occur over the entire migration season. At hatcheries, fish to tag are obtained across as wide a set of ponds and raceways as possible to allow effective

  5. Impact of phenolic substrate and growth temperature on the arthrobacter chlorophenolicus proteome

    SciTech Connect (OSTI)

    Unell, Maria; Abraham, Paul E.; Shah, Manesh; Zhang, Bing; Ruckert, Christian; VerBerkmoes, Nathan C.; Jansson, Janet K.

    2009-02-15

    We compared the Arthrobacter chlorophenolicus proteome during growth on 4-chlorophenol, 4-nitrophenol or phenol at 5 C and 28 C; both for the wild type and a mutant strain with mass spectrometry based proteomics. A label free workflow employing spectral counting identified 3749 proteins across all growth conditions, representing over 70% of the predicted genome and 739 of these proteins form the core proteome. Statistically significant differences were found in the proteomes of cells grown under different conditions including differentiation of hundreds of unknown proteins. The 4-chlorophenol-degradation pathway was confirmed, but not that for phenol.

  6. Characterization of Sugar Insensitive (sis) Mutants of Arabidopsis

    SciTech Connect (OSTI)

    Gibson, Susan I.

    2009-06-08

    Despite the fact that soluble sugar levels have been postulated to play an important role in the control of a wide variety of plant metabolic and developmental pathways, the mechanisms by which plants respond to soluble sugar levels remain poorly understood. Plant responses to soluble sugar levels are also important in bioenergy production, as plant sugar responses are believed to help regulate both carbon fixation and carbon partitioning. For example, accumulation of soluble sugars, such as sucrose and glucose, in source tissues leads to feedback inhibition of photosynthesis, thereby decreasing rates of carbon fixation. Soluble sugar levels can also affect sink strengths, affecting the rates of accumulation of carbon-based compounds into both particular molecular forms (e.g. carbohydrates versus lipids versus proteins) and particular plant organs and tissues. Mutants of Arabidopsis that are defective in the ability to respond to soluble sugar levels were isolated and used as tools to identify some of the factors involved in plant sugar response. These sugar insensitive (sis) mutants were isolated by screening mutagenized seeds for those that were able to germinate and develop relatively normal shoot systems on media containing 0.3 M glucose or 0.3 M sucrose. At these sugar concentrations, wild-type Arabidopsis germinate and produce substantial root systems, but show little to no shoot development. Twenty-eight sis mutants were isolated during the course of four independent mutant screens. Based on a preliminary characterization of all of these mutants, sis3 and sis6 were chosen for further study. Both of these mutations appear to lie in previously uncharacterized loci. Unlike many other sugar-response mutants, sis3 mutants exhibit a wild-type or near wild-type response in all phytohormone-response assays conducted to date. The sis6-1 mutation is unusual in that it appears to be due to overexpression of a gene, rather than representing a loss of function mutation

  7. Microsoft Word - FeMoco.doc

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Fig. 1. Fourier transforms calculated over the k-range 2-16 Å -1 of EXAFS data (dotted) and fits (solid) from (left) MoFe protein- bound FeMoco and (right) the NifEN-bound FeMoco precursor. The EXAFS data were obtained, respectively, by subtraction of ΔnifB MoFe protein EXAFS from wild-type MoFe protein EXAFS and ΔnifB NifEN EXAFS from NifEN EXAFS. The insets show the structure of FeMoco (left) and a structural model consistent with the XAS analysis of the NifEN-bound FeMoco precursor

  8. LA-13859-MS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    13859-MS Issued: September 2001 Nevada Test Site Radionuclide Inventory, 1951-1992 Scott M. Bowen David L. Finnegan Joseph L. Thompson Charles M. Miller (Deceased) Phyllis L. Baca Loretta F. Olivas Carmen G. Geoffrion David K. Smith* Wataru Goishi* Bradley K. Esser* Jesse W. Meadows* Neil Namboodiri* John F. Wild* *Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550-9234 Los Alamos N A T I O N A L L A B O R A T O R Y Los Alamos, New Mexico 87545 Nevada Test Site

  9. Effect of the L499M mutation of the ascomycetous Botrytis aclada laccase on redox potential and catalytic properties

    SciTech Connect (OSTI)

    Osipov, Evgeny [A. N. Bach Institute of Biochemistry, Leninsky Prospect 33/2, Moscow 119071 (Russian Federation); Polyakov, Konstantin [A. N. Bach Institute of Biochemistry, Leninsky Prospect 33/2, Moscow 119071 (Russian Federation); Engelhardt Institute of Molecular Biology, Vavilova Str. 32, Moscow 119991 (Russian Federation); Kittl, Roman [BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Wien (Austria); Shleev, Sergey [RSC Kurchatov Institute, Acad. Kurchatov Sq. 1, Moscow 123182 (Russian Federation); Malm University, 205 06 Malm (Sweden); Dorovatovsky, Pavel [RSC Kurchatov Institute, Acad. Kurchatov Sq. 1, Moscow 123182 (Russian Federation); Tikhonova, Tamara, E-mail: ttikhonova@inbi.ras.ru [A. N. Bach Institute of Biochemistry, Leninsky Prospect 33/2, Moscow 119071 (Russian Federation); Hann, Stephan; Ludwig, Roland [BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Wien (Austria); Popov, Vladimir [A. N. Bach Institute of Biochemistry, Leninsky Prospect 33/2, Moscow 119071 (Russian Federation); RSC Kurchatov Institute, Acad. Kurchatov Sq. 1, Moscow 123182 (Russian Federation)

    2014-11-01

    The structures of the ascomycetous B. aclada laccase and its L499M T1-site mutant have been solved at 1.7 resolution. The mutant enzyme shows a 140 mV lower redox potential of the type 1 copper and altered kinetic behaviour. The wild type and the mutant have very similar structures, which makes it possible to relate the changes in the redox potential to the L499M mutation Laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. These enzymes contain four Cu atoms per molecule organized into three sites: T1, T2 and T3. In all laccases, the T1 copper ion is coordinated by two histidines and one cysteine in the equatorial plane and is covered by the side chains of hydrophobic residues in the axial positions. The redox potential of the T1 copper ion influences the enzymatic reaction and is determined by the nature of the axial ligands and the structure of the second coordination sphere. In this work, the laccase from the ascomycete Botrytis aclada was studied, which contains conserved Ile491 and nonconserved Leu499 residues in the axial positions. The three-dimensional structures of the wild-type enzyme and the L499M mutant were determined by X-ray crystallography at 1.7 resolution. Crystals suitable for X-ray analysis could only be grown after deglycosylation. Both structures did not contain the T2 copper ion. The catalytic properties of the enzyme were characterized and the redox potentials of both enzyme forms were determined: E{sub 0} = 720 and 580 mV for the wild-type enzyme and the mutant, respectively. Since the structures of the wild-type and mutant forms are very similar, the change in the redox potential can be related to the L499M mutation in the T1 site of the enzyme.

  10. Tested by Fire - How two recent Wildfires affected Accelerator Operations at LANL

    SciTech Connect (OSTI)

    Spickermann, Thomas

    2012-08-01

    In a little more than a decade two large wild fires threatened Los Alamos and impacted accelerator operations at LANL. In 2000 the Cerro Grande Fire destroyed hundreds of homes, as well as structures and equipment at the DARHT facility. The DARHT accelerators were safe in a fire-proof building. In 2011 the Las Conchas Fire burned about 630 square kilometers (250 square miles) and came dangerously close to Los Alamos/LANL. LANSCE accelerator operations Lessons Learned during Las Conchas fire: (1) Develop a plan to efficiently shut down the accelerator on short notice; (2) Establish clear lines of communication in emergency situations; and (3) Plan recovery and keep squirrels out.

  11. The LMNA mutation p.Arg321Ter associated with dilated cardiomyopathy leads to reduced expression and a skewed ratio of lamin A and lamin C proteins

    SciTech Connect (OSTI)

    Al-Saaidi, Rasha; Rasmussen, Torsten B.; Palmfeldt, Johan; Nissen, Peter H.; Beqqali, Abdelaziz; Hansen, Jakob; Pinto, Yigal M.; Boesen, Thomas; Mogensen, Jens; Bross, Peter

    2013-11-15

    Dilated cardiomyopathy (DCM) is a disease of the heart muscle characterized by cardiac chamber enlargement and reduced systolic function of the left ventricle. Mutations in the LMNA gene represent the most frequent known genetic cause of DCM associated with disease of the conduction systems. The LMNA gene generates two major transcripts encoding the nuclear lamina major components lamin A and lamin C by alternative splicing. Both haploinsuffiency and dominant negative effects have been proposed as disease mechanism for premature termination codon (PTC) mutations in LMNA. These mechanisms however are still not clearly established. In this study, we used a representative LMNA nonsense mutation, p.Arg321Ter, to shed light on the molecular disease mechanisms. Cultured fibroblasts from three DCM patients carrying this mutation were analyzed. Quantitative reverse transcriptase PCR and sequencing of these PCR products indicated that transcripts from the mutant allele were degraded by the nonsense-mediated mRNA decay (NMD) mechanism. The fact that no truncated mutant protein was detectable in western blot (WB) analysis strengthens the notion that the mutant transcript is efficiently degraded. Furthermore, WB analysis showed that the expression of lamin C protein was reduced by the expected approximately 50%. Clearly decreased lamin A and lamin C levels were also observed by immunofluorescence microscopy analysis. However, results from both WB and nano-liquid chromatography/mass spectrometry demonstrated that the levels of lamin A protein were more reduced suggesting an effect on expression of lamin A from the wild type allele. PCR analysis of the ratio of lamin A to lamin C transcripts showed unchanged relative amounts of lamin A transcript suggesting that the effect on the wild type allele was operative at the protein level. Immunofluorescence microscopy analysis showed no abnormal nuclear morphology of patient fibroblast cells. Based on these data, we propose that

  12. Comparative Survival Study (CSS) of PIT-Tagged Spring/Summer Chinook and Summer Steelhead : 2008 Annual Report.

    SciTech Connect (OSTI)

    Comparative Survival Study Oversight Committee and Fish Passage Center

    2008-12-02

    The Comparative Survival Study (CSS; BPA Project 199602000) began in 1996 with the objective of establishing a long term dataset of the survival rate of annual generations of salmon from their outmigration as smolts to their return to freshwater as adults to spawn (smolt-to-adult return rate; SAR). The study was implemented with the express need to address the question whether collecting juvenile fish at dams and transporting them downstream in barges and trucks and releasing them downstream of Bonneville Dam was compensating for the effect of the Federal Columbia River Power System (FCRPS) on survival of Snake Basin spring/summer Chinook salmon migrating through the hydrosystem. The Completion of this annual report for the CSS signifies the 12th outmigration year of hatchery spring/summer Chinook salmon marked with Passive Integrated Transponder (PIT) tags as part of the CSS and the 9th complete brood year return as adults of those PIT-tagged fish (report covers adult returns from 1997-2006 hatchery Chinook juvenile migrations). In addition, the CSS has provided PIT-tags to on-going tagging operations for wild Chinook since 2002 (report covers adult returns from 1994-2006 wild Chinook juvenile migrations). The CSS tags wild steelhead on the lower Clearwater River and utilized wild and hatchery steelhead from other tagging operations in evaluations of transportation (report covers adult returns from 1997-2005 wild and hatchery steelhead migrations). The primary purpose of this report is to update the time series of smolt-to-adult survival rate data and related parameters with additional years of data since the completion of the CSS 10-yr retrospective analysis report (Schaller et al 2007). The 10-yr report provided a synthesis of the results from this ongoing study, the analytical approaches employed, and the evolving improvements incorporated into the study as reported in CSS annual progress reports. This current report specifically addresses the constructive

  13. ALSNews Vol. 276

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    6 ALSNews Vol. 276 Print Wednesday, 30 May 2007 00:00 Contents Particles from Comet 81P/Wild 2 viewed by ALS microscopes Nature and origin of the cuprate pseudogap In Memoriam: Gary Krebs Director's update at all-hands meeting First light for ultrafast Beamline 6.0.1 COSMIC/MAESTRO reviewers enthusiastic Users' Meeting, October 4-6 General user proposals submission deadline ALS Fellowship Program: doctoral deadline and new postdoctoral fellowship News Links Carbon joins the magnetic club

  14. Industry Perspective

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    idatech.com info@idatech.com 63065 NE 18 th Street Bend, OR 97701 541.383.3390 Industry Perspective Biogas and Fuel Cell Workshop National Renewable Energy Laboratory June 11 - 13, 2012 Mike Hicks Chairman of the Board of Directors, FCHEA Treasurer of the Board of Directors, FCS&E Engineering Manager, Technology Development & Integration, IdaTech Outline 1. Critical Factors * Fuel Purity * Fuel Cost 2. Natural Gas - The Wild Card & Competition 3. IdaTech's Experience Implementing

  15. Regioselective alkane hydroxylation with a mutant CYP153A6 enzyme

    DOE Patents [OSTI]

    Koch, Daniel J.; Arnold, Frances H.

    2013-01-29

    Cytochrome P450 CYP153A6 from Myobacterium sp. strain HXN1500 was engineered using in-vivo directed evolution to hydroxylate small-chain alkanes regioselectively. Mutant CYP153A6-BMO1 selectively hydroxylates butane and pentane at the terminal carbon to form 1-butanol and 1-pentanol, respectively, at rates greater than wild-type CYP153A6 enzymes. This biocatalyst is highly active for small-chain alkane substrates and the regioselectivity is retained in whole-cell biotransformations.

  16. 2003 - 07 | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    7 Jul 2003 Mon, 2003-07-28 00:00 Catching T-waves: Terahertz radiation is gentle but piercing (US News) Tue, 2003-07-08 00:00 Ohio University professors receive publicity for role in discovery of new type of particle matter (Ohio University) Sun, 2003-07-06 00:00 Lab finds evidence of tinier part of matter (Daily Press) Sat, 2003-07-05 00:00 Wild Bunch: First five-quark particle turns up (Science News) Fri, 2003-07-04 00:00 Five-quark particle may exist 9Goleta Valley Voice) Thu, 2003-07-03

  17. Compositions of Stardust Impact Tracks and Terminal Particles in Aerogel by

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Hard X-ray Microprobe at SSRL Compositions of Stardust Impact Tracks and Terminal Particles in Aerogel by Hard X-ray Microprobe at SSRL Until 1974, Comet 81P/Wild 2 orbited beyond Jupiter, but a gravitational kick from that planet altered its orbit transforming it into a short-period comet in the inner solar system. This allowed NASA's solar-powered Stardust spacecraft to intercept the comet's tail within the orbit of Mars. The fly-by was completed at a relative speed of 6.1 km/s passing

  18. Effects of nutritional status on metabolic rate, exercise and recovery in a freshwater fish

    SciTech Connect (OSTI)

    Gingerich, Andrew J.; Philipp, D. P.; Suski, C. D.

    2010-11-20

    The influence of feeding on swimming performance and exercise recovery in fish is poorly understood. Examining swimming behavior and physiological status following periods of feeding and fasting is important because wild fish often face periods of starvation. In the current study, researchers force fed and fasted groups of largemouth bass (Micropterus salmoides) of similar sizes for a period of 16 days. Following this feeding and fasting period, fish were exercised for 60 s and monitored for swimming performance and physiological recovery. Resting metabolic rates were also determined. Fasted fish lost an average of 16 g (nearly 12%) of body mass, while force fed fish maintained body mass. Force fed fish swam 28% further and required nearly 14 s longer to tire during exercise. However, only some physiological conditions differed between feeding groups. Resting muscle glycogen concentrations was twofold greater in force fed fish, at rest and throughout recovery, although it decreased in both feeding treatments following exercise. Liver mass was nearly three times greater in force fed fish, and fasted fish had an average of 65% more cortisol throughout recovery. Similar recovery rates of most physiological responses were observed despite force fed fish having a metabolic rate 75% greater than fasted fish. Results are discussed as they relate to largemouth bass starvation in wild systems and how these physiological differences might be important in an evolutionary context.

  19. Knockdown of hepatoma-derived growth factor-related protein-3 induces apoptosis of H1299 cells via ROS-dependent and p53-independent NF-κB activation

    SciTech Connect (OSTI)

    Yun, Hong Shik; Baek, Jeong-Hwa; Yim, Ji-Hye; Lee, Su-Jae; Lee, Chang-Woo; Song, Jie-Young; Um, Hong-Duck; Park, Jong Kuk; Park, In-Chul; Hwang, Sang-Gu

    2014-07-11

    Highlights: • HRP-3 is a radiation- and anticancer drug-responsive protein in H1299 cells. • Depletion of HRP-3 induces apoptosis of radio- and chemoresistant H1299 cells. • Depletion of HRP-3 promotes ROS generation via inhibition of the Nrf2/HO-1 pathway. • ROS generation enhances NF-κB activity, which acts as an upstream signal in the c-Myc/Noxa apoptotic pathway. - Abstract: We previously identified hepatoma-derived growth factor-related protein-3 (HRP-3) as a radioresistant biomarker in p53 wild-type A549 cells and found that p53-dependent induction of the PUMA pathway was a critical event in regulating the radioresistant phenotype. Here, we found that HRP-3 knockdown regulates the radioresistance of p53-null H1299 cells through a distinctly different molecular mechanism. HRP-3 depletion was sufficient to cause apoptosis of H1299 cells by generating substantial levels of reactive oxygen species (ROS) through inhibition of the Nrf2/HO-1 antioxidant pathway. Subsequent, ROS-dependent and p53-independent NF-κB activation stimulated expression of c-Myc and Noxa proteins, thereby inducing the apoptotic machinery. Our results thus extend the range of targets for the development of new drugs to treat both p53 wild-type or p53-null radioresistant lung cancer cells.

  20. Global warming accelerates drought-induced forest death

    ScienceCinema (OSTI)

    McDowell, Nathan; Pockman, William

    2014-06-02

    Many southwestern forests in the United States will disappear or be heavily altered by 2050, according to a series of joint Los Alamos National Laboratory-University of New Mexico studies. Nathan McDowell, a Los Alamos plant physiologist, and William Pockman, a UNM biology professor, explain that their research, and more from scientists around the world, is forecasting that by 2100 most conifer forests should be heavily disturbed, if not gone, as air temperatures rise in combination with drought. "Everybody knows trees die when there's a drought, if there's bark beetles or fire, yet nobody in the world can predict it with much accuracy." McDowell said. "What's really changed is that the temperature is going up," thus the researchers are imposing artificial drought conditions on segments of wild forest in the Southwest and pushing forests to their limit to discover the exact processes of mortality and survival. The study is centered on drought experiments in woodlands at both Los Alamos and the Sevilleta National Wildlife Refuge in central New Mexico. Both sites are testing hypotheses about how forests die on mature, wild trees, rather than seedlings in a greenhouse, through the ecosystem-scale removal of 50 percent of yearly precipitation through large water-diversion trough systems.

  1. Decreasing transmembrane segment length greatly decreases perfringolysin O pore size

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lin, Qingqing; Li, Huilin; Wang, Tong; London, Erwin

    2015-04-08

    Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakagemore » assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.« less

  2. Superoxide reduction by a superoxide reductase lacking the highly conserved lysine residue

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Teixeira, Miguel; Cabelli, Diane; Pinto, Ana F.; Romao, Celia V.; Pinto, Liliana C.; Huber, Harald; Saraiva, Ligia M.; Todorovic, Smilja

    2014-12-05

    Superoxide reductases (SORs) are the most recently identified superoxide detoxification systems, being found in microorganisms from the three domains of life. These enzymes are characterized by a catalytic mononuclear iron site, with one cysteine and four histidine ligands of the ferrous active form. A lysine residue in the –EKHVP– motif, located close to the active site, has been considered to be essential for the enzyme function, by contributing to the positive surface patch that attracts the superoxide anion and by controlling the chemistry of the catalytic mechanism through a hydrogen bond network. However, we show here that this residue ismore » substituted by non-equivalent amino acids in several putative SORs from Archaea and unicellular Eukarya. In this work, we focus on mechanistic and spectroscopic studies of one of these less common enzymes, the SOR from the hyperthermophilic crenarchaeon Ignicoccus hospitalis. We employ pulse radiolysis fast kinetics and spectroscopic approaches to study the wild-type enzyme (₋E₂₃T₂₄HVP₋), and two mutants, T24K and E23A, the later mimicking enzymes lacking both the lysine and glutamate (a ferric ion ligand) of the motif. The efficiency of the wild type protein and mutants in reducing superoxide is comparable to other SORs, revealing the robustness of these enzymes to single mutations.« less

  3. Kokanee Stock Status and Contribution Cabinet Gorge Hatchery, Lake Pend Oreille, Idaho, 1988 Annual Progress Report.

    SciTech Connect (OSTI)

    Bowles, Edward C.

    1989-02-01

    The kokanee Oncorhynchus nerka rehabilitation program for Lake Pend Oreille continued to show progress during 1988. Estimated kokanee abundance in early September was 10.2 million fish. This estimate is 70% higher than 1987 and 140% higher than the populations's low point in 1986. Increased population size over the past two years is the result of two consecutive strong year classes produced from high recruitment of hatchery and wild fry. High recruitment of wild fry in 1988 resulted from good parental escapement (strong year class) in 1987 and relatively high fry survival. Hatchery fry made up 51% of total fry recruitment (73% of total fry biomass), which is the largest contribution since hatchery supplementation began in the 1970s. High hatchery fry abundance resulted from a large release (13 million fry) from Cabinet Gorge Hatchery and excellent fry survival (29%) during their first summer in Lake Pend Oreille. Improved fry release strategies enhanced survival, which doubled from 1987 to 1988 and was ten times higher than survival in 1986. Our research goal is to maintain 30% survival so we are very optimistic, but need to replicate additional years to address annual variability. 27 refs., 24 figs., 3 tabs.

  4. Crystallization and preliminary X-ray analysis of binary and ternary complexes of Haloferax mediterranei glucose dehydrogenase

    SciTech Connect (OSTI)

    Esclapez, Julia; Britton, K. Linda; Baker, Patrick J.; Fisher, Martin; Pire, Carmen; Ferrer, Juan; Bonete, María José; Rice, David W.

    2005-08-01

    Single crystals of binary and ternary complexes of wild-type and D38C mutant H. mediterranei glucose dehydrogenase have been obtained by the hanging-drop vapour-diffusion method. Haloferax mediterranei glucose dehydrogenase (EC 1.1.1.47) belongs to the medium-chain alcohol dehydrogenase superfamily and requires zinc for catalysis. In the majority of these family members, the catalytic zinc is tetrahedrally coordinated by the side chains of a cysteine, a histidine, a cysteine or glutamate and a water molecule. In H. mediterranei glucose dehydrogenase, sequence analysis indicates that the zinc coordination is different, with the invariant cysteine replaced by an aspartate residue. In order to analyse the significance of this replacement and to contribute to an understanding of the role of the metal ion in catalysis, a range of binary and ternary complexes of the wild-type and a D38C mutant protein have been crystallized. For most of the complexes, crystals belonging to space group I222 were obtained using sodium/potassium citrate as a precipitant. However, for the binary and non-productive ternary complexes with NADPH/Zn, it was necessary to replace the citrate with 2-methyl-2,4-pentanediol. Despite the radical change in conditions, the crystals thus formed were isomorphous.

  5. Biofuel and chemical production by recombinant microorganisms via fermentation of proteinaceous biomass

    DOE Patents [OSTI]

    Liao, James C.; Cho, Kwang Myung; Yan, Yajun; Huo, Yixin

    2016-03-15

    Provided herein are metabolically modified microorganisms characterized by having an increased keto-acid flux when compared with the wild-type organism and comprising at least one polynucleotide encoding an enzyme that when expressed results in the production of a greater quantity of a chemical product when compared with the wild-type organism. The recombinant microorganisms are useful for producing a large number of chemical compositions from various nitrogen containing biomass compositions and other carbon sources. More specifically, provided herein are methods of producing alcohols, acetaldehyde, acetate, isobutyraldehyde, isobutyric acid, n-butyraldehyde, n-butyric acid, 2-methyl-1-butyraldehyde, 2-methyl-1-butyric acid, 3-methyl-1-butyraldehyde, 3-methyl-1-butyric acid, ammonia, ammonium, amino acids, 2,3-butanediol, 1,4-butanediol, 2-methyl-1,4-butanediol, 2-methyl-1,4-butanediamine, isobutene, itaconate, acetoin, acetone, isobutene, 1,5-diaminopentane, L-lactic acid, D-lactic acid, shikimic acid, mevalonate, polyhydroxybutyrate (PHB), isoprenoids, fatty acids, homoalanine, 4-aminobutyric acid (GABA), succinic acid, malic acid, citric acid, adipic acid, p-hydroxy-cinnamic acid, tetrahydrofuran, 3-methyl-tetrahydrofuran, gamma-butyrolactone, pyrrolidinone, n-methylpyrrolidone, aspartic acid, lysine, cadeverine, 2-ketoadipic acid, and/or S-adenosyl-methionine (SAM) from a suitable nitrogen rich biomass.

  6. The Magnificent Journey.

    SciTech Connect (OSTI)

    United States. Bonneville Power Administration.

    1995-01-01

    The annual run of Northwest salmon--from the vast Pacific Ocean to the mountain streams where their lives began--is one of Nature`s most awe-inspiring events. Now that modern science has discovered some of the salmon`s secrets, their journey seems even more miraculous. So unlikely is the survival of a single returning salmon that Nature compensates heavily. Of the other 3,000 to 7,000 eggs in a nest, only one spawning pair, on average, will make it back. Too much or too little water at hatching can wipe out great swarms of young fish life. Bigger fish, bears, seals--all take their share of salmon. Nature allows for these natural events. But Nature alone cannot make up for what people have done. Dams in the Columbia River Basin have blocked huge areas of the wild salmon`s spawning grounds. Roads and towns sprouted up along rivers and streams. Logging and farming practices fouled rivers and creeks. So did pollution from the cities. And it became too easy to catch fish. Salmon runs became smaller and smaller. Some types of salmon disappeared forever. Having nearly destroyed the salmon, people are now coming to their rescue. Still, important runs of Northwest native salmon are in real danger of extinction. Much remains to be done. This brochure presents a close look at the life of a wild salmon, Oncorhynchus tshawystcha.

  7. Mutations Abrogating VP35 Interaction with Double-Stranded RNA Render Ebola Virus Avirulent in Guinea Pigs

    SciTech Connect (OSTI)

    Prins, Kathleen C.; Delpeut, Sebastien; Leung, Daisy W.; Reynard, Olivier; Volchkova, Valentina A.; Reid, St. Patrick; Ramanan, Parameshwaran; Cárdenas, Washington B.; Amarasinghe, Gaya K.; Volchkov, Viktor E.; Basler, Christopher F.

    2010-10-11

    Ebola virus (EBOV) protein VP35 is a double-stranded RNA (dsRNA) binding inhibitor of host interferon (IFN)-{alpha}/{beta} responses that also functions as a viral polymerase cofactor. Recent structural studies identified key features, including a central basic patch, required for VP35 dsRNA binding activity. To address the functional significance of these VP35 structural features for EBOV replication and pathogenesis, two point mutations, K319A/R322A, that abrogate VP35 dsRNA binding activity and severely impair its suppression of IFN-{alpha}/{beta} production were identified. Solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography reveal minimal structural perturbations in the K319A/R322A VP35 double mutant and suggest that loss of basic charge leads to altered function. Recombinant EBOVs encoding the mutant VP35 exhibit, relative to wild-type VP35 viruses, minimal growth attenuation in IFN-defective Vero cells but severe impairment in IFN-competent cells. In guinea pigs, the VP35 mutant virus revealed a complete loss of virulence. Strikingly, the VP35 mutant virus effectively immunized animals against subsequent wild-type EBOV challenge. These in vivo studies, using recombinant EBOV viruses, combined with the accompanying biochemical and structural analyses directly correlate VP35 dsRNA binding and IFN inhibition functions with viral pathogenesis. Moreover, these studies provide a framework for the development of antivirals targeting this critical EBOV virulence factor.

  8. John Day River Sub-Basin Fish Habitat Enhancement Project; 2008 Annual Report

    SciTech Connect (OSTI)

    Powell, Russ M.; Alley, Pamela D.; Goin Jr, Lonnie

    2009-07-15

    Work undertaken in 2008 included: (1) Seven new fence projects were completed thereby protecting approximately 10.97 miles of streams with 16.34 miles of riparian fence; (2) Renewal of one expired lease was completed thereby continuing to protect 0.75 miles of stream with 1.0 mile of riparian fence. (3) Maintenance of all active project fences (106.54 miles), watergaps (78), spring developments (33) were checked and repairs performed; (3) Planted 1000 willow/red osier on Fox Creek/Henslee property; (4) Planted 2000 willows/red osier on Middle Fork John Day River/Coleman property; (5) Planted 1000 willow/red osier cuttings on Fox Creek/Johns property; (6) Since the initiation of the Fish Habitat Project in 1984 we have 126.86 miles of stream protected using 211.72 miles of fence protecting 5658 acres. The purpose of the John Day Fish Habitat Enhancement Program is to enhance production of indigenous wild stocks of spring Chinook and summer steelhead within the sub basin through habitat protection, enhancement and fish passage improvement. The John Day River system supports the largest remaining wild runs of spring chinook salmon and summer steelhead in Northeast Oregon.

  9. Analysis of the influence of subcellular localization of the HIV Rev protein on Rev-dependent gene expression by multi-fluorescence live-cell imaging

    SciTech Connect (OSTI)

    Wolff, Horst; Hadian, Kamyar; Ziegler, Manja; Weierich, Claudia; Kramer-Hammerle, Susanne; Kleinschmidt, Andrea; Erfle, Volker; Brack-Werner, Ruth . E-mail: brack@gsf.de

    2006-02-15

    The human immunodeficiency virus Rev protein is a post-transcriptional activator of HIV gene expression. Rev is a nucleocytoplasmic shuttle protein that displays characteristic nuclear/nucleolar subcellular localization in various cell lines. Cytoplasmic localization of Rev occurs under various conditions disrupting Rev function. The goal of this study was to investigate the relationship between localization of Rev and its functional activity in living cells. A triple-fluorescent imaging assay, called AQ-FIND, was established for automatic quantitative evaluation of nucleocytoplasmic distribution of fluorescently tagged proteins. This assay was used to screen 500 rev genes generated by error-prone PCR for Rev mutants with different localization phenotypes. Activities of the Rev mutants were determined with a second quantitative, dual-fluorescent reporter assay. In HeLa cells, the majority of nuclear Rev mutants had activities similar to wild-type Rev. The activities of Rev mutants with abnormal cytoplasmic localization ranged from moderately impaired to nonfunctional. There was no linear correlation between subcellular distribution and levels of Rev activity. In astrocytes, nuclear Rev mutants showed similar impaired activities as the cytoplasmic wild-type Rev. Our data suggest that steady-state subcellular localization is not a primary regulator of Rev activity but may change as a secondary consequence of altered Rev function. The methodologies described here have potential for studying the significance of subcellular localization for functions of other regulatory factors.

  10. Analysis of Leaf and Root Transcriptome of Soil Grown Avena barbata Plants

    SciTech Connect (OSTI)

    Swarbreck, St; phanie; Lindquist, Erika; Ackerly, David; Andersen, Gary

    2011-02-01

    Slender wild oat (Avena barbata) is an annual grass dominant in many grassland ecosystems in Mediterranean climate. This species has been the subject of ecological studies that aim at understanding the effect of global climate change on grassland ecosystems and the genetic basis for adaptation under varying environmental conditions. We present the sequencing and analysis of cDNA libraries constructed from leaf and root samples collected from A. barbata grown on natural soil and under varying rainfall patterns. More than one million expressed sequence tags (ESTs) were generated using both GS 454-FLX pyrosequencing and Sanger sequencing, and these tags were assembled into consensus sequences. We identified numerous candidate polymorphic markers in the dataset, providing possibilities for linking the genomic and the existing genetic information for A. barbata. Using the digital northern method, we showed that genes involved in photosynthesis were down regulated under high rainfall while stress- related genes were up regulated. We also identified a number of genes unique to the root library with unknown function. Real-time RT-PCR was used to confirm the root specificity of some of these transcripts such as two genes encoding O-methyl transferase. Also we showed differential expression under three water levels. Through a combination of Sanger and 454-based sequencing technologies, we were able to generate a large set of transcribed sequences for A. barbata. This dataset provides a platform for further studies of this important wild grass species

  11. Raptor Use of the Rio Grande Gorge

    SciTech Connect (OSTI)

    Ponton, David A.

    2015-03-20

    The Rio Grande Gorge is a 115 km long river canyon located in Southern Colorado (15 km) and Northern New Mexico (100 km). The majority of the canyon is under the administration of the Bureau of Land Management {BLM), and 77 km of the canyon south of the Colorado/New Mexico border are designated Wild River under the National Wild and Scenic Rivers Act of 1968. Visits I have made to the Rio Grande Gorge over the past 15 .years disclosed some raptor utilization. As the Snake River Birds of Prey Natural Area gained publicity, its similarity to the Rio Grande Gorge became obvious, and I was intrigued by the possibility of a high raptor nesting density in the Gorge. A survey in 1979 of 20 km of the northern end of the canyon revealed a moderately high density of red-tailed hawks and prairie falcons. With the encouragement of that partial survey, and a need to assess the impact of river-running on nesting birds of prey, I made a more comprehensive survey in 1980. The results of my surveys, along with those of a 1978 helicopter survey by the BLM, are presented in this report, as well as general characterization of the area, winter use by raptors, and an assessment of factors influencing the raptor population.

  12. The HPr Proteins from the Thermophile Bacillus stearothermophilus Can Form Domain-swapped Dimers

    SciTech Connect (OSTI)

    Sridharan, Sudharsan; Razvi, Abbas; Scholtz, J. Martin; Sacchettini, James C. (TAM)

    2010-07-20

    The study of proteins from extremophilic organisms continues to generate interest in the field of protein folding because paradigms explaining the enhanced stability of these proteins still elude us and such studies have the potential to further our knowledge of the forces stabilizing proteins. We have undertaken such a study with our model protein HPr from a mesophile, Bacillus subtilis, and a thermophile, Bacillus stearothermophilus. We report here the high-resolution structures of the wild-type HPr protein from the thermophile and a variant, F29W. The variant proved to crystallize in two forms: a monomeric form with a structure very similar to the wild-type protein as well as a domain-swapped dimer. Interestingly, the structure of the domain-swapped dimer for HPr is very different from that observed for a homologous protein, Crh, from B. subtilis. The existence of a domain-swapped dimer has implications for amyloid formation and is consistent with recent results showing that the HPr proteins can form amyloid fibrils. We also characterized the conformational stability of the thermophilic HPr proteins using thermal and solvent denaturation methods and have used the high-resolution structures in an attempt to explain the differences in stability between the different HPr proteins. Finally, we present a detailed analysis of the solution properties of the HPr proteins using a variety of biochemical and biophysical methods.

  13. Ecological Interactions Between Metals and Microbes That Impact Bioremediation

    SciTech Connect (OSTI)

    Konopka, Allan E.

    1998-06-01

    Samples have been obtained from (a) soil highly contaminated with Cr (tannery site) and (b) soils contaminated with petroleum, Cr, and Pb (Seymour, IN). Microcosm experiments with the tannery site soil indicated that microbial biomass (assayed as phospholipid-phosphate) and activity (assayed as carbon dioxide evolution) were primarily determined by organic carbon availability, but not total Cr concentration. The toxicity of metals to the indigenous microbial populations of the Seymour soils was determined by measuring microbial activity (incorporation of tritiated leucine into protein) of cells extracted from soil particles in solutions of increasing metal concentration. Although total Cr concentration varied 100-fold in these soils, the inhibition constant for Cr toxicity varied < 3-fold. Of additional interest in one soil was the dose-response function; the response suggests the soil contains a complex mixture of microbes with different Cr resistance levels. Cr and Pb resistant bacteria have been isolated from these soil samples. In Arthrobacter sp. Cr15, Cr resistance was spontaneously lost at a frequency of ca. 0.5% after growth for 20 generations in non-selective medium. The wild-type contained a 60 kb plasmid. In two Cr sensitive strains, restriction fragment analysis has shown that 15 kb of the plasmid have been lost. Matings between the wild type and cured strains result in transfer of the Cr resistance phenotype at a frequency of 1%.

  14. Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhu, Xueyong; Viswanathan, Karthik; Raman, Rahul; Yu, Wenli; Sasisekharan, Ram; Wilson, Ian A.

    2015-11-01

    Avian H5N1 influenza viruses continue to spread in wild birds and domestic poultry with sporadic infection in humans. Receptor binding specificity changes are a prerequisite for H5N1 viruses and other zoonotic viruses to be transmitted among humans. Previous reported hemagglutinin (HA) mutants from ferret-transmissible H5N1 viruses of A/Viet Nam/1203/04 and A/Indonesia/5/05 showed slightly increased, but still very weak, binding to human receptors. From mutagenesis and glycan array studies, we previously identified two H5N1 HA mutants that could more effectively switch receptor specificity to human-like α2-6 linked sialosides with avidity comparable to wild-type H5 HA binding to avian-like α2-3 linked sialosides.more »Here, crystal structures of these two H5 HA mutants free and in complex with human and avian glycan receptor analogues reveal the structural basis for their preferential binding to human receptors. These findings suggest continuous surveillance should be maintained to monitor and assess human-to-human transmission potential of H5N1 viruses.« less

  15. A Zinc-Finger-Family Transcription Factor, AbVf19, Is Required for the Induction of a Gene Subset Important for Virulence in Alternaria brassicicola

    SciTech Connect (OSTI)

    Srivastava, Akhil; Ohm, Robin A.; Oxiles, Lindsay; Brooks, Fred; Lawrence, Christopher B.; Grigoriev, Igor V.; Cho, Yangrae

    2011-10-26

    Alternaria brassicicola is a successful saprophyte and necrotrophic plant pathogen with a broad host range within the family Brassicaceae. It produces secondary metabolites that marginally affect virulence. Cell wall degrading enzymes (CDWE) have been considered important for pathogenesis but none of them individually have been identified as significant virulence factors in A. brassicicola. In this study, knockout mutants of a gene, AbVf19, were created and produced considerably smaller lesions than the wild type on inoculated host plants. The presence of tandem zinc-finger domains in the predicted amino acid sequence and nuclear localization of AbVf19- reporter protein suggested that it was a transcription factor. Gene expression comparisons using RNA-seq identified 74 genes being downregulated in the mutant during a late stage of infection. Among the 74 downregulated genes, 28 were putative CWDE genes. These were hydrolytic enzyme genes that composed a small fraction of genes within each family of cellulases, pectinases, cutinases, and proteinases. The mutants grew slower than the wild type on an axenic medium with pectin as a major carbon source. This study demonstrated the existence and the importance of a transcription factor that regulates a suite of genes that are important for decomposing and utilizing plant material during the late stage of plant infection.

  16. Calmodulin Methionine Residues are Targets For One-Electron Oxidation by Hydroxyl Radicals: Formation of S therefore N three-electron bonded Radical Complexes

    SciTech Connect (OSTI)

    Nauser, Thomas; Jacoby, Michael E.; Koppenol, Willem H.; Squier, Thomas C.; Schoneich, Christian

    2005-02-01

    The one-electron (1e) oxidation of organic sulfides and methionine (Met) constitutes an important reaction mechanism in vivo.1,2 Evidence for a Cu(II)-catalyzed oxidation of Met35 in the Alzheimer's disease -amyloid peptide was obtained,3 and, based on theoretical studies, Met radical cations were proposed as intermediates.4 In the structure of -amyloid peptide, the formation of Met radical cations appears to be facilitated by a preexisting close sulfur-oxygen (S-O) interaction between the Met35 sulfur and the carbonyl oxygen of the peptide bond C-terminal to Ile31.5 Substitution of Ile31 with Pro31 abolishes this S-O interaction,5 significantly reducing the ability of -amyloid to reduce Cu(II), and converts the neurotoxic wild-type -amyloid into a non-toxic peptide.6 The preexisting S-O bond characterized for wild-type -amyloid suggests that electron transfer from Met35 to Cu(II) is supported through stabilization of the Met radical cation by the electron-rich carbonyl oxygen, generating an SO-bonded7 sulfide radical cation (Scheme 1, reaction 1).5

  17. Superoxide reduction by a superoxide reductase lacking the highly conserved lysine residue

    SciTech Connect (OSTI)

    Teixeira, Miguel; Cabelli, Diane; Pinto, Ana F.; Romao, Celia V.; Pinto, Liliana C.; Huber, Harald; Saraiva, Ligia M.; Todorovic, Smilja

    2014-12-05

    Superoxide reductases (SORs) are the most recently identified superoxide detoxification systems, being found in microorganisms from the three domains of life. These enzymes are characterized by a catalytic mononuclear iron site, with one cysteine and four histidine ligands of the ferrous active form. A lysine residue in the EKHVP motif, located close to the active site, has been considered to be essential for the enzyme function, by contributing to the positive surface patch that attracts the superoxide anion and by controlling the chemistry of the catalytic mechanism through a hydrogen bond network. However, we show here that this residue is substituted by non-equivalent amino acids in several putative SORs from Archaea and unicellular Eukarya. In this work, we focus on mechanistic and spectroscopic studies of one of these less common enzymes, the SOR from the hyperthermophilic crenarchaeon Ignicoccus hospitalis. We employ pulse radiolysis fast kinetics and spectroscopic approaches to study the wild-type enzyme (?E??T??HVP?), and two mutants, T24K and E23A, the later mimicking enzymes lacking both the lysine and glutamate (a ferric ion ligand) of the motif. The efficiency of the wild type protein and mutants in reducing superoxide is comparable to other SORs, revealing the robustness of these enzymes to single mutations.

  18. Generation of transgenic wheat (Triticum aestivum L.) accumulating heterologous endo-xylanase or ferulic acid esterase in the endosperm

    SciTech Connect (OSTI)

    Harholt, Jesper; Bach, Inga C; Lind-Bouquin, Solveig; Nunan, Kylie J.; Madrid, Susan M.; Brinch-Pedersen, Henrik; Holm, Preben B.; Scheller, Henrik V.

    2009-12-08

    Endo-xylanase (from Bacillus subtilis) or ferulic acid esterase (from Aspergillus niger) were expressed in wheat under the control of the endosperm specific 1DX5 glutenin promoter. Constructs both with and without the endoplasmic reticulum retention signal KDEL were used. Transgenic plants were recovered in all four cases but no qualitative differences could be observed whether KDEL was added or not. Endo-xylanase activity in transgenic grains was increased between two and three fold relative to wild type. The grains were shriveled and had a 25-33% decrease in mass. Extensive analysis of the cell walls showed a 10-15% increase in arabinose to xylose ratio, a 50% increase in the proportion of water extractable arabinoxylan, and a shift in the MW of the water extractable arabinoxylan from being mainly larger than 85 kD to being between 2 kD and 85 kD. Ferulic acid esterase expressing grains were also shriveled and the seed weight was decreased by 20-50%. No ferulic acid esterase activity could be detected in wild type grains whereas ferulic acid esterase activity was detected in transgenic lines. The grain cell walls had 15-40% increase in water unextractable arabinoxylan and a decrease in monomeric ferulic acid between 13 and 34%. In all the plants the observed changes are consistent with a plant response that serves to minimize the effect of the heterologously expressed enzymes by increasing arabinoxylan biosynthesis and cross-linking.

  19. Consolidated bioprocessing of transgenic switchgrass by an engineered and evolved Clostridium thermocellum strain

    SciTech Connect (OSTI)

    Yee, Kelsey L; Rodriguez Jr, Miguel; Thompson, Olivia A; Fu, Chunxiang; Wang, Zeng-Yu; Davison, Brian H; Mielenz, Jonathan R

    2014-01-01

    Background: Switchgrass is an abundant and dedicated bioenergy feedstock however its inherent recalcitrance is one of the economic hurdles for producing biofuels. The down-regulation of the caffeic acid O-methyl transferase (COMT) gene in the lignin pathway of switchgrass reduced lignin content and S/G ratio, and the transgenic lines showed improved fermentation yield with S. cerevisiae and C. thermocellum (ATCC 27405) in comparison to the wild-type switchgrass. Results: Here we examine the fermentation potential of the COMT transgenic switchgrass and its wild-type line, with an engineered and evolved Clostridium thermocellum (M1570) strain. The fermentation of the transgenic switchgrass had superior conversion relative to the control line with an increase of 20% and ethanol was the primary metabolite accounting for 90% of the total metabolites measured by HPLC. Conclusions: The down-regulation of the COMT gene in switchgrass reduced recalcitrance and improved microbial bioconversion yield. Moreover, these results showed ethanol as the main fermentation metabolite produced by an engineered and evolved C. thermocellum strain grown on a transgenic switchgrass.

  20. Direct Conversion of Plant Biomass to Ethanol by Engineered Caldicellulosiruptor bescii

    SciTech Connect (OSTI)

    Chung, Daehwan; Cha, Minseok; Guss, Adam M; Westpheling, Janet

    2014-01-01

    Ethanol is the most widely used renewable transportation biofuel in the United States, with the production of 13.3 billion gallons in 2012 [John UM (2013) Contribution of the Ethanol Industry to the Economy of the United States]. Despite considerable effort to produce fuels from lignocellulosic biomass, chemical pretreatment and the addition of saccharolytic enzymes before microbial bioconversion remain economic barriers to industrial deployment [Lynd LR, et al. (2008) Nat Biotechnol 26(2):169-172]. We began with the thermophilic, anaerobic, cellulolytic bacterium Caldicellulosiruptor bescii, which efficiently uses unpretreated biomass, and engineered it to produce ethanol. Here we report the direct conversion of switchgrass, a nonfood, renewable feedstock, to ethanol without conventional pretreatment of the biomass. This process was accomplished by deletion of lactate dehydrogenase and heterologous expression of a Clostridium thermocellum bifunctional acetaldehyde/alcohol dehydrogenase. Whereas wild-type C. bescii lacks the ability to make ethanol, 70% of the fermentation products in the engineered strain were ethanol [12.8 mM ethanol directly from 2% (wt/vol) switchgrass, a real-world substrate] with decreased production of acetate by 38% compared with wild-type. Direct conversion of biomass to ethanol represents a new paradigm for consolidated bioprocessing, offering the potential for carbon neutral, cost-effective, sustainable fuel production.

  1. Global warming accelerates drought-induced forest death

    SciTech Connect (OSTI)

    McDowell, Nathan; Pockman, William

    2013-07-09

    Many southwestern forests in the United States will disappear or be heavily altered by 2050, according to a series of joint Los Alamos National Laboratory-University of New Mexico studies. Nathan McDowell, a Los Alamos plant physiologist, and William Pockman, a UNM biology professor, explain that their research, and more from scientists around the world, is forecasting that by 2100 most conifer forests should be heavily disturbed, if not gone, as air temperatures rise in combination with drought. "Everybody knows trees die when there's a drought, if there's bark beetles or fire, yet nobody in the world can predict it with much accuracy." McDowell said. "What's really changed is that the temperature is going up," thus the researchers are imposing artificial drought conditions on segments of wild forest in the Southwest and pushing forests to their limit to discover the exact processes of mortality and survival. The study is centered on drought experiments in woodlands at both Los Alamos and the Sevilleta National Wildlife Refuge in central New Mexico. Both sites are testing hypotheses about how forests die on mature, wild trees, rather than seedlings in a greenhouse, through the ecosystem-scale removal of 50 percent of yearly precipitation through large water-diversion trough systems.

  2. Uses of Ku70

    DOE Patents [OSTI]

    Li, Gloria C.; Cordon-Cardo, Carlos; Ouyang, Honghai

    2004-10-26

    This invention provides a method of diagnosing a predisposition to cancer in a subject comprising: (a) obtaining a nucleic acid sample from the subject; and; (b) determining whether one or more of the subject's Ku70 alleles or regulatory regions to those alleles are deleted or different from the wild type so as to reduce or eliminate the subject's expression of polypeptide having tumor suppressor activity. This invention also provides a method of assessing the severity of cancer in a subject comprising: (a) obtaining a nucleic acid sample from the subject; and (b) determining whether one or more of the subject's Ku70 alleles or regulatory regions to those alleles are deleted or different from the wild type so as to reduce or eliminate the subject's expression of polypeptide having tumor suppressor activity. This invention also provides a method of assessing the severity of cancer in a subject comprising: determining the subcellular localization of Ku70 in the subject, wherein an abnormal subcellular localization of Ku70 indicates a predisposition to cancer.

  3. Structure of adenovirus bound to cellular receptor car

    DOE Patents [OSTI]

    Freimuth, Paul I.

    2004-05-18

    Disclosed is a mutant adenovirus which has a genome comprising one or more mutations in sequences which encode the fiber protein knob domain wherein the mutation causes the encoded viral particle to have significantly weakened binding affinity for CARD1 relative to wild-type adenovirus. Such mutations may be in sequences which encode either the AB loop, or the HI loop of the fiber protein knob domain. Specific residues and mutations are described. Also disclosed is a method for generating a mutant adenovirus which is characterized by a receptor binding affinity or specificity which differs substantially from wild type. In the method, residues of the adenovirus fiber protein knob domain which are predicted to alter D1 binding when mutated, are identified from the crystal structure coordinates of the AD12knob:CAR-D1 complex. A mutation which alters one or more of the identified residues is introduced into the genome of the adenovirus to generate a mutant adenovirus. Whether or not the mutant produced exhibits altered adenovirus-CAR binding properties is then determined.

  4. Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Yoneda, Aki; Henson, William R.; Goldner, Nicholas K.; Park, Kun Joo; Forsberg, Kevin J.; Kim, Soo Ji; Pesesky, Mitchell W.; Foston, Marcus; Dantas, Gautam; Moon, Tae Seok

    2016-02-02

    Lignin-derived (e.g. phenolic) compounds can compromise the bioconversion of lignocellulosic biomass to fuels and chemicals due to their toxicity and recalcitrance. The lipid-accumulating bacterium Rhodococcus opacus PD630 has recently emerged as a promising microbial host for lignocellulose conversion to value-added products due to its natural ability to tolerate and utilize phenolics. To gain a better understanding of its phenolic tolerance and utilization mechanisms, we adaptively evolved R. opacus over 40 passages using phenol as its sole carbon source (up to 373% growth improvement over wild-type), and extensively characterized two strains from passages 33 and 40. The two adapted strains showedmore » higher phenol consumption rates (~20 mg/l/h) and ~2-fold higher lipid production from phenol than the wild-type strain.Whole-genome sequencing and comparative transcriptomics identified highly-upregulated degradation pathways and putative transporters for phenol in both adapted strains, highlighting the important linkage between mechanisms of regulated phenol uptake, utilization, and evolved tolerance. Our study shows that the R. opacus mutants are likely to use their transporters to import phenol rather than export them, suggesting a new aromatic tolerance mechanism. The identified tolerance genes and pathways are promising candidates for future metabolic engineering in R. opacus for improved lignin conversion to lipid-based products.« less

  5. Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis

    SciTech Connect (OSTI)

    Pletneva, Nadya V.; Pletnev, Vladimir Z. Souslova, Ekaterina; Chudakov, Dmitry M.; Lukyanov, Sergey; Martynov, Vladimir I.; Arhipova, Svetlena; Artemyev, Igor; Wlodawer, Alexander; Dauter, Zbigniew; Pletnev, Sergei

    2013-06-01

    The yellow fluorescent protein phiYFPv with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The yellow fluorescent protein phiYFPv (λ{sub em}{sup max} ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow–orange range (535–555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The ‘yellow’ chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adopts the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.

  6. Decreasing transmembrane segment length greatly decreases perfringolysin O pore size

    SciTech Connect (OSTI)

    Lin, Qingqing; Li, Huilin; Wang, Tong; London, Erwin

    2015-04-08

    Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakage assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.

  7. Palmitoylation of the feline immunodeficiency virus envelope glycoprotein and its effect on fusion activity and envelope incorporation into virions

    SciTech Connect (OSTI)

    Gonzalez, Silvia A.; Paladino, Monica G.; Affranchino, Jose L.

    2012-06-20

    The feline immunodeficiency virus (FIV) envelope glycoprotein (Env) possesses a short cytoplasmic domain of 53 amino acids containing four highly conserved cysteines at Env positions 804, 811, 815 and 848. Since palmitoylation of transmembrane proteins occurs at or near the membrane anchor, we investigated whether cysteines 804, 811 and 815 are acylated and analyzed the relevance of these residues for Env functions. Replacement of cysteines 804, 811 and 815 individually or in combination by serine residues resulted in Env glycoproteins that were efficiently expressed and processed. However, mutations C804S and C811S reduced Env fusogenicity by 93% and 84%, respectively, compared with wild-type Env. By contrast, mutant C815S exhibited a fusogenic capacity representing 50% of the wild-type value. Remarkably, the double mutation C804S/C811S abrogated both Env fusion activity and Env incorporation into virions. Finally, by means of Click chemistry assays we demonstrated that the four FIV Env cytoplasmic cysteines are palmitoylated.

  8. Systems Level Approaches to Understanding and Manipulating Heterocyst Differentiation in Nostoc Punctiforme: Sites of Hydrogenase and Nitrogenase Synthesis and Activity

    SciTech Connect (OSTI)

    Meeks, John C.

    2015-04-02

    Heterocysts are specialized cells that establish a physiologically low oxygen concentration; they function as the sites of oxygen-sensitive nitrogen fixation and hydrogen metabolism in certain filamentous cyanobacteria. They are present at a frequency of less than 10% of the cells and singly in a nonrandom spacing pattern in the filaments. The extent of differential gene expression during heterocyst differentiation was defined by DNA microarray analysis in wild type and mutant cultures of Nostoc punctiforme. The results in wild-type cultures identified two groups of genes; approximately 440 that are unique to heterocyst formation and function, and 500 that respond positively and negatively to the transient stress of nitrogen starvation. Nitrogen fixation is initiated within 24 h after induction, but the cultures require another 24 h before growth is reinitiated. Microarray analyses were conducted on strains with altered expression of three genes that regulate the presence and spacing of heterocysts in the filaments; loss of function or over expression of these genes increases the heterocyst frequency 2 to 3 fold compared to the wild-type. Mutations in the genes hetR and hetF result in the inability to differentiate heterocysts, whereas over expression of each gene individually yields multiple contiguous heterocysts at sites in the filaments; they are positive regulatory elements. Mutation of the gene patN results in an increase in heterocysts frequency, but, in this case, the heterocysts are singly spaced in the filaments with a decrease in the number of vegetative cells in the interval between heterocysts; this is a negative regulatory element. However, over expression of patN resulted in the wild-type heterocyst frequency and spacing pattern. Microarray results indicated HetR and HetF influence the transcription of a common set of about 395 genes, as well as about 350 genes unique to each protein. HetR is known to be a transcriptional regulator and HetF is

  9. Kelt Reconditioning: A Research Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss), 2001 Annual Report.

    SciTech Connect (OSTI)

    Hatch, Douglas R.; Anders, Paul J., Evans, Allen F.

    2002-12-01

    Repeat spawning is a life history strategy that is expressed by some species from the family Salmonidae. Rates of repeat spawning for post-development Columbia River steelhead (Oncorhynchus mykiss) populations range from 1.6 to 17%. It is expected that currently observed iteroparity rates for wild steelhead in the Basin are artificially and in some cases severely depressed due to development and operation of the hydropower system and various additional anthropogenic factors. Increasing the natural expression of historical repeat spawning rates using fish culturing means could be a viable technique to assist the recovery of depressed steelhead populations. Reconditioning is the process of culturing post-spawned fish (kelts) in a captive environment until they are able to reinitiate feeding, growth, and again develop mature gonads. Kelt reconditioning techniques were initially developed for Atlantic salmon (Salmo salar) and sea-trout (S. trutta). The recent Endangered Species Act listing of many Columbia Basin steelhead populations has prompted interest in developing reconditioning methods for wild steelhead populations within the Basin. To address recovery, we captured wild emigrating steelhead kelts from the Yakima River and tested reconditioning and the effects of several diet formulations on its success at Prosser Hatchery on the Yakama Reservation. Steelhead kelts from the Yakima River were collected at the Chandler Juvenile Evaluation Facility (CJEF, located at Yakima River kilometer 48) from 12 March to 5 July 2001. Kelts were reconditioned in circular tanks and fed a mixed diet of starter paste, adult sized trout pellets, and freeze-dried krill. Formalin was used to control outbreaks of fungus and we tested the use of Ivermectin{trademark}to control internal parasites (e.g., Salmincola spp.). Surviving specimens were released for natural spawning in two groups on 15 November 2001 and 18 January 2002. Overall success of the reconditioning process was based on

  10. Survival Estimates for the Passage of Spring-Migrating Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2004-2005 Annual Report.

    SciTech Connect (OSTI)

    Smith, Steven G.; Muir, William D.; Marsh, Douglas M.

    2005-10-01

    In 2004, the National Marine Fisheries Service and the University of Washington completed the twelfth year of a study to estimate survival and travel time of juvenile salmonids (Oncorhynchus spp.) passing through dams and reservoirs on the Snake and Columbia Rivers. All estimates were derived from detections of fish tagged with passive integrated transponder tags (PIT tags). We PIT tagged and released a total of 19,621 hatchery steelhead, 8,128 wild steelhead, and 9,227 wild yearling Chinook salmon at Lower Granite Dam. In addition, we utilized fish PIT tagged by other agencies at traps and hatcheries upstream from the hydropower system and sites within the hydropower system. PIT-tagged smolts were detected at interrogation facilities at Lower Granite, Little Goose, Lower Monumental, McNary, John Day, and Bonneville Dams and in the PIT-tag detector trawl operated in the Columbia River estuary. Survival estimates were calculated using a statistical model for tag-recapture data from single release groups (the single-release model). Primary research objectives in 2004 were to (1) estimate reach survival and travel time in the Snake and Columbia Rivers throughout the migration period of yearling Chinook salmon O. tshawytscha and steelhead O. mykiss; (2) evaluate relationships between survival estimates and migration conditions; and (3) evaluate the survival-estimation models under prevailing conditions. This report provides reach survival and travel time estimates for 2004 for PIT-tagged yearling Chinook salmon (hatchery and wild), hatchery sockeye salmon O. nerka, hatchery coho salmon O. kisutch, and steelhead (hatchery and wild) in the Snake and Columbia Rivers. Results are reported primarily in the form of tables and figures; details on methodology and statistical models used are provided in previous reports cited here. Survival and detection probabilities were estimated precisely for most of the 2004 yearling Chinook salmon and steelhead migrations. Hatchery and

  11. evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation ans a consolidated bioprocessing approach

    SciTech Connect (OSTI)

    Yee, Kelsey L; Rodriguez, Jr., Miguel; Tschaplinski, Timothy J; Engle, Nancy L; Martin, Madhavi Z; Fu, Chunxiang; Wang, Zeng-Yu; Hamilton-Brehm, Scott; Mielenz, Jonathan R

    2012-01-01

    Abstract Background: The inherent recalcitrance of lignocellulosic biomass is one of the major economic hurdles for the production of fuels and chemicals from biomass. Additionally, lignin is recognized as having a negative impact on enzymatic hydrolysis of biomass, and as a result much interest has been placed on modifying the lignin pathway to improve bioconversion of lignocellulosic feedstocks. Results: Previous results showed down-regulation of the caffeic acid 3-O-methyl transferase (COMT) gene in the lignin pathway yielded switchgrass (Panicum virgatum) that was more susceptible to bioconversion after dilute acid pretreatment. Here we examined the response of these plant lines to milder pretreatment conditions with yeast-based SSF, CBP with Clostridium thermocellum, and fermentations with the cellulolytic extreme thermophiles, Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Unlike the S. cerevisiae SSF conversions, fermentations of pretreated down-regulated COMT transgenic switchgrass with C. thermocellum showed an apparent inhibition of fermentation not observed in the wild-type switchgrass. This inhibition can be eliminated by hot water extraction of the pretreated biomass which resulted in superior conversion yield with transgenic versus wild-type switchgrass for C. thermocellum, also exceeding the yeast-based SSF yield. Further fermentation evaluation of the transgenic switchgrass indicated differential inhibition for the Caldicellulosiruptor strains, which could not be rectified by additional processing conditions. Gas chromatography-mass spectrometry metabolite profiling was used to examine the fermentation broth to elucidate the relative abundance of lignin derived aromatic compounds. The types and abundance of fermentation-derived lignin constituents varied between C. thermocellum and each of the Caldicellulosiruptor strains. Conclusions: The down-regulation of the COMT gene improves the bioconversion of switchgrass relative to the

  12. Yakima River Spring Chinook Enhancement Study, 1987 Annual Report.

    SciTech Connect (OSTI)

    Fast, David E.

    1988-01-01

    The smelt outmigration was monitored at wapatox on the Naches River and Prosser on the lower Yakima. The spring outmigration at Wapatox was estimated to be 16,141 smolts. The 1987 spring outmigration of wild spring chinook from the Yakima Basin was estimated to be 251,975 smolts at Prosser. The survival from egg to smelt was calculated using the 1985 redd counts and the 1987 smolt outmigration at Prosser. The estimated survival was 4.16%, which gives a mean egg to smolt survival over four years of 6.32%. In 1987 a total of 3,683 adult and 335 jack spring chinook salmon returning to the Yakima River were counted at Prosser fish ladder. This gives a total of 4,018 salmon returning to Prosser Dam. The median dates of passage were May 12 and May 16 for adults and jacks respectively. An additional 372 fish were estimated to have been caught in the Yakima River subsistence dipnet fishery below Horn Rapids and Prosser Dams. Therefore, total return to the Yakima system was 4,390 spring chinook salmon. Spring chinook were counted at Roza Dam from May 1 to September 30, 1987. Passage at Roza Dam was 1,610 adult and 67 jack spring chinook for a total of 1,677 wild fish. The median dates of passage at Roza Dam were May 29 and May 26 for spring chinook adults and jacks respectively. The smolt to adult (S{sub sa}) survival was calculated based on the 1983 smelt outmigration estimated at Prosser and the 1984 return of jacks (3 year old fish) the 1985 return of four year old adults, and the 1986 return of five year old fish to the Yakima River. It was estimated that 6,012 wild three, four, and five year old fish returned from an estimated smolt outmigration of 135,548 fish in 1983. This gives an estimated survival from smolt to adult of 4.4%. The smolt to adult survival for the 1984 smolt outmigration was 5.3% with 423 jacks returning in 1985, 5,163 four year old adults returning in 1986, and 983 five year old fish returning in 1987 fran an estimated 123,732 smolts in 1984. Spring

  13. Oxygen isotope variability within Nautilus shell growth bands

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Linzmeier, Benjamin J.; Kozdon, Reinhard; Peters, Shanan E.; Valley, John W.

    2016-04-21

    Nautilus is often used as an analogue for the ecology and behavior of extinct externally shelled cephalopods. Nautilus shell grows quickly, has internal growth banding, and is widely believed to precipitate aragonite in oxygen isotope equilibrium with seawater. Pieces of shell from a wild-caught Nautilus macromphalus from New Caledonia and from a Nautilus belauensis reared in an aquarium were cast in epoxy, polished, and then imaged. Growth bands were visible in the outer prismatic layer of both shells. The thicknesses of the bands are consistent with previously reported daily growth rates measured in aquarium reared individuals. In situ analysis ofmore » oxygen isotope ratios using secondary ion mass spectrometry (SIMS) with 10 μm beam-spot size reveals inter- and intra-band δ18O variation. In the wild-caught sample, a traverse crosscutting 45 growth bands yielded δ18O values ranging 2.5‰, from +0.9 to -1.6 ‰ (VPDB), a range that is larger than that observed in many serial sampling of entire shells by conventional methods. The maximum range within a single band (~32 μm) was 1.5‰, and 27 out of 41 bands had a range larger than instrumental precision (±2 SD = 0.6‰). The results from the wild individual suggest depth migration is recorded by the shell, but are not consistent with a simple sinusoidal, diurnal depth change pattern. In addition, to create the observed range of δ18O, however, this Nautilus must have traversed a temperature gradient of at least ~12°C, corresponding to approximately 400 m depth change. Isotopic variation was also measured in the aquarium-reared sample, but the pattern within and between bands likely reflects evaporative enrichment arising from a weekly cycle of refill and replacement of the aquarium water. Overall, this work suggests that depth migration behavior in ancient nektonic mollusks could be elucidated by SIMS analysis across individual growth bands.« less

  14. Establishment of an oil and gas database for increased recovery and characterization of oil and gas carbonate reservoir heterogeneity. [Jurassic Smackover Formation

    SciTech Connect (OSTI)

    Kopasaka-Merkel, D.C.; Moore, H.E. Jr.; Mann, S.D; Hall, D.R.

    1992-06-01

    This volume contains maps, well log correlated to lithology, porosity and permeability, structural cross section, graph of production history, porosity vs. natural log permeability plots; detailed core log, porosity vs. natural permeability plot for one lithofacies, paragenetic sequence and reservoir characterization sheet for the following fields in southwest Alabama: Stave Creek oil field; Sugar Ridge oil field; Toxey oil field, Turkey Creed oil field; Turnerville oil field, Uriah oil field; Vocation oil field; Wallace oil field; Wallers Creek oil field; West Appleton oil field; West Barrytown oil field; West Bend oil field; West Okatuppa Creed oil field; Wild Fork Creek oil field; Wimberly oil field; Womack Hill oil field; and Zion Chapel oil field. (AT)

  15. Establishment of an oil and gas database for increased recovery and characterization of oil and gas carbonate reservoir heterogeneity. Appendix 1, Volume 4

    SciTech Connect (OSTI)

    Kopasaka-Merkel, D.C.; Moore, H.E. Jr.; Mann, S.D; Hall, D.R.

    1992-06-01

    This volume contains maps, well log correlated to lithology, porosity and permeability, structural cross section, graph of production history, porosity vs. natural log permeability plots; detailed core log, porosity vs. natural permeability plot for one lithofacies, paragenetic sequence and reservoir characterization sheet for the following fields in southwest Alabama: Stave Creek oil field; Sugar Ridge oil field; Toxey oil field, Turkey Creed oil field; Turnerville oil field, Uriah oil field; Vocation oil field; Wallace oil field; Wallers Creek oil field; West Appleton oil field; West Barrytown oil field; West Bend oil field; West Okatuppa Creed oil field; Wild Fork Creek oil field; Wimberly oil field; Womack Hill oil field; and Zion Chapel oil field. (AT)

  16. Establishment of an oil and gas database for increased recovery and characterization of oil and gas carbonate reservoir heterogeneity. [Jurassic Smackover Formation

    SciTech Connect (OSTI)

    Kopaska-Merkel, D.C.; Moore, H.E. Jr.; Mann, S.D.; Hall, D.R.

    1992-06-01

    This volume contains maps, well logging, structural cross section, graph of production history, porosity vs. natural log permeability plots, detailed core log, paragenetic sequence, and reservoir characterization sheet for the following fields in southwest Alabama: North Smiths Church oil field; North Wallers Creek oil field; Northeast Barnett oil field; Northwest Range oil field; Pace Creek oil field; Palmers Crossroads oil field; Perdido oil field; Puss Cuss Creek oil field; Red Creek gas condensate field; Robinson Creek oil field; Silas oil field; Sizemore Creek gas condensate field; Smiths Church gas condensate field; South Burnt Corn Creek oil field; South Cold Creek oil field; South Vocation oil field; South Wild Fork Creek gas condensate field; South Womack Hill oil field; Southeast Chatom gas condensate field; Southwest Barrytown oil field; and Souwilpa Creek gas condensate field.

  17. Establishment of an oil and gas database for increased recovery and characterization of oil and gas carbonate reservoir heterogeneity. Appendix 1, Volume 3

    SciTech Connect (OSTI)

    Kopaska-Merkel, D.C.; Moore, H.E. Jr.; Mann, S.D.; Hall, D.R.

    1992-06-01

    This volume contains maps, well logging, structural cross section, graph of production history, porosity vs. natural log permeability plots, detailed core log, paragenetic sequence, and reservoir characterization sheet for the following fields in southwest Alabama: North Smiths Church oil field; North Wallers Creek oil field; Northeast Barnett oil field; Northwest Range oil field; Pace Creek oil field; Palmers Crossroads oil field; Perdido oil field; Puss Cuss Creek oil field; Red Creek gas condensate field; Robinson Creek oil field; Silas oil field; Sizemore Creek gas condensate field; Smiths Church gas condensate field; South Burnt Corn Creek oil field; South Cold Creek oil field; South Vocation oil field; South Wild Fork Creek gas condensate field; South Womack Hill oil field; Southeast Chatom gas condensate field; Southwest Barrytown oil field; and Souwilpa Creek gas condensate field.

  18. Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

    SciTech Connect (OSTI)

    Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.; Machius, Mischa; Szyperski, Thomas; Kuhlman, Brian

    2015-10-15

    Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helix bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).

  19. Identification of the nucleophile catalytic residue of GH51 α-l-arabinofuranosidase from Pleurotus ostreatus

    SciTech Connect (OSTI)

    Amore, Antonella; Iadonisi, Alfonso; Vincent, Florence; Faraco, Vincenza

    2015-12-21

    In this paper, the recombinant α-l-arabinofuranosidase from the fungus Pleurotus ostreatus (rPoAbf) was subjected to site-directed mutagenesis in order to identify the catalytic nucleophile residue. Based on bioinformatics and homology modelling analyses, E449 was revealed to be the potential nucleophilic residue. Thus, the mutant E449G of PoAbf was recombinantly expressed in Pichia pastoris and its recombinant expression level and reactivity were investigated in comparison to the wild-type. The design of a suitable set of hydrolysis experiments in the presence or absence of alcoholic arabinosyl acceptors and/or formate salts allowed to unambiguously identify the residue E449 as the nucleophile residue involved in the retaining mechanism of this GH51 arabinofuranosidase. 1H NMR analysis was applied for the identification of the products and the assignement of their anomeric configuration.

  20. Laboratory evaluation of the hazard to wood mice, Apodemus sylvaticus, from the agricultural use of methiocarb molluscicide pellets

    SciTech Connect (OSTI)

    Tarrant, K.A.; Westlake, G.E.

    1988-01-01

    Laboratory studies have been carried out to determine the toxicity of methiocarb pellets to wild trapped wood mice in order to provide some background data prior to any further evaluation of hazard in the field. In this study, wood mice were exposed to dry and to dampened methiocarb pellets in order to reproduce field trial application conditions. Field observations of methiocarb pellets indicate that the physical character changes under dry and wet weather conditions. This may affect their relative attractiveness and potential toxicity to wood mice. The laboratory assessment of exposed wood mice included measurement of brain esterase activities, methiocarb residues in selected mouse tissue, carcasses, and histological evaluation of kidney, liver and lungs.

  1. EIS-0163-S: Supplemental EIS/1993 Interim Columbia and Snake Rivers Flow Improvement Measures for Salmon

    Broader source: Energy.gov [DOE]

    The U.S. Army Corps of Engineers – Walla Walla District has prepared this statement to assess alternatives to improve flows of water in the lower Columbia-Snake rivers in 1993 and future years to assist the migration of juvenile and adult anadromous fish past eight hydropower dams. The U.S. Department of Energy’s Bonneville Power Administration served as a cooperating agency in developing this supplement due to its key role in direct operation of the integrated and coordinated Columbia-Snake River System, and adopted this statement in March of 1993. This statement supplements the 1992 Columbia River Salmon Flow Measures Options Analysis Environmental Impact Statement, which evaluated ways to alter water management operations in 1992 on the lower Columbia and Snake rivers to enhance the survival of wild Snake River salmon.

  2. Effects of polychlorinated biphenyls and nutritional restriction on barbituate-induced sleeping times and selected blood characteristics in raccoons (Procyon lotor)

    SciTech Connect (OSTI)

    Montz, W.E.; Card, W.C.; Kirkpatrick, R.L.

    1982-05-01

    Hepatic microsomal enzyme activity was induced in wild-trapped raccoons (Procyon lotor) and selected blood characteristics were measured in an effort to detect responses due to PCB ingestion, nutritional restriction, and their interactions. Barbiturate-induced sleeping times were used as an index of hepatic microsomal activity because they have been used reliably by other workers. Blood characteristics examined in the study were nonesterified fatty acids (NEFA), cholesterol, and three ketone bodies (D-(-)-3-hydroxybutyrate, acetoacetate, and acetone). Results show a reduction in sleeping times, elevated NEFA and D-(-)-3-hydroxybutyrate concentrations, and lower cholesterol concentrations in PCB-treated groups. A highly significant interaction between PCB treatment and nutritional restriction was observed in acetoacetate concentrations. (JMT)

  3. Lipidomic and proteomic analysis of Caenorhabditis elegans lipid droplets and identification of ACS-4 as a lipid droplet-associated protein

    SciTech Connect (OSTI)

    Vrablik, Tracy L.; Petyuk, Vladislav A.; Larson, Emily M.; Smith, Richard D.; Watts, Jennifer

    2015-06-27

    Lipid droplets are cytoplasmic organelles that store neutral lipids for membrane synthesis and energy reserves. In this study, we characterized the lipid and protein composition of purified C. elegans lipid droplets. These lipid droplets are composed mainly of triacylglycerols, surrounded by a phospholipid monolayer composed primarily of phosphatidylcholine and phosphatidylethanolamine. The fatty acid composition of the triacylglycerols was rich in fatty acid species obtained from the dietary E. coli, including cyclopropane fatty acids and cis-vaccenic acid. Unlike other organisms, C. elegans lipid droplets contain very little cholesterol or cholesterol esters. Comparison of the lipid droplet proteomes of wild type and high-fat daf-2 mutant strains shows a relative decrease of MDT-28 abundance in lipid droplets isolated from daf-2 mutants. Functional analysis of lipid droplet proteins identified in our proteomic studies indicated an enrichment of proteins required for growth and fat homeostasis in C. elegans.

  4. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    SciTech Connect (OSTI)

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  5. Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis

    SciTech Connect (OSTI)

    Pomraning, Kyle R.; Wei, Siwei; Karagiosis, Sue A.; Kim, Young-Mo; Dohnalkova, Alice; Arey, Bruce W.; Bredeweg, Erin L.; Orr, Galya; Metz, Thomas O.; Baker, Scott E.

    2015-04-23

    Yarrowia lipolytica is an oleaginous ascomycete yeast that accumulates large amounts of lipids and has potential as a biofuel producing organism. Despite a growing scientific literature focused on lipid production by Y. lipolytica, there remain significant knowledge gaps regarding the key biological processes involved. We applied a combination of metabolomic and lipidomic profiling approaches as well as microscopic techniques to identify and characterize the key pathways involved in de novo lipid accumulation from glucose in batch cultured, wild-type Y. lipolytica. We found that lipids accumulated rapidly and peaked at 48 hours during the five day experiment, concurrent with a shift in amino acid metabolism. We also report that Y. lipolytica secretes disaccharides early in batch culture and reabsorbs them when extracellular glucose is depleted. Exhaustion of extracellular sugars coincided with thickening of the cell wall, suggesting that genes involved in cell wall biogenesis may be a useful target for improving the efficiency of lipid producing yeast strains.

  6. National Uranium Resource Evaluation: Wells Quadrangle, Nevada, Idaho, and Utah

    SciTech Connect (OSTI)

    Proffitt, J.L.; Mayerson, D.L.; Parker, D.P.; Wolverson, N.; Antrim, D.; Berg, J.; Witzel, F.

    1982-08-01

    The Wells 2/sup 0/ Quadrangle, Nevada, Idaho, and Utah, was evaluated using National Uranium Resource Evaluation criteria to delineate areas favorable for uranium deposits. Our investigation has resulted in the delineation of areas that contain Tertiary sedimentary rocks favorable for hydroallogenic deposits in the Mountain City area (Favorable Area A) and in the Oxley Peak area north of Wells (Favorable Area B). Environments considered to be unfavorable for uranium deposits include Tertiary felsic volcanic, felsic plutonic, intermediate to mafic volcanic, Paleozoic and Mesozoic sedimentary rocks, Precambrian rocks, and most Tertiary sedimentary rocks located outside the favorable areas. Present-day basins are unevaluated environments because of a paucity of adequate outcrop and subsurface data. However, the scarce data indicate that some characteristics favorable for uranium deposits are present in the Susie Creek-Tule Valley-Wild Horse basin, the Contact-Granite Range-Tijuana John stocks area, the Charleston Reservoir area, and the Wells-Marys River basin.

  7. Determining Home Range and Preferred Habitat of Feral Horses on the Nevada National Security Site Using Geographic Information Systems

    SciTech Connect (OSTI)

    Burns, Ashley V.

    2014-05-30

    Feral horses (Equus caballus) are free-roaming descendants of domesticated horses and legally protected by the Wild and Free-Roaming Horses and Burros Act of 1971, which mandates how feral horses and burros should be managed and protected on federal lands. Using a geographic information system to determine the home range and suitable habitat of feral horses on the federally managed Nevada National Security Site can enable wildlife biologists in making best management practice recommendations. Home range was estimated at 88.1 square kilometers. Site suitability was calculated for elevation, forage, slope, water presence and horse observations. These variables were combined in successive iterations into one polygon. Suitability rankings established that 85 square kilometers are most suitable habitat, with 2,052 square kilometers of good habitat 1,252 square kilometers of fair habitat and 122 square kilometers of least suitable habitat.

  8. Identifying Event Impacts by Monitoring the News Media

    SciTech Connect (OSTI)

    Patton, Robert M; Potok, Thomas E

    2008-01-01

    Assessing the potential property and social impacts of an event, such as tornado or wildfire, continues to be a challenging research area. From financial markets to disaster management to epidemiology, the importance of understanding the impacts that events create cannot be understated. Our work describes an approach to fuse information from multiple sources, then to analyze the information cycles to identify prior temporal patterns related to the impact of an event. This approach is then applied to the analysis of news reports from multiple news sources pertaining to several different natural disasters. Results show that our approach can project the severity of the impacts of certain natural disasters, such as heat waves on droughts and wild fires. In addition, results show that specific types of disaster consistently produce similar impacts when each time they occur.

  9. Waste characterization study for the Kemp's Ridley sea turtle. Technical memo

    SciTech Connect (OSTI)

    Malone, R.F.; Guarisco, M.

    1988-02-01

    The Kemp's Ridley sea turtle, Lepidochelys kempi, is an endangered species. The National Marine Fisheries Service's Head Start program is part of an international operation to save the turtles from extinction. Under the Head Start program, eggs from the Ridley's only known wild nesting beach at Rancho Nuevo in Mexico are transported to Padre Island on the Texas coast to be hatched. The head start enables the turtles to develop a survival advantage. The principal objective was to develop baseline waste-characterization data required to design a waste-water treatment scheme for the Galveston Head Start facility. As a secondary objective, preliminary testing of some filtration components was undertaken to determine which units were most appropriate for inclusion in a wastewater treatment scheme.

  10. Economic evaluation of rural woodlots in a developing country: Tanzania

    SciTech Connect (OSTI)

    Kihiyo, V.B.M.S.

    1996-03-01

    Rural areas in developing countries use wood as their main source of energy. Previously, wood has been obtained free from natural forests and woodlands. The pressure of increased demand through population growth, and the fact that natural trees take longer to grow, has made this resource scarce. Thus, raising trees in woodlots has been adopted as the solution to its shortage in the wild. However, growing trees in woodlots will inevitably require resources in terms of capital, land and manpower. Economic evaluation becomes necessary to ascertain that these resources are used economically. This paper dwells on some of the salient features of the economic evaluation of woodlots, such as interest rates, shadow prices of factors of production, social opportunity, cost of capital and sensitivity analysis of such woodlots in a developing country such as Tanzania. 19 refs., 5 tabs.

  11. Sabin-to-Mahoney Transition Model of Quasispecies Replication

    Energy Science and Technology Software Center (OSTI)

    2009-05-31

    Qspp is an agent-based stochastic simulation model of the Poliovirus Sabin-to-Mahoney transition. This code simulates a cell-to-cell model of Poliovirus replication. The model tracks genotypes (virus genomes) as they are replicated in cells, and as the cells burst and release particles into the medium of a culture dish. An inoculum is then taken from the pool of virions and is used to inoculate cells on a new dish. This process repeats. The Sabin genotype comprisesmore » the initial inoculum. Nucleotide positions that match the Sabin1 (vaccine strain) and Mahoney (wild type) genotypes, as well as the neurovirulent phenotype (from the literature) are enumerated as constants.« less

  12. Comparative Survival Study (CSS) of Hatchery PIT-tagged Spring/Summer Chinook; Migration Years 1997-2002 Mark/Recapture Activities and Bootstrap Analysis, 2003-2004 Biennial Report.

    SciTech Connect (OSTI)

    Berggren, Thomas J.; Franzoni, Henry; Basham, Larry R.

    2003-11-01

    The Comparative Survival Study (CSS) was initiated in 1996 as a multi-year program of the fishery agencies and tribes to estimate survival rates over different life stages for spring and summer Chinook (hereafter, Chinook) produced in major hatcheries in the Snake River basin and from selected hatcheries in the lower Columbia River. Much of the information evaluated in the CSS is derived from fish tagged with Passive Integrated Transponder (PIT) tags. A comparison of survival rates of Chinook marked in two different regions (which differ in the number of dams Chinook have to migrate through) provides insight into the effects of the Snake/Columbia hydroelectric system (hydrosystem). The CSS also compares the smolt-to-adult survival rates (SARs) for Snake River Chinook that were transported versus those that migrated in-river to below Bonneville Dam. Additional comparisons can be made within in-river experiences as well as comparison between the different collector projects from which smolts are transported. CSS also compares survival rates for wild Snake River spring and summer Chinook. These comparisons generate information regarding the relative effects of the current management actions used to recover this listed species. Scientists and managers have recently emphasized the importance of delayed hydrosystem mortality to long-term management decisions. Delayed hydrosystem mortality may be related to the smolts experience in the Federal Columbia River Power System, and could occur for both smolts that migrate in-river and smolts that are transported. The CSS PIT tag information on in-river survival rates and smolt-to-adult survival rates (SARs) of transported and in-river fish are relevant to estimation of ''D'', which partially describes delayed hydrosystem mortality. The parameter D is the differential survival rate of transported fish relative to fish that migrate in-river, as measured from below Bonneville Dam to adults returning to Lower Granite Dam. When D

  13. Sandwiched Rnyi divergence satisfies data processing inequality

    SciTech Connect (OSTI)

    Beigi, Salman [School of Mathematics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5746, Tehran (Iran, Islamic Republic of)] [School of Mathematics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5746, Tehran (Iran, Islamic Republic of)

    2013-12-15

    Sandwiched (quantum) ?-Rnyi divergence has been recently defined in the independent works of Wilde et al. [Strong converse for the classical capacity of entanglement-breaking channels, preprint http://arxiv.org/abs/arXiv:1306.1586 (2013)] and Mller-Lennert et al. [On quantum Rnyi entropies: a new definition, some properties and several conjectures, preprint http://arxiv.org/abs/arXiv:1306.3142v1 (2013)]. This new quantum divergence has already found applications in quantum information theory. Here we further investigate properties of this new quantum divergence. In particular, we show that sandwiched ?-Rnyi divergence satisfies the data processing inequality for all values of ? > 1. Moreover we prove that ?-Holevo information, a variant of Holevo information defined in terms of sandwiched ?-Rnyi divergence, is super-additive. Our results are based on Hlder's inequality, the Riesz-Thorin theorem and ideas from the theory of complex interpolation. We also employ Sion's minimax theorem.

  14. Real-Time Water Quality Monitoring and Habitat Assessment in theSan Luis National Wildlife Refuge

    SciTech Connect (OSTI)

    Quinn, Nigel W.T.; Hanlon, Jeremy S.; Burns, Josephine R.; Stromayer, Karl A.K.; Jordan, Brandon M.; Ennis, Mike J.; Woolington,Dennis W.

    2005-08-28

    The project report describes a two year experiment to control wetland drainage to the San Joaquin River of California from the San Luis National Wildlife Refuge using a decision support system for real-time water quality management. This system required the installation and operation of one inlet and three drainage flow and water quality monitoring stations which allowed a simple mass balance model to be developed of the seasonally managed wetlands in the study area. Remote sensing methods were developed to document long-term trends in wetland moist soil vegetation and soil salinity in response to management options such as delaying the initiation of seasonal wetland drainage. These environmental management tools provide wetland managers with some of the tools necessary to improve salinity conditions in the San Joaquin River and improve compliance with State mandated salinity objectives without inflicting long-term harm on the wild fowl habitat resource.

  15. Constraints on the Formation Age of Cometary Material from the NASA Stardust Mission

    SciTech Connect (OSTI)

    Matzel, J; Ishii, H; Joswiak, D; Hutcheon, I; Bradley, J; Brownlee, D; Weber, P K; Teslich, N; Matrajt, G; McKeegan, K; MacPherson, G

    2009-11-13

    We measured the {sup 26}Al-{sup 26}Mg isotope systematics of a {approx} 5-micrometer refractory particle, Coki, returned from comet 81P/Wild 2 in order to relate the time scales of formation of cometary inclusions to their meteoritic counterparts. The data show no evidence of radiogenic {sup 26}Mg and define an upper limit to the abundance of {sup 26}Al at the time of particle formation: {sup 26}Al/{sup 27}Al < 1 x 10-5. The absence of {sup 26}Al indicates that Coki formed >1.7 million years after the oldest solids in the solar system, calcium- and aluminum-rich inclusions (CAIs). The data suggest that high-temperature inner solar system material formed, was subsequently transferred to the Kuiper Belt, and was incorporated into comets several million years after CAI formation.

  16. Genetic manipulation of lignin reduces recalcitrance and improves biomass ethanol production from switchgrass

    SciTech Connect (OSTI)

    Hamilton, Choo Yieng; Fu, Chunxiang; Xiao, Xirong; Ge, Yaxin; Chen, Fang; Bouton, Joseph; Foston, Marcus; Dixon, Richard A; Wang, Zeng-Yu; Mielenz, Jonathan R

    2011-01-01

    Switchgrass is a leading dedicated bioenergy feedstock because it is a native, high yielding, perennial prairie grass with broad cultivation range and low agronomic input requirements. Biomass conversion research has developed pilot scale processes for production of ethanol and other alcohols but they remain costly primarily due to the intrinsic recalcitrance of biomass. We show here that switchgrass genetic modification can produce normal plants that have reduced thermochemical and enzymatic recalcitrance. Downregulation of the switchgrass caffeic O-methyltransferase gene decreases lignin content modestly, reduces the syringyl to guaiacyl lignin monomer ratio and increases the ethanol yield by up to a third using conventional biomass fermentation processes. The downregulated lines have wild-type biomass yields but require reduced pretreatment severity and 300-400% lower cellulase dosages for equivalent product yields significantly lowering processing costs. Alternately, our modified transgenic switchgrass lines should yield significantly more fermentation chemicals per hectare under identical process conditions.

  17. Optimal measurement of surface shortwave irradiance using current instrumentation -- the ARM experience

    SciTech Connect (OSTI)

    Michalsky, J.; Rubes, M.; Stoffel, T.; Wesley, M.; Splitt, M.; DeLuisi, J.

    1997-03-01

    Shortwave (solar) measurements of surface irradiance for clear sky conditions disagree with a number of different models. Betts used the European Center for Medium-range Forecasts (ECMWF) shortwave model to calculate surface irradiance that were 5-10 percent higher than measurements. Wild used a different formulation of the ECMWF shortwave model, but found that the model overpredicted clear-sky shortwave and average of 3 percent. Ding and Wang used data from the Atmospheric Radiation Measurement (ARM) program and found that the GENESIS GCM shortwave model, likewise, overpredicted clear-sky irradiance by about 4 percent. To help resolve the measurement dilemma, reference instruments were deployed in April 1996 at the Southern Great Plains ARM site central facility very near the shortwave measurements. The rest of the paper describes the experiment undertaken to ascertain total horizontal shortwave irradiance at the surface, including a separation of the direct normal and diffuse horizontal components. Results and a discussion of same concludes the paper.

  18. Monitoring the Reproductive Success of Naturally Spawning Hatchery and Natural Spring Chinook Salmon in the Wenatchee River, 2008-2009 Progress Report.

    SciTech Connect (OSTI)

    Ford, Michael J.; Williamson, Kevin S.

    2009-05-28

    We investigated differences in the statistical power to assign parentage between an artificially propagated and wild salmon population. The propagated fish were derived from the wild population, and are used to supplement its abundance. Levels of genetic variation were similar between the propagated and wild groups at 11 microsatellite loci, and exclusion probabilities were >0.999999 for both groups. The ability to unambiguously identify a pair of parents for each sampled progeny was much lower than expected, however. Simulations demonstrated that the proportion of cases the most likely pair of parents were the true parents was lower for propagated parents than for wild parents. There was a clear relationship between parentage assignment ability and the degree of linkage disequilibrium, the estimated effective number of breeders that produced the parents, and the size of the largest family within the potential parents. If a stringent threshold for parentage assignment was used, estimates of relative fitness were biased downward for the propagated fish. The bias appeared to be largely eliminated by either fractionally assigning progeny among parents in proportion to their likelihood of parentage, or by assigning progeny to the most likely set of parents without using a statistical threshold. We used a DNA-based parentage analysis to measure the relative reproductive success of hatchery- and natural-origin spring Chinook salmon in the natural environment. Both male and female hatchery-origin fish produced far fewer juvenile progeny per parent when spawning naturally than did natural origin fish. Differences in age structure, spawning location, weight and run timing were responsible for some of the difference in fitness. Male size and age had a large influence on fitness, with larger and older males producing more offspring than smaller or younger individuals. Female size had a significant effect on fitness, but the effect was much smaller than the effect of size on

  19. Distribution of Polycyclic Aromatic Hydrocarbons in Soils and Terrestrial Biota After a Spill of Crude Oil in Trecate, Italy

    SciTech Connect (OSTI)

    Brandt, Charles A. ); Becker, James M. ); Porta, Augusto C.

    2001-12-01

    Following a large blowout of crude oil in northern Italy in 1994, the distribution of polyaromatic hydrocarbons (PAHs) was examined over time and space in soils, uncultivated wild vegetation, insects, mice, and frogs in the area. Within 2 y of the blowout, PAH concentrations declined to background levels over much of the area where initial concentrations were within an order of magnitude above background, but had not declined to background in areas where starting concentrations exceeded background by two orders of magnitude. Octanol-water partitioning and extent of alkylation explained much of the variance in uptake of PAHs by plants and animals. Lower Kow PAHs and higher-alkylated PAHs had higher soil-to-biota accumulation factors (BSAFs) than did high-Kow and unalkylated forms. BSAFs for higher Kow PAHs were very low for plants, but much higher for animals, with frogs accumulating more of these compounds than other species.

  20. A novel approach to make homogeneous protease-stable monovalent streptavidin

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhang, M.; Shao, J; Xiao, J.; Deng, W.; Yu, H.

    2015-06-11

    The interaction between the tetramer streptavidin and biotin is recognized as one of the strongest non-covalent associations. Owing to the tight and specific binding, the streptavidin-biotin system has been used widely for bimolecular labeling, purification, immobilization, and even for targeted delivery of therapeutics drugs. Here, we report a novel approach to make homogeneous monovalent tetramer streptavidin. The purified monovalent protein showed both thermal stability and protease stability. Unexpectedly, we found that two proteases, Proteinase K (PK) and Subtilisin (SU), can efficiently remove the His8-tag from the wild-type subunit without affecting the tetramer architecture of monovalent streptavidin, thus making it moremore » homogeneous. In addition, crystallization was performed to assure the homogeneity of the monovalent protein prepared. Overall, monovalent streptavidin shows increased homogeneity and will likely be valuable for many future applications in a wide range of research areas.« less

  1. Molecular ageing: Free radical initiated epimerization of thymopentin A case study

    SciTech Connect (OSTI)

    Sheykhkarimli, Dayag; Choo, Ken-Loon; Owen, Michael; Csizmadia, Imre G.; Fiser, Bla; Jjrt, Balzs; Viskolcz, Bla

    2014-05-28

    The epimerization of amino acid residues increases with age in living organisms. In the present study, the structural consequences and thermodynamic functions of the epimerization of thymopentin (TP-5), the active site of the thymic hormone thymopoietin, were studied using molecular dynamics and density functional theory methods. The results show that free radical-initiated D-amino acid formation is energetically favoured (?130 kJmol{sup ?1}) for each residue and induces significant changes to the peptide structure. In comparison to the wild-type (each residue in the L-configuration), the radius of gyration of the D-Asp{sup 3} epimer of the peptide decreased by 0.5 , and disrupted the intramolecular hydrogen bonding of the native peptide. Beyond establishing important structural, energetic and thermodynamic benchmarks and reference data for the structure of TP-5, these results disseminate the understanding of molecular ageing, the epimerization of amino acid residues.

  2. Mapping site-specific endonuclease binding to DNA by direct imaging with AFM

    SciTech Connect (OSTI)

    Allison, D.P.; Thundat, T.; Doktycz, M.J.; Kerper, P.S.; Warmack, R.J.; Modrich, P.; Isfort, R.J.

    1995-12-31

    Physical mapping of DNA can be accomplished by direct AFM imaging of site specific proteins bound to DNA molecules. Using Gln-111, a mutant of EcoRI endonuclease with a specific affinity for EcoRI sites 1,000 times greater than wild type enzyme but with cleavage rate constants reduced by a factor of 10{sup 4}, the authors demonstrate site-specific mapping by direct AFM imaging. Images are presented showing specific-site binding of Gln-111 to plasmids having either one (pBS{sup +}) or two (pMP{sup 32}) EcoRI sites. Identification of the Gln-111/DNA complex is greatly enhanced by biotinylation of the complex followed by reaction with streptavidin gold prior to imaging. Image enhancement coupled with improvements in the preparation techniques for imaging large DNA molecules, such as lambda DNA (47 kb), has the potential to contribute to direct AFM restriction mapping of cosmid-sized genomic DNAs.

  3. Hood River and Pelton Ladder Evaluation Studies, Annual Report 2000-2001.

    SciTech Connect (OSTI)

    Olsen, Erik

    2009-09-01

    The Bonneville Power Administration (BPA) funded the development of two master plans which outline the rationale, and general approach, for implementing a defined group of projects that are an integral part of a comprehensive watershed goal to 'Protect, enhance and restore wild and natural populations of anadromous and resident fish within the Hood River Subbasin'. The Hood River Production Master Plan and the Pelton Ladder Master Plan were completed in 1991 and subsequently approved by the Northwest Power Planning Council in 1992. Action items identified in the two master plans, as well as in a later document entitled 'Hood River/Pelton Ladder Master Agreement' (ODFW and CTWSRO Undated), are designed to achieve two biological fish objectives: (1) to increase production of wild summer and winter steelhead (Oncorhynchus mykiss) to levels commensurate with the subbasins current carrying capacity and (2) re-establishing a self-sustaining population of spring chinook salmon (Oncorhynchus tshawytscha). Numerical fish objectives for subbasin escapement, spawner escapement, and subbasin harvest are defined for each of these species in Coccoli (2000). Several projects are presently funded by the BPA to achieve the Hood River subbasin's numerical fish objectives for summer and winter steelhead and spring chinook salmon. They include BPA project numbers 1998-021-00 (Hood River Fish Habitat), 1998-053-03 (Hood River Production Program - CTWSRO: M&E), 1998-053-07 (Parkdale Fish Facility), 1998-053-08 (Powerdale/Oak Springs O&M), and 1998-053-12 (Hood River Steelhead Genetics Study). Collectively, they are implemented under the umbrella of what has come to be defined as the Hood River Production Program (HRPP). The HRPP is jointly implemented by the Oregon Department of Fish and Wildlife (ODFW) and The Confederated Tribes of the Warm Springs Reservation of Oregon (CTWSRO). Strategies for achieving the HRPP's biological fish objectives for the Hood River subbasin were initially

  4. Transposable Elements and Genetic Instabilities in Crop Plants

    DOE R&D Accomplishments [OSTI]

    Burr, B.; Burr, F.

    1981-04-10

    Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

  5. Identification of the nucleophile catalytic residue of GH51 α-l-arabinofuranosidase from Pleurotus ostreatus

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Amore, Antonella; Iadonisi, Alfonso; Vincent, Florence; Faraco, Vincenza

    2015-12-21

    In this paper, the recombinant α-l-arabinofuranosidase from the fungus Pleurotus ostreatus (rPoAbf) was subjected to site-directed mutagenesis in order to identify the catalytic nucleophile residue. Based on bioinformatics and homology modelling analyses, E449 was revealed to be the potential nucleophilic residue. Thus, the mutant E449G of PoAbf was recombinantly expressed in Pichia pastoris and its recombinant expression level and reactivity were investigated in comparison to the wild-type. The design of a suitable set of hydrolysis experiments in the presence or absence of alcoholic arabinosyl acceptors and/or formate salts allowed to unambiguously identify the residue E449 as the nucleophile residue involvedmore » in the retaining mechanism of this GH51 arabinofuranosidase. 1H NMR analysis was applied for the identification of the products and the assignement of their anomeric configuration.« less

  6. Kelt Reconditioning: A Research Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss), 2002 Annual Report.

    SciTech Connect (OSTI)

    Hatch, Douglas R.; Branstetter, Ryan; Blodgett, Joe

    2003-07-01

    Repeat spawning is a life history strategy that is expressed by some species from the family Salmonidae. Rates of repeat spawning for post-development Columbia River steelhead Oncorhynchus mykiss populations range from 1.6 to 17%. It is expected that currently observed iteroparity rates for wild steelhead in the Basin are severely depressed due to development and operation of the hydropower system and various additional anthropogenic factors. Increasing the natural expression of historical repeat spawning rates using fish culturing means could be a viable technique to assist the recovery of depressed steelhead populations. Reconditioning is the process of culturing post-spawned fish (kelts) in a captive environment until they are able to reinitiate feeding, growth, and again develop mature gonads. Kelt reconditioning techniques were initially developed for Atlantic salmon Salmo salar and sea-trout S. trutta. The recent Endangered Species Act listing of many Columbia Basin steelhead populations has prompted interest in developing reconditioning methods for wild steelhead populations within the Basin. To test kelt steelhead reconditioning as a potential recovery tool, we captured wild emigrating steelhead kelts from the Yakima River and evaluated reconditioning (short and long-term) success and diet formulations at Prosser Hatchery on the Yakima River. Steelhead kelts from the Yakima River were collected at the Chandler Juvenile Evaluation Facility (CJEF, located at Yakima River kilometer 48) from March 12 to June 13, 2002. In total, 899 kelts were collected for reconditioning at Prosser Hatchery. Captive specimens represented 19.8% (899 of 4,525) of the entire 2001-2002 Yakima River wild steelhead population, based on fish ladder counts at Prosser Dam. Kelts were reconditioned in circular tanks and were fed freeze-dried krill, Moore-Clark pellets, altered Moore-Clark pellets (soaked in krill extract and dyed), or a combination of the altered Moore

  7. Kelt Reconditioning: A Research Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss), 2003 Annual Report.

    SciTech Connect (OSTI)

    Hatch, Douglas R.; Branstetter, Ryan; Blodgett, Joe

    2004-03-01

    Repeat spawning is a life history strategy that is expressed by some species from the family Salmonidae. Rates of repeat spawning for post-development Columbia River steelhead Oncorhynchus mykiss populations range from 1.6 to 17%. It is expected that currently observed iteroparity rates for wild steelhead in the Basin are severely depressed due to development and operation of the hydropower system and various additional anthropogenic factors. Increasing the natural expression of historical repeat spawning rates using fish culturing methods could be a viable technique to assist the recovery of depressed steelhead populations. Reconditioning is the process of culturing post-spawned fish (kelts) in a captive environment until they are able to reinitiate feeding, growth, and redevelop mature gonads. Kelt reconditioning techniques were initially developed for Atlantic salmon Salmo salar and sea-trout S. trutta. The recent Endangered Species Act listing of many Columbia Basin steelhead populations has prompted interest in developing reconditioning methods for wild steelhead populations within the Basin. To test kelt steelhead reconditioning as a potential recovery tool, we captured wild emigrating steelhead kelts from the Yakima River and evaluated reconditioning (short and long-term) success and diet formulations at Prosser Hatchery on the Yakima River. Steelhead kelts from the Yakima River were collected at the Chandler Juvenile Monitoring Facility (CJMF, located on the Yakima River at river kilometer 75.6) from 12 March to 28 May 2003. In total, 690 kelts were collected for reconditioning at Prosser Hatchery. Captive specimens represented 30.8% (690 of 2,235) of the entire 2002-2003 Yakima River wild steelhead population, based on fish ladder counts at Prosser Dam. All steelhead kelts were reconditioned in circular tanks, fed freeze-dried krill and received hw-wiegandt multi vit dietary supplement; long-term steelhead kelts also received Moore-Clark pellets

  8. Behavioural response of juvenile Chinook salmon Oncorhynchus tshawytscha during a sudden temperature increase and implications for survival

    SciTech Connect (OSTI)

    Bellgraph, Brian J.; McMichael, Geoffrey A.; Mueller, Robert P.; Monroe, Jennifer L.

    2010-01-01

    The behaviours of juvenile Chinook salmon Oncorhynchus tshawytscha were evaluated during a temperature increase from 8.8 to 23.2°C, which was designed to simulate unique thermal conditions present in a hydroelectric reservoir. The percent of fish with an active swimming behaviour increased from 26 to 93 % and mean opercular beat rates increased from 76 to 159 beats per minute between basal and maximum temperatures. Fish equilibrium did not change significantly throughout the experiment and relatively little mortality (12 %) occurred. Thermal stress is likely incurred by juvenile salmon experiencing a temperature change of this magnitude; however, stress induced in this study was primarily sublethal. Behavioural changes accompanying thermal stress (e.g., erratic swimming) may increase predation potential in the wild despite being sublethal during laboratory experiments.

  9. Kelt Reconditioning: A Research Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss), 2005 Annual Report.

    SciTech Connect (OSTI)

    Branstetter, Ryan; Whiteaker, John; Hatch, Douglas R.

    2006-01-01

    Iteroparity, the ability to repeat spawn, is a natural life history strategy that is expressed by some species from the family Salmonidae. Estimated rates of repeat spawning for post-development Columbia River steelhead Oncorhynchus mykiss populations range from 1.6 to 17%. It is expected that currently observed iteroparity rates for wild steelhead in the Basin are severely depressed due to development and operation of the hydropower system and various additional anthropogenic factors. Increasing the current expression of repeat spawning rates using fish culturing methods could be a viable technique to assist the recovery of depressed steelhead populations, and could help reestablish this naturally occurring life history trait. Reconditioning is the process of culturing post-spawned fish (kelts) in a captive environment until they are able to reinitiate feeding, growth, and redevelop mature gonads. Reconditioning techniques were initially developed for Atlantic salmon Salmo salar and sea-trout S. trutta. The recent Endangered Species Act listing of many Columbia River Basin steelhead populations has prompted interest in developing reconditioning methods for wild steelhead populations within the Basin. To test kelt steelhead reconditioning as a potential recovery tool, wild emigrating steelhead kelts were placed into one of four study groups (in river release, direct capture and transport, short-term reconditioning, or long-term reconditioning). Steelhead kelts from the Yakima River were collected at the Chandler Juvenile Monitoring Facility (CJMF, located on the Yakima River at river kilometer 75.6) from 11 March to 23 June 2005. In total, 519 kelts were collected for reconditioning at Prosser Hatchery. Captive specimens represented 15.0% (519 of 3,451) of the entire 2004-2005 Yakima River wild steelhead population, based on fish ladder counts at Prosser Dam. Steelhead kelts were reconditioned in 20-foot circular tanks, and fed freeze-dried krill initially (first 2

  10. Kelt Reconditioning: A Research Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss), 2005-2006 Annual Report.

    SciTech Connect (OSTI)

    Branstetter, Ryan; Whiteaker, John; Hatch, Douglas R.

    2006-12-01

    Iteroparity, the ability to repeat spawn, is a natural life history strategy that is expressed by some species from the family Salmonidae. Estimated rates of repeat spawning for post-development Columbia River steelhead Oncorhynchus mykiss populations range from 1.6 to 17%. It is expected that currently observed iteroparity rates for wild steelhead in the Basin are severely depressed due to development and operation of the hydropower system and various additional anthropogenic factors. Increasing the current expression of repeat spawning rates using fish culturing methods could be a viable technique to assist the recovery of depressed steelhead populations, and could help reestablish this naturally occurring life history trait. Reconditioning is the process of culturing post-spawned fish (kelts) in a captive environment until they are able to reinitiate feeding, growth, and redevelop mature gonads. Reconditioning techniques were initially developed for Atlantic salmon Salmo salar and sea-trout S. trutta. The recent Endangered Species Act listing of many Columbia River Basin steelhead populations has prompted interest in developing reconditioning methods for wild steelhead populations within the Basin. To test kelt steelhead reconditioning as a potential recovery tool, wild emigrating steelhead kelts were placed into one of four study groups (in river release, direct capture and transport, short-term reconditioning, or long-term reconditioning). Steelhead kelts from the Yakima River were collected at the Chandler Juvenile Monitoring Facility (CJMF, located on the Yakima River at river kilometer 75.6) from 7 March to 8 June 2006. In total, 348 kelts were collected for reconditioning at Prosser Hatchery. Captive specimens represented 17.0% (348 of 2,002) of the entire 2005-2006 Yakima River wild steelhead population, based on fish ladder counts at Prosser Dam. Steelhead kelts were reconditioned in 20-foot circular tanks, and fed freeze-dried krill initially (first 2

  11. Willamette Hatchery Oxygen Supplementation Studies : Annual Report 1993.

    SciTech Connect (OSTI)

    Ewing, R.D.; Ewing, S.K.; Sheahan, J.E.

    1993-11-01

    Hydropower development and operations in the Columbia River basin have caused the loss of 5 million to 11 million salmonids. An interim goal of the Northwest Power Planning Council is to reestablish these historical numbers by doubling the present adult runs from 2.5 million to 5.0 million fish. This increase in production will be accomplished through comprehensive management of both wild and hatchery fish, but artificial propagation will play a major role in the augmentation process. The current husbandry techniques in existing hatcheries require improvements that may include changes in rearing densities, addition of oxygen, removal of excess nitrogen, and improvement in raceway design. Emphasis will be placed on the ability to increase the number of fish released from hatcheries that survive to return as adults.

  12. Formation of mushrooms and lignocellulose degradation encoded in the genome sequence of Schizophyllum commune

    SciTech Connect (OSTI)

    Ohm, Robin A.; de Jong, Jan F.; Lugones, Luis G.; Aerts, Andrea; Kothe, Erika; Stajich, Jason E.; de Vries, Ronald P.; Record, Eric; Levasseur, Anthony; Baker, Scott E.; Bartholomew, Kirk A.; Coutinho, Pedro M.; Erdmann, Susann; Fowler, Thomas J.; Gathman, Allen C.; Lombard, Vincent; Henrissat, Bernard; Knabe, Nicole; Kues, Ursula; Lilly, Walt W.; Lindquist, Erika; Lucas, Susan; Magnuson, Jon K.; Piumi, Francois; Raudaskoski, Marjatta; Salamov, Asaf; Schmutz, Jeremy; Schwarze, Francis W.M.R.; van Kuyk, Patricia A.; Horton, J. Stephen; Grigoriev, Igor V.; Wosten, Han A.B.

    2010-07-12

    The wood degrading fungus Schizophyllum commune is a model system for mushroom development. Here, we describe the 38.5 Mb assembled genome of this basidiomycete and application of whole genome expression analysis to study the 13,210 predicted genes. Comparative analyses of the S. commune genome revealed unique wood degrading machinery and mating type loci with the highest number of reported genes. Gene expression analyses revealed that one third of the 471 identified transcription factor genes were differentially expressed during sexual development. Two of these transcription factor genes were deleted. Inactivation of fst4 resulted in the inability to form mushrooms, whereas inactivation of fst3 resulted in more but smaller mushrooms than wild-type. These data illustrate that mechanisms underlying mushroom formation can be dissected using S. commune as a model. This will impact commercial production of mushrooms and the industrial use of these fruiting bodies to produce enzymes and pharmaceuticals.

  13. Idaho Steelhead Monitoring and Evaluation Studies : Annual Progress Report 2007.

    SciTech Connect (OSTI)

    Copeland, Timothy; Putnam, Scott

    2008-12-01

    The goal of Idaho Steelhead Monitoring and Evaluation Studies is to collect monitoring data to evaluate wild and natural steelhead populations in the Clearwater and Salmon river drainages. During 2007, intensive population data were collected in Fish Creek (Lochsa River tributary) and Rapid River (Little Salmon River tributary); extensive data were collected in other selected spawning tributaries. Weirs were operated in Fish Creek and Rapid River to estimate adult escapement and to collect samples for age determination and genetic analysis. Snorkel surveys were conducted in Fish Creek, Rapid River, and Boulder Creek (Little Salmon River tributary) to estimate parr density. Screw traps were operated in Fish Creek, Rapid River, Secesh River, and Big Creek to estimate juvenile emigrant abundance, to tag fish for survival estimation, and to collect samples for age determination and genetic analysis. The estimated wild adult steelhead escapement in Fish Creek was 81 fish and in Rapid River was 32 fish. We estimate that juvenile emigration was 24,127 fish from Fish Creek; 5,632 fish from Rapid River; and 43,674 fish from Big Creek. The Secesh trap was pulled for an extended period due to wildfires, so we did not estimate emigrant abundance for that location. In cooperation with Idaho Supplementation Studies, trap tenders PIT tagged 25,618 steelhead juveniles at 18 screw trap sites in the Clearwater and Salmon river drainages. To estimate age composition, 143 adult steelhead and 5,082 juvenile steelhead scale samples were collected. At the time of this report, 114 adult and 1,642 juvenile samples have been aged. Project personnel collected genetic samples from 122 adults and 839 juveniles. We sent 678 genetic samples to the IDFG Eagle Fish Genetics Laboratory for analysis. Water temperature was recorded at 37 locations in the Clearwater and Salmon river drainages.

  14. Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter sulfurreducens PCA

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Qian, Chen; Johs, Alexander; Chen, Hongmei; Mann, Benjamin F.; Lu, Xia; Abraham, Paul E.; Hettich, Robert L.; Gu, Baohua

    2016-07-27

    Geobacter sulfurreducens PCA can reduce, sorb, and methylate mercury (Hg); however, the underlying biochemical mechanisms of these processes and interdependent metabolic pathways remain unknown. In this study, shotgun proteomics was used to compare global proteome profiles between wild-type G. sulfurreducens PCA and two mutant strains: a ΔhgcAB mutant, which is deficient in two genes known to be essential for Hg methylation and a ΔomcBESTZ mutant, which is deficient in five outer membrane c-type cytochromes and thus impaired in its ability for dissimilatory metal ion reduction. We were able to delineate the global response of G. sulfurreducens PCA in both mutantsmore » and identify cellular networks and metabolic pathways that were affected by the loss of these genes. Deletion of hgcAB increased the relative abundances of proteins implicated in extracellular electron transfer, including most of the c-type cytochromes, PilA-C, and OmpB, and is consistent with a previously observed increase in Hg reduction in the hgcAB mutant. Deletion of omcBESTZ was found to significantly increase relative abundances of various methyltransferases, suggesting that a loss of dissimilatory reduction capacity results in elevated activity among one-carbon metabolic pathways and thus increased methylation. We show that G. sulfurreducens PCA encodes only the folate branch of the Wood Ljungdahl pathway, and proteins associated with the folate branch were found at lower abundance in the ΔhgcAB mutant strain than the wild type. In conclusion, this observation supports the hypothesis that the function of HgcA and HgcB may be linked to one carbon metabolism through the folate branch of the Wood-Ljungdahl pathway by providing methyl groups required for Hg methylation.« less

  15. Elimination of hydrogenase post-translational modification blocks H2 production and increases ethanol yield in Clostridium thermocellum

    SciTech Connect (OSTI)

    Biswas, Ranjita; Zheng, Tianyong; Olson, Daniel G.; Lynd, Lee R; Guss, Adam M

    2015-01-01

    The native ability of Clostridium thermocellum to rapidly consume cellulose and produce ethanol makes it a leading candidate for a consolidated bioprocessing (CBP) biofuel production strategy. C. thermocellum also synthesizes lactate, formate, acetate, H2, and amino acids that compete with ethanol production for carbon and electrons. Elimination of H2 production could redirect carbon flux towards ethanol production by making more electrons available for acetyl-CoA reduction to ethanol. C. thermocellum encodes four hydrogenases and rather than delete each individually, we targeted a hydrogenase maturase gene (hydG), involved in converting the three [FeFe] hydrogenase apoenzymes into holoenzymes. Further deletion of the [NiFe] hydrogenase (ech) resulted in a mutant that functionally lacks all four hydrogenases. H2 production in hydG ech was undetectable and ethanol yield increased nearly 2-fold compared to wild type. Interestingly, mutant growth improved upon the addition of acetate, which led to increased expression of genes related to sulfate metabolism, suggesting these mutants may use sulfate as a terminal electron acceptor to balance redox reactions. Genomic analysis of hydG revealed a mutation in adhE, resulting in a strain with both NADH- and NADPH-dependent alcohol dehydrogenase activities. While this same adhE mutation is found in ethanol tolerant C. thermocellum strain E50C, hydG and hydG ech are not more ethanol tolerant than wild type, illustrating the complicated interactions between redox balancing and ethanol tolerance in C. thermocellum. The dramatic increase in ethanol production here suggests that targeting protein post-translational modification is a promising new approach for inactivation of multiple enzymes simultaneously for metabolic engineering.

  16. A combinatorial histidine scanning library approach to engineer highly pH-dependent protein switches

    SciTech Connect (OSTI)

    Murtaugh, Megan L.; Fanning, Sean W.; Sharma, Tressa M.; Terry, Alexandra M.; Horn, James R.

    2012-09-05

    There is growing interest in the development of protein switches, which are proteins whose function, such as binding a target molecule, can be modulated through environmental triggers. Efforts to engineer highly pH sensitive protein-protein interactions typically rely on the rational introduction of ionizable groups in the protein interface. Such experiments are typically time intensive and often sacrifice the protein's affinity at the permissive pH. The underlying thermodynamics of proton-linkage dictate that the presence of multiple ionizable groups, which undergo a pK{sub a} change on protein binding, are necessary to result in highly pH-dependent binding. To test this hypothesis, a novel combinatorial histidine library was developed where every possible combination of histidine and wild-type residue is sampled throughout the interface of a model anti-RNase A single domain VHH antibody. Antibodies were coselected for high-affinity binding and pH-sensitivity using an in vitro, dual-function selection strategy. The resulting antibodies retained near wild-type affinity yet became highly sensitive to small decreases in pH, drastically decreasing their binding affinity, due to the incorporation of multiple histidine groups. Several trends were observed, such as histidine 'hot-spots,' which will help enhance the development of pH switch proteins as well as increase our understanding of the role of ionizable residues in protein interfaces. Overall, the combinatorial approach is rapid, general, and robust and should be capable of producing highly pH-sensitive protein affinity reagents for a number of different applications.

  17. Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport

    SciTech Connect (OSTI)

    Wang, Zhongshan; Xiang, Quanju; Zhu, Xiaofeng; Dong, Haohao; He, Chuan; Wang, Haiyan; Zhang, Yizheng; Wang, Wenjian; Dong, Changjiang

    2014-09-26

    Highlights: • Determination of the structure of the wild-type LptB in complex with ATP and Mg{sup 2+}. • Demonstrated that ATP binding residues are essential for LptB’s ATPase activity and LPS transport. • Dimerization is required for the LptB’s function and LPS transport. • Revealed relationship between activity of the LptB and the vitality of E. coli cells. - Abstract: Lipopolysaccharide (LPS) is the main component of the outer membrane of Gram-negative bacteria, which plays an essential role in protecting the bacteria from harsh conditions and antibiotics. LPS molecules are transported from the inner membrane to the outer membrane by seven LPS transport proteins. LptB is vital in hydrolyzing ATP to provide energy for LPS transport, however this mechanism is not very clear. Here we report wild-type LptB crystal structure in complex with ATP and Mg{sup 2+}, which reveals that its structure is conserved with other nucleotide-binding proteins (NBD). Structural, functional and electron microscopic studies demonstrated that the ATP binding residues, including K42 and T43, are crucial for LptB’s ATPase activity, LPS transport and the vitality of Escherichia coli cells with the exceptions of H195A and Q85A; the H195A mutation does not lower its ATPase activity but impairs LPS transport, and Q85A does not alter ATPase activity but causes cell death. Our data also suggest that two protomers of LptB have to work together for ATP hydrolysis and LPS transport. These results have significant impacts in understanding the LPS transport mechanism and developing new antibiotics.

  18. Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection

    SciTech Connect (OSTI)

    Nakayasu, Ernesto S.; Tempel, Rebecca; Cambronne, Xiaolu A.; Petyuk, Vladislav A.; Jones, Marcus B.; Gritsenko, Marina A.; Monroe, Matthew E.; Yang, Feng; Smith, Richard D.; Adkins, Joshua N.; Heffron, Fred

    2013-09-22

    Francisella tularensis is a facultative intracellular bacterium that causes the deadly disease tularemia. Most evidence suggests that Francisella is not well recognized by the innate immune system that normally leads to cytokine expression and cell death. In previous work, we identified new bacterial factors that were hyper-cytotoxic to macrophages. Four of the identified hyper-cytotoxic strains (lpcC, manB, manC and kdtA) had an impaired lipopolysaccharide (LPS) synthesis and produced an exposed lipid A lacking the O-antigen. These mutants were not only hyper-cytotoxic but also were phagocytosed at much higher rates compared to the wild type parent strain. To elucidate the cellular signaling underlying this enhanced phagocytosis and cell death, we performed a large-scale comparative phosphoproteomic analysis of cells infected with wild-type and delta-lpcC F. novicida. Our data suggest that not only actin but also intermediate filaments and microtubules are important for F. novicida entry into the host cells. In addition, we observed differential phosphorylation of tristetraprolin (TTP), a key component of the mRNA-degrading machinery that controls the expression of a variety of genes including many cytokines. Infection with the delta-lpcC mutant induced the hyper-phosphorylation and inhibition of TTP, leading to the production of cytokines such as IL-1beta and TNF-alpha which may kill the host cells by triggering apoptosis. Together, our data provide new insights for Francisella invasion and a post-transcriptional mechanism that prevents the expression of host immune response factors that controls infection by this pathogen.

  19. Compensatory Paracrine Mechanisms That Define The Urothelial Response to Injury in Partial Bladder Outlet Obstruction

    SciTech Connect (OSTI)

    Bassuk, James; Lendvay, Thomas S.; Sweet, Robert; Han, Chang-Hee; Soygur, Tarkan; Cheng, Jan-Fang; Plaire, J. Chadwick; Charleston, Jay S.; Charleston, Lynne B.; Bagai, Shelly; Cochrane, Kimberly; Rubio, Eric; Bassuk, James A.; Fuchs, Elaine

    2007-06-21

    Diseases and conditions affecting the lower urinary tract are a leading cause of dysfunctional sexual health, incontinence, infection, and kidney failure. The growth, differentiation, and repair of the bladder's epithelial lining are regulated, in part, by fibroblast growth factor (FGF)-7 and -10 via a paracrine cascade originating in the mesenchyme (lamina propria) and targeting the receptor for FGF-7 and -10 within the transitional epithelium (urothelium). The FGF-7 gene is located at the 15q15-q21.1 locus on chromosome 15 and four exons generate a 3.852-kb mRNA. Five duplicated FGF-7 gene sequences that localized to chromosome 9 were predicted not to generate functional protein products, thus validating the use of FGF-7-null mice as an experimental model. Recombinant FGF-7 and -10 induced proliferation of human urothelial cells in vitro and transitional epithelium of wild-type and FGF-7-null mice in vivo.To determine the extent that induction of urothelial cell proliferation during the bladder response to injury is dependent on FGF-7, an animal model of partial bladder outlet obstruction was developed. Unbiased stereology was used to measure the percentage of proliferating urothelial cells between obstructed groups of wild-type and FGF-7-null mice. The stereological analysis indicated that a statistical significant difference did not exist between the two groups, suggesting that FGF-7 is not essential for urothelial cell proliferation in response to partial outlet obstruction. In contrast, a significant increase in FGF-10 expression was observed in the obstructed FGF-7-null group, indicating that the compensatory pathway that functions in this model results in urothelial repair.

  20. Statistical Survival Analysis of Fish and Wildlife Tagging Studies; SURPH.1 Manual - Analysis of Release-Recapture Data for Survival Studies, 1994 Technical Manual.

    SciTech Connect (OSTI)

    Smith, Steven G.; Skalski, John R.; Schelechte, J. Warren

    1994-12-01

    Program SURPH is the culmination of several years of research to develop a comprehensive computer program to analyze survival studies of fish and wildlife populations. Development of this software was motivated by the advent of the PIT-tag (Passive Integrated Transponder) technology that permits the detection of salmonid smolt as they pass through hydroelectric facilities on the Snake and Columbia Rivers in the Pacific Northwest. Repeated detections of individually tagged smolt and analysis of their capture-histories permits estimates of downriver survival probabilities. Eventual installation of detection facilities at adult fish ladders will also permit estimation of ocean survival and upstream survival of returning salmon using the statistical methods incorporated in SURPH.1. However, the utility of SURPH.1 far exceeds solely the analysis of salmonid tagging studies. Release-recapture and radiotelemetry studies from a wide range of terrestrial and aquatic species have been analyzed using SURPH.1 to estimate discrete time survival probabilities and investigate survival relationships. The interactive computing environment of SURPH.1 was specifically developed to allow researchers to investigate the relationship between survival and capture processes and environmental, experimental and individual-based covariates. Program SURPH.1 represents a significant advancement in the ability of ecologists to investigate the interplay between morphologic, genetic, environmental and anthropogenic factors on the survival of wild species. It is hoped that this better understanding of risk factors affecting survival will lead to greater appreciation of the intricacies of nature and to improvements in the management of wild resources. This technical report is an introduction to SURPH.1 and provides a user guide for both the UNIX and MS-Windows{reg_sign} applications of the SURPH software.

  1. Genetic disruption of KSHV major latent nuclear antigen LANA enhances viral lytic transcriptional program

    SciTech Connect (OSTI)

    Li Qiuhua; Zhou Fuchun; Ye Fengchun; Gao Shoujiang

    2008-09-30

    Following primary infection, KSHV establishes a lifelong persistent latent infection in the host. The mechanism of KSHV latency is not fully understood. The latent nuclear antigen (LANA or LNA) encoded by ORF73 is one of a few viral genes expressed during KSHV latency, and is consistently detected in all KSHV-related malignancies. LANA is essential for KSHV episome persistence, and regulates the expression of viral lytic genes through epigenetic silencing, and inhibition of the expression and transactivation function of the key KSHV lytic replication initiator RTA (ORF50). In this study, we used a genetic approach to examine the role of LANA in regulating KSHV lytic replication program. Deletion of LANA did not affect the expression of its adjacent genes vCyclin (ORF72) and vFLIP (ORF71). In contrast, the expression levels of viral lytic genes including immediate-early gene RTA, early genes MTA (ORF57), vIL-6 (ORF-K2) and ORF59, and late gene ORF-K8.1 were increased before and after viral lytic induction with 12-O-tetradecanoyl-phorbol-13-acetate and sodium butyrate. This enhanced expression of viral lytic genes was also observed following overexpression of RTA with or without simultaneous chemical induction. Consistent with these results, the LANA mutant cells produced more infectious virions than the wild-type virus cells did. Furthermore, genetic repair of the mutant virus reverted the phenotypes to those of wild-type virus. Together, these results have demonstrated that, in the context of viral genome, LANA contributes to KSHV latency by regulating the expression of RTA and its downstream genes.

  2. Isolation and characterization of two cellulose morphology mutants of Gluconacetobacter hansenii ATCC23769 producing cellulose with lower crystallinity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Deng, Ying; Nagachar, Nivedita; Fang, Lin; Luan, Xin; Catchmark, Jeffrey M.; Tien, Ming; Kao, Teh -hui; Lai, Hsin -Chih

    2015-03-19

    Gluconacetobacter hansenii, a Gram-negative bacterium, produces and secrets highly crystalline cellulose into growth medium, and has long been used as a model system for studying cellulose synthesis in higher plants. Cellulose synthesis involves the formation of β-1,4 glucan chains via the polymerization of glucose units by a multi-enzyme cellulose synthase complex (CSC). These glucan chains assemble into ordered structures including crystalline microfibrils. AcsA is the catalytic subunit of the cellulose synthase enzymes in the CSC, and AcsC is required for the secretion of cellulose. However, little is known about other proteins required for the assembly of crystalline cellulose. To addressmore » this question, we visually examined cellulose pellicles formed in growth media of 763 individual colonies of G. hansenii generated via Tn5 transposon insertion mutagenesis, and identified 85 that produced cellulose with altered morphologies. X-ray diffraction analysis of these 85 mutants identified two that produced cellulose with significantly lower crystallinity than wild type. The gene disrupted in one of these two mutants encoded a lysine decarboxylase and that in the other encoded an alanine racemase. Solid-state NMR analysis revealed that cellulose produced by these two mutants contained increased amounts of non-crystalline cellulose and monosaccharides associated with non-cellulosic polysaccharides as compared to the wild type. Monosaccharide analysis detected higher percentages of galactose and mannose in cellulose produced by both mutants. Field emission scanning electron microscopy showed that cellulose produced by the mutants was unevenly distributed, with some regions appearing to contain deposition of non-cellulosic polysaccharides; however, the width of the ribbon was comparable to that of normal cellulose. As both lysine decarboxylase and alanine racemase are required for the integrity of peptidoglycan, we propose a model for the role of peptidoglycan

  3. Structural characterization of a mixed-linkage glucan deficient mutant reveals alteration in cellulose microfibril orientation in rice coleoptile mesophyll cell walls

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Smith-Moritz, Andreia M.; Hao, Zhao; Fernández-Nino, Susana G.; Fangel, Jonatan U.; Verhertbruggen, Yves; Holman, Hoi-Ying N.; Willats, William G. T.; Ronald, Pamela C.; Scheller, Henrik V.; Heazlewood, Joshua L.; et al

    2015-08-18

    The CELLULOSE SYNTHASE-LIKE F6 (CslF6) gene was previously shown to mediate the biosynthesis of mixed-linkage glucan (MLG), a cell wall polysaccharide that is hypothesized to be tightly associated with cellulose and also have a role in cell expansion in the primary cell wall of young seedlings in grass species. We have recently shown that loss-of-function cslf6 rice mutants do not accumulate MLG in most vegetative tissues. Despite the absence of a structurally important polymer, MLG, these mutants are unexpectedly viable and only show a moderate growth compromise compared to wild type. Therefore these mutants are ideal biological systems to testmore » the current grass cell wall model. In order to gain a better understanding of the role of MLG in the primary wall, we performed in-depth compositional and structural analyses of the cell walls of 3 day-old rice seedlings using various biochemical and novel microspectroscopic approaches. We found that cellulose content as well as matrix polysaccharide composition was not significantly altered in the MLG deficient mutant. However, we observed a significant change in cellulose microfibril bundle organization in mesophyll cell walls of the cslf6 mutant. Using synchrotron source Fourier Transform Mid-Infrared (FTM-IR) Spectromicroscopy for high-resolution imaging, we determined that the bonds associated with cellulose and arabinoxylan, another major component of the primary cell walls of grasses, were in a lower energy configuration compared to wild type, suggesting a slightly weaker primary wall in MLG deficient mesophyll cells. Finally, taken together, these results suggest that MLG may influence cellulose deposition in mesophyll cell walls without significantly affecting anisotropic growth thus challenging MLG importance in cell wall expansion.« less

  4. Inhibition of SH2-domain-containing inositol 5-phosphatase (SHIP2) ameliorates palmitate induced-apoptosis through regulating Akt/FOXO1 pathway and ROS production in HepG2 cells

    SciTech Connect (OSTI)

    Gorgani-Firuzjaee, Sattar; Adeli, Khosrow; Meshkani, Reza

    2015-08-21

    The serine–threonine kinase Akt regulates proliferation and survival by phosphorylating a network of protein substrates; however, the role of a negative regulator of the Akt pathway, the SH2-domain-containing inositol 5-phosphatase (SHIP2) in apoptosis of the hepatocytes, remains unknown. In the present study, we studied the molecular mechanisms linking SHIP2 expression to apoptosis using overexpression or suppression of SHIP2 gene in HepG2 cells exposed to palmitate (0.5 mM). Overexpression of the dominant negative mutant SHIP2 (SHIP2-DN) significantly reduced palmitate-induced apoptosis in HepG2 cells, as these cells had increased cell viability, decreased apoptotic cell death and reduced the activity of caspase-3, cytochrome c and poly (ADP-ribose) polymerase. Overexpression of the wild-type SHIP2 gene led to a massive apoptosis in HepG2 cells. The protection from palmitate-induced apoptosis by SHIP2 inhibition was accompanied by a decrease in the generation of reactive oxygen species (ROS). In addition, SHIP2 inhibition was accompanied by an increased Akt and FOXO-1 phosphorylation, whereas overexpression of the wild-type SHIP2 gene had the opposite effects. Taken together, these findings suggest that SHIP2 expression level is an important determinant of hepatic lipoapotosis and its inhibition can potentially be a target in treatment of hepatic lipoapoptosis in diabetic patients. - Highlights: • Lipoapoptosis is the major contributor to the development of NAFLD. • The PI3-K/Akt pathway regulates apoptosis in different cells. • The role of negative regulator of this pathway, SHIP2 in lipoapoptosis is unknown. • SHIP2 inhibition significantly reduces palmitate-induced apoptosis in HepG2 cells. • SHIP2 inhibition prevents palmitate induced-apoptosis by regulating Akt/FOXO1 pathway.

  5. Acetaminophen-induced acute liver injury in HCV transgenic mice

    SciTech Connect (OSTI)

    Uehara, Takeki; Kosyk, Oksana; Jeannot, Emmanuelle; Bradford, Blair U.; Tech, Katherine; Macdonald, Jeffrey M.; Boorman, Gary A.; Chatterjee, Saurabh; Mason, Ronald P.; Melnyk, Stepan B.; Tryndyak, Volodymyr P.; Pogribny, Igor P.; Rusyn, Ivan

    2013-01-15

    The exact etiology of clinical cases of acute liver failure is difficult to ascertain and it is likely that various co-morbidity factors play a role. For example, epidemiological evidence suggests that coexistent hepatitis C virus (HCV) infection increased the risk of acetaminophen-induced acute liver injury, and was associated with an increased risk of progression to acute liver failure. However, little is known about possible mechanisms of enhanced acetaminophen hepatotoxicity in HCV-infected subjects. In this study, we tested a hypothesis that HCV-Tg mice may be more susceptible to acetaminophen hepatotoxicity, and also evaluated the mechanisms of acetaminophen-induced liver damage in wild type and HCV-Tg mice expressing core, E1 and E2 proteins. Male mice were treated with a single dose of acetaminophen (300 or 500 mg/kg in fed animals; or 200 mg/kg in fasted animals; i.g.) and liver and serum endpoints were evaluated at 4 and 24 h after dosing. Our results suggest that in fed mice, liver toxicity in HCV-Tg mice is not markedly exaggerated as compared to the wild-type mice. In fasted mice, greater liver injury was observed in HCV-Tg mice. In fed mice dosed with 300 mg/kg acetaminophen, we observed that liver mitochondria in HCV-Tg mice exhibited signs of dysfunction showing the potential mechanism for increased susceptibility. -- Highlights: ? Acetaminophen-induced liver injury is a significant clinical challenge. ? HCV-infected subjects may be at higher risk for acetaminophen-induced liver injury. ? We used HCV transgenics to test if liver injury due to acetaminophen is exacerbated.

  6. Effect of a C298D Mutation in CaHydA [FeFe]-Hydrogenase: Insights into the Protein-Metal Cluster Interaction by EPR and FTIR Spectroscopic Investigation

    SciTech Connect (OSTI)

    Morra, Simone; Maurelli, Sara; Chiesa, Mario; Mulder, David W.; Ratzloff, Michael W.; Giamello, Elio; King, Paul W.; Gilardi, Gianfranco; Valettia, Francesca

    2016-01-01

    A conserved cysteine located in the signature motif of the catalytic center (H-cluster) of [FeFe]-hydrogenases functions in proton transfer. This residue corresponds to C298 in Clostridium acetobutylicum CaHydA. Despite the chemical and structural difference, the mutant C298D retains fast catalytic activity, while replacement with any other amino acid caused significant activity loss. Given the proximity of C298 to the H-cluster, the effect of the C298D mutation on the catalytic center was studied by continuous wave (CW) and pulse electron paramagnetic resonance (EPR) and by Fourier transform infrared (FTIR) spectroscopies. Comparison of the C298D mutant with the wild type CaHydA by CW and pulse EPR showed that the electronic structure of the center is not altered. FTIR spectroscopy confirmed that absorption peak values observed in the mutant are virtually identical to those observed in the wild type, indicating that the H-cluster is not generally affected by the mutation. Significant differences were observed only in the inhibited state Hox-CO: the vibrational modes assigned to the COexo and Fed-CO in this state are shifted to lower values in C298D, suggesting different interaction of these ligands with the protein moiety when C298 is changed to D298. More relevant to the catalytic cycle, the redox equilibrium between the Hox and Hred states is modified by the mutation, causing a prevalence of the oxidized state. This work highlights how the interactions between the protein environment and the H-cluster, a dynamic closely interconnected system, can be engineered and studied in the perspective of designing bio-inspired catalysts and mimics.

  7. Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Biswas, Ranjita; Zheng, Tianyong; Olson, Daniel G.; Lynd, Lee R.; Guss, Adam M.

    2015-02-01

    The native ability of Clostridium thermocellum to rapidly consume cellulose and produce ethanol makes it a leading candidate for a consolidated bioprocessing (CBP) biofuel production strategy. C. thermocellum also synthesizes lactate, formate, acetate, H2, and amino acids that compete with ethanol production for carbon and electrons. Elimination of H2 production could redirect carbon flux towards ethanol production by making more electrons available for acetyl-CoA reduction to ethanol. C. thermocellum encodes four hydrogenases and rather than delete each individually, we targeted a hydrogenase maturase gene (hydG), involved in converting the three [FeFe] hydrogenase apoenzymes into holoenzymes. Further deletion of the [NiFe]more » hydrogenase (ech) resulted in a mutant that functionally lacks all four hydrogenases. H2 production in hydG ech was undetectable and ethanol yield increased nearly 2-fold compared to wild type. Interestingly, mutant growth improved upon the addition of acetate, which led to increased expression of genes related to sulfate metabolism, suggesting these mutants may use sulfate as a terminal electron acceptor to balance redox reactions. Genomic analysis of hydG revealed a mutation in adhE, resulting in a strain with both NADH- and NADPH-dependent alcohol dehydrogenase activities. While this same adhE mutation is found in ethanol tolerant C. thermocellum strain E50C, hydG and hydG ech are not more ethanol tolerant than wild type, illustrating the complicated interactions between redox balancing and ethanol tolerance in C. thermocellum. The dramatic increase in ethanol production here suggests that targeting protein post-translational modification is a promising new approach for inactivation of multiple enzymes simultaneously for metabolic engineering.« less

  8. Carbonic anhydrase activity in isolated chloroplasts of chlamydomonas reinhardtii

    SciTech Connect (OSTI)

    Katzman, G.; Togasaki, R.K. ); Marcus, Y. ); Moroney, J.V. )

    1989-04-01

    In a new assay of carbonic anhydrase, NaH{sup 14}CO{sub 3} solution at the bottom of a sealed vessel releases {sup 14}CO{sub 3} which diffuses to the top of the vessel to be assimilated by actively photosynthesizing Chlamydomonas cells. The assay is initiated by illuminating cells and stopped by turning the light off and killing the cells with acid. Enzyme activity was estimated from acid stable radioactivity above the uncatalyzed background level. With bovine carbonic anhydrase, 1.5 Wilbur Anderson Unit (WAU) can be consistantly measured at 5-6 fold above background. Sonicated whole cells of air adapted wild type (+)gave 741.1 {plus minus} 12.4 WAU/mg chl. Intact washed cells of mixotrophically grown wall-less mutant CWD(-) and a high CO2 requiring wall-less double mutant CIA-3/CW15 (-) gave 7.1 {plus minus} 1.9 and 2.8 {plus minus} 7.8 WAU/mg chl respectively. Chloroplasts isolated from CWD and CIA-3/CW15 and subsequently disrupted gave 64.0 {plus minus} 14.7 and 2.8 {plus minus} 3.2 WAU/mg chl respectively. Chloroplast sonicate from another wall-less mutant CW15(-) gave activity comparable to CWD. Thus on a chlorophyll basis, enzyme activity in chloroplasts from mixotrophically grown cells is about 1/10th of the level found in air adapted wild type cells. CIA-3 seems to lack this activity.

  9. Assessment of High Rates of Precocious Male Maturation in a Spring Chinook Salmon Supplementation Hatchery Program, Annual Report 2002-2003.

    SciTech Connect (OSTI)

    Larsen, Donald; Beckman, Brian; Cooper, Kathleen

    2003-08-01

    The Yakima River Spring Chinook Salmon Supplementation Project in Washington State is currently one of the most ambitious efforts to enhance a natural salmon population in the United States. Over the past five years we have conducted research to characterize the developmental physiology of naturally- and hatchery-reared wild progeny spring chinook salmon (Oncorhynchus tshawytscha) in the Yakima River basin. Fish were sampled at the main hatchery in Cle Elum, at remote acclimation sites and, during smolt migration, at downstream dams. Throughout these studies the maturational state of all fish was characterized using combinations of visual and histological analysis of testes, gonadosomatic index (GSI), and measurement of plasma 11-ketotestosterone (11-KT). We established that a plasma 11-KT threshold of 0.8 ng/ml could be used to designate male fish as either immature or precociously maturing approximately 8 months prior to final maturation (1-2 months prior to release as 'smolts'). Our analyses revealed that 37-49% of the hatchery-reared males from this program undergo precocious maturation at 2 years of age and a proportion of these fish appear to residualize in the upper Yakima River basin throughout the summer. An unnaturally high incidence of precocious male maturation may result in loss of potential returning anadromous adults, skewing of female: male sex ratios, ecological, and genetic impacts on wild populations and other native species. Precocious male maturation is significantly influenced by growth rate at specific times of year and future studies will be conducted to alter maturation rates through seasonal growth rate manipulations.

  10. Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum

    SciTech Connect (OSTI)

    Biswas, Ranjita; Zheng, Tianyong; Olson, Daniel G.; Lynd, Lee R.; Guss, Adam M.

    2015-02-01

    The native ability of Clostridium thermocellum to rapidly consume cellulose and produce ethanol makes it a leading candidate for a consolidated bioprocessing (CBP) biofuel production strategy. C. thermocellum also synthesizes lactate, formate, acetate, H2, and amino acids that compete with ethanol production for carbon and electrons. Elimination of H2 production could redirect carbon flux towards ethanol production by making more electrons available for acetyl-CoA reduction to ethanol. C. thermocellum encodes four hydrogenases and rather than delete each individually, we targeted a hydrogenase maturase gene (hydG), involved in converting the three [FeFe] hydrogenase apoenzymes into holoenzymes. Further deletion of the [NiFe] hydrogenase (ech) resulted in a mutant that functionally lacks all four hydrogenases. H2 production in hydG ech was undetectable and ethanol yield increased nearly 2-fold compared to wild type. Interestingly, mutant growth improved upon the addition of acetate, which led to increased expression of genes related to sulfate metabolism, suggesting these mutants may use sulfate as a terminal electron acceptor to balance redox reactions. Genomic analysis of hydG revealed a mutation in adhE, resulting in a strain with both NADH- and NADPH-dependent alcohol dehydrogenase activities. While this same adhE mutation is found in ethanol tolerant C. thermocellum strain E50C, hydG and hydG ech are not more ethanol tolerant than wild type, illustrating the complicated interactions between redox balancing and ethanol tolerance in C. thermocellum. The dramatic increase in ethanol production here suggests that targeting protein post-translational modification is a promising new approach for inactivation of multiple enzymes simultaneously for metabolic engineering.

  11. Total Dissolved Gas Effects on Incubating Chum Salmon Below Bonneville Dam

    SciTech Connect (OSTI)

    Arntzen, Evan V.; Hand, Kristine D.; Carter, Kathleen M.; Geist, David R.; Murray, Katherine J.; Dawley, Earl M.; Cullinan, Valerie I.; Elston, Ralph A.; Vavrinec, John

    2009-01-29

    At the request of the U.S. Army Corps of Engineers (USACE; Portland District), Pacific Northwest National Laboratory (PNNL) undertook a project in 2006 to look further into issues of total dissolved gas (TDG) supersaturation in the lower Columbia River downstream of Bonneville Dam. In FY 2008, the third year of the project, PNNL conducted field monitoring and laboratory toxicity testing to both verify results from 2007 and answer some additional questions about how salmonid sac fry respond to elevated TDG in the field and the laboratory. For FY 2008, three objectives were 1) to repeat the 2006-2007 field effort to collect empirical data on TDG from the Ives Island and Multnomah Falls study sites; 2) to repeat the static laboratory toxicity tests on hatchery chum salmon fry to verify 2007 results and to expose wild chum salmon fry to incremental increases in TDG, above those of the static test, until external symptoms of gas bubble disease were clearly present; and 3) to assess physiological responses to TDG levels in wild chum salmon sac fry incubating below Bonneville Dam during spill operations. This report summarizes the tasks conducted and results obtained in pursuit of the three objectives. Chapter 1 discusses the field monitoring, Chapter 2 reports the findings of the laboratory toxicity tests, and Chapter 3 describes the field-sampling task. Each chapter contains an objective-specific introduction, description of the study site and methods, results of research, and discussion of findings. Literature cited throughout this report is listed in Chapter 4. Additional details on the monitoring methodology and results are provided in Appendices A and B included on the compact disc bound inside the back cover of the printed version of this report.

  12. Survival Estimates for the Passage of Juvenile Salmonids through Snake and Columbia River Dams and Reservoirs, 2002-2003 Annual Report.

    SciTech Connect (OSTI)

    Muir, William D.; Smith, Steven G.; Zabel, Richard W.

    2003-07-01

    In 2002, the National Marine Fisheries Service and the University of Washington completed the tenth year of a study to estimate survival and travel time of juvenile salmonids (Oncorhynchus spp.) passing through dams and reservoirs on the Snake and Columbia Rivers. All estimates were derived from detections of fish tagged with passive integrated transponder tags (PIT tags). We PIT tagged and released a total of 19,891 hatchery steelhead at Lower Granite Dam. In addition, we utilized fish PIT tagged by other agencies at traps and hatcheries upstream from the hydropower system and sites within the hydropower system. PIT-tagged smolts were detected at interrogation facilities at Lower Granite, Little Goose, Lower Monumental, McNary, John Day, and Bonneville Dams and in the PIT-tag detector trawl operated in the Columbia River estuary. Survival estimates were calculated using a statistical model for tag-recapture data from single release groups (the ''Single-Release Model''). Primary research objectives in 2002 were to (1) estimate reach and project survival and travel time in the Snake and Columbia Rivers throughout the migration period of yearling chinook salmon O. tshawytscha and steelhead O. mykiss; (2) evaluate relationships between survival estimates and migration conditions; and (3) evaluate the survival-estimation models under prevailing conditions. This report provides reach survival and travel time estimates for 2002 for PIT-tagged yearling chinook salmon (hatchery and wild), hatchery sockeye salmon O. nerka, hatchery coho salmon O. kisutch, and steelhead (hatchery and wild) in the Snake and Columbia Rivers. Results are reported primarily in the form of tables and figures; details on methodology and statistical models used are provided in previous reports cited here. Results for summer-migrating chinook salmon will be reported separately.

  13. Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock

    SciTech Connect (OSTI)

    Egli, Martin; Pattanayek, Rekha; Sheehan, Jonathan H.; Xu, Yao; Mori, Tetsuya; Smith, Jarrod A.; Johnson, Carl H.

    2013-01-25

    We found that the Synechococcus elongatus KaiA, KaiB, and KaiC proteins in the presence of ATP generate a post-translational oscillator that runs in a temperature-compensated manner with a period of 24 h. KaiA dimer stimulates phosphorylation of KaiC hexamer at two sites per subunit, T432 and S431, and KaiB dimers antagonize KaiA action and induce KaiC subunit exchange. Neither the mechanism of KaiA-stimulated KaiC phosphorylation nor that of KaiB-mediated KaiC dephosphorylation is understood in detail at present. We demonstrate here that the A422V KaiC mutant sheds light on the former mechanism. It was previously reported that A422V is less sensitive to dark pulse-induced phase resetting and has a reduced amplitude of the KaiC phosphorylation rhythm in vivo. A422 maps to a loop (422-loop) that continues toward the phosphorylation sites. By pulling on the C-terminal peptide of KaiC (A-loop), KaiA removes restraints from the adjacent 422-loop whose increased flexibility indirectly promotes kinase activity. We found in the crystal structure that A422V KaiC lacks phosphorylation at S431 and exhibits a subtle, local conformational change relative to wild-type KaiC. Molecular dynamics simulations indicate higher mobility of the 422-loop in the absence of the A-loop and mobility differences in other areas associated with phosphorylation activity between wild-type and mutant KaiCs. Finally, the A-loop–422-loop relay that informs KaiC phosphorylation sites of KaiA dimer binding propagates to loops from neighboring KaiC subunits, thus providing support for a concerted allosteric mechanism of phosphorylation.

  14. Improved protocol to purify untagged amelogenin – Application to murine amelogenin containing the equivalent P70→T point mutation observed in human amelogenesis imperfecta

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Buchko, Garry W.; Shaw, Wendy J.

    2014-10-13

    Amelogenin is the predominant extracellular protein responsible for converting carbonated hydroxyapatite into dental enamel, the hardest and most heavily mineralized tissue in vertebrates. Despite much effort, the precise mechanism by which amelogenin regulates enamel formation is not fully understood. To assist efforts aimed at understanding the biochemical mechanism of enamel formation, more facile protocols to purify recombinantly expressed amelogenin, ideally without any tag to assist affinity purification, are advantageous. Here we describe an improved method to purify milligram quantities of amelogenin that exploits its high solubility in 2% glacial acetic acid under conditions of low ionic strength. The method involvesmore » heating the frozen cell pellet for two 15 min periods at ~70 ºC with two minutes of sonication in between, dialysis twice in 2% acetic acid (1:250 v/v), and reverse phase chromatography. A further improvement in yield is obtained by resuspending the frozen cell pellet in 6 M guanidine hydrochloride in the first step. The acetic acid heating method is illustrated with a murine amelogenin containing the corresponding P70→T point mutation observed in an human amelogenin associated with amelogenesis imperfecta (P71T), while the guanidine hydrochloride heating method is illustrated with wild type murine amelogenin (M180). The self-assembly properties of P71T were probed by NMR chemical shift perturbation studies as a function of protein (0.1 to 1.8 mM) and NaCl (0 to 367 mM) concentration. In conclusion, relative to similar studies with wild type murine amelogenin, P71T self-associates at lower protein or salt concentrations with the interactions initiated near the N-terminus.« less

  15. Distinct Luminal-Type Mammary Carcinomas Arise from Orthotopic Trp53-Null Mammary Transplantation of Juvenile versus Adult Mice

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Nguyen, David H.; Ouyang, Haoxu; Mao, Jian-Hua; Hlatky, Lynn; Barcellos-Hoff, M. H.

    2014-12-01

    Age and physiologic status, such as menopause, are risk factors for breast cancer. Less clear is what factors influence the diversity of breast cancer. In this study, we investigated the effect of host age on the distribution of tumor subtypes in mouse mammary chimera consisting of wild-type hosts and Trp53 nullizygous epithelium, which undergoes a high rate of neoplastic transformation. Wild-type mammary glands cleared of endogenous epithelium at 3 weeks of age were subsequently transplanted during puberty (5 weeks) or at maturation (10 weeks) with syngeneic Trp53-null mammary tissue fragments and monitored for one year. Tumors arose sooner from adultmore » hosts (AH) compared with juvenile hosts (JH). However, compared with AH tumors, JH tumors grew several times faster, were more perfused, exhibited a two-fold higher mitotic index, and were more highly positive for insulin-like growth factor receptor phosphorylation. Most tumors in each setting were estrogen receptor (ER)-positive (80% JH vs. 70% AH), but JH tumors were significantly more ER-immunoreactive (P = 0.0001) than AH tumors. A differential expression signature (JvA) of juvenile versus adult tumors revealed a luminal transcriptional program. Centroids of the human homologs of JvA genes showed that JH tumors were more like luminal A tumors and AH tumors were more like luminal B tumors. Hierarchical clustering with the JvA human ortholog gene list segregated luminal A and luminal B breast cancers across datasets. Lastly, these data support the notion that age-associated host physiology greatly influences the intrinsic subtype of breast cancer.« less

  16. Performance and value of CAD-deficient pine- Final Report

    SciTech Connect (OSTI)

    Bailian Li; Houmin Chang; Hasan Jameel

    2007-02-28

    The southern US produces 58% of the nation's timber, much of it grown in intensively managed plantations of genetically improved loblolly pine. One of the fastest-growing loblolly pine selections made by the NCSU-Industry Cooperative Tree Improvement Program, whose progeny are widely planted, is also the only known natural carrier of a rare gene, cadn1. This allele codes for deficiency in an enzyme, cinnamyl alcohol dehydrogenase, which catalyzes the last step in the biosynthesis of lignin precursors. This study is to characterize this candidate gene for marker-assisted selection and deployment in the breeding program. This research will enhance the sustainability of forest production in the South, where land-use pressures will limit the total area available in the future for intensively managed plantations. Furthermore, this research will provide information to establish higher-value plantation forests with more desirable wood/fiber quality traits. A rare mutant allele (cad-n1) of the cad gene in loblolly pine (Pinus taeda L.) causes a deficiency in the production of cinnamyl alcohol dehydrogenase (CAD). The effects of this allele were examined by comparing wood density and growth traits of cad-n1 heterozygous trees with those of wild-type trees in a 10-year-old open-pollinated family trial growing under two levels of fertilization in Scotland County, North Carolina. In all, 200 trees were sampled with 100 trees for each treatment. Wood density measurements were collected from wood cores at breast height using x-ray densitometry. We found that the substitution of cad-n1 for a wild-type allele (Cad) was associated with a significant effect on wood density. The cad-n1 heterozygotes had a significantly higher wood density (+2.6%) compared to wild-type trees. The higher density was apparently due to the higher percentage of latewood in the heterozygotes. The fertilization effect was highly significant for both growth and wood density traits. While no cad genotype x

  17. Enumeration of Juvenile Salmonids in the Okanogan Basin Using Rotary Screw Traps, Performance Period: March 15, 2006 - July 15, 2006.

    SciTech Connect (OSTI)

    Johnson, Peter N.; Rayton, Michael D.

    2007-05-01

    The Colville Tribes identified the need for collecting baseline census data on the timing and abundance of juvenile salmonids in the Okanogan River basin for the purpose of documenting local fish populations, augmenting existing fishery data and assessing natural production trends of salmonids. This report documents and assesses the pilot year of rotary trap capture of salmonid smolts on the Okanogan River. The project is a component of the Colville Tribes Okanogan Basin Monitoring and Evaluation Program (OBMEP) which began in 2004. Trapping for outmigrating fish began on 14 March 2006 and continued through 11 July 2006. Anadromous forms of Oncorhynchus, including summer steelhead (O. mykiss), Chinook (O. tshawytscha), and sockeye (O. nerka), were targeted for this study; all have verified, natural production in the Okanogan basin. Both 8-ft and 5-ft rotary screw traps were deployed on the Okanogan River from the Highway 20 Bridge and typically fished during evening hours or 24 hours per day, depending upon trap position and discharge conditions. Juvenile Chinook salmon were the most abundant species trapped in 2006 (10,682 fry and 2,024 smolts), followed by sockeye (205 parr and 3,291 smolts) and steelhead (1 fry and 333 smolts). Of the trapped Chinook, all fry were wild origin and all but five of the smolts were hatchery-reared. All trapped sockeye were wild origin and 88% of the steelhead smolts were hatchery-reared. Mark-recapture experiments were conducted using Chinook fry and hatchery-reared steelhead smolts (sockeye were not used in 2006 because the peak of the juvenile migration occurred prior to the onset of the mark-recapture experiments). A total of 930 chinook fry were marked and released across eight separate release dates (numbers of marked Chinook fry released per day ranged from 34 to 290 fish). A total of 11 chinook fry were recaptured for an overall trap efficiency of 1.18%. A total of 710 hatchery-reared steelhead were marked and released across

  18. Steelhead Supplementation Studies; Steelhead Supplementation in Idaho Rivers, Annual Report 2002.

    SciTech Connect (OSTI)

    Byrne, Alan

    2003-03-01

    The Steelhead Supplementation Study (SSS) has two broad objectives: (1) investigate the feasibility of supplementing depressed wild and natural steelhead populations using hatchery populations, and (2) describe the basic life history and genetic characteristics of wild and natural steelhead populations in the Salmon and Clearwater Basins. Idaho Department of Fish and Game (IDFG) personnel stocked adult steelhead from Sawtooth Fish Hatchery into Frenchman and Beaver creeks and estimated the number of age-1 parr produced from the outplants since 1993. On May 2, 2002, both Beaver and Frenchman creeks were stocked with hatchery adult steelhead. A SSS crew snorkeled the creeks in August 2002 to estimate the abundance of age-1 parr from brood year (BY) 2001. I estimated that the yield of age-1 parr per female stocked in 2001 was 7.3 and 6.7 in Beaver and Frenchman creeks, respectively. SSS crews stocked Dworshak hatchery stock fingerlings and smolts from 1993 to 1999 in the Red River drainage to assess which life stage produces more progeny when the adults return to spawn. In 2002, Clearwater Fish Hatchery personnel operated the Red River weir to trap adults that returned from these stockings. Twelve PIT-tagged adults from the smolt releases and one PIT-tagged adult from fingerling releases were detected during their migration up the mainstem Columbia and Snake rivers, but none from either group were caught at the weir. The primary focus of the study has been monitoring and collecting life history information from wild steelhead populations. An adult weir has been operated annually since 1992 in Fish Creek, a tributary of the Lochsa River. The weir was damaged by a rain-on-snow event in April 2002 and although the weir remained intact, some adults were able to swim undetected through the weir. Despite damage to the weir, trap tenders captured 167 adult steelhead, the most fish since 1993. The maximum likelihood estimate of adult steelhead escapement was 242. A screw trap

  19. Smolt Condition and Timing of Arrival at Lower Granite Reservoir, 1983-1984 Technical Report.

    SciTech Connect (OSTI)

    Scully, Richard J.; Buettner, Edwin W.

    1985-12-01

    Hatcheries released 9.3 million chinook salmon and 6.3 million steelhead smolts and presmolts upriver from Lower Granite Reservoir for migration In spring, 1984. We operated smolt monitoring traps at Whitebird from March 14 to May 12, Snake River from March 22 to May 15 and Clearwater from March 29 to May 13. Peak passage of yearling chinook salmon occurred the third week In April at both Whitebird and Snake River traps. Passage of steelhead was still increasing when high water stopped trapping in mid-May. Median migration rates for branded chinook salmon between release sites and Whitebird were 3, 17 and 15 miles/day for Rapid River, South Fork Salmon and Decker Flat smolts, respectively, an average of 11.6 miles/day. Average migration rate for these three groups between Whitebird and Snake River trap was 28 miles/day. Average migration rate between release sites and Snake River (the head of Lower Granite Reservoir) was 13.2 miles/day and from that point on through the reservoir to the dam, 1.9 miles/day. Salmon River discharge, when considered along with other environmental factors, had the greatest effect on migration rate of smolts branded both at hatcheries and at the Whitebird trap and migrating to the head of Lower Granite Reservoir. Migration rate for steelhead released from Dworshak Hatchery and recaptured at the Clearwater trap was 34 miles/day. Survival rates to the Snake River trap of branded chinook salmon smolts released at Hells Canyon Dam, Rapid River, South Fork Salmon and Decker Flat were 52%, 65%, 68% and 35%, respectively. Classical descaling, where at least 40% of the scales are missing from at least two of five areas on the side of a smolt, ranged from 0 to 5.3% at hatcheries for chinook salmon and was less than 1% for steelhead. Descaling rate often Increased about 1% at release sites. Classical descaling at Whitebird, Clearwater and Snake River traps averaged 4.5, 2.5 and 1.5% for chinook salmon, 2.1, 0.4 and 1.4% for wild steelhead and 8

  20. Deletion of Caldicellulosiruptor bescii CelA reveals its crucial role in the deconstruction of lignocellulosic biomass

    SciTech Connect (OSTI)

    Young, Jenna; Chung, Daehwan; Bomble, Yannick J.; Himmel, Michael E.; Westpheling, Janet

    2014-10-09

    Background: Members of the bacterial genus Caldicellulosiruptor are the most thermophilic cellulolytic organisms described to date, and have the ability to grow on lignocellulosic biomass without conventional pretreatment. Different species vary in their abilities to degrade cellulose, and the presence of CelA, a bifunctional glycoside hydrolase that contains a Family 48 and a Family 9 catalytic domain, correlates well with cellulolytic ability in members of this genus. For example, C. hydrothermalis, which does not contain a CelA homolog, or a GH48 Family or GH9 Family glycoside hydrolase, is the least cellulolytic of the Caldicellulosiruptor species so far described. C. bescii, which contains CelA and expresses it constitutively, is among the most cellulolytic. In fact, CelA is the most abundant extracellular protein produced in C. bescii. The enzyme contains two catalytic units, a Family 9A-CBM3c processive endoglucanase and a Family 48 exoglucanase, joined by two Family 3b carbohydrate-binding domains. Although there are two non-reducing end-specific Family 9 and three reducing end-specific Family 48 glycoside hydrolases (producing primarily glucose and cellobiose; and cellobiose and cellotriose, respectively) in C. bescii, CelA is the only protein that combines both enzymatic activities. Results: A deletion of the celA gene resulted in a dramatic reduction in the microorganism’s ability to grow on crystalline cellulose (Avicel) and diminished growth on lignocellulosic biomass. A comparison of the overall endoglucanase and exoglucanase activities of the mutant compared with the wild-type suggests that the loss of the endoglucanase activity provided by the GH9 family domain is perhaps compensated for by other enzymes produced by the cell. In contrast, it appears that no other enzymes in the C. bescii secretome can compensate for the loss of exoglucanase activity. The change in enzymatic activity in the celA mutant resulted in a 15-fold decrease in sugar

  1. The Small Ethylene Response Factor ERF96 is Involved in the Regulation of the Abscisic Acid Response in Arabidopsis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wang, Xiaoping; Liu, Shanda; Tian, Hainan; Wang, Shucai; Chen, Jin-Gui

    2015-11-26

    Ethylene regulates many aspects of plant growth and development including seed germination, leaf senescence, and fruit ripening, and of plant responses to environmental stimuli including both biotic and abiotic stresses. Ethylene response factors (ERFs) are plant-specific transcription factors and are a subfamily of the AP2 (APETALA2)/ERF transcription factor family. The function of many members in this large gene family remains largely unknown. ERF96, a member of the Group IX ERF family transcription factors, has recently been shown to be a transcriptional activator that is involved in plant defense response in Arabidopsis. In this article, we provide evidence that ERF96 ismore » a positive regulator of abscisic acid (ABA) responses. Bioinformatics analysis indicated that there are a total four small ERFs in Arabidopsis including ERF95, ERF96, ERF97, and ERF98, and that ERF96 forms a cluster with ERF95 and ERF97. By using quantitative RT-PCR, we found that ERF96 is expressed in all tissues and organs examined except roots, with relatively high expression in flowers and seeds. Results from the protoplast transfection assay indicated that the EDLL motif-containing C-terminal domain is responsible for ERF96’s transcriptional activity. Although loss-of-function mutant of ERF96 was morphologically similar to wild type plants, transgenic plants overexpressing ERF96 had smaller rosette size and were delayed in flowering time. In ABA sensitivity assays, we found that ERF96 overexpression plants were hypersensitive to ABA in terms of ABA inhibition of seed germination, early seedling development and root elongation. Consistent with these observations, elevated transcript levels of some ABA-responsive genes including RD29A, ABI5, ABF3, ABF4, P5CS, and COR15A were observed in the transgenic plants in the presence of ABA. However, in the absence of ABA treatment, the transcript levels of these ABA-responsive genes remained largely unchanged. Our experiments also showed

  2. Ovate family protein1 interaction with BLH3 regulates transition timing from vegetative to reproductive phase in Arabidopsis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhang, Liguo; Zhang, Xiaofei; Ju, Hanxun; Chen, Jingui; Wang, Shucai; Wang, Hemeng; Zhao, Yuanling; Chang, Ying

    2016-01-23

    We study the Three-Amino-acid-Loop-Extension(TALE) homeodomain transcription factor BLH3 that regulates timing of transition from vegetative to reproductive phase. Previous preliminary results obtained using large-scale yeast two-hybrids indicate that BLH3 protein possibly interact with Ovate Family Proteins(OFPs) transcription co-regulators. Nevertheless, it is uncertain whether OFP1–BLH3 complex is involved in regulation of timing of transition from vegetative to reproductive phase in Arabidopsis. The interaction between BLH3 and OFP1 was re-tested and verified by a yeast two-hybrid system. We found that the BLH3–OFP1 interaction was mainly mediated through the BLH3 homeodomain. Meanwhile, this interaction was further confirmed by bimolecular fluorescence complementation (BiFC) inmore » vivo. In addition, by establishing protoplast transient expression, we discovered that BLH3 acts as a transcriptional activator, whereas OFP1 functioned as a repressor. The interactions between OFP1 and BLH3 can reduce BLH3 transcriptional activity. The ofp1 mutant lines and blh3 mutant lines, OFP1 overexpress lines and BLH3 overexpress lines can both influence timing of transition from vegetative to reproductive phase. Furthermore, 35s:OFP1/blh3 plants exhibited flowering and leaf quantity similar to that of the wild-type controls. 35s:BLH3/ofp1 plants flowered earlier and had less leaves than wild-type controls, indicating that OFP1 protein might depend partially on BLH3 in its function to regulate the timing of transition from vegetative to reproductive phase. In conclusion, these results support our assumption that, by interacting with OFP1, BLH3 forms a functional protein complex that controls timing of progression from vegetative to reproductive phase, and OFP1 might negatively regulate BLH3 or the BLH-KNOX complex, an important interaction for sustaining the normal transition from vegetative to reproductive phase.« less

  3. The Small Ethylene Response Factor ERF96 is Involved in the Regulation of the Abscisic Acid Response in Arabidopsis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wang, Xiaoping; Liu, Shanda; Tian, Hainan; Wang, Shucai; Chen, Jin-Gui

    2015-11-26

    We report that ethylene regulates many aspects of plant growth and development including seed germination, leaf senescence, and fruit ripening, and of plant responses to environmental stimuli including both biotic and abiotic stresses. Ethylene response factors (ERFs) are plant-specific transcription factors and are a subfamily of the AP2 (APETALA2)/ERF transcription factor family. The function of many members in this large gene family remains largely unknown. ERF96, a member of the Group IX ERF family transcription factors, has recently been shown to be a transcriptional activator that is involved in plant defense response in Arabidopsis. Here we provide evidence that ERF96more » is a positive regulator of abscisic acid (ABA) responses. Bioinformatics analysis indicated that there are a total four small ERFs in Arabidopsis including ERF95, ERF96, ERF97, and ERF98, and that ERF96 forms a cluster with ERF95 and ERF97. By using quantitative RT-PCR, we found that ERF96 is expressed in all tissues and organs examined except roots, with relatively high expression in flowers and seeds. Results from the protoplast transfection assay indicated that the EDLL motif-containing C-terminal domain is responsible for ERF96’s transcriptional activity. Although loss-of-function mutant of ERF96 was morphologically similar to wild type plants, transgenic plants overexpressing ERF96 had smaller rosette size and were delayed in flowering time. In ABA sensitivity assays, we found that ERF96 overexpression plants were hypersensitive to ABA in terms of ABA inhibition of seed germination, early seedling development and root elongation. Consistent with these observations, elevated transcript levels of some ABA-responsive genes including RD29A, ABI5, ABF3, ABF4, P5CS, and COR15A were observed in the transgenic plants in the presence of ABA. However, in the absence of ABA treatment, the transcript levels of these ABA-responsive genes remained largely unchanged. Our experiments also showed

  4. Reproductive biomarkers responses induced by xenoestrogens in the characid fish Astyanax fasciatus inhabiting a South American reservoir: An integrated field and laboratory approach

    SciTech Connect (OSTI)

    Prado, Paula S.; Pinheiro, Ana Paula B.; Bazzoli, Nilo; Rizzo, Elizete

    2014-05-01

    Field studies evaluating the effects of endocrine disruption chemicals (EDCs) on the fish reproduction are scarce worldwide. The goal of this study was to assess hepatic levels of vitellogenin (Vtg), zona radiata proteins (Zrp) and insulin-like growth factors (IGF-I and IGF-II), and relating them to reproductive endpoints in a wild fish population habiting a reservoir that receive domestic sewage, agricultural and industrial residues. Adult fish Astyanax fasciatus were sampled during the reproductive season in five sites from the Furnas Reservoir, Grande River, and Paraguay–Paraná basin. As a control to field data, fish were experimentally exposed via dietary intake, to oestradiol benzoate (OB) for 7 days. Fish from site with little anthropogenic interference showed hepatic levels of Vtg, Zrp and IGF-I and IGF-II similar to those from the non-treated experimental group. In sites located immediately downstream from the municipal wastewater discharges, the water total oestrogen was >120 ng/l, and male fish displayed increased Vtg and Zrp and decreased IGF-I levels similar to OB treated fish. In females, levels of Vtg, Zrp, IGF-I and IGF-II suggest an impairment of final oocyte maturation and spawning, as also detected by frequency of over-ripening, follicular atresia and fecundity. At the sites that receive agricultural and industrial residues, the water total oestrogen was <50 ng/l and females showed decreased Zrp and increased IGF-II levels associated to reduced diameter of vitellogenic follicles, indicating an inhibition of oocyte growth. Overall, the current study reports oestrogenic contamination impairing the reproduction of a wild fish from a hydroeletric reservoir and, the data contribute to improving the current knowledge on relationship between hepatic Vtg, Zrp and IGF-I and IGF-II, and reproductive endpoints in a teleost fish. In addition, our data point out novel reproductive biomarkers (IGF-I, IGF-II and over-ripening) to assessing xenoestrogenic

  5. Detection of genotoxic and non-genotoxic carcinogens in Xpc{sup −/−}p53{sup +/−} mice

    SciTech Connect (OSTI)

    Melis, Joost P.M.; Leiden University Medical Center, Department of Toxicogenetics, Leiden ; Speksnijder, Ewoud N.; Kuiper, Raoul V.; Dutch Molecular Pathology Center, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht ; Salvatori, Daniela C.F.; Schaap, Mirjam M.; Leiden University Medical Center, Department of Toxicogenetics, Leiden ; Maas, Saskia; Robinson, Joke; Verhoef, Aart; Benthem, Jan van; Luijten, Mirjam; Steeg, Harry van

    2013-01-15

    An accurate assessment of the carcinogenic potential of chemicals and pharmaceutical drugs is essential to protect humans and the environment. Therefore, substances are extensively tested before they are marketed to the public. Currently, the rodent two-year bioassay is still routinely used to assess the carcinogenic potential of substances. However, over time it has become clear that this assay yields false positive results and also has several economic and ethical drawbacks including the use of large numbers of animals, the long duration, and the high cost. The need for a suitable alternative assay is therefore high. Previously, we have proposed the Xpa*p53 mouse model as a very suitable alternative to the two-year bioassay. We now show that the Xpc*p53 mouse model preserves all the beneficial traits of the Xpa*p53 model for sub-chronic carcinogen identification and can identify both genotoxic and non-genotoxic carcinogens. Moreover, Xpc*p53 mice appear to be more responsive than Xpa*p53 mice towards several genotoxic and non-genotoxic carcinogens. Furthermore, Xpc*p53 mice are far less sensitive than Xpa*p53 mice for the toxic activity of DNA damaging agents and as such clearly respond in a similar way as wild type mice do. These advantageous traits of the Xpc*p53 model make it a better alternative for in vivo carcinogen testing than Xpa*p53. This pilot study suggests that Xpc*p53 mice are suited for routine sub-chronic testing of both genotoxic and non-genotoxic carcinogens and as such represent a suitable alternative to possibly replace the murine life time cancer bioassay. Highlights: ► The Xpc*p53 mouse model is able to identify genotoxic and non-genotoxic carcinogens. ► Time, animals and cost can be significantly reduced compared to the 2-year bioassay. ► Xpc*p53 mice are more advantageous for carcinogen identification than Xpa*p53 mice. ► Xpc*p53 mice exhibit a wild type response upon exposure to genotoxicants.

  6. The Small Ethylene Response Factor ERF96 is Involved in the Regulation of the Abscisic Acid Response in Arabidopsis

    SciTech Connect (OSTI)

    Wang, Xiaoping; Liu, Shanda; Tian, Hainan; Wang, Shucai; Chen, Jin-Gui

    2015-11-26

    We report that ethylene regulates many aspects of plant growth and development including seed germination, leaf senescence, and fruit ripening, and of plant responses to environmental stimuli including both biotic and abiotic stresses. Ethylene response factors (ERFs) are plant-specific transcription factors and are a subfamily of the AP2 (APETALA2)/ERF transcription factor family. The function of many members in this large gene family remains largely unknown. ERF96, a member of the Group IX ERF family transcription factors, has recently been shown to be a transcriptional activator that is involved in plant defense response in Arabidopsis. Here we provide evidence that ERF96 is a positive regulator of abscisic acid (ABA) responses. Bioinformatics analysis indicated that there are a total four small ERFs in Arabidopsis including ERF95, ERF96, ERF97, and ERF98, and that ERF96 forms a cluster with ERF95 and ERF97. By using quantitative RT-PCR, we found that ERF96 is expressed in all tissues and organs examined except roots, with relatively high expression in flowers and seeds. Results from the protoplast transfection assay indicated that the EDLL motif-containing C-terminal domain is responsible for ERF96’s transcriptional activity. Although loss-of-function mutant of ERF96 was morphologically similar to wild type plants, transgenic plants overexpressing ERF96 had smaller rosette size and were delayed in flowering time. In ABA sensitivity assays, we found that ERF96 overexpression plants were hypersensitive to ABA in terms of ABA inhibition of seed germination, early seedling development and root elongation. Consistent with these observations, elevated transcript levels of some ABA-responsive genes including RD29A, ABI5, ABF3, ABF4, P5CS, and COR15A were observed in the transgenic plants in the presence of ABA. However, in the absence of ABA treatment, the transcript levels of these ABA-responsive genes remained largely unchanged. Our experiments also showed that

  7. Trps1 deficiency inhibits the morphogenesis of secondary hair follicles via decreased Noggin expression

    SciTech Connect (OSTI)

    Sun, Yujing; Nakanishi, Masako; Sato, Fuyuki; Oikawa, Kosuke; Muragaki, Yasuteru; Zhou, Gengyin

    2015-01-16

    Highlights: • The number of secondary hair follicles is reduced by half in Trps1 KO embryonic skin compared to wild-type skin. • Noggin expression is significantly decreased and BMP signaling is promoted in Trps1 KO embryonic skin. • Treatment with a Noggin or BMP inhibitor rescued the decreased number of hair follicles in Trps1 KO skin graft cultures. • Cell proliferation and apoptosis of the epidermis were normalized by Noggin treatment. - Abstract: A representative phenotype of patients with tricho-rhino-phalangeal syndrome (TRPS) is sparse hair. To understand the developmental defects of these patient’s hair follicles, we analyzed the development of hair follicles histologically and biochemically using Trps1 deficient (KO) mice. First, we compared the numbers of primary hair follicles in wild-type (WT) and KO embryos at different developmental stages. No differences were observed in the E14.5 skins of WT and KO mice. However, at later time points, KO fetal skin failed to properly develop secondary hair follicles, and the number of secondary hair follicles present in E18.5 KO skin was approximately half compared to that of WT skin. Sonic hedgehog expression was significantly decreased in E17.5 KO skin, whereas no changes were observed in Eda/Edar expression in E14.5 or E17.5 skins. In addition, Noggin expression was significantly decreased in E14.5 and E17.5 KO skin compared to WT skin. In parallel with the suppression of Noggin expression, BMP signaling was promoted in the epidermal cells of KO skins compared to WT skins as determined by immunohistochemistry for phosphorylated Smad1/5/8. The reduced number of secondary hair follicles was restored in skin graft cultures treated with a Noggin and BMP inhibitor. Furthermore, decreased cell proliferation, and increased apoptosis in KO skin was rescued by Noggin treatment. Taken together, we conclude that hair follicle development in Trps1 KO embryos is impaired directly or indirectly by decreased Noggin

  8. Lactose-Inducible System for Metabolic Engineering of Clostridium ljungdahlii

    SciTech Connect (OSTI)

    Banerjee, A; Leang, C; Ueki, T; Nevin, KP; Lovley, DR

    2014-03-25

    The development of tools for genetic manipulation of Clostridium ljungdahlii has increased its attractiveness as a chassis for autotrophic production of organic commodities and biofuels from syngas and microbial electrosynthesis and established it as a model organism for the study of the basic physiology of acetogenesis. In an attempt to expand the genetic toolbox for C. ljungdahlii, the possibility of adapting a lactose-inducible system for gene expression, previously reported for Clostridium perfringens, was investigated. The plasmid pAH2, originally developed for C. perfringens with a gusA reporter gene, functioned as an effective lactose-inducible system in C. ljungdahlii. Lactose induction of C. ljungdahlii containing pB1, in which the gene for the aldehyde/alcohol dehydrogenase AdhE1 was downstream of the lactose-inducible promoter, increased expression of adhE1 30-fold over the wild-type level, increasing ethanol production 1.5-fold, with a corresponding decrease in acetate production. Lactose-inducible expression of adhE1 in a strain in which adhE1 and the adhE1 homolog adhE2 had been deleted from the chromosome restored ethanol production to levels comparable to those in the wild-type strain. Inducing expression of adhE2 similarly failed to restore ethanol production, suggesting that adhE1 is the homolog responsible for ethanol production. Lactose-inducible expression of the four heterologous genes necessary to convert acetyl coenzyme A (acetyl-CoA) to acetone diverted ca. 60% of carbon flow to acetone production during growth on fructose, and 25% of carbon flow went to acetone when carbon monoxide was the electron donor. These studies demonstrate that the lactose-inducible system described here will be useful for redirecting carbon and electron flow for the biosynthesis of products more valuable than acetate. Furthermore, this tool should aid in optimizing microbial electrosynthesis and for basic studies on the physiology of acetogenesis.

  9. Deletion of Caldicellulosiruptor bescii CelA reveals its crucial role in the deconstruction of lignocellulosic biomass

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Young, Jenna; Chung, Daehwan; Bomble, Yannick J.; Himmel, Michael E.; Westpheling, Janet

    2014-10-09

    Background: Members of the bacterial genus Caldicellulosiruptor are the most thermophilic cellulolytic organisms described to date, and have the ability to grow on lignocellulosic biomass without conventional pretreatment. Different species vary in their abilities to degrade cellulose, and the presence of CelA, a bifunctional glycoside hydrolase that contains a Family 48 and a Family 9 catalytic domain, correlates well with cellulolytic ability in members of this genus. For example, C. hydrothermalis, which does not contain a CelA homolog, or a GH48 Family or GH9 Family glycoside hydrolase, is the least cellulolytic of the Caldicellulosiruptor species so far described. C. bescii,more » which contains CelA and expresses it constitutively, is among the most cellulolytic. In fact, CelA is the most abundant extracellular protein produced in C. bescii. The enzyme contains two catalytic units, a Family 9A-CBM3c processive endoglucanase and a Family 48 exoglucanase, joined by two Family 3b carbohydrate-binding domains. Although there are two non-reducing end-specific Family 9 and three reducing end-specific Family 48 glycoside hydrolases (producing primarily glucose and cellobiose; and cellobiose and cellotriose, respectively) in C. bescii, CelA is the only protein that combines both enzymatic activities. Results: A deletion of the celA gene resulted in a dramatic reduction in the microorganism’s ability to grow on crystalline cellulose (Avicel) and diminished growth on lignocellulosic biomass. A comparison of the overall endoglucanase and exoglucanase activities of the mutant compared with the wild-type suggests that the loss of the endoglucanase activity provided by the GH9 family domain is perhaps compensated for by other enzymes produced by the cell. In contrast, it appears that no other enzymes in the C. bescii secretome can compensate for the loss of exoglucanase activity. The change in enzymatic activity in the celA mutant resulted in a 15-fold decrease in

  10. Active site proton delivery and the lyase activity of human CYP17A1

    SciTech Connect (OSTI)

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G.

    2014-01-03

    Highlights: The disruption of PREG/PROG hydroxylation activity by T306A showed the participation of Cpd I. T306A supports the involvement of a nucleophilic peroxo-anion during lyase activity. The presence of cytochrome b{sub 5} augments CC lyase activity. ?5-Steroids are preferred substrates for CYP17 catalysis. -- Abstract: Cytochrome P450 CYP17A1 catalyzes a series of reactions that lie at the intersection of corticoid and androgen biosynthesis and thus occupies an essential role in steroid hormone metabolism. This multifunctional enzyme catalyzes the 17?-hydroxylation of ?4- and ?5-steroids progesterone and pregnenolone to form the corresponding 17?-hydroxy products through its hydroxylase activity, and a subsequent 17,20-carboncarbon scission of pregnene-side chain produce the androgens androstenedione (AD) and dehydroepiandrosterone (DHEA). While the former hydroxylation reaction is believed to proceed through a conventional Compound I rebound mechanism, it has been suggested that the latter carbon cleavage is initiated by an iron-peroxy intermediate. We report on the role of Thr306 in CYP17 catalysis. Thr306 is a member of the conserved acid/alcohol pair thought to be essential for the efficient delivery of protons required for hydroperoxoanion heterolysis and formation of Compound I in the cytochromes P450. Wild type and T306A CYP17A1 self-assembled in Nanodiscs were used to quantitate turnover and coupling efficiencies of CYP17s physiological ?4- and ?5-substrates. We observed that T306A co-incorporated in Nanodiscs with its redox partner cytochrome P450 oxidoreductase, coupled NADPH only by 0.9% and 0.7% compared to the wild type (97% and 22%) during the conversion of pregnenolone and progesterone, respectively, to the corresponding 17-OH products. Despite increased oxidation of pyridine nucleotide, hydroxylase activity was drastically diminished in the T306A mutant, suggesting a high degree of uncoupling in which reducing equivalents and protons

  11. Genetic Improvement of Switchgrass and Other Herbaceous Plants for Use as Biomass Fuel Feedstock

    SciTech Connect (OSTI)

    Vogel, K.P.

    2001-01-11

    It should be highly feasible to genetically modify the feedstock quality of switchgrass and other herbaceous plants using both conventional and molecular breeding techniques. Effectiveness of breeding to modify herbages of switchgrass and other perennial and annual herbaceous species has already been demonstrated. The use of molecular markers and transformation technology will greatly enhance the capability of breeders to modify the plant structure and cell walls of herbaceous plants. It will be necessary to monitor gene flow to remnant wild populations of plants and have strategies available to curtail gene flow if it becomes a potential problem. It also will be necessary to monitor plant survival and long-term productivity as affected by genetic changes that improve forage quality. Information on the conversion processes that will be used and the biomass characteristics that affect conversion efficiency and rate is absolutely essential as well as information on the relative economic value of specific traits. Because most forage or biomass quality characteristics are highly affected by plant maturity, it is suggested that plant material of specific maturity stages be used in research to determining desirable feedstock quality characteristics. Plant material could be collected at various stages of development from an array of environments and storage conditions that could be used in conversion research. The same plant material could be used to develop NIRS calibrations that could be used by breeders in their selection programs and also to develop criteria for a feedstock quality assessment program. Breeding for improved feedstock quality will likely affect the rate of improvement of biomass production per acre. If the same level of resources are used, multi-trait breeding simply reduces the selection pressure and hence the breeding progress that can be made for a single trait unless all the traits are highly correlated. Since desirable feedstock traits are likely

  12. Western Pond Turtle Head-starting and Reintroduction, 2005-2006 Annual Report.

    SciTech Connect (OSTI)

    Van Leuven, Susan; Allen, Harriet; Slavens, Kate

    2006-11-01

    This report covers the results of the western pond turtle head-starting and reintroduction project for the period of October 2005-September 2006. Wild hatchling western pond turtles from the Columbia River Gorge were reared at the Woodland Park and Oregon zoos in 2005 and 2006 as part of the recovery effort for this Washington State endangered species. The objective of the program is to reduce losses to introduced predators like bullfrogs and largemouth bass by raising the hatchlings to a size where they are too large to be eaten by most of these predators. Twenty-six turtles were placed at the Woodland Park Zoo and 62 at the Oregon Zoo in fall 2005. These turtles joined two that were held back from release in summer 2005 due to their small size. All 90 juvenile turtles were released at three sites in the Columbia Gorge in 2006. Twenty-eight juvenile turtles were released at the Klickitat ponds, 22 at the Klickitat lake, 21 at the Skamania site, and 19 at Pierce National Wildlife Refuge (NWR). This brought the total number of head-start turtles released since 1991 to 944; 285 for the Klickitat ponds, 158 for the Klickitat lake, 227 for the Skamania pond complex, and 274 at Pierce NWR. In 2006, 20 females from the Klickitat population were equipped with transmitters and monitored for nesting activity. Fifteen nests were located and protected; these produced 55 hatchlings. The hatchlings were collected in September and transported to the Oregon and Woodland Park zoos for rearing in the head-start program. One wild hatchling captured in spring 2006 was placed in the head-start program to attain more growth in captivity. During the 2006 field season trapping effort, 414 western pond turtles were captured in the Columbia Gorge, including 374 previously head-started turtles. These recaptures, together with confirmed nesting by head-start females and visual resightings, indicate the program is succeeding in boosting juvenile recruitment to increase the populations

  13. Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

    SciTech Connect (OSTI)

    Langkilde, Annette; Kristensen, Søren M.; Lo Leggio, Leila; Mølgaard, Anne; Jensen, Jan H.; Houk, Andrew R.; Navarro Poulsen, Jens-Christian; Kauppinen, Sakari; Larsen, Sine

    2008-08-01

    The short hydrogen bonds in rhamnogalacturonan acetylesterase have been investigated by structure determination of an active-site mutant, {sup 1}H NMR spectra and computational methods. Comparisons are made to database statistics. A very short carboxylic acid carboxylate hydrogen bond, buried in the protein, could explain the low-field (18 p.p.m.) {sup 1}H NMR signal. An extremely low-field signal (at approximately 18 p.p.m.) in the {sup 1}H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theoretical calculations of chemical shift values were used in the interpretation of the experimental {sup 1}H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 Å resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 Å) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor–acceptor distances of different types of hydrogen bonds. The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pK{sub a} values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest

  14. Synergized resmethrin and corticosterone alter the chicken's response to west nile virus

    SciTech Connect (OSTI)

    Jankowski, Mark David; Franson, J Christian; Mostl, Erich; Porter, Warren P; Hofmeister, Erik K

    2009-01-01

    Debate concerning arbovirus control strategies remains contentious because concern regarding the relative risk of viral infection and environmental toxicant exposure is high but inadequately characterized. Taking this into account, mosquito control agencies employ aerial insecticides only after arbovirus surveillance data indicate high local mosquito-infection-rates. Successfully mitigating the risk of adult-mosquito-control insecticides ('adulticides') to non-target species such as humans, domestic animals, fish, beneficial insects and wildlife, while increasing their efficacy to reduce arbovirus outbreak intensity requires targeted scientific data from animal toxicity studies and environmental monitoring activities. Wild birds are an important reservoir host for WNv and are potentially exposed to insecticides used for mosquito control. However, no risk assessments have evaluated whether insecticides augment or extend the potential transmissibility of West Nile virus (WNv) in birds. In order to augment existing resmethrin risk assessments, we aimed to determine whether synergized resmethrin (SR) may cause chickens to develop an elevated or extended WN viremia and if subacute stress may affect its immunotoxicity. We distributed 40 chickens into four groups then exposed them prior to and during WNv infection with SR (50 {mu}g/l resmethrin + 150 {mu}g/l piperonyl butoxide) and/or 20 mg/I corticosterone (CORT) in their drinking-water. Corticosterone was given for 10 continuous days and SR was given for 3 alternate days starting the 3rd day of CORT exposure, then chickens were subcutaneously inoculated with WNv on the 5th day of CORT treatment. Compared to controls, CORT treatment extended and elevated viremia, enhanced WNv-specific antibody and increased the percentage of birds that shed oral virus, whereas SR treatment extended viremia, depressed WNv-specific IgG, and increased the percentage of CORT-treated birds that shed oral virus. Corticosterone and SR

  15. Study on the reduction of atmospheric mercury emissions from mine waste enriched soils through native grass cover in the Mt. Amiata region of Italy

    SciTech Connect (OSTI)

    Fantozzi, L.; Dini, F.; Tamburello, L.; Pirrone, N.; Sprovieri, F.

    2013-08-15

    Atmospheric mercury emissions from mine-waste enriched soils were measured in order to compare the mercury fluxes of bare soils with those from other soils covered by native grasses. Our research was conducted near Mt. Amiata in central Italy, an area that was one of the largest and most productive mining centers in Europe up into the 1980s. To determine in situ mercury emissions, we used a Plexiglas flux chamber connected to a portable mercury analyzer (Lumex RA-915+). This allowed us to detect, in real time, the mercury vapor in the air, and to correlate this with the meteorological parameters that we examined (solar radiation, soil temperature, and humidity). The highest mercury flux values (8000 ng m{sup −2} h{sup −1}) were observed on bare soils during the hours of maximum insulation, while lower values (250 ng m{sup −2} h{sup −1}) were observed on soils covered by native grasses. Our results indicate that two main environmental variables affect mercury emission: solar radiation intensity and soil temperature. The presence of native vegetation, which can shield soil surfaces from incident light, reduced mercury emissions, a result that we attribute to a drop in the efficiency of mercury photoreduction processes rather than to decreases in soil temperature. This finding is consistent with decreases in mercury flux values down to 3500 ng m{sup −2} h{sup −1}, which occurred under cloudy conditions despite high soil temperatures. Moreover, when the soil temperature was 28 °C and the vegetation was removed from the experimental site, mercury emissions increased almost four-fold. This increase occurred almost immediately after the grasses were cut, and was approximately eight-fold after 20 h. Thus, this study demonstrates that enhancing wild vegetation cover could be an inexpensive and effective approach in fostering a natural, self-renewing reduction of mercury emissions from mercury-contaminated soils. -- Highlights: ► Mercury air/surface exchange

  16. DECOMMISSIONING THE HIGH PRESSURE TRITIUM LABORATORY AT LOS ALAMOS NATIONAL LABORATORY

    SciTech Connect (OSTI)

    Peifer, M.J.; Rendell, K.; Hearnsberger, D.W.

    2003-02-27

    In May 0f 2000, the Cerro Grande wild land fire burned approximately 48,000 acres in and around Los Alamos. In addition to the many buildings that were destroyed in the town site, many structures were also damaged and destroyed within the 43 square miles that comprise the Los Alamos National Laboratory (LANL). A special Act of Congress provided funding to remove Laboratory structures that were damaged by the fire, or that could be threatened by subsequent catastrophic wild land fires. The High Pressure Tritium Laboratory (HPTL) is located at Technical Area (TA) 33, building 86 in the far southeast corner of the Laboratory property. It is immediately adjacent to Bandelier National Park. Because it was threatened by both the Cerro Grande fire in 2000, and the 16,000- acre Dome fire in 1996, the former tritium processing facility was placed on the list of facilities scheduled for Decontamination and Decommissioning under the Cerro Grande Rehabilitation Project. The work was performed through the Facilities and Waste Operations (FWO) Division and is integrated with other Laboratory D&D efforts. The primary demolition contractor was Clauss Construction of San Diego, California. Earth Tech Global Environmental Services of San Antonio, Texas was sub-contracted to Clauss Construction, and provided radiological decontamination support to the project. Although the forty-seven year old facility had been in a state of safe-shutdown since operations ceased in 1990, a significant amount of tritium remained in the rooms where process systems were located. Tritium was the only radiological contaminant associated with this facility. Since no specific regulatory standards have been set for the release of volumetrically contaminated materials, concentration guidelines were derived in order to meet other established regulatory criteria. A tritium removal system was developed for this project with the goal of reducing the volume of tritium concentrated in the concrete of the building

  17. Ortho-aminoazotoluene activates mouse constitutive androstane receptor (mCAR) and increases expression of mCAR target genes

    SciTech Connect (OSTI)

    Smetanina, Mariya A.; Pakharukova, Mariya Y.; Kurinna, Svitlana M.; Dong, Bingning; Hernandez, Juan P.; Moore, David D.; Merkulova, Tatyana I.

    2011-08-15

    2'-3-dimethyl-4-aminoazobenzene (ortho-aminoazotoluene, OAT) is an azo dye and a rodent carcinogen that has been evaluated by the International Agency for Research on Cancer (IARC) as a possible (class 2B) human carcinogen. Its mechanism of action remains unclear. We examined the role of the xenobiotic receptor Constitutive Androstane Receptor (CAR, NR1I3) as a mediator of the effects of OAT. We found that OAT increases mouse CAR (mCAR) transactivation in a dose-dependent manner. This effect is specific because another closely related azo dye, 3'-methyl-4-dimethyl-aminoazobenzene (3'MeDAB), did not activate mCAR. Real-time Q-PCR analysis in wild-type C57BL/6 mice revealed that OAT induces the hepatic mRNA expression of the following CAR target genes: Cyp2b10, Cyp2c29, Cyp3a11, Ugt1a1, Mrp4, Mrp2 and c-Myc. CAR-null (Car{sup -/-}) mice showed no increased expression of these genes following OAT treatment, demonstrating that CAR is required for their OAT dependent induction. The OAT-induced CAR-dependent increase of Cyp2b10 and c-Myc expression was confirmed by Western blotting. Immunohistochemistry analysis of wild-type and Car{sup -/-} livers showed that OAT did not acutely induce hepatocyte proliferation, but at much later time points showed an unexpected CAR-dependent proliferative response. These studies demonstrate that mCAR is an OAT xenosensor, and indicate that at least some of the biological effects of this compound are mediated by this nuclear receptor. - Highlights: > The azo dye and mouse carcinogen OAT is a very effective mCAR activator. > OAT increases mCAR transactivation in a dose-dependent manner. > OAT CAR-dependently increases the expression of a specific subset of CAR target genes. > OAT induces an unexpectedly deferred, but CAR-dependent hepatocyte proliferation.

  18. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of L-lactate dehydrogenase and its H171C mutant from Bacillus subtilis

    SciTech Connect (OSTI)

    Zhang, Yanfeng; Gao, Xiaoli

    2012-08-31

    L-Lactate dehydrogenase (LDH) is an important enzyme involved in the last step of glycolysis that catalyzes the reversible conversion of pyruvate to L-lactate with the simultaneous oxidation of NADH to NAD{sup +}. In this study, wild-type LDH from Bacillus subtilis (BsLDH-WT) and the H171C mutant (BsLDH-H171C) were expressed in Escherichia coli and purified to near-homogeneity. BsLDH-WT was crystallized in the presence of fructose 1,6-bisphosphate (FBP) and NAD{sup +} and the crystal diffracted to 2.38 {angstrom} resolution. The crystal belonged to space group P3, with unit-cell parameters a = b = 171.04, c = 96.27 {angstrom}. BsLDH-H171C was also crystallized as the apoenzyme and in complex with NAD{sup +}, and data sets were collected to 2.20 and 2.49 {angstrom} resolution, respectively. Both BsLDH-H171C crystals belonged to space group P3, with unit-cell parameters a = b = 133.41, c = 99.34 {angstrom} and a = b = 133.43, c = 99.09 {angstrom}, respectively. Tetramers were observed in the asymmetric units of all three crystals.

  19. The influence of TRP53 in the dose response of radiation-induced apoptosis, DNA repair and genomic stability in murine haematopoietic cells

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lemon, Jennifer A.; Taylor, Kristina; Verdecchia, Kyle; Phan, Nghi; Boreham, Douglas R.

    2014-01-01

    Apoptotic and DNA damage endpoints are frequently used as surrogate markers of cancer risk, and have been well-studied in the Trp53+/- mouse model. We report the effect of differing Trp53 gene status on the dose response of ionizing radiation exposures (0.01-2 Gy), with the unique perspective of determining if effects of gene status remain at extended time points. Here we report no difference in the dose response for radiation-induced DNA double-strand breaks in bone marrow and genomic instability (MN-RET levels) in peripheral blood, between wild-type (Trp53+/+) and heterozygous (Trp53+/-) mice. The dose response for Trp53+/+ mice showed higher initial levelsmore » of radiation-induced lymphocyte apoptosis relative to Trp53+/- between 0 and 1 Gy. Although this trend was observed up to 12 hours post-irradiation, both genotypes ultimately reached the same level of apoptosis at 14 hours, suggesting the importance of late-onset p53-independent apoptotic responses in this mouse model. Expected radiation-induced G1 cell cycle delay was observed in Trp53+/+ but not Trp53+/-. Although p53 has an important role in cancer risk, we have shown its influence on radiation dose response can be temporally variable. This research highlights the importance of caution when using haematopoietic endpoints as surrogates to extrapolate radiation-induced cancer risk estimation.« less

  20. Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dao, E. Han; Sierra, Raymond G.; Laksmono, Hartawan; Lemke, Henrik T.; Alonso-Mori, Roberto; Coey, Aaron; Larsen, Kevin; Baxter, Elizabeth L.; Cohen, Aina E.; Soltis, S. Michael; et al

    2015-04-30

    In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecondmore » X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.« less

  1. Statistical Analysis of Microarray Data with Replicated Spots: A Case Study withSynechococcusWH8102

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Thomas, E. V.; Phillippy, K. H.; Brahamsha, B.; Haaland, D. M.; Timlin, J. A.; Elbourne, L. D. H.; Palenik, B.; Paulsen, I. T.

    2009-01-01

    Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in partmoreto the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting biological outcome of this experiment is the indication of the extent to which the phosphorus regulatory system of this cyanobacterium affects the expression of multiple genes beyond those strictly involved in phosphorus acquisition.less

  2. Scientific Data Management (SDM) Center for Enabling Technologies. 2007-2012

    SciTech Connect (OSTI)

    Ludascher, Bertram; Altintas, Ilkay

    2013-09-06

    Over the past five years, our activities have both established Kepler as a viable scientific workflow environment and demonstrated its value across multiple science applications. We have published numerous peer-reviewed papers on the technologies highlighted in this short paper and have given Kepler tutorials at SC06,SC07,SC08,and SciDAC 2007. Our outreach activities have allowed scientists to learn best practices and better utilize Kepler to address their individual workflow problems. Our contributions to advancing the state-of-the-art in scientific workflows have focused on the following areas. Progress in each of these areas is described in subsequent sections. Workflow development. The development of a deeper understanding of scientific workflows "in the wild" and of the requirements for support tools that allow easy construction of complex scientific workflows; Generic workflow components and templates. The development of generic actors (i.e.workflow components and processes) which can be broadly applied to scientific problems; Provenance collection and analysis. The design of a flexible provenance collection and analysis infrastructure within the workflow environment; and, Workflow reliability and fault tolerance. The improvement of the reliability and fault-tolerance of workflow environments.

  3. SITE ENVIRONMENTAL REPORT 2000 (SEPTEMBER 2001).

    SciTech Connect (OSTI)

    BROOKHAVEN NATIONAL LABORTORY; PROJECT MANAGER BARBARA COX

    2001-09-27

    Brookhaven National Laboratory (BNL) strives for excellence in both its science research and its facility operations. BNL manages its world-class scientific research with particular sensitivity to environmental and community issues through its internationally recognized Environmental Management System (EMS) and award-winning community relations program. The Site Environmental Report 2000 (SER) summarizes the status of the Laboratory's environmental programs and performance, including the steady progress towards cleaning up the Laboratory site and fully integrating environmental stewardship into all facets of BNL's mission. BNL's motto, ''Exploring Earth's Mysteries... Protecting its Future,'' describes how the Laboratory approaches its work, with balance between science and the environment. One of the newest initiatives at the Laboratory, the Upton Ecological and Research Reserve, will permanently preserve 530 acres (212 hectares) of the Long Island Central Pine Barrens, a unique ecosystem of forests and wetlands. The Reserve sets aside 10% of BNL property for conservation and ecological research through a partnership between the U.S. Department of Energy (DOE) and the U.S. Fish and Wildlife Service. The Reserve provides habitat for approximately 27 endangered, threatened, or species of special concern, including the state-endangered eastern tiger salamander, state-threatened banded sunfish, and swamp darter, along with a number of other species found onsite, such as the wild turkey and red-tailed hawk.

  4. Decreased cell adhesion promotes angiogenesis in a Pyk2-dependent manner

    SciTech Connect (OSTI)

    Shen, Colette J.; Raghavan, Srivatsan; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 ; Xu, Zhe; Baranski, Jan D.; Yu, Xiang; Wozniak, Michele A.; Miller, Jordan S.; Gupta, Mudit; Buckbinder, Leonard; Chen, Christopher S.

    2011-08-01

    Angiogenesis is regulated by both soluble growth factors and cellular interactions with the extracellular matrix (ECM). While cell adhesion via integrins has been shown to be required for angiogenesis, the effects of quantitative changes in cell adhesion and spreading against the ECM remain less clear. Here, we show that angiogenic sprouting in natural and engineered three-dimensional matrices exhibited a biphasic response, with peak sprouting when adhesion to the matrix was limited to intermediate levels. Examining changes in global gene expression to determine a genetic basis for this response, we demonstrate a vascular endothelial growth factor (VEGF)-induced upregulation of genes associated with vascular invasion and remodeling when cell adhesion was limited, whereas cells on highly adhesive surfaces upregulated genes associated with proliferation. To explore a mechanistic basis for this effect, we turned to focal adhesion kinase (FAK), a central player in adhesion signaling previously implicated in angiogenesis, and its homologue, proline-rich tyrosine kinase 2 (Pyk2). While FAK signaling had some impact, our results suggested that Pyk2 can regulate both gene expression and endothelial sprouting through its enhanced activation by VEGF in limited adhesion contexts. We also demonstrate decreased sprouting of tissue explants from Pyk2-null mice as compared to wild type mice as further confirmation of the role of Pyk2 in angiogenic sprouting. These results suggest a surprising finding that limited cell adhesion can enhance endothelial responsiveness to VEGF and demonstrate a novel role for Pyk2 in the adhesive regulation of angiogenesis.

  5. Nez Perce Tribal Hatchery Program : Draft Environmental Impact Statement.

    SciTech Connect (OSTI)

    United States. Bonneville Power Administration; Nez Perce Tribal Hatchery .

    1996-06-01

    Bonneville Power Administration, the Bureau of Indian Affairs, the Nez Perce Tribe propose a supplementation program to restore chinook salmon to the Clearwater River Subbasin in Idaho. The Clearwater River is a tributary to the Snake River, which empties into the Columbia River. The Nez Perce Tribe would build and operate two central incubation and rearing hatcheries and six satellite facilities. Spring, summer and fall chinook salmon would be reared and acclimated to different areas in the Subbasin and released at the hatchery and satellite sites or in other watercourses throughout the Subbasin. The supplementation program differs from other hatchery programs because the fish would be released at different sizes and would return to reproduce naturally in the areas where they are released. Several environmental issues were identified during scoping: the possibility that the project would fail if mainstem Columbia River juvenile and adult passage problems are not solved; genetic risks to fish listed as endangered or threatened; potential impacts to wild and resident fish stocks because of increase competition for food and space; and water quality. The Proposed Action would affect several important aspects of Nez Perce tribal life, primarily salmon harvest, employment, and fisheries management.

  6. Engineering Ascorbate Peroxidase Activity Into Cytochrome C Peroxidase

    SciTech Connect (OSTI)

    Meharenna, Y.T.; Oertel, P.; Bhaskar, B.; Poulos, T.L.

    2009-05-26

    Cytochrome c peroxidase (CCP) and ascorbate peroxidase (APX) have very similar structures, and yet neither CCP nor APX exhibits each others activities with respect to reducing substrates. APX has a unique substrate binding site near the heme propionates where ascorbate H-bonds with a surface Arg and one heme propionate (Sharp et al. (2003) Nat. Struct. Biol. 10, 303--307). The corresponding region in CCP has a much longer surface loop, and the critical Arg residue that is required for ascorbate binding in APX is Asn in CCP. In order to convert CCP into an APX, the ascorbate-binding loop and critical arginine were engineered into CCP to give the CCP2APX mutant. The mutant crystal structure shows that the engineered site is nearly identical to that found in APX. While wild-type CCP shows no APX activity, CCP2APX catalyzes the peroxidation of ascorbate at a rate of {approx}12 min{sup -1}, indicating that the engineered ascorbate-binding loop can bind ascorbate.

  7. Global Analysis of Salmonella Alternative Sigma Factor E on Protein Translation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Li, Jie; Nakayasu, Ernesto S.; Overall, Christopher C.; Johnson, Rudd C.; Kidwai, Afshan S.; McDermott, Jason E.; Ansong, Charles; Heffron, Fred; Cambronne, Eric D.; Adkins, Joshua N.

    2015-02-16

    The alternative sigma factor E (σE) is critical for response to extracytoplasmic stress in Salmonella. Extensive studies have been conducted on σE-regulated gene expression, particularly at the transcriptional level. Increasing evidence suggests however that σE may indirectly participate in post-transcriptional regulation. Here in this study, we conducted sample-matched global proteomic and transcriptomic analyses to determine the level of regulation mediated by σE in Salmonella. We analysed samples from wild type and isogenic rpoE mutant Salmonella cultivated in three different conditions; nutrient-rich and conditions that mimic early and late intracellular infection. We found that 30% of the observed proteome was regulatedmore » by σE combining all three conditions. In different growth conditions, σE affected the expression of a broad spectrum of Salmonella proteins required for miscellaneous functions. Those involved in transport and binding, protein synthesis, and stress response were particularly highlighted. By comparing transcriptomic and proteomic data, we identified genes post-transcriptionally regulated by σE and found that post-transcriptional regulation was responsible for a majority of changes observed in the σE-regulated proteome. Further, comparison of transcriptomic and proteomic data from hfq mutant of Salmonella demonstrated that σE–mediated post-transcriptional regulation was partially dependent on the RNA-binding protein Hfq.« less

  8. Global Analysis of Salmonella Alternative Sigma Factor E on Protein Translation

    SciTech Connect (OSTI)

    Li, Jie; Nakayasu, Ernesto S.; Overall, Christopher C.; Johnson, Rudd C.; Kidwai, Afshan S.; McDermott, Jason E.; Ansong, Charles; Heffron, Fred; Cambronne, Eric D.; Adkins, Joshua N.

    2015-02-16

    The alternative sigma factor E (σE) is critical for response to extracytoplasmic stress in Salmonella. Extensive studies have been conducted on σE-regulated gene expression, particularly at the transcriptional level. Increasing evidence suggests however that σE may indirectly participate in post-transcriptional regulation. Here in this study, we conducted sample-matched global proteomic and transcriptomic analyses to determine the level of regulation mediated by σE in Salmonella. We analysed samples from wild type and isogenic rpoE mutant Salmonella cultivated in three different conditions; nutrient-rich and conditions that mimic early and late intracellular infection. We found that 30% of the observed proteome was regulated by σE combining all three conditions. In different growth conditions, σE affected the expression of a broad spectrum of Salmonella proteins required for miscellaneous functions. Those involved in transport and binding, protein synthesis, and stress response were particularly highlighted. By comparing transcriptomic and proteomic data, we identified genes post-transcriptionally regulated by σE and found that post-transcriptional regulation was responsible for a majority of changes observed in the σE-regulated proteome. Further, comparison of transcriptomic and proteomic data from hfq mutant of Salmonella demonstrated that σE–mediated post-transcriptional regulation was partially dependent on the RNA-binding protein Hfq.

  9. Evolution of context dependent regulation by expansion of feast/famine regulatory proteins

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Plaisier, Christopher L.; Lo, Fang -Yin; Ashworth, Justin; Brooks, Aaron N.; Beer, Karlyn D.; Kaur, Amardeep; Pan, Min; Reiss, David J.; Facciotti, Marc T.; Baliga, Nitin S.

    2014-11-14

    Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how the expansion of the Feast/Famine Regulatory Protein (FFRP) or Lrp-like proteins into an eight-member family in Halobacterium salinarum NRC-1 has aided in niche-adaptation of this archaeon to a complex and dynamically changing hypersaline environment. We mapped genome-wide binding locations for all eight FFRPs, investigated their preference for binding different effector molecules, and identified the contexts in which they act by analyzing transcriptional responses across 35 growth conditions thatmore » mimic different environmental and nutritional conditions this organism is likely to encounter in the wild. Integrative analysis of these data constructed an FFRP regulatory network with conditionally active states that reveal how interrelated variations in DNA-binding domains, effector-molecule preferences, and binding sites in target gene promoters have tuned the functions of each FFRP to the environments in which they act. We demonstrate how conditional regulation of similar genes by two FFRPs, AsnC (an activator) and VNG1237C (a repressor), have striking environment-specific fitness consequences for oxidative stress management and growth, respectively. This study provides a systems perspective into the evolutionary process by which gene duplication within a transcription factor family contributes to environment-specific adaptation of an organism.« less

  10. Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kole, Chittaranjan; Muthamiliarasan, Mehanathan; Henry, Robert; Edwards, David; Sharma, Rishu; Abberton, Michael; Batley, Jacqueline; Bentley, Alison; Blakeney, Michael; Bryant, John; et al

    2015-08-11

    Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful inmore » enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.« less

  11. The Adipose Renin-Angiotensin System Modulates Systemic Markers of Insulin Sensitivity and Activates the Intrarenal Renin-Angiotensin System

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kim, Suyeon; Soltani-Bejnood, Morvarid; Quignard-Boulange, Annie; Massiera, Florence; Teboul, Michele; Ailhaud, Gerard; Kim, Jung Han; Moustaid-Moussa, Naima; Voy, Brynn H.

    2006-01-01

    Background . The adipose tissue renin-angiotensin system (RAS) contributes to regulation of fat mass and may also impact systemic functions such as blood pressure and metabolism. Methods and results . A panel of mouse models including mice lacking angiotensinogen, Agt ( Agt -KO), mice expressing Agt solely in adipose tissue (aP2- Agt/Agt -KO), and mice overexpressing Agt in adipose tissue (aP2- Agt ) was studied. Total body weight, epididymal fat pad weight, and circulating levels of leptin, insulin, and resistin were significantly decreased in Agt -KO mice, while plasma adiponectin levels were increased. aP2- Agt mice exhibited increased adipositymore » and plasma leptin and insulin levels compared to wild type (WT) controls. Angiotensinogen and type I Ang II receptor protein levels were also elevated in kidney of aP2- Agt mice. Conclusion . These findings demonstrate that alterations in adipose RAS activity significantly impact both local and systemic physiology in a way that may contribute to the detrimental health effects of obesity.« less

  12. A comprehensive collection of systems biology data characterizing the host response to viral infection

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Aevermann, Brian D.; Pickett, Brett E.; Kumar, Sanjeev; Klem, Edward B.; Agnihothram, Sudhakar; Askovich, Peter S.; Bankhead, Armand; Bolles, Meagan; Carter, Victoria; Chang, Jean H.; et al

    2014-10-14

    The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archivedmore » at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). As a result, by comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.« less

  13. cAMP-response-element-binding protein positively regulates breast cancer metastasis and subsequent bone destruction

    SciTech Connect (OSTI)

    Son, Jieun; Lee, Jong-Ho; Kim, Ha-Neui; Ha, Hyunil Lee, Zang Hee

    2010-07-23

    Research highlights: {yields} CREB is highly expressed in advanced breast cancer cells. {yields} Tumor-related factors such as TGF-{beta} further elevate CREB expression. {yields} CREB upregulation stimulates metastatic potential of breast cancer cells. {yields} CREB signaling is required for breast cancer-induced bone destruction. -- Abstract: cAMP-response-element-binding protein (CREB) signaling has been reported to be associated with cancer development and poor clinical outcome in various types of cancer. However, it remains to be elucidated whether CREB is involved in breast cancer development and osteotropism. Here, we found that metastatic MDA-MB-231 breast cancer cells exhibited higher CREB expression than did non-metastatic MCF-7 cells and that CREB expression was further increased by several soluble factors linked to cancer progression, such as IL-1, IGF-1, and TGF-{beta}. Using wild-type CREB and a dominant-negative form (K-CREB), we found that CREB signaling positively regulated the proliferation, migration, and invasion of MDA-MB-231 cells. In addition, K-CREB prevented MDA-MB-231 cell-induced osteolytic lesions in a mouse model of cancer metastasis. Furthermore, CREB signaling in cancer cells regulated the gene expression of PTHrP, MMPs, and OPG, which are closely involved in cancer metastasis and bone destruction. These results indicate that breast cancer cells acquire CREB overexpression during their development and that this CREB upregulation plays an important role in multiple steps of breast cancer bone metastasis.

  14. Somatic mutational analysis of FAK in breast cancer: A novel gain-of-function mutation due to deletion of exon 33

    SciTech Connect (OSTI)

    Fang, Xu-Qian; Liu, Xiang-Fan; Yao, Ling; Chen, Chang-Qiang; Gu, Zhi-Dong; Ni, Pei-Hua; Zheng, Xin-Min; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY ; Fan, Qi-Shi

    2014-01-10

    Highlights: A novel FAK splicing mutation identified in breast tumor. FAK-Del33 mutation promotes cell migration and invasion. FAK-Del33 mutation regulates FAK/Src signal pathway. -- Abstract: Focal adhesion kinase (FAK) regulates cell adhesion, migration, proliferation, and survival. We identified a novel splicing mutant, FAK-Del33 (exon 33 deletion, KF437463), in both breast and thyroid cancers through colony sequencing. Considering the low proportion of mutant transcripts in samples, this mutation was detected by TaqMan-MGB probes based qPCR. In total, three in 21 paired breast tissues were identified with the FAK-Del33 mutation, and no mutations were found in the corresponding normal tissues. When introduced into a breast cell line through lentivirus infection, FAK-Del33 regulated cell motility and migration based on a wound healing assay. We demonstrated that the expression of Tyr397 (main auto-phosphorylation of FAK) was strongly increased in FAK-Del33 overexpressed breast tumor cells compared to wild-type following FAK/Src RTK signaling activation. These results suggest a novel and unique role of the FAK-Del33 mutation in FAK/Src signaling in breast cancer with significant implications for metastatic potential.

  15. INSL5 may be a unique marker of colorectal endocrine cells and neuroendocrine tumors

    SciTech Connect (OSTI)

    Mashima, Hirosato; Ohno, Hideki; Yamada, Yumi; Sakai, Toshitaka; Ohnishi, Hirohide

    2013-03-22

    Highlights: ► INSL5 is expressed in enteroendocrine cells along the colorectum. ► INSL5 is expressed increasingly from proximal colon to rectum. ► INSL5 co-localizes rarely with chromogranin A. ► All rectal neuroendocrine tumors examined expressed INSL5. -- Abstract: Insulin-like peptide 5 (INSL5) is a member of the insulin superfamily, and is a potent agonist for RXFP4. We have shown that INSL5 is expressed in enteroendocrine cells (EECs) along the colorectum with a gradient increase toward the rectum. RXFP4 is ubiquitously expressed along the digestive tract. INSL5-positive EECs have little immunoreactivity to chromogranin A (CgA) and might be a unique marker of colorectal EECs. CgA-positive EECs were distributed normally along the colorectum in INSL5 null mice, suggesting that INSL5 is not required for the development of CgA-positive EECs. Exogenous INSL5 did not affect the proliferation of human colon cancer cell lines, and chemically-induced colitis in INSL5 null mice did not show any significant changes in inflammation or mucosal healing compared to wild-type mice. In contrast, all of the rectal neuroendocrine tumors examined co-expressed INSL5 and RXFP4. INSL5 may be a unique marker of colorectal EECs, and INSL5–RXFP4 signaling might play a role in an autocrine/paracrine fashion in the colorectal epithelium and rectal neuroendocrine tumors.

  16. Nuclear localization of the DNA repair scaffold XRCC1: Uncovering the functional role of a bipartite NLS

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kirby, Thomas W.; Gassman, Natalie R.; Smith, Cassandra E.; Pedersen, Lars C.; Gabel, Scott A.; Sobhany, Mack; Wilson, Samuel H.; London, Robert E.

    2015-08-25

    We have characterized the nuclear localization signal (NLS) of XRCC1 structurally using X-ray crystallography and functionally using fluorescence imaging. Crystallography and binding studies confirm the bipartite nature of the XRCC1 NLS interaction with Importin α (Impα) in which the major and minor binding motifs are separated by >20 residues, and resolve previous inconsistent determinations. Binding studies of peptides corresponding to the bipartite NLS, as well as its major and minor binding motifs, to both wild-type and mutated forms of Impα reveal pronounced cooperative binding behavior that is generated by the proximity effect of the tethered major and minor motifs ofmore » the NLS. The cooperativity stems from the increased local concentration of the second motif near its cognate binding site that is a consequence of the stepwise binding behavior of the bipartite NLS. We predict that the stepwise dissociation of the NLS from Impα facilitates unloading by providing a partially complexed intermediate that is available for competitive binding by Nup50 or the Importin β binding domain. This behavior gives a basis for meeting the intrinsically conflicting high affinity and high flux requirements of an efficient nuclear transport system.« less

  17. Characterization of key triacylglycerol biosynthesis processes in rhodococci

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Amara, Sawsan; Seghezzi, Nicolas; Otani, Hiroshi; Diaz-Salazar, Carlos; Liu, Jie; Eltis, Lindsay D.

    2016-04-29

    In this study, oleaginous microorganisms have considerable potential for biofuel and commodity chemical production. Under nitrogen-limitation, Rhodococcus jostii RHA1 grown on benzoate, an analog of lignin depolymerization products, accumulated triacylglycerols (TAGs) to 55% of its dry weight during transition to stationary phase, with the predominant fatty acids being C16:0 and C17:0. Transcriptomic analyses of RHA1 grown under conditions of N-limitation and N-excess revealed 1,826 dysregulated genes. Genes whose transcripts were more abundant under N-limitation included those involved in ammonium assimilation, benzoate catabolism, fatty acid biosynthesis and the methylmalonyl-CoA pathway. Of the 16 atf genes potentially encoding diacylglycerol O-acyltransferases, atf8 transcriptsmore » were the most abundant during N-limitation (~50-fold more abundant than during N-excess). Consistent with Atf8 being a physiological determinant of TAG accumulation, a Δatf8 mutant accumulated 70% less TAG than wild-type RHA1 while atf8 overexpression increased TAG accumulation 20%. Genes encoding type-2 phosphatidic acid phosphatases were not significantly expressed. By contrast, three genes potentially encoding phosphatases of the haloacid dehalogenase superfamily and that cluster with, or are fused with other Kennedy pathway genes were dysregulated. Overall, these findings advance our understanding of TAG metabolism in mycolic acid-containing bacteria and provide a framework to engineer strains for increased TAG production.« less

  18. Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects

    SciTech Connect (OSTI)

    Kole, Chittaranjan; Muthamiliarasan, Mehanathan; Henry, Robert; Edwards, David; Sharma, Rishu; Abberton, Michael; Batley, Jacqueline; Bentley, Alison; Blakeney, Michael; Bryant, John; Cai, Hongwei; Cakir, Mehmet; Cseke, Leland J.; Cockram, James; de Oliveira, Antonio Costa; De Pace, Ciro; Dempewolf, Hannes; Ellison, Shelby; Gepts, Paul; Greenland, Andy; Hall, Anthony; Hori, Kiyosumi; Hughes, Stephen; Humphreys, Mike W.; Iorizzo, Massimo; Ismail, Abdelgabi M.; Marshall, Athole; Mayes, Sean; Nguyen, Henry T.; Ogbannaya, Francis C.; Ortiz, Rodomiro; Paterson, Andrew H.; Simon, Philipp W.; Tohme, Joe; Tuberosa, Roberto; Valliyodan, Babu; Varshney, Rajeev K.; Wullschleger, Stan D.; Yano, Masahiro; Prasad, Manoj

    2015-08-11

    Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.

  19. Use of prolines for improving growth and other properties of plants and algae

    DOE Patents [OSTI]

    Unkefer, Pat J.; Knight, Thomas J.; Martinez, Rodolfo A.

    2003-04-29

    Increasing the concentration of prolines such as 2-hydroxy-5-oxoproline, in the foliar portions of plants has been shown to cause an increase in carbon dioxide fixation, growth rate, dry weight, nutritional value (amino acids), nodulation and nitrogen fixation, photosynthetically derived chemical energy, and resistance to insect pests over the same properties for wild type plants. This can be accomplished in four ways: (1) the application of a solution of the proline directly to the foliar portions of the plant by spraying these portions; (2) applying a solution of the proline to the plant roots; (3) genetically engineering the plant and screening to produce lines that overexpress glutamine synthetase in the leaves which gives rise to increased concentration of the metabolite, 2-hydroxy-5-oxoproline (this proline is also known as 2-oxoglutaramnate); and (4) impairing the glutamine synthetase activity in the plant roots which causes increased glutamine synthetase activity in the leaves which gives rise to increased concentration of 2-hydroxy-5-oxoproline. Prolines have also been found to induce similar effects in algae.

  20. Use of prolines for improving growth and other properties of plants and algae

    DOE Patents [OSTI]

    Unkefer, Pat J.; Knight, Thomas J.; Martinez, Rodolfo A.

    2003-07-15

    Increasing the concentration of prolines, such as 2-hydroxy-5-oxoproline, in the foliar portions of plants has been shown to cause an increase in carbon dioxide fixation, growth rate, dry weight, nutritional value (amino acids), nodulation and nitrogen fixation, photosynthetically derived chemical energy, and resistance to insect pests over the same properties for wild type plants. This can be accomplished in four ways: (1) the application of a solution of the proline directly to the foliar portions of the plant by spraying these portions; (2) applying a solution of the proline to the plant roots; (3) genetically engineering the plant and screening to produce lines that over-express glutamine synthetase in the leaves which gives rise to increased concentration of the metabolite, 2-hydroxy-5-oxoproline (this proline is also known as 2-oxoglutaramate); and (4) impairing the glutamine synthetase activity in the plant roots which causes increased glutamine synthetase activity in the leaves which gives rise to increased concentration of 2-hydroxy-5-oxoproline. Prolines have also been found to induce similar effects in algae.