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Browsing Faculty Research Publications (Botany and Plant Pathology) by Title

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Browsing Faculty Research Publications (Botany and Plant Pathology) by Title

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  • Cheng, Xu; de Bruijn, Irene; van der Voort, Menno; Loper, Joyce E.; Raaijmakers, Jos M. (John Wiley & Sons Ltd and Society for Applied Microbiology, 2013-08)
    Transcriptome analysis of Pseudomonas fluorescensSBW25 showed that 702 genes were differentially regulated in a gacS::Tn5 mutant, with 300 and 402 genes up- and downregulated respectively. Similar to the Gac regulon of o ...
  • Gene Ontology Consortium; Berardini, Tanya Z.; Li, Donghui; Jaiswal, Pankaj; et al. (Oxford University Press, 2009-11-17)
    The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The G ...
  • Bruskiewich, Richard; Senger, Martin; Davenport, Guy; Jaiswal, Pankaj; et al. (Hindawi Publishing Corporation, 2008)
    The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A k ...
  • Xie, Zhixin; Johansen, Lisa K.; Gustafan, Adam M.; Kasschau, Kristin D.; Lellis, Andrew D.; Zilberman, Daniel; Jacobsen, Steven E.; Carrington, James C. (Public Library of Science, 2004-05)
    Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to ...
  • Alexander, J. Andrew; Liston, Aaron; Popovich, Steve J. (Botanical Society of America, Inc., 2004-12)
    Astragalus oniciformis Barneby is a narrow endemic xerophyte of the upper Snake River Plain of central Idaho, USA, where it inhabits stabilized, aeolian sand deposits and previously burned, sandy sites over Quaternary b ...
  • Goyer, Aymeric; Sweek, Kortney (American Chemical Society, 2011-12-28)
    Biofortification of staple crops like potato via breeding is an attractive strategy to reduce human micronutrient deficiencies. A prerequisite is metabolic phenotyping of genetically diverse material which can potentiall ...
  • Lee, Hanna; Yoo, Seong Jeon; Lee, Jeong Hwan; Kim, Wanhui; Yoo, Seung Kwan; Fitzgerald, Heather; Carrington, James C.; Ahn, Ji Hoon (Oxford University Press, 2010-01-12)
    Flowering is the primary trait affected by ambient temperature changes. Plant microRNAs (miRNAs) are small non-coding RNAs playing an important regulatory role in plant development. In this study, to elucidate the me ...
  • Torto-Alalibo, Trudy; Purwantini, Endang; Lomax, Jane; Setubal, João C.; Mukhopadhyay, Biswarup; Tyler, Brett M. (Frontiers Research Foundation, 2014-10-10)
    Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and ...
  • Halgren, Anne; Maselko, Maciej; Azevedo, Mark; Mills, Dallice; Armstrong, Donald; Banowetz, Gary (Society for General Microbiology, 2012-11-01)
    The genetic basis of the biosynthesis of the germination-arrest factor (GAF) produced by Pseudomonas fluorescens WH6, and previously identified as 4-formylaminooxyvinylglycine, has been investigated here. In addition to ...
  • Padamsee, Mahajabeen; Kumar, T. K. Arun; Riley, Robert; Binder, Manfred; Boyd, Alex; Calvo, Ana M.; Furukawa, Kentaro; Hesse, Cedar; Hohmann, Stefan; James, Tim Y.; LaButti, Kurt; Lapidus, Alla; Lindquist, Erika; Lucas, Susan; Miller, Kari; Shantappa, Sourabha; Grigoriev, Igor V.; Hibbett, David S.; McLaughlin, David J.; Spatafora, Joseph W.; Aime, M. Catherine (Elsevier, 2012-03)
    Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from h ...
  • Bushley, Kathryn E.; Raja, Rajani; Jaiswal, Pankaj; Cumbie, Jason S.; Nonogaki, Mariko; Boyd, Alexander E.; Owensby, C. Alisha; Knaus, Brian J.; Elser, Justin; Miller, Daniel; Di, Yanming; McPhail, Kerry L.; Spatafora, Joseph W. (Public Library of Science, 2013-06-20)
    The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isola ...
  • Dharmawardhana, Palitha; Ren, Liya; Amarasinghe, Vindhya; Monaco, Marcela; Thomason, Jim; Ravenscroft, Dean; McCouch, Susan; Ware, Doreen; Jaiswal, Pankaj (Springer, 2013)
    Background: Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in associa ...
  • Grunwald, Niklaus J. (Canadian Phytopathological Society, 2012-02-23)
    Whole and partial genome sequences are becoming available at an ever-increasing pace. For many plant pathogen systems, we are moving into the era of genome resequencing. The first Phytophthora genomes, P. ramorum and P. ...
  • Toome, Merje; Ohm, Robin A.; Riley, Robert W.; Boyd, Alexander; Spatafora, Joseph W.; et al. (John Wiley & Sons Ltd., 2014-04)
    Mixia osmundae (Basidiomycota, Pucciniomycotina) represents a monotypic class containing an unusual fern pathogen with incompletely understood biology. We sequenced and analyzed the genome of M. osmundae, focusing on g ...
  • Li, Lin; Eichten, Steven R.; Shimizu, Rena; Cole, Rex A.; Fowler, John E.; et al. (BioMed Central Ltd., 2014-02-27)
    BACKGROUND: Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and ...
  • Kasschau, Kristin D.; Fahlgren, Noah; Chapman, Elisabeth J.; Sullivan, Christopher M.; Cumbie, Jason S.; Givan, Scott A.; Carrington, James C. (PLoS ONE, 2007-03)
    Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNA ...
  • Klevebring, Daniel; Street, Nathaniel R.; Fahlgren, Noah; Kasschau, Krisitin D.; Carrington, James C.; Lundeberg, Joakim; Jansson, Stefan (BioMed Central, 2009-12-20)
    Background: Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18- ...
  • Al Rwahnih, Maher; Doljab, Valerian V.; Dauberta, Steve; Koonin, Eugene V.; Rowhania, Adib (Elsevier, 2012-01)
    Deep sequencing analysis of an asymptomatic grapevine revealed a virome containing five RNA viruses and a viroid. Of these, Grapevine leafroll-associated virus 7 (GLRaV-7), an unassigned closterovirus, was by far the mos ...
  • McCune, Bruce; Schoch, Conrad; Root, Heather T.; Kageyama, Stacie A.; Miadlikowska, Jolanta (American Bryological and Lichenological Society, Inc., 2011)
    Hypogymnia imshaugii is one of the most common, conspicuous and morphologically variable epiphytic lichens of the Pacific coastal states and provinces. The species varies greatly in morphology and chemistry, suggesting m ...
  • O'Malley, Robert T.; Behrenfeld, Michael J.; Westberry, Toby K.; Milligan, Allen J.; Shang, Shaoling; Yan, Jing (American Geophysical Union, 2014-07-17)
    Since June 2010, the Geostationary Ocean Color Imager (GOCI) has been collecting the first diurnally resolved satellite ocean measurements. Here GOCI retrievals of phytoplankton chlorophyll concentration and fluorescen ...

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