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Search Results: 1 - 10 of 464832 matches for " Ralph A Dean "
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The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes
Jixin Deng, Ignazio Carbone, Ralph A Dean
BMC Evolutionary Biology , 2007, DOI: 10.1186/1471-2148-7-30
Abstract: A total of 376 P450 genes were assigned to 168 families according to standard nomenclature. On average, only 1 to 2 genes per family were in each genome. To resolve conflicting results between different clustering analyses and standard family designation, a higher order relationship was formulated. 376 genes were clustered into 115 clans. Subsequently a novel approach based on parsimony was developed to build the evolutionary models. Based on these analyses, a core of 30 distinct clans of P450s was defined. The core clans experienced contraction in all four fungal lineages while new clans expanded in all with exception of NC. MG experienced more genes and clans gains compared to the other fungi. Parsimonious analyses unanimously supported one species topology for the four fungi.The four studied fungi exhibit unprecedented diversity in their P450omes in terms of coding sequence, intron-exon structures and genome locations, suggesting a complicated evolutionary history of P450s in filamentous Ascomycetes. Clan classification and a novel strategy were developed to study evolutionary history. Contraction of core clans and expansion of novel clans were identified. The exception was the NC lineage, which exhibited pure P450 gene loss.Fungi comprise a large and diverse kingdom of organisms. It is estimated that as many as 1.5 million species exist in the planet today [1,2]. Most described fungi grow by producing long, multi-celled hyphae, and are known as filamentous fungi. Filamentous fungi occupy a wide range of ecological niches with diverse life histories and physiological processes. Many live as saprotrophs decomposing and absorbing nutrients from dead materials while others have evolved the ability to be pathogens deriving their nutrients from living or dying hosts. Taking advantage of available genome sequences to explore the evolution of important gene families may help shed light on the processes that have allowed fungi to exploit diverse habitats.The P450-contain
Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites
Sailsbery Joshua K,Dean Ralph A
BMC Evolutionary Biology , 2012, DOI: 10.1186/1471-2148-12-154
Abstract: Background The highly conserved bHLH (basic Helix-Loop-Helix) domain, found in many transcription factors, has been well characterized separately in Plants, Animals, and Fungi. While conserved, even functionally constrained sites have varied since the Eukarya split. Our research identifies those slightly variable sites that were highly characteristic of Plants, Animals, or Fungi. Results Through discriminant analysis, we identified five highly discerning DNA-binding amino acid sites. Additionally, by incorporating Kingdom specific HMMs, we were able to construct a tool to quickly and accurately identify and classify bHLH sequences using these sites. Conclusions We conclude that highly discerning sites identified through our analysis were likely under functional constraints specific to each Kingdom. We also demonstrated the utility of our tool by identifying and classifying previously unknown bHLH domains in both characterized genomes and from sequences in a large environmental sample.
Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea
Resham D Kulkarni, Michael R Thon, Huaqin Pan, Ralph A Dean
Genome Biology , 2005, DOI: 10.1186/gb-2005-6-3-r24
Abstract: Proteins with significant similarity to fungus-specific and other eukaryotic GPCRs were identified in M. grisea. These included homologs of known fungal GPCRs, the cAMP receptors from Dictyostelium, and a steroid receptor mPR. We also identified a novel class of receptors typified by PTH11, a cell-surface integral membrane protein required for pathogenicity. PTH11 has seven transmembrane regions and an amino-terminal extracellular cysteine-rich EGF-like domain (CFEM domain), a characteristic also seen in human GPCRs. Sixty-one PTH11-related proteins were identified in M. grisea that shared a common domain with homologs in Neurospora crassa and other fungi belonging to this subphylum of the Ascomycota (the Pezizomycotina). None was detected in other fungal groups (Basidiomycota or other Ascomycota subphyla, including yeasts) or any other eukaryote. The subclass of PTH11 containing the CFEM domain is highly represented in M. grisea.In M. grisea we identified homologs of known GPCRs and a novel class of GPCR-like receptors specific to filamentous ascomycetes. A member of this new class, PTH11, is required for pathogenesis, thus suggesting roles in pathogenicity for other members. The identified classes constitute the largest number of GPCR-like proteins reported in fungi to date.Cell-surface G-protein-coupled receptors (GPCRs) bind exogenous as well as endogenous ligands such as photons, odorants, lipids, nucleotides, hormones, pheromones, peptides and proteins. Interaction with these ligands drives diverse processes such as photoreception, taste and olfactory sensations in animals, mating in fungi and cell-cell communications in slime molds [1-3]. These receptors are characterized by seven transmembrane α-helices that upon ligand binding relay the signal by bringing about conformational changes in bound G proteins. The extracellular amino terminus in most cases interacts with the ligand and the carboxyl terminus with G proteins. The G proteins in turn activate differe
Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses
Sandra M Mathioni, André Beló, Christopher J Rizzo, Ralph A Dean, Nicole M Donofrio
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-49
Abstract: We identified 4,973 genes that were differentially expressed in at least one of the in planta and in vitro stress conditions when compared to fungal mycelia grown in complete medium, which was used as reference. From those genes, 1,909 showed similar expression patterns between at least one of the in vitro stresses and rice and/or barley. Hierarchical clustering of these 1,909 genes showed three major clusters in which in planta conditions closely grouped with the nutrient starvation conditions. Out of these 1,909 genes, 55 genes and 129 genes were induced and repressed in all treatments, respectively. Functional categorization of the 55 induced genes revealed that most were either related to carbon metabolism, membrane proteins, or were involved in oxidoreduction reactions. The 129 repressed genes showed putative roles in vesicle trafficking, signal transduction, nitrogen metabolism, or molecular transport.These findings suggest that M. oryzae is likely primarily coping with nutrient-limited environments at the invasive growth stage 72 hours post-inoculation, and not with oxidative or temperature stresses.Magnaporthe oryzae is the causal agent of rice blast, the most threatening disease of cultivated rice worldwide. Spores of this filamentous ascomycete fungus, after landing on the leaf surface, form a germination tube. This tube senses the hydrophobicity and hardness of the host surface resulting in the formation of a penetration structure called an appressorium [1]. The accumulation of melanin in the appressorium cell wall and subsequent increase of glycerol levels in its interior generates high turgor pressure [2], which then leads to the formation of a penetration peg, a specialized hypha that is responsible for puncturing the plant epidermis and entering the plant cell [3,4]. Once inside the host, the fungus forms intracellular invasive hyphae (IH), from which filamentous hyphae emerge and follow a cell-to-cell growth pattern [5]. As a hemi-biotrophic organism
Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens
Amy J Powell, Gavin C Conant, Douglas E Brown, Ignazio Carbone, Ralph A Dean
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-147
Abstract: To determine if patterns of gene duplication differed between pathogens and non-pathogens, we identified gene families across nine euascomycete and two basidiomycete species. Gene family size distributions were fit to power laws to compare gene duplication trends in pathogens versus non-pathogens. Fungal phytopathogens showed globally altered patterns of gene duplication, as indicated by differences in gene family size distribution. We also identified sixteen examples of gene family expansion and five instances of gene family contraction in pathogenic lineages. Expanded gene families included those predicted to be important in melanin biosynthesis, host cell wall degradation and transport functions. Contracted families included those encoding genes involved in toxin production, genes with oxidoreductase activity, as well as subunits of the vacuolar ATPase complex. Surveys of the functional distribution of gene duplicates indicated that pathogens show enrichment for gene duplicates associated with receptor and hydrolase activities, while euascomycete pathogens appeared to have not only these differences, but also significantly more duplicates associated with regulatory and carbohydrate binding functions.Differences in the overall levels of gene duplication in phytopathogenic species versus non-pathogenic relatives implicate gene inventory flux as an important virulence-associated process in fungi. We hypothesize that the observed patterns of gene duplicate enrichment, gene family expansion and contraction reflect adaptation within pathogenic life histories. These adaptations were likely shaped by ancient, as well as contemporary, intimate associations with monocot hosts.Change in gene inventory in pathogenic genomes is an important evolutionary signal. Previous studies have documented the relationship between virulence and differential gene gain and/or loss in bacteria and viruses [1-8]. However, this phenomenon remains unexamined at a genomic scale in fungal pathoge
GT-Miner: a graph-theoretic data miner, viewer, and model processor
Douglas E. Brown,Amy J. Powell,Ignazio Carbone,Ralph A. Dean
Bioinformation , 2008,
Abstract: Inexpensive computational power combined with high-throughput experimental platforms has created a wealth of biological information requiring analytical tools and techniques for interpretation. Graph-theoretic concepts and tools have provided an important foundation for information visualization, integration, and analysis of datasets, but they have often been relegated to background analysis tasks. GT-Miner is designed for visual data analysis and mining operations, interacts with other software, including databases, and works with diverse data types. It facilitates a discovery-oriented approach to data mining wherein exploration of alterations of the data and variations of the visualization is encouraged. The user is presented with a basic iterative process, consisting of loading, visualizing, transforming, and then storing the resultant information. Complex analyses are built-up through repeated iterations and user interactions. The iterative process is optimized by automatic layout following transformations and by maintaining a current selection set of interest for elements modified by the transformations. Multiple visualizations are supported including hierarchical, spring, and force-directed self-organizing layouts. Graphs can be transformed with an extensible set of algorithms or manually with an integral visual editor. GT-Miner is intended to allow easier access to visual data mining for the non-expert.
Collaboration Policies: Access Control Management in Decentralized Heterogeneous Workflows
Mine Altunay,Douglas E. Brown,Gregory T. Byrd,Ralph A. Dean
Journal of Software , 2006, DOI: 10.4304/jsw.1.1.11-22
Abstract: Service-oriented computing promotes collaboration by defining the standards layer that allows compatibility between disparate domains. Workflows, by taking advantage of the service oriented framework, provide the necessary tools to harness services in order to tackle complicated problems. As a result, a service is no longer exposed to a small pre-determined homogeneous pool of users; instead it has a large, undefined, and heterogeneous pool of users. This paradigm shift in computing results in increased service exposure. The interactions among the services of a workflow must be carefully evaluated against the security risks associated with them. Classical security problems, such as delegation of rights, conflict of interest, and access control in general, become more complicated due to multiple autonomous security domains and the absence of pre- established trust relationships among the domains. Our work tackles these problems in two aspects: it provides a service owner with the necessary means to express and evaluate its trust requirements from a workflow (collaboration policies), and it incorporates these trust requirements into the workflow-planning framework (workflow authorization framework). Our policy-based framework allows bilateral peer-level trust evaluations that are based on each peer’s collaboration policies, and incorporates the outcome of these evaluations into the workflow planning logic. As a result, our work provides the necessary tools for promoting multi-party ad-hoc collaborations, and aims to reduce the reluctance and hesitation towards these collaborations by attacking the security risks associated with them.
Experimental Evolution Reveals Genome-Wide Spectrum and Dynamics of Mutations in the Rice Blast Fungus, Magnaporthe oryzae
Junhyun Jeon, Jaeyoung Choi, Gir-Won Lee, Ralph A. Dean, Yong-Hwan Lee
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0065416
Abstract: Knowledge on mutation processes is central to interpreting genetic analysis data as well as understanding the underlying nature of almost all evolutionary phenomena. However, studies on genome-wide mutational spectrum and dynamics in fungal pathogens are scarce, hindering our understanding of their evolution and biology. Here, we explored changes in the phenotypes and genome sequences of the rice blast fungus Magnaporthe oryzae during the forced in vitro evolution by weekly transfer of cultures on artificial media. Through combination of experimental evolution with high throughput sequencing technology, we found that mutations accumulate rapidly prior to visible phenotypic changes and that both genetic drift and selection seem to contribute to shaping mutational landscape, suggesting the buffering capacity of fungal genome against mutations. Inference of mutational effects on phenotypes through the use of T-DNA insertion mutants suggested that at least some of the DNA sequence mutations are likely associated with the observed phenotypic changes. Furthermore, our data suggest oxidative damages and UV as major sources of mutation during subcultures. Taken together, our work revealed important properties of original source of variation in the genome of the rice blast fungus. We believe that these results provide not only insights into stability of pathogenicity and genome evolution in plant pathogenic fungi but also a model in which evolution of fungal pathogens in natura can be comparatively investigated.
Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus
Soonok Kim,Jinnan Hu,Yeonyee Oh,Jongsun Park,Jinhee Choi,Yong-Hwan Lee,Ralph A. Dean,Thomas K. Mitchell
PLOS Pathogens , 2010, DOI: 10.1371/journal.ppat.1000909
Abstract: Significant progress has been made in defining the central signaling networks in many organisms, but collectively we know little about the downstream targets of these networks and the genes they regulate. To reconstruct the regulatory circuit of calcineurin signal transduction via MoCRZ1, a Magnaporthe oryzae C2H2 transcription factor activated by calcineurin dephosphorylation, we used a combined approach of chromatin immunoprecipitation - chip (ChIP-chip), coupled with microarray expression studies. One hundred forty genes were identified as being both a direct target of MoCRZ1 and having expression concurrently differentially regulated in a calcium/calcineurin/MoCRZ1 dependent manner. Highly represented were genes involved in calcium signaling, small molecule transport, ion homeostasis, cell wall synthesis/maintenance, and fungal virulence. Of particular note, genes involved in vesicle mediated secretion necessary for establishing host associations, were also found. MoCRZ1 itself was a target, suggesting a previously unreported autoregulation control point. The data also implicated a previously unreported feedback regulation mechanism of calcineurin activity. We propose that calcium/calcineurin regulated signal transduction circuits controlling development and pathogenicity manifest through multiple layers of regulation. We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen.
Polyubiquitin Is Required for Growth, Development and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae
Yeonyee Oh, William L. Franck, Sang-Oh Han, Angela Shows, Emine Gokce, David C. Muddiman, Ralph A. Dean
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0042868
Abstract: Protein ubiquitination, which is highly selective, regulates many important biological processes including cellular differentiation and pathogenesis in eukaryotic cells. Here, we integrated pharmacological, molecular and proteomic approaches to explore the role of ubiquitination in Magnaporthe oryzae, the leading fungal disease of rice world-wide. Inhibition of ubiquitin-mediated proteolysis using the 26S proteasome inhibitor, Bortezomib, significantly attenuated conidia germination, appressorium formation and pathogenicity in M. oryzae. Gene expression analysis revealed that many genes associated with protein ubiquitination were developmentally regulated during conidia germination. Only a few, including a polyubiquitin encoding gene, MGG_01282, were more abundantly expressed during appressorium formation and under nitrogen starvation. Targeted gene deletion of MGG_01282, in addition to a significant reduction in protein ubiquitination as determined by immuno blot assays, resulted in pleiotropic effects on M. oryzae including reduced growth and sporulation, abnormal conidia morphology, reduced germination and appressorium formation, and the inability to cause disease. Mutants were also defective in sexual development and were female sterile. Using mass spectrometry, we identified 63 candidate polyubiquitinated proteins under nitrogen starvation, which included overrepresentation of proteins involved in translation, transport and protein modification. Our study suggests that ubiquitination of target proteins plays an important role in nutrient assimilation, development and pathogenicity of M. oryzae.
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