Difference between revisions of "Hivanson Week 12"

From LMU BioDB 2024
Jump to navigation Jump to search
(→‎Defining 10 unknown biological terms: all words to define)
(→‎Presentation Prep: RNA treatment, math, and where available.)
Line 1: Line 1:
 
==Presentation Prep==
 
==Presentation Prep==
 +
 +
===Purpose===
 +
This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.
 +
 
===Defining 10 unknown biological terms===
 
===Defining 10 unknown biological terms===
 
#Thioredoxin system:
 
#Thioredoxin system:
Line 36: Line 40:
 
# '''How many replicates did they perform per treatment or timepoint?'''
 
# '''How many replicates did they perform per treatment or timepoint?'''
 
#*3
 
#*3
−
# What method did they use to prepare the RNA, label it and hybridize it to the microarray?  
+
# '''What method did they use to prepare the RNA, label it and hybridize it to the microarray?'''
−
#*
+
#*Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
−
# What mathematical/statistical method did they use to analyze the data?
+
#*Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
−
# Are the data publicly available for download?  From which web site?
+
#*Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
 +
# '''What mathematical/statistical method did they use to analyze the data?'''
 +
#*ANOVA
 +
# '''Are the data publicly available for download?  From which web site?'''
 +
#*GEO Database and SGD.
 
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
 
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
 
#* What do the X and Y axes represent (if applicable)?
 
#* What do the X and Y axes represent (if applicable)?

Revision as of 17:08, 17 April 2024

Presentation Prep

Purpose

This week's purpose is to understand, analyze, and communicate the findings of the article that our data will be coming from. This paper is the source of the data that will be used by the Data Analysts to make a gene regulatory network.

Defining 10 unknown biological terms

  1. Thioredoxin system:
  2. Glutathione system:
  3. Leucine zipper proteins:
  4. Lignin:
  5. Capillariy electrophoresis:
  6. Photodiode Array Detector:
  7. Trehalose:
  8. MAPK signaling:
  9. Regulon:
  10. Isoenzymes:
  11. Rho zero petites:

Questions about your article

  1. What is the main result presented in this paper?
    • CHP exposure changes the transcriptional response of yeast via its oxidative stress response. The researchers observed the changes in yeast transcription from minutes 0-20, noting many significant changes in minutes 0-6.
      • Implicated pathways include oxidative phosphorylation, galactose metabolism, ATP synthesis, proteasome proteolysis, and glutathione & thioredoxin systems.
  2. What is the importance or significance of this work?
    • This paper was the first to note the early (0-6 minutes post-exposure) transcriptional response by yeast to CHP.
    • The researchers found that Yap3, 5, and 7 are involved in the yeast OSR, and that their functions were not previously known.
  3. What were the limitations in previous studies that led them to perform this work?
    • Some similar studies did not have biological replicates, nor control groups.
    • This study is unique as there was no incubation with CHP before monitoring the transcriptional change. Some other studies waited 10+ minutes to begin analyzing the changes in transcription.
  4. How did they treat the yeast cells (what experiment were they doing?)
    • CHP, or cumene hydroperoxide, exposure (CHP in 95% (w/v) ethanol)
  5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
    • Diploid strain BY4743 was used.
  6. What media did they grow them in? What temperature? What type of incubator? For how long?
    • 2% (w/v) sucrose supplemented with uracil L-leucine, and L-histidine
    • 30ºC
    • New Brunswick BioFlo fermentors
    • Grown until OD600 of 1.5
  7. What controls did they use?
    • The same strain of yeast was grown and monitored exactly the same way as the treatment group, but not exposed to CHP.
  8. How many replicates did they perform per treatment or timepoint?
    • 3
  9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?
    • Preparation of RNA: Once collected, the samples were centrifuged and freeze-dried, then RNA was extracted by modified "hot phenol protocol."
    • Labeling RNA: S98 arrays by Affymetrix, a well as a quality control check, and then the GeneChip One-Cycle cDNA synthesis kit were used to label the RNA.
    • Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
  10. What mathematical/statistical method did they use to analyze the data?
    • ANOVA
  11. Are the data publicly available for download? From which web site?
    • GEO Database and SGD.
  12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
    • What do the X and Y axes represent (if applicable)?
    • How were the measurements made?
    • What trends are shown by the plots and what conclusions can you draw from the data?
  13. How does this work compare with previous studies?
  14. What are the important implications of this work?
  15. What future directions should the authors take?
  16. Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

Presentation

Ivanson, Kaplan, Miller on Sha et al., 2013

Acknowledgments

References

Template:Hivanson

Retrieved from "https://xmlpipedb.lmucs.org/biodb/spring2024/index.php?title=Hivanson_Week_12&oldid=3296"