Bobak Seddighzadeh Week 11

From OpenWetWare

Revision as of 03:16, 12 April 2010 by Bobak Seddighzadeh (Talk | contribs)
(diff) ←Older revision | Current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search

Media:Yeast_paper_journal_club2.ppt

Terms:

  1. acclimation: adaptation to prolongued exposure
  2. trehalose: disaccharide that is involved in the ability of plants/animals to withstand desiccation due to its hight water retention
  3. batch culture: a large-scale closed culture in which cells are grown in a fixed volume of nutrient medium under specific environmental conditions
  4. cis-regulatory motif: a motif is a nucleotide/ amino acid sequence that is widespread and is believed to have biological significance
  5. specific growth rate: increase in cell mass per unit cell mass per unit time-- unites = reciprocal time
  6. desaturase: an enzyme that removes two hydrogens from a fatty acid, resulting in a carbon-carbon double bond
  7. Mannoproteins: yeast cell wall components that contain large numbers of mannose groups
  8. chemostat : a bioreactor to which fresh medium is continuously added, while culture liquid is continuously removed to keep the culture volume constant
  9. catabolite repression: repression of certain sugar metabolizing operons in favor of glucose utilization when glucose is predominant carbon source
  10. Sphingolipids: a class of lipids derived from the aliphatic amino alcohol sphingosine.

Introduction

  • optimum growth range fro S Cerevisiae is 25-35 degrees Celsius
  • Suboptimal temperaturs affect varous cellular process such as growth phase, respiration, lipid composition
  • time scale of exposure important in interpretation
    • cold shock versus prolonged exposure produce different responses
  • Other studies found two distinct phases during cold shock: early and late
    • Trehalose consistently observed in studies as a increased response
  • Problems with other studies:
    • Transcriptome data reveals major discrepancies
    • Trehalose accumulation only essential below ten degrees Celsius
    • Differences between adaptation and acclimation haven’t been thoroughly investigated
  • Main results presented in study:
    • S cerevisiae was grown at 12 to 30 degrees Celsius in anaerobic chemostat cultures
    • Fixed growth rate
    • Transcription analyzed in both glucose and ammonium limited conditions for both temperatures
  • The signifigance of their study is that they found better insight on S Cerevisiae adaptations to cold exposure by creating a more accurate and reliable data set by growing the cultures in a chemostat

Methods

  • The prototrophic haploid reference S. cerevisiae strain were grown at 12 or 30 degrees Celsius
  • Concetrations of metabolites were analyzed using high performaance liquid chromatography
  • Results from each growth condition were collected from three independent culture replicates and were hybridized to the chip for the microarray
  • They hypridized four microarray chips. One for each growth condition
  • Three individually cultured biological replicates were used
  • They do not list the steps found in Overview of Microarray Data Analysis section

Results:

  • Table 1: Shows that biomass yields were similar at both temperatures indicated growth rates were not affected severely by growth temperature
  • Figure 1: Shows the transcriptome responses glocuse and ammonium limited chemostat cultures.
    • Glucose limited cultures yielded 494 different genes compared to 806 nitrogen limited cultures
    • 235 genes showed up or down regulations in both conditions
    • 16% of genome included in temperature response genes
  • Figure 2: Analyzed temperature-responsive genes (1065) for specific functional categories and cis-regulatory motifs
    • Growth limiting nutrient kinetics were alerted.
    • High affinity ammonia permeases were expressed less in 12C sample and the low affinity was expressed more in 12C sample
    • Protein synthesis genes were more expressed at 12C than 30C, especially for N-limiting cultures
    • Increased concentration of limiting nutrients resulted in catabolite repression
  • Table 2: Trehalose and glycogen levels were significantly lower at 12C (except for glycogen in glucose-limited culture)
  • Table 3: The small number of genes that showed a consistent transcriptional response to low temperature during acclimation and adaptation
    • 91 were consistently up regulated at low temperature, and only 48 were consistently down-regulated
  • Figure 4: Twenty-nine genes were transcriptionally regulated during both adaptation and acclimation to low temperature
    • only 11 genes showed a consistent pattern of regulation in all four situations
  • Figure 5: Negligible Overlap with Growth-rate–responsive Genes was Observed
    • 25% of down-regulated genes and 10% of up-regulated are likely to be only related to specific growth rate.
  • Figure 6: A Significant Overlap Between Regulated Genes in Batch Cultures Exist


Discussion

  • the transcriptional response to a stimulus has been shown to be dependent on other environmental parameters
  • Using combinatorial approaches, core sets of genes can be defined
  • There is a growing body of evidence that specific growth rate itself has a strong effect on genome-wide transcription
  • less than 1% of the temperature-responsive genes identified in the present chemostat

study showed a growth-rate–dependent transcript level

  • In batch cultures of S. cerevisiae, exposure to low temperatures causes an increased synthesis of storage carbohydrates (in particular trehalose) and transcriptional up-regulation of genes involved in storage carbohydrate metabolism
    • These effects weren’t observed in their studies
  • Chemostat-based transcriptome analysis at 12 and 30°C

yielded a set of 235 genes that showed a consistent transcriptional response to low temperature

  • The only clearly defined group of genes that was regulated in chemostats and batchculture studies on low-temperature adaptation had to do with lipid metabolism
  • chaperone-encoding genes were transcriptionally down-regulated at low temperature in the chemostat cultures in contrast to being upregulated in other batch culture studies
  • Electronic Journal
  1. Bobak Seddighzadeh Week 2
  2. Bobak Seddighzadeh Week 3
  3. Bobak Seddighzadeh Week 4
  4. Bobak Seddighzadeh Week 5
  5. Bobak Seddighzadeh Week 6
  6. Bobak Seddighzadeh Week 7
  7. Bobak Seddighzadeh Week 8
  8. Bobak Seddighzadeh Week 9
  9. Bobak Seddighzadeh Week 10
  10. Bobak Seddighzadeh Week 11
  11. Bobak Seddighzadeh Week 12
  12. Bobak Seddighzadeh Week 13
  • Shared Journal
  1. BIOL398-01/S10:Class Journal Week 2
  2. BIOL398-01/S10:Class Journal Week 3
  3. BIOL398-01/S10:Class Journal Week 4
  4. BIOL398-01/S10:Class Journal Week 5
  5. BIOL398-01/S10:Class Journal Week 6
  6. BIOL398-01/S10:Class Journal Week 7
  7. BIOL398-01/S10:Class Journal Week 8
  8. BIOL398-01/S10:Class Journal Week 9
  9. BIOL398-01/S10:Class Journal Week 10
  10. BIOL398-01/S10:Class Journal Week 11
  11. BIOL398-01/S10:Class Journal Week 12
  12. BIOL398-01/S10:Class Journal Week 13
  • Assignments
  1. BIOL398-01/S10:Week 2
  2. BIOL398-01/S10:Week 3
  3. BIOL398-01/S10:Week 4
  4. BIOL398-01/S10:Week 5
  5. BIOL398-01/S10:Week 6
  6. BIOL398-01/S10:Week 7
  7. BIOL398-01/S10:Week 8
  8. BIOL398-01/S10:Week 9
  9. BIOL398-01/S10:Week 10
  10. BIOL398-01/S10:Week 11
  11. BIOL398-01/S10:Week 12
  12. BIOL398-01/S10:Week 13

User Pager

Personal tools