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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)

    of Fungal Polyketide Cyclization Print Polyketide natural products produced by bacteria and fungi are often characterized by the presence of multiple aromatic rings that are...

  2. Chemistry & Biology Aryl-aldehyde Formation in Fungal Polyketides

    E-Print Network [OSTI]

    Zhao, Huimin

    Chemistry & Biology Article Aryl-aldehyde Formation in Fungal Polyketides: Discovery at Urbana-Champaign, Urbana, IL 61801, USA 2Department of Chemistry, University of Illinois at Urbana

  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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home RoomPreservation ofAlbuquerque|SensitiveAprilPhoton SourceSuperconductorsSRS StructuralStructure

  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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effect Photovoltaics -7541C.3X-rays3EnergyParameterFilaments Joshuaand

  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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effect Photovoltaics -7541C.3X-rays3EnergyParameterFilaments JoshuaandStructure

  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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effect Photovoltaics -7541C.3X-rays3EnergyParameterFilaments

  7. 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust,Field-effect Photovoltaics -7541C.3X-rays3EnergyParameterFilamentsStructure

  8. Characterization of the Biosynthetic Pathway of Fungal Aromatic Polyketides

    E-Print Network [OSTI]

    Li, Yanran

    2012-01-01

    2011). Comparative Characterization of Fungal Anthracenone2011). Comparative Characterization of Fungal AnthracenoneCA (2002) Initial characterization of a type I fatty acid

  9. Producing biofuels using polyketide synthases

    DOE Patents [OSTI]

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

    2013-04-16

    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.

  10. 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent Bonding Low-Cost2 DOENERSC Overview * Na#onalDeadly Carcinogen

  11. 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 ...

  12. Producing dicarboxylic acids using polyketide synthases

    DOE Patents [OSTI]

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

    2013-10-29

    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.

    2012-02-01

    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. Engineered polyketide biosynthesis and biocatalysis in Escherichia coli

    E-Print Network [OSTI]

    Gao, Xue; Wang, Peng; Tang, Yi

    2010-01-01

    metabolic pathway engineering. Biochemistry 42(48):14342–biochemistry, structural biology, genetics, and meta- bolic engineering,engineering of a methylmalonyl-coa mutase- epimerase pathway for complex polyketide biosynthesis in Escherichia coli. Biochemistry

  15. Mechanism Studies on Fungal Type I Highly-Reducing Polyketide Synthases and Polyketide Synthase-Nonribosomal Peptide Synthetase Hybrids

    E-Print Network [OSTI]

    Xu, Wei

    2013-01-01

    185(14): p. 4136-4143. Asturias, F.J. , et al. , StructureS. Smith, and F.J. Asturias, Conformational flexibility of

  16. Mechanism Studies on Fungal Type I Highly-Reducing Polyketide Synthases and Polyketide Synthase-Nonribosomal Peptide Synthetase Hybrids

    E-Print Network [OSTI]

    Xu, Wei

    2013-01-01

    include caffeine, nicotine, quinine and cocaine (Figure 1).98]; and a zinc-free quinine reductase (ER) from Thermus

  17. Pd-Catalyzed Wacker Cyclizations Palladium-Catalyzed Oxidative Wacker

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Pd-Catalyzed Wacker Cyclizations Palladium-Catalyzed Oxidative Wacker Cyclizations in Nonpolar stoichiometric oxidant. Palladium-catalyzed bond-forming constructions have become indispensable in organic chemistry.[4] A favorable property of palladium is that it can serve as both a nucleophile (i.e., Pd0

  18. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2012-01-01

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

  19. JGI Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01

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

  20. Fungal Genomics Program

    E-Print Network [OSTI]

    Grigoriev, Igor

    2012-01-01

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

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

    E-Print Network [OSTI]

    Lam, Tin Yiu

    2008-01-01

    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 ...

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

    E-Print Network [OSTI]

    Zabala, Angelica Obusan

    2014-01-01

    and the antioxidant resveratrol from plants (Figure 1.1).example of which is resveratrol (Figure 1.1) commonly found

  3. Producing a trimethylpentanoic acid using hybrid polyketide synthases

    SciTech Connect (OSTI)

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

    2014-10-07

    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.

  4. Cloning and characterization of a type III polyketide synthase from Aspergillus niger

    E-Print Network [OSTI]

    Zhao, Huimin

    of Illinois, 600 South Mathews Avenue, Urbana, IL 61801, USA a r t i c l e i n f o Article history: Received synthases (PKSs) are the condensing enzymes that catalyze the formation of a myriad of aromatic polyketides

  5. Construction of a Part of a 3-Hydroxypropionate Cycle for Heterologous Polyketide Biosynthesis in Escherichia coli

    SciTech Connect (OSTI)

    Yuzawa, S; Chiba, N; Katz, L; Keasling, JD

    2012-12-11

    Polyketides, an important class of natural products with, complex chemical structures, are widely used as antibiotics and other pharmaceutical agents. A clear barrier to heterologous polyketide biosynthesis in Escherichia coli is the lack of (2S)-methylmalonyl-CoA, a common substrate of multimodular polyketide synthases. Here we report a route for synthesizing (2S)-methylmalonyl-CoA from malonyl-CoA with a 3-hydroxypropionate cycle in thermoacidophilic crenarchaeon. The engineered E. coli strain produced both propionyl-CoA and methylmalonyl-CoA at intracellular levels similar to those of acetyl-CoA and succinyl-CoA, respectively. This approach may open a way to produce a variety of polyketide drugs in E. coli from renewable carbon sources.

  6. 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.

    2008-10-07

    locus, highlighting the plasticity of this region and its potential for combina- torial polyketide biochemistry. Results Overview of pMUM002 from M. liflandii 128FXT Assembly of the complete DNA sequence of pMUM002 from four overlapping BAC clones (06A07... of each two-carbon unit. Shaded modules indicate that the DNA sequence of these regions is unknown or not yet confirmed. *Organisation of mlsA1 and mlsA2 for all pMUM examined to date, based upon toxin structures.Page 6 of 15 (page number not for citation...

  7. Can fungal biopesticides control malaria? 

    E-Print Network [OSTI]

    Thomas, Matt B; Read, Andrew F

    2007-01-01

    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 ...

  8. A diverse family of type III polyketide synthases in Eucalyptus speciesw Sheryl B. Rubin-Pitel,za

    E-Print Network [OSTI]

    Zhao, Huimin

    A diverse family of type III polyketide synthases in Eucalyptus speciesw Sheryl B. Rubin published as an Advance Article on the web 1st June 2010 DOI: 10.1039/c004992a Eucalyptus species synthesize to hyperforin, respectively. Trees of the genus Eucalyptus represent a group of plants in which acyl

  9. Palladium-Catalyzed Enantioselective Cyclization of Silyloxy-1,6-Enynes Britton K. Corkey and F. Dean Toste*

    E-Print Network [OSTI]

    Toste, Dean

    Palladium-Catalyzed Enantioselective Cyclization of Silyloxy-1,6-Enynes Britton K. Corkey and F silyloxy-substituted olefins. On the basis of our recent report on palladium-catalyzed enantio- selective 5

  10. Trend, Ramtohul and Stoltz. Supporting Information S1 Oxidative Cyclizations in a Nonpolar Solvent Using

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Oxidative Cyclization of 1. Palladium source and additive optimization reactions shown in Tables 1 and S1. A thick-walled oven-dried 25 mL 15 cm-long tube equipped with magnetic stir bar was charged with powdered molecular sieves (MS3Å, 125 mg, 500 mg MS3Å/mmol substrate), palladium source (0.0125 mmol, 0.05 equiv

  11. Mesoscale Analyses of Fungal Networks

    E-Print Network [OSTI]

    Lee, Sang Hoon; Porter, Mason A

    2014-01-01

    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.

  12. Sequencing the Fungal Tree of Life

    E-Print Network [OSTI]

    Martin, Francis

    2014-01-01

    SA (2008) Extending genomics to natural communities andFueling the future with fungal genomics. Mycology, in press.Fifteen years of microbial genomics: meeting the challenges

  13. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01

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

  14. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01

    engineering of fungal biocontrol agents to achieve greatersymbionts, potential biocontrol agents and inhabitants ofpathogens, or biocontrol agents, play a very important role.

  15. Predicting multidimensional distributive properties of hyperbranched polymer resulting from AB2 polymerization with substitution, cyclization and shielding

    E-Print Network [OSTI]

    Ivan Kryven; Piet D. Iedema

    2013-05-05

    A deterministic mathematical model for the polymerization of hyperbranched molecules accounting for substitution, cyclization, and shielding effect has been developed as a system of nonlinear population balances. The solution obtained by a novel approximation method shows perfect agreement with the analytical solution in limiting cases and provides, for the first time in this class of polymerization problems, full multidimensional results.

  16. Biochem. J. (2000) 350, 229235 (Printed in Great Britain) 229 Identification of amino acid residues important in the cyclization reactions

    E-Print Network [OSTI]

    Suh, Dae-Yeon

    2000-01-01

    cyclization reactions to produce naringenin chalcone and resveratrol respectively. On the basis of sequence inter- mediate). Meanwhile, resveratrol production by STS-P$(&G strongly decreased to give various products in the order CTAL resveratrol$ bisnoryangonin naringenin. As a result, narin- INTRODUCTION

  17. 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.

    2009-11-30

    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.

  18. 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

    2011-01-01

    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 ...

  19. 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 ...

  20. Fungal Diversity Identification of Botryosphaeriaceae from Eucalyptus, Acacia

    E-Print Network [OSTI]

    Fungal Diversity 103 Identification of Botryosphaeriaceae from Eucalyptus, Acacia and Pinus). Identification of Botryosphaeriaceae from Eucalyptus, Acacia and Pinus in Venezuela. Fungal Diversity 25: 103, Eucalyptus and Pinus. Some anamorphs associated with the Botryosphaeriaceae have been reported from Venezuela

  1. MycoCosm, an Integrated Fungal Genomics Resource (Conference...

    Office of Scientific and Technical Information (OSTI)

    In-Document Search Title: MycoCosm, an Integrated Fungal Genomics Resource MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in...

  2. PLPA4380 Fungal Genetics and Genomics B. Gillian Turgeon

    E-Print Network [OSTI]

    Chen, Tsuhan

    PLPA4380 Fungal Genetics and Genomics B. Gillian Turgeon Spring 2016 Date Topic Wed Jan 27 Feb 22 Quiz Wed Feb 24 Sequenced fungal genomes: JGI Mycocosm tools Characteristics/ typical features/ comparative genomics/annotation Fri Feb 26 Sequenced fungal genomes: JGI Mycocosm tools Characteristics

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

    E-Print Network [OSTI]

    Jones, Carrie Preston

    2007-01-01

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

  4. JGI Fungal Genomics Program (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis....

  5. Intercropped silviculture systems, a key to achieving soil fungal...

    Office of Scientific and Technical Information (OSTI)

    Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations Citation Details In-Document Search Title: Intercropped...

  6. USING DNA SEQUENCE DATA TO CHARACTERISE FUNGAL PATHOGENS OF TREES

    E-Print Network [OSTI]

    fungal leaf pathogens of trees, and more specifically Eucalyptus trees, are a group of fungi that belong to the fungal genus Mycosphaerella. Many Mycosphaerella species cause a leaf disease of Eucalyptus trees defoliation of Eucalyptus trees and it can ultimately retard tree growth. Eucalyptus trees are widely grown

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

    E-Print Network [OSTI]

    Fungal Diversity Chrysoporthe doradensis sp. nov. pathogenic to Eucalyptus in Ecuador Marieka. and Wingfield, M.J. (2005). Chrysoporthe doradensis sp. nov. pathogenic to Eucalyptus in Ecuador. Fungal Eucalyptus in various South American countries. This disease has not previously been recorded from Ecuador

  8. MycoCosm, an Integrated Fungal Genomics Resource Shabalov, Igor...

    Office of Scientific and Technical Information (OSTI)

    Resource Shabalov, Igor; Grigoriev, Igor 59 BASIC BIOLOGICAL SCIENCES MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in...

  9. 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, ...

  10. 28 CITRUS INDUSTRY February 2012 he season for fungal foliar

    E-Print Network [OSTI]

    Burns, Jacqueline K.

    28 CITRUS INDUSTRY · February 2012 T he season for fungal foliar diseases is just around the corner-Drive · Heavy duty Stainless Steel Pump ­ handles virtually any tank mix · Multi-Directional, Adjustable Nozzles

  11. Fungal biology: compiling genomes and exploiting them

    SciTech Connect (OSTI)

    Labbe, Jessy L; Uehling, Jessie K; Payen, Thibaut; Plett, Jonathan

    2014-01-01

    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).

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

    E-Print Network [OSTI]

    Vesk, Peter

    Dispersed Polyphosphate in Fungal Vacuoles in Eucalyptus pilularis/Pisolithus tinctorius. 1999. Dispersed polyphos- phate in fungal vacuoles in Eucalyptus pilularis/ Pisolithus tinctorius and Eucalyptus pilularis under axenic conditions were rapidly frozen, freeze- substituted in tetrahydrofuran

  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

    2011-01-01

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

  14. Fungal biomass associated with the phyllosphere of bryophytes and vascular plants

    E-Print Network [OSTI]

    Laudal, Arnfinn

    Fungal biomass associated with the phyllosphere of bryophytes and vascular plants M. L. DAVEYa Epiphytes Ergosterol Erogsterol extraction Fungal biomass Phyllosphere Vascular plants a b s t r a c t Little is known about the amount of fungal biomass in the phyllosphere of bryophytes compared to higher

  15. Do chlorophyllous orchids heterotrophically use mycorrhizal fungal carbon?

    E-Print Network [OSTI]

    Do chlorophyllous orchids heterotrophically use mycorrhizal fungal carbon? Marc-Andre´ Selosse1 ISYEB), CP 50, 45 rue Buffon, 75005 Paris, France 2 School of Life Sciences, University of Kwa with mycorrhizal fungi, the rhizoctonias, which are considered to exchange min- eral nutrients against plant carbon

  16. 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 Data Center Home Page on Delicious Rank EERE:FinancingPetroleum12, 2015ExecutiveFluorescentDanKathyEnergydetailsof Energy Fungal

  17. Dereplicating and Mapping Secondary Metabolites Directly on Fungal Cultures

    SciTech Connect (OSTI)

    Kertesz, Vilmos [ORNL; Van Berkel, Gary J [ORNL; Sica, Vincent P [University of North Carolina at Greensboro; Raja, Huzefa A [University of North Carolina at Greensboro; El-Elimat, Tamam [University of North Carolina at Greensboro; Oberlies, Nicholas H [University of North Carolina at Greensboro; Pearce, Cedric J [Mycosynthetix, Inc., North Carolina

    2015-01-01

    Ambient ionization techniques coupled to mass spectrometry have recently become prevalent in natural product research due to their ability to examine secondary metabolites in situ. Identifying, mapping, and monitoring secondary metabolites directly on an organism provides invaluable spatial and temporal details that are lost through traditional extraction processes. Most ambient ionization techniques do not collect mutually supportive data, such as chromatographic retention times and/or UV/VIS spectra, and this can limit the ability to identify certain metabolites, such as differentiating isomers. To overcome this, the droplet liquid microjunction surface sampling probe (droplet LMJ SSP) was coupled with UPLC PDA HRMS MS/MS, thus providing separation, retention times, and UV/VIS data used in traditional dereplication protocols. By capturing these mutually supportive data, the identity of secondary metabolites could be confidently and rapidly assigned in situ. Using the droplet LMJ SSP, a protocol was constructed to analyze the secondary metabolite profile of fungal cultures directly without any sample preparation. The results demonstrate that fungal cultures can be dereplicated from the Petri dish, thus identifying secondary metabolites, including isomers, and confirming them against reference standards. Furthermore, heat maps, similar to mass spectrometry imaging, can be used to ascertain the location and relative concentration of secondary metabolites directly on the surface and/or surroundings of a fungal culture.

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

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

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

    2014-11-18

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

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

    SciTech Connect (OSTI)

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

    2014-11-18

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

  20. Cyclization phenomena in the sol-gel polymerization of {alpha},{omega}-bis(triethoxysilyl)alkanes and incorporation of the cyclic structures into network silsesquioxane polymers

    SciTech Connect (OSTI)

    Loy, D.A.; Carpenter, J.P.; Alam, T.M.; Shaltout, R. [Sandia National Labs., Albuquerque, NM (United States)] [Sandia National Labs., Albuquerque, NM (United States); Dorhout, P.K. [Colorado State Univ., Fort Collins, CO (United States). Dept. of Chemistry] [Colorado State Univ., Fort Collins, CO (United States). Dept. of Chemistry; Greaves, J.; Shea, K.J. [Univ. of California, Irvine, CA (United States). Dept. of Chemistry] [Univ. of California, Irvine, CA (United States). Dept. of Chemistry; Small, J.H. [Los Alamos National Lab., NM (United States). Polymers and Coatings Group] [Los Alamos National Lab., NM (United States). Polymers and Coatings Group

    1999-06-16

    Intramolecular cyclizations during acid-catalyzed sol-gel polymerizations of {alpha},{omega}-bis(triethoxysilyl)alkanes substantially lengthen gel times for monomers with ethylene (1), propylene (2), and butylene (3) bridging groups. These cyclization reactions were found, using mass spectrometry and {sup 29}Si NMR spectroscopy, to lead preferentially to monomeric and dimeric products based on six- and seven-membered disilsesquioxane rings. 1,2-Bis(triethoxysilyl)ethane (1) reacts under acidic conditions to give a bicyclic dimer (5) that is composed of two annelated seven-membered rings. Under the same conditions, 1,3-bis(triethoxysilyl)propane (2), 1,4-bis(triethoxysilyl)butane (3), and Z-1,4-bis(triethoxysilyl)but-2-ene (10) undergo an intramolecular condensation reaction to give the six- and seven-membered cyclic disilsesquioxanes 6, 7, and 11. Subsequently, these cyclic monomers slowly react to form the tricyclic dimers 8, 9, and 12. With NaOH as polymerization catalyst, these cyclic silsesquioxanes readily reacted to afford gels that were shown by CP MAS {sup 29}Si NMR and infrared spectroscopies to retain some cyclic structures. Comparison of the porosity and microstructure of xerogels prepared from the cyclic monomers 6 and 7 with those of gels prepared directly from their acyclic precursors 2 and 3 indicates that the final pore structure of the xerogels is markedly dependent on the nature of the precursor. In addition, despite the fact that the monomeric cyclic disilsesquioxane species cannot be isolated from 1--3 under basic conditions due to their rapid rate of gelation, spectroscopic techniques also detected the presence of the cyclic structures in the resulting polymeric gels.

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

    SciTech Connect (OSTI)

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

    1999-01-04

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

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

    SciTech Connect (OSTI)

    Walton, Jonathan

    2013-03-17

    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.).

  3. 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

  4. 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

  5. INHIBITION OF FUNGAL POlYGALACTURONASES BY EXTRACTS OF Eucalyptus grandis WITH DIFFERENT DISEASE SUSCEPTIBILITIES

    E-Print Network [OSTI]

    INHIBITION OF FUNGAL POlYGALACTURONASES BY EXTRACTS OF Eucalyptus grandis WITH DIFFERENT DISEASE and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria.- 0002, (South Africa) Eucalyptus by fungal pathogens are an important constraint' to the productivity of Eucalyptus plantations, Fungi

  6. Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities

    E-Print Network [OSTI]

    Detection of forest stand-level spatial structure in ectomycorrhizal fungal communities Erik A First published online 10 May 2004 Abstract Ectomycorrhizal fungal (EMF) communities are highly diverse, we investigated the spatial structure of these communities. We used EMF community data from a number

  7. COMPARATIVE ANALYSIS OF GENE PREDICTION METHODS AND DEVELOPMENT OF A FUNGAL GENOME DATABASE SYSTEM

    E-Print Network [OSTI]

    Moriyama, Etsuko

    COMPARATIVE ANALYSIS OF GENE PREDICTION METHODS AND DEVELOPMENT OF A FUNGAL GENOME DATABASE SYSTEM;COMPARATIVE ANALYSIS OF GENE PREDICTION METHODS AND DEVELOPMENT OF A FUNGAL GENOME DATABASE SYSTEM Skanth genome projects have been planned and some new draft genomes have been recently completed. Multiple gene

  8. Cyclization of N-alkyl azinium cations with bifunctional nucleophiles. 21. Regioisomeric 1,3,4-thiadiazino(5,6-b)quinoxalines

    SciTech Connect (OSTI)

    Baklykov, V.G.; Charushin, V.N.; Chupakhin, O.N.; Drozd, V.N.

    1987-10-01

    Thiobenzyhydrazides undergo cyclization with N-alkyl-quinoxalinium salts to give 5-alkyl-substituted 1,4,4a,5,10,10a-hexahydro-1,3,4-thiadiazino(5,6-b)quinoxalines, which undergo isomerization to 10-alkyl-substituted thiadiazinoquinoxalines when they are heated in ethanol or in the presence of acids. The IR spectra of suspensions of the compounds in mineral oil were recorded with a UR-20 spectrometer. The PMR spectra of solutions in d/sub 6/-DMSO were recorded with Perkin-Elmer R-12B (60 MHz) and Brucker WP-80 (80 MHz) spectrometers with tetramethylsilane (TMS) and hexamethyldisiloxane (HMDS) as the internal standards. The /sup 13/C NMR spectra of solutions in d/sub 6/-DMSO were recorded with Brucker WH-90 (22.62 MHz) and Varian FT-80A (20.13 MHz) spectrometers. The chemical shifts were measured with respect to the signal of the solvent (d/sub 6/-DMSO, 39.6 ppm).

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

    DOE Patents [OSTI]

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

    2013-10-15

    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.

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

    DOE Patents [OSTI]

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

    2012-01-17

    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.

  11. 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

  12. 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.

    2007-01-01

    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.

  13. 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.

    2015-02-23

    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

  14. Fungi in the future: Interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities

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

    Cotton, T. E. Anne; Fitter, Alastair H.; Miller, R. Michael; Dumbrell, Alex J.; Helgason, Thorunn

    2015-01-05

    Understanding the natural dynamics of arbuscular mycorrhizal (AM) fungi and their response to global environmental change is essential for the prediction of future plant growth and ecosystem functions. We investigated the long-term temporal dynamics and effect of elevated atmospheric carbon dioxide (CO2) and ozone (O3) concentrations on AM fungal communities. Molecular methods were used to characterize the AM fungal communities of soybean (Glycine max) grown under elevated and ambient atmospheric concentrations of both CO2 and O3 within a free air concentration enrichment experiment in three growing seasons over 5 yr. Elevated CO2 altered the community composition of AM fungi, increasingmore »the ratio of Glomeraceae to Gigasporaceae. By contrast, no effect of elevated O3 on AM fungal communities was detected. However, the greatest compositional differences detected were between years, suggesting that, at least in the short term, large-scale interannual temporal dynamics are stronger mediators than atmospheric CO2 concentrations of AM fungal communities. We conclude that, although atmospheric change may significantly alter AM fungal communities, this effect may be masked by the influences of natural changes and successional patterns through time. We suggest that changes in carbon availability are important determinants of the community dynamics of AM fungi.« less

  15. 2012 CELLULAR & MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 17 - 22, 2012

    SciTech Connect (OSTI)

    Judith Berman

    2012-06-22

    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.

  16. Field tolerance to fungal pathogens of Brassica napus constitutively expressing a chimeric chitinase gene

    SciTech Connect (OSTI)

    Grison, R.; Grezes-Besset, B.; Lucante, N.

    1996-05-01

    Constitutive overexpression of a protein involved in plant defense mechanisms to disease is one of the strategies proposed to increase plant tolerance to fungal pathogens. A hybrid endochitinase gene under a constitutive promoter was introduced by Agrobacterium-mediated transformation into a winter-type oilseed rape (Brassica napus var. oleifera) inbred line. Progeny from transformed plants was challenged using three different fungal pathogens (Cylindrosporium concentricum, Phoma lingam, Sclerotinia sclerotiorum) in field trials at two different geographical locations. These plants exhibited an increased tolerance to disease as compared with the nontransgenic parental plants. 31 refs., 1 fig., 2 tabs.

  17. 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

  18. 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

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

    E-Print Network [OSTI]

    Fierer, Noah

    Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks Krista L of Colorado, Boulder, Colorado, United States of America Abstract In urban environments, green roofs provide. However, little research has been done on the non-plant biota associated with green roofs, which likely

  20. Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by

    E-Print Network [OSTI]

    Snow, Christopher

    Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence has been used to generate active, thermostable cellobiohy- drolase class I (CBH I) enzymes from., 2007). Class I cellobiohydrolases (CBH Is or family 7 glycosyl hydrolases) are the principal components

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

    E-Print Network [OSTI]

    Hibbett, David S.

    of interacting communities, with thousands of species of animals, plants, fungi and bacteria. In soils, this complex web of life is responsible for the cycling of carbon (C), for water and nutrients, for soil, the US Department of Energy Joint Genome Institute (JGI) launched the Fungal Genomics Program (FGP

  2. 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

  3. 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

  4. 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

  5. Fungal and algal gene expression in early developmental stages of lichen-symbiosis

    E-Print Network [OSTI]

    Lutzoni, François M.

    -fungal interactions, symbiosis INTRODUCTION Members of kingdom Chloroplastida are ubiquitous in terrestrial, aquatic with Chloroplastida in which they have diversified into an array of terrestrial niches (Selosse and Le Tacon 1998) on the signaling pathways connecting lichen symbionts and on morphogenesis. The initial stages in the development

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

    E-Print Network [OSTI]

    Thomas, David D.

    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

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

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

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

    2015-04-23

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

  8. This article is from the April 2008 issue of

    E-Print Network [OSTI]

    Burns, Jacqueline K.

    of EfPKS1 is involved in the biosynthesis of elsinochromes via a fungal polyketide pathway, perylenequinone toxins are unique because they contain a core chromophore of phenolic quinone that is able

  9. A radioisotope based methodology for plant-fungal interactions in the rhizosphere

    SciTech Connect (OSTI)

    Weisenberger, A. G.; Bonito, G.; Lee, S.; McKisson, J. E.; Gryganskyi, A.; Reid, C. D.; Smith, M. F.; Vaidyanathan, G.; Welch, B.

    2013-10-01

    In plant ecophysiology research there is interest in studying the biology of the rhizosphere because of its importance in plant nutrient-interactions. The rhizosphere is the zone of soil surrounding a plant's root system where microbes (such as fungi) are influenced by the root and the roots by the microbes. We are investigating a methodology for imaging the distribution of molecular compounds of interest in the rhizosphere without disturbing the root or soil habitat. Our intention is to develop a single photon emission computed tomography (SPECT) system (PhytoSPECT) to image the bio-distribution of fungi in association with a host plant's roots. The technique we are exploring makes use of radioactive isotopes as tracers to label molecules that bind to fungal-specific compounds of interest and to image the fungi distribution in the plant and/or soil. We report on initial experiments designed to test the ability of fungal-specific compounds labeled with an iodine radioisotope that binds to chitin monomers (N-acetylglucosamine). Chitin is a compound not found in roots but in fungal cell walls. We will test the ability to label the compound with radioactive isotopes of iodine ({sup 125}I, and {sup 123}I).

  10. Methods for transforming and expression screening of filamentous fungal cells with a DNA library

    DOE Patents [OSTI]

    Teter, Sarah; Lamsa, Michael; Cherry, Joel; Ward, Connie

    2015-06-02

    The present invention relates to methods for expression screening of filamentous fungal transformants, comprising: (a) isolating single colony transformants of a DNA library introduced into E. coli; (b) preparing DNA from each of the single colony E. coli transformants; (c) introducing a sample of each of the DNA preparations of step (b) into separate suspensions of protoplasts of a filamentous fungus to obtain transformants thereof, wherein each transformant contains one or more copies of an individual polynucleotide from the DNA library; (d) growing the individual filamentous fungal transformants of step (c) on selective growth medium, thereby permitting growth of the filamentous fungal transformants, while suppressing growth of untransformed filamentous fungi; and (e) measuring activity or a property of each polypeptide encoded by the individual polynucleotides. The present invention also relates to isolated polynucleotides encoding polypeptides of interest obtained by such methods, to nucleic acid constructs, expression vectors, and recombinant host cells comprising the isolated polynucleotides, and to methods of producing the polypeptides encoded by the isolated polynucleotides.

  11. 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.

    2012-09-17

    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.

  12. Synthetic studies applied to polyketide natural products

    E-Print Network [OSTI]

    Mandel, Alexander

    2008-01-01

    synthesis of two keystone diastereomers . . . . . . . 3.5.23.11: Synthesis of two keystone diastereomers 115a andhas been dubbed the “keystone” as this piece is available

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

    E-Print Network [OSTI]

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

  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.

    2013-11-01

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

    SciTech Connect (OSTI)

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

    2013-01-01

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

  16. Pd-Catalyzed Cyclizations Direct Oxidative Heck

    E-Print Network [OSTI]

    Stoltz, Brian M.

    events: 1) halogenation of an aryl or vinyl precursor and 2) palladium(0)-catalyzed CÀC bond formation to develop palladium(ii)-catalyzed dehydrogenation as a general oxidation method,[6,7] we recently described with subsequent olefin insertion and b-hydrogen elimina- tion.[9] Importantly, this mechanism is analogous

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

    SciTech Connect (OSTI)

    Kingsley, Mark T

    2001-03-13

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

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

    SciTech Connect (OSTI)

    Kingsley, Mark T.

    2001-03-13

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

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

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

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

    2015-09-04

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

  20. 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

    2011-12-29

    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.

  1. 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

  2. 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.

    2014-08-26

    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.

  3. Active site mapping of iterative polyketide synthases and the detection of polyketide intermediates using high- resolution Fourier Transform mass spectrometry

    E-Print Network [OSTI]

    Meehan, Michael Joseph

    2009-01-01

    be ejected during thermal activation methods and that thisPEA is accomplished using thermal activation methods.are a large number of thermal activation methods that could

  4. 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 ...

  5. 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.

    2006-08-30

    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.

  6. 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.

    2012-05-04

    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.

  7. Enrichment and broad representation of plant biomass-degrading enzymes in the specialized hyphal swellings of Leucoagaricus gongylophorus, the fungal symbiont of leaf-cutter ants

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

    Aylward, Frank O.; Khadempour, Lily; Tremmel, Daniel M.; McDonald, Bradon R.; Nicora, Carrie D.; Wu, Si; Moore, Ronald J.; Orton, Daniel J.; Monroe, Matthew E.; Piehowski, Paul D.; et al

    2015-08-28

    Leaf-cutter ants are prolific and conspicuous constituents of Neotropical ecosystems that derive energy from specialized fungus gardens they cultivate using prodigious amounts of foliar biomass. The basidiomycetous cultivar of the ants, Leucoagaricus gongylophorus, produces specialized hyphal swellings called gongylidia that serve as the primary food source of ant colonies. Gongylidia also contain plant biomass-degrading enzymes that become concentrated in ant digestive tracts and are deposited within fecal droplets onto fresh foliar material as ants incorporate it into the fungus garden. Although the enzymes concentrated by L. gongylophorus within gongylidia are thought to be critical to the initial degradation of plantmore »biomass, only a few enzymes present in these hyphal swellings have been identified. Here we use proteomic methods to identify proteins present in the gongylidia of three Atta cephalotes colonies. Our results demonstrate that a diverse but consistent set of enzymes is present in gongylidia, including numerous plant biomass-degrading enzymes likely involved in the degradation of polysaccharides, plant toxins, and proteins. Overall, gongylidia contained over three quarters of all biomass-degrading enzymes identified in the L. gongylophorus genome, demonstrating that the majority of the enzymes produced by this fungus for biomass breakdown are ingested by the ants. We also identify a set of 40 of these enzymes enriched in gongylidia compared to whole fungus garden samples, suggesting that certain enzymes may be particularly important in the initial degradation of foliar material. Our work sheds light on the complex interplay between leaf-cutter ants and their fungal symbiont that allows for the host insects to occupy an herbivorous niche by indirectly deriving energy from plant biomass.« less

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

    E-Print Network [OSTI]

    Willumstad, Thomas P. (Thomas Paul)

    2013-01-01

    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 ...

  9. The Development and Application of Gold(I)-Catalyzed Cyclization Cascades

    E-Print Network [OSTI]

    Sethofer, Steven Gregory

    2011-01-01

    lithium trimethylsilylacetylide to give tertiary alcohol 4.43. Deprotection and esterification then provided acetate

  10. Mechanistic and Reactivity Studies of Cationic Cyclizations Catalyzed by Supramolecular Encapsulation

    E-Print Network [OSTI]

    Hastings, Courtney James

    2010-01-01

    lithium wire ( 45.2 mmol), 2.3 mL 2-bromo-2- butene (22.6 mmol), and 1.0 g ethyl acetate-lithium wire (27.7 mmol), 1.87 g (E)-2-bromo-2-butene (13.9 mmol), and 0.680 mL ethyl acetate (

  11. The effect of host structure on the selectivity and mechanism of supramolecular catalysis of Prins cyclizations

    SciTech Connect (OSTI)

    Hart-Cooper, William M.; Zhao, Chen; Triano, Rebecca M.; Yaghoubi, Parastou; Ozores, Haxel Lionel; Burford, Kristen N.; Toste, F. Dean; Bergman, Robert G.; Raymond, Kenneth N.

    2014-11-28

    The effect of host structure on the selectivity and mechanism of intramolecular Prins reactions is evaluated using K12Ga4L6 tetrahedral catalysts. The host structure was varied by modifying the structure of the chelating moieties and the size of the aromatic spacers. While variation in chelator substituents was generally observed to affect changes in rate but not selectivity, changing the host spacer afforded differences in efficiency and product diastereoselectivity. An extremely high number of turnovers (up to 840) was observed. Maximum rate accelerations were measured to be on the order of 105, which numbers among the largest magnitudes of transition state stabilization measured with a synthetic host-catalyst. Host/guest size effects were observed to play an important role in host-mediated enantioselectivity.

  12. The effect of host structure on the selectivity and mechanism of supramolecular catalysis of Prins cyclizations

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

    Hart-Cooper, William M.; Zhao, Chen; Triano, Rebecca M.; Yaghoubi, Parastou; Ozores, Haxel Lionel; Burford, Kristen N.; Toste, F. Dean; Bergman, Robert G.; Raymond, Kenneth N.

    2014-11-28

    The effect of host structure on the selectivity and mechanism of intramolecular Prins reactions is evaluated using K12Ga4L6 tetrahedral catalysts. The host structure was varied by modifying the structure of the chelating moieties and the size of the aromatic spacers. While variation in chelator substituents was generally observed to affect changes in rate but not selectivity, changing the host spacer afforded differences in efficiency and product diastereoselectivity. An extremely high number of turnovers (up to 840) was observed. Maximum rate accelerations were measured to be on the order of 105, which numbers among the largest magnitudes of transition state stabilizationmore »measured with a synthetic host-catalyst. Host/guest size effects were observed to play an important role in host-mediated enantioselectivity.« less

  13. Mechanistic and Reactivity Studies of Cationic Cyclizations Catalyzed by Supramolecular Encapsulation

    E-Print Network [OSTI]

    Hastings, Courtney James

    2010-01-01

    the maximum reaction velocity (V max ) will be equal to thatto reach the maximum reaction velocity in the presence ofthe maximum velocity of the reaction, K m is the Michaelis

  14. The Development and Application of Gold(I)-Catalyzed Cyclization Cascades

    E-Print Network [OSTI]

    Sethofer, Steven Gregory

    2011-01-01

    79B) C(79)-H(79C) C(80)- H(80A) C(80)-H(80B) C(80)-H(80C) C(C(79)-H(79C) H(79B)-C(79)-H(79C) C(77)-C(80)-H(80A) C(77)-C(80)-H(80B) H(80A)-C(80)-H(80B) C(77)-C(80)-H(80C) H(80A)-C(

  15. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01

    strains. Appl. Microbiol. Biotech. 74:937-953. Hahn-HägerdalJ Indust Microbiol Biotech. 30:279-291. Schneider H, WangPachysolen tannophilus. Biotech Letts. 3:89-92. Sharon E,

  16. Understanding the Forest Microbiome: A Fungal Perspective

    SciTech Connect (OSTI)

    Vilgalys, Rytas [Duke University

    2014-03-19

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

  17. 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.

    2011-04-29

    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.

  18. ORIGINAL PAPER Ectomycorrhizal fungal sporocarp diversity

    E-Print Network [OSTI]

    Henkel, Terry

    monodominant forests of the Guiana Shield Terry W. Henkel · M. Catherine Aime · Mimi M. L. Chin · Steven L. Miller · Rytas Vilgalys · Matthew E. Smith Received: 8 July 2011 / Accepted: 23 September 2011 Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA S. L. Miller

  19. Transcriptome and Biochemical Analyses of Fungal Degradation...

    Office of Scientific and Technical Information (OSTI)

    proposal is aimed at identifying the enzymes which are known to depolymerize woody biomass. Fundamental understanding of how nature gains access to cellulose and hemicellulose...

  20. Fueling the Future with Fungal Genomics

    E-Print Network [OSTI]

    Grigoriev, Igor V.

    2011-01-01

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

  1. The FungalWeb Ontology The Core of a Semantic Web Application for Fungal Genomics

    E-Print Network [OSTI]

    Haarslev, Volker

    -Nejad, Christopher J.O Baker, Greg Butler, Volker Haarslev Department of Computer Science and Software Engineering and knowledge, but most of the information generated by biologists is in the contextual form e.g. natural specification of biological knowledge to make the information computationally accessible and semantically clear

  2. Selective Monoterpene-like Cyclization Reactions Achieved by Water Exclusion from Reactive Intermediates in a Supramolecular Catalyst

    E-Print Network [OSTI]

    Hart-Cooper, William

    2014-01-01

    9  has  been  observed when water is absent.   (31)  For the  exclusion  of  water  from  reactive  intermediates Reactions Achieved by Water Exclusion from Reactive

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

    E-Print Network [OSTI]

    Ariyarathna, Yamuna Kumari

    2014-08-31

    heteronuclear multiple bond correlation HMPA hexamethylphosphoramide HPLC high performance liquid chromatography HSQC heteronuclear single quantum coherence K2CO3 potassium carbonate Ln ligand LAH lithium aluminum hydride LG....13 Synthesis of acyl pyrroles Use of pre-prepared lithium pyrrolide proved to be successful for the nucleophilic substitution of the acyl chloride. The synthesized acyl pyrrole ester was subjected to the decarboxylative allylation conditions. To our delight...

  4. 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 ...

  5. MycoCosm, an Integrated Fungal Genomics Resource (Conference...

    Office of Scientific and Technical Information (OSTI)

    service. Visit OSTI to utilize additional information resources in energy science and technology. A paper copy of this document is also available for sale to the public from...

  6. Fungal Genomics Presentation for BETO 2015 Project Peer Review

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

    Maximize TRY: high Titer for downstream processing efficiency high Rate to minimize CAPEXOPEX high Yield to maximize use of costly biomass feedstocks Robust organisms for...

  7. Fungal Diversity Diversity of saprobic hyphomycetes on Proteaceae and

    E-Print Network [OSTI]

    Institute, 2 Professor Popov Street, 197376 St. Petersburg, Russia 3 Department of Biological Sciences. In South Africa they are used for landscaping and floral decoration, and the flowers are exported

  8. Fungal Genomics Program Grigoriev, Igor 59 BASIC BIOLOGICAL SCIENCES...

    Office of Scientific and Technical Information (OSTI)

    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...

  9. Fungal Genomics Program (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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...

  10. Fungal Diversity Pseudocercospora flavomarginata sp. nov., from Eucalyptus

    E-Print Network [OSTI]

    countries, where timber is used primarily for the paper and pulp industry. In South-East Asia, the forestry industry is expanding rapidly, and it has been estimated that there are approximately 2 million ha

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

    SciTech Connect (OSTI)

    Berbee, Mary [University of British Columbia

    2014-03-19

    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.

  12. Anthocyanins Reduce Fungal Growth in Fruits H. Martin Schaefera*

    E-Print Network [OSTI]

    Schaefer, Martin

    is to impart colors, the adaptive significance of anthocyanins in plant reproductive organs is invariably, cyanidin, seed dispersal, fruit color, plant interaction, fruit pathogens. The adaptive functions of non as light screens protecting the photosynthetic apparatus against excess light because they absorb light

  13. 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

  14. Surface tension propulsion of fungal spores by use of microdroplets

    E-Print Network [OSTI]

    Noblin, Xavier; Dumais, Jacques

    2010-01-01

    Many edible mushrooms eject their spores (about 10 microns in size) at high speed (about 1 m/s) using surface tension forces in a few microseconds. Basically the coalescence of a droplet with the spore generates the necessary momentum to eject the spore. We have detailed this mechanism in \\cite{noblin2}. In this article, we give some details about the high speed movies (up to 250000 fps) of mushrooms' spores ejection attached to this submission. This video was submitted as part of the Gallery of Fluid Motion 2010 which is showcase of fluid dynamics videos.

  15. JGI Fungal Genomics Program Grigoriev, Igor V. 99; BIOFUELS;...

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  16. JGI Fungal Genomics Program (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  17. Fungal Genomics Program (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  18. Intercropped silviculture systems, a key to achieving soil fungal community

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing(Journal Article)lasers(JournalatBaBartheExpansionSciTechmanagement in eucalyptus

  19. Intercropped silviculture systems, a key to achieving soil fungal community

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing(Journal Article)lasers(JournalatBaBartheExpansionSciTechmanagement in

  20. Transcriptome and Biochemical Analyses of Fungal Degradation of Wood

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory of rare Kaon and PionExperiments (Journallithium ionToxin-eating

  1. Transcriptome and Biochemical Analyses of Fungal Degradation of Wood

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory of rare Kaon and PionExperiments (Journallithium ionToxin-eating(Technical

  2. 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

    2010-01-01

    3 ). Dialkenyl zinc 2.53. E-2-butenyl bromide (1.80 mL, 17.7zinc species was added as slowly as possible to the refluxing solution of bromide

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

    SciTech Connect (OSTI)

    Neurock, Matthew

    2011-05-26

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

  4. Synthetic studies toward complex Schisandraceae and zoanthamine natural products

    E-Print Network [OSTI]

    Fischer, Derek A.

    2008-01-01

    cycloaddition with 1,3 butadiene, stereo and regioselective163). The 2-amino-1,3-butadiene cyclization substrate (404)examples of 2-amino-1,3 butadienes as cyclization substrates

  5. Evidence for Catalytic CysteineHistidine Dyad in Chalcone Synthase

    E-Print Network [OSTI]

    Suh, Dae-Yeon

    -CoA, but catalyze differ- ent cyclization reactions to produce naringenin chal- cone and resveratrol, respectively

  6. In vitro reconstitution and crystal structure of p-aminobenzoate N-oxygenase (AurF) involved

    E-Print Network [OSTI]

    Zhao, Huimin

    for Biophysics and Computational Biology, and Institute for Genomic Biology, University of Illinois at Urbana Streptomyces thiolu- teus catalyzes the formation of unusual polyketide synthase starter unit p

  7. 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.

    2010-01-01

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

  8. Host resistance and pathogen-derived hormone affect the outcome of a fungal-plant interaction

    E-Print Network [OSTI]

    Cole, Stephanie Joy

    2012-01-01

    microorganisms are referred to as microbe-associated molecular patterns (MAMPs), formerly referred to as pathogen-

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

    E-Print Network [OSTI]

    Sain, Divya

    2013-01-01

    Reviews 23(1–2): 1-8. Duo-Chuan, L. (2006). "Review ofexpression in bacteria." Yi Chuan 33( 10): 1029-38. Figure 1Wiwat et al. 2004; Duo-Chuan 2006; Gan, Yang et al. 2007).

  10. 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

  11. Peach Leaf CurlPeach Leaf Curl Peach leaf curl is a fungal disease that

    E-Print Network [OSTI]

    Ishida, Yuko

    to increase effectiveness. Bordeaux mixture is a home-made copper sulfate and lime mixture that must

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

    E-Print Network [OSTI]

    disease in Oman and Pakistan Marelize van Wyk1* , Ali O. Al Adawi2 , Iqrar A. Khan3 , Michael L. Deadman4 and Biology (NIAB), P.O. Box 128, Jhang Road, Faisalabad, Pakistan 4 Department of Crop Sciences, P.O. Box 34). Ceratocystis manginecans sp. nov., causal agent of a destructive mango wilt disease in Oman and Pakistan

  13. Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest

    E-Print Network [OSTI]

    functioning, but the determinates of their diversity and functional interactions are not well known) food webs (Kaspari et al. 2008). While litter decomposition is mediated by both biotic and abiotic

  14. Soil fungal effects on floral signals, rewards, and aboveground interactions in an alpine pollination web

    E-Print Network [OSTI]

    Becklin, Katie M.; Gamez, Guadelupe; Uelk, Brian; Raguso, Robert A.; Galen, Candace

    2011-08-01

    • Premise of the study: Plants interact with above- and belowground organisms; the combined effects of these interactions determine plant fitness and trait evolution. To better understand the ecological and evolutionary implications of multispecies...

  15. Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey

    E-Print Network [OSTI]

    Seidl, Verena

    2010-01-01

    Secondary metabolites influence Arabidopsis/Botrytis interactions: variation in host production and pathogen sensitivity. Plant

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

    E-Print Network [OSTI]

    of the bacterial pathogen Pseudomonas syringae pv. maculicola (Psm). All three mutants develop a hypersensitive response when in®ltrated with Psm expressing the avirulence gene avrRpt2, which activates resistance via the LZ-NBS/LRR resistance protein encoded by RPS2. The growth of Psm(avrRpt2), while somewhat greater

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

    E-Print Network [OSTI]

    Husted, James Ross

    2005-02-17

    red or white discharge). Upon evisceration the reproductive tract was removed and the vagina was opened up to reveal the vaginal fornix. Each tract was swabbed twice circumferentially around the vaginal fornix, and then the swab (BBL Sparks...

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

    E-Print Network [OSTI]

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

    2012-01-01

    , diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania...

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

    E-Print Network [OSTI]

    Wang, Chih-Li

    2012-10-19

    -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...

  20. Fungal inoculation and methyl jasmonate application induce highly variable terpene accumulation in Norway spruce

    E-Print Network [OSTI]

    in Norway spruce Tao Zhao 1, Paal Krokene 2, Niklas Björklund 3, Nadir Erbilgin 4 , Erik Christiansen 2 Bo of Chemistry, KTH, SE-100 44 Stockholm, Sweden 2 Norwegian Forest and Landscape Institute, N-1431 Ås, Norway 3 healthy forests. With the aims of characterizing the defensive chemical induction in Norway spruce Picea

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

    E-Print Network [OSTI]

    Shefferson, Richard P.

    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

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

    E-Print Network [OSTI]

    Sain, Divya

    2013-01-01

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

  3. DISEASED EUPHORBIA TREES IN SOUTH AFRICA HARBOURS UNEXPLORED FUNGAL AND INSECT BIODIVERSITY, INCLUDING

    E-Print Network [OSTI]

    alarming reports of large-scale decline and death of Euphorbia ingens trees in South Africa. Mortality of these iconic trees as part of an MSc project. During investigations into the death of E. ingens, as well as E identified and are associated with die-back symptoms on E. ingens. L. theobromae was isolated from Cossonus

  4. PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution

    E-Print Network [OSTI]

    Boyer, Edmond

    alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-a high no role in study design, data collection and analysis, decision to publish, or preparation, The Netherlands, 4 Universite´ de Rennes I, CNRS, UMR 6074 IRISA, Campus de Beaulieu, Rennes, France, 5 Centre

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

    E-Print Network [OSTI]

    and are classified by the Centers for Disease Control and Prevention as one of the six highest risk threat agents in the Supporting Information) of the MLSMR was performed using Docking- based Virtual Screening Pipeline (DOVIS).5

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

    SciTech Connect (OSTI)

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

    2013-11-01

    This techno-economic analysis assesses the process economics of ethanol production from lignocellulosic feedstock by fungi in order 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. Organism performance and technology readiness are split into three groups: near-term (<5 years), mid-term (5-10 years) and long-term (>10 years) process deployment. Processes classified as near-term could reasonably be developed in this shorter time frame, as suggested by recent literature. Mid-term technology process models are based on lab-scale experimental data, and yields near the theoretical limit are used to estimate long-term technology goals. Further research and economic evaluation on the integrated production of chemicals and fuels in biorefineries are recommended.

  7. Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey

    E-Print Network [OSTI]

    Seidl, Verena

    2010-01-01

    Development of improved biocontrol agents for agricul- turalment or selection of biocontrol agents. We also expect that

  8. Distribution and drivers of ectomycorrhizal fungal communities across the North American Arctic

    E-Print Network [OSTI]

    Taylor, Lee

    of the North American Arctic. We collected roots from two principal arctic ectomycorrhizal host plants, Salix, and Pyronemataceae. Both host plants showed similar species richness, with 176 OTUs on Salix arctica and 154 OTUs

  9. Asthma and the Diversity of Fungal Spores in Air Anne Pringle*

    E-Print Network [OSTI]

    Pringle, Anne

    diversity of fungi involved in asthma. What Is Asthma? Asthma is a complex disease without a single cause inhalation of allergens, but atopic asthmas are caused by the body's interaction with allergens outside in causing asthma is unknown. Why Do Fungi Make Spores? And a Guide to Terminology The jargon associated

  10. 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

  11. 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

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

    E-Print Network [OSTI]

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

    2007-01-01

    38,39] and long [40,41] evo- lutionary timescales; however,Koonin EV: Analysis of evo- lution of exon-intron structure

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

    E-Print Network [OSTI]

    Sain, Divya

    2013-01-01

    109(Pt 2): 150-8. Araujo-Palomares, C. L. , M. Riquelme, etthe Spitzenkörper (Araujo-Palomares, Riquelme et al. 2009).

  14. Short communication Microsite differences in fungal hyphal length, glomalin, and soil

    E-Print Network [OSTI]

    Rilli, Matthias C.

    , 2001). Soil structure has a prevailing role in soil infiltration and biogeochem- ical processes), lower temperature (Maestre et al., 2001), higher infiltration capacity (Maestre et al., 2002a), a larger in semiarid steppes of SE Spain. This study was conducted at three S. tenacissima steppes located

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

    E-Print Network [OSTI]

    King, Alison

    2011-04-01

    stress on the oats. These water additions did not produce leachate. Once weekly, pots 18 were inundated with either 40 or 60 mL water, and leachate was collected in scintillation vials, which were then stored at 4° C. At the end of six weeks all... with lactophenol cotton blue, mounting on slides, and examining roots at 10x-40x magnification. Dry oat biomass was collected after one week at 60° C. Nitrate and ammonium content were then measured from leachate samples on a Lachat Quickchem Autoanalyzer...

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

    E-Print Network [OSTI]

    Robertson, L. D.

    1998-01-01

    Bioaerosol concentrations between 200 - 450 CFU/m3 have remained largely uncharacterized with respect to potential indoor air quality concerns. This research provides for further description of indoor bioaerosol concentrations and concludes that 3 0...

  17. Deleterious activity of cultivated grasses (Poaceae) and residues on soilborne fungal, nematode and weed pests

    E-Print Network [OSTI]

    Stapleton, James J.; Summers, Charles G.; Mitchell, Jeffrey P.; Prather, Timothy S.

    2010-01-01

    on wheat seedlings. Crop Science, 35, 1652–1656. Burgos, N.system with cover crops. Weed Science, 44, 355–361. Cheema,

  18. Host resistance and pathogen-derived hormone affect the outcome of a fungal-plant interaction

    E-Print Network [OSTI]

    Cole, Stephanie Joy

    2012-01-01

    resistance and pathogen-derived hormone affect the outcomeresistance and pathogen-derived hormone affect the outcomemetabolites. These pathogen-derived hormones can alter plant

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

    E-Print Network [OSTI]

    Nguyen, Henry

    2010-11-17

    .2.4. Hatakeyama ? s Enantiosel e c t i v e Sy nthe sis of (?)-1.1a Hatakeyama?s synthesis of ( ? )-1.1a 6h began with propargyl alcohol 1.37 by a palladium mediated addition to an acetal dehyde derivative to give ether 1.38 . The PMB protection group...

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

    E-Print Network [OSTI]

    Heffron, Timothy Paul

    2005-01-01

    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 ...

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

    DOE Patents [OSTI]

    Dai, Ziyu (Richland, WA); Lasure, Linda L. (Fall City, WA); Magnuson, Jon K. (Pasco, WA)

    2008-11-11

    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.

  2. Isolated Fungal Promoters and Gene Transcription Terminators and Methods of Protein and Chemical Production in a Fungus

    DOE Patents [OSTI]

    Dai, Ziyu (Richland, WA); Lasure, Linda L. (Fall City, WA); Magnuson, Jon K. (Pasco, WA)

    2008-11-11

    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.

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

    SciTech Connect (OSTI)

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

    2014-05-27

    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.

  4. The contribution of fungal spores and bacteria to regional and global aerosol number and ice nucleation immersion freezing rates

    E-Print Network [OSTI]

    Spracklen, D. V.

    Primary biological aerosol particles (PBAPs) may play an important role in aerosol–climate interactions, in particular by affecting ice formation in mixed phase clouds. However, the role of PBAPs is poorly understood because ...

  5. 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

    2009-05-15

    LOL is a novel secondary metabolite gene cluster associated with the production of loline alkaloids (saturated 1-aminopyrrolizidine alkaloids with an oxygen bridge) exclusively in closely related grass-endophyte species in the genera Epichloë...

  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

    2011-01-01

    on request from PLoS (Public Library of Science) by sendingrequest to PLoS ONE, Public Library of Science, 1160 Batteryand postage) payable to ‘‘Public Library of Science’’. This

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

    E-Print Network [OSTI]

    Subbarao, Krishna V

    2011-01-01

    Centre, Charlottetown, Prince Edward Island, Canada Abstractstrain PD747 (Canada: Prince Edward Island; potato fieldsoil), PD747 (Canada: Prince Edward Island; potato field

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

    E-Print Network [OSTI]

    Subbarao, Krishna V

    2011-01-01

    Centre, Charlottetown, Prince Edward Island, Canada AbstractPD747 (Canada: Prince Edward Island; potato field soil)PD747 (Canada: Prince Edward Island; potato field soil) and

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

    E-Print Network [OSTI]

    Elisabet Ottosson Community ecology in a changing world 120614 Natalija Ashipova Monocultures of the mind

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

    E-Print Network [OSTI]

    The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA National Laboratory, United States of America Received February 23, 2013; Accepted October 16, 2013

  11. Rapid genome resequencing of an atoxigenic strain of Aspergillus

    Office of Scientific and Technical Information (OSTI)

    de Barcelona, Bellaterra, Catalonia (Spain) 59 BASIC BIOLOGICAL SCIENCES fungal genomics; gene regulatory networks fungal genomics; gene regulatory networks In...

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

    E-Print Network [OSTI]

    Liu, Qingsong

    2009-05-15

    Apoptolidin 1.1 was isolated in 1997 by Hayakawa and co-workers from a soil bacterium Nocardiopsis sp. during screening for specific apoptosis inducers. The primary biological test revealed that this polyketide macrolide induced apoptosis in cells...

  13. Template Synthesis, Properties, and Crystal Structure of a Trigonal Bipyramidal Cobalt(II)

    E-Print Network [OSTI]

    Paik Suh, Myunghyun

    (II) Octaazamacrobicyclic Complex Myunghyun Paik Suh,* Jaeho Lee, Mi Young Han, and Tea Sung Yoon Department of Chemistry under a nitrogen atmosphere. While the cyclization reaction proceeded, the brownish green color

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

    SciTech Connect (OSTI)

    Eisenbraun, E.J.

    1991-02-15

    The synthesis route for preparing the title compound, has been carried out on a small scale for the preparation of a mixture of isomers. Alternative routes for the cyclization are being explored. (DLC)

  15. Synthesis of 6-Methyl-9-propyldibenzothiophene-4-ol. Technical progress report No. 2, October 25, 1990--January 25, 1991

    SciTech Connect (OSTI)

    Eisenbraun, E.J.

    1991-02-15

    The synthesis route for preparing the title compound, has been carried out on a small scale for the preparation of a mixture of isomers. Alternative routes for the cyclization are being explored. (DLC)

  16. 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 ...

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

    E-Print Network [OSTI]

    Armbrust, Kurt W. (Kurt Willes)

    2014-01-01

    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 ...

  18. 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 ...

  19. vol. 164, supplement the american naturalist november 2004 The Rise and Fall of a Six-Year Coral-Fungal Epizootic

    E-Print Network [OSTI]

    Harvell, Catherine Drew

    marine ecosystems. Although pathogens and other microorganisms now dominate the ecology of some coastal the following hypotheses for decline of the epizootic: change in environment, change in pathogen input of pathogen input, or environmental conditions (water quality and temperature), is likely to promote

  20. 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

    2014-07-07

    ^(lon) -linked. To enable large-scale SNP applications, we developed inexpensive methods for high-throughput non-destructive seed DNA extraction for PCR-based genotyping. We then high-resolution mapped 10 SNPs in the proximal alien segment near Ren^(lon). We...

  1. 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

    2011-01-01

    by beadbeating with 0.3g zirconia/silica beads (BioSpeccontaining 0.3 g of 0.5 mm zirconia/silica beads (Biospec

  2. The influence of bacterial and fungal isolates from the rhizosphere of Tamcot CAMD-E on host response to Phymatotrichum root rot of cotton 

    E-Print Network [OSTI]

    Lazo, Gerard Raymond

    1984-01-01

    with the water-only treatment had the highest incidence of disease, and also had the lowest seed cotton yield; but the RW-E+Fu-E treated plants had the lowest incidence of root rot and one of the lowest yields (Table 3). Trends apparent in this experiment... inoculation' 105 110 115 120 125 130 1 Control 2 T-E 3 SW-E 4 WA-E 5 RW-E 6 Fu-E 7 T-E+Fu-E 8 SW-E+Fu-E 9 WA-E+Fu-E 10 RW-E+Fu-E 'A total of 12 plants were inoculated for each treatment. The experiment had an average of 23 I incidence of dead...

  3. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    Aut noma de Barcelona Bellaterra Catalonia Spain BASIC BIOLOGICAL SCIENCES fungal genomics gene regulatory networks fungal genomics gene regulatory networks In microorganisms...

  4. Trichoderma: the genomics of opportunistic success

    E-Print Network [OSTI]

    Druzhinina, Irina S.

    2011-01-01

    and plant responses to fungal biocontrol agents. Annu. Rev.about how fungal biocontrol agents stimulate the plantsativus L. ) by the biocontrol agent Trichoderma harzianum.

  5. 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)

    2009-09-15

    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.

  6. 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)

    2009-10-06

    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.

  7. Protist, Vol. 159, 21--30, January 2008 http://www.elsevier.de/protis

    E-Print Network [OSTI]

    Gent, Universiteit

    acid synthases involved in lipid metabolism. Polyketide biosynthesis of secondary metabolites and hence). Numerous functions in nature have been pro- posed for these secondary metabolites, ranging from chemical 44, 66651 Banyuls sur mer cedex, France c Department of Plant Systems Biology, Flanders

  8. Acta Cryst. (2000). D56, 16471651 Beynon et al. Tetracenomycin A2 oxygenase 1647 crystallization papers

    E-Print Network [OSTI]

    Fisher, Andrew J.

    2000-01-01

    biosynthesis John Beynon,a Elpidio R. Rafanan Jr,a Ben Shena and Andrew J. Fishera,b * a Department Polyketide biosynthesis is responsible for a large number of biologically active molecules. In many cases, such as p-hydroxybenzoate hydroxylase (PHBH, 27.4% identity; Schreuder et al., 1988) and phenol hydroxylase

  9. Microbial Metabolism Databases of Microbial

    E-Print Network [OSTI]

    Huang, Ching-Tsan

    1 Microbial Metabolism Databases of Microbial Metabolism & Degradation Ching-Tsan Huang () Office://www.ebi.ac.uk/ http://umbbd.msi.umn.edu/index.html #12;9 http://umbbd.msi.umn.edu/meta/meta_map.html #12;10 Microbial, Energy, Lipids, Nucleotides, Amino acids, Glycans, Polyketides/Nonribosome peptides, Secondary

  10. Cryptosporidium parvum: enhancing our understanding of its unique fatty acid metabolism and the elucidation of putative new inhibitors 

    E-Print Network [OSTI]

    Fritzler, Jason Michael

    2008-10-10

    synthase (CpFAS1), C. parvum also possesses an enormous type I polyketide synthase (CpPKS1). Because of the size of this megasynthase, functional characterization of the complete enzyme is not possible. We have isolated and characterized the loading unit...

  11. Total synthesis of gracilioether F. Development and application of Lewis acid promoted ketene–alkene [2+2] cycloadditions and late-stage C—H oxidation

    SciTech Connect (OSTI)

    Rasik, Christopher M.; Brown, M. Kevin

    2014-12-22

    The first synthesis of gracilioether F, a polyketide natural product with an unusual tricyclic core and five contiguous stereocenters, is described. Key steps of the synthesis include a Lewis acid promoted ketene–alkene [2+2] cycloaddition and a late-stage carboxylic acid directed C(sp³)—H oxidation. The synthesis requires only eight steps from norbornadiene.

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

    SciTech Connect (OSTI)

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

    2008-05-22

    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.

  13. Copyright 2010 CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. You are free to share -to copy, distribute and transmit the work, under the following conditions

    E-Print Network [OSTI]

    , Polizzi & Vitale 2001, Crous 2002, Polizzi et al. 2006, 2007, 2009, Vitale et al. 2009), where it causes, Crous 2002, Polizzi et al. 2006, 2007, 2009, Vitale et al. 2009). Schoch et al. (2001) considered female

  14. Limnol. Oceanogr., 49(3), 2004, 680685 2004, by the American Society of Limnology and Oceanography, Inc.

    E-Print Network [OSTI]

    Kagami, Maiko

    and Oceanography, Inc. Daphnia can protect diatoms from fungal parasitism Maiko Kagami,1 Ellen Van Donk, Arnout de

  15. www.newphytologist.org 169 Blackwell Publishing, Ltd.

    E-Print Network [OSTI]

    -year seedlings of Salix reinii with ECM mother trees that had been inoculated with one of 11 dominant ECM fungal

  16. Carbon-Carbon Bond Formation Promoted by Organoruthenium Complexes. The First Unsubstituted

    E-Print Network [OSTI]

    Girolami, Gregory S.

    metallabenzene complexes have been de- scribed. Stable sulfide- or thiol-substituted osmabenzene complexes have been obtained via a cyclization reaction from two molecules of acetylene and an osmium-thio- carbonyl group on a carbonyl ligand; the dienediyl group can be in the form of an external reagent

  17. Science in China Series B: Chemistry 2009 SCIENCE IN CHINA PRESS

    E-Print Network [OSTI]

    Wang, Jianbo

    found that -carbonyl allenic sulfides can cyclize to generate furan products with high efficiency when metal-catalyzed rearrangement of -carbonyl allenic sulfides to form furans. Scheme 3 Synthesis of furan.springerlink.com Synthesis of furan from allenic sulfide derivatives PENG LingLing, ZHANG Xiu, MA Jie, ZHONG ZhenZhen, ZHANG

  18. Frontiers in Catalysis Science and Engineering Seminar Series

    E-Print Network [OSTI]

    Frontiers in Catalysis Science and Engineering Seminar Series H· Transfer from Transition-Metal Hydrides. Applications to Radical Polymerizations and Cyclizations Presented by... Jack R. Norton(II) metalloradical, but both the metalloradical and the hydride are present during the operation of newer (Cr

  19. Synthesis of (-)-Tetracycline Mark G. Charest, Dionicio R. Siegel, and Andrew G. Myers*

    E-Print Network [OSTI]

    group of the Diels-Alder adduct 5 (triethyl- amine trihydrofluoride, 76%) and oxidized the hydroxyl to bring about the cycloaddition of hydroxyl-protected variants of enone 3 (or 2) with the diene precursor R-hydroxyl group within enone 3 is an important feature of the successful Diels-Alder cyclization

  20. University of Southern California Dornsife College of Letters, Arts and Sciences

    E-Print Network [OSTI]

    Rohs, Remo

    , University of Southern California "Towards Oil Independence through Renewable Methanol Chemistry" 9 Szantay, Technical University of Budapest "Methylene Insertion into the Aromatic Ring in Place:30-11:50 Tomohiko Ohwada, The University of Tokyo "Acid-Catalyzed Cyclization Reactions to Functionalize Aromatic

  1. Communications J,Org. Chem., Vol.40, No. 14, 1975 2141 for 7 hr led quantitatively to a mixture of the pseudo-acid

    E-Print Network [OSTI]

    Keinan, Ehud

    , and the resulting amide mixture was cyclized using as medium 10% sodium acetate-acetic acid for 20 hr at 25'. After of 12a was removed by reaction with lithium mercaptide in HMPAZ2yielding 90% of 20(S)-camptothec- in (12

  2. Synthetic and Biosynthetic Studies of Natural Products

    E-Print Network [OSTI]

    Ve?liz Chanis, Eduardo Alberto

    1992-05-01

    of 4-Demethoxy -A-Homodaunorubicin Analogs Part II. Biosynthesis of Coloradocin. Origin of the Carbons Part III. Total Synthesis of the Naturally Occurring Prenylated Bibenzyl Amorfrutin A Eduardo Alberto Veliz Chanis B.S., University of Panama... to the intractable behavior of some of the intermediates. Part II describes the elucidation of the biosynthesis of coloradocin by the use of stable isotopes. The major carbon chain is polyketide and derived from acetate-propionate and methionine as shown...

  3. Probing the Biosynthesis and Mode of Action of Azinomycin B 

    E-Print Network [OSTI]

    Kelly, Gilbert Thomson

    2010-10-12

    5. Typical Examples of Natural Product Structures from the Polyketide, Alkaloid, NRPS, Terpene, and Shikimate Pathway Families. ....................................8? Figure 6. The Building Blocks, Arrangement, and Nonmevalonate Biosynthesis... for Carzinophilin A/Azinomycin B. Compounds isolated from Streptomyces sahachiroi culture broths and identified: (A) azinomycin A (B) azinomycin B and naphthoate group derivatives (C-F) adapted from Yokoi et al. 1986 [17]. After complete structural...

  4. A Mechanistic Investigation of Gelation. The Sol-Gel Polymerization of Bridged Silsesquioxane Monomers

    SciTech Connect (OSTI)

    SHEA,KENNETH J.; LOY,DOUGLAS A.

    2000-07-14

    The study of a homologous series of silsesquioxane monomers has uncovered striking discontinuities in gelation behavior. An investigation of the chemistry during the early stages of the polymerization has provided a molecular basis for these observations. Monomers containing from one to four carbon atoms exhibit a pronounced tendency to undergo inter or intramolecular cyclization. The cyclic intermediates have been characterized by {sup 29}Si NMR, chemical ionization mass spectrometry and isolation from the reaction solution. These carbosiloxanes are local thermodynamic sinks that produce kinetic bottlenecks in the production of high molecular weight silsesquioxanes. The formation of cyclics results in slowing down or in some cases completely shutting down gelation. An additional finding is that the cyclic structures are incorporated intact into the final xerogel. Since cyclization alters the structure of the building block that eventually makes up the xerogel network, it is expected that this will contribute importantly to the bulk properties of the xerogel as well.

  5. Methods for monitoring multiple gene expression

    DOE Patents [OSTI]

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

    2012-05-01

    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.

  6. Methods for monitoring multiple gene expression

    DOE Patents [OSTI]

    Berka, Randy; Bachkirova, Elena; Rey, Michael

    2013-10-01

    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.

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

    DOE Patents [OSTI]

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

    1993-08-31

    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. 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)

    1993-01-01

    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.

  9. Development of Epipolythiodiketopiperazine syntheses and the total synthesis of diketopiperazine alkaloids

    E-Print Network [OSTI]

    Adams, Timothy C. (Timothy Cho)

    2015-01-01

    I. The Development of Epipolythiodiketopiperazine (ETP) Syntheses Epipolythiodiketopiperazine (ETP) alkaloids represent a structurally complex and biologically potent class of secondary fungal metabolites and these molecules ...

  10. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    Genomics Resource Shabalov Igor Grigoriev Igor BASIC BIOLOGICAL SCIENCES MycoCosm is a web based interactive fungal genomics resource which was first released in March in...

  11. Genomic Encyclopedia of Fungi (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis....

  12. Kjiersten Fagnan Appointed NERSC/JGI Engagement Lead

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

    systems to assemble and perform comparative analysis for genomes from plant, fungal, microbial and metagenome communities. In her new role, Fagnan will coordinate NERSC...

  13. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    and Environmental Research (BER) (SC-23)","59 BASIC BIOLOGICAL SCIENCES fungal genomics; gene regulatory networks",,"In microorganisms, Ion Torrent sequencing technology has...

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

    E-Print Network [OSTI]

    Wohlbach, Dana J.

    2011-01-01

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

  15. Rapid genome resequencing of an atoxigenic strain of Aspergillus...

    Office of Scientific and Technical Information (OSTI)

    United States Language: English Subject: 59 BASIC BIOLOGICAL SCIENCES fungal genomics; gene regulatory networks Word Cloud More Like This Free Publicly Accessible Full...

  16. 282 PHYTOPATHOLOGY Use of Pyrosequencing to Quantify Incidence of

    E-Print Network [OSTI]

    Cotty, Peter J.

    culturing methods. Additional keywords: biocontrol, population genetics. Aflatoxins are highly toxic is the most important causal agent of aflatoxin con- tamination. However, this fungal species is highly

  17. Biocontrol of Lettuce Drop Caused by Sclerotinia sclerotiorum and S. minor in Desert Agroecosystems

    E-Print Network [OSTI]

    Subbarao, Krishna V

    2008-01-01

    application of fungal biocontrol agents for the control ofpure cultures of each biocontrol agent and transferred intoFig. 3). The other biocontrol agents and Rovral did not

  18. Isolation of a significant fraction of non-phototroph diversity...

    Office of Scientific and Technical Information (OSTI)

    strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised...

  19. Polymerization of bis(triethoxysilyl)ethenes. Impact of substitution geometry on the formation of ethenylene- and vinylidene-bridged polysilsesquioxanes

    SciTech Connect (OSTI)

    Loy, D.A.; Carpenter, J.P.; Yamanaka, S.A.; McClain, M.D. [Sandia National Labs., Albuquerque, NM (United States). Encapsulants and Foams Dept.] [Sandia National Labs., Albuquerque, NM (United States). Encapsulants and Foams Dept.; Greaves, J.; Hobson, S.; Shea, K.J. [Univ. of California, Irvine, CA (United States). Dept. of Chemistry] [Univ. of California, Irvine, CA (United States). Dept. of Chemistry

    1998-12-01

    In this study, the authors utilized the substitution geometry of triethoxysilyl groups about an organic bridging group to control the outcome of the sol-gel polymerization process. The substitution geometry of two triethoxysilyl groups about a carbon-carbon double bond was determined to have a profound effect on sol-gel polymerizations of the E (1) and Z (2) ethenylene-bridged monomers and vinylidene-bridged monomer (3) and on the porosity in the resulting xerogels. {sup 29}Si NMR and chemical ionization mass spectrometry were used to elucidate the early sol-gel chemistry in the acid-catalyzed polymerizations of 1--3. Trans substitution about the ethenylene-bridging group in 1 led to acyclic and monocyclic dimers and trimers as condensation products under acidic conditions and only microporous gels under both acidic and basic conditions. In contrast, cyclization reactions dominated the sol-gel chemistry of 2 beginning with intramolecular cyclization to give the cyclic disilsesquioxane (4) and continued with the formation of cyclic oligomers, including a bicyclic dimer. The cyclization of 2 slowed the rate of gelation compared to 1 and afforded microporous xerogels under acidic conditions and mesoporous gels under basic conditions. The sol-gel chemistry of the vinylidene monomer (3) was strongly retarded by the formation of a cyclic dimer (5). Only mesoporous gels were formed under basic conditions after 9 months; no gels were obtained under acidic conditions.

  20. This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon.

    E-Print Network [OSTI]

    Bhattacharyya, Madan Kumar

    immunity against an oomycete and a fungal pathogen but not a bacterial pathogen that cause diseases an oomycete and a fungal pathogen but not a bacterial pathogen that cause diseases in soybean Rishi Sumit1 resistance (NHR) provides immunity to all members of a plant species against all isolates of a microorganism

  1. Tue 12/16/03 2:05 PM A Biosafety Discussion List [BIOSAFTY@MITVMA.MIT.EDU]; on behalf of; Scott, Rick

    E-Print Network [OSTI]

    , Rick [SCOTTWI@MAIL.ECU.EDU] BIOSAFTY@MITVMA.MIT.EDU fungal contaminated cell culture... I am helping a PI who is suffering from a fungal contamination problem. He is culturing murine 3T3 cells on DMEM, "my car is squeaking, what's wrong with it?" So- I am not asking for a definitive answer, just ideas

  2. Organic Acid Production by Filamentous Fungi

    E-Print Network [OSTI]

    12 Organic Acid Production by Filamentous Fungi Jon K. Magnuson and Linda L. Lasure 1. Introduction Many of the commercial production processes for organic acids are excellent examples of fungal overshadowed by the successful deploy- ment of the -lactam processes.Yet, in terms of productivity, fungal

  3. (33)V O L U M E 4 N O . 2 he November issue of Molecular

    E-Print Network [OSTI]

    Hibbett, David S.

    with a wonderful News and Views piece from the architects of the UNITE project (http:// uite.ut.ee) and a diverse cation of fungal communities using the latest tools from the UNITE consortium. For more than a dec- ade, UNITE has worked to provide a curat- ed database of fungal ITS sequences that can be used to identify

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

    SciTech Connect (OSTI)

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

    2015-01-01

    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.

  5. Revised 9/8/14 Fall 2014 Seminar Schedule

    E-Print Network [OSTI]

    Zhou, Pei

    UNIVERSITY LEE OCTOBER 24 "WEIRD ION...WEIRD ION CHANNEL: FLUORIDE RESISTANCE IN MICROORGANISMS" CHRISTOPHER ADAPTATIONS TO METALS AND OXIDATIVE STRESS IN THE HUMAN FUNGAL PATHOGEN CANDIDA ALBICANS" SVETLANA LUTSENKO

  6. Translational Control Mechanisms Analyzed in Neurospora crassa 

    E-Print Network [OSTI]

    Wei, Jiajie

    2013-07-11

    The Neurospora crassa arg-2 gene encodes the small subunit of carbamoyl phosphate synthetase, the first enzyme in fungal arginine (Arg) biosynthesis. The arginine attenuator peptide (AAP), specified by an upstream open ...

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

    E-Print Network [OSTI]

    Cheng, Johnathan Zandrew

    2011-01-01

    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 ...

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

    E-Print Network [OSTI]

    Ramaswamy, Anitha

    2002-01-01

    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...

  9. Inhibition of Tau Aggregation by Three Aspergillus nidulans Secondary Metabolites: 2,?-Dihydroxyemodin, Asperthecin, and Asperbenzaldehyde

    E-Print Network [OSTI]

    Paranjape, Smita Ramesh; Chiang, Yi-Ming; Sanchez, James F.; Entwistle, Ruth; Wang, Clay C. C.; Oakley, Berl R.; Gamblin, Truman Chris

    2014-01-10

    for these diseases. Fungal natural products have proven to be a rich source of useful compounds having wide varieties of biological activity. We have screened Aspergillus nidulans secondary metabolites containing aromatic ring structures for their ability to inhibit...

  10. Position Announcement Professor and Head, Department of Entomology and Plant Pathology

    E-Print Network [OSTI]

    Tennessee, University of

    , agricultural industries, state and federal agencies, and professional organizations), and the administration, or virology. Current research projects and extension programs focus on fungal, insect, nematode and viral faculty members, 7 research assistant professors and postdoctoral associates and 15 professional, support

  11. DOI: 10.1126/science.1136237 , 513 (2007);315Science

    E-Print Network [OSTI]

    2007-01-01

    to extreme environments (1). A plant-fungal symbiosis between a tropical panic grass from geothermal soils temperatures in Yellowstone National Park (YNP) (2). Field and laboratory experiments have shown that when root

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

    E-Print Network [OSTI]

    Saleska, Scott

    to extreme environments (1). A plant-fungal symbiosis between a tropical panic grass from geothermal soils temperatures in Yellowstone National Park (YNP) (2). Field and laboratory experiments have shown that when root

  13. Characterization of the Tri10 gene from Fusarium sporotrichioides 

    E-Print Network [OSTI]

    Tag, Andrew George

    2004-09-30

    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 ...

  14. Karnal Bunt: A Disease of Wheat 

    E-Print Network [OSTI]

    Schuster, Greta; Krausz, Joseph P.; Rush, Charlie

    2002-11-20

    Karnal bunt is a fungal disease that affects wheat, durum wheat and triticale. This publication explains the life cycle of the disease, how it spreads, and methods of control....

  15. The roles of N-myristoylation in cell morphogenesis in Aspergillus nidulans 

    E-Print Network [OSTI]

    Lee, Soo Chan

    2009-05-15

    Polarized hyphal growth dominates the life cycle of filamentous fungi and is essential to disease progression for many fungal pathogens. Despite its importance, much of the basic biology controlling the process remains to ...

  16. Comparison of the infection biology and transcriptome of wild-type and single gene deletion strains of Fusarium graminearum 

    E-Print Network [OSTI]

    Brown, Neil Andrew

    2012-06-22

    Fusarium Ear Blight is a devastating fungal disease of cereals and due to the contamination of the harvested grain with a range of trichothecene mycotoxins presents a risk to human and animal health. The re-emergence of ...

  17. Pharmacokinetics of cyclosporine A in normal and carrier dogs for Alport Syndrome and transdermal absorption of cyclosporine A in normal dogs 

    E-Print Network [OSTI]

    Inan, Guvenc

    2002-01-01

    Cyclosporine A is a fungal 11 amino acid cyclic polypeptide characterized by potent immunosuppressive activity. CsA selectively inhibits T lymphocytes, without any direct effect on B lymphocytes. Allograft and patient survival rates for all solid...

  18. FABI LAUNCHES PARTNERSHIP WITH CBS FABI has entered into a research partnership agreement with

    E-Print Network [OSTI]

    is an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW). Its Fungal Biodiversity Centre of a scientific, health-related or industrial nature. It offers various services including identifications, patent

  19. Convergent Evolution of Calcineurin Pathway Roles in Thermotolerance and Virulence in Candida glabrata

    E-Print Network [OSTI]

    Regev, Aviv

    Candida glabrata is an emerging human fungal pathogen that is frequently drug tolerant, resulting in difficulties in treatment and a higher mortality in immunocompromised patients. The calcium-activated protein phosphatase ...

  20. 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

  1. Total synthesis of cyclotryptamine and diketopiperazine alkaloids

    E-Print Network [OSTI]

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

    2013-01-01

    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 ...

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

    E-Print Network [OSTI]

    2012-01-01

    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

  3. Effects of Oilseed Meals on the Germination, Growth, and Survival of Crop and Weed Species 

    E-Print Network [OSTI]

    Rothlisberger, Katie Lynn

    2012-02-14

    ...................................................................................... 90 VIII SUMMARY AND CONCLUSIONS ................................................... 92 REFERENCES .......................................................................................................... 95 VITA... ....................................................................................................... 72 Figure 23 Bacterial copy numbers for treatments at preplant and harvest 1 ............. 89 Figure 21 Fungal copy number for treatments at preplant and harvest 1 .................. 90 xi LIST OF TABLES...

  4. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    MycoCosm, an Integrated Fungal Genomics Resource","Shabalov, Igor; Grigoriev, Igor","2012-03-16T04:00:00Z",1165859,,"LBNL-6823E","DE-AC02-05CH11231",,"Conference",,,"Conference:...

  5. The mechanics and functional consequences of hyphal fusion in Neurospora crassa; from genes to nutrient and nuclear translocation

    E-Print Network [OSTI]

    Simonin, Anna Ruth

    2011-01-01

    Eur. J. Cell Biol. 23, 208–223. Rayner, A. D. M. (1996)Jennings and A.D.M. Rayner, eds. ). Cambridge UniversityFungal Genet. Biol. 37:171– Rayner, A. (1991). THE CHALLENGE

  6. Trichoderma: the genomics of opportunistic success

    E-Print Network [OSTI]

    Druzhinina, Irina S.

    2011-01-01

    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,

  7. Devonian Fungi: Interactions with the Green Alga Palaeonitella

    E-Print Network [OSTI]

    Taylor, Thomas N.; Hass, Hagen; Remy, Winfried

    1992-11-01

    This paper describes three new taxa of fossil aquatic fungi preserved in 400-million-year-old Lower Devonian Rhynie Chert. All of the fungal morphotypes are attached to cells of the green alga Palaeonitella cranii. Milleromyces rhyniensis...

  8. A version of this article appeared in GreenMaster 41(3):28-30 (June 2006) A New Rhizoctonia Fungus on Turfgrass in Ontario

    E-Print Network [OSTI]

    Hsiang, Tom

    on Turfgrass in Ontario By Tom Hsiang, Darcy Olds and Russ Gowan The fungal genus Rhizoctonia contains many, 2003, 2004). It has not been previously documented in any other part of Canada. Outbreak in Ontario

  9. REU MENTORS & THEIR RESEARCH PROJECTS JONATHAN ARNOLD (Genetics) systems biology of the biological clock

    E-Print Network [OSTI]

    Arnold, Jonathan

    , innate defense mechanisms, and genome stability. djgarf@bmb.uga.edu TONY GLYNN (USDA) ­ Fungal genomics). Evolutionary systems biology, comparative genomics, protein structure, function and evolution. kannan & Institute of Bioinformatics) Microbial comparative genomics, prokaryotic genome composition, structure

  10. 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 ...

  11. Integrated genomic and transcriptomic analysis reveals mycoparasitism as the ancestoral life style of Trichoderma

    E-Print Network [OSTI]

    Kubicek, Christian P.

    2011-01-01

    to  fungal biocontrol agents.  Annu Rev Phytopathol 2010, the most studied biocontrol agents are species of the the most studied biocontrol agents (BCAs) are species of 

  12. AQUATIC PLANT CONTROL L,A'.IVRESEARCH PROGRAM , TECHNICAL REPORT A-91-6

    E-Print Network [OSTI]

    US Army Corps of Engineers

    demonstrated potential as a biocontrol agent for the noxious submersed aquatic macrophyte HydriLla vertici Biocontrol HydriLla verticil/ata 21 Fungal pathogen Macrophomina phaseolina 16. PRICE CODe yy ~. I ~ . 17

  13. 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

  14. Low-level Laser Therapy to the Mouse Femur Enhances the Fungicidal Response of Neutrophils against Paracoccidioides brasiliensis

    E-Print Network [OSTI]

    Burger, Eva

    Neutrophils (PMN) play a central role in host defense against the neglected fungal infection paracoccidioidomycosis (PCM), which is caused by the dimorphic fungus Paracoccidioides brasiliensis (Pb). PCM is of major importance, ...

  15. Soil Biology & Biochemistry 40 (2008) 434442 Species-specific impacts of collembola grazing on

    E-Print Network [OSTI]

    2008-01-01

    velutina and Hypholoma fasciculare morphology, that of Resinicium bicolor was only markedly affected by F collembola reduce fungal biomass (Hanlon and Anderson, 1979), but at low to moderate densities they often

  16. Arthropod population and community dynamics in turfgrass 

    E-Print Network [OSTI]

    Wang, Yong

    1998-01-01

    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...

  17. 1366 Plant Disease / Vol. 88 No. 121366 Aspergillus flavus in Soils and Corncobs in South Texas

    E-Print Network [OSTI]

    Cotty, Peter J.

    fungal metabolites that are limited in food and feed by government regulations throughout most. KG, Staufen, Germany). Both the sieve and the mill were vacuumed to remove loose contaminants

  18. GENERAL TECHNICAL REPORT PSW-GTR-240 Are Needle Reactions in Resistance to

    E-Print Network [OSTI]

    , it has been presumed that HR-mediated cell death near the point of C. ribicola entry confines fungal. Generally, HR phenotypes are visible as yellow or brown necrotic lesions at the site of pathogen entry

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

    E-Print Network [OSTI]

    Johnson, Natalie Malek

    2011-10-21

    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...

  20. Ecosystem engineers activate mycorrhizal mutualism in salt marshes

    E-Print Network [OSTI]

    Bertness, Mark D.

    Departamento de Biologi´a (FCEyN), UNMdP, CC 573 Correo Central, B7600WAG, Mar del Plata, Rivadavia 1917, 1033-product of burrowing. Field experiments demonstrate that fungal colonization is dependent on crab burrowing

  1. RESEARCH Open Access Reduction in host-finding behaviour in fungus-

    E-Print Network [OSTI]

    Read, Andrew

    and to a lesser degree, to CO2. Conclusions: Fungal infection reduces the responsiveness of mosquitoes to host- ness and sustainability of insecticide-based interventions, such as indoor residual sprays (IRS

  2. Microtubule organization requires cell-cycle dependent nucleation at dispersed cytoplasmic sites, polar and perinuclear MTOCs in the plant pathogen Ustilago maydis

    E-Print Network [OSTI]

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

    2003-02-01

    Growth of most eukaryotic cells requires directed transport along microtubules (MTs) that are nucleated at nuclear-associated microtubule organizing centers (MTOCs), such as the centrosome and the fungal spindle pole body (SPB). Herein, we show...

  3. Formation of sporangia and zoospores by a Labyrinthomyxa sp. parasitic in Macoma Balthica Linne 

    E-Print Network [OSTI]

    Valiulis, George Arvidas

    1968-01-01

    in sea water. Cells isolated from the host by the Waring blender isolation method. 1125X 35 FORMATION OF SPORANGIA AND ZOOSPORES BY A LABYRINTHOMYXA SP. PARASITIC IN MACOMA BALTHICA LINNE INTRODUCTION A technique for diagnosing oysters infected... with the fungal pathogen Labyrinthomyza marina was developed by Ray (1952), This method consisted of placing sections of oyster tissue in Fluid Thioglycollate Medium (F. T. M. ) for 48 hrs then staining with Lugol's iodine. This caused the fungal cells...

  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)

    2012-01-17

    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. Understanding the Role of Histidine in the GHSxG Acyltransferase Active Site Motif: Evidence for Histidine Stabilization of the Malonyl-Enzyme Intermediate

    SciTech Connect (OSTI)

    Poust, S; Yoon, I; Adams, PD; Katz, L; Petzold, CJ; Keasling, JD

    2014-10-06

    Acyltransferases determine which extender units are incorporated into polyketide and fatty acid products. The ping-pong acyltransferase mechanism utilizes a serine in a conserved GHSxG motif. However, the role of the conserved histidine in this motif is poorly understood. We observed that a histidine to alanine mutation (H640A) in the GHSxG motif of the malonyl-CoA specific yersiniabactin acyltransferase results in an approximately seven-fold higher hydrolysis rate over the wildtype enzyme, while retaining transacylation activity. We propose two possibilities for the reduction in hydrolysis rate: either H640 structurally stabilizes the protein by hydrogen bonding with a conserved asparagine in the ferredoxin-like subdomain of the protein, or a water-mediated hydrogen bond between H640 and the malonyl moiety stabilizes the malonyl-O-AT ester intermediate.

  6. Understanding the role of histidine in the GHSxG acyltransferase active site motif: Evidence for histidine stabilization of the malonyl-enzyme intermediate

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

    Poust, Sean; Yoon, Isu; Adams, Paul D.; Katz, Leonard; Petzold, Christopher J.; Keasling, Jay D.

    2014-10-06

    Acyltransferases determine which extender units are incorporated into polyketide and fatty acid products. Thus, the ping-pong acyltransferase mechanism utilizes a serine in a conserved GHSxG motif. However, the role of the conserved histidine in this motif is poorly understood. We observed that a histidine to alanine mutation (H640A) in the GHSxG motif of the malonyl-CoA specific yersiniabactin acyltransferase results in an approximately seven-fold higher hydrolysis rate over the wildtype enzyme, while retaining transacylation activity. We propose two possibilities for the reduction in hydrolysis rate: either H640 structurally stabilizes the protein by hydrogen bonding with a conserved asparagine in the ferredoxin-likemore »subdomain of the protein, or a water-mediated hydrogen bond between H640 and the malonyl moiety stabilizes the malonyl-O-AT ester intermediate.« less

  7. Hydroconversion of liquid hydrocarbons in a staged autothermal reactor

    SciTech Connect (OSTI)

    Blass, SD; Bhan, A; Schmidt, LD

    2013-01-31

    An autothermal staged reactor was assembled containing a top stage of Rh-Ce/alpha-Al2O3 which generated heat and H-2 by reacting CH4 and air that passed through a downstream stage containing 0.5 wt% Pt/gamma-Al2O3 mixed with either HBEA, HZSM-5, or USY in a heat-integrated non-isothermal reactor. The H-2 produced subsequently reacts in a 20:1 ratio with a co-feed of hexane or decane or 2-decanone fed to the reactor between the stages. The large-sized pores of HBEA and USY allowed deoxygenation of 2-decanone to form decene isomers which can crack or cyclize to form up to a 36% yield of methylated and ethylated monoaromatics. The medium-sized pores of HZSM-5 restricted decene formation from 2-decanone by catalyzing cracking reactions to C2-6 compounds which can cyclize to form aromatics. By contrast, the reactor effluent from non-oxygenated reactants decane and hexane contained less than 5% aromatics. Thus, we extend the scope of staged autothermal reactor functionality to hydrocracking and hydroisomerization of higher saturated and oxygenated hydrocarbons. (C) 2012 Elsevier B.V. All rights reserved.

  8. 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

    2012-12-17

    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

  9. New Palladium-Catalyzed Approaches to Heterocycles and Carbocycles

    SciTech Connect (OSTI)

    Qinhua Huang

    2004-12-19

    The tert-butylimines of o-(1-alkynyl)benzaldehydes and analogous pyridinecarbaldehydes have been cyclized under very mild reaction conditions in the presence of I{sub 2}, ICl, PhSeCl, PhSCl and p-O{sub 2}NC{sub 6}H{sub 4}SCl to give the corresponding halogen-, selenium- and sulfur-containing disubstituted isoquinolines and naphthyridines, respectively. Monosubstituted isoquinolines and naphthyridines have been synthesized by the metal-catalyzed ring closure of these same iminoalkynes. This methodology accommodates a variety of iminoalkynes and affords the anticipated heterocycles in moderate to excellent yields. The Pd(II)-catalyzed cyclization of 2-(1-alkynyl)arylaldimines in the presence of various alkenes provides an efficient way to synthesize a variety of 4-(1-alkenyl)-3-arylisoquinolines in moderate to excellent yields. The introduction of an ortho-methoxy group on the arylaldimine promotes the Pd-catalyzed cyclization and stabilizes the resulting Pd(II) intermediate, improving the yields of the isoquinoline products. Highly substituted naphthalenes have been synthesized by the palladium-catalyzed annulation of a variety of internal alkynes, in which two new carbon-carbon bonds are formed in a single step under relatively mild reaction conditions. This method has also been used to synthesize carbazoles, although a higher reaction temperature is necessary. The process involves arylpalladation of the alkyne, followed by intramolecular Heck olefination and double bond isomerization. This method accommodates a variety of functional groups and affords the anticipated highly substituted naphthalenes and carbazoles in good to excellent yields. Novel palladium migratiodarylation methodology for the synthesis of complex fused polycycles has been developed, in which one or more sequential Pd-catalyzed intramolecular migration processes involving C-H activation are employed. The chemistry works best with electron-rich aromatics, which is in agreement with the idea that these palladium-catalyzed C-H activation reactions parallel electrophilic aromatic substitution. A relatively efficient synthesis of cyclopropanes has been developed using palladium-catalyzed C-H activation chemistry, in which two new carbon-carbon bonds are formed in a single step. This method involves the palladium-catalyzed activation of relatively unreactive C-H bonds, and provides a very efficient way to synthesize cyclopropapyrrolo[1,2-a]indoles, analogues of the mitomycin antibiotics.

  10. Fungi from geothermal soils in Yellowstone National Park

    SciTech Connect (OSTI)

    Redman, R.S.; Litvintseva, A.; Sheehan, K.B.; Henson, J.M.; Rodriguez, R.J.

    1999-12-01

    Geothermal soils near Amphitheater Springs in Yellowstone National Park were characterized by high temperatures (up to 70 C), high heavy metal content, low pH values (down to pH 2.7), sparse vegetation, and limited organic carbon. From these soils the authors cultured 16 fungal species. Two of these species were thermophilic, and six were thermotolerant. They cultured only three of these species from nearby cool (0 to 22 C) soils. Transect studies revealed that higher numbers of CFUs occurred in and below the root zone of the perennial plant Dichanthelium lanuginosum (hot springs panic grass). The dynamics of fungal CFUs in geothermal soil and nearby nongeothermal soil were investigated for 12 months by examining soil cores and in situ mesocosms. For all of the fungal species studied, the temperature of the soil from which the organisms were cultured corresponded with their optimum axenic growth temperature.

  11. Structures and functions of oligosaccharins. Progress report, June 15, 1993--March 14, 1995

    SciTech Connect (OSTI)

    Albersheim, P.

    1995-03-01

    This research focuses on the following: Purification, characterization, and cell wall localization of an {alpha}-fucosidase that inactivates a xyloglucan oligosaccharin; Oligogalacturonides inhibit the formation of roots on tobacco explants; Activation of a tobacco glycine-rich protein gene by a fungal glucan preparation; Fusarium moniliforme secretes four endopolygalacturonases derived from a single gene product; Polygalacturonase-inhibiting protein accumulates in Phaseolus vulgaris L. in response to wounding, elicitors and fungal infection; Generation of {beta}-glucan elicitors by plant enzymes and inhibition of the enzymes by a fungal protein; Polygalacturonase inhibitor proteins from bean (Phaseolus vulgaris L.), pear (Pyrus communis L.) and tomato (Lycopersicon esculentum): Immunological relatedness and specificity of polygalacturonase inhibition; Fungi protect themselves against plant pathogenesis-related glycanases; Purification, cloning, and characterization of two xylanases from Magnaporthe grisea, the rice blast fungus; and Molecular cloning and expression pattern of an {alpha}-fucosidase gene from pea seedlings.

  12. Emissive sensors and devices incorporating these sensors

    SciTech Connect (OSTI)

    Swager, Timothy M; Zhang, Shi-Wei

    2013-02-05

    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.

  13. Evaluate reformer performance at a glance

    SciTech Connect (OSTI)

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

    1996-02-01

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

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

    SciTech Connect (OSTI)

    Schoendorff, George

    2012-04-02

    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.

  15. Microbial Pathogens Trigger Host DNA Double-Strand Breaks Whose Abundance Is Reduced by Plant Defense

    E-Print Network [OSTI]

    of an alternative mediator of pathogen-induced H2AX phosphorylation. In summary, pathogenic microorganisms canMicrobial Pathogens Trigger Host DNA Double-Strand Breaks Whose Abundance Is Reduced by Plant largely unknown. We report that multiple bacterial, fungal and oomycete plant pathogen species induce

  16. Cortes-Barco AM, Goodwin PH, Hsiang T. in press. Induced systemic resistance against three foliar diseases of Agrostis stolonifera by (2R,3R)-Butanediol or an isoparaffin mixture. Annals of Applied

    E-Print Network [OSTI]

    Hsiang, Tom

    defense mechanism typically activated by non- pathogenic root-associated microorganisms and systemic priming of gene expression in response to subsequent pathogen challenge. ISR was found to be activated)-butanediol to the soil reduced the diseased leaf area of Agrostis stolonifera by 20 to 40% for the fungal pathogens

  17. Molecular Ecology (2008) 17, 40684078 doi: 10.1111/j.1365-294X.2008.03894.x 2008 The Authors

    E-Print Network [OSTI]

    Harvell, Catherine Drew

    2008-01-01

    in allowing opportunistic pathogens to increase and actual introductions of new pathogenic microorganisms structure in the opportunistic fungal pathogen Aspergillus sydowii KRYSTAL L. RYPIEN, JASON P. ANDRAS and C pathogens, impaired host immunity, or changing environmental conditions. Identifying the source of emergent

  18. Vol. 25, No. 6, 2012 / 817 MPMI Vol. 25, No. 6, 2012, pp. 817824. http://dx.doi.org/10.1094/MPMI-12-11-0317. 2012 The American Phytopathological Society

    E-Print Network [OSTI]

    Bhattacharyya, Madan Kumar

    of pathogenic microorganisms. How- ever, transgenic plants can assemble mammalian antibodies correctly (Hiatt et by pathogen toxins. One such disease is the soy- bean sudden death syndrome (SDS). SDS is a serious dis- ease caused by the fungal pathogen Fusarium virguli- forme. The pathogen, however, has never been isolated

  19. 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

  20. Major perturbation of ocean chemistry and a `Strangelove Ocean' after the end-Permian mass extinction

    E-Print Network [OSTI]

    of the negative isotope excursion and the eventual recovery of life in the Triassic Period is the pace at a level marked by a flood of fungal spores (Visscher et al., 1996). In fact, coal deposits are unknown in Lower Triassic strata, and recovery of plant diversity appar- ently took c. 4 million years (Retallack

  1. This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research

    E-Print Network [OSTI]

    Center for Advanced Microstructure and Devices, Louisiana State University, Baton Rouge, LA 70806, USA online 8 January 2008 Abstract Wood­polymer composites (WPC) have been extensively used for building to fungal and termite attacks due to wood components enveloped in the thermoplastic matrix. Much effort has

  2. Proceedings of 7th Pacific Rim Bio-based Composite Symposium. Nanjing, China. October Mechanical Properties and Decay Resistance of Wood-Polymer

    E-Print Network [OSTI]

    Agricultural Center, Baton Rouge, LA 70803, USA. wuqing@lsu.edu 3 Assistant Professor, Center for Advanced-polymer composites (WPC) have been extensively used for building products, automotive, packaging materials, and other applications. WPC is subject to fungal and termite attacks due to wood components enveloped

  3. EINDHOVEN UNIVERSITY OF TECHNOLOGY Department of Mathematics and Computer Science

    E-Print Network [OSTI]

    Hulshof, Joost

    EINDHOVEN UNIVERSITY OF TECHNOLOGY Department of Mathematics and Computer Science CASA-Report 09 and Computer Science Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven, The Netherlands ISSN for the dynamics of the vesicle supply center model of tip growth in fungal hyphae is derived. For this we

  4. 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

  5. Multiple locus genealogies and phenotypic characters reappraise the causal agents of apple ring rot in China

    E-Print Network [OSTI]

    Biggs, Alan R.

    Multiple locus genealogies and phenotypic characters reappraise the causal agents of apple ring rot # School of Science 2014 Abstract Apple ring rot inflicts severe economic losses in the main apple phylogenetic species recognition (GCPSR) was applied to pathogenic fungal isolates from apple and pear from

  6. Crabapples Resistant to Apple Scab and Japanese Beetle in Indiana

    E-Print Network [OSTI]

    Pittendrigh, Barry

    Crabapples Resistant to Apple Scab and Japanese Beetle in Indiana Cliff Sadof, Department pests, apple scab and Japanese beetle, have also given this plant a reputation of being prone to insect and disease problems. Both these pests are widely distributed in Indiana. Apple scab is a fungal disease

  7. 3.1.1.2 Feed Processing and Handling DL2 Final Report

    SciTech Connect (OSTI)

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

    2006-09-30

    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.

  8. REVIEW ARTICLE published: 27 March 2013

    E-Print Network [OSTI]

    Raizada, Manish N.

    -microbial secondary metabolites produced by fungal endophytes: an interdisciplinary perspective Walaa Kamel Mousa1 are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing

  9. cis-and trans-Regulation of miR163 and Target Genes Confers Natural Variation of Secondary Metabolites in Two Arabidopsis

    E-Print Network [OSTI]

    Tholl, Dorothea

    involved in secondary metabolite biosynthetic pathways that are inducible by a fungal elicitor, alamethicin and secondary metabolite profiles. We suggest that cis- and trans-regulation of miRNA and other genes providescis- and trans-Regulation of miR163 and Target Genes Confers Natural Variation of Secondary

  10. Bacterial extracellular lignin peroxidase

    DOE Patents [OSTI]

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

    1993-01-01

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

  11. 23USDA Forest Service Proceedings, RMRS-P-72. 2014 Introduction

    E-Print Network [OSTI]

    members of the kingdom of fungi for many applications in bioremediation (a process collectively called "fungal bioremediation" or "mycoremediation") has been well established (Gadd 2001; Singh 2006). Many. The incorporation of these organisms into engineered water treatment ecosystems and biofiltration media have

  12. Department of Botany, 3359 Mississauga Road

    E-Print Network [OSTI]

    Anderson, James B.

    as resistance to antibacterial agents in bacteria1 , one long-term concern is that the number of fundamentally EVOLUTION OF ANTIFUNGAL DRUG RESISTANCE: MECHANISMS AND PATHOGEN FITNESS James B. Anderson Abstract | Like by antifungal drugs, drug-sensitive fungal pathogens frequently evolve resistance. Although the molecular

  13. Eukaryotic microbes, species recognition and the geographic limits of species: examples

    E-Print Network [OSTI]

    Eukaryotic microbes, species recognition and the geographic limits of species: examples from of eukaryotic microbes, the Fungi. We show that inferred geographic range of a fungal species depends upon structure (Finlay & Fenchel 2004). Finlay & Fenchel's claim of global ranges for eukaryotic microbes echoes

  14. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

    E-Print Network [OSTI]

    Hibbett, David S.

    polysaccharides, phenolic compounds, and enzyme inhibitors from fungal tissue lysates. Purified DNA is suitable reducing plastic waste and hands-on time to allow multiple samples to be processed in parallel. Overview remove trace contaminants such as residual polysaccharides and pure DNA is eluted in water or low ionic

  15. doi:10.1130/G25699A.1 2009;37;615-618Geology

    E-Print Network [OSTI]

    Benning, Liane G.

    a reference to the article's full citation. GSA provides this and other forums for the the abstracts only;GEOLOGY, July 2009 615 ABSTRACT Plant-driven fungal weathering is a major pathway of soil formation, yet. Our study demonstrates the biomechanical-chemical alteration interplay at the fungus-biotite interface

  16. 21st Century Directions in Biology Fungi play pivotal roles in all terrestrial environ-

    E-Print Network [OSTI]

    that break down complex organic polymers into simpler forms that can be taken up by the fungi or by other organisms. This process is an essential step in the carbon cycle; without it, plant detritus would quickly of terrestrial food webs. Fungal mycelia serve as the primary carbon source in a number of soil food webs (Wardle

  17. 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

  18. 245V.S.F.T. Merckx (ed.), Mycoheterotrophy: The Biology of Plants Living on Fungi, DOI 10.1007/978-1-4614-5209-6_6, Springer Science+Business Media New York 2013

    E-Print Network [OSTI]

    Taylor, Lee

    245V.S.F.T. Merckx (ed.), Mycoheterotrophy: The Biology of Plants Living on Fungi, DOI 10.1007/978-1-4614-5209-6_6, © Springer Science+Business Media New York 2013 6.1 Introduction Mycoheterotrophic plants provide fascinating of mycoheterotrophic plants always target different fungal clades (Taylor and Bruns 1999;BidartondoandBruns2001

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

    E-Print Network [OSTI]

    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

  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. Limiting Abnormal Mold Growth in Buildings 

    E-Print Network [OSTI]

    Graham, C. W.

    2002-01-01

    in wood, or rusting and corrosion of metals. Abnormal mold or fungal growth, then, can create major problems for building owners. Moisture is the key factor that building designers and owners can manage in order to limit mold growth. This paper introduces...

  2. Auritella foveata, a new species of Inocybaceae (Agaricales) from tropical India

    E-Print Network [OSTI]

    Matheny, P. Brandon

    Auritella foveata, a new species of Inocybaceae (Agaricales) from tropical India P. Brandon Matheny & Matheny is described as new from mixed evergreen forests in tropical India. The species is distinctive due, systematics. Introduction India is exceedingly rich in fungal diversity (Manoharachary et al. 2005). Indeed

  3. Cellulose 8: 91-97,200/. (i) 2001 Kluwer AcademIc Publishers. Printed in the Netherlands.

    E-Print Network [OSTI]

    Brown Jr., R. Malcolm

    91 Cellulose 8: 91-97,200/. (i) 2001 Kluwer AcademIc Publishers. Printed in the Netherlands. Rotation of cellulose ribbons during degradation with fungal cellulase Andrew J. Bowling}, Yoshihiko Amano2; accepted 15 March 2001 Key words: bacterial cellulose, cellulose, cellulase, Celluclast, chira

  4. Strong Cellulase Inhibition by Mannan Polysaccharides in Cellulose Conversion to Sugars

    E-Print Network [OSTI]

    California at Riverside, University of

    Strong Cellulase Inhibition by Mannan Polysaccharides in Cellulose Conversion to Sugars Rajeev and their enzymatically prepared hydrolyzates were discovered to be strongly inhibitory to fungal cellulase in cellulose; galactomannan; oligomers; xylan Introduction Lignocellulosic biomass comprised of three major compo- nents--cellulose

  5. 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

  6. Plant and Soil 253: 293299, 2003. 2003 Kluwer Academic Publishers. Printed in the Netherlands.

    E-Print Network [OSTI]

    Rilli, Matthias C.

    Plant and Soil 253: 293­299, 2003. © 2003 Kluwer Academic Publishers. Printed in the Netherlands. 293 Glomalin, an arbuscular-mycorrhizal fungal soil protein, responds to land-use change Matthias C 2003 Key words: decomposition, forest soil, glycoprotein, soil carbon storage Abstract Glomalin

  7. Colony Collapse Disorder Over the fall, winter, and spring of 2006-07, many beekeepers across the U.S. were

    E-Print Network [OSTI]

    Ishida, Yuko

    , not previously demonstrated from U.S. colonies, Nosema ceranae (fungal invader of adult bee intestinal tract that ovarian nurse cells were involved may help explain the problem beekeepers face with early queen #12;failures. Perhaps those ovarian cells continue to eliminate themselves when adult queens are exposed

  8. 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)

    2013-06-15

    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}.

  9. Population genetic analyses suggest that the Eucalyptus

    E-Print Network [OSTI]

    Population genetic analyses suggest that the Eucalyptus fungal pathogen Ceratocystis fimbriata has , Brenda D. Wingfield a , Gilbert N. Kamgan b and Michael J. Wingfield a Introduction Eucalyptus species, with Eucalyptus comprising about 40% of the total area.3 This is an important crop that sustains large pulp, sawn

  10. TPCP: Botryosphaeria canker and die-back of Eucalyptus BOTRYOSPHAERIA CANKER AND DIE-

    E-Print Network [OSTI]

    TPCP: Botryosphaeria canker and die-back of Eucalyptus BOTRYOSPHAERIA CANKER AND DIE- BACK OF EUCALYPTUS INTRODUCTION Botryosphaeria canker and die- back is one of the most important diseases of Eucalyptus spp. in South Africa. This disease is caused by the fungal pathogen Botryosphaeria dothidea

  11. Taxonomy and pathogenicity of Ceratocystis species on Eucalyptus trees in South China, including

    E-Print Network [OSTI]

    Taxonomy and pathogenicity of Ceratocystis species on Eucalyptus trees in South China, including C Research Foundation 2012 Abstract Commercial plantations of Eucalyptus species have been established economy. As part of a survey of fungal diseases affecting Eucalyptus species in South China, Ceratocystis

  12. Molecular Analysis of an Endopolygalacturonase Gene from a Eucalyptus Canker Pathogen, Cryphonectria cubensis

    E-Print Network [OSTI]

    Molecular Analysis of an Endopolygalacturonase Gene from a Eucalyptus Canker Pathogen a serious Eucalyptus canker disease. Fungal cell wall degrading enzymes (CWDEs) are important during the early stages of interaction of the fungus with Eucalyptus. To improve our understanding of the molecular

  13. Ann. N.Y. Acad. Sci. ISSN 0077-8923 ANNALS OF THE NEW YORK ACADEMY OF SCIENCES

    E-Print Network [OSTI]

    Cotty, Peter J.

    of contaminated food and feed. Aspergillus flavus, the primary causal agent of crop aflatoxin contamination; aflatoxin; food safety; biocontrol; competitive exclusion Introduction The filamentous fungus Aspergillus flavus is the pri- mary causal agent of food and feed contamination with the severely toxic fungal

  14. 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

  15. , ..1.'tf.VI:f "'UU:> J.~:4U t"AJ..+27317642494 TAPPSA 14102 APPLICATIONOF FUNGI AN)) Fl!NGAL PRODU(T~ I.N BIOPULPING

    E-Print Network [OSTI]

    -actives to improve penetration of pulping chemicals. Wood chips have also been treated successtUlly with fungal on a mill sc.le~'. These procedures are aimed at the tr..tmenl of wood chips in a solid-substrate fermenta- steri1iz!11ionof wood chips isregnzdedas u~. Freshiy cut wood also contains inhibirory compounds such .s

  16. Atmos. Chem. Phys., 12, 1110711123, 2012 www.atmos-chem-phys.net/12/11107/2012/

    E-Print Network [OSTI]

    Meskhidze, Nicholas

    and Ecosystem Sciences, S¨olvegatan 12, Lund University, 223 62 Lund, Sweden 3Asthma-Allergy Denmark large amounts of air- borne fungal spores. It is likely that such harvesting periods can cause- tral Europe causes episodes of high airborne Alternaria spore concentrations in Copenhagen as well

  17. Some Fungi and Water Molds in Waters of Lake Michigan with Emphasis on Those Associated with the Benthic Amphipod Diporeia spp.

    E-Print Network [OSTI]

    NOTE Some Fungi and Water Molds in Waters of Lake Michigan with Emphasis on Those Associated) were used to grow fungi in Lake Michigan water, a rich and diverse fungal and water mold community occur within the division Oomycota (water molds). The *Corresponding author. E-mail: Thomas

  18. INTRODUCTORY MYCOLOGY: BIOM 423 Fall 2010, 3 cr. LEC 2 LAB 1, PGC, Rm 214, M W 1:00-4:00 (1 hr lecture and 2 hr lab), field trips.

    E-Print Network [OSTI]

    Cripps, Cathy

    20* White-spored Mushrooms Mushroom ID D2L, Web W Sept 22 Dark-spored Mushrooms Mushroom ID D2L, Web mycology. Lecture Lab Reading M Aug 30 Introduction: the Fungal Lifestyle Movie, or movie clips D2L, Web W Sept 1 Phylogeny of Fungi Microscopic technique D2L, Web W Sept 8 BASIDIOMYCOTA introduction tissue

  19. Cellular Responses in Sea Fan Corals: Granular Amoebocytes React to Pathogen and Climate Stressors

    E-Print Network [OSTI]

    Harvell, Catherine Drew

    Cellular Responses in Sea Fan Corals: Granular Amoebocytes React to Pathogen and Climate Stressors amoebocyte responses indicate that sea fan corals use cellular defenses to combat fungal infection SF, Peters EC, Harvell CD (2008) Cellular Responses in Sea Fan Corals: Granular Amoebocytes React

  20. Calcium Montmorillonite for the Mitigation of Aflatoxicosis and Gastrointestinal Inflammation 

    E-Print Network [OSTI]

    Zychowski, Katherine E

    2014-08-06

    calcium montmorillonite clay to reduce the risk of aflatoxicosis in farm-raised fish and alleviate gastrointestinal inflammation and dysbiosis in a mouse model of Crohn’s disease (CD). Aflatoxin B_(1) (AFB_(1)) is a fungal mycotoxin that commonly...

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

    E-Print Network [OSTI]

    Ross, Sharon

    1997-01-01

    amplification with PCR primers specific for P. sorghi, demonstrating that the primers could amplify fungal DNA from infected callus. A dual culture of P. sparsa and rose callus was sought to provide pure DNA for sequencing and primer development but could...

  2. 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 a comprehensive set of best management practices for the control of anthracnose disease on golf courses. Host). Seedhead development requires con- siderable metabolic energy, which reallocates pho- tosynthate away from

  3. ORIGINAL ARTICLE doi:10.1111/j.1558-5646.2007.00003.x

    E-Print Network [OSTI]

    ORIGINAL ARTICLE doi:10.1111/j.1558-5646.2007.00003.x SPECIALIZATION AND LOCAL ADAPTATION 7, 2006 Accepted October 1, 2006 We investigate the geographic pattern of adaptation of a fungal and aggressivity on local versus allopatric plant­fungus combinations. We found evidence for local adaptation

  4. Plant-driven weathering of apatite the role of an ectomycorrhizal fungus

    E-Print Network [OSTI]

    Benning, Liane G.

    , Diepenbeek, Belgium 3 Earth and Biosphere Institute, School of Earth and Environment, University of Leeds, Leeds, UK 4 Biogeochimie ­ Systeme Terre, Departement des Sciences de la Terre et de l in plastic wells that were only accessed by their fungal partner. Under P limitation, pulse labelling

  5. REGULAR ARTICLE Testing the ecological stability of ectomycorrhizal symbiosis

    E-Print Network [OSTI]

    outweigh the benefits of mycorrhizal nutrient acquisition. In this study, we simulated the effects of post-fire than unheated controls, reduced percent colonization did not cause any decrease in fungal biomass11104-009-0200-1 Responsible Editor: Erik A. Hobbie. Electronic supplementary material The online

  6. Airlift bioreactors. (Latest citations from the Biobusiness database). Published Search

    SciTech Connect (OSTI)

    Not Available

    1993-04-01

    The bibliography contains citations concerning industrial and research applications of airlift bioreactors. Citations include biofilm formation, patents, pharmaceutical production, oxygen mass transfer studies, antibiotic production, wastewater treatment, culture media aspects, and growth kinetics. Topics also explore the culturing of bacterial, fungal, insect, and animal cells. (Contains a minimum of 99 citations and includes a subject term index and title list.)

  7. Doctoral Candidates/ PhD (as structured or as supervised doctoral project)

    E-Print Network [OSTI]

    Schüler, Axel

    process. The surface of PET materials can be modified by hydrolytic bacterial and fungal enzymes-hydrolyzing microbial enzymes, and their employment in a novel biocatalytic PET functionalization process. The project of Leipzig in Leipzig, Germany Institute for Biochemistry Chair for Microbiology and Bioprocess Technology

  8. Post-Doctorates Postdoctoral stay up to 12 months

    E-Print Network [OSTI]

    Schüler, Axel

    in a finishing process. The surface of PET materials can be modified by hydrolytic bacterial and fungal enzymes-hydrolyzing microbial enzymes, and their employment in a novel biocatalytic PET functionalization process. The project Technology Programme website http://www.biochemie.uni-leipzig.de/agz/ Research project description

  9. Exploring structural definitions of mycorrhizas, with emphasis on nutrient-exchange interfaces1

    E-Print Network [OSTI]

    Massicotte, Hugues

    Exploring structural definitions of mycorrhizas, with emphasis on nutrient-exchange interfaces1 R for symbiotic associations of some leafy liverworts. An important feature of mycorrhizas is the interface and ectendomycorrhizas. In ectomycorrhizas, the apoplastic interface consists of plant cell wall and fungal cell wall

  10. Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

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

    Calteau, Alexandra; Fewer, David P.; Latifi, Amel; Coursin, Thérèse; Laurent, Thierry; Jokela, Jouni; Kerfeld, Cheryl A.; Sivonen, Kaarina; Piel, Jörn; Gugger, Muriel

    2014-11-18

    Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary forces driving their remarkable chemical diversity are poorly understood. We carried out a phylum-wide investigation of genetic diversification of the cyanobacterial NRPS and PKS pathways formore »the production of bioactive compounds. 452 NRPS and PKS gene clusters were identified from 89 cyanobacterial genomes, revealing a clear burst in late-branching lineages. Our genomic analysis further grouped the clusters into 286 highly diversified cluster families (CF) of pathways. Some CFs appeared vertically inherited, while others presented a more complex evolutionary history. Only a few horizontal gene transfers were evidenced amongst strongly conserved CFs in the phylum, while several others have undergone drastic gene shuffling events, which could result in the observed diversification of the pathways. In addition to toxin production, several NRPS and PKS gene clusters are devoted to important cellular processes of these bacteria such as nitrogen fixation and iron uptake. The majority of the biosynthetic clusters identified here have unknown end products, highlighting the power of genome mining for the discovery of new natural products.« less

  11. Studies on the biology of the crisamicin-producing organism Micromonospora purpureochromogenes subsp. celinoensis

    SciTech Connect (OSTI)

    Pope, J.A. Jr.

    1985-01-01

    A Micromonospora isolate, RV-101, obtained from the Red V Coconut Company in the Philippines, produces a new complex of antibiotics, the crisamicins. Using standard taxonomic methods for the genus Micromonospora, including micromorphology, growth characteristics on select media, whole cell analysis of chemical composition, and carbohydrate utilization patterns, the organism was classified as Micromonospora purpureochromogenes subsp. celinoensis. The chief character used in this classification was the production of a dark-brown diffusible pigment on media containing complex sources of nitrogen. The biosynthesis of crisamicin A was investigated by the technique of /sup 13/C acetate feeding and /sup 13/C NMR spectroscopy. Crisamicin A was found to be synthesized from acetate via the polyketide biosynthetic pathway. In addition, the assignment of one of two possible structures, differing in the position of phenolic hydroxyl groups, and in the point of linkage between the two monomers of the molecule, was made using the labeling data. The structure determined demonstrates that crisamicin A is unique among the benzoisochromanequinone antibiotics, in that it lacks an oxygen atom at position C-8.

  12. Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

    SciTech Connect (OSTI)

    Calteau, Alexandra; Fewer, David P.; Latifi, Amel; Coursin, Thérèse; Laurent, Thierry; Jokela, Jouni; Kerfeld, Cheryl A.; Sivonen, Kaarina; Piel, Jörn; Gugger, Muriel

    2014-11-18

    Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary forces driving their remarkable chemical diversity are poorly understood. We carried out a phylum-wide investigation of genetic diversification of the cyanobacterial NRPS and PKS pathways for the production of bioactive compounds. 452 NRPS and PKS gene clusters were identified from 89 cyanobacterial genomes, revealing a clear burst in late-branching lineages. Our genomic analysis further grouped the clusters into 286 highly diversified cluster families (CF) of pathways. Some CFs appeared vertically inherited, while others presented a more complex evolutionary history. Only a few horizontal gene transfers were evidenced amongst strongly conserved CFs in the phylum, while several others have undergone drastic gene shuffling events, which could result in the observed diversification of the pathways. In addition to toxin production, several NRPS and PKS gene clusters are devoted to important cellular processes of these bacteria such as nitrogen fixation and iron uptake. The majority of the biosynthetic clusters identified here have unknown end products, highlighting the power of genome mining for the discovery of new natural products.

  13. Methods of increasing secretion of polypeptides having biological activity

    DOE Patents [OSTI]

    Merino, Sandra

    2015-04-14

    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.

  14. Methods of increasing secretion of polypeptides having biological activity

    DOE Patents [OSTI]

    Merino, Sandra

    2014-10-28

    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.

  15. 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)

    2010-11-02

    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.

  16. 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

    2010-04-20

    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.

  17. Methods of increasing secretion of polypeptides having biological activity

    DOE Patents [OSTI]

    Merino, Sandra

    2013-10-01

    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.

  18. Methods of increasing secretion of polypeptides having biological activity

    DOE Patents [OSTI]

    Merino, Sandra

    2014-05-27

    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.

  19. Disease in Natural Plant Populations, Communities, and Ecosystems: Insights into Ecological and Evolutionary Processes

    E-Print Network [OSTI]

    Alexander, Helen M.

    2010-05-01

    for a pathogen can lead to par- ticularly interesting effects if one or more plant species harbors the pathogen but is not greatly impacted. As noted by Haldane, “a non- specific parasite…is a powerful competitive weapon” (58). For example, infected... multiple approaches. For example, Mitchell and Power (85) ex- plored the use of pathogen databases and concluded that 84% fewer fungal pathogens and 24% fewer virus species infect plant species in their naturalized ranges in North America than...

  20. Fossil fungi from America Pennsylvanian coal balls

    E-Print Network [OSTI]

    Baxter, R. W.

    1975-05-29

    THE UNIVERSITY OF KANSAS PALEONTOLOGICAL CONTRIBUTIONS May 29, 1975 Paper 77 FOSSIL FUNGI FROM AMERICAN PENNSYLVANIAN COAL BALLS' ROBERT W. BAXTER University of Kansas, Lawrence, Kansas ABSTRACT The current status of knowledge regarding fossil... 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...

  1. Response to aflatoxin and grain composition of exotic maize germplasm 

    E-Print Network [OSTI]

    Corn, Rebecca Joann

    2009-06-02

    fulfillment of the requirements for the degree of MASTER OF SCIENCE Approved by: Co-Chairs of Committee, Javier Betran William Rooney Committee Members, Thomas Isakeit Lloyd Rooney Head of Department, David Baltensperger.... Javier Betran Dr. William L. Rooney Exotic germplasm has potential to provide new alleles for disease and insect resistance. US maize (Zea mays L.) currently lacks genetic resistance to Aspergillus flavus, a fungal pathogen that produces...

  2. Is there reduction in disease and predispersal seed predation at the border of a host plant’s range? - field and herbarium studies of Carex blanda

    E-Print Network [OSTI]

    Alexander, Helen M.

    2007-01-01

    . blanda. The smut fungus Anthracoidea blanda (V?nky and H. Alexander) causes localised ovary infections (V?nky 2005). Individual infected flowers are sterilised with the ovaries replaced by sori that consist of fungal teliospores around remnant ovary... tissue. An infected plant can range from having a single infected flower to over 50% of flowers sterilised. Based on Scandianvian studies of other Anthracoidea species (Kukkonen 1972; Ericson et al.1993; Ingvarsson & Ericson 1998, 2000), we expect...

  3. Calling on a million minds for community annotation in WikiProteins

    E-Print Network [OSTI]

    Mons, Barend; Ashburner, Michael; Chichester, Christine; van Mulligen, Erik; Weeber, Marc; den Dunnen, Johan T.; Musen, Marc; Cockerill, Matthew; Hermjakob, Henning; Packer, Abel; Pacheco, Roberto; Lewis, Suzanna; Berkeley, Alfred; Melton, William; Barris, Nickolas; Borner, Katy; Meijssen, Gerard; Moeller, Erik; Roes, Peter Jan; Mons, Albert; van Ommen, Gert; Wales, Jimmy; Bairoch, Amos

    2008-05-28

    -etching primers such as 'Clearfil Liner Bond 2' [PMID: 9522695, 12601887], on the Clb1 gene in the fungal pathogen Ustilago maydis [PMID: 14679309] and on cal- cineurin B-like proteins, such as CLB1 in Arabidopsis [PMID: 14617077]. For computational meta... profile' has been constructed and, subsequently, an Author Knowlet. These will be augmented by a highly curated database from Latin America, CV Lattes [27], which contains considerable overlap with the PubMed Author collection, but will also enrich...

  4. The Application of Ultraviolet Germicidal Technology in HVAC Systems 

    E-Print Network [OSTI]

    Taylor, M. J.

    2000-01-01

    ) filtration is another alternative. HEPA filters have the ability to intercept many fungal spores. However, they also intercept nutrients, and if damp, provide a site for the spores to grow and multiply. The spores may grow through the filter material..., releasing spores on the downstream side of the filter.12 The result is that the filter contributes to the increase in the number of spores in the occupied space rather than decreases them. HEPA filters are unable to remove viruses. Typical HEPA filters...

  5. Predicting drug metabolism: experiment and/or computation?

    E-Print Network [OSTI]

    Kirchmair, Johannes; Göller, Andreas H.; Lang, Dieter; Kunze, Jens; Testa, Bernard; Wilson, Ian D.; Glen, Robert C.; Schneider, Gisbert

    2015-04-24

    metabolites. These xenobiotics also include synthetic drugs, in addition to naturally occurring substances (e.g. bacterial, fungal and herbal toxins), often produced as part of a specific defence mechanism. Recent studies have highlighted the often... Metabolic enzymes and effectors involved in their regulation are known for remarkable ligand promiscuity. The plasticity and size of their binding sites (some of them have two or more) is a direct result of their function, which in the case of xenobiotic...

  6. Microorganisms having enhanced tolerance to inhibitors and stress

    DOE Patents [OSTI]

    Brown, Steven D.; Yang, Shihui

    2014-07-29

    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.

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

    SciTech Connect (OSTI)

    Dodge, Robert L.; Cournoyer, Michael E.

    2012-07-01

    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)

  8. 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.

    1992-02-17

    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.

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

    E-Print Network [OSTI]

    Hossein Salari; B. Eslami-Mossallam; M. S. Naderi; M. R. Ejtehadi

    2015-05-23

    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 which is in excellent agreement with recent experimental data.

  10. Structure-Based Design of Novel HIV-1 Protease Inhibitors to Combat Drug Resistance

    SciTech Connect (OSTI)

    Ghosh,A.; Sridhar, P.; Leshchenko, S.; Hussain, A.; Li, J.; Kovalevsky, A.; Walters, D.; Wedelind, J.; Grum-Tokars, V.; et al.

    2006-01-01

    Structure-based design and synthesis of novel HIV protease inhibitors are described. The inhibitors are designed specifically to interact with the backbone of HIV protease active site to combat drug resistance. Inhibitor 3 has exhibited exceedingly potent enzyme inhibitory and antiviral potency. Furthermore, this inhibitor maintains impressive potency against a wide spectrum of HIV including a variety of multi-PI-resistant clinical strains. The inhibitors incorporated a stereochemically defined 5-hexahydrocyclopenta[b]furanyl urethane as the P2-ligand into the (R)-(hydroxyethylamino)sulfonamide isostere. Optically active (3aS,5R,6aR)-5-hydroxy-hexahydrocyclopenta[b]furan was prepared by an enzymatic asymmetrization of meso-diacetate with acetyl cholinesterase, radical cyclization, and Lewis acid-catalyzed anomeric reduction as the key steps. A protein-ligand X-ray crystal structure of inhibitor 3-bound HIV-1 protease (1.35 Angstroms resolution) revealed extensive interactions in the HIV protease active site including strong hydrogen bonding interactions with the backbone. This design strategy may lead to novel inhibitors that can combat drug resistance.

  11. The effect of rhenium, sulfur and alumina on the conversion of hydrocarbons over platinum single crystals: Surface science and catalytic studies

    SciTech Connect (OSTI)

    Kim, C.

    1992-04-01

    Conversion reactions of hydrocarbons over Pt-Re model catalyst surfaces modified by sulfur and alumina have been studied. A plasma deposition source has been developed to deposit Pt, Re, and Al on metal substrates variable coverage in ultrahigh vacuum without excessive heating. Conversion of n-hexane was performed over the Re-covered Pt and Pt-covered Re surfaces. The presence of the second metal increased hydrogenolysis activity of both Pt-Re surfaces. Addition of sulfur on the model Catalyst surfaces suppressed hydrogenolysis activity and increased the cyclization rate of n-hexane to methylcyclopentane over Pt-Re surfaces. Sulfiding also increased the dehydrogenation rate of cyclohexane to benzene Over Pt-Re surfaces. It has been proposed that the PtRe bimetallic catalysts show unique properties when combined with sulfur, and electronic interactions exist between platinum, rhenium and sulfur. Decomposition of hydrocarbons on the sulfur-covered Pt-Re surfaces supported that argument. For the conversion of 1-butene over the planar Pt/AlO[sub x], the addition of Pt increased the selectivity of hydrogenation over isomerization.

  12. The effect of rhenium, sulfur and alumina on the conversion of hydrocarbons over platinum single crystals: Surface science and catalytic studies

    SciTech Connect (OSTI)

    Kim, C.

    1992-04-01

    Conversion reactions of hydrocarbons over Pt-Re model catalyst surfaces modified by sulfur and alumina have been studied. A plasma deposition source has been developed to deposit Pt, Re, and Al on metal substrates variable coverage in ultrahigh vacuum without excessive heating. Conversion of n-hexane was performed over the Re-covered Pt and Pt-covered Re surfaces. The presence of the second metal increased hydrogenolysis activity of both Pt-Re surfaces. Addition of sulfur on the model Catalyst surfaces suppressed hydrogenolysis activity and increased the cyclization rate of n-hexane to methylcyclopentane over Pt-Re surfaces. Sulfiding also increased the dehydrogenation rate of cyclohexane to benzene Over Pt-Re surfaces. It has been proposed that the PtRe bimetallic catalysts show unique properties when combined with sulfur, and electronic interactions exist between platinum, rhenium and sulfur. Decomposition of hydrocarbons on the sulfur-covered Pt-Re surfaces supported that argument. For the conversion of 1-butene over the planar Pt/AlO{sub x}, the addition of Pt increased the selectivity of hydrogenation over isomerization.

  13. Static and dynamic pressure effects on the thermolysis of nitroalkanes in solution

    SciTech Connect (OSTI)

    Brower, K.R. [New Mexico Inst. of Mining and Technology, Socorro, NM (United States). Dept. of Chemistry; Davis, L.L.; Naud, D.L. [Los Alamos National Lab., NM (United States); Wang, J. [Univ. of Southern California, Los Angeles, CA (United States). Dept. of Chemistry

    1998-12-31

    The authors have measured the effects of static and shock-induced pressures on the decomposition rates and mechanisms of various nitroalkanes dissolved in different solvents with and without organic amine catalysts. While nitroalkanes without {alpha}-hydrogen decompose by homolysis of the C-NO{sub 2} bond over a wide range of conditions, the decomposition pathway of nitroalkanes having {alpha}-hydrogens (i.e., acidic nitroalkanes) is complicated and follows different decomposition mechanisms depending on the availability of organic base and reaction pressure. The Nef reaction is also an important reaction pathway. The five known decomposition pathways, homolysis of the C-NO{sub 2} bond, bimolecular reaction between the aci-form and aci-ion, cyclization of the aci-form, elimination of nitrous acid, and the Nef reaction, are highly dependent on the reaction conditions, such as pressure, presence of organic amines, water, alcohols, and polarity of solvent. The authors discuss the results of several tests used to support these various decomposition mechanisms.

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

    SciTech Connect (OSTI)

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

    2009-06-08

    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.

  15. 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.

    2008-01-01

    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.

  16. Process for the preparation of benozotriazoles and their polymers, and 2(2-hydroxy-5-isopropenylphenyl)2H-benzotriazole produced thereby

    DOE Patents [OSTI]

    Vogl, Otto (Brooklyn, NY); Nir, Zohar (Beer Sheva, IL)

    1989-03-14

    The compound 2(2-hydroxy-5-isopropenylphenyl)2H-benzotriazole (2H5P) is produced by azo coupling of o-nitrophenyl diazonium chloride with p-hydroxyacetophenone, subjecting the resulting isolated azo compound to reductive cyclization with zinc in the presence of sodium hydroxide at a temperature of about 50.degree.-70.degree. C., acidifying the resulting mixture so as to produce (2(2-hydroxy-5-acetylphenyl)2H-benzotriazole (2H5A), acetylating the isolated 2(2-hydroxy-5-acetylphenyl)2H-benzotriazole (2H5A), so as to produce 2(2-acetoxy-5-acetylphenyl)2H-benzotriazole (2A5A), methylating the isolated 2(2-acetoxy-5-acetylphenyl(2H-benzotriazole (2A5A) with a methyl Grignard reagent and dehydrating the isolated reaction product with potassium hydrogen sulfate so as to produce 2(2-hydroxy-5-isopropenylphenyl)2H-benzotriazole (2H5P). The compound is used as a polymerizable ultra violet light stabilizer.

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

    E-Print Network [OSTI]

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

    2015-01-01

    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. Formation and polymerization of cyclic disilsesquioxanes

    SciTech Connect (OSTI)

    Loy, D.A.; Carpenter, J.P.; Myers, S.A. [Sandia National Labs., Albuquerque, NM (United States)] [and others

    1996-12-31

    Under acidic sol-gel polymerization conditions, 1,3-bis(triethoxysilyl)-propane 1 and 1,4-bis(triethoxysilyl)butane 2 were shown to preferentially form cyclic disilsesquioxanes 3 and 4 rather than the expected 1,3-propylene- and 1,4-butylene-bridged polysilsesquioxane gels. Formation of 3 and 4 is driven by a combination of an intramolecular cyclization to six and seven membered rings, and a pronounced reduction in reactivity under acidic conditions as a function of increasing degree of condensation. The stability of cyclic disilsesquioxanes was confirmed with the synthesis of 3 and 4 in gram quantities; the cyclic disilsesquioxanes react slowly to give tricyclic dimers containing a thermodynamically stable eight membered siloxane ring. Continued reactions were shown to perserve the cyclic structure, opening up the possibility of utilizing cyclic disilsesquioxanes as sol-gel monomers. Preliminary polymerization studies with these new, carbohydrate-like monomers revealed the formation of network poly(cyclic disilsesquioxanes) under acidic conditions and polymerization with ring-opening under basic conditions.

  19. Intramolecular condensation reactions of {alpha},{omega}-bis(triethoxysilyl)alkanes. Formation of cyclic disilsesquioxanes

    SciTech Connect (OSTI)

    Loy, D.A.; Carpenter, J.P.; Myers, S.A.; Assink, R.A. [Sandia National Lab., Albuquerque, NM (United States)] [Sandia National Lab., Albuquerque, NM (United States); Small, J.H.; Greaves, J.; Shea, K.J. [Univ. of California, Irvine, CA (United States)] [Univ. of California, Irvine, CA (United States)

    1996-09-04

    In this paper, we used mass spectrometry and {sup 29}Si NMR spectroscopy to discover that the length of the alkylene-bridging groups had a pronounced effect on the competition between cyclization and polymerization of {alpha},{omega}-bis(triethoxysilyl)alkanes and on the formation of polymeric gels. While the intramolecular reaction clearly slows gelation, the cyclic disilsesquioxanes are still tetrafunctional monomers theoretically capable of forming polymeric gels. If the ring structures, which bear a striking resemblence to carbohydrates, are preserved through the polymerization, the resulting poly(cyclic disilsesquioxane) gels may have structural similarities to branched or cross-linked carbohydrates, such as cellulose or chitosan. Under base-catalyzed sol-gel polymerization conditions, 3 and 4 (six- and seven-membered cyclic disilsesquioxanes, respectively) quickly reacted to give gels with significant ring opening as determined from the {sup 29}Si chemical shifts in solid-state (CP MAS) NMR spectra. However, gels prepared under acidic conditions reveal some or all of the cyclic disilsesquioxane functionality was preserved in the polymers. 13 refs., 1 fig.

  20. Intramolecular condensation reactions of {alpha}, {omega}- bis(triethoxy-silyl)alkanes. Formation of cyclic disilsesquioxanes

    SciTech Connect (OSTI)

    Loy, D.A.; Carpenter, J.P.; Myers, S.A.; Assink, R.A.; Small, J.H. [Sandia National Labs., Albuquerque, NM (United States); Greaves, J.; Shea, K.J. [California Univ., Irvine, CA (United States). Dept. of Chemistry

    1996-08-01

    Under acidic sol-gel polymerization conditions, 1,3-bis(triethoxysilyl)-propane (1) and 1,4-bis(triethoxysilyl)butane (2) were shown to preferentially form cyclic disilsesquioxanes 3 and 4 rather than the expected 1,3-propylene- and 1,4-butylene-bridged polysilsesquioxane gels. Formation of 3 and 4 is driven by a combination of an intramolecular cyclization to six and seven membered rings, and a pronounced reduction in reactivity under acidic conditions as a function of increasing degree of condensation. The ease with which these relatively unreactive cyclic monomers and dimers are formed (under acidic conditions) helps to explain the difficulties in forming gels from 1 and 2. The stability of cyclic disilsesquioxanes was confirmed withe the synthesis of 3 and 4 in gram quantities; the cyclic disilsesquioxanes react slowly to give tricyclic dimers containing a thermodynamically stable eight membered siloxane ring. Continued reactions were shown to perserve the cyclic structure, opening up the possibility of utilizing cyclic disilsesquioxanes as sol-gel monomers. Preliminary polymerization studies with these new, carbohydrate-like monomers revealed the formation of network poly(cyclic disilsesquioxanes) under acidic conditions and polymerization with ring-opening under basic conditions.

  1. Mechanism of protein splicing of the Pyrococcus abyssi lon protease intein

    SciTech Connect (OSTI)

    O'Brien, Kevin M.; Schufreider, Ann K.; McGill, Melissa A.; O'Brien, Kathryn M.; Reitter, Julie N.; Mills, Kenneth V.

    2010-12-17

    Research highlights: {yields} The Pyrococcus abyssi lon protease intein promotes efficient protein splicing. {yields} Inteins with mutations that interfere with individual steps of splicing do not promote unproductive side reactions. {yields} The intein splices with Lys in place of the highly conserved penultimate His. {yields} The intein is flanked by a Gly-rich region at its C terminus that may increase the efficiency of the third step of splicing, Asn cyclization coupled to peptide bond cleavage. -- Abstract: Protein splicing is a post-translational process by which an intervening polypeptide, the intein, excises itself from the flanking polypeptides, the exteins, coupled to ligation of the exteins. The lon protease of Pyrococcus abyssi (Pab) is interrupted by an intein. When over-expressed as a fusion protein in Escherichia coli, the Pab lon protease intein can promote efficient protein splicing. Mutations that block individual steps of splicing generally do not lead to unproductive side reactions, suggesting that the intein tightly coordinates the splicing process. The intein can splice, although it has Lys in place of the highly conserved penultimate His, and mutants of the intein in the C-terminal region lead to the accumulation of stable branched-ester intermediate.

  2. Spatial regulation of a common precursor from two distinct genes generates metabolite diversity

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

    Guo, Chun -Jun; Sun, Wei -Wen; Bruno, Kenneth S.; Oakley, Berl R.; Keller, Nancy P.; Wang, Clay C. C.

    2015-07-13

    In secondary metabolite biosynthesis, core synthetic genes such as polyketide synthase genes usually encode proteins that generate various backbone precursors. These precursors are modified by other tailoring enzymes to yield a large variety of different secondary metabolites. The number of core synthesis genes in a given species correlates, therefore, with the number of types of secondary metabolites the organism can produce. In our study, heterologous expression of all the A. terreus NRPSlike genes showed that two NRPS-like proteins, encoded by atmelA and apvA, release the same natural product, aspulvinone E. In hyphae this compound is converted to aspulvinones whereas inmore »conidia it is converted to melanin. The genes are expressed in different tissues and this spatial control is probably regulated by their own specific promoters. Comparative genomics indicates that atmelA and apvA might share a same ancestral gene and the gene apvA is located in a highly conserved region in Aspergillus species that contains genes coding for life-essential proteins. Our data reveal the first case in secondary metabolite biosynthesis in which the tissue specific production of a single compound directs it into two separate pathways, producing distinct compounds with different functions. Our data also reveal that a single trans-prenyltransferase, AbpB, prenylates two substrates, aspulvinones and butyrolactones, revealing that genes outside of contiguous secondary metabolism gene clusters can modify more than one compound thereby expanding metabolite diversity. Our study raises the possibility of incorporation of spatial, cell-type specificity in expression of secondary metabolites of biological interest and provides new insight into designing and reconstituting their biosynthetic pathways.« less

  3. 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

    2010-06-10

    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

  4. 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.

    2010-12-07

    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.

  5. Trichoderma: the genomics of opportunistic success

    SciTech Connect (OSTI)

    Druzhinina, Irina S.; Seiboth, Verena Seidl; Estrella, Alfredo Herrera; Horwitz, Benjamin A.; Kenerley, Charles M.; Monte, Enrique; Mukherjee, Prasun K.; Zeilinger, Susanne; Grigoriev, Igor V.; Kubicek, Christian P.

    2011-01-01

    Trichoderma is a genus of common filamentous fungi that display a remarkable range of lifestyles and interactions with other fungi, animals and plants. Because of their ability to antagonize plant-pathogenic fungi and to stimulate plant growth and defence responses, some Trichoderma strains are used for biological control of plant diseases. In this Review, we discuss recent advances in molecular ecology and genomics which indicate that the interactions of Trichoderma spp. with animals and plants may have evolved as a result of saprotrophy on fungal biomass (mycotrophy) and various forms of parasitism on other fungi (mycoparasitism), combined with broad environmental opportunism.

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

    E-Print Network [OSTI]

    Jones, Richard Worth

    1983-01-01

    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...

  7. Trichomycetes in Argentinean Aquatic Insect Larvae

    E-Print Network [OSTI]

    Lichtwardt, Robert W.; Ferrington, Leonard C. Jr.; Lastra, Claudia Ló pez

    1999-11-01

    were preserved in 70% ethanol for later iden-tification. Attempts to culture some of the Harpellales were made by selecting pieces of gut in which fungal thalli were grow-ing and washing them at least twice in 35-mm petri dishes containing sterile.... 8. Pattern of folding backward typical of more mature thalli, the posterior part of the hindgut cuticle is at the upper right. Scale bar: 7 = 20 |jim; 8 = 80 \\im. ing in a posterior direction, as normally happens in other Harpellales. However...

  8. Deciphering the relative contributions of multiple functions within plant-microbe symbioses

    E-Print Network [OSTI]

    Sikes, Benjamin A.; Powell, Jeff R.; Rillig, Matthias C.

    2010-06-01

    Ecology, 91(6), 2010, pp. 1591–1597 #2; 2010 by the Ecological Society of America Deciphering the relative contributions of multiple functions within plant–microbe symbioses BENJAMIN A. SIKES,1,3 JEFF R. POWELL,2 AND MATTHIAS C. RILLIG2 1Department... positive, with the Gigasporaceae variable indi- cating a stronger association (Fig. 2); paths originating from both AM fungal variables were necessary to ensure adequate model fit (Table 1). For S. glauca, only species June 2010 1593PLANT–MICROBE SYMBIOSES...

  9. Oomycete Interactions with Plants: Infection Strategies and Resistance Principles

    E-Print Network [OSTI]

    Fawke, Stuart; Doumane, Mehdi; Schornack, Sebastian

    2015-06-03

    75 The Oomycota are a distinct class of fungal-like eukaryotic microbes, many of which are 76 highly destructive plant or animal pathogens. They share a range of morphological features 77 with fungi, but possess various unique characteristics which... common and contrasting 95 mechanisms of pathogenic and mutualistic filamentous microbes. 96 97 Phylogeny 98 Analysis of conserved DNA sequences such as mitochondrial COX2 (10-12), LSU rDNA (13) 99 and SSU rDNA (14) have confirmed that oomycetes...

  10. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    SciTech Connect (OSTI)

    Gilbert, David

    2013-01-01

    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.

  11. 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

    2009-07-17

    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.

  12. Refined understanding of sulfur amino acid nutrition in hybrid striped bass, Morone chrysops (male symbol) x M. saxatilis (female symbol) 

    E-Print Network [OSTI]

    Kelly, Mark Christopher

    2005-08-29

    of mortality and vulnerability to fungal disease compared to bass fed diets containing higher levels of methionine. In contrast, Griffin et al. (1994) estimated the requirement of hybrid striped bass for TSAA to be 0.7% of diet which is considerably lower... fed a diet containing L-methionine. Feed efficiency, expressed as g gain/g dry feed, for fish fed MHA was 0.66 compared to 0.77 for fish fed L- methionine. Thus, MHA was not as efficiently used as L-methionine by hybrid striped bass. In channel...

  13. Diseases of Peaches and Plums. 

    E-Print Network [OSTI]

    Johnson, Jerral D.

    1980-01-01

    the possibility of root injury during cultivation as much as possible. Mushroom Root Rot Mushroom root rot is a fungal disease commonly known as "post oak root rot," "shoestring root rot" or "mushroom root rot." It attacks peach, pear, plum, apple and many... trees. Do not replant trees in old orchard sites infested with mushroom root rot. Cotton Root Rot Peach and plum trees die suddenly after show ing first symptoms of wilting. When roots are pulled from the soil, the bark is decayed, and covered...

  14. Parasites may help stabilize cooperative relationships

    E-Print Network [OSTI]

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

    2009-06-01

    . The fungus is vertically transmitted between genera- tions, with new queens carrying a fungal pellet, collected from their natal garden, on the nuptial flight [36]. In exchange for these benefits, the fungus serves as the pri- mary food source for the ant... AB, Pan JJ, Villesen P, Mueller UG, Blackwell M, McLaughlin DJ: Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants. Proc Roy Soc Lond B Bio 2004, 271(1550):1777-1782. 36. Weber NA: Gardening Ants: The Attines...

  15. 2012 MITOCHONDRIA AND CHLOROPLASTS GORDON RESEARCH CONFERENCE & GORDON RESEARCH SEMINAR, JULY 29 - AUGUST 3, 2012

    SciTech Connect (OSTI)

    Barkan, Alice

    2012-08-03

    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.

  16. Expanding genomics of mycorrhizal symbiosis

    SciTech Connect (OSTI)

    Kuo, Alan; Kohler, Annegret; Martin, Francis M.; Grigoriev, Igor V.

    2014-11-04

    The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.

  17. 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.

    2014-04-01

    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.

  18. Structure of Protein Geranylgeranyltransferase-I from the Human Pathogen Candida albicans Complexed with a Lipid Substrate

    SciTech Connect (OSTI)

    Hast, Michael A.; Beese, Lorena S. (Duke)

    2008-11-21

    Protein geranylgeranyltransferase-I (GGTase-I) catalyzes the transfer of a 20-carbon isoprenoid lipid to the sulfur of a cysteine residue located near the C terminus of numerous cellular proteins, including members of the Rho superfamily of small GTPases and other essential signal transduction proteins. In humans, GGTase-I and the homologous protein farnesyltransferase (FTase) are targets of anticancer therapeutics because of the role small GTPases play in oncogenesis. Protein prenyltransferases are also essential for many fungal and protozoan pathogens that infect humans, and have therefore become important targets for treating infectious diseases. Candida albicans, a causative agent of systemic fungal infections in immunocompromised individuals, is one pathogen for which protein prenylation is essential for survival. Here we present the crystal structure of GGTase-I from C. albicans (CaGGTase-I) in complex with its cognate lipid substrate, geranylgeranylpyrophosphate. This structure provides a high-resolution picture of a non-mammalian protein prenyltransferase. There are significant variations between species in critical areas of the active site, including the isoprenoid-binding pocket, as well as the putative product exit groove. These differences indicate the regions where specific protein prenyltransferase inhibitors with antifungal activity can be designed.

  19. Novel Aryne Chemistry in Organic Synthesis

    SciTech Connect (OSTI)

    Zhijian Liu

    2006-12-12

    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.

  20. Status report on a solar photovoltaic concentrating energy system for a hospital in Hawaii

    SciTech Connect (OSTI)

    Seki, A.; Curtis, G.; Yuen, P.

    1983-06-01

    The largest parabolic concentrating photovoltaic/solar thermal system in the U.S. began producing electricity and hot water for a hospital on the island of Kauai, Hawaii in November 1981. Each of the 80 parabolic collectors is 6 feet by 10 feet and concentrates incident sunlight on photovoltaic cells mounted on two faces of the receiver at the focus. Although the 35 kilowatt system has been designed to produce 22,000 net kilowatt-hours per year of electricity and 620,000 gallons of 180 F water, electrical output (12 to 15 kilowatt-hours per day) is only 20 percent of that expected, primarily because insolation at the site has been only 40 percent of predicted values. A second problem with fungal attack on the receivers has been solved by better sealing. The system has also withstood a hurricane with negligible damage.

  1. 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)

    2007-12-11

    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.

  2. 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)

    2010-08-10

    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.

  3. 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)

    2011-04-12

    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.

  4. 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)

    2012-04-03

    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.

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

    SciTech Connect (OSTI)

    Kumar, Manoj

    2012-12-20

    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.

  6. Accumulation of several heavy metals and lanthanides in mushrooms (Agaricales) from the Chicago region.

    SciTech Connect (OSTI)

    Aruguete, D. M.; Aldstadt, J. H., III; Mueller, G. M.; Environmental Research; Univ. of Chicago; Field Museum of Natural History

    1998-01-01

    This study explored the differences in metal uptake in sporocarps of ectomycorrhizae-forming fungi relative to (1) fungal species; (2) collection location; (3) differential metal uptake and variation within single-species, single-area populations; and (4) mobile metal content of soil substrate for the fungi. In addition, this study examined levels of some of the lanthanides in these mushrooms, as lanthanide uptake in higher fungi has not been quantified to date. In 1995 and 1996, sporocarps from three species of ectomycorrhizal fungi (Amanita flavorubescens, Amanita rubescens, and Russula pectinatoides) were collected from Cowles Bog, Indiana Dunes National Lakeshore (near an industrial area) and the Palos forest preserves (near a residential area). Soil was also collected from the Cowles Bog plots; metals were extracted from the soil, either with local Lake Michigan water or with nitric acid. These two extractions were meant to simulate the natural soil equilibrium concentrations of soluble metals and the maximum possible effects of any fungal chelating chemicals, respectively. An inductively coupled plasma mass spectrometer was used to analyze soil extracts and nitric acid digests of whole sporocarps for the target analytes. The metals found at elevated levels in the mushrooms included four of environmental interest (Ag, Cd, Ba, and Pb) and three lanthanides (La, Ce, and Nd). Significant differences in uptake of metals were observed between A. rubescens and R. pectinatoides, while A. rubescens and A. flavorubescens were not significantly different. With regard to location, more cadmium was found in Cowles Bog collections of A. rubescens, while Palos forest A. rubescens had more of the lanthanides and barium. Significant specimen-to-specimen variation occurred in all populations examined. Correlation analysis between pairs of trace elements within each sporocarp population revealed strong positive correlations between the lanthanides. Sporocarps concentrated more metal than was made available by the lake water extraction of soil and less metal than was made available by the nitric acid extraction of soil.

  7. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust

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

    Nunes da Rocha, Ulisses; Cadillo-Quiroz, Hinsby; Karaoz, Ulas; Rajeev, Lara; Klitgord, Niels; Dunn, Sean; Truong, Viet; Buenrostro, Mayra; Bowen, Benjamin P.; Garcia-Pichel, Ferran; et al

    2015-04-14

    Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration ofmore »BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.« less

  8. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust

    SciTech Connect (OSTI)

    Nunes da Rocha, Ulisses; Cadillo-Quiroz, Hinsby; Karaoz, Ulas; Rajeev, Lara; Klitgord, Niels; Dunn, Sean; Truong, Viet; Buenrostro, Mayra; Bowen, Benjamin P.; Garcia-Pichel, Ferran; Mukhopadhyay, Aindrila; Northen, Trent R.; Brodie, Eoin L.

    2015-04-14

    Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.

  9. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    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.

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

    SciTech Connect (OSTI)

    SLACK, JEFFREY, M.

    2012-12-06

    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.

  11. Biotechnology and genetic optimization of fast-growing hardwoods

    SciTech Connect (OSTI)

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

    1991-02-01

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

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

    SciTech Connect (OSTI)

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

    2004-01-01

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

  13. The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1

    SciTech Connect (OSTI)

    Cao, Yangrong; Liang, Yan; Tanaka, Kiwamu; Nguyen, Cuong T.; Jedrzejczak, Robert P.; Joachimiak, Andrzej; Stacey, Gary

    2014-10-23

    Chitin is a fungal microbe-associated molecular pattern recognized in Arabidopsis by a lysin motif receptor kinase (LYK), AtCERK1. Previous research suggested that AtCERK1 is the major chitin receptor and mediates chitin-induced signaling through homodimerization and phosphorylation. However, the reported chitin binding affinity of AtCERK1 is quite low, suggesting another receptor with high chitin binding affinity might be present. Here, we propose that AtLYK5 is the primary chitin receptor in Arabidopsis. Mutations in AtLYK5 resulted in a significant reduction in chitin response. AtLYK5 shares overlapping function with AtLYK4 and, therefore, Atlyk4/Atlyk5-2 double mutants show a complete loss of chitin response. AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. AtLYK5 binds chitin at a much higher affinity than AtCERK1. The data suggest that AtLYK5 is the primary receptor for chitin, forming a chitin inducible complex with AtCERK1 to induce plant immunity.

  14. The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1

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

    Cao, Yangrong; Liang, Yan; Tanaka, Kiwamu; Nguyen, Cuong T.; Jedrzejczak, Robert P.; Joachimiak, Andrzej; Stacey, Gary

    2014-10-23

    Chitin is a fungal microbe-associated molecular pattern recognized in Arabidopsis by a lysin motif receptor kinase (LYK), AtCERK1. Previous research suggested that AtCERK1 is the major chitin receptor and mediates chitin-induced signaling through homodimerization and phosphorylation. However, the reported chitin binding affinity of AtCERK1 is quite low, suggesting another receptor with high chitin binding affinity might be present. Here, we propose that AtLYK5 is the primary chitin receptor in Arabidopsis. Mutations in AtLYK5 resulted in a significant reduction in chitin response. AtLYK5 shares overlapping function with AtLYK4 and, therefore, Atlyk4/Atlyk5-2 double mutants show a complete loss of chitin response. AtLYK5more »interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. AtLYK5 binds chitin at a much higher affinity than AtCERK1. The data suggest that AtLYK5 is the primary receptor for chitin, forming a chitin inducible complex with AtCERK1 to induce plant immunity.« less

  15. Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius

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

    Cabañes, F. Javier; Sanseverino, Walter; Castellá, Gemma; Bragulat, M. Rosa; Cigliano, Riccardo Aiese; Sánchez, Armand

    2015-03-13

    In microorganisms, Ion Torrent sequencing technology has been proved to be useful in whole-genome sequencing of bacterial genomes (5 Mbp). In our study, for the first time we used this technology to perform a resequencing approach in a whole fungal genome (36 Mbp), a non-ochratoxin A producing strain of Aspergillus carbonarius. Ochratoxin A (OTA) is a potent nephrotoxin which is found mainly in cereals and their products, but it also occurs in a variety of common foods and beverages. Due to the fact that this strain does not produce OTA, we focused some of the bioinformatics analyses in genes involvedmore »in OTA biosynthesis, using a reference genome of an OTA producing strain of the same species. This study revealed that in the atoxigenic strain there is a high accumulation of nonsense and missense mutations in several genes. Importantly, a two fold increase in gene mutation ratio was observed in PKS and NRPS encoding genes which are suggested to be involved in OTA biosynthesis.« less

  16. Proteomics based compositional analysis of complex cellulase-hemicellulase mixtures

    SciTech Connect (OSTI)

    Chundawat, Shishir P.; Lipton, Mary S.; Purvine, Samuel O.; Uppugundla, Nirmal; Gao, Dahai; Balan, Venkatesh; Dale, Bruce E.

    2011-10-07

    Efficient deconstruction of cellulosic biomass to fermentable sugars for fuel and chemical production is accomplished by a complex mixture of cellulases, hemicellulases and accessory enzymes (e.g., >50 extracellular proteins). Cellulolytic enzyme mixtures, produced industrially mostly using fungi like Trichoderma reesei, are poorly characterized in terms of their protein composition and its correlation to hydrolytic activity on cellulosic biomass. The secretomes of commercial glycosyl hydrolase producing microbes was explored using a proteomics approach with high-throughput quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Here, we show that proteomics based spectral counting approach is a reasonably accurate and rapid analytical technique that can be used to determine protein composition of complex glycosyl hydrolase mixtures that also correlates with the specific activity of individual enzymes present within the mixture. For example, a strong linear correlation was seen between Avicelase activity and total cellobiohydrolase content. Reliable, quantitative and cheaper analytical methods that provide insight into the cellulosic biomass degrading fungal and bacterial secretomes would lead to further improvements towards commercialization of plant biomass derived fuels and chemicals.

  17. Glionitrin A, an antibiotic-antitumor metabolite derived from competitive interaction between abandoned mine microbes

    SciTech Connect (OSTI)

    Park, H.B.; Kown, H.C.; Lee, C.H.; Yang, H.O.

    2009-02-15

    The nutrient conditions present in abandoned coal mine drainages create an extreme environment where defensive and offensive microbial interactions could be critical for survival and fitness. Coculture of a mine drainage-derived Sphingomonas bacterial strain, KMK-001, and a mine drainage-derived Aspergillus fumigatus fungal strain, KMC-901, resulted in isolation of a new diketopiperazine disulfide, glionitrin A (1). Compound 1 was not detected in monoculture broths of KMK-001 or KMC-901. The structure of 1, a (3S,10aS) diketopiperazine disulfide containing a nitro aromatic ring, was based on analysis of MS, NMR, and circular dichroism spectra and confirmed by X-ray crystal data. Glionitrin A displayed significant antibiotic activity against a series of microbes including methicillin-resistant Staphylococcus aureus. An in vitro MTT cytotoxicity assay revealed that 1 had potent submicromolar cytotoxic activity against four human cancer cell lines: HCT-116, A549, AGS, and DU145. The results provide further evidence that microbial coculture can produce novel biologically relevant molecules.

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

    SciTech Connect (OSTI)

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

    2012-09-01

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

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

    SciTech Connect (OSTI)

    Not Available

    1993-07-01

    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.

  20. Trichodermin induces cell apoptosis through mitochondrial dysfunction and endoplasmic reticulum stress in human chondrosarcoma cells

    SciTech Connect (OSTI)

    Su, Chen-Ming; Wang, Shih-Wei; Lee, Tzong-Huei; Tzeng, Wen-Pei; Hsiao, Che-Jen; Liu, Shih-Chia; Tang, Chih-Hsin

    2013-10-15

    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.

  1. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

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

    2012-03-03

    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.

  2. Underground and earth sheltered food storage: historical, geographic, and economic considerations

    SciTech Connect (OSTI)

    Dunkel, F.V.

    1985-01-01

    Storage structures now used for bulk grain and beans have been derived from a combination of scientific experiments and tradition. Recent generations of US farmers have grown up with the understanding that grain is best stored in round metal bins or wooden cribs aboveground. It is generally thought that natural wind movements in the crib structures and forced air flow from aeration fans in metal bins will keep grain and beans safe, i.e., free of moisture accumulation and the resulting insect and fungal growth, and protected from germination, all of which deteriorate the commodity. North American farmers further believe that the low temperature of northern winters combined with careful use of aerating fans will keep the grain dry or beans safe (less than 14% moisture content) for years of storage. Traditional forms of grain and bean storage in other parts of the world have evolved differently. With the exception of North America, the people of every continent in the world have developed underground structures for long-term storage of food. A review of the varieties of underground structures that have evolved throughout the world, and research related to underground storage of grain and beans is presented.

  3. Book review of Insect Symbiosis. Volume 2. Bourtzis, K.A. and Miller, T.A. editros. 2006 CRC Press, Taylor and Francis Group, Boca Raton, FL, 276 pp. ISBN 0-8493-1286-8

    SciTech Connect (OSTI)

    Hoy, M.A. [Department of Entomology and Nematology, University of Florida, Gainesville, FL (United States)

    2007-03-15

    There are several definitions of symbiosis, but in this book it involves an association where one organism (the symbiont) lives within or on the body of another organism (the host), regardless of the actual effect on the host. Some symbioses are mutualistic, some parasitic, and some involve commensalism, in which one partner derives some benefit without either harming or benefiting the other. This is the second volume in this exciting and rapidly advancing topic by these editors. The first volume was published in 2003 and during the intervening three years additional data have been produced that make this book a useful addition to your library. The first book provided chapters that provided an overview of insect symbiosis, discussions of the primary aphid symbiont Buchnera and other aphid symbionts, symbiosis in tsetse, symbionts in the weevil Sitophilus , the possible use of paratransgenic symbionts of Rhodnius prolixis to prevent disease transmission, bark beetle and fungal symbiosis, symbionts of tephritid fruit flies, symbionts affecting termite behavior, an overview of microsporidia as symbionts (parasites?) of insects, an overview of a newly discovered bacterium that causes sex-ratio distortion in insects and mites (from the Bacteroides group), symbionts that selectively kill male insects, and several chapters on the ubiquitous endosymbiont Wolbachia.

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

    SciTech Connect (OSTI)

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

    2011-05-01

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

  5. 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.

    2007-12-07

    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.

  6. Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility

    SciTech Connect (OSTI)

    Serer, María I.; Bonomi, Hernán R.; Guimarães, Beatriz G.; Rossi, Rolando C.; Goldbaum, Fernando A.; Klinke, Sebastián

    2014-05-01

    This work reports crystal structures of trimeric riboflavin synthase from the pathogen B. abortus both as the apo protein and in complex with several ligands of interest. It is shown that ligand binding drives the assembly of the unique active site of the trimer, and these findings are complemented by a detailed kinetic study on this enzyme, in which marked inhibition by substrate and product was observed. Riboflavin synthase (RS) catalyzes the last step of riboflavin biosynthesis in microorganisms and plants, which corresponds to the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine to yield one molecule of riboflavin and one molecule of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. Owing to the absence of this enzyme in animals and the fact that most pathogenic bacteria show a strict dependence on riboflavin biosynthesis, RS has been proposed as a potential target for antimicrobial drug development. Eubacterial, fungal and plant RSs assemble as homotrimers lacking C{sub 3} symmetry. Each monomer can bind two substrate molecules, yet there is only one active site for the whole enzyme, which is located at the interface between two neighbouring chains. This work reports the crystallographic structure of RS from the pathogenic bacterium Brucella abortus (the aetiological agent of the disease brucellosis) in its apo form, in complex with riboflavin and in complex with two different product analogues, being the first time that the structure of an intact RS trimer with bound ligands has been solved. These crystal models support the hypothesis of enhanced flexibility in the particle and also highlight the role of the ligands in assembling the unique active site. Kinetic and binding studies were also performed to complement these findings. The structural and biochemical information generated may be useful for the rational design of novel RS inhibitors with antimicrobial activity.

  7. Melanin, a promising radioprotector: Mechanisms of actions in a mice model

    SciTech Connect (OSTI)

    Kunwar, A.; Adhikary, B.; Jayakumar, S.; Barik, A.; Chattopadhyay, S.; Raghukumar, S.; Priyadarsini, K.I.

    2012-10-15

    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.

  8. A model for motor-mediated bidirectional transport along an antipolar microtubule bundle

    E-Print Network [OSTI]

    Congping Lin; Peter Ashwin; Gero Steinberg

    2012-11-21

    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.

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

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

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

    2014-10-07

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

  10. Nickel biosorption from aqueous systems: Studies on single and multimetal equilibria, kinetics, and recovery

    SciTech Connect (OSTI)

    Suhasini, I.P.; Sriram, G.; Asolekar, S.R.; Sureshkumar, G.K.

    1999-10-01

    This paper reports studies on the removal of toxic trace metals (nickel separately, and simultaneously with cobalt) from aqueous solutions by employing fungal biosorbents, PFB1 and PFB2, which were developed in the authors' laboratory. The observed maximum equilibrium uptake of nickel on the biosorbent was 214 mg/g (PFB1) and 110 mg/g (PFB2). The average efficiency for nickel removal was 84.5% (PFB1) and 60.8% (PFB2). The equilibrium uptake of nickel followed first-order Langmuir kinetics in the case of PFB1 and second-order Langmuir kinetics in the case of PFB2. Studies on simultaneous removal of cobalt and nickel indicated that the extent of secondary interactions between cobalt and nickel can be quantified by the change in Langmuir equilibrium constants for both metals. A mathematical model based on Fick's law of diffusion and Langmuir adsorption was developed to simulate the kinetics of nickel removal. The model was able to predict the experimentally observed kinetics well. From the simulations, the diffusivity of nickel in PFB1 was found to be 1.6 x 10{sup {minus}8} m{sup 2}/s. Desorption studies indicated that it was possible to reuse the biosorbent over three sorption-desorption cycles, and that acidic solutions desorbed better than basic or salt solutions. Among the desorbents studied, HCl and CaCl{sub 2}, with desorption efficiencies equal to 73.2 and 74.1%, respectively, for PFB1 and 70.0 and 63.1%, respectively, for PFB2 at the end of three cycles, were found to be the best desorbents.

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

    SciTech Connect (OSTI)

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

    2011-04-18

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

  12. Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness

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

    Zaborin, A.; Smith, D.; Garfield, K.; Quensen, J.; Shakhsheer, B.; Kade, M.; Tirrell, M.; Tiedje, J.; Gilbert, J. A.; Zaborina, O.; et al

    2014-09-23

    We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candidamore »taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a “commensal lifestyle.” However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.« less

  13. The mechanism of patulin's cytotoxicity and the antioxidant activity of indole tetramic acids

    SciTech Connect (OSTI)

    Riley, R.T.; Showker, J.L. )

    1991-06-01

    In LLC-PK1 cells exposed to patulin (50 microM), lipid peroxidation, abrupt calcium influx, extensive blebbing, and total LDH release appeared to be serially connected events with each representing a step in the loss of structural integrity of the plasma membrane. The aforementioned patulin-induced events were prevented by concurrent incubation with butylated hydroxytoluene, deferoxamine, and cyclopiazonic acid, a fungal metabolite. Patulin also caused depletion of nonprotein sulfhydryls, increased 86Rb+ efflux, dome collapse, and eventually the loss of cell viability. These events were not prevented by antioxidants, results consistent with the hypothesis that they were also serially connected but occurring parallel to those previously mentioned. The earliest events observed in patulin-treated cells were the decrease in nonprotein sulfhydryls and increase in 86Rb+ efflux (5 min) which occurred before statistically significant alterations in protein-bound sulfhydryls. The increased potassium efflux (86Rb+ efflux) occurred via a pathway distinct from BaCl2, quinine, or tetraethylammonium sensitive potassium channels. This is the first published report of the antioxidant activity of indole tetramic acids (cyclopiazonic acid and cyclopiazonic acid imine). The protective effect of tetramic acids in LLC-PK1 cells was restricted to indole tetramic acids, and their prevention of lipid peroxidation did not involve iron chelation. The results of this study demonstrate that cyclopiazonic acid is a potent inhibitor of azide-insensitive, ATP-dependent, a23187-sensitive calcium uptake by the lysate of LLC-PK1 cells. This result is consistent with the hypothesis that the endoplasmic reticulum calcium transport ATPase is a sensitive target for cyclopiazonic acid in LLC-PK1 cells.

  14. 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

    2011-02-17

    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.

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

    SciTech Connect (OSTI)

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

    2009-01-01

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

  16. 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

    2014-04-01

    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.

  17. Effect of hydroxamate siderophores on Fe release and Pb(II) adsorption by goethite

    SciTech Connect (OSTI)

    Kraemer, Stephan M.; Cheah, Sing-Foong; Zapf, Rita; Xu, Jide; Raymond, Kenneth N.; Sposito, Garrison

    1998-08-01

    Hydroxamate siderophores are biologically-synthesized, Fe(III)-specific ligands which are common in soil environments. In this paper, we report an investigation of their adsorption by the iron oxyhydroxide, goethite; their influence on goethite dissolution kinetics; and their ability to affect Pb(II) adsorption by the goethite surface. The siderophores used were desferrioxamine B (DFO-B), a fungal siderophore, and desferrioxamine D1, an acetyl derivative of DFO-B (DFO-D1). Siderophore adsorption isotherms yielded maximum surface concentrations of 1.5 (DFO-B) or 3.5 (DFO-D1) mu-mol/g at pH 6.6, whereas adsorption envelopes showed either cation-like (DFO-B) or ligand-like (DFO-D1) behavior. Above pH 8, the adsorbed concentrations of both siderophores were similar. The dissolution rate of goethite in the presence of 240 mu M DFO-B or DFO-D1 was 0.02 or 0.17 mu-mol/g hr, respectively. Comparison of these results with related literature data on the reactions between goethite and acetohydroxamic acid, a monohydroxamate ligand, suggested that the three hydroxamate groups in DFO-D1 coordinate to Fe(III) surface sites relatively independently. The results also demonstrated a significant depleting effect of 240 mu-M DFO-B or DFO-D1 on Pb(II) adsorption by goethite at pH > 6.5, but there was no effect of adsorbed Pb(II) on the goethite dissolution rate.

  18. Revealing the Differences Between Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance

    SciTech Connect (OSTI)

    Resch, M.

    2014-09-08

    Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution imaging techniques. Also, translating findings between model substrates to intact biomass is critical for evaluating enzyme performance. Here we employ a fungal free enzyme cocktail, a complexed cellulosomal system, and a combination of the two to investigate saccharification mechanisms on cellulose I, II and III along with corn stover from Clean Fractionation (CF), which is an Organosolv pretreatment. The insoluble Cellulose Enriched Fraction (CEF) from CF contains mainly cellulose with minor amounts of residual hemicellulose and lignin, the amount of which depends on the CF pretreatment severity. Enzymatic digestions at both low and high-solids loadings demonstrate that CF reduces the amount of enzyme required to depolymerize polysaccharides relative to deacetylated, dilute acid pretreated corn stover. Transmission and scanning electron microscopy of the biomass provides evidence for the different mechanisms of enzymatic deconstruction between free and complexed enzyme systems, and reveals the basis for the synergistic relationship between the two enzyme paradigms on a process-relevant substrate for the first time. These results also demonstrate that the presence of lignin, rather than cellulose morphology, is more detrimental to cellulosome action than to free cellulases. As enzyme costs are a major economic driver for biorefineries, this study provides key inputs for the evaluation of CF as a pretreatment method for biomass conversion.

  19. Solid phase immobilization of optically responsive liposomes insol-gel materials for chemical and biological sensing

    SciTech Connect (OSTI)

    Yamanaka, Stacey A.; Charych, Deborah H.; Loy, Douglas A.; Sasaki, Darryl Y.

    1997-04-01

    Liposomes enhanced with surface recognition groups have previously been found to have high affinity for heavy metal ions and virus particles with unique fluorescent and colorimetric responses, respectively. These lipid aggregate systems have now been successfully immobilized in a silica matrix via the sol-gel method, affording sensor materials that are robust, are easily handled, and offer optical clarity. The mild processing conditions allow quantitative entrapment of preformed liposomes without modification of the aggregate structure. Lipid extraction studies of immobilized nonpolymerized liposomes showed no lipid leakage in aqueous solution over a period of 3 months. Heavy metal fluorescent sensor materials prepared with 5 percent N-[8-[1-octadecyl-2-(9-(1-pyrenyl)nonyl)-rac-glyceroyl]-3,6-dioxaoctyl]imino acid/distearylphosphatidylcholineliposomes exhibited a 4-50-fold enhancement in sensitivity to various metal ions compared to that of the liposomes in free solution. Through ionic attraction the anionic silicate surface, at the experimental pH of 7.4, may act as a preconcentrator of divalent metal ions, boosting the gel's internal metal concentration. Entrapped sialic acid-coated polydiacetylene liposomes responded with colorimetric signaling to influenza virus X31, although slower than the free liposomes in solution. The successful transport of the virus (50-100 nm diameter) reveals a large pore diameter of the gel connecting the liposome to the bulk solution. The porous and durable silica matrix additionally provides a protective barrier to biological attack (bacterial, fungal) and allows facile recycling of the liposome heavy metal sensor.

  20. Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness

    SciTech Connect (OSTI)

    Zaborin, A.; Smith, D.; Garfield, K.; Quensen, J.; Shakhsheer, B.; Kade, M.; Tirrell, M.; Tiedje, J.; Gilbert, J. A.; Zaborina, O.; Alverdy, J. C.

    2014-09-23

    We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candida taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a “commensal lifestyle.” However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.

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

    SciTech Connect (OSTI)

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

    2014-10-07

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

  2. 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

    2014-11-20

    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.

  3. 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, II, David G.; Smith, Richard D.; Glass, N. Louise; Heitman, Joseph

    2014-11-20

    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.

  4. 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

    2011-04-28

    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

  5. Soil microbial responses to nitrogen addition in arid ecosystems

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

    Sinsabaugh, Robert L.; Belnap, Jayne; Rudgers, Jennifer; Kuske, Cheryl R.; Martinez, Noelle; Sandquist, Darren

    2015-08-14

    The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg N ha-1 y-1 from March 2012 to March 2013. In March 2013, biocrust (0–0.5 cm) and bulk soils (0–10 cm) were collected beneath Ambrosia canopies and in the interspaces betweenmore »plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. With most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha-1 y-1 and 159 kg ha-1, respectively, for biomass, and 70 kg ha-1 y-1 and 114 kg ha-1, respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration reported in broader meta-analyses of N amendment effects in mesic ecosystems. The large effect sizes at low N addition rates indicate that arid ecosystems are sensitive to modest increments in anthropogenic N deposition.« less

  6. HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa

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

    Jonkers, Wilfried; Leeder, Abigail C.; Ansong, Charles; Wang, Yuexi; Yang, Feng; Starr, Trevor L.; Camp, II, David G.; Smith, Richard D.; Glass, N. Louise; Heitman, Joseph

    2014-11-20

    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) thatmore »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.« less

  7. 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

    2014-11-17

    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

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

    SciTech Connect (OSTI)

    Donal F. Day

    2009-03-31

    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.

  9. Microbial Cell Imaging

    SciTech Connect (OSTI)

    Doktycz, Mitchel John; Sullivan, Claretta; Mortensen, Ninell P; Allison, David P

    2011-01-01

    Atomic force microscopy (AFM) is finding increasing application in a variety of fields including microbiology. Until the emergence of AFM, techniques for ivnestigating processes in single microbes were limited. From a biologist's perspective, the fact that AFM can be used to generate high-resolution images in buffers or media is its most appealing feature as live-cell imaging can be pursued. Imaging living cells by AFM allows dynamic biological events to be studied, at the nanoscale, in real time. Few areas of biological research have as much to gain as microbiology from the application of AFM. Whereas the scale of microbes places them near the limit of resolution for light microscopy. AFM is well suited for the study of structures on the order of a micron or less. Although electron microscopy techniques have been the standard for high-resolution imaging of microbes, AFM is quickly gaining favor for several reasons. First, fixatives that impair biological activity are not required. Second, AFM is capable of detecting forces in the pN range, and precise control of the force applied to the cantilever can be maintained. This combination facilitates the evaluation of physical characteristics of microbes. Third, rather than yielding the composite, statistical average of cell populations, as is the case with many biochemical assays, the behavior of single cells can be monitored. Despite the potential of AFM in microbiology, there are several limitations that must be considered. For example, the time required to record an image allows for the study of gross events such as cell division or membrane degradation from an antibiotic but precludes the evaluation of biological reactions and events that happen in just fractions of a second. Additionally, the AFM is a topographical tool and is restricted to imaging surfaces. Therefore, it cannot be used to look inside cells as with opticla and transmission electron microscopes. other practical considerations are the limitation on the maximum scan size (roughly 100 x 100 {mu}m) and the restricted movement of the cantilever in the Z (or height) direction. In most commercial AFMs, the Z range is restricted to roughly 10 {mu}m such that the height of cells to be imaged must be seriously considered. Nevertheless, AFM can provide structural-functional information at nanometer resolution and do so in physiologically relevant environments. Further, instrumentation for scanning probe microscopy continues to advance. Systems for high-speed imaging are becoming available, and techniques for looking inside the cells are being demonstrated. The ability to combine AFM with other imaging modalities is likely to have an even greater impact on microbiological studies. AFM studies of intact microbial cells started to appear in the literature in the 1990s. For example, AFM studies of Saccharomyces cerevisiae examined buddings cars after cell division and detailed changes related to cell growth processes. Also, the first AFM studies of bacterial biofilms appeared. In the late 1990s, AFM studies of intact fungal spores described clear changes in spore surfaces upon germination, and studies of individual bacterial cells were also described. These early bacterial imaging studies examined changes in bacterial morphology due to antimicrobial peptides exposure and bacterial adhesion properties. The majority of these early studies were carried out on dried samples and took advantage of the resolving power of AFM. The lack of cell mounting procedures presented an impediment for cell imaging studies. Subsequently, several approaches to mounting microbial cells have been developed, and these techniques are described later. Also highlighted are general considerations for microbial imaging and a description of some of the various applications of AFM to microbiology.

  10. Missing links in the root-soil organic matter continuum

    SciTech Connect (OSTI)

    O'Brien, Sarah L.; Iversen, Colleen M

    2009-01-01

    The soil environment remains one of the most complex and poorly understood research frontiers in ecology. Soil organic matter (SOM), which spans a continuum from fresh detritus to highly processed, mineral-associated organic matter, is the foundation of sustainable terrestrial ecosystems. Heterogeneous SOM pools are fueled by inputs from living and dead plants, driven by the activity of micro- and mesofauna, and are shaped by a multitude of abiotic factors. The specialization required to measure unseen processes that occur on a wide range of spatial and temporal scales has led to the partitioning of soil ecology research across several disciplines. In the organized oral session 'Missing links in the root-soil organic matter continuum' at the annual Ecological Society of America meeting in Albuquerque, NM, USA, we joined the call for greater communication and collaboration among ecologists who work at the root-soil interface (e.g. Coleman, 2008). Our goal was to bridge the gap between scientific disciplines and to synthesize disconnected pieces of knowledge from root-centric and soil-centric studies into an integrated understanding of belowground ecosystem processes. We focused this report around three compelling themes that arose from the session: (1) the influence of the rhizosphere on SOM cycling, (2) the role of soil heterotrophs in driving the transformation of root detritus to SOM, and (3) the controlling influence of the soil environment on SOM dynamics. We conclude with a discussion of new approaches for gathering data to bridge gaps in the root-SOM continuum and to inform the next generation of ecosystem models. Although leaf litter has often been considered to be the main source of organic inputs to soil, Ann Russell synthesized a convincing body of work demonstrating that roots, rather than surface residues, control the accumulation of SOM in a variety of ecosystems. Living roots, which are chemically diverse and highly dynamic, also influence a wide range of soil processes, from the exudation of labile C compounds to the development of fungal associations. For example, Zoe Cardon demonstrated that the root-mediated redistribution of deep soil water to relatively dry shallower soil, increased soil CO{sub 2} efflux and nutrient cycling near the surface in an arid ecosystem. Andrew Kulmatiski also discussed the importance of rooting distribution throughout the soil profile for strategies of water uptake by different species in an African savanna. Later, Julie Jastrow demonstrated that living roots shape soil physical structure by promoting the formation of soil aggregates, which facilitated accrual of SOM in restored grasslands. Taken together, the evidence is compelling that living roots, and organic matter derived from root detritus, are important parts of the continuum of organic matter in the soil. Larger soil organisms (i.e. 50 {micro}m to many cm in body size) play an important role in the root-SOM continuum by grazing on roots and microbes, comminuting organic matter and aggregating soil in fecal pellets. However, litterbag and soil incubation studies necessarily exclude invertebrates, and research on faunal activity and trophic dynamics tends to be independent from research on the biogeochemistry of SOM cycling. Tim Filley used plant-derived biomarkers in invertebrate residues to bridge the gap between larger soil organisms, such as earthworms and beetle larvae, and SOM distribution. He found that larger soil organisms help to stabilize root-derived organic matter in soil aggregates. Similar coupling of biogeochemistry with food web studies could prove fruitful for describing mechanisms that underlie critical ecosystem processes. Despite considerable research efforts, the breadth of the microbial role in the root-SOM continuum remains unresolved. Using advanced pyrosequencing techniques, David Nelson demonstrated the importance of archea as nitrifiers in agricultural systems exposed to elevated [CO{sub 2}]. Rising atmospheric [CO{sub 2}] and other changing environmental factors add a layer of complexity t

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

    SciTech Connect (OSTI)

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

    2011-09-16

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