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Andrew Fletcher Thesis with Changes Microarray analysis of DV10 Saccharomyces cerevisiae during Second Fermentation under Oenological Conditions by Andrew Fletcher A Thesis Presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Bioinformatics Guelph, Ontario, Canada © Andrew S. Fletcher, May, 2015 ABSTRACT Microarray Analysis of DV10 Saccharomyces cerevisiae During Second Fermentation Under Oenological Conditions Andrew S. Fletcher Advisors: University of Guelph, 2014 Dr. G van der Merwe Dr. P McNicholas During aging of high quality sparkling wine, yeasts that have finished fermentation slowly die and release metabolites into the wine that are responsible for characteristic taste and foaming properties. Two of the main processes that aid in aging are autolysis and autophagy but their regulation during secondary fermentation remains largely unknown. Microarray analysis of the Saccharomyces cerevisiae strain DV10 during secondary fermentation yielded some potential targets for future studies regarding these processes. Several stress pathways were identified as well as the GATA transcription factors GAT2, GAT3, and GAT4. Many proposed targets of GATA transcription factors are part of the ATG family of autophagy genes, which had one or more copies of the GATA consensus sequence in their promoters. This possible relationship is of particular interest due to the poorly understood roles of these GATA factors and could lead to better understanding of the regulatory processes of autophagy. ACKNOWLEDGMENTS I did not expect to be writing a thesis during post secondary studies. For this experience I owe thanks to my two advisors. Without them I would have graduated a long time ago. Instead I was given the “opportunity” to transfer into a M.Sc. program. But kidding aside, I would do it all again. My project was the envy of everyone I met. So thank you Dr. George van der Merwe, for choosing me to be the lucky grad student, and for introducing me to a world I always wanted to be a part of. Also, for not laughing in my face when I insisted I could work full time on the other side of the country and still write a thesis (even though I obviously couldn’t). Thank you to Paul McNicholas for offering to take me on, and providing funding to give me an opportunity I wouldn’t have otherwise had. Despite being impossibly busy, I could always get the help I needed. Every meeting we had left me feeling more encouraged. I also must recognize the efforts of Gavin Robertson and the crew at the Niagara College Teaching Winery for producing the sparkling wine necessary for my experiments. A big thanks, also, to Angus Ross for getting me started in the van der Merwe lab, and always being there to help me find things. And to Richard Priess for the brainstorming help. Finally, I have to thank my friends and family for keeping me alive and sane through the whole ordeal. Most importantly, I must express my appreciation for Mel. Without her I would have been a model grad student. However, she showed me that pursuing a master’s degree and the rest of life’s goals needn’t be mutually exclusive. iii Table of Contents ABSTRACT ............................................................................................................................................ i Table of Contents ............................................................................................................................. iv List of Tables .................................................................................................................................... vii List of Figures ...................................................................................................................................... x List of Abbreviations ..................................................................................................................... xii Chapter 1 – Introduction ....................................................................................................... 1 1.1. Overview of sparkling wine production ........................................................................... 1 1.1.1. Methods of production ..................................................................................................................... 2 1.1.2. Base wine production ....................................................................................................................... 2 1.1.3 Secondary fermentation .................................................................................................................... 5 1.1.4. Alternative methods of sparkling wine production ............................................................. 8 1.2. Overview of Saccharomyces cerevisiae .............................................................................. 9 1.2.1 Yeast strains used in sparkling wine production ................................................................ 10 1.2.2. Carbon Metabolism ......................................................................................................................... 11 1.2.2.1. Glycolysis ......................................................................................................................................... 12 1.2.2.2. Fermentation .................................................................................................................................. 13 1.2.3. Stress response and consequences .......................................................................................... 15 1.2.4. Osmotic stress response ............................................................................................................... 16 1.2.5. Autolysis .............................................................................................................................................. 17 1.2.6. Yeast cell wall .................................................................................................................................... 19 1.2.7. Autophagy ........................................................................................................................................... 20 1.2.8. Autophagy regulation ..................................................................................................................... 23 1.2.9. GATA family of transcription factors ....................................................................................... 25 1.3. Microarrays .............................................................................................................................. 26 1.3.1. In-situ synthesized oligonucleotide arrays ........................................................................... 27 1.3.2. Hybridization ..................................................................................................................................... 27 1.4 Data Analysis ............................................................................................................................. 28 1.4.1. Pre-processing .................................................................................................................................. 28 1.4.2. Background noise and correction ............................................................................................. 29 1.4.3. Normalization .................................................................................................................................... 31 1.4.4. Cluster analysis ................................................................................................................................. 34 1.4.5. Model-based clustering ................................................................................................................. 35 1.4.6. Longitudinal Clustering ................................................................................................................. 36 1.4.7. Gene ontology .................................................................................................................................... 38 1.5. Previous microarray studies of S. cerevisiae during secondary sparkling wine fermentation .................................................................................................................................... 38 1.6. Hypothesis and Objectives .................................................................................................. 39 Chapter 2 - Materials and Methods ................................................................................. 40 2.1. Sparkling wine production: ................................................................................................ 40 2.1.1. Base wine fermentation ................................................................................................................ 40 2.1.2. Second Fermentation ..................................................................................................................... 41 2.2. Yeast collection ....................................................................................................................... 42 2.2.1. Cell viability analysis ...................................................................................................................... 43 2.2.2. RNA isolation ..................................................................................................................................... 44 2.3. Microarray Methods .............................................................................................................
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