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Fred Samuel Dietrich

Associate Professor of Molecular Genetics and Microbiology
Molecular Genetics and Microbiology
Duke Box 3568, Durham, NC 27710
421 Jones Building, Durham, NC 27710

Selected Publications


RNA viruses, M satellites, chromosomal killer genes, and killer/nonkiller phenotypes in the 100-genomes S. cerevisiae strains.

Journal Article G3 (Bethesda) · September 30, 2023 We characterized previously identified RNA viruses (L-A, L-BC, 20S, and 23S), L-A-dependent M satellites (M1, M2, M28, and Mlus), and M satellite-dependent killer phenotypes in the Saccharomyces cerevisiae 100-genomes genetic resource population. L-BC was ... Full text Link to item Cite

Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries.

Journal Article G3 (Bethesda) · October 19, 2021 RNA sequencing (RNA-Seq) experiments focused on gene expression involve removal of ribosomal RNA (rRNA) because it is the major RNA constituent of cells. This process, called RNA enrichment, is done primarily to reduce cost: without rRNA removal, deeper se ... Full text Link to item Cite

HGT in the human and skin commensal Malassezia: A bacterially derived flavohemoglobin is required for NO resistance and host interaction.

Journal Article Proc Natl Acad Sci U S A · July 7, 2020 The skin of humans and animals is colonized by commensal and pathogenic fungi and bacteria that share this ecological niche and have established microbial interactions. Malassezia are the most abundant fungal skin inhabitant of warm-blooded animals and hav ... Full text Open Access Link to item Cite

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.

Journal Article BMC Genomics · July 23, 2019 BACKGROUND: Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobi ... Full text Link to item Cite

Mitochondrial Genome Variation Affects Multiple Respiration and Nonrespiration Phenotypes in Saccharomyces cerevisiae.

Journal Article Genetics · February 2019 Mitochondrial genome variation and its effects on phenotypes have been widely analyzed in higher eukaryotes but less so in the model eukaryote Saccharomyces cerevisiae Here, we describe mitochondrial genome variation in 96 diverse S. cerevisiae strains and ... Full text Link to item Cite

2μ plasmid in Saccharomyces species and in Saccharomyces cerevisiae.

Journal Article FEMS Yeast Res · December 2015 We determined that extrachromosomal 2μ plasmid was present in 67 of the Saccharomyces cerevisiae 100-genome strains; in addition to variation in the size and copy number of 2μ, we identified three distinct classes of 2μ. We identified 2μ presence/absence a ... Full text Link to item Cite

The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen.

Journal Article Genome Res · May 2015 Saccharomyces cerevisiae, a well-established model for species as diverse as humans and pathogenic fungi, is more recently a model for population and quantitative genetics. S. cerevisiae is found in multiple environments-one of which is the human body-as a ... Full text Link to item Cite

Structures of naturally evolved CUP1 tandem arrays in yeast indicate that these arrays are generated by unequal nonhomologous recombination.

Journal Article G3 (Bethesda) · September 17, 2014 An important issue in genome evolution is the mechanism by which tandem duplications are generated from single-copy genes. In the yeast Saccharomyces cerevisiae, most strains contain tandemly duplicated copies of CUP1, a gene that encodes a copper-binding ... Full text Link to item Cite

Cryptococcus gattii VGIII Isolates Causing Infections in HIV/AIDS Patients in Southern California: Identification of the Local Environmental Source as Arboreal

Journal Article PLoS Pathogens · August 21, 2014 Ongoing Cryptococcus gattii outbreaks in the Western United States and Canada illustrate the impact of environmental reservoirs and both clonal and recombining propagation in driving emergence and expansion of microbial pathogens. C. gattii comprises four ... Full text Open Access Cite

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

Journal Article PLoS Genet · April 2014 Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and ... Full text Open Access Link to item Cite

The reference genome sequence of Saccharomyces cerevisiae: then and now.

Journal Article G3 (Bethesda) · March 20, 2014 The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively stu ... Full text Link to item Cite

The deacetylase Sir2 from the yeast Clavispora lusitaniae lacks the evolutionarily conserved capacity to generate subtelomeric heterochromatin.

Journal Article PLoS Genet · October 2013 Deacetylases of the Sir2 or sirtuin family are thought to regulate life cycle progression and life span in response to nutrient availability. This family has undergone successive rounds of duplication and diversification, enabling the enzymes to perform a ... Full text Link to item Cite

Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans.

Journal Article PLoS Biol · September 2013 Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down's syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug resistanc ... Full text Link to item Cite

Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications.

Journal Article G3 (Bethesda) · August 7, 2013 The filamentous fungus Ashbya gossypii is a cotton pathogen transmitted by insects. It is readily grown and manipulated in the laboratory and is commercially exploited as a natural overproducer of vitamin B2. Our previous genome analysis of A. gossypii iso ... Full text Link to item Cite

High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family.

Journal Article BMC Genomics · April 4, 2013 BACKGROUND: Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ... Full text Link to item Cite

Cryptococcus neoformans Rim101 is associated with cell wall remodeling and evasion of the host immune responses.

Journal Article mBio · January 15, 2013 UNLABELLED: Infectious microorganisms often play a role in modulating the immune responses of their infected hosts. We demonstrate that Cryptococcus neoformans signals through the Rim101 transcription factor to regulate cell wall composition and the host-p ... Full text Link to item Cite

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen.

Journal Article Nat Commun · 2013 Responsible for the Irish potato famine of 1845-49, the oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the p ... Full text Link to item Cite

High-resolution genome-wide analysis of irradiated (UV and γ-rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events.

Journal Article Genetics · April 2012 In diploid eukaryotes, repair of double-stranded DNA breaks by homologous recombination often leads to loss of heterozygosity (LOH). Most previous studies of mitotic recombination in Saccharomyces cerevisiae have focused on a single chromosome or a single ... Full text Link to item Cite

Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification.

Journal Article Mol Biol Evol · January 2012 The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are dista ... Full text Link to item Cite

Discovery of a modified tetrapolar sexual cycle in Cryptococcus amylolentus and the evolution of MAT in the Cryptococcus species complex.

Journal Article PLoS Genet · 2012 Sexual reproduction in fungi is governed by a specialized genomic region called the mating-type locus (MAT). The human fungal pathogenic and basidiomycetous yeast Cryptococcus neoformans has evolved a bipolar mating system (a, α) in which the MAT locus is ... Full text Link to item Cite

RNA viruses, M satellites, chromosomal killer genes, and killer/nonkiller phenotypes in the 100-genomes S. cerevisiae strains.

Journal Article G3 (Bethesda) · September 30, 2023 We characterized previously identified RNA viruses (L-A, L-BC, 20S, and 23S), L-A-dependent M satellites (M1, M2, M28, and Mlus), and M satellite-dependent killer phenotypes in the Saccharomyces cerevisiae 100-genomes genetic resource population. L-BC was ... Full text Link to item Cite

Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries.

Journal Article G3 (Bethesda) · October 19, 2021 RNA sequencing (RNA-Seq) experiments focused on gene expression involve removal of ribosomal RNA (rRNA) because it is the major RNA constituent of cells. This process, called RNA enrichment, is done primarily to reduce cost: without rRNA removal, deeper se ... Full text Link to item Cite

HGT in the human and skin commensal Malassezia: A bacterially derived flavohemoglobin is required for NO resistance and host interaction.

Journal Article Proc Natl Acad Sci U S A · July 7, 2020 The skin of humans and animals is colonized by commensal and pathogenic fungi and bacteria that share this ecological niche and have established microbial interactions. Malassezia are the most abundant fungal skin inhabitant of warm-blooded animals and hav ... Full text Open Access Link to item Cite

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata.

Journal Article BMC Genomics · July 23, 2019 BACKGROUND: Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobi ... Full text Link to item Cite

Mitochondrial Genome Variation Affects Multiple Respiration and Nonrespiration Phenotypes in Saccharomyces cerevisiae.

Journal Article Genetics · February 2019 Mitochondrial genome variation and its effects on phenotypes have been widely analyzed in higher eukaryotes but less so in the model eukaryote Saccharomyces cerevisiae Here, we describe mitochondrial genome variation in 96 diverse S. cerevisiae strains and ... Full text Link to item Cite

2μ plasmid in Saccharomyces species and in Saccharomyces cerevisiae.

Journal Article FEMS Yeast Res · December 2015 We determined that extrachromosomal 2μ plasmid was present in 67 of the Saccharomyces cerevisiae 100-genome strains; in addition to variation in the size and copy number of 2μ, we identified three distinct classes of 2μ. We identified 2μ presence/absence a ... Full text Link to item Cite

The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen.

Journal Article Genome Res · May 2015 Saccharomyces cerevisiae, a well-established model for species as diverse as humans and pathogenic fungi, is more recently a model for population and quantitative genetics. S. cerevisiae is found in multiple environments-one of which is the human body-as a ... Full text Link to item Cite

Structures of naturally evolved CUP1 tandem arrays in yeast indicate that these arrays are generated by unequal nonhomologous recombination.

Journal Article G3 (Bethesda) · September 17, 2014 An important issue in genome evolution is the mechanism by which tandem duplications are generated from single-copy genes. In the yeast Saccharomyces cerevisiae, most strains contain tandemly duplicated copies of CUP1, a gene that encodes a copper-binding ... Full text Link to item Cite

Cryptococcus gattii VGIII Isolates Causing Infections in HIV/AIDS Patients in Southern California: Identification of the Local Environmental Source as Arboreal

Journal Article PLoS Pathogens · August 21, 2014 Ongoing Cryptococcus gattii outbreaks in the Western United States and Canada illustrate the impact of environmental reservoirs and both clonal and recombining propagation in driving emergence and expansion of microbial pathogens. C. gattii comprises four ... Full text Open Access Cite

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

Journal Article PLoS Genet · April 2014 Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and ... Full text Open Access Link to item Cite

The reference genome sequence of Saccharomyces cerevisiae: then and now.

Journal Article G3 (Bethesda) · March 20, 2014 The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively stu ... Full text Link to item Cite

The deacetylase Sir2 from the yeast Clavispora lusitaniae lacks the evolutionarily conserved capacity to generate subtelomeric heterochromatin.

Journal Article PLoS Genet · October 2013 Deacetylases of the Sir2 or sirtuin family are thought to regulate life cycle progression and life span in response to nutrient availability. This family has undergone successive rounds of duplication and diversification, enabling the enzymes to perform a ... Full text Link to item Cite

Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans.

Journal Article PLoS Biol · September 2013 Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down's syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug resistanc ... Full text Link to item Cite

Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications.

Journal Article G3 (Bethesda) · August 7, 2013 The filamentous fungus Ashbya gossypii is a cotton pathogen transmitted by insects. It is readily grown and manipulated in the laboratory and is commercially exploited as a natural overproducer of vitamin B2. Our previous genome analysis of A. gossypii iso ... Full text Link to item Cite

High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family.

Journal Article BMC Genomics · April 4, 2013 BACKGROUND: Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ... Full text Link to item Cite

Cryptococcus neoformans Rim101 is associated with cell wall remodeling and evasion of the host immune responses.

Journal Article mBio · January 15, 2013 UNLABELLED: Infectious microorganisms often play a role in modulating the immune responses of their infected hosts. We demonstrate that Cryptococcus neoformans signals through the Rim101 transcription factor to regulate cell wall composition and the host-p ... Full text Link to item Cite

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen.

Journal Article Nat Commun · 2013 Responsible for the Irish potato famine of 1845-49, the oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the p ... Full text Link to item Cite

High-resolution genome-wide analysis of irradiated (UV and γ-rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events.

Journal Article Genetics · April 2012 In diploid eukaryotes, repair of double-stranded DNA breaks by homologous recombination often leads to loss of heterozygosity (LOH). Most previous studies of mitotic recombination in Saccharomyces cerevisiae have focused on a single chromosome or a single ... Full text Link to item Cite

Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification.

Journal Article Mol Biol Evol · January 2012 The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are dista ... Full text Link to item Cite

Discovery of a modified tetrapolar sexual cycle in Cryptococcus amylolentus and the evolution of MAT in the Cryptococcus species complex.

Journal Article PLoS Genet · 2012 Sexual reproduction in fungi is governed by a specialized genomic region called the mating-type locus (MAT). The human fungal pathogenic and basidiomycetous yeast Cryptococcus neoformans has evolved a bipolar mating system (a, α) in which the MAT locus is ... Full text Link to item Cite

A whole-genome analysis of premature termination codons.

Journal Article Genomics · November 2011 We sequenced the genomes of ten unrelated individuals and identified heterozygous stop codon-gain variants in protein-coding genes: we then sequenced their transcriptomes and assessed the expression levels of the stop codon-gain alleles. An ANOVA showed st ... Full text Link to item Cite

A diverse population of Cryptococcus gattii molecular type VGIII in southern Californian HIV/AIDS patients.

Journal Article PLoS Pathog · September 2011 Cryptococcus gattii infections in southern California have been reported in patients with HIV/AIDS. In this study, we examined the molecular epidemiology, population structure, and virulence attributes of isolates collected from HIV/AIDS patients in Los An ... Full text Link to item Cite

Oxidative stress survival in a clinical Saccharomyces cerevisiae isolate is influenced by a major quantitative trait nucleotide.

Journal Article Genetics · July 2011 One of the major challenges in characterizing eukaryotic genetic diversity is the mapping of phenotypes that are the cumulative effect of multiple alleles. We have investigated tolerance of oxidative stress in the yeast Saccharomyces cerevisiae, a trait sh ... Full text Link to item Cite

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).

Journal Article Proc Natl Acad Sci U S A · June 29, 2010 The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages ... Full text Link to item Cite

Evolution of the sex-related locus and genomic features shared in microsporidia and fungi.

Journal Article PLoS One · May 7, 2010 BACKGROUND: Microsporidia are obligate intracellular, eukaryotic pathogens that infect a wide range of animals from nematodes to humans, and in some cases, protists. The preponderance of evidence as to the origin of the microsporidia reveals a close relati ... Full text Open Access Link to item Cite

Morphological and genomic characterization of Filobasidiella depauperata: a homothallic sibling species of the pathogenic cryptococcus species complex.

Journal Article PLoS One · March 10, 2010 The fungal species Cryptococcus neoformans and Cryptococcus gattii cause respiratory and neurological disease in animals and humans following inhalation of basidiospores or desiccated yeast cells from the environment. Sexual reproduction in C. neoformans a ... Full text Open Access Link to item Cite

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production.

Journal Article Genome Res · December 2009 Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the suga ... Full text Link to item Cite

Non-coding RNA prediction and verification in Saccharomyces cerevisiae.

Journal Article PLoS Genet · January 2009 Non-coding RNA (ncRNA) play an important and varied role in cellular function. A significant amount of research has been devoted to computational prediction of these genes from genomic sequence, but the ability to do so has remained elusive due to a lack o ... Full text Link to item Cite

Saccharomyces cerevisiae: population divergence and resistance to oxidative stress in clinical, domesticated and wild isolates.

Journal Article PLoS One · 2009 BACKGROUND: Saccharomyces cerevisiae has been associated with human life for millennia in the brewery and bakery. Recently it has been recognized as an emerging opportunistic pathogen. To study the evolutionary history of S. cerevisiae, the origin of clini ... Full text Link to item Cite

Microsporidia evolved from ancestral sexual fungi.

Journal Article Curr Biol · November 11, 2008 Microsporidia are obligate, intracellular eukaryotic pathogens that infect animal cells, including humans [1]. Previous studies suggested microsporidia share a common ancestor with fungi [2-7]. However, the exact nature of this phylogenetic relationship is ... Full text Link to item Cite

Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans.

Journal Article Genome Biol · 2008 BACKGROUND: Genome variability can have a profound influence on the virulence of pathogenic microbes. The availability of genome sequences for two strains of the AIDS-associated fungal pathogen Cryptococcus neoformans presented an opportunity to use compar ... Full text Link to item Cite

Computational and experimental identification of novel human imprinted genes.

Journal Article Genome Res · December 2007 Imprinted genes are essential in embryonic development, and imprinting dysregulation contributes to human disease. We report two new human imprinted genes: KCNK9 is predominantly expressed in the brain, is a known oncogene, and may be involved in bipolar d ... Full text Link to item Cite

The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering.

Journal Article Genetics · December 2007 The synthesis of biotin, a vitamin required for many carboxylation reactions, is a variable trait in Saccharomyces cerevisiae. Many S. cerevisiae strains, including common laboratory strains, contain only a partial biotin synthesis pathway. We here report ... Full text Link to item Cite

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.

Journal Article Proc Natl Acad Sci U S A · July 31, 2007 We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensi ... Full text Link to item Cite

Evolution of budding yeast prion-determinant sequences across diverse fungi.

Journal Article J Mol Biol · April 20, 2007 Prions are transmissible self-replicating alternative states of proteins. Four prions ([PSI+], [URE3], [RNQ+] and [NU+]) can be inherited cytoplasmically in Saccharomyces cerevisiae laboratory strains. In the case of [PSI+], there is increasing evidence th ... Full text Link to item Cite

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists.

Journal Article BMC Genomics · January 9, 2007 BACKGROUND: The Ashbya Genome Database (AGD) 3.0 is an innovative cross-species genome and transcriptome browser based on release 40 of the Ensembl developer environment. DESCRIPTION: AGD 3.0 provides information on 4726 protein-encoding loci and 293 non-c ... Full text Link to item Cite

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

Journal Article Genome Biol · 2007 BACKGROUND: Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from transcripts before protein translation. Many facets of spliceosomal intron evolution, including age, mechanisms of origins, the role of natural sele ... Full text Link to item Cite

The genome of the filamentous fungus ashbya gossypii: Annotation and evolutionary implications

Journal Article Topics in Current Genetics · December 1, 2006 The 9.2 Mb genome of the filamentous fungus Ashbya gossypii consists of seven chromosomes carrying 4718 protein coding genes, 194 tRNA genes, at least 60 small RNA genes, and 40-50 copies of rRNA genes. With respect to both, the size and the number of gene ... Full text Cite

Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus.

Journal Article Gene · November 15, 2006 Fungi from the genus Aspergillus are important saprophytes and opportunistic human fungal pathogens that contribute in these and other diverse ways to human well-being. Part of their impact on human well-being stems from the production of small molecular w ... Full text Link to item Cite

Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment.

Journal Article Mol Biol Evol · October 2006 The availability of the whole-genome sequence from the 2 known varieties of the human pathogenic fungus Cryptococcus neoformans provides an opportunity to study the relative contribution of divergence and introgression during the process of speciation in a ... Full text Link to item Cite

The Cryptococcus neoformans catalase gene family and its role in antioxidant defense.

Journal Article Eukaryot Cell · September 2006 In the present study, we sought to elucidate the contribution of the Cryptococcus neoformans catalase gene family to antioxidant defense. We employed bioinformatics techniques to identify four members of the C. neoformans catalase gene family and created m ... Full text Link to item Cite

Yeast diversity sampling on the San Juan Islands reveals no evidence for the spread of the Vancouver Island Cryptococcus gattii outbreak to this locale.

Journal Article FEMS Yeast Res · June 2006 Biological diversity has been estimated for various phyla of life, such as insects and mammals, but in the microbe world is has been difficult to determine species richness and abundance. Here we describe a study of species diversity of fungi with a yeast- ... Full text Link to item Cite

Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans.

Journal Article Eukaryot Cell · May 2006 Introns are a defining feature of eukaryotic genomes, though the mechanism of intron gain or loss is not well understood. Reverse transcription of mRNA followed by homologous recombination with the genome has been posited as a mechanism of intron loss, tho ... Full text Link to item Cite

Morphogenesis in skin is governed by discrete sets of differentially expressed microRNAs.

Journal Article Nat Genet · March 2006 During embryogenesis, multipotent progenitors within the single-layered surface epithelium differentiate to form the epidermis and its appendages. Here, we show that microRNAs (miRNAs) have an essential role in orchestrating these events. We cloned more th ... Full text Link to item Cite

Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak.

Journal Article Nature · October 27, 2005 Genealogy can illuminate the evolutionary path of important human pathogens. In some microbes, strict clonal reproduction predominates, as with the worldwide dissemination of Mycobacterium leprae, the cause of leprosy. In other pathogens, sexual reproducti ... Full text Link to item Cite

Genomic convergence to identify candidate genes for Parkinson disease: SAGE analysis of the substantia nigra.

Journal Article Mov Disord · October 2005 Genomic convergence is a multistep approach that combines gene expression with genomic linkage to identify and prioritize susceptibility genes for complex disease. As a first step, we previously performed linkage analysis on 174 multiplex Parkinson's disea ... Full text Link to item Cite

Clinical and environmental isolates of Cryptococcus gattii from Australia that retain sexual fecundity.

Journal Article Eukaryot Cell · August 2005 Cryptococcus gattii is a primary pathogenic yeast that causes disease in both animals and humans. It is closely related to Cryptococcus neoformans and diverged from a common ancestor approximately 40 million years ago. While C. gattii has a characterized s ... Full text Link to item Cite

Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae.

Journal Article Curr Genet · August 2005 We have taken advantage of recently sequenced hemiascomycete fungal genomes to computationally identify additional genes potentially regulated by upstream open reading frames (uORFs). Our approach is based on the observation that the structure, including t ... Full text Link to item Cite

Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae.

Journal Article Eukaryot Cell · June 2005 The genomes of the hemiascomycetes Saccharomyces cerevisiae and Ashbya gossypii have been completely sequenced, allowing a comparative analysis of these two genomes, which reveals that a small number of genes appear to have entered these genomes as a resul ... Full text Link to item Cite

Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE.

Journal Article Nucleic Acids Res · 2005 A minimally addressed area in Saccharomyces cerevisiae research is the mapping of transcription start sites (TSS). Mapping of TSS in S.cerevisiae has the potential to contribute to our understanding of gene regulation, transcription, mRNA stability and asp ... Full text Link to item Cite

Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms.

Journal Article PLoS Biol · December 2004 Sexual identity is governed by sex chromosomes in plants and animals, and by mating type (MAT) loci in fungi. Comparative analysis of the MAT locus from a species cluster of the human fungal pathogen Cryptococcus revealed sequential evolutionary events tha ... Full text Link to item Cite

Identification of Cryptococcus neoformans temperature-regulated genes with a genomic-DNA microarray.

Journal Article Eukaryot Cell · October 2004 The ability to survive and proliferate at 37 degrees C is an essential virulence attribute of pathogenic microorganisms. A partial-genome microarray was used to profile gene expression in the human-pathogenic fungus Cryptococcus neoformans during growth at ... Full text Link to item Cite

Cryptococcus neoformans mitochondrial genomes from serotype A and D strains do not influence virulence.

Journal Article Curr Genet · October 2004 Cryptococcus neoformans is an encapsulated pathogenic yeast producing meningoencephalitis. Two primary strains in genetic studies, serotype A H99 and serotype D JEC21, possess dramatic differences in virulence. Since it has been shown that mitochondrial ge ... Full text Link to item Cite

Phylogenetic footprint analysis of IGF2 in extant mammals.

Journal Article Genome Res · September 2004 Genomic imprinting results in monoallelic gene transcription that is directed by cis-acting regulatory elements epigenetically marked in a parent-of-origin-dependent manner. We performed phylogenetic sequence and epigenetic comparisons of IGF2 between the ... Full text Link to item Cite

Complete genomic nucleotide sequence of the temperate bacteriophage Aa Phi 23 of Actinobacillus actinomycetemcomitans.

Journal Article J Bacteriol · August 2004 The entire double-stranded DNA genome of the Actinobacillus actinomycetemcomitans bacteriophage Aa Phi 23 was sequenced. Linear DNA contained in the phage particles is circularly permuted and terminally redundant. Therefore, the physical map of the phage g ... Full text Link to item Cite

The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome.

Journal Article Science · April 9, 2004 We have sequenced and annotated the genome of the filamentous ascomycete Ashbya gossypii. With a size of only 9.2 megabases, encoding 4718 protein-coding genes, it is the smallest genome of a free-living eukaryote yet characterized. More than 90% of A. gos ... Full text Link to item Cite

Maximal polar growth potential depends on the polarisome component AgSpa2 in the filamentous fungus Ashbya gossypii.

Journal Article Mol Biol Cell · October 2003 We used actin staining and videomicroscopy to analyze the development from a spore to a young mycelium in the filamentous ascomycete Ashbya gossypii. The development starts with an initial isotropic growth phase followed by the emergence of germ tubes. The ... Full text Link to item Cite

Verification of a new gene on Saccharomyces cerevisiae chromosome III.

Journal Article Yeast · June 2003 We present verification of the existence of a previously unannotated, intron-containing gene of 134 amino acids (predicted molecular weight approximately 15.5 kDa) located on chromosome III of Saccharomyces cerevisiae. Strains carrying a deletion of this g ... Full text Link to item Cite

Regulation of cytochrome c oxidase subunit 1 (COX1) expression in Cryptococcus neoformans by temperature and host environment.

Journal Article Microbiology (Reading) · April 2003 In the study of differential gene expression of Cryptococcus neoformans, a transcript of COX1 (cytochrome oxidase c subunit 1) was identified in a serotype A strain. The transcript was upregulated at 37 degrees C compared to 30 degrees C and expressed by y ... Full text Link to item Cite

Genomic convergence: identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage.

Journal Article Hum Mol Genet · March 15, 2003 We present a multifactorial, multistep approach called genomic convergence that combines gene expression with genomic linkage analysis to identify and prioritize candidate susceptibility genes for Parkinson's disease (PD). To initiate this process, we used ... Link to item Cite

Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii.

Journal Article Genome Biol · 2003 BACKGROUND: The recently sequenced genome of the filamentous fungus Ashbya gossypii revealed remarkable similarities to that of the budding yeast Saccharomyces cerevisiae both at the level of homology and synteny (conservation of gene order). Thus, it beca ... Full text Link to item Cite

BARD: A visualization tool for biological sequence analysis

Journal Article Proceedings - IEEE Symposium on Information Visualization, INFO VIS · January 1, 2003 We present BARD (biological arc diagrams), a visualization tool for biological sequence analysis. The development of BARD began with the application of Wattenberg's arc diagrams [Wattenberg 2002] to results from sequence analysis programs, such as BLAST [A ... Full text Cite

A framework for integrating the songbird brain.

Journal Article J Comp Physiol A Neuroethol Sens Neural Behav Physiol · December 2002 Biological systems by default involve complex components with complex relationships. To decipher how biological systems work, we assume that one needs to integrate information over multiple levels of complexity. The songbird vocal communication system is i ... Full text Open Access Link to item Cite

Mating-type locus of Cryptococcus neoformans: a step in the evolution of sex chromosomes.

Journal Article Eukaryot Cell · October 2002 The sexual development and virulence of the fungal pathogen Cryptococcus neoformans is controlled by a bipolar mating system determined by a single locus that exists in two alleles, alpha and a. The alpha and a mating-type alleles from two divergent variet ... Full text Link to item Cite

Cytoplasmic dynein is required to oppose the force that moves nuclei towards the hypal tip in the filamentous ascomycete Ashbya gossypii

Journal Article Journal of Cell Science · April 17, 2001 We have followed the migration of GFP-labelled nuclei in multinucleate hyphae of Ashbya gossypii. For the first time we could demonstrate that the mode of long range nuclear migration consists of oscillatory movements of nuclei with, on average, higher amp ... Cite

Cytoplasmic dynein is required to oppose the force that moves nuclei towards the hyphal tip in the filamentous ascomycete Ashbya gossypii.

Journal Article J Cell Sci · March 2001 We have followed the migration of GFP-labelled nuclei in multinucleate hyphae of Ashbya gossypii. For the first time we could demonstrate that the mode of long range nuclear migration consists of oscillatory movements of nuclei with, on average, higher amp ... Full text Link to item Cite

A PAK-like protein kinase is required for maturation of young hyphae and septation in the filamentous ascomycete Ashbya gossypii.

Journal Article J Cell Sci · December 2000 Filamentous fungi grow by hyphal extension, which is an extreme example of polarized growth. In contrast to yeast species, where polarized growth of the tip of an emerging bud is temporally limited, filamentous fungi exhibit constitutive polarized growth o ... Full text Link to item Cite

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.

Journal Article Science · August 6, 1999 The functions of many open reading frames (ORFs) identified in genome-sequencing projects are unknown. New, whole-genome approaches are required to systematically determine their function. A total of 6925 Saccharomyces cerevisiae strains were constructed, ... Full text Link to item Cite

Compact organization of rRNA genes in the filamentous fungus Ashbya gossypii.

Journal Article Curr Genet · July 1999 The rDNA cluster in the phytopathogenic fungus Ashbya gossypii consists of approximately 50 tandem repeat units of 8197 bp. Each unit carries a gene for the 35S pre-rRNA, processed into 18S, 5.8S and 25S rRNA, and a divergently transcribed gene for 5S rRNA ... Full text Link to item Cite

The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.

Journal Article Nature · May 29, 1997 The nucleotide sequence of the 948,061 base pairs of chromosome XVI has been determined, completing the sequence of the yeast genome. Chromosome XVI was the last yeast chromosome identified, and some of the genes mapped early to it, such as GAL4, PEP4 and ... Link to item Cite

The nucleotide sequence of Saccharomyces cerevisiae chromosome V.

Journal Article Nature · May 29, 1997 Here we report the sequence of 569,202 base pairs of Saccharomyces cerevisiae chromosome V. Analysis of the sequence revealed a centromere, two telomeres and 271 open reading frames (ORFs) plus 13 tRNAs and four small nuclear RNAs. There are two Tyl transp ... Link to item Cite

The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI

Journal Article Nature · May 29, 1997 The nucleotide sequence of the 948,061 base pairs of chromosome XVI has been determined, completing the sequence of the yeast genome. Chromosome XVI was the last yeast chromosome identified, and some of the genes mapped early to it, such as GAL4, PEP4 and ... Full text Cite

The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.

Journal Article Nature · May 29, 1997 The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1-2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, whic ... Link to item Cite

The nucleotide sequence of Saccharomyces cerevisiae chromosome V

Journal Article Nature · May 29, 1997 Here we report the sequence of 569,202 base pairs of Saccharomyces cerevisiae chromosome V. Analysis of the sequence revealed a centromere, two telomeres and 271 open reading frames (ORFs) plus 13 tRNAs and four small nuclear RNAs. There are two Ty1 transp ... Full text Cite

Efficient random subcloning of DNA sheared in a recirculating point-sink flow system.

Journal Article Nucleic Acids Res · October 15, 1996 Based on a high-performance liquid chromatographic pump, we have built a device that allows recirculation of DNA through a 63-microm orifice with ensuing fractionation to a minimum fragment size of approximately 300 base pairs. Residence time of the DNA fr ... Full text Link to item Cite

Two distinct genes encode small isoproteolipids affecting plasma membrane H(+)-ATPase activity of Saccharomyces cerevisiae.

Journal Article J Biol Chem · August 19, 1994 A small proteolipid called PMP1 is associated with yeast plasma membrane H(+)-ATPase (Navarre, C., Ghislain, M., Leterme, S., Ferroud, C., Dufour, J.-P., and Goffeau, A. (1992) J. Biol. Chem. 267, 6425-6428). We have identified a second Saccharomyces cerev ... Link to item Cite

The rRNA-encoding DNA array has an altered structure in topoisomerase I mutants of Saccharomyces cerevisiae.

Journal Article Proc Natl Acad Sci U S A · August 15, 1993 All the chromosomes from isogenic TOP1 and top1 strains have similar mobility on pulsed-field gels except for chromosome XII, which fails to migrate into the gels in top1 mutants. Chromosome XII contains the tandem repeats of rRNA-encoding DNA (rDNA). When ... Full text Link to item Cite

Mitotic recombination in the rDNA of S. cerevisiae is suppressed by the combined action of DNA topoisomerases I and II.

Journal Article Cell · November 4, 1988 We have found that mitotic recombination within the S. cerevisiae rDNA cluster (200 tandemly repeated 9.1 kb units) is strongly suppressed and that this suppression requires the combined action of DNA topoisomerases I and II. Strains with a null mutation i ... Full text Link to item Cite