Matthew E. Jurek Week 11: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(→Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analyis: outlined materials and methods) |
|||
Line 25: | Line 25: | ||
#*Chemostat cultures allow for control of specific growth rate independent of culture conditions such as metabolites, pH, and oxygen availability. | #*Chemostat cultures allow for control of specific growth rate independent of culture conditions such as metabolites, pH, and oxygen availability. | ||
#*Overall Goal: Focus on genome-wide transcriptional regulation by exploring steady-state acclimatized growth of yeast at low temps | #*Overall Goal: Focus on genome-wide transcriptional regulation by exploring steady-state acclimatized growth of yeast at low temps | ||
#Materials and Methods | |||
#*Haploid strain CEN.PK113-7D was grown at both 12 and 30 degrees C, anaerobically, in a chemostat | |||
#*The chemstat contained a dilution rate of .03/h, pH of 5.0 and stirrer speed of 600rpm. | |||
#*The cultures were contained in a synthetic medium that limited either carbon or nitrogen. Every other requirement was in excess. | |||
#*Each growth condition consisted of 3 independent replicates. | |||
#*Microarray data was analyzed using Fisher's exact test with a Bonferroni correction in order to acheive a p value threshold of .01. | |||
#*This data was then compared to previously published low-temperature transcriptome datasets. |
Revision as of 21:27, 3 April 2013
Matthew E. Jurek BIOL398-03/S13
Assignment Page
- BIOL398-03/S13:Week_2
- BIOL398-03/S13:Week 3
- BIOL398-03/S13:Week 4
- BIOL398-03/S13:Week_5
- BIOL398-03/S13:Week_6
- BIOL398-03/S13:Week_8
- BIOL398-03/S13:Week_9
- BIOL398-03/S13:Week_11
- BIOL398-03/S13:Week_12
- BIOL398-03/S13:Week_13
- BIOL398-03/S13:Week_14
User Page
- Matthew E. Jurek Week 2
- Matthew E. Jurek Week 3
- Matthew E. Jurek Week 4
- Matthew E. Jurek Week 5
- Matthew E. Jurek Week 6
- Anthony J. Wavrin/Matthew E. Jurek Metabolic Pathways Project
- Matthew E. Jurek Week 8
- Matthew E. Jurek Week 9
- Matthew E. Jurek Week 11
- Matthew E. Jurek Week 12
- Matthew E. Jurek Week 13
- Matthew E. Jurek Week 14
- Final Presentation
Biological Terms
- trehalose- also known as mycose or tremalose, is a natural alpha-linked disaccharide formed by an α,α-1,1-glucoside bond between two α-glucose units.
- mannoprotein- component of yeast cell walls; protein covalently linked to polymers of mannose.
- chromatography- the separation of mixtures into their constituents by preferential adsorption by a solid, as a column of silica (column chromatography) or a strip of filter paper (paper chromatography) or by a gel.
- immunoprecipitation- the separation of an antigen from a solution by the formation of a large complex with its specific antibody.
- catabolite- a product of catabolic action.
- kinetics- the branch of mechanics that deals with the actions of forces in producing or changing the motion of masses.
- ceramides- ceramides are a family of lipid molecules. A ceramide is composed of sphingosine and a fatty acid.
- orthologue- one of two or more homologous gene sequences found in different species.
- ergosterol- a compound present in ergot and many other fungi. A steroid alcohol, it is converted to vitamin D2 when irradiated with ultraviolet light.
- transcriptome- the transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and non-coding RNA produced in one or a population of cells.
Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analyis
Tai et al. (2007) Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analysis. Molecular Biology of the Cell 18: 5100–5112.
- Introduction
- On the cellular level, yeast responds in a number of ways to temperature changes (temps outside the 25-30 degree C optimum).
- Temperatures below the optimum range slow cellular processes.
- Effects of low temperature depend on exposure time
- Sudden exposure results in adaptaion
- Prolonged exposure results in acclimation
- Previous studies have focused on cold shock (sudden exposure) and found 2 phases of cold-shock response
- Current low-temp transcriptome databases contain major discrepancies
- Previous studies have focused on batch culutures: hard to distinguish temp effects on transcription from effects of specific growth rate
- Chemostat cultures allow for control of specific growth rate independent of culture conditions such as metabolites, pH, and oxygen availability.
- Overall Goal: Focus on genome-wide transcriptional regulation by exploring steady-state acclimatized growth of yeast at low temps
- Materials and Methods
- Haploid strain CEN.PK113-7D was grown at both 12 and 30 degrees C, anaerobically, in a chemostat
- The chemstat contained a dilution rate of .03/h, pH of 5.0 and stirrer speed of 600rpm.
- The cultures were contained in a synthetic medium that limited either carbon or nitrogen. Every other requirement was in excess.
- Each growth condition consisted of 3 independent replicates.
- Microarray data was analyzed using Fisher's exact test with a Bonferroni correction in order to acheive a p value threshold of .01.
- This data was then compared to previously published low-temperature transcriptome datasets.