Carmen E. Castaneda: Week 9

Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). List the citation(s) for the dictionary(s) you use, providing a URL to the page is fine.

1. trehalose (1)
2. osmolarity (2)
3. dendrogram (3)
4. ribosome biogenesis (4)
5. glycogen (5)
6. diauxic (6)

1. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can check this by clicking on "Print preview" in your browser). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
   • What is the main result presented in this paper?
   • What is the importance or significance of this work?
   • How did they treat the cells (what experiment were they doing?)
   • What strain(s) of yeast did they use? Was the strain haploid or diploid?
   • What media did they grow them in? What temperature? What type of incubator? For how long?
   • What controls did they use?
   • How many replicates did they perform per timepoint?
   • What mathematical/statistical method did they use to analyze the data?
   • What transcription factors did they talk about?
   • Briefly state the result shown in each of the figures and tables.

Outline

Abstract

• transcriptional response of budding yeast to cold
  • exposed to 10°C for different lengths of time
  • DNA microarrays were used characterize the changes in transcript abundance
    • two main groups were identified, early cold response, ERC, and late cold response, LRC
  • overlap between environmental stress response, ESR, genes and LRC
  • acoomulation of the carbohydrate reserve trehalose and glycogen is indunced during LRC
  • strand munipulation
    • Msn2p and Msn4p involvement with the inductionof genes common to stress responses
      • recognition of paterns during LRC and comparirison between ERC

Introduction

• Unicellular organisms are affected by a variety of extreme changes in their environments
  • Changes in their environment like nutrients, acidity, osmolarity temperature, toxins and radiation
• Developed programmed responses to stress into the genetic code, not random
  • The transcription of genes is changed
    • which is general stress response.
• ~10% of the genome responds
  • Genes involved are defined as environmental stress response, ESR
    • Induced ESR genes tend to be those involved in a variety of cell functions like protein folding &degradation, transport, & carbohydrate metabolism
    • Repressed deal with cell growth
• Little known about mechanisms responsible for growth and survival at low temperatures
• Cold causes different changes in the physical and biochemical properties
• Ability to adapt is determined by different regulatory mechanisms
• We'll compare cold responses to the responses of other stress stimuli and accumulation of trehalose and glycogen in cold stress

Materials and Methods

• Strains
  • BY4743 (wild type)
  • BSY25
    • derived from a cross of the two single-mutant strains
  • W303
    • for growth curve experiments
• growth medium and culture condition
  • YPD medium - 2% glucose, 2% bactopeptone, 1% yeast extract
  • culture inoculated from fresh colony and grown overnight at 30°C in 50 ml of medium in Erlenmeyer flasks shaken at 170rpm
    • these were the diluted to 0.05 OD in 500ml of fresh medium, grown to 0.6 OD at 30°C in 1500ml flasks shaken 170rpm
      • transferred to a 10°C water bath shaker, in which they were incubated for 10, 30 or 120 min at 170rpm before being harvested
  • temperature dropped 4°C per minute
• isolation of RNA
  • isolated using hot-phenol method with modifications
    • 500ml cells were processed in 50 ml tubes by extracting phenol

1. Each group of students will be assigned one section of the paper. The group will be responsible for preparing that portion of the PowerPoint presentation and explaining the assigned section and figures in detail to the class. Groups will be assigned on 3/10/11 in class.
   • Introduction, Figures 1, 2: Sarah, Carmen
   • Methods, Figures 3, 4: Alondra, Nick
   • Discussion, Figures 5, 6: James