Difference between revisions of "Eyoung20 journal week 11"
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==Definitions of terms== | ==Definitions of terms== | ||
| − | # Mutagenicity | + | # Mutagenicity:was not on any of the sites. |
| − | # 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. | + | # 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). |
| − | # Salmonella typhimurium :A gram-negative pathogenic bacterium associated in gastroenteritis in humans and other mammals ( | + | # Salmonella typhimurium :A gram-negative pathogenic bacterium associated in gastroenteritis in humans and other mammals(customers 2014). |
| − | # disulfirams | + | # disulfirams:was not on any of the sites. |
| − | # erythrocyte aldehyde dehydrogenase activity | + | # erythrocyte aldehyde dehydrogenase activity: was not on any of the sites. |
| − | + | # sulfhydryl (SH) enzymes: was not on any of the sites. | |
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| − | # sulfhydryl (SH) enzymes | ||
# model eukaryotic cell | # model eukaryotic cell | ||
| − | # alkylating agent: A highly reactive substance that replaces hydrogen by an alkyl group especially in a biologically important molecule (e.g. DNA). | + | # alkylating agent: A highly reactive substance that replaces hydrogen by an alkyl group especially in a biologically important molecule (e.g. DNA)(customers 2014). |
# biomarkers: biomarkers are used to detect the presence of DNA sequence associated with specific diseases, such as by genetic markers. | # biomarkers: biomarkers are used to detect the presence of DNA sequence associated with specific diseases, such as by genetic markers. | ||
| − | # sporulation: (Science: biology) The act or process of forming spores; spore formation. | + | # sporulation: (Science: biology) The act or process of forming spores; spore formation(customers 2014). |
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==Outline== | ==Outline== | ||
Revision as of 01:06, 14 November 2019
Contents
- 1 Purpose
- 2 Team and Journal Information
- 3 Definitions of terms
- 4 Outline
- 4.1 Introduction
- 4.2 Methods
- 4.2.1 How did they treat the yeast cells (what experiment were they doing?)
- 4.2.2 What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
- 4.2.3 What media did they grow them in? What temperature? What type of incubator? For how long?
- 4.2.4 What controls did they use?
- 4.2.5 How many replicates did they perform per treatment or timepoint?
- 4.2.6 What method did they use to prepare the RNA, label it and hybridize it to the microarray?
- 4.2.7 What mathematical/statistical method did they use to analyze the data?
- 4.2.8 Are the data publicly available for download? From which web site?
- 4.3 Results
- 4.4 Conclusions
- 4.4.1 How does this work compare with previous studies?
- 4.4.2 What are the important implications of this work?
- 4.4.3 What future directions should the authors take?
- 4.4.4 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?
- 5 Conclusion
- 6 Documents and files
- 7 Acknowledgements
- 8 References
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
- 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
- Mutagenicity:was not on any of the sites.
- 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).
- Salmonella typhimurium :A gram-negative pathogenic bacterium associated in gastroenteritis in humans and other mammals(customers 2014).
- disulfirams:was not on any of the sites.
- erythrocyte aldehyde dehydrogenase activity: was not on any of the sites.
- sulfhydryl (SH) enzymes: was not on any of the sites.
- model eukaryotic cell
- alkylating agent: A highly reactive substance that replaces hydrogen by an alkyl group especially in a biologically important molecule (e.g. DNA)(customers 2014).
- biomarkers: biomarkers are used to detect the presence of DNA sequence associated with specific diseases, such as by genetic markers.
- 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:
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
Documents and files
Acknowledgements
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.
