Difference between revisions of "Eyoung20 journal week 11"

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== Individual Journal Assignment ==
+
==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.
  
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* Store this journal entry as "''username'' Week 11" (i.e., this is the text to place between the square brackets when you link to this page).
+
==Team and Journal Information==
−
* Invoke your template on your journal entry page so that you:
 
−
** Link from your journal entry page to this Assignment page.
 
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** Link from your journal entry to your user page.
 
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** Add the "Journal Entry" category to the end of your wiki page.
 
−
* Because you have invoked your template on your user page, you should also have a:
 
−
** Link from your user page to this Assignment page.
 
−
** Link to your journal entry from your user page.
 
−
* '''''Note that this week, we will add two new categories, "Group Projects" and a category for your team's name.'''  Please do not add these to your individual templates because we want these categories to be precisely used for the Group Projects and your team, respectively.''
 
−
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
 
−
* The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, Outline of your journal article, Annotated Bibliography, Conclusion, Acknowledgments, and References (as specified by the [[Week_1 | Week 1]] assignment).
 
−
** All files generated in the protocol must be uploaded to the wiki and linked to from your journal entry page in a "Data and Files" section.
 
−
** You will write a summary paragraph that gives the conclusions from this week's analysis.
 
−
 
 
−
=== Team Membership ===
 
−
 
 
−
The project groups and roles are are:
 
 
# 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
 
# 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
 
#* Project Manager: Mike
Line 23: Line 8:
 
#* Data Analysis: Emma, Kaitlyn
 
#* Data Analysis: Emma, Kaitlyn
 
#* Coder: Mike
 
#* Coder: Mike
−
# Arseknights: Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006
+
==Definitions of terms==
−
#* Project Manager: Naomi
+
# Mutagenicity:was not on any of the sites.  
−
#* Quality Assurance: Naomi, Joey
+
# 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).
−
#* Data Analysis: Marcus, Ivy
+
# Salmonella typhimurium :A gram-negative pathogenic bacterium associated in gastroenteritis in humans and other mammals(customers 2014).
−
#* Designer: DeLisa
+
# disulfirams:was not on any of the sites. 
−
# Team 3: Barreto, L., Canadell, D., Valverde‐Saubí, D., Casamayor, A., & Ariño, J. (2012). The short‐term response of yeast to potassium starvation. Environmental microbiology, 14(11), 3026-3042. DOI: 10.1111/j.1462-2920.2012.02887.x
+
# erythrocyte aldehyde dehydrogenase activity: was not on any of the sites.
−
#* Project Manager: TBA
+
# sulfhydryl (SH) enzymes: was not on any of the sites.
−
#* Quality Assurance: Christina, Jonar
+
# model eukaryotic cell
−
#* Data Analysis: David, Aby
+
# alkylating agent: A highly reactive substance that replaces hydrogen by an alkyl group especially in a biologically important molecule (e.g. DNA)(customers 2014).
−
#* Coder: Mihir
+
# 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
  
−
==== Presentation Prep: Individual Journal Pages ====
+
====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
  
−
In preparation for your journal club presentation, you will each '''''individually''''' complete the following assignment on your individual journal page.
+
====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.
  
−
# 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.
+
====How many replicates did they perform per treatment or timepoint?====
−
#* Online Biological Dictionaries
+
* 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.
−
#** Web sites
 
−
#*** [http://www.biology-online.org/dictionary/Main_Page biology-online.org dictionary]
 
−
#*** [http://www.geneontology.org Gene Ontology]
 
−
#*** [http://www.cancer.gov/dictionary/ NCI Dictionary of Cancer Terms]
 
−
#** eBooks
 
−
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170 Oxford Dictionary of Biochemistry and Molecular Biology eBook]
 
−
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199204625.001.0001/acref-9780199204625 Dictionary of Biology Oxford Reference eBook]
 
−
#*** [http://site.ebrary.com/lib/loyolamarymount/detail.action?docID=10188656 Dictionary of Cell and Molecular Biology eBook]
 
−
#*** [http://www.oxfordreference.com/view/10.1093/acref/9780199766444.001.0001/acref-9780199766444 Dictionary of Genetics Oxford Reference eBook]
 
−
# 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.
 
−
## What is the main result presented in this paper?
 
−
## What is the importance or significance of this work?
 
−
## What were the limitations in previous studies that led them to perform this work?
 
−
## 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?
 
−
## 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 treatment or timepoint?
 
−
## What method did they use to prepare the RNA, label it and hybridize it 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?
 
−
##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?
 
−
## 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?
 
  
−
===== How to Read a Primary Research Article =====
+
====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.
  
−
A primary research article is divided into sections that each have a different purpose.  Articles in ''Science'' and ''Nature'' are written in a single narrative format and do not explicitly have these headers.  However, the information for each of these sections is still there. 
+
====What mathematical/statistical method did they use to analyze the data?====
−
<!-- In the future, I should modify this for different types of articles; hypothesis-driven original research, discovery-based original research, methods/tool article, review. --KD -->
+
They used the MIPS database to look at the results but they do not outline what statistical analysis they used on the data.
  
−
====== Abstract ======
+
====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.
  
−
The abstract provides a brief summary of the paper. It states the significance and background, methods, major results, and conclusions from the paper. Different journals have different word limits for the abstract. The abstract is indexed on [http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed PubMed] and may be the only part of the text publicly available.
+
===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
 +
* 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: online 
 +
* Did LMU pay a fee for this article: Yes
  
−
====== Introduction ======
+
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.
 +
* PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Allicin-induced+global+gene+expression+profile+of+Saccharomyces+cerevisiae
 +
* PubMed Central: N/A
 +
* Publisher Full Text (HTML): https://idp.springer.com/authorize/casa?redirect_uri=https://link.springer.com/article/10.1007/s00253-010-2709-x&casa_token=SfdWs-dtgecAAAAA:K4K36vTMMaZUiCVFiN65kVzjjVYthNh5-HbuCdHtlRBZOAdjicci5Rx6J6P4ZkOoZ4i0VUewUMTdZ5t-b0w
 +
* Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00253-010-2709-x.pdf
 +
* Copyright: Springer-Verlag 2010
 +
* Publisher:  Springer
 +
* Availability: online and in article 
 +
* Did LMU pay a fee for this article: Yes
  
−
The introduction gives the background information necessary to understand the paper.
+
====Use a keyword search for the first three databases/tools and answer the following:====
−
The introduction should be in the form of a logical argument that “funnels” from broad to narrow:
+
=====PubMed=====
−
[[Image:Funnel.jpg|right]]
+
*What original keyword(s) did you use? How many results did you get?
−
* States importance of the problem
+
** pesticide thiuram 737 results
−
* States what is known about the problem
+
** Saccharomyces cerevisiae 127,609 results
−
* States what is unknown about the problem
+
** pesticide thiuram Saccharomyces cerevisiae 10 results
−
* States clues that suggest how to approach the unknown
+
*Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
−
* States the question the paper is trying to address
+
** pesticide thiuram Saccharomyces cerevisiae 10 results
−
* States the experimental approach
 
−
* Sometimes briefly states the answer they found
 
  
−
====== Materials and Methods======
+
=====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
  
−
Describes the experiments used in the paper with enough detail so that another investigator could reproduce the experiments.  However, it is usually written in a "shorthand" style that relies heavily on references to previous literature.  Articles in ''Science'' and ''Nature'' severely restrict the amount of methods that can be included in the paper.  In those articles, the information is embedded in the figure legends or references or is available as supplemental online material.
+
=====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
  
−
====== 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
  
−
Describes the experiments performed and the results of the experiments.  The text can take the form of question, experiment, results from that experiment, repeated several times. Each main experiment should be represented by a figure or table of results.  Some people read papers by looking at the figures and reading the legends, then going back to the text for details.
+
=====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
  
−
====== Discussion ======
+
=====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
  
−
States the answer to the question the paper is trying to address.  It explains and defends the answer, if necessary.  It puts the results in a broader perspective by comparing with previous results or models.  The implications of the results are discussed and the next steps for future research are suggested.
+
=====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
  
−
====== References ======
+
===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.
  
−
List of references cited in the main text of the paper. Different journals have different styles of references, but all the essential information should be there, authors, year of publication, journal name, volume, and page numbers. The title of the article is sometimes omitted. This list is a useful resource to look for further reading on the subject of the paper.
+
====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.
  
−
====== Caveat Emptor ======
+
==== 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.
  
−
Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent).  The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.
+
====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.
  
−
==== Journal Club Presentation ====
 
  
−
Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, November 14.
 
−
* Please follow the [http://brightspace.lmu.edu Presentation Guidelines PowerPoint on Brightspace] for how to format your slides.
 
−
* You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
 
−
* You need to present the information in the outline of your journal article listed above, but organized as a presentation.
 
−
* ''Your PowerPoint slides must be uploaded to the wiki and linked to from your '''individual''' journal page '''and''' your '''team''' page by 12:01am on Thursday, November 14'''''
 
−
** You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
 
−
* Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the [[Presentation Rubric]].
 
−
* Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
 
−
*# What is the speaker's take-home message (one short sentence)?
 
−
*# What is the best thing about this presentation?
 
−
*# What needs improvement?
 
−
*# Please comment on the speaking style (language and delivery) of each presenter.
 
−
* Although you may be working with different partners on this presentation than before, we expect that you will take the feedback from your previous presentation into account when doing this one.
 
  
−
=== Annotated Bibliography ===
 
  
−
This exercise will be primarily performed in class on Tuesday, November 12.  The purpose of this exercise is to annotate a bibliography of papers related to your assigned paper, that report microarray data from yeast subjected to a timecourse treatment. You will also use these articles to write the Introduction and Discussion sections of your final group report. You will complete the bibliography on your individual journal entry, and summarize it on your team's page.
+
==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.
  
−
'''Resource:''' [http://libguides.lmu.edu/BIOL367 BIOL/CMSI 367 LibGuide]
+
==Documents and files==
 +
[[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
 +
==Acknowledgements==
 +
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|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.
  
−
# Create a bibliography of a minimum of 8-10 citations to primary research articles related to your assigned article (2 per group member). 
+
"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
−
#* Each of the 8-10 references in your bibliography needs to have the following information (an example is given in the section below):
+
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 00:17, 14 November 2019 (PST)
−
#** The complete bibliographic reference in the APA style (see [https://owl.purdue.edu/owl/research_and_citation/apa_style/apa_formatting_and_style_guide/reference_list_basic_rules.html this link]).  You will be using one of three formats, journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
 
−
#** The link to the abstract from PubMed.
 
−
#** The link to the full text of the article in PubMedCentral.
 
−
#** The link to the full text of the article (HTML format) from the publisher web site.
 
−
#** The link to the full PDF version of the article from the publisher web site.
 
−
#** Who owns the rights to the article and what is the availability?
 
−
#*** Does the journal or the authors own the copyright?
 
−
#*** Is the article available “Open Access” upon publication under a Creative Commons license?
 
−
#*** If the article is not Open Access, is it available for free after a certain period of time has elapsed?
 
−
#** What organization is the publisher of the article? 
 
−
#*** What type of organization is it?  (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization; see http://oaspa.org/membership/members/ for a list of members of the Open Access Scholarly Publishers Association)
 
−
#** Is this article available in print or online only?
 
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#*** Has LMU paid a subscription or other fee for your access to this article?
 
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#** Are the data associated with this article available?  If so, provide a link to the dataset.
 
−
# You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
 
−
#* 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?
 
−
#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 
−
#** Google Scholar
 
−
#*** What original keyword(s) did you use?  How many results did you get?
 
−
#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 
−
#** Web of Science
 
−
#*** What original keyword(s) did you use?  How many results did you get?
 
−
#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 
−
#* 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?  How many results did you get?
 
−
#** Google Scholar
 
−
#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
−
#** Web of Science
 
−
#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
−
#** Perform a prospective search on the following three review articles in Web of Science and answer the following:
 
−
#*** Aguilera, J., Randez-Gil, F., & Prieto, J.A. (2007).  Cold Response in Saccharomyces cerevisiae:  New Functions for Old Mechanisms.  FEMS Microbiological Reviews,  31, 327–341.  doi: 10.1111/j.1574-6976.2007.00066.x
 
−
#**** How many articles does this article cite?
 
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#**** How many articles cite this article?
 
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#*** Al-Fageeh, M.B. & Smales, C.M. (2006).  Control and Regulation of the Cellular Responses to Cold Shock:  the Responses in Yeast and Mammalian Systems.  Biochemical Journal, 397, 247–259.  doi: 10.1042/BJ20060166
 
−
#**** How many articles does this article cite?
 
−
#**** How many articles cite this article?
 
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#*** Thieringer, H.A., Jones, P.G.,& Inouye, M. (1998).  Cold shock and adaptation.  BioEssays, 20, 49–57.  doi: 10.1002/(SICI)1521-1878(199801)20:1<49::AID-BIES8>3.0.CO;2-N
 
−
#**** How many articles does this article cite?
 
−
#**** How many articles cite this article?
 
  
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==== Sample Bibliographic Entry ====
+
==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
  
−
For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:
+
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
  
−
Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast.  ''Molecular Biology of the Cell'', 15, 5492-5502. doi:  10.1091/mbc.E04-03-0167
+
Customers. “Salmonella Typhimurium.” Biology, 12 May 2014, www.biology-online.org/dictionary/Salmonella_typhimurium.
−
* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/15483057
 
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* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
 
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* Publisher Full Text (HTML):  http://www.molbiolcell.org/content/15/12/5492.long
 
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* Publisher Full Text (PDF):  http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
 
−
* Copyright:  2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
 
−
* Publisher:  American Society for Cell Biology (scientific society)
 
−
* Availability:  in print and online
 
−
* Did LMU pay a fee for this article: no
 
  
 +
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.
  
 
{{Template:eyoung20}}
 
{{Template:eyoung20}}

Latest revision as of 23:05, 18 November 2019

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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