Eyoung20 journal week 11
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Contents
- 1 Purpose
- 2 Team and Journal Information
- 3 Definitions of terms
- 4 Outline
- 5 =Method
- 5.1 How did they treat the yeast cells (what experiment were they doing?)
- 5.2 What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
- 5.3 What media did they grow them in? What temperature? What type of incubator? For how long?
- 5.4 What controls did they use?
- 5.5 How many replicates did they perform per treatment or timepoint?
- 5.6 What method did they use to prepare the RNA, label it and hybridize it to the microarray?
- 5.7 What mathematical/statistical method did they use to analyze the data?
- 5.8 Are the data publicly available for download? From which web site?
- 5.9 Results
- 5.10 Colclusions
- 5.10.1 How does this work compare with previous studies?
- 5.10.2 What are the important implications of this work?
- 5.10.3 What future directions should the authors take?
- 5.10.4 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?
- 6 Annotated Bibliography
- 7 Conclusion
- 8 Acknowledgements
- 9 References
Purpose
Team and Journal Information
- Team 1: Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
- Project Manager: Mike
- Quality Assurance: Iliana
- Data Analysis: Emma, Kaitlyn
- Coder: Mike
Definitions of terms
- 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). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
- Online Biological Dictionaries
Outline
- Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). 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. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
Introduction
What is the main result presented in this paper?
- The main result of this paper is the genes are activated when the cells are exposed to the pesticide Thiuram determined using DNA microarray screening.
What is the importance or significance of this work?
- This work is important due to the fact that it sets the ground work for further studies on Thiuram. The pesticide Thiuram is a fungicide that meany studies say is toxic and mutagenic. However there is little known on the mechanisms of the toxicity or mutagenicity. This study sets up the ground work for doing research in how thiuram interacts to create this toxicity and mutagenicity. By finding the genes that are effected by thiuram, it creates a list of genes to research and map. Then hopefully by networking and mapping these genes answers on how thiuram is toxic and mutagenic can be found.
- The genes they screen can also be biological indicators to detect pollutants like thiuram and many others.
What were the limitations in previous studies that led them to perform this work?
- previous studied were limited by technology and were unable to look at the entire genome in one single experiment. This slide with 6000 open reading frames allows for the entire cells function to be analyzed .
=Method
How did they treat the yeast cells (what experiment were they doing?)
What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
- Saccharomyces cerevisiae S288C (alpha SUC2 mal mel gal2 CUP1) was the indicator strain.
- It is not stated in the article if the stain was haploid to diploid
What media did they grow them in? What temperature? What type of incubator? For how long?
- They used YPD medium made of (2% polypeptone, 1% yeast extract, 2% glucose)
- Temperature was 25 °C
- Type of incubator was Biomek 2000 Laboratory Automation Workstation (Beck- man Coulter, Inc., Fullerton, CA)
- Incubated for 24 hours
What controls did they use?
- The control was a yeast genome collected from cells grown in the same medium as the others that had no thiuram or anything else added to the medium.
How many replicates did they perform per treatment or timepoint?
- It is not clarified in the paper how many replicated were preformed per time point. The results were collected at time points of 15, 30, and 120 minutes.
What method did they use to prepare the RNA, label it and hybridize it to the microarray?
- The RNA was extracted with the hot phenol method, then cDNA was synthesized from the RNA.
- the cDNA was then linke with a fluorescent label.
- The cDNA of the control was labeled differnently then the cDNA of the thiuram treated cDNA. The control was labeled with Cy3 while the treatment samples were labeled with Cy5.
- The hybridization solution 20× SSC and 2 μL of 10% SDS was added to the cDNA, so it would hybridize to the microarray.
What mathematical/statistical method did they use to analyze the data?
Are the data publicly available for download? From which web site?
Results
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?
How were the measurements made?
What trends are shown by the plots and what conclusions can you draw from the data?
Colclusions
How does this work compare with previous studies?
What are the important implications of this work?
What future directions should the authors take?
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?
Annotated Bibliography
Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the structures of agricultural fungicides to gene expression in Saccharomyces cerevisiae upon exposure to toxic doses. Environmental science & technology, 37(12), 2788-2793 DOI:10.1021/es026156b
- PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/12854720
- PubMed Central: N/A
- Publisher Full Text (HTML): https://pubs.acs.org/doi/10.1021/es026156b
- Publisher Full Text (PDF): https://pubs.acs.org/doi/pdf/10.1021/es026156b
- Copyright: copyright © 2003, American Chemical Society
- Publisher: American Chemical Society
- Availability:
- Did LMU pay a fee for this article:
APA + DOI number
- PubMed Abstract:
- PubMed Central:
- Publisher Full Text (HTML):
- Publisher Full Text (PDF):
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