Sample records for fungal polyketide cyclization

  1. Structure Illuminates Mechanism of Fungal Polyketide Cyclization

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

    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...

  2. Structure Illuminates Mechanism of Fungal Polyketide Cyclization

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over Our Instagram Secretary900SteepStrengtheningFunctions | StanfordAnchoredand

  3. Structure Illuminates Mechanism of Fungal Polyketide Cyclization

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over Our Instagram Secretary900SteepStrengtheningFunctions | StanfordAnchoredandStructure

  4. Structure Illuminates Mechanism of Fungal Polyketide Cyclization

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over Our Instagram Secretary900SteepStrengtheningFunctions |

  5. Structure Illuminates Mechanism of Fungal Polyketide Cyclization

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over Our Instagram Secretary900SteepStrengtheningFunctions |Structure Illuminates

  6. Structure Illuminates Mechanism of Fungal Polyketide Cyclization

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del SolStrengthening a solid ... Strengthening a solidRadiationStructure Illuminates

  7. Heterocycles 1999, 51, 13 -16 SYNTHESIS AND CYCLIZATION OF NOVEL

    E-Print Network [OSTI]

    Rusell, K.C.

    with a Bergman cyclization.2 Semmelhack et al.3a demonstrated that the cyclization of anthraquinone (1) underwent

  8. Producing biofuels using polyketide synthases

    DOE Patents [OSTI]

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

    2013-04-16T23:59:59.000Z

    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.

  9. Polycyclic Aromatic Triptycenes: Oxygen Substitution Cyclization Strategies

    E-Print Network [OSTI]

    VanVeller, Brett

    The cyclization and planarization of polycyclic aromatic hydrocarbons with concomitant oxygen substitution was achieved through acid catalyzed transetherification and oxygen-radical reactions. The triptycene scaffold ...

  10. Characterization of the Biosynthetic Pathway of Fungal Aromatic Polyketides

    E-Print Network [OSTI]

    Li, Yanran

    2012-01-01T23:59:59.000Z

    act KR with the anthraquinone emodin and suggested that actacid 52 which is the anthraquinone precursor of the well-fren minimal PKS, the anthraquinone compound 63 is formed

  11. Deadly Carcinogen Unraveled: The Molecular Origami of Fungal Polyketide

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration wouldDECOMPOSITION OFSupplementalC. L.Deadly Carcinogen Unraveled: The

  12. Producing dicarboxylic acids using polyketide synthases

    DOE Patents [OSTI]

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

    2013-10-29T23:59:59.000Z

    The present invention provides for a polyketide synthase (PKS) capable of synthesizing a dicarboxylic acid (diacid). Such diacids include diketide-diacids and triketide-diacids. The invention includes recombinant nucleic acid encoding the PKS, and host cells comprising the PKS. The invention also includes methods for producing the diacids.

  13. Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

    SciTech Connect (OSTI)

    Brown, Daren W.; Butchko, Robert A.; Baker, Scott E.; Proctor, Robert H.

    2012-02-01T23:59:59.000Z

    Fusarium species are ubiquitous in nature, cause a range of plant diseases, and produce a variety of chemicals often referred to as secondary metabolites. Although some fungal secondary metabolites affect plant growth or protect plants from other fungi and bacteria, their presence in grain based food and feed is more often associated with a variety of diseases in plants and in animals. Many of these structurally diverse metabolites are derived from a family of related enzymes called polyketide synthases (PKSs). A search of genomic sequence of Fusarium verticillioides, F. graminearum, F. oxysporum and Nectria haematococca (anamorph F. solani) identified a total of 58 PKS genes. To gain insight into how this gene family evolved and to guide future studies, we conducted a phylogenomic and functional domain analysis. The resulting genealogy suggested that Fusarium PKSs represent 34 different groups responsible for synthesis of different core metabolites. The analyses indicate that variation in the Fusarium PKS gene family is due to gene duplication and loss events as well as enzyme gain-of-function due to the acquisition of new domains or of loss-of-function due to nucleotide mutations. Transcriptional analysis indicate that the 16 F. verticillioides PKS genes are expressed under a range of conditions, further evidence that they are functional genes that confer the ability to produce secondary metabolites.

  14. Effects of Sequence Disorder on DNA Looping and Cyclization

    E-Print Network [OSTI]

    Yuri O. Popov; Alexei V. Tkachenko

    2007-06-08T23:59:59.000Z

    Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of cyclization probabilities. For short DNA segments, the range of the distribution reaches several orders of magnitude for even completely random sequences. The ensemble averaged values of the cyclization probability are also calculated, and the connection to the recent experiments is discussed.

  15. angucyclinone polyketide ws5995b: Topics by E-print Network

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

    6 July, 2009 Environmental Sciences and Ecology Websites Summary: , glandular trichome, hemp, hop, Humulus lupulus, marijuana, polyketide synthase, trichomes. Introduction...

  16. Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius

    SciTech Connect (OSTI)

    Gallo, Antonia; Knox, Benjamin P.; Bruno, Kenneth S.; Solfrizzo, Michele; Baker, Scott E.; Perrone, Giancarlo

    2014-06-02T23:59:59.000Z

    Ochratoxin A (OTA) is a potent mycotoxin produced by Aspergillus and Penicillium species and is a common contaminant of a wide variety of food commodities, with Aspergillus carbonarius being the main producer of OTA contamination in grapes and wine. The molecular structure of OTA is composed of a dihydroisocoumarin ring linked to phenylalanine and, as shown in different producing fungal species, a polyketide synthase (PKS) is a component of the OTA biosynthetic pathway. Similar to observations in other filamentous ascomycetes, the genome sequence of A. carbonarius contains a large number of genes predicted to encode PKSs. In this work a pks gene identified within the putative OTA cluster of A. carbonarius, designated as AcOTApks, was inactivated and the resulting mutant strain was unable to produce OTA, confirming the role of AcOTApks in this biosynthetic pathway. AcOTApks protein is characteristic of the highly reduced (HR)-PKS family, and also contains a putative methyltransferase domain likely responsible for the addition of the methyl group to the OTA polyketide structure. AcOTApks is different from the ACpks protein that we previously described which showed an expression profile compatible with OTA production. We performed phylogenetic analyses of the ?-ketosynthase and acyl-transferase domains of the OTA PKSs which had been identified and characterized in different OTA producing fungal species. The phylogenetic results were similar for both the two domains analyzed and showed that OTA PKS of A. carbonarius, Aspergillus niger, and Aspergillus ochraceus clustered in a monophyletic group with 100% bootstrap support suggesting a common origin, while the other OTA PKSs analyzed were phylogenetically distant. A qRT-PCR assay monitored AcOTApks expression during fungal growth and concomitant production of OTA by A. carbonarius in synthetic grape medium. A clear correlation between the expression profile of AcOTApks and kinetics of OTA production was observed with AcOTApks which reached its maximum level of transcription before OTA accumulation in mycelium reached its highest level, confirming the fact that gene transcription always precedes phenotypic production.

  17. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2012-01-01T23:59:59.000Z

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

  18. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01T23:59:59.000Z

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

  19. Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor

    2012-01-01T23:59:59.000Z

    strains Comparative genomics and transcriptomics of xyloseFungal Genomics Program Igor Grigoriev 1 * (complex communities Fungal Genomics Program Igor Grigoriev

  20. Synthesis of indoles via a tandem benzannulation-cyclization strategy

    E-Print Network [OSTI]

    Lam, Tin Yiu

    2008-01-01T23:59:59.000Z

    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 ...

  1. Bridging the Gap: Studying Sequence to Product Correlation among Fungal Polyketide Synthases

    E-Print Network [OSTI]

    Zabala, Angelica Obusan

    2014-01-01T23:59:59.000Z

    Citric and gluconic acid production from fig by Aspergillus niger using solid-state fermentation."industrial fermentation for the production of citric acid,

  2. Producing a trimethylpentanoic acid using hybrid polyketide synthases

    DOE Patents [OSTI]

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

    2014-10-07T23:59:59.000Z

    The present invention provides for a polyketide synthase (PKS) capable of synthesizing trimethylpentanoic acid. The present invention also provides for a host cell comprising the PKS and when cultured produces the trimethylpentanoic acid. The present invention also provides for a method of producing the trimethylpentanoic acid, comprising: providing a host cell of the present invention, and culturing said host cell in a suitable culture medium such that the trimethylpentanoic acid is produced, optionally isolating the trimethylpentanoic acid, and optionally, reducing the isolated trimethylpentanoic acid into a trimethylpentanol or an iso-octane.

  3. Fungal Genomics Program

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-03-12T23:59:59.000Z

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  4. JGI Fungal Genomics Program

    SciTech Connect (OSTI)

    Grigoriev, Igor V.

    2011-03-14T23:59:59.000Z

    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

  5. Can fungal biopesticides control malaria? 

    E-Print Network [OSTI]

    Thomas, Matt B; Read, Andrew F

    2007-01-01T23:59:59.000Z

    Recent research has raised the prospect of using insect fungal pathogens for the control of vector-borne diseases such as malaria. In the past, microbial control of insect pests in both medical and agricultural sectors ...

  6. Origin of Selectivity in the Antibody 20F10-Catalyzed Yang Cyclization

    E-Print Network [OSTI]

    Keinan, Ehud

    identified that can act as local sensitizers to enhance the cyclization process. Introduction Although life pathway. Biocatalysis represents an attractive strategy to restrain mechanistic manifolds and channel of lowering the activation energy barrier is irrelevant. Other concepts of enzyme catalysis such as entropic

  7. Synthesis of a 7-Azaindole by Chichibabin Cyclization: Reversible Base-Mediated Dimerization of 3-Picolines

    E-Print Network [OSTI]

    Collum, David B.

    Synthesis of a 7-Azaindole by Chichibabin Cyclization: Reversible Base-Mediated Dimerization of 3 of heteroannulation- appending a pyrrole to a pyridine or vice versa.1,2 In connection with a program at Sanofi-Aventis to synthesize polycyclic pyrrole derivatives to be tested for the treatment of asthma,2c the conversion of 2

  8. Mesoscale Analyses of Fungal Networks

    E-Print Network [OSTI]

    Lee, Sang Hoon; Porter, Mason A

    2014-01-01T23:59:59.000Z

    We give a brief application of mesoscopic response functions (MRFs) to a large set of networks of fungi and slime moulds. We construct "structural networks" by estimating cord conductances (which yield edge weights) from experimental data and "functional networks" by calculating edge weights based on how much nutrient traffic is predicted to occur on each edge. Both types of networks have the same topology, and we compute MRFs for both families of networks to illustrate two different ways of constructing taxonomies to compare large sets of fungal and slime-mould networks to each other. We demonstrate that network taxonomies allow objective groupings of networks across species, treatments, and laboratories. We believe that the groupings that we have derived through our structural and functional taxonomic analyses of fungal networks could be of considerable assistance to biologists in their attempts to capture the impact of treatment combinations on network behaviour.

  9. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01T23:59:59.000Z

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

  10. Enzyme-Like Catalysis of the Nazarov Cyclization by Supramolecular Encapsulation

    SciTech Connect (OSTI)

    Hastings, Courtney; Pluth, Michael; Bergman, Robert; Raymond, Kenneth

    2010-03-29T23:59:59.000Z

    A primary goal in the design and synthesis of molecular hosts has been the selective recognition and binding of a variety of guests using non-covalent interactions. Supramolecular catalysis, which is the application of such hosts towards catalysis, has much in common with many enzymatic reactions, chiefly the use of both spatially appropriate binding pockets and precisely oriented functional groups to recognize and activate specific substrate molecules. Although there are now many examples which demonstrate how selective encapsulation in a host cavity can enhance the reactivity of a bound guest, all have failed to reach the degree of increased reactivity typical of enzymes. We now report the catalysis of the Nazarov cyclization by a self-assembled coordination cage, a carbon-carbon bond-forming reaction which proceeds under mild, aqueous conditions. The acceleration in this system is over a million-fold, and represents the first example of supramolecular catalysis that achieves the level of rate enhancement comparable to that observed in several enzymes. We explain the unprecedented degree of rate increase as due to the combination of (a) preorganization of the encapsulated substrate molecule, (b) stabilization of the transition state of the cyclization by constrictive binding, and (c) increase in the basicity of the complexed alcohol functionality.

  11. PNNL Fungal Biotechnology Core DOE-OBP Project

    SciTech Connect (OSTI)

    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

    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.

  12. 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]

    Underwood, Brian Saxton

    2011-01-01T23:59:59.000Z

    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 ...

  13. Room Temperature Copper(II)-Catalyzed Oxidative Cyclization of Enamides to 2,5-Disubstituted Oxazoles via Vinylic C–H Functionalization

    E-Print Network [OSTI]

    Cheung, Chi Wai

    A copper(II)-catalyzed oxidative cyclization of enamides to oxazoles via vinylic C–H bond functionalization at room temperature is described. Various 2,5-disubstituted oxazoles bearing aryl, vinyl, alkyl, and heteroaryl ...

  14. Are tropical fungal endophytes hyperdiverse? Fungal endophytes are ubiquitous fungi that inhabit healthy plant tissues without

    E-Print Network [OSTI]

    California at Berkeley, University of

    Are tropical fungal endophytes hyperdiverse? Abstract Fungal endophytes are ubiquitous fungi that inhabit healthy plant tissues without causing disease. Endophytes have been found in every plant species sites in a lowland, moist tropical forest of central Panama, we quantified endophyte colonization

  15. E-Print Network 3.0 - assess fungal metabolic Sample Search Results

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

    3 4 5 > >> 1 The FungalWeb Ontology The Core of a Semantic Web Application for Fungal Genomics Summary: 1 The FungalWeb Ontology The Core of a Semantic Web Application for Fungal...

  16. MycoCosm, an Integrated Fungal Genomics Resource

    SciTech Connect (OSTI)

    Shabalov, Igor; Grigoriev, Igor

    2012-03-16T23:59:59.000Z

    MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/month or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.

  17. ENDOPHYTIC FUNGAL COMMUNITIES OF BROMUS TECTORUM: MUTUALISMS, COMMUNITY ASSEMBLAGES

    E-Print Network [OSTI]

    ENDOPHYTIC FUNGAL COMMUNITIES OF BROMUS TECTORUM: MUTUALISMS, COMMUNITY ASSEMBLAGES in Environmental Science and titled "ENDOPHYTIC FUNGAL COMMUNITIES OF BROMUS TECTORUM: MUTUALISMS, COMMUNITY with endophytic fungi. Cheatgrass populations were sampled across North America and endophytes were isolated from

  18. RESEARCH ARTICLE Open Access A fungal endophyte induces transcription of

    E-Print Network [OSTI]

    Raizada, Manish N.

    RESEARCH ARTICLE Open Access A fungal endophyte induces transcription of genes encoding a redundant trees, proposed ecologically to act as a fungicide. Taxus is host to fungal endophytes, defined as organisms that inhabit plants without causing disease. The Taxus endophytes have been shown to synthesize

  19. Fungal endophytes limit pathogen damage in a tropical tree

    E-Print Network [OSTI]

    Bermingham, Eldredge

    Fungal endophytes limit pathogen damage in a tropical tree A. Elizabeth Arnold* , Luis Carlos Meji species examined to date harbors endophytic fungi within its asymptomatic aerial tissues, such that endophytes rep- resent a ubiquitous, yet cryptic, component of terrestrial plant communities. Fungal

  20. Detoxification of aromatic pollutants by fungal enzymes

    SciTech Connect (OSTI)

    Bollag, J.M.; Dec, J. [Pennsylvania State Univ., University Park, PA (United States)

    1995-12-31T23:59:59.000Z

    Fungal enzymes, such as laccase, peroxidase, and tyrosinase, play a prominent role in catalyzing the transformation of various aromatic compounds in the environment. The enzyme-mediated oxidative coupling reaction results in covalent binding of chlorinated phenols and anilines to soil organic matter or polymerization of the substrates in aquatic systems. Both of these processes are accompanied by a detoxification effect. Therefore, it has been postulated that they be exploited for the treatment of polluted soil and water. The mechanism and efficiency of oxidative coupling in pollutant removal were studied by incubation of chlorinated phenols and anilines with various humic substances or soil and analysis of the reaction products by chromatography and mass and {sup 13}C nuclear magnetic resonance (NMR) spectrometry. The decontamination effect could be enhanced by optimization of the reaction conditions and immobilization of enzymes on solid materials. The results obtained strongly support the concept of using enzymes for control of environmental pollution.

  1. The intramolecular cyclization of bis-2,5-dimethylene-2,5-dihydrofurans and bis-2,5-dimethylene-2,5-dihydrothiophenes: An approach to macrocycles

    SciTech Connect (OSTI)

    Klumpp, D.A.

    1994-01-11T23:59:59.000Z

    The first two papers of this dissertation present our work with the intramolecular cyclizations of a pair of p-quinodimethanes. The p-quinodimethanes were generated by flash vacuum pyrolysis (FVP) and were linked by a bridging chain. The third paper of this dissertation presents our work in the synthetic manipulation of the products formed from the intramolecular reactions of the p-quinodimethanes.

  2. Leaf endophyte load influences fungal garden development in leaf-cutting ants

    E-Print Network [OSTI]

    Bermingham, Eldredge

    Leaf endophyte load influences fungal garden development in leaf-cutting ants Van Bael et al. Van Open Access Leaf endophyte load influences fungal garden development in leaf-cutting ants Sunshine with relatively low fungal endophyte content. This preference suggests that fungal endophytes exact a cost

  3. Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

    E-Print Network [OSTI]

    Holder, Jason W.

    Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, ...

  4. arbuscular mycorrhizal fungal: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  5. Fungal biology: compiling genomes and exploiting them

    SciTech Connect (OSTI)

    Labbe, Jessy L [ORNL; Uehling, Jessie K [ORNL; Payen, Thibaut [INRA; Plett, Jonathan [University of Western Sydney, Australia

    2014-01-01T23:59:59.000Z

    The last 10 years have seen the cost of sequencing complete genomes decrease at an incredible speed. This has led to an increase in the number of genomes sequenced in all the fungal tree of life as well as a wide variety of plant genomes. The increase in sequencing has permitted us to study the evolution of organisms on a genomic scale. A number of talks during the conference discussed the importance of transposable elements (TEs) that are present in almost all species of fungi. These TEs represent an especially large percentage of genomic space in fungi that interact with plants. Thierry Rouxel (INRA, Nancy, France) showed the link between speciation in the Leptosphaeria complex and the expansion of TE families. For example in the Leptosphaeria complex, one species associated with oilseed rape has experienced a recent and massive burst of movement by a few TE families. The alterations caused by these TEs took place in discrete regions of the genome leading to shuffling of the genomic landscape and the appearance of genes specific to the species, such as effectors useful for the interactions with a particular plant (Rouxel et al., 2011). Other presentations showed the importance of TEs in affecting genome organization. For example, in Amanita different species appear to have been invaded by different TE families (Veneault-Fourrey & Martin, 2011).

  6. Phylogenetics and Taxonomy of the Fungal Vascular Wilt Pathogen Verticillium, with the Descriptions of Five New Species

    E-Print Network [OSTI]

    Subbarao, Krishna V

    2011-01-01T23:59:59.000Z

    have MAT1-2 idiomorphs. Taxonomy The genus VerticilliumPhylogenetics and Taxonomy of the Fungal Vascular Wilt2011) Phylogenetics and Taxonomy of the Fungal Vascular Wilt

  7. Host identity impacts rhizosphere fungal communities associated with three alpine plant species

    E-Print Network [OSTI]

    Becklin, Katie M.; Hertweck, Kate L.; Jumpponen, Ari

    2012-01-01T23:59:59.000Z

    Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses we ...

  8. Two fungal symbioses collide: endophytic fungi are not welcome in leaf-cutting ant gardens

    E-Print Network [OSTI]

    Bermingham, Eldredge

    Two fungal symbioses collide: endophytic fungi are not welcome in leaf-cutting ant gardens Sunshine with their fungal garden, while the leaf material they provide to their garden is usually filled with endophytic fungi. The ants and their cultivar may interact with hundreds of endophytic fungal species, yet little

  9. Fungal endophytes in woody roots of Douglas-fir (Pseudotsuga menziesii) and ponderosa pine (Pinus ponderosa)

    E-Print Network [OSTI]

    Fungal endophytes in woody roots of Douglas-fir (Pseudotsuga menziesii) and ponderosa pine (Pinus baseline data for future surveys of fungal endophytes. Examination of internal transcribed spacer (ITS1 evidence of host species or plant association effects on total recovery of fungal endophytes or recovery

  10. Fungal Diversity Characterization of Fusarium oxysporum isolates from Ethiopia

    E-Print Network [OSTI]

    Fungal Diversity 51 Characterization of Fusarium oxysporum isolates from Ethiopia using AFLP, SSR.D., Wingfield, M.J. and Steenkamp, E.T. (2006). Characterization of Fusarium oxysporum isolates from Ethiopia Sequence Repeat (SSR) markers and DNA sequence analyses to study 32 strains of F. oxysporum from Ethiopia

  11. Managing plant symbiosis: fungal endophyte genotype alters plant community composition

    E-Print Network [OSTI]

    Rudgers, Jennifer

    Managing plant symbiosis: fungal endophyte genotype alters plant community composition Jennifer A hosts the foliar endophytic fungus, Neotypho- dium coenophialum. We quantified vegetation development of the endophyte (KY-31, AR-542) in two tall fescue cultivars (Georgia-5, Jesup). The KY-31 endophyte produces

  12. West Nile virus (WNV) genome RNAs with up to three adjacent mutations that disrupt long distance 5'-3' cyclization sequence basepairs are viable

    SciTech Connect (OSTI)

    Basu, Mausumi; Brinton, Margo A., E-mail: mbrinton@gsu.ed

    2011-03-30T23:59:59.000Z

    Mosquito-borne flavivirus genomes contain conserved 5' and 3' cyclization sequences (CYC) that facilitate long distance RNA-RNA interactions. In previous studies, flavivirus replicon RNA replication was completely inhibited by single or multiple mismatching CYC nt substitutions. In the present study, full-length WNV genomes with one, two or three mismatching CYC substitutions showed reduced replication efficiencies but were viable and generated revertants with increased replication efficiency. Several different three adjacent mismatching CYC substitution mutant RNAs were rescued by a second site mutation that created an additional basepair (nts 147-10913) on the internal genomic side of the 5'-3' CYC. The finding that full-length genomes with up to three mismatching CYC mutations are viable and can be rescued by a single nt spontaneous mutation indicates that more than three adjacent CYC basepair substitutions would be required to increase the safety of vaccine genomes by creating mismatches in inter-genomic recombinants.

  13. Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks

    E-Print Network [OSTI]

    Fierer, Noah

    microbes across the greater New York City area is locally variable. Green roof fungal communities wereDigging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks Krista L a number of benefits, including decreased urban heat island effects and reduced energy costs for buildings

  14. Bioactivity of Fungal Endophytes as a Function of Endophyte Taxonomy and the Taxonomy and

    E-Print Network [OSTI]

    Coley, Phyllis

    Bioactivity of Fungal Endophytes as a Function of Endophyte Taxonomy and the Taxonomy taxonomy and forest type to tailor plant collections, and selecting endophytes from specific orders C, Coley PD, et al. (2013) Bioactivity of Fungal Endophytes as a Function of Endophyte Taxonomy

  15. Twenty-Seventh Fungal Genetics Conference, Asilomar, CA, March 12-17, 2013

    SciTech Connect (OSTI)

    Walton, Jonathan

    2013-03-17T23:59:59.000Z

    This meeting brings together ~900 international scientists to discuss the latest research on fungal genetics. Sessions of particular relevance to DOE include lignocellulose degradation, cellulose conversion to fermentable sugars, fermentation of sugars to fuel molecules. Other sessions cover fungal diseases of biomass crops (miscanthus, corn, switchgrass, etc.).

  16. Fungal Diversity Ceratocystis neglecta sp. nov., infecting Eucalyptus trees in Colombia

    E-Print Network [OSTI]

    Fungal Diversity 73 Ceratocystis neglecta sp. nov., infecting Eucalyptus trees in Colombia Rodas, C Eucalyptus trees in Colombia. Fungal Diversity 28: 73-84. Commercial plantation forestry utilising species of non-native Eucalyptus trees forms an important industry in Colombia. These trees are, however

  17. Two fungal symbioses collide: endophytic fungi are not welcome in leaf-cutting ant gardens

    E-Print Network [OSTI]

    Bermingham, Eldredge

    Two fungal symbioses collide: endophytic fungi are not welcome in leaf-cutting ant gardens Sunshine, while the leaf material they provide to their garden is usually filled with endophytic fungi. The ants and their cultivar may interact with hundreds of endophytic fungal species, yet little is known about

  18. PLANT-ANIMAL INTERACTIONS -ORIGINAL PAPER Fungal endophytes of native grasses decrease insect herbivore

    E-Print Network [OSTI]

    Rudgers, Jennifer

    PLANT-ANIMAL INTERACTIONS - ORIGINAL PAPER Fungal endophytes of native grasses decrease insect March 2010 / Accepted: 2 June 2010 Ó Springer-Verlag 2010 Abstract Endophytic fungal symbionts of studies on endophyte­ grass symbioses have been conducted on economically important, agricultural species

  19. Balancing multiple mutualists: asymmetric interactions among plants, arbuscular mycorrhizal fungi, and fungal endophytes

    E-Print Network [OSTI]

    Rudgers, Jennifer

    , and fungal endophytes Keenan M. L. Mack and Jennifer A. Rudgers K. M. L. Mack and J. A. Rudgers (jrudgers, a protective fungal endophyte aboveground, Neotyphodium coenophialum, and nutritional symbionts (arbuscular and applied a fertilizer treatment to individual plants. Endophyte presence in host plants strongly reduced

  20. Does a toxic fungal endophyte of tall fescue affect reproduction of

    E-Print Network [OSTI]

    Jamieson, Ian

    Does a toxic fungal endophyte of tall fescue affect reproduction of takahe on offshore islands? DOC. References 9 #12;4 Jamieson & Easton--Tall fescue-endophytes and takahe reproction on offshore islands Final of Conservation. This paper may be cited as: Jamieson, I.; Sydney Easton, H. 2002: Does a toxic fungal endophyte

  1. Communities of fungal endophytes in tropical forest grasses: highly diverse host-and habitat

    E-Print Network [OSTI]

    Coley, Phyllis

    Communities of fungal endophytes in tropical forest grasses: highly diverse host- and habitat: Charles W. Bacon Keywords: Barro Colorado Island Biodiversity Community assembly Fungal endophytes Poaceae- studied endophytes in the lowland forests of Panama. We used sequence data for 402 isolates from two

  2. 13:00:09:11:10 Fungal endophytes protect grass seedlings against

    E-Print Network [OSTI]

    Kramarz, Paulina

    13:00:09:11:10 Page 769 Page 769 Fungal endophytes protect grass seedlings against herbivory-transmitted fungal endophytes, some grasses produce a larger quantity of seeds, although these seeds are smaller than if the infection reduces predation pressure. Question: Does the endophyte protect grass seedlings against herbivory

  3. Role of fungal ligninolytic enzymes in pollutant degradation

    SciTech Connect (OSTI)

    Hammel, K.E.; Tardone, P.J.; Price, L.A.

    1989-02-01T23:59:59.000Z

    The ligninolytic fungi that cause white rot of wood have recently become the object of increasing attention from hazardous waste management specialists. The metabolic pathways that they employ for ligninolysis appear to have unusual xenobiotic capabilities, and there is some preliminary evidence that their extracellular lignin peroxidases, which normally catalyze the depolymerization of lignin, could bring about the initial oxidation of certain aromatic pollutants in vivo. However, it remains to be demonstrated that high levels of lignin peroxidase activity will necessarily lead to improved rates of pollutant degradation, or indeed that these enzymes are actually involved in any of the fungal xenobiotic oxidations that have been observed. To address these questions, the authors have begun a study of anthracene metabolism in the lignin degrader Phanerochaete chrysosporium: this simple model pollutant is quantitatively oxidized to anthraquinone by purified lignin peroxidases, is at least to some extent oxidized to the same quinone by whole fungal cultures, and is also mineralized at appreciable rates in vivo. The results point to a role for lignin peroxidases in organopollutant degradation by Phanerochaete, but more work is required to elucidate the pathways involved.

  4. LysM receptor-like kinases to improve plant defense response against fungal pathogens

    SciTech Connect (OSTI)

    Wan, Jinrong; Stacey, Gary; Stacey, Minviluz; Zhang, Xuecheng

    2013-10-15T23:59:59.000Z

    Perception of chitin fragments (chitooligosaccharides) is an important first step in plant defense response against fungal pathogen. LysM receptor-like kinases (LysM RLKs) are instrumental in this perception process. LysM RLKs also play a role in activating transcription of chitin-responsive genes (CRGs) in plants. Mutations in the LysM kinase receptor genes or the downstream CRGs may affect the fungal susceptibility of a plant. Mutations in LysM RLKs or transgenes carrying the same may be beneficial in imparting resistance against fungal pathogens.

  5. LysM receptor-like kinases to improve plant defense response against fungal pathogens

    SciTech Connect (OSTI)

    Wan, Jinrong (Columbia, MO); Stacey, Gary (Columbia, MO); Stacey, Minviluz (Columbia, MO); Zhang, Xuecheng (Columbia, MO)

    2012-01-17T23:59:59.000Z

    Perception of chitin fragments (chitooligosaccharides) is an important first step in plant defense response against fungal pathogen. LysM receptor-like kinases (LysM RLKs) are instrumental in this perception process. LysM RLKs also play a role in activating transcription of chitin-responsive genes (CRGs) in plants. Mutations in the LysM kinase receptor genes or the downstream CRGs may affect the fungal susceptibility of a plant. Mutations in LysM RLKs or transgenes carrying the same may be beneficial in imparting resistance against fungal pathogens.

  6. X-ray Crystal Structure of Aristolochene Synthase from Aspergillus terreus and Evolution of Templates for the Cyclization of Farnesyl Diphosphate

    SciTech Connect (OSTI)

    Shishova,E.; Di Costanzo, L.; Cane, D.; Christianson, D.

    2007-01-01T23:59:59.000Z

    Aristolochene synthase from Aspergillus terreus catalyzes the cyclization of the universal sesquiterpene precursor, farnesyl diphosphate, to form the bicyclic hydrocarbon aristolochene. The 2.2 {angstrom} resolution X-ray crystal structure of aristolochene synthase reveals a tetrameric quaternary structure in which each subunit adopts the {alpha}-helical class I terpene synthase fold with the active site in the 'open', solvent-exposed conformation. Intriguingly, the 2.15 {angstrom} resolution crystal structure of the complex with Mg{sup 2+}{sub 3}-pyrophosphate reveals ligand binding only to tetramer subunit D, which is stabilized in the 'closed' conformation required for catalysis. Tetramer assembly may hinder conformational changes required for the transition from the inactive open conformation to the active closed conformation, thereby accounting for the attenuation of catalytic activity with an increase in enzyme concentration. In both conformations, but especially in the closed conformation, the active site contour is highly complementary in shape to that of aristolochene, and a catalytic function is proposed for the pyrophosphate anion based on its orientation with regard to the presumed binding mode of aristolochene. A similar active site contour is conserved in aristolochene synthase from Penicillium roqueforti despite the substantial divergent evolution of these two enzymes, while strikingly different active site contours are found in the sesquiterpene cyclases 5-epi-aristolochene synthase and trichodiene synthase. Thus, the terpenoid cyclase active site plays a critical role as a template in binding the flexible polyisoprenoid substrate in the proper conformation for catalysis. Across the greater family of terpenoid cyclases, this template is highly evolvable within a conserved {alpha}-helical fold for the synthesis of terpene natural products of diverse structure and stereochemistry.

  7. Sequencing the fungal tree Terrestrial ecosystems host a complex array of interacting

    E-Print Network [OSTI]

    Hibbett, David S.

    with heterotrophic and autotrophic organisms alike, and play an integral and growing role in the development in three areas: plant health, biorefinery and fungal diversity. Plant health depends on interactions

  8. Population structure of the fungal pathogen Holocryphia eucalypti in Australia and South Africa

    E-Print Network [OSTI]

    Population structure of the fungal pathogen Holocryphia eucalypti in Australia and South Africa, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa. B Institute, University of Pretoria, Pretoria 0002, South Africa. C School of Biological Sciences

  9. Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations

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

    Rachid, Caio T. C. C.; Balieiro, Fabiano C.; Fonseca, Eduardo S.; Peixoto, Raquel Silva; Chaer, Guilherme M.; Tiedje, James M.; Rosado, Alexandre S.

    2015-02-23T23:59:59.000Z

    Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments:more »monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that.« less

  10. 2012 CELLULAR & MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 17 - 22, 2012

    SciTech Connect (OSTI)

    Judith Berman

    2012-06-22T23:59:59.000Z

    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.

  11. Biodegradation by bioaugmentation of dairy wastewater by fungal consortium on a bioreactor lab-scale and on a pilot-scale

    E-Print Network [OSTI]

    Boyer, Edmond

    1 Biodegradation by bioaugmentation of dairy wastewater by fungal consortium on a bioreactor lab 257 and 153% after bio-augmentation with fungi. An inoculated bioreactor with fungal consortium

  12. Sesquiterpene Quinones and Related Metabolites from Phyllosticta spinarum, a Fungal Strain Endophytic in Platycladus orientalis of the Sonoran Desert1

    E-Print Network [OSTI]

    Arnold, A. Elizabeth

    Endophytic in Platycladus orientalis of the Sonoran Desert1 E. M. Kithsiri Wijeratne, Priyani A. Paranagama, a fungal strain endophytic in Platycladus orientalis. The structures of the new compounds were determined of Phyllosticta spinarum (Botry- osphaeriaceae), a fungal strain endophytic in the leaf tissue of oriental arbor

  13. Effects of elevated CO2 , nitrogen deposition, and decreased species diversity on foliar fungal plant disease

    E-Print Network [OSTI]

    Crews, Stephen

    Effects of elevated CO2 , nitrogen deposition, and decreased species diversity on foliar fungal Three components of global change, elevated CO2 , nitrogen addition, and decreased plant species increasing more in pathogen load. Elevated CO2 increased pathogen load of C3 grasses, perhaps by decreasing

  14. ORIGINAL ARTICLE Fungal Diversity of Norway Spruce Litter: Effects of Site

    E-Print Network [OSTI]

    Minnesota, University of

    ORIGINAL ARTICLE Fungal Diversity of Norway Spruce Litter: Effects of Site Conditions and Premature duplicatus). The study was conducted in 37-year-old Norway spruce [Picea abies (L.) Karst.] stands as endophytes of Norway spruce in prior studies. During spring of 2005, we found less than half the number

  15. Evidence that chytrids dominate fungal communities in high-elevation soils

    E-Print Network [OSTI]

    Schmidt, Steven K.

    - out the world. In a more focused study of our sites in Colorado, we show that carbon sources reservoirs of undocumented biodiversity (4, 5). High-elevation soils are unique and may be challenging never been characterized (9). A majority of molecular surveys of fungal community com- position have

  16. Issues in Comparative Fungal Genomics Tom Hsiang1 and David L. Baillie2

    E-Print Network [OSTI]

    Hsiang, Tom

    Issues in Comparative Fungal Genomics Tom Hsiang1 and David L. Baillie2 1 Department. By the middle of 2005, there were almost 300 complete genomes that were publicly accessible. Most of these were archeal or bacterial since prokaryotic genomes are much smaller than eukaryotic genomes. Among eukaryotes

  17. Effect of sampling height on the concentration of airborne fungal spores

    E-Print Network [OSTI]

    Levetin, Estelle

    and possible sources of air pollution.8 In addition, it is high enough to avoid vandalism and bothering aeroallergens. Airborne fungal spores are commonly collected from the outdoor air at the rooftop level of high respiration level (1.5 m above the ground) and at roof level (12 m height). Methods: Air samples were

  18. Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal

    E-Print Network [OSTI]

    Kohn, Linda M.

    SYNTHESIS Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using in tissue (e.g., Stone et al. 2000; Arnold 2007). Most mem- bers of these communities are endophytes asymptomatic (Stone et al. 2000; Schulz and Boyle 2005). Designation as an endophyte therefore depends

  19. Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes of tropical forest grasses

    E-Print Network [OSTI]

    Coley, Phyllis

    Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes examining endophytic fungi associated with grasses (Poaceae) have focused on agronomically important species and forest-edge communities. To provide a broader context for understanding grass-endophyte associations we

  20. Analysis of the Fungal Virulence of Cryptococcus and Exploration of Novel Antifungals Against Cryptococcosis

    E-Print Network [OSTI]

    Zhai, Bing

    2014-08-01T23:59:59.000Z

    burden in the lungs, and works synergistically with fluconazole in an intranasal infection model ............................................. 84 3.4. Discussion... Figure 19 Polymyxin B is effective in reducing lung fungal burden and modestly prolongs animal survival in a murine model of pulmonary cryptococcosis ..... 86 Figure 20 Sertraline is fungicidal against both proliferative and quiescent...

  1. Soil fungal pathogens and the relationship between plant diversity and productivity

    E-Print Network [OSTI]

    Cleveland, Cory

    LETTER Soil fungal pathogens and the relationship between plant diversity and productivity John L community productivity often increases with increasing plant diversity. Most frequently, resource- based or competitive interactions are thought to drive this positive diversity­productivity relationship. Here, we ask

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

    E-Print Network [OSTI]

    Colorado at Boulder, University of

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

  3. Ion Torrent PGM as Tool for Fungal Community Analysis: A Case Study of Endophytes in Eucalyptus grandis

    E-Print Network [OSTI]

    Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa, 2 Department of Zoology and Entomology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South environmental strains into culture, fungal communities are difficult to characterize. This is especially true

  4. Enzymatic Digestibility of Corn Stover Fractions in Response to Fungal Pretreatment

    SciTech Connect (OSTI)

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

    2012-05-30T23:59:59.000Z

    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 < 0.05). For all fractions, xylan and glucan degradation followed a pattern similar to lignin degradation, with leaves having a significantly higher percentage of degradation (p < 0.05). Hydrolytic enzyme activity also revealed that the fungus was more active in the degradation of carbohydrates in leaves. As a result of fungal pretreatment, the highest sugar yield, however, was obtained with corn cobs.

  5. Nutrient Losses in Agriculture: the Role of Biochar and Fungal Associations

    E-Print Network [OSTI]

    King, Alison

    2011-04-01T23:59:59.000Z

    whole oat plants were harvested, their live biomass recorded, and root samples taken for mycorrhizal testing. These roots were stored in a 1:1 solution on ethanol and water at 4° C. Mycorrhizal infection was assessed by staining roots segments...?? 16 Nutrient Losses in Agriculture: the Role of Biochar and Fungal Associations Alison King (Faculty Advisor: Dr. Sharon Billings) Ecology & Evolutionary Biology INTRODUCTION Agriculture is a system of extraction: through it we capture...

  6. 2010 CELL AND MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 13-18, 2010

    SciTech Connect (OSTI)

    Michelle Momany

    2010-06-18T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    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

    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.

  8. Fungal species on baobabs in Western Australia Prepared by: Draginja Pavlic (PhD student working on a project entitled

    E-Print Network [OSTI]

    Fungal species on baobabs in Western Australia Prepared by: Draginja Pavlic (PhD student working species endemic in Australia and is restricted to the north-western parts of the country. Baobabs belong is a single species from the family Bombaceae present in Australia. A recent study revealed that A. gibbosa

  9. Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR

    E-Print Network [OSTI]

    Lutzoni, François M.

    Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred endophytic fungi in asymp- tomatic foliage of loblolly pine (Pinus taeda) in North Carolina, USA, with four (environmental PCR of surface sterilized foliage) for estimating endophyte diversity and species composition

  10. Short title: Endophytes of grasses Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes of

    E-Print Network [OSTI]

    Arnold, A. Elizabeth

    Short title: Endophytes of grasses Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes of tropical forest grasses K. Lindsay Higgins Phyllis D. Coley Thomas A. Kursar: Most studies examining endophytic fungi associated with grasses (Poaceae) have focused on agronomically

  11. Automated fungal DNA sequence comparison Dylan Glotzer `11, Anders Ohman `10, Darcy Young '11 Faculty Sponsor: David Hibbett

    E-Print Network [OSTI]

    Hibbett, David S.

    Automated fungal DNA sequence comparison Dylan Glotzer `11¹, Anders Ohman `10¹, Darcy Young '11 sequences were downloaded from the NCBI's GenBank, which is a database of publicly available DNA sequences. These sequences were categorized as "environmental" or "specimen-based" submissions based on a number of keywords

  12. An Extensive Study of Mutation and Selection on the Wobble Nucleotide in tRNA Anticodons in Fungal Mitochondrial Genomes

    E-Print Network [OSTI]

    Xia, Xuhua

    An Extensive Study of Mutation and Selection on the Wobble Nucleotide in tRNA Anticodons in Fungal hypotheses aim to predict the wobble nucleotide of tRNA anticodons in mitochondrion. The codon-anticodon adaptation hypothesis predicts that the wobble nucleotide of tRNA anticodon should evolve toward maximizing

  13. The Paleozoic origin of enzymatic mechanisms for lignin degradation reconstructed using 31 fungal genomes

    SciTech Connect (OSTI)

    Floudas, Dimitrios; Binder, Manfred; Riley, Robert; Barry, Kerrie; Blanchette, Robert A; Henrissat, Bernard; Martinez, Angel T.; Otillar, Robert; Spatafora, Joseph W.; Yadav, Jagit S.; Aerts, Andrea; Benoit, Isabelle; Boyd, Alex; Carlson, Alexis; Copeland, Alex; Coutinho, Pedro M.; de Vries, Ronald P.; Ferreira, Patricia; Findley, Keisha; Foster, Brian; Gaskell, Jill; Glotzer, Dylan; Gorecki, Pawel; Heitman, Joseph; Hesse, Cedar; Hori, Chiaki; Igarashi, Kiyohiko; Jurgens, Joel A.; Kallen, Nathan; Kersten, Phil; Kohler, Annegret; Kues, Ursula; Kumar, T. K. Arun; Kuo, Alan; LaButti, Kurt; Larrondo, Luis F.; Lindquist, Erika; Ling, Albee; Lombard, Vincent; Lucas, Susan; Lundell, Taina; Martin, Rachael; McLaughlin, David J.; Morgenstern, Ingo; Morin, Emanuelle; Murat, Claude; Nagy, Laszlo G.; Nolan, Matt; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Rokas, Antonis; Ruiz-Duenas, Francisco J.; Sabat, Grzegorz; Salamov, Asaf; Samejima, Masahiro; Schmutz, Jeremy; Slot, Jason C.; St. John, Franz; Stenlid, Jan; Sun, Hui; Sun, Sheng; Syed, Khajamohiddin; Tsang, Adrian; Wiebenga, Ad; Young, Darcy; Pisabarro, Antonio; Eastwood, Daniel C.; Martin, Francis; Cullen, Dan; Grigoriev, Igor V.; Hibbett, David S.

    2012-03-12T23:59:59.000Z

    Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non?lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.

  14. Techno-economic analysis of corn stover fungal fermentation to ethanol

    SciTech Connect (OSTI)

    Meyer, Pimphan A.; Tews, Iva J.; Magnuson, Jon K.; Karagiosis, Sue A.; Jones, Susanne B.

    2013-11-01T23:59:59.000Z

    This techno-economic analysis assesses the process economics of ethanol production from lignocellulosic feedstock by fungi to identify promising opportunities, and the research needed to achieve them. Based on literature derived data, four different ethanologen strains are considered in this study: native and recombinant Saccharomyces cerevisiae, the natural pentose-fermenting yeast, Pichia stipitis and the filamentous fungus Fusarium oxysporum. In addition, filamentous fungi are applied in multi-organism and consolidated process configurations. Organism performance and technology readiness are categorized as near-term (<5 years), mid-term (5-10 years), and long-term (>10 years) process deployment. The results of the analysis suggest that the opportunity for fungal fermentation exists for lignocellulosic ethanol production.

  15. Thermal Stabilization of an Endoglucanase by Cyclization

    E-Print Network [OSTI]

    Lieshout, Johan F. T.

    An intein-driven protein splicing approach allowed for the covalent linkage between the N- and C-termini of a polypeptide chain to create circular variants of the endo-?-1,3-1,4-glucanase, LicA, from Bacillus licheniformis. ...

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

    SciTech Connect (OSTI)

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

    2011-08-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Kingsley, Mark T.

    2001-03-13T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Kingsley, Mark T

    2001-03-13T23:59:59.000Z

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

  19. 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

    SciTech Connect (OSTI)

    Klobukowski, Erik

    2011-12-29T23:59:59.000Z

    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.

  20. Trap cultures reveal higher species richness of arbuscular mycorrhizal fungi in comparison to soil samples in the Phoenix metropolitan area.Arbuscular mycorrhizal fungal and dark septate endophytes colonization of plant roots from urban desert preserves a

    E-Print Network [OSTI]

    Hall, Sharon J.

    samples in the Phoenix metropolitan area.Arbuscular mycorrhizal fungal and dark septate endophytes mycorrhizal fungal and dark septate endophytes colonization of plant roots from urban desert preserves (Brundett 1999). Dark septate endophytes (DSE) are another type of root colonizing fungi mainly classified

  1. Promoter sequence of 3-phosphoglycerate kinase gene 2 of lactic acid-producing fungus rhizopus oryzae and a method of expressing a gene of interest in fungal species

    DOE Patents [OSTI]

    Gao, Johnway [Richland, WA; Skeen, Rodney S [Pendleton, OR

    2003-03-04T23:59:59.000Z

    The present invention provides the promoter clone discovery of phosphoglycerate kinase gene 2 of a lactic acid-producing filamentous fungal strain, Rhizopus oryzae. The isolated promoter can constitutively regulate gene expression under various carbohydrate conditions. In addition, the present invention also provides a design of an integration vector for the transformation of a foreign gene in Rhizopus oryzae.

  2. Promoter sequence of 3-phosphoglycerate kinase gene 1 of lactic acid-producing fungus rhizopus oryzae and a method of expressing a gene of interest in fungal species

    DOE Patents [OSTI]

    Gao, Johnway [Richland, WA; Skeen, Rodney S [Pendleton, OR

    2002-10-15T23:59:59.000Z

    The present invention provides the promoter clone discovery of phosphoglycerate kinase gene 1 of a lactic acid-producing filamentous fungal strain, Rhizopus oryzae. The isolated promoter can constitutively regulate gene expression under various carbohydrate conditions. In addition, the present invention also provides a design of an integration vector for the transformation of a foreign gene in Rhizopus oryzae.

  3. Structural and functional studies of a phosphatidic acid-binding antifungal plant defensin MtDef4: Identification of an RGFRRR motif governing fungal cell entry

    SciTech Connect (OSTI)

    Sagaram, Uma S.; El-Mounadi, Kaoutar; Buchko, Garry W.; Berg, Howard R.; Kaur, Jagdeep; Pandurangi, Raghoottama; Smith, Thomas J.; Shah, Dilip

    2013-12-04T23:59:59.000Z

    A highly conserved plant defensin MtDef4 potently inhibits the growth of a filamentous fungus Fusarium graminearum. MtDef4 is internalized by cells of F. graminearum. To determine its mechanism of fungal cell entry and antifungal action, NMR solution structure of MtDef4 has been determined. The analysis of its structure has revealed a positively charged patch on the surface of the protein consisting of arginine residues in its ?-core signature, a major determinant of the antifungal activity of MtDef4. Here, we report functional analysis of the RGFRRR motif of the ?-core signature of MtDef4. The replacement of RGFRRR to AAAARR or to RGFRAA not only abolishes fungal cell entry but also results in loss of the antifungal activity of MtDef4. MtDef4 binds strongly to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Mutations of RGFRRR which abolish fungal cell entry of MtDef4 also impair its binding to PA. Our results suggest that RGFRRR motif is a translocation signal for entry of MtDef4 into fungal cells and that this positively charged motif likely mediates interaction of this defensin with PA as part of its antifungal action.

  4. Vertical transmission of fungal endophytes is widespread in Susan Hodgson, Catherine de Cates, Joshua Hodgson, Neil J. Morley, Brian C. Sutton &

    E-Print Network [OSTI]

    Chittka, Lars

    Vertical transmission of fungal endophytes is widespread in forbs Susan Hodgson, Catherine de Cates(8): 1199­ 1208 doi: 10.1002/ece3.953 Abstract To date, it has been thought that endophytic fungi in forbs field- grown plants and endophytes isolated from these, and from subsequent cotyle- dons and true leaves

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

    E-Print Network [OSTI]

    Shefferson, Richard P.

    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

  6. Ice Nucleation of Fungal Spores from the Classes Agaricomycetes, Ustilaginomycetes, and Eurotiomycetes, and the effect on the Atmospheric Transport of these Spores

    SciTech Connect (OSTI)

    Haga, D. I.; Burrows, Susannah M.; Iannone, R.; Wheeler, M. J.; Mason, R.; Chen, J.; Polishchuk, E. A.; Poschl, U.; Bertram, Allan K.

    2014-08-26T23:59:59.000Z

    Ice nucleation on fungal spores may affect the frequency and properties of ice and mixed-phase clouds. We studied the ice nucleation properties of 12 different species of fungal spores chosen from three classes: Agaricomycetes, Ustilagomycetes, and Eurotiomycetes. Agaricomycetes include many types of mushroom species and are cosmopolitan all over the globe. Ustilagomycetes are agricultural pathogens and have caused widespread damage to crops. Eurotiomycetes are found on all types of decaying material and include important human allergens. We focused on these classes since they are thought to be abundant in the atmosphere and because there is very little information on the ice nucleation ability of these classes of spores in the literature. All of the fungal spores investigated were found to cause freezing of water droplets at temperatures warmer than homogeneous freezing. The cumulative number of ice nuclei per spore was 0.001 at temperatures between -19 °C and -29 °C, 0.01 between -25.5 °C and -31 °C, and 0.1 between -26 °C and -36 °C. On average, the order of ice nucleating ability for these spores is Ustilagomycetes > Agaricomycetes ? Eurotiomycetes. We show that at temperatures below -20 °C, all of the fungal spores studied here are less efficient ice nuclei compared to Asian mineral dust on a per surface area basis. We used our new freezing results together with data in the literature to compare the freezing temperatures of spores from the phyla Basidiomycota and Ascomycota, which together make up 98 % of known fungal species found on Earth. The data show that within both phyla (Ascomycota and Basidiomycota) there is a wide range of freezing properties, and also that the variation within a phylum is greater than the variation between the average freezing properties of the phyla. Using a global chemistry-climate transport model, we investigated whether ice nucleation on the studied spores, followed by precipitation, can influence the atmospheric transport and global distributions of these spores in the atmosphere. Simulations show that inclusion of ice nucleation scavenging of fungal spores in mixed-phase clouds can decrease the surface annual mean mixing ratios of fungal spores over the oceans and polar regions and decrease annual mean mixing ratios in the upper troposphere.

  7. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

    SciTech Connect (OSTI)

    Olson, Ake; Aerts, Andrea; Asiegbu, Fred; Belbahri, Lassaad; Bouzid, Ourdia; Broberg, Anders; Canback, Bjorn; Coutinho, Pedro M.; Cullen, Dan; Dalman, Kerstin; Deflorio, Giuliana; van Diepen, Linda T. A.; Dunand, Christophe; Duplessis, Sebastien; Durling, Mikael; Gonthier, Paolo; Grimwood, Jane; Fossdal, Carl Gunnar; Hansson, David; Henrissat, Bernard; Hietala, Ari; Himmelstrand, Kajsa; Hoffmeister, Dirk; Hogberg, Nils; James, Timothy Y.; Karlsson, Magnus; Kohler, Annegret; Lucas, Susan; Lunden, Karl; Morin, Emmanuelle; Murat, Claude; Park, Jongsun; Raffaello, Tommaso; Rouze, Pierre; Salamov, Asaf; Schmutz, Jeremy; Solheim, Halvor; Stahlberg, Jerry; Velez, Heriberto; de Vries, Ronald P.; Wiebenga, Ad; Woodward, Steve; Yakovlev, Igor; Garbelotto, Matteo; Martin, Francis; Grigoriev, Igor V.; Stenlid, Jan

    2012-01-01T23:59:59.000Z

    Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.

  8. Quantifying fungal viability in air and water samples using quantitative PCR after treatment with propidium monoazide (PMA)

    SciTech Connect (OSTI)

    Vesper, Stephen; McKinstry, Craig A.; Hartmann, Chris; Neace, Michelle; Yoder, Stephanie; Vesper, Alex

    2007-11-28T23:59:59.000Z

    A method is described to discriminate between live and dead cells of the infectious fungi Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus, Mucor racemosus, Rhizopus stolonifer and Paecilomyces variotii. To test the method, conidial suspensions were heat inactivated at 85 °C or held at 5 °C (controls) for 1 h. Polycarbonate filters (25 mm diameter, 0.8 ?m pore size) were placed on "welled" slides (14 mm diameter) and the filters treated with either PBS or PMA. Propidium monoazide (PMA), which enters dead cells but not live cells, was incubated with cell suspensions, exposed to blue wavelength light-emitting diodes (LED) to inactivate remaining PMA and secure intercalation of PMAwith DNA of dead cells. Treated cells were extracted and the live and dead cells evaluated with quantitative PCR (QPCR). After heat treatment and DNA modification with PMA, all fungal species tested showed an approximate 100- to 1000-fold difference in cell viability estimated by QPCR analysis which was consistent with estimates of viability based on culturing.

  9. a32 modular polyketide: Topics by E-print Network

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

    systems and its optimization for applications to quantum repeaters and entanglement distribution and sharing. Gualdi, Giulia; Illuminati, Fabrizio 2010-01-01 6 Modular Entanglement...

  10. allyl alcohol cyclization: Topics by E-print Network

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

    second, the efficacy of three psychotherapies for alcoholism in treating extreme West, Mike 333 Characterization of Catalysts for the Synthesis of Higher Alcohols using...

  11. A Dioxane Template for Highly Selective Epoxy Alcohol Cyclizations

    E-Print Network [OSTI]

    Mousseau, James J.

    Ladder polyether natural products are a class of natural products denoted by their high functional-group density and large number of well-defined stereocenters. They comprise the toxic component of harmful algal blooms ...

  12. Intramolecular Cyclization Strategies Towards the Synthesis of Zoanthamine Alkaloids

    E-Print Network [OSTI]

    Theodorakis, Emmanuel

    and purified through a silica plug. The crude aldehyde was obtained as oil and used without further chromatography. NMR spectra were recorded on the Varian Mercury 400, 300 and/or Jeol Unity 500 MHz instruments 11 as oil (3.37 g, 57%, 2 steps). TLC (ethyl acetate/hexanes 2:3): Rf = 0.5; 1 H NMR (400 MHz, CDCl3

  13. aryl radical cyclization: Topics by E-print Network

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

    organizational transformation, new organizational forms and the new public management (NPM) in a novel way. Data reveal important limits to intended organizational transformation...

  14. Cyclization and Catenation Directed by Molecular Self-Assembly

    SciTech Connect (OSTI)

    Wang, Wei; Wang, Li Q.; Palmer, Bruce J.; Exarhos, Gregory J.; Li, Alexander D.

    2006-08-30T23:59:59.000Z

    We report here that molecular self-assembly can effectively direct and enhance specific reaction pathways. Using perylene??-??stacking weak attractive forces, we succeeded in synthesizing perylene bisimide macrocyclic dimer and a concatenated dimer-dimer ring from dynamic self-assembly of monomeric bis-N, N’-(2-(2-(2-(2-thioacetyl ethoxy) ethoxy) ethoxy) ethyl) perylene tetracarboxylic diimide. The monocyclic ring closure and the dimer-dimer ring concatenation were accomplished through formation of disulfide bonds, which was readily triggered by air oxidization under basic deacetylation conditions. The perylene cyclic dimer and its concatenated tetramer were characterized using both structural methods (NMR, mass spectroscopy) and photophysical measurements (UV-vis spectroscopy). Kinetic analyses offer informative insights about reaction pathways and possible mechanisms, which lead to the formation of fascinating concatenated rings. Molecular dynamic behaviors of both the monocyclic dimer and the concatenated dimer-dimer ring were modeled with the NWChem molecular dynamics software module, which shows distinct stacking activities for the monocyclic dimer and the concatenated tetramer.

  15. Quantitation of fungal mRNAs in complex substrates by reverse transciption pcr and its application to Phanerochaete chrysosporium-colonized soil

    SciTech Connect (OSTI)

    Lamar, R.T.; Schoenike, B.; Dietrich, D.M. [Univ. of Wisconsin, Madison, WI (United States)] [and others

    1995-06-01T23:59:59.000Z

    Thorough analysis of fungi in complex substrates has been hampered by inadequate experimental tools for assessing physiological activity and estimating biomass. We report a method for the quantitative assessment of specific fungal mRNAs in soil. The method was applied to complex gene families of Phanerochaete chrysosporium, a white-rot fungus widely used in studies of organopollutant degradation. Among the genes implicated in pollutant degradation, two closely related lignin peroxidase transcripts were detected in soil. The pattern of lignin peroxidase gene expression was unexpected; certain transcripts abundant in defined cultures were not detected in soil cultures. Transcripts encoding cellobiohydrolases and{beta}-tubulin were also detected. The method will aid in defining the roles of specific genes in complex biological processes such as organopollutant degradation, developing strategies for strain improvement, and identifying specific fungi in environmental samples. 45 refs., 3 figs., 1 tab.

  16. The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

    SciTech Connect (OSTI)

    de Wit, Pierre J. G. M.; van der Burgt, Ate; Okmen, Bilal; Stergiopoulos, Ioannis; Abd-Elsalam, Kamel A.; Aerts, Andrea L.; Bahkali, Ali H.; Beenen, Henriek G.; Chettri, Oranav; Cos, Murray P.; Datema, Erwin; de Vries, Ronald P.; DHillon, Braham; Ganley, Austen R.; Griffiths, Scott A.; Guo, Yanan; Gamelin, Richard C.; Henrissat, Bernard; Kabir, M. Shahjahan; Jashni, Mansoor Karimi; Kema, Gert; Klaubauf, Sylvia; Lapidus, Alla; Levasseur, Anthony; Lindquist, Erika; Mehrabi, Rahim; Ohm, Robin A.; Owen, Timothy J.; Salamov, Asaf; Schwelm, Arne; Schijlen, Elio; Sun, Hui; van den Burg, Harrold A.; van Burg, Roeland C. H. J.; Zhang, Shuguang; Goodwin, Stephen B.; Grigoriev, Igor V.; Collemare, Jerome; Bradshaw, Rosie E.

    2012-05-04T23:59:59.000Z

    We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70percent of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2percent in Cfu versus 3.2percent in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.

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

    SciTech Connect (OSTI)

    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

    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.

  18. Deciphering the genetic basis for polyketide variation among mycobacteria producing mycolactones

    E-Print Network [OSTI]

    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

    . Chembiochem 2003, 4:654-657. 24. Kaser M, Rondini S, Naegeli M, Stinear T, Portaels F, Certa U, Pluschke G: Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans. BMC Evol Biol 2007, 7:177. 25. Nei M, Rooney AP... . Nucleic Acids Research 1995, 23:4992-4999. 35. Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolu- tionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 2007, 24:1596-1599. 36. Sonnhammer EL, Durbin R: A dot-matrix program...

  19. acid-promoted cyclization reactions: Topics by E-print Network

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

    After an introduction to the controversial problem of Low Energy Nuclear Reactions (LENR) catalyzed by neutrons on metallic hydride surfaces we present the results of an...

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

    E-Print Network [OSTI]

    Marcus, Andrew Peter

    2009-01-01T23:59:59.000Z

    nones were exposed to 25 mol % AlCl 3 in toluene. ?-Methyl-2.9 was exposed to 10 mol % AlCl 3 in toluene at 80 ºC to

  1. Antitumor activity of a membrane lytic peptide cyclized with a linker sensitive to membrane

    E-Print Network [OSTI]

    Chau, Ying

    a concen- tration of 5 Mmol/L, suppressed activity to MCF-7 and RBC was observed, whereas the toxicity of the cyclic peptide was shown by comparing cytotoxicity results on RBC and two human breast cancer cell lines of different malignancy and MT1-MMP expression: highly invasive MDA-MB-435 and noninvasive MCF-7. Above

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

    E-Print Network [OSTI]

    Marcus, Andrew Peter

    2009-01-01T23:59:59.000Z

    2.145a The Paal-Knorr pyrrole synthesis involves the acid-perform the Paal-Knorr pyrrole synthesis with aniline 2.145a

  3. Synthesis of highly substituted benzo-fused nitrogen heterocycles via tandem benzannulation/cyclization strategies

    E-Print Network [OSTI]

    Willumstad, Thomas P. (Thomas Paul)

    2013-01-01T23:59:59.000Z

    Benzannulations employing ynamides and vinylketenes (generated in situ from [alpha]-diazo ketones) were investigated. Irradiation of the diazo ketones using a batch or continuous-flow reactor leads to the formation of ...

  4. Structure of the Product from a Novel Cyclization Reaction Involving a C(6)-Substituted Uridine Analog

    E-Print Network [OSTI]

    Wang, Binghe; Takusagawa, Fusao; Mertes, Mathias P.; Bowman-James, Kristin

    1993-01-01T23:59:59.000Z

    {Received 10 January 1992; accepted 23 April 1993) Abstract. 5,6,7,7a,9,10,14b, 14c-0ctahydr0-4-[2,3-0- (1 -methylethylidene)-^-D-ribofuranosyl]cyclopenta- * Current address: Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045....5380 (1) 4.71 C(8) 0.0127 (3) -0 .1702 (4) 0.5363 (1) 5.55 C(9) -0 .0155 (3) -0.0678 (3) 0.5607 (1) 4.93 C(10) 0.0623 (3) -0 .0646(3) 0.5998 (1) 3.94 N(1I) 0.0188 (2) -0 .1154(2) 0.64071 (8) 3.72 C(12) -0 .0329 (3) -0.0412 (3) 0.6717 (1) 4.61 C(13) 0...

  5. Fueling the Future with Fungal Genomics

    SciTech Connect (OSTI)

    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

    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.

  6. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01T23:59:59.000Z

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

  7. Understanding the Forest Microbiome: A Fungal Perspective

    SciTech Connect (OSTI)

    Vilgalys, Rytas [Duke University

    2014-03-19T23:59:59.000Z

    Rytas Vilgalys, Duke University, speaking at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif

  8. PALLADIUM-CATALYZED DECARBOXYLATIVE ALLYLATIONS OF ESTER ENOLATE EQUIVALENTS AND PALLADIUM-CATALYZED CYCLIZATIONS VIA CO2 AND SILYL ACTIVATION

    E-Print Network [OSTI]

    Ariyarathna, Yamuna Kumari

    2014-08-31T23:59:59.000Z

    (diphenylphosphino)-1,1’-binaphthyl SN2 bimolecular nucleophilic substitution t-Bu tert-butyl t-BuOK potassium tert-butoxide TfOH trifluoromethanesulfonic acid TFP trifurylphosphine THF tetrahydrofuran tol toluene TPO triphenylphosphine...A). Coordination of the Pd(0) catalyst to the allyl moiety facilitates the oxidative addition to produce a palladium ?-allyl intermediate and carboxylate 1.1.4. Upon decarboxylation the carboxylate will expose the active nucleophile, which then couple...

  9. A Concise and Versatile Double-Cyclization Strategy for the Highly Stereoselective Synthesis and Arylative Dimerization of Aspidosperma Alkaloids

    E-Print Network [OSTI]

    Medley, Jonathan William

    Building cycles: A strategy for the concise, stereoselective synthesis of aspidosperma alkaloids and related structures via a common putative diiminium ion intermediate is reported. The approach enables the dimerization ...

  10. Fungal Diversity Identification and pathogenicity of Graphium and Pesotum

    E-Print Network [OSTI]

    wounds on Schizolobium parahybum in Ecuador Maria M. Geldenhuis1 , Jolanda Roux1 , Fernando Montenegro3, Quito, Ecuador Geldenhuis, M.M., Roux, J., Montenegro, F., De Beer, Z.W., Wingfield, M.J. and Wingfield

  11. Fungal Diversity Chrysoporthe doradensis sp. nov. pathogenic to Eucalyptus in

    E-Print Network [OSTI]

    Gryzenhout1* , Henrietta Myburg2 , Brenda D. Wingfield2 , Fernando Montenegro3 and Michael J. Wingfield1 1 Juan Manuel Durini, Quito, Ecuador Gryzenhout, M., Myburg, H., Wingfield, B.D., Montenegro, F

  12. Fungal diversity within the Populus rhizosphere and endosphere...

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

    Symbiosis Conference Speaker and Attendee List Integrating Environmental, Safety, and Quality Management System Audits NYC Taxi Drive Cycle Development and Simulation Study...

  13. Pectinases Link Early Fungal Evolution to the Land Plant Lineage

    SciTech Connect (OSTI)

    Berbee, Mary [University of British Columbia

    2014-03-19T23:59:59.000Z

    Mary Berbee, University of British Columbia, Canada, speaking at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif.

  14. Biology and Management of Fungal Pathogens of Vegetables Program Leader

    E-Print Network [OSTI]

    Lazzaro, Brian

    of cucurbit and solanaceous crops. This water mold was recently found on snap beans in New York on Long Island Summary: Biology and management of Sclerotinia sclerotiorum (cause of white mold) on beans (snap, soy strategies for control of Phytophthora capsici on snap beans (cause of Phytophthora blight), including

  15. allergic fungal sinusitis: Topics by E-print Network

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

    and Rhinitis (Montpellier Paris-Sud XI, Universit de 344 Interference of a short-term exposure to nitrogen dioxide with allergic airways responses to allergenic Physics...

  16. Ris-PhD-20(EN) Interactions Between Fungal Plant

    E-Print Network [OSTI]

    This thesis is submitted in partial fulfilment of the requirements for the Ph.D. degree at the Royal together on the same plants in the field. This PhD thesis concludes, that interaction between different assessment, where disease severities are determined as averages over the crop. The work presented in the PhD

  17. Fungal Genomics Presentation for BETO 2015 Project Peer Review

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport inEnergy0.pdfTechnologies ProgramOutfittedof EnergydetailsDepartment

  18. Fungal diversity within the Populus rhizosphere and endosphere | Department

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport inEnergy0.pdfTechnologies ProgramOutfittedof EnergydetailsDepartmentof

  19. Biosynthetic investigations of ansamycin natural products from marine-derived actinomycetes

    E-Print Network [OSTI]

    Wilson, Micheal Christopher

    2011-01-01T23:59:59.000Z

    Polyketide Pathways in an Endophyte. Angew Chem Int Ed (114)Polyketide Pathways in an Endophyte. Angew Chem Int EdA-D from a Mangrove Endophyte Reveal an Unparalleled

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

    E-Print Network [OSTI]

    Sofiyev, Vladimir

    2010-01-01T23:59:59.000Z

    synthesis began with tetrahydroindole 3.23 (Scheme 3.4), which is readily available in multigram quantities from pyrrole

  1. Evidence That Epoxide-Opening Cascades Promoted by Water Are Stepwise and Become Faster and More Selective After the First Cyclization

    E-Print Network [OSTI]

    Morten, Christopher J.

    A detailed kinetic study of the endo-selective epoxide-opening cascade reaction of a diepoxy alcohol in neutral water was undertaken using 1H NMR spectroscopy. The observation of monoepoxide intermediates resulting from ...

  2. annua glandular trichome: Topics by E-print Network

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

    6 July, 2009 Environmental Sciences and Ecology Websites Summary: , glandular trichome, hemp, hop, Humulus lupulus, marijuana, polyketide synthase, trichomes. Introduction...

  3. Biosynthetic investigations of ansamycin natural products from marine-derived actinomycetes

    E-Print Network [OSTI]

    Wilson, Micheal Christopher

    2011-01-01T23:59:59.000Z

    pigment antioxidant SA cym non-ribosomal peptide cyclomarinantioxidant 1.3: Polyketides and Non-ribosomal Peptidesantioxidant cytotoxic mactolactam cytotoxic benzoxazole antibacterial, cytotoxic cyclic peptides

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

    E-Print Network [OSTI]

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

    2010-01-01T23:59:59.000Z

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

  5. Journal of Experimental Botany, Vol. 60, No. 13, pp. 37153726, 2009 doi:10.1093/jxb/erp210 Advance Access publication 6 July, 2009

    E-Print Network [OSTI]

    Weiblen, George D

    , glandular trichome, hemp, hop, Humulus lupulus, marijuana, polyketide synthase, trichomes. Introduction substantially in economic traits that range from marijuana, arguably the most widespread illicit drug, to hemp

  6. Three unique mutants of Arabidopsis identify eds loci required for limiting growth of a biotrophic fungal

    E-Print Network [OSTI]

    Wildermuth, Mary C

    with enhanced disease susceptibility to Erysiphe orontii. Our initial characterization focused on three mutants, mutant. Introduction When plants are attacked by pathogens they mount a battery of defenses, including

  7. Daldinia decipiens and Entonaema cinnabarina as fungal symbionts of Xiphydria wood wasps

    E-Print Network [OSTI]

    e s e a r c h 1 1 1 ( 2 0 0 7 ) 2 2 4 ­ 2 3 1 0953-7562/$ ­ see front matter ª 2006 The British or species `declines', e.g. Dutch-elm disease and oak decline in central and southern Europe, Fraxinus de

  8. arachidonate-rich fungal oil: Topics by E-print Network

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

    simulation to optimize carbon dioxide (CO2) sequestration and enhance oil recovery (CO2-EOR) based on known 224 Algeria's New Oil Strategy Lahouari ADDI Physics Websites...

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

    E-Print Network [OSTI]

    204 Sohar, 311, Sultanate of Oman 3 Plant Protection Division, Nuclear Institute for Agriculture of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa 2 Ghadafan Agriculture Research Station, Ministry of Agriculture and Fisheries, P. O. Box

  10. Comparative genomic analysis of fungal genomes reveals intron-rich ancestors

    E-Print Network [OSTI]

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

    2007-01-01T23:59:59.000Z

    previously proposed meth- ods. Dollo parsimony assumes aNYK. Results for all meth- ods are given in Additional dataa convergence of the four meth- ods on better estimates (and

  11. Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

    E-Print Network [OSTI]

    Kohn, Linda M.

    , Elisabeth Fournier2,11 , Lilian Gout2 , Matthias Hahn12 , Linda Kohn13 , Nicolas Lapalu1 , Kim M. Plummer14

  12. Fungal Genetics and Biology 43 (2006) 545559 www.elsevier.com/locate/yfgbi

    E-Print Network [OSTI]

    2006-01-01T23:59:59.000Z

    (arthro- conidia), produced by the saprobic phase of the fungus. Within the lungs of the host, the barrel

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

    E-Print Network [OSTI]

    Zhao, Huimin

    of lignocellulosic biomass to value-added products such as bioethanol and xylitol. Saccharomyces cerevisiae is a suitable organism for bioethanol production (Almeida and Hahn-Hägerdal 2009; Matsushika et al. 2009a

  14. Gene expression in human fungal pathogen Coccidioides immitis changes as arthroconidia differentiate into spherules and mature

    E-Print Network [OSTI]

    Viriyakosol, Suganya; Singhania, Akul; Fierer, Joshua; Goldberg, Jonathan; Kirkland, Theo N; Woelk, Christopher H

    2013-01-01T23:59:59.000Z

    a 40 ?M nylon cell strainer (BD Falcon). The strainedcultures through a 40 ?M nylon cell strainer (BD Falcon).picked up from the cell strainer using a sterile disposable

  15. Dispersed Polyphosphate in Fungal Vacuoles in Eucalyptus pilularis/Pisolithus tinctorius

    E-Print Network [OSTI]

    Vesk, Peter

    . Stained sections of ether­acrolein freeze-substituted mycorrhizas also showed only dis- persed material

  16. Fungus Threatens the Viability of Cotton For more than a century, the fungal disease cotton root

    E-Print Network [OSTI]

    , and subsequently validating and expanding the promising results, AgriLife Extension compiled data from the 2010,000 acres of dryland cotton (230,000 total acres). The total net economic benefit to growers was estimated

  17. Discovery of Fungal Cell Wall Components Using Evolutionary and Functional Genomics

    E-Print Network [OSTI]

    Sain, Divya

    2013-01-01T23:59:59.000Z

    profiling and comparative genomics approaches." Eukaryotcerevisiae." Comp Funct Genomics 2(3): 124-42. Dinsdale, E.profiling and comparative genomics approaches." Eukaryot

  18. E-Print Network 3.0 - anti-fungal drug design Sample Search Results

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

    Pg. 1: Eligible Expenses & Documentation Pg. 2: Over-The-Counter Changes due to Health Care Reform Summary: Allergy & sinus medicines and products Feminine anti-fungalanti-itch...

  19. Monitoring Viable Fungal and Bacterial Bioaerosol Concentrations to Identify Acceptable Levels for Common Indoor Environments

    E-Print Network [OSTI]

    Robertson, L. D.

    1998-01-01T23:59:59.000Z

    and enumerated using several sampling methodologies, yet the specific effects of many airborne microorganisms on human health is not clearly understood. The lack of understanding is in part due to the extreme complexities that exists with respect to sampling... while sterile hyphae averaged 29 CFUlm3. Penicillium was observed in 50% if the indoor samples and averaged 48 CFUlm3. Aspergillus was documented to occur in 33% of the indoor samples and demonstrated an average airborne concentration of 20 CFUlm3...

  20. Fungal Diversity A new bark canker disease of the tropical hardwood tree Cedrelinga cateniformis

    E-Print Network [OSTI]

    in Ecuador Lombard, L.1* , Bogale, M.2 , Montenegro, F.3 , Wingfield, B.D.2 and Wingfield, M.J.1 1 Department, L., Bogale, M., Montenegro, F., Wingfield, B.D. and Wingfield, M.J. (2008). A new bark canker

  1. Assessing the Roles of Striatin Orthologs in Fungal Morphogenesis, Sexual Development and Pathogenicity

    E-Print Network [OSTI]

    Wang, Chih-Li

    2012-10-19T23:59:59.000Z

    -utilizing mutants demonstrates that Str1 is required for hyphal fusion. In pathogenicity, ?str1 is less virulent in maize anthracnose leaf blight and stalk rot. The phenotypes of ?str1 are complemented by the Fusarium verticillioides striatin ortholog (fsr1...

  2. A novel test for host-symbiont codivergence indicates ancient origin of fungal endophytes in grasses

    E-Print Network [OSTI]

    Schardl, Chris L; Lindstrom, Adam; Speakman, Skyler; Stromberg, Arnold; Yoshida, Ruriko

    2007-01-01T23:59:59.000Z

    Significant phylogenetic codivergence between plant or animal hosts ($H$) and their symbionts or parasites ($P$) indicate the importance of their interactions on evolutionary time scales. However, valid and realistic methods to test for codivergence are not fully developed. One of the systems where possible codivergence has been of interest involves the large subfamily of temperate grasses (Pooideae) and their endophytic fungi (epichloae). These widespread symbioses often help protect host plants from herbivory and stresses, and affect species diversity and food web structures. Here we introduce the MRCALink (most-recent-common-ancestor link) method and use it to investigate the possibility of grass-epichlo\\"e codivergence. MRCALink applied to ultrametric $H$ and $P$ trees identifies all corresponding nodes for pairwise comparisons of MRCA ages. The result is compared to the space of random $H$ and $P$ tree pairs estimated by a Monte Carlo method.

  3. Species of Mycosphaerellaceae and Teratosphaeriaceae on native Myrtaceae in Uruguay: evidence of fungal host jumps

    E-Print Network [OSTI]

    Blanchette, Robert A.

    Species of Mycosphaerellaceae and Teratosphaeriaceae on native Myrtaceae in Uruguay: evidence Proteccion Vegetal, Facultad de Agronomia, Universidad de la Republica, Uruguay b Forestry and Agricultural Agropecuaria (INIA), Uruguay d Department of Plant Pathology, University of Minnesota, USA a r t i c l e i n f

  4. Bacterial and fungal organisms in the vagina of normal cows and cows with vaginitis

    E-Print Network [OSTI]

    Husted, James Ross

    2005-02-17T23:59:59.000Z

    frequent aerobic isolates included Acinetobacter lwoffii, Arcanobacterium pyogenes, Escherichia coli, Corynebacterium spp., and Streptococcus spp. These organisms were isolated from both groups of cows, but more frequently from the vaginitis group...

  5. Comparative Genomics Suggests that the Fungal Pathogen Pneumocystis Is an Obligate Parasite

    E-Print Network [OSTI]

    Alvarez, Nadir

    of Microbiology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland, 2, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland Abstract for the management of patients susceptible to P. jirovecii infection given that the only source of infection would

  6. Bacterial and fungal organisms in the vagina of normal cows and cows with vaginitis 

    E-Print Network [OSTI]

    Husted, James Ross

    2005-02-17T23:59:59.000Z

    AND LITERATURE REVIEW ??????. 1 II MATERIALS AND METHODS ?????????????. 6 Collection???...??????????????????.. 6 Identification of Aerobic Bacteria?????????????. 7 Identification of Anaerobic Bacteria????????????. 8 Identification... of Microaerophilic Bacteria?????????? 8 Identification of Campylobacter sp????????????.. 9 Aerotolerance Test??????????????????? 9 Identification of Ureaplasma Bacteria???????????.. 10 Identification of Mycoplasma Bacteria???????????. 10 Identification...

  7. Mycoflora of pecans and microscopic studies of host-fungal interactions

    E-Print Network [OSTI]

    Wang, Huey-Ming

    1975-01-01T23:59:59.000Z

    Dec 24 Dec 31 Jan 7 Jan 14 Jan 21 0 1 2 3 4 5 6 7 8 9 10 10 25 19 4 24 20 21 21 27 44 32 28 42 35 48 35 25 44 55 58 68 67 10 15 23 26 0 22 50' 29 33 20 38 1 2 1 4 2 8 3 5 5 5 6 6 5 7 0 5 5 3 4 6 8 3 5 5 5 6...nd 3rd 4th 6th 7th 8th 9th 10th 11th Nov 20 Nov 23 Nov 24 Nov 26 Dec 3 Dec 19 Dec 23 Dec 25 Jan 3 Jan 6 Jan 8 Jan 9 Jan 10 Jan 13 Jan 18 Jan 21 0. 60 0. 82 0. 35 0. 33 0. 70 0. 78 l. 18 0. 08 0. 06 0. 12 0. 11 0. 02...

  8. Affinity Purification and Characterization of a Cutinase from the Fungal Plant Pathogen Monilinia fructicola (Wint.) Honey

    E-Print Network [OSTI]

    Hammock, Bruce D.

    fructicola (Wint.) Honey Guang-Yi Wang,* Themis J. Michailides,* Bruce D. Hammock, Young-Moo Lee, and Richard

  9. Fungal bis-Naphthopyrones as Inhibitors of Botulinum Neurotoxin John H. Cardellina II,

    E-Print Network [OSTI]

    -5011 Biotechnology High Performance Computer Software Applications Institute, Telemedicine and Advanced Technology, chaetochromin, talaroderxine, binding free energy, thermodynamic integration Botulinum neurotoxins (Bo and are classified by the Centers for Disease Control and Prevention as one of the six highest risk threat agents

  10. Diversity of Orchid Fungal Symbionts in Estonian Mine Tailings Sam Willis, Charles Cowden and Richard Shefferson

    E-Print Network [OSTI]

    Gittleman, John

    little more than burnt oil soaked shale and ash. We extracted all DNA in soil samples taken from multiple samples were taken is on a barren hill that was created when Estonia burned oil soaked shale to produce the fungi are utilizing the nutrients from the burnt oil and shale to support the orchids (Shefferson et al

  11. The Ecophysiology and Evolution of Mycoheterotrophic Plants in the Tribe Pyroleae (Ericaceae)

    E-Print Network [OSTI]

    Hynson, Nicole

    2010-01-01T23:59:59.000Z

    species. Fungal endophytes in the genus Phialocephala andfungus, Endo=fungal endophyte, ErM=ericoid mycorrhizalFlagelloscypha sp. OTU # Fungal endophyte Fungus sp.1 Fungus

  12. The development of iterative and cascade methods for the rapid synthesis of ladder polyether natural products

    E-Print Network [OSTI]

    Heffron, Timothy Paul

    2005-01-01T23:59:59.000Z

    I. The Development of Methods for the Iterative Synthesis of Polytetrahydropyrans An iterative method comprising chain homologation, epoxidation, 6-endo cyclization, and protiodesilylation was developed. Notable achievements ...

  13. Phylogenetics and Taxonomy of the Fungal Vascular Wilt Pathogen Verticillium, with the Descriptions of Five New Species

    E-Print Network [OSTI]

    Subbarao, Krishna V

    2011-01-01T23:59:59.000Z

    alfalfae Inderb. , H. W. Platt, R. M. Bostock, R. M. Davis &RM, Davis RM, Usami T, Platt HW, et al. (2011) Phylogeneticsnonalfalfae Inderb. , H. W. Platt, R. M. Bostock, R. M.

  14. Isolated fungal promoters and gene transcription terminators and methods of protein and chemical production in a fungus

    DOE Patents [OSTI]

    Dai, Ziyu; Lasure, Linda L; Magnuson, Jon K

    2014-05-27T23:59:59.000Z

    The present invention encompasses isolated gene regulatory elements and gene transcription terminators that are differentially expressed in a native fungus exhibiting a first morphology relative to the native fungus exhibiting a second morphology. The invention also encompasses a method of utilizing a fungus for protein or chemical production. A transformed fungus is produced by transforming a fungus with a recombinant polynucleotide molecule. The recombinant polynucleotide molecule contains an isolated polynucleotide sequence linked operably to another molecule comprising a coding region of a gene of interest. The gene regulatory element and gene transcription terminator may temporally and spatially regulate expression of particular genes for optimum production of compounds of interest in a transgenic fungus.

  15. November 2008 www.aznps.org The Plant Press ARIZONA NATIVE PLANT SOCIETY 13 Introduction to fungal endophytes

    E-Print Network [OSTI]

    Arnold, A. Elizabeth

    endophytes When first introduced in 1866, "endophyte" was used broadly to refer to any organism found within, but modern mycologists generally agree that endophytes are organisms that colonize internal plant tissues without causing apparent harm to their host. Research in my group (http://www.endophytes.org) focuses

  16. Phylogenetics and Taxonomy of the Fungal Vascular Wilt Pathogen Verticillium, with the Descriptions of Five New Species

    E-Print Network [OSTI]

    Subbarao, Krishna V

    2011-01-01T23:59:59.000Z

    known as dark septate endophyte Type 1. Mycologia 97: 628–pathogens from asymptomatic endophytes. Mycologia 102: 1318–

  17. Broad Knowledge seminars at Forest Pathology and Plant Pathology 130608 Georgios Tzelepis Fungal diseases: A threat to human life

    E-Print Network [OSTI]

    goes the limit? Or where are the insects 100528 Ulises Blandon Diaz Genetically modified food: Peril of genetically modified plants #12;

  18. The evolution of LOL, the secondary metabolite gene cluster for insecticidal loline alkaloids in fungal endophytes of grasses.

    E-Print Network [OSTI]

    Kutil, Brandi Lynn

    2009-05-15T23:59:59.000Z

    .......................................... 24 3 Determination of repetitive DNA content for the E. festucae BAC library ........................................................ 26 4 A set of contiguous BAC clones associated with the odc probe....... 29 5 Microsynteny... and sequencing............................................. 43 4 Species binomen and accession numbers for taxa in Cys/Met Metab PP gene family trees............................................... 66 5 Species binomen and accession numbers for taxa...

  19. Syntheses and conformational studies of peptidomimetics of B-turns

    E-Print Network [OSTI]

    Wang, Zhicheng

    1999-01-01T23:59:59.000Z

    not work well on solid supports. The S[]Ar and S[]2 reactions were used to synthesize macrocycles on solid phases. By using S[]Ar cyclization, libraries were made by parallel method on Geysen's pins. The products formed via different S[]2 cyclization...

  20. Studies on taxadiene synthase

    E-Print Network [OSTI]

    Chow, Siew Yin

    2006-08-16T23:59:59.000Z

    and 2D NMR. These results support the intermediacy and the existence of the cembrenyl cation in the cyclization of GGPP to taxadiene, and indicate that modifications at the 10,11 double bond of GGPP are tolerable in the cyclization....

  1. Received 24 Jul 2013 | Accepted 7 Nov 2013 | Published 5 Dec 2013 Activation and characterization of a cryptic

    E-Print Network [OSTI]

    Zhao, Huimin

    strains and contains an unusual hybrid polyketide synthase-nonribosomal peptide synthetase, which diverse biological activities such as antifungal, antibiotic and antioxidant proper- ties1­7. PTMs were

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

    E-Print Network [OSTI]

    Liu, Qingsong

    2009-05-15T23:59:59.000Z

    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 ...

  3. New strategies for the synthesis of azepine-containing alkaloids

    E-Print Network [OSTI]

    Tallant, Matthew David

    2001-01-01T23:59:59.000Z

    of dimethyltritylsilyl ether 35. . . . . . . . . . Diels-Alder cyclization of 18 with dimethyl fumarate. . . . . Intramolecular Heck cyclization of enamide 32. . . . . . . , . . . . . Page 23 24 26 27 28 28 30 30 32 33 34 43 xn1 LIST OF TABLES TABLE 1.... 11: Diels-Alder cyclization of 27 with dimethyl fumarate and X-ray structure of dimethyltritylsilyl ether 35. Iicc Or Me Me or C LiBHe, Beo, PhH, gg 'C, 24h ~ "CO Me H 27 87% CO, Me 61% 32 OH Ph, CSiMe2Br DMF, rl, 24 h AgNO3, Iree Ofr...

  4. Rhodium-catalyzed epoxide-opening cascades toward brevisin and hemibrevetoxin B

    E-Print Network [OSTI]

    Armbrust, Kurt W. (Kurt Willes)

    2014-01-01T23:59:59.000Z

    CHAPTER I. Rhodium-Catalyzed Epoxide-Opening Cascades: Formal Synthesis of (-)-Brevisin [chemical formula inserted] [Rh(CO)?Cl]? was found to be an effective catalyst for endo-selective cyclizations and cascades of ...

  5. Synthesis of oxygen-containing heterocyclic compounds based on the intramolecular OH insertion and Wolff rearrangement

    E-Print Network [OSTI]

    Wang, Jianbo

    of tetrahydrofuran derivatives.2 Palladium- catalyzed cyclization of allylic 2-alkynoates has been utilized to build of rhodium (II) acetate, with the expectation that Rh(II)-carbene intra- molecular O­H insertion should occur

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

    E-Print Network [OSTI]

    Gehling, Victor S. (Victor Scott)

    2008-01-01T23:59:59.000Z

    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 ...

  7. Gilbert Stork: Explorations into Position Selectivity

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Regiospecific deprotonation & trapping with saturated ketones · -Vetivone Cyano-epoxide and allylic-Patchouli alcohol · (+)-Digitoxigenin Radical cyclization to form a temporary ring Mixed acetal linkage · 12a

  8. ‘Bioinspired’ Total Synthesis of Agelastatin A and Derivatives for Cellular Target Identification; Syntheses of ^(15)N-labeled Oroidin and Keramadine Analog for ‘Metabiosynthetic’ Studies

    E-Print Network [OSTI]

    Reyes, Jeremy Chris Punzalan

    2013-11-08T23:59:59.000Z

    , to agelastatin A. A facile and highly diastereoselective C-ring formation via a 5-exo-trig cyclization or a Nazarov 4pi electrocyclization, proceeding through a deep-red colored N-acyliminium intermediate, constructs the three contiguous...

  9. Efficient and Selective Formation of Macrocyclic Disubstituted Z Alkenes by Ring-Closing Metathesis (RCM) Reactions Catalyzed by Mo- or W-Based Monoaryloxide Pyrrolide (MAP) Complexes: Applications to Total Syntheses of Epilachnene, Yuzu Lactone, Ambrettolide, Epothilone C, and Nakadomarin A

    E-Print Network [OSTI]

    Wang, Chenbo

    The first broadly applicable set of protocols for efficient Z-selective formation of macrocyclic disubstituted alkenes through catalytic ring-closing metathesis (RCM) is described. Cyclizations are performed with 1.2–7.5?mol?% ...

  10. Mechanism and Transition-State Structures for Nickel-Catalyzed Reductive Alkyne?Aldehyde Coupling Reactions

    E-Print Network [OSTI]

    McCarren, P. R.

    The mechanism of nickel-catalyzed reductive alkyne?aldehyde coupling reactions has been investigated using density functional theory. The preferred mechanism involves oxidative cyclization to form the nickeladihydrofuran ...

  11. Poly(Pyridinium Phenylene)s: Water-Soluble N-Type Polymers

    E-Print Network [OSTI]

    Swager, Timothy Manning

    Poly(pyridinium phenylene) conjugated polymers are synthesized by a cross-coupling and cyclization sequence. These polyelectrolytes are freely soluble in water and display high degrees of electroactivity. When reduced ...

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

    E-Print Network [OSTI]

    Swager, Timothy Manning

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

  13. Batch and Flow Photochemical Benzannulations Based on the Reaction of Ynamides and Diazo Ketones. Application to the Synthesis of Polycyclic Aromatic and Heteroaromatic Compounds

    E-Print Network [OSTI]

    Willumstad, Thomas P.

    Highly substituted polycyclic aromatic and heteroaromatic compounds are produced via a two-stage tandem benzannulation/cyclization strategy. The initial benzannulation step proceeds via a pericyclic cascade mechanism ...

  14. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J. (Waukee, IA); Ellanskaya, Irina (Kyiv, UA); Ellanskaya, legal representative, Natalia (Kyiv, UA); Gilliam, Jacob T. (Norwalk, IA); Hunter-Cevera, Jennie (Elliott City, MD); Presnail, James K. (Avondale, PA); Schepers, Eric (Port Deposit, MD); Simmons, Carl R. (Des Moines, IA); Torok, Tamas (Richmond, CA); Yalpani, Nasser (Johnston, IA)

    2009-09-15T23:59:59.000Z

    The invention relates to antifungal compositions and methods for protecting a plant from a fungal pathogen. Compositions including antifungal polypeptides isolated from a fungal fermentation broth are provided.

  15. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J. (Granger, IA); Crane, Virginia C. (Des Moines, IA); Ellanskaya, Irina (Kyiv, UA); Ellanskaya, legal representative, Natalia (Kyiv, UA); Gilliam, Jacob T. (Norwalk, IA); Hunter-Cevera, Jennie (Elliott City, MD); Presnail, James K. (Avondale, PA); Schepers, Eric J. (Port Deposit, MD); Simmons, Carl R. (Des Moines, IA); Torok, Tamas (Richmond, CA); Yalpani, Nasser (Johnston, IA)

    2009-10-06T23:59:59.000Z

    The invention relates to compositions including amino acid sequences isolated from fungal fermentation broths and methods for protecting a plant from a pathogen, particularly a fungal pathogen.

  16. Biological Interfaces | Clean Energy | ORNL

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

    of renewable energy sources. The PMI SFA integrates expertise in the areas of plant genomics, fungal and bacterial research, fungal ecology, analytical tool development, and...

  17. Diversification of NRT2 and the Origin of Its Fungal Homolog Jason C. Slot,* Kelly Hallstrom,* Patrick B. Matheny,* and David S. Hibbett*

    E-Print Network [OSTI]

    Matheny, P. Brandon

    in the ectomycorrhizal mushroom genus, Hebeloma. Introduction 35 Nitrogen is a limiting nutrient in most forest soils (including diatoms and oomy- cetes, but not yet kelp), and fungi. NRT2 belongs to the Nitrate/Nitrite Porter

  18. Diversification of NRT2 and the Origin of Its Fungal Homolog Jason C. Slot,* Kelly N. Hallstrom,* Patrick B. Matheny,* and David S. Hibbett*

    E-Print Network [OSTI]

    Hibbett, David S.

    in the ectomycorrhizal mushroom genus, Hebeloma. Introduction Nitrogen is a limiting nutrient in most forest soils (including diatoms and oomy- cetes, but not yet kelp), and fungi. NRT2 belongs to the Nitrate/Nitrite Porter

  19. Bacillus simplex—A Little Known PGPB with Anti-Fungal Activity—Alters Pea Legume Root Architecture and Nodule Morphology When Coinoculated with Rhizobium leguminosarum bv. viciae

    E-Print Network [OSTI]

    2013-01-01T23:59:59.000Z

    promoting bacterial endophytes. Appl. Soil Ecol. 2012, 61,phyllosphere, or as endophytes [10,26,27]. In a survey ofBLAST. Previously, an endophyte identified as B. simplex

  20. Investigations into the mycoheterotrophic symbiosis between Rhizopogon salebrosus and Pterospora andromedea and development of bioinformatic tools related to non-assembled fungal genomes

    E-Print Network [OSTI]

    Wong, Valerie

    2011-01-01T23:59:59.000Z

    the hybrid assembly using Bowtie. Up to 50 alignments werethe read-mapping program Bowtie (Langmead, Trapnell, Pop, ®ions by requiring Bowtie to discard all alignments for

  1. A P-loop Mutation in G[alpha] Subunits Prevents Transition to the Active State: Implications for G-protein Signaling in Fungal Pathogenesis

    SciTech Connect (OSTI)

    Bosch, Dustin E.; Willard, Francis S.; Ramanujam, Ravikrishna; Kimple, Adam J.; Willard, Melinda D.; Naqvi, Naweed I.; Siderovski, David P. (UNC); (Singapore)

    2012-10-23T23:59:59.000Z

    Heterotrimeric G-proteins are molecular switches integral to a panoply of different physiological responses that many organisms make to environmental cues. The switch from inactive to active G{alpha}{beta}{gamma} heterotrimer relies on nucleotide cycling by the G{alpha} subunit: exchange of GTP for GDP activates G{alpha}, whereas its intrinsic enzymatic activity catalyzes GTP hydrolysis to GDP and inorganic phosphate, thereby reverting G{alpha} to its inactive state. In several genetic studies of filamentous fungi, such as the rice blast fungus Magnaporthe oryzae, a G42R mutation in the phosphate-binding loop of G{alpha} subunits is assumed to be GTPase-deficient and thus constitutively active. Here, we demonstrate that G{alpha}(G42R) mutants are not GTPase deficient, but rather incapable of achieving the activated conformation. Two crystal structure models suggest that Arg-42 prevents a typical switch region conformational change upon G{alpha}{sub i1}(G42R) binding to GDP {center_dot} AlF{sub 4}{sup -} or GTP, but rotameric flexibility at this locus allows for unperturbed GTP hydrolysis. G{alpha}(G42R) mutants do not engage the active state-selective peptide KB-1753 nor RGS domains with high affinity, but instead favor interaction with G{beta}{gamma} and GoLoco motifs in any nucleotide state. The corresponding G{alpha}{sub q}(G48R) mutant is not constitutively active in cells and responds poorly to aluminum tetrafluoride activation. Comparative analyses of M. oryzae strains harboring either G42R or GTPase-deficient Q/L mutations in the G{alpha} subunits MagA or MagB illustrate functional differences in environmental cue processing and intracellular signaling outcomes between these two G{alpha} mutants, thus demonstrating the in vivo functional divergence of G42R and activating G-protein mutants.

  2. Towards Stunt-Free Lonren Reniform Nematode Resistance by Dissection of an Alien R-Gene Chromosome Segment and Detection of Significant Fungal Interactions

    E-Print Network [OSTI]

    Zheng, Xiuting

    2014-07-07T23:59:59.000Z

    . Starr Shuhua Yuan Hongbin Zhang Head of Department, David D. Baltensperger August 2014 Major Subject: Plant Breeding Copyright 2014 Xiuting Zheng ii ABSTRACT Reniform (Rotylenchulus... two years of my Ph.D. study, I learned a lot of pathology from Dr. Bell. I take this opportunity to thank my other committee members, Dr. James Starr, Dr. Patricia Klein, Dr. Hongbin Zhang, and Dr. Joshua Yuan, for their guidance through the course...

  3. Nombramientos SECRETARIOS

    E-Print Network [OSTI]

    types of fungal bioreactors with inmmobilized Trametes versicolor for post-treated weak black liquor

  4. Natural Product Synthesis DOI: 10.1002/anie.201006154

    E-Print Network [OSTI]

    Trauner, Dirk

    an unprecedented 9,10-anthraquinone methide moiety fused to a dihydropyran (Scheme 1). This flat tetracyclic ring polyketide pathway (for the anthraquinone derivative), and Scheme 1. Racemic natural products featuring N) and hydroxyviocristin (5), an anthrone and a 1,4-anthraquinone, respectively, that bear a substitution pattern

  5. Enantioselective Intramolecular Hydroarylation of Alkenes via Directed C-H Bond Activation

    SciTech Connect (OSTI)

    Harada, Hitoshi; Thalji, Reema; Bergman, Robert; Ellman, Jonathan

    2008-05-22T23:59:59.000Z

    Highly enantioselective catalytic intramolecular ortho-alkylation of aromatic imines containing alkenyl groups tethered at the meta position relative to the imine directing group has been achieved using [RhCl(coe){sub 2}]{sub 2} and chiral phosphoramidite ligands. Cyclization of substrates containing 1,1- and 1,2-disubstituted as well as trisubstituted alkenes were achieved with enantioselectivities >90% ee for each substrate class. Cyclization of substrates with Z-alkene isomers proceeded much more efficiently than substrates with E-alkene isomers. This further enabled the highly stereoselective intramolecular alkylation of certain substrates containing Z/E-alkene mixtures via a Rh-catalyzed alkene isomerization with preferential cyclization of the Z-isomer.

  6. Copper (I)-catalyzed carbon-hydogen insertion reactions of diazoesters: an asymmetric approach to the mitosene ring system

    E-Print Network [OSTI]

    Cha, Kobporn Lulu

    1997-01-01T23:59:59.000Z

    of mitosenes 16 and 17 from the cyclization of diazoester 15 followed by DDQ oxidation The HPLC chromatograms of mitosenes 24 and 25 from the cyclization of diazoester 23 followed by DDQ oxidation . . . . . . . The 200 MHz 'H NMR spectrum of pantolactone 2...-nitrophenylacetate 10 in CDCI, . The 50 MHz "C NMR spectrum of pantolactone 2-nitrophenylacetate 10 in CDCI, The IR spectrum of pantolactone 2-nitrophenylacetate 10 in CH, CI, . The 200 MHz 'H NMR spectrum of pantolactone 2-(2, 5-dihydro)pyrrolophenylacetate 12...

  7. SHORT COMMUNICATION Production of Minima Workers by Gynes of Atta colombica Guerin-Meneville

    E-Print Network [OSTI]

    Bermingham, Eldredge

    SHORT COMMUNICATION Production of Minima Workers by Gynes of Atta colombica Gue´rin-Me´ne´ville (Hymenoptera: Formicidae: Attini) that Lack a Fungal Pellet HERMO´ GENES FERNA´ NDEZ-MARI´N 1 AND WILLIAM T showed that gynes sometimes lose their fungal pellets, or the fungal garden fails before workers emerge

  8. Synthesis of 6-Methyl-9-n-propyldibenzothiophene-4-ol. Quarterly technical progress report No. 4, April 25--July 25, 1991

    SciTech Connect (OSTI)

    Eisenbraun, E.J.

    1991-07-25T23:59:59.000Z

    The material covered in this report is divided into two parts: further cyclization experiments on 1,4-diethyl-2-[(2`- methoxyphenyl)thio]benzene and its sulfone both by chemical and photochemical means, and progress toward synthesis of modified target molecule, 9-isopropyl-4-methoxy-6-methyldibenzo-thiophene. 8 refs, figs.

  9. Synthesis of 6-Methyl-9-n-propyldibenzothiophene-4-ol

    SciTech Connect (OSTI)

    Eisenbraun, E.J.

    1991-07-25T23:59:59.000Z

    The material covered in this report is divided into two parts: further cyclization experiments on 1,4-diethyl-2-[(2'- methoxyphenyl)thio]benzene and its sulfone both by chemical and photochemical means, and progress toward synthesis of modified target molecule, 9-isopropyl-4-methoxy-6-methyldibenzo-thiophene. 8 refs, figs.

  10. Methods for monitoring multiple gene expression

    SciTech Connect (OSTI)

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

    2012-05-01T23:59:59.000Z

    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.

  11. Methods for monitoring multiple gene expression

    DOE Patents [OSTI]

    Berka, Randy; Bachkirova, Elena; Rey, Michael

    2013-10-01T23:59:59.000Z

    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.

  12. Food Research Institute University of WisconsinMadison 1550 Linden Drive Madison, Wisconsin 53706

    E-Print Network [OSTI]

    Sheridan, Jennifer

    Staphylococcus aureus Fungi and Mycotoxins Fungal/Bacterial genomics Cryptosporidia, Toxoplasma Novel detection) Genomic and proteomic analyses of Clostridium botulinum endospore resistance (Johnson) Human and plant

  13. 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

  14. Scott Baker | EMSL

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

    nearly 80 peer-reviewed journal articles related to fungal biotechnology and genomics applied to production of biofuels and bioproducts. He has managed multidisciplinary...

  15. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

    E-Print Network [OSTI]

    Wohlbach, Dana J.

    2011-01-01T23:59:59.000Z

    et al. (2009) Comparative genomics of the fungal pathogensComparative genomics of xylose-fermenting fungi for enhancedapplications. BMC Genomics Wisselink HW, Toirkens MJ, Wu Q,

  16. The Ascomycete Verticillium longisporum Is a Hybrid and a Plant Pathogen with an Expanded Host Range

    E-Print Network [OSTI]

    Subbarao, Krishna V

    2011-01-01T23:59:59.000Z

    of three new Neotyphodium endophyte species from grassesal. (2007) New Neotyphodium endophyte species from the grassamongst asexual fungal endophytes of grasses. Mol Ecol 13:

  17. Trichoderma: the genomics of opportunistic success

    E-Print Network [OSTI]

    Druzhinina, Irina S.

    2011-01-01T23:59:59.000Z

    et al. The beneficial endophyte Trichoderma hamatum isolateRedman, R.S. Fungal endophytes: diversity and functionalet al. The beneficial endophyte Trichoderma hamatum isolate

  18. Feasibility of Biodegradation of Polyfluoroalkyl and Perfluoroalkyl Substances

    E-Print Network [OSTI]

    Tseng, Nancy Shiao-lynn

    2012-01-01T23:59:59.000Z

    general suite of fungal endophytes dominate the roots of twohas been shown to be an endophyte, growing on the roots ofand both fungi are endophytes [255] (Genbank Accession

  19. International Agriculture Fellowship: A Gates Foundation Grand Challenges Exploration in Endophytic Biological Control

    E-Print Network [OSTI]

    Ferrara, Katherine W.

    International Agriculture Fellowship: A Gates Foundation Grand Challenges Exploration in Endophytic Challenges Explorations Grant (see program overview) to develop crop seeds with endophytic fungal

  20. Understanding Free and Complexed Enzyme Mechanisms and Factors...

    Office of Scientific and Technical Information (OSTI)

    Understanding Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance (Presentation) Re-direct Destination: Fungal free enzymes and bacterial...

  1. apple scab resistance: Topics by E-print Network

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

    scab, caused by the ascomycete fungal pathogen Venturia inaequalis, is one of the most Biggs, Alan R. 6 Crop Conditions Apple Diseases: What To Do? Environmental Sciences and...

  2. alters suberin composition: Topics by E-print Network

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

    Branches offield-grown peach cultivars were mechanically wounded and degree Biggs, Alan R. 3 Managing plant symbiosis: fungal endophyte genotype alters plant community...

  3. E-Print Network 3.0 - aspergillus oryzae learning Sample Search...

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

    domestication on the fungal proteome Summary: , 2331-2336 9 Machida, M. et al. (2008) Genomics of Aspergillus oryzae: learning from the history of Koji... of domestication on...

  4. arbuscular mycorrhizal colonization: Topics by E-print Network

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

    significant plant carbon sink (Jakobsen and Rosendahl, 1990) and contribute to the fungal energy Rilli, Matthias C. 5 Mycorrhizae Effects of fertilizers and arbuscular mycorrhizal...

  5. arvensis obscurus hymenoptera: Topics by E-print Network

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

    J. MEHDIABADI & Ted R. SCHULTZ Abstract Ants species that obligately depend on the cultivation of fungus for food. In return, the ants nourish, protect, and disperse their fungal...

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

    DOE Patents [OSTI]

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

    1993-01-01T23:59:59.000Z

    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.

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

    DOE Patents [OSTI]

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

    1993-08-31T23:59:59.000Z

    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.

  8. Xyolide, a bioactive nonenolide from an Amazonian endophytic fungus, Xylaria feejeensis

    E-Print Network [OSTI]

    Handelsman, Jo

    Xyolide, a bioactive nonenolide from an Amazonian endophytic fungus, Xylaria feejeensis Ezra G Fungal endophyte Pythium ultimum a b s t r a c t Endophytes isolated from tropical plants represent a largely untapped reservoir of bioactive secondary metabolites. We screened a library of fungal endophyte

  9. 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]

    Arnold, A. Elizabeth

    ://www.elsevier.com/copyright #12;Author's personal copy Geographic locality and host identity shape fungal endophyte communities Cupressaceae Molecular phylogeny Species richness Symbiosis a b s t r a c t Understanding how fungal endophyte ranges of their hosts is key to understanding the ecology and evolutionary context of endophyte

  10. www.newphytologist.org 147 Blackwell Publishing LtdOxford, UKNPHNew Phytologist0028-646X The Authors (2008). Journal compilation New Phytologist (2008)235010.1111/j. 1469-8137.2008.02350.xDecember 200700147???156???Original ArticlesXX XX

    E-Print Network [OSTI]

    Bruns, Tom

    2008-01-01T23:59:59.000Z

    on the fungal endophyte community of maize (Zea mays) Jean J. Pan1,2 , Andrew M. Baumgarten3 and Georgiana May2 fungal endophyte studies has been how plants benefit from endophyte infection. Few studies have investigated the role of the host plant as an environment in shaping endophyte community diversity

  11. Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes

    E-Print Network [OSTI]

    Lutzoni, François M.

    Culture-based study of endophytes associated with rubber trees in Peru reveals a new class: Ascomycota Endophytes Fungal phylogeny Hevea Sapwood Tropical forest a b s t r a c t Through a culture foliar endophytes. Because its origin is nested within this major burst of fungal diversification, we

  12. Tall fescue (Festuca arundinacea Schreb.) is the pre-dominant forage species on over one million acres of

    E-Print Network [OSTI]

    Liskiewicz, Maciej

    Fungal Endophyte While occasional negative responses of animals con- suming tall fescue were observed an endophyte because it is found within tissue and does not affect the outward appear- ance of the grass. In the scientific community, the tall fescue fungal endophyte was formerly known as Acremonium coenophialum, but has

  13. Mycologia, 95(3), 2003, pp. 388398. 2003 by The Mycological Society of America, Lawrence, KS 66044-8897

    E-Print Network [OSTI]

    Arnold, A. Elizabeth

    66044-8897 Canopy cover and leaf age affect colonization by tropical fungal endophytes: Ecological Research Institute, Apartado 2072, Balboa, Republic of Panama Abstract: Fungal endophytes inhabit healthy of endophyte infection in leaves of tropical forest trees. However, ecological factors underlying

  14. to the Midwest Regional Center of Excellence for Biodefense and Emerging Infectious Disease Research

    E-Print Network [OSTI]

    Saleska, Scott

    ,4 Marilyn J. Roossinck1 * A mutualistic association between a fungal endophyte and a tropical panic grass­8). However, the effect of mycoviruses on mutualistic fungal endophytes is unknown. There is only one report of a mycovirus from the well- known mutualistic endophyte, Epichloë festucae, but no phenotype has been

  15. Fossil fungi from America Pennsylvanian coal balls

    E-Print Network [OSTI]

    Baxter, R. W.

    1975-05-29T23:59:59.000Z

    fungi from American Pennsylvanian coal balls is discussed under the following general headings: 1) Phycomycetes, 2) Asco- mycetes, 3) Basidiomycetes, 4) fungal sclerotia, 5) mycorrhizal fungi, and 6) "fleshy fungi." Protoascon missouriensis... fungi from American Pennsylvanian coal balls is discussed under the following general headings: 1) Phycomycetes, 2) Asco- mycetes, 3) Basidiomycetes, 4) fungal sclerotia, 5) mycorrhizal fungi, and 6) "fleshy fungi." Protoascon missouriensis...

  16. Global diversity and geography of soil fungi: minus one widespread group

    SciTech Connect (OSTI)

    Schadt, Christopher Warren [ORNL; Rosling, Anna [Uppsala University, Uppsala, Sweden

    2015-01-01T23:59:59.000Z

    IN THEIR RESEARCH ARTICLE Global diversity and geography of soil fungi Tedersoo et al. (28 November, 2014) present a compelling study regarding patterns of biodiversity of fungi, at a scale unprecedented to date for fungal biogeographical studies. The study demonstrates strong global biogeographic patterns in richness and community composition of soil fungi, what concerns us with the study is what we don t see. Unfortunately this study underestimates fungal diversity of at least one key group of soil fungi due to reliance on a single traditional primer with known flaws, and as a consequence the overall relative abundance of fungal groups may also be skewed.

  17. Photocatalyzed multiple additions of amines to {alpha}, {beta}-unsaturated esters and nitriles

    SciTech Connect (OSTI)

    Das, S.; Kumar, J.S.D.; Thomas, K.G.; Shivaramayya, K. [Regional Research Lab., Trivandrum (India); George, M.V. [Regional Research Lab., Trivandrum (India)]|[Univ. of Notre Dame, IN (United States)

    1994-02-11T23:59:59.000Z

    Photoelectron-transfer-catalyzed intermolecular carbon-carbon bond formation of primary, secondary, and tertiary amines with {alpha}, {beta}-unsaturated esters and nitriles using photosensitizers such as anthraquinone, acridone, and dicyanoanthracene has been investigated. The addition of {alpha}-aminoalkyl radicals, generated via photoelectron-transfer processes, to olefinic substrates and the subsequent 1,5-hydrogen abstraction reactions of the amine-olefin adduct radicals lead to a number of interesting multiple-olefin-added products. The adducts of the primary and secondary amines with {alpha}, {beta}-unsaturated esters undergo further cyclizations to give spiro and cyclic lactams, respectively.

  18. Thermally-generated reactive intermediates: Trapping of the parent ferrocene-based o-quinodimethane and reactions of diradicals generated by hydrogen-atom transfers

    SciTech Connect (OSTI)

    Ferguson, J.M.

    1993-09-01T23:59:59.000Z

    Ferrocenocyclobutene is prepared by flash vacuum pyrolysis (FVP) of the N-amino-2-phenylaziridine hydrazone of 2-methylferrocenealdehyde. In the second section of this dissertation, a series of hydrocarbon rearrangements were observed. FVP of o-allyltoluene at 0.1 Torr (700--900 C) gives 2-methylindan and indene, accompanied by o-propenyltoluene. FVP of 2-methyl-2`-vinylbiphenyl gives 9-methyl-9,10-dihydrophenanthrene, which fits the proposed mechanism. However, FVP of 2-(o-methylbenzyl)styrene gives mainly anthracene and 1-methylanthracene. This cyclization reaction was also successful with o-allylphenol and o-(2-methylallyl)phenol.

  19. Allylation of acetanilides with allyl acetate under conditions of metal-complex catalysis combined with phase-transfer catalysis

    SciTech Connect (OSTI)

    Lebedev, S.A.; Leonova, Yu.P.; Berestova, S.S.; Petrov, E.S.

    1988-10-20T23:59:59.000Z

    Acetanilides are alkylated at the nitrogen atom under the conditions of phase-transfer catalysis. For the case of the reaction of acetanilides with allyl acetate the authors showed that 2-alkenyl esters can be used for the alkylation of acetanilides under the conditions of phase-transfer catalysis in the presence of the complexes of zero valent palladium. N-Acetylskatole was obtained with a yield of 50% from N-allyl-2-bromoacetanilide by intramolecular cyclization in the presence of Od(OAc)/sub 2/ as catalyst.

  20. An approach to catalytic asymmetric electrocyclization

    E-Print Network [OSTI]

    Kothari, Abhishek

    2010-02-09T23:59:59.000Z

    3.4 Solid state conformation 56 3.5 Synthesis of mixed oligomers 57 3.5.1 Synthesis of mixed dimer 57 vi 3.5.2 Synthesis of mixed tetramer 58 3.6 Structural assignments & investigation of conformations 59 3.7 Cyclopropane... to trigger these cyclizations, which disfavours the use of this elegant and efficient transformation in the synthesis of complex and delicate molecules. Thus, it is important to investigate systems with a lower energy barrier to hexatriene electrocyclization...

  1. Proceedings of the Sudden Oak Death Third Science Symposium New Relationships Among the Sudden Oak

    E-Print Network [OSTI]

    Standiford, Richard B.

    extract agar and water agar. We separated and purified morphologically distinct fungal colonies. In January and July of 2006, we randomly selected and harvested three P. ramorum- inoculated trees and three

  2. Ecological analysis of secondary metabolite production in Aspergillus spp.

    E-Print Network [OSTI]

    Ramaswamy, Anitha

    2002-01-01T23:59:59.000Z

    A complex and fascinating aspect of fungal development is the production of secondary metabolites. One of the best characterized secondary metabolite pathway is the aflatoxin (AF) and sterigmatocystin (ST) pathway, found in many Aspergillus spp...

  3. african virus adapting: Topics by E-print Network

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

    African hosts. Fungal Biology 118: 168-179. www 382 Cowpox Virus in CiteSeer Summary: depression and lethargy, anorexia, and recumbency until death. A short time later, another...

  4. Seed metabolites alter the development of Aspergillus ssp.

    E-Print Network [OSTI]

    Hinze, Lori Lynn

    2013-02-22T23:59:59.000Z

    of conidiophores and sexually through the formation of cleistothecia. Both A. parasiticus and A. flavus reproduce asexually via the conidiophore. The development of these reproductive structures seems to bepartially dependent upon the fungal molecule called psi...

  5. RESEARCH ARTICLE Managing grey mould on raspberry grown under protection

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    -harvest cooling and cold storage is used to delay the onset of fungal rotting. This new strategy was evaluated . Raspberry. Grey mould . Cold storage . Zero residues 1 Introduction Raspberry fruit are very susceptible

  6. AQUATIC MICROBIAL ECOLOGY Aquat Microb Ecol

    E-Print Network [OSTI]

    Ilan, Micha

    -tumor, anti- fungal, anti-viral, and anti-bacterial properties (Wal- lace 1997). Several antibiotics have been organism. Several recent reports on antimicrobial ac- tivity of sponges and corals have examined

  7. Baker elected SIMB president-elect | EMSL

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

    at the Torrey Mesa Research InstituteSyngenta, where he was on a team that used a genomics-based approach to study fungal plant pathogens. Baker received his doctorate in Cell...

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

    E-Print Network [OSTI]

    Cheng, Johnathan Zandrew

    2011-01-01T23:59:59.000Z

    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 ...

  9. Top 10 plant pathogenic bacteria in molecular plant pathology.

    E-Print Network [OSTI]

    2012-01-01T23:59:59.000Z

    Foster, G.D. (2012) The top 10 fungal pathogens in molecularBLACKWELL PUBLISHING LTD Top 10 plant pathogenic bacteriaC. and Foster, G.D. (2011) Top 10 plant viruses in molecular

  10. Total synthesis of cyclotryptamine and diketopiperazine alkaloids

    E-Print Network [OSTI]

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

    2013-01-01T23:59:59.000Z

    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 ...

  11. Presidential address Geomycology: biogeochemical transformations

    E-Print Network [OSTI]

    Ahmad, Sajjad

    Corresponding Editor: David L. Hawksworth Keywords: Carbonates Clay minerals Environmental biotechnology Lichens of the fungal transformations discussed have beneficial applications in environmental biotechnology, e and radionuclides by fungi, bioweathering and bioremediation Geoffrey M. GADD* Division of Environmental and Applied

  12. Trichoderma: the genomics of opportunistic success

    E-Print Network [OSTI]

    Druzhinina, Irina S.

    2011-01-01T23:59:59.000Z

    of a fungal prey. BMC Genomics 10, 567 (2009). This studythe TrichoEST functional genomics approach. Curr. Genet. 51,in Hypocrea jecorina. BMC Genomics. 9, 430 (2008) Mukherjee,

  13. Genomic Encyclopedia of Fungi

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-08-10T23:59:59.000Z

    Genomes of fungi relevant to energy and environment 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 150 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.

  14. Arthropod population and community dynamics in turfgrass

    E-Print Network [OSTI]

    Wang, Yong

    1998-01-01T23:59:59.000Z

    Non-target arthropod and nematode populations in ographics. fungal and nematode treated bermudagrass were contrasted with populations in a chlorpyrifos and an untreated control treatment. Fifty-five arthropod families or suborder, herein referred...

  15. Palynology and Paleoecology of the Lake Somerville spillway section, Late Eocene Manning Formation (Jackson Group), east-central Texas

    E-Print Network [OSTI]

    Sancay, Recep Hayrettin

    2000-01-01T23:59:59.000Z

    Analysis of lignites, freshwater and marine siliciclastic sediments from the Lake Somerville spillway section (Late Eocene, Jackson Group, Manning Formation) yielded a diverse assemblage of terrestrial palynomorphs including fungal spores (84 genera...

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

    E-Print Network [OSTI]

    Johnson, Natalie Malek

    2011-10-21T23:59:59.000Z

    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...

  17. Mycopathologia 140: 5158, 1997. 1997 Kluwer Academic Publishers. Printed in the Netherlands.

    E-Print Network [OSTI]

    Hammock, Bruce D.

    of Food Science and Technology, University of California, Davis, California Received 8 September 1997 solani pisi and fungal EHs have been used in organic synthesis for enantioselective hydrolysis [14­ 17

  18. Syntrophic exchange in synthetic microbial communities Michael T. Meea,b

    E-Print Network [OSTI]

    Collins, James J.

    recently described including the bioconversion of unprocessed cellulolytic feedstocks into biofuel isobutanol using fungal­bacterial communities (4) and biofuel precursor methyl halides using yeast using engineered quorum-sensing Escherichia coli (7, 8). These advances paint an exciting future

  19. ANNUAL SYMBIOSIS WORKSHOP ---MAY 19-20TH , 2012

    E-Print Network [OSTI]

    Sachs, Joel

    :20-1:40 Sharon Lafferty Doty Nitrogen-Fixing Endophytes of Poplar and Willow:10 ­ 2:30 Carolin Frank Bacterial Endophytes of Forest Conifers: Specificity Interacting symbioses: leaf endophyte load and fungal garden development in leaf

  20. Endomelanconiopsis, a new anamorph genus in the Botryosphaeriaceae Enith I. Rojas

    E-Print Network [OSTI]

    Arnold, A. Elizabeth

    discomycete. Endomelanconiopsis endo- phytica was isolated as an endophyte from healthy leaves of Theobroma microspora was isolated from soil in Europe. Key words: Austrocenangium, Endomelanconium, endophytic fungi, Heisteria concinna, systematics, Theobroma cacao INTRODUCTION Fungal endophytes live inside plant tissues

  1. Endophyte Microbiome Diversity in Micropropagated Atriplex canescens and Atriplex torreyi var griffithsii

    E-Print Network [OSTI]

    Endophyte Microbiome Diversity in Micropropagated Atriplex canescens and Atriplex torreyi var to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could, Cooke P, Dowd S, Sun S (2011) Endophyte Microbiome Diversity in Micropropagated Atriplex canescens

  2. ANNUAL SYMBIOSIS WORKSHOP ---MAY 19-20TH , 2012

    E-Print Network [OSTI]

    Sachs, Joel

    :20-1:40 Sharon Lafferty Doty Nitrogen-Fixing Endophytes of Poplar and Willow Frank Bacterial Endophytes of Forest Conifers: Specificity and Adaptive symbioses: leaf endophyte load and fungal garden development in leaf-cutting ants · 2

  3. Parasites may help stabilize cooperative relationships

    E-Print Network [OSTI]

    Little, Ainslie E. F.; Currie, Cameron R.

    2009-06-01T23:59:59.000Z

    . 50. Tanaka A, Tapper BA, Popay A, Parker EJ, Scott B: A symbiosis expressed non-ribosomal peptide synthetase from a mutual- istic fungal endophyte of perennial ryegrass confers protec- tion to the symbiotum from insect herbivory. Mol Microbiol 2005...

  4. Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages

    E-Print Network [OSTI]

    Arnold, A. Elizabeth

    Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes Although associated with all plants, fungal endophytes (microfungi that live within healthy plant tissues, or phylogenetic relationships. We surveyed endophytic Ascomycota from healthy photosyn- thetic tissues of three

  5. ARM - Field Campaign - Observations and Modeling of the Green...

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

    as well as coarse particles such as fragments of plants and insects, pollen grains, algae, fern spores, and fungal spores in Amazonia and near Manaus; 2) develop new TEM...

  6. Cellulases and coding sequences

    DOE Patents [OSTI]

    Li, Xin-Liang (Athens, GA); Ljungdahl, Lars G. (Athens, GA); Chen, Huizhong (Lawrenceville, GA)

    2001-02-20T23:59:59.000Z

    The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

  7. Letter from the organizers Welcome to the 5th

    E-Print Network [OSTI]

    Chen, Kuang-Yu

    and seek to aid graduate career development. The goal of the symposium is to present cutting edge research: The Role of a Chromodomain in the Function of the Fungal Specific Translation Elongation Factor eEF3

  8. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes

    E-Print Network [OSTI]

    van het Hoog, Marco

    Background: The 10.9× genomic sequence of Candida albicans, the most important human fungal pathogen, was published in 2004. Assembly 19 consisted of 412 supercontigs, of which 266 were a haploid set, since this fungus is ...

  9. Major Nitrogen Loss Pathways in Upland Blueberry Soils

    E-Print Network [OSTI]

    Vano, Imre

    2009-01-01T23:59:59.000Z

    2 O production in an arable peat soil in Central KalimantanTateyama brown forest soil + peat moss (1:1), SC- Soil +the tropical and boreal peat soils have a wide fungal

  10. Investigation of microbicidal activity of surface-immobilized hydrophobic polycations

    E-Print Network [OSTI]

    Hsu, Bryan Boen

    2011-01-01T23:59:59.000Z

    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 ...

  11. Journal of Food,Agriculture & Environment, Vol.7 (2),April 2009 103 Antimicrobial activity against pathogenic microorganisms by extracts from herbal

    E-Print Network [OSTI]

    Khalil, Amjad

    Journal of Food,Agriculture & Environment, Vol.7 (2),April 2009 103 Antimicrobial activity against-fungal activity. www.world-food.netJournal of Food, Agriculture & Environment Vol.7 (2) : 103-106. 2009

  12. Effect of Virulence Factors on the Photodynamic Inactivation of Cryptococcus neoformans

    E-Print Network [OSTI]

    Prates, Renato A.

    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 ...

  13. arbuscular mycorrhizal populations: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  14. arbuscular mycorrhizal symbiosis: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  15. arbuscular mycorrhizal hyphae: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  16. arbuscular mycorrhizal status: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  17. arbuscular mycorrhizal symbiosis1woa: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  18. arbuscular mycorrhizal fungus: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  19. arbuscular mycorrhiza cultures1: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  20. arbuscular mycorrhizae improves: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  1. arachis wild species: Topics by E-print Network

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

    factors particularly diseases play a major role in limiting the yield of groundnut. The crop is known to be attacked by a number of fungal and bacterial diseases. Most of the...

  2. arbuscular mycorrhiza enhanced: Topics by E-print Network

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

    C, aggregate stability percentage, pH and electrical conductivity) were changed with the cultivation of both crop species. The AM fungal small sub-unit (SSU) rRNA genes were...

  3. Characterization of the Tri10 gene from Fusarium sporotrichioides 

    E-Print Network [OSTI]

    Tag, Andrew George

    2004-09-30T23:59:59.000Z

    The trichothecene mycotoxins are secondary metabolites produced by a variety of fungal genera including Fusarium, Myrothecium, Trichothecium, and Stachybotyris, that are toxic to humans and animals that ingest them by ...

  4. Exo-endo cellulase fusion protein

    DOE Patents [OSTI]

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

    2012-01-17T23:59:59.000Z

    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.

  5. Overproduction of ligninolytic enzymes

    SciTech Connect (OSTI)

    Elisashvili, Vladimir; Kachlishvili, Eva; Torok, Tamas

    2014-06-17T23:59:59.000Z

    Methods, compositions, and systems for overproducing ligninolytic enzymes from the basidiomycetous fungus are described herein. As described, the method can include incubating a fungal strain of Cerrena unicolor IBB 303 in a fermentation system having growth medium which includes lignocellulosic material and then cultivating the fungal strain in the fermentation system under conditions wherein the fungus expresses the ligninolytic enzymes. In some cases, the lignocellulosic material is mandarin peel, ethanol production residue, walnut pericarp, wheat bran, wheat straw, or banana peel.

  6. Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein

    SciTech Connect (OSTI)

    Dong Hongping; Zhang Bo [Wadsworth Center, New York State Department of Health, Albany, New York 12201 (United States); Shi Peiyong [Wadsworth Center, New York State Department of Health, Albany, New York 12201 (United States); Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, New York 12201 (United States)], E-mail: pei_yong.shi@novartis.com

    2008-11-10T23:59:59.000Z

    Genome cyclization is essential for flavivirus replication. We used RNases to probe the structures formed by the 5'-terminal 190 nucleotides and the 3'-terminal 111 nucleotides of the West Nile virus (WNV) genomic RNA. When analyzed individually, the two RNAs adopt stem-loop structures as predicted by the thermodynamic-folding program. However, when mixed together, the two RNAs form a duplex that is mediated through base-pairings of two sets of RNA elements (5'CS/3'CSI and 5'UAR/3'UAR). Formation of the RNA duplex facilitates a conformational change that leaves the 3'-terminal nucleotides of the genome (position - 8 to - 16) to be single-stranded. Viral NS5 binds specifically to the 5'-terminal stem-loop (SL1) of the genomic RNA. The 5'SL1 RNA structure is essential for WNV replication. The study has provided further evidence to suggest that flavivirus genome cyclization and NS5/5'SL1 RNA interaction facilitate NS5 binding to the 3' end of the genome for the initiation of viral minus-strand RNA synthesis.

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

    SciTech Connect (OSTI)

    Manna, Kuntal [Ames Laboratory

    2012-12-17T23:59:59.000Z

    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

  8. Field evaluation of the lignin-degrading fungus 'phanerochaete sordida' to treat creosote-contaminated soil

    SciTech Connect (OSTI)

    Davis, M.W.; Glaser, J.A.; Evans, J.W.; Lamar, R.T.

    1993-01-01T23:59:59.000Z

    A field study to determine the ability of selected lignin-degrading fungi to remediate soil contaminated with pentachlorophenol and creosote was performed at a wood treating facility in south central Mississippi in the Autumn of 1991. The study was designed to evaluate 7 fungal treatments and appropriate control treatments. Soil concentrations of 14 priority pollutant polycyclic aromatic hydrocarbon (PAH) components of creosote were measured over time to determine treatment efficacies. Fungal treatments involved mixing fungal inocula and aspen chips into the contaminated soil and maintaining moisture by irrigation and aeration by tillage. PAHs of more than 4 rings persisted at their original concentrations during the 8 wk course of the study for all treatments and controls.

  9. Methods for producing secreted polypeptides

    DOE Patents [OSTI]

    Maiyuran, Suchindra (Gold River, CA); Fidantsef, Ana (Davis, CA); Brody, Howard (Davis, CA)

    2008-07-01T23:59:59.000Z

    The present invention relates to methods for producing a polypeptide, comprising: (a) cultivating a fungal host cell in a medium conducive for the production of the polypeptide, wherein the fungal host cell comprises a nucleic acid construct comprising a first nucleotide sequence encoding a signal peptide operably linked to a second nucleotide sequence encoding the polypeptide, wherein the first nucleotide sequence is foreign to the second nucleotide sequence and the 3' end of the first nucleotide sequence is immediately upstream of the initiator codon of the second nucleotide sequence. The present invention also relates to the isolated signal peptide sequences and to constructs, vectors, and fungal host cells comprising the signal peptide sequences operably linked to nucleotide sequences encoding polypeptides.

  10. Emissive sensors and devices incorporating these sensors

    DOE Patents [OSTI]

    Swager, Timothy M; Zhang, Shi-Wei

    2013-02-05T23:59:59.000Z

    The present invention generally relates to luminescent and/or optically absorbing compositions and/or precursors to those compositions, including solid films incorporating these compositions/precursors, exhibiting increased luminescent lifetimes, quantum yields, enhanced stabilities and/or amplified emissions. The present invention also relates to sensors and methods for sensing analytes through luminescent and/or optically absorbing properties of these compositions and/or precursors. Examples of analytes detectable by the invention include electrophiles, alkylating agents, thionyl halides, and phosphate ester groups including phosphoryl halides, cyanides and thioates such as those found in certain chemical warfare agents. The present invention additionally relates to devices and methods for amplifying emissions, such as those produced using the above-described compositions and/or precursors, by incorporating the composition and/or precursor within a polymer having an energy migration pathway. In some cases, the compositions and/or precursors thereof include a compound capable of undergoing a cyclization reaction.

  11. The Structure of the L-myo-inositol-1-phosphate Synthase-NAD[superscript +]-2-deoxy-D-glucitol 6-(E)-Vinylhomophosphonate Complex Demands a Revision of the Enzyme Mechanism

    SciTech Connect (OSTI)

    Jin, Xiangshu; Foley, Kathleen M.; Geiger, James H. (MSU)

    2010-11-16T23:59:59.000Z

    1l-myo-inositol 1-phosphate (MIP) synthase catalyzes the conversion of D-glucose 6-phosphate to 1l-myo-inositol 1-phosphate, the first and rate-limiting step in the biosynthesis of all inositol-containing compounds. It involves an oxidation, enolization, intramolecular aldol cyclization, and reduction. Here we present the structure of MIP synthase in complex with NAD{sup +} and a high-affinity inhibitor, 2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate. This structure reveals interactions between the enzyme active site residues and the inhibitor that are significantly different from that proposed for 2-deoxy-D-glucitol 6-phosphate in the previously published structure of MIP synthase-NAD{sup +}-2-deoxy-D-glucitol 6-phosphate. There are several other conformational changes in NAD{sup +} and the enzyme active site as well. Based on the new structural data, we propose a new and completely different mechanism for MIP synthase.

  12. United abominations: Density functional studies of heavy metal chemistry

    SciTech Connect (OSTI)

    Schoendorff, George

    2012-04-02T23:59:59.000Z

    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.

  13. Large scale solubilization of coal and bioconversion to utilizable energy. Eighth quarterly technical progress report, July 1, 1995--September 30, 1995

    SciTech Connect (OSTI)

    Mishra, N.C.

    1996-02-01T23:59:59.000Z

    In order to develop a system for a large scale coal solubilization and its bioconversion to utilizable fuel, we plan to clone the genes encoding Neurospora protein that facilitate depolymerization of coal. We also plan to use desulfurizing bacteria to remove the sulfur in situ and use other microorganisms to convert biosolubilized coal into utilizable energy following an approach utilizing several microorganisms. In addition the product of coal solubilized by fungus will be characterized to determine their chemical nature and the mechanism of reaction catalyzed by fungal product during in vivo and in vitro solubilization by the fungus or purified fungal protein.

  14. Large scale solubilization of coal and bioconversion to utilizable energy. Quarterly report, October 1--December 31, 1996

    SciTech Connect (OSTI)

    Mishra, N.C.

    1996-12-22T23:59:59.000Z

    In order to develop a system for a large scale coal solubilization and its bioconversion to utilizable fuel, the author plans to clone the genes encoding Neurospora protein that facilitate depolymerization of coal. He also plans to use desulfurizing bacteria to remove the sulfur in situ and use other microorganisms to convert biosolubilized coal into utilizable energy following an approach utilizing several microorganisms. In addition the product of coal solubilized by fungus will be characterized to determine their chemical nature and the mechanism of reaction catalyzed by fungal product during in vivo and in vitro solubilization by the fungus or purified fungal protein.

  15. Large scale solubilization of coal and bioconversion to utilizable energy. Fifth quarterly technical report, January 1, 1995--March 31, 1995

    SciTech Connect (OSTI)

    Mishra, N.C.

    1995-12-01T23:59:59.000Z

    In order to develop a system for a large scale coal solubilization and its bioconversion to utilizable fuel, we plan to clone the genes encoding Neurospora protein that facilitate depolymerization of coal. We also plan to use desulfurizing bacteria to remove the sulfur in situ and use other microorganisms to convert biosolubilized coal into utilizable energy following an approach utilizing several microorganisms. In addition the product of coal solubilized by fungus will be characterized to determine their chemical nature and the mechanism of reaction catalyzed by fungal product during in vivo and in vitro solubilization by the fungus or purified fungal protein.

  16. Large scale solubilization of coal and bioconversion to utilizable energy. Seventh quarterly technical progress report, April 1, 1995--June 30, 1995

    SciTech Connect (OSTI)

    Mishra, N.C.

    1995-12-01T23:59:59.000Z

    In order to develop a system for a large scale coal solubilization and its bioconversion to utilizable fuel, we plan to clone the genes encoding Neurospora protein that facilitate depolymerization of coal. We also plan to use desulfurizing bacteria to remove the sulfur in situ and use other microorganisms to convert biosolubilized coal into utilizable energy following an approach utilizing several microorganisms. In addition the product of coal solubilized by fungus will be characterized to determine their chemical nature and the mechanism of reaction catalyzed by fungal product during in vivo and in vitro solubilization by the fungus or purified fungal protein.

  17. Effectiveness of Infection Control Barriers for Construction in Healthcare

    E-Print Network [OSTI]

    Huo, Jinyun

    2014-08-12T23:59:59.000Z

    OF FIGURES Page Figure 1. Aspergillus spore (after David Gregory and Debbie Marshall, 2012) ............... 7 Figure 2. Diagram of the ventilation system ................................................................. 17 Figure 3. Fungal growth... half of these occurred with construction activities around the hospital. Figure 1 shows the picture of the Aspergillus spores from Franzblau (2012). Figure 1. Aspergillus spore (after David Gregory and Debbie Marshall, 2012) 8 Gregory...

  18. responses to environmental changes that are significantly more abrupt than those that would occur in nature. A

    E-Print Network [OSTI]

    Kaspari, Mike

    to a different growth chamber after every five weeks, and the appropriate [CO2] was re-set. Plants were watered weeks. At harvest, soil was collected using a 10-cm diameter corer. This soil core was then used to trap colonization26 . The total length of fungal hyphae was determined after extraction from a subsample of soil

  19. C.M. Brasier -Refereed Publications Brasier, C.M. (1986). Some genetical aspects of necrotophy with special reference to

    E-Print Network [OSTI]

    1986-01-01T23:59:59.000Z

    1 C.M. Brasier - Refereed Publications General Brasier, C.M. (1986). Some genetical aspects.J. Jellis, Eds.) pp. 297-310. Blackwells, Oxford. Brasier, C.M. (1987). The dynamics of fungal speciation. In `Evolutionary biology of the fungi' (A.D.M. Rayner, C.M. Brasier and D. Moore, Eds.) pp. 231-260. Cambridge

  20. Microbial communities and greenhouse gas emissions associated with the biodegradation of specified risk material in compost

    SciTech Connect (OSTI)

    Xu, Shanwei [Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5 (Canada); Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada); Reuter, Tim [Alberta Agriculture and Rural Development, Lethbridge, Alberta, Canada T1J 4V6 (Canada); Gilroyed, Brandon H. [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada); Tymensen, Lisa [Alberta Agriculture and Rural Development, Lethbridge, Alberta, Canada T1J 4V6 (Canada); Hao, Yongxin; Hao, Xiying [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada); Belosevic, Miodrag [Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 (Canada); Leonard, Jerry J. [Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5 (Canada); McAllister, Tim A., E-mail: tim.mcallister@agr.gc.ca [Agriculture and Agri-Food Canada, Lethbridge Research Centre, P.O. Box 3000, Lethbridge, Alberta, Canada T1J 4B1 (Canada)

    2013-06-15T23:59:59.000Z

    Highlights: ? Addition of feathers altered bacterial and fungal communities in compost. ? Microbial communities degrading SRM and compost matrix were distinct. ? Addition of feathers may enrich for microbial communities that degrade SRM. ? Inclusion of feather in compost increased both CH{sub 4} and N{sub 2}O emissions from compost. ? Density of methanogens and methanotrophs were weakly associated with CH{sub 4} emissions. - Abstract: Provided that infectious prions (PrP{sup Sc}) are inactivated, composting of specified risk material (SRM) may be a viable alternative to rendering and landfilling. In this study, bacterial and fungal communities as well as greenhouse gas emissions associated with the degradation of SRM were examined in laboratory composters over two 14 day composting cycles. Chicken feathers were mixed into compost to enrich for microbial communities involved in the degradation of keratin and other recalcitrant proteins such as prions. Feathers altered the composition of bacterial and fungal communities primarily during the first cycle. The bacterial genera Saccharomonospora, Thermobifida, Thermoactinomycetaceae, Thiohalospira, Pseudomonas, Actinomadura, and Enterobacter, and the fungal genera Dothideomycetes, Cladosporium, Chaetomium, and Trichaptum were identified as candidates involved in SRM degradation. Feathers increased (P < 0.05) headspace concentrations of CH{sub 4} primarily during the early stages of the first cycle and N{sub 2}O during the second. Although inclusion of feathers in compost increases greenhouse gas emissions, it may promote the establishment of microbial communities that are more adept at degrading SRM and recalcitrant proteins such as keratin and PrP{sup Sc}.

  1. RESEARCH ARTICLES DothideomycetePlant Interactions Illuminated by Genome

    E-Print Network [OSTI]

    McDonald, Bruce

    to foliar pathogens in Western Australia and north central and northeastern North America (Solomon et al a Australian Centre for Necrotrophic Fungal Pathogens, Murdoch University, WA 6150, Australia b Department the carbon skeletons and energy for the synthesis of proteins and other components destined

  2. Novel species of Celoporthe from Eucalyptus and Syzygium trees in China and Indonesia

    E-Print Network [OSTI]

    Novel species of Celoporthe from Eucalyptus and Syzygium trees in China and Indonesia ShuaiFei Chen cumini. Three morphologically similar fungal isolates collected previously from Indonesia also were analyses showed that the Chinese isolates and those from Indonesia reside in a clade close to previously

  3. ABSTRACT: The effect of the cotton storage trisaccharide raf-finose and cottonseed storage protein (CSP) in combination on

    E-Print Network [OSTI]

    Cotty, Peter J.

    ABSTRACT: The effect of the cotton storage trisaccharide raf- finose and cottonseed storage protein of ground whole cottonseed and water-extracted cotton- seed meal to support fungal biosynthesis of aflatoxin in raffinose refer- ence media. Results with ground whole cottonseed as a sole carbon/nitrogen source

  4. Bacterial extracellular lignin peroxidase

    DOE Patents [OSTI]

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

    1993-01-01T23:59:59.000Z

    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.

  5. Trees (2007) 21:239247 DOI 10.1007/s00468-006-0116-9

    E-Print Network [OSTI]

    Minnesota, University of

    2007-01-01T23:59:59.000Z

    or excess of irradiance, and nutrient un- balance, and soil communities are in initial stages of de to drive sufficient C gain to provide energy for themselves and fungal symbionts. Keywords Betula pendula- tal flora of a city. For example, 162 plant species or nearly one-sixth of the total flora

  6. Organic Acid Production by Filamentous Fungi

    E-Print Network [OSTI]

    -being. Indeed, organic acid fermentations are often not even identified as fungal bioprocesses, having been Aspergillus niger in aerated stirred-tank-reactors can convert glucose to citric acid with greater than 80 lipolytica, and related yeast species, may be in use commercially to produce citric acid (Lopez-Garcia, 2002

  7. PUBLICATION 600-080 Fish Health and Disease

    E-Print Network [OSTI]

    Liskiewicz, Maciej

    PUBLICATION 600-080 Fish Health and Disease Striped bass (Morone saxitilis) and hybrid striped bass these fish are commonly raised in high densities under intensive aquaculture situations (e.g., cages, ponds of the viral, bacterial, fungal, and parasitic pathogens, but the fish become increasingly susceptible

  8. Human Antimicrobial Peptide LL-37 Inhibits Adhesion of Candida albicans by Interacting with Yeast Cell-Wall

    E-Print Network [OSTI]

    University (Taiwan). The funders had no role in study design, data collection and analysis, decision by LL-37 provides a new strategy to prevent C. albicans infection, and LL-37 is a useful, new tool of patients receiving antibiotic and immunosuppressive therapies, there is an increased risk of fungal

  9. A threshold area ratio of organic to conventional agriculture causes recurrent pathogen outbreaks in organic agriculture

    E-Print Network [OSTI]

    Kolokolnikov, Theodore

    A threshold area ratio of organic to conventional agriculture causes recurrent pathogen outbreaks in organic agriculture S. Adl a, , D. Iron b , T. Kolokolnikov b a Department of Biology, Dalhousie Fungal spores Organic agriculture Pathogen dispersal Conventional agriculture uses herbicides, pesticides

  10. Ann. For. Sci. 67 (2010) 802 Available online at: c INRA, EDP Sciences, 2010 www.afs-journal.org

    E-Print Network [OSTI]

    , threatened by several factors, including fungal pathogens that reduce timber quality and cause tree mortality, commercial companies and research and educational organiza- tions in the country. 1. INTRODUCTION Increasing, wealth creation, the production of export capital as well as fuel and construction timber

  11. Also inside this issue: Bioengineering Better Biomass

    E-Print Network [OSTI]

    Also inside this issue: Bioengineering Better Biomass DOE JGI/EMSL Collaborative Science Projects and degrade carbon. This is an image of the Mn(II)-oxidizing fungus Stilbella aciculosa ­ the fungal biomass Better Biomass Feedstock Science Highlights 15 Clouds up Close Improving Catalysts Pore Challenge

  12. Volume 102, pp. 209220 OctoberDecember 2007 Observations in Pluteus section Pluteus in Spain

    E-Print Network [OSTI]

    Hibbett, David S.

    in Spain: two new records for Europe A. Justo & M.L. Castro fjusto@uvigo.es or alfredo de Vigo E-36310 Vigo Spain Abstract -- Pluteus atropungens and Pluteus brunneidiscus are recorded in studies of fungal biodiversity in the Iberian Peninsula (Spain, Portugal) and Balearic Islands (Spain

  13. Paleogene Radiation of a Plant Pathogenic Mushroom Martin P. A. Coetzee1

    E-Print Network [OSTI]

    Paleogene Radiation of a Plant Pathogenic Mushroom Martin P. A. Coetzee1 *, Paulette Bloomer2 dating placed the initial radiation of the genus at 54 million years ago within the Early Paleogene role of long-distance dispersal in the radiation of fungal pathogens from the Southern Hemisphere

  14. Oregon State University Sun Grant Western Regional Center

    E-Print Network [OSTI]

    Tullos, Desiree

    and Cellulases in the Bioconversion of Lignocellulosic Feedstocks to Ethanol Christine Kelly, Oregon State to ethanol. The team will examine fungal heme peroxidases to discover new "accessory" enzymes that function of conversion of softwoods to ethanol. Progress to Date · Bioreactor runs and analyses: Dr. Kelly and her

  15. RESEARCH Open Access Agave proves to be a low recalcitrant

    E-Print Network [OSTI]

    California at Riverside, University of

    : Here, we report sugar release data from fungal enzymatic hydrolysis of non-pretreated and hydrothermally pretreated biomass that shows agave to be much less recalcitrant to deconstruction than poplar or switchgrass. In fact, non-pretreated agave has a sugar release five to eight times greater than that of poplar

  16. REGULAR ARTICLE Soil nitrogen cycling rates in low arctic shrub tundra

    E-Print Network [OSTI]

    Grogan, Paul

    of the soil microbial community in both ecosystems indicat- ed similar fungal dominance (epifluorescence landscape. Keywords 15 Nitrogen . Gross N mineralization . Arctic tundra . Litter. Soil microbial community). For example, remote sensing studies have characterized an increase in peak-season biomass across the Arctic

  17. GENERAL TECHNICAL REPORT PSW-GTR-240 Breeding for Resistance in Norway Spruce to the

    E-Print Network [OSTI]

    Standiford, Richard B.

    GENERAL TECHNICAL REPORT PSW-GTR-240 162 Breeding for Resistance in Norway Spruce to the Root Results from previous studies of resistance in Norway spruce (Picea abies (L.) Karst.) to the pathogens Heterobasidion spp. show significant genotypic variation in fungal growth and spore susceptibility among Norway

  18. Annu. Rev. Entomol. 1997. 42:179206 Copyright c 1997 by Annual Reviews Inc. All rights reserved

    E-Print Network [OSTI]

    Harrington, Thomas C.

    , Scolytus ventralis, Dendroctonus rufipennis, Dendroctonus pseudotsugae, Dendroctonus simplex, or Tomicus p University, Ames, Iowa 50011 KEY WORDS: plant-insect interactions, insect-fungal interactions, Dendroctonus with fungi: primary, secondary, and saprophytic. Primary bark beetles in the genus Dendroctonus (e.g. D

  19. Effects of supplementary feed enzymes on the laying performance and fecal moisture of a commercial incrossbred egg stock

    E-Print Network [OSTI]

    Ibarbia, Ramon Amador

    1964-01-01T23:59:59.000Z

    offeots of eater treatment of barley and fungal snmpne suyylsmsntation on Che metabolisahle . nf- %he raMonx-' ai-ref&i+ted bf Cha-:perfc~- of -gi ouing- ohkobd:: ?. The authors reported inoreassi-in the msCaboliga&e energy-as a rema& of the addition...

  20. Bridging mycorrhizal genomics, metagenomics and forest ecology

    E-Print Network [OSTI]

    Pringle, Anne

    Meetings Bridging mycorrhizal genomics, metagenomics and forest ecology 6th New Phytologist of easily cultured saprotrophic fungi (among the first three published genomes were the models Saccharomyces or biotechnological interest, genomics is now poised to rapidly permeate the fields of fungal ecology and evolution

  1. A Study of Dust Movement through Construction Barriers

    E-Print Network [OSTI]

    Zhang, Wei

    2014-12-12T23:59:59.000Z

    Airborne infection agents can and do infect patients who have a lung disease or who are coping with a weakened immune systems or in some circumstances otherwise apparently healthy people. A rise in the rate of fungal infection for a particular class...

  2. FINDINGS IN BRIEF THEME: Water, aquaculture and fish

    E-Print Network [OSTI]

    to farming protocols, local environment effects, food safety and nutritive quality of fish as food. Jana carnivorous fish can thrive and grow on alternative food sources such as mussel meal and fungal protein. Photo treatment,with bacteria that break down organic matter. *EHEC is an aggre

  3. Microbial Diversity of the Harvard Yard Soil Ecosystem Ectomycorrhizalfungiofpinoak

    E-Print Network [OSTI]

    Pringle, Anne

    As the management of the Harvard Yard steers towards more sustainable approaches, there is a growing interest of the soil microbial communities in Harvard Yard improve our ability to sustainably manage this system? We-1492r), archaeal (21f-958r) or fungal (ITS1f-ITS4) specific primers. Clone libraries of PCR amplicons

  4. Treena BURGESS1,2 *, Brenda D. WINGFIELD2

    E-Print Network [OSTI]

    sapinea is an endophyte and latent pathogen of pines, assumedly introduced to the Southern Hemisphere. radiata has acquired this fungal endophyte from other Pinus within the exotic environment. INTRODUCTION Sphaeropsis sapinea is a ubiquitous endophyte and latent pathogen of Pinus (Smith & Stanosz 1995, Smith et al

  5. www.ext.vt.edu Produced by Communications and Marketing, College of Agriculture and Life Sciences,

    E-Print Network [OSTI]

    Liskiewicz, Maciej

    , the primary forage base is endophyte- infected (E+) Kentucky 31 (KY31) tall fescue. Tall fescue sets performance and disorders caused by the presence of the fungal endophyte Neotyphodium coenophialum reduces its-infected. The endophytic fungus produces ergot alkaloids that are toxic to livestock (Ball, Hoveland, and Lacefield 2002

  6. GLOMEROMYCOTEAN ASSOCIATIONS IN LIVERWORTS: A MOLECULAR, CELLULAR, AND TAXONOMIC ANALYSIS

    E-Print Network [OSTI]

    Bruns, Tom

    End Road, London E1 4NS, UK Liverworts form endophytic associations with fungi that mirror mycorrhizal (except a few mostly derived clades), and part of the Metzgeriidae. Fungal endophytes from Haplomitrium, Conocephalum, Fossombronia, and Pellia were related to Glomus Group A, while the endophyte from Monoclea

  7. Functional Ecology 2008, 22, 706713 doi: 10.1111/j.1365-2435.2008.01395.x 2008 The Authors. Journal compilation 2008 British Ecological Society

    E-Print Network [OSTI]

    Rudgers, Jennifer

    . Journal compilation © 2008 British Ecological Society Blackwell Publishing Ltd Endophyte symbiosis investigated how a fungal endophyte symbiosis affects the growth and survival of a rare, mid-western United compared the performance of endophyte-infected and endophyte- disinfected grove bluegrass (Poa alsodes

  8. Endophytic fungi as biocontrol agents of Theobroma cacao pathogens Luis C. Mejia a,b

    E-Print Network [OSTI]

    Arnold, A. Elizabeth

    Endophytic fungi as biocontrol agents of Theobroma cacao pathogens Luis C. Meji´a a,b , Enith I; accepted 18 January 2008 Available online 31 January 2008 Abstract Fungal endophytes isolated from healthy endophytic morphospecies, 40% (21/52), 65% (28/43) and 27% percent (4/15) showed in vitro antagonism against

  9. Ecology, 00(0), 0000, pp. 000000 0000 by the Ecological Society of America

    E-Print Network [OSTI]

    Bermingham, Eldredge

    IMPLICATIONS OF ANTI-PATHOGEN EFFECTS OF TROPICAL FUNGAL ENDOPHYTES AND MYCORRHIZAE EDWARD ALLEN HERRE,1,3 LUIS Jersey 08901 USA Abstract. We discuss studies of foliar endophytic fungi (FEF) and arbuscular mycorrhizal of endophyte free (EÀ) and endophyte containing (Eþ) plant tissues in T. cacao show that foliar endophytes (FEF

  10. The Authors (2009) New Phytologist (2009) 182: 229238 229 Journal compilation New Phytologist (2009) www.newphytologist.org 229

    E-Print Network [OSTI]

    Kohn, Linda M.

    2009-01-01T23:59:59.000Z

    -8137.2008.02746.xDecember 200800229???238???Original ArticleXX XX Evidence for alteration of fungal endophyte, Canada Summary · Plant defense compounds are common stressors encountered by endophytes. Fungi readily variation in defense compound production on endophyte colonization. We compared the influence of defense

  11. Potential for endophyte symbiosis to increase resistance of the native grass Poa alsodes to invasion by the non-native

    E-Print Network [OSTI]

    Whitney, Kenneth

    Potential for endophyte symbiosis to increase resistance of the native grass Poa alsodes grass, Poa alsodes, and a fungal endophyte (Neotyphodium sp.) improved the grass's ability to compete naturally endophyte-symbiotic and experi- mentally endophyte-free P. alsodes plants with the invader

  12. Ecology, 88(1), 2007, pp. 1825 2007 by the Ecological Society of America

    E-Print Network [OSTI]

    Rudgers, Jennifer

    arundinaceum (tall fescue), hosts a fungal endophyte that is toxic to herbivores. In replicated experimental grasslands, the presence of the endophyte in tall fescue reduced tree abundance and size, altered tree spp.) was 65% higher in plots with the endophyte at the one grassland site where these data were

  13. Ecology, 93(1), 2012, pp. 38 2012 by the Ecological Society of America

    E-Print Network [OSTI]

    Aschehoug, Erik

    Reports Ecology, 93(1), 2012, pp. 3­8 Ó 2012 by the Ecological Society of America Fungal endophytes conditions. Here we tested the effects of two phylotypes of Alternaria endophytes on the growth, competitive in the absence of endophytes. However, one endophyte both increased the biomass of C. stoebe and reduced

  14. www.newphytologist.org 413 Blackwell Publishing, Ltd.

    E-Print Network [OSTI]

    Alvarez, Nadir

    endophyte Epichloë glyceriae has a positive effect on clonal growth of its host (Pan & Clay, 2002; 2003 in hosts infected by E. glyceriae may function as one mechanism by which endophytic fungi could increase, AMF and leaf- inhabiting fungal endophytes are widely distributed in some ecologically important

  15. Original article Creation of stable associations between perennial

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    and fungal endophytes Walid Naffaaa Claude Astierb Catherine Ravelb Jean-Jacques Guillaumin a Unité de - The ability of 15 isolates of endophytic fungi isolated from ten species of grasses to form compatible asso-like endophyte, could be associated with both L. perenne and F. arundinacea. Acremonium sp. from L. persicum

  16. Purdue University Name of Student: Department of Entomology

    E-Print Network [OSTI]

    Ginzel, Matthew

    was to examine how tall fescue cultivar and endophyte strain influence feeding behavior and survival of four endophyte Neotyphodium coenophialum. Neotyphodium endophytes are symbiotic fungal mutualists of many cool. There are alkaloids that are associated with endophytes that provide insect resistance. The only problem is that some

  17. INSECTSYMBIONT INTERACTIONS Endophyte-Mediated Resistance to Herbivores Depends on Herbivore

    E-Print Network [OSTI]

    Rudgers, Jennifer

    INSECTÐSYMBIONT INTERACTIONS Endophyte-Mediated Resistance to Herbivores Depends on Herbivore, herbivore identity can alter the outcome of plantÐsymbiont interactions. Symbiotic foliar fungal endophytes the production of alkaloids. Although endophytes are common in nature, relatively little is known about

  18. Copyright c Society of Systematic Biologists DOI:10.1093/sysbio/syp001

    E-Print Network [OSTI]

    Arnold, A. Elizabeth

    endophytes associated with foliage of plants). Fungal endophytes are ubiquitous among all lineages of land the evolution of endophytism and the diversification of the most species-rich phylum of Fungi (Ascomycota) lies in endophyte-like fungi that can be isolated from the interior of apparently healthy lichens

  19. Open Archive TOULOUSE Archive Ouverte (OATAO) OATAO is an open access repository that collects the work of Toulouse researchers and

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    endophyte of black spruce (Picea mariana) needles is also an aquatic hyphomycete. (2006) Molecular Ecology #12;Blackwell Publishing Ltd A fungal endophyte of black spruce (Picea mariana) needles is also spacer (ITS) sequence of this fungus and of a com- monly encountered foliar endophyte isolated from P

  20. JMB--MS 467 Cust. Ref. No. CAM 517/94 [SGML] J. Mol. Biol. (1995) 248, 402413

    E-Print Network [OSTI]

    1995-01-01T23:59:59.000Z

    dynamics (X-PLOR). The final model has an R-value of 18.1% for the 5.0 to 1.8 Å data shell and 19 bonds; 129 water molecules are included in the final model. We show structural comparisons confirming of many fungal hyphae. We previouslyTexas, Austin, TX 78712 U.S.A. reported the three

  1. Concentrations de carbonate de calcium sur les parois des hyphes mycliens

    E-Print Network [OSTI]

    Boyer, Edmond

    Concentrations de carbonate de calcium sur les parois des hyphes mycéliens Gabriel CALLOT, Daniel possibilité de formation de carbonate de calcium sur les parois des filaments mycéliens. Parallèlement à ces, minéralogenèse. SUMMARY Concentration of calcium carbonate on the walls of fungal hyphae. The structure

  2. George W. Bird, Professor Michigan State University

    E-Print Network [OSTI]

    /Rhizosphere Energy CO2 H2O Nutrients Role of nematodes et al. in nutrient transport and transformation. #12;Vertical Crop Shoot System Nutrient Inputs Bacterial Feeding Nematodes, Amoebae, Flagellates and Ciliates Fungal Ground System. . Bacteria #12; Essential Component of Organic Agriculture. Climbing Mt. Organic Phase

  3. Author's personal copy Dendrochronology of two butternut (Juglans cinerea) populations

    E-Print Network [OSTI]

    Grissino-Mayer, Henri D.

    since the last ice-age, but an exotic fungal pathogen (Sirococcus clavigignenti-juglandacearum) has been nuts, and as a mast source for wildlife (Clark, 1958; Rink, 1990; Ostry and Pijut, 2000). In the southern part of its range, butternut has comprised 1­3% of arboreal pollen since the last ice

  4. The DogWoodFall 2009 Best Management Practices for Anthracnose on Annual Bluegrass Turf

    E-Print Network [OSTI]

    Hsiang, Tom

    (causedbyColletotrichumcereale)isadestructive fungal disease of weakened turf that occurs throughout the U.S., Canada and Western Europe (15, chemical growth regulation, mowing, rolling, topdressing, verticutting and irrigation as well). Seedhead development requires considerable metabolic energy, which reallocates photosynthate away from

  5. August 2008 GCM 93 Anthracnose (caused by Colletotrichum cere-

    E-Print Network [OSTI]

    Hsiang, Tom

    fungal disease of weakened turf that occurs throughout the U.S., Canada and Western Europe (15 fertility, chemical growth regulation, mowing, rolling, topdressing, verticutting and irrigation as well). Seedhead development requires con- siderable metabolic energy, which reallocates pho- tosynthate away from

  6. Pcp1p, an Spc110p-related Calmodulin Target at the Centrosome of the Fission Yeast

    E-Print Network [OSTI]

    Davis, Trisha N.

    Pcp1p, an Spc110p-related Calmodulin Target at the Centrosome of the Fission Yeast.] Abstract In the budding yeast Saccharomyces cerevisiae, the calmodulin-binding protein Spc110p/Nuf1p facilitates mitotic spindle formation from the fungal centrosome or spindle pole body (SPB). The human Spc110p

  7. Functional diversity of soil microbial community, rock phosphate dissolution and growth of Acacia seyal as influenced by grass-,

    E-Print Network [OSTI]

    Thioulouse, Jean

    soil amended or not with rock phosphate. Results indicated a stimulation of plant growth with rock phosphate alone. Leaf content in N was also increased in the termite treatments (except was hypothesized to be related to the production of large quantities of oxalic acid by fungal populations

  8. Comparative Transcriptomics of the Saprobic and Parasitic Growth Phases in Coccidioides pp

    E-Print Network [OSTI]

    phase in the environment and as spherules in the parasitic phase in the mammalian host. In this study unrestricted use, distribution, and reproduction in any medium, provided the original author and source in many fungal pathogens to identify genes critical to growth in a host environment [1

  9. Published Ahead of Print 6 September 2013. 10.1128/AEM.01702-13.

    E-Print Network [OSTI]

    Ickert-Bond, Steffi

    sites where the effect of climate warming is under investigation. A total of 226,695 reads were at the genus level were subjected to BLAST analysis against the ARB-SILVA database, where 50% most closely effect after 1 year of warming on the fungal community struc- ture at both sites, except perhaps

  10. This article is from the October 2007 issue of

    E-Print Network [OSTI]

    where parameter values for wind and gravitation lead to expo- nentially or polynomially decreasing explicitly in terms of parameters for diffusion, wind, gravitation, and spore release height. Additional keywords: dispersal gradient, power law. The dispersal of airborne fungal spores within a field has been

  11. Regulation of plant defense responses in Arabidopsis by EDR2, a PH and START domain-containing protein

    E-Print Network [OSTI]

    Innes, Roger

    Regulation of plant defense responses in Arabidopsis by EDR2, a PH and START domain resistance (edr2) to the biotrophic powdery mildew pathogen Erysiphe cichoracearum. Inhibition of fungal growth on edr2 mutant leaves occurred at a late stage of the infection process and coincided

  12. Doctoral Thesis Defense Speaker: Christine Houry Kehyayan

    E-Print Network [OSTI]

    Doedel, Eusebius

    :00 Place: EV 1.162 ABSTRACT With the rapid development of genome sequencing technologies, complete genomes experimentally characterized enzymes from fungal genomes in the mycoCLAP database. Our study shows that the MCLAPhy, a novel approach for clustering proteins by leveraging the global context of complete genomes

  13. Fermentation technology targets the use of microorganisms and/or enzymes for the production of value added

    E-Print Network [OSTI]

    Auckland, University of

    of value added compounds that can have applications in the food, chemical, biomedical, bio-energy. Software control and real time data logging. Bacterial, yeast and fungal cultures. Parallel fermentations. PC2 containment allows for fermentation of risk group 2 and recombinant microbes. The Centre

  14. 3.1.1.2 Feed Processing and Handling DL2 Final Report

    SciTech Connect (OSTI)

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

    2006-09-30T23:59:59.000Z

    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.

  15. Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in

    E-Print Network [OSTI]

    Zhao, Huimin

    at Urbana-Champaign, Urbana, Illinois, United States of America Abstract Biofuels derived from- xylose and L-arabinose into biofuels such as ethanol through heterologous expression of the fungal D and hexose sugars for biofuels production. Experimental switching of cofactor usage in enzymes has been

  16. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

    SciTech Connect (OSTI)

    Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

    2012-05-02T23:59:59.000Z

    The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

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

    SciTech Connect (OSTI)

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

    2012-11-26T23:59:59.000Z

    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.

  18. Large scale solubilization of coal and bioconversion to utilizable energy. Technical progress report, January 1--March 31, 1996

    SciTech Connect (OSTI)

    Mishra, N.C.

    1996-05-01T23:59:59.000Z

    In order develop a system for a large scale coal solubilization and its bioconversion to utilizable fuel, the authors plan to clone the genes encoding Neurospora protein that facilitates depolymerization of coal. They also plan to use desulfurizing bacteria to remove the sulfur in situ and use other microorganisms to convert biosolubilized coal into utilizable energy following an approach utilizing several microorganisms. In addition the products of coal solubilized by fungus will be characterized to determine their chemical nature and the mechanism of reaction catalyzed by fungal product during in vivo and in vitro solubilization by the fungus or purified fungal protein. Results are presented for the cloning of genes for Neurospora CSA-protein.

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

    SciTech Connect (OSTI)

    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

    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.

  20. Methods of increasing secretion of polypeptides having biological activity

    DOE Patents [OSTI]

    Merino, Sandra

    2014-05-27T23:59:59.000Z

    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.

  1. Methods of increasing secretion of polypeptides having biological activity

    DOE Patents [OSTI]

    Merino, Sandra

    2014-10-28T23:59:59.000Z

    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.

  2. Isolated nucleic acids encoding antipathogenic polypeptides and uses thereof

    DOE Patents [OSTI]

    Altier, Daniel J.; Crane, Virginia C.; Ellanskaya, Irina; Ellanskaya, Natalia; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K.; Schepers, Eric J.; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-04-20T23:59:59.000Z

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from fungal fermentation broths. Nucleic acids that encode the antipathogenic polypeptides are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  3. Nucleic acids encoding antifungal polypeptides and uses thereof

    DOE Patents [OSTI]

    Altier, Daniel J. (Granger, IA); Ellanskaya, I. A. (Kyiv, UA); Gilliam, Jacob T. (Norwalk, IA); Hunter-Cevera, Jennie (Elliott City, MD); Presnail, James K (Avondale, PA); Schepers, Eric (Port Deposit, MD); Simmons, Carl R. (Des Moines, IA); Torok, Tamas (Richmond, CA); Yalpani, Nasser (Johnston, IA)

    2010-11-02T23:59:59.000Z

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  4. Methods of increasing secretion of polypeptides having biological activity

    DOE Patents [OSTI]

    Merino, Sandra

    2013-10-01T23:59:59.000Z

    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.

  5. THE ROLE FUNGI AND YEAST IN MONITORED NATURAL ATTENUATION

    SciTech Connect (OSTI)

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

    2010-01-26T23:59:59.000Z

    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.

  6. Genetically engineered pesticide biodegradation by Gliocladium virens

    E-Print Network [OSTI]

    Supak, Janet Marie

    1990-01-01T23:59:59.000Z

    There is an increased awareness of the potential for hazardous chemicals contaminating food, water, air, and soil. Some of Lhese pollutants are agricultural pesticides. Pesc. icides are potential hazards when they are introduced into the environment in high... that cannot naturally degrade chis environmental pollutant. Preparatory steps for fungal transformation included determining the sensitivity of Gliocladium vireos to target pesticides and de. termining the ability of the fungus to naturally degrade...

  7. Sorghum Ergot - Field Identification

    E-Print Network [OSTI]

    Krausz, Joseph P.

    1997-07-21T23:59:59.000Z

    a dirty- white, brittle crust on the panicle and leaf surfaces. Prepared by: Joseph Krausz, Thomas Isakeit, and Harold Kaufman, Department of Plant Pathology and Microbiol- ogy, The Texas A&M University System. Photos by T. Isakeit. In moist..._lower may be replaced by a hard, dense fungal mass (sclerotium) which may be capable of overwintering (Photo not available). E-463 Texas AgriLife Extension Service ? Zerle L. Carpenter, Director ? The Texas A&M University System, College Station, Texas...

  8. Effects of soil solarization on yields of celery, pepper, onion, control of soil-borne pathogens, and chemical changes in the soil

    E-Print Network [OSTI]

    Avila, Francisco Antonio

    1989-01-01T23:59:59.000Z

    of sublethal temperatures or a combination of thermal and biological control (36). In some of the same experiments, Fusarium spp. were also controlled by solarization (36, 67). Katan et al. (36) found that preheating the soil 45 to 50'C, allowing it to cool... (16) . Effective disease control is correlated with a corresponding reduction in inoculum density of pathogenic fungal propagules in solari zed soil (27, 32, 36, 71, 49, 3, 67, 22 ) . The reduction in inoculum density in solarized soil by thermal...

  9. Microorganisms having enhanced tolerance to inhibitors and stress

    DOE Patents [OSTI]

    Brown, Steven D.; Yang, Shihui

    2014-07-29T23:59:59.000Z

    The present invention provides genetically modified strains of microorganisms that display enhanced tolerance to stress and/or inhibitors such as sodium acetate and vanillin. The enhanced tolerance can be achieved by increasing the expression of a protein of the Sm-like superfamily such as a bacterial Hfq protein and a fungal Sm or Lsm protein. Further, the present invention provides methods of producing alcohol from biomass materials by using the genetically modified microorganisms of the present invention.

  10. Texas Rice, Volume IV, Number 6

    E-Print Network [OSTI]

    Texas A&M University System Agricultural Research and Extension Center Beaumont, Texas August 2004 Volume IV Number 6 Texas Rice Bacterial and Fungal Endophytes in Rice Endophytes are plant-associ- ated organisms that often form... plant/endophyte associations, may infer resistance to insects such as aphids and armyworms. The following is a layman’s review of research conducted by scientists worldwide on endophytic continued on page 4 associations that pertain to rice pro- duction...

  11. Probing the Conformational Distributions of Sub-Persistence Length DNA

    SciTech Connect (OSTI)

    Mastroianni, Alexander; Sivak, David; Geissler, Phillip; Alivisatos, Paul

    2009-06-08T23:59:59.000Z

    We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle X-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average value (as in ensemble FRET) or an extreme value (as in cyclization), and in principle provides a more robust data set for assessing the suitability of theoretical models. Our experimental results for dsDNA comprising 42-94 basepairs (bp) are consistent with a simple worm-like chain model of dsDNA elasticity, whose behavior we have determined from Monte Carlo simulations that explicitly represent nanoparticles and their alkane tethers. A persistence length of 50 nm (150 bp) gave a favorable comparison, consistent with the results of single-molecule force-extension experiments on much longer dsDNA chains, but in contrast to recent suggestions of enhanced flexibility at these length scales.

  12. Directed metalation of N,N-diethylbenzamides. Silylated benzamides for the synthesis of naturally occurring peri-methylanthraquinones and peri-methyl polycyclic aromatic hydrocarbons

    SciTech Connect (OSTI)

    Mills, R.J.; Snieckus, V. (Univ. of Waterloo, Ontario (Canada))

    1989-09-01T23:59:59.000Z

    Efficient methodologies based on directed ortho metalation, fluoride-induced carbodesilylation, and metal-halogen exchange processes (Scheme I) are reported for the synthesis of peri-methyl-substituted anthraquinone natural products 5 and polycyclic aromatic hydrocarbons 6, 7. Benzamide 8 (Scheme II) is converted in a one-pot sequence into the disilylated derivative 10, which upon metalation, condensation with 3,5-dimethoxybenzaldehyde, CsF desilylation, and TsOH cyclization leads to the key phthalide 11. Compound 11 is transformed into deoxyerythrolaccin tris(methyl ether) 5c, which has been previously converted into the natural product 5a. For the synthesis of erythrolaccin tetrakis(methyl ether) 5d, the silyl and bromo benzamides 14 and 15 (Scheme III) are condensed with 3,5-dimethoxybenzaldehyde by CsF-induced carbodesilylation and metal-halogen exchange expedients, respectively, to give the phthalide 16, which is transformed into the target anthraquinone 55d by methods identical with those used in 5c. Along similar lines, the synthesis of 11-methyl-7,12-benz(a)anthraquinone (6a, Scheme IV), 8-methyl-7,12-benz(a)anthraquinone (6b), and 10-methyl-9,14-dibenz(a,c)anthraquinone (7) is described.

  13. Synthesis of 6-Methyl-9-propyldibenzothiophene-4-ol amended to 9-isopropyl-6-methyldibenzothiophene-4-ol. Final technical report, July 25, 1991--January 25, 1993

    SciTech Connect (OSTI)

    Eisenbraun, E.J.

    1992-02-17T23:59:59.000Z

    This is a draft final technical report on Task 1 of a contract to synthesize 6-Methyl-9-propyldibenzothiophene-4-ol, as amended to 9- isopropyl-6-methyldibenzothiophene-4-ol. This report is a compilation of data presented in earlier reports. The first annual report dealt with an attempted synthesis of 4-methoxy-6-methyl-9- propyldibenzothiophene (the original target compound), the successful synthesis and delivery of 200 grams of the sulfide 1,4-diethyl-2- [(2{prime}-methoxyphenyl)-thio]benzene, and initial work on a new synthesis route for the preparation of the new target compound 9- isopropyl-6-methyldibenzothiophene-4-ol. The change to the new target compound and the new synthesis route became necessary when it was learned that the sulfide mixture could not be cyclized to the substituted dibenzothiophene mixture. The second annual report described the successful preparation of 45 g of the new target compound using the new synthesis route. Subsequently funds were provided to synthesize an additional 45 g of the new target using the same reaction scheme. This task was recently completed.

  14. The nature and fate of natural resins in the geosphere - VIII - NMR and Py-GC-MS characterization of soluble labdanoid polymers isolated from holocene class I resins.

    SciTech Connect (OSTI)

    Clifford, D. J.; Hatcher, P. G.; Botto, R. E.; Muntean, J. V.; Michaels, B.; Anderson, K. B.; Chemistry; Pennsylvania State Univ.; Amoco Oil Co.

    1997-01-01T23:59:59.000Z

    Soluble polylabdanoids isolated by sequential solvent extraction have been characterized by liquid-state {sup 13}C- and {sup 1}H NMR and {sup 13}C-{sup 1}H HMQC (heteronuclear correlation) NMR spectroscopy in addition to solid-state NMR and Py-GC-MS techniques. Two Holocene resins originating from Santander, Colombia and Mombasa, Kenya were analyzed. Soluble polymers were isolated by extraction with a 1:1 (v/v) methylene chloride-methanol mixture following sequential extractions with methylene chloride and methanol. The molecular weight of polymer extracts was shown by GPC analyses to exceed that of non-polymeric occluded terpenoids. Py-GC-MS, solid-state {sup 13}C CP/MAS and {sup 13}C cross-polarization/depolarization NMR spectroscopy results indicated that chemical compositions of soluble polymers isolated from immature resins are highly representative of the structure of corresponding insoluble polymers, i.e. polylabdatrienes. These data provide evidence for cross-linking or cyclization of side-chain olefinic carbons during or shortly after polymerization. Generally, the characterization of soluble resin polymers by liquid-state NMR spectroscopy has proven to be an excellent means for investigating the maturation mechanism of polylabdanoid resinites, and has potential for furthering the application of Class I resinites as geothermal indicators.

  15. Self-avoiding worm-like chain model for dsDNA loop formation

    E-Print Network [OSTI]

    Yaroslav Pollak; Sarah Goldberg; Roee Amit

    2014-11-06T23:59:59.000Z

    We compute for the first time the effects of excluded volume on the probability for double-stranded DNA to form a loop. We utilize a Monte-Carlo algorithm for generation of large ensembles of self- avoiding worm-like chains, which are used to compute the J-factor for varying lengthscales. In the entropic regime, we confirm the scaling-theory prediction of a power-law drop off of -1.92, which is significantly stronger than the -1.5 power-law predicted by the non-self-avoiding worm-like chain model. In the elastic regime, we find that the angle-independent end-to-end chain distribution is highly anisotropic. This anisotropy, combined with the excluded volume constraints, lead to an increase in the J-factor of the self-avoiding worm-like chain by about half an order of magnitude relative to its non-self-avoiding counterpart. This increase could partially explain the anomalous results of recent cyclization experiments, in which short dsDNA molecules were found to have an increased propensity to form a loop.

  16. Non-Markovian polymer reaction kinetics

    E-Print Network [OSTI]

    Thomas Guérin; Olivier Bénichou; Raphaël Voituriez

    2012-09-07T23:59:59.000Z

    Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in nucleic acids or polypeptides, is complicated by the structural dynamics of their chains. Although both intramolecular reactions, such as cyclization, and intermolecular reactions have been studied extensively, both experimentally and theoretically, there is to date no exact explicit analytical treatment of transport-limited polymer reaction kinetics, even in the case of the simplest (Rouse) model of monomers connected by linear springs. We introduce a new analytical approach to calculate the mean reaction time of polymer reactions that encompasses the non-Markovian dynamics of monomer motion. This requires that the conformational statistics of the polymer at the very instant of reaction be determined, which provides, as a by-product, new information on the reaction path. We show that the typical reactive conformation of the polymer is more extended than the equilibrium conformation, which leads to reaction times significantly shorter than predicted by the existing classical Markovian theory.

  17. Extreme bendability of DNA double helix due to bending asymmetry

    E-Print Network [OSTI]

    Salari, Hossein; Naderi, M S; Ejtehadi, M R

    2015-01-01T23:59:59.000Z

    Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model w...

  18. Thermolysis of surface-attached 1,3-diphenylpropane: impact of surface immobilization on thermal reaction mechanisms

    SciTech Connect (OSTI)

    Buchanan, A.C. III; Biggs, C.A.

    1988-01-01T23:59:59.000Z

    Attempts to understand the thermal chemistry of coal at the molecular level are severely complicated by its inherent properties: a diverse array of structural units (e.g., aromatic, hydroaromatic, and heterocyclic aromatic clusters connected by short aliphatic and ether links) and functional groups (e.g., phenolic hydroxyls, carboxyls, and basic nitrogens) in a cross-linked macromolecular framework with no repeating units. One simplifying experimental approach has been the study of individual model compounds that highlight structural features in coal. We are studying the thermolysis of model compounds that are immobilized by covalent attachment to an inert surface. Previous studies of surface-immobilized bibenzyl (1,2-diphenylethane) showed that immobilization can profoundly alter free-radical reaction pathways compared with the corresponding fluid phase behavior. In particular, free-radical chain pathways became dominant decay routes leading to rearrangement, cyclization, and hydrogenolysis of the bibenzyl groups. In this paper we describe preliminary results on the effects of surface immobilization on the thermolysis of 1,3-diphenylpropane, whose fluid phase behavior has been extensively investigated.

  19. Thermolysis of surface-attached 1,3-diphenylpropane: Impact of surface immobilization on thermal reaction mechanisms

    SciTech Connect (OSTI)

    Buchanan, A.C. III; Biggs, C.A.

    1987-01-01T23:59:59.000Z

    Attempts to understand the thermal chemistry of coal at the molecular level are severely complicated by its inherent properties: a diverse array of structural units (e.g., aromatic, hydroaromatic, and heterocyclic aromatic clusters connected by short aliphatic and ether links) and functional groups (e.g., phenolic hydroxyls, carboxyls, and basic nitrogens) in a cross-linked macromolecular framework with no repeating units. One simplifying experimental approach has been the study of individual model compounds that highlight structural features in coal. A complicating feature in the interpretive extrapolation of model compound behavior to coal is the possible modifications in free-radical reactivity patterns resulting from restricted translational mobility in the coal where breaking one bond in the macromolecular structure will result in radical centers that are still attached to the residual framework. We are modeling this phenomenon by studying the thermolysis of model compounds that are immobilized by covalent attachment to an inert surface. Previous studies of surface-immobilized bibenzyl (1,2-diphenylethane) showed that immobilization can profoundly alter free-radical reaction pathways compared with the corresponding fluid phase behavior. In particular, free-radical chain pathways became dominant decay routes leading to rearrangement, cyclization, and hydrogenolysis of the bibenzyl groups. In this paper we describe preliminary results on the effects of surface immobilization on the thermolysis of 1,3-diphenylpropane, whose fluid phase behavior has been extensively investigated. 9 refs., 1 fig.

  20. The Greening of a Plutonium Facility through Personnel Safety, Operational Efficiency, and Infrastructure Improvements - 12108

    SciTech Connect (OSTI)

    Dodge, Robert L.; Cournoyer, Michael E. [Los Alamos National Laboratory, P.O. Box 1163, Los Alamos, NM 87545 (United States)

    2012-07-01T23:59:59.000Z

    Chemical and metallurgical operations involving plutonium and other hazardous materials account for most activities performed at the Los Alamos National Laboratory's Plutonium Facility (TA-55). Engineered barriers provide the most effective protection from hazardous materials. These safety features serve to protect workers and provide defense in depth against the hazards associated with operations. Although not designed to specifically meet environmental requirements the safety-based design does meet or exceed the requirements of the environmental regulations enacted during and since its construction. TA-55's Waste Services Group supports this safety methodology by ensuring safe, efficient and compliant management of all radioactive and hazardous wastes generated at the TA-55. A key function of this group is the implementation of measures that lower the overall risk of radiological and hazardous material operations. Processes and procedures that reduce waste generation compared to current, prevalent processes or procedures used for the same purpose are identified. Some of these 'Best Practices' include implementation of a chemical control system, elimination of aerosol cans, reduction in hazardous waste, implementation of zero liquid discharge, and the re-cyclization of nitric acid. P2/WMin opportunities have been implemented in the areas of personnel and facility attributes, environmental compliance, energy conservation, and green focused infrastructure expansion with the overall objective of minimizing raw material and energy consumption and waste generation. This increases technical knowledge and augments operational safety. (authors)

  1. X-ray Crystallographic Studies of Substrate Binding to Aristolochene Synthase Suggest a Metal Ion Binding Sequence for Catalysis

    SciTech Connect (OSTI)

    Shishova,E.; Yu, F.; Miller, D.; Faraldos, J.; Zhao, Y.; Coates, R.; Allemann, R.; Cane, D.; Christianson, D.

    2008-01-01T23:59:59.000Z

    The universal sesquiterpene precursor, farnesyl diphosphate (FPP), is cyclized in an Mg2+-dependent reaction catalyzed by the tetrameric aristolochene synthase from Aspergillus terreus to form the bicyclic hydrocarbon aristolochene and a pyrophosphate anion (PPi) coproduct. The 2.1- Angstroms resolution crystal structure determined from crystals soaked with FPP reveals the binding of intact FPP to monomers A-C, and the binding of PPi and Mg2+B to monomer D. The 1.89- Angstroms resolution structure of the complex with 2-fluorofarnesyl diphosphate (2F-FPP) reveals 2F-FPP binding to all subunits of the tetramer, with Mg2+Baccompanying the binding of this analogue only in monomer D. All monomers adopt open activesite conformations in these complexes, but slight structural changes in monomers C and D of each complex reflect the very initial stages of a conformational transition to the closed state. Finally, the 2.4- Angstroms resolution structure of the complex with 12,13-difluorofarnesyl diphosphate (DF-FPP) reveals the binding of intact DF-FPP to monomers A-C in the open conformation and the binding of PPi, Mg2+B, and Mg2+C to monomer D in a predominantly closed conformation. Taken together, these structures provide 12 independent 'snapshots' of substrate or product complexes that suggest a possible sequence for metal ion binding and conformational changes required for catalysis.

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

    SciTech Connect (OSTI)

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

    2010-06-10T23:59:59.000Z

    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

  3. In vitro activity of sorghum non-tannin polyphenols against grain molding and weathering fungi

    E-Print Network [OSTI]

    Leungchaikul, Patcharin

    1982-01-01T23:59:59.000Z

    moniliforme (Castor 1981). Grain weather1ng 1s a colonizat1on of mature kernels by saprophytic field fungi such as Alternaria spp. The difference be- tween grain molding and weathering 1s not perfectly distinct and the fungi that cause grain molding can... also cause grain weathering. For example, C. lunata and F. moniliforme can 1nfect sorghum late in kernel development or after maturity and, therefore, cause grain weather1ng (Castor 1981) . Fungal infect1on of grain in the field and/or dur1ng...

  4. Chromosomal characterizations in a restricted population of Geomys bursarius (Rodentia: Geomyidae)

    E-Print Network [OSTI]

    Stallings, Raymond L

    1978-01-01T23:59:59.000Z

    added as a precaution against possible fungal contamination because the tissue was collected in the field. The fetal calf serum, penicillin-streptomycin and Mycostatin were obtained from Grand island. Biological Supply Co. Cells were harvested... of these regions differ [y, , !'j~gl )~~ i~i! %alii'. , f~jg, . ' p~~::. iij' jg', : (4': j&'t"ig, !jj, iffy. ; f%":, (pl~i. (p'. ;: fi, , ". . . jpQ& $ 1s? . . l ~ e b. ' 23 in cesium salt, density gradients from unique sequences and are termed. satellite...

  5. Development and evaluation of a lignite-stillage carrier system for application and study of biological control agents 

    E-Print Network [OSTI]

    Jones, Richard Worth

    1983-01-01T23:59:59.000Z

    Approved as to style and content by: (Chairman of Committee) (Member) (Member) (Head of Department) December 1983 ABSTRACT Development and Evaluation of a Lignite-Sti liege Carrier System for Application and Study of Biological Agents. (December 1983.... The carrier system consisted of lignite granules amended with thin liquid sti llage. This carrier system supported fungal propagule production as high as 2. 0 x 10g propagules/g carrier. Thin liquid sti llage supported the production of 4. 0-4. 5 mg of g...

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

    E-Print Network [OSTI]

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

    2009-07-17T23:59:59.000Z

    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.

  7. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    SciTech Connect (OSTI)

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

    2013-01-01T23:59:59.000Z

    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.

  8. Effects of grain deterioration on sorghum food quality

    E-Print Network [OSTI]

    Domanski, Cristian Estanislao

    1983-01-01T23:59:59.000Z

    and Bechtel 1978). Storage fungi common on grains grow most rapidly at about 30-32 C, and their growth rate decreases as temperature decreases. Qasem and Christensen (1960), working with samples of maize stored in the laboratory at moisture contents of 16... deteriorated grain was set at about 18%, which allowed fungal growth but not sprouting. Under field conditions, the moisture content is much higher, after a rain or dew, for example. TADI 1. 2 Effeii of Cruin Deterroraciun on tlir I'hysicai amd Chemical...

  9. Interaction between NOD2 and CARD9 involves the NOD2 NACHT and the linker region between the NOD2 CARDs and NACHT domain

    E-Print Network [OSTI]

    Parkhouse, Rhiannon; Boyle, Joseph P.; Mayle, Sophie; Sawmynaden, Kovilen; Rittinger, Katrin; Monie, Tom P.

    2014-05-21T23:59:59.000Z

    except for GB1-RIP2– CARD which used 4 h at 37 #4;C. Cultures were pelleted, frozen over- night and resuspended in standard lysis buffer (100 mM NaCl, 25 mM sodium phosphate, 20 mM imidazole, 5 mM b-mercap- toethanol, 0.1 % Triton-X100). Appropriate... -I results in activation of CARD9 and inflammasome signaling for interleukin 1 beta production. Nat. Immunol. 11, 63–69. [15] Glocker, E.-O. et al. (2009) A homozygous CARD9 mutation in a family with susceptibility to fungal infections. N. Engl. J. Med. 361...

  10. Variation in, inheritance of, and correlations between a number of growth and form traits in three sycamore populations

    E-Print Network [OSTI]

    Nebgen, Russell James

    1980-01-01T23:59:59.000Z

    comb1nation of these factors (Lee 1972). American sycamore (Platanus occidentalis L . ) has si 1 v1 cal characteri st1cs -- rapid growth, abundant seeding, relative intolerance, ease of propagat1on and plant1ng -- which makes it an excellent choice...) . In the past, it has been rel at1 vely free of pests in natural stands although several fungal d1seases (which cause top d1e-back and lethal bole cankers) appear to be ser 1ous in plantations under intensive culture. Improvement of a species through select1...

  11. Methods for recalibration of mass spectrometry data

    DOE Patents [OSTI]

    Tolmachev, Aleksey V. (Richland, WA); Smith, Richard D. (Richland, WA)

    2009-03-03T23:59:59.000Z

    Disclosed are methods for recalibrating mass spectrometry data that provide improvement in both mass accuracy and precision by adjusting for experimental variance in parameters that have a substantial impact on mass measurement accuracy. Optimal coefficients are determined using correlated pairs of mass values compiled by matching sets of measured and putative mass values that minimize overall effective mass error and mass error spread. Coefficients are subsequently used to correct mass values for peaks detected in the measured dataset, providing recalibration thereof. Sub-ppm mass measurement accuracy has been demonstrated on a complex fungal proteome after recalibration, providing improved confidence for peptide identifications.

  12. Part I. Halichondrin B: Studies on the total synthesis. Part II. Levuglandins: Generation from PGH sub 2 and binding with proteins

    SciTech Connect (OSTI)

    Jirousek, M.R.

    1989-01-01T23:59:59.000Z

    Halichondrins are a new family of extremely bioactive marine natural products present in minute quantities in a sponge, Halichondria Okadai Kadota. Halichondrin B is the most biologically active member of this family and shows remarkably effective in vivo antitumor activity. A practical synthesis would allow clinical testing of this rare molecule. The C6-C12 fragment corresponds to a heptulose which might cyclize to the required polyheterocycle in analogy with the presumed biosynthesis of halichondrin B. The key heptulose intermediate was prepared from D-ribose. A novel mixed ethyl dimethoxybenzyl acetal of formylmethylenetriphenylphosphorane stereoselectively gave a cis alkene upon reaction with the aldehyde obtained from oxidation of methyl isopropylidene D-riboside. Osmium tetraoxide-catalyzed vicinal hydroxylation of the resulting cis alkene, protection of the diol as an acetonide, and hydrolysis of the acetal under neutral conditions using DDQ delivered two diastereomers of the desired aldehyde in excellent yield. Absolute stereochemical characterization of these diastereomers was achieved by correlation with derivatives of D-allose and L-talose. An effective new method was developed for purification of the prostaglandin endoperoxide PGH{sub 2} based on centrifugal partition chromatography and a novel aprotic two phase ternary solvent system. Recent studies showed that solvent-induced decomposition of PGH{sub 2} produces levuglandins, {gamma}-ketoaldehydes with 10,11-seco prostanoic acid (levuglandin E{sub 2} LGE{sub 2}) or 9,10-seco prostanoic acid (levuglandin D{sub 2},LGD{sub 2}) structures. The abundant supply of pure PGH{sub 2} now available and a simple HPLC assay procedure developed for detection of levuglandins allowed a reexamination of the silica gel-catalyzed decomposition of PGH{sub 2}.

  13. Analytical Methodologies for Detection of Gamma-Valerolactone, Delta-Valerolactone, Acephate and Azinphos Methyl and Their Associated Metabolites in Complex Biological Matrices

    SciTech Connect (OSTI)

    Zink, E.; Clark, R.; Grant, K.; Campbell, J.; Hoppe, E.

    2005-01-01T23:59:59.000Z

    Non-invasive biomonitoring for chemicals of interest in law enforcement and similar monitoring of pesticides, together with their metabolites, can not only save money but can lead to faster medical attention for individuals exposed to these chemicals. This study describes methods developed for the analysis of gamma-valerolactone (GVL), delta-valerolactone (DVL), acephate, and azinphos methyl in saliva and serum. Liquid chromatography/mass spectrometry (LC/MS) operated in the negative and positive ion mode and gas chromatography/mass spectrometry (GC/MS) were used to analyze GVL and DVL. Although both analytical techniques worked well, lower detection limits were obtained with GC/MS. The lactones and their corresponding sodium salts were spiked into both saliva and serum. The lactones were isolated from saliva or serum using newly developed extraction techniques and then subsequently analyzed using GC/MS. The sodium salts of the lactones are nonvolatile and require derivatization prior to analysis by this method. N-methyl-N-(t-butyldimethylsilyl)-trifluoroacetamide (MTBSTFA) was ultimately selected as the reagent for derivatization because the acidic conditions required for reactions with diazomethane caused the salts to undergo intramolecular cyclization to the corresponding lactones. In vitro studies were conducted using rat liver microsomes to determine other metabolites associated with these compounds. Azinphos methyl and acephate are classified as organophosphate pesticides, and are known to be cholinesterase inhibitors in humans and insects, causing neurotoxicity. For this reason they have both exposure and environmental impact implications. These compounds were spiked into serum and saliva and prepared for analysis by GC/MS. Continuation of this research would include analysis by GC/MS under positive ion mode to determine the parent ions of the unknown metabolites. Further research is planned through an in vivo analysis of the lactones and pesticides. These methodologies could be extended for further analysis of other similar compounds.

  14. SYNTHESIS OF NOVEL CROWN ETHERS BEARING THE exo-cis-2,3-NORBORNYL GROUP AS POTENTIAL Na+ AND K+ EXTRACTANTS

    SciTech Connect (OSTI)

    Robeson, R.M.; Bonnesen, P.

    2007-01-01T23:59:59.000Z

    The synthesis of a series of novel dinorbornyl-16-crown-5 and dinorbornyl-18-crown-6 ethers that incorporate the exo-cis-2,3-norbornyl moiety within the macrocycle framework is described. The key starting material for the crown ethers, exo-cis-2,3-norbornanediol, was successfully prepared on a large (>30g) scale in 88% yield from norbornylene by osmium tetroxide-catalyzed hydroxylation. The syn and anti isomers of the dinorbornyl-16-crown-5 ether family were prepared using diethylene glycol with ring closure achieved using a methallyl linkage. The isomers cis-syn-cis and cis-anti-cis di-norbornano-15-methyleno-16-crown-5 (6A and 6B) could be separated using column chromatography, and a single crystal of the syn isomer 6A suitable for X-ray crystal structure analysis was obtained, thereby confi rming the syn orientation. The syn and anti isomers of the dinorbornyl-18-crown-6 ether family were successfully prepared employing a different synthetic strategy, involving the potassium–templated cyclization of two bis-hydroxyethoxy-substituted exo-cis-2,3-norbornyl groups under high dilution conditions. Attempts to fully separate cis-syn-cis di-norbornano-18-crown-6 (10A) and cis-anti-cis di-norbornano-18-crown-6 (10B) from one another using column chromatography were unsuccessful. All intermediates and products were checked for purity using either thin layer chromatography or gas chromatography, and characterized by proton and carbon NMR. Crown ethers 6AB and 10AB are to our knowledge the fi rst crown ethers to incorporate the exo-cis-2,3-norbornyl moiety into the crown ring to be successfully synthesized and characterized.

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

    SciTech Connect (OSTI)

    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

    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.

  16. Large scale solubilization of coal and bioconversion to utilizable energy. Third quarterly technical progress report, April 1, 1994--June 30, 1994

    SciTech Connect (OSTI)

    Mishra, N.C.

    1994-08-01T23:59:59.000Z

    In order to develop a system for a large scale coal solubilization and its bioconversion to utilizable fuel, the investigators plan to clone the genes encoding Neurospora protein that facilitate depolymerization of coal. They also plan to use desulfurizing bacteria to remove the sulfur in situ and use other microorganisms to convert biosolubilized coal into utilizable energy following an approach utilizing several microorganisms. In addition the product of coal solubilized by fungus will be characterized to determine their chemical nature and the mechanism of reaction catalyzed by fungal product during in vivo and in vitro solubilization by the fungus or purified fungal protein. Main objectives are: (1) cloning of Neurospora gene for coal depolymerization protein controlling solubilization in different host cells, utilizing Neurospora plasmid and other vector(s); (2) (a) development of a large scale electrophoretic separation of coal drived products obtained after microbial solubilization; (b) identification of the coal derived products obtained after biosolubilization by Neurospora cultures or obtained after Neurospora enzyme catalyzed reaction in in vitro by the wildtype and mutant enzymes; (3) bioconversion of coal drived products into utilizable fuel; and (4) characterization of Neurospora wildtype and mutant CSA protein(s) involved in solubilization of coal in order to assess the nature of the mechanism of solubilization and the role of Neurospora proteins in this process.

  17. Ring fission of anthracene by a eukaryota

    SciTech Connect (OSTI)

    Hammel, K.E.; Green, B.; Gai, W.Z.

    1993-01-01T23:59:59.000Z

    Ligninolytic fungi are unique among eukaryotes in their ability to degrade polycyclic aromatic hydrocarbons (PAHs), but the mechanism for this process is unknown. Although certain PAHs are oxidized in vitro by the fungal lignin peroxidases (LiPs) that catalyze ligninolysis, it has never been shown that LiPs initiate PAH degradation in vivo. To address these problems, the metabolism of anthracene (AC) and its in vitro oxidation product, 9,10-anthraquinone (AQ), was examined by chromatographic and isotope dilution techniques in Phanerochaete chrysosporium. The fungal oxidation of AC to AQ was rapid, and both AC and AQ were significantly mineralized. Both compounds were cleaved by the fungus to give the same ring-fission metabolite, phthalic acid, and phthalate production from AQ was shown to occur only under ligninolytic culture conditions. These results show that the major pathway for AC degradation in Phanerochaete proceeds AC -> AQ -> phthalate + CO2 and that it is probably mediated by LiPs and other enzymes of ligninolytic metabolism.

  18. Ring fission of anthracene by a eukaryote

    SciTech Connect (OSTI)

    Hammel, K.E.; Green, B.; Wen Zhi Gai (State Univ. of New York, Syracuse (United States))

    1991-12-01T23:59:59.000Z

    Ligninolytic fungi are unique among eukaryotes in their ability to degrade polycyclic aromatic hydrocarbons (PAHs), but the mechanism for this process is unknown. Although certain PAHs are oxidized in vitro by the fungal lignin peroxidases (LiPs) that catalyze ligninolysis, it has never been shown that LiPs initiate PAH degradation in vivo. To address these problems, the metabolism of anthracene (AC) and its in vitro oxidation product, 9,10-anthraquinone (AQ), was examined by chromatographic and isotope dilution techniques in Phanerochaete chrysosporium. The fungal oxidation of AC to AQ was rapid, and both AC and AQ were significantly mineralized. Both compounds were cleaved by the fungus to give the same ring-fission metabolite, phthalic acid, and phthalate production from AQ was shown to occur only under ligninolytic culture conditions. These results show that the major pathway for AC degradation in Phanerochaete proceeds AC {yields} AQ {yields} phthalate + CO{sub 2} and that it is probably mediated by LiPs and other enzymes of ligninolytic metabolism.

  19. 2010 GORDON RESEARCH CONFERENCE ON MITOCHONDRIA & CHLOROPLASTS, LUCCA, ITALY, JULY 11-16, 2010

    SciTech Connect (OSTI)

    Alice Barkan

    2010-07-16T23:59:59.000Z

    The 2010 GRC on Mitochondria & Chloroplasts will assemble an international group of molecular, structural and cellular biologists, biochemists and geneticists investigating a broad spectrum of fundamental problems related to the biology of these organelles in animal, plant and fungal cells. This field has witnessed an extraordinary expansion in recent years, fueled by the discovery of the role of mitochondria in human disease and ageing, and of the synergy of chloroplasts and mitochondria in energetic output, the identification of novel factors involved in organelle division, movement, signaling and acclimation to changing environmental conditions, and by the powerful tools of organelle proteomics. The 2010 GRC will highlight advances in the elucidation of molecular mechanisms of organelle biogenesis including regulation of genome structure, evolution and expression, organellar protein import, assembly and turnover of respiratory and photosynthetic complexes, bidirectional signaling between organelles and nucleus, organelle morphology and dynamics, and the integration of cellular metabolism. We will also explore progress in mechanisms of disease and ageing/ senescence in animals and plants. The organellar field has forged new fronts toward a global and comprehensive understanding of mitochondrial and chloroplast biology at the molecular level. Many of the molecules under study in model organisms are responsible for human diseases, providing significant impetus for a meeting that encourages interactions between mammalian, fungal and plant organellar biologists.

  20. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

    SciTech Connect (OSTI)

    Wohlbach, Dana J.; Kuo, Alan; Sato, Trey K.; Potts, Katlyn M.; Salamov, Asaf A.; LaButti, Kurt M.; Sun, Hui; Clum, Alicia; Pangilinan, Jasmyn L.; Lindquist, Erika A.; Lucas, Susan; Lapidus, Alla; Jin, Mingjie; Gunawan, Christa; Balan, Venkatesh; Dale, Bruce E.; Jeffries, Thomas W.; Zinkel, Robert; Barry, Kerrie W.; Grigoriev, Igor V.; Gasch, Audrey P.

    2011-02-24T23:59:59.000Z

    Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative capacity pales in comparison with glucose, limiting the economic feasibility of industrial fermentations. To better understand xylose utilization for subsequent microbial engineering, we sequenced the genomes of two xylose-fermenting, beetle-associated fungi, Spathaspora passalidarum and Candida tenuis. To identify genes involved in xylose metabolism, we applied a comparative genomic approach across 14 Ascomycete genomes, mapping phenotypes and genotypes onto the fungal phylogeny, and measured genomic expression across five Hemiascomycete species with different xylose-consumption phenotypes. This approach implicated many genes and processes involved in xylose assimilation. Several of these genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrating the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology.

  1. Defining the Effectiveness of UV Lamps Installed in Circulating Air Ductwork

    SciTech Connect (OSTI)

    Douglas VanOsdell; Karin Foarde

    2002-11-30T23:59:59.000Z

    Germicidal ultraviolet (UVGI) lamps have a long history of use for inactivating microbial aerosols. Most reports have focused on the control of infectious diseases, such as tuberculosis (TB), in the occupied spaces of medical facilities. Ventilation duct use of UVGI has been increasing. In-duct applications are generally more concerned with controlling environmental organisms than with controlling infections agents. This document reports the results of a project to investigate the ability of UVGI lamps to inactivate representative environmental microbial aerosols in ventilation ducts. During this research, UVGI lamps were experimentally demonstrated to inactivate bioaerosols composed of vegetative bacteria, bacteria spores, or fungal spores to a reproducible degree under conditions of fixed dose. Vegetative bacteria were most susceptible to UVGI, with bacteria and fungal spores being substantially more resistant. The performance equation commonly cited in the literature for UVGI inactivation was found to generally apply, provided its parameters were known. Revision of final report DOE/OR22674/610-40030-01. Revised table 5 on page 33.

  2. 2012 MITOCHONDRIA AND CHLOROPLASTS GORDON RESEARCH CONFERENCE & GORDON RESEARCH SEMINAR, JULY 29 - AUGUST 3, 2012

    SciTech Connect (OSTI)

    Barkan, Alice

    2012-08-03T23:59:59.000Z

    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.

  3. Understanding Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance (Presentation)

    SciTech Connect (OSTI)

    Resch, M.; Donohoe, B.; Katahira, R.; Ashutosh, M.; Beckham, G.; Himmel, M.; Decker, S.

    2014-04-01T23:59:59.000Z

    Fungal free enzymes and bacterial complexed cellulosomes deconstruct biomass using different physical mechanisms. Free enzymes, which typically contain a large proportion of GH7 cellobiohydrolase, diffuse throughout the substrate and hydrolyze primarily from the cellulose reducing end, resulting in 'sharpened' macrofibrils. In contrast, complexed cellulosomes contain a diverse array of carbohydrate binding modules and multiple catalytic specificities leading to delamination and physical peeling of the cellulose macrofibril structures. To investigate how cellulose structure contributes to recalcitrance, we compared the deconstruction of cellulose I, II, and III; using free and complexed enzyme systems. We also evaluated both systems on Clean Fractionation and alkaline pretreated biomass, which remove much of the lignin, to determine the impact on enzyme loading reduction. Free fungal enzymes demonstrated a swelling of the outer surface of the plant cell walls while removing localized disruptions, resulting in a smooth surface appearance. Cellulosomes produced cell wall surfaces with localized areas of disruption and little surface layer swelling. These studies contribute to the overall understanding of biomass recalcitrance and how combining different enzymatic paradigms may lead to the formulation of new enzyme cocktails to reduce the cost of producing sugars from plant cell wall carbohydrates.

  4. Novel Aryne Chemistry in Organic Synthesis

    SciTech Connect (OSTI)

    Zhijian Liu

    2006-12-12T23:59:59.000Z

    Arynes are among the most intensively studied systems in chemistry. However, many aspects of the chemistry of these reactive intermediates are not well understood yet and their use as reagents in synthetic organic chemistry has been somewhat limited, due to the harsh conditions needed to generate arynes and the often uncontrolled reactivity exhibited by these species. Recently, o-silylaryl triflates, which can generate the corresponding arynes under very mild reaction conditions, have been found very useful in organic synthesis. This thesis describes several novel and useful methodologies by employing arynes, which generate from o-silylaryl triflates, in organic synthesis. An efficient, reliable method for the N-arylation of amines, sulfonamides and carbamates, and the O-arylation of phenols and carboxylic acids is described in Chapter 1. Amines, sulfonamides, phenols, and carboxylic acids are good nucleophiles, which can react with arynes generated from a-silylaryl triflates to afford the corresponding N- and O-arylated products in very high yields. The regioselectivity of unsymmetrical arynes has also been studied. A lot of useful, functional groups can tolerate our reaction conditions. Carbazoles and dibenzofurans are important heteroaromatic compounds, which have a variety of biological activities. A variety of substituted carbazoles and dibenzofwans are readily prepared in good to excellent yields starting with the corresponding o-iodoanilines or o-iodophenols and o-silylaryl triflates by a treatment with CsF, followed by a Pd-catalyzed cyclization, which overall provides a one-pot, two-step process. By using this methodology, the carbazole alkaloid mukonine has been concisely synthesized in a very good yield. Insertion of an aryne into a {sigma}-bond between a nucleophile and an electrophile (Nu-E) should potentially be a very beneficial process from the standpoint of organic synthesis. A variety of substituted ketones and sulfoxides have been synthesized in good yields via the intermolecular C-N {sigma}-bond addition of amides and S-N {sigma}-bond addition of sulfinamides to arynes under mild reaction conditions. The indazole moiety is a frequently found subunit in drug substances with important biological activities. Indazole analogues have been readily synthesized under mild reaction conditions by the [3+2] cycloaddition of a variety of diazo compounds with o-silylaryl triflates in the presence of CsF or TBAF. Polycyclic aromatic and heteroaromatic hydrocarbons have been synthesized in high yields by two different processes involving the Pd-catalyzed annulation of arynes. Both processes appear to involve the catalytic, stepwise coupling of two very reactive substrates, an aryne and an organopalladium species, to generate excellent yields of cross-coupled products.

  5. Process for producing ethanol

    SciTech Connect (OSTI)

    Lantero, O.J.; Fish, J.J.

    1993-07-27T23:59:59.000Z

    A process is described for producing ethanol from raw materials containing a high dry solid mash level having fermentable sugars or constituents which can be converted into sugars, comprising the steps of: (a) liquefaction of the raw materials in the presence of an alpha amylase to obtain liquefied mash; (b) saccharification of the liquefied mash in the presence of a glucoamylase to obtain hydrolysed starch and sugars; (c) fermentation of the hydrolysed starch and sugars by yeast to obtain ethanol; and (d) recovering the obtained ethanol, wherein an acid fungal protease is introduced to the liquefied mash during the saccharification and/or to the hydrolysed starch and sugars during the fermentation, thereby increasing the rate of production of ethanol as compared to a substantially similar process conducted without the introduction of the protease.

  6. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J. (Waukee, IA); Dahlbacka, Glen (Oakland, CA); Ellanskaya, legal representative, Natalia (Kyiv, IL); Herrmann, Rafael (Wilmington, DE); Hunter-Cevera, Jennie (Elliott City, MD); McCutchen, Billy F. (Clive, IA); Presnail, James K. (Avondale, PA); Rice, Janet A. (Wilmington, DE); Schepers, Eric (Port Deposit, MD); Simmons, Carl R. (Des Moines, IA); Torok, Tamas (Richmond, CA); Yalpani, Nasser (Johnston, IA); Ellanskaya, deceased, Irina (Kyiv, IL)

    2007-12-11T23:59:59.000Z

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  7. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J. (Waukee, IA); Dahlbacka, Glen (Oakland, CA); Elleskaya, Irina (Kyiv, UA); Ellanskaya, legal representative; Natalia (Kyiv, UA); Herrmann, Rafael (Wilmington, DE); Hunter-Cevera, Jennie (Elliott City, MD); McCutchen, Billy F. (College Station, IA); Presnail, James K. (Avondale, PA); Rice, Janet A. (Wilmington, DE); Schepers, Eric (Port Deposit, MD); Simmons, Carl R. (Des Moines, IA); Torok, Tamas (Richmond, CA); Yalpani, Nasser (Johnston, IA)

    2010-08-10T23:59:59.000Z

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  8. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J. (Waukee, IA); Dahlbacka, Glen (Oakland, CA); Elleskaya, Irina (Kyiv, UA); Ellanskaya, legal representative, Natalia (Kyiv, UA); Herrmann, Rafael (Wilmington, DE); Hunter-Cevera, Jennie (Elliott City, MD); McCutchen, Billy F. (College Station, IA); Presnail, James K. (Avondale, PA); Rice, Janet A. (Wilmington, DE); Schepers, Eric (Port Deposit, MD); Simmons, Carl R. (Des Moines, IA); Torok, Tamas (Richmond, CA); Yalpani, Nasser (Johnston, IA)

    2011-04-12T23:59:59.000Z

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  9. Antifungal polypeptides

    DOE Patents [OSTI]

    Altier, Daniel J. (Granger, IA); Dahlbacka, Glen (Oakland, CA); Ellanskaya, Irina (Kyiv, UA); Ellanskaya, legal representative, Natalia (Kyiv, UA); Herrmann, Rafael (Wilmington, DE); Hunter-Cevera, Jennie (Elliott City, MD); McCutchen, Billy F. (College Station, TX); Presnail, James K. (Avondale, PA); Rice, Janet A. (Wilmington, DE); Schepers, Eric (Port Deposit, MD); Simmons, Carl R. (Des Moines, IA); Torok, Tamas (Richmond, CA); Yalpani, Nasser (Johnston, IA)

    2012-04-03T23:59:59.000Z

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  10. Titration-based screening for evaluation of natural product extracts: identification of an aspulvinone family of luciferase inhibitors

    SciTech Connect (OSTI)

    Cruz, P.G.; Auld, D.S.; Schultz, P.J.; Lovell, S.; Battaile, K.P.; MacArthur, R.; Shen, M.; Tamayo-Castillo, G.; Inglese, J.; Sherman, D.H. (Michigan); (NIH); (Kansas); (Costa Rica); (HWMRI)

    2011-11-28T23:59:59.000Z

    The chemical diversity of nature has tremendous potential for the discovery of molecular probes and medicinal agents. However, sensitivity of HTS assays to interfering components of crude extracts derived from plants, and macro- and microorganisms has curtailed their use in lead discovery. Here, we describe a process for leveraging the concentration-response curves obtained from quantitative HTS to improve the initial selection of actives from a library of partially fractionated natural product extracts derived from marine actinomycetes and fungi. By using pharmacological activity, the first-pass CRC paradigm improves the probability that labor-intensive subsequent steps of reculturing, extraction, and bioassay-guided isolation of active component(s) target the most promising strains and growth conditions. We illustrate how this process identified a family of fungal metabolites as potent inhibitors of firefly luciferase, subsequently resolved in molecular detail by X-ray crystallography.

  11. The plant cell wall decomposing machinery underlies the functional diversity of forest fungi

    SciTech Connect (OSTI)

    Eastwood, Daniel C.; Floudas, Dimitrios; Binder, Manfred; Majcherczyk, Andrzej; Schneider, Patrick; Aerts, Andrea; Asiegbu, Fred O.; Baker, Scott E.; Barry, Kerrie; Bendiksby, Mika; Blumentritt, Melanie; Coutinho, Pedro M.; Cullen, Dan; Vries, Ronald P. de; Gathman, Allen; Goodell, Barry; Henrissat, Bernard; Ihrmark, Katarina; Kauserud, Hä; vard; Kohler, Annegret; LaButti, Kurt; Lapidus, Alla; Lavin, José; L.; Lee, Yong-Hwan; Lindquist, Erika; Lilly, Walt; Lucas, Susan; Morin, Emmanuelle; Murat, Claude; Oguiza, José; A.; Park, Jongsun; Pisabarro, Antonio G.; Riley, Robert; Rosling, Anna; Salamov, Asaf; Schmidt, Olaf; Schmutz, Jeremy; Skrede, Inger; Stenlid, Jan; Wiebenga, Ad; Xie, Xinfeng; Kü; es, Ursula; Hibbett, David S.; Hoffmeister, Dirk; Hö; gberg, Nils; Martin, Francis; Grigoriev, Igor V.; Watkinson, Sarah C.

    2011-05-01T23:59:59.000Z

    Brown rot decay removes cellulose and hemicellulose from wood?residual lignin contributing up to 30percent of forest soil carbon?and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the ?dry rot? fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota

  12. Development of a commercial enzymes system for lignocellulosic biomass saccharification

    SciTech Connect (OSTI)

    Kumar, Manoj

    2012-12-20T23:59:59.000Z

    DSM Innovation Inc., in its four year effort was able to evaluate and develop its in-house DSM fungal cellulolytic enzymes system to reach enzyme efficiency mandates set by DoE Biomass program MYPP goals. DSM enzyme cocktail is uniquely active at high temperature and acidic pH, offering many benefits and product differentiation in 2G bioethanol production. Under this project, strain and process development, ratio optimization of enzymes, protein and genetic engineering has led to multitudes of improvement in productivity and efficiency making development of a commercial enzyme system for lignocellulosic biomass saccharification viable. DSM is continuing further improvement by additional biodiversity screening, protein engineering and overexpression of enzymes to continue to further lower the cost of enzymes for saccharification of biomass.

  13. The importance of integration and scale in the arbuscular mycorrhizal symbiosis.

    SciTech Connect (OSTI)

    Miller, R. M.; Kling, M.; Environmental Research; Swedish Univ. of Agricultural Sciences

    2000-01-01T23:59:59.000Z

    The arbuscular mycorrhizal (AM) fungus contributes to system processes and functions at various hierarchical organizational levels, through their establishment of linkages and feedbacks between whole-plants and nutrient cycles. Even though these fungal mediated feedbacks and linkages involve lower-organizational level processes (e.g. photo-assimilate partitioning, interfacial assimilate uptake and transport mechanisms, intraradical versus extraradical fungal growth), they influence higher-organizational scales that affect community and ecosystem behavior (e.g. whole-plant photosynthesis, biodiversity, nutrient and carbon cycling, soil structure). Hence, incorporating AM fungi into research directed at understanding many of the diverse environmental issues confronting society will require knowledge of how these fungi respond to or initiate changes in vegetation dynamics, soil fertility or both. Within the last few years, the rapid advancement in the development of analytical tools has increased the resolution by which we are able to quantify the mycorrhizal symbiosis. It is important that these tools are applied within a conceptual framework that is temporally and spatially relevant to fungus and host. Unfortunately, many of the studies being conducted on the mycorrhizal symbiosis at lower organizational scales are concerned with questions directed solely at understanding fungus or host without awareness of what the plant physiologist or ecologist needs for integrating the mycorrhizal association into larger organizational scales or process levels. We show by using the flow of C from plant-to-fungus-to-soil, that through thoughtful integration, we have the ability to bridge different organizational scales. Thus, an essential need of mycorrhizal research is not only to better integrate the various disciplines of mycorrhizal research, but also to identify those relevant links and scales needing further investigation for understanding the larger-organizational level responses.

  14. Enhanced bioremediation process: A case study of effectiveness on PAH contamination in soils at a former wood-treating site

    SciTech Connect (OSTI)

    Mills, W.F. [Miltech Environmental, Inc., Tucker, GA (United States); Matens, B.L. [Dames and Moore, Baton Rouge, LA (United States); Buchalter, D.S. [EMCON, Norcross, GA (United States); Montgomery, D.N. [Georgia Dept. of Transportation, Forest Park, GA (United States). Office of Materials and Research

    1997-12-31T23:59:59.000Z

    The Enhanced Bioremediation Process (EBP) technology is an exsitu biodegradation process that utilizes bacterial and fungal inoculants to effectively oxidize and bioremediate persistent hard to degrade organics in contaminated soils. The EBP fungal inoculants produce highly reactive extracellular peroxidase enzymes that can oxidize and degrade lignin, a complex, natural polymer composed of phenylpropane units that is resistant to decay. The lignin peroxidase enzymes are highly nonspecific because of their ability to oxidize the heterogenic lignin molecule, and are capable of degrading a wide variety of complex organic compounds. Because the chemical sub-structure of lignin (1,2-aryl diethers, alkyl sidechains and connected aryl systems) resembles that of many persistent organic compounds, the EBP inoculants are very effective in biodegrading similar hazardous organic pollutants in contaminated soils. As an inadvertent by-product of these biochemical processes, the EBP organisms reduce the organic constituents to a soluble form. In a soluble form, the indigenous organisms can further degrade the contaminants. The technology is applied in such a manner as to maximize the activity of the indigenous organisms by establishing optimum growth conditions. The efficacy of the EBP technology in degrading persistent environmental pollutants has been documented at both the bench scale and pilot demonstration levels. A recently completed field pilot demonstration was conducted at a creosote contaminated site. The demonstration entailed the treatment of approximately 700 tons of soil contaminated with PAH constituents. Laboratory analyses of pre and post-treated soils indicate that total average PAH concentrations in many samples were reduced by greater than 91 percent over a two month treatment period.

  15. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17T23:59:59.000Z

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  16. Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe

    SciTech Connect (OSTI)

    Bulfer, Stacie L.; Hendershot, Jenna M.; Trievel, Raymond C. (Michigan); (UCSF)

    2013-09-18T23:59:59.000Z

    Lysine biosynthesis in fungi, euglena, and certain archaebacteria occurs through the {alpha}-aminoadipate pathway. Enzymes in the first steps of this pathway have been proposed as potential targets for the development of antifungal therapies, as they are absent in animals but are conserved in several pathogenic fungi species, including Candida, Cryptococcus, and Aspergillus. One potential antifungal target in the {alpha}-aminoadipate pathway is the third enzyme in the pathway, homoisocitrate dehydrogenase (HICDH), which catalyzes the divalent metal-dependent conversion of homoisocitrate to 2-oxoadipate (2-OA) using nicotinamide adenine dinucleotide (NAD{sup +}) as a cofactor. HICDH belogns to a family of {beta}-hydroxyacid oxidative decarboxylases that includes malate dehydrogenase, tartrate dehydrogenase, 6-phosphogluconate dehydrogenase, isocitrate dehydrogenase (ICDH), and 3-isopropylmalte dehydrogenase (IPMDH). ICDH and IPMDH are well-characterized enzymes that catalyze the decarboxylation of isocitrate to yield 2-oxoglutarate (2-OG) in the citric acid cycle and the conversion of 3-isopropylmalate to 2-oxoisovalerate in the leucine biosynthetic pathway, respectively. Recent structural and biochemical studies of HICDH reveal that this enzyme shares sequence, structural, and mechanistic homology with ICDH and IPMDH. To date, the only published structures of HICDH are from the archaebacteria Thermus thermophilus (TtHICDH). Fungal HICDHs diverge from TtHICDH in several aspects, including their thermal stability, oligomerization state, and substrate specificity, thus warranting further characterization. To gain insights into these differences, they determined crystal structures of a fungal Schizosaccharomyces pombe HICDH (SpHICDH) as an apoenzyme and as a binary complex with additive tripeptide glycyl-glycyl-glycine (GGG) to 1.55 {angstrom} and 1.85 {angstrom} resolution, respectively. Finally, a comparison of the SpHICDH and TtHICDH structures reveal differences in their active sites that help explain the variations in their respective substrate specificities.

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

    SciTech Connect (OSTI)

    SLACK, JEFFREY, M.

    2012-12-06T23:59:59.000Z

    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.

  18. Old-field Community, Climate and Atmospheric Manipulation

    SciTech Connect (OSTI)

    Aimee Classen

    2009-11-01T23:59:59.000Z

    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.

  19. Degradation of 4,4{prime}-Dichlorobiphenyl, 3,3{prime}, 4,4{prime}-Tetrachlorobiphenyl, and 2,2{prime},4,4{prime},5,5{prime}-Hexachlorobiphenyl by the white rot fungus Phanerochaete chrysosporium

    SciTech Connect (OSTI)

    Dietrich, D.; Lamar, R. [Dept. of Agriculture, Madison, WI (United States); Hickey, W.J. [Univ. of Wisconsin, Madison, WI (United States)

    1995-11-01T23:59:59.000Z

    The white rot fungus Phanerochaete chrysosporium has demonstrated abilities to degrade many xenobiotic chemicals. In this study, the degradation of three model polychlorinated biphenyl (PCB) congeners (4,4{prime}- dichlorobiphenyl [DCB], 3,3{prime},4,4{prime}-tetrachlorobiphenyl, and 2,2{prime},4,4{prime},5,5{prime}-hexachlorobiphenyl) by P. chrysosporium in liquid culture was examined. After 28 days of incubation, {sup 14}C partitioning analysis indicated extensive degradation of DCB, including 11% mineralization. In contrast, there was negligible mineralization of the tetrachloro- or hexachlorobiphenyl and little evidence for any significant metabolism. With all of the model PCBs, a large fraction of the {sup 14}C was determined to be biomass bound. Results from a time course study done with 4,4{prime}-[{sup 14}C]DCB to examine {sup 14}C partitioning dynamics indicated that the biomass-bound {sup 14}C was likely attributable to nonspecific adsorption of the PCBs to the fungal hyphae. In a subsequent isotope trapping experiment, 4-chlorobenzoic acid and 4-chlorobenzyl alcohol were identified as metabolites produced from 4,4{prime}-[{sup 14}C]DCB. To the best of our knowledge, this the first report describing intermediates formed by P. chrysosporium during PCB degradation. Results from these experiments suggested similarities between P. chrysosporium and bacterial systems in terms of effects of congener chlorination degree and pattern on PCB metabolism and intermediates characteristic of the PCB degradation process. 23 refs., 4 figs., 2 tabs.

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

    SciTech Connect (OSTI)

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

    2011-05-01T23:59:59.000Z

    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.

  1. Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen suppressive soil

    SciTech Connect (OSTI)

    Hjort, K.; Bergstrom, M.; Adesina, M.F.; Jansson, J.K.; Smalla, K.; Sjoling, S.

    2009-09-01T23:59:59.000Z

    Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal-restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal-restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF{sup 103} of the isolate, Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.

  2. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

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

    2012-03-03T23:59:59.000Z

    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.

  3. Physiological, toxicological, and population responses of smallmouth bass to acidification

    SciTech Connect (OSTI)

    Marcus, M.D.; Gulley, D.D. (eds.); Christensen, S.W.; McDonald, D.G.; Van Winkle, W.; Mount, D.R.; Wood, C.M.; Bergman, H.L. (Wyoming Univ., Laramie, WY (United States). Dept. of Zoology and Physiology)

    1992-08-01T23:59:59.000Z

    The Lake Acidification and Fisheries (LAF) project examined effects of acidic water chemistries on four fish species. This report presents an overview of investigations on smallmouth bass (Micropterus dolomieui). Experiments conducted with this species included as many as 84 exposure combinations of acid, aluminum, and low calcium. In egg, fry, and juvenile stages of smallmouth bass, increased acid and aluminum concentrations increased mortality and decreased growth, while increased calcium concentrations often improved survival. Relative to the juvenile life stages of smallmouth bass tested, yolksac and swim-up fry were clearly more sensitive to stressful exposure conditions. While eggs appeared to be the most sensitive life stage, this conclusion was compromised by heavy mortalities of eggs due to fungal infestations during experimental exposures. As found in our earlier studies with brook and rainbow trout, acid-aluminum stressed smallmouth bass exhibited net losses of electrolytes across gills and increased accumulation of aluminum on gill tissues. Overall, our results indicated that smallmouth bass were generally more sensitive to increased exposure concentrations of aluminum than to increased acidities. Compared to toxicology results from earlier LAF project studies, smallmouth bass were more sensitive than brook trout and slightly less sensitive than rainbow trout when exposed to water quality conditions associated with acidification.An example application of the LAF modeling framework shows how different liming scenarios can improve survival probabilities for smallmouth bass in a set of lakes sensitive to acidification.

  4. Interspecific Comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    SciTech Connect (OSTI)

    Millenbaugh, Bonnie A; Pangilinan, Jasmyn L.; Torriani, Stefano F.F.; Goodwin, Stephen B.; Kema, Gert H.J.; McDonald, Bruce A.

    2007-12-07T23:59:59.000Z

    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has shown discordant patterns of nuclear and mitochondrial diversity. The mitochondrial genome of M. graminicola is a circular molecule of approximately 43,960 bp containing the typical genes coding for 14 proteins related to oxidative phosphorylation, one RNA polymerase, two rRNA genes and a set of 27 tRNAs. The mitochondrial DNA of M. graminicola lacks the gene encoding the putative ribosomal protein (rps5-like), commonly found in fungal mitochondrial genomes. Most of the tRNA genes were clustered with a gene order conserved with many other ascomycetes. A sample of thirty-five additional strains representing the known global mt diversity was partially sequenced to measure overall mitochondrial variability within the species. Little variation was found, confirming previous RFLP-based findings of low mitochondrial diversity. The mitochondrial sequence of M. graminicola is the first reported from the family Mycosphaerellaceae or the order Capnodiales. The sequence also provides a tool to better understand the development of fungicide resistance and the conflicting pattern of high nuclear and low mitochondrial diversity in global populations of this fungus.

  5. Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

    SciTech Connect (OSTI)

    Aylward, Frank O.; Burnum-Johnson, Kristin E.; Tringe, Susannah G.; Teiling, Clotilde; Tremmel, Daniel; Moeller, Joseph; Scott, Jarrod J.; Barry, Kerrie W.; Piehowski, Paul D.; Nicora, Carrie D.; Malfatti, Stephanie; Monroe, Matthew E.; Purvine, Samuel O.; Goodwin, Lynne A.; Smith, Richard D.; Weinstock, George; Gerardo, Nicole; Suen, Garret; Lipton, Mary S.; Currie, Cameron R.

    2013-06-12T23:59:59.000Z

    Plants represent a large reservoir of organic carbon comprised largely of recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access to nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants are a paradigmatic example. These ants use fresh foliar biomass as manure to cultivate fungus gardens composed primarily of Leucoagaricus gongylophorus, a basidiomycetous symbiont that produces specialized hyphal swellings that serve as a food source for the host ant colony. Although leaf-cutter ants are conspicuous herbivores that contribute substantially to carbon turnover in Neotropical ecosystems, the process through which plant biomass is degraded in their fungus gardens is not well understood. Here we present the first draft genome of L. gongylophorus, and using genomic, metaproteomic, and phylogenetic tools we investigate its role in lignocellulose degradation in the fungus gardens of both Atta cephalotes and Acromyrmex echinatior leaf-cutter ants. We show that L. gongylophorus produces a diversity of lignocellulases in fungus gardens, and is likely the primary driver of plant biomass degradation in these ecosystems. We also show that this fungus produces distinct sets of lignocellulases throughout the different stages of biomass degradation, including numerous cellulases and laccases that may be playing an important but previously uncharacterized role in lignocellulose degradation. Our study provides a comprehensive analysis of plant biomass degradation in leaf-cutter ant fungus gardens and provides insight into the molecular dynamics underlying the symbiosis between these dominant herbivores and their obligate fungal cultivar.

  6. Improvements In Ethanologenic Escherichia Coli and Klebsiella Oxytoca

    SciTech Connect (OSTI)

    Dr. David Nunn

    2010-09-30T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Not Available

    1993-07-01T23:59:59.000Z

    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.

  8. Producing a True Lignin Depolymerase for Biobleaching Softwood Kraft Pulp

    SciTech Connect (OSTI)

    Simo Sarkanen

    2002-02-04T23:59:59.000Z

    This project constituted an intensive effort devoted to producing, from the white-rot fungus Tramets Cingulata, a lignin degrading enzyme (lignin depolymerase) that is directly able to biobleach or delignify softwood kraft pulp brownstock. To this end, the solutions in which T. cingulata was grown contained dissolved kraft lignin which fulfilled two functions; it behaved as a lignin deploymerase substrate and it also appeared to act as an inducer of enzyme expression. However, the lignin depolymerase isoenzymes (and other extracellular T. cingulata enzymes) interacted very strongly with both the kraft lignin components and the fungal hypae, so the isolating these proteins from the culture solutions proved to be unexpectedly difficult. Even after extensive experimentation with a variety of protein purification techniques, only one approach appeared to be capable of purifying lignin depolymerases to homogeneity. Unfortunately the procedure was extremely laborious; it involved the iso electric focusing of concentrated buffer-exchanged culture solutions followed by electro-elution of the desired protein bands from the appropriate polyacrylamide gel segments

  9. Trichodermin induces cell apoptosis through mitochondrial dysfunction and endoplasmic reticulum stress in human chondrosarcoma cells

    SciTech Connect (OSTI)

    Su, Chen-Ming [Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan (China); Wang, Shih-Wei [Department of Medicine, Mackay Medical College, New Taipei City, Taiwan (China); Lee, Tzong-Huei [Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan (China); Tzeng, Wen-Pei [Graduate Institute of Sports and Health, National Changhua University of Education, Changhua, Taiwan (China); Hsiao, Che-Jen [School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Liu, Shih-Chia [Department of Orthopaedics, Mackay Memorial Hospital, Taipei, Taiwan (China); Tang, Chih-Hsin, E-mail: chtang@mail.cmu.edu.tw [Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan (China); Department of Pharmacology, School of Medicine, China Medical University, Taichung, Taiwan (China); Department of Biotechnology, College of Health Science, Asia University, Taichung, Taiwan (China)

    2013-10-15T23:59:59.000Z

    Chondrosarcoma is the second most common primary bone tumor, and it responds poorly to both chemotherapy and radiation treatment. Nalanthamala psidii was described originally as Myxosporium in 1926. This is the first study to investigate the anti-tumor activity of trichodermin (trichothec-9-en-4-ol, 12,13-epoxy-, acetate), an endophytic fungal metabolite from N. psidii against human chondrosarcoma cells. We demonstrated that trichodermin induced cell apoptosis in human chondrosarcoma cell lines (JJ012 and SW1353 cells) instead of primary chondrocytes. In addition, trichodermin triggered endoplasmic reticulum (ER) stress protein levels of IRE1, p-PERK, GRP78, and GRP94, which were characterized by changes in cytosolic calcium levels. Furthermore, trichodermin induced the upregulation of Bax and Bid, the downregulation of Bcl-2, and the dysfunction of mitochondria, which released cytochrome c and activated caspase-3 in human chondrosarcoma. In addition, animal experiments illustrated reduced tumor volume, which led to an increased number of terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL)-positive cells and an increased level of cleaved PARP protein following trichodermin treatment. Together, this study demonstrates that trichodermin is a novel anti-tumor agent against human chondrosarcoma cells both in vitro and in vivo via mitochondrial dysfunction and ER stress. - Highlights: • Trichodermin induces chondrosarcoma apoptosis. • ER stress is involved in trichodermin-induced cell death. • Trichodermin induces chondrosarcoma death in vivo.

  10. Automated detection of Karnal bunt teliospores

    SciTech Connect (OSTI)

    Linder, K.D.; Baumgart, C.; Creager, J.; Heinen, B.; Troupe, T.; Meyer, D.; Carr, J.; Quint, J.

    1998-02-01T23:59:59.000Z

    Karnal bunt is a fungal disease which infects wheat and, when present in wheat crops, yields it unsatisfactory for human consumption. Due to the fact that Karnal bunt (KB) is difficult to detect in the field, samples are taken to laboratories where technicians use microscopes and methodically search for KB teliospores. AlliedSignal Federal Manufacturing and Technologies (FM and T), working with the Kansas Department of Agriculture, created a system which utilizes pattern recognition, feature extraction, and neural networks to prototype an automated detection system for identifying KB teliospores. System hardware consists of a biological compound microscope, motorized stage, CCD camera, frame grabber, and a PC. Integration of the system hardware with custom software comprises the machine vision system. Fundamental processing steps involve capturing an image from the slide, while concurrently processing the previous image. Features extracted from the acquired imagery are then processed by a neural network classifier which has been trained to recognize spore-like objects. Images with spore-like objects are reviewed by trained technicians. Benefits of this system include: (1) reduction of the overall cycle-time; (2) utilization of technicians for intelligent decision making (vs. manual searching); (3) a regulatory standard which is quantifiable and repeatable; (4) guaranteed 100% coverage of the cover slip; and (5) significantly enhanced detection accuracy.

  11. 3-Nitropropionic Acid is a Suicide Inhibitor of MitochondrialRespiration that, Upon Oxidation by Complex II, Forms a Covalent AdductWith a Catalytic Base Arginine in the Active Site of the Enzyme

    SciTech Connect (OSTI)

    Huang, Li-shar; Sun, Gang; Cobessi, David; Wang, Andy C.; Shen,John T.; Tung, Eric Y.; Anderson, Vernon E.; Berry, Edward A.

    2005-12-01T23:59:59.000Z

    We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 {angstrom} resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg297 as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator of succinate dehydrogenase, forms a covalent adduct with the side chain of Arg297. The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg 297 to be increased by 83 Da and to have potential of losing 44 Da, consistent with decarboxylation, during fragmentation.

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

    SciTech Connect (OSTI)

    Whisler, Howard C.

    1997-06-01T23:59:59.000Z

    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.

  13. Structural characterization of a ?-hydroxyacid dehydrogenase from Geobacter sulfurreducens and Geobacter metallireducens with succinic semialdehyde reductase activity

    SciTech Connect (OSTI)

    Zhang, Yanfeng; Zheng, Yi; Qin, Ling; Wang, Shihua; Buchko, Garry W.; Garavito, Michael R.

    2014-07-30T23:59:59.000Z

    Beta-hydroxyacid dehydrogenase (?-HAD) genes have been identified in all sequenced genomes of eukaryotes and prokaryotes. Their gene products catalyze the NAD+- or NADP+-dependent oxidation of various ?-hydroxy acid substrates into their corresponding semialdehyde. In many fungal and bacterial genomes, multiple ?-HAD genes are observed leading to the hypothesis that these gene products may have unique, uncharacterized metabolic roles specific to their species. The genomes of Geobacter sulfurreducens and Geobacter metallireducens each contain two potential ?-HAD genes. The protein sequences of one pair of these genes, Gs-?HAD (Q74DE4) and Gm-?HAD (Q39R98), have 65% sequence identity and 77% sequence similarity with each other. Both proteins reduce succinic semialdehyde, a metabolite of the GABA shunt. To further explore the structural and functional characteristics of these two ?-HADs with a potentially unique substrate specificity, crystal structures for Gs-?HAD and Gm-?HAD in complex with NADP+ were determined to a resolution of 1.89 Å and 2.07 Å, respectively. The structure of both proteins are similar, composed of 14 ?-helices and nine ?-strands organized into two domains. Domain One (1-165) adopts a typical Rossmann fold composed of two ?/? units: a six-strand parallel ?-sheet surrounded by six ?-helices (?1 – ?6) followed by a mixed three-strand ?-sheet surrounded by two ?-helices (?7 and ?8). Domain Two (166-287) is composed of a bundle of seven ?-helices (?9 – ?14). Four functional regions conserved in all ?-HADs are spatially located near each other at the interdomain cleft in both Gs-?HAD and Gm-?HAD with a buried molecule of NADP+. The structural features of Gs-?HAD and Gm-?HAD are described in relation to the four conserved consensus sequences characteristic of ?-HADs and the potential biochemical importance of these enzymes as an alternative pathway for the degradation of succinic semialdehyde.

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

    SciTech Connect (OSTI)

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

    1991-12-01T23:59:59.000Z

    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.

  15. Characterization of trapped lignin-degrading microbes in tropical forest soil

    SciTech Connect (OSTI)

    DeAngelis, K.M.; Allgaier, M.; Chavarria, Y.; Fortney, J.L.; Hugenholz, P.; Simmons, B.; Sublette, K.; Silver, W.L.; Hazen, T.C.

    2011-03-01T23:59:59.000Z

    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.

  16. Melanin, a promising radioprotector: Mechanisms of actions in a mice model

    SciTech Connect (OSTI)

    Kunwar, A., E-mail: amitbio@rediffmail.com [Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India); Adhikary, B. [Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India)] [Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India); Jayakumar, S. [Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India)] [Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India); Barik, A. [Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India)] [Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India); Chattopadhyay, S. [Bio-Organic Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India)] [Bio-Organic Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India); Raghukumar, S. [Myko Tech Private Limited, Dona Paula, Goa?403004 (India)] [Myko Tech Private Limited, Dona Paula, Goa?403004 (India); Priyadarsini, K.I., E-mail: kindira@barc.gov.in [Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India)

    2012-10-15T23:59:59.000Z

    The radioprotective effect of extracellular melanin, a naturally occurring pigment, isolated from the fungus Gliocephalotrichum simplex was examined in BALB/C mice, and the probable mechanism of action was established. At an effective dose of 50 mg/kg body weight, melanin exhibited both prophylactic and mitigative activities, increasing the 30-day survival of mice by 100% and 60%, respectively, after exposure to radiation (7 Gy, whole body irradiation (WBI)). The protective activity of melanin was primarily due to inhibition of radiation-induced hematopoietic damages as evidenced by improvement in spleen parameters such as index, total cellularity, endogenous colony forming units, and maintenance of circulatory white blood cells and platelet counts. Melanin also reversed the radiation-induced decrease in ERK phosphorylation in splenic tissue, which may be the key feature in its radioprotective action. Additionally, our results indicated that the sustained activation of AKT, JNK and P38 proteins in splenic tissue of melanin pre-treated group may also play a secondary role. This was also supported by the fact that melanin could prevent apoptosis in splenic tissue by decreasing BAX/Bcl-XL ratio, and increasing the expressions of the proliferation markers (PCNA and Cyclin D1), compared to the radiation control group. Melanin also reduced the oxidative stress in hepatic tissue and abrogated immune imbalance by reducing the production of pro-inflammatory cytokines (IL6 and TNF?). In conclusion, our results confirmed that fungal melanin is a very effective radioprotector against WBI and the probable mechanisms of radioprotection are due to modulation in pro-survival (ERK) signaling, prevention of oxidative stress and immunomodulation. -- Highlights: ? Melanin showed promising radioprotection under pre and post irradiation condition. ? Melanin protects the hematopoietic system from radiation induced damage. ? Melanin modulates pro-survival pathways, immune system and prevents oxidative stress.

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

    SciTech Connect (OSTI)

    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

    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.

  18. Influence of Airflow on Laboratory Storage of High Moisture Corn Stover

    SciTech Connect (OSTI)

    Lynn M. Wendt; Ian J. Bonner; Amber N. Hoover; Rachel M. Emerson; William A. Smith

    2014-04-01T23:59:59.000Z

    Storing high moisture biomass for bioenergy use is a reality in many areas of the country where wet harvest conditions and environmental factors prevent dry storage from being feasible. Aerobic storage of high moisture biomass leads to microbial degradation and self-heating, but oxygen limitation can aid in material preservation. To understand the influence of oxygen presence on high moisture biomass (50 %, wet basis), three airflow rates were tested on corn stover stored in laboratory reactors. Temperature, carbon dioxide production, dry matter loss, chemical composition, fungal abundance, pH, and organic acids were used to monitor the effects of airflow on storage conditions. The results of this work indicate that oxygen availability impacts both the duration of self-heating and the severity of dry matter loss. High airflow systems experienced the greatest initial rates of loss but a shortened microbially active period that limited total dry matter loss (19 %). Intermediate airflow had improved preservation in short-term storage compared to high airflow systems but accumulated the greatest dry matter loss over time (up to 27 %) as a result of an extended microbially active period. Low airflow systems displayed the best performance with the lowest rates of loss and total loss (10 %) in storage at 50 days. Total structural sugar levels of the stored material were preserved, although glucan enrichment and xylan loss were documented in the high and intermediate flow conditions. By understanding the role of oxygen availability on biomass storage performance, the requirements for high moisture storage solutions may begin to be experimentally defined.

  19. Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

    SciTech Connect (OSTI)

    DeAngelis, Kristen M.; Allgaier, Martin; Chavarria, Yaucin; Fortney, Julian L.; Hugenholtz, Philip; Simmons, Blake A.; Sublette, Kerry; Silver, Whendee; Hazen, Terry C.

    2011-04-29T23:59:59.000Z

    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.

  20. Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

    SciTech Connect (OSTI)

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

    2011-07-14T23:59:59.000Z

    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.

  1. A model for motor-mediated bidirectional transport along an antipolar microtubule bundle

    E-Print Network [OSTI]

    Congping Lin; Peter Ashwin; Gero Steinberg

    2012-11-21T23:59:59.000Z

    Long-distance bidirectional transport of organelles depends on the motor proteins kinesin and dynein. Using quantitative data obtained from a fungal model system, we previously developed ASEP-models of bidirectional motion of motors along unipolar microtubules (MTs) near the cell ends of the elongated hyphal cells (herein referred as "unipolar section"). However, recent quantitative live cell imaging in this system has demonstrated that long-range motility of motors and their endosomal cargo mainly occurs along extended antipolar microtubule bundles within the central part of the cell (herein referred to as "bipolar section"). Dynein and kinesin-3 motors coordinate their activity to move early endosomes (EEs) in a bidirectional fashion, with dynein mediating retrograde motility along the unipolar section near the cell poles, whereas kinesin-3 is responsible for bidirectional motions along the antipolar section. Here we extend our modelling approach to simulate bidirectional motility along an antipolar microtubule bundle. In our model, cargos (particles) change direction on each MT with a turning rate $\\Omega$ and the MTs are linked to each other at the minus ends where particles can hop between MTs with a rate $q_1$ (obstacle-induced switching rate) or $q_2$ (end-induced switching rate). By numerical simulations and mean-field approximations, we investigate the distribution of particles along the MTs for different overall densities $\\Theta$. We find that even if $\\Theta$ is low, the system can exhibit shocks in the density profiles near plus and minus ends caused by queueing of particles. We also discuss how the switching rates $q_{1,2}$ influence the type of motor that dominates the active transport in the bundle.

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

    SciTech Connect (OSTI)

    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

    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.

  3. Crystal structure of the Candida albicans Kar3 kinesin motor domain fused to maltose-binding protein

    SciTech Connect (OSTI)

    Delorme, Caroline; Joshi, Monika [Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6 (Canada)] [Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6 (Canada); Allingham, John S., E-mail: allinghj@queensu.ca [Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6 (Canada)

    2012-11-30T23:59:59.000Z

    Highlights: Black-Right-Pointing-Pointer The Candida albicans Kar3 motor domain structure was solved as a maltose-binding protein fusion. Black-Right-Pointing-Pointer The electrostatic surface and part of the ATPase pocket of the motor domain differs markedly from other kinesins. Black-Right-Pointing-Pointer The MBP-Kar3 interface highlights a new site for intramolecular or intermolecular interactions. -- Abstract: In the human fungal pathogen Candida albicans, the Kinesin-14 motor protein Kar3 (CaKar3) is critical for normal mitotic division, nuclear fusion during mating, and morphogenic transition from the commensal yeast form to the virulent hyphal form. As a first step towards detailed characterization of this motor of potential medical significance, we have crystallized and determined the X-ray structure of the motor domain of CaKar3 as a maltose-binding protein (MBP) fusion. The structure shows strong conservation of overall motor domain topology to other Kar3 kinesins, but with some prominent differences in one of the motifs that compose the nucleotide-binding pocket and the surface charge distribution. The MBP and Kar3 modules are arranged such that MBP interacts with the Kar3 motor domain core at the same site where the neck linker of conventional kinesins docks during the 'ATP state' of the mechanochemical cycle. This site differs from the Kar3 neck-core interface in the recent structure of the ScKar3Vik1 heterodimer. The position of MBP is also completely distinct from the Vik1 subunit in this complex. This may suggest that the site of MBP interaction on the CaKar3 motor domain provides an interface for the neck, or perhaps a partner subunit, at an intermediate state of its motile cycle that has not yet been observed for Kinesin-14 motors.

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

    SciTech Connect (OSTI)

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

    1991-12-01T23:59:59.000Z

    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.

  5. Effect of a heavy metal on ecto- and vesicular-arbuscular mycorrhizal fungi: The physiology, ultrastructure, and ecology of copper stress and tolerance

    SciTech Connect (OSTI)

    Gruhn, C.M.

    1989-01-01T23:59:59.000Z

    The first chapter examines the enzyme tyrosinase in several ectomycorrhizal fungi and shows that its activity is altered in these fungi in response to copper. Polyamines are also examined, and it is shown that their levels are altered in some ectomycorrhizal fungi due to copper stress but not in others. The second chapter uses transmission electron microscopy to demonstrate that copper is bound to the hyphae of ectomycorrhizal fungi grown on solid media, but the location of the binding varies between fungal species. In vitro copper tolerances of a number of ectomycorrhizal species are compared and differences in tolerance are evident between species and between different isolates of the same species. In the third chapter, four ectomycorrhizal fungi and one nonmycorrhizal fungus are evaluated for their ability to improve the growth of Japanese Red Pine under conditions of copper stress. Improvement of pine seedling growth is not correlated with in vitro copper tolerance of the fungus, but is related to the degree of compatibility between host and fungus. Despite differences in in vitro tolerance between three isolates of the same species, there are no differences in the effect of the isolates on the tree host under conditions of copper stress. Ectomycorrhizal fungi were also inoculated in pairs on pine seedlings and the competitive abilities of the fungi are compared under stressed and nonstressed conditions. The fourth chapter discusses the results of inoculation of pine with a nonhost fungus which stimulates dichotomous branching of the root system. The compound responsible for the branching is demonstrated to be indole-3-acetic acid (IAA), a plant growth hormone. The final two chapters deal with endomycorrhizal fungi.

  6. Comparative genomics of citric-acid producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

    SciTech Connect (OSTI)

    Grigoriev, Igor V.; Baker, Scott E.; Andersen, Mikael R.; Salazar, Margarita P.; Schaap, Peter J.; Vondervoot, Peter J.I. van de; Culley, David; Thykaer, Jette; Frisvad, Jens C.; Nielsen, Kristen F.; Albang, Richard; Albermann, Kaj; Berka, Randy M.; Braus, Gerhard H.; Braus-Stromeyer, Susanna A.; Corrochano, Luis M.; Dai, Ziyu; Dijck, Piet W.M. van; Hofmann, Gerald; Lasure, Linda L.; Magnusson, Jon K.; Meijer, Susan L.; Nielsen, Jakob B.; Nielsen, Michael L.; Ooyen, Albert J.J. van; Panther, Kathyrn S.; Pel, Herman J.; Poulsen, Lars; Samson, Rob A.; Stam, Hen; Tsang, Adrian; Brink, Johannes M. van den; Atkins, Alex; Aerts, Andrea; Shapiro, Harris; Pangilinan, Jasmyn; Salamov, Asaf; Lou, Yigong; Lindquist, Erika; Lucas, Susan; Grimwood, Jane; Kubicek, Christian P.; Martinez, Diego; Peij, Noel N.M.E. van; Roubos, Johannes A.; Nielsen, Jens

    2011-04-28T23:59:59.000Z

    The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compels additional exploration. We therefore undertook whole genome sequencing of the acidogenic A. niger wild type strain (ATCC 1015), and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was utilized to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 megabase of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis revealed up-regulation of the electron transport chain, specifically the alternative oxidative pathway in ATCC 1015, while CBS 513.88 showed significant up-regulation of genes relevant to glucoamylase A production, such as tRNA-synthases and protein transporters. Our results and datasets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.[Supplemental materials (10 figures, three text documents and 16 tables) have been made available. The whole genome sequence for A. niger ATCC 1015 is available from NBCI under acc. no ACJE00000000. The up-dated sequence for A. niger CBS 513.88 is available from EMBL under acc. no AM269948-AM270415. The sequence data from the phylogeny study has been submitted to NCBI (GU296686-296739). Microarray data from this study is submitted to GEO as series GSE10983. Accession for reviewers is possible through: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi token GSE10983] The dsmM_ANIGERa_coll511030F library and platform information is deposited at GEO under number GPL6758

  7. HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa

    SciTech Connect (OSTI)

    Jonkers, Wilfried; Leeder, Abigail C.; Ansong, Charles; Wang, Yuexi; Yang, Feng; Starr, Trevor L.; Camp, David G.; Smith, Richard D.; Glass, N. Louise

    2014-11-20T23:59:59.000Z

    Cell fusion in genetically identical Neurospora crassa germlings and in hyphae is a highly regulated process involving the activation of a conserved MAP kinase cascade that includes NRC1, MEK2 and MAK2. During chemotrophic growth in germlings, the MAP kinase cascade members localize to conidial anastomosis tube (CAT) tips every 4 minutes, perfectly out of phase with another protein that is recruited to the tip: SOFT, a protein of unknown biochemical function. How this oscillation process is initiated, maintained and what proteins regulate the MAP kinase cascade is currently unclear. A global phosphoproteomics approach using an allele of mak-2 (mak-2Q100G) that can be specifically inhibited by the ATP analog 1NM-PP1 was utilized to identify MAK2 kinase targets in germlings that were potentially involved in this process. One such putative target was HAM5, a protein of unknown biochemical function. Previously, ?ham-5 mutants were shown to be deficient for hyphal fusion. Here we show that HAM5-GFP co-localized with NRC1, MEK2 and MAK2 and oscillated with identical dynamics from the cytoplasm to CAT tips during chemotropic interactions. In the ?mak-2 strain, HAM5-GFP localized to punctate complexes that did not oscillate, but still localized to the germling tip, suggesting that MAK2 activity influences HAM5 function/localization. However, MAK2-GFP showed only cytoplasmic and nuclear localization in a ?ham-5 strain and did not localize to puncta, as observed in wild type germlings. Via co-immunoprecipitation experiments, HAM5 was shown to physically interact with MAK2, MEK2 and NRC1, suggesting that it functions as a scaffold/transport hub for the MAP kinase cascade members during oscillation and chemotropic interactions during both germling and hyphal fusion in N. crassa. The identification of HAM5 as a scaffold-like protein will help to link the activation of MAK2 to upstream factors and other proteins involved in this intriguing process of fungal communication.

  8. Interactive Effects of Climate Change and Decomposer Communities on the Stabilization of Wood-Derived Carbon Pools: Catalyst for a New Study

    SciTech Connect (OSTI)

    Resh, Sigrid C. [Michigan Technological University

    2014-11-17T23:59:59.000Z

    Globally, forest soils store ~two-thirds as much carbon (C) as the atmosphere. Although wood makes up the majority of forest biomass, the importance of wood contributions to soil C pools is unknown. Even with recent advances in the mechanistic understanding of soil processes, integrative studies tracing C input pathways and biological fluxes within and from soils are lacking. Therefore, our research objectives were to assess the impact of different fungal decay pathways (i.e., white-rot versus brown-rot)—in interaction with wood quality, soil temperature, wood location (i.e., soil surface and buried in mineral soil), and soil texture—on the transformation of woody material into soil CO2 efflux, dissolved organic carbon (DOC), and soil C pools. The use of 13C-depleted woody biomass harvested from the Rhinelander, WI free-air carbon dioxide enrichment (Aspen-FACE) experiment affords the unique opportunity to distinguish the wood-derived C from other soil C fluxes and pools. We established 168 treatment plots across six field sites (three sand and three loam textured soil). Treatment plots consisted of full-factorial design with the following treatments: 1. Wood chips from elevated CO2, elevated CO2 + O3, or ambient atmosphere AspenFACE treatments; 2. Inoculated with white rot (Bjerkandera adusta) or brown rot (Gloeophyllum sepiarium) pure fungal cultures, or the original suite of endemic microbial community on the logs; and 3. Buried (15cm in soil as a proxy for coarse roots) or surface applied wood chips. We also created a warming treatment using open-topped, passive warming chambers on a subset of the above treatments. Control plots with no added wood (“no chip control”) were incorporated into the research design. Soils were sampled for initial ?13C values, CN concentrations, and bulk density. A subset of plots were instrumented with lysimeters for sampling soil water and temperature data loggers for measuring soil temperatures. To determine the early pathways of decomposition, we measured soil surface CO2 efflux, dissolved organic C (DOC), and DO13C approximately monthly over two growing seasons from a subsample of the research plots. To determine the portion of soil surface CO2 efflux attributable to wood-derived C, we used Keeling plot techniques to estimate the associated ?13C values of the soil CO2 efflux. We measured the ?13CO2 once during the peak of each growing season. Initial values for soil ?13C values and CN concentrations averaged across the six sites were -26.8‰ (standard error = 0.04), 2.46% (se = 0.11), and 0.15% (se = 0.01), respectively. The labeled wood chips from the Aspen FACE treatments had an average ?13C value of -39.5‰ (se 0.10). The >12 ‰ isotopic difference between the soil and wood chip ?13C values provides the basis for tracking the wood-derived C through the early stages of decomposition and subsequent storage in the soil. Across our six research sites, average soil surface CO2 efflux ranged from 1.04 to 2.00 g CO2 m-2 h-1 for the first two growing seasons. No wood chip controls had an average soil surface CO2 efflux of 0.67 g CO2 m-2 h-1 or about half of that of the wood chip treatment plots. Wood-derived CO2 efflux was higher for loam textured soils relative to sands (0.70 and 0.54 g CO2 m-2 h-1, respectively; p = 0.045)), for surface relative to buried wood chip treatments (0.92 and 0.39 g CO2 m-2 h-1, respectively; p < 0.001), for warmed relative to ambient temperature treatments (0.99 and 0.78 g CO2 m-2 h-1, respectively; 0.004), and for natural rot relative to brown and white rots (0.93, 0.82, and 0.78 g CO2 m-2 h-1, respectively; p = 0.068). Our first two growing seasons of soil surface CO2 efflux data show that wood chip location (i.e., surface vs. buried chip application) is very important, with surface chips loosing twice the wood-derived CO2. The DOC data support this trend for greater loss of ecosystem C from surface chips. This has strong implications for the importance of root and buried wood for ecosystem C retention. This strong chip location effect

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

    SciTech Connect (OSTI)

    Donal F. Day

    2009-03-31T23:59:59.000Z

    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.