@misc{torto-alalibo_collmer_gwinn-giglio_lindeberg_meng_chibucos_tseng_lomax_biehl_ireland_et al._2010, title={Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology}, volume={74}, ISSN={["1098-5557"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78650086447&partnerID=MN8TOARS}, DOI={10.1128/mmbr.00017-10}, abstractNote={SUMMARYMicrobes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community.}, number={4}, journal={MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS}, author={Torto-Alalibo, Trudy and Collmer, Candace W. and Gwinn-Giglio, Michelle and Lindeberg, Magdalen and Meng, Shaowu and Chibucos, Marcus C. and Tseng, Tsai-Tien and Lomax, Jane and Biehl, Bryan and Ireland, Amelia and et al.}, year={2010}, month={Dec}, pages={479–503} }
 @misc{meng_torto-alalibo_chibucos_tyler_dean_2009, title={Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms}, volume={9}, ISSN={["1471-2180"]}, DOI={10.1186/1471-2180-9-s1-s7}, abstractNote={Abstract}, journal={BMC MICROBIOLOGY}, author={Meng, Shaowu and Torto-Alalibo, Trudy and Chibucos, Marcus C. and Tyler, Brett M. and Dean, Ralph A.}, year={2009}, month={Feb} }
 @misc{meng_brown_ebbole_torto-alalibo_oh_deng_mitchell_dean_2009, title={Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae}, volume={9}, ISSN={["1471-2180"]}, DOI={10.1186/1471-2180-9-s1-s8}, abstractNote={Abstract}, journal={BMC MICROBIOLOGY}, author={Meng, Shaowu and Brown, Douglas E. and Ebbole, Daniel J. and Torto-Alalibo, Trudy and Oh, Yeon Yee and Deng, Jixin and Mitchell, Thomas K. and Dean, Ralph A.}, year={2009}, month={Feb} }
 @misc{torto-alalibo_meng_dean_2009, title={Infection strategies of filamentous microbes described with the Gene Ontology}, volume={17}, ISSN={["1878-4380"]}, DOI={10.1016/j.tim.2009.05.003}, abstractNote={Filamentous microbes that form highly developed symbiotic associations (ranging from pathogenesis to mutualism) with their hosts include fungi, oomycetes and actinomycete bacteria. These organisms share many common features in growth, development and infection and have evolved similar strategies for neutralizing host defense responses to establish symbioses. Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced genomes of filamentous organisms. Analysis of the available genomes has provided useful information about genes that might be important for host infection and colonization. However, because many functional similarities among these organisms have arisen by convergent evolution, sequence-based genomic comparisons will miss many genes that are functionally analogous. In the absence of sequence similarity, annotating genes with standardized terms from the Gene Ontology (GO) can facilitate functional comparisons. Here, we review common strategies employed by filamentous organisms during colonization of their hosts, with reference to GO terms that best describe the processes involved. Filamentous microbes that form highly developed symbiotic associations (ranging from pathogenesis to mutualism) with their hosts include fungi, oomycetes and actinomycete bacteria. These organisms share many common features in growth, development and infection and have evolved similar strategies for neutralizing host defense responses to establish symbioses. Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced genomes of filamentous organisms. Analysis of the available genomes has provided useful information about genes that might be important for host infection and colonization. However, because many functional similarities among these organisms have arisen by convergent evolution, sequence-based genomic comparisons will miss many genes that are functionally analogous. In the absence of sequence similarity, annotating genes with standardized terms from the Gene Ontology (GO) can facilitate functional comparisons. Here, we review common strategies employed by filamentous organisms during colonization of their hosts, with reference to GO terms that best describe the processes involved. filamentous or rod-shaped bacteria of the order Actinomycetales. extracellular component around mesophyll cells in a plant. swollen dome-shaped structure differentiated from germ tube to facilitate penetration of the host plant. symbionts that depend entirely on their host for their nutrients and as such preserve the viability of their host. a class of mostly aquatic fungi. non-motile asexual spores that develop off conidiophores in certain oomycetes and fungi. fungi that live asymptomatically within a plant tissue for part of its life. germination hypha, which emerges from a spore and often penetrates the host tissue. specialized branch of a hypha formed inside a host cell by certain fungi and oomycetes in order to obtain nourishment from their host. symbionts that initially inhabit living host cells and as infection proceeds, actively kill the host to obtain nutrients from dead tissues. a class of cysteine-rich proteins that form hydrophobic coating on surfaces. fungi that form mutualistic association with the roots of plants. symbiont that kills host tissues during colonization and obtains nutrients from the dead matter. organisms that resemble filamentous fungi but are evolutionarily related to heterokont biflagellate algae in the kingdom Stramenopila. molecules that are found in microorganisms but not in the host. a serine protease similar to subtilisin and characterized by a catalytic triad of amino acids that include aspartate, histidine and serine. a spherical vesicle found in the cytoplasm of zoospores. asexual spores which use flagella for locomotion.}, number={7}, journal={TRENDS IN MICROBIOLOGY}, author={Torto-Alalibo, Trudy and Meng, Shaowu and Dean, Ralph A.}, year={2009}, month={Jul}, pages={320–327} }
 @misc{oh_donofrio_pan_coughlan_brown_meng_mitchell_dean_2008, title={Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae}, volume={9}, ISSN={["1474-760X"]}, DOI={10.1186/gb-2008-9-5-r85}, abstractNote={Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood.We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection.We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.}, number={5}, journal={GENOME BIOLOGY}, author={Oh, Yeonyee and Donofrio, Nicole and Pan, Huaqin and Coughlan, Sean and Brown, Douglas E. and Meng, Shaowu and Mitchell, Thomas and Dean, Ralph A.}, year={2008} }