354 research outputs found
Patterns of Cell Division During Morphogenesis of the Sea Urchin Lytechinus variegatus
No full text(Statement of Responsibility) by Corey Nislow(Thesis) Thesis (B.A.) -- New College of Florida, 1987(Electronic Access) RESTRICTED TO NCF STUDENTS, STAFF, FACULTY, AND ON-CAMPUS USE(Bibliography) Includes bibliographical references.(Source of Description) This bibliographic record is available under the Creative Commons CC0 public domain dedication. The New College of Florida, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.(Local) Faculty Sponsor: Morrill, Joh
Understanding cellular response to drugs and toxins with yeast genomics tools
No full textAdvances in genomics and drug discovery have been accelerated by the introduction of new technologies for screens of increasing complexity. A key test bed for these technologies is yeast (Saccharomyces cerevisiae), a valuable experimental model for understanding the mechanism of action (MOA) of compounds. Unfortunately, some of these screening approaches are, by necessity, biased, while others may not be suitable to address the intended research questions. This thesis used the unbiased yeast chemical genomics and phenomics tools to investigate cellular response to diverse drugs, toxins and mycoparasite-prey interactions. First, I characterized the genome-wide effects of N-nitrosamines and their metabolites, and revealed diverse evolutionarily conserved genes and pathways that mediate their toxicity, including arginine biosynthesis, DNA damage repair, mitochondrial genome integrity and vacuolar protein sorting. I further showed that overexpression of ARG3 (ornithine carbamoyltransferase) confers resistance to N-nitrosamines.
In my second project, I identified candidate genes and pathways that could mediate interactions between two yeasts. I observed that resistance and sensitivity to predation by Saccharomycopsis schoenii could be time-dependent, and identified Saccharomyces cerevisiae deletion strains (hits) that were resistant and sensitive to S. schoenii. Genes lacking in the resistant strains are involved in cell wall integrity, arginine/lysine biosynthesis, and oxidative stress response. Conversely, the sensitive strains lack genes involved in endocytosis, vacuolar protein sorting, and cell size regulation.
The third project provided data that can help define MOA of anthracycline chemotherapeutics using a multipronged approach. The data showed that some anthracyclines (doxorubicin, daunorubicin and epirubicin) exhibited higher potency in cells grown on glycerol versus glucose media. It further indicated that doxorubicin and daunorubicin MOA may involve mitochondrial processes that are not linked to mitochondrial DNA. I uncovered a spectrum of anthracycline response profiles, and showed that cellular effects of anthracyclines can be distinguished. Using whole genome sequencing, I identified mutations from doxorubicin-resistant clones, and showed that overexpression of ARL1 (ADP ribosylation factor like GTPase 1) and SSL2 (member of RNA polymerase transcription factor TFIIH complex) confers resistance to anthracyclines.
Together, my work characterized candidate genes and pathways that could be required in cellular response to chemical perturbation.Science, Faculty ofGraduat
Pharmacogenomics : from experimental design through patient interactions
No full textIn this study 180 patients were consented and enrolled for pharmacogenomic testing based on their current antidepressant/antipsychotic usage. Samples from patients were genotyped by PCR, massARRAY, and targeted for next generation sequencing. We also conducted a quantitative, frequency-based analysis of participants’ perceptions using simple surveys. Pharmacogenomic information, including medication changes and altered dosing recommendations were returned to the pharmacists and used to direct patient therapy. Overwhelmingly, patients perceived pharmacists/pharmacies as an appropriate healthcare provider to deliver pharmacogenomic services. In total, there were 81 medication changes in 33 unique patients, representing 22% of all genotyped participants. We performed a simple drug cost analysis and found that medication adjustments and dosing changes across the entire cohort added $24.15CAD per patient per year for those that required an adjustment. Comparing different platforms, we uncovered a small number (1.7%) of genotype discrepancies, none of which impacted medication suggestions. We conclude that: 1) Pharmacists are competent providers of pharmacogenomic services. 2) The potential reduction in adverse drug responses and optimization of drug selection and dosing comes at a minimal cost to the health care system. 3) Changes in drug therapy, based on PGx tests, result in inconsequential changes in annual drug therapy cost with small cost increases just as likely as costs savings. 4) Pharmacogenomic services offered by pharmacists are ready for wide commercial implementation. This thesis details the methods and results from this study in relation to pharmacogenomics as a concept and its practice across British Columbia and Canada.Pharmaceutical Sciences, Faculty ofGraduat
Supplemental Material for Coutin, Giaever, and Nislow, 2020
No full textSupplementary Materials for G3/2019/400898. The 'supplementary-materials.pdf' contains additional tables, figures, text and listings referred to in the main article. Individual supplementary figures and a movie are also available as individual files
Development of a high-throughput genome-wide method to assess Ty1 retrotransposon insertion upstream of tRNA genes in Saccharomyces cerevisiae
No full textThe full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.Science, Faculty ofGraduat
Chemogenomic screening of topoisomerase inhibitors : mechanistic insights and cellular interactions
No full textThe full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.Pharmaceutical Sciences, Faculty ofGraduat
Exploring AdoMet-dependent Methyltransferases in Yeast
No full textThis work presents the investigation of fungal AdoMet-dependent methyltransferases. The first part of the dissertation focuses on two distinct methyltransferases with previously unknown functions in the budding yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans. To characterize these enzymes I used a combinatorial approach that exploits contemporary high-throughput techniques available in yeast (chemical genetics, expression, lipid profiling and genetic interaction analysis) combined with rigorous biological follow-up. First, I showed that S. cerevisiae CRG1 (ScCRG1) is a small molecule methyltransferase that methylates cytotoxic drug cantharidin and is important for maintaining lipid homeostasis and actin cytoskeleton integrity in response to small-molecule cantharidin in the baker’s yeast. Similarly to ScCRG1, orf19.633 in the human fungal pathogen C. albicans (CaCRG1) methylates cantharidin and is important for GlcCer biosynthesis. I also demonstrated that CaCrg1 is a ceramide- and PIP-binding methyltransferase involved in Candida’s morphogenesis, membrane trafficking and fungal virulence. Together, the analysis of two genes in yeast illuminated the important roles of the novel small molecule methyltransferases in coupling drug response to lipid biosynthesis and fungal virulence. In the second part of my dissertation, I present the systematic characterization of the genetic architecture of the yeast methyltransferome by examining fitness of double-deletion methyltransferase mutants in standard and under environmental stress conditions. This analysis allowed me to describe specific properties of the methyltransferome network and to uncover functional relationships among methyltransferases inspiring multiple hypotheses and expanding the current knowledge of this family of enzymes.Ph
Exploring AdoMet-dependent Methyltransferases in Yeast
No full textThis work presents the investigation of fungal AdoMet-dependent methyltransferases. The first part of the dissertation focuses on two distinct methyltransferases with previously unknown functions in the budding yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans. To characterize these enzymes I used a combinatorial approach that exploits contemporary high-throughput techniques available in yeast (chemical genetics, expression, lipid profiling and genetic interaction analysis) combined with rigorous biological follow-up. First, I showed that S. cerevisiae CRG1 (ScCRG1) is a small molecule methyltransferase that methylates cytotoxic drug cantharidin and is important for maintaining lipid homeostasis and actin cytoskeleton integrity in response to small-molecule cantharidin in the baker’s yeast. Similarly to ScCRG1, orf19.633 in the human fungal pathogen C. albicans (CaCRG1) methylates cantharidin and is important for GlcCer biosynthesis. I also demonstrated that CaCrg1 is a ceramide- and PIP-binding methyltransferase involved in Candida’s morphogenesis, membrane trafficking and fungal virulence. Together, the analysis of two genes in yeast illuminated the important roles of the novel small molecule methyltransferases in coupling drug response to lipid biosynthesis and fungal virulence. In the second part of my dissertation, I present the systematic characterization of the genetic architecture of the yeast methyltransferome by examining fitness of double-deletion methyltransferase mutants in standard and under environmental stress conditions. This analysis allowed me to describe specific properties of the methyltransferome network and to uncover functional relationships among methyltransferases inspiring multiple hypotheses and expanding the current knowledge of this family of enzymes.Ph
Defining Nucleosome Occupancy and Positioning: Evolution and the Role of Trans-acting Factors
No full textThe fundamental repeating unit of all eukaryotic chromatin is the 147bp DNA:histone complex known as the nucleosome. Genome-wide studies have demonstrated that nucleosomes are organized with the 5’ promoter being nucleosome depleted and the transcribed region is occupied by a periodic array of positioned nucleosomes.
While this organization is well described, the determinants, particularly trans-acting factors that contribute to this architecture are only partly described with gene expression, however, while the connection between chromatin and the various facets of gene expression regulation, especially in evolution, is apparent the detailed mechanisms remain to be described. In this thesis, I describe 1) The role of nucleosomes in gene expression evolution in closely related yeast species 2) The role of trans-acting factors (particularly transcription factors and co-factors) in determining the nucleosome depleted region of promoters and 3) The role of trans-acting factors in nucleosome spacing within genes.Ph
Defining Nucleosome Occupancy and Positioning: Evolution and the Role of Trans-acting Factors
No full textThe fundamental repeating unit of all eukaryotic chromatin is the 147bp DNA:histone complex known as the nucleosome. Genome-wide studies have demonstrated that nucleosomes are organized with the 5’ promoter being nucleosome depleted and the transcribed region is occupied by a periodic array of positioned nucleosomes.
While this organization is well described, the determinants, particularly trans-acting factors that contribute to this architecture are only partly described with gene expression, however, while the connection between chromatin and the various facets of gene expression regulation, especially in evolution, is apparent the detailed mechanisms remain to be described. In this thesis, I describe 1) The role of nucleosomes in gene expression evolution in closely related yeast species 2) The role of trans-acting factors (particularly transcription factors and co-factors) in determining the nucleosome depleted region of promoters and 3) The role of trans-acting factors in nucleosome spacing within genes.Ph
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