National Library of Energy BETA

Sample records for bacterial biofilm development

  1. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    Real-Time Chemical Imaging of Bacterial Biofilm Development Real-Time Chemical Imaging of Bacterial Biofilm Development Print Wednesday, 25 August 2010 00:00 Scientists have...

  2. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of...

  3. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing...

  4. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    that shapes biofilm development. This combination of synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy and the microfluidic platform will...

  5. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMassR&D100 Winners * Impacts onReal-Time Chemical Imaging of Bacterial Biofilm

  6. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMassR&D100 Winners * Impacts onReal-Time Chemical Imaging of Bacterial BiofilmReal-Time

  7. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    SR-FTIR spectromicroscopy measurements. Future applications of the SR-FTIR-based microfluidics approach may help explain why some bacteria maintain biofilms in given...

  8. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    chemical-scale information on biofilm phenotype and function, including Berkeley Lab's bioenergy efforts and subsurface biogeochemical studies. Studying Living Cells For...

  9. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    chronic bacterial infections and beneficial processes such as those enabling biofuel production by microbes. A cartoon of the open-channel microfluidic platform used with SR-FTIR...

  10. A microfluidic device for high throughput bacterial biofilm studies Jeongyun Kim,a

    E-Print Network [OSTI]

    Wood, Thomas K.

    A microfluidic device for high throughput bacterial biofilm studies Jeongyun Kim,a Manjunath Hegde of biofilm community formation. Here, we describe the development of a PDMS-based two-layer microfluidic flow

  11. Analysis and Simulation of a Meso-scale Model of Diffusive Resistance of Bacterial Biofilms to

    E-Print Network [OSTI]

    Demaret, Laurent

    Analysis and Simulation of a Meso-scale Model of Diffusive Resistance of Bacterial Biofilms Most bacteria live in biofilm communities, which offer protection against harmful external impacts mathematical model that focuses on the diffusive resistance that a growing biofilm exerts against penetration

  12. Laser-Generated Shockwaves for the Disruption of Bacterial Biofilms

    E-Print Network [OSTI]

    Navarro, Artemio

    2013-01-01

    Costerton, “Antibiotic resistance of bacteria in biofilms,”28] D. L. Paterson, “Resistance in gram-negative bacteria:Antimicrobial resistance in gram-positive bacteria. ,” Am J

  13. Spatially resolved characterization of biogenic manganese oxideproduction within a bacterial biofilm

    SciTech Connect (OSTI)

    Toner, Brandy; Fakra, Sirine; Villalobos, Mario; Warwick, Tony; Sposito, Garrison

    2004-10-01

    Pseudomonas putida strain MnB1, a biofilm forming bacteria, was used as a model for the study of bacterial Mn oxidation in freshwater and soil environments. The oxidation of Mn{sub (aq)}{sup +2} by P. putida was characterized by spatially and temporally resolving the oxidation state of Mn in the presence of a bacterial biofilm using scanning transmission x-ray microscopy (STXM) combined with near edge x-ray absorption fine structure (NEXAFS) spectroscopy at the Mn-L{sub 2,3} absorption edges. Subsamples were collected from growth flasks containing 0.1 mM and 1 mM total Mn at 16, 24, 36 and 48 hours after inoculation. Immediately after collection, the unprocessed hydrated subsamples were imaged at 40 nm resolution. Manganese NEXAFS spectra were extracted from x-ray energy sequences of STXM images (stacks) and fit with linear combinations of well characterized reference spectra to obtain quantitative relative abundances of Mn(II), Mn(III) and Mn(IV). Careful consideration was given to uncertainty in the normalization of the reference spectra, choice of reference compounds, and chemical changes due to radiation damage. The STXM results confirm that Mn{sub (aq)}{sup +2} was removed from solution by P. putida and was concentrated as Mn(III) and Mn(IV) immediately adjacent to the bacterial cells. The Mn precipitates were completely enveloped by bacterial biofilm material. The distribution of Mn oxidation states was spatially heterogeneous within and between the clusters of bacterial cells. Scanning transmission x-ray microscopy is a promising tool to advance the study of hydrated interfaces between minerals and bacteria, particularly in cases where the structure of bacterial biofilms needs to be maintained.

  14. Laser Desorption Postionization Mass Spectrometry of Antibiotic-Treated Bacterial Biofilms using Tunable Vacuum Ultraviolet Radiation

    SciTech Connect (OSTI)

    Gasper, Gerald L.; Takahashi, Lynelle K.; Zhou, Jia; Ahmed, Musahid; Moore, Jerry F.; Hanley, Luke

    2010-08-04

    Laser desorption postionization mass spectrometry (LDPI-MS) with 8.0 ? 12.5 eV vacuum ultraviolet synchrotron radiation is used to single photon ionize antibiotics andextracellular neutrals that are laser desorbed both neat and from intact bacterial biofilms. Neat antibiotics are optimally detected using 10.5 eV LDPI-MS, but can be ionized using 8.0 eV radiation, in agreement with prior work using 7.87 eV LDPI-MS. Tunable vacuum ultraviolet radiation also postionizes laser desorbed neutrals of antibiotics and extracellular material from within intact bacterial biofilms. Different extracellular material is observed by LDPI-MS in response to rifampicin or trimethoprim antibiotic treatment. Once again, 10.5 eV LDPI-MS displays the optimum trade-off between improved sensitivity and minimum fragmentation. Higher energy photons at 12.5 eV produce significant parent ion signal, but fragment intensity and other low mass ions are also enhanced. No matrix is added to enhance desorption, which is performed at peak power densities insufficient to directly produce ions, thus allowing observation of true VUV postionization mass spectra of antibiotic treated biofilms.

  15. APPLICATIONS OF BIOTECHNOLOGY IN DEVELOPMENT OF BIOMATERIALS: NANOTECHNOLOGY AND BIOFILMS

    SciTech Connect (OSTI)

    Brigmon, R.; Berry, T.; Narayan, R.

    2010-11-29

    Biotechnology is the application of biological techniques to develop new tools and products for medicine and industry. Due to various properties including chemical stability, biocompatibility, and specific activity, e.g. antimicrobial properties, many new and novel materials are being investigated for use in biosensing, drug delivery, hemodialysis, and other medical applications. Many of these materials are less than 100 nanometers in size. Nanotechnology is the engineering discipline encompassing designing, producing, testing, and using structures and devices less than 100 nanometers. One of the challenges associated with biomaterials is microbial contamination that can lead to infections. In recent work we have examined the functionalization of nanoporous biomaterials and antimicrobial activities of nanocrystalline diamond materials. In vitro testing has revealed little antimicrobial activity against Pseudomonas fluorescens bacteria and associated biofilm formation that enhances recalcitrance to antimicrobial agents including disinfectants and antibiotics. Laser scanning confocal microscopy studies further demonstrated properties and characteristics of the material with regard to biofilm formation.

  16. Microfluidic Systems for Investigating Bacterial Chemotaxis and Colonization 

    E-Print Network [OSTI]

    Englert, Derek Lynn

    2011-02-22

    The overall goal of this work was to develop and utilize microfluidic models for investigating bacterial chemotaxis and biofilm formation - phenotypes that play key roles in bacterial infections. Classical methods for investigating chemotaxis...

  17. Influence of sulfate reducing bacterial biofilm on corrosion behavior of low-alloy, high-strength steel (API-5L X80)

    E-Print Network [OSTI]

    ). Microbiologically influenced corrosion (MIC) is one of the most damaging mechanisms to pipeline steel materials deposit corrosion, cracking, enhanced erosion corrosion and dealloying (Little and Lee, 2007). PipelinesInfluence of sulfate reducing bacterial biofilm on corrosion behavior of low-alloy, high

  18. BslA is a self-assembling bacterial hydrophobin that coats the Bacillus subtilis biofilm

    E-Print Network [OSTI]

    van Aalten, Daan

    that the ability of B. subtilis to function as a biocontrol agent in the rhizosphere and reduce infection by funga-positive soil bacterium that functions as an effective plant growth- promoting agent. The biofilm matrix infections (4) but conversely have critical roles in bioremediation (5) and biocontrol processes (6, 7

  19. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    has led to unprecedented study of dynamic processes. The ability to image the chemical reactions in living cells in real time, especially in parallel with fluorescence...

  20. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMassR&D100 Winners * Impacts on GlobalRachel2RateCaseElementsOxideTransformations

  1. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration wouldMassR&D100 Winners * Impacts on

  2. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) by Carbon-RichProton DeliveryRadioactiveRare | NationalEnvironment

  3. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) by Carbon-RichProton DeliveryRadioactiveRare |

  4. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) by Carbon-RichProton DeliveryRadioactiveRare |Real-Time Chemical Imaging

  5. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) by Carbon-RichProton DeliveryRadioactiveRare |Real-Time Chemical

  6. Real-Time Chemical Imaging of Bacterial Biofilm Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation of Fe(II) by Carbon-RichProton DeliveryRadioactiveRare |Real-Time ChemicalReal-Time

  7. Differential growth of wrinkled biofilms

    E-Print Network [OSTI]

    Espeso, D R; Einarsson, B

    2015-01-01

    Biofilms are antibiotic-resistant bacterial aggregates that grow on moist surfaces and can trigger hospital-acquired infections. They provide a classical example in biology where the dynamics of cellular communities may be observed and studied. Gene expression regulates cell division and differentiation, which affect the biofilm architecture. Mechanical and chemical processes shape the resulting structure. We gain insight into the interplay between cellular and mechanical processes during biofilm development on air-agar interfaces by means of a hybrid model. Cellular behavior is governed by stochastic rules informed by a cascade of concentration fields for nutrients, waste and autoinducers. Cellular differentiation and death alter the structure and the mechanical properties of the biofilm, which is deformed according to Foppl-Von Karman equations informed by cellular processes and the interaction with the substratum. Stiffness gradients due to growth and swelling produce wrinkle branching. We are able to repr...

  8. Inter- and Intra-kingdom Signaling in Bacterial Chemotaxis, Biofilm Formation, and Virulence 

    E-Print Network [OSTI]

    Hegde, Manjunath

    2012-02-14

    , houses up to 1000 distinct bacterial species and an estimated excess of ~1014 resident microbes existing in homeostasis with the host's immune system (3). Therefore, the gut microbiome is one of the most complex microbial ecosystems, in which a diverse... suggest this number may be as large as 35,000 (35). The interactions of microbes with the host have evolved into a complex balance of host genes, gut environment, and microbes defined as the microbiome (4, 36). These microbes modulate the normal...

  9. The Fundamentals and Applications of Biofilms

    E-Print Network [OSTI]

    Huang, Ching-Tsan

    Affecting Microbial Growth #12;15 Microbial Nutrition Purpose To obtain energy and construct new cellular #12;4 #12;5 http://www.biofilm.montana.edu #12;6 Reference Books: General Microbial biofilms (1996) H. Bryers (Ed.) #12;7 Reference Books: Bacterial Biofilms Microbial biofilms (2004) M. Ghannoum & G. A. O

  10. Dynamic Metabolism Studies of Live Bacterial Films

    SciTech Connect (OSTI)

    Majors, Paul D.; Mclean, Jeffrey S.

    2008-11-01

    Bacterial film (biofilm) microbes exist within spatial (nutrient, electron-acceptor, pH, etc.) gradients of their own making. Correspondingly, biofilm bacteria are physiologically and functionally distinct from free-floating bacteria and from their own species at differing biofilm depths. This article describes our efforts to develop noninvasive nuclear magnetic resonance (NMR) technologies for biofilm-metabolism studies. This involves integrating NMR with controlled-cultivation methods to interrogate microbial physiology live and under known growth conditions. NMR is uniquely capable of providing depth-resolved metabolic and transport information in a non-invasive, non-sample-consuming fashion, providing information required for experimental reactive transport studies. We have studied mono-species biofilms relevant to environment remediation and human health. We describe these technologies, discuss their advantages and limitations, and give examples of their application.

  11. Fundamentals and Applications of Biofilms

    E-Print Network [OSTI]

    Huang, Ching-Tsan

    Water treatment For limiting biological growth and biofilm formation Wastewater treatment Remove toxic chemicals via the formation of biofilms Bioremediation Remove or detoxify pollutants that have found;3 International Water Association Water Cycle #12;4 Water Treatment Bacterial growth in purified water Growth

  12. Permeabilizing biofilms

    DOE Patents [OSTI]

    Soukos, Nikolaos S. (Revere, MA); Lee, Shun (Arlington, VA); Doukas,; Apostolos G. (Belmont, MA)

    2008-02-19

    Methods for permeabilizing biofilms using stress waves are described. The methods involve applying one or more stress waves to a biofilm, e.g., on a surface of a device or food item, or on a tissue surface in a patient, and then inducing stress waves to create transient increases in the permeability of the biofilm. The increased permeability facilitates delivery of compounds, such as antimicrobial or therapeutic agents into and through the biofilm.

  13. Image-Based Screening in Vibrio Cholerae: Platform Development, Image Analysis, and Small Molecule Biofilm Modulators

    E-Print Network [OSTI]

    Peach, Kelly Corbus

    2013-01-01

    8 1.3.2. Antimicrobial Resistance Bacteria in the biofilm1.3.1. Host Resistance The nature of bacteria in the biofilmadditional resistance mechanisms employed by bacteria in the

  14. Combating biofilms and antibiotic resistance using synthetic biology

    E-Print Network [OSTI]

    Lu, Timothy K. (Timothy Kuan-Ta), 1981-

    2008-01-01

    Bacterial infections represent a significant source of morbidity and mortality. Biofilms and antibiotic resistance pose challenges to our future ability to treat bacterial diseases with antibiotics (1). Bacteria frequently ...

  15. Mesoscale Elucidation of Biofilm Shear Behavior

    E-Print Network [OSTI]

    Barai, Pallab; Mukherjee, Partha P

    2015-01-01

    Formation of bacterial colonies as biofilm on the surface/interface of various objects has the potential to impact not only human health and disease but also energy and environmental considerations. Biofilms can be regarded as soft materials, and comprehension of their shear response to external forces is a key element to the fundamental understanding. A mesoscale model has been presented in this article based on digitization of a biofilm microstructure. Its response under externally applied shear load is analyzed. Strain stiffening type behavior is readily observed under high strain loads due to the unfolding of chains within soft polymeric substrate. Sustained shear loading of the biofilm network results in strain localization along the diagonal direction. Rupture of the soft polymeric matrix can potentially reduce the intercellular interaction between the bacterial cells. Evolution of stiffness within the biofilm network under shear reveals two regions: a) initial increase in stiffness due to strain stiffe...

  16. Role of AI-2 in oral biofilm formation using microfluidic devices 

    E-Print Network [OSTI]

    Kim, Sun Ho

    2009-05-15

    Biofilms are highly organized bacterial structures that are attached to a surface. They are ubiquitous in nature and may be detrimental, causing numerous types of illnesses in living organisms. Biofilms in the human oral cavity are the main cause...

  17. Bacterial flagella explore microscale hummocks and hollows to increase adhesion

    E-Print Network [OSTI]

    Friedlander, Ronn Samuel

    Biofilms, surface-bound communities of microbes, are economically and medically important due to their pathogenic and obstructive properties. Among the numerous strategies to prevent bacterial adhesion and subsequent biofilm ...

  18. Support Analytical Infrastructure and Further Development of a Statewide Bacterial Source Tracking Library 

    E-Print Network [OSTI]

    DiGiovanni, G.; Casarez, E.; Gentry, T.; Martin, E.; Gregory, L.; Wagner, K.

    2013-01-01

    The project titled Support Analytical Infrastructure and Further Development of a Statewide Bacterial Source Tracking Library funded by the Texas State Soil and Water Conservation Board was established to provide needed resources to expand...

  19. Microscale Confinement features in microfluidic devices can affect biofilm

    SciTech Connect (OSTI)

    Kumar, Aloke; Karig, David K; Neethirajan, Suresh; Acharya, Rajesh K; Mukherjee, Partha P; Retterer, Scott T; Doktycz, Mitchel John

    2013-01-01

    Biofilms are aggregations of microbes that are encased by extra-cellular polymeric substances (EPS) and adhere to surfaces and interfaces. Biofilm development on abiotic surfaces is a dynamic process, which typically proceeds through an initial phase of adhesion of plankntonic microbes to the substrate, followed by events such as growth, maturation and EPS secretion. However, the coupling of hydrodynamics, microbial adhesion and biofilm growth remain poorly understood. Here, we investigate the effect of semiconfined features on biofilm formation. Using a microfluidic device and fluorescent time-lapse microscopy, we establish that confinement features can significantly affect biofilm formation. Biofilm dynamics change not only as a function of confinement features, but also of the total fluid flow rate, and our combination of experimental results and numerical simulations reveal insights into the link between hydrodynamics and biofilm formation.

  20. IMPACTS OF BIOFILM FORMATION ON CELLULOSE FERMENTATION

    SciTech Connect (OSTI)

    Leschine, Susan

    2009-10-31

    This project addressed four major areas of investigation: i) characterization of formation of Cellulomonas uda biofilms on cellulose; ii) characterization of Clostridium phytofermentans biofilm development; colonization of cellulose and its regulation; iii) characterization of Thermobifida fusca biofilm development; colonization of cellulose and its regulation; and iii) description of the architecture of mature C. uda, C. phytofermentans, and T. fusca biofilms. This research is aimed at advancing understanding of biofilm formation and other complex processes involved in the degradation of the abundant cellulosic biomass, and the biology of the microbes involved. Information obtained from these studies is invaluable in the development of practical applications, such as the single-step bioconversion of cellulose-containing residues to fuels and other bioproducts. Our results have clearly shown that cellulose-decomposing microbes rapidly colonize cellulose and form complex structures typical of biofilms. Furthermore, our observations suggest that, as cells multiply on nutritive surfaces during biofilms formation, dramatic cell morphological changes occur. We speculated that morphological changes, which involve a transition from rod-shaped cells to more rounded forms, might be more apparent in a filamentous microbe. In order to test this hypothesis, we included in our research a study of biofilm formation by T. fusca, a thermophilic cellulolytic actinomycete commonly found in compost. The cellulase system of T. fusca has been extensively detailed through the work of David Wilson and colleagues at Cornell, and also, genome sequence of a T. fusca strain has been determine by the DOE Joint Genome Institute. Thus, T. fusca is an excellent subject for studies of biofilm development and its potential impacts on cellulose degradation. We also completed a study of the chitinase system of C. uda. This work provided essential background information for understanding how C. uda colonizes and degrades insoluble substrates. Major accomplishments of the project include: • Development of media containing dialysis tubing (described by the manufacturer as “regenerated cellulose”) as sole carbon and energy source and a nutritive surface for the growth of cellulolytic bacteria, and development of various microscopic methods to image biofilms on dialysis tubing. • Demonstration that cultures of C. phytofermentans, an obligate anaerobe, C. uda, a facultative aerobe, and T. fusca, a filamentous aerobe, formed microbial communities on the surface of dialysis tubing, which possessed architectural features and functional characteristics typical of biofilms. • Demonstration that biofilm formation on the nutritive surface, cellulose, involves a complex developmental processes, including colonization of dialysis tubing, formation of cell clusters attached to the nutritive surface, cell morphological changes, formation of complex structures embedded in extracellular polymeric matrices, and dispersal of biofilm communities as the nutritive surface is degraded. • Determination of surface specificity and regulatory aspects of biofilm formation by C. phytofermentans, C. uda, and T. fusca. • Demonstration that biofilm formation by T. fusca forms an integral part of the life cycle of this filamentous cellulolytic bacterium, including studies on the role of mycelial pellet formation in the T. fusca life cycle and a comparison of mycelial pellets to surface-attached T. fusca biofilms. • Characterization of T. fusca biofilm EPS, including demonstration of a functional role for EPS constituents. • Correlation of T. fusca developmental life cycle and cellulase gene expression.

  1. Development of a Vaccine for Bacterial Kidney Disease in Salmon, 1987 Annual Report.

    SciTech Connect (OSTI)

    Kaattari, Stephen

    1988-06-01

    Bacterial kidney disease (BKD) has been and remains a chronic contributory problem limiting the productivity of salmon in the Columbia River Basin. Control of this disease will not come easily, but it would lead to a tremendous increase in the health and numbers of salmon populations. Vaccination of salmon to Renibacterium salmoninarum (KDB) is a potentially successful method of controlling this disease. To date, however, no successful vaccine has been developed for general use. A possible solution to this problem, and thus the goal of this research, is to isolate the antigenic components of KDB and enhance their ability to activate the host defenses. This will be accomplished by the chemical modification of these antigens with potent immunomodulatory substances. These modified antigens will then be tested for their effectiveness in inducing immunity to BKD and thereby preventing the disease. The goal of the project's fourth year was to test the immunogenicity and prophylactic value in coho salmon (Oncorhynchus kisutch) of various--chemical conjugates of Renibacterium salmoninarum cell and major antigens. This was accomplished by assessing the serum antibody response, the cellular immune response (chemiluminescence), and the kinetics of mortality after lethal injections of the bacteria. The studies completed this year have: (1) identified immunization procedures which enhance the induction of high levels of antibody; (2) identified functionally distinct serum antibodies which may possess different abilities to protect salmon against BKD; (3) begun the isolation and characterization of anti-R. salmoninarum antibodies which may correlate with varying degrees of protection; (4) identified chemiluminescence as a potential method for assessing cellular immunity to bacterial kidney disease; and (5) characterized two monoclonal antibodies to R. salmoninarum which will be of benefit in the diagnosis of this disease.

  2. EFFECT OF MECHANICAL STRESS ON BACTERIAL ADHESION

    E-Print Network [OSTI]

    Ribot, Magali

    EFFECT OF MECHANICAL STRESS ON BACTERIAL ADHESION AND EARLY BIOFILM GROWTH Sigolène LECUYER-4. growth and maturation (h-days) 5. dispersion (days-months) #12;MECHANICAL STRESS DURING ADHESION stress can be transmitted: ·by the underlying substrate (adhesion, friction) time PART I PART II #12

  3. Bacterial Source Tracking to Support the Development and Implementation of Watershed Protection Plans for the Lampasas and Leon Rivers: Lampasas River Watershed Final Report 

    E-Print Network [OSTI]

    Gregory, L.; Casarez, E.; Truesdale, J.; Di Giovanni, G.; Owen, T.; Wolfe, J.

    2013-04-25

    The Bacterial Source Tracking to Support the Development and Implementation of Watershed Protection Plans for the Lampasas and Leon Rivers project was developed to provide supplemental information to stakeholders engaged ...

  4. Development of a Low Input and sustainable Switchgrass Feedstock Production System Utilizing Beneficial Bacterial Endophytes

    SciTech Connect (OSTI)

    Mei, Chuansheng; Nowak, Jerzy; Seiler, John

    2014-10-24

    Switchgrass represents a promising feedstock crop for US energy sustainability. However, its broad utilization for bioenergy requires improvements of biomass yields and stress tolerance. In this DOE funded project, we have been working on harnessing beneficial bacterial endophytes to enhance switchgrass performance and to develop a low input feedstock production system for marginal lands that do not compete with the production of food crops. We have demonstrated that one of most promising plant growth-promoting bacterial endophytes, Burkholderia phytofirmans strain PsJN, is able to colonize roots and significantly promote growth of switchgrass cv. Alamo under in vitro, growth chamber, greenhouse, as well as field conditions. Furthermore, PsJN bacterization improved growth and development of switchgrass seedlings, significantly stimulated plant root and shoot growth, and tiller number in the field, and enhanced biomass accumulation on both poor (p<0.001) and rich (p<0.05) soils, with more effective stimulation of plant growth in low fertility soil. Plant physiology measurements showed that PsJN inoculated Alamo had consistently lower transpiration, lower stomatal conductance, and higher water use efficiency in greenhouse conditions. These physiological changes may significantly contribute to the recorded growth enhancement. PsJN inoculation rapidly results in an increase in photosynthetic rates which contributes to the advanced growth and development. Some evidence suggests that this initial growth advantage decreases with time when resources are not limited such as in greenhouse studies. Additionally, better drought resistance and drought hardening were observed in PsJN inoculated switchgrass. Using the DOE-funded switchgrass EST microarray, in a collaboration with the Genomics Core Facility at the Noble Foundation, we have determined gene expression profile changes in both responsive switchgrass cv. Alamo and non-responsive cv. Cave-in-Rock (CR) following PsJN bacterization. With the MapMan software to analyze microarray data, the number of up- and down-regulated probes was calculated. The number of up-regulated probes in Alamo was 26, 14, 14, and 12% at 0.5, 2, 4 and 8 days after inoculation (DAI) with PsJN, respectively while the corresponding number in CR was 24, 22, 21, and 19%, respectively. In both cultivars, the largest number of up-regulated probes occurred at 0.5 DAI. Noticeable differences throughout the timeframe between Alamo and CR were that the number was dramatically decreased to half (12%) in Alamo but remained high in CR (approximately 20%). The number of down regulated genes demonstrated different trends in Alamo and CR. Alamo had an increasing trend from 9% at 0.5 DAI to 11, 17, and 28% at 2, 4, and 8 DAI, respectively. However, CR had 13% at 0.5 and 2 DAI, and declined to 10% at 4 and 8 DAI. With the aid of MapMan and PageMan, we mapped the response of the ID probes to the observed major gene regulatory network and major biosynthetic pathway changes associated with the beneficial bacterial endophyte infection, colonization, and early growth promotion process. We found significant differences in gene expression patterns between responsive and non-responsive cultivars in many pathways, including redox state regulation, signaling, proteolysis, transcription factors, as well as hormone (SA and JA in particular)-associated pathways. Form microarray data, a total of 50 key genes have been verified using qPCR. Ten of these genes were chosen for further functional study via either overexpression and/or RNAi knockout technologies. These genes were calmodulin-related calcium sensor protein (CAM), glutathione S-transferase (GST), histidine-containing phosphotransfer protein (H-221), 3 different zinc finger proteins (ZF-371, ZF131 and ZF242), EF hand transcription factor (EF-622), peroxidase, cellulose synthase catalytic submit A2 (CESA2), and Aux/IAA family. A total of 8 overexpression and 5 RNAi transgenic plants have been regenerated, and their gene expression levels determined using qPCR. Consequently

  5. Artificial teeth : dental biofilm analysis on a chip

    E-Print Network [OSTI]

    Lam, Raymond Hiu-wai

    2010-01-01

    In this thesis, an "artificial teeth" microfluidic device is developed that provides unprecedented control over the conditions required to simulate the growth of complex dental biofilm. Dental plaque formation is not only ...

  6. In situ biofilm coupon device

    DOE Patents [OSTI]

    Peyton, Brent M. (Kennewick, WA); Truex, Michael J. (Richland, WA)

    1997-01-01

    An apparatus for characterization of in-situ microbial biofilm populations in subsurface groundwater. The device permits biofilm-forming microorganisms to adhere to packing material while emplaced in a groundwater strata, so that the packing material can be later analyzed for quantity and type of microorganisms, growth rate, and nutrient requirements.

  7. In situ biofilm coupon device

    DOE Patents [OSTI]

    Peyton, B.M.; Truex, M.J.

    1997-06-24

    An apparatus is disclosed for characterization of in-situ microbial biofilm populations in subsurface groundwater. The device permits biofilm-forming microorganisms to adhere to packing material while emplaced in a groundwater strata, so that the packing material can be later analyzed for quantity and type of microorganisms, growth rate, and nutrient requirements. 3 figs.

  8. FAST CARS Developing a Laser Spectroscopic Technique for Rapid Identification of Bacterial Spores

    E-Print Network [OSTI]

    Scully, M O; Lucht, R P; Opatrny, T; Pilloff, H; Rebane, A; Sokolov, A V; Zubairy, M S

    2002-01-01

    Airborne contaminants, e.g., bacterial spores, are usually analyzed by time consuming microscopic, chemical and biological assays. Current research into real time laser spectroscopic detectors of such contaminants is based on e.g. resonant Raman spectroscopy. The present approach derives from recent experiments in which atoms and molecules are prepared by one (or more) coherent laser(s) and probed by another set of lasers. The connection with previous studies based on "Coherent Anti-Stokes Raman Spectroscopy" (CARS) is to be noted. However generating and utilizing maximally coherent oscillation in macromolecules having an enormous number of degrees of freedom is much more challenging. This extension of the CARS technique is called FAST CARS (Femtosecond Adaptive Spectroscopic Techniques for Coherent Anti-Stokes Raman Spectroscopy), and the present paper proposes and analyses ways in which it could be used to rapidly identify pre-selected molecules in real time.

  9. Adhesion and formation of microbial biofilms in complex microfluidic devices

    SciTech Connect (OSTI)

    Kumar, Aloke [ORNL; Karig, David K [ORNL; Neethirajan, Suresh [University of Guelph; Suresh, Anil K [ORNL; Srijanto, Bernadeta R [ORNL; Mukherjee, Partha P [ORNL; Retterer, Scott T [ORNL; Doktycz, Mitchel John [ORNL

    2012-01-01

    Shewanella oneidensis is a metal reducing bacterium, which is of interest for bioremediation and clean energy applications. S. oneidensis biofilms play a critical role in several situations such as in microbial energy harvesting devices. Here, we use a microfluidic device to quantify the effects of hydrodynamics on the biofilm morphology of S. oneidensis. For different rates of fluid flow through a complex microfluidic device, we studied the spatiotemporal dynamics of biofilms, and we quantified several morphological features such as spatial distribution, cluster formation and surface coverage. We found that hydrodynamics resulted in significant differences in biofilm dynamics. The baffles in the device created regions of low and high flow in the same device. At higher flow rates, a nonuniform biofilm develops, due to unequal advection in different regions of the microchannel. However, at lower flow rates, a more uniform biofilm evolved. This depicts competition between adhesion events, growth and fluid advection. Atomic force microscopy (AFM) revealed that higher production of extra-cellular polymeric substances (EPS) occurred at higher flow velocities.

  10. Adhesion of Bacterial Exopolymers to r-FeOOH: Inner-Sphere Complexation of Phosphodiester Groups

    E-Print Network [OSTI]

    Chorover, Jon

    Adhesion of Bacterial Exopolymers to r-FeOOH: Inner-Sphere Complexation of Phosphodiester Groups of polyelectrolytes that mediate biomineralization and bacterial adhesion and stabilize biofilm matrixes in natural-FeOOH) surface, providing an energetically stable bond for further EPS or cell adhesion. 1. Introduction

  11. Characterization of Biofilm in 200W

    E-Print Network [OSTI]

    PNNL-23679 Characterization of Biofilm in 200W Fluidized Bed Reactors September 2014 MH Lee E ER Eisenhauer SD Saurey EA Cordova BD Lee EC Golovich KE Parker #12;#12;PNNL-23679 Characterization of Biofilm

  12. From Nanowires to Biofilms: An Exploration of Novel Mechanisms of Uranium Transformation Mediated by Geobacter Bacteria

    SciTech Connect (OSTI)

    REGUERA, GEMMA [Michigan State University

    2014-01-16

    One promising strategy for the in situ bioremediation of radioactive groundwater contaminants that has been identified by the SBR Program is to stimulate the activity of dissimilatory metal-reducing microorganisms to reductively precipitate uranium and other soluble toxic metals. The reduction of U(VI) and other soluble contaminants by Geobacteraceae is directly dependent on the reduction of Fe(III) oxides, their natural electron acceptor, a process that requires the expression of Geobacter’s conductive pili (pilus nanowires). Expression of conductive pili by Geobacter cells leads to biofilm development on surfaces and to the formation of suspended biogranules, which may be physiological closer to biofilms than to planktonic cells. Biofilm development is often assumed in the subsurface, particularly at the matrix-well screen interface, but evidence of biofilms in the bulk aquifer matrix is scarce. Our preliminary results suggest, however, that biofilms develop in the subsurface and contribute to uranium transformations via sorption and reductive mechanisms. In this project we elucidated the mechanism(s) for uranium immobilization mediated by Geobacter biofilms and identified molecular markers to investigate if biofilm development is happening in the contaminated subsurface. The results provided novel insights needed in order to understand the metabolic potential and physiology of microorganisms with a known role in contaminant transformation in situ, thus having a significant positive impact in the SBR Program and providing novel concept to monitor, model, and predict biological behavior during in situ treatments.

  13. Laser-Generated Shockwaves for the Disruption of Bacterial Biofilms

    E-Print Network [OSTI]

    Navarro, Artemio

    2013-01-01

    illuminated by three high power LEDs centered at 850 nm in aHigh power light emitting diodes (LEDs), however, provide aThe optical power of the three LED light was measured by a

  14. Laser-Generated Shockwaves for the Disruption of Bacterial Biofilms

    E-Print Network [OSTI]

    Navarro, Artemio

    2013-01-01

    into microcentrifuge tubes 9. Vortex and store in cryogenicthe 50 mL test tube with TSB 4. Vortex to evenly mix then

  15. Laser-Generated Shockwaves for the Disruption of Bacterial Biofilms

    E-Print Network [OSTI]

    Navarro, Artemio

    2013-01-01

    CCD and prevents ambient light pollution that exist at otherrange. This causes light pollution in the acquired images.filtering prevents light pollution from other wavelengths,

  16. When to clean and how to clean biofilms in heat exchangers

    E-Print Network [OSTI]

    Pogiatzis, T.A.; Vassiliadis, V.S.; Mergulhão, F.J.; Wilson, D.I.

    2014-07-02

    .M. Generalized Benders decomposition. Journal Of Optimization Theory Applications. 1972, 10, 237 - 60. [23] Nebot, E., Casanueva, J.F., Casanueva, T., Sales, D. Model for fouling deposition on power plant steam condensers cooled with seawater: effect of water... .K., Pokroy, B., Seminara, A., Aizenberg, J. Bacterial biofilm shows persistent resistance to liquid wetting and gas penetration. Proceedings of the National Academy of Sciences of the United States of America. 2011, 108, 995-1000. [19] Marchand, S., De Block...

  17. Studies of protein adsorption on implant materials in relation to biofilm formation I. Activity of Pseudomonas aeruginosa on Polypropylene and High density Polyethylene in presence of serum albumin

    E-Print Network [OSTI]

    Sinha, S Dutta; Maity, P K; Tarafdar, S; Moulik, S P

    2014-01-01

    The surface of biomaterials used as implants are highly susceptible to bacterial colonization and subsequent infection. The amount of protein adsorption on biomaterials, among other factors, can affect the nature and quality of biofilms formed on them. The variation in the adsorption time of the protein on the biomaterial surface produces a phenotypic change in the bacteria by alteration of the production of EPS (exoplysaccharide) matrix. Knowledge of the effects of protein adsorption on implant infection will be very useful in understanding the chemistry of the biomaterial surfaces, which can deter the formation of biofilms. It is observed that the adsorption of BSA on the biomaterial surfaces increases with time and concentration, irrespective of their type and the nature of the EPS matrix of the bacterial biofilm is dependent on the amount of protein adsorbed on the biomaterial surface. The adsorption of protein (BSA) on the biomaterials, polypropylene (PP) and high density polyethylene (HDPE) has been stu...

  18. Modeling for Anaerobic Fixed-Bed Biofilm Reactors

    SciTech Connect (OSTI)

    Liu, B. Y. M.; Pfeffer, J. T.

    1989-06-01

    The specific objectives of this research were: 1. to develop an equilibrium model for chemical aspects of anaerobic reactors; 2. to modify the equilibrium model for non-equilibrium conditions; 3. to incorporate the existing biofilm models into the models above to study the biological and chemical behavior of the fixed-film anaerobic reactors; 4. to experimentally verify the validity of these models; 5. to investigate the biomass-holding ability of difference packing materials for establishing reactor design criteria.

  19. Bacterial hydrodynamics

    E-Print Network [OSTI]

    Lauga, Eric

    2015-01-01

    Bacteria predate plants and animals by billions of years. Today, they are the world's smallest cells yet they represent the bulk of the world's biomass, and the main reservoir of nutrients for higher organisms. Most bacteria can move on their own, and the majority of motile bacteria are able to swim in viscous fluids using slender helical appendages called flagella. Low-Reynolds-number hydrodynamics is at the heart of the ability of flagella to generate propulsion at the micron scale. In fact, fluid dynamic forces impact many aspects of bacteriology, ranging from the ability of cells to reorient and search their surroundings to their interactions within mechanically and chemically-complex environments. Using hydrodynamics as an organizing framework, we review the biomechanics of bacterial motility and look ahead to future challenges.

  20. Bacterial hydrodynamics

    E-Print Network [OSTI]

    Eric Lauga

    2015-09-07

    Bacteria predate plants and animals by billions of years. Today, they are the world's smallest cells yet they represent the bulk of the world's biomass, and the main reservoir of nutrients for higher organisms. Most bacteria can move on their own, and the majority of motile bacteria are able to swim in viscous fluids using slender helical appendages called flagella. Low-Reynolds-number hydrodynamics is at the heart of the ability of flagella to generate propulsion at the micron scale. In fact, fluid dynamic forces impact many aspects of bacteriology, ranging from the ability of cells to reorient and search their surroundings to their interactions within mechanically and chemically-complex environments. Using hydrodynamics as an organizing framework, we review the biomechanics of bacterial motility and look ahead to future challenges.

  1. Effect of micro-patterning on bacterial adhesion on PET (polyethylene terephthalate) surface

    E-Print Network [OSTI]

    Wang, Liyun; Chen, Wei; Terentjev, Eugene

    2014-12-16

    medical devices and food processing facilities 4 are prone to infections caused by the attached microbes, and eventually - biofilms, leading to a direct threat to 5 health and food contamination.3-6 Hence, a host of biological and chemical strategies... -Tasciuc DA, et al. Effect of micro-and nanoscale topography on the adhesion of 6 bacterial cells to solid surfaces. Appl Environ Microb 2013;79:2703-12. 7 4. Antoci Jr V, Adams CS, Parvizi J, et al. The inhibition of Staphylococcus epidermidis biofilm...

  2. Mechanical robustness of Pseudomonas aeruginosa biofilms

    E-Print Network [OSTI]

    Lieleg, Oliver

    Biofilms grow on various surfaces and in many different environments, a phenomenon that constitutes major problems in industry and medicine. Despite their importance little is known about the viscoelastic properties of ...

  3. Gene Expression in Bacillus subtilis Surface Biofilms With and Without

    E-Print Network [OSTI]

    Wood, Thomas K.

    . subtilis and its sporula- tion mutant (ÁspoIIGB::erm) were investigated to discern the important biofilm

  4. Bacterial motility on abiotic surfaces

    E-Print Network [OSTI]

    Gibiansky, Maxsim

    2013-01-01

    J Costerton. Antibiotic resistance of bacteria in biofilms.bacteria are extremely resistant to many forms of stress, including a greatly heightened antibiotic resistance.

  5. Bacterial Polybydroxyalkanoates Sang Yup Lee

    E-Print Network [OSTI]

    Review Bacterial Polybydroxyalkanoates Sang Yup Lee Department of Chemical Engineering and BioProcess- pared with petrochemical derived plastics. Among the candidates for biodegradable plastics, PHAs have, much effort has been devoted to develop a process for the economical production of PHAs. Here we review

  6. Studies of protein adsorption on implant materials in relation to biofilm formation I. Activity of Pseudomonas aeruginosa on Polypropylene and High density Polyethylene in presence of serum albumin

    E-Print Network [OSTI]

    S Dutta Sinha; Susmita Chatterjee; P. K. Maity; S. Tarafdar; S. P. Moulik

    2014-11-19

    The surface of biomaterials used as implants are highly susceptible to bacterial colonization and subsequent infection. The amount of protein adsorption on biomaterials, among other factors, can affect the nature and quality of biofilms formed on them. The variation in the adsorption time of the protein on the biomaterial surface produces a phenotypic change in the bacteria by alteration of the production of EPS (exoplysaccharide) matrix. Knowledge of the effects of protein adsorption on implant infection will be very useful in understanding the chemistry of the biomaterial surfaces, which can deter the formation of biofilms. It is observed that the adsorption of BSA on the biomaterial surfaces increases with time and concentration, irrespective of their type and the nature of the EPS matrix of the bacterial biofilm is dependent on the amount of protein adsorbed on the biomaterial surface. The adsorption of protein (BSA) on the biomaterials, polypropylene (PP) and high density polyethylene (HDPE) has been studied and the formation of the biofilms of Pseudomonas aeruginosa on them has been examined.

  7. Mechanics of torque generation in the bacterial flagellar motor

    E-Print Network [OSTI]

    Mandadapu, Kranthi K; Berry, Richard M; Oster, George

    2015-01-01

    The bacterial flagellar motor (BFM) is responsible for driving bacterial locomotion and chemotaxis, fundamental processes in pathogenesis and biofilm formation. In the BFM, torque is generated at the interface between transmembrane proteins (stators) and a rotor. It is well-established that the passage of ions down a transmembrane gradient through the stator complex provides the energy needed for torque generation. However, the physics involved in this energy conversion remain poorly understood. Here we propose a mechanically specific model for torque generation in the BFM. In particular, we identify two fundamental forces involved in torque generation: electrostatic and steric. We propose that electrostatic forces serve to position the stator, while steric forces comprise the actual 'power stroke'. Specifically, we predict that ion-induced conformational changes about a proline 'hinge' residue in an $\\alpha$-helix of the stator are directly responsible for generating the power stroke. Our model predictions f...

  8. Community Genomic, Proteomic, and Transcriptomic Analyses of Acid Mine Drainage Biofilm Communities

    E-Print Network [OSTI]

    Goltsman, Daniela

    2013-01-01

    T, Banfield J. 2004. Acid mine drainage biogeochemistry atof eukaryotes in acid mine drainage biofilm communities.III) bacteria in acid mine drainage biofilms. Appl Environ

  9. DEVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION

    SciTech Connect (OSTI)

    Bill W. Bogan; Brigid M. Lamb; Gemma Husmillo; Kristine Lowe; J. Robert Paterek; John J. Kilbane II

    2004-12-01

    The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Various chemicals that inhibit the growth and/or the metabolism of corrosion-associated microbes such as sulfate reducing bacteria, denitrifying bacteria, and methanogenic bacteria were evaluated to determine their ability to inhibit corrosion in experiments utilizing pure and mixed bacterial cultures, and planktonic cultures as well as mature biofilms. Planktonic cultures are easier to inhibit than mature biofilms but several compounds were shown to be effective in decreasing the amount of metal corrosion. Of the compounds tested hexane extracts of Capsicum pepper plants and molybdate were the most effective inhibitors of sulfate reducing bacteria, bismuth nitrate was the most effective inhibitor of nitrate reducing bacteria, and 4-((pyridine-2-yl)methylamino)benzoic acid (PMBA) was the most effective inhibitor of methanogenic bacteria. All of these compounds were demonstrated to minimize corrosion due to MIC, at least in some circumstances. The results obtained in this project are consistent with the hypothesis that any compound that disrupts the metabolism of any of the major microbial groups present in corrosion-associated biofilms shows promise in limiting the amount/rate of corrosion. This approach of controlling MIC by controlling the metabolism of biofilms is more environmentally benign than the current approach involving the use of potent biocides, and warrants further investigation.

  10. Bacterial Source Tracking to Support the Development and Implementation of Watershed Protection Plans for the Lampasas and Leon Rivers: Lampasas River Watershed Final Report 

    E-Print Network [OSTI]

    Gregory, L.; Casarez, E.; Truesdale, J.; Di Giovanni, G.; Owen, T; Wolfe, J.

    2013-04-25

    . iv Acronyms ADCM Acoustic Doppler Current Meter ARCC Average Rate of Correct Classification AgriLife-TP Blackland Research and Extension Center in Temple BST Bacterial Source Tracking CAFO Concentrated Animal Feeding Operation CFS...&M AgriLife Research?s - Water Science Laboratory located at the Blackland Research and Extension Center in Temple (AgriLife-TP) cooperated with the University of Texas Health Science Center at Houston School of Public Health, El Paso Regional Campus...

  11. RESPONSES OF STREAM BIOFILM TO PACIFIC SALMON (ONCORHYNCHUS SPP.) SPAWNERS

    E-Print Network [OSTI]

    Lamberti, Gary A.

    Pacific Rim. The dynam- ics of salmon runs and environmental conditions of streams in which they spawn canRESPONSES OF STREAM BIOFILM TO PACIFIC SALMON (ONCORHYNCHUS SPP.) SPAWNERS: THE ROLE by Janine R¨uegg 2011 All Rights Reserved #12;RESPONSES OF STREAM BIOFILM TO PACIFIC SALMON (ONCORHYNCHUS

  12. Microfluidics for bacterial chemotaxis

    E-Print Network [OSTI]

    Ahmed, Tanvir, Ph. D. Massachusetts Institute of Technology

    2011-01-01

    Bacterial chemotaxis, a remarkable behavioral trait which allows bacteria to sense and respond to chemical gradients in the environment, has implications in a broad range of fields including but not limited to disease ...

  13. Annual progress Report on research related to our research project “Stabilization of Plutonium in Subsurface Environments via Microbial Reduction and Biofilm Formation” funded by the Environmental Remediation Sciences Division (ERSD)

    SciTech Connect (OSTI)

    New, Mary

    2006-06-01

    The overarching goal of this research project is to investigate and optimize the mechanisms for in situ immobilization of Pu species by naturally-occurring bacteria. Specific research objectives are: (a) investigate the mechanism of bacterial accumulation and immobilization of plutonium species by biofilm formation under aerobic conditions and (b) to demonstrate the direct and indirect stabilization of Pu via dissimilatory reduction by Geobacter metallireducens.

  14. TPCP: Bacterial Blight of Eucalyptus BACTERIAL BLIGHT OF EUCALYPTUS

    E-Print Network [OSTI]

    TPCP: Bacterial Blight of Eucalyptus BACTERIAL BLIGHT OF EUCALYPTUS Typical symptoms of bacterial and commercial plantations and was reported from different Eucalyptus species, hybrids and clones. The causal Eucalyptus spp. It also records a serious new disease problem affecting one of the most widely planted forest

  15. Bacterial extracellular lignin peroxidase

    DOE Patents [OSTI]

    Crawford, Donald L. (Moscow, ID); Ramachandra, Muralidhara (Moscow, ID)

    1993-01-01

    A newly discovered lignin peroxidase enzyme is provided. The enzyme is obtained from a bacterial source and is capable of degrading the lignin portion of lignocellulose in the presence of hydrogen peroxide. The enzyme is extracellular, oxidative, inducible by lignin, larch wood xylan, or related substrates and capable of attacking certain lignin substructure chemical bonds that are not degradable by fungal lignin peroxidases.

  16. Magnetic Particle Induction and Its Importance in Biofilm Research

    E-Print Network [OSTI]

    Cirpka, Olaf Arie

    ). While the existence of a biofilm is beneficial in many settings, for example in waste water treatment years. Publications in the fields of biomedicine (Guo et al., 2008; Morton et al., 1998), waste water

  17. The Effect of Packing Hydrophilization on Bacterial Attachment and the Relationship With the

    E-Print Network [OSTI]

    in biotrickling filters for air pollution control. The intent was to modify the ring surface and in which biofilm development is particularly important is bioreactors for air pollution control. In the past decade, there has been major progress on the development of high-performance bioreactors for air

  18. Bacterial Bleeding Canker of Horse Chestnut

    E-Print Network [OSTI]

    Bacterial Bleeding Canker of Horse Chestnut -unraveling its secrets through genomics Sarah Green bleeding canker 3. Sequenced the genome of Pae to gain insights into its evolution and biology 1. Developed) #12;Genome sequencing Pae What does genomics mean? `Genomics' is the study of the genomes of organisms

  19. Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium

    E-Print Network [OSTI]

    Arnold, Frances H.

    biofilms, and vast reaches of the earth are coated in these living films. In many cases, the microorganisms (16) found in Pseudomonas aeruginosa, an opportunistic pathogen that forms a biofilm in the lungs

  20. Single particle tracking reveals spatial and dynamic organization of the Escherichia coli biofilm matrix

    E-Print Network [OSTI]

    Birjiniuk, Alona

    Biofilms are communities of surface-adherent bacteria surrounded by secreted polymers known as the extracellular polymeric substance. Biofilms are harmful in many industries, and thus it is of great interest to understand ...

  1. Engineering Escherichia coli to Control Biofilm Formation, Dispersal, and Persister Cell Formation 

    E-Print Network [OSTI]

    Hong, Seok Hoon

    2012-02-14

    Biofilms are formed in aquatic environments by the attachment of bacteria to submerged surfaces, to the air/liquid interface, and to each other. Although biofilms are associated with disease and biofouling, the robust ...

  2. ForPeerReview A mixed-culture model of a probiotic biofilm control system

    E-Print Network [OSTI]

    Demaret, Laurent

    ForPeerReview Only A mixed-culture model of a probiotic biofilm control system Journal; Helmholtz Centre Munich, Biomathematics and Biometry Keywords: biofilm, probiotics, mathematical model;ForPeerReview Only A mixed-culture model of a probiotic biofilm control system Hermann J. Eberl1

  3. Mechanics of torque generation in the bacterial flagellar motor

    E-Print Network [OSTI]

    Kranthi K. Mandadapu; Jasmine A. Nirody; Richard M. Berry; George Oster

    2015-01-13

    The bacterial flagellar motor (BFM) is responsible for driving bacterial locomotion and chemotaxis, fundamental processes in pathogenesis and biofilm formation. In the BFM, torque is generated at the interface between transmembrane proteins (stators) and a rotor. It is well-established that the passage of ions down a transmembrane gradient through the stator complex provides the energy needed for torque generation. However, the physics involved in this energy conversion remain poorly understood. Here we propose a mechanically specific model for torque generation in the BFM. In particular, we identify two fundamental forces involved in torque generation: electrostatic and steric. We propose that electrostatic forces serve to position the stator, while steric forces comprise the actual 'power stroke'. Specifically, we predict that ion-induced conformational changes about a proline 'hinge' residue in an $\\alpha$-helix of the stator are directly responsible for generating the power stroke. Our model predictions fit well with recent experiments on a single-stator motor. Furthermore, we propose several experiments to elucidate the torque-speed relationship in motors where the number of stators may not be constant. The proposed model provides a mechanical explanation for several fundamental features of the flagellar motor, including: torque-speed and speed-ion motive force relationships, backstepping, variation in step sizes, and the puzzle of swarming experiments.

  4. Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

    SciTech Connect (OSTI)

    Wang, Jianjun; Shen, Jianhaua; Wu, Yucheng; Tu, Chen; Soininen , Janne; Stegen, James C.; He, Jizheng; Liu, Xingqi; Zhang, Lu; Zhang, Enlou

    2013-02-28

    Increasing evidence emerged for non-random spatial distributions for microbes, but the underlying processes resulting in microbial assemblage variation among and within Earth’s ecosystems is still lacking. For instance, some studies showed that the deterministic processes by habitat specialization are important, while other studies hold that bacterial communities are assembled by neutral forces. Here we examine the relative importance of deterministic and stochastic processes for bacterial communities from subsurface environments, as well as stream biofilm, lake water, lake sediment and soil using pyrosequencing of 16S rRNA gene. We show that there is a general pattern in phylogenetic signal in species niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups, and for three sample groups, that spatial distance reflects unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

  5. A biofilm microreactor system for simultaneous electrochemical and nuclear magnetic resonance techniques

    SciTech Connect (OSTI)

    Renslow, Ryan S.; Babauta, Jerome T.; Majors, Paul D.; Mehta, Hardeep S.; Ewing, R. James; Ewing, Thomas; Mueller, Karl T.; Beyenal, Haluk

    2014-03-01

    In order to fully understand electrochemically active biofilms and the limitations to their scale-up in industrial biofilm reactors, a complete picture of the microenvironments inside the biofilm is needed. Nuclear magnetic resonance (NMR) techniques are ideally suited for the study of biofilms and for probing their microenvironments because these techniques allow for non-invasive interrogation and in situ monitoring with high resolution. By combining NMR with simultaneous electrochemical techniques, it is possible to sustain and study live electrochemically active biofilms. Here, we introduce a novel biofilm microreactor system that allows for simultaneous electrochemical and NMR techniques (EC-NMR) at the microscale. Microreactors were designed with custom radiofrequency resonator coils, which allowed for NMR measurements of biofilms growing on polarized gold electrodes. For an example application of this system, we grew Geobacter sulfurreducens biofilms. NMR was used to investigate growth media flow velocities, which were compared to simulated laminar flow, and electron donor concentrations inside the biofilms. We use Monte Carlo error analysis to estimate standard deviations of the electron donor concentration measurements within the biofilm. The EC-NMR biofilm microreactor system can ultimately be used to correlate extracellular electron transfer rates with metabolic reactions and explore extracellular electron transfer mechanisms.

  6. LATERAL GENE TRANSFER AND THE HISTORY OF BACTERIAL GENOMES

    SciTech Connect (OSTI)

    Howard Ochman

    2006-02-22

    The aims of this research were to elucidate the role and extent of lateral transfer in the differentiation of bacterial strains and species, and to assess the impact of gene transfer on the evolution of bacterial genomes. The ultimate goal of the project is to examine the dynamics of a core set of protein-coding genes (i.e., those that are distributed universally among Bacteria) by developing conserved primers that would allow their amplification and sequencing in any bacterial taxa. In addition, we adopted a bioinformatic approach to elucidate the extent of lateral gene transfer in sequenced genome.

  7. Exploring the reactivity of bacterial multicomponent monooxygenases

    E-Print Network [OSTI]

    Tinberg, Christine Elaine

    2010-01-01

    Chapter 1. Introduction: The Reactivity of Bacterial Multicomponent Monooxygenases Bacterial multicomponent monooxygenases constitute a remarkable family of enzymes that oxidize small, inert hydrocarbon substrates using ...

  8. Bacteria, Biofilms and Fluid Dynamics: Elementary Flows and Unexpected Phenomena

    E-Print Network [OSTI]

    Fisher, Frank

    Bacteria, Biofilms and Fluid Dynamics: Elementary Flows and Unexpected Phenomena Wednesday February the migration of bacteria along surfaces when exposed to a shear flow. In particular, we identify an unusual response where flow produces a directed motion of twitching bacteria in the upstream direction. (ii) We

  9. Attoyac Bayou Bacterial Source Tracking Report 

    E-Print Network [OSTI]

    Martin, E.; Gentry, T.; Gregory, L.; Wagner, K.

    2014-01-01

    ...................................................................................... 2 Bacterial Source Tracking ................................................................................................... 4 Library-Independent BST... ............................................................................................... 4 Library-Dependent BST .................................................................................................. 4 Results...

  10. ORIGINAL ARTICLE Convergent development of anodic bacterial

    E-Print Network [OSTI]

    treatment plant sample known to produce consistent power densities, a second wastewater treatment plant Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel). The aerobic effluent (1.16 mW mÀ 2 ) and river water (1.14 mW mÀ 2 ) inocula produced a higher maximum power

  11. Hyperbolic chemotaxis Hyperbolic chemotaxis on networks Models for biofilms Models for algae Some issues in the modeling of movement

    E-Print Network [OSTI]

    Ribot, Magali

    Hyperbolic chemotaxis Hyperbolic chemotaxis on networks Models for biofilms Models for algae Some issues in the modeling of movement of cells : chemotaxis, biofilms, algae, etc... Magali Ribot;Hyperbolic chemotaxis Hyperbolic chemotaxis on networks Models for biofilms Models for algae Hyperbolic

  12. The Hydrogen-Based Hollow-Fiber Membrane Biofilm Reactor (HFMBfR) for Removing Oxidized

    E-Print Network [OSTI]

    Nerenberg, Robert

    The Hydrogen-Based Hollow-Fiber Membrane Biofilm Reactor (HFMBfR) for Removing Oxidized documents that the hydrogen-based hollow-fiber membrane-biofilm reactor (HFMBfR) is technically. The hydrogen pressure to the hollow fibers is a key control parameter that can be adjusted rapidly and easily

  13. Evaluation of chlorines' impact on biofilms on scratched stainless steel surfaces

    E-Print Network [OSTI]

    Schreuders, Paul

    Evaluation of chlorines' impact on biofilms on scratched stainless steel surfaces Andrea Lomander Escherichia coli were grown on 316 stainless steel slides in a nutrient starved medium. The stainless steel 6 and 24 h. A 3­6 h old biofilm on a polished stainless steel surface detached when 200 ppm sodium

  14. Cell cycle: The bacterial approach to coordination

    E-Print Network [OSTI]

    Levin, Petra Anne

    Despite the power of bacterial genetics, the prokaryotic cell cycle has remained poorly understood. But recent work with three different bacterial species has shed light on how chromosomes and plasmids are oriented and ...

  15. On attractant scheduling in networks based on bacterial communication

    E-Print Network [OSTI]

    Sivakumar, Raghupathy

    On attractant scheduling in networks based on bacterial communication Yunlong Gao Shanghai Jiaotong on bacterial communication. Bacterial communication is a communication paradigm between biological cells which using chemical attractants. Although bacterial communication occurs in nature, engineering

  16. Systemic Acquired Tolerance to Virulent Bacterial Pathogens in Tomato1

    E-Print Network [OSTI]

    Klee, Harry J.

    and pathogenic microorganisms indicate that the processes of disease symptom development and pathogen growth canSystemic Acquired Tolerance to Virulent Bacterial Pathogens in Tomato1 Anna Block, Eric Schmelz to the presence of a pathogen. These host responses are frequently mediated by phytohormones. For example

  17. Microscale electronic detection of bacterial metabolism Rafael Gomeza

    E-Print Network [OSTI]

    Bashir, Rashid

    efforts to reduce bacterial infections in developed countries, their incidence has tended to remain K. Bhuniac a School of Electrical and Computer Engineering, Purdue University, West Lafayette has become a national security issue for many countries. Detecting pathogenic bacteria in food

  18. Activated ClpP kills persisters and eradicates a chronic biofilm infection.

    SciTech Connect (OSTI)

    Conlon, Brian P.; Nakayasu, Ernesto S.; Fleck, Laura E.; LaFleur, Michael D.; Isabella, Vincent M.; Coleman, K.; Leonard, Steve N.; Smith, Richard D.; Adkins, Joshua N.; Lewis, Kim

    2013-11-21

    The current antibiotic crisis stems from two distinct phenomena-drug resistance, and drug tolerance. Resistance mechanisms such as drug efflux or modification prevent antibiotics from binding to their targets 1, allowing pathogens to grow. Antibiotic tolerance is the property of persister cells, phenotypic variants of regular bacteria 2. Antibiotics kill by corrupting targets, but these are inactive in dormant persisters, leading to tolerance. Persisters were first identified by Joseph Bigger in 1944, when he discovered a surviving sub-population of Staphylococcus following treatment with penicillin3. Persisters are largely responsible for recalcitrance of chronic diseases such as tuberculosis, and various infections associated with biofilms - endocarditis, osteomyelitis, infections of catheters and indwelling devices, and deep-seated infections of soft tissues 4. There are a number of redundant pathways involved in persister formation5,6 precluding development of drugs inhibiting their formation. The acyldepsipeptide antibiotic (ADEP 4) has been shown to activate the ClpP protease resulting in death of growing cells 7. Here we show that ADEP4 activated ClpP becomes a fairly non-specific protease and kills persister cells by degradation of over 400 intracellular targets. clpP mutants are resistant to ADEP4 7, but we find that they display increased susceptibility to killing by a range of conventional antibiotics. Combining ADEP4 with rifampicin leads to eradication of persisters, stationary and biofilm populations of Staphylococcus aureus in vitro and in a deep-seated murine infection. Target corruption/activation provides an approach to killing persisters and eradicating chronic infections.

  19. Molecular Characterization of Bacterial Respiration on Minerals

    SciTech Connect (OSTI)

    Blake, Robert C.

    2013-04-26

    The overall aim of this project was to contribute to our fundamental understanding of proteins and biological processes under extreme environmental conditions. We sought to define the biochemical and physiological mechanisms that underlie biodegradative and other cellular processes in normal, extreme, and engineered environments. Toward that end, we sought to understand the substrate oxidation pathways, the electron transport mechanisms, and the modes of energy conservation employed during respiration by bacteria on soluble iron and insoluble sulfide minerals. In accordance with these general aims, the specific aims were two-fold: To identify, separate, and characterize the extracellular biomolecules necessary for aerobic respiration on iron under strongly acidic conditions; and to elucidate the molecular principles whereby these bacteria recognize and adhere to their insoluble mineral substrates under harsh environmental conditions. The results of these studies were described in a total of nineteen manuscripts. Highlights include the following: 1. The complete genome of Acidithiobacillus ferrooxidans ATCC 23270 (type strain) was sequenced in collaboration with the DOE Joint Genome Institute; 2. Genomic and mass spectrometry-based proteomic methods were used to evaluate gene expression and in situ microbial activity in a low-complexity natural acid mine drainage microbial biofilm community. This was the first effort to successfully analyze a natural community using these techniques; 3. Detailed functional and structural studies were conducted on rusticyanin, an acid-stable electron transfer protein purified from cell-free extracts of At. ferrooxidans. The three-dimensional structure of reduced rusticyanin was determined from a combination of homonuclear proton and heteronuclear 15N- and 13C-edited NMR spectra. Concomitantly, the three-dimensional structure of oxidized rusticyanin was determined by X-ray crystallography to a resolution of 1.9 A by multiwavelength anomalous dispersion (MAD) phasing; 4. An acid-stable red cytochrome with a novel absorbance peak at 579 nm was purified from cell-free extracts of L. ferriphilum. Functional studies demonstrated that this cytochrome was an important component of the aerobic iron respiratory chain in this organism; 5. The specific adhesion of At. ferrooxidans to pyrite is mediated by an extracellular protein that was identified as aporusticyanin. The adhesion of At. ferrooxidans to minerals was characterized by high affinity binding that exhibited a high specificity for pyrite over other sulfide minerals. The principal biopolymer involved in this high-affinity adhesion to pyrite was isolated by mineral affinity chromatography and identified as aporusticyanin. The adhesion of purified aporusticyanin to minerals was observed to adhere to different mineral with a pattern of reactivity identical to that observed with the intact bacterium. Further, preincubation of pyrite with excess exogenous aporusticyanin served to inhibit the adherence of intact cells to the surface of the mineral, indicating that the protein and the cells adhered to the pyrite in a mutually exclusive manner. Taken together, these observations support a model where aporusticyanin located on the surface of the bacterial cell acts as a mineral-specific receptor for the initial adherence of At. ferrooxidans to solid pyrite; 6. The specific adhesion of L. ferriphilum to pyrite was mediated by a different acid-stable extracellular protein than aporusticyanin; and 7. A prototype integrating cavity absorption meter (ICAM) was assembled to determine whether this novel spectrophotometer could be used to study cellular respiration in situ.

  20. Electromagnetic Signals from Bacterial DNA

    E-Print Network [OSTI]

    A. Widom; J. Swain; Y. N. Srivastava; S. Sivasubramanian

    2012-02-09

    Chemical reactions can be induced at a distance due to the propagation of electromagnetic signals during intermediate chemical stages. Although is is well known at optical frequencies, e.g. photosynthetic reactions, electromagnetic signals hold true for muck lower frequencies. In E. coli bacteria such electromagnetic signals can be generated by electric transitions between energy levels describing electrons moving around DNA loops. The electromagnetic signals between different bacteria within a community is a "wireless" version of intercellular communication found in bacterial communities connected by "nanowires". The wireless broadcasts can in principle be of both the AM and FM variety due to the magnetic flux periodicity in electron energy spectra in bacterial DNA orbital motions.

  1. Comparing Vacuum and Extreme Ultraviolet Radiation for Postionization of Laser Desorbed Neutrals from Bacterial Biofilms and Organic Fullerene

    E-Print Network [OSTI]

    Gaspera, Gerald L.

    2011-01-01

    Laboratory, USA Comparing Vacuum and Extreme Ultravioletradiation, extreme ultraviolet, vacuum ultravioletAbstract Vacuum and extreme ultraviolet radiation from 8 -

  2. Force-extension curves of bacterial flagella

    E-Print Network [OSTI]

    Reinhard Vogel; Holger Stark

    2010-11-10

    Bacterial flagella assume different helical shapes during the tumbling phase of a bacterium but also in response to varying environmental conditions. Force-extension measurements by Darnton and Berg explicitly demonstrate a transformation from the coiled to the normal helical state [N.C. Darnton and H.C. Berg, Biophys. J. {92}, 2230 (2007)]. We here develop an elastic model for the flagellum based on Kirchhoff's theory of an elastic rod that describes such a polymorphic transformation and use resistive force theory to couple the flagellum to the aqueous environment. We present Brownian dynamics simulations that quantitatively reproduce the force-extension curves and study how the ratio $\\Gamma$ of torsional to bending rigidity and the extensional rate influence the response of the flagellum. An upper bound for $\\Gamma$ is given. Using clamped flagella, we show in an adiabatic approximation that the mean extension, where a local coiled-to-normal transition occurs first, depends on the logarithm of the extensional rate.

  3. Bacterial Population Genetics in a Forensic Context

    SciTech Connect (OSTI)

    Velsko, S P

    2009-11-02

    This report addresses the recent Department of Homeland Security (DHS) call for a Phase I study to (1) assess gaps in the forensically relevant knowledge about the population genetics of eight bacterial agents of concern, (2) formulate a technical roadmap to address those gaps, and (3) identify new bioinformatics tools that would be necessary to analyze and interpret population genetic data in a forensic context. The eight organisms that were studied are B. anthracis, Y. pestis, F. tularensis, Brucella spp., E. coli O157/H7, Burkholderia mallei, Burkholderia pseudomallei, and C. botulinum. Our study focused on the use of bacterial population genetics by forensic investigators to test hypotheses about the possible provenance of an agent that was used in a crime or act of terrorism. Just as human population genetics underpins the calculations of match probabilities for human DNA evidence, bacterial population genetics determines the level of support that microbial DNA evidence provides for or against certain well-defined hypotheses about the origins of an infecting strain. Our key findings are: (1) Bacterial population genetics is critical for answering certain types of questions in a probabilistic manner, akin (but not identical) to 'match probabilities' in DNA forensics. (2) A basic theoretical framework for calculating likelihood ratios or posterior probabilities for forensic hypotheses based on microbial genetic comparisons has been formulated. This 'inference-on-networks' framework has deep but simple connections to the population genetics of mtDNA and Y-STRs in human DNA forensics. (3) The 'phylogeographic' approach to identifying microbial sources is not an adequate basis for understanding bacterial population genetics in a forensic context, and has limited utility, even for generating 'leads' with respect to strain origin. (4) A collection of genotyped isolates obtained opportunistically from international locations augmented by phylogenetic representations of relatedness will not and enzootic outbreaks noted through international outbreak surveillance systems, and 'representative' genetic sequences from each outbreak. (5) Interpretation of genetic comparisons between an attack strain and reference strains requires a model for the network structure of maintenance foci, enzootic outbreaks, and human outbreaks of that disease, coupled with estimates of mutational rate constants. Validation of the model requires a set of sequences from exemplary outbreaks and laboratory data on mutation rates during animal passage. The necessary number of isolates in each validation set is determined by disease transmission network theory, and is based on the 'network diameter' of the outbreak. (6) The 8 bacteria in this study can be classified into 4 categories based on the complexity of the transmission network structure of their natural maintenance foci and their outbreaks, both enzootic and zoonotic. (7) For B. anthracis, Y. pestis, E. coli O157, and Brucella melitensis, and their primary natural animal hosts, most of the fundamental parameters needed for modeling genetic change within natural host or human transmission networks have been determined or can be estimated from existing field and laboratory studies. (8) For Burkholderia mallei, plausible approaches to transmission network models exist, but much of the fundamental parameterization does not. In addition, a validated high-resolution typing system for characterizing genetic change within outbreaks or foci has not yet been demonstrated, although a candidate system exists. (9) For Francisella tularensis, the increased complexity of the transmission network and unresolved questions about maintenance and transmission suggest that it will be more complex and difficult to develop useful models based on currently available data. (10) For Burkholderia pseudomallei and Clostridium botulinum, the transmission and maintenance networks involve complex soil communities and metapopulations about which very little is known. It is not clear that these pathogens can be brought into the in

  4. Biofilms as sources of fecal bacteria contamination in the stormwater drainage system in Singapore

    E-Print Network [OSTI]

    Burkhart, Tsung Hwa (Tsung Hwa Sophia)

    2013-01-01

    A study was performed to examine a possible source of fecal bacteria contamination originating from within the stormwater drainage system in Singapore. The extent of fecal bacteria presence in storm drain biofilms was ...

  5. The effect of adjacent layers like biofilms on mass transport through nanofiltration membranes

    E-Print Network [OSTI]

    Bothe, Dieter

    , which is always present on the membrane surface in crossflow filtration processes, as well as a feed to high tangential flow velocities in crossflow filtrations, the size of this biofilm is limited to values

  6. The dynamics of surface detachment and quorum sensing in spatially controlled biofilm colonies of Pseudomonas aeruginosa

    E-Print Network [OSTI]

    Jang, Hongchul

    2014-01-01

    Biofilms represent a highly successful life strategy of bacteria in a very broad range of environments and often have negative implications for industrial and clinical applications, as their removal from surfaces and the ...

  7. Natural bacterial communities serve as quantitative geochemical...

    Office of Scientific and Technical Information (OSTI)

    approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior...

  8. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

    E-Print Network [OSTI]

    2013-01-01

    genomics in acid mine drainage biofilm communities revealsextreme acidophiles from acid mine drainage and industrialacidophile important in acid mine drainage. Science 2000,

  9. Recombinant production of bacterial toxins and their derivatives in the methylotrophic yeast Pichia pastoris

    E-Print Network [OSTI]

    Gurkan, Cemal; Ellar, David J.

    2005-12-07

    -expression of the cholera toxin subunit B (CTB) and CTB-viral antigen fusion protein using the native bacterial DNA sequence (SF) [4] N.D. LTB (Escherichia coli) secreted expression of the heat-labile enterotoxin subunit B (LTB) using the native bacterial DNA sequence... -specific antibody fragment fused to a gene coding for a highly potent bacterial toxin or its subunits [5]. Despite their crucial roles in vaccine development, thera- peutic applications, control of crop pests and disease vec- Published: 07 December 2005 Microbial...

  10. Leading Edge Bacterial Genomics and Pathogen Evolution

    E-Print Network [OSTI]

    Mekalanos, John

    Leading Edge Review Bacterial Genomics and Pathogen Evolution David M. Raskin,1 Rekha Seshadri,2 Medical School, Boston, MA 02115, USA 2 The Institute for Genomic Research, 9712 Medical Center Drive.02.002 The availability of hundreds of bacterial genome sequences has altered the study of bacte- rial pathogenesis

  11. Magnetic microbes: Bacterial magnetite biomineralization

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

    Prozorov, Tanya

    2015-09-14

    Magnetotactic bacteria are a diverse group of prokaryotes with the ability to orient and migrate along the magnetic field lines in search for a preferred oxygen concentration in chemically stratified water columns and sediments. These microorganisms produce magnetosomes, the intracellular nanometer-sized magnetic crystals surrounded by a phospholipid bilayer membrane, typically organized in chains. Magnetosomes have nearly perfect crystal structures with narrow size distribution and species-specific morphologies, leading to well-defined magnetic properties. As a result, the magnetite biomineralization in these organisms is of fundamental interest to diverse disciplines, from biotechnology to astrobiology. As a result, this article highlights recent advances inmore »the understanding of the bacterial magnetite biomineralization.« less

  12. Identification of Molecular and Cellular Responses of Desulfovibrio vulgaris Biofilms under Culture Conditions Relevant to Field Conditions for Bioreduction

    SciTech Connect (OSTI)

    Fields, Matthew W.

    2006-06-01

    Desulfovibrio vulgaris ATCC29579 is a sulfate- reducing bacterium (SRB) that is commonly used as a model for direct and indirect heavy metal reduction, and can also be a causitative agent of metal corrosion. During growth with lactate and sulfate, internal carbohydrate levels increased throughout exponential-phase, and peaked as the cells transitioned to stationary-phase. The carbohydrate to protein ratio (C:P) peaked at 0.05 ug/ug as the cells transitioned to stationary-phase, and then declined to 0.02 ug/ug during extended stationary-phase. In contrast, a strain of D. vulgaris that does not contain the megaplasmid, maintained higher internal carbohydrate levels and the C:P ratio peaked at 0.1 ug/ug (2-fold increase compared to wild-type). Under the tested growth conditions, we observed biofilm formation in wild-type cells, but the plasmid-less strain formed less biofilm (2-fold decrease). We hypothesized that carbohydrate was re-allocated to the external cell proper for biofilm formation. However, biofilm contained relatively little carbohydrate (0.6 to 1.0 ug/ml) and had a similar C:P ratio compared to wild-type early stationary-phase cells. Staining with calcafluor white also indicated the presence of little external carbohydrate in D. vulgaris biofilms. Less biofilm was formed in the presence of protinease K, trypsin, and chymotrypsin, however, the growth of planktonic cells was not affected. In addition, when D. vulgaris biofilm was treated with a protease, less biofilm was observed. Electron micrographs suggested the presence of filaments between the biofilm cells, and filaments appeared to be susceptible to protease treatment. Biofilm filtrates contained soluble protein, and SDS-PAGE analysis suggested different polypeptide profiles between a filtrate, a planktonic, and a biofilm sample.

  13. Characterization of Biofilm in 200W Fluidized Bed Reactors

    SciTech Connect (OSTI)

    Lee, Michelle H.; Saurey, Sabrina D.; Lee, Brady D.; Parker, Kent E.; Eisenhauer, Emalee ER; Cordova, Elsa A.; Golovich, Elizabeth C.

    2014-09-29

    Contaminated groundwater beneath the 200 West Area at the Hanford Site in Southeast Washington is currently being treated using a pump and treat system to remove organics, inorganics, radionuclides, and metals. A granular activated carbon-based fluidized bed reactor (FBR) has been added to remove nitrate, hexavalent chromium and carbon tetrachloride. Initial analytical results indicated the microorganisms effectively reduced many of the contaminants to less than cleanup levels. However shortly thereafter operational upsets of the FBR include carbon carry over, over production of microbial extracellular polymeric substance (biofilm) materials, and over production of hydrogen sulfide. As a result detailed investigations were undertaken to understand the functional diversity and activity of the microbial community present in the FBR over time. Molecular analyses including terminal restriction fragment length polymorphism analysis, quantitative polymerase chain reaction and fluorescent in situ hybridization analyses were performed on the microbial community extracted from the biofilm within the bed and from the inoculum, to determine functional dynamics of the FBR bed over time and following operational changes. Findings from these analyses indicated: 1) the microbial community within the bed was completely different than community used for inoculation, and was likely from the groundwater; 2) analyses early in the testing showed an FBR community dominated by a few Curvibacter and Flavobacterium species; 3) the final sample taken indicated that the microbial community in the FBR bed had become more diverse; and 4) qPCR analyses indicated that bacteria involved in nitrogen cycling, including denitrifiers and anaerobic ammonia oxidizing bacteria, were dominant in the bed. These results indicate that molecular tools can be powerful for determining functional diversity within FBR type reactors. Coupled with micronutrient, influent and effluent chemistry evaluations, a more complete understanding of the balance between system additions (nutrients, groundwater) and biology can be achieved, thus increasing long-term predictions of performance. These analyses uniquely provide information that can be used in optimizing the overall performance, efficiency, and stability of the system both in real time as well as over the long-term, as the system design is altered or improved and/or new streams are added.

  14. HYDROGEN-BASED, HOLLOW-FIBER MEMBRANE BIOFILM REACTOR FOR REDUCTION OF PERCHLORATE AND OTHER OXIDIZED CONTAMINANTS

    E-Print Network [OSTI]

    Nerenberg, Robert

    HYDROGEN-BASED, HOLLOW-FIBER MEMBRANE BIOFILM REACTOR FOR REDUCTION OF PERCHLORATE AND OTHER be added. Hydrogen is an ideal electron donor, as it is non-toxic, inexpensive, and sparsely soluble. We tested a hydrogen-based, hollow-fiber membrane biofilm reactor (MBfR) for reduction of perchlorate

  15. Aquatic microenvironments in bacterial ecology and diversity

    E-Print Network [OSTI]

    Hunt, Dana E., Ph. D. Massachusetts Institute of Technology

    2008-01-01

    Molecular surveys have revealed tremendous bacterial diversity in the world's oceans; yet how do these diverse bacteria with the same essential nutrient requirements co-exist in the same environment? This study examines ...

  16. Performance and microbial ecology of the hybrid membrane biofilm process for concurrent nitrification

    E-Print Network [OSTI]

    Nerenberg, Robert

    into existing treatment plants. This is especially attractive for older plants unable to achieve the long b sludge tank, with suppressed aeration, to allow concurrent nitrification and denitrification. We waters. This research reports on a novel process for TN removal, the hybrid membrane biofilm process

  17. Application of a moving bed biofilm reactor for tertiary ammonia treatment in high temperature industrial wastewater

    E-Print Network [OSTI]

    industrial wastewater Jennifer L. Shore a,b , William S. M'Coy b , Claudia K. Gunsch a , Marc A. Deshusses a 2012 Available online 17 February 2012 Keywords: Moving bed biofilm reactor Industrial wastewater and industrial wastewater. No biotreatment was observed at 45 °C, although effective nitrification was rapidly

  18. Innovative Porous Media Approach in Modeling Biofilm Applications, Human Eye and Nanofluid Based Heat Pipes

    E-Print Network [OSTI]

    Shafahi, Maryam

    2010-01-01

    water treatment, enhanced oil recovery, groundwater recharge and in situ bioremediation.bioremediation, microbial enhanced oil recovery and metal extraction; yet they can be damaging in waterbioremediation, microbial enhanced oil recovery, and metal extraction. On the other hand, biofilms are damaging for water

  19. Degree project Single-cell analysis of attached microbes in sediment, soil, and biofilms

    E-Print Network [OSTI]

    Uppsala Universitet

    Degree project Single-cell analysis of attached microbes in sediment, soil, and biofilms Keywords with a phylogenetic screen and sequencing to gain further information about the microbes possibly involved with another group, if the student has a particular interest in other metabolic functions or microbes

  20. Impact of sediment grain-size and biofilm age on epipelic microphytobenthos resuspension

    E-Print Network [OSTI]

    Impact of sediment grain-size and biofilm age on epipelic microphytobenthos resuspension Martin polymeric Substances Sediment Intertidal zones are dynamic areas, where tidal currents and wind-induced waves are responsible of resuspension of the sediment and associated microphytobenthos (MPB). Sediment

  1. Hydrogen-based, hollow-fiber membrane biofilm reactor for reduction of perchlorate and other oxidized

    E-Print Network [OSTI]

    Nerenberg, Robert

    Hydrogen-based, hollow-fiber membrane biofilm reactor for reduction of perchlorate and other. For drinking water treatment, an electron donor must be added. Hydrogen is an ideal electron donor, as it is non-toxic, inexpensive, and sparsely soluble. We tested a hydrogen-based, hollow-fiber membrane

  2. Environmental variability and the ecological effects of spawning Pacific salmon on stream biofilm

    E-Print Network [OSTI]

    Tiegs, Scott

    , combining data from different North Pacific Rim ecoregions inflated the confidence interval as comparedEnvironmental variability and the ecological effects of spawning Pacific salmon on stream biofilm of organisms delivering resource subsidies, such as ecosystem engineering by Pacific salmon spawners

  3. Candida albicans Ethanol Stimulates Pseudomonas aeruginosa WspR-Controlled Biofilm Formation as Part of

    E-Print Network [OSTI]

    Dietrich, Lars

    Candida albicans Ethanol Stimulates Pseudomonas aeruginosa WspR-Controlled Biofilm Formation formation and phenazine production were strongly influenced by ethanol produced by the fungus C. albicans. Ethanol stimulated phenotypes that are indicative of increased levels of cyclic- di-GMP (c

  4. BIOENERGY AND BIOFUELS Anodic biofilms in microbial fuel cells harbor low numbers

    E-Print Network [OSTI]

    BIOENERGY AND BIOFUELS Anodic biofilms in microbial fuel cells harbor low numbers of higher a higher-power density (17.4 mW/m2 ) than the mixed culture, although voltage generation was variable. Our; Kiely et al. 2010; Parameswaran et al. 2009a, b). In general, power densities for acetic acid

  5. Synthetic analogs of bacterial quorum sensors

    DOE Patents [OSTI]

    Iyer, Rashi S.; Ganguly, Kumkum; Silks, Louis A.

    2013-01-08

    Bacterial quorum-sensing molecule analogs having the following structures: ##STR00001## and methods of reducing bacterial pathogenicity, comprising providing a biological system comprising pathogenic bacteria which produce natural quorum-sensing molecule; providing a synthetic bacterial quorum-sensing molecule having the above structures and introducing the synthetic quorum-sensing molecule into the biological system comprising pathogenic bacteria. Further is provided a method of targeted delivery of an antibiotic, comprising providing a synthetic quorum-sensing molecule; chemically linking the synthetic quorum-sensing molecule to an antibiotic to produce a quorum-sensing molecule-antibiotic conjugate; and introducing the conjugate into a biological system comprising pathogenic bacteria susceptible to the antibiotic.

  6. Synthetic analogs of bacterial quorum sensors

    DOE Patents [OSTI]

    Iyer, Rashi (Los Alamos, NM); Ganguly, Kumkum (Los Alamos, NM); Silks, Louis A. (Los Alamos, NM)

    2011-12-06

    Bacterial quorum-sensing molecule analogs having the following structures: ##STR00001## and methods of reducing bacterial pathogenicity, comprising providing a biological system comprising pathogenic bacteria which produce natural quorum-sensing molecule; providing a synthetic bacterial quorum-sensing molecule having the above structures and introducing the synthetic quorum-sensing molecule into the biological system comprising pathogenic bacteria. Further is provided a method of targeted delivery of an antibiotic, comprising providing a synthetic quorum-sensing molecule; chemically linking the synthetic quorum-sensing molecule to an antibiotic to produce a quorum-sensing molecule-antibiotic conjugate; and introducing the conjugate into a biological system comprising pathogenic bacteria susceptible to the antibiotic.

  7. Investigations of Structure and Metabolism within Shewanella oneidensis MR-1 Biofilms

    SciTech Connect (OSTI)

    Mclean, Jeffrey S.; Majors, Paul D.; Reardon, Catherine L.; Bilskis, Christina L.; Reed, Samantha B.; Romine, Margaret F.; Fredrickson, Jim K.

    2008-07-01

    Biofilms are known to possess spatially and temporally varying metabolite concentration profiles at the macroscopic and microscopic scales. This results in varying growth environments within that may ultimately drive species diversity, determine biofilm structure and also the spatial arrangement of the community members. Using noninvasive nuclear magnetic resonance (NMR) microscopic imaging/spectroscopy and confocal imaging, we investigated anaerobic reduction kinetics, structural variation, and the stratification of metabolism within live biofilms of the facultative anaerobic dissimilatory metal-reducing Shewanella oneidensis strain MR-1. Biofilms were pregrown using a defined minimal media in a homebuilt constant depth film fermenter and subsequently transferred to an in-magnet sample chamber under laminar flow for NMR measurements. The sample was subjected to various, rapidly switched substrate/ anaerobic electron acceptor combinations (fumarate, dimethyl sulfoxide, and nitrate electron acceptors). Localized NMR spectroscopy was used to non-invasively monitored the spectra of hydrogen-containing metabolites at high temporal resolution (4.5 min) under oxygen-limited conditions. Anaerobic reduction was immediately observed upon switching feed solutions indicate that no gene induction (transcriptional response) was needed for MR-1 to switch between fumarate, dimethyl sulfoxide (DMSO) and nitrate electron acceptors. In parallel experiments, confocal microscopy was used with constitutively expressed fluorescent reporters to independently investigate structural changes in response to the availability of electron acceptor and also the outcome of metabolic competition under oxygen-limited conditions. A clearer understanding of the metabolic diversity and plasticity of the biofilm mode of growth as well as how this possibly translates to the environmental fitness is made possible through the use of non-invasive and non-destructive techniques such as described here.

  8. Photo Gallery: Argonne OutLoud: "Invisible Influence: A Bacterial...

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

    Photo Gallery: Argonne OutLoud: "Invisible Influence: A Bacterial Guide to Your Health" Argonne OutLoud Invisible Influence: A Bacterial Guide to Your Health 1 of 10 Argonne...

  9. Torquespeed relationship of the bacterial flagellar motor

    E-Print Network [OSTI]

    Oster, George

    Torque­speed relationship of the bacterial flagellar motor Jianhua Xing* , Fan Bai , Richard Berry swimming bacteria are propelled by flagellar filaments driven by a rotary motor. Each of these tiny motors can generate an impressive torque. The motor torque vs. speed relationship is considered one

  10. Bacterial Production Lab State variables and processes

    E-Print Network [OSTI]

    Vallino, Joseph J.

    . · Bacteria must utilize for growth · Must be able to measure at low concentrations. Low detection limitsI) 8.06 d , Iodine-125 (125I) 60 d Types Helium nuclei Electron Gamma ray For bacterial in counts per min. (CPM) Due to some losses, CPM detection SA: 371 mCi (mmol 14C)-1 Measure

  11. Analysis of Bacterial Communities in Seagrass Bed Sediments by Double-Gradient Denaturing Gradient Gel Electrophoresis

    E-Print Network [OSTI]

    Sherman, Tim

    . Devereux1 (1) Office of Research and Development, US Environmental Protection Agency, NHEERL­Gulf Ecology. The work presented here investigated several factors and their impact on bacterial community diversity the waters contig- uous with the Gulf of Mexico in the USA. Seagrasses found in the northern Gulf of Mexico

  12. Bacterial resistance to antibiotics continues to pose a serious threat to human and animal

    E-Print Network [OSTI]

    Singer, Randall

    of resistance15 . In addition to exposure to naturally produced antibiotics, bacteria at a given site canBacterial resistance to antibiotics continues to pose a serious threat to human and animal health. The relationship between antibiotic use and the development of resistance has been studied extensively, with some

  13. Application of Bacterial Biocathodes in Microbial Fuel Cells Zhen He, Largus T. Angenent*

    E-Print Network [OSTI]

    Review Application of Bacterial Biocathodes in Microbial Fuel Cells Zhen He, Largus T. Angenent* Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis Abstract This review addresses the development and experimental progress of biocathodes in microbial fuel

  14. Elucidating the Role of Small Molecule Signals in Bacterial Development 

    E-Print Network [OSTI]

    Ababneh, Qutaiba O

    2015-08-10

    protein is DisA, an octameric protein from B. subtilis that has two functions; first, it binds DNA via its C-terminal helix–hairpin–helix DNA-binding domain (HhH) and scans DNA integrity. Second, it synthesizes c-di-AMP using the N-terminal DAC 26... domain (151). The DAC domain in DisA protein is connected to the HhH domain through a specific linker domain (150). Therefore, c-di-AMP synthesis by DAC domain is allosterically inhibited when the HhH domain binds damaged DNA (152). Failure...

  15. New information about bacterial enzymes to help scientists develop...

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

    5, 2015 Tweet EmailPrint Scientists studying the biosynthesis and production of microbial natural products now have a greater insight into the process thanks to research...

  16. New information about bacterial enzymes to help scientists develop more

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformationJessework usesofPublications64 2.251 2.211NewNew exhibit

  17. Stages common to all biofilms (medical and environmental) Stages unique to aquatic biofouling BiofilmThickness(m)

    E-Print Network [OSTI]

    . Develop better antifouling surfaces to improve shipping fuel efficiency, reduce invasive species transport

  18. An in-vivo study of electrical charge distribution on the bacterial cell wall by Atomic Force Microscopy in vibrating force mode

    E-Print Network [OSTI]

    Christian Marliere; Samia Dhahri

    2015-04-13

    We report an in-vivo electromechanical Atomic Force Microscopy (AFM) study of charge distribution on the cell wall of Gram plus Rhodococcus wratislaviensis bacteria, naturally adherent to a glass substrate, in physiological conditions. The method presented in this paper relies on a detailed study of AFM approach-retract curves giving the variation of the interaction force versus distance between tip and sample. In addition to classical height and mechanical (as stiffness) data, mapping of local electrical properties, as bacterial surface charge, was proved to be feasible at a spatial resolution better than few tens of nanometers. This innovative method relies on the measurement of the cantilever's surface stress through its deflection far from (higher than 10nm) the repulsive contact zone. The variations of surface stress come from modification of electrical surface charge of the cantilever (as in classical electrocapillary measurements) likely stemming from its charging during contact of both tip and sample electrical double layers. This method offers an important improvement in local electrical and electrochemical measurements at the solid-liquid interface particularly in high-molarity electrolytes when compared to technics focused on the direct use of electrostatic force. It thus opens a new way to directly investigate in-situ biological electrical surface processes involved in numerous practical and fundamental problems as bacterial adhesion, biofilm formation, microbial fuel cell, etc.

  19. A polymer-solvent model of biofilm growth H. F. Winstanley1, M. Chapwanya2, M. J. McGuinness3, A. C. Fowler1

    E-Print Network [OSTI]

    McGuinness, Mark

    A polymer-solvent model of biofilm growth H. F. Winstanley1, M. Chapwanya2, M. J. McGuinness3, A. C with pure solvent across a semi-permeable membrane. This osmotic pressure is given in the relevant limit of polymer. Polymer-Solvent Model I We consider a biofilm in 0

  20. Detoxification of organophosphate nerve agents by bacterial phosphotriesterase

    SciTech Connect (OSTI)

    Ghanem, Eman; Raushel, Frank M. . E-mail: raushel@tamu.edu

    2005-09-01

    Organophosphates have been widely used as insecticides and chemical warfare agents. The health risks associated with these agents have necessitated the need for better detoxification and bioremediation tools. Bacterial enzymes capable of hydrolyzing the lethal organophosphate nerve agents are of special interest. Phosphotriesterase (PTE) isolated from the soil bacteria Pseudomonas diminuta displays a significant rate enhancement and substrate promiscuity for the hydrolysis of organophosphate triesters. Directed evolution and rational redesign of the active site of PTE have led to the identification of new variants with enhanced catalytic efficiency and stereoselectivity toward the hydrolysis of organophosphate neurotoxins. PTE has been utilized to protect against organophosphate poisoning in vivo. Biotechnological applications of PTE for detection and decontamination of insecticides and chemical warfare agents are developing into useful tools. In this review, the catalytic properties and potential applications of this remarkable enzyme are discussed.

  1. Metallization of bacterial cellulose for electrical and electronic device manufacture

    DOE Patents [OSTI]

    Evans, Barbara R. (Oak Ridge, TN); O'Neill, Hugh M. (Knoxville, TN); Jansen, Valerie Malyvanh (Memphis, TN); Woodward, Jonathan (Knoxville, TN)

    2011-06-07

    A method for the deposition of metals in bacterial cellulose and for the employment of the metallized bacterial cellulose in the construction of fuel cells and other electronic devices is disclosed. The method for impregnating bacterial cellulose with a metal comprises placing a bacterial cellulose matrix in a solution of a metal salt such that the metal salt is reduced to metallic form and the metal precipitates in or on the matrix. The method for the construction of a fuel cell comprises placing a hydrated bacterial cellulose support structure in a solution of a metal salt such that the metal precipitates in or on the support structure, inserting contact wires into two pieces of the metal impregnated support structure, placing the two pieces of metal impregnated support structure on opposite sides of a layer of hydrated bacterial cellulose, and dehydrating the three layer structure to create a fuel cell.

  2. Metallization of bacterial cellulose for electrical and electronic device manufacture

    DOE Patents [OSTI]

    Evans, Barbara R. (Oak Ridge, TN) [Oak Ridge, TN; O'Neill, Hugh M. (Knoxville, TN) [Knoxville, TN; Jansen, Valerie Malyvanh (Memphis, TN) [Memphis, TN; Woodward, Jonathan (Knoxville, TN) [Knoxville, TN

    2010-09-28

    A method for the deposition of metals in bacterial cellulose and for the employment of the metallized bacterial cellulose in the construction of fuel cells and other electronic devices is disclosed. The method for impregnating bacterial cellulose with a metal comprises placing a bacterial cellulose matrix in a solution of a metal salt such that the metal salt is reduced to metallic form and the metal precipitates in or on the matrix. The method for the construction of a fuel cell comprises placing a hydrated bacterial cellulose support structure in a solution of a metal salt such that the metal precipitates in or on the support structure, inserting contact wires into two pieces of the metal impregnated support structure, placing the two pieces of metal impregnated support structure on opposite sides of a layer of hydrated bacterial cellulose, and dehydrating the three layer structure to create a fuel cell.

  3. Metallization of bacterial cellulose for electrical and electronic device manufacture

    DOE Patents [OSTI]

    Evans, Barbara R.; O'Neill, Hugh M.; Jansen, Valerie Malyvanh; Woodward, Jonathan

    2006-01-17

    The employment of metallized bacterial cellulose in the construction of fuel cells and other electronic devices is disclosed. The fuel cell includes an electrolyte membrane comprising a membrane support structure comprising bacterial cellulose, an anode disposed on one side of the electrolyte membrane, and a cathode disposed on an opposite side of the electrolyte membrane. At least one of the anode and the cathode comprises an electrode support structure comprising bacterial cellulose, and a catalyst disposed in or on the electrode support structure.

  4. The Carboxysome and Other Bacterial Microcompartments

    SciTech Connect (OSTI)

    Kerfeld, Cheryl A.; Greenleaf, William B.; Kinney, James N.

    2010-06-23

    - Carboxysomes are part of the carbon concentrating mechanism in cyanobacteria and chemoautotrophs. - Carboxysomes are a subclass of bacterial microcompartments (BMCs); BMCs can encapsulate a range of metabolic processes. - Like some viral particles, the carboxysome can be modeled as an icosahedron-in its case, having 4,000-5,000 hexameric shell subunits and 12 surface pentamers to generate curvature. - The threefold axis of symmetry of the CsoS1D protein in carboxysomes forms a pore that can open and close, allowing for selective diffusion. - Genetic modules encoding BMC shell proteins and the enzymes that they encapsulate are horizontally transferable, suggesting they enable bacteria to adapt to diverse environments.

  5. Harnessing the Bacterial Power of Nanomagnets

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverse (Journalvivo Low-Dose Lowï‚—34OctoberK West60Harnessing the Bacterial Power

  6. Harnessing the Bacterial Power of Nanomagnets

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverse (Journalvivo Low-Dose Lowï‚—34OctoberK West60Harnessing the Bacterial

  7. Fluorescence-Enhancement Based Detection and Identification of Bacterial Contaminants

    E-Print Network [OSTI]

    Upadhyayula, Srigokul

    2012-01-01

    and Eukaryotes. Analytical Chemistry 80:5312-5319. Gill, M.and bacterial spores. Analytical Chemistry 72:2428-2432.Biological Materials. Analytical Chemistry Plomp, M. , T. J.

  8. Bacterial and Protozoal Contamination of Nearshore Marine Environments

    E-Print Network [OSTI]

    Atwill, Rob; Conrad, Patricia A.

    2010-01-01

    Tate. Reducing microbial contamination in storm runoff fromManagement of microbial contamination in storm runoff fromBacterial and Protozoal Contamination of Nearshore Marine

  9. A Viscoelastic Fluid Description of Bacterial Biofilm Material I. Klapper \\Lambda , C.J. Rupp y , R. Cargo y , B. Purvedorj y , P. Stoodley yz

    E-Print Network [OSTI]

    Klapper, Isaac

    pipelines where they are associated with increased pressure drop, product contamination, and corrosion

  10. Reconstruction of a Bacterial Genome from DNA Cassettes

    SciTech Connect (OSTI)

    Christopher Dupont; John Glass; Laura Sheahan; Shibu Yooseph; Lisa Zeigler Allen; Mathangi Thiagarajan; Andrew Allen; Robert Friedman; J. Craig Venter

    2011-12-31

    This basic research program comprised two major areas: (1) acquisition and analysis of marine microbial metagenomic data and development of genomic analysis tools for broad, external community use; (2) development of a minimal bacterial genome. Our Marine Metagenomic Diversity effort generated and analyzed shotgun sequencing data from microbial communities sampled from over 250 sites around the world. About 40% of the 26 Gbp of sequence data has been made publicly available to date with a complete release anticipated in six months. Our results and those mining the deposited data have revealed a vast diversity of genes coding for critical metabolic processes whose phylogenetic and geographic distributions will enable a deeper understanding of carbon and nutrient cycling, microbial ecology, and rapid rate evolutionary processes such as horizontal gene transfer by viruses and plasmids. A global assembly of the generated dataset resulted in a massive set (5Gbp) of genome fragments that provide context to the majority of the generated data that originated from uncultivated organisms. Our Synthetic Biology team has made significant progress towards the goal of synthesizing a minimal mycoplasma genome that will have all of the machinery for independent life. This project, once completed, will provide fundamentally new knowledge about requirements for microbial life and help to lay a basic research foundation for developing microbiological approaches to bioenergy.

  11. Modelling and Analysis of Phase Variation in Bacterial Colony Growth

    E-Print Network [OSTI]

    Gilbert, David

    Modelling and Analysis of Phase Variation in Bacterial Colony Growth Ovidiu P^arvu1 , David Gilbert, Brandenburg University of Technology monika.heiner@informatik.tu-cottbus.de 3 Harbin Institute of Technology case study, namely phase variation patterning in bacterial colony growth, forming circular colonies

  12. Bacterial Diversity in Livestock Manure Composts as Characterized by Terminal

    E-Print Network [OSTI]

    Tiquia-Arashiro, Sonia M.

    Bacterial Diversity in Livestock Manure Composts as Characterized by Terminal Restriction Fragment in the decomposition of organic matter during the composting process. However, microbial communities active in composts of bacterial communities in livestock manure compost was determined based on terminal restriction fragment

  13. Bacterial phytopathogens and genome science Joa~ o C Setubal1

    E-Print Network [OSTI]

    Setubal, João Carlos

    Bacterial phytopathogens and genome science Joa~ o C Setubal1 , Leandro M Moreira2 and Ana CR da Silva3 There are now fourteen completed genomes of bacterial phytopathogens, all of which have been generated in the past six years. These genomes come from a phylogenetically diverse set of organisms

  14. Comparing Bacterial Genomes by Searching their Common Intervals

    E-Print Network [OSTI]

    Fertin, Guillaume

    Comparing Bacterial Genomes by Searching their Common Intervals S´ebastien Angibaud, Damien. Comparing bacterial genomes implies the use of a dedicated measure. It relies on comparing circular genomes genomes that takes into account duplications. Its application on a concrete case, comparing E. coli and V

  15. Development Development

    E-Print Network [OSTI]

    Programme 2007 - 2010 The aim of the Timber Development Programme (TDP) is "to contribute to the sustainable development to underpin sustainable forest management and support economic growth and employment acrossDevelopment Timber Development Programme 2007 - 2010 #12;2 | Timber Development Programme 2007

  16. The effect of deuteration on the structure of bacterial cellulose

    SciTech Connect (OSTI)

    Bali, Garima [Georgia Institute of Technology; Foston, Marcus [Georgia Institute of Technology; O'Neill, Hugh Michael [ORNL; Evans, Barbara R [ORNL; He, Junhong [ORNL; Ragauskas, Arthur [Georgia Institute of Technology

    2013-01-01

    ABSTRACT In vivo generated deuterated bacterial cellulose, cultivated from 100% deuterated glycerol in D2O medium, was analyzed for deuterium incorporation by ionic liquid dissolution and 2H and 1H nuclear magnetic resonance (NMR). A solution NMR method of the dissolved cellulose was used to determine that this bacterial cellulose had 85 % deuterium incorporation. Acetylation and 1H and 2H NMR of deuterated bacterial cellulose indicated near equal deuteration at all sites of the glucopyranosyl ring except C-6 which was partly deuterated. Despite the high level of deuterium incorporation there were no significant differences in the molecular and morphological properties were observed for the deuterated and protio bacterial cellulose samples. The highly deuterated bacterial cellulose presented here can be used as a model substrate for studying cellulose biopolymer properties via future small angle neutron scattering (SANS) studies.

  17. Steps in the bacterial flagellar motor

    E-Print Network [OSTI]

    Thierry Mora; Howard Yu; Yoshiyuki Sowa; Ned S. Wingreen

    2009-04-02

    The bacterial flagellar motor is a highly efficient rotary machine used by many bacteria to propel themselves. It has recently been shown that at low speeds its rotation proceeds in steps [Sowa et al. (2005) Nature 437, 916--919]. Here we propose a simple physical model that accounts for this stepping behavior as a random walk in a tilted corrugated potential that combines torque and contact forces. We argue that the absolute angular position of the rotor is crucial for understanding step properties, and show this hypothesis to be consistent with the available data, in particular the observation that backward steps are smaller on average than forward steps. Our model also predicts a sublinear torque-speed relationship at low torque, and a peak in rotor diffusion as a function of torque.

  18. Transcriptomic Analysis for Genetic Mechanisms of the Factors Related to Biofilm Formation in Escherichia coli O157:H7

    E-Print Network [OSTI]

    Wood, Thomas K.

    coli serotype O157:H7 is the most common human pathogen responsible for out- breaks of hemorrhagic cystitis by pathogenic E. coli due to their high resistance to antimi- crobial agents [8]. Food-borne microorganisms, such as E. coli O157:H7, can readily attach to and form biofilms on various surfaces

  19. Effects of age and composition of field-produced biofilms on oyster larval setting Alaina H. Campbella

    E-Print Network [OSTI]

    Franklin, Rima B.

    no inhibitory effect. In contrast, the percentage of organic matter was negatively correlated with oyster set. An important negative effect observed during the study period was heavy predation by Stylochus ellipticusEffects of age and composition of field-produced biofilms on oyster larval setting Alaina H

  20. H-NOX regulation of c-di-GMP metabolism and biofilm formation in Legionella pneumophilammi_7259 930..942

    E-Print Network [OSTI]

    Vance,. Russell

    -EAL protein, lpg1057, and overexpression in L. pneumophila of this protein, or the well-studied diguanylate cyclase, vca0956, results in a hyper-biofilm phenotype; (iv) the Lpg1057 protein displays diguanylate state, but not the Fe(II) unligated state; and (v) consistent with the Hnox1 regulation of Lpg1057

  1. Associations between bacterial communities of house dust and infant gut

    SciTech Connect (OSTI)

    Konya, T.; Koster, B.; Maughan, H.; Escobar, M.; Azad, M.B.; Guttman, D.S.; Sears, M.R.; Becker, A.B.; Brook, J.R.; Takaro, T.K.; Kozyrskyj, A.L.; Scott, J.A.

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  2. Escherichia coli Enhanced Hydrogen Production, Genome-wide Screening for Extracellular DNA, and Influence of GGDEF Proteins on Early Biofilm Formation 

    E-Print Network [OSTI]

    Sanchez Torres, Viviana

    2012-02-14

    for applications such as production of biofuels and biofilm control. The aims of this work were the application of protein engineering to increase E. coli hydrogen production, the identification of the proteins regulating extracellular DNA production (e...

  3. Bacteria-Phytoplankton Competition Bacterial immobilization or remineralization of N.

    E-Print Network [OSTI]

    Vallino, Joseph J.

    Bacteria-Phytoplankton Competition Overview: · Bacterial immobilization or remineralization of N. · Competition between bacteria and phytoplankton for DIN. · Experimentally examine how dissolved organic carbon (DOC) affects the competition between bacteria and phytoplankton for limiting nutrients. · Demonstrate

  4. Studies of bacterial homeostasis Sinorhizobium meliloti and Escherichia coli

    E-Print Network [OSTI]

    Davies, Bryan William

    2008-01-01

    The symbiosis between Sinorhizobium meliloti and its plant host Medicago sativa, offers a tractable model to explore the bacterial requirements for endocytic survival in a eukaryotic host. It has been shown that during ...

  5. Use of Optical Mapping in Bacterial Genome Finishing

    SciTech Connect (OSTI)

    Kumar, Dibyendu [University of Florida

    2010-06-03

    Dibyendu Kumar from the University of Florida discusses whole-genome optical mapping to help validate bacterial genome assemblies on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  6. Motor-Driven Bacterial Flagella and Buckling Instabilities

    E-Print Network [OSTI]

    Reinhard Vogel; Holger Stark

    2012-01-03

    Many types of bacteria swim by rotating a bundle of helical filaments also called flagella. Each filament is driven by a rotary motor and a very flexible hook transmits the motor torque to the filament. We model it by discretizing Kirchhoff's elastic-rod theory and develop a coarse-grained approach for driving the helical filament by a motor torque. A rotating flagellum generates a thrust force, which pushes the cell body forward and which increases with the motor torque. We fix the rotating flagellum in space and show that it buckles under the thrust force at a critical motor torque. Buckling becomes visible as a supercritical Hopf bifurcation in the thrust force. A second buckling transition occurs at an even higher motor torque. We attach the flagellum to a spherical cell body and also observe the first buckling transition during locomotion. By changing the size of the cell body, we vary the necessary thrust force and thereby obtain a characteristic relation between the critical thrust force and motor torque. We present a sophisticated analytical model for the buckling transition based on a helical rod which quantitatively reproduces the critical force-torque relation. Real values for motor torque, cell body size, and the geometry of the helical filament suggest that buckling should occur in single bacterial flagella. We also find that the orientation of pulling flagella along the driving torque is not stable and comment on the biological relevance for marine bacteria.

  7. Assessment Of Bacterial Sources Impacting Lake Waco And Belton Lake 

    E-Print Network [OSTI]

    Giovanni, G.

    2006-01-01

    Of Bacterial Sources Impacting Lake Waco And Belton Lake Prepared for: TEXAS FARM BUREAU Prepared by: PARSONS TEXAS A&M UNIVERSITY AGRICULTURAL RESEARCH & EXTENSION CENTER AT EL PASO, TEXAS AGRICULTURAL EXPERIMENT STATION TEXAS A&M UNIVERSITY ? CORPUS CHRISTI... Authority, and the City of Waco. FEBRUARY 2006 ASSESSMENT OF BACTERIAL SOURCES IMPACTING LAKE WACO AND BELTON LAKE Prepared for: TEXAS FARM BUREAU Prepared by: PARSONS TEXAS A&M UNIVERSITY AGRICULTURAL RESEARCH & EXTENSION CENTER AT EL PASO...

  8. Sociological adaptation among bacterial populations in an activated sludge ecosystem 

    E-Print Network [OSTI]

    Forrest, Robert George

    1970-01-01

    SOCIOLOGICAL ADAPTATION AMONG BACTERIAL POPULATIONS IN AN ACT1VATED SLUDGE ECOSYSTEM A Thesis by Robert George Forrest Submitted to the Graduate College of Texas ARK University in partial flilfillment of the requirements for the degree... of MASTER OF SCIENCE January, 1970 Major Subject& Microbiology SOCIOLOGICAL ADAPTATION AMONG BACTERIAL POPULkTIONS IN AN ACTIVATE) SLUDGE ECOSYSTEM A Thesis by Robert George Forrest Approved as to style and content by& (Co-Chairman of Committee) (Co...

  9. Bacterial and Protozoal Contamination of Nearshore Marine Environments in California, with Ecologically Sustainable Management

    E-Print Network [OSTI]

    Atwill, Edward R.; Conrad, Patricia A.

    2008-01-01

    Title: Reducing microbial contamination in runoff fromBacterial and Protozoal Contamination of Nearshore Marine

  10. DEVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION

    SciTech Connect (OSTI)

    Bill W. Bogan; Brigid M. Lamb; John J. Kilbane II

    2004-10-30

    The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Previous testing indicated that the growth, and the metal corrosion caused by pure cultures of sulfate reducing bacteria were inhibited by hexane extracts of some pepper plants. This quarter tests were performed to determine if chemical compounds other than pepper extracts could inhibit the growth of corrosion-associated microbes and to determine if pepper extracts and other compounds can inhibit corrosion when mature biofilms are present. Several chemical compounds were shown to be capable of inhibiting the growth of corrosion-associated microorganisms, and all of these compounds limited the amount of corrosion caused by mature biofilms to a similar extent. It is difficult to control corrosion caused by mature biofilms, but any compound that disrupts the metabolism of any of the major microbial groups present in corrosion-associated biofilms shows promise in limiting the amount/rate of corrosion.

  11. A polymer-solvent model of biofilm growth H. F. Winstanley,

    E-Print Network [OSTI]

    McGuinness, Mark

    and man-made (Chapelle 2001). In wastewater and sewage treatment, bacterial action causes the breakdown, both in the environment and in industrial processes. In soil, bacteria play a primary r in the medical and pharmaceu- tical industries, as well being a primary cause of disease in the human body

  12. Insights from twenty years of bacterial genome sequencing

    SciTech Connect (OSTI)

    Land, Miriam L; Hauser, Loren John; Jun, Se Ran; Nookaew, Intawat; Leuze, Michael Rex; Ahn, Tae-Hyuk; Karpinets, Tatiana V; Lund, Ole; Kora, Guruprasad H; Wassenaar, Trudy; Poudel, Suresh; Ussery, David W

    2015-01-01

    Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.

  13. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

    SciTech Connect (OSTI)

    Hodkinson, Brendan P; Gottel, Neil R; Schadt, Christopher Warren; Lutzoni, Francois

    2011-01-01

    Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e. green algal vs. cyanobacterial), mycobiont-types and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.

  14. Low-temperature solgel-derived nanosilver-embedded silane coating as biofilm inhibitor This article has been downloaded from IOPscience. Please scroll down to see the full text article.

    E-Print Network [OSTI]

    Cao, Wenwu

    Low-temperature sol­gel-derived nanosilver-embedded silane coating as biofilm inhibitor.1088/0957-4484/22/15/155602 Low-temperature sol­gel-derived nanosilver-embedded silane coating as biofilm inhibitor A Babapour1.iop.org/Nano/22/155602 Abstract Silver nanocomposite coatings are prepared by the sol­gel method

  15. Bacterial Monitoring for the Buck Creek Watershed 

    E-Print Network [OSTI]

    2008-01-01

    personnel to conduct this study. With the help and cooperation of the Texas AgriLife Research and Extension Center at Vernon, a work plan was developed to collect water samples and conduct water quality monitoring every other week at 13 different sites along...

  16. The Dynamics of Cooperative Bacterial Virulence in the Field

    E-Print Network [OSTI]

    West, Stuart

    of microorganisms can depend on cooperation between cells. Although this insight has revolutionized our populations. We investigated the sociality of essential virulence factors (crystal toxins) in the pathogen growth and virulence of pathogenic bacteria often depends on cooperation be- tween bacterial cells (1

  17. Bacterial batteries By Birmingham Science News Examiner, Paul

    E-Print Network [OSTI]

    Lovley, Derek

    Bacterial batteries By Birmingham Science News Examiner, Paul Hamaker September 14, 5:44 AM in remote areas, conversion of waste to electricity, and longer battery life in harsh environments. KN400 greatly increases the power output of batteries and electric cells. More electron flow per unit area

  18. SGM Special Moving folded proteins across the bacterial cell

    E-Print Network [OSTI]

    Palmer, Tracy

    -containing proteins are essential for most types of bacterial respiratory and photo- synthetic energy metabolism by the transmembrane proton electrochemical gradient. The TatA protein probably forms the transport channel while metabolism in most environments depends upon the bacterium being able to produce cofactor-containing pro

  19. Making Drinking Water Safer from Bacterial Contamination in Emergency Situations

    E-Print Network [OSTI]

    drinking water. However, this protection may break down during emergencies caused by natural disastersMaking Drinking Water Safer from Bacterial Contamination in Emergency Situations Monty C. Dozier, such as hurricanes. Water supplies to your home may be shut off or become dangerous to use. You must then know what

  20. COMMUNICATION TO THE EDITOR Chiral Compounds from Bacterial

    E-Print Network [OSTI]

    COMMUNICATION TO THE EDITOR Chiral Compounds from Bacterial Polyesters: Sugars to Plastics to Fine Research Center, Korea Advanced Institute of Science and Technology, 373-1 Kusong-dong, Yusong-gu, Taejon, 1996). PHAs have drawn much attention because they can be used as truly biodegradable plastics

  1. Cell Host & Microbe Bacterial Effectors Target the Common Signaling

    E-Print Network [OSTI]

    Sheen, Jen

    Cell Host & Microbe Article Bacterial Effectors Target the Common Signaling Partner BAK1 to Disrupt and Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA 6These convergent innate immune responses stimulated by multiple microbe-associ- ated molecular patterns (MAMPs

  2. Molecular Cell The Three-Dimensional Architecture of a Bacterial

    E-Print Network [OSTI]

    Church, George M.

    Molecular Cell Article The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration have determined the three-dimensional (3D) architecture of the Caulobacter crescentus genome segregation. INTRODUCTION The three-dimensional (3D) architecture of the genome both reflects and regulates

  3. Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

    SciTech Connect (OSTI)

    Gladden, J.M.; Allgaier, M.; Miller, C.S.; Hazen, T.C.; VanderGheynst, J.S.; Hugenholtz, P.; Simmons, B.A.; Singer, S.W.

    2011-05-01

    Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60 C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80 C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

  4. Natural bacterial communities serve as quantitative geochemical biosensors

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

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; et al

    2015-05-12

    Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination,more »even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.« less

  5. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method

    SciTech Connect (OSTI)

    Axen, Seth D.; Erbilgin, Onur; Kerfeld, Cheryl A.; Tanaka, Mark M.

    2014-10-23

    Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications.

  6. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method

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

    Axen, Seth D.; Erbilgin, Onur; Kerfeld, Cheryl A.; Tanaka, Mark M.

    2014-10-23

    Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found inmore »seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications.« less

  7. Differentiation of Microbial Species and Strains in Coculture Biofilms by Multivariate Analysis of Laser Desorption Postionization Mass Spectra

    SciTech Connect (OSTI)

    University of Illinois at Chicago; Montana State University; Bhardwaj, Chhavi; Cui, Yang; Hofstetter, Theresa; Liu, Suet Yi; Bernstein, Hans C.; Carlson, Ross P.; Ahmed, Musahid; Hanley, Luke

    2013-04-01

    7.87 to 10.5 eV vacuum ultraviolet (VUV) photon energies were used in laser desorption postionization mass spectrometry (LDPI-MS) to analyze biofilms comprised of binary cultures of interacting microorganisms. The effect of photon energy was examined using both tunable synchrotron and laser sources of VUV radiation. Principal components analysis (PCA) was applied to the MS data to differentiate species in Escherichia coli-Saccharomyces cerevisiae coculture biofilms. PCA of LDPI-MS also differentiated individual E. coli strains in a biofilm comprised of two interacting gene deletion strains, even though these strains differed from the wild type K-12 strain by no more than four gene deletions each out of approximately 2000 genes. PCA treatment of 7.87 eV LDPI-MS data separated the E. coli strains into three distinct groups two ?pure? groups and a mixed region. Furthermore, the ?pure? regions of the E. coli cocultures showed greater variance by PCA when analyzed by 7.87 eV photon energies than by 10.5 eV radiation. Comparison of the 7.87 and 10.5 eV data is consistent with the expectation that the lower photon energy selects a subset of low ionization energy analytes while 10.5 eV is more inclusive, detecting a wider range of analytes. These two VUV photon energies therefore give different spreads via PCA and their respective use in LDPI-MS constitute an additional experimental parameter to differentiate strains and species.

  8. Development and Integration of Genome-Enabled Techniques to Track and Predict the Cycling of Carbon in Model Microbial Communities

    SciTech Connect (OSTI)

    Banfield, Jillian

    2014-11-26

    The primary objective of this project was to establish widely applicable, high-throughput “omics” methods for tracking carbon flow in microbial communities at a strain-resolved molecular level. We developed and applied these methods to study a well-established microbial community model system with a long history of “omics” innovation: chemoautotrophic biofilms grown in an acid mine drainage (AMD) environment. The methods are now being transitioned (in a new project) to study soil. Using metagenomics, stable-isotope proteomics, stable-isotope metabolomics, transcriptomics, and microscopy, we tracked carbon flow during initial biofilm growth involving CO2 fixation, through the maturing biofilm community consisting of multiple trophic levels, and during an anaerobic degradative phase after biofilms sink. This work included explicit consideration of the often overlooked roles of archaea and microbial eukaryotes (fungi) in carbon turnover. We also analyzed where the eosystem begins to fail in response to thermal perturbation, and how perturbation propagates through a carbon cycle. We investigated the form of strain variation in microbial communities, the importance of strain variants, and the rate and form of strain evolution. Overall, the project generated an array of new, integrated ‘omics’ approaches and provided unprecedented insight into the functioning of a natural ecosystem. This project supported graduate training for five Ph.D. students and three post doctoral fellows and contributed directly to at least 26 publications (two in Science).

  9. Spatial organization of bacterial transcription and translation

    E-Print Network [OSTI]

    Michele Castellana; Ned S. Wingreen

    2015-10-29

    In bacteria such as $\\textit{Escherichia coli}$, DNA is compacted into a nucleoid near the cell center, while ribosomes - molecular complexes that translate messenger RNAs (mRNAs) into proteins - are mainly localized at the poles. We study the impact of this spatial organization using a minimal reaction-diffusion model for the cellular transcriptional-translational machinery. Our model predicts that $\\sim90\\%$ of mRNAs are segregated to the poles and reveals a "circulation" of ribosomes driven by the flux of mRNAs, from synthesis in the nucleoid to degradation at the poles. To address the existence of non-specific, transient interactions between ribosomes and mRNAs, we developed a novel method to efficiently incorporate such transient interactions into reaction-diffusion equations, which allowed us to quantify the biological implications of such non-specific interactions, e.g. for ribosome efficiency.

  10. Method for construction of bacterial strains with increased succinic acid production

    DOE Patents [OSTI]

    Donnelly, Mark I. (Warrenville, IL); Sanville-Millard, Cynthia (Plainfield, IL); Chatterjee, Ranjini (Park Ridge, IL)

    2000-01-01

    A fermentation process for producing succinic acid is provided comprising selecting a bacterial strain that does not produce succinic acid in high yield, disrupting the normal regulation of sugar metabolism of said bacterial strain, and combining the mutant bacterial strain and selected sugar in anaerobic conditions to facilitate production of succinic acid. Also provided is a method for changing low yield succinic acid producing bacteria to high yield succinic acid producing bacteria comprising selecting a bacterial strain having a phosphotransferase system and altering the phosphotransferase system so as to allow the bacterial strain to simultaneously metabolize different sugars.

  11. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity

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

    Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; Osipiuk, Jerzy; Gu, Minyi; Zhang, Minjia; Mandapati, Kavitha; Gollapalli, Deviprasad R.; Gorla, Suresh Kumar; Hedstrom, Lizbeth; et al

    2015-01-09

    The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes withmore »different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. As a result, these findings offer a potential strategy for further ligand optimization.« less

  12. The Limiting Speed of the Bacterial Flagellar Motor

    E-Print Network [OSTI]

    Nirody, Jasmine A; Oster, George

    2015-01-01

    Recent experiments on the bacterial flagellar motor have shown that the structure of this nanomachine, which drives locomotion in a wide range of bacterial species, is more dynamic than previously believed. Specifically, the number of active torque-generating units (stators) was shown to vary across applied loads. This finding invalidates the experimental evidence reporting that limiting (zero-torque) speed is independent of the number of active stators. Here, we propose that, contrary to previous assumptions, the maximum speed of the motor is not universal, but rather increases as additional torque-generators are recruited. This result arises from our assumption that stators disengage from the motor for a significant portion of their mechanochemical cycles at low loads. We show that this assumption is consistent with current experimental evidence and consolidate our predictions with arguments that a processive motor must have a high duty ratio at high loads.

  13. The Limiting Speed of the Bacterial Flagellar Motor

    E-Print Network [OSTI]

    Jasmine A. Nirody; Richard M. Berry; George Oster

    2015-05-22

    Recent experiments on the bacterial flagellar motor have shown that the structure of this nanomachine, which drives locomotion in a wide range of bacterial species, is more dynamic than previously believed. Specifically, the number of active torque-generating units (stators) was shown to vary across applied loads. This finding invalidates the experimental evidence reporting that limiting (zero-torque) speed is independent of the number of active stators. Here, we propose that, contrary to previous assumptions, the maximum speed of the motor is not universal, but rather increases as additional torque-generators are recruited. This result arises from our assumption that stators disengage from the motor for a significant portion of their mechanochemical cycles at low loads. We show that this assumption is consistent with current experimental evidence and consolidate our predictions with arguments that a processive motor must have a high duty ratio at high loads.

  14. Ferromagnetic and antiferromagnetic order in bacterial vortex lattices

    E-Print Network [OSTI]

    Hugo Wioland; Francis G. Woodhouse; Jörn Dunkel; Raymond E. Goldstein

    2015-11-16

    Despite their inherent non-equilibrium nature, living systems can self-organize in highly ordered collective states that share striking similarities with the thermodynamic equilibrium phases of conventional condensed matter and fluid systems. Examples range from the liquid-crystal-like arrangements of bacterial colonies, microbial suspensions and tissues to the coherent macro-scale dynamics in schools of fish and flocks of birds. Yet, the generic mathematical principles that govern the emergence of structure in such artificial and biological systems are elusive. It is not clear when, or even whether, well-established theoretical concepts describing universal thermostatistics of equilibrium systems can capture and classify ordered states of living matter. Here, we connect these two previously disparate regimes: Through microfluidic experiments and mathematical modelling, we demonstrate that lattices of hydrodynamically coupled bacterial vortices can spontaneously organize into distinct phases of ferro- and antiferromagnetic order. The preferred phase can be controlled by tuning the vortex coupling through changes of the inter-cavity gap widths. The emergence of opposing order regimes is tightly linked to the existence of geometry-induced edge currents, reminiscent of those in quantum systems. Our experimental observations can be rationalized in terms of a generic lattice field theory, suggesting that bacterial spin networks belong to the same universality class as a wide range of equilibrium systems.

  15. Bacterial Immobilization for Imaging by Atomic Force Microscopy

    SciTech Connect (OSTI)

    Allison, David P [ORNL; Sullivan, Claretta [Eastern Virginia Medical School; Mortensen, Ninell P [ORNL; Retterer, Scott T [ORNL; Doktycz, Mitchel John [ORNL

    2011-01-01

    AFM is a high-resolution (nm scale) imaging tool that mechanically probes a surface. It has the ability to image cells and biomolecules, in a liquid environment, without the need to chemically treat the sample. In order to accomplish this goal, the sample must sufficiently adhere to the mounting surface to prevent removal by forces exerted by the scanning AFM cantilever tip. In many instances, successful imaging depends on immobilization of the sample to the mounting surface. Optimally, immobilization should be minimally invasive to the sample such that metabolic processes and functional attributes are not compromised. By coating freshly cleaved mica surfaces with porcine (pig) gelatin, negatively charged bacteria can be immobilized on the surface and imaged in liquid by AFM. Immobilization of bacterial cells on gelatin-coated mica is most likely due to electrostatic interaction between the negatively charged bacteria and the positively charged gelatin. Several factors can interfere with bacterial immobilization, including chemical constituents of the liquid in which the bacteria are suspended, the incubation time of the bacteria on the gelatin coated mica, surface characteristics of the bacterial strain and the medium in which the bacteria are imaged. Overall, the use of gelatin-coated mica is found to be generally applicable for imaging microbial cells.

  16. Convergent bacterial microbiotas in the fungal agricultural systems of insects

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

    Aylward, Frank O.; Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; Glavina del Rio, Tijana; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; et al

    2014-11-18

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associatedmore »with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes.« less

  17. Convergent bacterial microbiotas in the fungal agricultural systems of insects

    SciTech Connect (OSTI)

    Aylward, Frank O.; Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; Glavina del Rio, Tijana; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; Klepzig, Kier D.; Currie, Cameron R.

    2014-11-18

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes.

  18. Distance matters: the impact of gene proximity in bacterial gene regulation

    E-Print Network [OSTI]

    Otto Pulkkinen; Ralf Metzler

    2013-05-13

    Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product formation is increasingly recognized. We here show from analytical and numerical analysis that the distance between a transcription factor (TF) gene and its target gene drastically affects the speed and reliability of transcriptional regulation in bacterial cells. For an explicit model system we develop a general theory for the interactions between a TF and a transcription unit. The observed variations in regulation efficiency are linked to the magnitude of the variation of the TF concentration peaks as a function of the binding site distance from the signal source. Our results support the role of rapid binding site search for gene colocalization and emphasize the role of local concentration differences.

  19. Production of extremophilic bacterial cellulase enzymes in aspergillus niger.

    SciTech Connect (OSTI)

    Gladden, John Michael

    2013-09-01

    Enzymes can be used to catalyze a myriad of chemical reactions and are a cornerstone in the biotechnology industry. Enzymes have a wide range of uses, ranging from medicine with the production of pharmaceuticals to energy were they are applied to biofuel production. However, it is difficult to produce large quantities of enzymes, especially if they are non-native to the production host. Fortunately, filamentous fungi, such as Aspergillus niger, are broadly used in industry and show great potential for use a heterologous enzyme production hosts. Here, we present work outlining an effort to engineer A. niger to produce thermophilic bacterial cellulases relevant to lignocellulosic biofuel production.

  20. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters

    E-Print Network [OSTI]

    2006-01-01

    Metabolic Complementarity and Genomics of the Dual BacterialMetabolic complementarity and genomics of the dual bacterialthe other. ) Comparative genomics. The predicted proteomes

  1. Effect of Divalent Cation Removal on the Structure of Gram-Negative Bacterial Outer Membrane Models

    SciTech Connect (OSTI)

    Clifton, Luke A.; Skoda, Maximilian W. A.; Le Brun, Anton P.; Ciesielski, Filip; Kuzmenko, Ivan; Holt, Stephen A.; Lakey, Jeremy H.

    2014-12-09

    The Gram-negative bacterial outer membrane (GNB-OM) is asymmetric in its lipid composition with a phospholipid-rich inner leaflet and an outer leaflet predominantly composed of lipopolysaccharides (LPS). LPS are polyanionic molecules, with numerous phosphate groups present in the lipid A and core oligosaccharide regions. The repulsive forces due to accumulation of the negative charges are screened and bridged by the divalent cations (Mg2+ and Ca2+) that are known to be crucial for the integrity of the bacterial OM. Indeed, chelation of divalent cations is a well-established method to permeabilize Gram-negative bacteria such as Escherichia coli. Here, we use X-ray and neutron reflectivity (XRR and NR, respectively) techniques to examine the role of calcium ions in the stability of a model GNB-OM. Using XRR we show that Ca2+ binds to the core region of the rough mutant LPS (RaLPS) films, producing more ordered structures in comparison to divalent cation free monolayers. Using recently developed solid-supported models of the GNB-OM, we study the effect of calcium removal on the asymmetry of DPPC:RaLPS bilayers. We show that without the charge screening effect of divalent cations, the LPS is forced to overcome the thermodynamically unfavorable energy barrier and flip across the hydrophobic bilayer to minimize the repulsive electrostatic forces, resulting in about 20% mixing of LPS and DPPC between the inner and outer bilayer leaflets. These results reveal for the first time the molecular details behind the well-known mechanism of outer membrane stabilization by divalent cations. This confirms the relevance of the asymmetric models for future studies of outer membrane stability and antibiotic penetration.

  2. Effect of Divalent Cation Removal on the Structure of Gram-Negative Bacterial Outer Membrane Models

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

    Clifton, Luke A.; Skoda, Maximilian W. A.; Le Brun, Anton P.; Ciesielski, Filip; Kuzmenko, Ivan; Holt, Stephen A.; Lakey, Jeremy H.

    2014-12-09

    The Gram-negative bacterial outer membrane (GNB-OM) is asymmetric in its lipid composition with a phospholipid-rich inner leaflet and an outer leaflet predominantly composed of lipopolysaccharides (LPS). LPS are polyanionic molecules, with numerous phosphate groups present in the lipid A and core oligosaccharide regions. The repulsive forces due to accumulation of the negative charges are screened and bridged by the divalent cations (Mg2+ and Ca2+) that are known to be crucial for the integrity of the bacterial OM. Indeed, chelation of divalent cations is a well-established method to permeabilize Gram-negative bacteria such as Escherichia coli. Here, we use X-ray and neutronmore »reflectivity (XRR and NR, respectively) techniques to examine the role of calcium ions in the stability of a model GNB-OM. Using XRR we show that Ca2+ binds to the core region of the rough mutant LPS (RaLPS) films, producing more ordered structures in comparison to divalent cation free monolayers. Using recently developed solid-supported models of the GNB-OM, we study the effect of calcium removal on the asymmetry of DPPC:RaLPS bilayers. We show that without the charge screening effect of divalent cations, the LPS is forced to overcome the thermodynamically unfavorable energy barrier and flip across the hydrophobic bilayer to minimize the repulsive electrostatic forces, resulting in about 20% mixing of LPS and DPPC between the inner and outer bilayer leaflets. These results reveal for the first time the molecular details behind the well-known mechanism of outer membrane stabilization by divalent cations. This confirms the relevance of the asymmetric models for future studies of outer membrane stability and antibiotic penetration.« less

  3. Genomic approaches to understanding bacterial virulence Laura S Burrack and Darren E Higgins

    E-Print Network [OSTI]

    Higgins, Darren

    complete deletion mutant set for a bacterial species. In addition to defined libraries of of virulence factors through the use of bioinformatics, targeted mutant library construction, screening of libraries of bacterial proteins within model organisms such as yeast. Host genomic information has also

  4. Influence of bacterial uptake on deep-ocean dissolved organic Jrgen Bendtsen and Claus Lundsgaard

    E-Print Network [OSTI]

    loop in the aphotic zone based on new measurements of deep ocean bacterial metabolism. These together ocean circulation, we show that the observed gradient of DOC in the deep North Atlantic can be explained by the temperature dependence of bacterial metabolic activity in conjunction with the formation of deep-water at high

  5. Organic loading rates affect composition of soil-derived bacterial communities during continuous, fermentative

    E-Print Network [OSTI]

    , fermentative biohydrogen production Yonghua Luoa,1 , Husen Zhangb,2 , Michael Salernob,3 , Bruce E. Loganb: Biohydrogen Fermentation Renewable Bacterial community Clostridium Selenomonas a b s t r a c t Bacterial community composition during steady-state, fermentative H2 production was compared across a range of organic

  6. Molecular characterization of intestinal bacteria in healthy cats and a comparison of the fecal bacterial flora between healthy cats and cats with inflammatory bowel disease (IBD) 

    E-Print Network [OSTI]

    Ritchie, Lauren Elizabeth

    2009-05-15

    specific pathogen free cat (SPF) and the bacterial composition was identified by direct sequencing of bacterial 16S rDNA amplicons. A predominant anaerobic microflora was observed in all evaluated segments of the intestine. Fourteen different bacterial...

  7. Structure-based receptor MIMICS targeted against bacterial superantigen toxins

    DOE Patents [OSTI]

    Gupta, Goutam (Santa Fe, NM); Hong-Geller, Elizabeth (Los Alamos, NM); Shiflett, Patrick R. (Los Alamos, NM); Lehnert, Nancy M. (Albuquerque, NM)

    2009-08-18

    The invention provides therapeutic compositions useful in the treatment of bacterial superantigen mediated conditions, such as Toxic Shock Syndrome. The compositions comprise genetically engineered bifunctional polypeptides containing a specific T-cell receptor binding domain and a specific MHC class II receptor binding domain, each targeting non-overlapping epitopes on a superantigen molecule against which they are designed. The anti-superantigen "receptor mimetics" or "chimeras" are rationally designed to recreate the modality of superantigen binding directly to both the TCR and the MHC-II receptor, and are capable of acting as decoys for superantigen binding, effectively out-competing the host T-cell and MHC-II receptors, the natural host receptors.

  8. ASSESSMENT OF MARKER PROTEINS IDENTIFIED IN WHOLE CELL EXTRACTS FOR BACTERIAL SPECIATION USING LIQUID CHROMATOGRAPHY ELECTROSPRAY IONIZATION TANDEM MASS SPECTROMETRY

    SciTech Connect (OSTI)

    Kooken, Jennifer M.; Fox, Karen F.; Fox, Alvin; Wunschel, David S.

    2014-02-02

    ASSESSMENT OF MARKER PROTEINS IDENTIFIED IN WHOLE CELL EXTRACTS FOR BACTERIAL SPECIATION USING LIQUID CHROMATOGRAPHY ELECTROSPRAY IONIZATION TANDEM MASS SPECTROMETRY

  9. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    SciTech Connect (OSTI)

    Kingsley, Mark T

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, an d analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: (1) to assess the potential terrorist threat to U.S. agricultural crops, (2) to determine whether suitable assays exist to monitor that threat, and (3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  10. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    SciTech Connect (OSTI)

    Kingsley, Mark T.

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, and analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: 1) to assess the potential terrorist threat to U.S. agricultural crops, 2) to determine whether suitable assays exist to monitor that threat, and 3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  11. Towards an informative mutant phenotype for every bacterial gene

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

    Deutschbauer, Adam; Price, Morgan N.; Wetmore, Kelly M.; Tarjan, Daniel R.; Xu, Zhuchen; Shao, Wenjen; Leon, Dacia; Arkin, Adam P.; Skerker, Jeffrey M.

    2014-08-11

    Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, inmore »Z. mobilis, most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness.« less

  12. Bacterial microcompartment assembly: The key role of encapsulation peptides

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

    Aussignargues, Clément; Paasch, Bradley C.; Gonzalez-Esquer, Raul; Erbilgin, Onur; Kerfeld, Cheryl A.

    2015-06-23

    Bacterial microcompartments (BMCs) are proteinaceous organelles used by a broad range of bacteria to segregate and optimize metabolic reactions. Their functions are diverse, and can be divided into anabolic (carboxysome) and catabolic (metabolosomes) processes, depending on their cargo enzymes. The assembly pathway for the ?-carboxysome has been characterized, revealing that biogenesis proceeds from the inside out. The enzymes coalesce into a procarboxysome, followed by encapsulation in a protein shell that is recruited to the procarboxysome by a short (~17 amino acids) extension on the C-terminus of one of the encapsulated proteins. A similar extension is also found on the N-more »or C-termini of a subset of metabolosome core enzymes. These encapsulation peptides (EPs) are characterized by a primary structure predicted to form an amphipathic ?-helix that interacts with shell proteins. In this study, we review the features, function and widespread occurrence of EPs among metabolosomes, and propose an expanded role for EPs in the assembly of diverse BMCs.« less

  13. Design of a microfluidic device for the analysis of biofilm behavior in a microbial fuel cell

    E-Print Network [OSTI]

    Jones, A-Andrew D., III (Akhenaton-Andrew Dhafir)

    2014-01-01

    This thesis presents design, manufacturing, testing, and modeling of a laminar-flow microbial fuel cell. Novel means were developed to use graphite and other bulk-scale materials in a microscale device without loosing any ...

  14. Microbial studies of compost: bacterial identification, and their potential for turfgrass pathogen suppression

    E-Print Network [OSTI]

    Boland, Greg J.

    , diversity, fungi pathogen, pink snow mould, phospholipid analysis, plant microorganism, turfgrass SummaryMicrobial studies of compost: bacterial identification, and their potential for turfgrass pathogen Composting is the degradation of organic materials through the activities of diverse microorganisms

  15. Oil bioremediation in salt marsh mesocosms as influenced by nitrogen, phosphorus, and bacterial seeding 

    E-Print Network [OSTI]

    Wright, Alan Lee

    1995-01-01

    Glasshouse experiments were conducted to determine the effects of N and P fertilization and bacterial seeding on crude oil degradation in salt marsh mesocosms containing marsh soil and Spartina alterniflora. Fertilization with urea, NH4, and N03...

  16. Siderophore production by heterotrophic bacterial isolates from the Costa Rica upwelling dome

    E-Print Network [OSTI]

    Krey, Whitney B. (Whitney Blair)

    2008-01-01

    (cont) An increased understanding of heterotrophic bacterial strategies for acquiring nutrients and trace elements is critical for elucidating their impact on biogeochemical cycling in the ocean. It is estimated that iron ...

  17. Comparison of the mechanism of transmembrane signaling in bacterial chemoreceptors and sensor kinases 

    E-Print Network [OSTI]

    Ward, Scott Michael

    2006-10-30

    Membrane-bound receptors transmit information from the cell exterior to the cell interior. Bacterial receptors capable of transmitting this information include sensor kinases, which control gene expression via response regulators, and methyl...

  18. A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction for

    E-Print Network [OSTI]

    Korban, Schuyler S.

    A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction of 31 584 clones has been constructed from M. floribunda 821. From the analysis of 88 randomly selected

  19. Aboveground-belowground interactions: Investigating the role of plant communities in structuring soil bacterial communities

    E-Print Network [OSTI]

    Murphy, Cheryl A.

    2012-08-31

    and by plant communities through litter inputs and root exudation. This dissertation focuses on investigating the role that plant communities play in potentially creating environmental heterogeneity within the soil and how that impacts soil bacterial community...

  20. FapR, a Bacterial Transcription Factor Involved in Global Regulation of Membrane Lipid Biosynthesis

    E-Print Network [OSTI]

    Schujman, Gustavo E

    Bacterial cells exert exquisite control over the biosynthesis of their membrane lipids, but the mechanisms are obscure. We describe the identification and purification from Bacillus subtilis of a transcription factor, FapR, ...

  1. Structural investigations of hydroxylase proteins and complexes in bacterial multicomponent monooxygenase systems

    E-Print Network [OSTI]

    McCormick, Michael S. (Michael Scott)

    2008-01-01

    Bacterial multicomponent monooxgenases (BMMs) such as toluene/o-xylene monooxygenase (ToMO), phenol hydroxylase (PH), and soluble methane monooxygenase (sMMO) catalyze hydrocarbon oxidation reactions at a carboxylatebridged ...

  2. Soil Biology & Biochemistry 38 (2006) 16081614 Endogeic earthworms differentially influence bacterial communities

    E-Print Network [OSTI]

    Rilli, Matthias C.

    2006-01-01

    Soil Biology & Biochemistry 38 (2006) 1608­1614 Endogeic earthworms differentially influence bacterial communities associated with different soil aggregate size fractions Daniel L. Mummeya,Ã, Matthias influence soil structure. Although soil microorganisms are thought to be central to earthworm

  3. Citrus Bioactive Compounds: Isolation, Characterization and Modulation of Bacterial Intercellular Communication and Pathogenicity 

    E-Print Network [OSTI]

    Vikram, Amit

    2012-07-16

    The secondary metabolites of citrus such as limonoids and flavonoids constitute an important part of human diet. The present work was undertaken to elucidate the effect of citrus limonoids and flavonoids on the bacterial cell-cell signaling...

  4. Adaptable functionality of transcriptional feedback in bacterial two-component systems

    E-Print Network [OSTI]

    Ray, J. Christian J.; Igoshin, Oleg A.

    2010-02-12

    A widespread mechanism of bacterial signaling occurs through two-component systems, comprised of a sensor histidine kinase (SHK) and a transcriptional response regulator (RR). The SHK activates RR by phosphorylation. The ...

  5. Bacterial influence on uranium oxidation reduction reactions : implications for environmental remediation and isotopic composition

    E-Print Network [OSTI]

    Mullen, Lisa Maureen

    2007-01-01

    The bacterial influence on the chemistry and speciation of uranium has some important impacts on the environment, and can be exploited usefully for the purposes of environmental remediation of uranium waste contamination. ...

  6. A keystone predator controls bacterial diversity in the pitcher-plant (Sarracenia purpurea) microecosystem

    E-Print Network [OSTI]

    Pringle, Anne

    A keystone predator controls bacterial diversity in the pitcher-plant (Sarracenia purpurea of the keystone predator in this food web, larvae of the pitcher-plant mosquito Wyeomyia smithii. Results were

  7. Quantitative and qualitative evaluation of the aerobic and facultative bacterial flora of voided canine urine 

    E-Print Network [OSTI]

    Biggerstaff, Jane

    1978-01-01

    QUANTITATIVE AND QUALITATIVE EVALUATION OF THE AEROBIC AND FACULTATIVE BACTERIAL FLORA OF VOIDED CANINE URINE A Thesis by JANE BIGGERSTAFF Submitted to the Graduate College of Texas ARM University in partial fulfillment of the requirements... and content by Chairman of gs}mmittoe) (Head of Department) (Nember (Nember) August 1978 443163 ABSTRACT Quantitative and Qualitative Evaluation of the Aerobic and Facultative Bacterial Flora of Voided Canine Urine. (August, 1978) Jane Biggerstaff, B...

  8. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

    SciTech Connect (OSTI)

    Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.; Santee, C.A.; Bradford, M.A.; Treseder, K.K.; Wallenstein, M.D.; Brodie, E.L.

    2011-04-18

    Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.

  9. Coulter counter determination of bacterial growth and cellular size change following ??Co gamma irradiation 

    E-Print Network [OSTI]

    Gaston, Gary W

    1976-01-01

    COULTER COUNTER DETERMINATION OF BACTERIAL GROWTH AND CELLULAR SIZE CHANGE FOLLOWING Co GAMMA IRRADIATION A Thesis by GARY W. GASTON Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirement... for the degree of MASTER OF SCIENCE December 1976 Ma)or Subject: Biophysics COULTER COUNTER DETERMINATION OF BACTERIAL GROWTH AND CELLULAR SIZE CHANGE FOLLOWING Co GAMMA IRRADIATION A Thesis by GARY W. GASTON APPROVED as to style and content by: ead...

  10. Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs: Arg- and Gln-type Bacterial CDO Homologs

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

    Driggers, Camden M.; Hartman, Steven J.; Karplus, P. Andrew

    2015-01-01

    In some bacteria, cysteine is converted to cysteine sulfinic acid by cysteine dioxygenases (CDO) that are only ~15–30% identical in sequence to mammalian CDOs. Among bacterial proteins having this range of sequence similarity to mammalian CDO are some that conserve an active site Arg residue (“Arg-type” enzymes) and some having a Gln substituted for this Arg (“Gln-type” enzymes). Here, we describe a structure from each of these enzyme types by analyzing structures originally solved by structural genomics groups but not published: a Bacillus subtilis “Arg-type” enzyme that has cysteine dioxygenase activity (BsCDO), and a Ralstonia eutropha “Gln-type” CDO homolog ofmore »uncharacterized activity (ReCDOhom). The BsCDO active site is well conserved with mammalian CDO, and a cysteine complex captured in the active site confirms that the cysteine binding mode is also similar. The ReCDOhom structure reveals a new active site Arg residue that is hydrogen bonding to an iron-bound diatomic molecule we have interpreted as dioxygen. Notably, the Arg position is not compatible with the mode of Cys binding seen in both rat CDO and BsCDO. As sequence alignments show that this newly discovered active site Arg is well conserved among “Gln-type” CDO enzymes, we conclude that the “Gln-type” CDO homologs are not authentic CDOs but will have substrate specificity more similar to 3-mercaptopropionate dioxygenases.« less

  11. Lubricating bacteria model for the growth of bacterial colonies exposed to ultraviolet radiation

    SciTech Connect (OSTI)

    Zhang Shengli; Zhang Lei; Liang Run; Zhang Erhu; Liu Yachao; Zhao Shumin

    2005-11-01

    In this paper, we study the morphological transition of bacterial colonies exposed to ultraviolet radiation by modifying the bacteria model proposed by Delprato et al. Our model considers four factors: the lubricant fluid generated by bacterial colonies, a chemotaxis initiated by the ultraviolet radiation, the intensity of the ultraviolet radiation, and the bacteria's two-stage destruction rate with given radiation intensities. Using this modified model, we simulate the ringlike pattern formation of the bacterial colony exposed to uniform ultraviolet radiation. The following is shown. (1) Without the UV radiation the colony forms a disklike pattern and reaches a constant front velocity. (2) After the radiation is switched on, the bacterial population migrates to the edge of the colony and forms a ringlike pattern. As the intensity of the UV radiation is increased the ring forms faster and the outer velocity of the colony decreases. (3) For higher radiation intensities the total population decreases, while for lower intensities the total population increases initially at a small rate and then decreases. (4) After the UV radiation is switched off, the bacterial population grows both outward as well as into the inner region, and the colony's outer front velocity recovers to a constant value. All these results agree well with the experimental observations [Phys. Rev. Lett. 87, 158102 (2001)]. Along with the chemotaxis, we find that lubricant fluid and the two-stage destruction rate are critical to the dynamics of the growth of the bacterial colony when exposed to UV radiation, and these were not previously considered.

  12. Towards an informative mutant phenotype for every bacterial gene

    SciTech Connect (OSTI)

    Deutschbauer, Adam; Price, Morgan N.; Wetmore, Kelly M.; Tarjan, Daniel R.; Xu, Zhuchen; Shao, Wenjen; Leon, Dacia; Arkin, Adam P.; Skerker, Jeffrey M.

    2014-08-11

    Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, in Z. mobilis, most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness.

  13. Identification and characterization of a bacterial hydrosulphide ion channel

    SciTech Connect (OSTI)

    Czyzewski, Bryan K.; Wang, Da-Neng (NYUSM)

    2012-10-26

    The hydrosulphide ion (HS{sup -}) and its undissociated form, hydrogen sulphide (H{sub 2}S), which are believed to have been critical to the origin of life on Earth, remain important in physiology and cellular signalling. As a major metabolite in anaerobic bacterial growth, hydrogen sulphide is a product of both assimilatory and dissimilatory sulphate reduction. These pathways can reduce various oxidized sulphur compounds including sulphate, sulphite and thiosulphate. The dissimilatory sulphate reduction pathway uses this molecule as the terminal electron acceptor for anaerobic respiration, in which process it produces excess amounts of H{sub 2}S. The reduction of sulphite is a key intermediate step in all sulphate reduction pathways. In Clostridium and Salmonella, an inducible sulphite reductase is directly linked to the regeneration of NAD{sup +}, which has been suggested to have a role in energy production and growth, as well as in the detoxification of sulphite. Above a certain concentration threshold, both H{sub 2}S and HS{sup -} inhibit cell growth by binding the metal centres of enzymes and cytochrome oxidase, necessitating a release mechanism for the export of this toxic metabolite from the cell. Here we report the identification of a hydrosulphide ion channel in the pathogen Clostridium difficile through a combination of genetic, biochemical and functional approaches. The HS{sup -} channel is a member of the formate/nitrite transport family, in which about 50 hydrosulphide ion channels form a third subfamily alongside those for formate (FocA) and for nitrite (NirC). The hydrosulphide ion channel is permeable to formate and nitrite as well as to HS{sup -} ions. Such polyspecificity can be explained by the conserved ion selectivity filter observed in the channel's crystal structure. The channel has a low open probability and is tightly regulated, to avoid decoupling of the membrane proton gradient.

  14. Antibiotic persistence in Salmonella enterica serovar Typhimurium; involvement of the CspA paralogues 

    E-Print Network [OSTI]

    Shrimpton, Sarah Elaine

    2011-06-27

    Chronic infections are often attributed to bacterial biofilms. These biofilms are extremely tolerant to antimicrobial treatment due to the presence of dormant persister cells. Whilst a number of persister genes and ...

  15. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

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

    Hesse, Cedar N.; Mueller, Rebecca C.; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D.; Zak, Donald R.; Kuske, Cheryl R.

    2015-04-23

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes)more »in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.« less

  16. LLNL Genomic Assessment: Viral and Bacterial Sequencing Needs for TMTI, Tier 1 Report

    SciTech Connect (OSTI)

    Slezak, T; Borucki, M; Lenhoff, R; Vitalis, E

    2009-09-29

    The Lawrence Livermore National Lab Bioinformatics group has recently taken on a role in DTRA's Transformation Medical Technologies Initiative (TMTI). The high-level goal of TMTI is to accelerate the development of broad-spectrum countermeasures. To achieve those goals, TMTI has a near term need to obtain more sequence information across a large range of pathogens, near neighbors, and across a broad geographical and host range. Our role in this project is to research available sequence data for the organisms of interest and identify critical microbial sequence and knowledge gaps that need to be filled to meet TMTI objectives. This effort includes: (1) assessing current genomic sequence for each agent including phylogenetic and geographical diversity, host range, date of isolation range, virulence, sequence availability of key near neighbors, and other characteristics; (2) identifying Subject Matter Experts (SME's) and potential holders of isolate collections, contacting appropriate SME's with known expertise and isolate collections to obtain information on isolate availability and specific recommendations; (3) identifying sequence as well as knowledge gaps (eg virulence, host range, and antibiotic resistance determinants); (4) providing specific recommendations as to the most valuable strains to be placed on the DTRA sequencing queue. We acknowledge that criteria for prioritization of isolates for sequencing falls into two categories aligning with priority queues 1 and 2 as described in the summary. (Priority queue 0 relates to DTRA operational isolates whose availability is not predictable in advance.) 1. Selection of isolates that appear to have likelihood to provide information on virulence and antibiotic resistance. This will include sequence of known virulent strains. Particularly valuable would be virulent strains that have genetically similar yet avirulent, or non human transmissible, counterparts that can be used for comparison to help identify key virulence or host range genes. This approach will provide information that can be used by structural biologists to help develop therapeutics and vaccines. We have pointed out such high priority strains of which we are aware, and note that if any such isolates should be discovered, they will rise to the top priority. We anticipate difficulty locating samples with unusual resistance phenotypes, in particular. Sequencing strategies for isolates in queue 1 should aim for as complete finishing status as possible, since high-quality initial annotation (gene-calling) will be necessary for the follow-on protein structure analyses contributing to countermeasure development. Queue 2 for sequencing determination will be more dynamic than queue 1, and samples will be added to it as they become available to the TMTI program. 2. Selection of isolates that will provide broader information about diversity and phylogenetics and aid in specific detection as well as forensics. This approach focuses on sequencing of isolates that will provide better resolution of variants that are (or were) circulating in nature. The finishing strategy for queue 2 does not require complete closing with annotation. This queue is more static, as there is considerable phylogenetic data, and in this report we have sought to reveal gaps and make suggestions to fill them given existing sequence data and strain information. In this report we identify current sequencing gaps in both priority queue categories. Note that this is most applicable to the bacterial pathogens, as most viruses are by default in queue 1. The Phase I focus of this project is on viral hemorrhagic fever viruses and Category A bacterial agents as defined to us by TMTI. We have carried out individual analyses on each species of interest, and these are included as chapters in this report. Viruses and bacteria are biologically very distinct from each other and require different methods of analysis and criteria for sequencing prioritization. Therefore, we will describe our methods, analyses and conclusions separately for each category.

  17. Functional genomics of the bacterial degradation of the emerging water contaminants: 1,4-dioxane and N-nitrosodimethylamine (NDMA)

    E-Print Network [OSTI]

    Sales, Christopher Michael

    2012-01-01

    demonstration with propane to remediate trichloroethene andTrichloroethylene degradation by propane-oxidizing bacteria.Bacterial oxidation of propane. FEMS Micro- biology Letters,

  18. Bacterial inosine 5'-monophosphate dehydrogenase ("IMPDH") DNA as a dominant selectable marker in mammals and other eukaryotes

    DOE Patents [OSTI]

    Huberman, Eliezer (Chicago, IL); Baccam, Mekhine J. (Woodridge, IL)

    2007-02-27

    The present invention relates to a nucleic acid sequence and its corresponding protein sequence useful as a dominant selectable marker in eukaryotes. More specifically the invention relates to a nucleic acid encoding a bacterial IMPDH gene that has been engineered into a eukaryotic expression vectors, thereby permitting bacterial IMPDH expression in mammalian cells. Bacterial IMPDH expression confers resistance to MPA which can be used as dominant selectable marker in eukaryotes including mammals. The invention also relates to expression vectors and cells that express the bacterial IMPDH gene as well as gene therapies and protein synthesis.

  19. The calcification of staphylococcus aureus bacteria by the mineralization by inhibitor exclusion mechanism : a potential defense mechanism against bacterial infections

    E-Print Network [OSTI]

    Truong, Linh Y.

    2011-01-01

    in Serum: A Possible Mechanism for Biomineralization. J.by Inhibitor Exclusion mechanism targets the bacterial cellto become mineralized by the MIE mechanism. The goal of our

  20. Bacterially induced precipitation of CaCO sub 3 : An example from studies of cyanobacterial mats

    SciTech Connect (OSTI)

    Chafetz, H.S.

    1990-04-30

    Bacteria induce the precipitation of calcium carbonate in the laboratory and in nature by altering their chemical environment. Geologists are recognizing the possibility that bacterially induced precipitates may form significant mineral deposits, unfortunately, there are currently no sound criteria by which they can be recognized in recent sediments, or in the rock record. Cultures of aerobic and facultative bacteria from cyanobacterial mats on Andros Island, Bahamas, and Baffin Bay, Texas, induced the precipitation of calcium carbonate under controlled conditions. Crusts, the largest features formed, are composed of 5--200{mu}m diameter bundles which are, in turn, composed of numerous individual crystals. The smallest observed features are 0.1--0.4{mu}m spheres and rods which comprise some individual crystals and crystal bundles. Crystal bundles resembling rhombohedra, tetragonal disphenoids, tetragonal dipyramids, and calcite dumbbells appear to be uniquely bacterial in origin, and they have all been observed in recent sediments. Swollen rods, discs, curved dumbbells, and 50--200{mu}m optically continuous crystals resembling brushes may be uniquely bacterial in origin, however, they have not been reported by other laboratories nor observed in natural settings. Presence of any of these forms in recent sediments should be taken as strong evidence for bacterial influence. Spheres and aragonite dumbbells have also been observed in natural environments, however, they are not always bacterial in origin. Precipitation of calcium carbonate occurs preferentially on dead cyanobacteria in the presence of bacteria. Lithification of algal mats to form stromatolites may take place in the zone of decaying organic matter due to bacterial activity.

  1. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

    SciTech Connect (OSTI)

    Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.; Wong, J.; DeSantis, T.Z.; Brodie, E.L.; Hazen, T.C.; Holden, P.A.; Andersen, G.L.

    2010-03-01

    Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

  2. Bacterial infection causes stress-induced memory dysfunction in mice

    E-Print Network [OSTI]

    Gareau, Melanie G.

    Background: The brain–gut axis is a key regulator of normal intestinal physiology; for example, psychological stress is linked to altered gut barrier function, development of food allergies and changes in behaviour. Whether ...

  3. Predicting Protective Bacterial Antigens Using Random Forest Classifiers

    E-Print Network [OSTI]

    Honavar, Vasant

    feature representations us- ing three classification methods (Logistic Regression, Sup- port Vector, and bioinformatics have led to a new approach for vaccine development called Reverse Vac- cinology (RV) [2, 3, 4, 5

  4. Multi-Scale Imaging of Respiratory Bacterial Infection Using Fiber Microendoscopy and Whole-Animal Imaging 

    E-Print Network [OSTI]

    Bixler, Joel Nathan

    2014-08-27

    microendoscope that was constructed for bacterial detection. The basic design is similar to the system previously reported for use in bacterial imaging in situ (29). A light emitting diode (Thorlabs M530L2) centered at 530 nm with a 31 nm bandwidth was used... of the microendoscope system. LED: light emitting diode; L1: collimating lens; F1: excitation filter; D: dichroic beamsplitter; Obj: Microscope objective; F2: Emission filter; L2: focusing lens. 10 3.2 Incorporation of Fiber Microendoscope Into Whole...

  5. Bacterial Colony Counting by Convolutional Neural Networks Alessandro Ferrari1,2, Stefano Lombardi1, Alberto Signoroni1

    E-Print Network [OSTI]

    Signoroni, Alberto

    Bacterial Colony Counting by Convolutional Neural Networks Alessandro Ferrari1,2, Stefano Lombardi1 Convolutional Neural Networks (CNN) for counting the number of colonies contained in confluent agglomerates of bacterial cultures on Petri dishes to be screened daily. Computer vision tech- niques are optimal candidates

  6. Engineered enzymatically active bacteriophages and methods of uses thereof

    DOE Patents [OSTI]

    Collins, James J (Newton, MA); Kobayashi, Hideki (Yokohama, JP); Kearn, Mads (Ottawa, CA); Araki, Michihiro (Minatoku, JP); Friedland, Ari (Boston, MA); Lu, Timothy Kuan-Ta (Palo Alto, CA)

    2012-05-22

    The present invention provides engineered bacteriophages that express at least one biofilm degrading enzyme on their surface and uses thereof for degrading bacterial biofilms. The invention also provides genetically engineered bacteriophages expressing the biofilm degrading enzymes and proteins necessary for the phage to replicate in different naturally occurring biofilm producing bacteria. The phages of the invention allow a method of biofilm degradation by the use of one or only a few administration of the phage because the system using these phages is self perpetuating, and capable of degrading biofilm even when the concentration of bacteria within the biofilm is low.

  7. Bacterial Water Contamination: Associated Risk Factors and Beliefs in a Rural Community in Northern Evan Torline

    E-Print Network [OSTI]

    Zhou, Yaoqi

    Bacterial Water Contamination: Associated Risk Factors and Beliefs in a Rural Community in Northern of its residents are living without access to clean drinking water. This simple issue causes terrible community of Mol, Haiti before the implementation of a chlorine water filtration system in it. A handful

  8. Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting

    E-Print Network [OSTI]

    Colorado at Boulder, University of

    Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times Deborah A. Neher1 *, Thomas R. Weicht1 , Scott T. Bates2 , Jonathan W. Leff3 , Noah Fierer3 of Colorado, Boulder, Colorado, United States of America Abstract Compost production is a critical component

  9. Phylogenetic Screening of Ribosomal RNA Gene-Containing Clones in Bacterial Artificial Chromosome (BAC) Libraries from

    E-Print Network [OSTI]

    de la Torre, José R.

    (BAC) Libraries from Different Depths in Monterey Bay M.T. Suzuki1 , C.M. Preston2 , O. Be´ja`2 , J processes, but much of their biology and ecology remains ill defined. One approach to better defining. Previously, we constructed and phylogenetically screened a Bacterial Artificial Chromosome (BAC) library from

  10. Improved Yield and Diverse Finished Bacterial Genomes using Pacific Biosciences RS II SMRT Sequencing

    E-Print Network [OSTI]

    Weber, David J.

    Improved Yield and Diverse Finished Bacterial Genomes using Pacific Biosciences RS II SMRT-Cruz, Alvaro Godinez, Luke J. Tallon Institute for Genome Sciences, University of Maryland School of Medicine, effective, and highly accurate platform for generation of complete microbial genome sequences. As early

  11. Exploring the Energy Landscape for QA to QB Electron Transfer in Bacterial

    E-Print Network [OSTI]

    Gunner, Marilyn

    ) is rate-limited by conformational changes rather than electron tunneling. QB movement from a distal trapped in a different conformation. Now electron transfer from QA - to QB occurs even below 40 KExploring the Energy Landscape for QA - to QB Electron Transfer in Bacterial Photosynthetic

  12. Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source

    E-Print Network [OSTI]

    Bohannan, Brendan

    , is an energy-efficient way to simultaneously cool building mass and avoid overnight and weekend microbial an intensive temporal study of indoor airborne bacterial communities in a high-traffic university building associated with differing ventilation strategies relevant to modern building design. Our results indicate

  13. Dynamic viscoelastic behavior of individual Gram-negative bacterial cells Virginia Vadillo-Rodriguezabc

    E-Print Network [OSTI]

    Dutcher, John

    parameters were used to generate a full description of the dynamic viscoelastic behavior of the cells overDynamic viscoelastic behavior of individual Gram-negative bacterial cells Virginia Vadillo) to measure the viscoelastic properties of individual Escherichia coli K12 cells under fully hydrated

  14. Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the

    E-Print Network [OSTI]

    their metabolic activities, microbial populations mediate the impact of high gradient regions on ecologicalSeasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in nitrogen and carbon metabolism in the CRCM. Initial experiments with the environmental microarrays were

  15. Modeling Torque Versus Speed, Shot Noise, and Rotational Diffusion of the Bacterial Flagellar Motor

    E-Print Network [OSTI]

    Mora, Thierry

    Modeling Torque Versus Speed, Shot Noise, and Rotational Diffusion of the Bacterial Flagellar Motor for the flagellar motor that enables bacteria to swim. Our model explains the experimentally measured torque-speed relationship of the proton-driven E. coli motor at various pH and temperature conditions. In particular

  16. Bacterial traits, organism mass, and numerical abundance in the detrital soil food web of Dutch

    E-Print Network [OSTI]

    Cohen, Joel E.

    LETTER Bacterial traits, organism mass, and numerical abundance in the detrital soil food web.mulder@rivm.nl Abstract This paper compares responses to environmental stress of the ecophysiological traits of organisms in the detrital soil food webs of grasslands in the Netherlands, using the relationship between average body mass

  17. Local Environmental Pollution Strongly Influences Culturable Bacterial Aerosols at an Urban Aquatic Superfund Site

    E-Print Network [OSTI]

    Uriarte, Maria

    or aquatic environments contaminated with sewage, hydrocarbons, heavy metals, and other industrial waste communities containing contaminated soil and water. INTRODUCTION In 1978, Bovallius and colleagues observed aerosol fallout rate and surface water bacterial concentrations were at least an order of magnitude

  18. The Rate of Osmotic Downshock Determines the Survival Probability of Bacterial Mechanosensitive Channel Mutants

    E-Print Network [OSTI]

    Phillips, Rob

    The Rate of Osmotic Downshock Determines the Survival Probability of Bacterial Mechanosensitive and respond to environmental changes. In bacteria, these channels are be- lieved to protect against an osmotic that the protection provided by MS channels depends strongly on the rate of osmotic change, revealing that, under

  19. Bacterial volatiles promote growth in Arabidopsis Choong-Min Ryu*, Mohamed A. Farag

    E-Print Network [OSTI]

    Paré, Paul W.

    Bacterial volatiles promote growth in Arabidopsis Choong-Min Ryu*, Mohamed A. Farag , Chia-Hui Hu of agricultural species for the purposes of growth enhance- ment, including increased seed emergence, plant weight when seeds were coated with PGPR before planting (1), and plant weight of tuber-treated potatoes

  20. Bacterial Stimulation in Mixed Cultures of Bacteria and Organic Carbon from River and Lake Waters

    E-Print Network [OSTI]

    Jacquet, Stéphan

    (rivers or lakes) and blended (different proportions of river and lake water) batch cultures. In each those of either of the individual components and certainly important to an overall understanding. The simple mixing of water from different systems with the resulting blending of bacterial populations

  1. This journal is c The Royal Society of Chemistry 2010 Integr. Biol. Microfluidics for bacterial chemotaxisw

    E-Print Network [OSTI]

    Shimizu, Tom

    This journal is c The Royal Society of Chemistry 2010 Integr. Biol. Microfluidics for bacterial 2010 DOI: 10.1039/c0ib00049c Microfluidics is revolutionizing the way we study the motile behavior system to understand how cells and organisms sense and respond to gradients. Using microfluidics to study

  2. Dynamics of marine pelagic bacterial communities on the Texas-Louisiana shelf 

    E-Print Network [OSTI]

    Anitsakis, Erin Colleen

    2009-05-15

    Clone Library and Sequencing.......................................................... 18 Results and Discussion............................................................................ 19 Seawater Culture Growth...?............................................................................................ 11 2.1 Seawater-culture bacterial abundances over incubation ......................... 20 2.2 Seawater-culture protozoa abundance over incubation........................... 20 2.3 Fingerprints of total and BrdU-labeled seawater...

  3. The shielding effect of wild type iron reducing bacterial flora on the corrosion of linepipe steel

    E-Print Network [OSTI]

    , pipeline networks are subjected to different corrosion deterioration mechanisms that result fromThe shielding effect of wild type iron reducing bacterial flora on the corrosion of linepipe steel 28 May 2013 Available online 7 June 2013 Keywords: Corrosion Impedance Iron reducing bacteria IRB

  4. First report of bacterial wilt caused by Ralstonia solanacearumon eucalypts in South Africa

    E-Print Network [OSTI]

    First report of bacterial wilt caused by Ralstonia solanacearumon eucalypts in South Africa BY T. A of Pretoria, 0002 Pretoria, South Africa. E-mail: Teresa. Coutinho@FABI.up.ac.za; 3 Department of Microbiology and Biochemistry, University of the Orange Free State, PO Box 339, Bloemfontein 9300, South Africa; 4 Agricultural

  5. Bacterial Blight and Dieback of Eucalyptus Species, Hybrids, and Clones in South Africa

    E-Print Network [OSTI]

    Bacterial Blight and Dieback of Eucalyptus Species, Hybrids, and Clones in South Africa T. A- technology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; ,I, I\\lergaert and 1\\1. C University for Christian Higher Education, Private Bag X6001, Potchefstroom 2520, South Africa;,. Swings

  6. texas bacterial source tracking library Protection of our water resources is one of the most

    E-Print Network [OSTI]

    ) of pollution greatly affect water quality. Identifying and assessing sources of fecal pollution is a key for identifying human and animal sources of fecal pollution. Texas Water Resources Institute 1500 Research Parkwaytexas bacterial source tracking library Protection of our water resources is one of the most

  7. Associations between marine invertebrates and their cooperative bacterial symbionts offer access to an

    E-Print Network [OSTI]

    McFall-Ngai, Margaret

    venture onto land and radiate into terrestrial habitats. In spite of these historical facts, because of our own phylogenetic position as land mammals, both a terrestrial bias and a vertebrate bias have come pathways associated with animal­bacterial interactions have recently revealed that certain ancient

  8. ORIGINAL ARTICLE The structure of the bacterial and archaeal community in a

    E-Print Network [OSTI]

    Lovley, Derek

    ORIGINAL ARTICLE The structure of the bacterial and archaeal community in a biogas digester. Anaerobic fermentation of waste biomass not only gen- erates biogas fuel for cooking, lighting and heating biogas digesters at different scales and for different applications for treating rural wastes is well

  9. Modeling of rate-dependent phase transition in bacterial flagellar filament Xiaoling Wang a

    E-Print Network [OSTI]

    Sun, Qing-Ping

    Modeling of rate-dependent phase transition in bacterial flagellar filament Xiaoling Wang for bacteria. The long helical filament is the propeller made up of only one kind of protein called flagellin [2,3]. Macroscopically the filament can be viewed as a hollow tube with an outer diameter of 20 nm

  10. Pseudomonas syringae pv. actinidiae (PSA) Isolates from Recent Bacterial Canker of Kiwifruit Outbreaks Belong to

    E-Print Network [OSTI]

    Guttman, David S.

    Pseudomonas syringae pv. actinidiae (PSA) Isolates from Recent Bacterial Canker of Kiwifruit fruit (Actinidia deliciosa and A. chinensis) caused by Pseudomonas syringae pv. actinidiae (PSA, Taratufolo MC, Cai R, Almeida NF, et al. (2012) Pseudomonas syringae pv. actinidiae (PSA) Isolates from

  11. Quadrature conductivity: A quantitative indicator of bacterial abundance in porous media

    SciTech Connect (OSTI)

    Chi Zhang; Andre Revil; Yoshiko Fujita; Junko Munakata-Marr; George Redden

    2014-09-01

    ABSTRACT The abundance and growth stages of bacteria in subsurface porous media affect the concentrations and distributions of charged species within the solid-solution interfaces. Therefore, spectral induced polarization (SIP) measurements can be used to monitor changes in bacterial biomass and growth stage. Our goal was to gain a better understanding of the SIP response of bacteria present in a porous material. Bacterial cell surfaces possess an electric double layer and therefore become polarized in an electric field. We performed SIP measurements over the frequency range of 0.1–1 kHz on cell suspensions alone and cell suspensions mixed with sand at four pore water conductivities. We used Zymomonas mobilis at four different cell densities (in- cluding the background). The quadrature conductivity spectra exhibited two peaks, one around 0.05–0.10 Hz and the other around 1–10 Hz. Because SIP measurements on bacterial suspensions are typically made at frequencies greater than 1 Hz, these peaks have not been previously reported. In the bac-terial suspensions in growth medium, the quadrature conduc-tivity at peak I was linearly proportional to the density of the bacteria. For the case of the suspensions mixed with sands, we observed that peak II presented a smaller increase in the quadrature conductivity with the cell density. A comparison of the experiments with and without sand grains illustrated the effect of the porous medium on the overall quadrature con- ductivity response (decrease in the amplitude and shift of the peaks to the lower frequencies). Our results indicate that for a given porous medium, time-lapse SIP has potential for mon- itoring changes in bacterial abundance within porous media.

  12. Steven Chu's Wigner Lecture | ornl.gov

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

    work that could lead to effective measures against bacterial biofilms -- colonies of bacteria protected by protein fortresses -- to reduce their resistance to treatment, and...

  13. A functional gene array for detection of bacterial virulence elements

    SciTech Connect (OSTI)

    Jaing, C

    2007-11-01

    We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

  14. Bacterial Effector HopF2 Suppresses Arabidopsis Immunity by Targeting BAK1 

    E-Print Network [OSTI]

    Zhou, Jinggeng

    2013-07-19

    -associated molecular patterns (PAMPs or MAMPs) through membrane- localized receptor-like kinases (RLKs) (Boller and Felix, 2009; Jones and Dangl, 2006). PAMP-triggered immunity (PTI) plays a pivotal role in defense against a broad spectrum of potential pathogens... (Boller and Felix, 2009; Jones and Dangl, 2006). A 22-amino- acid peptide from N-terminus of bacterial flagellin, flg22, can be perceived by Arabidopsis RLK flagellin-sensing 2 (FLS2), and induces FLS2 association with another plasma membrane...

  15. Bacterial production and microbial food web structure in a large arctic river and the coastal Arctic Ocean

    E-Print Network [OSTI]

    Vincent, Warwick F.

    in the surface waters decreased across the salinity gradient, dropping from 51,000 (river) to 30 (sea) cells m. Glucose enrichment experiments indicated that bacterial metabolism was carbon limited in the Mackenzie

  16. Epidemiology of Bacterial Food-borne Pathogens: Linking Intermittent Pathogen Shedding and Transmission in Their Animal Hosts 

    E-Print Network [OSTI]

    Gautam, Raju

    2013-04-30

    Most bacterial foodborne pathogens are shed intermittently from their animal hosts and are able to grow and persist in the environment. Cattle and pigs constitute the major animal reservoirs for these pathogens. The overall ...

  17. Elucidation of the pathways responsible for the biosynthesis of UDP-N,N'-diacetylbacillosamine in bacterial pathogens

    E-Print Network [OSTI]

    Morrison, Michael James

    2014-01-01

    The highly-modified, bacterial sugar N,N'-diacetylbacillosamine (diNAcBac) has been implicated in the pathogenicity of certain microbes through its incorporation onto various protein virulence factors. In particular, ...

  18. Sustainable Development

    E-Print Network [OSTI]

    Brierley, Andrew

    150 Sustainable Development Sustainable Development Degree options BSc or MA (Single Honours Degree) Sustainable Development Contributing Schools Biology; Chemistry; Computer Science; Geography & Geosciences within Sustainable Development, then you should apply for the MA degree; if you are most interested

  19. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

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

    Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; Trimble, William; Meyer, Folker; Guglielmini, Julien; Rocha, Eduardo P. C.; Polz, Martin F.

    2015-05-05

    Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells.more »Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.« less

  20. Sustainable Development

    E-Print Network [OSTI]

    Brierley, Andrew

    ) Sustainable Development Contributing Schools Biology; Chemistry; Computer Science; Geography & Geosciences enquiries Dr Emilia Ferraro, Department of Geography & Sustainable Development E: gg. Resources Very few universities currently offer undergraduate degrees in Sustainable Development. Uniquely

  1. Bioinspired Engineering for Microbial Sensing: The Development of Bacterial Sensing Methodologies Based on Fluorescence Staining and Microfluidic Emission Spectroscopy

    E-Print Network [OSTI]

    Nunez, Vicente

    2015-01-01

    Chemical Science and Analytical Chemistry respectively. ivOptical Tweezers. Analytical Chemistry 2010, 82 (9), 3840-and Eukaryotes. Analytical Chemistry 2008, 80 (14), 5312-

  2. Bacterial total maximum daily load (TMDL): development and evaluation of a new classification scheme for impaired waterbodies of Texas 

    E-Print Network [OSTI]

    Paul, Sabu

    2005-02-17

    with the impaired waterbodies. The main characteristics considered for the classification of waterbodies were designated use of the waterbody, land use distribution, density of stream network, average distance of a land of a particular use to the closest stream...

  3. Clone Bacterial Thermal Stable Enzymes in T. Reesei: Cooperative Research and Development Final Report, CRADA Number CRD-01-00105

    SciTech Connect (OSTI)

    Himmel, M. E.

    2010-08-01

    The focus of this CRADA was on improving the efficacy of GCI's primary host for commercial cellulase production, Trichoderma reesei.

  4. Bioinspired Engineering for Microbial Sensing: The Development of Bacterial Sensing Methodologies Based on Fluorescence Staining and Microfluidic Emission Spectroscopy

    E-Print Network [OSTI]

    Nunez, Vicente

    2015-01-01

    Journal of Biological Engineering 2010, 4, No pp given;Annals of biomedical engineering 2009, 37 (6), 1190-205.new biomaterials and tissue engineering in ophthalmology.

  5. Bioinspired Engineering for Microbial Sensing: The Development of Bacterial Sensing Methodologies Based on Fluorescence Staining and Microfluidic Emission Spectroscopy

    E-Print Network [OSTI]

    Nunez, Vicente

    2015-01-01

    pg. 155 3. Chapter 3. Microfluidics for Biosensing andand-peel fabrication for microfluidics: what's in it forcross-section PDMS microfluidics system for replication of

  6. Bioinspired Engineering for Microbial Sensing: The Development of Bacterial Sensing Methodologies Based on Fluorescence Staining and Microfluidic Emission Spectroscopy

    E-Print Network [OSTI]

    Nunez, Vicente

    2015-01-01

    of the liquid. The energy of the water molecules at thecomparable to the energy of the water molecule in the bulk

  7. Bioinspired Engineering for Microbial Sensing: The Development of Bacterial Sensing Methodologies Based on Fluorescence Staining and Microfluidic Emission Spectroscopy

    E-Print Network [OSTI]

    Nunez, Vicente

    2015-01-01

    and phosphobetaines. Biomaterials 2004, 25 (7-8), of Zhao,silicone elastomers. Biomaterials 2010, 31 (13), Eleni, P.Ratner, B. D. , Biomaterials science : an introduction to

  8. Improved Bacterial and Viral Recoveries from 'Complex' Samples using Electrophoretically Assisted Acoustic Focusing

    SciTech Connect (OSTI)

    Ness, K; Rose, K; Jung, B; Fisher, K; Mariella, Jr., R P

    2008-03-27

    Automated front-end sample preparation technologies can significantly enhance the sensitivity and reliability of biodetection assays [1]. We are developing advanced sample preparation technologies for biowarfare detection and medical point-of-care diagnostics using microfluidic systems with continuous sample processing capabilities. Here we report an electrophoretically assisted acoustic focusing technique to rapidly extract and enrich viral and bacterial loads from 'complex samples', applied in this case to human nasopharyngeal samples as well as simplified surrogates. The acoustic forces capture and remove large particles (> 2 {micro}m) such as host cells, debris, dust, and pollen from the sample. We simultaneously apply an electric field transverse to the flow direction to transport small ({le} 2 {micro}m), negatively-charged analytes into a separate purified recovery fluid using a modified H-filter configuration [Micronics US Patent 5,716,852]. Hunter and O'Brien combined transverse electrophoresis and acoustic focusing to measure the surface charge on large particles, [2] but to our knowledge, our work is the first demonstration combining these two techniques in a continuous flow device. Marina et al. demonstrated superimposed dielectrophoresis (DEP) and acoustic focusing for enhanced separations [3], but these devices have limited throughput due to the rapid decay of DEP forces. Both acoustic standing waves and electric fields exert significant forces over the entire fluid volume in microchannels, thus allowing channels with larger dimensions (> 100 {micro}m) and high throughputs (10-100 {micro}L/min) necessary to process real-world volumes (1 mL). Previous work demonstrated acoustic focusing of microbeads [4] and biological species [5] in various geometries. We experimentally characterized our device by determining the biological size-cutoff where acoustic radiation pressure forces no longer transport biological particles. Figure 1 shows images of E.Coli ({approx}1 {micro}m) and yeast ({approx}4-5 {micro}m) flowing in a microchannel (200 {micro}m deep, 500 {micro}m wide) at a flow rate of 10 {micro}L/min. The E.Coli does not focus in the acoustic field while the yeast focuses at the channel centerline. This result suggests the acoustic size-cutoff for biological particles in our device lies between 2 and 3 {micro}m. Transverse electrophoresis has been explored extensively in electric field flow fractionation [6] and isoelectric focusing devices [7]. We demonstrated transverse electrophoretic transport of a wide variety of negatively-charged species, including fluorophores, beads, viruses, E.Coli, and yeast. Figure 2 shows the electromigration of a fluorescently labeled RNA virus (MS2) from the lower half of the channel to the upper half region with continuous flow. We demonstrated the effectiveness of our electrophoretically assisted acoustic focusing device by separating virus-like particles (40 nm fluorescent beads, selected to aid in visualization) from a high background concentration of yeast contaminants (see Figure 3). Our device allows for the efficient recovery of virus into a pre-selected purified buffer while background contaminants are acoustically captured and removed. We also tested the device using clinical nasopharyngeal samples, both washes and lavages, and demonstrated removal of unknown particulates (>2 ?m size) from the sample. Our future research direction includes spiking known amounts of bacteria and viruses into clinical samples and performing quantitative off-chip analysis (real-time PCR and flow cytometry).

  9. Career Development

    Broader source: Energy.gov [DOE]

    The career development objective is to produce better employees and maximizing employee potential. DOE Leadership & Career Development Programs can help provide employees with the skills and...

  10. Characterization of the bacterial metagenome in an industrial algae bioenergy production system

    SciTech Connect (OSTI)

    Huang, Shi; Fulbright, Scott P; Zeng, Xiaowei; Yates, Tracy; Wardle, Greg; Chisholm, Stephen T; Xu, Jian; Lammers, Peter

    2011-03-16

    Cultivation of oleaginous microalgae for fuel generally requires growth of the intended species to the maximum extent supported by available light. The presence of undesired competitors, pathogens and grazers in cultivation systems will create competition for nitrate, phosphate, sulfate, iron and other micronutrients in the growth medium and potentially decrease microalgal triglyceride production by limiting microalgal health or cell density. Pathogenic bacteria may also directly impact the metabolism or survival of individual microalgal cells. Conversely, symbiotic bacteria that enhance microalgal growth may also be present in the system. Finally, the use of agricultural and municipal wastes as nutrient inputs for microalgal production systems may lead to the introduction and proliferation of human pathogens or interfere with the growth of bacteria with beneficial effects on system performance. These considerations underscore the need to understand bacterial community dynamics in microalgal production systems in order to assess microbiome effects on microalgal productivity and pathogen risks. Here we focus on the bacterial component of microalgal production systems and describe a pipeline for metagenomic characterization of bacterial diversity in industrial cultures of an oleaginous alga, Nannochloropsis salina. Environmental DNA was isolated from 12 marine algal cultures grown at Solix Biofuels, a region of the 16S rRNA gene was amplified by PCR, and 16S amplicons were sequenced using a 454 automated pyrosequencer. The approximately 70,000 sequences that passed quality control clustered into 53,950 unique sequences. The majority of sequences belonged to thirteen phyla. At the genus level, sequences from all samples represented 169 different genera. About 52.94% of all sequences could not be identified at the genus level and were classified at the next highest possible resolution level. Of all sequences, 79.92% corresponded to 169 genera and 70 other taxa. We apply a principal component analysis across the initial sample set to draw correlations between sample variables and changes in microbiome populations.

  11. Natural Organic Matter (NOM) in Aquatic Systems: Interactions with Radionuclides (234Th (IV), 129 I) and Biofilms 

    E-Print Network [OSTI]

    Zhang, Saijin

    2011-10-21

    as interactions with 129I. A method involving cross flow ultrafiltration, followed by a three-step cartridge soaking and stirred-cell diafiltration, was developed for isolating EPS from phytoplankton cultures, especially in seawater media. EPS isolated from a...

  12. Cutability, bacterial control and packaging effects on the merchandising of lamb 

    E-Print Network [OSTI]

    Varnadore, William Lee

    1972-01-01

    and increasing storage life, yet had no effect on the ultimate palat- abilityy of cooked lamb. Polyvinyl chloride film (PVC) effectively reduced carcass weight loss as shrinkage and improved the appearance of the subcutaneous fat cover. However, the use... in 7, 6 and 7 comparisons, 18 Table 4. Comparison of Bacterial Counts (log&0/ 1 in. Z) from Lamb Cuts in Experiment 2. Treatmenta Period of Day of Storageb retail dis la c (da s) 0 5 Chamber type, high vacuum, barrier bag Soft film wrap, PVC...

  13. Construction of force measuring optical tweezers instrumentation and investigations of biophysical properties of bacterial adhesion organelles

    E-Print Network [OSTI]

    Andersson, Magnus

    2015-01-01

    Optical tweezers are a technique in which microscopic-sized particles, including living cells and bacteria, can be non-intrusively trapped with high accuracy solely using focused light. The technique has therefore become a powerful tool in the field of biophysics. Optical tweezers thereby provide outstanding manipulation possibilities of cells as well as semi-transparent materials, both non-invasively and non-destructively, in biological systems. In addition, optical tweezers can measure minute forces (Adhesive bacterial organelles, so called pili, mediate adhesion to host cells and are therefore crucial...

  14. Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater

    E-Print Network [OSTI]

    Mouser, P.J.

    2010-01-01

    heterogeneous ammonium availability on bacterial communityThe impact of ammonium availability on microbial communityin response to ammonium availability to ensure an adequate

  15. Coupling between switching regulation and torque generation in bacterial flagellar motor

    E-Print Network [OSTI]

    Fan Bai; Tohru Minamino; Zhanghan Wu; Keiichi Namba; Jianhua Xing

    2013-07-25

    The bacterial flagellar motor plays a crucial role in both bacterial locomotion and chemotaxis. Recent experiments reveal that the switching dynamics of the motor depends on the motor rotation speed, and thus the motor torque, non-monotonically. Here we present a unified mathematical model which models motor torque generation based on experimental torque-speed curves and torque-dependent switching based on the conformational spread model. The model successfully reproduces the observed switching rate as a function of the rotation speed, and provides a generic physical explanation independent of most details. A stator affects the switching dynamics through two mechanisms: accelerating the conformation flipping rates of individual rotor switching units, which favours slower motor speed and thus increasing torque; and affecting more switching units within unit time, which favours faster speed. Consequently, the switching rate shows a maximum at intermediate speed. Our model predicts that a motor switches more often with more stators. The load-switching relation may serve as a mechanism for sensing the physical environment, similar to the chemotaxis system for sensing the chemical environment. It may also coordinate the switch dynamics of motors within a cell.

  16. Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

    SciTech Connect (OSTI)

    Aylward, Frank O.; Burnum, Kristin E.; Scott, Jarrod J.; Suen, Garret; Tringe, Susannah G.; Adams, Sandra M.; Barry, Kerrie W.; Nicora, Carrie D.; Piehowski, Paul D.; Purvine, Samuel O.; Starrett, Gabriel J.; Goodwin, Lynne A.; Smith, Richard D.; Lipton, Mary S.; Currie, Cameron R.

    2012-09-01

    Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant Neotropical herbivores cultivate symbiotic fungus gardens on massive quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers in mature Atta colonies. Here we use metagenomic, and metaproteomic techniques to characterize the bacterial diversity and overall physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that, in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter, and Escherichia. We show that these bacterial communities possess genes commonly associated with lignocellulose degradation, and likely participate in the processing of plant biomass. Additionally, we demonstrate that bacteria in these environments encode a diverse suite of biosynthetic pathways, and that they may enrich the nitrogen-poor forage of the ants with B-vitamins, amino acids, and proteins. These results are consistent with the hypothesis that fungus gardens are highly-specialized fungus-bacteria communities that efficiently convert plant material into usable energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities to the ecology and evolution of herbivorous metazoans.

  17. Solid State Electron Transfer via Bacterial Nanowires: Contributions Toward a Mechanistic Understanding of Geophysical Response of Biostimulated Subsurface

    SciTech Connect (OSTI)

    Estella Atekwana

    2012-05-08

    The degradation of organic matter by microorganisms provides a source of electrical potential or so-called 'self potential' (SP) that can be measured by using a voltmeter. During this process electrons are being produced as a waste-product and bacterial cells have to dispose of these to allow for the complete biodegradation of organic matter. Especially in anaerobic microbial communities, exo-cellular electron transfer is the most important driving force behind this process and organisms have developed different, but also similar, ways to transfer electrons to other microorganisms. Recently, it has been postulated that direct electron transfer from cell-to-cell is actually done by 'hard-wired' microorganisms. This shuttling of electrons is most likely done by certain c-type cytochromes that form the functional part of electrically conductive nanowires. In this study we investigated if nanowires can explain the geoelectrical (self potential and spectral induced polarization) signals observed at some biostimulated environments such as DOE sites. The objectives of our project are to: (1) investigate any temporal changes in the geophysical signatures (Self Potential (SP) and Induced Polarization (IP)) associated with nanowires of the bacterium Shewanella oneidensis MR-1, wild type and mtrc/omcA deletion mutant, (2) demonstrate that mutant strains of bacteria that produce nonconductive nanowires do not contribute to geoelectrical responses. We accomplished the following: (1) Provided training to students and a postdoctoral fellow that worked on the project, (2) Conducted several SP & IP measurements correlating the distribution of nanowires and SIP/SP signals in partial fulfillment of object No. 1 and 2. On the following we will report and discuss the results of our last experiment with some emphasis on the source mechanisms of both SP and IP associated with Shewanella oneidensis MR-1, wild type in sand columns.

  18. Bacterially induced precipitation of CaCO{sub 3}: An example from studies of cyanobacterial mats. Final report

    SciTech Connect (OSTI)

    Chafetz, H.S.

    1990-04-30

    Bacteria induce the precipitation of calcium carbonate in the laboratory and in nature by altering their chemical environment. Geologists are recognizing the possibility that bacterially induced precipitates may form significant mineral deposits, unfortunately, there are currently no sound criteria by which they can be recognized in recent sediments, or in the rock record. Cultures of aerobic and facultative bacteria from cyanobacterial mats on Andros Island, Bahamas, and Baffin Bay, Texas, induced the precipitation of calcium carbonate under controlled conditions. Crusts, the largest features formed, are composed of 5--200{mu}m diameter bundles which are, in turn, composed of numerous individual crystals. The smallest observed features are 0.1--0.4{mu}m spheres and rods which comprise some individual crystals and crystal bundles. Crystal bundles resembling rhombohedra, tetragonal disphenoids, tetragonal dipyramids, and calcite dumbbells appear to be uniquely bacterial in origin, and they have all been observed in recent sediments. Swollen rods, discs, curved dumbbells, and 50--200{mu}m optically continuous crystals resembling brushes may be uniquely bacterial in origin, however, they have not been reported by other laboratories nor observed in natural settings. Presence of any of these forms in recent sediments should be taken as strong evidence for bacterial influence. Spheres and aragonite dumbbells have also been observed in natural environments, however, they are not always bacterial in origin. Precipitation of calcium carbonate occurs preferentially on dead cyanobacteria in the presence of bacteria. Lithification of algal mats to form stromatolites may take place in the zone of decaying organic matter due to bacterial activity.

  19. Bruce Walcheck: Role of neutrophils in acute lung injury, bacterial lung infection, and sepsis (cell based assays and in vivo studies in mice).

    E-Print Network [OSTI]

    Blanchette, Robert A.

    Bruce Walcheck: Role of neutrophils in acute lung injury, bacterial lung infection, and sepsis, eosinophils, and macrophages in the ( ) oapplie lungs (cell based assays and in vivo studies in mice) Alice). Mike Murtaugh: Pathogenesis of lung inflammation during bacterial and viral pneumonia (cell based

  20. Program Development

    SciTech Connect (OSTI)

    Atencio, Julian J.

    2014-05-01

    This presentation covers how to go about developing a human reliability program. In particular, it touches on conceptual thinking, raising awareness in an organization, the actions that go into developing a plan. It emphasizes evaluating all positions, eliminating positions from the pool due to mitigating factors, and keeping the process transparent. It lists components of the process and objectives in process development. It also touches on the role of leadership and the necessity for audit.

  1. Conservation of Modules but not Phenotype in Bacterial Response to Environmental Stress

    SciTech Connect (OSTI)

    Timberlake, Sonia; Joachimiak, Marcin; Joyner, Dominique; Chakraborty, Romy; Baumohl, Jason; Dehal, Paramvir; Arkin, Adam; Hazen, Terry; Alm, Eric

    2010-05-17

    Microbes live in changing environments and change their phenotype via gene regulation in response. Although this transcriptional response is important for fitness, very little is known about how it evolves in microbes. We started by asking a number of high-level questions about the evolution of transcriptional phenotype: (1) To what extent is transcriptional response conserved, i.e. do conserved genes respond similarly to the same condition; (2) To what extent are transcriptional modules conserved; and (3) Does there exist a general stress response to a variety of stressors? To illuminate these questions, we analyzed more than 500 microarray experiments across the bacterial domain. We looked for conservation of transcriptional regulation both in close sister species and vastly divergent clades. In addition, we produced and analyzed an extensive in-house compendium of environmental stress data in three metal-reducing bacteria.

  2. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity

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

    Payne, Samuel H.; Monroe, Matthew E.; Overall, Christopher C.; Kiebel, Gary R.; Degan, Michael G.; Gibbons, Bryson C.; Fujimoto, Grant M.; Purvine, Samuel O.; Adkins, Joshua N.; Lipton, Mary S.; et al

    2015-08-18

    This dataset deposition announces the submission to public repositories of the PNNL Biodiversity Library, a large collection of global proteomics data for 112 bacterial and archaeal organisms. The data comprises 35,162 tandem mass spectrometry (MS/MS) datasets from ~10 years of research. All data has been searched, annotated and organized in a consistent manner to promote reuse by the community. Protein identifications were cross-referenced with KEGG functional annotations which allows for pathway oriented investigation. We present the data as a freely available community resource. A variety of data re-use options are described for computational modeling, proteomics assay design and bioengineering. Instrumentmore »data and analysis files are available at ProteomeXchange via the MassIVE partner repository under the identifiers PXD001860 and MSV000079053.« less

  3. Structure of the Transmembrane Regions of a Bacterial Cyclic Nucleotide-Regulated Channel

    SciTech Connect (OSTI)

    Clayton,G.; Latieri, S.; Heginbotham, L.; Unger, V.; Morais-Cabral, J.

    2008-01-01

    The six-transmembrane helix (6 TM) tetrameric cation channels form the largest ion channel family, some members of which are voltage-gated and others are not. There are no reported channel structures to match the wealth of functional data on the non-voltage-gated members. We determined the structure of the transmembrane regions of the bacterial cyclic nucleotide-regulated channel MlotiK1, a non-voltage-gated 6 TM channel. The structure showed how the S1-S4 domain and its associated linker can serve as a clamp to constrain the gate of the pore and possibly function in concert with ligand-binding domains to regulate the opening of the pore. The structure also led us to hypothesize a new mechanism by which motions of the S6 inner helices can gate the ion conduction pathway at a position along the pore closer to the selectivity filter than the canonical helix bundle crossing.

  4. Seasonal dynamics of bacterial biomass and production in a coastal arctic ecosystem: Franklin Bay, western Canadian Arctic

    E-Print Network [OSTI]

    Vincent, Warwick F.

    Seasonal dynamics of bacterial biomass and production in a coastal arctic ecosystem: Franklin Bay 2008. [1] The Canadian Arctic Shelf Exchange Study (CASES) included the overwintering deployment biomass and production in a coastal arctic ecosystem: Franklin Bay, western Canadian Arctic, J. Geophys

  5. Structural Analysis of a Chimeric Bacterial R-Amylase. High-Resolution Analysis of Native and Ligand Complexes,

    E-Print Network [OSTI]

    Structural Analysis of a Chimeric Bacterial R-Amylase. High-Resolution Analysis of Native ReceiVed April 26, 2000 ABSTRACT: Several chimeric R-amylases genes were constructed by an in vivo amylases (hereafter BA2), consisting of residues 1-300 from B. amyloliquefaciens and 301-483 from B

  6. The bacterial world contains much metabolic bio diversity. If life was present on Earth at least 3.5 billion

    E-Print Network [OSTI]

    Higgins, Darren

    , releasing O2 . The oxygenic photosynthetic apparatus probably evolved from a functional pairing of the two hundreds of cells8 . Most cyanobacteria divide by binary fission, but some exhibit alternatives to the standard mode of bacterial division, reproducing by budding or by multiple fission of enlarged cells8

  7. Resolving the Electron Transfer Kinetics in the Bacterial Reaction Center by Pulse Polarized 2-D Photon Echo Spectroscopy

    E-Print Network [OSTI]

    Mukamel, Shaul

    of photosynthesis is excitation energy transfer toward and charge separation within highly conserved reaction modeling of the nonlinear optical response of the bacterial RC B. viridis incorporating electron and energy of artificial photochemical devices. While the RCs of higher plants operate at high band gaps (680-700 nm

  8. Fungal, bacterial, and archaeal communities mediating C cycling and trace gas flux in peatland ecosystems subject to climate change

    E-Print Network [OSTI]

    Fungal, bacterial, and archaeal communities mediating C cycling and trace gas flux in peatland microbial community profiling in a network of natural peatland ecosystems spanning large-scale climate the drivers of microbial community composition via metagenomic and metatranscriptomic analysis of samples from

  9. 604 Integr. Biol., 2010, 2, 604629 This journal is c The Royal Society of Chemistry 2010 Microfluidics for bacterial chemotaxisw

    E-Print Network [OSTI]

    Entekhabi, Dara

    Microfluidics for bacterial chemotaxisw Tanvir Ahmed,a Thomas S. Shimizub and Roman Stocker*a Received 1st June 2010, Accepted 11th August 2010 DOI: 10.1039/c0ib00049c Microfluidics is revolutionizing the way we to gradients. Using microfluidics to study chemotaxis of free-swimming bacteria presents experimental

  10. Development Tools

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB Packet HanfordDOEDanielDeSmall BusinessDeveloperDevelopingTools

  11. Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants

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

    Berni Canani, Roberto; Sangwan, Naseer; Stefka, Andrew T.; Nocerino, Rita; Paparo, Lorella; Aitoro, Rosita; Calignano, Antonio; Khan, Aly A.; Gilbert, Jack A.; Nagler, Cathryn R.

    2015-09-22

    Dietary intervention with extensively hydrolyzed casein formula supplemented with Lactobacillus rhamnosus GG (EHCF+LGG) accelerates tolerance acquisition in infants with cow’s milk allergy (CMA). We examined whether this effect is attributable, at least in part, to an influence on the gut microbiota. Fecal samples from healthy controls (n=20) and from CMA infants (n=19) before and after treatment with EHCF with (n=12) and without (n=7) supplementation with LGG were compared by 16S rRNA-based operational taxonomic unit clustering and oligotyping. Differential feature selection and generalized linear model fitting revealed that the CMA infants have a diverse gut microbial community structure dominated by Lachnospiraceaemore »(20.5±9.7%) and Ruminococcaceae (16.2±9.1%). Blautia, Roseburia and Coprococcus were significantly enriched following treatment with EHCF and LGG, but only one genus, Oscillospira, was significantly different between infants that became tolerant and those that remained allergic. However, most tolerant infants showed a significant increase in fecal butyrate levels, and those taxa that were significantly enriched in these samples, Blautia and Roseburia, exhibited specific strain-level demarcations between tolerant and allergic infants. As a result, our data suggest that EHCF+LGG promotes tolerance in infants with CMA, in part, by influencing the strain-level bacterial community structure of the infant gut.« less

  12. Thermodynamics of Electron Flow in the Bacterial Deca-heme Cytochrome MtrF

    SciTech Connect (OSTI)

    Breuer, Marian; Zarzycki, Piotr P.; Blumberger, Jochen; Rosso, Kevin M.

    2012-07-01

    Electron transporting multiheme cytochromes are essential to the metabolism of microbes that inhabit soils and carry out important biogeochemical processes. Recently the first crystal structure of a prototype bacterial deca-heme cytochrome (MtrF) has been resolved and its electrochemistry characterized. However, the molecular details of electron conductance along heme chains in the cytochrome are difficult to access via experiment due to the nearly identical chemical nature of the heme cofactors. Here we employ large-scale molecular dynamics simulations to compute the reduction potentials of the ten hemes of MtrF in aqueous solution. We find that as a whole they fall within a range of about 0.3 V in agreement with experiment. Individual reduction potentials give rise to a free energy profile for electron conduction that is approximately symmetric with respect to the center of the protein. Our calculations indicate that there is no significant potential bias along the orthogonal octa- and tetra-heme chains suggesting that under aqueous conditions MtrF is a nearly reversible two-dimensional conductor.

  13. Real-time Bacterial Detection by Single Cell Based Sensors UsingSynchrotron FTIR Spectromicroscopy

    SciTech Connect (OSTI)

    Veiseh, Mandana; Veiseh, Omid; Martin, Michael C.; Bertozzi,Carolyn; Zhang, Miqin

    2005-08-10

    Microarrays of single macrophage cell based sensors weredeveloped and demonstrated for real time bacterium detection bysynchrotron FTIR microscopy. The cells were patterned on gold-SiO2substrates via a surface engineering technique by which the goldelectrodes were immobilized with fibronectin to mediate cell adhesion andthe silicon oxide background were passivated with PEG to resist proteinadsorption and cell adhesion. Cellular morphology and IR spectra ofsingle, double, and triple cells on gold electrodes exposed tolipopolysaccharide (LPS) of different concentrations were compared toreveal the detection capabilities of these biosensors. The single-cellbased sensors were found to generate the most significant IR wave numbervariation and thus provide the highest detection sensitivity. Changes inmorphology and IR spectrum for single cells exposed to LPS were found tobe time- and concentration-dependent and correlated with each other verywell. FTIR spectra from single cell arrays of gold electrodes withsurface area of 25 mu-m2, 100 mu-m2, and 400 mu-m2 were acquired usingboth synchrotron and conventional FTIR spectromicroscopes to study thesensitivity of detection. The results indicated that the developedsingle-cell platform can be used with conventional FTIRspectromicroscopy. This technique provides real-time, label-free, andrapid bacterial detection, and may allow for statistic and highthroughput analyses, and portability.

  14. Guanidino groups greatly enhance the action of antimicrobial peptidomimetics against bacterial cytoplasmic membranes

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

    Andreev, Konstantin; Bianchi, Christopher; Laursen, Jonas S.; Citterio, Linda; Hein-Kristensen, Line; Gram, Lone; Kuzmenko, Ivan; Olsen, Christian A.; Gidalevitz, David

    2014-05-28

    In this study, antimicrobial peptides or their synthetic mimics are a promising class of potential new antibiotics. Herein we assess the effect of the type of cationic side chain (i.e., guanidino vs. amino groups) on the membrane perturbing mechanism of antimicrobial ?-peptide–?-peptoid chimeras. Langmuir monolayers composed of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylglycerol (DPPG) were used to model cytoplasmic membranes of both Gram-positive and Gram-negative bacteria, while lipopolysaccharide Kdo2-lipid A monolayers were mimicking the outer membrane of Gram-negative species. We report the results of the measurements using an array of techniques, including high-resolution synchrotron surface X-ray scattering, epifluorescence microscopy, and in vitro antimicrobial activity tomore »study the molecular mechanisms of peptidomimetic interaction with bacterial membranes. We found guanidino group-containing chimeras to exhibit greater disruptive activity on DPPG monolayers than the amino group-containing analogues. However, this effect was not observed for lipopolysaccharide monolayers where the difference was negligible. Furthermore, the addition of the nitrobenzoxadiazole fluorophore did not reduce the insertion activity of these antimicrobials into both model membrane systems examined, which may be useful for future cellular localization studies.« less

  15. Software Developers

    Broader source: Energy.gov [DOE]

    Because SEED will provide a common, open-source data framework, software developers will be able to write applications that access the data in a consistent way (with proper permissions), or build functionalities onto the SEED platform in a replicable way.

  16. Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

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

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Andersen, Gary L.; Mormile, Melanie R.

    2014-10-07

    Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean ismore »the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.« less

  17. A multifactor analysis of fungal and bacterial community structure of the root microbiome of mature Populus deltoides trees

    SciTech Connect (OSTI)

    Shakya, Migun; Gottel, Neil R; Castro Gonzalez, Hector F; Yang, Zamin; Gunter, Lee E; Labbe, Jessy L; Muchero, Wellington; Bonito, Gregory; Vilgalys, Rytas; Tuskan, Gerald A; Podar, Mircea; Schadt, Christopher Warren

    2013-01-01

    Bacterial and fungal communities associated with plant roots are central to the host- health, survival and growth. However, a robust understanding of root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to it s associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall genotypic distances did not have a significant effect on corresponding communities that could be separated from other measured effects.

  18. Application of PSO, Artificial Bee Colony and Bacterial Foraging Optimization algorithms to economic load dispatch: An analysis

    E-Print Network [OSTI]

    Baijal, Anant; Jayabarathi, T

    2011-01-01

    This paper illustrates successful implementation of three evolutionary algorithms, namely- Particle Swarm Optimization(PSO), Artificial Bee Colony (ABC) and Bacterial Foraging Optimization (BFO) algorithms to economic load dispatch problem (ELD). Power output of each generating unit and optimum fuel cost obtained using all three algorithms have been compared. The results obtained show that ABC and BFO algorithms converge to optimal fuel cost with reduced computational time when compared to PSO for the two example problems considered.

  19. Impact of bacteria and bacterial components on osteogenic and adipogenic differentiation of adipose-derived mesenchymal stem cells

    SciTech Connect (OSTI)

    Fiedler, Tomas; Salamon, Achim; Adam, Stefanie; Herzmann, Nicole; Taubenheim, Jan; Peters, Kirsten

    2013-11-01

    Adult mesenchymal stem cells (MSC) are present in several tissues, e.g. bone marrow, heart muscle, brain and subcutaneous adipose tissue. In invasive infections MSC get in contact with bacteria and bacterial components. Not much is known about how bacterial pathogens interact with MSC and how contact to bacteria influences MSC viability and differentiation potential. In this study we investigated the impact of three different wound infection relevant bacteria, Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes, and the cell wall components lipopolysaccharide (LPS; Gram-negative bacteria) and lipoteichoic acid (LTA; Gram-positive bacteria) on viability, proliferation, and osteogenic as well as adipogenic differentiation of human adipose tissue-derived mesenchymal stem cells (adMSC). We show that all three tested species were able to attach to and internalize into adMSC. The heat-inactivated Gram-negative E. coli as well as LPS were able to induce proliferation and osteogenic differentiation but reduce adipogenic differentiation of adMSC. Conspicuously, the heat-inactivated Gram-positive species showed the same effects on proliferation and adipogenic differentiation, while its cell wall component LTA exhibited no significant impact on adMSC. Therefore, our data demonstrate that osteogenic and adipogenic differentiation of adMSC is influenced in an oppositional fashion by bacterial antigens and that MSC-governed regeneration is not necessarily reduced under infectious conditions. - Highlights: • Staphylococcus aureus, Streptococcus pyogenes and Escherichia coli bind to and internalize into adMSC. • Heat-inactivated cells of these bacterial species trigger proliferation of adMSC. • Heat-inactivated E. coli and LPS induce osteogenic differentiation of adMSC. • Heat-inactivated E. coli and LPS reduce adipogenic differentiation of adMSC. • LTA does not influence adipogenic or osteogenic differentiation of adMSC.

  20. NMR STUDIES OF BACTERIAL TYPE III SECRETION APPARATUS NEEDLE AND TIP PROTEINS AND THE NMR STRUCTURE OF THE HANTAVIRUS NUCLEOCAPSID COILED-COIL DOMAIN

    E-Print Network [OSTI]

    Wang, Yu

    2009-04-28

    Many Gram-negative bacterial pathogens utilize type III secretion systems (TTSSs) for subverting the normal cellular functions of their target eukaryotic cells. The type III secretion apparatus (TTSA) functions like a ...

  1. Investigations of Rhizobium biofilm formation

    E-Print Network [OSTI]

    Fujishige, Nancy A; Kapadia, Neel N; De Hoff, Peter L; Hirsch, Ann M

    2006-01-01

    on a glass slide buried in compost soil. Fluorescent image.on a glass slide buried in compost soil. Fluorescent image.organic matter, found in the compost. Bare spots on the PVC

  2. Nozzle development

    SciTech Connect (OSTI)

    Dodge, F.T.; Dodge, L.G.; Johnson, J.E.

    1989-06-01

    The objective of this program has been the development of experimental techniques and data processing procedures to allow for the characterization of multi-phase fuel nozzles using laboratory tests. Test results were to be used to produce a single value coefficient-of-performance that would predict the performance of the fuel nozzles independent of system application. Several different types of fuel nozzles capable of handling multi-phase fuels have been characterized for: (a) fuel flow rate versus delivery pressure, (b) fuel-air ratio throughout the fuel spray or plume and the effective cone angle of the injector, and (c) fuel drop- or particle-size distribution as a function of fluid properties. Fuel nozzles which have been characterized on both single-phase liquids and multi-phase liquid-solid slurries include a variable-film-thickness nozzle, a commercial coal-water slurry (CWS) nozzle, and four diesel injectors of different geometries (tested on single-phase fluids only). Multi-phase mixtures includes CWS with various coal loadings, surfactant concentrations, and stabilizer concentrations, as well as glass-bead water slurries with stabilizing additives. Single-phase fluids included glycerol-water mixtures to vary the viscosity over a range of 1 to 1500 cP, and alcohol-water mixtures to vary the surface tension from about 22 to 73 dyne/cm. In addition, tests were performed to characterize straight-tube gas-solid nozzles using two differences size distributions of glass beads in air. Standardized procedures have been developed for processing measurements of spray drop-size characteristics and the overall cross-section average drop or particle size. 43 refs., 60 figs., 7 tabs.

  3. An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

    SciTech Connect (OSTI)

    Song, Zhen; Kenney, Janice P.L.; Fein, Jeremy B.; Bunker, Bruce A.

    2015-02-09

    Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has been observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.

  4. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

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

    Srinivasan, Ramya; Karaoz, Ulas; Volegova, Marina; MacKichan, Joanna; Kato-Maeda, Midori; Miller, Steve; Nadarajan, Rohan; Brodie, Eoin L.; Lynch, Susan V.; Heimesaat, Markus M.

    2015-02-06

    According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n =more »617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.« less

  5. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

    SciTech Connect (OSTI)

    Srinivasan, Ramya; Karaoz, Ulas; Volegova, Marina; MacKichan, Joanna; Kato-Maeda, Midori; Miller, Steve; Nadarajan, Rohan; Brodie, Eoin L.; Lynch, Susan V.; Heimesaat, Markus M.

    2015-02-06

    According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.

  6. Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

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

    Mueller, Rebecca C.; Belnap, Jayne; Kuske, Cheryl R.

    2015-09-04

    Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing ofmore »ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0–0.5 or 0–10 cm) across the N-amendment gradient (0, 7, and 15 kg ha–1 yr–1). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Provided the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.« less

  7. The Siderocalin/Enterobactin Interaction: A Link between Mammalian Immunity and Bacterial Iron Transport

    SciTech Connect (OSTI)

    Meux, Susan C.

    2008-05-12

    The siderophore enterobactin (Ent) is produced by enteric bacteria to mediate iron uptake. Ent scavenges iron and is taken up by the bacteria as the highly stable ferric complex [Fe{sup III}(Ent)]{sup 3-}. This complex is also a specific target of the mammalian innate immune system protein, Siderocalin (Scn), which acts as an anti-bacterial agent by specifically sequestering siderophores and their ferric complexes during infection. Recent literature suggesting that Scn may also be involved in cellular iron transport has increased the importance of understanding the mechanism of siderophore interception and clearance by Scn; Scn is observed to release iron in acidic endosomes and [Fe{sup III}(Ent)]{sup 3-} is known to undergo a change from catecholate to salicylate coordination in acidic conditions, which is predicted to be sterically incompatible with the Scn binding pocket (also referred to as the calyx). To investigate the interactions between the ferric Ent complex and Scn at different pH values, two recombinant forms of Scn with mutations in three residues lining the calyx were prepared: Scn-W79A/R81A and Scn-Y106F. Binding studies and crystal structures of the Scn-W79A/R81A:[Fe{sup III}(Ent)]{sup 3-} and Scn-Y106F:[Fe{sup III}(Ent)]{sup 3-} complexes confirm that such mutations do not affect the overall conformation of the protein but do weaken significantly its affinity for [Fe{sup III}(Ent)]{sup 3-}. Fluorescence, UV-Vis and EXAFS spectroscopies were used to determine Scn/siderophore dissociation constants and to characterize the coordination mode of iron over a wide pH range, in the presence of both mutant proteins and synthetic salicylate analogs of Ent. While Scn binding hinders salicylate coordination transformation, strong acidification results in the release of iron and degraded siderophore. Iron release may therefore result from a combination of Ent degradation and coordination change.

  8. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    SciTech Connect (OSTI)

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Ta?, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.

  9. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

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

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Ta?, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy numbermore »of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.« less

  10. Novel Bacterial Diversity in an Anchialine Blue Hole on Abaco Island, Bahamas 

    E-Print Network [OSTI]

    Gonzalez, Brett Christopher

    2012-02-14

    in the interior of the island (Raeisi and Mylroie, 1995). This mixing of water masses has aggressive dissolutional properties and aids in the forming of karstic features such as flank margin caves. Mylroie et al., (2001) proposed and developed the ?Carbonate... towards the geologic development and glacial eustatic events on the island. 10 Anchialine Environment Anchialine habitats are known to exist throughout the world often underground, forming a halocline where freshwater mixes with the intruding...

  11. Laboratory Directed Research and Development Program

    SciTech Connect (OSTI)

    Ogeka, G.J.; Romano, A.J.

    1992-12-01

    This report briefly discusses the following research: Advances in Geoexploration; Transvenous Coronary Angiography with Synchrotron X-Rays; Borehole Measurements of Global Warming; Molecular Ecology: Development of Field Methods for Microbial Growth Rate and Activity Measurements; A New Malaria Enzyme - A Potential Source for a New Diagnostic Test for Malaria and a Target for a New Antimalarial Drug; Basic Studies on Thoron and Thoron Precursors; Cloning of the cDNA for a Human Serine/Threonine Protein Kinase that is Activated Specifically by Double-Stranded DNA; Development of an Ultra-Fast Laser System for Accelerator Applications; Cluster Impact Fusion; Effect of a Bacterial Spore Protein on Mutagenesis; Structure and Function of Adenovirus Penton Base Protein; High Resolution Fast X-Ray Detector; Coherent Synchrotron Radiation Longitudinal Bunch Shape Monitor; High Grain Harmonic Generation Experiment; BNL Maglev Studies; Structural Investigations of Pt-Based Catalysts; Studies on the Cellular Toxicity of Cocaine and Cocaethylene; Human Melanocyte Transformation; Exploratory Applications of X-Ray Microscopy; Determination of the Higher Ordered Structure of Eukaryotic Chromosomes; Uranium Neutron Capture Therapy; Tunneling Microscopy Studies of Nanoscale Structures; Nuclear Techiques for Study of Biological Channels; RF Sources for Accelerator Physics; Induction and Repair of Double-Strand Breaks in the DNA of Human Lymphocytes; and An EBIS Source of High Charge State Ions up to Uranium.

  12. Application of Fibrolytic Enzymes and Bacterial Inoculants to Sorghum Silage and Small-Grain Hay 

    E-Print Network [OSTI]

    Thomas, Martha 1980-

    2013-01-17

    in maximizing nutritive value, therefore, harvest should be performed at the correct stage of development (Table 2.1). Grain sorghum should be cut at late milk to late dough stage and forage sorghums should be 1.02 m tall or at late boot stage when forage...

  13. Accelerated Publications Photocycle of the Flavin-Binding Photoreceptor AppA, a Bacterial Transcriptional

    E-Print Network [OSTI]

    van Stokkum, Ivo

    - photolysis spectroscopy. Time-resolved fluorescence experiments revealed four components of flavin adenine- tion and transduction of UV, visible, and near-IR radiation, for growing, developing, and adjusting of J.A.I. is supported by European Community's Human Potential Program Grant HPRN-CT-2002-00248 (PSICO

  14. Coimmunopurification of Phosphorylated Bacterial-and Plant-Type Phosphoenolpyruvate Carboxylases with the

    E-Print Network [OSTI]

    Plaxton, William

    with the Plastidial Pyruvate Dehydrogenase Complex from Developing Castor Oil Seeds1,2[W][OA] R. Glen Uhrig, Brendan O (R.G.U., B.O., H.E.S., W.C.P.), Department of Chemistry (Y.-M.S.), and Department of Biochemistry (W

  15. Removal of Eutrophic Nutrients from Wastewater and their UNIVERSITY OF THE DISTRICT OF COLUMBIA Bioconversion to Bacterial Single Cell Protein for Animal

    E-Print Network [OSTI]

    District of Columbia, University of the

    as end products of anaerobic sludge digestion as well as many common cyclic amino acids such as histidine .........................................................9 2. Biochemical analysis of the dried bacterial biomass grown on digester Elutriate ......................................................................................................10 3. Nutritive quality of A. eutrophus biomass grown in wastewater (digester elutriate) as a protein

  16. Geochemical assessment of gaseous hydrocarbons: mixing of bacterial and thermogenic methane in the deep subsurface petroleum system, Gulf of Mexico continental slope 

    E-Print Network [OSTI]

    Ozgul, Ercin

    2004-09-30

    Mixtures of bacterial and thermogenic methane are found both at vents at the seafloor and in reservoirs in the deep subsurface of the Gulf of Mexico continental slope. The C1-C5 gas that most recently charged reservoirs of Jolliet (GC 184), Genesis...

  17. A Novel Phosphorylation Event Activates Bacterial Type VI Secretion A research team led by Dr. Erh-Min Lai, an Associate Research Fellow at the Institute

    E-Print Network [OSTI]

    Chen, Sheng-Wei

    A Novel Phosphorylation Event Activates Bacterial Type VI Secretion A research team led by Dr. Erh-Min Lai, an Associate Research Fellow at the Institute of Plant and Microbial Biology, and Dr. Ming-Daw Tsai, a Distinguished Research Fellow at the Institute of Biological Chemistry, recently reported

  18. Plasmid DNA minipreps (alkaline lysis method) 1. Centrifuge 1 mL of overnight bacterial culture in eppi tube for 2 min at 10,000 x g

    E-Print Network [OSTI]

    Pace, Norman

    Plasmid DNA minipreps (alkaline lysis method) 1. Centrifuge 1 mL of overnight bacterial culture. Incubate on ice 5 min (or longer). 7. Centrifuge for 10 min at 16,000 x g at 4°C. 8. Transfer supernatant to new eppi tube; add equal volume PCI; mix by vortex. 9. Centrifuge for 5 min at 16,000 x g at room

  19. Ecosystems and Sustainable Development

    E-Print Network [OSTI]

    Tufford, Dan

    1999-01-01

    Ecosystems and Sustainable Development Editors: J.L. Uso,Ecosystems and Sustainable Development. Southhampton, UK:ISBN: 1-85312-502-4. Sustainable development research is a

  20. Psychology of Sustainable Development

    E-Print Network [OSTI]

    Milfont, Taciano Lemos

    2003-01-01

    to achieve sustainable development: economic, environmental,Psychology of Sustainable Development By Peter Schmuck andPsychology of Sustainable Development. Norwell, MA: Kluwer

  1. 2012 Bacterial Source Tracking - State of the Science Conference Conference Proceedings 

    E-Print Network [OSTI]

    Smith, C.; Wagner, K.; Warrick, L.

    2012-01-01

    ; evaluation and development of a feral hog marker; and evaluation of grazing management practices. An ongoing project in Texas that Dr. Gentry expanded on was source tracking or Little Brazos River tributaries. He described library-independent and library...-dependent approaches and analysis for this study area. For the library-independent analysis, the hog marker was detected most frequently. Texas has a population of nearly two million feral hogs with approximately $52 million in damages each year and Joy Archuleta...

  2. Individual Development and Excutive Development Plan Resources

    Broader source: Energy.gov [DOE]

    According to OPM, an individual development plan (IDP) is a tool to assist employees in career and personal development. Its primary purpose is to help employees reach short and long-term career...

  3. Final Report Grant No. DE-FG02-98ER20307 Lipopolysaccharide Structures and Genes Required for Root Nodule Development August 1, 2004 to July 31, 2008

    SciTech Connect (OSTI)

    Noel, K. Dale

    2008-12-07

    This project dealt with the plant-bacterial symbiosis that gives rise to root nodules on leguminous plants in which the bacteria carry out nitrogen fixation. Nitrogen fixation, like carbon dioxide fixation, is essential for life on planet earth, and this symbiosis is estimated to account for half of all nitrogen fixed on land. Aside from being important for the sustenance of global life, this ability allows legumes to grow without nitrogen fertilizers. Basic studies such as this project are aimed at understanding the symbiosis well enough that eventually it can be engineered into important crop species so that they no longer depend on nitrogen fertilizer for growth. The production and distribution of excessive fertilizer needed for optimal crop yields is responsible for a significant portion of the energy costs in agriculture. The specific aims of this work were to further the understanding of a bacterial factor that is essential for the symbiotic infection process. This factor is a bacterial surface molecule, lipopolysaccharide O antigen. In this project we showed that, not only the presence, but the specific structure of this molecule is crucial for infection. Although the success of bacterial infections in many pathogenic and mutualistic interactions have been shown to depend on intact O antigen, it has been very rare to establish that specific features of the structure are important. One of the features in this case is the presence of one additional methyl group on one sugar in the O antigen. It is very surprising that such a minor change should have an observable effect. This work sets the stage for biochemical studies of possible plant receptors that may be involved. During the course of this grant period, we developed a method of testing the importance of this bacterial component at stages of nodule development beyond the step that is blocked by null mutation. The method works adequately for this purpose and is being improved. It has implications for testing the roles of other important bacterial factors at multiple stages of nodule development. The project also investigated the biosynthesis of this bacterial factor. It has a complex structure and the first accomplishment was the determination of the sequences of genetic regions known to be important. Next the discovered genes were mutated to identify the 26 that are required for its synthesis. In addition, six others were discovered that are believed to change its structure under various environmental conditions. By studying mutants affected in specific genes, genes were associated with each of the predicted steps in the biosynthesis. Current work is testing the predicted biosynthetic model with studies conducted in vitro with bacterial extracts. Overall, the work funded by this grant establishes this system as a model for host-bacterial interactions based on specific polysaccharide structure. All areas that are needed for a comprehensive model have been significantly advanced: the biological function, the structural features that are crucial, the complete set of bacterial genes involved, and a model for the biosynthesis.

  4. Tanpopo cosmic dust collector: Silica aerogel production and bacterial DNA contamination analysis

    E-Print Network [OSTI]

    Tabata, Makoto; Yokobori, Shin-ichi; Kawai, Hideyuki; Takahashi, Jun-ichi; Yano, Hajime; Yamagishi, Akihiko

    2011-01-01

    Hydrophobic silica aerogels with ultra-low densities have been designed and developed as cosmic dust capture media for the Tanpopo mission which is proposed to be carried out on the International Space Station. Glass particles as a simulated cosmic dust with 30 \\mu m in diameter and 2.4 g/cm^3 in density were successfully captured by the novel aerogel at a velocity of 6 km/s. Background levels of contaminated DNA in the ultra-low density aerogel were lower than the detection limit of a polymerase chain reaction assay. These results show that the manufactured aerogel has good performance as a cosmic dust collector and sufficient quality in respect of DNA contamination. The aerogel is feasible for the biological analyses of captured cosmic dust particles in the astrobiological studies.

  5. Insights into substrate specificity of NlpC/P60 cell wall hydrolases containing bacterial SH3 domains

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

    Xu, Qingping; Mengin-Lecreulx, Dominique; Liu, Xueqian W.; Patin, Delphine; Farr, Carol L.; Grant, Joanna C.; Chiu, Hsiu -Ju; Jaroszewski, Lukasz; Knuth, Mark W.; Godzik, Adam; et al

    2015-09-15

    Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. In addition, these enzymes all have ?-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (ordl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminall-Ala. Their crystal structures revealed a highly conserved structure consisting ofmore »two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation.Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.« less

  6. Clean development mechanism: Perspectives from developing countries

    SciTech Connect (OSTI)

    Sari, Agus P.; Meyers, Stephen

    1999-06-01

    This paper addresses the political acceptability and workability of CDM by and in developing countries. At COP-3 in Kyoto in 1997, the general position among developing countries changed from strong rejection of joint implementation to acceptance of CDM. The outgrowth of CDM from a proposal from Brazil to establish a Clean Development Fund gave developing countries a sense of ownership of the idea. More importantly, establishing support for sustainable development as a main goal for CDM overcame the resistance of many developing countries to accept a carbon trading mechanism. The official acceptance of CDM is not a guarantee of continued acceptance, however. Many developing countries expect CDM to facilitate a substantial transfer of technology and other resources to support economic growth. There is concern that Annex I countries may shift official development assistance into CDM in order to gain carbon credits, and that development priorities could suffer as a result. Some fear that private investments could be skewed toward projects that yield carbon credits. Developing country governments are wary regarding the strong role of the private sector envisioned for CDM. Increasing the awareness and capacity of the private sector in developing countries to initiate and implement CDM projects needs to be a high priority. While private sector partnerships will be the main vehicle for resource transfer in CDM, developing country governments want to play a strong role in overseeing and guiding the process so that it best serves their development goals. Most countries feel that establishment of criteria for sustainable development should be left to individual countries. A key issue is how CDM can best support the strengthening of local capacity to sustain and replicate projects that serve both climate change mitigation and sustainable development objectives.There is support among developing countries for commencing CDM as soon as possible. Since official commencement must await the entry into force of the Kyoto Protocol, many developing countries support the establishment of an Interim Phase starting in 2000, with possible retroactive crediting once the Protocol enters into force.

  7. Direct Metal Transfer Between Periplasmic Proteins Identifies a Bacterial Copper Chaperone

    SciTech Connect (OSTI)

    Bagai, I.; Rensing, C.; Blackburn, N.; McEvoy, M.M.

    2009-05-11

    Transition metals require exquisite handling within cells to ensure that cells are not harmed by an excess of free metal species. In Gram-negative bacteria, copper is required in only small amounts in the periplasm, not in the cytoplasm, so a key aspect of protection under excess metal conditions is to export copper from the periplasm. Additional protection could be conferred by a periplasmic chaperone to limit the free metal species prior to export. Using isothermal titration calorimetry, we have demonstrated that two periplasmic proteins, CusF and CusB, of the Escherichia coli Cu(I)/Ag(I) efflux system undergo a metal-dependent interaction. Through the development of a novel X-ray absorption spectroscopy approach using selenomethionine labeling to distinguish the metal sites of the two proteins, we have demonstrated transfer of Cu(I) occurs between CusF and CusB. The interaction between these proteins is highly specific, as a homologue of CusF with a 51% identical sequence and a similar affinity for metal, did not function in metal transfer. These experiments establish a metallochaperone activity for CusF in the periplasm of Gram-negative bacteria, serving to protect the periplasm from metal-mediated damage.

  8. Essays in Development Economics

    E-Print Network [OSTI]

    Hicks, Joan Hamory

    2009-01-01

    Handbook of Development Economics, Volume I (pp. 713-762).Journal of Development Economics, 81, 80-96. Behrman, JereJournal of Development Economics, 79, 349-373. Dercon,

  9. Training and Organizational Development

    E-Print Network [OSTI]

    Stephens, Graeme L.

    Training and Organizational Development Contact: Ellen Audley Assistant, 491-1376, Ellen coordinates training and development opportunities for personal and professional growth for Colorado State. Customized training and organizational development consulting services are also available. Class Locations

  10. Training and Organizational Development

    E-Print Network [OSTI]

    Stephens, Graeme L.

    Training and Organizational Development Contact: Ellen Audley Assistant, 491-1376, Ellen coordinates training and development opportunities for personal and professional growth for Colorado State. Customized training and organizational development consulting services are also available. Class Location

  11. Training and Organizational Development

    E-Print Network [OSTI]

    Training and Organizational Development Contact: Ellen Audley Assistant, (970) 491-1376, Ellen 1 of 5 This office coordinates training and development opportunities for personal and professional and state classified personnel. Customized training and orga- nizational development consulting services

  12. Training and Organizational Development

    E-Print Network [OSTI]

    Training and Organizational Development Contact: Ellen Audley Assistant, (970) 491-1376, Ellen training and development opportunities for personal and professional growth for Colorado State University training and organiza- tional development consulting services are also available. Class Location: Johnson

  13. Training and Organizational Development

    E-Print Network [OSTI]

    Stephens, Graeme L.

    Training and Organizational Development Contact: Ellen Audley Assistant, 491-1376, Ellen training and development opportunities for personal and professional growth for Colorado State University training and organizational development consulting services are also available. Class Location: Johnson

  14. What is Community Development

    E-Print Network [OSTI]

    Taylor, Greg

    2009-04-01

    This publication offers a practical definition of community development for county Extension educators. It also offers examples of goals and objectives for various resource development areas in a community. A list of community development...

  15. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site

    SciTech Connect (OSTI)

    Green, Stefan [Florida State University; Prakash, Om [Florida State University; Jasrotia, Puja [Florida State University; Overholt, Will [Florida State University; Cardenas, Erick [Michigan State University, East Lansing; Hubbard, Daniela [Florida State University; Tiedje, James M. [Michigan State University, East Lansing; Watson, David B [ORNL; Schadt, Christopher Warren [ORNL; Brooks, Scott C [ORNL; Kostka, Joel [Florida State University

    2011-01-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of ribosomal RNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure, and denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as concentration of nitrogen species, oxygen and sampling season did not appear to strongly influence the distribution of Rhodanobacter. Results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  16. Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants

    SciTech Connect (OSTI)

    Berni Canani, Roberto; Sangwan, Naseer; Stefka, Andrew T.; Nocerino, Rita; Paparo, Lorella; Aitoro, Rosita; Calignano, Antonio; Khan, Aly A.; Gilbert, Jack A.; Nagler, Cathryn R.

    2015-09-22

    Dietary intervention with extensively hydrolyzed casein formula supplemented with Lactobacillus rhamnosus GG (EHCF+LGG) accelerates tolerance acquisition in infants with cow’s milk allergy (CMA). We examined whether this effect is attributable, at least in part, to an influence on the gut microbiota. Fecal samples from healthy controls (n=20) and from CMA infants (n=19) before and after treatment with EHCF with (n=12) and without (n=7) supplementation with LGG were compared by 16S rRNA-based operational taxonomic unit clustering and oligotyping. Differential feature selection and generalized linear model fitting revealed that the CMA infants have a diverse gut microbial community structure dominated by Lachnospiraceae (20.5±9.7%) and Ruminococcaceae (16.2±9.1%). Blautia, Roseburia and Coprococcus were significantly enriched following treatment with EHCF and LGG, but only one genus, Oscillospira, was significantly different between infants that became tolerant and those that remained allergic. However, most tolerant infants showed a significant increase in fecal butyrate levels, and those taxa that were significantly enriched in these samples, Blautia and Roseburia, exhibited specific strain-level demarcations between tolerant and allergic infants. As a result, our data suggest that EHCF+LGG promotes tolerance in infants with CMA, in part, by influencing the strain-level bacterial community structure of the infant gut.

  17. Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

    SciTech Connect (OSTI)

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Andersen, Gary L.; Mormile, Melanie R.

    2014-10-07

    Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.

  18. NITINOL ENGINE DEVELOPMENT

    E-Print Network [OSTI]

    Banks, Ridgway

    2013-01-01

    20, 1976 LBL-5293 NITINOL ENGINE DEVELOPMENT Ridgway Banksof California. NITINOL ENGINE DEVELOPMENT Ridgway Banks andof practical heat engines based on this phenomenon is

  19. Clean Energy Development Fund

    Office of Energy Efficiency and Renewable Energy (EERE)

    Vermont's Clean Energy Development Fund (CEDF) was established in 2005 to promote the development and deployment of cost-effective and environmentally sustainable electric power and thermal...

  20. ORISE: Web Development

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

    Web Development As computer-based applications become increasingly popular for the delivery of health care training and information, the need for Web development in support of...

  1. NITINOL ENGINE DEVELOPMENT

    E-Print Network [OSTI]

    Banks, Ridgway

    2013-01-01

    16-20, 1976 LBL-5293 NITINOL ENGINE DEVELOPMENT RidgwayUniversity of California. NITINOL ENGINE DEVELOPMENT Ridgwaynickel-titanium alloy "55-Nitinol." Details of the current

  2. Developing Alaskan Sustainable Housing

    Office of Energy Efficiency and Renewable Energy (EERE)

    The Association of Alaska Housing Authorities is holding a 3-day training event for housing development professionals titled Developing Alaskan Sustainable Housing (DASH). This is a unique...

  3. Context-dependent protein folding of a virulence peptide in the bacterial and host environments: structure of an SycH–YopH chaperone–effector complex

    SciTech Connect (OSTI)

    Vujanac, Milos; Stebbins, C. Erec, E-mail: stebbins@rockefeller.edu [The Rockefeller University, New York, NY 10065 (United States)

    2013-04-01

    The structure of a SycH–YopH chaperone–effector complex from Yersinia reveals the bacterial state of a protein that adopts different folds in the host and pathogen environments. Yersinia pestis injects numerous bacterial proteins into host cells through an organic nanomachine called the type 3 secretion system. One such substrate is the tyrosine phosphatase YopH, which requires an interaction with a cognate chaperone in order to be effectively injected. Here, the first crystal structure of a SycH–YopH complex is reported, determined to 1.9 Å resolution. The structure reveals the presence of (i) a nonglobular polypeptide in YopH, (ii) a so-called ?-motif in YopH and (iii) a conserved hydrophobic patch in SycH that recognizes the ?-motif. Biochemical studies establish that the ?-motif is critical to the stability of this complex. Finally, since previous work has shown that the N-terminal portion of YopH adopts a globular fold that is functional in the host cell, aspects of how this polypeptide adopts radically different folds in the host and in the bacterial environments are analysed.

  4. for the future DEVELOPMENT

    E-Print Network [OSTI]

    Birmingham, University of

    . Metallurgy and Materials development continues The iconic building before refurbishment The welcoming new

  5. Options for developing countries in mining development

    SciTech Connect (OSTI)

    Walrond, G.W.; Kumar, R.

    1985-01-01

    This book is a study of the issues that developing countries face in planning and implementing mineral development, taking as case studies Botswana, Sierra Leone, Zambia, Tanzania, Malaysia, Papua New Guinea and the developed states of Quebec and Western Australia. The authors consider the major aspects of the matter including organization and administration; regulation; taxation and surplus distribution; the dynamics of such instruments as royalty, rent resource tax and capital allowances under various cost/price scenarios; and selected mining agreements and their key provisions. They stress throughout the need for foreign investment while maximizing the economic benefits reaped from exhaustible resources.

  6. Comparison of availability of copper(II) complexes with organic ligands to bacterial cells and to chitin

    SciTech Connect (OSTI)

    Vasconcelos, M.T.S.D.; Azenha, M.A.O.; Cabral, J.P.S.

    1997-10-01

    Bacterial cells or chitin were exposed to solutions with 100 {micro}M total but only 5 {micro}M free copper, due to the presence of a proper concentration of proline, lysine, cysteine, or ethylenediamine tetraacetate (EDTA). The influence of the nature and concentration of the particles and soluble ligands, on the sorption and on the desorption of the copper, at pH 6.50 and 25.0 C, was investigated. The metal sorbed by the particles and that left in the solution were measured by atomic absorption spectrometry, after different periods of contact between particles and solution. The interpretation of the results was based on the copper(II) speciation calculated through equilibrium approaches applied to homogeneous or heterogeneous systems. A significant fraction of copper bound to the organic ligands was displaced to the bacteria or chitin, and the extent of chemical reaction depended on the nature of both the soluble (or leaving) ligands and sites on the particle surface (or entering ligands), as expected by the equilibrium theory. But with chitin, the uptake of copper in the presence of cysteine or EDTA was higher than expected, which may be due to the adsorption of the soluble copper complexes on the particle surface. In consequence of a competition between soluble and particulate ligands (cells or chitin), the free copper(II) concentration decreased in the solution, even in the presence of very strong chelators. The results indicate that copper availability is not a simple function of the initial free copper concentration in the solution. Desorption of the previously fixed copper, originated by free soluble ligands indicated that the sorption of copper was quasireversible for both particles, though a larger dismissal of the equilibrium position occurred for the cells, probably due to their biological activity.

  7. Hanford Site Development Plan

    SciTech Connect (OSTI)

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J. ); Yancey, E.F. )

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs.

  8. Internet Polling Development Report 

    E-Print Network [OSTI]

    Klima, P.; Lockhart, D.; Haberl, J. S.

    2001-01-01

    This is the final report which documents the development of Internet-based data logger polling. The project consists of two main tasks: the development of automated polling procedures that can be launched remotely with no operator input...

  9. Intel Architecture Software Developer's

    E-Print Network [OSTI]

    Dinda, Peter A.

    Intel Architecture Software Developer's Manual Volume 1: Basic Architecture NOTE: The Intel Architecture Software Developer's Manual consists of three volumes: Basic Architecture, Order Number 243190 sustaining applications. Intel may make changes to specifications and product descriptions at any time

  10. Developing a Marketing Plan 

    E-Print Network [OSTI]

    Bevers, Stan; Waller, Mark L.; Amosson, Stephen H.; McCorkle, Dean

    2009-03-02

    Developing a good marketing plan will help you identify and quantify costs, set price goals, determine potential price outlook, examine production and price risk, and develop a strategy for marketing your crop. This publication describes...

  11. Essays in development economics

    E-Print Network [OSTI]

    Keniston, Daniel Eben

    2011-01-01

    Chapter 1 looks at the empirical estimation of the welfare impacts of bargaining. Bargaining for retail goods is common in developing countries, but rare in the developed world. The welfare implications of this difference ...

  12. Essays in Development Economics

    E-Print Network [OSTI]

    Keats, Anthony

    2012-01-01

    Discontinuity Designs in Economics," Journal of EconomicJournal of Development Economics 87(1): 57-75. [21] Ozier,Journal of Development Economics 94, 151-163. [9] Delavande,

  13. RELAP-7 Development

    Broader source: Energy.gov [DOE]

    During the second quarter, the Reactor team drafted software development guidance documents and a software quality assurance plan.

  14. Gammasphere software development

    SciTech Connect (OSTI)

    Piercey, R.B.

    1993-01-01

    Activities of the nuclear physics group are described. Progress was made in organizing the Gammasphere Software Working Group, establishing a nuclear computing facility, participating in software development at Lawrence Berkeley, developing a common data file format, and adapting the ORNL UPAK software to run at Gammasphere. A universal histogram object was developed that defines a file format and provides for an objective-oriented programming model. An automated liquid nitrogen fill system was developed for Gammasphere (110 Ge detectors comprise the sphere).

  15. 2013 Nuclear Workforce Development ...

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

    Nuclear Workforce Development Day Tuesday, October 22, 2013 Nuclear Medicine Topics: Pathways of Practice in Nuclear Medicine Radiopharmacy Patient Care ...

  16. DEVELOPING STATE POLICIES SUPPORTIVE OF BIOENERGY DEVELOPMENT

    SciTech Connect (OSTI)

    Kathryn Baskin

    2004-10-31

    Working within the context of the Southern States Biobased Alliance (SSBA) and with officials in each state, the Southern States Energy Board (SSEB) is identifying bioenergy-related policies and programs within each state to determine their impact on the development, deployment or use of bioenergy. In addition, SSEB will determine which policies have impacted industry's efforts to develop, deploy or use biobased technologies or products. As a result, SSEB will work with the Southern States Biobased Alliance to determine how policy changes might address any negative impacts or enhance positive impacts. In addition to analysis of domestic policies and programs, this project will include the development of a U.S.-Brazil Biodiesel Pilot Project. The purpose of this effort is to promote and facilitate the commercialization of biodiesel and bioenergy production and demand in Brazil.

  17. DEVELOPING STATE POLICIES SUPPORTIVE OF BIOENERGY DEVELOPMENT

    SciTech Connect (OSTI)

    Kathryn Baskin

    2005-04-30

    Working within the context of the Southern States Biobased Alliance (SSBA) and with officials in each state, the Southern States Energy Board (SSEB) is identifying bioenergy-related policies and programs within each state to determine their impact on the development, deployment or use of bioenergy. In addition, SSEB will determine which policies have impacted industry's efforts to develop, deploy or use biobased technologies or products. As a result, SSEB will work with the Southern States Biobased Alliance to determine how policy changes might address any negative impacts or enhance positive impacts. In addition to analysis of domestic policies and programs, this project will include the development of a U.S.-Brazil Biodiesel Pilot Project. The purpose of this effort is to promote and facilitate the commercialization of biodiesel and bioenergy production and demand in Brazil.

  18. DEVELOPING STATE POLICIES SUPPORTIVE OF BIOENERGY DEVELOPMENT

    SciTech Connect (OSTI)

    Kathryn Baskin

    2005-01-31

    Working within the context of the Southern States Biobased Alliance (SSBA) and with officials in each state, the Southern States Energy Board (SSEB) is identifying bioenergy-related policies and programs within each state to determine their impact on the development, deployment or use of bioenergy. In addition, SSEB will determine which policies have impacted industry's efforts to develop, deploy or use biobased technologies or products. As a result, SSEB will work with the Southern States Biobased Alliance to determine how policy changes might address any negative impacts or enhance positive impacts. In addition to analysis of domestic policies and programs, this project will include the development of a U.S.-Brazil Biodiesel Pilot Project. The purpose of this effort is to promote and facilitate the commercialization of biodiesel and bioenergy production and demand in Brazil.

  19. DEVELOPING STATE POLICIES SUPPORTIVE OF BIOENERGY DEVELOPMENT

    SciTech Connect (OSTI)

    Kathryn Baskin

    2004-07-28

    Working within the context of the Southern States Biobased Alliance (SSBA) and with officials in each state, the Southern States Energy Board (SSEB) is identifying bioenergy-related policies and programs within each state to determine their impact on the development, deployment or use of bioenergy. In addition, SSEB will determine which policies have impacted industry's efforts to develop, deploy or use biobased technologies or products. As a result, SSEB will work with the Southern States Biobased Alliance to determine how policy changes might address any negative impacts or enhance positive impacts. In addition to analysis of domestic policies and programs, this project will include the development of a U.S.-Brazil Biodiesel Pilot Project. The purpose of this effort is to promote and facilitate the commercialization of biodiesel and bioenergy production and demand in Brazil.

  20. performance development and compensation

    E-Print Network [OSTI]

    Dennett, Daniel

    · ProvidinginputtothePerformanceReviewprocess. Human Resources serves as a resource for school/division leadershipperformance development and compensation programs @WorkGuidebook #12;4 | Tufts University Human performance development program Tufts Competencies 5 The @Work Performance Development and Compensation Cycle

  1. Mechanisms in Plant Development

    SciTech Connect (OSTI)

    Hake, Sarah

    2013-08-21

    This meeting has been held every other year for the past twenty-two years and is the only regularly held meeting focused specifically on plant development. Topics covered included: patterning in developing tissues; short and long distance signaling; differentiation of cell types; the role of epigenetics in development; evolution; growth.

  2. Scienceandthe DevelopingWorld

    E-Print Network [OSTI]

    -quality research and to provide education in order to promote science in the developing world. As we celebrate our to evolve in response to a changing world, initiating efforts where new priorities--and new potential and supporting science in the developing world. 2 New Research Areas: Develop new research areas

  3. Coated Conductor Technology Development

    E-Print Network [OSTI]

    Coated Conductor Technology Development Roadmap Priority Research & Development Activities Leading for Electric Systems Program Prepared by: Energetics, Incorporated #12;Coated Conductor Development Roadmap of high-quality, low-cost coated conductors that will lead to industrial-scale commercial manufacturing

  4. Bacterial extracellular lignin peroxidase

    DOE Patents [OSTI]

    Crawford, D.L.; Ramachandra, M.

    1993-08-03

    DNA constructs are provided for the production of Streptomyces lignin peroxidase. The enzyme finds use in the degradation of lignin and oxidation of organic substrates.

  5. Bacterial Sulfur Storage Globules

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 OutreachProductswsicloudwsiclouddenDVA N C E D B L O OLaura BeaneCardwell,Production - Energyby I. J. Pickering

  6. Sandia Energy - Advanced Research & Development

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

    & Development Home Stationary Power Energy Conversion Efficiency Solar Energy Photovoltaics Advanced Research & Development Advanced Research & DevelopmentCoryne...

  7. The developer`s competitive advantage

    SciTech Connect (OSTI)

    DeLugo, E.M. Jr. [Ridgewood Power Corp., NJ (United States)

    1994-09-01

    When developers seek funding for power projects today, they are entering a financial market that is well versed in the risk and reward characteristics of independent power projects. Over the past several years, a high demand for project funding, combined with a variety of well-publicized fiascoes has caused many investors and lenders to adopt a more cautious posture toward leveraged ventures.

  8. Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway

    SciTech Connect (OSTI)

    Webb, N.A.; Mulichak, A.M.; Lam, J.S.; Rocchetta, H.L.; Garavito, R.M. (MSU); (Guelph); (PG)

    2010-03-08

    D-Rhamnose is a rare 6-deoxy monosaccharide primarily found in the lipopolysaccharide of pathogenic bacteria, where it is involved in host-bacterium interactions and the establishment of infection. The biosynthesis of D-rhamnose proceeds through the conversion of GDP-D-mannose by GDP-D-mannose 4,6-dehydratase (GMD) to GDP-4-keto-6-deoxymannose, which is subsequently reduced to GDP-D-rhamnose by a reductase. We have determined the crystal structure of GMD from Pseudomonas aeruginosa in complex with NADPH and GDP. GMD belongs to the NDP-sugar modifying subfamily of the short-chain dehydrogenase/reductase (SDR) enzymes, all of which exhibit bidomain structures and a conserved catalytic triad (Tyr-XXX-Lys and Ser/Thr). Although most members of this enzyme subfamily display homodimeric structures, this bacterial GMD forms a tetramer in the same fashion as the plant MUR1 from Arabidopsis thaliana. The cofactor binding sites are adjoined across the tetramer interface, which brings the adenosyl phosphate moieties of the adjacent NADPH molecules to within 7 {angstrom} of each other. A short peptide segment (Arg35-Arg43) stretches into the neighboring monomer, making not only protein-protein interactions but also hydrogen bonding interactions with the neighboring cofactor. The interface hydrogen bonds made by the Arg35-Arg43 segment are generally conserved in GMD and MUR1, and the interacting residues are highly conserved among the sequences of bacterial and eukaryotic GMDs. Outside of the Arg35-Arg43 segment, residues involved in tetrameric contacts are also quite conserved across different species. These observations suggest that a tetramer is the preferred, and perhaps functionally relevant, oligomeric state for most bacterial and eukaryotic GMDs.

  9. Essays in Development Economics

    E-Print Network [OSTI]

    Bazzi, Samuel Ali

    are weak,” Review of Economics and Statistics, 2004, 86,Essays in Development Economics A dissertation submitted indegree Doctor of Philosophy in Economics by Samuel Ali Bazzi

  10. Laboratory Directed Research & Development

    E-Print Network [OSTI]

    Ohta, Shigemi

    ......................................................................5 Photovoltaics: Nanostructure, Solvent Annealing and Performance..............................................7 Solar Energy Source Evaluation for Smart Grid Development of a Collaborative NREL, BNL, LDRD........................................................................17

  11. Synergizing in Cyberinfrastructure Development

    E-Print Network [OSTI]

    Bietz, Matthew J.; Baumer, Eric P.; Lee, Charlotte P.

    2010-01-01

    relationships with grantees to develop new collaborations (approach potential grantees directly and work with them towith and among its grantees. The project was designed around

  12. NMR bioreactor development for live in-situ microbial functional analysis

    SciTech Connect (OSTI)

    Majors, Paul D.; Mclean, Jeffrey S.; Scholten, Johannes C.

    2008-05-01

    A live in-situ metabolomics capability was developed for prokaryotic cultures under controlled-growth conditions. Toward this goal, a radiofrequency-transparent bioreactor was developed and integrated with a commercial wide-bore nuclear magnetic resonance (NMR) imaging spectrometer and a commercial bioreactor controller. Water suppressed 1H NMR spectroscopy was used to monitor glucose and fructose utilization and byproduct excretion by Eubacterium aggregans (an anaerobic bacterial species relevant for biofuels production) under controlled batch and continuous culture conditions. The resulting metabolite profiles (short chain organic acids and ethanol) and trends are consistent with existing knowledge of its metabolism. However, our study showed the Eubacterium aggregans produces lactate end product in significant concentrations – a result not previously reported. The advantages of live in-situ microbial metabolomics analysis and its complementariness with functional genomics / systems biology methods are discussed.

  13. Laboratory Directed Research and Development Program. Annual report

    SciTech Connect (OSTI)

    Ogeka, G.J.; Romano, A.J.

    1992-12-01

    This report briefly discusses the following research: Advances in Geoexploration; Transvenous Coronary Angiography with Synchrotron X-Rays; Borehole Measurements of Global Warming; Molecular Ecology: Development of Field Methods for Microbial Growth Rate and Activity Measurements; A New Malaria Enzyme - A Potential Source for a New Diagnostic Test for Malaria and a Target for a New Antimalarial Drug; Basic Studies on Thoron and Thoron Precursors; Cloning of the cDNA for a Human Serine/Threonine Protein Kinase that is Activated Specifically by Double-Stranded DNA; Development of an Ultra-Fast Laser System for Accelerator Applications; Cluster Impact Fusion; Effect of a Bacterial Spore Protein on Mutagenesis; Structure and Function of Adenovirus Penton Base Protein; High Resolution Fast X-Ray Detector; Coherent Synchrotron Radiation Longitudinal Bunch Shape Monitor; High Grain Harmonic Generation Experiment; BNL Maglev Studies; Structural Investigations of Pt-Based Catalysts; Studies on the Cellular Toxicity of Cocaine and Cocaethylene; Human Melanocyte Transformation; Exploratory Applications of X-Ray Microscopy; Determination of the Higher Ordered Structure of Eukaryotic Chromosomes; Uranium Neutron Capture Therapy; Tunneling Microscopy Studies of Nanoscale Structures; Nuclear Techiques for Study of Biological Channels; RF Sources for Accelerator Physics; Induction and Repair of Double-Strand Breaks in the DNA of Human Lymphocytes; and An EBIS Source of High Charge State Ions up to Uranium.

  14. Technical Assistance to Developers

    SciTech Connect (OSTI)

    Rockward, Tommy; Borup, Rodney L.; Garzon, Fernando H.; Mukundan, Rangachary; Spernjak, Dusan

    2012-07-17

    This task supports the allowance of technical assistance to fuel-cell component and system developers as directed by the DOE. This task includes testing of novel materials and participation in the further development and validation of single cell test protocols. This task also covers technical assistance to DOE Working Groups, the U.S. Council for Automotive Research (USCAR) and the USCAR/DOE Driving Research and Innovation for Vehicle efficiency and Energy sustainability (U.S. Drive) Fuel Cell Technology Team. Assistance includes technical validation of new fuel cell materials and methods, single cell fuel cell testing to support the development of targets and test protocols, and regular advisory participation in other working groups and reviews. This assistance is made available to PEM fuel cell developers by request and DOE Approval. The objectives are to: (1) Support technically, as directed by DOE, fuel cell component and system developers; (2) Assess fuel cell materials and components and give feedback to developers; (3) Assist the DOE Durability Working Group with the development of various new material durability Testing protocols; and (4) Provide support to the U.S. Council for Automotive Research (USCAR) and the USCAR/DOE Fuel Cell Technology Team. FY2012 specific technical objectives are: (1) Evaluate novel MPL materials; (2) Develop of startup/ shutdown protocol; (3) Test the impact of hydrophobic treatment on graphite bi-polar plates; (4) Perform complete diagnostics on metal bi-polar plates for corrosion; and (5) Participate and lead efforts in the DOE Working Groups.

  15. Wind Economic Development (Postcard)

    SciTech Connect (OSTI)

    Not Available

    2011-08-01

    The U.S. Department of Energy's Wind Powering America initiative provides information on the economic development benefits of wind energy. This postcard is a marketing piece that stakeholders can provide to interested parties; it will guide them to the economic development benefits section on the Wind Powering America website.

  16. Developments in Human Communication

    E-Print Network [OSTI]

    Thompson, Michael

    CMST 1B03 Developments in Human Communication: Part & Present Amanda Etches-Johnson Mills Research in Human Communication Session Outline 1. Finding Books Using MORRIS 2. Finding Journal Articles using: Developments in Human Communication What is MORRIS anyway? · MORRIS is McMaster's library catalogue · Shows

  17. Introducing Web Application Development

    E-Print Network [OSTI]

    Ding, Wei

    Introducing Web Application Development Instructor: Dr Wei Ding Development Instructor: Dr.Wei Ding Fall 2009 1CS 437/637 Database-BackedWeb Sites andWeb Services Introduction: Internet vs. World Wide Web Internet is an interconnected network of thousands ofInternet is an interconnected network

  18. Sun Academic Developer Program

    E-Print Network [OSTI]

    Davenport, James

    Sun Academic Developer Program Kim Jones Vice President Government, Education & Health Care Sun Microsystems, Inc. FY08 Campus Ambassador Programme Your Name Here Sun Microsystems, Inc. #12;2 FY08 Campus Ambassador Programme #12;3 Sun Academic Developer Initiative On-Campus Events and Contests Open Source

  19. Aggressive development plans

    SciTech Connect (OSTI)

    McCandless, D.H.

    1993-11-01

    Hydropower developments are capital-intensive, are subject to uncertainty in water availability, and have a somewhat higher construction-cost risk than thermal projects. However, a developer who selects an attractive site, arranges a good financial package, and designs and constructs a well-conceived hydropower project can earn an attractive long-term return while providing a dependable, low-cost source of energy to consumers. In the Philippines, many attractive hydropower sites are now available. As demonstrated by the attendance at the US Trade and Development Agency-sponsored Symposium on Power Development and Investment Opportunities in the Philippines, in Washington, D.C., on Sept. 21 and 22, 1993, there is a growing interest in private hydropower. Following its successful record in implementing thermal private power developments, the Philippines now offers many attractive opportunities to exploit its tremendous potential in the hydropower sector.

  20. Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation

    E-Print Network [OSTI]

    Chen, Mark

    N-linked glycosylation modulates protein folding and stability through a variety of mechanisms. As such there is considerable interest in the development of general rules to predict the structural consequences of site-specific ...

  1. Liga developer apparatus system

    DOE Patents [OSTI]

    Boehme, Dale R. (Pleasanton, CA); Bankert, Michelle A. (San Francisco, CA); Christenson, Todd R. (Albuquerque, NM)

    2003-01-01

    A system to fabricate precise, high aspect ratio polymeric molds by photolithograpic process is described. The molds for producing micro-scale parts from engineering materials by the LIGA process. The invention is a developer system for developing a PMMA photoresist having exposed patterns comprising features having both very small sizes, and very high aspect ratios. The developer system of the present invention comprises a developer tank, an intermediate rinse tank and a final rinse tank, each tank having a source of high frequency sonic agitation, temperature control, and continuous filtration. It has been found that by moving a patterned wafer, through a specific sequence of developer/rinse solutions, where an intermediate rinse solution completes development of those portions of the exposed resist left undeveloped after the development solution, by agitating the solutions with a source of high frequency sonic vibration, and by adjusting and closely controlling the temperatures and continuously filtering and recirculating these solutions, it is possible to maintain the kinetic dissolution of the exposed PMMA polymer as the rate limiting step.

  2. Microsystem product development.

    SciTech Connect (OSTI)

    Polosky, Marc A.; Garcia, Ernest J.

    2006-04-01

    Over the last decade the successful design and fabrication of complex MEMS (MicroElectroMechanical Systems), optical circuits and ASICs have been demonstrated. Packaging and integration processes have lagged behind MEMS research but are rapidly maturing. As packaging processes evolve, a new challenge presents itself, microsystem product development. Product development entails the maturation of the design and all the processes needed to successfully produce a product. Elements such as tooling design, fixtures, gages, testers, inspection, work instructions, process planning, etc., are often overlooked as MEMS engineers concentrate on design, fabrication and packaging processes. Thorough, up-front planning of product development efforts is crucial to the success of any project.

  3. Microsystem Product Development

    E-Print Network [OSTI]

    Polosky, M -A

    2007-01-01

    Over the last decade the successful design and fabrication of complex MEMS (MicroElectroMechanical Systems), optical circuits and ASICs have been demonstrated. Packaging and integration processes have lagged behind MEMS research but are rapidly maturing. As packaging processes evolve, a new challenge presents itself, microsystem product development. Product development entails the maturation of the design and all the processes needed to successfully produce a product. Elements such as tooling design, fixtures, gages, testers, inspection, work instructions, process planning, etc., are often overlooked as MEMS engineers concentrate on design, fabrication and packaging processes. Thorough, up-front planning of product development efforts is crucial to the success of any project.

  4. Sustainable Development Conference

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

    The event drew more that 1,000 participants and speakers, including the presidents of Liberia, Malta and Rwanda; the First Lady of Panama; and U.N. Sustainable Development...

  5. Political elites and development

    E-Print Network [OSTI]

    Querubín Borrero, Pablo

    2010-01-01

    This dissertation consists of three essays on the behavior of political elites and their effect on economic development. The first two chapters focus on political dynasties in the Philippines while the third chapter analyzes ...

  6. Essays on development finance

    E-Print Network [OSTI]

    Fischer, Gregory M. (Gregory Mark)

    2008-01-01

    This thesis consists of three essays that examine investment choices in less developed countries. Chapter 1 examines how the structure of existing microfinance contracts may discourage risky but high-expected return ...

  7. Essays on development economics

    E-Print Network [OSTI]

    Ruthbah, Ummul Hasanath

    2007-01-01

    This dissertation is a collection of three independent papers in empirical development economics. The first chapter studies the effect of a family planning program in Bangladesh, which successfully reduced fertility, on ...

  8. Acquisition Career Development Program

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2004-04-19

    This Order establishes training and certification requirements and career development programs under the Acquisition Career Development (ACD) Program for DOE and NNSA acquisition workforce. The acquisition workforce includes contracting, purchasing, personal property management, program management, Contracting Officers and Contracting Officer Representatives. The ACD Program implements the Office of Federal Procurement Policy (OFPP) requirements, Federal Acquisition Regulation (FAR) requirements, Federal Acquisition Reform Act (FARA) requirements, and the objectives of Executive Order (E.O.) 129231, Federal Procurement Reform, dated 10-13-1994. This order cancels DOE O 361.1, Acquisition Career Development Program, dated 11-10-99, AND Acquisition Letter 2003-05, Personal Property Management Career Development, Training, and Certification Program, dated 9-10-03. Cancels DOE O 361.1 Chg 2. Canceled by DOE O 361.1B.

  9. Arthropod Growth & Development

    E-Print Network [OSTI]

    Brown, Christopher A.

    pathways in insects Ametabolous insects resemble small adults at hatching, lacking only fully developed, a stadium 1st instar may not always be the one to emerge from egg In nearly all terrestrial arthropods

  10. Sustaining development in Detroit

    E-Print Network [OSTI]

    Resnick, Noah Samuel, 1977-

    2004-01-01

    The intent of this thesis is to propose a strategy for stabilizing and increasing the disparate pieces of development that form the traces of the once great industrial city of Detroit. It focuses primarily on Fordism as a ...

  11. Training and Development

    E-Print Network [OSTI]

    California at Santa Cruz, University of

    Training and Development Administration Assistant Vice Chancellor Lori Castro VC Business Senior Manager Conflict Resolution Nancy Heischman Training Coordinator Vacant Principal Technical Training Consultant Frank Widman Health Care Facilitator / Interim Benefits Manager Frank Trueba Disability

  12. Development of Portable Detectors

    SciTech Connect (OSTI)

    None

    2006-12-01

    The purpose of this Cooperative Research and Development Agreement (CRADA) between UT-Battelle, LLC (the “Contractor”) and Sense Holdings, Inc. (the “Participant”) was for the development of hand-held detectors with high sensitivity and selectivity for the detection of explosives, toxic industrial chemicals and materials, and other materials of interest for security applications. The two parties built a series of demonstration and prototype handheld sensors based upon micoelectromechanical systems (MEMS) with electronic readout.

  13. Acquisition Career Development Program

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2003-06-13

    To set forth requirements and responsibilities for the Department of Energy (DOE) Acquisition Career Development (ACD) Program, which implements Office of Federal Procurement Policy (OFPP) requirements, Federal Acquisition Regulation (FAR) requirements, Federal Acquisition Reform Act (FARA) requirements, and the career development objectives of Executive Order (E.O.) 12931. Change 1 approved 12-20-2001. Change 2 approved 06-13-03. Cancels DOE O 361.1 Chg 1. Canceled by DOE O 361.1A.

  14. Acquisition Career Development Program

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2001-12-20

    To set forth requirements and responsibilities for the Department of Energy (DOE) Acquisition Career Development (ACD) Program, which implements Office of Federal Procurement Policy (OFPP) requirements, Federal Acquisition Regulation (FAR) requirements, Federal Acquisition Reform Act (FARA) requirements, and the career development objectives of Executive Order (E.O.) 12931. Change 1 approved 12-20-2001. Cancels DOE O 361.1. Canceled by DOE O 361.1 Chg 2.

  15. Review: Theories of Sustainable Development

    E-Print Network [OSTI]

    Laberge, Yves

    2015-01-01

    Review: Theories of Sustainable Development Edited By JudithTheories of Sustainable Development. Abingdon: Routledge,Routledge Studies in Sustainable Development. Theories of

  16. Sustainable Development Summer Intern Report 2013 Sustainable Development Summer Intern

    E-Print Network [OSTI]

    Sustainable Development Summer Intern Report 2013 Sustainable Development Summer Intern Final amongst university's invested in sustainable development. Our small but mighty size allows us to build through positive sustainable practices. As the Sustainable Development Summer Intern I am fortunate enough

  17. Sustainable Development Summer Intern Report 2010 Sustainable Development Summer Intern

    E-Print Network [OSTI]

    Sustainable Development Summer Intern Report 2010 1 Sustainable Development Summer Intern Final of Bishop's University. The role of the Sustainable Development Summer Intern (SDSI) is to coordinate and organize sustainable development information and activities during the summer months. Ensuring

  18. Emergency Response Guideline Development

    SciTech Connect (OSTI)

    Gary D. Storrick

    2007-09-30

    Task 5 of the collaborative effort between ORNL, Brazil, and Westinghouse for the International Nuclear Energy Research Initiative entitled “Development of Advanced Instrumentation and Control for an Integrated Primary System Reactor” focuses on operator control and protection system interaction, with particular emphasis on developing emergency response guidelines (ERGs). As in the earlier tasks, we will use the IRIS plant as a specific example of an integrated primary system reactor (IPSR) design. The present state of the IRIS plant design – specifically, the lack of a detailed secondary system design – precludes establishing detailed emergency procedures at this time. However, we can create a structure for their eventual development. This report summarizes our progress to date. Section 1.2 describes the scope of this effort. Section 2 compares IPSR ERG development to the recent AP1000 effort, and identifies three key plant differences that affect the ERGs and control room designs. The next three sections investigate these differences in more detail. Section 3 reviews the IRIS Safety-by-Design™ philosophy and its impact on the ERGs. Section 4 looks at differences between the IRIS and traditional loop PWR I&C Systems, and considers their implications for both control room design and ERG development. Section 5 examines the implications of having one operating staff control multiple reactor units. Section 6 provides sample IRIS emergency operating procedures (EOPs). Section 7 summarizes our conclusions.

  19. Economic Development | ornl.gov

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

    Economic Development Carbon Fiber Cluster Strategy Additive Manufacturing Cluster Strategy Entrepreneurial Development Programs Oak Ridge Science and Technology Park Economic...

  20. Power Systems Development Facility

    SciTech Connect (OSTI)

    Southern Company Services

    2009-01-31

    In support of technology development to utilize coal for efficient, affordable, and environmentally clean power generation, the Power Systems Development Facility (PSDF), located in Wilsonville, Alabama, has routinely demonstrated gasification technologies using various types of coals. The PSDF is an engineering scale demonstration of key features of advanced coal-fired power systems, including a Transport Gasifier, a hot gas particulate control device, advanced syngas cleanup systems, and high-pressure solids handling systems. This final report summarizes the results of the technology development work conducted at the PSDF through January 31, 2009. Twenty-one major gasification test campaigns were completed, for a total of more than 11,000 hours of gasification operation. This operational experience has led to significant advancements in gasification technologies.

  1. Graphite Technology Development Plan

    SciTech Connect (OSTI)

    W. Windes; T. Burchell; M.Carroll

    2010-10-01

    The Next Generation Nuclear Plant (NGNP) will be a helium-cooled High Temperature Gas Reactor (HTGR) with a large graphite core. Graphite physically contains the fuel and comprises the majority of the core volume. Graphite has been used effectively as a structural and moderator material in both research and commercial high-temperature gas-cooled reactors. This development has resulted in graphite being established as a viable structural material for HTGRs. While the general characteristics necessary for producing nuclear grade graphite are understood, historical “nuclear” grades no longer exist. New grades must be fabricated, characterized, and irradiated to demonstrate that current grades of graphite exhibit acceptable non-irradiated and irradiated properties upon which the thermomechanical design of the structural graphite in NGNP is based. This Technology Development Plan outlines the research and development (R&D) activities and associated rationale necessary to qualify nuclear grade graphite for use within the NGNP reactor.

  2. Hydropower research and development

    SciTech Connect (OSTI)

    NONE

    1997-03-01

    This report is a compilation of information on hydropower research and development (R and D) activities of the Federal government and hydropower industry. The report includes descriptions of on-going and planned R and D activities, 1996 funding, and anticipated future funding. Summary information on R and D projects and funding is classified into eight categories: fish passage, behavior, and response; turbine-related; monitoring tool development; hydrology; water quality; dam safety; operations and maintenance; and water resources management. Several issues in hydropower R and D are briefly discussed: duplication; priorities; coordination; technical/peer review; and technology transfer/commercialization. Project information sheets from contributors are included as an appendix.

  3. Cities and Sustainable Development

    E-Print Network [OSTI]

    . The information and communications revolution has spawned the idea of the "smart city," which places the relevant technologies at the heart of systems that collect and respond to information: smart power grids, smartCities and Sustainable Development By: Jeffrey D. Sachs NOV 25, 2013 NEW YORK ­ Tacloban

  4. JAGUAR developer's manual.

    SciTech Connect (OSTI)

    Chan, Ethan

    2011-06-01

    JAGUAR (JAva GUi for Applied Research) is a Java software tool providing an advanced text editor and graphical user interface (GUI) to manipulate DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) input specifications. This document focuses on the technical background necessary for a developer to understand JAGUAR.

  5. Accelerator Development @ Daresbury Laboratory

    E-Print Network [OSTI]

    -injectors ­ Superconducting RF acceleration ­ Cryogenic systems ­ Advanced diagnostics ­ Free Electron Lasers ­ Photon beam radioisotopes. 2 Treatment & Diagnostics #12;Basic Accelerator Configuration 3 Beam Source Low Energy Capture electron beam technology development. 4 Booster Compressor IR-FEL Photoinjector Laser Linac Acceleration

  6. Developing hydropower overseas

    SciTech Connect (OSTI)

    Smith, W.B. (Benham-Holway Power Group, Tulsa, OK (United States))

    1991-10-01

    This article examines how the National Hydropower Association (NHA) has found ways to support its members who desire to expand their business programs to foreign markets through participation in a wide range of government programs. The topics of the article include the market in developing countries, the certificate of review, products and services, and domestic and international competition.

  7. ECH Technology Development

    SciTech Connect (OSTI)

    Temkin, Richard

    2014-12-24

    Electron Cyclotron Heating (ECH) is needed for plasma heating, current drive, plasma stability control, and other applications in fusion energy sciences research. The program of fusion energy sciences supported by U. S. DOE, Office of Science, Fusion Energy Sciences relies on the development of ECH technology to meet the needs of several plasma devices working at the frontier of fusion energy sciences research. The largest operating ECH system in the world is at DIII-D, consisting of six 1 MW, 110 GHz gyrotrons capable of ten second pulsed operation, plus two newer gyrotrons. The ECH Technology Development research program investigated the options for upgrading the DIII-D 110 GHz ECH system. Options included extending present-day 1 MW technology to 1.3 – 1.5 MW power levels or developing an entirely new approach to achieve up to 2 MW of power per gyrotron. The research consisted of theoretical research and designs conducted by Communication and Power Industries of Palo Alto, CA working with MIT. Results of the study would be validated in a later phase by research on short pulse length gyrotrons at MIT and long pulse / cw gyrotrons in industry. This research follows a highly successful program of development that has led to the highly reliable, six megawatt ECH system at the DIII-D tokamak. Eventually, gyrotrons at the 1.5 megawatt to multi-megawatt power level will be needed for heating and current drive in large scale plasmas including ITER and DEMO.

  8. International Policy International Development

    E-Print Network [OSTI]

    Watson, Andrew

    Research Strategy 2006-2009 International Policy Energy Adaptation International Development Coasts Change Research. Our strategy builds upon our previous work on integrated assessment, energy, adaptation of time. In this spirit, the Centre reconfirms its vision statement: "The Tyndall Centre is the UK network

  9. Renewable Energy Economic Development

    E-Print Network [OSTI]

    Renewable Energy Economic Development Dick Sheehy & Nate Monosoff, CH2M HILL March, 2010 #12;Contents 1. Who is CH2M HILL? 2. Why Do We Need Renewables? 3. Where Is The Wind Blowing? 4. Where Is The Sun Shining? 5. How To Catch Some Rays? 6. Renewable Related 2 Proprietary & Confidential #12;Where

  10. Leadership Development Readings

    Broader source: Energy.gov [DOE]

    The Leadership Development Readings is a comprehensive list of more than 700 ECQ-related leadership readings organized by ECQ intended to assist all current and aspiring government leaders’ efforts to broaden their organizational and management experience and expand their knowledge in the five Executive Core Qualifications as well as Fundamental Competencies.

  11. Developing the Environmental Health

    E-Print Network [OSTI]

    Developing the Environmental Health Workforce Direct from CDC's Environmental Health Services Branch CAPT Michael E. Herring, R.E.H.S., M.P.H. Editor's note: NEHA strives to provide up-to-date and relevant information on environmental health and to build part- nerships

  12. Energy Efficiency Project Development

    SciTech Connect (OSTI)

    IUEP

    2004-03-01

    The International Utility Efficiency Partnerships, Inc. (IUEP) has been a leader among the industry groups that have supported voluntary initiatives to promote international energy efficiency projects and address global climate change. The IUEP maintains its leadership by both supporting international greenhouse gas (GHG) reduction projects under the auspices of the U.S. Department of Energy (DOE) and by partnering with U.S. and international organizations to develop and implement strategies and specific energy efficiency projects. The goals of the IUEP program are to (1) provide a way for U.S. industry to maintain a leadership role in international energy efficiency infrastructure projects; (2) identify international energy project development opportunities to continue its leadership in supporting voluntary market-based mechanisms to reduce GHG emissions; and (3) demonstrate private sector commitment to voluntary approaches to global climate issues. The IUEP is dedicated to identifying, promoting, managing, and assisting in the registration of international energy efficiency projects that result in demonstrated voluntary reductions of GHG emissions. This Final Technical Report summarizes the IUEP's work in identifying, promoting, managing, and assisting in development of these projects and IUEP's effort in creating international cooperative partnerships to support project development activities that develop and deploy technologies that (1) increase efficiency in the production, delivery and use of energy; (2) increase the use of cleaner, low-carbon fuels in processing products; and (3) capture/sequester carbon gases from energy systems. Through international cooperative efforts, the IUEP intends to strengthen partnerships for energy technology innovation and demonstration projects capable of providing cleaner energy in a cost-effective manner. As detailed in this report, the IUEP met program objectives and goals during the reporting period January 1, 2001 through December 31, 2002. At the request of the DOE, we have also included in this report additional activities during the reporting period January, 1999 through January, 2001. This additional information had been reported earlier in the Final Technical Reports that summarized activities undertaken in those earlier periods.

  13. e+ e- Factory Developments

    SciTech Connect (OSTI)

    Sullivan, Michael; /SLAC

    2010-08-26

    The impressive performance of current (KEKB) and recent (PEP-II) B-Factory colliders has increased interest in developing even higher luminosity B-factories. Two new designs are being developed (SuperKEKB and SuperB). Both designs plan to deliver a luminosity in the range of 1 x 10{sup 36} cm{sup -2}s{sup -1}, nearly 100 times the present B-factory level. Achieving this high luminosity requires high-current beams and short bunch lengths and/or a new way of colliding the beams. The SuperB design employs a crabbed magnetic waist with a large crossing angle and the SuperKEKB design is looking at crab cavities with high-current beams and/or a travelling focus. I describe the designs being studied to achieve the high luminosity needed for the next generation of B-Factories.

  14. ADVANCED SORBENT DEVELOPMENT PROGRAM

    SciTech Connect (OSTI)

    Unknown

    1998-06-16

    The overall objective of this program was to develop regenerable sorbents for use in the temperature range of 343 to 538 C (650 to 1000 F) to remove hydrogen sulfide (H{sub 2}S) from coal-derived fuel gases in a fluidized-bed reactor. The goal was to develop sorbents that are capable of reducing the H{sub 2}S level in the fuel gas to less than 20 ppmv in the specified temperature range and pressures in the range of 1 to 20 atmospheres, with chemical characteristics that permit cyclic regeneration over many cycles without a drastic loss of activity, as well as physical characteristics that are compatible with the fluidized bed application.

  15. Update on INSIGHTS Development

    SciTech Connect (OSTI)

    Not Listed; Eric Burgett

    2011-09-01

    INSIGHTS is a transformational separate effects testing capability to perform in situ irradiation studies and characterization of the microscale behavior of nuclear fuel materials under a wide variety of in-pile conditions. Separate effects testing including growth, irradiation, and monitoring of these materials, and encompasses the full science based approach for fuels development from the nanoscale to the mesoscale behavior of the sample material and other defects driven by the modeling and simulation efforts of INL.

  16. Issue Development sheet Example

    Broader source: Energy.gov [DOE]

    ISSUE DEVELOPMENT SHEET INFORMATION ONLY The information provided below indicates that a potential concern for finding has been identified. Please provide any objective evidence you may have that could either alleviate the concern or eliminate the finding. If no objective evidence is available/can be provided by the end of this audit (at the scheduled end of field work), this information will be included in the audit report and reported as a concern or an audit finding as appropriate.

  17. Acquisition Career Development Program

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    1999-11-10

    The Order implements the Department's Acquisition Career Development program, mandatory for professionals in the GS-1102 and 1105 occupational procurement series, as well as others with significant procurement responsibilities. The Order also ensures that members of the acquisition workforce are aware of and adhere to the mandatory training and certification requirements. Cancels Acquisition Letter 98-06. Canceled by DOE O 361.1 Chg 1.

  18. Developing the Business of Technology

    E-Print Network [OSTI]

    Finley Jr., Russell L.

    -a-Company Find-a-Company vs. #12;Business Model What Combination of Business Activities? Research ProductDeveloping the Business of Technology #12;Developing the Business of Technology Universities Business Development Year 1 Year 2 Year 3 Year 4 Product Development Business Development Naïve Planning

  19. Central DevelopmentCentral Development LaboratoryLaboratory

    E-Print Network [OSTI]

    Groppi, Christopher

    efficiencyImprove production efficiency Develop InP amplifiers forDevelop InP amplifiers for bands down to 1

  20. NOx Sensor Development

    SciTech Connect (OSTI)

    Woo, L Y; Glass, R S

    2010-11-01

    NO{sub x} compounds, specifically NO and NO{sub 2}, are pollutants and potent greenhouse gases. Compact and inexpensive NO{sub x} sensors are necessary in the next generation of diesel (CIDI) automobiles to meet government emission requirements and enable the more rapid introduction of more efficient, higher fuel economy CIDI vehicles. Because the need for a NO{sub x} sensor is recent and the performance requirements are extremely challenging, most are still in the development phase. Currently, there is only one type of NO{sub x} sensor that is sold commercially, and it seems unlikely to meet more stringent future emission requirements. Automotive exhaust sensor development has focused on solid-state electrochemical technology, which has proven to be robust for in-situ operation in harsh, high-temperature environments (e.g., the oxygen stoichiometric sensor). Solid-state sensors typically rely on yttria-stabilized zirconia (YSZ) as the oxygen-ion conducting electrolyte and then target different types of metal or metal-oxide electrodes to optimize the response. Electrochemical sensors can be operated in different modes, including amperometric (a current is measured) and potentiometric (a voltage is measured), both of which employ direct current (dc) measurements. Amperometric operation is costly due to the electronics necessary to measure the small sensor signal (nanoampere current at ppm NO{sub x} levels), and cannot be easily improved to meet the future technical performance requirements. Potentiometric operation has not demonstrated enough promise in meeting long-term stability requirements, where the voltage signal drift is thought to be due to aging effects associated with electrically driven changes, both morphological and compositional, in the sensor. Our approach involves impedancemetric operation, which uses alternating current (ac) measurements at a specified frequency. The approach is described in detail in previous reports and several publications. Briefly, impedancemetric operation has shown the potential to overcome the drawbacks of other approaches, including higher sensitivity towards NO{sub x}, better long-term stability, potential for subtracting out background interferences, total NO{sub x} measurement, and lower cost materials and operation. Past LLNL research and development efforts have focused on characterizing different sensor materials and understanding complex sensing mechanisms. Continued effort has led to improved prototypes with better performance, including increased sensitivity (to less than 5 ppm) and long-term stability, with more appropriate designs for mass fabrication, including incorporation of an alumina substrate with an imbedded heater. Efforts in the last year to further improve sensor robustness have led to successful engine dynamometer testing with prototypes mounted directly in the engine manifold. Previous attempts had required exhaust gases to be routed into a separate furnace for testing due to mechanical failure of the sensor from engine vibrations. A more extensive cross-sensitivity study was also undertaken this last year to examine major noise factors including fluctuations in water, oxygen, and temperature. The quantitative data were then used to develop a strategy using numerical algorithms to improve sensor accuracy. The ultimate goal is the transfer of this technology to a supplier for commercialization. Due to the recent economic downturn, suppliers are demanding more comprehensive data and increased performance analysis before committing their resources to take the technology to market. Therefore, our NO{sub x} sensor work requires a level of technology development more thorough and extensive than ever before. The objectives are: (1) Develop an inexpensive, rapid-response, high-sensitivity and selective electrochemical sensor for oxides of nitrogen (NO{sub x}) for compression-ignition, direct-injection (CIDI) exhaust gas monitoring; (2) Explore and characterize novel, effective sensing methodologies based on impedance measurements and designs and manufacturing metho

  1. Product development practices that matter

    E-Print Network [OSTI]

    Gupta, Nisheeth

    2010-01-01

    Product Development consists of activities to transforms a market opportunity and technological innovation into successful products. Several waves of improvements in technological innovation and product development have ...

  2. Developer Resources | Department of Energy

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

    Library EPA: Developer Resources EPA: Data Finder EPA: eGrid Electricity Generation Environmental Impact Data Labor: Developer Tools NOAA: Climate Data Energy Department EIA:...

  3. Advanced Integrated Systems Technology Development

    E-Print Network [OSTI]

    2013-01-01

    Renewable Energy Technologies Transportation Advanced Integrated Systems Technology Development is the final report for the Advanced Integrated Systems Technology Development project (

  4. Conservation and economic development

    SciTech Connect (OSTI)

    Sullivan, M.J.

    1992-05-01

    This oral presentation is about the Espanola Power Savers Project which involves both the utility and for the community. I`m going to spend much of my time today discussing why this project makes sense for the community, but I would like to start with a brief word about why community-based conservation makes sense for utilities. A number of reasons are listed to show why conservation is today`s energy resource of choice. But if, for a moment, we take that as a given and ask why community-based conservation programs are the right way to develop that resource, the answer is simple: They work!

  5. Conservation and economic development

    SciTech Connect (OSTI)

    Sullivan, M.J.

    1992-05-01

    This oral presentation is about the Espanola Power Savers Project which involves both the utility and for the community. I'm going to spend much of my time today discussing why this project makes sense for the community, but I would like to start with a brief word about why community-based conservation makes sense for utilities. A number of reasons are listed to show why conservation is today's energy resource of choice. But if, for a moment, we take that as a given and ask why community-based conservation programs are the right way to develop that resource, the answer is simple: They work

  6. Photonics Research and Development

    SciTech Connect (OSTI)

    Pookpanratana, Sujitra; Shlayan, Neveen; Venkat, Rama; Das, Bisjwajit; Boehm, Bob; Heske, Clemens; Fraser, Donald; Moustakas, Theodore

    2010-01-15

    During the period August 2005 through October 2009, the UNLV Research Foundation (UNLVRF), a non-profit affiliate of the University of Nevada, Las Vegas (UNLV), in collaboration with UNLVâ??s Colleges of Science and Engineering; Boston University (BU); Oak Ridge National Laboratory (ORNL); and Sunlight Direct, LLC, has managed and conducted a diverse and comprehensive research and development program focused on light-emitting diode (LED) technologies that provide significantly improved characteristics for lighting and display applications. This final technical report provides detailed information on the nature of the tasks, the results of the research, and the deliverables. It is estimated that about five percent of the energy used in the nation is for lighting homes, buildings and streets, accounting for some 25 percent of the average homeâ??s electric bill. However, the figure is significantly higher for the commercial sector. About 60 percent of the electricity for businesses is for lighting. Thus replacement of current lighting with solid-state lighting technology has the potential to significantly reduce this nationâ??s energy consumption â?? by some estimates, possibly as high as 20%. The primary objective of this multi-year R&D project has been to develop and advance lighting technologies to improve national energy conversion efficiencies; reduce heat load; and significantly lower the cost of conventional lighting technologies. The UNLVRF and its partners have specifically focused these talents on (1) improving LED technologies; (2) optimizing hybrid solar lighting, a technology which potentially offers the benefits of blending natural with artificial lighting systems, thus improving energy efficiency; and (3) building a comprehensive academic infrastructure within UNLV which concentrates on photonics R&D. Task researchers have reported impressive progress in (1) the development of quantum dot laser emitting diodes (QDLEDs) which will ultimately improve energy efficiency and lower costs for display and lighting applications (UNLV College of Engineering); (2) advancing green LED technology based on the Indium-Gallium-Nitride system (BU), thus improving conversion efficiencies; (3) employing unique state-of-the-art X-ray, electron and optical spectroscopies with microscopic techniques to learn more about the electronic structure of materials and contacts in LED devices (UNLV College of Science); (4) establishing a UNLV Display Lighting Laboratory staffed with a specialized team of academic researchers, students and industrial partners focused on identifying and implementing engineering solutions for lighting display-related problems; and (5) conducting research, development and demonstration for HSL essential to the resolution of technological barriers to commercialization.

  7. Agricultural Market Development Abroad. 

    E-Print Network [OSTI]

    Kirby, James E.; McNeely, John G.

    1965-01-01

    for the repeal of the Smoot-Hawley Act in 1934 vith the passage of the Reciprocal Trade Agreement .kt. This new act marked a beginning of a liberal 1 ~rade policy based on reciprocal trade agreements. The Trade Expansion Act of 1962 was the culmin- ation... of organizations with which FAS entered into planning and (5) research in the physical sciences as Italian market development activities. a broad and cautious generalization to include al- l moft any type of study of the physical sciences. not 1. The ~ational...

  8. WINDExchange: Workforce Development

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservationBio-Inspired SolarAbout /Two0 -UsingHeatInformationDevelopment Resources

  9. SRNL LDRD - Developed Technologies

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis of Protein1-0845*RV6 Commercial value of4Developed Technologies

  10. Economic Development - SRSCRO

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory ofDid you not find what you wereDisclaimersMailEconomic Development As the

  11. Exciting new PDSF developments

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submitKansasCommunitiesof Energy8) Wigner HomeExampleDevelopments UsingExciting

  12. Development of active porous medium filters based on plasma textiles

    SciTech Connect (OSTI)

    Kuznetsov, Ivan A.; Saveliev, Alexei V.; Rasipuram, Srinivasan; Kuznetsov, Andrey V.; Brown, Alan; Jasper, Warren

    2012-05-15

    Inexpensive, flexible, washable, and durable materials that serve as antimicrobial filters and self-decontaminating fabrics are needed to provide active protection to people in areas regularly exposed to various biohazards, such as hospitals and bio research labs working with pathogens. Airlines and cruise lines need such material to combat the spread of infections. In households these materials can be used in HVAC filters to fight indoor pollution, which is especially dangerous to people suffering from asthma. Efficient filtering materials are also required in areas contaminated by other types of hazardous dust particulates, such as nuclear dust. The primary idea that guided the undertaken study is that a microplasma-generating structure can be embedded in a textile fabric to generate a plasma sheath (''plasma shield'') that kills bacterial agents coming in contact with the fabric. The research resulted in the development of a plasma textile that can be used for producing new types of self-decontaminating garments, fabrics, and filter materials, capable of activating a plasma sheath that would filter, capture, and destroy any bacteriological agent deposited on its surface. This new material relies on the unique antimicrobial and catalytic properties of cold (room temperature) plasma that is benign to people and does not cause thermal damage to many polymer textiles, such as Nomex and polypropylene. The uniqueness of cold plasma as a disinfecting agent lies in the inability of bacteria to develop resistance to plasma exposure, as they can for antibiotics. Plasma textiles could thus be utilized for microbial destruction in active antimicrobial filters (for continuous decontamination and disinfection of large amounts of air) as well as in self-decontaminating surfaces and antibacterial barriers (for example, for creating local antiseptic or sterile environments around wounds and burns).

  13. Department of Development Sociology Development Sociology Minor Application

    E-Print Network [OSTI]

    Chen, Tsuhan

    - Rethinking Global Development DSOC 3240 ­ Environment and Society DSOC 3311 - Environmental Governance DSOC

  14. MARSAME Develop A Survey Design 4 DEVELOP A SURVEY DESIGN

    E-Print Network [OSTI]

    MARSAME Develop A Survey Design 4 DEVELOP A SURVEY DESIGN 4.1 Introduction Once a decision rule has been developed, a disposition survey can be designed for the impacted materials and equipment (M costly and time-consuming development of redundant survey designs. The evaluation of existing SOPs

  15. Inter-American Development Bank Sustainable Development Department

    E-Print Network [OSTI]

    Inter-American Development Bank Sustainable Development Department Environment Division Forest Correa Pertti Veijalainen Harri Ahveninen Inter-American Development Bank Washington, D.C. Sustainable. At the IDB the work was supervised by Kari Keipi of the Sustainable Development Department (SDS). Bank staff

  16. Downhole Fluid Analyzer Development

    SciTech Connect (OSTI)

    Bill Turner

    2006-11-28

    A novel fiber optic downhole fluid analyzer has been developed for operation in production wells. This device will allow real-time determination of the oil, gas and water fractions of fluids from different zones in a multizone or multilateral completion environment. The device uses near infrared spectroscopy and induced fluorescence measurement to unambiguously determine the oil, water and gas concentrations at all but the highest water cuts. The only downhole components of the system are the fiber optic cable and windows. All of the active components--light sources, sensors, detection electronics and software--will be located at the surface, and will be able to operate multiple downhole probes. Laboratory testing has demonstrated that the sensor can accurately determine oil, water and gas fractions with a less than 5 percent standard error. Once installed in an intelligent completion, this sensor will give the operating company timely information about the fluids arising from various zones or multilaterals in a complex completion pattern, allowing informed decisions to be made on controlling production. The research and development tasks are discussed along with a market analysis.

  17. Eltron Research & Development

    SciTech Connect (OSTI)

    Evenson, Carl; Mackay, Richard; Faull, John

    2014-03-01

    This topical report covers technical work conducted under contract DE-FC26-05NT42469 between FY06 Q1 through FY14 Q2. The project evolved through several budget periods, budget revisions and continuation applications. This report covers work performed under the “base” program. In 2010 ARRA funding was added to the project. A separate report covering the ARRA portion of the project was submitted to DOE. The original project was focused on research and development for scale-up of hydrogen separation membrane for a FutureGen type power plant. The work included membrane testing and evaluation of metal alloy flat plates vs. tubes and metal membranes vs. cermet membranes. In addition, economic analysis and process modeling was performed. The original project team included CoorsTek, NORAM, and Praxair. In FY10Q2 a continuation application was filed for conducting a scale-up test at Eastman Chemical. In this part of the project a Subscale Engineering Prototype (SEP) membrane skid was designed, fabricated, and operated on a gasified coal slip-stream on Eastman’s site in Kingsport, TN. Following operation, the project was reorganized and a second continuation application with a new statement of work was initiated in FY12Q1. Finally, based on DOE’s decision not to proceed with a Process Development Unit (PDU) field test, a third continuation application and statement of work was initiated in FY13Q1 to close out the project.

  18. Advanced Hydrogen Turbine Development

    SciTech Connect (OSTI)

    Joesph Fadok

    2008-01-01

    Siemens has developed a roadmap to achieve the DOE goals for efficiency, cost reduction, and emissions through innovative approaches and novel technologies which build upon worldwide IGCC operational experience, platform technology, and extensive experience in G-class operating conditions. In Phase 1, the technologies and concepts necessary to achieve the program goals were identified for the gas turbine components and supporting technology areas and testing plans were developed to mitigate identified risks. Multiple studies were conducted to evaluate the impact in plant performance of different gas turbine and plant technologies. 2015 gas turbine technologies showed a significant improvement in IGCC plant efficiency, however, a severe performance penalty was calculated for high carbon capture cases. Thermodynamic calculations showed that the DOE 2010 and 2015 efficiency targets can be met with a two step approach. A risk management process was instituted in Phase 1 to identify risk and develop mitigation plans. For the risks identified, testing and development programs are in place and the risks will be revisited periodically to determine if changes to the plan are necessary. A compressor performance prediction has shown that the design of the compressor for the engine can be achieved with additional stages added to the rear of the compressor. Tip clearance effects were studied as well as a range of flow and pressure ratios to evaluate the impacts to both performance and stability. Considerable data was obtained on the four candidate combustion systems: diffusion, catalytic, premix, and distributed combustion. Based on the results of Phase 1, the premixed combustion system and the distributed combustion system were chosen as having the most potential and will be the focus of Phase 2 of the program. Significant progress was also made in obtaining combustion kinetics data for high hydrogen fuels. The Phase 1 turbine studies indicate initial feasibility of the advanced hydrogen turbine that meets the aggressive targets set forth for the advanced hydrogen turbine, including increased rotor inlet temperature (RIT), lower total cooling and leakage air (TCLA) flow, higher pressure ratio, and higher mass flow through the turbine compared to the baseline. Maintaining efficiency with high mass flow Syngas combustion is achieved using a large high AN2 blade 4, which has been identified as a significant advancement beyond the current state-of-the-art. Preliminary results showed feasibility of a rotor system capable of increased power output and operating conditions above the baseline. In addition, several concepts were developed for casing components to address higher operating conditions. Rare earth modified bond coat for the purpose of reducing oxidation and TBC spallation demonstrated an increase in TBC spallation life of almost 40%. The results from Phase 1 identified two TBC compositions which satisfy the thermal conductivity requirements and have demonstrated phase stability up to temperatures of 1850 C. The potential to join alloys using a bonding process has been demonstrated and initial HVOF spray deposition trials were promising. The qualitative ranking of alloys and coatings in environmental conditions was also performed using isothermal tests where significant variations in alloy degradation were observed as a function of gas composition. Initial basic system configuration schematics and working system descriptions have been produced to define key boundary data and support estimation of costs. Review of existing materials in use for hydrogen transportation show benefits or tradeoffs for materials that could be used in this type of applications. Hydrogen safety will become a larger risk than when using natural gas fuel as the work done to date in other areas has shown direct implications for this type of use. Studies were conducted which showed reduced CO{sub 2} and NOx emissions with increased plant efficiency. An approach to maximize plant output is needed in order to address the DOE turbine goal for 20-30% reduction o

  19. Ripeness sensor development

    SciTech Connect (OSTI)

    Not Available

    1992-11-01

    About 20--25% of the total production of fruits and vegetables in the USA must be discarded after harvest About 25--30% of this loss is the result of over-ripening and this loss represents about 8.39 [times] 10[sup 12] BTU of invested energy every year. This invested energy could be saved by non-destructive ripeness sensing. Sweetness is an important indicator of fruit quality and highly correlated with ripeness in most fruits. Research to develop a non-destructive fruit ripeness sensor has been conducted in the Agricultural Engineering Department at Purdue University. It is based on [sup 1]H-MR (proton Magnetic Resonance). A first generation prototype of the ripeness sensor based on [sup 1]H-MR was built and tested with. Results show that the sensor can discriminate small fruit (0.75 in diameter or smaller) differing in sugar content by 6%. This prototype can separate the fruit into at least two groups: one ripe and the other not ripe. The estimated cost for such a ripeness sensor is around $4,000. The signal sensitivity of the prototype can be improved to enable it to differentiate between fruits varying in sugar content by only 1 or 2% by using water peak suppression techniques to recover relatively weak sugar resonance signals in intact fruits, modifying circuits to eliminate noise, leakage and distortion of input/output signals, improving the magnetic console to get a higher magnetic field and better homogeneity, and designing a probe to achieve a higher signal-to-noise (S/N) ratio. As research continues a second generation ripeness sensor will be developed which will incorporate many of the improvements and which will be suitable for commercial use. Additional research will allow application of the technique to a wider range of fruit sizes (from blueberries to watermelons). This report describes estimated energy savings, feasibility studies, development of the initial prototype, and preliminary evaluation of the first generation prototype.

  20. Breakthrough Vehicle Development - Fuel Cells

    Fuel Cell Technologies Publication and Product Library (EERE)

    Document describing research and development program for fuel cell power systems for transportation applications.

  1. Process Development for Nanostructured Photovoltaics

    SciTech Connect (OSTI)

    None

    2011-05-31

    Fact sheet describing low-cost nanofabrication method to develop nanostructured, dye-sensitized solar cells

  2. RESEARCH AND DEVELOPMENT ACTIVITIES IN

    E-Print Network [OSTI]

    Hasýrcý, Vasýf

    COOPERATION DEVELOPMENT PROGRAMMES FOR CENTERS (MGEP) 35 INITIATIVE FOR RENEWABLE ENERGY, ECOSYSTEMS BY THE MINISTRY OF DEVELOPMENT 14 RESEARCH INFRASTRUCTURE DEVELOPMENT PROJECTS 15 NATIONAL AND INTERNATIONAL-going research and development projects in METU, excluding the projects supported within BAP (Scientific Research

  3. Alloys in energy development

    SciTech Connect (OSTI)

    Frost, B.R.T.

    1984-02-01

    The development of new and advanced energy systems often requires the tailoring of new alloys or alloy combinations to meet the novel and often stringent requirements of those systems. Longer life at higher temperatures and stresses in aggressive environments is the most common goal. Alloy theory helps in achieving this goal by suggesting uses of multiphase systems and intermediate phases, where solid solutions were traditionally used. However, the use of materials under non-equilibrium conditions is now quite common - as with rapidly solidified metals - and the application of alloy theory must be modified accordingly. Under certain conditions, as in a reactor core, the rate of approach to equilibrium will be modified; sometimes a quasi-equilibrium is established. Thus an alloy may exhibit enhanced general diffusion at the same time as precipitate particles are being dispersed and solute atoms are being carried to vacancy sinks. We are approaching an understanding of these processes and can begin to model these complex systems.

  4. Advanced servomanipulator development

    SciTech Connect (OSTI)

    Kuban, D.P.

    1985-01-01

    The Advanced Servomanipulator (ASM) System consists of three major components: the ASM slave, the dual arm master controller (DAMC) or master, and the control system. The ASM is remotely maintainable force-reflecting servomanipulator developed at the Oak Ridge National Laboratory (ORNL) as part of the Consolidated Fuel Reprocessing Program. This new manipulator addresses requirements of advanced nuclear fuel reprocessing with emphasis on force reflection, remote maintainability, reliability, radiation tolerance, and corrosion resistance. The advanced servomanipulator is uniquely subdivided into remotely replaceable modules which will permit in situ manipulator repair by spare module replacement. Manipulator modularization and increased reliability are accomplished through a force transmission system that uses gears and torque tubes. Digital control algorithms and mechanical precision are used to offset the increased backlash, friction, and inertia resulting from the gear drives. This results in the first remotely maintainable force-reflecting servomanipulator in the world.

  5. Policy and IT Standards Development Process Development ApprovalInitiation

    E-Print Network [OSTI]

    New Mexico, University of

    Policy and IT Standards Development Process Development ApprovalInitiation Main Campus Health Sciences Audit Academic, Technology, Project, Legal or Administrative Need IT Standard or UNM Policy? Policy Office convenes committee, vetting process with stakeholders and groups Campus Executives, Regents

  6. Power Systems Development Facility

    SciTech Connect (OSTI)

    None

    2003-07-01

    This report discusses Test Campaign TC12 of the Kellogg Brown & Root, Inc. (KBR) Transport Gasifier train with a Siemens Westinghouse Power Corporation (SW) particle filter system at the Power Systems Development Facility (PSDF) located in Wilsonville, Alabama. The Transport Gasifier is an advanced circulating fluidized-bed reactor designed to operate as either a combustor or a gasifier using a particulate control device (PCD). While operating as a gasifier, either air or oxygen can be used as the oxidant. Test run TC12 began on May 16, 2003, with the startup of the main air compressor and the lighting of the gasifier start-up burner. The Transport Gasifier operated until May 24, 2003, when a scheduled outage occurred to allow maintenance crews to install the fuel cell test unit and modify the gas clean-up system. On June 18, 2003, the test run resumed when operations relit the start-up burner, and testing continued until the scheduled end of the run on July 14, 2003. TC12 had a total of 733 hours using Powder River Basin (PRB) subbituminous coal. Over the course of the entire test run, gasifier temperatures varied between 1,675 and 1,850 F at pressures from 130 to 210 psig.

  7. Developing product platforms:analysis of the development process

    E-Print Network [OSTI]

    Roveda, Marco

    1999-12-08

    Several authors have highlighted the importance of companies enhancing their new product development process through a multiproduct

  8. GEOGRAPHY 288: POPULATION, ENVIRONMENT, AND DEVELOPMENT IN THE DEVELOPING WORLD

    E-Print Network [OSTI]

    Lopez-Carr, David

    literature and 2) students receive feedback towards the improved development of their own research projectsGEOGRAPHY 288: POPULATION, ENVIRONMENT, AND DEVELOPMENT IN THE DEVELOPING WORLD Winter 2005 Class@geog.ucsb.edu phone: 4219 Office: Ellison 5714 Office hours: M 11-12; W 1-2 . NATURE OF THE COURSE This seminar

  9. IEED Tribal Energy Development to Build Tribal Energy Development Capacity

    Broader source: Energy.gov [DOE]

    The Assistant Secretary - Indian Affairs for the U.S. Department of the Interior, through the Office of Indian Energy and Economic Development, is soliciting grant proposals from Indian tribes to build tribal capacity for energy resource development or management under the Department of the Interior's (DOl's) Tribal Energy Development Capacity (TEDC) grant program.

  10. POWER SYSTEMS DEVELOPMENT FACILITY

    SciTech Connect (OSTI)

    Unknown

    2002-11-01

    This report discusses test campaign GCT4 of the Kellogg Brown & Root, Inc. (KBR) transport reactor train with a Siemens Westinghouse Power Corporation (Siemens Westinghouse) particle filter system at the Power Systems Development Facility (PSDF) located in Wilsonville, Alabama. The transport reactor is an advanced circulating fluidized-bed reactor designed to operate as either a combustor or a gasifier using one of two possible particulate control devices (PCDs). The transport reactor was operated as a pressurized gasifier during GCT4. GCT4 was planned as a 250-hour test run to continue characterization of the transport reactor using a blend of several Powder River Basin (PRB) coals and Bucyrus limestone from Ohio. The primary test objectives were: Operational Stability--Characterize reactor loop and PCD operations with short-term tests by varying coal-feed rate, air/coal ratio, riser velocity, solids-circulation rate, system pressure, and air distribution. Secondary objectives included the following: Reactor Operations--Study the devolatilization and tar cracking effects from transient conditions during transition from start-up burner to coal. Evaluate the effect of process operations on heat release, heat transfer, and accelerated fuel particle heat-up rates. Study the effect of changes in reactor conditions on transient temperature profiles, pressure balance, and product gas composition. Effects of Reactor Conditions on Synthesis Gas Composition--Evaluate the effect of air distribution, steam/coal ratio, solids-circulation rate, and reactor temperature on CO/CO{sub 2} ratio, synthesis gas Lower Heating Value (LHV), carbon conversion, and cold and hot gas efficiencies. Research Triangle Institute (RTI) Direct Sulfur Recovery Process (DSRP) Testing--Provide syngas in support of the DSRP commissioning. Loop Seal Operations--Optimize loop seal operations and investigate increases to previously achieved maximum solids-circulation rate.

  11. Tools for dynamic model development

    E-Print Network [OSTI]

    Schaber, Spencer Daniel

    2014-01-01

    For this thesis, several tools for dynamic model development were developed and analyzed. Dynamic models can be used to simulate and optimize the behavior of a great number of natural and engineered systems, from the ...

  12. Herty Advanced Materials Development Center

    Broader source: Energy.gov [DOE]

    Session 1-B: Advancing Alternative Fuels for the Military and Aviation Sector Breakout Session 1: New Developments and Hot Topics Jill Stuckey, Acting Director, Herty Advanced Materials Development Center

  13. Automotive Component Product Development Enhancement

    E-Print Network [OSTI]

    de Weck, Olivier L.

    Automotive Component Product Development Enhancement Through Multi-Attribute System Design Engineering Systems Division #12;Automotive Component Product Development Enhancement Through Multi of Science in Engineering and Management February 2005 ABSTRACT Automotive industry is facing a tough period

  14. Mechanisms of brain ventricle development

    E-Print Network [OSTI]

    Lowery, Laura Anne

    2008-01-01

    The brain ventricles are a conserved system of fluid-filled cavities within the brain that form during the earliest stages of brain development. Abnormal brain ventricle development has been correlated with neurodevelopmental ...

  15. Development of a high-throughput microfluidic integrated microarray for the detection of chimeric bioweapons.

    SciTech Connect (OSTI)

    Sheppod, Timothy; Satterfield, Brent; Hukari, Kyle W.; West, Jason A. A.; Hux, Gary A.

    2006-10-01

    The advancement of DNA cloning has significantly augmented the potential threat of a focused bioweapon assault, such as a terrorist attack. With current DNA cloning techniques, toxin genes from the most dangerous (but environmentally labile) bacterial or viral organism can now be selected and inserted into robust organism to produce an infinite number of deadly chimeric bioweapons. In order to neutralize such a threat, accurate detection of the expressed toxin genes, rather than classification on strain or genealogical decent of these organisms, is critical. The development of a high-throughput microarray approach will enable the detection of unknowns chimeric bioweapons. The development of a high-throughput microarray approach will enable the detection of unknown bioweapons. We have developed a unique microfluidic approach to capture and concentrate these threat genes (mRNA's) upto a 30 fold concentration. These captured oligonucleotides can then be used to synthesize in situ oligonucleotide copies (cDNA probes) of the captured genes. An integrated microfluidic architecture will enable us to control flows of reagents, perform clean-up steps and finally elute nanoliter volumes of synthesized oligonucleotides probes. The integrated approach has enabled a process where chimeric or conventional bioweapons can rapidly be identified based on their toxic function, rather than being restricted to information that may not identify the critical nature of the threat.

  16. Development of MP3 Technologies

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

    Development of MP3 Technologies Impact of Basic Research on Innovation - Edited excerpts from American Competitiveness Initiative, February 2006...

  17. Climate Change, Adaptation, and Development

    E-Print Network [OSTI]

    Cole, Daniel H.

    2008-01-01

    Climate Change, Adaptation, and Development Daniel H. Cole*THE COSTS OF CLIMATE CHANGE . ADAPTATIONCONVENTION ON CLIMATE CHANGE . IV. A.

  18. Gammasphere software development. Progress report

    SciTech Connect (OSTI)

    Piercey, R.B.

    1993-05-01

    Activities of the nuclear physics group are described. Progress was made in organizing the Gammasphere Software Working Group, establishing a nuclear computing facility, participating in software development at Lawrence Berkeley, developing a common data file format, and adapting the ORNL UPAK software to run at Gammasphere. A universal histogram object was developed that defines a file format and provides for an objective-oriented programming model. An automated liquid nitrogen fill system was developed for Gammasphere (110 Ge detectors comprise the sphere).

  19. OFFICE OF SUPPLIER DIVERSITY DEVELOPMENT

    E-Print Network [OSTI]

    Pittendrigh, Barry

    OFFICE OF SUPPLIER DIVERSITY DEVELOPMENT STRATEGIC PLAN JESSE MOORE, MANAGER August, 2005 Mission Statement Provide leadership and develop relationships that will result in Purdue's campus' supplier base is a recognized national leader in developing a diverse supplier base. All staff involved with purchasing

  20. Small Talk: Cell-to-Cell Communication in Bacteria

    ScienceCinema (OSTI)

    Bassler, Bonnie [Princeton University, Princeton, New Jersey, United States

    2010-01-08

    Cell-cell communication in bacteria involves the production, release, and subsequent detection of chemical signaling molecules called autoinducers. This process, called quorum sensing, allows bacteria to regulate gene expression on a population-wide scale. Processes controlled by quorum sensing are usually ones that are unproductive when undertaken by an individual bacterium but become effective when undertaken by the group. For example, quorum sensing controls bioluminescence, secretion of virulence factors, biofilm formation, sporulation, and the exchange of DNA. Thus, quorum sensing is a mechanism that allows bacteria to function as multi-cellular organisms. Bacteria make, detect, and integrate information from multiple autoinducers, some of which are used exclusively for intra-species communication while others enable communication between species. Research is now focused on the development of therapies that interfere with quorum sensing to control bacterial virulence.

  1. The Effects of Stator Compliance, Backs Steps, Temperature, and Clockwise Rotation on the Torque-Speed Curve of Bacterial Flagellar Motor

    E-Print Network [OSTI]

    Giovanni Meacci; Ganhui Lan; Yuhai Tu

    2010-08-13

    Rotation of a single bacterial flagellar motor is powered by multiple stators tethered to the cell wall. In a "power-stroke" model the observed independence of the speed at low load on the number of stators is explained by a torque-dependent stepping mechanism independent of the strength of the stator tethering spring. On the other hand, in models that depend solely on the stator spring to explain the observed behavior, exceedingly small stator spring constants are required. To study the dynamics of the motor driven by external forces (such as those exerted by an optical tweezer), back-stepping is introduced when stators are driven far out of equilibrium. Our model with back-stepping reproduces the observed absence of a barrier to backward rotation, as well the behaviors in the high-speed negative-torque regime. Recently measured temperature dependence of the motor speed near zero load (Yuan & Berg 2010 Biophys J) is explained quantitatively by the thermally activated stepping rates in our model. Finally, we suggest that the general mechanical properties of all molecular motors (linear and rotary), characterized by their force(torque)-speed curve, can be determined by their power-stroke potentials and the dependence of the stepping rates on the mechanical state of the motor (force or speed). The torque-speed curve for the clockwise rotating flagellar motor has been observed for the first time recently (Yuan et al. 2010 PNAS). Its quasi-linear behavior is quantitatively reproduced by our model. In particular, we show that concave and convex shapes of the torque-speed curve can be achieved by changing the interaction potential from linear to quadratic form. We also show that reversing the stepping rate dependence on force (torque) can lead to non-monotonicity in the speed-load dependency.

  2. POWER SYSTEMS DEVELOPMENT FACILITY

    SciTech Connect (OSTI)

    Unknown

    2002-05-01

    This report discusses test campaign GCT3 of the Halliburton KBR transport reactor train with a Siemens Westinghouse Power Corporation (Siemens Westinghouse) particle filter system at the Power Systems Development Facility (PSDF) located in Wilsonville, Alabama. The transport reactor is an advanced circulating fluidized-bed reactor designed to operate as either a combustor or a gasifier using one of two possible particulate control devices (PCDs). The transport reactor was operated as a pressurized gasifier during GCT3. GCT3 was planned as a 250-hour test run to commission the loop seal and continue the characterization of the limits of operational parameter variations using a blend of several Powder River Basin coals and Bucyrus limestone from Ohio. The primary test objectives were: (1) Loop Seal Commissioning--Evaluate the operational stability of the loop seal with sand and limestone as a bed material at different solids circulation rates and establish a maximum solids circulation rate through the loop seal with the inert bed. (2) Loop Seal Operations--Evaluate the loop seal operational stability during coal feed operations and establish maximum solids circulation rate. Secondary objectives included the continuation of reactor characterization, including: (1) Operational Stability--Characterize the reactor loop and PCD operations with short-term tests by varying coal feed, air/coal ratio, riser velocity, solids circulation rate, system pressure, and air distribution. (2) Reactor Operations--Study the devolatilization and tar cracking effects from transient conditions during transition from start-up burner to coal. Evaluate the effect of process operations on heat release, heat transfer, and accelerated fuel particle heat-up rates. Study the effect of changes in reactor conditions on transient temperature profiles, pressure balance, and product gas composition. (3) Effects of Reactor Conditions on Syngas Composition--Evaluate the effect of air distribution, steam/coal ratio, solids circulation rate, and reactor temperature on CO/CO{sub 2} ratio, H{sub 2}/converted carbon ratio, gasification rates, carbon conversion, and cold and hot gas efficiencies. Test run GCT3 was started on December 1, 2000, with the startup of the thermal oxidizer fan, and was completed on February 1, 2001. This test was conducted in two parts; the loop seal was commissioned during the first part of this test run from December 1 through 15, which consisted of hot inert solids circulation testing. These initial tests provided preliminary data necessary to understand different parameters associated with the operation and performance of the loop seal. The loop seal was tested with coal feed during the second part of the test run and additional data was gathered to analyze reactor operations and to identify necessary modifications to improve equipment and process performance. In the second part of GCT3, the gasification portion of the test, from January 20 to February 1, 2001, the mixing zone and riser temperatures were varied between 1,675 and 1,825 F at pressures ranging from 200 to 240 psig. There were 306 hours of solid circulation and 184 hours of coal feed attained in GCT3.

  3. Recent Developments in SHERPA

    SciTech Connect (OSTI)

    Archibald, Jennifer; Gleisberg, Tanju; Hoeche, Stefan; Krauss, Frank; Schonherr, Marek; Schumann, Steffen; Siegert, Frank; Winter, Jan; /Fermilab

    2011-11-15

    Some recent QCD-related developments in the SHERPA event generator are presented. In the past decades, event generators such as PYTHIA [1, 2] and HERWIG [3, 4] have been central for nearly all physics analyses at particle physics experiments at the high-energy frontier. This will also hold true at the LHC, where a large number of interesting signals for new particles or new phenomena (the Higgs boson or any other manifestation of the mechanism behind electro-weak symmetry breaking, supersymmetry, extra dimensions etc.) is hampered by a plethora of severe, sometimes overwhelming backgrounds. Nearly all of them are largely influenced by QCD. Therefore it seems fair to say that the success of the LHC in finding new physics may very well depend on a deep and detailed understanding of old physics, like QCD. Examples for this include, among others, the central-jet veto for the vector boson fusion channel for Higgs production or topologies, where gauge bosons emerge in association with many jets, a background for many search channels. In a reflection on increased needs by the experimental community, aiming at higher precision, incorporation of new physics models and so on, the work horses of old have undergone serious renovation efforts, resulting in new, improved versions of the respective codes, namely PYTHIA8 [5] and HERWIG++ [6]. In addition a completely new code, SHERPA [7], has been constructed and is in the process of maturing. The status of this code is the topic of this contribution. SHERPA's hallmark property is the inclusion of higher-order tree-level QCD contributions, leading to an improved modelling of jet production. They are introduced through a full-fledged matrix element generator, AMEGIC++ [8], which is capable of generating matrix elements and corresponding phase space mappings for processes with multi-particle final states in various models, including the Standard Model, anomalous gauge triple and quadruple couplings according to [9, 10], the Minimal Supersymmetric Standard Model with Feynman rules from [11], the ADD-model of extra dimensions [12, 13], and a model with an extra U(1) singlet coupling to the Higgs boson only [14]. The code has been thoroughly tested and validated [15]. This code, however, is limited, especially in the treatment of many ({ge} 6) external QCD particles. Therefore, in the near future, SHERPA will incorporate another, new matrix element generator, COMIX, which is based on Berends-Giele recursion relations [16] and color-dressing [17] rather than color-ordering. In Tabs. 1 and 2 some example cross sections for gg {yields} ng at fixed energies and pp {yields} b{bar b} + n jets obtained with this program are exhibited and compared to those from other programs. In addition, concerning the calculation of higher-order matrix elements and cross sections, there have been first steps towards an automation of such calculations at truly next-to leading order accuracy. They manifest themselves in the implementation of a procedure [19] to fully automatically construct and evaluate Catani-Seymour dipole subtraction terms [20] for the real part of such NLO calculations. The results from the matrix element calculations are merged with the subsequent parton shower through the formalism of [21, 22]. The results of its implementation in SHERPA [23] has recently been compared with other algorithms [24]. Although there remains some dispute about the theoretical equivalence of the different approaches, the overall results show satisfying agreement with each other, such that they can be used with confidence for data analysis.

  4. Research, Development, Demonstration, and Deployment | Department...

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

    Research, Development, Demonstration, and Deployment Research, Development, Demonstration, and Deployment The Bioenergy Technologies Office's research, development, demonstration,...

  5. Project Management Career Development Program | Department of...

    Office of Environmental Management (EM)

    You are here Home Operational Management Certifications and Professional Development Project Management Career Development Program Project Management Career Development...

  6. Transaction Costs, Information Technology and Development

    E-Print Network [OSTI]

    Singh, Nirvikar

    2004-01-01

    Transaction Costs, Information Technology and Development 1.Transaction Costs, Information Technology and DevelopmentTransaction Costs, Information Technology and Development *

  7. Transaction Costs, Information Technology and Development

    E-Print Network [OSTI]

    Singh, Nirvikar

    2004-01-01

    Transaction Costs, Information Technology and Development 1.Transaction Costs, Information Technology and DevelopmentTransaction Costs, Information Technology and Development

  8. Bacterial Abundance Measure bacterial numbers and mass per unit volume.

    E-Print Network [OSTI]

    Vallino, Joseph J.

    at all). Basic method: · Aseptically collect and filter water onto sterile filter. · Place filter-methylene blue dye) · Incubate filter at 40ºC (or higher) · Count colonies to determine colonies/100 ml water EPA for isolation or water testing, such as coliform test. 9 ml 100 #12;Dilution Plate Calculations N: Number

  9. Pompano subsea development -- Testing program

    SciTech Connect (OSTI)

    Nelson, R.; Berger, R.; Tyer, C.

    1996-12-31

    System reliability is essential for the economic success of any subsea oil and gas development. Testing programs can be developed to prove system reliability while still adhering to cost and schedule constraints. This paper describes a three-tiered equipment testing program that was employed for the Pompano Phase 2 subsea system. Program objectives, test descriptions, procedure development and test execution are discussed in detail. Lessons learned throughout the tests are also presented.

  10. MPAS-Ocean Development Update

    SciTech Connect (OSTI)

    Jacobsen, Douglas W.; Ringler, Todd D.; Petersen, Mark R.; Jones, Philip W.; Maltrud, Mathew E.

    2012-06-13

    The Model for Prediction Across Scales (MPAS) is a modeling framework developed jointly between NCAR and LANL, built to allow core developers to: rapidly develop new dynamical cores, and leverage improvements made to shared codes. MPAS-Ocean (MPAS-O) is a functioning ocean model capable of high resolution, or highly vairable resolution simulations. The first MPAS-O publication is expected by the end of the year.

  11. Climate change: comparative impact on developing and developed countries

    E-Print Network [OSTI]

    Climate change: comparative impact on developing and developed countries PAUL CHINOWSKY1 , CAROLYN. In these projections, climate change is a global issue with potential impacts for every country. However, the relative levels to determine the relative impact of climate change in the context of a single infrastructure

  12. ME2801 Planning -Developing a Venture Planning -Developing a Venture

    E-Print Network [OSTI]

    Arvestad, Lars

    models for business process analysis develop and argue for a business/business model Kursens huvudsakliga to independently: identify a feasible business idea evaluate market opportunities for the idea in terms of market discuss and critically assess the steps necessary for realizing the business. develop and write a complete

  13. ME2801 Planning -Developing a Venture Planning -Developing a Venture

    E-Print Network [OSTI]

    Arvestad, Lars

    advanced models for business process analysis - Develop and argue for a complete business model Kursens to be able to independently: - Identify a feasible business idea - Perform a market analysis of a business idea - Discuss and critically assess the necessary steps for realizing a business idea - Develop

  14. Laboratory Directed Research and Development

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2015-04-30

    To establish Department of Energy (DOE) requirements for laboratory directed research and development (LDRD) while providing the laboratory director broad flexibility for program implementation

  15. Illinois Coal Development Program (Illinois)

    Broader source: Energy.gov [DOE]

    The Illinois Coal Development Program seeks to advance promising clean coal technologies beyond research and towards commercialization. The program provides a 50/50 match with private industry...

  16. Economic Development | ornl.gov

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

    security categories at the 2010 GVC hosted by ORNL March 24-26. The competition, in its fourth year, attracts students developing new technologies and venture investors with...

  17. Renewable Natural Gas- Developer Perspective

    Broader source: Energy.gov [DOE]

    Breakout Session 3-C: Renewable Gaseous FuelsRenewable Natural Gas - Developer PerspectiveDavid Ross, Managing Director, MultiGen International, LLC

  18. Developing Alaskan Sustainable Housing Training

    Broader source: Energy.gov [DOE]

    Hosted by the Association of Alaska Housing Authorities (AAHA), this three-day training event covers strategies and technical issues related to sustainable housing development.

  19. Laboratory Directed Research and Development

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    To establish Department of Energy (DOE) requirements for laboratory directed research and development (LDRD) while providing the laboratory director broad flexibility for program implementation.

  20. Geothermal Research and Development Programs

    Broader source: Energy.gov [DOE]

    Here you'll find links to laboratories, universities, and colleges conducting research and development (R&D) in geothermal energy technologies.