Eyoung20 journal week 11

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Contents

Purpose

To review in-depth and critically analyzed the paper the data for the rest of the project is coming from. To create the foundational work for the rest of the project.

Team and Journal Information

  1. 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

  1. Mutagenicity:was not on any of the sites.
  2. Ames test: A test to determine the effects of a chemical on the rate of mutation in bacterial cells, and hence its likely potential for causing cancer in other organisms, including humans. Devised by US biologist Bruce Ames (1928– ), it is widely used in screening chemicals occurring in the environment for possible carcinogenic activity (see xenobiotic). The chemical is applied to plates inoculated with a special mutant strain of bacteria, usually Salmonella typhimurium, that require the amino acid histidine for growth. Cells that mutate back to the wild type are detected by the occurrence of colonies able to synthesize their own histidine and therefore to grow on the medium(Martin et.al .2008).
  3. Salmonella typhimurium :A gram-negative pathogenic bacterium associated in gastroenteritis in humans and other mammals(customers 2014).
  4. disulfirams:was not on any of the sites.
  5. erythrocyte aldehyde dehydrogenase activity: was not on any of the sites.
  6. sulfhydryl (SH) enzymes: was not on any of the sites.
  7. model eukaryotic cell
  8. alkylating agent: A highly reactive substance that replaces hydrogen by an alkyl group especially in a biologically important molecule (e.g. DNA)(customers 2014).
  9. biomarkers: biomarkers are used to detect the presence of DNA sequence associated with specific diseases, such as by genetic markers.
  10. sporulation: (Science: biology) The act or process of forming spores; spore formation(customers 2014).

Outline

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 .

Methods

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?

They used the MIPS database to look at the results but they do not outline what statistical analysis they used on the data.

Are the data publicly available for download? From which web site?

  • As of right now the link for the download of the data has not been found.

Results

Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.

  • Figure 1A
  • Figure 1B
  • Figure 2A
  • Figure 2B
  • Figure 2C
  • Figure 3A
  • Figure 3B
  • Figure 4A
  • Figure 4B
  • Table 1
  • Table 2
  • Table 3
  • Table 4: shows the results of the promoter activity assay.
What do the X and Y axes represent?
  • Figure 1A
  • Figure 1B
  • Figure 2A
  • Figure 2B
  • Figure 2C
  • Figure 3A
  • Figure 3B
  • Figure 4A
  • Figure 4B
  • Table 1
  • Table 2
  • Table 3
  • Table 4: The results are listed by promoter inserted (y) and then the data for each on fluorescent vs. non fluorescent per interaction and then the overall ratio(x)
How were the measurements made?
  • Figure 1A
  • Figure 1B
  • Figure 2A
  • Figure 2B
  • Figure 2C
  • Figure 3A
  • Figure 3B
  • Figure 4A
  • Figure 4B
  • Table 1
  • Table 2
  • Table 3
  • Table 4: The data was measured using relative intensity of the fluorescence.
What trends are shown by the plots and what conclusions can you draw from the data?
  • Figure 1A
  • Figure 1B
  • Figure 2A
  • Figure 2B
  • Figure 2C
  • Figure 3A
  • Figure 3B
  • Figure 4A
  • Figure 4B
  • Table 1
  • Table 2
  • Table 3
  • Table 4:

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

Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.

Use a keyword search for the first three databases/tools and answer the following:

PubMed
  • What original keyword(s) did you use? How many results did you get?
    • pesticide thiuram 737 results
    • Saccharomyces cerevisiae 127,609 results
    • pesticide thiuram Saccharomyces cerevisiae 10 results
  • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
    • pesticide thiuram Saccharomyces cerevisiae 10 results
Google Scholar
  • What original keyword(s) did you use? How many results did you get?
    • pesticide thiuram 4,470 results
    • Saccharomyces cerevisiae 1,190,000
    • pesticide thiuram Saccharomyces cerevisiae 204 results
  • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
    • pesticide thiuram Saccharomyces cerevisiae 204 results
Web of Science
  • What original keyword(s) did you use? How many results did you get?
    • pesticide thiuram 35 results
    • Saccharomyces cerevisiae 151,883 results
    • pesticide thiuram Saccharomyces cerevisiae 3 results
  • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
    • pesticide thiuram Saccharomyces cerevisiae 3 results

Use the advanced search functions for each of these three databases/tools and answer the following:

PubMed
  • Which advanced search functions were most useful to narrow down the search?
    • Didn't use the advanced search functions since the the key words narrowed the results down so much.
  • How many results did you get?
    • The thing was 10 results
Google Scholar
  • Which advanced search functions were most useful to narrow down the search?
    • The advanced function for narrowing down the results for words present in the title was extremely useful.
  • How many results did you get?
    • 1 result
Web of Science
  • Which advanced search functions were most useful to narrow down the search?
    • narrowing it down to articles in english was all that had to be used to narrow down the results.
  • How many results did you get?
    • 3 results
Perform a prospective search on your article in the Web of Science and answer the following:
  • How many articles does this article cite?
    • The first article cites 11 other articles
    • The second article cites 64 there articles
  • How many articles cite this article?
    • 53 articles cite the first article
    • 17 articles cite the second article

Conclusions

How does this work compare with previous studies?

  • this work covers a lot more of the genome than previous studies in a very effective manner.

What are the important implications of this work?

As stated in the indroduction section 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 future directions should the authors take?

  • The authors should create a larger data set and then move onto the next step of seeing how these genes they flagged mapped. Then they can look into what mechanisms the thuiram is using to harm organisms.

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?

  • The authors seemed to have accurately presented the data they collected, however the paper lacks a formal discussion and synopsis of the results. This makes it lack a concrete result of the experiment. A major flaw of this paper is the method is spastic with confusing language and very hard to follow. It would be really hard to replicate this experiment.



Conclusion

The exercise with this journal article allowed use to review and get to know the paper the data for the rest of the project is coming from. It created a familiarity with the research that went into getting this data which helps to understand the overall implications of the work. The in-depth look at the paper also allowed for critique. Overall the paper seems fairly scientifically sound, however there are several aspects that are not the ideal. The method of the research is messy, confusing, and hard to follow. Also overall the paper is very complexly written and the writing could be simplified while remaining scientific.

Documents and files

Group Presentation

Acknowledgements

This section is in acknowledgement to partner Michael Armas, Iliana Crespin, and Kaitlyn Nguyen. I would also like to acknowledge Dr. Dahlquist for introducing and teaching the topic and direction of this assignment.I would like to acknowledge that the methods were taken from week 11 and then adapted to fit the actual lab methods preformed.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Eyoung20 (talk) 00:17, 14 November 2019 (PST)

References

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

Dahlquist, K. (2019, November 13). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11

Customers. “Salmonella Typhimurium.” Biology, 12 May 2014, www.biology-online.org/dictionary/Salmonella_typhimurium.

Martin, E., & Hine, R. (2008). Ames test. In A Dictionary of Biology. : Oxford University Press. Retrieved 14 Nov. 2019, from https://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625-e-180.

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week 3 ASP1/YDR321W Week 3 Class Journal Week 3
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