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  • Duke University Center for Microbial Pathogenesis
    more about basic fungal biology we are taking a somewhat different approach By characterizing the genomes of related organisms starting with the filamentous fungus Ashbya gossypii we hope to more precisely define what are the set of genes in S cerevisiae as well as to identify genes found in related fungi that have been lost from the genome of this yeast Considerably more than 90 of the genes found in S cerevisiae are found in Ashbya gossypii and likewise well over 90 of the genes found in Ashbya gossypii are found in S cerevisiae This suggests that the set of genes found in this family of fungi is somewhat larger than the set of genes found in the standard research yeast but not by very much How much genetic variation is there within a fungal pathogen species Our interest in this human pathogen is to expand beyond looking at one isolate and to investigate the diversity in the population Are there genes found in some Cryptococcus neoformans isolates but not in others Are there regions of the genome or individual genes which are highly diverged between Cryptococcus isolates Efforts are now underway at Stanford University to sequence the genome of

    Original URL path: http://mgm.duke.edu/microbial/mycology/dietrich/ (2014-06-13)
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  • Duke University Center for Microbial Pathogenesis
    emerging opportunistic pathogen Clinically derived strains of S cerevisiae resemble more commonly observed pathogenic fungi in that they have traits associated with virulence such as profuse pseudohyphal formation and high temperature growth Also clinically derived strains of S cerevisiae proliferate and persist in immunocompetent mice and kill complement factor five deficient mice The ease of genetically manipulating S cerevisiae relative to the more commonly observed pathogenic fungi makes S cerevisiae a powerful genetically tractable model system to identify pathways required for fungal survival in the mammalian host environment We test S cerevisiae mutants to find those that are severely deficient in their ability to survive in the host environment which provides insight into the basic processes of fungal pathogenesis We then apply these results to other less genetically tractable fungi S cerevisiae a microbial model for quantitative genetics One observes a range of phenotypes quantitative traits in natural populations which is due to the complex interaction of multiple alleles of many different genes Although these quantitative traits are very important the genetic complexity of quantitative traits has made the identification of the genes underlying quantitative traits difficult To better understand quantitative traits we developed S cerevisiae as a microbial model

    Original URL path: http://mgm.duke.edu/microbial/mycology/mccusker/ (2014-06-13)
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  • Duke University Center for Microbial Pathogenesis
    of intersterility between related species population biology of fungi estimation of breeding systems and measurement of gene flow in natural populations Fungi currently under investigation include the oyster mushroom Pleurotus ostreatus as well as several species of medically important fungi Candida albicans and Cryptococcus neoformans Phylogeny The major research effort in our laboratory for the last 10 years is still aimed at understanding molecular evolution of ribosomal RNA genes in fungi and their use for estimating evolutionary relationships of the higher Basidiomycotina We are presently surveying rDNA sequence variation from various families of the Agaricales mushrooms and related fungi Speciation Saprobic basidiomycetes offer an excellent system for studying the meaning of what is a species in fungi Our research combines the study of morphology mating behavior genetics and molecular systematics to try and understand how species differ and how they evolve Mating compatibility studies have repeatedly demonstrated strong intersterility barriers among most species Our previous studies on DNA level variation in the mushroom Collybia dryophila revealed a surprisingly high degree of genetic divergence associated with speciation among intersterility groups More recently our studies of speciation in the oyster mushroom genus Pleurotus have examined the importance of biogeography as a primary factor associate with speciation At the molecular level genomes of mushroom species also appear to turn over more rapidly than other eukaryotes We are currently employing molecular approaches to study genetic mechanisms which may operate during speciation These methods include the use of DNA restriction fragment polymorphisms RFLPs and Amplified Fragment Length Polymorphisms AFLP to estimate genetic diversity and along with electrophoretic karyotyping as well as more conventional methods based on mating compatibility studies One of the current objectives of this research will be to develop a generalized model for genome evolution in Basidiomycotina and its role in the development

    Original URL path: http://mgm.duke.edu/microbial/mycology/vilgalys/ (2014-06-13)
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  • Duke University Center for Microbial Pathogenesis
    mice and is using positional cloning and positional candidate gene studies to define genetic polymorphisms that contribute to aspergillus susceptibility At present Dr Zaas has active collaborations with Roche PaloAlto and the Fred Hutchinson Cancer Research Center to elucidate the role of human genetic polymorphisms in aspergillus susceptibility Additionally she is evaluating the role of toll like receptors in the response to Aspergillus fumigatus Dr Zaas is one of 6

    Original URL path: http://mgm.duke.edu/microbial/mycology/zaas/ (2014-06-13)
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  • Duke University Center for Microbial Pathogenesis
    meeting itself will typically last 60 90 minutes allowing the trainee to present an oral summary of the project followed by questions and discussion Once yearly the mentor will submit a report to the EC which will conduct an annual review of each trainee Required Activities In both Track I or II the paramount activity of each postdoctoral trainee is the mentored research project However the MMPTP has designed several activities to complement the research experience During the three years that most trainees are supported by the program concurrent with the research they will accomplish the following complementary goals and activities Each trainee is required to take the DUMC course in Responsible Conduct of Research at the earliest opportunity This short course is offered in both the fall and spring semesters The course covers a variety of topics including data integrity and reporting authorship animal and human subjects IACUC IRB HIPAA conflicts of interest mentoring and laboratory supervision harassment diversity misconduct in research and other topics Most trainees will take the half day two week course in Medical Mycology that is taught in the late spring This informal course provides an overview of fungal diseases their epidemiology and clinical impact The content highlights clinical controversies areas of uncertainty research needs and diagnostic priorities and imperatives In the laboratory portion students learn to examine a variety of yeasts and molds in culture and to recognize pathogenic fungi in tissue Trainees will apply in March of their first year for acceptance to the Molecular Pathogenic Mycology Course at the Marine Biological Laboratory at Woods Hole MA which is given annually in mid August This 17 day course provides concepts and practice in the manipulation molecular tools genetics immunology and genomics of medical fungi Trainees attend the monthly DUMRU seminars which are hosted

    Original URL path: http://mgm.duke.edu/microbial/training/mmptp/postdoc/mentors.htm (2014-06-13)
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  • Duke University Center for Microbial Pathogenesis
    Molecular Pathogenic Mycology Course at Woods Hole and in May take the Medical Mycology course at Duke That spring the trainee may also attend the workshop on Mentoring and Career Issues at UNC CH and then recruit an undergraduate student to supervise for 10 weeks during the summer If the trainee is accepted to the Woods Hole course which he or she will learn in April the undergraduate mentoring experience will be deferred to the following summer to ensure uninterrupted supervision during this internship By the second year the trainee will have presented his or her research at local seminars and a national meeting At the end of the second year the trainee will be assisted by the mentor and RAC to plan the next career move either application for an individual fellowship alternative grant support or if ready a permanent position Year 1 Fall Take Responsible Conduct Course 4 days in August Select mentor s RAC and obtain approval of research project Begin full time research in the mentor s laboratory Attend and participate in DUMRU and other seminars Spring Pursue full time research in the mentor s laboratory Attend and participate in DUMRU and other seminars Apply for Molecular Pathogenic Mycology Course at Woods Hole Attend the UNC CH Workshop on career issues and mentoring Select undergraduate research assistant for the summer Summer Full time research in the mentor s laboratory Attend and participate in DUMRU and other Seminars Take the Medical Mycology mini course at Duke 10 half day sessions Supervise undergraduate summer research project May to August or Attend the Molecular Pathogenic Mycology Course at Woods Hole in August Year 2 Fall Spring Full time research in the mentor s laboratory Attend and participate in DUMRU and other seminars Complete research projects submit papers attend and

    Original URL path: http://mgm.duke.edu/microbial/training/mmptp/postdoc/track1.htm (2014-06-13)
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  • Duke University Center for Microbial Pathogenesis
    research experience will follow the second track which is designed to develop clinician scientists These trainees will be those with the M D or equivalent clinical degree who have completed internship and residency and are board certified or board eligible The track II training program is flexible and the type and amount of courses laboratory work or clinical research will vary to accommodate each trainee This track offers either basic

    Original URL path: http://mgm.duke.edu/microbial/training/mmptp/postdoc/track2.htm (2014-06-13)
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  • Duke University Department of Molecular Genetics & Microbiology
    used a comprehensive dataset of genomic data from fungi plants animals and bacteria along with gene location and gene similarity data to compare potential evolutionary scenarios for these enzymes Phylogenetic analysis allowed me to conclude that the urea amidolyase genes in fungi were the result of a horizontal gene transfer event from bacteria to fungi I used similar molecular evolution analyses in understanding the evolution of the sterol sensing domain proteins in eukaryotes As a postdoctoral scholar my current research topic involves the analysis of the genotypic and phenotypic variations among S cerevisiae strains Due to the importance of S cerevisiae both as a model organism and an emerging opportunistic pathogen the analyses will be useful in elucidating the genetic basis for many of the traits In our labs we have sequenced 93 haploid or self diploidized S cerevisiae strains These 93 strains were isolated from diverse geographical locations and origins such as trees soil wine and human infections I assembled the 93 sequenced genomes Illumina Hiseq 35x 600x coverage de novo and used the S288c reference genome to scaffold the contigs and annotate the sequences I annotated all the chromosomes from the 93 genomes and they have been deposited at Genbank From my analysis of the 93 S cerevisiae genomes I have found interesting results such as Aneuploidy Translocations Introgressions Variation in the number of Ty s Genes that are absent in some strains Novel genes in some strains Inactivating SNPs in several genes Variation in the 2 micron and rDNA Variation in the types and positions of introns in the mitochondrial genes I will use the sequence variation data along with high throughput quantitative phenotyping including antifungal drug resistance phenotypes of the 93 strains to identify candidate quantitative trait genes by haplotype association mapping I have been supported

    Original URL path: http://mgm.duke.edu/faculty/dietrich/lab/strope.html (2014-06-13)
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