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Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
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We encourage you to perform a real-time search of NLEBeta
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1

Structure Illuminates Mechanism of Fungal Polyketide Cyclization  

NLE Websites -- All DOE Office Websites (Extended Search)

Structure Illuminates Mechanism of Fungal Polyketide Cyclization Print Structure Illuminates Mechanism of Fungal Polyketide Cyclization Print Polyketide natural products produced by bacteria and fungi are often characterized by the presence of multiple aromatic rings that are responsible for the activity of polyketides as both beneficial antibiotic and anticancer agents and as dangerous toxic compounds, such as the highly carcinogenic aflatoxins that are produced by fungal species from the Aspergillus family of molds. Polyketide ring formation by fungal enzymes called polyketide synthases (PKSs) is mediated by the enzyme's product template (PT) domain. However, the mechanism for aromatic ring formation from a linear intermediate with high fidelity has remained unclear. To reveal the cyclization mechanism, researchers at the University of California, Irvine, and The Johns Hopkins University solved the structure of the isolated PT domain of the PKS involved in aflatoxin production (PksA) to 1.8 Å using data from ALS Beamline 8.2.2 and SSRL Beamline 9-1. The crystal structure, along with biochemical studies, provides a paradigm for polyketide cyclization by fungal PKSs, an event that is necessary for imparting biological activity to this large class of clinically relevant natural products.

2

Structure Illuminates Mechanism of Fungal Polyketide Cyclization  

NLE Websites -- All DOE Office Websites (Extended Search)

Structure Illuminates Mechanism of Fungal Polyketide Cyclization Print Structure Illuminates Mechanism of Fungal Polyketide Cyclization Print Polyketide natural products produced by bacteria and fungi are often characterized by the presence of multiple aromatic rings that are responsible for the activity of polyketides as both beneficial antibiotic and anticancer agents and as dangerous toxic compounds, such as the highly carcinogenic aflatoxins that are produced by fungal species from the Aspergillus family of molds. Polyketide ring formation by fungal enzymes called polyketide synthases (PKSs) is mediated by the enzyme's product template (PT) domain. However, the mechanism for aromatic ring formation from a linear intermediate with high fidelity has remained unclear. To reveal the cyclization mechanism, researchers at the University of California, Irvine, and The Johns Hopkins University solved the structure of the isolated PT domain of the PKS involved in aflatoxin production (PksA) to 1.8 Å using data from ALS Beamline 8.2.2 and SSRL Beamline 9-1. The crystal structure, along with biochemical studies, provides a paradigm for polyketide cyclization by fungal PKSs, an event that is necessary for imparting biological activity to this large class of clinically relevant natural products.

3

Structure Illuminates Mechanism of Fungal Polyketide Cyclization  

NLE Websites -- All DOE Office Websites (Extended Search)

Structure Illuminates Mechanism Structure Illuminates Mechanism of Fungal Polyketide Cyclization Structure Illuminates Mechanism of Fungal Polyketide Cyclization Print Wednesday, 31 March 2010 00:00 Polyketide natural products produced by bacteria and fungi are often characterized by the presence of multiple aromatic rings that are responsible for the activity of polyketides as both beneficial antibiotic and anticancer agents and as dangerous toxic compounds, such as the highly carcinogenic aflatoxins that are produced by fungal species from the Aspergillus family of molds. Polyketide ring formation by fungal enzymes called polyketide synthases (PKSs) is mediated by the enzyme's product template (PT) domain. However, the mechanism for aromatic ring formation from a linear intermediate with high fidelity has remained unclear. To reveal the cyclization mechanism, researchers at the University of California, Irvine, and The Johns Hopkins University solved the structure of the isolated PT domain of the PKS involved in aflatoxin production (PksA) to 1.8 Å using data from ALS Beamline 8.2.2 and SSRL Beamline 9-1. The crystal structure, along with biochemical studies, provides a paradigm for polyketide cyclization by fungal PKSs, an event that is necessary for imparting biological activity to this large class of clinically relevant natural products.

4

Deadly Carcinogen Unraveled: The Molecular Origami of Fungal Polyketide  

NLE Websites -- All DOE Office Websites (Extended Search)

Deadly Carcinogen Unraveled: The Molecular Origami Deadly Carcinogen Unraveled: The Molecular Origami of Fungal Polyketide Aflatoxin is an unavoidable food contaminant in grains and nuts produced in developing countries. Chronic ingestion of nuts and grains contaminated with aflatoxin-producing molds such as Aspergillus parasiticus leads to a high rate of liver cancer, and is a large problem in developing countries. Aflatoxins belong to a class of natural products called polyketides, which are biosynthesized in many bacteria and fungi (1,2). Polyketide natural products produced by bacteria and fungi are often characterized by the presence of multiple aromatic rings that are responsible for the activity of polyketides as antibiotic, anticancer, and toxic compounds (2). Polyketide ring formation by fungal PKSs results from regiospecific cyclizations of reactive poly-beta-keto intermediates of specific length that is mediated by the product template (PT) domain (Fig. 1). The mechanism for aromatic ring formation, where a linear intermediate is transformed into a multicyclic product with high fidelity, has remained unclear. To reveal the cyclization mechanism, the Tsai lab at the University of California, Irvine, in collaboration with the Townsend lab at The Johns Hopkins University, solved the structure of the isolated PT domain of PksA to 1.8 Å using data from the SSRL beamline 9.1 and ALS beamline 8.2.2. The work was reported in the Oct 22 issue of Nature.

5

Available Technologies: JBEI Polyketide Synthases Portfolio ...  

Researchers at the Joint BioEnergy Institute (JBEI) have developed a suite of technologies employing Type 1 polyketide synthases (PKS) ...

6

Producing biofuels using polyketide synthases  

DOE Patents (OSTI)

The present invention provides for a non-naturally occurring polyketide synthase (PKS) capable of synthesizing a carboxylic acid or a lactone, and a composition such that a carboxylic acid or lactone is included. The carboxylic acid or lactone, or derivative thereof, is useful as a biofuel. The present invention also provides for a recombinant nucleic acid or vector that encodes such a PKS, and host cells which also have such a recombinant nucleic acid or vector. The present invention also provides for a method of producing such carboxylic acids or lactones using such a PKS.

Katz, Leonard; Fortman, Jeffrey L; Keasling, Jay D

2013-04-16T23:59:59.000Z

7

JGI Fungal Genomics Program  

E-Print Network (OSTI)

View Supports functional genomics, user data deposition andJGI Fungal Genomics Program Igor V. Grigoriev 1 DOE Jointof California. JGI Fungal Genomics Program Contact: Igor

Grigoriev, Igor V.

2011-01-01T23:59:59.000Z

8

JGI Fungal Genomics Program  

E-Print Network (OSTI)

JGI Fungal Genomics Program Igor V. Grigoriev 1 Lawrenceof California. JGI Fungal Genomics Program Contact: IgorJGI). Its key project, the Genomics Encyclopedia of Fungi,

Grigoriev, Igor V.

2012-01-01T23:59:59.000Z

9

Synthesis of indoles via a tandem benzannulation-cyclization strategy  

E-Print Network (OSTI)

Vinylketenes (generated in situ from cyclobutenones or a-diazo ketones) react with ynamides via a pericyclic cascade process to produce highly-substituted aniline derivatives. Cyclization of the benzannulation products can ...

Lam, Tin Yiu

2008-01-01T23:59:59.000Z

10

Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-?-pyrone.  

SciTech Connect

The genome sequencing of the fungus Aspergillus niger, an industrial workhorse, uncovered a large cache of genes encoding enzymes thought to be involved in the production of secondary metabolites yet to be identified. Identification and structural characterization of many of these predicted secondary metabolites are hampered by their low concentration relative to the known A. niger metabolites such as the naphtho-?-pyrone family of polyketides. We deleted a nonreducing PKS gene in A. niger strain ATCC 11414, a daughter strain of A. niger ATCC strain 1015 whose genome was sequenced by the DOE Joint Genome Institute. This PKS encoding gene is a predicted ortholog of alb1 from Aspergillus fumigatus which is responsible for production of YWA1, a precursor of fungal DHN melanin. Our results show that the A. niger alb1 PKS is responsible for the production of the polyketide precursor for DHN melanin biosynthesis. Deletion of alb1 elimnates the production of major metabolites, naphtho-?-pyrones. The generation of an A. niger strain devoid of naphtho-?-pyrones will greatly facilitate the elucidation of cryptic biosynthetic pathways in this organism.

Chiang, Yi Ming; Meyer, Kristen M.; Praseuth , Michael; Baker, Scott E.; Bruno, Kenneth S.; Wang, Clay C.

2010-12-06T23:59:59.000Z

11

JGI Fungal Genomics Program  

SciTech Connect

Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

Grigoriev, Igor V.

2011-03-14T23:59:59.000Z

12

Exploiting genetic diversity by directed evolution: molecular breeding of type III polyketide synthases improves productivityw z  

E-Print Network (OSTI)

Exploiting genetic diversity by directed evolution: molecular breeding of type III polyketide 2008 DOI: 10.1039/b717705d Applying directed evolution to the phloroglucinol synthase PhlD from activity and the productivity goals for industrial application,5 and several examples of applying directed

Zhao, Huimin

13

Fueling the Future with Fungal Genomics  

E-Print Network (OSTI)

genome sequencing and bioenergy. Fungal Biology Reviews. 22:of fungal pathogens of bioenergy crops with sequenced hostand improve them to make bioenergy production efficient on

Grigoriev, Igor V.

2011-01-01T23:59:59.000Z

14

Fueling the Future with Fungal Genomics  

E-Print Network (OSTI)

et al. 2008. Fungal genome sequencing and bioenergy. FungalCullen D, et al. 2008. Genome sequencing and analysis of theand lessons learned from genome sequencing. Methods Enzymol.

Grigoriev, Igor V.

2011-01-01T23:59:59.000Z

15

Why sequence census of fungal biology?  

NLE Websites -- All DOE Office Websites (Extended Search)

sequence census of fungal biology? Despite the large number of sequenced fungal genomes, the current taxonomic sampling is limited to well-characterized lineages of the Kingdom and...

16

Fueling the Future with Fungal Genomics  

E-Print Network (OSTI)

JW. 2010. China's fungal genomics initiative: a whitepaper.and Saccharomycotina. BMC Genomics. 8, 325. Bailly J,Harnessing ectomycorrhizal genomics for ecological insights.

Grigoriev, Igor V.

2011-01-01T23:59:59.000Z

17

Semantic web infrastructure for fungal enzyme biotechnologists  

Science Conference Proceedings (OSTI)

The FungalWeb Ontology seeks to support various data integration needs of enzyme biotechnology from inception to product roll. Serving as a knowledgebase for decision support, the conceptualization seeks to link fungal species with enzymes, enzyme substrates, ... Keywords: Description logic, Enzyme, Fungi, Ontology, Semantic Web

Christopher J. O. Baker; Arash Shaban-Nejad; Xiao Su; Volker Haarslev; Greg Butler

2006-09-01T23:59:59.000Z

18

PNNL Fungal Biotechnology Core DOE-OBP Project  

DOE Green Energy (OSTI)

In 2009, we continued to address barriers to fungal fermentation in the primary areas of morphology control, genomics, proteomics, fungal hyperproductivity, biomass-to-products via fungal based consolidated bioprocesses, and filamentous fungal ethanol. Alternative renewable fuels from fungi was added as a new subtask. Plans were also made to launch a new advanced strain development subtask in FY2010.

Baker, Scott E.; Bruno, Kenneth S.; Butcher, Mark G.; Collett, James R.; Culley, David E.; Dai, Ziyu; Magnuson, Jon K.; Panisko, Ellen A.

2009-11-30T23:59:59.000Z

19

Synthesis and determination of the absolute configuration of Armatol A through a polyepoxide cyclization cascade : revision of the proposed structures of Armatols A-F  

E-Print Network (OSTI)

Cyclization Cascades Leading to the Tricyclic Fragment of Armatol A The synthesis of the fused 6,7,7-tricycle of armatol A was investigated. Fragments containing both a ketone and an aldehyde for subsequent fragment coupling ...

Underwood, Brian Saxton

2011-01-01T23:59:59.000Z

20

Why sequence fungal pathogen Cochliobolus sativus?  

NLE Websites -- All DOE Office Websites (Extended Search)

fungal pathogen Cochliobolus sativus? fungal pathogen Cochliobolus sativus? Wheat and barley have been and will continue to be the cereal crops of major importance in the United States and around the world. In 2008, the U.S. produced over 130 million tons of wheat, third in the world behind China and India. Fungal diseases such as spot blotch are a consistent source of economic losses for the cereal crops. Spot blotch caused by C. sativus in barley and wheat is one of the most important diseases and remains a problem in many regions of the world. The fungus Cochliobolus sativus is the sexual stage of Bipolaris sorokiniana, which is the causal agent of a wide variety of cereal diseases. In its asexual stage, the pathogen can infect and cause disease on the root (where it is known as common root rot), leaf and stem, and head

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Melanoma Therapy with Rhenium-Cyclized Alpha Melanocyte Stimulating Hormone Peptide Analogs  

SciTech Connect

Malignant melanoma is the 6th most commonly diagnosed cancer with increasing incidence in the United States. It is estimated that 54,200 cases of malignant melanoma will be newly diagnosed and 7,600 cases of death will occur in the United States in the year 2003 (1). At the present time, more than 1.3% of Americans will develop malignant melanoma during their lifetime (2). The average survival for patients with metastatic melanoma is about 6-9 months (3). Moreover, metastatic melanoma deposits are resistant to conventional chemotherapy and external beam radiation therapy (3). Systematic chemotherapy is the primary therapeutic approach to treat patients with metastatic melanoma. Dacarbazine is the only single chemotherapy agent approved by FDA for metastatic melanoma treatment (5). However, the response rate to Dacarbazine is only approximately 20% (6). Therefore, there is a great need to develop novel treatment approaches for metastatic melanoma. The global goal of this research program is the rational design, characterization and validation of melanoma imaging and therapeutic radiopharmaceuticals. Significant progress has been made in the design and characterization of metal-cyclized radiolabeled alpha-melanocyte stimulating hormone peptides. Therapy studies with {sup 188}Re-CCMSH demonstrated the therapeutic efficacy of the receptor-targeted treatment in murine and human melanoma bearing mice (previous progress report). Dosimetry calculations, based on biodistribution data, indicated that a significant dose was delivered to the tumor. However, {sup 188}Re is a very energetic beta-particle emitter. The longer-range beta-particles theoretically would be better for larger tumors. In the treatment of melanoma, the larger primary tumor is usually surgically removed leaving metastatic disease as the focus of targeted radiotherapy. Isotopes with lower beta-energies and/or shorter particle lengths should be better suited for targeting metastases. The {sup 177}Lu-DOTA-Re(Arg11)CCMSH and {sup 212}Pb-DOTA-Re(Arg11)CCMSH complexes were developed and synthesized to investigate its ability to target and deliver an effective dose to small melanoma tumors and metastatic deposits. Dosimetry calculations for {sup 188}Re-CCMSH and {sup 212}Pb/{sup 212}Bi[DOTA]-Re(Arg11)CCMSH were compared in the B16/F1 mouse melanoma flank tumor model to analyze the delivered dose to tumor and normal organs.

Thomas P Quinn

2005-11-22T23:59:59.000Z

22

DOE Joint Genome Institute: Formidable Fungal Force Counters...  

NLE Websites -- All DOE Office Websites (Extended Search)

applications, fungi provide a source of enzymes to catalyze such processes as generating biofuels from plant biomass. One large fungal group with such enzymes are the rust plant...

23

Development of a copper-catalyzed amidation-base-promoted cyclization sequence for the synthesis of 2-aryl- and 2-vinyl1-4 quinolones  

E-Print Network (OSTI)

A direct two-step method for the preparation of 2-aryl- and 2-vinyl-4-quinolones that utilizes a copper-catalyzed amidation of ortho-halophenones followed by a base-promoted Camps cyclization of the resulting N-(2-keto-aryl)amides ...

Jones, Carrie Preston

2007-01-01T23:59:59.000Z

24

Cyclization Phenomena in the Sol-Gel Polymerization of a,w-Bis(triethoxysilyl)alkanes and Incorporation of the Cyclic Structures into Network Silsesquioxane Polymers  

Science Conference Proceedings (OSTI)

Intramolecular cyclizations during acid-catalyzed, sol-gel polymerizations of ct,co- bis(tietioxysilyl)aWmes substintidly lengtien gelties formonomers witietiylene- (l), propylene- (2), and butylene-(3)-bridging groups. These cyclizations reactions were found, using mass spectrometry and %i NMR spectroscopy, to lead preferentially to monomeric and dimeric products based on six and seven membered disilsesquioxane rings. 1,2- Bis(triethoxysilyl)ethane (1) reacts under acidic conditions to give a bicyclic drier (5) that is composed of two annelated seven membered rings. Under the same conditions, 1,3- bis(triethoxysilyl)propane (2), 1,4-bis(triethoxysilyl)butane (3), and z-1,4- bis(triethoxysilyl)but-2-ene (10) undergo an intramolecular condensation reaction to give the six membemd and seven membered cyclic disilsesquioxanes 6, 7, and 11. Subsequently, these cyclic monomers slowly react to form the tricyclic dirners 8,9 and 12. With NaOH as polymerization catalyst these cyclic silsesquioxanes readily ~aeted to afford gels that were shown by CP MAS z%i NMR and infr=d spectroscopes to retain some cyclic structures. Comparison of the porosity and microstructwe of xerogels prepared from the cyclic monomers 6 and 7 with gels prepared directly from their acyclic precursors 2 and 3, indicate that the final pore structure of the xerogels is markedly dependent on the nature of the precursor. In addition, despite the fact that the monomeric cyclic disilsesquioxane species can not be isolated from 1-3 under basic conditions due to their rapid rate of gelation, spectroscopic techniques also detected the presence of the cyclic structures in the resulting polymeric gels.

Alam, T.M.; Carpenter, J.P.; Dorhout, P.K.; Greaves, J.; Loy, D.A.; Shaltout, R.; Shea, K.J.; Small, J.H.

1999-01-04T23:59:59.000Z

25

Modelling the global distribution of fungal species: new insights into microbial cosmopolitanism  

E-Print Network (OSTI)

Modelling the global distribution of fungal species: new insights into microbial cosmopolitanism cosmopolitan distributions. However, for estimating the global distributions of microorganisms, discriminating

Bruns, Tom

26

A Fungal End to Coal in the Carboniferous Period? | U.S. DOE...  

Office of Science (SC) Website

A Fungal End to Coal in the Carboniferous Period? Biological and Environmental Research (BER) BER Home About BER Research Facilities Science Highlights Searchable Archive of BER...

27

ALSNews Vol. 307  

NLE Websites -- All DOE Office Websites (Extended Search)

7 Print 7 Print In This Issue ALS Social Media is Here Structures of the Ribosome in Intermediate States of Ratcheting Structure Illuminates Mechanism of Fungal Polyketide Cyclization New Infrared Beamline 5.4, BSISB Facility Open ALS Controls Upgrade: Meeting the Needs of a Growing Facility Ring Leaders: Accelerator Operations and Development Announcements: Guest House Special Extended, and VUVX 2010 Who's in the News Operations Update UEC Corner News Links RingLeaders Ring Leaders Accelerator Operations and Development Division Deputy for Accelerator Operations and Development David Robin gives an overview of the Accelerator Physics Group, Accelerator and Floor Operations Sections, and the ALS Procedure Center. Read the Article announcements Announcements Guest House Special

28

ALSNews Vol. 307  

NLE Websites -- All DOE Office Websites (Extended Search)

7 Print 7 Print In This Issue ALS Social Media is Here Structures of the Ribosome in Intermediate States of Ratcheting Structure Illuminates Mechanism of Fungal Polyketide Cyclization New Infrared Beamline 5.4, BSISB Facility Open ALS Controls Upgrade: Meeting the Needs of a Growing Facility Ring Leaders: Accelerator Operations and Development Announcements: Guest House Special Extended, and VUVX 2010 Who's in the News Operations Update UEC Corner News Links RingLeaders Ring Leaders Accelerator Operations and Development Division Deputy for Accelerator Operations and Development David Robin gives an overview of the Accelerator Physics Group, Accelerator and Floor Operations Sections, and the ALS Procedure Center. Read the Article announcements Announcements Guest House Special

29

ALSNews Vol. 307  

NLE Websites -- All DOE Office Websites (Extended Search)

7 Print 7 Print In This Issue ALS Social Media is Here Structures of the Ribosome in Intermediate States of Ratcheting Structure Illuminates Mechanism of Fungal Polyketide Cyclization New Infrared Beamline 5.4, BSISB Facility Open ALS Controls Upgrade: Meeting the Needs of a Growing Facility Ring Leaders: Accelerator Operations and Development Announcements: Guest House Special Extended, and VUVX 2010 Who's in the News Operations Update UEC Corner News Links RingLeaders Ring Leaders Accelerator Operations and Development Division Deputy for Accelerator Operations and Development David Robin gives an overview of the Accelerator Physics Group, Accelerator and Floor Operations Sections, and the ALS Procedure Center. Read the Article announcements Announcements Guest House Special

30

ALSNews Vol. 307  

NLE Websites -- All DOE Office Websites (Extended Search)

7 Print 7 Print In This Issue ALS Social Media is Here Structures of the Ribosome in Intermediate States of Ratcheting Structure Illuminates Mechanism of Fungal Polyketide Cyclization New Infrared Beamline 5.4, BSISB Facility Open ALS Controls Upgrade: Meeting the Needs of a Growing Facility Ring Leaders: Accelerator Operations and Development Announcements: Guest House Special Extended, and VUVX 2010 Who's in the News Operations Update UEC Corner News Links RingLeaders Ring Leaders Accelerator Operations and Development Division Deputy for Accelerator Operations and Development David Robin gives an overview of the Accelerator Physics Group, Accelerator and Floor Operations Sections, and the ALS Procedure Center. Read the Article announcements Announcements Guest House Special

31

e-Fungi: a data resource for comparative analysis of fungal genomes  

E-Print Network (OSTI)

ic ho de rm a re es ei G ib be re lla ze ae Ch ae to m iu m gl o bo su m M ag na po rth e gr is ea Ne ur os po ra cr as sa En ce ph al ito zo o n cu n ic u li p450 RVT_1 Fungal_trans Helicase_C Pkinase p450 RVT_1 Fungal_trans Helicase_C Pkinase...

Hedeler, Cornelia; Wong, Han Min; Cornell, Michael J; Alam, Intikhab; Soanes, Darren M; Rattray, Magnus; Hubbard, Simon J; Talbot, Nicholas J; Oliver, Stephen G; Paton, Norman W

2007-11-20T23:59:59.000Z

32

Twenty-second Fungal Genetics Conference - Asilomar, 2003  

SciTech Connect

The purpose of the Twenty Second Fungal Genetics Conference is to bring together scientists and students who are interested in genetic approaches to studying the biology of filamentous fungi. It is intended to stimulate thinking and discussion in an atmosphere that supports interactions between scientists at different levels and in different disciplines. Topics range from the basic to the applied. Filamentous fungi impact human affairs in many ways. In the environment they are the most important agents of decay and nutrient turnover. They are used extensively in the food industry for the production of food enzymes such as pectinase and food additives such as citric acid. They are used in the production of fermented foods such as alcoholic drinks, bread, cheese, and soy sauce. More than a dozen species of mushrooms are used as foods directly. Many of our most important antibiotics, such as penicillin, cyclosporin, and lovastatin, come from fungi. Fungi also have many negative impacts on human health and economics. Fungi are serious pathogens in immuno-compromised patients. Fungi are the single largest group of plant pathogens and thus a serious limit on crop productivity throughout the world. Many fungi are allergenic, and mold contamination of residences and commercial buildings is now recognized as a serious public health threat. As decomposers, fungi cause extensive damage to just about all natural and synthetic materials.

Jonathan D. Walton

2003-06-30T23:59:59.000Z

33

Transcriptome and Biochemical Analyses of Fungal Degradation of Wood  

SciTech Connect

Lignocellulosic accounts for a large percentage of material that can be utilized for biofuels. The most costly part of lignocellulosic material processing is the initial hydrolysis of the wood which is needed to circumvent the lignin barrier and the crystallinity of cellulose. Enzymes will play an increased role in this conversion in that they potentially provide an alternative to costly and caustic high temperature and acid treatment. The increasing use of enzymes in biotechnology is facilitated by both continued improvements in enzyme technology but also in the discovery of new and novel enzymes. The present proposal is aimed at identifying the enzymes which are known to depolymerize woody biomass. Fundamental understanding of how nature gains access to cellulose and hemicellulose will impact all applications. Because fungi are the only known microbes capable of circumventing the lignin barrier, knowledge of the enzyme they use is of great potential for biofuel processing. Nature has evolved different fungal mechanisms for enzymatic hydrolysis of wood. Most notable are the white-rot fungi (wrf) and the brown-rot fungi (brf). This proposed research aims at determining the complete transcriptome of three wrf and two brf to determine the enzymes involved in lignocellulose degradation. The transcriptome work will be supported by enzyme characterization (and zymograms) and finally analysis of the lignin component to determine the mode of lignin modification. In this proposed research, we hypothesize that: 1) Determination of the complete transcriptome of closely related white and brown rot fungi will lead to knowledge of the relevant enzymes involved in wood degradation. 2) Knowledge of the extracellular transcriptome and the mechanism of wood decay can only be obtained if the products of the decay are known. As such, characterization of the lignin oxidation products will correlate the enzymes involved (obtained from the transcriptome) to the lignin oxidation products. The Department of Energy has sequenced the P. chrysosporium genome and has approved the sequencing of the genome of the closely-related brown rot fungus P. placenta. This comparative genomics approach will yield important information on differences between these two fungi. Analysis of gene unique to each fungus (which have been lost or gained) can potentially lead to determining the enzymes which are responsible for each type of decay. This comparison, however, would not be complete without comparing the transcriptome and the proteome/enzymes. Comparative genomics may tell us which genes may be important, but it will not tell us when these genes are expressed, at what levels and will not necessarily tell us what these genes do.

Tien, Ming

2009-03-14T23:59:59.000Z

34

2012 CELLULAR & MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 17 - 22, 2012  

SciTech Connect

The Gordon Research Conference on CELLULAR & MOLECULAR FUNGAL BIOLOGY was held at Holderness School, Holderness New Hampshire, June 17 - 22, 2012. The 2012 Gordon Conference on Cellular and Molecular Fungal Biology (CMFB) will present the latest, cutting-edge research on the exciting and growing field of molecular and cellular aspects of fungal biology. Topics will range from yeast to filamentous fungi, from model systems to economically important organisms, and from saprophytes and commensals to pathogens of plants and animals. The CMFB conference will feature a wide range of topics including systems biology, cell biology and morphogenesis, organismal interactions, genome organisation and regulation, pathogenesis, energy metabolism, biomass production and population genomics. The Conference was well-attended with 136 participants. Gordon Research Conferences does not permit publication of meeting proceedings.

Judith Berman

2012-06-22T23:59:59.000Z

35

Enzymatic Digestibility of Corn Stover Fractions in Response to Fungal Pretreatment  

Science Conference Proceedings (OSTI)

Corn stover fractions (leaves, cobs, and stalks) were studied for enzymatic digestibility after pretreatment with a white rot fungus, Ceriporiopsis subvermispora. Among the three fractions, leaves had the least recalcitrance to fungal pretreatment and the lignin degradation reached 45% after 30 days of pretreatment. The lignin degradation of stalks and cobs was similar but was significantly lower than that of leaves (p corn cobs.

Cui, Z. F.; Wan, C. X.; Shi, J.; Sykes, R. W.; Li, Y. B.

2012-05-30T23:59:59.000Z

36

DOE Joint Genome Institute: Fungal Map of Mutations Key to Increasing  

NLE Websites -- All DOE Office Websites (Extended Search)

September 1, 2009 September 1, 2009 Fungal Map of Mutations Key to Increasing Enzyme Production for Bioenergy Use Download a podcast of this release! WALNUT CREEK, CA-In half a century, one fungus has gone from being the bane of the Army quartermasters' existence in the Pacific to industry staple and someday, as part of the U.S. Department of Energy's mission to promote national energy security through clean, renewable energy development, a biofuel producers' best friend. Trichoderma reesei's makeover is due in part to scientific explorations that led to the development of mutant fungal strains that produce large quantities of biomass-degrading enzymes. T. reesei Image: T. reesei, courtesy of Irma Salovuori, VTT Biotechnology Now an international team of researchers led by scientists at the DOE Joint

37

Soil carbon sequestration and changes in fungal and bacterial biomass following incorporation of forest residues.  

SciTech Connect

Sequestering carbon (C) in forest soils can benefit site fertility and help offset greenhouse gas emissions. However, identifying soil conditions and forest management practices which best promote C accumulation remains a challenging task. We tested whether soil incorporation of masticated woody residues alters short-term C storage at forested sites in western and southeastern USA. Our hypothesis was that woody residues would preferentially stimulate soil fungal biomass, resulting in improved C use efficiency and greater soil C storage. Harvest slash at loblolly pine sites in South Carolina was masticated (chipped) and either (1) retained on the soil surface, (2) tilled to a soil depth of 40 cm, or (3) tilled using at least twice the mass of organics. At comparative sites in California, live woody fuels in ponderosa pine stands were (1) masticated and surface applied, (2) masticated and tilled, or (3) left untreated. Sites with clayey and sandy soils were compared in each region, with residue additions ranging from 20 to 207 Mg ha_1. Total and active fungal biomass were not strongly affected by residue incorporation despite the high input of organics. Limited response was also found for total and active bacterial biomass. As a consequence, fungal:bacterial (F:B) biomass ratios were similar among treatments at each site. Total soil C was elevated at one California site following residue incorporation, yet was significantly lower compared to surface-applied residues at both loblolly pine sites, presumably due to the oxidative effects of tilling on soil organic matter. The findings demonstrated an inconsequential effect of residue incorporation on fungal and bacterial biomass and suggest a limited potential of such practices to enhance long-term soil C storage in these forests.

Busse, Matt, D.; Sanchez, Felipe G.; Ratcliff, Alice W.; Butnor, John R.; Carter, Emily A.; Powers, Robert F.

2009-01-01T23:59:59.000Z

38

Structures of Cryptococcus neoformans Protein Farnesyltransferase Reveal Strategies for Developing Inhibitors That Target Fungal Pathogens  

Science Conference Proceedings (OSTI)

Cryptococcus neoformans is a fungal pathogen that causes life-threatening infections in immunocompromised individuals, including AIDS patients and transplant recipients. Few antifungals can treat C. neoformans infections, and drug resistance is increasing. Protein farnesyltransferase (FTase) catalyzes post-translational lipidation of key signal transduction proteins and is essential in C. neoformans. We present a multidisciplinary study validating C. neoformans FTase (CnFTase) as a drug target, showing that several anticancer FTase inhibitors with disparate scaffolds can inhibit C. neoformans and suggesting structure-based strategies for further optimization of these leads. Structural studies are an essential element for species-specific inhibitor development strategies by revealing similarities and differences between pathogen and host orthologs that can be exploited. We, therefore, present eight crystal structures of CnFTase that define the enzymatic reaction cycle, basis of ligand selection, and structurally divergent regions of the active site. Crystal structures of clinically important anticancer FTase inhibitors in complex with CnFTase reveal opportunities for optimization of selectivity for the fungal enzyme by modifying functional groups that interact with structurally diverse regions. A substrate-induced conformational change in CnFTase is observed as part of the reaction cycle, a feature that is mechanistically distinct from human FTase. Our combined structural and functional studies provide a framework for developing FTase inhibitors to treat invasive fungal infections.

Hast, Michael A.; Nichols, Connie B.; Armstrong, Stephanie M.; Kelly, Shannon M.; Hellinga, Homme W.; Alspaugh, J. Andrew; Beese, Lorena S. (Duke)

2012-09-17T23:59:59.000Z

39

2010 CELL AND MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 13-18, 2010  

DOE Green Energy (OSTI)

The Cellular and Molecular Fungal Biology Conference provides a forum for presentation of the latest advances in fungal research with an emphasis on filamentous fungi. This open-registration scientific meeting brings together the leading scientists from academia, government and industry to discuss current research results and future directions at Holderness School, an outstanding venue for scientific interaction. A key objective of the conference is to foster interaction among scientists working on model fungi such as Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa and Aspergillus nidulans and scientists working on a variety of filamentous fungi whose laboratory tractability is often inversely proportional to their medical, industrial or ecological importance. Sessions will be devoted to Systems Biology, Fungi and Cellulosic Biomass, Small RNAs, Population Genomics, Symbioses, Pathogenesis, Membrane Trafficking and Polarity, and Cytoskeleton and Motors. A session will also be devoted to hot topics picked from abstracts. The CMFB conference provides a unique opportunity to examine the breadth of fungal biology in a small meeting format that encourages in-depth discussion among the attendees.

Michelle Momany

2010-06-18T23:59:59.000Z

40

I. A1,3-Strain Enabled Retention of Chirality During Bis-Cyclization of ?-Ketoamides: Asymmetric Synthesis and Bioactivity of Salinosporamide A and Derivatives II. Optimization of an Organic Syntheses: Asymmetric Nucleophile-Catalyzed Aldol- Lactonization of Aldehyde Acids  

E-Print Network (OSTI)

The potential of human 20S proteasome inhibitors continues to be of interest for anticancer chemotherapy and the recent FDA approval of bortezomib (Velcade) validates the proteasome as a target for cancer chemotherapy. Salinosporamide A, a marine unique bicycle [3.2.0] Beta-lactone-containing natural product, is not only a potent nanomolar inhibitor of the human proteasome but also active against bortezomibresistant multiple myeloma cells. The racemic and asymmetric syntheses of salinosporamide A and derivatives were targeted. In this dissertation, we successfully accomplished the shortest route to date with only a 9-step total synthesis of ()-salinosporamide A. The conciseness of this strategy arises from the key bis-cyclization of a Beta-keto tertiary amide, amenable to gram scale, constructs both the Gamma-lactam and the fused-Beta-lactone in one operation with high enantiopurity, which was enabled by A^1,3-strain. Several derivatives were synthesized and their inhibition activity toward chymotripsin-like, caspase-like, and trypsin-like of the human 20S proteasome was evaluated. This dissertation also included a successfully optimized Organic Syntheses procedure for asymmetric synthesis of (1S,5R)-6-oxaspiro[bicyclo[3.2.0]heptane-3,2'- [1,3]dioxolan]-7-one via the nucleophile-catalyzed aldol-lactonization.

Nguyen, Henry

2010-12-01T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

Two-Stage Fungal Pre-Treatment for Improved Biogas Production from Sisal Leaf Decortication Residues  

E-Print Network (OSTI)

Abstract: Sisal leaf decortications residue (SLDR) is amongst the most abundant agroindustrial residues in Tanzania and is a good feedstock for biogas production. Pretreatment of the residue prior to its anaerobic digestion (AD) was investigated using a twostage pre-treatment approach with two fungal strains, CCHT-1 and Trichoderma reesei in succession in anaerobic batch bioreactors. AD of the pre-treated residue with CCTH-1 at 10 % (wet weight inoculum/SLDR) inoculum concentration incubated for four days followed by incubation for eight days with 25 % (wet weight inoculum/SLDR) of T. reesei gave a methane yield of 0.292 0.04 m 3 CH4/kg volatile solids (VS)added. On reversing the pre-treatment succession of the fungal inocula using the same parameters followed by AD, methane yield decreased by about 55%. Generally, an increment in the range of 30101% in methane yield in comparison to the un-treated SLDR was obtained. The results confirmed the potential of CCHT-1 followed by Trichoderma reesei fungi pre-treatment prior to AD to achieve significant improvement in biogas production from SLDR.

Mutemi Muthangya; Anthony Manoni Msh; Amelia Kajumulo Kivaisi

2009-01-01T23:59:59.000Z

42

Synthetic studies applied to polyketide natural products  

E-Print Network (OSTI)

D. H. ; Smith, J. L. Nat. Chem. Bio. 2006, 2, 537542. 94.Iwata, M. ; Mizui, Y. Nat. Chem. Bio. 2007, 3, 570575. 218.B and FD-895 Bio. Org. Med. Chem. Lett. 2007, 17, 5159

Mandel, Alexander

2008-01-01T23:59:59.000Z

43

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

44

Application of neural networks to discriminate fungal infection levels in rice panicles using hyperspectral reflectance and principal components analysis  

Science Conference Proceedings (OSTI)

Detecting plant health condition is an important step in controlling disease and insect stress in agricultural crops. In this study, we applied neural network and principal components analysis techniques for discriminating and classifying different fungal ... Keywords: Derivative spectra, Neural networks, Principal component analysis, Remote sensing, Rice false smut disease, Rice glume blight disease, Spectral reflectance

Zhan-Yu Liu; Hong-Feng Wu; Jing-Feng Huang

2010-07-01T23:59:59.000Z

45

DOE Joint Genome Institute. Pulp NonFiction: Fungal Analysis Reveals Clues  

NLE Websites -- All DOE Office Websites (Extended Search)

March 22, 2012 March 22, 2012 Pulp NonFiction: Fungal Analysis Reveals Clues for Targeted Biomass Deconstruction Without fungi and microbes to break down dead trees and leaf litter in nature, the forest floor might look like a scene from TV's "Hoarders." Ceriporiopsis subvermispora mycelium on wood Photo: Scanning electron micrograph of Ceriporiopsis subvermispora mycelium on wood. (R. Blanchette, University of Minnesota) Massive-scale genome sequencing projects supported by the U.S. Department of Energy (DOE) and being carried out at the DOE Joint Genome Institute (JGI) highlight the importance of learning how the cellulose, hemicellulose and lignin that serve as a plant's infrastructure can be broken down by these forest organisms to extract needed nutrients. Among the fungi being

46

Gourmet and Health-Promoting Specialty OilsChapter 7 Borage, Evening Primrose, Blackcurrant, and Fungal Oils: Gamma-Linolenic Acid-rich Oils  

Science Conference Proceedings (OSTI)

Gourmet and Health-Promoting Specialty Oils Chapter 7 Borage, Evening Primrose, Blackcurrant, and Fungal Oils: Gamma-Linolenic Acid-rich Oils Health Nutrition Biochemistry eChapters Health - Nutrition - Biochemistry Press ...

47

Edge effects, not connectivity, determine the incidence and development of a foliar fungal plant disease.  

Science Conference Proceedings (OSTI)

Using a model plant-pathogen system in a large-scale habitat corridor experiment, we found that corridors do not facilitate the movement of wind-dispersed plant pathogens, that connectivity of patches does not enhance levels of foliar fungal plant disease, and that edge effects are the key drivers of plant disease dynamics. Increased spread of infectious disease is often cited as a potential negative effect of habitat corridors used in conservation, but the impacts of corridors on pathogen movement have never been tested empirically. Using sweet corn (Zea mays) and southern corn leaf blight (Cochliobolus heterostrophus) as a model plant-pathogen system, we tested the impacts of connectivity and habitat fragmentation on pathogen movement and disease development at the Savannah River Site, South Carolina, USA. Over time, less edgy patches had higher proportions of diseased plants, and distance of host plants to habitat edges was the greatest determinant of disease development. Variation in average daytime temperatures provided a possible mechanism for these disease patterns. Our results show that worries over the potentially harmful effects of conservation corridors on disease dynamics are misplaced, and that, in a conservation context, many diseases can be better managed by mitigating edge effects.

Johnson, Brenda, L.; Haddad, Nick, M.

2011-08-01T23:59:59.000Z

48

Bulk gold catalyzed oxidation reactions of amines and isocyanides and iron porphyrin catalyzed N-H and O-H bond insertion/cyclization reactions of diamines and aminoalcohols  

Science Conference Proceedings (OSTI)

This work involves two projects. The first project entails the study of bulk gold as a catalyst in oxidation reactions of isocyanides and amines. The main goal of this project was to study the activation and reactions of molecules at metal surfaces in order to assess how organometallic principles for homogeneous processes apply to heterogeneous catalysis. Since previous work had used oxygen as an oxidant in bulk gold catalyzed reactions, the generality of gold catalysis with other oxidants was examined. Amine N-oxides were chosen for study, due to their properties and use in the oxidation of carbonyl ligands in organometallic complexes. When amine N-oxides were used as an oxidant in the reaction of isocyanides with amines, the system was able to produce ureas from a variety of isocyanides, amines, and amine N-oxides. In addition, the rate was found to generally increase as the amine N-oxide concentration increased, and decrease with increased concentrations of the amine. Mechanistic studies revealed that the reaction likely involves transfer of an oxygen atom from the amine N-oxide to the adsorbed isocyanide to generate an isocyanate intermediate. Subsequent nucleophilic attack by the amine yields the urea. This is in contrast to the bulk gold-catalyzed reaction mechanism of isocyanides with amines and oxygen. Formation of urea in this case was proposed to proceed through a diaminocarbene intermediate. Moreover, formation of the proposed isocyanate intermediate is consistent with the reactions of metal carbonyl ligands, which are isoelectronic to isocyanides. Nucleophilic attack at coordinated CO by amine N-oxides produces CO{sub 2} and is analogous to the production of an isocyanate in this gold system. When the bulk gold-catalyzed oxidative dehydrogenation of amines was examined with amine N-oxides, the same products were afforded as when O{sub 2} was used as the oxidant. When the two types of oxidants were directly compared using the same reaction system and conditions, it was found that the oxidative dehydrogenation of dibenzylamine to Nbenzylidenebenzylamine, with N-methylmorpholine N-oxide (NMMO), was nearly quantitative (96%) within 24 h. However, the reaction with oxygen was much slower, with only a 52% yield of imine product over the same time period. Moreover, the rate of reaction was found to be influenced by the nature of the amine N-oxide. For example, the use of the weakly basic pyridine N-oxide (PyNO) led to an imine yield of only 6% after 24 h. A comparison of amine N-oxide and O2 was also examined in the oxidation of PhCH{sub 2}OH to PhCHO catalyzed by bulk gold. In this reaction, a 52% yield of the aldehyde was achieved when NMMO was used, while only a 7% product yield was afforded when O{sub 2} was the oxidant after 48 h. The bulk gold-catalyzed oxidative dehydrogenation of cyclic amines generates amidines, which upon treatment with Aerosil and water were found to undergo hydrolysis to produce lactams. Moreover, 5-, 6-, and 7-membered lactams could be prepared through a one-pot reaction of cyclic amines by treatment with oxygen, water, bulk gold, and Aerosil. This method is much more atom economical than industrial processes, does not require corrosive acids, and does not generate undesired byproducts. Additionally, the gold and Aerosil catalysts can be readily separated from the reaction mixture. The second project involved studying iron(III) tetraphenylporphyrin chloride, Fe(TPP)Cl, as a homogeneous catalyst for the generation of carbenes from diazo reagents and their reaction with heteroatom compounds. Fe(TPP)Cl, efficiently catalyzed the insertion of carbenes derived from methyl 2-phenyldiazoacetates into O-H bonds of aliphatic and aromatic alcohols. Fe(TPP)Cl was also found to be an effective catalyst for tandem N-H and O-H insertion/cyclization reactions when 1,2-diamines and 1,2-alcoholamines were treated with diazo reagents. This approach provides a one-pot process for synthesizing piperazinones and morpholinones and related analogues such as quinoxalinones and benzoxazin-2-ones.

Klobukowski, Erik

2011-12-29T23:59:59.000Z

49

Mycorrhizal Species Dominate the Soil-Fungal Community in Estonian Oil Shale-Ash Hills Charles Cowden, Sam Willis, and Richard Shefferson  

E-Print Network (OSTI)

Mycorrhizal Species Dominate the Soil-Fungal Community in Estonian Oil Shale-Ash Hills Charles 30602 Introduction Estonia relies on vast reserves of oil shale to produce electricity. The mining and burning of oil shale is extremely inefficient and produces large quantities of tailings and ash (Vallner

Shefferson, Richard P.

50

Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains  

Science Conference Proceedings (OSTI)

In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt to characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.

Hollister, Emily B [ORNL; Schadt, Christopher Warren [ORNL; Palumbo, Anthony Vito [ORNL; Ansley, R J [Texas A& M University; Boutton, Thomas W [Texas A& M University

2010-01-01T23:59:59.000Z

51

Fungal glycoside hydrolases for saccharification of lignocellulose: outlook for new discoveries fueled by genomics and functional studies  

DOE Green Energy (OSTI)

Genome sequencing of a variety of fungi is a major initiative currently supported by the Department of Energys Joint Genome Institute. Encoded within the genomes of many fungi are upwards of 200+ enzymes called glycoside hydrolases (GHs). GHs are known for their ability to hydrolyze the polysaccharide components of lignocellulosic biomass. Production of ethanol and next generation biofuels from lignocellulosic biomass represents a sustainable route to biofuels production. However this process has to become more economical before large scale operations are put into place. Identifying and characterizing GHs with improved properties for biomass degradation is a key factor for the development of cost effective processes to convert biomass to fuels and chemicals. With the recent explosion in the number of GH encoding genes discovered by fungal genome sequencing projects, it has become apparent that improvements in GH gene annotation processes have to be developed. This will enable more informed and efficient decision making with regard to selection and utilization of these important enzymes in bioprocess that produce fuels and chemicals from lignocellulosic feedstocks.

Jovanovic, Iva; Magnuson, Jon K.; Collart, Frank R.; Robbertse, Barbara; Adney, William S.; Himmel, Michael E.; Baker, Scott E.

2009-08-01T23:59:59.000Z

52

Effects of multiple climate change factors on the tall fescue-fungal endophyte symbiosis: infection frequency and tissue chemistry.  

Science Conference Proceedings (OSTI)

Climate change (altered CO{sub 2}, warming, and precipitation) may affect plant-microbial interactions, such as the Lolium arundinaceum-Neotyphodium coenophialum symbiosis, to alter future ecosystem structure and function. To assess this possibility, tall fescue tillers were collected from an existing climate manipulation experiment in a constructed old-field community in Tennessee (USA). Endophyte infection frequency (EIF) was determined, and infected (E+) and uninfected (E-) tillers were analysed for tissue chemistry. The EIF of tall fescue was higher under elevated CO{sub 2} (91% infected) than with ambient CO{sub 2} (81%) but was not affected by warming or precipitation treatments. Within E+ tillers, elevated CO{sub 2} decreased alkaloid concentrations of both ergovaline and loline, by c. 30%; whereas warming increased loline concentrations 28% but had no effect on ergovaline. Independent of endophyte infection, elevated CO{sub 2} reduced concentrations of nitrogen, cellulose, hemicellulose, and lignin. These results suggest that elevated CO{sub 2}, more than changes in temperature or precipitation, may promote this grass-fungal symbiosis, leading to higher EIF in tall fescue in old-field communities. However, as all three climate factors are likely to change in the future, predicting the symbiotic response and resulting ecological consequences may be difficult and dependent on the specific atmospheric and climatic conditions encountered.

Brosi, Glade [University of Kentucky; McCulley, Rebecca L [University of Kentucky; Bush, L P [University of Kentucky; Nelson, Jim A [University of Kentucky; Classen, Aimee T [University of Tennessee, Knoxville (UTK); Norby, Richard J [ORNL

2011-01-01T23:59:59.000Z

53

Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers (2010) Fungal Genetics and Biology  

Science Conference Proceedings (OSTI)

The level of genetic diversity and genetic structure in the Perigord black truffle (Tuber melanosporum Vittad.) has been debated for several years, mainly due to the lack of appropriate genetic markers. Microsatellites or simple sequence repeats (SSRs) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers. In this study, we surveyed the T. melanosporum genome (1) to characterise its SSR pattern; (2) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and (3) to identify new polymorphic SSR markers for population genetics. The T. melanosporum genome is rich in SSRs with 22,425 SSRs with mono-nucleotides being the most frequent motifs. SSRs were found in all genomic regions although they are more frequent in non-coding regions (introns and intergenic regions). Sixty out of 135 PCR-amplified mono-, di-, tri-, tetra, penta, and hexanucleotides were polymorphic (44%) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain. The number of alleles varied from 2 to 18 and the expected heterozygosity from 0.124 to 0.815. One hundred and thirty-two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high (0.999). Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation. In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system.

Murat, Claude [INRA, Nancy, France; Riccioni, C [INRA, Nancy, France; Belfiori, B [INRA, Nancy, France; Cichocki, N [INRA, Nancy, France; Labbe, Jessy L [ORNL; Morin, Emmanuelle [INRA, Nancy, France; Tisserant, Emilie [INRA, Nancy, France; Paolocci, F [INRA, Nancy, France; Rubini, A [INRA, Nancy, France; Martin, Francis [INRA, Nancy, France

2011-01-01T23:59:59.000Z

54

Deciphering the genetic basis for polyketide variation among mycobacteria producing mycolactones  

E-Print Network (OSTI)

of MlsB from pMUM003. To test this hypothesis, we performed South- ern hybridisation analysis of BACs containing either mlsA or mlsB from pMUM001, pMUM002 and pMUM003 with probes for either the KR-A or KR-B domain, and as pre- dicted, Southern analysis... . For example, the 15 KS domains share > 99.1% nucleotide identity over 1257 nts, which translates to only nine variable amino acid residues among 419 aa. There are three types of domains (LM-KS, AT-I and AT-II) that have 100% intra-species nucleotide identity...

Pidot, Sacha J; Hong, Hui; Seemann, Torsten; Porter, Jessica L; Yip, Marcus J; Men, Artem; Johnson, Matthew; Wilson, Peter; Davies, John K; Leadlay, Peter F; Stinear, Timothy P

2008-10-07T23:59:59.000Z

55

Investigation into the Nazarov Cyclization of Aryl Dienyl Ketones and Synthetic Studies Toward Tetrapetalone A  

E-Print Network (OSTI)

pH were obtained by Color pHast Indi- cator Strips pH = 0 pH were obtained by Color pHast Indicator Strips pH = 0 pH were obtained by Color pHast Indicator Strips pH = 0

Marcus, Andrew Peter

2009-01-01T23:59:59.000Z

56

Fueling the Future with Fungal Genomics  

E-Print Network (OSTI)

submerged cultures into biodiesel. Energy Fuels. 24 (5):Martnez S, Garre V. 2009. Biodiesel production from biomassexample, production of biodiesel from Mucor circinelloides

Grigoriev, Igor V.

2011-01-01T23:59:59.000Z

57

Fueling the future with fungal genomics  

E-Print Network (OSTI)

Fungi play important roles across the range of current and future biofuel production processes. From crop/feedstock health to plant biomass saccharification, enzyme production to bioprocesses for producing ethanol, higher alcohols, or future hydrocarbon biofuels, fungi are involved. Research and development are underway to understand the underlying biological processes and improve them to make bioenergy production efficient on an industrial scale. Genomics is the foundation of the systems biology approach that is being used to accelerate the research and development efforts across the spectrum of topic areas that impact biofuels production. In this review, we discuss past, current, and future advances made possible by genomic analyses of the fungi that impact plant/feedstock health, degradation of lignocellulosic biomass, and fermentation of sugars to ethanol, hydrocarbon biofuels, and renewable chemicals.

Igor V. Grigoriev A; Daniel Cullen B; Stephen B. Goodwin C; David Hibbett D; Thomas W. Jeffries B; Christian P. Kubicek E; Cheryl Kuske F; Jon K. Magnuson G; Francis Martin H; Joseph W. Spatafora I; Adrian Tsang J; Scott E. Baker A

2011-01-01T23:59:59.000Z

58

JGI - Fungal Program User Advisory Committee  

NLE Websites -- All DOE Office Websites (Extended Search)

University of California, Berkeley Stephen Goodwin, Purdue University David Hibbett, Clark University Francis Martin, INRA (France) Joseph Spatafora, Oregon State University...

59

Fueling the Future with Fungal Genomics  

E-Print Network (OSTI)

yeast for improved biofuel production. Science. 330:84-86.current and future biofuel production processes. From crop/platforms for biomass-to-biofuel production on an industrial

Grigoriev, Igor V.

2011-01-01T23:59:59.000Z

60

Fueling the Future with Fungal Genomics  

E-Print Network (OSTI)

Saccharomyces cerevisiae. Biofuels. 108:147-177. Harman GE,or future hydrocarbon biofuels, fungi are involved. Researchtopic areas that impact biofuels production. In this review,

Grigoriev, Igor V.

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

Fueling the Future with Fungal Genomics  

SciTech Connect

Fungi play important roles across the range of current and future biofuel production processes. From crop/feedstock health to plant biomass saccharification, enzyme production to bioprocesses for producing ethanol, higher alcohols or future hydrocarbon biofuels, fungi are involved. Research and development are underway to understand the underlying biological processes and improve them to make bioenergy production efficient on an industrial scale. Genomics is the foundation of the systems biology approach that is being used to accelerate the research and development efforts across the spectrum of topic areas that impact biofuels production. In this review, we discuss past, current and future advances made possible by genomic analyses of the fungi that impact plant/feedstock health, degradation of lignocellulosic biomass and fermentation of sugars to ethanol, hydrocarbon biofuels and renewable chemicals.

Grigoriev, Igor V.; Cullen, Daniel; Hibbett, David; Goodwin, Stephen B.; Jeffries, Thomas W.; Kubicek, Christian P.; Kuske, Cheryl; Magnuson, Jon K.; Martin, Francis; Spatafora, Joey; Tsang, Adrian; Baker, Scott E.

2011-04-29T23:59:59.000Z

62

SSRL HEADLINES March 2010  

NLE Websites -- All DOE Office Websites (Extended Search)

9 March, 2010 9 March, 2010 __________________________________________________________________________ Contents of this Issue: Science Highlight - Researchers Directly Observe Oxygen Signature from the Oxygen-evolving Complex of Photosynthesis Science Highlight - Deadly Carcinogen Unraveled: The Molecular Origami of Fungal Polyketides Researchers Rediscover the Structure of Water SSRL Scientific Advisory Committee Convened in March Joachim Stöhr to Deliver the 2010 Robert Hofstadter Memorial Lectures April 12-13 The 5th Annual SSRL School on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences: Theory and Application The 37th International Conference on Vacuum Ultraviolet and X-ray Physics (VUVX2010) Workshop Wrap-up on Exploring X-ray Effects on Biological Samples

63

Synthetic studies of the Thio-Nazarov Cyclization, Biomimetic Total Syntheses of Shimalactones and Exiguamines, and Synthesis of Photoswitchable Dopamine Analogs  

E-Print Network (OSTI)

J. ; Trauner, D. Nat. Chem. Bio. 2008, 4, 535537. 3. Opitz,R. J. ; Trauner, D. Nat. Chem. Bio. 2008, 4, 535537. 8.

Sofiyev, Vladimir

2010-01-01T23:59:59.000Z

64

Final Technical Report for DOE Grant, number DE-FG02-05ER15701; Probing Surface Chemistry Under Catalytic Conditions: Olefin Hydrogenation,Cyclization and Functionalization.  

Science Conference Proceedings (OSTI)

The specific goal of this work was to understanding the catalytic reactions pathways for the synthesis of vinyl acetate over Pd, Au and PdAu alloys. A combination of both experimental methods (X-ray and Auger spectroscopies, low-energy ion scattering (LEIS), low-energy electron diffraction (LEED) and theory (Density Functional Theory (DFT) calculations and Monte Carlo methods under various different reactions) were used to track the surface chemistry and the influence of alloying. The surface intermediates involved in the various reactions were characterized using reflection-absorption infrared spectroscopy and LEED to identify the nature of the surface species and temperature-programmed desorption (TPD) to follow the decomposition pathways and measure heats of adsorption. These results along with those from density functional theoretical calculations were used determine the kinetics for elementary steps. The results from this work showed that the reaction proceeds via the Samanos mechanism over Pd surfaces whereby the ethylene directly couples with acetate to form an acetoxyethyl intermediate that subsequently undergoes a beta-hydride elimination to form the vinyl acetate monomer. The presence of Au was found to modify the adsorption energies and surface coverages of important surface intermediates including acetate, ethylidyne and ethylene which ultimately influences the critical C-H activation and coupling steps. By controlling the surface alloy composition or structure one can begin to control the steps that control the rate and even the mechanism.

Neurock, Matthew

2011-05-26T23:59:59.000Z

65

BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Cloning, characterization, and engineering of fungal  

E-Print Network (OSTI)

cerevisiae strains for second generation bioethanol: improving xylose fermentation and inhibitor tolerance. Keywords Arabinose fermentation . Xylitol production . Alcohol dehydrogenase . Cofactor specificity of lignocellulosic biomass to value-added products such as bioethanol and xylitol. Saccharomyces cerevisiae

Zhao, Huimin

66

Fungal radiation in the Cape Floristic Region: An analysis based on Gondwanamyces and Ophiostoma  

E-Print Network (OSTI)

Azerbaijan AY280481 AY280461 O. fusiforme CMW 10565 Larix decidua Austria AY280484 AY280465 O. gemellus CMW USA CMW 10564 O. lunatum Austria CMW 10563 O. lunatum Austria CMW 9968 O. fusiforme Azerbaijan CMW.W., Kirisits, T., 2004. Two new Ophiostoma species with Sporothrix anamorphs from Austria and Azerbaijan

67

Fungal spore-feeding thrips (Thysanoptera: Phlaeothripidae: Idolothripinae) from Iran with record of a fourth genus  

E-Print Network (OSTI)

The genus Allothrips Hood, with one species A. bournieri Mound, is reported for the first time in Iran and the generic classification of Phlaeothripidae is discussed briefly. A key is provided to distinguish the four genera recorded in Iran of the spore-feeding thrips in the Idolothripinae.

Kambiz Minaei

2010-01-01T23:59:59.000Z

68

Comparative genomic analysis of fungal genomes reveals intron-rich ancestors  

E-Print Network (OSTI)

Additional data file 7 is a zip file containing data for theAdditional data file 8 is a zip file containing multi-FASTA

Stajich, Jason E; Dietrich, Fred S; Roy, Scott W

2007-01-01T23:59:59.000Z

69

Comparative genomic analysis of fungal genomes reveals intron-rich ancestors  

E-Print Network (OSTI)

remain debated. Genome sequencing and comparative analysisInternational Human Genome Sequencing Consortium: Finishingreinhardtii genome structure using large-scale sequencing of

Stajich, Jason E; Dietrich, Fred S; Roy, Scott W

2007-01-01T23:59:59.000Z

70

Generation of reactive oxygen species by fungal NADPH oxidases is required for rice blast disease  

E-Print Network (OSTI)

utilizing all of the known techniques for NOx reduction. To be precise, the NOx formed within the flame] and several others [6, 7] have suggested certain reduction methods which are consistent with NOx formation, not solid waste. The results of NOx reduction techniques in coal combustion should be applied with caution

Talbot, Nicholas

71

Enhancing dry-grind corn ethanol production with fungal cultivation and ozonation.  

E-Print Network (OSTI)

??Public opinion of the U.S. fuel ethanol industry has suffered in recent years despite record ethanol production. Debates sparked over the environmental impacts of corn (more)

Rasmussen, Mary

2009-01-01T23:59:59.000Z

72

Enhanced bioprocessing of lignocellulose: Wood-rot fungal saccharification and fermentation of corn fiber to ethanol.  

E-Print Network (OSTI)

??The use of bio-based feedstock to support an economy based on renewable resources is becoming extremely important for generating biofuels and biobased products to reduce (more)

Shrestha, Prachand

2008-01-01T23:59:59.000Z

73

Fungal abundance spike and the Permian^Triassic boundary in the Karoo Supergroup (South Africa)  

E-Print Network (OSTI)

. Received 2000 April 13; in original form 1999 August 2 SUMMARY The Mana Pools and Lower Zambezi Karoo with no seismic expression is required. There is a conductive feature in the two basins in the Upper Karoo of Karoo basins within the mobile belt terranes. The main features controlling tectonic processes within

74

Fungal Diversity Ceratocystis manginecans sp. nov., causal agent of a destructive  

E-Print Network (OSTI)

disease in Oman and Pakistan Marelize van Wyk1* , Ali O. Al Adawi2 , Iqrar A. Khan3 , Michael L. Deadman4 204 Sohar, 311, Sultanate of Oman 3 Plant Protection Division, Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Jhang Road, Faisalabad, Pakistan 4 Department of Crop Sciences, P.O. Box 34

75

Available Technologies: Biological Production of Polymer Monomers  

Jay Keasling and Leonard Katz of the Joint BioEnergy Institute (JBEI) have invented polyketide synthases that can be introduced into a host organism for the ...

76

The Joint BioEnergy Institute (JBEI): Developing New Biofuels by Overcoming Biomass Recalcitrance  

E-Print Network (OSTI)

JD (2009) Producing biofuels using polyketide synthases.JBEI): Developing New Biofuels by Overcoming Biomassthe next-generation of biofuels liquid fuels derived from

Scheller, Henrik Vibe; Singh, Seema; Blanch, Harvey; Keasling, Jay D.

2010-01-01T23:59:59.000Z

77

INCITE Proposal Writing Tips  

E-Print Network (OSTI)

., Werner-Washburne, M., & Himmel, M. E. (2008). Fungal Genome Sequencing and Bioenergy. Fungal Biology

78

Research Article: In silico analyses of a new group of fungal and plant RecQ4-homologous proteins  

Science Conference Proceedings (OSTI)

Bacterial and eukaryotic RecQ helicases comprise a family of homologous proteins necessary for maintaining genomic integrity during the cell cycle and DNA repair. There is one known bacterial RecQ helicase, and five eukaryotic RecQ helicases that have ... Keywords: Hrq1 sequences, Hydrophobic cluster analysis, Protein phylogeny, RecQ4 sequences, Rothmund-Thompson syndrome, Three-dimensional protein modeling

Fernanda Barea; Simone Tessaro; Diego Bonatto

2008-10-01T23:59:59.000Z

79

Multistate Outbreak of Fungal Infection Associated with Injection of Methylprednisolone Acetate Solution from a Single Compounding Pharmacy  

E-Print Network (OSTI)

was alerted by a clinician regarding a patient with cultureconfirmed Aspergillus fumigatus meningitis diagnosed 46 days after epidural steroid injection at a Tennessee ambulatory surgical center. By September 27, the initial investigation, carried out by the Tennessee Department of Health in collaboration with CDC and the North Carolina Department of Health and Human Services, had identified an additional eight patients with clinically diagnosed, culture-negative meningitis: seven in Tennessee and one in North Carolina. All nine patients had received epidural steroid injection with preservative-free methylprednisolone acetate solution (MPA), compounded at New England Compounding Center (NECC) in Framingham, Massachusetts. All nine patients had received one or more injections from three lots of MPA (lot numbers 05212012@68;

unknown authors

2012-01-01T23:59:59.000Z

80

One-Pot Formation of Functionalized Indole and Benzofuran Derivatives Using a Single Bifunctional Ruthenium Catalyst  

E-Print Network (OSTI)

Bifunctional Ruthenium Catalyst Reji N. Nair Paul J. Lee bifunctional ruthenium catalyst for cyclization of terminalof transi- tion metal based catalysts have been reported to

Nair, Reji N.; Lee, Paul J.; Grotjahn, Douglas B.

2010-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Selection of Polyacrylonitrile Fibre Modification Parameters  

Science Conference Proceedings (OSTI)

of giving PAN fibres fluffiness and volume makes them suitable as substitutes for wool, and the cyclization capacity allows using them in production of carbon...

82

The Effects of Mercury Contamination on Tree, Fungal, and Soil Composition along East Fork Poplar Creek, Anderson and Roane Counties, Tennessee.  

E-Print Network (OSTI)

??The Oak Ridge Reservation established under The Atomic Energy Commission was the site for uranium enrichment and the construction of the atomic bomb during the (more)

Jean-Philippe, Sharon

2010-01-01T23:59:59.000Z

83

Evaluation of Indoor Air Quality Parameters and Airborne Fungal Spore Concentrations by Season and Type of HVAC System in a School Building.  

E-Print Network (OSTI)

??An indoor air quality survey has been conducted in a school building. Samples were collected inone room in each wing and each level on a (more)

McLeod, Jeffrey D.

2008-01-01T23:59:59.000Z

84

Studies directed towards the total synthesis of (+)-sieboldine A  

E-Print Network (OSTI)

Progress towards the total synthesis of sieboldine A is described. This synthetic approach uses a nickel-catalyzed alkyne-ketone reductive cyclization to form the hydrindane core of the natural product in good yield and ...

Gehling, Victor S. (Victor Scott)

2008-01-01T23:59:59.000Z

85

Bispyridinium-phenylene-based copolymers: low band gap n-type alternating copolymers  

E-Print Network (OSTI)

Bispyridinium-phenylene-based conjugated donoracceptor copolymers were synthesized by a Stille cross-coupling and cyclization sequence. These polyelectrolytes are freely soluble in organic solvents and display broad optical ...

Swager, Timothy Manning

86

Modeling Soybean Rust Spore Escape from Infected Canopies: Model Description and Preliminary Results  

Science Conference Proceedings (OSTI)

Asian soybean rust, caused by Phakopsora pachyrhizi, an airborne fungal pathogen, is an annual threat to U.S. soybean production. The disease is spread during the growing season by fungal spores that are transported from warm southern locations ...

David Andrade; Zaitao Pan; William Dannevik; Jeremy Zidek

2009-04-01T23:59:59.000Z

87

Instructions for use Kerogen morphology and geochemistry at the Permian-Triassic transition in the  

E-Print Network (OSTI)

.R., Schwindt, D.M., 2003. Fungal abundance spike and the Permian­Triassic boundary in the Karoo Supergroup

Tsunogai, Urumu

88

Multistage Evolution of Dolerites in the Karoo Large Igneous Province,  

E-Print Network (OSTI)

Fungal abundance spike and the Permian^Triassic boundary in the Karoo Supergroup (South Africa of the Carlton Heights section in the southern Karoo Basin of South Africa revealed a 1-m-thick fungal spike zone of the Dicynodont Zone at other Karoo sections. Using the fungal event as a time line in marine and non

Svensen, Henrik

89

Molecular Genetic Characterization of a Cluster in A. terreus for Biosynthesis of the Meroterpenoid Terretonin  

SciTech Connect

Meroterpenoids are natural products produced from polyketide and terpenoid precursors. A gene targeting system for A. terreus NIH2624 was developed, and a gene cluster for terretonin biosynthesis was characterized. The intermediates and shunt products were isolated from the mutant strains, and a pathway for terretonin biosynthesis is proposed. Analysis of two meroterpenoid pathways corresponding to terretonin in A. terreus and austinol in A. nidulans reveals that they are closely related evolutionarily.

Guo, Chun-Jun; Knox, Benjamin P.; Chiang, Yi Ming; Lo, Hsien-Chun; Sanchez, James F.; Lee, Kuan-Han; Oakley, Berl R.; Bruno, Kenneth S.; Wang, Clay C.

2012-11-01T23:59:59.000Z

90

Methods for monitoring multiple gene expression  

DOE Patents (OSTI)

The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

Berka, Randy; Bachkirova, Elena; Rey, Michael

2013-10-01T23:59:59.000Z

91

Methods for monitoring multiple gene expression  

DOE Patents (OSTI)

The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

Berka, Randy (Davis, CA); Bachkirova, Elena (Davis, CA); Rey, Michael (Davis, CA)

2008-06-01T23:59:59.000Z

92

An Approximation Algorithm for Computing a Parsimonious ... - CECM  

E-Print Network (OSTI)

Due to the large number of species in the real data set ? 6808 fungal gene trees from 23 species ? we applied only our approximation algorithm. We observed.

93

EMSL: Joint Call for Exploratory Collaborations between EMSL...  

NLE Websites -- All DOE Office Websites (Extended Search)

for pilot projects that integrate DOE-JGI and EMSL capabilities to address the following: Biofuels production - Projects that explore plant, fungal and microbial physiology and...

94

Injectable in Situ Cross-Linking Hydrogels for Local Antifungal Therapy  

E-Print Network (OSTI)

Invasive fungal infections can be devastating, particularly in immunocompromised patients, and difficult to treat with systemic drugs. Furthermore, systemic administration of those medications can have severe side effects. ...

Kohane, Daniel S.

95

Compost Tea for the Management of Dollar Spot (Sclerotinia homoeocarpa) on Turfgrass.  

E-Print Network (OSTI)

??Turfgrasses are unique in their capability of tolerating foot traffic and physical wear, while still remaining functional and aesthetically pleasing. Fungal disease represents one of (more)

Kelloway, Stephen

2012-01-01T23:59:59.000Z

96

Advantages of Enzyme Could Lead to Improved Biofuels Production...  

NLE Websites -- All DOE Office Websites (Extended Search)

may have several advantages over other fungal and bacterial cellulases for use in biofuels production: very high specific activity, stability at elevated tempera- tures, and a...

97

JGI - Why Sequence Phycomyces blakesleeanus?  

NLE Websites -- All DOE Office Websites (Extended Search)

of Phycomyces' precisely regulated responses. The full description of a zygomycete genome will provide key information about the evolution of fungal genomes. fungus with...

98

Improved Processes for the Production of Proteins and ...  

Summary. Researchers at PNNL have developed an improved process for the production of proteins and chemicals in fungal bioprocesses. The technology is ...

99

Why sequence a cereal grain pathogen?  

NLE Websites -- All DOE Office Websites (Extended Search)

component of the American economy, and not just because of the importance of maize for biofuel production. Additionally the fungal species selected for this project are also...

100

INITIAL RESEARCH TO ASSIST THE RESTORATION OF AMERICAN CHESTNUT TO VERMONT FORESTS.  

E-Print Network (OSTI)

??The American chestnut (Castanea dentata (Marsh.) Borkh.) is a tree species of unique ecologic and economic value that was virtually eliminated by a fungal blight (more)

Gurney, Kendra

2006-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

The role of arbuscular mycorrhizal fungi in the biotransformation of coal and application in dump rehabilitation.  

E-Print Network (OSTI)

??Fundamental processes underpinning the biotransformation of coal by fungal biocatalysts have been intensively investigated, however, limited large-scale industrial applications using such systems have been reported. (more)

Mukasa-Mugerwa, Thomas Tendo

2007-01-01T23:59:59.000Z

102

Assembly and Activity of Engineered Minicellulosomes (Poster)  

DOE Green Energy (OSTI)

This poster describes the optimization of reaction conditions for c thermocellum cellulase, a comparison of c thermocellum and fungal cellulases, and development of a library of cellulosomal enzymes.

Xu, Q.; Baker, J.; Michener, B.; Brunecky R.; Adney, B.; Ding, S.-Y.; Himmel, M. E.

2009-06-01T23:59:59.000Z

103

Conservation Tillage:  

E-Print Network (OSTI)

Hosford, R.M. Jr. 1976. Fungal Leaf Spot Diseases of Wheat in North Dakota. N.D. Agric. Exp. Sta. Bull.

Today Andtomorrow Southern; Southern Region; No-till Conference; Thomas J. Gerik; Thomas J. Gerik; Bill L. Harris; Bill L. Harris

1987-01-01T23:59:59.000Z

104

Synthetic route to meso-tetra hydrocarbyl or substituted hydrocarbyl porphyrins and derivatives  

DOE Patents (OSTI)

The hydroxyl group in a pyrrolic compound having in the 2-position thereof a group having the formula R(OH)CH--R is hydrocarbyl or substituted hydrocarbyl, is replaced by a group, for example a p-nitrobenzoate group, having better leaving properties than those of hydroxyl for a subsequent self-condensation and cyclization of the pyrrolic compound to form a meso-hydrocarbyl or meso-substituted hydrocarbyl porphyrin.

Wijesekera, Tilak P. (Glen Mills, PA); Wagner, Richard W. (Murrysville, PA)

1993-01-01T23:59:59.000Z

105

Synthetic route to meso-tetra hydrocarbyl or substituted hydrocarbyl porphyrins and derivatives  

DOE Patents (OSTI)

The hydroxyl group in a pyrrolic compound having in the 2-position thereof a group having the formula R(OH)CH-R is hydrocarbyl or substituted hydrocarbyl, is replaced by a group, for example a p-nitrobenzoate group, having better leaving properties than those of hydroxyl for a subsequent self-condensation and cyclization of the pyrrolic compound to form a meso-hydrocarbyl or meso-substituted hydrocarbyl porphyrin.

Wijesekera, T.P.; Wagner, R.W.

1993-08-31T23:59:59.000Z

106

Pyrolysis Research: Bioenergy Testing and Analysis Laboratory BIOENERGY PROGRAM  

E-Print Network (OSTI)

Depcik, Mechanical Engineering) Nutrient Losses in Agriculture: the Role of Biochar and Fungal Nutrient Losses in Agriculture: the Role of Biochar and Fungal Associations Alison King (Faculty Advisor farmers mixed charcoal with them. Today, the material is known as biochar, and is loosely defined

107

Sorghum Ergot: New Disease Threat to the Sorghum Industry  

E-Print Network (OSTI)

Sorghum ergot is caused by a fungus that infects the ovaries of sorghum flowers, converting each into a white fungal mass. First discovered in Texas in March 1997, the fungus can produce large amounts of honeydew that interferes with harvest and supports soprophytic fungal growth.

Krausz, Joseph P.; Isakeit, Thomas

1998-07-20T23:59:59.000Z

108

Exposure Assessment for Bioaerosols in Health Studies  

NLE Websites -- All DOE Office Websites (Extended Search)

Exposure Assessment for Bioaerosols in Health Studies Exposure Assessment for Bioaerosols in Health Studies Speaker(s): Carol Rao Date: July 9, 2004 - 12:00pm Location: Bldg. 90 Seminar Host/Point of Contact: Mark Mendell Exposures to fungi have been linked with asthma, toxicoses, hypersensitivity pneumonitis, and a range of non-specific symptoms. Definitive associations between indoor fungal exposure and health effects in population-based exposure-response studies, however, have not been well established. Issues in exposure assessment methods, both in collection and analysis, are major limitations. Classic methods for assessing airborne fungi rely upon collecting and analyzing whole fungal spores by culture. However, quantifying whole fungal spores may not fully describe fungal exposures, especially for purposes of investigating adverse respiratory

109

241_7 Borage, Evening Primrose.pdf  

Science Conference Proceedings (OSTI)

Borage, Evening Primrose, Blackcurrant, and Fungal Oils: g-Linolenic Acid-rich Oils D.E. Barre Cape Breton University, P.O. Box 5300, Sydney, Nova Scotia, Canada B1P-6L2 7

110

LIPABASE: a database for |true| lipase family enzymes  

Science Conference Proceedings (OSTI)

Lipase enzymes play an important role in lipid metabolism and are produced by a variety of species. Compared with animal, bacterial and fungal, little is known about plant lipases. Although lipases belong to many different protein families, they have ...

Abdelmonaem Messaoudi; Hatem Belguith; Imen Ghram; Jeannette Ben Hamida

2011-11-01T23:59:59.000Z

111

GASdb: a large-scale and comparative exploration database of...  

NLE Websites -- All DOE Office Websites (Extended Search)

genomes covering 23 phyla, 62.23% (1,1351,824) of which were from fungal genomes. A green plant phylum Strepto- phyta (664 FACs) contributes to 36.40% of the FACs. All the...

112

JOl/mol of Food Pmftclian. Vv/. 64. No. J. 200/. P/1ges 401-41)4 Research Note  

E-Print Network (OSTI)

occurring car- cinogens known. and, thus, crop contamination with the toxins poses a serious health hazard of fungal pectinases and other hydro- lases (1-3) in plant cell wall degradation is well established

Cotty, Peter J.

113

Molecular Ecology (2001) 10, 471479 2001 Blackwell Science Ltd  

E-Print Network (OSTI)

are the wide and often cosmopolitan distributions of fungal species, perhaps explained by aerobiology studies relate to the dispersal biology of a common, cosmopolitan mushroom species, Schizophyllum commune Fr

114

Deposition of Particles Liberated in Gusts of Wind  

Science Conference Proceedings (OSTI)

Theoretically, the aerial transport and deposition of fungal spores near to their source dependon the way in which they become airborne. Spores of some fungi are injected into the air, independentof wind speed, whereas others are blown from the ...

DONALD E. AYLOR; H. A. MCCARTNEY; A. BAINBRIOGE

1981-10-01T23:59:59.000Z

115

November/December 2001 CSBA Presentations Review  

E-Print Network (OSTI)

honey. 4. At the moment, there appear to be very few to no air lines that are willing to ship live bees of a beehive. Christine and resear- chers in three(?) other labs are working with potential fungal control

Hammock, Bruce D.

116

Marine Bioerosion Bibliography Compiled by Mark A. Wilson (Department of Geology, The College of Wooster,  

E-Print Network (OSTI)

, and fungal tissue; vegetative composition, above- and below-ground biomass, tree growth/mortality, litterfall and biomass of terrestrial and aquatic fauna. Many long-term data records are available on the Luquillo LTER

Wilson, Mark A.

117

Effect of Virulence Factors on the Photodynamic Inactivation of Cryptococcus neoformans  

E-Print Network (OSTI)

Opportunistic fungal pathogens may cause an array of superficial infections or serious invasive infections, especially in immunocompromised patients. Cryptococcus neoformans is a pathogen causing cryptococcosis in HIV/AIDS ...

Prates, Renato A.

118

Thermophilic Gram-Positive Biocatalysts for Biomass Conversion to Ethanol  

DOE Green Energy (OSTI)

These new second generation biocatalysts have the potential to reduce the cost of SSF by minimizing the amount of fungal cellulases, a significant cost component in the use of biomass as a renewable resource for production of fuels and chemicals.

Shanmugam, K.T.; Ingram, L.O.; Maupin-Furlow, J.A.; Preston, J.F.; Aldrich, H.C.

2003-12-01T23:59:59.000Z

119

Total synthesis of cyclotryptamine and diketopiperazine alkaloids  

E-Print Network (OSTI)

I. Total Synthesis of the (+)-12,12'-Dideoxyverticillin A The fungal metabolite (+)-12,12'-dideoxyverticillin A, a cytotoxic alkaloid isolated from a marine Penicillium sp., belongs to a fascinating family of densely ...

Kim, Justin, Ph. D. Massachusetts Institute of Technology

2013-01-01T23:59:59.000Z

120

Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison  

E-Print Network (OSTI)

Abstract Background Ustilago maydis is the basidiomycete fungus responsible for common smut of corn and is a model organism for the study of fungal phytopathogenesis. To aid in the annotation of the genome sequence of this organism, several...

Ho, Eric C H; Cahill, Matt J; Saville, Barry J

2007-09-24T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

PUBLICATIONS RECORD The University of British Columbia -Department of Civil Engineering  

E-Print Network (OSTI)

imparting substances in biologically treated pulp mill effluent using Aspergillus niger fungal biomass and requirements for jobs. Water Science and Technology, 59(4): 745-753. 61. Geng, Z., E.R. Hall and P. Bérubé

Froese, Thomas

122

Investigation of microbicidal activity of surface-immobilized hydrophobic polycations  

E-Print Network (OSTI)

Hydrophobic polycations have been shown to completely kill bacterial, fungal, and viral pathogens, on-contact. Herein we describe advances with this technology on two fronts: (1) innovation of a polycationic-derivative ...

Hsu, Bryan Boen

2011-01-01T23:59:59.000Z

123

Statistical Coupling Analysis of Aspartic Proteinases Based on Crystal Structures of the Trichoderma reesei  

E-Print Network (OSTI)

, such as sugars and bioethanol.1,2 Fungal APs have been shown to participate in the processing of secreted enzymes low- cost enzymes for the conversion of plant biomass materials into industrially useful bioproducts

Wlodawer, Alexander

124

Nature's approach toward ring formation and structural diversity in ergot alkaloid biosynthesis  

E-Print Network (OSTI)

Ergot alkaloids are fungal-derived secondary metabolites well known for a diverse array of pharmacological effects both beneficial and detrimental to human health. Historically, the ergot alkaloids have been known to cause ...

Cheng, Johnathan Zandrew

2011-01-01T23:59:59.000Z

125

Plant Pathogen Resistance  

Crop plants are infected by numerous fungal and bacterial pathogens that reduce crop quality and yield. Common methods for addessing this problem include time consuming processes such as genetic engeneering, and possibly enviromentally risky ...

126

Exo-endo cellulase fusion protein  

DOE Patents (OSTI)

The present invention relates to a heterologous exo-endo cellulase fusion construct, which encodes a fusion protein having cellulolytic activity comprising a catalytic domain derived from a fungal exo-cellobiohydrolase and a catalytic domain derived from an endoglucanase. The invention also relates to vectors and fungal host cells comprising the heterologous exo-endo cellulase fusion construct as well as methods for producing a cellulase fusion protein and enzymatic cellulase compositions.

Bower, Benjamin S. (Palo Alto, CA); Larenas, Edmund A. (Palo Alto, CA); Mitchinson, Colin (Palo Alto, CA)

2012-01-17T23:59:59.000Z

127

IDENTIFICATION, PRODUCTION AND CHARACTERIZATION OF NOVEL LIGNASE PROTEINS FROM TERMITES FOR DEPOLYMERIZATION OF LIGNOCELLULOSE  

DOE Green Energy (OSTI)

Commercial preparations of fungal enzymes currently are used to digest wood for ethanol production. We demonstrated in this study that termite enzymes could improve the efficiency of fungal enzyme cocktails. Although the economic feasibility of using caterpillar expressed termite enzymes alone to treat wood was not proven, this work points to the potential to combine C-PERLXpressed insect enzymes with industrial enzyme cocktails to boost their efficiency at treating wood for biofuels.

SLACK, JEFFREY, M.

2012-12-06T23:59:59.000Z

128

The effect of Sn on the reactions of n-hexane and cyclohexane over polycrystalline Pt foils  

Science Conference Proceedings (OSTI)

The modification of the catalytic properties of a polycrystalline platinum foil by the addition of tin was studied by the reactions of n-hexane and cyclohexane in excess H{sub 2}. The reactions were studied at 13.3 kPa of n-hexane, 450 kPa of H{sub 2} and 740 K, and 6.7 kPa of cyclohexane, 450 kPa of H{sub 2} and 573 K. The Pt-Sn catalyst was characterized by Auger electron spectroscopy and by temperature-programmed desorption of CO before and after the reactions. The sites that bind CO most strongly on the Pt foil also have the highest initial turnover rate and are the first ones to be poisoned by carbon deposits from hydrocarbon reactions or by sulfur when a sulfur-containing compound (thiophene) is present in the feed. The addition of tin can block these sites preferentially, thus decreasing the undesirable high initial hydrogenolysis rate of platinum catalysts in reforming reactions and eliminating the need for presulfiding the catalyst. Also, tin suppressed the hydrogenolysis reaction preferentially to the isomerization and cyclization reactions thus increasing the selectivities to isomerization and cyclization. The amount of carbon deposited was smaller on tin containing platinum catalysts during the dehydrogenation of cyclohexane and n-hexane.

Fujikawa, T.; Ribeiro, F.H.; Somorjai, G.A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley National Lab., CA (United States)

1998-08-15T23:59:59.000Z

129

Transition metal complexes of oxazolinylboranes and cyclopentadienyl-bis(oxazolinyl)borates: Catalysts for asymmetric olefin hydroamination and acceptorless alcohol decarbonylation  

Science Conference Proceedings (OSTI)

The research presented and discussed in this dissertation involves the synthesis of transition metal complexes of oxazolinylboranes and cyclopentadienyl-bis(oxazolinyl)borates, and their application in catalytic enantioselective olefin hydroamination and acceptorless alcohol decarbonylation. Neutral oxazolinylboranes are excellent synthetic intermediates for preparing new borate ligands and also developing organometallic complexes. Achiral and optically active bis(oxazolinyl)phenylboranes are synthesized by reaction of 2-lithio-2-oxazolide and 0.50 equiv of dichlorophenylborane. These bis(oxazolinyl)phenylboranes are oligomeric species in solid state resulting from the coordination of an oxazoline to the boron center of another borane monomer. The treatment of chiral bis(oxazolinyl)phenylboranes with sodium cyclopentadienide provide optically active cyclopentadienyl-bis(oxazolinyl)borates H[PhB(C{sub 5}H{sub 5})(Ox{sup R}){sub 2}] [Ox{sup R} = Ox{sup 4S-iPr,Me2}, Ox{sup 4R-iPr,Me2}, Ox{sup 4S-tBu]}. These optically active proligands react with an equivalent of M(NMe{sub 2}){sub 4} (M = Ti, Zr, Hf) to afford corresponding cyclopentadienyl-bis(oxazolinyl)borato group 4 complexes {PhB(C{sub 5}H{sub 4})(Ox{sup R}){sub 2}}M(NMe{sub 2}){sub 2} in high yields. These group 4 compounds catalyze cyclization of aminoalkenes at room temperature or below, providing pyrrolidine, piperidine, and azepane with enantiomeric excesses up to 99%. Our mechanistic investigations suggest a non-insertive mechanism involving concerted C?N/C?H bond formation in the turnover limiting step of the catalytic cycle. Among cyclopentadienyl-bis(oxazolinyl)borato group 4 catalysts, the zirconium complex {PhB(C{sub 5}H{sub 4})(Ox{sup 4S-iPr,Me2}){sub 2}}Zr(NMe{sub 2}){sub 2} ({S-2}Zr(NMe{sub 2}){sub 2}) displays highest activity and enantioselectivity. Interestingly, {S-2}Zr(NMe{sub 2}){sub 2} also desymmetrizes olefin moieties of achiral non-conjugated aminodienes and aminodiynes during cyclization. The cyclization of aminodienes catalyzed by {S-2}Zr(NMe{sub 2}){sub 2} affords diastereomeric mixture of cis and trans cylic amines with high diasteromeric ratios and excellent enantiomeric excesses. Similarly, the desymmetrization of alkyne moieties in {S-2}Zr(NMe{sub 2}){sub 2}-catalyzed cyclization of aminodiynes provides corresponding cyclic imines bearing quaternary stereocenters with enantiomeric excesses up to 93%. These stereoselective desymmetrization reactions are significantly affected by concentration of the substrate, temperature, and the presence of a noncyclizable primary amine. In addition, both the diastereomeric ratios and enantiomeric excesses of the products are markedly enhanced by N-deuteration of the substrates. Notably, the cationic zirconium-monoamide complex [{S-2}Zr(NMe{sub 2})][B(C{sub 6}F{sub 5}){sub 4}] obtained from neutral {S-2}Zr(NMe{sub 2}){sub 2} cyclizes primary aminopentenes providing pyrrolidines with S-configuration; whereas {S-2}Zr(NMe{sub 2}){sub 2} provides R-configured pyrrolidines. The yttrium complex {S-2}YCH{sub 2}SiMe{sub 3} also affords S-configured pyrrolidines by cyclization of aminopentenes, however the enantiomeric excesses of products are low. An alternative optically active yttrium complex {PhB(C{sub 5}H{sub 4})(Ox{sup 4S-tBu}){sub 2}}YCH{sub 2}SiMe{sub 3} ({S-3}YCH{sub 2}SiMe{sub 3}) is synthesized, which displays highly enantioselective in the cyclization of aminoalkenes at room temperature affording S-configured cyclic amines with enantiomeric excesses up to 96%. A noninsertive mechanism involving a six-membered transition state by a concerted C?N bond formation and N?H bond cleavage is proposed for {S-3}YCH{sub 2}SiMe{sub 3} system based on the kinetic, spectroscopic, and stereochemical features. In the end, a series of bis- and tris(oxazolinyl)borato iridium and rhodium complexes are synthesized with bis(oxazolinyl)phenylborane [PhB(Ox{sup Me2}){sub 2}]{sub n}, tris(oxazolinyl)borane [B(Ox{sup Me2}){sub 3}]n, and tris(4,4-dimethyl-2-oxazolinyl)phenylborate [To{sup M}]{sup ?}. All these new an

Manna, Kuntal [Ames Laboratory

2012-12-17T23:59:59.000Z

130

JGI - Product Offerings  

NLE Websites -- All DOE Office Websites (Extended Search)

Product Offerings Product Offerings Scientific Program Product Brief Description Deliverables FY14 target cycle time (median), days FY14 target cycle time (75th %), days Fungal Minimal Draft Low coverage whole genome shotgun sequencing for evaluation. May turn into a standard draft or improved standard draft. Assembly. Annotation optional (JGI portal); raw data submitted to SRA 250 400 Fungal Resequencing SNP and short indel calls, rearrangement detection, population analysis. Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files, tracks for upload to genome browser and fastq files; raw data submitted to SRA 140 200 Fungal Standard Draft Whole genome shotgun sequencing. Exact scope items and quality of finished product depend on genome. Selected genomes will be improved based on feasibility and scientific merit. Assembly, annotation (JGI Portal + Genbank); raw data submitted to SRA 250 400

131

Why Sequence Chestnut Blight Fungus?  

NLE Websites -- All DOE Office Websites (Extended Search)

Chestnut Blight Fungus? Chestnut Blight Fungus? Cryphonectria parasitica, the chestnut blight fungus, is responsible for epidemics that caused the destruction of hundreds of millions of mature chestnut trees in forests of North America and Europe during the first part of the 20th century. The discovery of a group of RNA viruses, now classified in the family Hypoviridae (hypoviruses), that reduce the virulence (hypovirulence) of this pathogen stimulated intensive research into the potential of using fungal viruses for the biological control of fungal disease. Subsequent epidemiologic and population genetic studies have established the chestnut/C. parasitica/hypovirus pathosystem as the textbook example of both the consequences of accidental introduction of an exotic organism and of hypovirulence-mediated biological control of fungal

132

c004817h_LR  

NLE Websites -- All DOE Office Websites (Extended Search)

PAPER PAPER www.rsc.org/obc | Organic & Biomolecular Chemistry Insights into lignin primary structure and deconstruction from Arabidopsis thaliana COMT (caffeic acid O-methyl transferase) mutant Atomt1† Syed G. A. Moinuddin,‡ Micha¨ el Jourdes,‡ Dhrubojyoti D. Laskar, Chanyoung Ki, Claudia L. Cardenas, Kye-Won Kim, Dianzhong Zhang, Laurence B. Davin and Norman G. Lewis* Received 31st March 2010, Accepted 19th May 2010 First published as an Advance Article on the web 22nd July 2010 DOI: 10.1039/c004817h The Arabidopsis mutant Atomt1 lignin differs from native lignin in wild type plants, in terms of sinapyl (S) alcohol-derived substructures in fiber cell walls being substituted by 5-hydroxyconiferyl alcohol (5OHG)-derived moieties. During programmed lignin assembly, these engender formation of benzodioxane substructures due to intramolecular cyclization

133

United abominations: Density functional studies of heavy metal chemistry  

Science Conference Proceedings (OSTI)

Carbonyl and nitrile addition to uranyl (UO{sup 2}{sup 2+}) are studied. The competition between nitrile and water ligands in the formation of uranyl complexes is investigated. The possibility of hypercoordinated uranyl with acetone ligands is examined. Uranyl is studied with diactone alcohol ligands as a means to explain the apparent hypercoordinated uranyl. A discussion of the formation of mesityl oxide ligands is also included. A joint theory/experimental study of reactions of zwitterionic boratoiridium(I) complexes with oxazoline-based scorpionate ligands is reported. A computational study was done of the catalytic hydroamination/cyclization of aminoalkenes with zirconium-based catalysts. Techniques are surveyed for programming for graphical processing units (GPUs) using Fortran.

Schoendorff, George

2012-04-02T23:59:59.000Z

134

Analogy and Difference between Gelation and Percolation Process  

E-Print Network (OSTI)

It has been verified that the theory of gelation with cyclization effects is in good accord with experimental observations of gel points and gel fractions. Encouraged by this success we scrutinize the prediction limit of the theory through the rigor of the bond percolation theory. Significant disparity is found between the prediction of the gelation theory and that of the percolation theory. To find the reason of the disparity, we re-examine the distribution function of bond animals; the analysis showing that the percolation process differs from real gelations in two points: (i) whereas the real gelation obeys the principle of equireactivity of functional units, the percolation process does not; (ii) the substantial reduction of functionality occurs through the percolation process. These make the lattice model intrinsically different from real chemical processes. As a result, one can not make use of the percolation theory for the purpose of examining the validity of the gelation theory.

Kazumi Suematsu

2004-10-06T23:59:59.000Z

135

Development of Lewis Base Catalyzed Stereoselective Methods for Synthesis of Beta- Lactones and Dyotropic Rearrangements of Tricyclic Beta-Lactones.  

E-Print Network (OSTI)

The recent finding that the FDA-approved antiobesity agent orlistat (tetrahydrolipstatin, Xenical) is a potent inhibitor of the thioesterase domain of fatty acid synthase (FAS) led us to develop a concise and practical asymmetric route to pseudosymmetric 3,4-dialkyl-cis-beta-lactones. The well-documented upregulation of FAS in cancer cells makes this enzyme complex an interesting therapeutic target for cancer. The described route to 3,4-dialkyl- beta -lactones is based on a two-step process involving Calter's catalytic, asymmetric ketene dimerization of acid chlorides followed by a facialselective hydrogenation leading to cis-substituted- beta -lactones. Importantly, the ketene dimer intermediates were found to be stable to flash chromatography, enabling opportunities for subsequent transformations of these optically active, reactive intermediates. Subsequent R-epimerization and R-alkylation or acylation led to trans- beta - lactones and beta -lactones bearing alpha-quaternary carbons, respectively. Several of the ketene dimers and beta-lactones displayed antagonistic activity (apparent Ki in the low micromolar range) in competition with a fluorogenic substrate toward a recombinant form of the thioesterase domain of fatty acid synthase. The best antagonist, a simple phenyl-substituted cis- beta -lactone, displayed an apparent Ki (2.5 ( 0.5 muM) of only 10- fold lower than that of orlistat (0.28 ( 0.06 muM). In addition, mechanistic studies of the ketene dimerization process by Reaction View infrared spectroscopy support previous findings that ketene formation is rate determining. A highly diastereoselective, nucleophile-promoted bis-cyclization process, employing readily available and tractable keto-acid substrates, is described. This methodology provides concise access to bicyclic- and tricyclic-beta-lactones bearing tertiary carbinol centers and quaternary carbons, greatly extending the scope of previous routes to bicyclic-beta-lactones from aldehyde acid substrates. This and related processes may be revealing a subtle interplay between [2 plus 2] cycloaddition and nucleophilecatalyzed aldol lactonization (NCAL) reaction manifolds. An early induction period in the bis-cyclization of keto-acids is confirmed via isolation of the complex between 4- pyrrolopyridine and Modified Mukaiyama reagent N-propyl-2-bromo pyridinium triflate. Dyotropic rearrangements of tricyclic keto beta-lactones derived in high yields and >19:1 diastereoselectivity from readily available 1, 3-dione acids is described. Zn (II) salts were found to be most efficient for affecting dyotropic 1, 2-acyl migrations where as sub stoichiometric TMSOTf was found to execute a delta-lactone migration providing bis gamma-lactone in modest yields. Enantioselective desymmetrization with inexpensive (S) - tetramisole has been demonstrated to provide direct evidence of Lewis base involvement in the Nucleophile Promoted Bis-cyclization of keto-acids. Further studies using TsCl as the carboxylate activating agent instead of modified Mukaiyama reagent and catalytic tetramisole are described for achieving practical, catalytic, enantioselective synthesis of beta-lactones from keto-acids. Preliminary studies toward conjugate addition- lactonization pathway provided a hint as to the complexity involved to affect this transformation under the bis-cyclization conditions. An alternate hypotheses concerning the possibility of isomerization-dienolate formation - lactonization is experimentally proven. Additionally, applications of these and related findings in the intramolecular Morita-Baylis-Hillman reaction with cyclic ketones have been investigated which provide new avenues of synthetic methodology development.

Purohit, Vikram C.

2008-12-01T23:59:59.000Z

136

Evaluate reformer performance at a glance  

Science Conference Proceedings (OSTI)

Catalytic reforming is becoming increasingly important in replacing octane lost as the removal of lead from worldwide gasoline pools continues. A method has been developed that can quickly evaluate the performance of any catalytic reformer. The catalytic naphtha reforming process primarily involves three well-known reactions. These are aromatization of naphthenes, cyclization of paraffins and hydrocracking of paraffins. Hydrogen is produced in the process of aromatization and dehydrocyclization of paraffins. Reformer performance is normally evaluated with a reformate analysis (PONA) and yield of C{sub 5{sup +}} reformate. This method of quick evaluation of reformer performance is based upon the main assumption that the increase in hydrocarbon moles in the process is equal to the number of C{single_bond}C bond ruptures and one mole of hydrogen is absorbed to saturate the same. This new method calculates aromatization efficiency, paraffin conversion, aromatic selectivity and finally the paraffin, naphthene and aromatic content of C{sub 5{sup +}} reformate.

Nag, A. [Indian Oil Corporation Ltd., Gujarat (India)

1996-02-01T23:59:59.000Z

137

Synthetic Studies Toward Selected Members of the Pyrrole-imidazole Alkaloids: Axinellamine, Konbuacidin and Palau' amine  

E-Print Network (OSTI)

The pyrrole imidazole alkaloids (PIA) is an ever-growing family of structurally related natural products isolated from several species of sponges which now features more than one hundred memebrs. Their complex molecular architectures, and in some cases, significant biological activities, have made these alkaloids the synthetic targets of a number of research groups across the world. In our approach, following early biosynthetic proposal by Kinnel and Scheuer and Al-Mourabit and Potier, it was envisioned that several of these alkaloids, namely palauamine, axinellamine, konbuacidin, styloguanidine and massadine, could be derived from a common chlorocyclopentane precursor through different modes of intramolecular cyclization. Building on the work done previously in our research group by Dr. Anja Dilley, Dr. Paul Dransfield, and Dr. Shaohui Wang, my investigations led to the synthesis of the angular aza-triquinane core of axinellamine and the peculiar transazabicyclo[ 3.3.0]octane core of palauamine. In my further studies mono- and bis-pyrrole advanced intermediates were synthesized that contain the complete carbon framework of the target natural products. However, attempts to induce the pivotal, potentially biomimetic cyclizations expected to deliver the cores of the target alkaloids proved to be rather challenging, resulting in inconsistent and irreproducible results and leading to the exploration of an alternative, abiotic approach. My efforts in this direction resulted in the synthesis of a pentacyclic enamine precursor to styloguanidine and a pentacyclic carbinolamine suitable for the synthesis of palauamine. Final attempts to complete the target natural products were however unsuccessful.

Zancanella, Manuel

2010-08-01T23:59:59.000Z

138

Toward the Total Synthesis of Norzoanthamine: The Development of a Transannular Michael Reaction Cascade  

E-Print Network (OSTI)

Norzoanthamine is a complex heptacyclic marine alkaloid isolated from colonial zoanthids. It potently inhibits loss of bone weight and strength in a postmenopausal osteoporosis mouse model, but its mode-of-action remains unknown. The scarcity of this natural product from its natural source and the need to access analogs for structure-activity relationship (SAR) study make it necessary to chemically synthesize this compound. However, the complex molecular skeleton, especially the highly functionalized and stereochemically complex ABC core structure of the natural product poses a significant challenge. As part of our efforts to develop a practical synthetic route to norzoanthamine, we systematically explored a transannular Michael reaction cascade in the context of the synthesis of angular 6-6-6 tricyclic ring system, a mimic of the ABC core structure of norzoanthamine. Using 1,7-bis-enones in the form of 14-membered macrocyclic lactone as model substrates, we demonstrated that both E,Z- and E,E-macrocycles underwent facile transannular reactions to give cis-syn-cis and trans-anti-trans ring systems, respectively. However, Z,E- and Z,Z- macrocycles did not cyclize under similar reactions. The similarities and differences between transannular Diels-Alder reactions and this transannular cyclization process were also disclosed. Building upon these preliminary studies, we developed a 12-linear step synthesis of the ABC carbocyclic core of norzoanthamine. It features an organocatalytic asymmetric intramolecular aldolization to set the stereochemistry of the entire molecule, a fragment coupling based on selective alkylation of a bis-enolate, and a transannular Michael reaction cascade for rapid and stereoselective synthesis of the polycyclic core. Subsequent Claisen rearrangement enabled installation of a handle for introduction of the bottom piece to complete the total synthesis. Other efforts toward the total synthesis have also been discussed.

Xue, Haoran

2013-05-01T23:59:59.000Z

139

OGI School of Science & Engineering www.ogi.edu/catalog  

E-Print Network (OSTI)

oxygen species; antioxidant; plant disease. Abstract Mannitol has been hypothesized to play a role; Witteveen & Visser, 1995). Mannitol also quenches reactive oxygen species (ROS) (Smirnoff & Cumbes, 1989 of Cryptococcus neoformans by human neutrophils: evidence that fungal mannitol protects by scavenging reactive

Chapman, Michael S.

140

This article was published in an Elsevier journal. The attached copy is furnished to the author for non-commercial research and  

E-Print Network (OSTI)

(Guillen et al., 1998) (77% similar, 67% identical for LePAR1 and 84% simi- lar/69% identical for LePAR2 reductase from V. radiata was shown to reduce the fungal toxin eutypine (Guillen et al., 1998). Again dehydro- genase in higher plants: molecular cloning and expression. Plant Mol. Biol. 36, 755­765. Guillen

Klee, Harry J.

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
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141

3.1.1.2 Feed Processing and Handling DL2 Final Report  

DOE Green Energy (OSTI)

This milestone report is the deliverable for our Feed Processing and Handling project. It includes results of wet biomass feedstock analysis, slurry pumping information, fungal processing to produce a lignin-rich biorefinery residue and two subcontracted efforts to quantify the amount of wet biomass feedstocks currently available within the corn processing and paper processing industries.

Elliott, Douglas C.; Magnuson, Jon K.; Wend, Christopher F.

2006-09-30T23:59:59.000Z

142

AnnualReport2009-2010 Beckman Institute for Advanced Science and Technology  

E-Print Network (OSTI)

(syphilis, Lyme), viral (HIV, hepatitis B, parvovirus, other), fungal, parasitic b. Whipple's disease c.Serologic and PCR tests for Lyme disease, HIV, Hepatitis B, Hepatitis C, parvovirus and other infectious streptococcal antibody tests, Lyme serologies, serum and urine uric acid levels, circulating immune complexes

Illinois at Urbana-Champaign, University of

143

The use of spectroscopic techniques (especially phosphorus-31 nuclear magnetic resonance [31  

E-Print Network (OSTI)

the apparent environmental problems. Spent mushroom compost (high fungal content) was applied to soil at a rate replaced by transplanting strawberry seedlings in plugs containing compost colonised by a mixture of bacteria, fungi and their respective consumers. This compost promoted the establishment of a complex food

Sparks, Donald L.

144

Competition Comments Commentaires  

E-Print Network (OSTI)

-native disease called the white pine blister rust that has killed many of these trees in the Park. Climate change is a non-native fungal disease introduced to North America in 1910 called the white pine blister rust (Tomback et al. 2001). The blister rust soon spread throughout most of the range of the whitebark pine

Le Roy, Robert J.

145

Bacterial extracellular lignin peroxidase  

DOE Patents (OSTI)

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.

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

1993-01-01T23:59:59.000Z

146

Bacterial metal leaching and bioaccumulation. (Latest citations from the Life Sciences Collection database). Published Search  

Science Conference Proceedings (OSTI)

The bibliography contains citations concerning bioleaching and bioaccumulation in metal recovery systems. References study bacterial oxidation, fungal metabolism, metal extraction, and metal recovery from deposits. Gold and uranium ore treatments are discussed. Toxicity characteristic leaching procedure (TCLP) tests and ultrasound pretreatment are examined. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

NONE

1996-06-01T23:59:59.000Z

147

The Crystal Structure and Mechanism of an Unusual Oxidoreductase, GilR, Involved in Gilvocarcin V Biosynthesis  

SciTech Connect

GilR is a recently identified oxidoreductase that catalyzes the terminal step of gilvocarcin V biosynthesis and is a unique enzyme that establishes the lactone core of the polyketide-derived gilvocarcin chromophore. Gilvocarcin-type compounds form a small distinct family of anticancer agents that are involved in both photo-activated DNA-alkylation and histone H3 cross-linking. High resolution crystal structures of apoGilR and GilR in complex with its substrate pregilvocarcin V reveals that GilR belongs to the small group of a relatively new type of the vanillyl-alcohol oxidase flavoprotein family characterized by bicovalently tethered cofactors. GilR was found as a dimer, with the bicovalently attached FAD cofactor mediated through His-65 and Cys-125. Subsequent mutagenesis and functional assays indicate that Tyr-445 may be involved in reaction catalysis and in mediating the covalent attachment of FAD, whereas Tyr-448 serves as an essential residue initiating the catalysis by swinging away from the active site to accommodate binding of the 6R-configured substrate and consequently abstracting the proton of the hydroxyl residue of the substrate hemiacetal 6-OH group. These studies lay the groundwork for future enzyme engineering to broaden the substrate specificity of this bottleneck enzyme of the gilvocarcin biosynthetic pathway for the development of novel anti-cancer therapeutics.

Noinaj, Nicholas; Bosserman, Mary A.; Schickli, M. Alexandra; Piszczek, Grzegorz; Kharel, Madan K.; Pahari, Pallab; Buchanan, Susan K.; Rohr, Jrgen (NIH); (Kentucky)

2012-11-26T23:59:59.000Z

148

Molecular genetic analysis reveals that a nonribosomal peptide synthetase-like (NRPS-like) gene in Aspergillus nidulans is responsible for microperfuranone biosynthesis  

SciTech Connect

Genome sequencing of Aspergillus species including A. nidulans has revealed that there are far more secondary metabolite biosynthetic gene clusters than secondary metabolites isolated from these organisms. This implies that these organisms can produce additional secondary metabolites have not yet been elucidated. The A. nidulans genome contains twelve nonribosomal peptide synthetase (NRPS), one hybrid polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS), and fourteen NRPS-like genes. The only NRPS-like gene in A. nidulans with a known product is tdiA which is involved in terrequinone A biosynthesis. To attempt to identify the products of these NRPS-like genes, we replaced the native promoters of the NRPS-like genes with the inducible alcohol dehydrogenase (alcA) promoter. Our results demonstrated that induction of the single NRPS-like gene AN3396.4 led to the enhanced production of microperfuranone. Furthermore, heterologous expression of AN3396.4 in A. niger confirmed that only one NRPS-like gene, AN3396.4, is necessary for the production of microperfuranone.

Yeh, Hsu-Hua; Chiang, Yi Ming; Entwistle, Ruth; Ahuja, Mammeet; Lee, Kuan-Han; Bruno, Kenneth S.; Wu, Tung-Kung; Oakley, Berl R.; Wang, Clay C.

2012-04-10T23:59:59.000Z

149

Large scale total synthesis of apoptolidinone and progress towards the total synthesis of ammocidin  

E-Print Network (OSTI)

Apoptolidin 1.1 was isolated in 1997 by Hayakawa and co-workers from a soil bacterium Nocardiopsis sp. during screening for specific apoptosis inducers. The primary biological test revealed that this polyketide macrolide induced apoptosis in cells transformed with the adenovirus type E1A oncognene, but not normal cells. This dissertation describes the latest studies in understanding of apoptolidins biological activity mechanism and previous contributions towards its total synthesis. Synthesizing apoptolidinone 1.26 by an intra-molecular Horner-Wadsworth-Emmons approach featuring a Suzuki coupling, cross metathesis and two diastereoselective aldol reactions is discussed. 15 mg apoptolidinone is prepared via our previously developed intramolecular Suzuking coupling approach. Ammocidin 3.1, which was found to induce apoptosis in Ba/F3-v12 cells in an IL- 3 free medium, is a specific apoptosis inducer discovered by Hayakawa and co-workers in 2001 from Saccharothrix sp. AJ9571. A strategy featuring Suzuki coupling, cross metathesis, Yamaguchi macrolactonization and three asymmetric aldol reactions was applied to the total synthesis of ammocidinone 3.6, the aglycone of ammocidin. The preparation of the key building blocks was discussed in the following chapter: aldehyde 3.8 (C14-C19) was synthesized via Sharpless asymmetric epoxidation; ethyl ketone 3.9 (C20-C28) was prepared via Kobayashi and Crimminss asymmetric aldol methodologies; aldehyde 3.14 (C7-C13) was generated by Brown crotylation and cross metathesis.

Liu, Qingsong

2006-12-01T23:59:59.000Z

150

Expanding beta-turn analogs for mimicking protein-protein hot spots  

E-Print Network (OSTI)

Solid-phase syntheses of two 14-membered ring peptidomimetics were done to determine whether or not a beta-turn structure can facilitate macrocyclization. NMR methods, together with CD and QMD calculations, do not fully support this assumption. However, cyclizations of more ordered structures like those of compounds 2 were more efficient than those for highly strained ring systems like 1. A small library of 18-membered ring peptidomimetics that accommodate an extra amino acid residue was synthesized on resin. Their syntheses were not complicated by head-to-tail dimer impurity, unlike those for previously synthesized 14-membered systems. These larger macrocycles exhibit beta-turn structures as verified by NMR, CD and QMD techniques. Moreover, two compounds in this series (3a and 3g) were shown to have agonistic properties for TrkC in cell survival assays. Dimerization of monovalent mimics was achieved first by modifying the organic template so that monovalent mimics with requisite functional groups can be synthesized. Second, the monovalent units were dimerized using sequential nucleophilic substitutions on fluorescently labeled dichlorotriazine. Our rationale to make bivalent compounds out of monovalent ones was justified when compound 4 was shown to bind TrkA with a 20 nM affinity. Reactions of amino acids with NH4SCN under acylating conditions produced 2-thiohydantoins in which the nitrogen of the amino acid (N1) was acylated. This was proven by 2-D NMR which showed no cross-peak between the NH signal observed and the C?-H of the amino acid. When the compound was deacylated, a new NH signal appeared and the corresponding cross-peak with the C?-H was observed. Solution-phase syntheses of non-peptidic mimics were achieved by doing a double substitution on a dihalogenated nitrobenzene scaffold. Sonogashira and SNAr reactions were done to install the required side-chains to give the desired compounds. These non-peptidic compounds can be easily adapted to our DTAF-Inp dimerization protocol since the nitro groups can be easily reduced. Attempts to make a spirotetracyclic peptidomimetic with three side chain mimics were done by synthesizing the spirocyclic diketopiperazine precursor. The synthesis of the DKP was achieved by making the cyclic quaternary amino acid that was coupled to another amino acid via the HOAt-EDC method. This protocol gave dipeptides in high yields. These dipeptides were deprotected and cyclized to the DKP under mildly acidic conditions in toluene.

Reyes, Samuel Onofre J.

2006-08-01T23:59:59.000Z

151

JGI - CSP Sequencing Plans for 2011  

NLE Websites -- All DOE Office Websites (Extended Search)

1 1 For status information, see the Genome Projects section. Proposer Affiliation Project Description Algae Kerfeld, Cheryl DOE JGI Genome and Transcriptome Analyses of Two Extremely Acidophilic and One Neutrophilic Eukaryotic Algal Species with Diverse Mechanism for CO2 Acquisition Lovejoy, Connie Laval University, Canada Small planktonic single celled eukaryotes from the Arctic Ocean Plants Muehlbauer, Gary University of Minnesota Whole genome shotgun sequencing of the barley genome Vogel, John USDA-ARS Surveying natural diversity of the model grass Brachypodium distachyon Fungi de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre, the Netherlands Comparative analysis of Aspergilli to facilitate novel strategies in fungal biotechnology Goodwin, Stephen Purdue University Sequencing of pathogens and extremophiles in the Dothideomycetes

152

Methods of increasing secretion of polypeptides having biological activity  

DOE Patents (OSTI)

The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

Merino, Sandra

2013-10-01T23:59:59.000Z

153

research 1..7  

NLE Websites -- All DOE Office Websites (Extended Search)

Digestibility Digestibility of Corn Stover Fractions in Response to Fungal Pretreatment Zhifang Cui, †,§ Caixia Wan, †,§ Jian Shi, † Robert W. Sykes, ‡ and Yebo Li* ,† † Department of Food, Agricultural, and Biological Engineering, The Ohio State University/Ohio Agricultural Research and Development Center, 1680 Madison Avenue, Wooster, Ohio 44691-4096, United States ‡ BioEnergy Science Center, National Renewable Energy Laboratory, Golden, Colorado 80401-3305, United States ABSTRACT: Corn stover fractions (leaves, cobs, and stalks) were studied for enzymatic digestibility after pretreatment with a white rot fungus, Ceriporiopsis subvermispora. Among the three fractions, leaves had the least recalcitrance to fungal pretreatment and the lignin degradation reached 45% after 30 days of pretreatment. The lignin degradation of stalks and cobs was similar but was significantly

154

Why sequence Postia placenta ?  

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Postia placenta? Postia placenta? Commonly found in forest ecosystems, brown rot fungi such as Postia placenta are a major cause of wood decay and are thought to be responsible for 10 percent of the wood decay in the annual timber harvest. Unlike white-rot fungi, however, brown-rot fungi can rapidly break down the cellulose in wood without affecting the lignin. The 33 Mbp genome of P. placenta was sequenced in 2006 using the tried-and-true Sanger method, and was published in 2009. The information allowed researchers to compare white-rot, brown-rot and soft-rot fungal genomes for the first time. Now researchers plan to resequence the genome using new sequencing technologies in order to further refine the genomic data collected during the assembly and annotation process. The fungal

155

Print  

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Fungi play key roles in DOE- Fungi play key roles in DOE- relevant missions of bioenergy production, bioremediation and carbon cycling. In bioenergy proj- ects alone, for example, fungal genome data have been used not only to ensure the health of crops that serve as biomass feedstocks but also provide enzymes that can break down the biomass as well as help convert it to transportation fuel. The DOE JGI has developed a Fungal Genomics Program headed by Igor Grigoriev. The program's first project, launched October 1, is the Genome Encyclopedia of Fungi (GEF). The program aims to explore fungi's ecological diversity and breadth across the Tree of Life for DOE-relevant science and applications. DOE JGI pioneered sequenc- ing and analysis of several fungi important for lignocellu- lose degradation, enzyme pro-

156

Novel Combination of Enzyme Systems Could Lower Biofuel Costs (Fact Sheet), Highlights in Science, NREL (National Renewable Energy Laboratory)  

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Two natural enzyme systems-one produced by Two natural enzyme systems-one produced by fungi and the other by bacteria-break down cel- lulose faster if used in combination. The resulting process shows promise for less expensive biofuels. Researchers from the National Renewable Energy Laboratory (NREL) and their partners studied a cocktail of individual fungal enzymes that depoly- merize biomass, and an alternative bacterial system in which multiple biomass-degrading enzymes, termed the cellulosome, are linked together by a protein scaffold. This study suggests that two of the most thoroughly studied and distinct paradigms of biomass degradation, namely free fungal enzymes and multi-enzyme bacterial cellulosomes, function together in an unexpected way to efficiently break down polysaccharides.

157

c3ee00019b 1..10  

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Fungal Fungal cellulases and complexed cellulosomal enzymes exhibit synergistic mechanisms in cellulose deconstruction† Michael G. Resch, * ab Bryon S. Donohoe, ab John O. Baker, ab Stephen R. Decker, ab Edward A. Bayer, c Gregg T. Beckham de and Michael E. Himmel ab Nature has evolved multiple enzymatic strategies for the degradation of plant cell wall polysaccharides, which are central to carbon flux in the biosphere and an integral part of renewable biofuels production. Many biomass-degrading organisms secrete synergistic cocktails of individual enzymes with one or several catalytic domains per enzyme, whereas a few bacteria synthesize large multi-enzyme complexes, termed cellulosomes, which contain multiple catalytic units per complex. Both enzyme systems employ similar catalytic chemistries; however, the physical mechanisms by which these enzyme systems degrade polysaccharides

158

Ghimire et al 2010.pdf  

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of of fungal endophyte communities inhabiting switchgrass (Panicum virgatum L.) growing in the native tallgrass prairie of northern Oklahoma Sita R. Ghimire & Nikki D. Charlton & Jeremey D. Bell & Yelugere L. Krishnamurthy & Kelly D. Craven Received: 24 November 2010 / Accepted: 12 December 2010 # Kevin D. Hyde 2010 Abstract This study was conducted to explore fungal endophyte communities inhabiting native switchgrass plants from the tallgrass prairie of northern Oklahoma. The primary focus was to isolate these endophytes in pure culture from surface-sterilized plant tissues and provide taxonomic identifications based on comparative analysis of ITS rDNA gene sequences. From these data, we evaluated the biodiversity of these potentially beneficial endosym- bionts from this rapidly disappearing habitat of the Great Plains. While important from a strictly

159

Enrichment, isolation and characterization of fungi tolerant to 1-ethyl-3-methylimidazolium acetate  

DOE Green Energy (OSTI)

This work aims to characterize microbial tolerance to 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), ionic liquid that has emerged as a novel biomass pretreatment for lignocellulosic biomass. Enrichment experiments performed using inocula treated with [C2mim][OAc] under solid and liquid cultivation yielded fungal populationsdominated by Aspergilli. Ionic liquid-tolerant Aspergillus isolates from these enrichments were capable of growing in a radial plate growth assay in the presence of 10% [C2mim][OAc]. When a [C2mim][OAc]-tolerant Aspergillus fumigatus strain was grown in the presence of switchgrass, endoglucanases and xylanases were secreted that retained residual enzymatic activity in the presence of 20% [C2mim][OAc]. The results of the study suggest tolerance to ionic liquids is a general property of Aspergilli. Tolerance to an industrially important ionic liquid was discovered in a fungal genera that is widely used in biotechnology, including biomass deconstruction.

Singer, S.W.; Reddy, A. P.; Gladden, J. M.; Guo, H.; Hazen, T.C.; Simmons, B. A.; VanderGheynst, J. S.

2010-12-15T23:59:59.000Z

160

Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum  

Science Conference Proceedings (OSTI)

Environmental and metabolic adaptability is critical for survival of the fungal human pathogen Aspergillus fumigatus in the immunocompromised lung. We employed an activity-based protein profiling (ABPP) approach utilizing a new aryl vinyl sulfonate probe and a serine hydrolase probe combined with quantitative LC-MS based accurate mass and time (AMT) tag proteomics for the identification of functional pathway adaptation of A. fumigatus to environmental variability relevant to pulmonary Invasive Aspergillosis. When the fungal pathogen was grown with human serum, metabolism and energy processes were markedly decreased compared to no serum culture. Additionally, functional pathways associated with amino acid and protein biosynthesis were limited as the fungus scavenged from the serum to obtain essential nutrients. Our approach revealed significant metabolic adaptation by A. fumigatus, and provides direct insight into this pathogens ability to survive and proliferate.

Wiedner, Susan D.; Burnum, Kristin E.; Pederson, Leeanna M.; Anderson, Lindsey N.; Fortuin, Suereta; Chauvigne-Hines, Lacie M.; Shukla, Anil K.; Ansong, Charles; Panisko, Ellen A.; Smith, Richard D.; Wright, Aaron T.

2012-08-03T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

Soil microbial community response to precipitation change in a semi-arid ecosystem  

SciTech Connect

Microbial communities regulate many belowground carbon cycling processes; thus, the impact of climate change on the struc- ture and function of soil microbial communities could, in turn, impact the release or storage of carbon in soils. Here we used a large-scale precipitation manipulation ( 18%, 50%, or ambient) in a pi on-juniper woodland (Pinus edulis-Juniperus mono- sperma) to investigate how changes in precipitation amounts altered soil microbial communities as well as what role seasonal variation in rainfall and plant composition played in the microbial community response. Seasonal variability in precipitation had a larger role in determining the composition of soil microbial communities in 2008 than the direct effect of the experimental precipitation treatments. Bacterial and fungal communities in the dry, relatively moisture-limited premonsoon season were compositionally distinct from communities in the monsoon season, when soil moisture levels and periodicity varied more widely across treatments. Fungal abundance in the drought plots during the dry premonsoon season was particularly low and was 4.7 times greater upon soil wet-up in the monsoon season, suggesting that soil fungi were water limited in the driest plots, which may result in a decrease in fungal degradation of carbon substrates. Additionally, we found that both bacterial and fungal communities beneath pi on pine and juniper were distinct, suggesting that microbial functions beneath these trees are different. We conclude that predicting the response of microbial communities to climate change is highly dependent on seasonal dynam- ics, background climatic variability, and the composition of the associated aboveground community.

Cregger, Melissa [ORNL; Schadt, Christopher Warren [ORNL; McDowell, Nathan [Los Alamos National Laboratory (LANL); Pockman, William [University of New Mexico, Albuquerque; Classen, Aimee T [University of Tennessee, Knoxville (UTK)

2012-01-01T23:59:59.000Z

162

Assessing Population-level Risks of Wind Power Development for the Indiana Bat (Myotis sodalis)  

Science Conference Proceedings (OSTI)

Continued development of wind energy must confront the challenge of managing risks to wildlife populations. Presently, construction of new wind facilities in much of the eastern United States is being hindered by concerns over possible impacts to the threatened Indiana bat (Myotis sodalis). These concerns are heightened by the emergence of a virulent fungal pathogen, white-nose syndrome, affecting hibernating colonies. While migratory tree bat fatalities at wind facilities are common, ...

2012-12-20T23:59:59.000Z

163

THE ROLE FUNGI AND YEAST IN MONITORED NATURAL ATTENUATION  

SciTech Connect

Fungi and yeast have been characterized as important components in the bioremediation of organic contaminants in soil and water including polyaromatic hydrocarbons (PAHs); however, research into their ability to metabolize these compounds in extreme environments has been limited. In this work forty-three fungi and yeasts were isolated from a PAH-contaminated sludge waste lagoon in Poland. The lagoon was part of a monitored natural attenuation (MNA) study where natural reduction of PAHs and associated toxicity over time in non-disturbed areas of the sludge lagoon indicated MNA activity. The microorganisms were initially isolated on minimal medium containing naphthalene as the sole carbon and energy source. Fungal isolates were then maintained on MEA and identified based on microscopic examination and BIOLOG{reg_sign}. The analysis identified several of the fungal isolates as belonging to the genera Penicillium, Paecilomyces, Aspergillus, and Eupenicillium. Yeasts included Candida parapsilosis and C. fluvialitis. Further microbial characterization revealed that several isolates were capable of rowing on acidified media of pH 4, 3, and 2.5. Over twenty percent of the fungi demonstrated growth as low as pH 2.5. Of the 43 isolates examined, 24 isolates exhibited growth at 5 C. Nine of the fungal isolates exhibiting growth at 5 C were then examined for metabolic activity using a respirometer testing metabolic activity at pH 3. Microcosm studies confirmed the growth of the fungi on PAH contaminated sediment as the sole carbon and energy source with elevated metabolic rates indicating evidence of MNA. Our findings suggest that many of the Poland fungal isolates may be of value in the bioremediation processes in acidic waste sites in northern climates typical of Northern Europe.

Brigmon, R.; Abe, M.; Johnson, B.; Simpson, W.; Mckinsey, P.

2010-01-26T23:59:59.000Z

164

Fifth international fungus spore conference. [Abstracts]: Final technical report  

DOE Green Energy (OSTI)

This folio contains the proceedings of the Fifth International Fungal Spore Conference held August 17-21, 1991 at the Unicoi State Park at Helen, Georgia. The volume contains abstracts of each oral presentation as well as a collection of abstracts describing the poster sessions. Presentations were organized around the themes (1) Induction of Sporulation, (2) Nuclear Division, (3) Spore Formation, (4) Spore Release and Dispersal, and (4) Spore Germination.

Timberlake, W.E.

1993-04-01T23:59:59.000Z

165

Fifth international fungus spore conference  

DOE Green Energy (OSTI)

This folio contains the proceedings of the Fifth International Fungal Spore Conference held August 17-21, 1991 at the Unicoi State Park at Helen, Georgia. The volume contains abstracts of each oral presentation as well as a collection of abstracts describing the poster sessions. Presentations were organized around the themes (1) Induction of Sporulation, (2) Nuclear Division, (3) Spore Formation, (4) Spore Release and Dispersal, and (4) Spore Germination.

Timberlake, W.E.

1993-04-01T23:59:59.000Z

166

Environmental Biology | Biosciences Division  

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Elevated CO2 and O3 effects on Carbon demand Elevated CO2 and O3 effects on Carbon demand BIO Home Page About BIO News Releases Research Publications People Contact Us Organization Chart Site Index Inside BIO BIO Safety About Argonne Elevated CO2 and O3 effects on Carbon demand of the Extramatrical Mycorrhizal Fungal Network Contact: R. Michael Miller (rmmiller@anl.gov) We are evaluating the interactive effects of elevated CO2 and O3 on the sequential growth and allocation of both ectomycorrhizal fungi (EMF) and arbuscular mycorrhizal fungi (AMF) associated with quaking aspen (Populus tremuloides), paper birch (Betula papyrifera), and sugar maple (Acer saccharum) at the Aspen FACE site. The Aspen FACE approach consists of 30 m diameter rings of gas-dispensing pipes that allow us to fumigate intact forest canopies with atmospheric pollutants and study the interaction of plants, soils and atmosphere (http://aspenface.mtu.edu/index.html). We have used several different approaches to quantifying treatment effects on the mycorrhizal fungal network, especially how host responses influence root associated colonization and extramatrical hyphal (EMH) production and symbiotic benefit. Over the last six years we have been developing and improving upon methods to better quantify root associated mycorrhizal fungal biomass and EMH production and standing crop. Because both AMF and EMF play a significant role in the system of study we also have had to develop a means of separating the production of these different mycorrhizae, especially quantification of the EMH.

167

Multiplexed Activity-Based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes Upon Exposure to Human Serum  

Science Conference Proceedings (OSTI)

Environmental adaptability is critical for survival of the fungal human pathogen Aspergillus fumigatus in the immunocompromised host lung. We hypothesized that exposure of the fungal pathogen to human serum would lead to significant alterations to the organisms physiology including metabolic activity and stress responses. Shifts in functional pathway and corresponding enzyme reactivity of A. fumigatus upon exposure to the human host may represent much needed prognostic indicators of fungal infection. To address this we employed a multiplexed activity-based protein profiling (ABPP) approach coupled to quantitative mass spectrometry-based proteomics to measure broad enzyme reactivity of the fungus cultured with and without human serum. ABPP showed a shift from aerobic respiration to ethanol fermentation and utilization over time in the presence of human serum, which was not observed in serum-free culture. Our approach provides direct insight into this pathogens ability to survive and proliferate. Additionally, our multiplexed ABPP approach captured a broad swath of enzyme reactivity and functional pathways and provides a method for rapid assessment of the A. fumigatus response to external stimuli.

Wiedner, Susan D.; Burnum, Kristin E.; Pederson, Leeanna M.; Anderson, Lindsey N.; Fortuin, Suereta; Chauvigne-Hines, Lacie M.; Shukla, Anil K.; Ansong, Charles; Panisko, Ellen A.; Smith, Richard D.; Wright, Aaron T.

2012-09-28T23:59:59.000Z

168

Controlled Synthesis  

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lUU lUU iIII---11111 q o m Controlled Synthesis of Polyenes by Catalytic Methods Progress Report for the period 12/01/92 - 11/30/93 Richard R. Schrock Five papers have appeared in the last year (see list at end), numbers 225,229, 233, 236, and 240. The living cyclopolymerization of dipropargyl derivatives has been reported for diethyl dipropargylmalonate (X = C(CO2Et)2; Scheme I; #225). We have found that c_ addition and [3 addition take place approximately to an equivalent degree, on the basis of the 13C NMR chemical shift for the quaternary carbon atom in the five or si×-membered ring, and in the presence of ethylene have isolated a molecule that contains a si×-membered ring that is formed when ethylene cleaves the cyclized species from the metal in a chain transfer-like reaction. On this basis also we can say that the polymer prepared from this monomer using classical catalysts contain

169

X-ray Photoelectron Spectroscopy and Kinetic Study: Pt-Group Metals and Bimetallic Surfaces  

E-Print Network (OSTI)

Pt-group metals were some of the first metals to be studied as catalysts for industrial use. The goal of these studies was to ascertain a fundamental understanding of CO oxidation and acetylene cyclotrimerization reactions on Ptgroup metals. A further goal was to determine the optimal conditions for each reaction. CO oxidation on Rh(111),Pt(100), and Pd(100) was scrutinized on various oxide surfaces from chemisorbed to bulk metal oxides. Low pressure reactions on Rh(111) reveal the highest activity was a CO uninhibited surface with oxidation revealed that only oxidation reactions on Pd(100) show oxygen penetration after CO has been consumed; however, during the highest activity XPS found only chemisorbed species. The cyclotrimerization of acetylene to benzene is another reaction found in industry typically carried out on Pd. The active site is considered to be a 7 atom configuration with 6 atoms surrounding a central atom. By adding relatively catalytically inert Au atoms to the active Pd(111) surface the acetylene coupling activity is enhanced. Cyclization activity is a function of the surface composition and the surface structure. A single Pd atom surrounded by six Au atoms is found to have the highest activity at 300K for acetylene cyclotrimerization.

Gath, Kerrie K.

2008-12-01T23:59:59.000Z

170

The experimental and theoretical determination of combinatorial kinetic isotope effects for mechanistic analysis  

E-Print Network (OSTI)

Unfortunately, chemists can never experimentally unravel a full reaction pathway. Even our ability to define key aspects of mechanisms, such as short-lived intermediates and the even more ephemeral transition states, is quite limited, requiring subtle experiments and subtle interpretations. Arguably the most important knowledge to be gained about the mechanism of a reaction is the structure and geometry of the transition state at the rate-limiting step, as this is where a reactions rate and selectivity are generally decided. The Singleton group has developed a methodology for predicting the combinatorial kinetic isotope effects (KIEs) at every atomic position, typically carbon or hydrogen, at natural abundance. A combination of experimental isotope effects and density functional theory (DFT) calculations has greatly aided our ability to predict and understand a reactions pathway and transition state geometries. Precise application of this method has allowed for the mechanistic investigation of a myriad of bioorganic, organic, and organometallic reactions. The technique has been applied in the analysis of the catalytic borylation of arenes via C-H bond activation, dynamic effects in the enyne allene cyclization, palladium catalyzed allylic alkylation, the nature of proton transfer in orotate decarboxylase, and the epoxidation of enones with t-butyl hydroperoxide.

Christian, Chad F.

2007-05-01T23:59:59.000Z

171

Heterotrophic Soil Respiration in Warming Experiments: Using Microbial Indicators to Partition Contributions from Labile and Recalcitrant Soil Organic Carbon. Final Report  

SciTech Connect

The central objective of the proposed work was to develop a genomic approach (nucleic acid-based) that elucidates the mechanistic basis for the observed impacts of experimental soil warming on forest soil respiration. The need to understand the mechanistic basis arises from the importance of such information for developing effective adaptation strategies for dealing with projected climate change. Specifically, robust predictions of future climate will permit the tailoring of the most effective adaptation efforts. And one of the greatest uncertainties in current global climate models is whether there will be a net loss of carbon from soils to the atmosphere as climate warms. Given that soils contain approximately 2.5 times as much carbon as the atmosphere, a net loss could lead to runaway climate warming. Indeed, most ecosystem models predict that climate warming will stimulate microbial decomposition of soil carbon, producing such a positive feedback to rising global temperatures. Yet the IPCC highlights the uncertainty regarding this projected feedback. The uncertainty arises because although warming-experiments document an initial increase in the loss of carbon from soils, the increase in respiration is short-lived, declining to control levels in a few years. This attenuation could result from changes in microbial physiology with temperature. We explored possible microbial responses to warming using experiments and modeling. Our work advances our understanding of how soil microbial communities and their activities are structured, generating insight into how soil carbon might respond to warming. We show the importance of resource partitioning in structuring microbial communities. Specifically, we quantified the relative abundance of fungal taxa that proliferated following the addition of organic substrates to soil. We added glycine, sucrose, cellulose, lignin, or tannin-protein to soils in conjunction with 3-bromo-deoxyuridine (BrdU), a nucleotide analog. Active microbes absorb BrdU from the soil solution; if they multiply in response to substrate additions, they incorporate the BrdU into their DNA. After allowing soils to incubate, we extracted BrdU-labeled DNA and sequenced the ITS regions of fungal rDNA. Fungal taxa that proliferated following substrate addition were likely using the substrate as a resource for growth. We found that the structure of active fungal communities varied significantly among substrates. The active fungal community under glycine was significantly different from those under other conditions, while the active communities under sucrose and cellulose were marginally different from each other and the control. These results indicate that the overall community structure of active fungi was altered by the addition of glycine, sucrose, and cellulose and implies that some fungal taxa respond to changes in resource availability. The community composition of active fungi is also altered by experimental warming. We found that glycine-users tended to increase under warming, while lignin-, tannin/protein-, and sucrose-users declined. The latter group of substrates requires extracellular enzymes for use, but glycine does not. It is possible that warming selects for fungal species that target, in particular, labile substrates. Linking these changes in microbial communities and resource partitioning to soil carbon dynamics, we find that substrate mineralization rates are, in general, significantly lower in soils exposed to long-term warming. This suggests that microbial use of organic substrates is impaired by warming. Yet effects are dependent on substrate identity. There are fundamental differences in the metabolic capabilities of the communities in the control and warmed soils. These differences might relate to the changes in microbial community composition, which appeared to be associated with groups specialized on different resources. We also find that functional responses indicate temperature acclimation of the microbial community. There are distinct seasonal patterns and to long-term soil warming, with

Bradford, M A; Melillo, J M; Reynolds, J F; Treseder, K K; Wallenstein, M D

2010-06-10T23:59:59.000Z

172

JGI - LSP Small-Scale Sequencing Plans for 2007  

NLE Websites -- All DOE Office Websites (Extended Search)

Laboratory Science Program Laboratory Science Program Small-Scale Sequencing Plans For status information, see the Genome Projects section. Organism Proposer Affiliation Five Archaea (Methanohalobium evestigatum, Methanobacterium formicicum, Halococcoides, Ferroglobus placidus, and Acidianus sp. JP7) Kyrpides LBNL Aspergillus terreus EST Baker PNNL Avena Barbata ESTs Anderson BNL Burkholderia cepacia Bu72 van der Lelie BNL ChIP-enriched binding sequences Stubbs LLNL CRISPR loci of Leptospirillum Banfield Cochliobolus heterostrophus Turgeon Cornell University Columbia River Microbiota Magnuson PNNL Dehalococcoides Brodie LBNL Etolico Lagoon in Greece Kyrpides LBNL Fungal comparative genomics (Orpinomyces) Baker PNNL Hypersaline microbial mat Raymond LLNL Leonotis nepetifolia Shanklin BNL

173

Biotechnology Regulatory Services public data file (permits, notifications,  

NLE Websites -- All DOE Office Websites (Extended Search)

Biotechnology Regulatory Services public data file (permits, notifications, Biotechnology Regulatory Services public data file (permits, notifications, and petitions) Agriculture Community Menu DATA APPS EVENTS DEVELOPER STATISTICS COLLABORATE ABOUT Agriculture You are here Data.gov » Communities » Agriculture » Data Biotechnology Regulatory Services public data file (permits, notifications, and petitions) Dataset Summary Description Public information on BRS applications for genetically engineered permits, notifications, and petitions. Tags {BRS,Permits,Notifications,Petitions,GE,"Agronomic Properties","Bacterial Resistance","Fungal Resistance","Herbicide Tolerance","Insect Resistance","Marker Gene","Nematode Resistance","Product Quality","Virus Resistance",Institution,Article,Phenotypes,"Genotypes "}

174

DOE JGI CSP 2012 PI Workshop  

NLE Websites -- All DOE Office Websites (Extended Search)

Organizers Organizers Workshop Organizers Nikos Kyrpides Prokaryotic Superprogram Lead, DOE JGI Susannah Tringe Metagenomics Program Lead, DOE JGI Tanja Woyke Microbial Genomics Program Lead, DOE JGI Igor Grigoriev Fungal Genomics Program Lead, DOE JGI Participants Heike Bucking, South Dakota State University Jeff Dangl, University of North Carolina Chapel Hill Kristen DeAngelis, University of Massachusetts University of Massachusetts, University of British Columbia Jorge Rodrigues, University of Texas Louis Tisa, University of New Hampshire Christopher Schadt, ORNL Jerry Tuskan, ORNL Eoin Brodie, LBNL Brendan Bohannan, University of Oregon Angela Kent, University of Illinois Urbana-Champaign James Tiedje, Michigan State University Nikos Kyrpides, DOE JGI Susannah Tringe, DOE JGI

175

JGI - Organization Structure  

NLE Websites -- All DOE Office Websites (Extended Search)

Organization Structure Organization Structure clickable organizational chart Dan Rokhsar Genomic Technologies Department Nikos Kyrpides Jeremy Schmutz Plant Program Metagenome Program Igor Grigoriev Fungal Program LBNL Director P. Alivisatos Scientific Advisory Committee JGI Director, Eddy Rubin Deputy Director of Science Programs, Jim Bristow S. Canon NERSC JGI Support Team Ray Turner Operations Department Prokaryote Super Program Genomic Technologies Department Len Pennacchio Microbial Program Tanja Woyke Dan Rokhsar Eukaryote Super Program Susannah Tringe Chia-lin Wei Executive Management DOE JGI Director: Eddy Rubin Deputy of Science: Jim Bristow Deputy of Operations: Ray Turner Deputy of Genomic Technologies: Len Pennacchio Departments Operations Deputy of Operations Ray Turner

176

Network Automata: Coupling structure and function in real-world networks  

E-Print Network (OSTI)

We introduce Network Automata, a framework which couples the topological evolution of a network to its structure. It is useful for dealing with networks in which the topology evolves according to some specified microscopic rules and, simultaneously, there is a dynamic process taking place on the network that both depends on its structure but is also capable of modifying it. It is a generic framework for modeling systems in which network structure, dynamics, and function are interrelated. At the practical level, this framework allows for easy implementation of the microscopic rules involved in such systems. To demonstrate the approach, we develop a class of simple biologically inspired models of fungal growth.

David M. D. Smith; Jukka-Pekka Onnela; Chiu Fan Lee; Mark Fricker; Neil F. Johnson

2007-01-26T23:59:59.000Z

177

2012 U.S. Department of Energy: Joint Genome Institute: Progress Report  

Science Conference Proceedings (OSTI)

The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is to serve the diverse scientific community as a user facility, enabling the application of large-scale genomics and analysis of plants, microbes, and communities of microbes to address the DOE mission goals in bioenergy and the environment. The DOE JGI's sequencing efforts fall under the Eukaryote Super Program, which includes the Plant and Fungal Genomics Programs; and the Prokaryote Super Program, which includes the Microbial Genomics and Metagenomics Programs. In 2012, several projects made news for their contributions to energy and environment research.

Gilbert, David [DOE JGI Public Affairs Manager] [DOE JGI Public Affairs Manager

2013-01-01T23:59:59.000Z

178

Complete genome sequence of the plant-associated Serratia plymuthica strain AS13  

Science Conference Proceedings (OSTI)

Serratia plymuthica AS13 is a plant-associated Gammaproteobacteria, isolated from rapeseed roots. It is of special interest because of its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The complete genome of S. plymuthica AS13 consists of a 5,442,549 bp circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced as part of the project enti- tled Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens within the 2010 DOE-JGI Community Sequencing Program (CSP2010).

Neupane, Saraswoti [Uppsala University, Uppsala, Sweden; Finlay, Roger D. [Uppsala University, Uppsala, Sweden; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Alstrom, Sadhna [Uppsala University, Uppsala, Sweden; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Han, James [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Held, Brittany [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J C [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Hogberg, Nils [Uppsala University, Uppsala, Sweden

2012-01-01T23:59:59.000Z

179

Process for preparing and using sweet sorghum in a fuel product  

Science Conference Proceedings (OSTI)

This patent describes a method of storing sweet sorghum preparatory to pelletizing it for use as a combustible fuel product comprising: removing a majority of sugar-containing fluid from the sorghum to leave a residue of ligno-cellulosic bagasse; piling the bagasse on a hard surface; compressing the piled bagasse to form a compacted mass, whereby the compressing frees air trapped within the bagasse to inhibit microbial and fungal oxidative degradation thereof; and storing the compacted mass preparatory to pelletizing the same.

Gunnerman, R.W.; Farone, W.A.

1986-09-23T23:59:59.000Z

180

Theoretical Investigations on the Formation and Dehydrogenation Reaction Pathways of H(NH2BH2)nH (n=1-4) Oligomers: Importance of Dihydrogen Interactions (DHI)  

DOE Green Energy (OSTI)

The H(NH2BH2)nH oligomers are possible products from dehydrogenation of ammonia borane (NH3BH3) and ammonium borohydride (NH4BH4), which belong to a class of boron-nitrogen-hydrogen (BNHx) compounds that are promising materials for chemical hydrogen storage. Understanding the kinetics and reaction pathways of formation of these oligomers and their further dehydrogenation is essential for developing BNHx-based hydrogen storage materials. We have performed computational modeling using density functional theory (DFT), ab initio wavefunction theory, and Car-Parrinello molecular dynamics (CPMD) simulations on the energetics and formation pathways for the H(NH2BH2)nH (n=1-4) oligomers, polyaminoborane (PAB), from NH3BH3 monomers and the subsequent dehydrogenation steps to form polyiminoborane (PIB). Through transition state searches and evaluation of the intrinsic reaction coordinates, we have investigated the B-N bond cleavage, the reactions of NH3BH3 molecule with intermediates, dihydrogen release through intra- and intermolecular hydrogen transfer, dehydrocoupling/cyclization of the oligomers, and the dimerization of NH3BH3 molecules. We discovered the formation mechanism of H(NH2BH2)n+1H oligomers through reactions of the H(NH2BH2)nH oligomers first with BH3 followed by reactions with NH3 and the release of H2, where the BH3 and NH3 intermediates are formed through dissociation of NH3BH3. We also found that the dimerization of the NH3BH3 molecules to form c-(NH2BH2)2 is slightly exothermic, with an unexpected transition state that leads to the simultaneous release of two H2 molecules. The dehydrogenations of the oligomers are also exothermic, typically by less than 10 kcal/(mol of H2), with the largest exothermicity for n=3. The transition state search shows that the one-step direct dehydrocoupling cyclization of the oligomers is not a favored pathway because of high activation barriers. The dihydrogen bonding, in which protic (HN) hydrogens interact with hydridic (HB) hydrogens, plays a vital role in stabilizing different structures of the reactants, transition states, and products. The dihydrogen interaction (DHI) within the -BH2(?2-H2) moiety accounts for both the formation mechanisms of the oligomers and for the dehydrogenation of ammonia borane. Support was provided from the U.S. Department of Energy, Office of Basic Energy Sciences, Chemical Sciences Division and from the U.S. Department of Energy, Energy Efficiency and Renewable Energy, Chemical Hydrogen Storage Center of Excellence. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

Li, Jun; Kathmann, Shawn M.; Hu, Han-Shi; Schenter, Gregory K.; Autrey, Thomas; Gutowski, Maciej S.

2010-09-06T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

An Exocyclic Methylene Group Acts As a Bioisostere of the 2?-Oxygen Atom in LNA  

DOE Green Energy (OSTI)

We show for the first time that it is possible to obtain LNA-like (Locked Nucleic Acid 1) binding affinity and biological activity with carbocyclic LNA (cLNA) analogs by replacing the 2{prime}-oxygen atom in LNA with an exocyclic methylene group. Synthesis of the methylene-cLNA nucleoside was accomplished by an intramolecular cyclization reaction between a radical at the 2{prime}-position and a propynyl group at the C-4{prime} position. Only methylene-cLNA modified oligonucleotides showed similar thermal stability and mismatch discrimination properties for complementary nucleic acids as LNA. In contrast, the close structurally related methyl-cLNA analogs showed diminished hybridization properties. Analysis of crystal structures of cLNA modified self-complementary DNA decamer duplexes revealed that the methylene group participates in a tight interaction with a 2{prime}-deoxyribose residue of the 5{prime}-terminal G of a neighboring duplex, resulting in the formation of a CH...O type hydrogen bond. This indicates that the methylene group retains a negative polarization at the edge of the minor groove in the absence of a hydrophilic 2{prime}-substituent and provides a rationale for the superior thermal stability of this modification. In animal experiments, methylene-cLNA antisense oligonucleotides (ASOs) showed similar in vivo activity but reduced toxicity as compared to LNA ASOs. Our work highlights the interchangeable role of oxygen and unsaturated moieties in nucleic acid structure and emphasizes greater use of this bioisostere to improve the properties of nucleic acids for therapeutic and diagnostic applications.

Seth, Punit P.; Allerson, Charles R.; Berdeja, Andres; Siwkowski, Andrew; Pallan, Pradeep S.; Gaus, Hans; Prakash, Thazha P.; Watt, Andrew T.; Egli, Martin; Swayze, Eric E. (Isis Pharm.); (Vanderbilt)

2010-12-07T23:59:59.000Z

182

Probing the Biosynthesis and Mode of Action of Azinomycin B  

E-Print Network (OSTI)

Since the isolation of azinomycins A and B in 1954 from the soil bacterium, Streptomyces sahachiroi, these natural products have been synthetic targets. Both compounds exhibit in vitro cytotoxic activity at submicromolar levels and demonstrate anti-tumor activities comparable to that of mitomycin C in vivo. Unique to this class of natural products is the presence of an aziridine [1,2-a] pyrrolidine ring system. Coupled with an epoxide moiety, these structural functionalities impart the ability to form interstrand cross-links with DNA via the electrophilic C10 and C21 carbons of azinomycin and the N7 positions of suitably disposed purine bases. This dissertation investigates the global impact of azinomycin B treatment in a yeast model with special emphasis on DNA damage response, the resulting cell cycle effects, and cellular localization of the compound. The results provide the first demonstration of the in vivo actions of azinomycin B and are consistent with the proposed role of the drug as a DNA crosslinking agent. Biosynthesis of azinomycin B was investigated and appears to have polyketide, non-ribosomal peptide synthetase and alkaloid origins. In pursuit of elucidating the biosynthetic origin we developed both a cell culturing system and a cell-free extract procedure capable of supporting azinomycin synthesis; we used these. These were employed with labeled metabolites to probe the biosynthetic origins of the molecule. Investigations with this enzyme preparation imparted important information regarding the substrate and cofactor requirements of the pathway. These results supported the premise of a mixed origin for the biosynthesis of the molecule and paved the way for expansive stable isotope labeling studies, which largely revealed the biosynthetic precursors and probable construction of the azinomycins. Some of these studies corroborate while other results conflict with initial proposed biosynthetic routes based upon the azinomycin biosynthetic gene cluster sequence. Future azinomycin biosynthetic gene cluster enzyme characterization, mechanistic investigations, and genetic modifications will ultimately provide definitive proof for the intermediacy of proposed biosynthetic precursors and the involvement of specific cofactors. Better understanding of how nature constructs unique molecule may provide insight into eventual chemoenzymatic/gene thearapy based approaches toward cancer therapy.

Kelly, Gilbert Thomson

2009-08-01T23:59:59.000Z

183

Studies toward biomimetic claisen condensation using nucleic acid templates and ribozyme catalysis  

E-Print Network (OSTI)

Many different experimental approaches were attempted to achieve carbon-carbon bond formation by nucleic acid template-directed reactions and ribozyme catalysis as potential lipid synthesizing machineries in the RNA world. A novel biomimetic condition for decarboxylative Claisen condensation in polyketide biosynthesis was discovered. The reaction of a malonic acid half oxyester with a Nhydroxysuccinmidyl ester forming reagent resulted in self-condensation to provide the corresponding 1,3-acetonedicarboxylic acid diester in the absence of a divalent metal chelator or a coordinating solvent. The decarboxylative Claisen condensation of malonyl adenosine using a poly-U template in solution or with immobilized poly-U was attempted. Various analytical methods demonstrated that malonyl adenosine underwent an exclusive hydrolysis reaction instead of condensation in the given conditions. Similar results were observed for the reaction of malonyl-CoA with acetyl-CoA on poly-U templates. No evidence for the decarboxylative Claisen condensation was observed by a DNA-templated system although a double helical structure of DNA duplex was proven to facilitate a bimolecular reaction by offering a favorable proximity effect. Therefore, it seems that the unsuccessful condensation resulted not from the bad template effect but from the intrinsic properties of the decarboxylative Claisen condensation reaction itself. Two tRNA molecules loaded with a malonic acid were prepared by ligation of truncated tRNAs with malonylated dinucletides. Our initial attempts to probe carbon-carbon bond formation by subjecting malonylated tRNAs to the in vitro translational machinery were not successful. Novel carbon isosteres of ?-amino acids are suggested as a potential source of a more stable and reactive carbanion for future experiments. Isoprenoid conjugates of nucleoside 5??-diphosphates, which were proposed as either an initiator nucleotide or substrate molecule for in vitro selection of prenyl-transferase ribozyme were prepared by one step nucleophilic displacement reactions. A random DNA pool was constructed for selection of a ketosynthase ribozyme. A substrate bearing a biotin tag was prepared by one-step conjugation. Hig-tagged T7 RNA polymerase was expressed and purified for a large scale transcription reaction. In vitro transcription of the random DNA pool with a 5??-thiol modified GMP analogue as an initiator nucleotide produced a thiol-modified random RNA library.

Ryu, Youngha

2003-05-01T23:59:59.000Z

184

2012 MITOCHONDRIA AND CHLOROPLASTS GORDON RESEARCH CONFERENCE & GORDON RESEARCH SEMINAR, JULY 29 - AUGUST 3, 2012  

Science Conference Proceedings (OSTI)

The 2012 Gordon Research Conference on Mitochondria and Chloroplasts will assemble an international group of scientists investigating fundamental properties of these organelles, and their integration into broader physiological processes. The conference will emphasize the many commonalities between mitochondria and chloroplasts: their evolution from bacterial endosymbionts, their genomes and gene expression systems, their energy transducing membranes whose proteins derive from both nuclear and organellar genes, the challenge of maintaining organelle integrity in the presence of the reactive oxygen species that are generated during energy transduction, their incorporation into organismal signaling pathways, and more. The conference will bring together investigators working in animal, plant, fungal and protozoan systems who specialize in cell biology, genetics, biochemistry, physiology, proteomics, genomics, and structural biology. As such, this conference will provide a unique forum that engenders cross-disciplinary discussions concerning the biogenesis, dynamics, and regulation of these key cellular structures. By fostering interactions among mammalian, fungal and plant organellar biologists, this conference also provides a conduit for the transmission of mechanistic insights obtained in model organisms to applications in medicine and agriculture. The 2012 conference will highlight areas that are moving rapidly and emerging themes. These include new insights into the ultrastructure and organization of the energy transducing membranes, the coupling of organellar gene expression with the assembly of photosynthetic and respiratory complexes, the regulatory networks that couple organelle biogenesis with developmental and physiological signals, the signaling events through which organellar physiology influences nuclear gene expression, and the roles of organelles in disease and development.

Barkan, Alice

2012-08-03T23:59:59.000Z

185

Structures and Functions of Oligosaccharins: The Role of Endoglycanases  

Science Conference Proceedings (OSTI)

The research proposed will investigate two projects that involve studies of the chemistry and biology of protein/protein and protein/carbohydrate interactions involved in host/pathogen interactions. Specifically, the projects involve (i) the interactions between fungal endopolygalacturonases and plant polygalacturonase-inhibiting proteins and (ii) the interactions between fungal endoxylanases and plant arabinoxylans. During pathogenesis fungi secrete families of endoglycanases that fragment the cell wall polysaccharides of the plant host. The result of endoglycanase action on cell wall polysaccharides can include weakening of the wall, penetration of host cells by the pathogen, solubilization of carbohydrate nutrients, and formation of oligosaccharins (oligosaccharides with regulatory function) that can stimulate plant defenses. We have made significant advances during the last funding period to support the hypothesis that the outcome of attempted pathogenesis can be influenced by protein/protein and protein/carbohydrate interactions in the extracellular matrices of the host and pathogen. We plan to expand on those successes by further exploring the mechanism of action of the endoglycanases and their plant-derived inhibitors, the expression of the various members of the endoglycanase families at various stages of infection and their role in the release of oligosaccharins and in pathogenicity, as well as the role played by the polysaccharide substrates in both pathogenicity and endoglycanase-inhibitor interactions.

Bergmann, Carl W. [University of Georgia

2008-12-05T23:59:59.000Z

186

An investigation of the influence of Trichoderma virens (hypocreales: hypocreaceae) on reticulitermes virginicus (isoptera: rhinotermitidae) feeding, with an evaluation of the use of labral morphology for identification of reticulitermes from Texas  

E-Print Network (OSTI)

Subterranean termites encounter numerous kinds of fungi during foraging and feeding activities. Nearly nine decades of research have exposed only a small fraction of the termitefungal interactions that exist in nature. The first portion of research presented here focused on how feeding behaviors of Reticulitermes virginicus (Banks) were affected by the fungus Trichoderma virens (Miller, Giddens & Foster) von Arx. Tests were performed with 'P' (GLT+) and 'Q'(GLT-) strains of T. virens. Both strains were applied to filter paper and wood disks cut from southern yellow pine and Sentricon?® monitoring devices. The first bioassay assessed the termites' feeding responses to fungal extracts removed from liquid media on days 2 through 7, and again on day 15. Only the GLT+ extracts from days 6 and 7 inhibited termite feeding significantly from the controls (16% and 54% less area loss, respectively). Response to wood covered by live T. virens mycelia was tested in the second bioassay. No significant differences in termite consumption were seen between fungal strains, but both substantially reduced the area loss due to termite feeding of treated wood by an average of 35%. A vacuum impregnation system was used to inoculate wood disks with fungal homogenate in the third bioassay. The wood treated with either GLT+ or GLT- homogenates did not have significant differences in area loss due to termite feeding. Overall, these results reiterated the plasticity that exists with termitefungal relationships. The second research topic addressed the applicability of labrum-based identification techniques to Reticulitermes Holmgren in Texas. Soldier labral morphology of four species, R. flavipes (Kollar), R. hageni (Banks), R. tibialis Banks, and R. virginicus (Banks), was evaluated as a character to separate species. Length and width measurements of five soldier labra were taken from each of the eight collection sites. These results were then judged against molecular analysis of the mtDNA 16S rRNA gene. Findings showed that labral shape was an unreliable diagnostic characteristic when comparing all species. A combination of length and length-towidth ratio successfully segregated all four Reticulitermes species. Comparison of a morphology-based dendogram to the phylogenetic analysis revealed a shared pattern between phenotypic and genotypic variations.

Heintschel, Bryan P.

2003-05-01T23:59:59.000Z

187

Characterization  

NLE Websites -- All DOE Office Websites (Extended Search)

Characterization Characterization of the Rust Fungus, Puccinia emaculata, and Evaluation of Genetic Variability for Rust Resistance in Switchgrass Populations Srinivasa Rao Uppalapati & Desalegn D. Serba & Yasuhiro Ishiga & Les J. Szabo & Shipra Mittal & Hem S. Bhandari & Joseph H. Bouton & Kirankumar S. Mysore & Malay C. Saha # The Author(s) 2012. This article is published with open access at Springerlink.com Abstract Several fungal pathogens have been identified on ornamental and native stands of switchgrass (Panicum virga- tum L.). Diseases of switchgrass, particularly rust, have been largely neglected and are likely to become the major limiting factor to biomass yield and quality, especially when monocul- tured over a large acreage. Based on teliospore morphology and internal transcribed spacer-based diagnostic primers, the rust pathogen collected

188

Why Sequence Paxillus involutus?  

NLE Websites -- All DOE Office Websites (Extended Search)

Paxillus involutus? Paxillus involutus? More than 75% of the carbon in terrestrial ecosystems is stored in forests. More than half of this carbon is found in soil organic matter (SOM). Recent studies have indicated that ectomycorrhizal (EM) fungi provide the dominant pathway through which carbon enters the SOM pool. The same fungi also drive the cycling of other nutrients within the forest community (microbiome) together with other soil microorganisms. Global climate changes as well as increasing anthropogenic nitrogen deposition are compelling reasons to study in detail how EM fungi and associated microflora mediate carbon as well as nitrogen cycling and deposition in terrestrial ecosystems. Likewise, EM fungi are known to protect plants from toxic metals. So, the development of metal-tolerant fungal associations would provide a strategy

189

U.S Department of Energy Joint Genome Institute Progress Report  

NLE Websites -- All DOE Office Websites (Extended Search)

S Department of Energy S Department of Energy Joint Genome Institute Progress Report 2009 Representatives of the four DOE JGI genome programs (plant, fungal, metagenome, and microbe) grace the cover of this annual report. Three of the organisms were among the 81 projects selected in 2009 for the 2010 Community Sequencing Program portfolio. Photo credits, clockwise from bottom left: Brachypodium distachyon by Roy Kaltschmidt, LBNL; Amanita thiersii fungus by Joe McFarland; Cow rumen metagenome by Gemma Henderson, AgResearch; Soybeans by Roy Kaltschmidt, LBNL; Zymomonas mobilis Z4 by Katherine Pappas, University of Athens U.S Department of Energy Joint Genome Institute Progress Report 2009 DOE JGI Mission . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Director's

190

Why Sequence Bacillus coagulans?  

NLE Websites -- All DOE Office Websites (Extended Search)

Bacillus coagulans? Bacillus coagulans? Bacilus coagulans strain 36D1 and its close relatives are ideal biocatalysts for fermentation of lignocellulosic biomass to fuels and chemicals. This bacterium is an acidophile and a moderate thermophile (grows at pH 5.0 and at 55°C). These characteristics are similar to the optimal conditions for the activity of fungal cellulases, which have been developed with significant support from DOE for simultaneous saccharification and fermentation (SSF) of cellulose to useful products (fuel ethanol, lactic acid, etc.). The optimal growth conditions for the biocatalysts currently used by industry for production of ethanol or lactic acid significantly differ from the optimal conditions for cellulase activity. This mismatch leads to higher usage of expensive cellulases than

191

JGI - CSP Sequencing Plans for 2014  

NLE Websites -- All DOE Office Websites (Extended Search)

Science Program Science Program Sequencing Plans for 2014 Proposer Affiliation Project Description Banfield, Jillian UC Berkeley, LBNL Community metagenomic and transcriptomic analyses of microbial carbon turnover in grassland soil profiles under two rainfall regimes Bonito, Gregory Duke University Comparative genomics of early diverging terrestrial fungi and their bacterial endosymbionts Brem, Rachel UC Berkeley Pioneering fungal mutagenesis using Tn-seq Brutnell, Thomas Donald Danforth Plant Science Center Doubling the number of Panicoideae genome sequences Canovas, David University of Seville, Spain Global genomic consequences of the deletion of the Aspergilli non-homologous end joining DNA repair mechanism employed as a genetic tool worldwide Chen, Jay Oak Ridge National Laboratory RNA-seq-Enabled Expression Quantitative Trait Locus (eQTL) in Populus

192

Could a Common Household Fungus Reduce Oil Imports? | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

a Common Household Fungus Reduce Oil Imports? a Common Household Fungus Reduce Oil Imports? Could a Common Household Fungus Reduce Oil Imports? June 21, 2011 - 11:37am Addthis A view of Aspergillus niger with the fungus’ DNA highlighted in green | Photo Courtesy of: PNNL. A view of Aspergillus niger with the fungus' DNA highlighted in green | Photo Courtesy of: PNNL. Ben Squires Analyst, Office of Energy Efficiency & Renewable Energy What does this mean for me? The Department's Pacific Northwest National Laboratory (PNNL) are working to harness the natural process that spoils fruits and vegetables as a way to make fuel and other petroleum substitutes from the parts of plants that we can't eat. The genetic bases of the behaviors and abilities of these two industrially relevant fungal strains will allow researchers to exploit

193

Interplay between function and structure in complex networks  

E-Print Network (OSTI)

We show that abrupt structural transitions can arise in functionally optimal networks, driven by small changes in the level of transport congestion. Our results offer an explanation as to why so many diverse species of network structure arise in Nature (e.g. fungal systems) under essentially the same environmental conditions. Our findings are based on an exactly solvable model system which mimics a variety of biological and social networks. We then extend our analysis by introducing a novel renormalization scheme involving cost motifs, to describe analytically the average shortest path across multiple-ring-and-hub networks. As a consequence, we uncover a 'skin effect' whereby the structure of the inner multi-ring core can cease to play any role in terms of determining the average shortest path across the network.

Jarrett, T C; Fricker, M; Johnson, N F; Jarrett, Timothy C.; Ashton, Douglas J.; Fricker, Mark; Johnson, Neil F.

2006-01-01T23:59:59.000Z

194

MINI-REVIEW Processive  

NLE Websites -- All DOE Office Websites (Extended Search)

Processive Processive and nonprocessive cellulases for biofuel production-lessons from bacterial genomes and structural analysis David B. Wilson Received: 23 September 2011 / Revised: 18 October 2011 / Accepted: 1 November 2011 / Published online: 24 November 2011 # Springer-Verlag 2011 Abstract Cellulases are key enzymes used in many processes for producing liquid fuels from biomass. Cur- rently there many efforts to reduce the cost of cellulases using both structural approaches to improve the properties of individual cellulases and genomic approaches to identify new cellulases as well as other proteins that increase the activity of cellulases in degrading pretreated biomass materials. Fungal GH-61 proteins are important new enzymes that increase the activity of current commercial cellulases leading to lower total protein loading and thus lower cost. Recent work has greatly increased

195

Cellulases: ambiguous nonhomologous enzymes in a genomic perspective  

NLE Websites -- All DOE Office Websites (Extended Search)

Cellulases: Cellulases: ambiguous nonhomologous enzymes in a genomic perspective Leonid O. Sukharnikov 1,2,4 , Brian J. Cantwell 1,4 , Mircea Podar 1,2,4 and Igor B. Zhulin 1,3,4,5 1 BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA 2 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA 3 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA 4 Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA 5 Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA The key material for bioethanol production is cellulose, which is one of the main components of the plant cell wall. Enzymatic depolymerization of cellulose is an essential step in bioethanol production, and can be accomplished by fungal and bacterial cellulases. Most

196

Why sequence Comparative analysis of Aspergilli species?  

NLE Websites -- All DOE Office Websites (Extended Search)

Comparative analysis of Aspergilli species? Comparative analysis of Aspergilli species? Aspergillus is not only one of the most important fungi for use in biotechnology it is also one of the most commonly found groups of fungi worldwide. This project seeks to sequence and annotate a series of additional Aspergillus species and Penicillium roqueforti to complement and strengthen the genomic data currently available for comparative studies. The data resulting from these species comparisonswill be of direct relevance to the DOE mission, particularly to howspecies have become adapted for utilization of specific carbon sources enabling efficientbiomass degradation. Principal Investigators: Ronald de Vries, CBS-KNAW Fungal Biodiversity Centre, the Netherlands Program: CSP 2011 Home > Sequencing > Why sequence Comparative analysis of Aspergilli

197

JGI - Why Sequence Poplar Leaf Rust?  

NLE Websites -- All DOE Office Websites (Extended Search)

Poplar Leaf Rust? Poplar Leaf Rust? The Populus (poplar tree) genome has been publicly released by the JGI, and the genomes of its symbiotic fungal associates Laccaria bicolor and Glomus intraradices are near completion. As part of the development of a broader community-based Populus genomics resource, and as a means of conducting informative comparative genomics among fungi, JGI will be sequencing Melampsora larici-populina (poplar leaf rust fungus), which causes widespread economic losses in poplar plantations worldwide and is a close relative of other economically important rusts (Uredinales), including Puccinia and other cereal rusts. There is a pressing need to develop a thorough understanding of the Melampsora species that are poplar pathogens so that new control approaches

198

Could a Common Household Fungus Reduce Oil Imports? | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Could a Common Household Fungus Reduce Oil Imports? Could a Common Household Fungus Reduce Oil Imports? Could a Common Household Fungus Reduce Oil Imports? June 21, 2011 - 11:37am Addthis A view of Aspergillus niger with the fungus’ DNA highlighted in green | Photo Courtesy of: PNNL. A view of Aspergillus niger with the fungus' DNA highlighted in green | Photo Courtesy of: PNNL. Ben Squires Analyst, Office of Energy Efficiency & Renewable Energy What does this mean for me? The Department's Pacific Northwest National Laboratory (PNNL) are working to harness the natural process that spoils fruits and vegetables as a way to make fuel and other petroleum substitutes from the parts of plants that we can't eat. The genetic bases of the behaviors and abilities of these two industrially relevant fungal strains will allow researchers to exploit

199

DOE JGI CSP 2012 PI Workshop  

NLE Websites -- All DOE Office Websites (Extended Search)

Agenda Agenda Monday, January 23 8:15am Shuttle bus departs from the Walnut Creek Marriott 8:30 Sign In and Continental Breakfast at JGI 9:00-9:15 Introductions, Workshop Overview and Goals Metagenome Program overview Susannah Tringe 9:15-9:30 JGI Prokaryotic Super Program Overview Nikos Kyrpides 9:30-9:45 JGI Microbial Program Overview Tanja Woyke 9:45-10:00 JGI Fungal Program Overview Igor Grigoriev 10:00-10:15 JGI Sequencing Technologies Feng Chen 10:15-10:30 Questions 10:30-10:45 Break 10:45-11:15 Rhizosphere Grand Challenge and CSP2012 Plant-Microbe interactions projects Susannah Tringe 11:15-11:35 CSP2012: Plant associated metagenomes--Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems Jeff Dangl

200

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (Extended Search)

1 Workshops 1 Workshops IMG Workshop Date: Monday, March 21 Time: 9:00 AM - 5:00 PM Location: Walnut Creek Marriott Audience: Users and potential users of the Integrated Microbial Genomes (IMG) data analysis systems. Description: 1-day workshop with hands-on tutorials on IMG. IMG-Metagenomes Workshop Date: Tuesday, March 22 Time: 9:00 AM - 12:00 PM Location: Walnut Creek Marriott Audience: Users and potential users of the Integrated Microbial Genomes (IMG) with Microbiome Samples (IMG/M) data analysis system. Description: half day workshop with hands-on tutorials on IMG/M. Mycocosm Workshop Date: Tuesday, March 22 Time: 9:00 AM - 12:00 PM Location: Walnut Creek Marriott Audience: Users and potential users of the Mycocosm fungal genomics portal. Description: The JGI Mycocosm web-portal provides data access,

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

Browse by Discipline -- E-print Network Subject Pathways: Fossil Fuels --  

Office of Scientific and Technical Information (OSTI)

E F G H I J K L M N O P Q R S E F G H I J K L M N O P Q R S T U V W X Y Z D'haeseleer, Patrik (Patrik D'haeseleer) - Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory Dabiri, John O. (John O. Dabiri) - Department of Aerospace, California Institute of Technology Dai, Yang (Yang Dai) - Department of Bioengineering, University of Illinois at Chicago Dal Palù, Alessandro (Alessandro Dal Palù) - Dipartimento di Matematica, Università degli Studi di Parma Dalkilic, Mehmet (Mehmet Dalkilic) - Center for Genomics and Bioinformatics & School of Informatics, Indiana University Daub, Margaret (Margaret Daub) - Center for Integrated Fungal Research & Department of Plant Biology, North Carolina State University Daugulis, Andrew J. (Andrew J. Daugulis) - Department of Chemical

202

Why sequence Pisolithus tinctorius and Pisolithus microcarpus?  

NLE Websites -- All DOE Office Websites (Extended Search)

Pisolithus tinctorius and Pisolithus microcarpus? Pisolithus tinctorius and Pisolithus microcarpus? The term Pisolithus is derived from Greek, where piso means pea-shaped and lithos means stone. The fungal species under this category get their name from the pea-shaped spore capsules that break down to disperse spores, and thrive in temperate regions as well as in less-than-ideal conditions such as high levels of heavy metals, highly acidic soils and drought. They form associations with a wide range of woody plants, including trees, which act as carbon sinks and could be feedstocks for cellulosic biofuels. Interactions with mycorrhizal fungi help trees access scarce nutrients such as nitrogen and phosphate. By sequencing the genomes of fungi related to others previously sequenced by the DOE JGI, researchers hope to better understand the symbiosis

203

The Annual DOE JGI User Meeting  

NLE Websites -- All DOE Office Websites (Extended Search)

Genomics of Energy & Environment Genomics of Energy & Environment The annual DOE JGI User Meeting March 18 - 20, 2014 in Walnut Creek, California Register now for the Meeting and Workshops Register Topics include: Microbial genomics, fungal genomics, metagenomics, and plant genomics; genome editing, natural products, pathway engineering, synthetic biology, high-throughput functional genomics, and societal impact of technological advances. State-of-the-art presentations by invited speakers as well as short talks selected from poster abstracts. In addition, tutorials on genomic informatics, data management, and new genomic technologies. Keynotes: Annalee Newitz, io9 Steve Quake, Stanford University Other confirmed speakers: Martin Ackermann, ETH Zurich Luke Alphey, Oxitec Mary Berbee, University of British Columbia

204

Cellulases: ambiguous nonhomologous enzymes in a genomic perspective  

Science Conference Proceedings (OSTI)

The key material for bioethanol production is cellulose, which is one of the main components of the plant cell wall. Enzymatic depolymerization of cellulose is an essential step in bioethanol production, and can be accomplished by fungal and bacterial cellulases. Most of the biochemically characterized bacterial cellulases come from only a few cellulose-degrading bacteria, thus limiting our knowledge of a range of cellulolytic activities that exist in nature. The recent explosion of genomic data offers a unique opportunity to search for novel cellulolytic activities; however, the absence of clear understanding of structural and functional features that are important for reliable computational identification of cellulases precludes their exploration in the genomic datasets. Here, we explore the diversity of cellulases and propose a genomic approach to overcome this bottleneck.

Sukharnikov, Leonid O [ORNL; Cantwell, Brian J [ORNL; Podar, Mircea [ORNL; Zhulin, Igor B [University of Tennessee (UTK) and Oak Ridge National Laboratory (ORNL)

2011-01-01T23:59:59.000Z

205

Analysis of cellulase and polyphenol oxidase production by southern pine beetle associated fungi  

E-Print Network (OSTI)

In this study, the production of extracellular enzymes by fungi associated with southern pine beetle was investigated for the first time. Cellulase and polyphenol oxidase production were analyzed for three beetle associated fungi. Only the mutualistic symbiont Entomocorticium sp. A was found to produce cellulases and polyphenol oxidase. In time course analyses of cellulase production in batch cultures, Entomocorticium sp. A showed maximum activity of 0.109 U/ml and 0.141 U/ml for total cellulase and endoglucanase activity respectively. Polyphenol oxidase production was simultaneous with fungal growth. Characterization of polyphenol oxidase by activity staining suggests that the enzyme is a tyrosinase/catechol oxidase. Enzyme assays in the presence of polyphenol oxidase inhibitors support the results of the activity staining. Keywords: Ceratocystiopsis, Entomocorticium, Ophiostoma, cellulase, tyrosinase/catechol oxidase

Abduvali Valiev; Zumrut B. Ogel; Kier D. Klepzig

2008-01-01T23:59:59.000Z

206

Intraspecific differentiation of Aureobasidium spp. using universally primed polymerase chain reaction  

Science Conference Proceedings (OSTI)

Universally primed polymerase chain reaction (UP-PCR) was used to analyze intraspecific variation in previously diagnosed biological species of yeastlike Aureobasidium fungi. No correlation between PCR-polymorphism and the origin of fungal strains was revealed. It is suggested that Aureobasidium species studied differ in the width of their ecological niches: species I is cosmopolitan, whereas species II demonstrates relative substrate specificity. The ability of different universal primers to operate as conservative or variable ones in experiments with different species and genera was confirmed. This ability is explained by different rates of evolution of amplified loci. Hybridization analysis of amplified DNA is suggested as a necessary step in classifying strains with insufficient similarity of PCR patterns as belonging to the same divergent species or to different species. 12 refs., 4 figs., 1 tab.

Mokrousov, I.V. [Pasteur Institute, St. Petersburg (Russian Federation)

1995-07-01T23:59:59.000Z

207

A model of hyphal tip growth involving microtubule-based transport  

E-Print Network (OSTI)

We propose a simple model for mass transport within a fungal hypha and its subsequent growth. Inspired by the role of microtubule-transported vesicles, we embody the internal dynamics of mass inside a hypha with mutually excluding particles progressing stochastically along a growing one-dimensional lattice. The connection between long range transport of materials for growth, and the resulting extension of the hyphal tip has not previously been addressed in the modelling literature. We derive and analyse mean-field equations for the model and present a phase diagram of its steady state behaviour, which we compare to simulations. We discuss our results in the context of the filamentous fungus, Neurospora crassa.

K. E. P. Sugden; M. R. Evans; W. C. K. Poon; N. D. Read

2006-05-09T23:59:59.000Z

208

Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9  

Science Conference Proceedings (OSTI)

Serratia plymuthica are plant-associated, plant beneficial species belonging to the family Enterobacteriaceae. The members of the genus Serratia are ubiquitous in nature and their life style varies from endophytic to free-living. S. plymuthica AS9 is of special interest for its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The genome of S. plymuthica AS9 comprises a 5,442,880 bp long circular chromosome that consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome is part of the project entitled Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens awarded through the 2010 DOE-JGI Community Sequencing Program (CSP2010).

Neupane, Saraswoti [Uppsala University, Uppsala, Sweden; Hogberg, Nils [Uppsala University, Uppsala, Sweden; Alstrom, Sadhna [Uppsala University, Uppsala, Sweden; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Lu, Megan [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Fiebig, Anne [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Finlay, Roger D. [Uppsala University, Uppsala, Sweden

2012-01-01T23:59:59.000Z

209

Saccharification of bamboo carbohydrates for the production of ethanol  

SciTech Connect

Bamboo carbohydrates were hydrolyzed with commercial amylases and a mixture of fungal culture broths containing cellulolytic and hemicellulolytic enzymes. The effects of cooking temperature and the size of fiber particles were also investigated. It was found that the higher the cooking temperature, the higher the rate of sugar formation and the lower the viscosity of the slurry. Additions of cellulose and hemicellulose digesting enzymes increased the sugar yield and decreased the viscosity of both the cooked and noncooked slurries. A smaller size of particle appeared to favor the average saccharification rate. Although glucose, xylose, and cellobiose were present in the hydrolysates, only 50% of the total carbohydrate was digested, and 78.9% of this was converted to reducing sugars. The alcohol efficiency for the fermentation of cooked and noncooked mashes by Saccharomyces was about 85%.

De Menezes, T.J.B.; Azzini, A.; Dos Santos, C.L.M.

1983-04-01T23:59:59.000Z

210

Summit-Watertown transmission line project, South Dakota. Final Environmental Assessment  

SciTech Connect

The Western Area Power Administration (Western) needs to rebuild the existing Summit-Watertown 115-kV transmission line, located in northeastern South Dakota, and western Minnesota. Nearly 60 percent of the existing facility was replaced in 1965 after severe ice-loading broke structures and wires. Because of the extensive loss of the line, surplus poles had to be used to replace the damaged H-frame structures. These were of varying sizes, causing improper structure loading. Additionally, the conductors and overhead shield wires have been spliced in numerous places. This provides additional space on these wires for icing and wind resistance, which in turn create problems for reliability. Finally, a progressive fungal condition has weakened the poles and, along with the improper loading, has created an unsafe condition for maintenance personnel and the general public.

1993-12-01T23:59:59.000Z

211

Evolution of Genes and Gene Networks in Filamentous Fungi  

E-Print Network (OSTI)

The Pezizomycotina, commonly known as the filamentous fungi, are a diverse group of organisms that have a major impact on human life. The filamentous fungi diverged from a common ancestor approximately 200 700 million years ago. Because of the diversity and the wealth of biological and genomic tools for the filamentous fungi it is possible to track the evolutionary history of genes and gene networks in these organisms. In this dissertation I focus on the evolution of two genes (lolC and lolD) in the LOL secondary metabolite gene cluster in Epichlo and Neotyphodium genera, the evolution of the MAP kinase-signaling cascade in the filamentous fungi, the regulation of the gene networks involved in asexual development in Neurospora crassa, and the identification of two genes in the N. crassa asexual development gene network, acon-2 and acon-3. I find that lolC and lolD originated as an ancient duplication in the ancestor of the filamentous fungi, which were later recruited in the LOL gene cluster in the fungal endophyte lineage. In the MAP kinase-signaling cascade, I find that the MAPK component is the most central gene in the gene network. I also find that the MAPK signaling cascade originated as three copies in the ancestor to eukaryotes, an arrangement that is maintained in filamentous fungi. My observations of gene expression profiling during N. crassa asexual development show tissue specific expression of genes. Both the vegetative mycelium and the aerial hyphae contribute to the formation of macroconidiophores. Also, with the help of genomic tools recently developed by researchers in the filamentous fungal community, I identified NCU00478 and NCU07617 as the genes with mutations responsible for two aconidial strains of N. crassa, acon-2 and acon-3 respectively.

Greenwald, Charles Joaquin

2010-08-01T23:59:59.000Z

212

Effects of Oilseed Meals and Isothiocyanates (ITCS) on Phymatotrichopsis omnivora (Cotton Root Rot) and Soil Microbial Communities  

E-Print Network (OSTI)

The meals from many oilseed crops contain biocidal chemicals that are known to inhibit the growth and activity of several soil pathogens, though little is known concerning impacts on whole soil microbial communities. We investigated the effect of oilseed meals (SMs) from both brassicaceous plants, including mustard and camelina, as well as non-brassicaceous plants, including jatropha and flax, on P. omnivora (the casual agent of cotton root rot) in Branyon clay soil (at 1 and 5% application rates). We also investigated the effect of SMs from camelina, jatropha, flax, and wheat straw on microbial communities in Weswood loam soil. We also used four types of isothiocyanates (ITCs) including allyl, butyl, phenyl, and benzyl ITC to test their effects on P. omnivora growth on potato dextrose agar (PDA), as well as on soil microbial communities in a microcosm study. Community qPCR assays were used to evaluate relative abundances of soil microbial populations. Soil microbial community composition was determined through tag-pyrosequencing using 454 GS FLX titanium technology, targeting ITS and 16S rRNA gene regions for fungal and bacterial communities, respectively. The results showed that all tested brassicaceous and jatropha SMs were able to inhibit P. omnivora sclerotial germination and hyphal growth, with mustard SM being the most effective. Flax didn't show any inhibitory effects on sclerotial germination. All tested ITCs inhibited P. omnivora OKAlf8 hyphal growth, and the level of inhibition varied with concentration and ITC type. Total soil fungal populations were reduced by ITC addition, and microbial community compositions were changed following SM and ITC application. These changes varied according to the type of SM or ITC added. Our results indicated that SMs of several brassicaceous species as well as jatropha may have potential for reducing cotton root rot as well as some other pathogens. Different SMs releasing varied ITCs may result in differential impacts on soil microorganisms including some pathogens.

Hu, Ping

2012-05-01T23:59:59.000Z

213

The effect of enzymes and starch damage on wheat flour tortilla quality  

E-Print Network (OSTI)

Specific enzymes have been used to improve flour quality for bread but enzyme action in tortilla flour has not been investigated. Two different wheat flours were prepared into tortillas using laboratory-scale, commercial equipment with fixed processing parameters. Dough and tortilla properties were evaluated using subjective and objective methods. Tortillas were stored in plastic bags at 22?°C for evaluation. The effects of nine enzymes (amyloglucosidase 1, amyloglucosidase 2, bacterial 1, bacterial 2, fungal, maltogenic 1, maltogenic 2, malted barley and xylanase) on quality of wheat flour tortillas were evaluated. Dough absorption was adjusted to attain uniform dough for tortillas. Enzyme addition to tortilla flour did not significantly affect tortilla weight, moisture and pH. Bacterial 2 amylase extended shelf stability while maltogenic 1 and xylanase exhibited smaller improvements in shelf stability and other tortilla properties. Addition of 0.05 activity unit bacterial 2 amylase improved tortilla diameter and improved tortilla shelf life from 12 to 28 days. Maltogenic 1 at 280 ppm improved tortilla diameter, opacity and shelf life. Addition of 100 ppm of xylanase effectively improved tortilla diameter and shelf life. Bacterial 1 amylase at 60 ppm improved tortilla diameter but did not improve shelf stability. Amyloglucosidase 2, maltogenic 2 and malted barley amylase did not improve tortilla quality at any of the evaluated levels. Amyloglucosidase 1 and fungal amylase reduced overall tortilla quality at all the evaluated levels. Bread-making quality of wheat flour is correlated with the damaged starch present in the flour. Damage was induced by grinding the samples for 0, 1, 4 and 8 hr to determine the effects of starch damage on tortilla quality. Processing increased starch damage of control tortilla flour from 5.4% to 12.6%. Damage starch increased dough water absorption, toughness and press rating and reduced diameter and opacity of tortillas. Damage starch improved tortilla rollability at higher levels but did not improve tortilla properties in combination with bacterial 2 amylase. Overall tortilla quality was not improved due to additional starch damage. Improved tortilla quality using bacterial 2 amylase at very low levels could be commercialized.

Arora, Sapna

2003-12-01T23:59:59.000Z

214

Land use and land cover change: the effects of woody plant encroachment and prescribed fire on biodiversity and ecosystem carbon dynamics in a southern great plains mixed grass savanna  

E-Print Network (OSTI)

In the southern Great Plains, the encroachment of grassland ecosystems by mesquite (Prosopis glandulosa), is widespread, and prescribed fire is commonly used in its control. Despite this, substantial quantitative information concerning their influences on the community composition, functional dynamics, and soil organic carbon (SOC) storage potential of grassland ecosystems is lacking. The objectives of this study were to: a) quantify the effects of seasonal prescribed fire treatments and mesquite encroachment on aboveground net primary productivity (ANPP) and herbaceous community composition; b) characterize SOC pool sizes, turnover, and storage potential relative to vegetation type and fire treatment; c) evaluate the structure and diversity of soil microbial communities relative to vegetation type; and d) characterize the functional diversity of these same microbes using the GeoChip functional gene microarray. Repeated winter and summer fires led to increased ANPP rates (average, 434 and 313 g m-2 y-1, respectively), relative to unburned controls (average, 238 g m-2 y-1), altered herbaceous community composition, and increased the storage of resistant forms of SOC, but did not affect overall SOC storage. Herbaceous ANPP rates did not differ significantly as a result of mesquite encroachment, but herbaceous community composition and SOC storage did. Mesquite soils contained significantly more total, slow-turnover, and resistant forms of SOC than those that occurred beneath C3 or C4 grasses. Similarity among the soil bacterial and fungal communities associated with the major vegetation types in this system was low to moderate. Significant differences were detected among soil fungi, with the mesquite-associated fungi harboring significant differences in community structure relative to the fungal communities associated with each of the other vegetation types examined. Despite this result, few significant differences were detected with respect to the functional diversity of these communities, suggesting either a high degree of functional redundancy, or that the functional differences harbored by these communities are beyond the scope of the GeoChip. The results of this study demonstrate that both fire and mesquite encroachment have the potential to alter ecosystem components and processes significantly, providing new insight regarding the effects of these widespread land use and land cover changes on ecosystem structure and function.

Hollister, Emily Brooke

2008-05-01T23:59:59.000Z

215

Neutron Reflectometry and QCM-D Study of the Interaction of Cellulase Enzymes with Films of Amorphous Cellulose  

Science Conference Proceedings (OSTI)

Improving the efficiency of enzymatic hydrolysis of cellulose is one of the key technological hurdles to reduce the cost of producing ethanol and other transportation fuels from lignocellulosic material. A better understanding of how soluble enzymes interact with insoluble cellulose will aid in the design of more efficient enzyme systems. We report a study involving neutron reflectometry (NR) and quartz crystal microbalance with dissipation (QCM-D) of the interaction of a commercial fungal enzyme extract (T. viride), two purified endoglucanses from thermophilic bacteria (Cel9A from A. acidocaldarius and Cel5A from T. maritima), and a mesophilic fungal endoglucanase (Cel45A from H. insolens) with amorphous cellulose films. The use of amorphous cellulose is motivated by the promise of ionic liquid pretreatment as a second generation technology that disrupts the native crystalline structure of cellulose. NR reveals the profile of water through the film at nm resolution, while QCM-D provides changes in mass and film stiffness. At 20 oC and 0.3 mg/ml, the T. viride cocktail rapidly digested the entire film, beginning from the surface followed by activity throughout the bulk of the film. For similar conditions, Cel9A and Cel5A were active for only a short period of time and only at the surface of the film, with Cel9A releasing 40 from the ~ 700 film and Cel5A resulting in only a slight roughening/swelling effect at the surface. Subsequent elevation of the temperature to the Topt in each case resulted in a very limited increase in activity, corresponding to the loss of an additional 60 from the film for Cel9A and 20 from the film for Cel5A, and very weak penetration into and digestion within the bulk of the film, before the activity again ceased. The results for Cel9A and Cel5A contrast sharply with results for Cel45A where very rapid and extensive penetration and digestion within the bulk of the film was observed at 20 C. We speculate that the large differences are due to the use of the thermophilic enzymes far below their optimal temperatures and also the presence of a cellulose binding module (CBM) on Cel45A while the thermophilic enzymes lack a CBM.

Halbert, Candice E [ORNL; Ankner, John Francis [ORNL; Kent, Michael S [Sandia National Laboratories (SNL); Jaclyn, Murton K [Sandia National Laboratories (SNL); Browning, Jim [ORNL; Cheng, Gang [Joint Bioenergy Institute; Liu, Zelin [Virginia Polytechnic Institute and State University (Virginia Tech); Majewski, Jaroslaw [Los Alamos National Laboratory (LANL); Supratim, Datta [Joint Bioenergy Institute; Michael, Jablin [Los Alamos National Laboratory (LANL); Bulent, Akgun [NIST Center for Neutron Research (NCRN), Gaithersburg, MD; Alan, Esker [Virginia Polytechnic Institute and State University (Virginia Tech); Simmons, Blake [Sandia National Laboratories (SNL)

2011-01-01T23:59:59.000Z

216

IDENTIFICATION, PRODUCTION AND CHARACTERIZATION OF NOVEL LIGNASE PROTEINS FROM TERMITES FOR DEPOLYMERIZATION OF LIGNOCELLULOSE  

SciTech Connect

Wood is a potential source for biofuels such as ethanol if it can be digested into sugars and fermented by yeast. Biomass derived from wood is a challenging substrate for ethanol production since it is made of lignin and cellulose which cannot be broken down easily into fermentable sugars. Some insects, and termites in particular, are specialized at using enzymes in their guts to digest wood into sugars. If termite gut enzymes could be made abundantly by a recombinant protein expression vector system, they could be applied to an industrial process to make biofuels from wood. In this study, a large cDNA library of relevant termite genes was made using termites fed a normal diet, or a diet with added lignin. A subtracted library yielded genes that were overexpressed in the presence of lignin. Termite gut enzyme genes were identified and cloned into recombinant insect viruses called baculoviruses. Using our PERLXpress system for protein expression, these termite gene recombinant baculoviruses were prepared and used to infect insect larvae, which then expressed abundant recombinant termite enzymes. Many of these expressed enzymes were prepared to very high purity, and the activities were studied in conjunction with collaborators at Purdue University. Recombinant termite enzymes expressed in caterpillars were shown to be able to release sugars from wood. Mixing different combinations of these enzymes increased the amount of sugars released from a model woody biomass substrate. The most economical, fastest and energy conserving way to prepare termite enzymes expressed by recombinant baculoviruses in caterpillars was by making crude liquid homogenates. Making enzymes stable in homogenates therefore was a priority. During the course of these studies, improvements were made to the recombinant baculovirus expression platform so that caterpillar-derived homogenates containing expressed termite enzymes would be more stable. These improvements in the baculoviruses included significantly reducing proteases and preventing blackening immune reactions that occur when caterpillars are homogenized. Proteases may degrade enzymes and immune reaction blackening may inactivate enzymes thus compromising the ability of these crude recombinant expressed termite enzyme preparations to release sugars. Commercial preparations of fungal enzymes currently are used to digest wood for ethanol production. We demonstrated in this study that termite enzymes could improve the efficiency of fungal enzyme cocktails. Although the economic feasibility of using caterpillar expressed termite enzymes alone to treat wood was not proven, this work points to the potential to combine C-PERLXpressed insect enzymes with industrial enzyme cocktails to boost their efficiency at treating wood for biofuels.

SLACK, JEFFREY, M.

2012-12-06T23:59:59.000Z

217

Development of PCR primers for the specific amplification of unique DNA sequences of Peronospora sparsa  

E-Print Network (OSTI)

A dual culture of Peronosclerospora sorghi and sorghum callus was established as a model system for a dual culture of Peronospora sparsa on rose callus. Though the identity of the fungus could not be verified microscopically, it was verified by DNA amplification with PCR primers specific for P. sorghi, demonstrating that the primers could amplify fungal DNA from infected callus. A dual culture of P. sparsa and rose callus was sought to provide pure DNA for sequencing and primer development but could not be established using similar procedures. Five inoculation techniques including callus inoculation with a conidial suspension, callus inoculation by transfer of conidia, callus inoculation with sections of a sporulating rose leaf, callus inoculation by sporulating leaves in a sporulation chamber, and use of infected rose leaf sections as explants for callus initiation were attempted. Calli were incubated under conditions favorable to fungal growth for two months, but no P. sparsa infection developed. Sufficient DNA from P. sparsa was extracted from conidia on sporulating rose leaves that a dual culture of the fungus was not necessary. The ITS regions of the RDNA were amplified by various combinations of conserved ITS primers. These products were cloned into a pNoTA/T7 vector and transformed into E. coli cc-complementation cells. Inserts from transformants were sequenced by the Gene Technologies Lab, Texas A&M University, and aligned using the Sequencher program to deten-nine the complete sequence of the ITS regions of P. sparsa. This sequence of P. sparsa was compared to fungi with similar sequences as well as common saprophytes of rose, using the BLAST search provided by Genbank, to select putative PCR primers unique to P. sparsa. The primers were tested against DNA from rose leaves infected with P. sparsa, plasmid DNA containing an insert of the ITS region of P. sparsa, rose callus, a water control, and the control fungi Fusarium oxysporum, Epicoccum sp., Alternaria sp., Cladosporium sp., Botrytis sp., and Pestalotia sp. A nested PCR protocol was used in which DNA was first amplified with conserved ITS primers I and 4, diluted 1: I 000 with water, and amplified with specific primers to yield a visible product only for samples containing P. sparsa DNA.

Ross, Sharon

1997-01-01T23:59:59.000Z

218

Heterocyclic small molecule peptidomimetics  

E-Print Network (OSTI)

Polymer-supported synthesis of a close analog (i.e. A) of an early lead, a 14- membered ring peptidomimetic D3, was described. The monovalent molecule was attached to different length linkers, and they were then paired sequentially on a triazine scaffold via our previously published methodology to give a small library of bivalent compounds 1 representing all combinations of linkers of the different lengths in a fast and efficient combinatorial manner. Cellular assays identified 1-ss as a TrkA receptor antagonist towards NGF and it was shown to bind TrkA with ~200 nM affinity and retains high selectivity towards TrkA in binding assays. A set of monovalent diketopiperazine (DKP) mimics 4-7 was synthesized efficiently from corresponding dipeptides via intramolecular SN2 cyclization reactions in solution. These DKP compounds contain two amino acid side-chain functionalities to mimic the sequences that occur at hot-spots in loop regions. The monovalent mimics were assembled into a library of biotin-labeled bivalent molecules 9 via the combinatorial strategy described above with some modification. In primary screening, compound 9gg showed preferential binding to TrkC receptors in FACScan assay and blocked the trophic activity of NT-3 in TrkC cells at 10 uM in cell survival assay. The preparation of monovalent 1,3,4-oxadizole-based mimics 12 was achieved from corresponding amino acid building blocks on gram scale in a highly efficient solution phase parallel synthesis manner in good yields. These heterocyclic compounds feature various natural amino acid side-chain functionalities including those occuring most frequently at hot-spots such as those of Tyr, Lys, Glu and Ser. Attempts to assemble them into bivalent molecules were done by coupling the monovalent mimics to the triazine scaffold sequentially in solution and simply manipulating the solvent systems. For some reasons, some reactions did not proceed cleanly. Studies have been carried out and the problems were partially solved. The biological activities of these oxadiazoles are under investigation. So far, six compounds have shown activities in four different bioassays. Two different peptidomimetic types that resemble protein A and protein G binding regions were generated and tested as binding factors in affinity columns for purification of IgG. They are cyclic hexapeptides 19, which were prepared via Fmoc- SPPS and solution phase intramoleculer macrocyclization, and heterocycle-based small molecules 22 and 23 featuring a variety of aromatic functionalities generated via solution phase parallel synthesis. Four compounds showed some affinity towards a Fab fragment of IgG in SAR screening, and they were attached to a dendrimer core on a solid support to give four multivalent mimetics 25.

Liu, Jing

2008-12-01T23:59:59.000Z

219

Urine definition  

NLE Websites -- All DOE Office Websites (Extended Search)

definition definition Name: durwood Status: N/A Age: N/A Location: N/A Country: N/A Date: Around 1993 Question: What material is urine composed of? Replies: Urine is normally composed of water and wasted products filtered form the body. The kidney produces urine. The other main function of the kidney is to regulate fluid balance in the body. It performs this function by using a selective osmosis system. Basically, the way it works is that electrolytes (dissolved salts like sodium, potassium, calcium, carbonate, chloride) are pumped back into or out of urine and blood so that in the end, just the right amounts of electrolyte and water exit the kidney blood vein. The rest ends up in urine. Interestingly, normal urine is sterile and has no bacteria. psych Urine contains 95% water and 5% solids. More than 1000 different mineral salts and compounds are estimated to be in urine. So far, our scientific community knows of about 200 elements. Some substances are: vitamins, amino acids, antibodies, enzymes, hormones, antigens, interleukins, proteins, immunoglobulins, gastric secretory depressants, tolergens, immunogens, uric acid, urea, proteoses, directin, H-11 (a growth inhibitory factor in human cancer), and urokinase. Believe it or not, scientists have know for years that urine is antibacterial, anti-protozoal, anti-fungal, anti- viral, and anti-tuberculostatic!

220

Development and demonstration of biosorbents for clean-up of uranium in water. CRADA final report  

SciTech Connect

Pseudomonas aeruginosa strain CSU, a nongenetically engineered bacterial strain known to bind dissolved hexavalent uranium, shows particular promise as the basis of an immobilized-cell process for removal of dissolved uranium from contaminated wastewaters. It was characterized with respect to its sorptive active. Living, heat-killed, permeabilized, and unreconstituted lyophilized cells were all capable of binding uranium. The uranium biosorption equilibrium could be described by the Langmuir isotherm. The rate of uranium adsorption increased following permeabilization of the outer and/or cytoplasmic membrane by organic solvents such as acetone. P. aeruginosa CSU biomass was significantly more sorptive toward uranium than certain novel, patented biosorbents derived from algal or fungal biomass sources. P. aeruginosa CSU biomass was also competitive with commercial cation-exchange resins, particularly in the presence of dissolved transition metals. Uranium binding by P. aeruginosa was clearly pH dependent. Uranium loading capacity increased with increasing pH under acidic conditions, presumably as a function of uranium speciation and due to the H{sup +} competition at some binding sites. Nevertheless, preliminary evidence suggests that this microorganism is also capable of binding anionic hexavalent uranium complexes. Ferric iron was a strong inhibitor of uranium binding to P. aeruginosa CSU biomass, and the presence of uranium also decreased the Fe{sup 3+} loading when the biomass was not saturated with Fe{sup 3+}, suggesting that Fe{sup 3+} and uranium may share the same binding sites on biomass.

Faison, B.D.; Hu, M.Z.C.; Norman, J.M.; Reeves, M.E.; Williams, L.; Schmidt-Kuster, W.; Darnell, K. [Oak Ridge National Lab., TN (United States)]|[Ogden Environmental Service, Oak Ridge, TN (United States)

1997-08-01T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
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221

Differential Expression in Phanerochaete chrysosporium of Membrane-Associated Proteins Relevant to Lignin Degradation  

DOE Green Energy (OSTI)

Fungal lignin-degrading systems must include membrane-associated proteins that participate in diverse processes such as uptake and oxidation of lignin fragments, secretion of ligninolytic secondary metabolites, and defense of the mycelium against ligninolytic oxidants. Despite their importance, little is known about the nature or regulation of these membrane-associated components. We grew the white rot basidiomycete Phanerochaete chrysosporium on cellulose or glucose as the carbon source and monitored the mineralization of a 14C-labeled synthetic lignin by these cultures to assess their ligninolytic competence. The results showed that the cellulose-grown cultures were ligninolytic, whereas the glucose-grown ones were not. We isolated microsomal membrane fractions from both types of culture and analyzed tryptic digests of them by shotgun liquid chromatography/tandem mass spectrometry. Comparison of the results against the predicted P. chrysosporium proteome showed that a catalase (Joint Genome Institute P. chrysosporium protein I.D. 124398), an alcohol oxidase (126879), two transporters (137220 and 132234), and two cytochrome P450s (5011 and 8912) were up-regulated under ligninolytic conditions. Real time reverse transcription polymerase chain reaction assays showed that RNA transcripts encoding all of these proteins were also up-regulated in ligninolytic cultures. Catalase 124398, alcohol oxidase 126879, and transporter 137220 were found in a proteomic analysis of partially purified plasma membranes from ligninolytic P. chrysosporium, and are therefore most likely associated with the outer envelope of the fungus.

Shary, Semarjit; Kapich, Alexander N.; Panisko, Ellen A.; Magnuson, Jon K.; Cullen, Dan; Hammel, Ken

2008-10-02T23:59:59.000Z

222

Biotechnology and genetic optimization of fast-growing hardwoods  

DOE Green Energy (OSTI)

A biotechnology research program was initiated to develop new clones of fast-growing Populus clones resistant to the herbicide glyphosate and resistant to the leaf-spot and canker disease caused by the fungus Septoria musiva. Glyphosate-resistant callus was selected from stem segments cultured in vitro on media supplemented with the herbicide. Plants were regenerated from the glyphosate-resistant callus tissue. A portion of plants reverted to a glyphosate susceptible phenotype during organogenesis. A biologically active filtrate was prepared from S. musiva and influenced fresh weight of Populus callus tissue. Disease-resistant plants were produced through somaclonal variation when shoots developed on stem internodes cultured in vitro. Plantlets were screened for disease symptoms after spraying with a suspension of fungal spores. A frequency of 0.83 percent variant production was observed. Genetically engineered plants were produced after treatment of plant tissue with Agrobacterium tumefasciens strains carrying plasmid genes for antibiotic resistance. Transformers were selected on media enriched with the antibiotic, kanamycin. Presence of foreign DNA was confirmed by Southern blot analysis. Protoplasts of popular were produced but did not regenerate into plant organs. 145 refs., 12 figs., 36 tabs.

Garton, S.; Syrkin-Wurtele, E.; Griffiths, H.; Schell, J.; Van Camp, L.; Bulka, K. (NPI, Salt Lake City, UT (United States))

1991-02-01T23:59:59.000Z

223

Prevention of Prespawning Mortality: Cause of Salmon Headburns and Cranial Lesions  

DOE Green Energy (OSTI)

This project was to undertaken to provide information about a condition known as ''headburn''. Information from the project will enable U.S. Corps of Engineers managers to make adjustments in operational procedures or facilities on the Columbia and Snake rivers to prevent loss of pre-spawning adult salmonids that migrate through the facilities. Headburn is a descriptive clinical term used by fishery biologists to describe scalping or exfoliation of skin and ulceration of underlying connective tissue and muscle, primarily of the jaw and cranial region of salmonids observed at fish passage facilities. Headburn lesions are primarily caused when fish collide with concrete or other structures at dams and fish passage facilities, and may be exacerbated in some fish that ''fallback'' or pass over spillways or through turbine assemblies after having passed the dam through a fish ladder. Prespawning mortality of headburned salmonids can be prevented or greatly reduced by therapeutic treatment of both hatchery and wild fish. Treatments would consist of topical application of an anti-fungal agent, injection of replacement plasma electrolytes into the peritoneal cavity, and injection of a broad-spectrum antibacterial agent at fish passage and trapping facilities or hatcheries.

Neitzel, Duane A.; Elston, R A.; Abernethy, Cary S.

2004-06-01T23:59:59.000Z

224

www.mdpi.com/journal/marinedrugs Anti-Phytopathogenic Activities of Macro-Algae Extracts  

E-Print Network (OSTI)

Abstract: Aqueous and ethanolic extracts obtained from nine Chilean marine macro-algae collected at different seasons were examined in vitro and in vivo for properties that reduce the growth of plant pathogens or decrease the injury severity of plant foliar tissues following pathogen infection. Particular crude aqueous or organic extracts showed effects on the growth of pathogenic bacteria whereas others displayed important effects against pathogenic fungi or viruses, either by inhibiting fungal mycelia growth or by reducing the disease symptoms in leaves caused by pathogen challenge. Organic extracts obtained from the brown-alga Lessonia trabeculata inhibited bacterial growth and reduced both the number and size of the necrotic lesion in tomato leaves following infection with Botrytis cinerea. Aqueous and ethanolic extracts from the red-alga Gracillaria chilensis prevent the growth of Phytophthora cinnamomi, showing a response which depends on doses and collecting-time. Similarly, aqueous and ethanolic extracts from the brown-alga Durvillaea antarctica were able to diminish the damage caused by tobacco mosaic virus (TMV) in tobacco leaves, and the aqueous procedure is, in addition, more effective and seasonally independent. These results suggest that macro-algae contain compounds with

Edra Jimnez; O Dorta; Cristian Medina; Alberto Ramrez; Ingrid Ramrez; Hugo Pea-corts

2011-01-01T23:59:59.000Z

225

Assessment of toxicological interactions of benzene and its primary degradation products (catechol and phenol) using a lux-modified bacterial bioassay  

Science Conference Proceedings (OSTI)

A bacterial bioassay has been developed to assess the relative toxicities of xenobiotics commonly found in contaminated soils, river waters, and ground waters. The assay utilized decline in luminescence of lux-marked Pseudomonas fluorescens on exposure to xenobiotics. Pseudomonas fluorescens is a common bacterium in the terrestrial environment, providing environmental relevance to soil, river, and ground water systems. Three principal environmental contaminants associated with benzene degradation were exposed to the luminescence-marked bacterial biosensor to assess their toxicity individually and in combination. Median effective concentration (EC50) values for decline in luminescence were determined for benzene, catechol, and phenol and were found to be 39.9, 0.77, and 458.6 mg/L, respectively. Catechol, a fungal and bacterial metabolite of benzene, was found to be significantly more toxic to the biosensor than was the parent compound benzene, showing that products of xenobiotic biodegradation may be more toxic than the parent compounds. Combinations of parent compounds and metabolites were found to be significantly more toxic to the bioassay than were the individual compounds themselves. Development of this bioassay has provided a rapid screening system suitable for assessing the toxicity of xenobiotics commonly found in contaminated soil, river, and ground-water environments. The assay can be utilized over a wide pH range is therefore more applicable to such environmental systems than bioluminescence-based bioassays that utilize marine organisms and can only be applied over a limited pH and salinity range.

Boyd, E.M. [Inst. of Terrestrial Ecology, Huntingdon (United Kingdom)]|[Univ. of Aberdeen (United Kingdom). Dept. of Plant and Soil Science; Meharg, A.A.; Wright, J. [Inst. of Terrestrial Ecology, Huntingdon (United Kingdom); Killham, K. [Univ. of Aberdeen (United Kingdom). Dept. of Plant and Soil Science

1997-05-01T23:59:59.000Z

226

Comparison Test for Infection Control Barriers for Construction in Healthcare  

E-Print Network (OSTI)

Understanding the extent of infection control measures to be taken to protect immunosuppressed and other types of patients from airborne infection agents during construction is crucial knowledge for both healthcare and construction professionals. The number of aspergillosis-related fatalities due to dust transmission during construction activity has decreased with the improvement of antifungal therapy, however the illness is particularly debilitating and the treatment is not always successful. This experimental work is the first stage in a research program to develop better dust controls for construction at existing medical facilities to reduce the incidence of dust borne fungi, such as Aspergillus spp. To better protect at-risk patients from exposure to Aspergillus spp. and other airborne fungal infections, an experiment was conducted to determine what materials can be used to create a barrier for infection control to moderate particle transmission from the construction area to the treatment area. This study investigated the relationship between construction barriers and particle transmission. A new experimental procedure and equipment simulates the transmission of disturbed dust from construction activity across a barrier. The effective of the barrier is determined from measured particle count on filter. The results show that an effective barrier manufactured from simple and readily available building supplies stops the transmission of 12-micron dust particles under a standard set of conditions. The test provides a simple and cost effective method to compare transmission rates for dust.

Bassett, Aimee

2013-05-01T23:59:59.000Z

227

Global coal gap between Permian-Triassic extinction and Middle Triassic recovery of peat-forming plants  

Science Conference Proceedings (OSTI)

Early Triassic coals are unknown, and Middle Triassic coals are rare and thin. The Early Triassic coal gap began with extinction of peat-forming plants at the end of the Permian (ca. 250 Ma), with no coal known anywhere until Middle Triassic (243 Ma). Permian levels of plant diversity and peat thickness were not recovered until Late Triassic (230 Ma). Tectonic and climatic explanations for the coal gap fail because deposits of fluctuating sea levels and sedimentary facies and paleosols commonly found in coal-bearing sequences are present also in Early Triassic rocks. Nor do we favor explanations involving evolutionary advances in the effectiveness of fungal decomposers, insects or tetrapod herbivores, which became cosmopolitan and much reduced in diversity across the Permian-Triassic boundary. Instead, we favor explanations involving extinction of peat-forming plants at the Permian-Triassic boundary, followed by a hiatus of some 10 m.y. until newly evolved peat-forming plants developed tolerance to the acidic dysaerobic conditions of wetlands. This view is compatible not only with the paleobotanical record of extinction of swamp plants, but also with indications of a terminal Permian productivity crash from {delta}{sup 13}C{sub org} and total organic carbon of both nonmarine and shallow marine shales. 205 refs., 3 figs., 3 tabs.

Retallack, G.J. [Univ. of Oregon, Eugene, OR (United States)] [Univ. of Oregon, Eugene, OR (United States); Veevers, J.J.; Morante, R. [Macquarie Univ., New South Wales (Australia)] [Macquarie Univ., New South Wales (Australia)

1996-02-01T23:59:59.000Z

228

Identification of Saprolegnia Spp. Pathogenic in Chinook Salmon : Final Report.  

SciTech Connect

This project has developed procedures to assess the role of the fungal parasite, Saprolegnia in the biology of salmon, particularly adult Chinook, in the Columbia River Basin. Both morphological and DNA ``fingerprinting`` surveys reveal that Saprolegnia parasitica (=S. diclina, Type I) is the most common pathogen of these fish. In the first phase of this study 92% of 620 isolates, from salmon lesions, conformed to this taxa of Saprolegnia. In the current phase, the authors have developed variants of DNA fingerprinting (RAPD and SWAPP analysis) that permit examination of the sub-structure of the parasite population. These results confirm the predominance of S. parasitica, and suggest that at least three different sub-groups of this fungus occur in the Pacific N.W., USA. The use of single and paired primers with PCR amplification permits identification of pathogenic types, and distinction from other species of the genus considered to be more saprophytic in character. A year`s survey of saprolegniaceous fungi from Lake Washington indicated that the fish-pathogen was not common in the water column. Where and how fish encounter this parasite can be approached with the molecular tags identified in this project.

Whisler, Howard C.

1997-06-01T23:59:59.000Z

229

D-erythroascorbic acid: Its preparations, chemistry, and metabolism (fungi and plants)  

SciTech Connect

The origin of oxalate in plants has received considerable attention and glycolate metabolism has been generally regarded as a prime precursor candidate although studies on the metabolism of L-ascorbic acid single out that plant constituent as well. Experiments with oxalate-accumulating plants that contain little or no tartaric acid revealed the presence of a comparable L-ascorbic acid metabolism with the exception that the cleavage products were oxalic acid and L-threonic acid or products of L-threonic acid metabolism. A reasonable mechanism for cleavage of L-ascorbic acid at the endiolic bond is found in studies on the photooxygenation of L-ascorbic acid. Presumably, analogs of L-ascorbic acid that differ only in the substituent at C4 also form a hydroperoxide in the presence of alkaline hydrogen peroxide and subsequently yield oxalic acid and the corresponding aldonic acid or its lactone. We became interested in such a possibility when we discovered that L-ascorbic acid was rare or absent in certain yeasts and fungi whereas a L-ascorbic acid analog, D-glycero-pent-2-enono- 1,4-lactone (D-erythroascorbic acid), was present. It has long been known that oxalate occurs in yeasts and fungi and its production plays a role in plant pathogenesis. As to the biosynthetic origin of fungal oxalic acid there is little information although it is generally assumed that oxaloacetate or possibly, glycolate, might be that precursor.

Loewus, F.A. (Washington State Univ., Pullman, WA (United States). Inst. of Biological Chemistry); Seib, P.A. (Kansas State Univ., Manhattan, KS (United States). Dept. of Grain Science and Industry)

1991-01-01T23:59:59.000Z

230

D-erythroascorbic acid: Its preparations, chemistry, and metabolism (fungi and plants). Final report  

SciTech Connect

The origin of oxalate in plants has received considerable attention and glycolate metabolism has been generally regarded as a prime precursor candidate although studies on the metabolism of L-ascorbic acid single out that plant constituent as well. Experiments with oxalate-accumulating plants that contain little or no tartaric acid revealed the presence of a comparable L-ascorbic acid metabolism with the exception that the cleavage products were oxalic acid and L-threonic acid or products of L-threonic acid metabolism. A reasonable mechanism for cleavage of L-ascorbic acid at the endiolic bond is found in studies on the photooxygenation of L-ascorbic acid. Presumably, analogs of L-ascorbic acid that differ only in the substituent at C4 also form a hydroperoxide in the presence of alkaline hydrogen peroxide and subsequently yield oxalic acid and the corresponding aldonic acid or its lactone. We became interested in such a possibility when we discovered that L-ascorbic acid was rare or absent in certain yeasts and fungi whereas a L-ascorbic acid analog, D-glycero-pent-2-enono- 1,4-lactone (D-erythroascorbic acid), was present. It has long been known that oxalate occurs in yeasts and fungi and its production plays a role in plant pathogenesis. As to the biosynthetic origin of fungal oxalic acid there is little information although it is generally assumed that oxaloacetate or possibly, glycolate, might be that precursor.

Loewus, F.A. [Washington State Univ., Pullman, WA (United States). Inst. of Biological Chemistry; Seib, P.A. [Kansas State Univ., Manhattan, KS (United States). Dept. of Grain Science and Industry

1991-12-31T23:59:59.000Z

231

ARBUSCULAR MYCORRHIZAL COLONIZATION OF LARREA TRIDENTATA AND AMBROSIA DUMOSA ROOTS VARIES WITH PRECIPITATION AND SEASON IN THE MOJAVE DESERT  

SciTech Connect

The percentage of fine roots colonized by arbuscular mycorrhizal (AM) fungi varied with season and with species in the co-dominant shrubs Lurreu tridentutu and Ambrosia dumosu at a site adjacent to the Nevada Desert FACE (Free-Air CO{sub 2} Enrichment) Facility (NDFF) in the Mojave Desert. We excavated downward and outward from the shrub bases in both species to collect and examine fine roots (< 1.0 mm diameter) at monthly intervals throughout 2001 and from October 2002 to September 2003. Fungal structures became visible in cleared roots stained with trypan blue. We quantified the percent colonization of roots by AM fungi via the line intercept method. In both years and for both species, colonization was highest in fall, relatively low in spring when root growth began, increased in late spring, and decreased during summer drought periods. Increases in colonization during summer and fall reflect corresponding increases in precipitation. Spring mycorrhizal colonization is low despite peaks in soil water availability and precipitation, indicating that precipitation is not the only factor influencing mycorrhizal colonization. Because the spring decrease in mycorrhizal colonization occurs when these shrubs initiate a major flush of fine root growth, other phenological events such as competing demands for carbon by fine root initiation, early season shoot growth, and flowering may reduce carbon availability to the fungus, and hence decrease colonization. Another possibility is that root growth exceeds the rate of mycorrhizal colonization.

M. E. APPLE; C. I. THEE; V. L. SMITH-LONGOZO; C. R. COGAR; C. E. WELLS; R. S. NOWAK

2004-01-01T23:59:59.000Z

232

Interactions of Endoglucanases with Amorphous Cellulose Films Resolved by Neutron Reflectometry and Quartz Crystal Microbalance with Dissipation Monitoring  

Science Conference Proceedings (OSTI)

A study of the interaction of four endoglucanases with amorphous cellulose films by neutron reflectometry (NR) and quartz crystal microbalance with dissipation monitoring (QCM-D) is reported. The endoglucanases include a mesophilic fungal endoglucanase (Cel45A from H. insolens), a processive endoglucanase from a marine bacterium (Cel5H from S. degradans), and two from thermophilic bacteria (Cel9A from A. acidocaldarius and Cel5A from T. maritima). The use of amorphous cellulose is motivated by the promise of ionic liquid pretreatment as a second generation technology that disrupts the native crystalline structure of cellulose. The endoglucanases displayed highly diverse behavior. Cel45A and Cel5H, which possess carbohydrate-binding modules (CBMs), penetrated and digested within the bulk of the films to a far greater extent than Cel9A and Cel5A, which lack CBMs. While both Cel45A and Cel5H were active within the bulk of the films, striking differences were observed. With Cel45A, substantial film expansion and interfacial broadening were observed, whereas for Cel5H the film thickness decreased with little interfacial broadening. These results are consistent with Cel45A digesting within the interior of cellulose chains as a classic endoglucanase, and Cel5H digesting predominantly at chain ends consistent with its designation as a processive endoglucanase.

Cheng, Gang [Joint Bioenergy Institute; Liu, Zelin [Virginia Polytechnic Institute and State University (Virginia Tech); Kent, Michael S [Sandia National Laboratories (SNL); Majewski, Jaroslaw [Los Alamos National Laboratory (LANL); Michael, Jablin [Los Alamos National Laboratory (LANL); Jaclyn, Murton K [Sandia National Laboratories (SNL); Halbert, Candice E [ORNL; Datta, Supratim [Joint Bioenergy Institute; Chao, Wang [Virginia Polytechnic Institute and State University (Virginia Tech); Brown, Page [Sandia National Laboratories (SNL)

2012-01-01T23:59:59.000Z

233

Old-field Community, Climate and Atmospheric Manipulation  

SciTech Connect

We are in the process of finishing a number of laboratory, growth chamber and greenhouse projects, analyzing data, and writing papers. The projects reported addressed these subjects: How do climate and atmospheric changes alter aboveground plant biomass and community structure; Effects of multiple climate changes factors on plant community composition and diversity: what did we learn from a 5-year open-top chamber experiment using constructed old-field communities; Do atmospheric and climatic change factors interact to alter woody seedling emergence, establishment and productivity; Soil moisture surpasses elevated CO{sub 2} and temperature in importance as a control on soil carbon dynamics; How do climate and atmospheric changes alter belowground root and fungal biomass; How do climate and atmospheric changes alter soil microarthropod and microbial communities; How do climate and atmospheric changes alter belowground microbial function; Linking root litter diversity and microbial functioning at a micro scale under current and projected CO{sub 2} concentrations; Multifactor climate change effects on soil ecosystem functioning depend on concurrent changes in plant community composition; How do climate and atmospheric changes alter aboveground insect populations; How do climate and atmospheric changes alter festuca endophyte infection; How do climate and atmospheric changes soil carbon stabilization.

Aimee Classen

2009-11-01T23:59:59.000Z

234

Fifteenth symposium on biotechnology for fuels and chemicals: Program and abstracts  

DOE Green Energy (OSTI)

This collection contains 173 abstracts from presented papers and poster sessions. The five sessions of the conference were on the subjects of: (1) Thermal, Chemical, and Biological Processing, (2) Applied Biological Research, (3) Bioprocessing Research (4), Process Economics and Commercialization, and (5) Environmental Biotechnology. Examples of specific topics in the first session include the kinetics of ripening cheese, microbial liquefaction of lignite, and wheat as a feedstock for fuel ethanol. Typical topics in the second session were synergism studies of bacterial and fungal celluloses, conversion of inulin from jerusalem artichokes to sorbitol and ethanol by saccharomyces cerevisiae, and microbial conversion of high rank coals to methane. The third session entertained topics such as hydrodynamic modeling of a liquid fluidized bed bioreactor for coal biosolubilization, aqueous biphasic systems for biological particle partitioning, and arabinose utilization by xylose-fermenting yeast and fungi. The fourth session included such topics as silage processing of forage biomass to alcohol fuels, economics of molasses to ethanol in India, and production of lactic acid from renewable resources. the final session contained papers on such subjects as bioluminescent detection of contaminants in soils, characterization of petroleum contaminated soils in coral atolls in the south Pacific, and landfill management for methane generation and emission control.

Not Available

1993-07-01T23:59:59.000Z

235

Microtubule organization requires cell cycle-dependent nucleation at dispersed cytoplasmic sites: Polar and perinuclear microtubule organizing centers in the plant pathogen Ustilago maydis  

E-Print Network (OSTI)

Growth of most eukaryotic cells requires directed transport along microtubules (MTs) that are nucleated at nuclear-associated microtubule organizing centers (MTOCs), such as the centrosome and the fungal spindle pole body (SPB). Herein, we show that the pathogenic fungus Ustilago maydis uses different MT nucleation sites to rearrange MTs during the cell cycle. In vivo observation of green fluorescent protein-MTs and MT plus-ends, tagged by a fluorescent EB1 homologue, provided evidence for antipolar MT orientation and dispersed cytoplasmic MT nucleating centers in unbudded cells. On budding ?-tubulin containing MTOCs formed at the bud neck, and MTs reorganized with ?85 % of all minus-ends being focused toward the growth region. Experimentally induced lateral budding resulted in MTs that curved out of the bud, again supporting the notion that polar growth requires polar MT nucleation. Depletion or overexpression of Tub2, the ?-tubulin from U. maydis, affected MT number in interphase cells. The SPB was inactive in G2 phase but continuously recruited ?-tubulin until it started to nucleate mitotic MTs. Taken together, our data suggest that MT reorganization in U. maydis depends on cell cycle-specific nucleation at dispersed cytoplasmic sites, at a polar MTOC and the SPB.

Anne Straube; Marianne Brill; Berl R. Oakley; Tetsuya Horio; Gero Steinberg

2003-01-01T23:59:59.000Z

236

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

DOE Green Energy (OSTI)

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.

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

2011-05-01T23:59:59.000Z

237

Improvements In Ethanologenic Escherichia Coli and Klebsiella Oxytoca  

DOE Green Energy (OSTI)

The current Verenium cellulosic ethanol process is based on the dilute-acid pretreatment of a biomass feedstock, followed by a two-stage fermentation of the pentose sugar-containing hydrolysate by a genetically modified ethanologenic Escherichia coli strain and a separate simultaneous saccharification-fermentation (SSF) of the cellulosic fraction by a genetically modified ethanologenic Klebsiella oxytoca strain and a fungal enzyme cocktail. In order to reduce unit operations and produce a fermentation beer with higher ethanol concentrations to reduce distillation costs, we have proposed to develop a simultaneous saccharification co-fermentation (SScF) process, where the fermentation of the pentose-containing hydrolysate and cellulosic fraction occurs within the same fermentation vessel. In order to accomplish this goal, improvements in the ethanologens must be made to address a number of issues that arise, including improved hydrolysate tolerance, co-fermentation of the pentose and hexose sugars and increased ethanol tolerance. Using a variety of approaches, including transcriptomics, strain adaptation, metagenomics and directed evolution, this work describes the efforts of a team of scientists from Verenium, University of Florida, Massachusetts Institute of Technology and Genomatica to improve the E. coli and K. oxytoca ethanologens to meet these requirements.

Dr. David Nunn

2010-09-30T23:59:59.000Z

238

Structure and Function of the Clostridium thermocellum Cellobiohydrolase A X1-Module Repeat: Enhancement Through Stabilization of the CbhA Complex  

DOE Green Energy (OSTI)

The efficient deconstruction of lignocellulosic biomass remains a significant barrier to the commercialization of biofuels. Whereas most commercial plant cell-wall-degrading enzyme preparations used today are derived from fungi, the cellulosomal enzyme system from Clostridium thermocellum is an equally effective catalyst, yet of considerably different structure. A key difference between fungal enzyme systems and cellulosomal enzyme systems is that cellulosomal enzyme systems utilize self-assembled scaffolded multimodule enzymes to deconstruct biomass. Here, the possible function of the X1 modules in the complex multimodular enzyme system cellobiohydrolase A (CbhA) from C. thermocellum is explored. The crystal structures of the two X1 modules from C. thermocellum CbhA have been solved individually and together as one construct. The role that calcium may play in the stability of the X1 modules has also been investigated, as well as the possibility that they interact with each other. Furthermore, the results show that whereas the X1 modules do not seem to act as cellulose disruptors, they do aid in the thermostability of the CbhA complex, effectively allowing it to deconstruct cellulose at a higher temperature.

Brunecky, R.; Alahuhta, M.; Bomble, Y. J.; Xu, Q.; Baker, J. O.; Ding, S. Y.; Himmel, M. E.; Lunin, V. V.

2012-03-01T23:59:59.000Z

239

Genome Improvement at JGI-HAGSC  

Science Conference Proceedings (OSTI)

Since the completion of the sequencing of the human genome, the JGI has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

Grimwood, Jane: Schmutz, Jeremy, J.: Myers, Richard, M.

2012-03-03T23:59:59.000Z

240

MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH (Session introduction)  

SciTech Connect

Pathogenic infections are a major cause of both human disease and loss of crop yields and animal stocks and thus cause immense damage to the worldwide economy. The significance of infectious diseases is expected to increase in an ever more connected warming world, in which new viral, bacterial and fungal pathogens can find novel hosts and ecologic niches. At the same time, the complex and sophisticated mechanisms by which diverse pathogenic agents evade defense mechanisms and subvert their hosts networks to suit their lifestyle needs is still very incompletely understood especially from a systems perspective [1]. Thus, understanding host-pathogen interactions is both an important and a scientifically fascinating topic. Recently, technology has offered the opportunity to investigate host-pathogen interactions on a level of detail and scope that offers immense computational and analytical possibilities. Genome sequencing was pioneered on some of these pathogens, and the number of strains and variants of pathogens sequenced to date vastly outnumbers the number of host genomes available. At the same time, for both plant and human hosts more and more data on population level genomic variation becomes available and offers a rich field for analysis into the genetic interactions between host and pathogen.

McDermott, Jason E.; Braun, Pascal; Bonneau, Richard A.; Hyduke, Daniel R.

2011-12-01T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

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

Science Conference Proceedings (OSTI)

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.

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.

2012-09-01T23:59:59.000Z

242

Identifying and characterizing the most significant ?-glucosidase of the novel species Aspergillus saccharolyticus  

Science Conference Proceedings (OSTI)

A newly discovered fungal species, Aspergillus saccharolyticus, was found to produce a culture broth rich in beta-glucosidase activity. In this present work, the main beta-glucosidase of A. saccharolyticus responsible for the efficient hydrolytic activity was identified, isolated, and characterized. Ion exchange chromatography was used to fractionate the culture broth, yielding fractions with high beta-glucosidase activity and only one visible band on an SDS-PAGE gel. Mass spectrometry analysis of this band gave peptide matches to beta-glucosidases from aspergilli. Through a PCR approach using degenerate primers and genome walking, a 2919 base pair sequence encoding the 860 amino acid BGL1 polypeptide was determined. BGL1 of A. saccharolyticus has 91% and 82% identity with BGL1 from Aspergillus aculeatus and BGL1 from Aspergillus niger, respectively, both belonging to Glycoside hydrolase family 3. Homology modeling studies suggested beta-glucosidase activity with preserved retaining mechanism and a wider catalytic pocket compared to other beta-glucosidases. The bgl1 gene was heterologously expressed in Trichoderma reesei QM6a, purified, and characterized by enzyme kinetics studies. The enzyme can hydrolyze cellobiose, pNPG, and cellodextrins. The enzyme showed good thermostability, was stable at 50C, and at 60C it had a half-life of approximately 6 hours.

Sorensen, Anette; Ahring, Birgitte K.; Lubeck, Mette; Ubhayasekera, Wimal; Bruno, Kenneth S.; Culley, David E.; Lubeck, Peter S.

2012-08-20T23:59:59.000Z

243

Complete genome of the cellyloytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evloutionary adaptations  

SciTech Connect

We present here the complete 2.4 Mb genome of the cellulolytic actinobacterial thermophile, Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized, and significantly elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. A novel feature of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes is that they are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. Interestingly, CBM3 was found to be always N-terminal to CBM2, suggesting a functional constraint driving this organization. While the catalytic domains of these modular enzymes are either diverse or unrelated, the CBMs were found to be highly conserved in sequence and may suggest selective substrate-binding interactions. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and non-coding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles, and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and presence of three laterally-acquired genomic islands of likely ecophysiological value.

Barabote, Ravi D.; Xie, Gary; Leu, David H.; Normand, Philippe; Necsulea, Anamaria; Daubin, Vincent; Medigue, Claudine; Adney, William S.; Xu,Xin Clare; Lapidus, Alla; Detter, Chris; Pujic, Petar; Bruce, David; Lavire, Celine; Challacombe, Jean F.; Brettin, Thomas S.; Berry, Alison M.

2009-01-01T23:59:59.000Z

244

The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling  

Science Conference Proceedings (OSTI)

Many studies have shown that changes in nitrogen (N) availability affect primary productivity in a variety of terrestrial systems, but less is known about the effects of the changing N cycle on soil organic matter (SOM) decomposition. We used a variety of techniques to examine the effects of chronic N amendments on SOM chemistry and microbial community structure and function in an alpine tundra soil. We collected surface soil (0-5 cm) samples from five control and five long-term N-amended plots established and maintained at the Niwot Ridge Long-term Ecological Research (LTER) site. Samples were bulked by treatment and all analyses were conducted on composite samples. The fungal community shifted in response to N amendments, with a decrease in the relative abundance of basidiomycetes. Bacterial community composition also shifted in the fertilized soil, with increases in the relative abundance of sequences related to the Bacteroidetes and Gemmatimonadetes, and decreases in the relative abundance of the Verrucomicrobia. We did not uncover any bacterial sequences that were closely related to known nitrifiers in either soil, but sequences related to archaeal nitrifiers were found in control soils. The ratio of fungi to bacteria did not change in the N-amended soils, but the ratio of archaea to bacteria dropped from 20% to less than 1% in the N-amended plots. Comparisons of aliphatic and aromatic carbon compounds, two broad categories of soil carbon compounds, revealed no between treatment differences. However, G-lignins were found in higher relative abundance in the fertilized soils, while proteins were detected in lower relative abundance. Finally, the activities of two soil enzymes involved in N cycling changed in response to chronic N amendments. These results suggest that chronic N fertilization induces significant shifts in soil carbon dynamics that correspond to shifts in microbial community structure and function.

Nemergut, Diana R [Institute of Arctic and Alpine Research; Townsend, Alan R [Institute of Arctic and Alpine Research; Taylor, John [University of California, Berkeley; Sattin, Sarah R [Institute of Arctic and Alpine Research; Freeman, Kristen R [University of Colorado, Boulder; Fierer, Noah [Institute of Arctic and Alpine Research; Neff, Jason [University of Colorado, Boulder; Bowman, William D [University of Colorado, Boulder; Schadt, Christopher Warren [ORNL; Weintraub, Michael N [University of Toledo, Toledo, OH; Schmidt, Steven K. [University of Colorado

2008-01-01T23:59:59.000Z

245

Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance  

DOE Green Energy (OSTI)

Some ionic liquids (ILs) have been shown to be very effective solvents for biomass pretreatment. It is known that some ILs can have a strong inhibitory effect on fungal cellulases, making the digestion of cellulose inefficient in the presence of ILs. The identification of IL-tolerant enzymes that could be produced as a cellulase cocktail would reduce the costs and water use requirements of the IL pretreatment process. Due to their adaptation to high salinity environments, halophilic enzymes are hypothesized to be good candidates for screening and identifying IL-resistant cellulases. Using a genome-based approach, we have identified and characterized a halophilic cellulase (Hu-CBH1) from the halophilic archaeon, Halorhabdus utahensis. Hu-CBH1 is present in a gene cluster containing multiple putative cellulolytic enzymes. Sequence and theoretical structure analysis indicate that Hu-CBH1 is highly enriched with negatively charged acidic amino acids on the surface, which may form a solvation shell that may stabilize the enzyme, through interaction with salt ions and/or water molecules. Hu-CBH1 is a heat tolerant haloalkaliphilic cellulase and is active in salt concentrations up to 5 M NaCl. In high salt buffer, Hu-CBH1 can tolerate alkali (pH 11.5) conditions and, more importantly, is tolerant to high levels (20percent w/w) of ILs, including 1-allyl-3-methylimidazolium chloride ([Amim]Cl). Interestingly, the tolerances to heat, alkali and ILs are found to be salt-dependent, suggesting that the enzyme is stabilized by the presence of salt. Our results indicate that halophilic enzymes are good candidates for the screening of IL-tolerant cellulolytic enzymes.

Zhang, Tao; Datta, Supratim; Eichler, Jerry; Ivanova, Natalia; Axen, Seth D.; Kerfeld, Cheryl A.; Chen, Feng; Kyrpides, Nikos; Hugenholtz, Philip; Cheng, Jan-Fang; Sale, Kenneth L.; Simmons, Blake; Rubin, Eddy

2011-02-17T23:59:59.000Z

246

Using next generation transcriptome sequencing to predict an ectomycorrhizal metablome.  

SciTech Connect

Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides) roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose. The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.

Larsen, P. E.; Sreedasyam, A.; Trivedi, G; Podila, G. K.; Cseke, L. J.; Collart, F. R. (Biosciences Division); (On Assignment, Scientific Staffing); (Univ. of Alabama at Huntsville)

2011-05-13T23:59:59.000Z

247

Genetic and Functional Analysis of Siderophores in Trichoderma virens  

E-Print Network (OSTI)

Trichoderma virens, an avirulent plant symbiotic fungus ubiquitous in soils worldwide, is remarkable as it induces systemic resistance in plants, enhances plant growth, and acts as a mycoparasite of plant-pathogenic fungi. For all microorganisms, the ability to acquire environmental iron is essential for fitness and survival. The ability of T. virens to acquire iron from the soil determines its success as a beneficial microorganism for plants and saprophyte of organic material. The most successful strategy developed by microbes for iron acquisition has been the production of siderophores, secondary metabolites that bind iron tightly and are produced in both intracellular and extracellular forms. Extensive genomic analysis of the genome sequence of T. virens revealed the presence of three genes, Tex10, Tex20, and Tex21 that encode siderophore-producing enzymes known as non-ribosomal peptide synthetases (NRPSs), but their regulation and function are largely unknown. To study the function of these secondary metabolites in the life strategy of T. virens, two genes encoding the NRPSs for the biosynthesis of siderophores (Tex10 and Tex20) were disrupted by fungal transformation. While the Tex20 mutants are phenotypically very similar to wild type, the Tex10 mutant shows some striking differences. Additionally, the Tex10 mutant shows less ability to respond to oxidative stress. Gene expression of these NRPSencoding genes was also analyzed in wild type and mutant strains. Siderophore production reaches a maximum at three days in iron depleted medium, while cultures grown in ferrated medium show a dramatic reduction in siderophore production, as well as NRPS gene expression. Correspondingly, several NRPS-encoding gene deletion strains reveal both lower mRNA and siderophore levels. Siderophore production at the peak expression time was corroborated by High Performance Liquid Chromatography. This information is essential for the enhancement of the beneficial capabilities of T. virens for global agricultural improvement.

Vittone, Gloria

2008-05-21T23:59:59.000Z

248

Bioremediation of aqueous pollutants using biomass embedded in hydrophilic foam. Final report  

Science Conference Proceedings (OSTI)

The major objective of this project was to examine the potential of a novel hydrophilic polyurethane foam as an immobilization medium for algal, bacteria, and other types of biomass, and to test the resulting foam/biomass aggregates for their use in cleaning up waters contaminated with heavy metals, radionuclides and toxic organic compounds. Initial investigations focused on the bioremoval of heavy metals from wastewaters at SRS using immobilized algal biomass. This effort met with limited success for reasons which included interference in the binding of biomass and target metals by various non-target constituents in the wastewater, lack of an appropriate wastewater at SRS for testing, and the unavailability of bioreactor systems capable of optimizing contact of target pollutants with sufficient biomass binding sites. Subsequent studies comparing algal, bacterial, fungal, and higher plant biomass demonstrated that other biomass sources were also ineffective for metal bioremoval under the test conditions. Radionuclide bioremoval using a Tc-99 source provided more promising results than the metal removal studies with the various types of biomass, and indicated that the alga Cyanidium was the best of the tested sources of biomass for this application. However, all of the biomass/foam aggregates tested were substantially inferior to a TEVA resin for removing Tc-99 in comparative testing. The authors also explored the use of hydrophilic polyurethane foam to embed Burkholderia cepacia, which is an efficient degrader of trichloroethylene (TCE), a contaminant of considerable concern at SRS and elsewhere. The embedded population proved to be incapable of growth on nutrient media, but retained respiratory activity. Lastly, the degradative capabilities of embedded G4 were examined. Phenol- or benzene-induced bacteria retained the ability to degrade TCE and benzene. The authors were successful in inducing enzyme activity after the organisms had already been embedded.

Wilde, E.W.; Radway, J.C.; Santo Domingo, J.; Zingmark, R.G.; Whitaker, M.J.

1996-12-31T23:59:59.000Z

249

Indirect health effects of relative humidity in indoor environments  

SciTech Connect

A review of the health effects of relative humidity in indoor environments suggests that relative humidity can affect the incidence of respiratory infections and allergies. Experimental studies on airborne-transmitted infectious bacteria and viruses have shown that the survival or infectivity of these organisms is minimized by exposure to relative humidities between 40 and 70%. Nine epidemiological studies examined the relationship between the number of respiratory infections or absenteeism and the relative humidity of the office, residence, or school. The incidence of absenteeism or respiratory infections was found to be lower among people working or living in environments with mid-range versus low or high relative humidities. The indoor size of allergenic mite and fungal populations is directly dependent upon the relative humidity. Mite populations are minimized when the relative humidity is below 50% and reach a maximum size at 80% relative humidity. Most species of fungi cannot grow unless the relative humidity exceeds 60%. Relative humidity also affects the rate of offgassing of formaldehyde from indoor building materials, the rate of formation of acids and salts from sulfur and nitrogen dioxide, and the rate of formation of ozone. The influence of relative humidity on the abundance of allergens, pathogens, and noxious chemicals suggests that indoor relative humidity levels should be considered as a factor of indoor air quality. The majority of adverse health effects caused by relative humidity would be minimized by maintaining indoor levels between 40 and 60%. This would require humidification during winter in areas with cold winter climates. Humidification should preferably use evaporative or steam humidifiers, as cool mist humidifiers can disseminate aerosols contaminated with allergens.

Arundel, A.V.; Sterling, E.M.; Biggin, J.H.; Sterling, T.D.

1986-03-01T23:59:59.000Z

250

Alcohol Fuels Program technical review, Spring 1984  

DOE Green Energy (OSTI)

The alcohol fuels program consists of in-house and subcontracted research for the conversion of lignocellulosic biomass into fuel alcohols via thermoconversion and bioconversion technologies. In the thermoconversion area, the SERI gasifier has been operated on a one-ton per day scale and produces a clean, medium-Btu gas that can be used to manufacture methanol with a relatively small gas-water shift reaction requirement. Recent research has produced catalysts that make methanol and a mixture of higher alcohols from the biomass-derived synthetic gas. Three hydrolysis processes have emerged as candidates for more focused research. They are: a high-temperature, dilute-acid, plug-flow approach based on the Dartmouth reactor; steam explosion pretreatment followed by hydrolysis using the RUT-C30 fungal organism; and direct microbial conversion of the cellulose to ethanol using bacteria in a single or mixed culture. Modeling studies, including parametric and sensitivity analyses, have recently been completed. The results of these studies will lead to a better definition of the present state-of-the-art for these processes and provide a framework for establishing the research and process engineering issues that still need resolution. In addition to these modeling studies, economic feasibility studies are being carried out by commercial engineering firms. Their results will supplement and add commercial validity to the program results. The feasibility contractors will provide input at two levels: Technical and economic assessment of the current state-of-the-art in alcohol production from lignocellulosic biomass via thermoconversion to produce methanol and higher alcohol mixtures and bioconversion to produce ethanol; and identification of research areas having the potential to significantly reduce the cost of production of alcohols.

Not Available

1984-10-01T23:59:59.000Z

251

The production of fuels and chemicals from food processing wastes using a novel fermenter separator  

Science Conference Proceedings (OSTI)

During 1991, considerable progress was made on the waste utilization project. Two small Wisconsin companies have expressed an interest in promoting and developing the ICRS technology. Pilot plant sites at (1) Hopkinton, IA, for a sweet whey plant, and Beaver Dam WI, for an acid whey site have been under development siting ICRS operations. The Hopkinton, IA site is owned and operated by Permeate Refining Inc., who have built a batch ethanol plant across the street from Swiss Valley Farms cheddar cheese operations. Permeate from Swiss Valley is piped across to PRI. PRI has signed a contract to site a 300--500,000 gallon/yr to ICRS pilot plant. They feel that the lower labor, lower energy, continuous process offered by the ICRS will substantially improve their profitability. Catalytics, Inc, is involved with converting whey from a Kraft cream cheese operation to ethanol and yeast. A complete project including whey concentration, sterilization, and yeast growth has been designed for this site. Process design improvements with the ICRS focussed on ethanol recovery techniques during this year's project. A solvent absorption/extractive distillation (SAED) process has been developed which offers the capability of obtaining an anhydrous ethanol product from vapors off 3 to 9% ethanol solutions using very little energy for distillation. Work on products from waste streams was also performed. a. Diacetyl as a high value flavor compound was very successfully produced in a Stirred Tank Reactor w/Separation. b. Yeast production from secondary carbohydrates in the whey, lactic acid, and glycerol was studied. c. Lactic acid production from cellulose and lactose studies continued. d. Production of anti-fungal reagents by immobilized plant cells; Gossypol has antifungal properties and is produced by G. arboretum.

Dale, M.C.; Venkatesh, K.V.; Choi, Hojoon; Moelhman, M.; Saliceti, L.; Okos, M.R.; Wankat, P.C.

1991-12-01T23:59:59.000Z

252

The production of fuels and chemicals from food processing wastes using a novel fermenter separator. Annual progress report, January 1991--December 1991  

Science Conference Proceedings (OSTI)

During 1991, considerable progress was made on the waste utilization project. Two small Wisconsin companies have expressed an interest in promoting and developing the ICRS technology. Pilot plant sites at (1) Hopkinton, IA, for a sweet whey plant, and Beaver Dam WI, for an acid whey site have been under development siting ICRS operations. The Hopkinton, IA site is owned and operated by Permeate Refining Inc., who have built a batch ethanol plant across the street from Swiss Valley Farms cheddar cheese operations. Permeate from Swiss Valley is piped across to PRI. PRI has signed a contract to site a 300--500,000 gallon/yr to ICRS pilot plant. They feel that the lower labor, lower energy, continuous process offered by the ICRS will substantially improve their profitability. Catalytics, Inc, is involved with converting whey from a Kraft cream cheese operation to ethanol and yeast. A complete project including whey concentration, sterilization, and yeast growth has been designed for this site. Process design improvements with the ICRS focussed on ethanol recovery techniques during this year`s project. A solvent absorption/extractive distillation (SAED) process has been developed which offers the capability of obtaining an anhydrous ethanol product from vapors off 3 to 9% ethanol solutions using very little energy for distillation. Work on products from waste streams was also performed. a. Diacetyl as a high value flavor compound was very successfully produced in a Stirred Tank Reactor w/Separation. b. Yeast production from secondary carbohydrates in the whey, lactic acid, and glycerol was studied. c. Lactic acid production from cellulose and lactose studies continued. d. Production of anti-fungal reagents by immobilized plant cells; Gossypol has antifungal properties and is produced by G. arboretum.

Dale, M.C.; Venkatesh, K.V.; Choi, Hojoon; Moelhman, M.; Saliceti, L.; Okos, M.R.; Wankat, P.C.

1991-12-01T23:59:59.000Z

253

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

Science Conference Proceedings (OSTI)

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.

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

2011-04-18T23:59:59.000Z

254

Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil  

DOE Green Energy (OSTI)

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.

DeAngelis, Kristen; Allgaier, Martin; Chavarria, Yaucin; Fortney, Julian; Hugenholtz, Phillip; Simmons, Blake; Sublette, Kerry; Silver, Whendee; Hazen, Terry

2011-07-14T23:59:59.000Z

255

Genetic Analysis of Chloroplast Translation  

DOE Green Energy (OSTI)

The assembly of the photosynthetic apparatus requires the concerted action of hundreds of genes distributed between the two physically separate genomes in the nucleus and chloroplast. Nuclear genes coordinate this process by controlling the expression of chloroplast genes in response to developmental and environmental cues. However, few regulatory factors have been identified. We used mutant phenotypes to identify nuclear genes in maize that modulate chloroplast translation, a key control point in chloroplast gene expression. This project focused on the nuclear gene crp1, required for the translation of two chloroplast mRNAs. CRP1 is related to fungal proteins involved in the translation of mitochondrial mRNAs, and is the founding member of a large gene family in plants, with {approx}450 members. Members of the CRP1 family are defined by a repeated 35 amino acid motif called a ''PPR'' motif. The PPR motif is closely related to the TPR motif, which mediates protein-protein interactions. We and others have speculated that PPR tracts adopt a structure similar to that of TPR tracts, but with a substrate binding surface adapted to bind RNA instead of protein. To understand how CRP1 influences the translation of specific chloroplast mRNAs, we sought proteins that interact with CRP1, and identified the RNAs associated with CRP1 in vivo. We showed that CRP1 is associated in vivo with the mRNAs whose translation it activates. To explore the functions of PPR proteins more generally, we sought mutations in other PPR-encoding genes: mutations in the maize PPR2 and PPR4 were shown to disrupt chloroplast ribosome biogenesis and chloroplast trans-splicing, respectively. These and other results suggest that the nuclear-encoded PPR family plays a major role in modulating the expression of the chloroplast genome in higher plants.

Barkan, Alice

2005-08-15T23:59:59.000Z

256

Efficient Graph Based Assembly of Short-Read Sequences on Hybrid Core Architecture  

Science Conference Proceedings (OSTI)

Advanced architectures can deliver dramatically increased throughput for genomics and proteomics applications, reducing time-to-completion in some cases from days to minutes. One such architecture, hybrid-core computing, marries a traditional x86 environment with a reconfigurable coprocessor, based on field programmable gate array (FPGA) technology. In addition to higher throughput, increased performance can fundamentally improve research quality by allowing more accurate, previously impractical approaches. We will discuss the approach used by Convey?s de Bruijn graph constructor for short-read, de-novo assembly. Bioinformatics applications that have random access patterns to large memory spaces, such as graph-based algorithms, experience memory performance limitations on cache-based x86 servers. Convey?s highly parallel memory subsystem allows application-specific logic to simultaneously access 8192 individual words in memory, significantly increasing effective memory bandwidth over cache-based memory systems. Many algorithms, such as Velvet and other de Bruijn graph based, short-read, de-novo assemblers, can greatly benefit from this type of memory architecture. Furthermore, small data type operations (four nucleotides can be represented in two bits) make more efficient use of logic gates than the data types dictated by conventional programming models.JGI is comparing the performance of Convey?s graph constructor and Velvet on both synthetic and real data. We will present preliminary results on memory usage and run time metrics for various data sets with different sizes, from small microbial and fungal genomes to very large cow rumen metagenome. For genomes with references we will also present assembly quality comparisons between the two assemblers.

Sczyrba, Alex; Pratap, Abhishek; Canon, Shane; Han, James; Copeland, Alex; Wang, Zhong; Brewer, Tony; Soper, David; D'Jamoos, Mike; Collins, Kirby; Vacek, George

2011-03-22T23:59:59.000Z

257

The recombinant expression and potential applications of bacterial organophosphate hydrolase in Zea mays L.  

E-Print Network (OSTI)

Organophosphate hydrolase (OPH, EC 3.1.8.1) is a bacterial enzyme with a broad spectrum of potential substrates that include organophosphorus pesticides, herbicides, and chemical warfare agents. OPH has been expressed successfully in bacterial, fungal, and insect cell culture systems; however, none of these systems produces amounts of enzyme suitable for applications outside of the research laboratory. Therefore, a transgenic Zea mays L. (maize) system was developed to express OPH as an alternate to the current OPH expression systems. The bacterial gene encoding the OPH protein was optimized for transcriptional and translational expression in maize. The optimized gene was inserted into the maize genome under the control of embryo specific, endosperm specific, and constitutive plant promoters. Select transformants were analyzed for the expression of OPH. Expression was observed in the seeds of plants transformed with each of the three constructs with the highest expression observed with the embryo specific and constitutive promoter constructs. The highest OPH expressing lines of transgenic maize had expression levels higher than those reported for the E. coli expression system. OPH was purified from transgenic maize seed and analyzed for posttranslational modification and kinetic properties. OPH was observed to undergo a glycosylation event when expressed in maize that yielded at least two forms of OPH homogolous dimer. The glycosylated form of OPH bound tightly to the Concanavalin A sepharose and remained active after months of storage at room temperature. OPH activity was checked against a number of organophosphate herbicides. Enzymatic activity was observed against the herbicide Amiprophos-methyl and kinetic properties were measured. Enzymatic activity was also tested against the organophosphate Haloxon. Transgenic maize callus, leaf, and seed tissue could be screened for the presence of the optimized opd gene by enzymatic activity. Comparison of the growth of transgenic and control callus on media containing organophosphates showed that the transgenic callus was resistant to the herbicidal effects of haloxon. Transgenic plants expressing OPH were also resistant to the herbicide bensulide when compared to control plants. This indicates that OPH can be used as a screenable marker in plant systems and may be a potential scorable marker system as well.

Pinkerton, Terrence Scott

2003-05-01T23:59:59.000Z

258

Chemistry and Biology of Aflatoxin-DNA Adducts  

Science Conference Proceedings (OSTI)

Aspergillus flavus is a fungal contaminant of stored rice, wheat, corn, and other grainstuffs, and peanuts. This is of concern to human health because it produces the mycotoxin aflatoxin B{sub 1} (AFB{sub 1}), which is genotoxic and is implicated in the etiology of liver cancer. AFB{sub 1} is oxidized in vivo by cytochrome P450 to form aflatoxin B{sub 1} epoxide, which forms an N7-dG adduct (AFB{sub 1}-N7-dG) in DNA. The latter rearranges to a formamidopyrimidine (AFB{sub 1}-FAPY) derivative that equilibrates between {alpha} and {beta} anomers of the deoxyribose. In DNA, both the AFB{sub 1}-N7-dG and AFB{sub 1}-{beta}-FAPY adducts intercalate above the 5'-face of the damaged guanine. Each produces G {yields} T transversions in Escherichia coli, but the AFB{sub 1}-{beta}-FAPY adduct is more mutagenic. The Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) provides a model for understanding error-prone bypass of the AFB{sub 1}-N7-dG and AFB{sub 1}-{beta}-FAPY adducts. It bypasses the AFB{sub 1}-N7-dG adduct, but it conducts error-prone replication past the AFB{sub 1}-FAPY adduct, including mis-insertion of dATP, consistent with the G {yields} T mutations characteristic of AFB{sub 1} mutagenesis in E. coli. Crystallographic analyses of a series of binary and ternary complexes with the Dpo4 polymerase revealed differing orientations of the N7-C8 bond of the AFB{sub 1}-N7-dG adduct as compared to the N{sup 5}-C8 bond in the AFB{sub 1}-{beta}-FAPY adduct, and differential accommodation of the intercalated AFB{sub 1} moieties within the active site. These may modulate AFB{sub 1} lesion bypass by this polymerase.

Stone, Michael P.; Banerjee, Surajit; Brown, Kyle L.; Egli, Martin (Vanderbilt)

2012-03-27T23:59:59.000Z

259

Directing ecological restoration: impact of organic amendments on above- and belowground ecosystem characteristics  

E-Print Network (OSTI)

Increasing interest among restoration ecologists exists in developing strategies that stimulate biotic interactions and promote self-regulation in restored systems. These approaches should target above- and belowground organisms because they interact to regulate ecosystem pattern and process. In the following dissertation, I compare the ability of organic amendments to alter above- and belowground biological community structure and function to promote prairie establishment on Castle Drive Landfill in Garland, Dallas County, Texas. Treatments included altering the location of organic amendments in the soil profile, either applied to surface or incorporated, and varying the amount applied. Plant community composition, grass population dynamics, soil nutrient conditions, and soil biological parameters were monitored for three growing seasons. Aboveground, the surface treatments were superior for the establishment of desired and undesired plant species. Plant density patterns can be attributed to the amelioration of physical conditions and the accidental burial of seed during incorporation. Grass population dynamics suggest that surface-amended plots supported establishment, but high-volume incorporated treatments were better for enhancing survival through seasonal and long-term drought. Belowground biological responses were affected by the plant community, and not by the amendment treatments. Soil microbial biomass and carbon mineralization potential were larger in those treatments with greater plant density. The structure of the nematode community suggests that decomposition in the surface-amended plots was directed through bacterial channels while decomposition in the incorporated plots was through fungal channels. It is likely that the higher rates of plant productivity in surface treatments stimulated root exudation, thereby favoring bacteria and the nematodes that feed on them. Treatment differences in decomposition pathway were attenuated after 17 months. The soil quality indicators, Cmic/Corg, qCO2, nematode family richness and nematode density, were not affected by the restoration treatments or plant density, but did increase over time. The results of this study suggest that restoration managers should direct their energies into establishing and promoting a high-quality plant community. This can be manipulated with amendments, but care is needed not to exceed thresholds within location treatments.

Biederman, Lori Ann

2007-05-01T23:59:59.000Z

260

Biomarkers of Exposure to Foodborne and Environmental Carcinogens: Enterosorbent Intervention in a High Risk Population  

E-Print Network (OSTI)

The need to assess human exposures to foodborne and environmental carcinogens, particularly in populations at high risk for cancer and disease, has led to the development of chemical-specific biomarkers. Sensitive biomarkers for aflatoxin and polycyclic aromatic hydrocarbons (PAHs) have been useful in providing information on population exposure and reducing associated public health impacts. Aflatoxins are fungal metabolites found in a variety of foods. Among these toxins, aflatoxin B1 (AFB1) is the most predominant and hepatocarcinogenic. Acutely, AFB1 can cause disease and death, necessitating safe and effective intervention strategies. Inclusion of NovaSil (NS) clay in the diet represents a practical, sustainable approach. NS has been shown to prevent aflatoxicosis in multiple animal species by binding aflatoxins in the gastrointestinal tract, reducing toxin bioavailability. Co-exposure to PAHs, hazardous environmental contaminants, has been shown to increase the risk for hepatocellular carcinoma (HCC). Therefore, objectives of this research were to utilize biomarkers to assess aflatoxin and PAH exposures in susceptible populations in Ghana and the U.S. and to evaluate the safety and efficacy of NS intervention in Ghana (a population at risk for aflatoxicosis). After 3-month intervention with 3.0g NS/day, median aflatoxin M1 (an AFB1 metabolite) was significantly reduced (up to 58 percent) compared to the placebo group. Furthermore, no significant differences were found in levels of nutrient minerals between NS and placebo groups at baseline and 3-months suggesting NS can be used to effectively sorb AFB1 without affecting serum concentrations of important minerals. PAH biomarker results showed participants in Ghana were significantly exposed to high levels of PAHs based on the presence of 1-hydroxypyrene (1-OHP) in the majority of urines (98.9 percent). NS treatment had no effect on 1-OHP levels, further confirming the preferential binding of aflatoxins by NS. U.S. population data from a Hispanic community in Texas with an elevated incidence of HCC demonstrated a lower percentage and level of aflatoxin and PAH biomarkers. Aflatoxin M1 excretion, however, was associated with increased consumption of certain foods prone to aflatoxin contamination; thus, some individuals may be more vulnerable to exposure and associated interactions that increase the risk for HCC (e.g., PAHs or hepatitis infection).

Johnson, Natalie Malek

2010-08-01T23:59:59.000Z

Note: This page contains sample records for the topic "fungal polyketide cyclization" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Pathogen Detection Lab-On-A-Chip (PADLOC) System for Plant Pathogen Diagnosis  

E-Print Network (OSTI)

Polymerase Chain Reaction (PCR) detection paves the way to reliable and rapid diagnosis of diseases and has been used extensively since its introduction. Many miniaturized PCR systems were presented by microfluidics and lab-on-a-chip community. However, most of the developed systems did not employ real-time detection and thus required post-PCR processes to obtain results. Among the few real-time PCR systems, almost all of them aimed for medical applications and those for plant pathogen diagnosis systems are almost non-existent in the literature. In this work, we are presenting a portable system that employs microfluidics PCR system with integrated optical systems to accomplish real-time quantitative PCR for plant pathogen diagnosis. The system is comprised of a PCR chip that has a chamber for PCR sample with integrated metal heaters fabricated by standard microfabrication procedures, an optical system that includes lenses, filters, a dichroic mirror and a photomultiplier tube (PMT) to achieve sensitive fluorescence measurement capability and a computer control system for Proportional Integral Derivative (PID) control and data acquisition. The optical detection system employs portable components and has a size of 3.9 x 5.9 x 11.9 cm which makes it possible to be used in field settings. On the device side, two different designs are used. The first design includes a single chamber in a 25.4 x 25.4 mm device and the capacity of the chamber is 9 micro-liters which is sufficient to do gel electrophoresis verification. The second design has three 2.2 micro-liter chambers squeezed in the same size device while having smaller volume to increase high throughput of the system. The operation of the system was demonstrated using Fusarium oxysporum spf. lycopersici which is a fungal plant pathogen that affects crops in the USA. In the presence of the plant pathogen, noticeable increases in the photomultiplier tube output were observed which means successful amplifications and detections occurred. The results were confirmed using gel electrophoresis which is a conventional post-PCR process to determine the existence and length of the amplified DNA. Clear bands located in the expected position were observed following the gel electrophoresis. Overall, we have presented a portable PCR system that has the capability of detecting plant pathogens.

Cifci, Osman

2012-08-01T23:59:59.000Z

262

Engineering Thermotolerant Biocatalysts for Biomass Conversion to Products  

DOE Green Energy (OSTI)

Lignocellulosic biomass is a promising feedstock for producing renewable chemicals and transportation fuels as petroleum substitutes. Fermentation of the cellulose in biomass in an SSF process requires that the properties of the microbial biocatalyst match the fungal cellulase activity optima for cost-effective production of products. Fermentation of the pentose sugars derived from hemicellulose in biomass is an additional asset of an ideal biocatalyst. The microbial biocatalyst used by the industry, yeast, lacks the ability to ferment pentose sugars. The optimum temperature for growth and fermentation of yeast is about 35C. The optimum temperature for commercially available cellulase enzymes for depolymerization of cellulose in biomass to glucose for fermentation is 50-55 C. Because of the mismatch in the temperature optima for the enzyme and yeast, SSF of cellulose to ethanol (cellulosic ethanol) with yeast is conducted at a temperature that is close to the optimum for yeast. We have shown that by increasing the temperature of SSF to 50-55 C using thermotolerant B. coagulans, the amount of cellulase required for SSF of cellulose to products can be reduced by 3-4 fold compared to yeast-based SSF at 35C with a significant cost savings due to lower enzyme loading. Thermotolerant Bacillus coagulans strains ferment hemicellulose-derived pentose sugars completely to L(+)-lactic acid, the primary product of fermentation. We have developed genetic tools to engineer B. coagulans for fermentation of all the sugars in biomass to ethanol. Using these tools, we have altered the fermentation properties of B. coagulans to produce ethanol as the primary product. The thermotolerant property of B. coagulans has been shown to also lower the cellulase requirement and associated cost in SSF of cellulose to lactic acid compared to lactic acid bacteria. Lactic acid is a potential petroleum substitute for bio-based renewable plastics production. This study has led to the development of B. coagulans as a thermotolerant microbial biocatalyst for production of ethanol as a transportation fuel and lactic acid as a starting material for bio-based plastics in a cost-effective manner from renewable biomass.

K. T. Shanmugam, L. O. Ingram and J. A. Maupin-Furlow

2010-05-20T23:59:59.000Z

263

Sugar-Based Ethanol Biorefinery: Ethanol, Succinic Acid and By-Product Production  

DOE Green Energy (OSTI)

Lignin from pretreatment seemed to offer a potential source of valuable by-products. Although a wide range of phenolic compounds were present in the effluent from dilute ammonia pretreatment, the concentrations of each (except for benzoic acid) were too low to consider for extraction. The cellulosic hydrolysis system was modified to produce commercially recoverable quantities of cellobiose, which has a small but growing market in the food process industries. A spin-off of this led to the production of a specific oligosaccharide which appears to have both medical and commercial implications as a fungal growth inhibitor. An alternate use of sugars produced from biomass hydrolysis would be to produce succinic acid as a chemical feedstock for other conversions. An organism was developed which can do this bioconversion, but the economics of succinic acid production were such that it could not compete with current commercial practice. To allow recovery of commercial amounts of ethanol from bagasse fermentation, research was conducted on high solids loading fermentations (using S. cerevisiae) with commercial cellulase on pretreated material. A combination of SHF/SSF treatment with fed-batch operation allowed fermentation at 30% solids loading. Supplementation of the fermentation with a small amount of black-strap molasses had results beyond expectation. There was an enhancement of conversion as well as production of ethanol levels above 6.0% w/w, which is required both for efficient distillation as well as contaminant repression. The focus of fermentation development was only on converting the cellulose to ethanol, as this yeast is not capable of fermenting both glucose and xylose (from hemicellulose). In anticipation of the future development of such an organism, we screened the commercially available xylanases to find the optimum mix for conversion of both cellulose and hemicellulose. A different mixture than the spezyme/novozyme mix used in our fermentation research was found to be more efficient at converting both cellulose and hemicellulose. Efforts were made to select a mutant of Pichia stipitis for ability to co-ferment glucose and xylose to ethanol. New mutation technology was developed, but an appropriate mutant has not yet been isolated. The ability to convert to stillage from biomass fermentations were determined to be suitable for anaerobic degradation and methane production. An economic model of a current sugar factory was developed in order to provide a baseline for the cost/benefit analysis of adding cellulosic ethanol production.

Donal F. Day

2009-03-31T23:59:59.000Z

264

Soil microbial response to glyphosate-base cotton pest management systems  

E-Print Network (OSTI)

Currently, 74% of cotton acres in the United States are planted with glyphosatetolerant varieties. The average glyphosate-tolerant cotton crop is treated with glyphosate 2.1 times each year in addition to other herbicides, insecticides, and fungicides. The primary objectives of this research were to: 1) describe the influence of glyphosate and pesticides commonly applied at or near the time of cotton planting on soil microbial activity and biomass; 2) study the effect of glyphosate on fluometuron degradation; 3) evaluate the response of Rhizoctonia solani to glyphosate and fluometuron; 4) study changes in glyphosate metabolism that occur as a result of repeated glyphosate applications; and 5) define shifts in the soil microbial community. Additionally, methods for accelerated solvent extraction (ASE) of fluometuron from soils were developed. In one experiment, the addition of glyphosate reduced C-mineralization in soils treated with fluometuron, aldicarb, or mefenoxam + PCNB formulations. However, in a second experiment, C-mineralization increased when glyphosate was applied with fluometuron relative to fluometuron applied alone. Accelerated solvent extraction was used in experiments which demonstrated that application of glyphosate with fluometuron increased the rate of fluometuron degradation in soil relative to fluometuron alone. When glyphosate was added to minimal medium, degradation of fluometuron by R. solani was reduced and less fungal biomass was produced. The total amount of 14C-glyphosate mineralized was reduced when glyphosate was applied 5 times relative to 1, 2, 3, or 4 times. Incorporation of 14Cglyphosate residues into soil microbial biomass was greater following five glyphosate applications than one application 3 and 7 days after application (DAA). Soil fatty acid methyl ester (FAME) profiles were altered by five glyphosate applications relative to one application. Additionally, FAMEs common to gram-negative bacteria were present in higher concentrations following five applications relative to 1, 2, 3, or 4 applications both 7 and 14 DAA. These studies indicated that: 1) glyphosate altered the soil microbial response to other pesticides; 2) fluometuron-degrading microorganisms in soil responded differently to glyphosate; 3) changes in the dissipation or distribution of glyphosate following repeated glyphosate applications were associated with changes in the structural diversity of the soil microbial community.

Lancaster, Sarah Renee

2008-05-01T23:59:59.000Z

265

Comparison of Tamspan 90 peanut component lines for aflatoxin production  

E-Print Network (OSTI)

The 38 lines that comprise 'Tamspan 90' peanut were studied for differential Aspet*llu,s flavus Links and A. parasiticus Spear growth and aflatoxin production under field and laboratory conditions. Required environmental conditions of temperature and moisture were not met for the production of sufficient aflatoxin for analytical studies in any of the three field experiments. Laboratory assays involving seed and pod inoculations with A. flavus and A. parasiticus mutants that produce norsolorinic acid (NOR), an orange-red pigmented precursor of aflatoxin, showed significant differences (P < 0.05) among lines when using immature and dried seed. Although relative NOR production, determined visually on the basis of orange-red pigment in the seed from the pod inoculations test, did not differ at P < 0.05, a three-fold difference was observed among the 38 lines. The relative ranking of the four checks showed Pronto to be the most susceptible followed by Starr, 55-437, and J-11, respectively, for production of NOR and aflatoxin. Comparing the reactions of the lines in three tests for NOR production, six lines were found constantly having low NOR production. Orange coloration in seed challenged by NOR A. flavus and A. parasiticus mutants was initially most prominent in the intercotyledonary cavity and the interfacial surface of cotyledons and testae. External fungal growth and coloration of pods did not consistently reflect seed infection. Orange coloration was consistently apparent in shells of immature pods. Mature pods varied from none to extensive, splotchy orange coloration. Visual assessments of individual seed for orange coloration, classified by color class, were highly correlated with quantity of aflatoxin and NOR as determined by HPLC (r = 0.83 and 0.95, respectively). Neither aflatoxin nor NOR were efficiently extracted from large samples (weight), and NOR was more difficult to extract from peanut seed than aflatoxin. Visual classification of seed for relative amount of aflatoxin contamination can be made successfully using A. parasiticus NOR mutants. Differentiating breeding lines to eliminate highly susceptible genotypes appears possible if laboratory assay and field performance are correlated.

Lopez, Yolanda

1994-01-01T23:59:59.000Z

266

Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638  

SciTech Connect

Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa x deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to improve establishment and sustainable production of poplar as an energy feedstock on marginal, non-agricultural soils using endophytic bacteria as growth promoting agents. Poplar is considered as the model tree species for the production of lignocellulosic biomass destined for biofuel production. The plant growth promoting endophytic bacterium Enterobacter sp. 638 can improve the growth of poplar on marginal soils by as much as 40%. This prompted us to sequence the genome of this strain and, via comparative genomics, identify functions essential for the successful colonization and endophytic association with its poplar host. Analysis of the genome sequence, combined with metabolite analysis and quantitative PCR, pointed to a remarkable interaction between Enterobacter sp. 638 and its poplar host with the endophyte responsible for the production of a phytohormone, and a precursor for another that poplar is unable to synthesize, and where the production of the plant growth promoting compounds depended on the presence of plant synthesized compounds, such as sucrose, in the growth medium. Our results provide the basis to better understanding the synergistic interactions between poplar and Enterobacter sp. 638. This information can be further exploited to improve establishment and sustainable production of poplar on marginal, non-agricultural soils using endophytic bacteria such as Enterobacter sp. 638 as growth promoting agents.

Taghavi, S.; van der Lelie, D.; Hoffman, A.; Zhang, Y.-B.; Walla, M. D.; Vangronsveld, J.; Newman, L.; Monchy, S.

2010-05-13T23:59:59.000Z

267

Sugar-Based Ethanol Biorefinery: Ethanol, Succinic Acid and By-Product Production  

SciTech Connect

The work conducted in this project is an extension of the developments itemized in DE-FG-36-04GO14236. This program is designed to help the development of a biorefinery based around a raw sugar mill, which in Louisiana is an underutilized asset. Some technical questions were answered regarding the addition of a biomass to ethanol facility to existing sugar mills. The focus of this work is on developing technology to produce ethanol and valuable by-products from bagasse. Three major areas are addressed, feedstock storage, potential by-products and the technology for producing ethanol from dilute ammonia pre-treated bagasse. Sugar mills normally store bagasse in a simple pile. During the off season there is a natural degradation of the bagasse, due to the composting action of microorganisms in the pile. This has serious implications if bagasse must be stored to operate a bagasse/biorefinery for a 300+ day operating cycle. Deterioration of the fermentables in bagasse was found to be 6.5% per month, on pile storage. This indicates that long term storage of adequate amounts of bagasse for year-round operation is probably not feasible. Lignin from pretreatment seemed to offer a potential source of valuable by-products. Although a wide range of phenolic compounds were present in the effluent from dilute ammonia pretreatment, the concentrations of each (except for benzoic acid) were too low to consider for extraction. The cellulosic hydrolysis system was modified to produce commercially recoverable quantities of cellobiose, which has a small but growing market in the food process industries. A spin-off of this led to the production of a specific oligosaccharide which appears to have both medical and commercial implications as a fungal growth inhibitor. An alternate use of sugars produced from biomass hydrolysis would be to produce succinic acid as a chemical feedstock for other conversions. An organism was developed which can do this bioconversion, but the economics of succinic acid production were such that it could not compete with current commercial practice. To allow recovery of commercial amounts of ethanol from bagasse fermentation, research was conducted on high solids loading fermentations (using S. cerevisiae) with commercial cellulase on pretreated material. A combination of SHF/SSF treatment with fed-batch operation allowed fermentation at 30% solids loading. Supplementation of the fermentation with a small amount of black-strap molasses had results beyond expectation. There was an enhancement of conversion as well as production of ethanol levels above 6.0% w/w, which is required both for efficient distillation as well as contaminant repression. The focus of fermentation development was only on converting the cellulose to ethanol, as this yeast is not capable of fermenting both glucose and xylose (from hemicellulose). In anticipation of the future development of such an organism, we screened the commercially available xylanases to find the optimum mix for conversion of both cellulose and hemicellulose. A different mixture than the spezyme/novozyme mix used in our fermentation research was found to be more efficient at converting both cellulose and hemicellulose. Efforts were made to select a mutant of Pichia stipitis for ability to co-ferment glucose and xylose to ethanol. New mutation technology was developed, but an appropriate mutant has not yet been isolated. The ability to convert to stillage from biomass fermentations were determined to be suitable for anaerobic degradation and methane production. An economic model of a current sugar factory was developed in order to provide a baseline for the cost/benefit analysis of adding cellulosic ethanol production.

Donal F. Day

2009-03-31T23:59:59.000Z

268

Surgically Implanted JSATS Micro-Acoustic Transmitters Effects on Juvenile Chinook Salmon and Steelhead Tag Expulsion and Survival, 2010  

DOE Green Energy (OSTI)

The purpose of this study was to evaluate survival model assumptions associated with a concurrent study - Acoustic Telemetry Evaluation of Dam Passage Survival and Associated Metrics at John Day, The Dalles, and Bonneville Dams, 2010 by Thomas Carlson and others in 2010 - in which the Juvenile Salmonid Acoustic Telemetry System (JSATS) was used to estimate the survival of yearling and subyearling Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) migrating through the Federal Columbia River Power System (FCRPS). The micro-acoustic transmitter used in these studies is the smallest acoustic transmitter model to date (12 mm long x 5 mm wide x 4 mm high, and weighing 0.43 g in air). This study and the 2010 study by Carlson and others were conducted by researchers from the Pacific Northwest National Laboratory and the University of Washington for the U.S. Army Corps of Engineers, Portland District, to meet requirements set forth by the 2008 FCRPS Biological Opinion. In 2010, we compared survival, tag burden, and tag expulsion in five spring groups of yearling Chinook salmon (YCH) and steelhead (STH) and five summer groups of subyearling Chinook salmon (SYC) to evaluate survival model assumptions described in the concurrent study. Each tagging group consisted of approximately 120 fish/species, which were collected and implanted on a weekly basis, yielding approximately 600 fish total/species. YCH and STH were collected and implanted from late April to late May (5 weeks) and SYC were collected and implanted from mid-June to mid-July (5 weeks) at the John Day Dam Smolt Monitoring Facility. The fish were collected once a week, separated by species, and assigned to one of three treatment groups: (1) Control (no surgical treatment), (2) Sham (surgical implantation of only a passive integrated transponder [PIT] tag), and (3) Tagged (surgical implantation of JSATS micro-acoustic transmitter [AT] and PIT tags). The test fish were held for 30 days in indoor circular tanks at the Bonneville Dam Juvenile Monitoring Facility. Overall mortality ranged weekly from 45 to 72% for YCH, 55 to 83% for STH, and 56 to 84% for SYC. The high background mortality in all groups and species made it difficult to discern tag effects. However, for YCH, STH, and SYC, the Tagged treatment groups had the highest overall mean mortality - 62%, 79%, and 76%, respectively. Fungal infections were found on 35% of all fish. Mean tag burden for the Tagged treatment group was relatively low for YCH (1.7%) and moderate for SYC (4.2%), while STH had a very low mean tag burden (0.7%). Tag burden was significantly higher in the Tagged treatment group for all species when compared to the Sham treatment group because of the presence of two tags. Surgeon performance did not contribute to the difference in mortality between the Sham and Tagged treatment groups. Tag expulsion from fish that survived to the end of the 30-day experiment was low but occurred in all species, with only two PIT tags and one AT lost, one tag per species. The high background mortality in this experiment was not limited to a treatment, temperature, or month. The decreased number of surviving fish influenced our experimental results and thus analyses. For future research, we recommend that a more natural exposure to monitor tag effects and other factors, such as swimming ability and predator avoidance, be considered to determine the effects of AT- and PIT- implantation on fishes.

Woodley, Christa M.; Carpenter, Scott M.; Carter, Kathleen M.; Wagner, Katie A.; Royer, Ida M.; Knox, Kasey M.; Kim, Jin A.; Gay, Marybeth E.; Weiland, Mark A.; Brown, Richard S.

2011-09-16T23:59:59.000Z

269

Kelt Reconditioning: A Research Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss), 2005-2006 Annual Report.  

DOE Green Energy (OSTI)

Iteroparity, the ability to repeat spawn, is a natural life history strategy that is expressed by some species from the family Salmonidae. Estimated rates of repeat spawning for post-development Columbia River steelhead Oncorhynchus mykiss populations range from 1.6 to 17%. It is expected that currently observed iteroparity rates for wild steelhead in the Basin are severely depressed due to development and operation of the hydropower system and various additional anthropogenic factors. Increasing the current expression of repeat spawning rates using fish culturing methods could be a viable technique to assist the recovery of depressed steelhead populations, and could help reestablish this naturally occurring life history trait. Reconditioning is the process of culturing post-spawned fish (kelts) in a captive environment until they are able to reinitiate feeding, growth, and redevelop mature gonads. Reconditioning techniques were initially developed for Atlantic salmon Salmo salar and sea-trout S. trutta. The recent Endangered Species Act listing of many Columbia River Basin steelhead populations has prompted interest in developing reconditioning methods for wild steelhead populations within the Basin. To test kelt steelhead reconditioning as a potential recovery tool, wild emigrating steelhead kelts were placed into one of four study groups (in river release, direct capture and transport, short-term reconditioning, or long-term reconditioning). Steelhead kelts from the Yakima River were collected at the Chandler Juvenile Monitoring Facility (CJMF, located on the Yakima River at river kilometer 75.6) from 7 March to 8 June 2006. In total, 348 kelts were collected for reconditioning at Prosser Hatchery. Captive specimens represented 17.0% (348 of 2,002) of the entire 2005-2006 Yakima River wild steelhead population, based on fish ladder counts at Prosser Dam. Steelhead kelts were reconditioned in 20-foot circular tanks, and fed freeze-dried krill initially (first 2 months of long-term reconditioning) or for the duration of the experiment. Long-term steelhead kelts also received Moore-Clark pellets to provide essential minerals and nutrients necessary for gonadal redevelopment. Oxytetracycline was administered to all reconditioned fish to boost immune system response following the stress of initial capture. To control parasitic infestations two methods were used: an intubation of Ivermectin{trademark} was administered to control internal parasites (e.g., Salmincola spp.) and, a Formalin drip system was administered via drip system for the duration of reconditioning to prevent fungal outbreaks. From the steelhead kelts collected at the CJMF, four experimental groups were established; in-river release, direct transport and release, short-term reconditioning and long-term reconditioning. Short-term kelts were reconditioned for 3 to 5 weeks. Surviving specimens were released on May 15, 2006 and June 27, 2006. Long-term steelhead kelts were held for a 6-9 month period with a release in October 18, 2006. No-term release kelts and short-term reconditioned kelts received PIT-tags with a portion of each group receiving hydro-acoustic tags to assess return survival, travel time, and migratory behavior below Bonneville Dam. In total, 49 No-term release kelts and 50 short-term reconditioned kelts were PIT-tagged, with all surviving No-term and short-term reconditioned kelts successfully receiving a surgically implanted hydroacoustic tag as well. With the conclusion of this third year we have completed a number of multi year analyses to better understand how kelts are faring in the lower river as well as laying the groundwork for a cost analysis.

Branstetter, Ryan; Whiteaker, John; Hatch, Douglas R. (Columbia River Inter-Tribal Fish Commission, Portland, OR)

2006-12-01T23:59:59.000Z

270

Kelt Reconditioning: A Research Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss), 2004 Annual Report.  

DOE Green Energy (OSTI)

Iteroparity, the ability to repeat spawn, is a life history strategy that is expressed by some species from the family Salmonidae. Rates of repeat spawning for post-development Columbia River steelhead Oncorhynchus mykiss populations range from 1.6 to 17%. It is expected that currently observed iteroparity rates for wild steelhead in the Basin are severely depressed due to development and operation of the hydropower system and various additional anthropogenic factors. Increasing the expression of historical repeat spawning rates using fish culturing methods could be a viable technique to assist the recovery of depressed steelhead populations, and could help reestablish this naturally occurring life history trait. Reconditioning is the process of culturing post-spawned fish (kelts) in a captive environment until they are able to reinitiate feeding, growth, and redevelop mature gonads. Kelt reconditioning techniques were initially developed for Atlantic salmon Salmo salar and sea-trout S. trutta. The recent Endangered Species Act listing of many Columbia River Basin steelhead populations has prompted interest in developing reconditioning methods for wild steelhead populations within the Basin. To test kelt steelhead reconditioning as a potential recovery tool, wild emigrating steelhead kelts were placed into one of three study groups (direct capture and transport, short-term reconditioning, or long-term reconditioning). Steelhead kelts from the Yakima River were collected at the Chandler Juvenile Monitoring Facility (CJMF, located on the Yakima River at river kilometer 75.6) from 15 March to 21 June 2004. In total, 842 kelts were collected for reconditioning at Prosser Hatchery. Captive specimens represented 30.5% (842 of 2,755) of the entire 2003-2004 Yakima River wild steelhead population, based on fish ladder counts at Prosser Dam. All steelhead kelts were reconditioned in 20-foot circular tanks, and fed freeze-dried krill initially or for the duration of the experiment. All steelhead kelts received hw-wiegandt multi vit dietary supplement as a means to improve initial nutrition. Long-term steelhead kelts received Moore-Clark pellets to provide essential minerals and nutrients necessary for gonadal redevelopment. Oxytetracycline was administered to all reconditioned fish to boost immune system response following the stress of initial capture. To control parasitic infestations two methods were used, first, after initial capture an intubation of Ivermectin{trademark} was administered to control internal parasites (e.g., Salmincola spp.). Next, a Formalin drip was used for the duration of reconditioning to prevent fungal outbreaks. Captured kelts were separated into three experimental groups: short-term reconditioning, long-term reconditioning, and direct transport and release. Success indicators for the short-term experiment include the proportion of fish that survived the reconditioning process and the proportion of fish that initiated a feeding response. Short-term kelts were reconditioned for 3 to 5 weeks. Surviving specimens were released for natural spawning on May 11, 2004. Survival-to-release was good for the short-term experiment, with a rate of 79.0%. Long-term steelhead kelts are currently being held for a 6-9 month period with a scheduled release in December 2004. Long-term success indicators include the proportion of fish that survived the reconditioning process and the proportion of surviving fish that successfully remature. Survival and rematuration for long-term kelts has not been determined and will be presented in the 2005 annual report. Direct transport and release kelts and short-term reconditioned kelts were radio or acoustic tagged to assess their travel time and migratory behaviors below Bonneville Dam. A total of 29 direct-transport and release kelts and 29 short-term reconditioned kelts received surgically implanted radio tags, and a total of 28 direct-transport/release and 26 short-term reconditioned fish received surgically implanted hydro acoustic tags. These tags will allow us to determine outm

Hatch, Douglas R.; Branstetter, Ryan; Whiteaker, John (Columbia River Inter-Tribal Fish Commission, Portland, OR)

2004-11-01T23:59:59.000Z

271

Kelt Reconditioning: A Research Project to Enhance Iteroparity in Columbia Basin Steelhead (Oncorhynchus mykiss), 2005 Annual Report.  

DOE Green Energy (OSTI)

Iteroparity, the ability to repeat spawn, is a natural life history strategy that is expressed by some species from the family Salmonidae. Estimated rates of repeat spawning for post-development Columbia River steelhead Oncorhynchus mykiss populations range from 1.6 to 17%. It is expected that currently observed iteroparity rates for wild steelhead in the Basin are severely depressed due to development and operation of the hydropower system and various additional anthropogenic factors. Increasing the current expression of repeat spawning rates using fish culturing methods could be a viable technique to assist the recovery of depressed steelhead populations, and could help reestablish this naturally occurring life history trait. Reconditioning is the process of culturing post-spawned fish (kelts) in a captive environment until they are able to reinitiate feeding, growth, and redevelop mature gonads. Reconditioning techniques were initially developed for Atlantic salmon Salmo salar and sea-trout S. trutta. The recent Endangered Species Act listing of many Columbia River Basin steelhead populations has prompted interest in developing reconditioning methods for wild steelhead populations within the Basin. To test kelt steelhead reconditioning as a potential recovery tool, wild emigrating steelhead kelts were placed into one of four study groups (in river release, direct capture and transport, short-term reconditioning, or long-term reconditioning). Steelhead kelts from the Yakima River were collected at the Chandler Juvenile Monitoring Facility (CJMF, located on the Yakima River at river kilometer 75.6) from 11 March to 23 June 2005. In total, 519 kelts were collected for reconditioning at Prosser Hatchery. Captive specimens represented 15.0% (519 of 3,451) of the entire 2004-2005 Yakima River wild steelhead population, based on fish ladder counts at Prosser Dam. Steelhead kelts were reconditioned in 20-foot circular tanks, and fed freeze-dried krill initially (first 2 months of long-term reconditioning) or for the duration of the experiment. Long-term steelhead kelts also received Moore-Clark pellets to provide essential minerals and nutrients necessary for gonadal redevelopment. Oxytetracycline was administered to all reconditioned fish to boost immune system response following the stress of initial capture. To control parasitic infestations two methods were used: an intubation of Ivermectin{trademark} was administered to control internal parasites (e.g., Salmincola spp). and, a Formalin drip system was administered via drip system for the duration of reconditioning to prevent fungal outbreaks. From the steelhead kelts collected at the CJMF, four experimental groups were established; in-river release, direct transport and release, short-term reconditioning and long-term reconditioning. Short-term kelts were reconditioned for 3 to 5 weeks. Surviving specimens were released on May 13, 2005 and June 30, 2005. Long-term steelhead kelts are currently being held for a 6-9 month period with a scheduled release in late November 2005.

Branstetter, Ryan; Whiteaker, John; Hatch, Douglas R. (Columbia River Inter-Tribal Fish Commission, Portland, OR)

2006-01-01T23:59:59.000Z

272

Augmented Fish Health Monitoring for Washington Department of Wildlife; Five-year Project Report, 1986-1991 Final Report.  

DOE Green Energy (OSTI)

The Augmented Fish Health Monitoring Project was funded by the Bonneville Power Administration (BPA) with the mandate to collect fish health data on the anadromous fish stocks of the Columbia River Basin in a standardized manner. The Washington Department of Wildlife began the project in 1986. Cumulative data and a final summary for this project are presented in this document. Fish stocks were examined monthly for length, weight, and health status at all Washington Department of Wildlife Columbia River Basin hatcheries. Assays for specific fish pathogens were conducted on all stocks of broodfish and smolts in the study area. Pathogens of interest were replicating viral agents, erythrocytic inclusion body syndrome virus (EIBSV), and Renibacterium salmoninarum. Sea-run cutthroat (SCT) were also sampled midway through the rearing cycle for R. salmoninarum. Juvenile fish were examined for the presence of any pathogen. Assays for Myxobolus cerebralis were conducted on fish stocks in several locations along the Columbia River. An organosomatic index analysis was made on each stock of smolts at the Cowlitz and Wells hatcheries. Results of the organosomatic index analysis were consistent between the years at each facility. However, the fish reared at Cowlitz displayed tissue changes associated with ceratomyxosis while those reared at Wells had a more desirable color and quality. Cell culture assays for viral agents in broodfish were positive for infectious hematopoeitic necrosis virus (IHNV) in all stocks at the Cowlitz Hatchery four out of five years in the study. Other stations were less consistent over the years. Only the sea-run cutthroat stock spawned at Beaver Creek was negative for any virus. Infectious pancreatic necrosis virus (IPNV) was isolated from summer-run steelhead (SS) broodfish at Wells in 1989 and 1991 and at Yakima in 1991. Inclusions that are characteristic of EIBSV were found in red blood cells of brood fish from the Wells Hatchery in 1990 and 1991. Data collected on EIBSV during the first two years of the project cannot be compared with the later three years due to changes in laboratory protocol. Isolations of IHNV in smolts were made from Cowlitz and Skamania hatcheries and the Gobar Rearing Pond. Epizootics of IHN occurred at Lyons Ferry, Beaver Creek, Cowlitz and Skamania hatcheries during the project, EIBSV inclusions were identified in very low levels from smolts from Beaver Creek, Chelan, Cowlitz, Eastbank, and Ringold. Assays for R. salmoninarum on broodfish and smolts revealed very low levels of infection and the disease was not a problem. Enteric redmouth disease was not observed in the project area. Cytophaga psychrophila was a chronic problem in young fish at Vancouver, Beaver Creek and Cowlitz hatcheries. Ceratomyxa Shasta was the only reportable parasite observed in the fish within the study area and caused yearly outbreaks of ceratomyxosis at the Cowlitz Hatchery. Fish at the Beaver Creek Hatchery were treated for furunculosis three of the five years of the project. An ozone water treatment plant has been installed to minimize the disease. Flow and density indexes and feed conversion did not vary significantly at the hatcheries during this project. Egg mortality averaged 12.94% throughout the project with a range from 4.39% to 29.10%. The mean fry mortality during the project was 15.08% with a range of 2.01 to 37.43%. The overall mortality for early rearing was 20.43%. Prespawning broodstock mortality was recorded for SS and SCT and averaged 5.18% with a range from 0 to 38.8%. Fungal invasion was the primary cause of death in adult fish. Epizootics of furunculosis, ceratomyxosis, bacterial coldwater disease, and IHN occurred during the project. Fewer cases were reported in more recent years. The BPA augmented fish health project helped WDW identify problem areas in fish health while they were occurring. This knowledge allowed us to develop strategies for improved fish quality. Overall the project has been invaluable in assisting us in the improvement of the health of our fish.

Kerwin, John; Roberts, Steve; Oman, Leni; Bolding, Bruce

1992-04-01T23:59:59.000Z

273

Statistical Analysis and Interpretation of Building Characterization, Indoor Environmental Quality Monitoring and Energy Usage Data from Office Buildings and Classrooms in the United States  

SciTech Connect

Three independent tasks had been performed (Stetzenbach 2008, Stetzenbach 2008b, Stetzenbach 2009) to measure a variety of parameters in normative buildings across the United States. For each of these tasks 10 buildings were selected as normative indoor environments. Task 1 focused on office buildings, Task 13 focused on public schools, and Task 0606 focused on high performance buildings. To perform this task it was necessary to restructure the database for the Indoor Environmental Quality (IEQ) data and the Sound measurement as several issues were identified and resolved prior to and during the transfer of these data sets into SPSS. During overview discussions with the statistician utilized in this task it was determined that because the selection of indoor zones (1-6) was independently selected within each task; zones were not related by location across tasks. Therefore, no comparison would be valid across zones for the 30 buildings so the by location (zone) data were limited to three analysis sets of the buildings within each task. In addition, differences in collection procedures for lighting were used in Task 0606 as compared to Tasks 01 & 13 to improve sample collection. Therefore, these data sets could not be merged and compared so effects by-day data were run separately for Task 0606 and only Task 01 & 13 data were merged. Results of the statistical analysis of the IEQ parameters show statistically significant differences were found among days and zones for all tasks, although no differences were found by-day for Draft Rate data from Task 0606 (p>0.05). Thursday measurements of IEQ parameters were significantly different from Tuesday, and most Wednesday measures for all variables of Tasks 1 & 13. Data for all three days appeared to vary for Operative Temperature, whereas only Tuesday and Thursday differed for Draft Rate 1m. Although no Draft Rate measures within Task 0606 were found to significantly differ by-day, Temperature measurements for Tuesday and Thursday showed variation. Moreover, Wednesday measurements of Relative Humidity within Task 0606 varied significantly from either Tuesday or Thursday. The majority of differences in IEQ measurements by-zone were highly significant (p<0.001), with the exception of Relative Humidity in some buildings. When all task data were combined (30 buildings) neither the airborne culturable fungi nor the airborne non-culturable spore data differed in the concentrations found at any indoor location in terms of day of collection. However, the concentrations of surface-associated fungi varied among the day of collection. Specifically, there was a lower concentration of mold on Tuesday than on Wednesday, for all tasks combined. As expected, variation was found in the concentrations of both airborne culturable fungi and airborne non-culturable fungal spores between indoor zones (1-6) and the outdoor zone (zone 0). No variation was found among the indoor zones of office buildings for Task 1 in the concentrations of airborne culturable fungi. However, airborne non-culturable spores did vary among zones in one building in Task 1 and variation was noted between zones in surface-associated fungi. Due to the lack of multiple lighting measurements for Tasks 13 and 0606, by-day comparisons were only performed for Task 1. No statistical differences were observed in lighting with respect to the day of collection. There was a wide range of variability by-zone among seven of the office buildings. Although few differences were found for the brightest illumination of the worksurface (IllumWkSfcBrtst) and the darkest illumination of the worksurface (IllumWkSfcDrkst) in Task 1, there was considerable variation for these variables in Task 13 and Task 0606 (p < 0.001). Other variables that differed by-zone in Task 13 include CombCCT and AmbCCT1 for S03, S07, and S08. Additionally, AmbChromX1, CombChromY, and CombChromX varied by-zone for school buildings S02, S04, and S05, respectively. Although all tasks demonstrated significant differences in sound measurements by zone, some of the buil

Linda Stetzenbach; Lauren Nemnich; Davor Novosel

2009-08-31T23:59:59.000Z