Individual Journal Week 11

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(Introduction)
(Materials & Methods)
Line 38: Line 38:
*Cultures analyzed through microarray and statistical analysis
*Cultures analyzed through microarray and statistical analysis
*Microarray analysis:
*Microarray analysis:
-
#*Determined RNA quality
+
**Determined RNA quality
-
#*growth condition derived from three independently cultured replicates
+
**growth condition derived from three independently cultured replicates
-
#*Northern analysis used
+
**Northern analysis used
*Statistical Analysis
*Statistical Analysis
-
#*Excel used to run significance of microarray add-in, through "pair-wise comparisons"
+
**Excel used to run significance of microarray add-in, through "pair-wise comparisons"
-
#*Data displayed in Venn diagrams and heat-maps
+
**Data displayed in Venn diagrams and heat-maps
-
#*Promoters analyzed through use of web-based software
+
**Promoters analyzed through use of web-based software
-
#*p-value calculated
+
**p-value calculated
-
#*Outside transcriptome datasets used for comparison
+
**Outside transcriptome datasets used for comparison
===Results===
===Results===

Revision as of 23:25, 3 April 2013

Contents

Terms

  • Batch-culture: A large-scale closed system culture in which cells are grown in a fixed volume of nutrient culture medium under specific environmental conditions (e.g. nutrient type, temperature, pressure, aeration, etc.) up to a certain density in a tank or airlift fermentor, harvested and processed as a batch, especially before all nutrients are used up. [1]
  • Catabolite: product of catabolism, the breakdown of complex molecules into simpler ones. [2]
  • Gene Regulatory Protein: Any protein that interacts with dna sequences of a gene and controls its transcription. [3]
  • Up-regulation:process that increases ligand/receptor interactions due to an increase in the number of available receptors. [4]
  • Down-regluation: the process that decreases ligand and receptor interactions or reduces the responsiveness of a cell to a stimulus following first exposure.This is often accompanied by an initial decrease in affinity of receptors for the agent and a subsequent reduction in the number of available receptors expressed on the surface which can result from internalisation of the ligand:receptor complex or from decreased expression of the receptor. [5]
  • Motif: The smallest group of atoms in a polymer that, when under the influence of a rotation-translation operator, will assemble the rest of the atoms in the chain. [6]
  • Desaturase: Any of several enzymes that putdouble bonds into the hydrocarbon areasof fatty acids. [7]
  • Biogenesis: The process in which life forms arise from similar life forms. [8]
  • Trehalose: a crystalline disaccharide C12H22O11 that is found in various organisms (as fungi and insects), is about half as sweet as sucrose, and is sometimes used as a sweetener in commercially prepared foods [9]
  • Transcriptome: the complement of mature messenger RNAs produced in a given cell in a given moment of its life. [10]

Outline

Introduction

  • The study observes the effects of suboptimal temperatures on transcriptional regulation in yeast.
  • Transcriptional responses were observed at temperatures 12C and 30C.
  • Lower temperatures, typically result in the slower cellular processes: growth phase, respiration, lipid composition of membranes, and trehalose content.
  • Time scale of exposure to cold-shock relevant:
    • Sudden exposure => adaptation
    • Prolonged exposure=> acclimation
    • Long term exposure => evolutionary adaptation
  • Two distinct phases during cold-shock response
  1. First 12 hours, early cold shock (ECS)
  2. After first 12 hours, Late cold response (LCR)
  • TPS1 and TPS2, commonly observed trehalose-biosynthetic transcriptional induction genes- observed in cold and heat shock conditions
  • Genes involved in cold-shock response typically involved in other stress response
  • Growth rate an important factor on transcription
  • Research seeks to control specific growth rate and other culture conditions, through use of chemostat, in order to establish steady-state and, thus, investigate transcription regulation influenced by suboptimal temperatures

Materials & Methods

  • Yeast was grown in one chemostat with temperature 12C as well as a second chemostat set at 30C, both set at a dilution rate of 0.03h-1 with a working volume of 1.0 L
  • Carbon or nitrogen limitations, other media/ nutrients in excess
  • pH constant at 5.0 by addition of 2 M KOH
  • Anaerobic growth
  • Stirrer set at constant 600 rpm
  • Grown in conditions in which ammonia was limiting at 12C, ammonia was limiting at 30C, glucose was limiting at 12C, and glucose was limiting at 30C
  • Cultures analyzed through microarray and statistical analysis
  • Microarray analysis:
    • Determined RNA quality
    • growth condition derived from three independently cultured replicates
    • Northern analysis used
  • Statistical Analysis
    • Excel used to run significance of microarray add-in, through "pair-wise comparisons"
    • Data displayed in Venn diagrams and heat-maps
    • Promoters analyzed through use of web-based software
    • p-value calculated
    • Outside transcriptome datasets used for comparison

Results

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