Difference between revisions of "Kzebrows Week 10"

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== Individual Journal Assignment ==
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==Electronic Lab Notebook==
  
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* Store this journal entry as "''username'' Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
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Information for this assignment can be found in the [[Week 10 | Week 10 assignment page]].
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* Link from your user page to this Assignment page.
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* Link to your journal entry from your user page.
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* Link back from your journal entry to your user page.
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* Don't forget to add the "Journal Entry" category to the end of your wiki page.
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**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
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* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week.  An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.
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'''Note that each person will complete an individual annotated bibliography.  Information from each team member's bibliography will then be compiled on your team's page.  This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.'''
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Information was further compiled into the group page for the [[Team_4 | Oregon Trail Survivors Week 10]].
  
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=== Annotated Bibliography of Genomics Papers for your Species ===
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===Creating the Annotated Bibliography===
  
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For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.
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In order to create an annotated bibliography of genomics papers for my team's species, ''Shigella flexneri'', I visited the following databases/tools and answered the following questions using keyword searches.
 +
 +
*[http://www.ncbi.nlm.nih.gov/pubmed '''PubMed''']
 +
** What original keyword(s) did you use?  How many results did you get?
 +
***When I searched "''Shigella flexneri''" I got 4,832 results.
 +
** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 +
***I searched "''Shigella flexneri'' genome" and got 664 results. "''Shigella flexneri'' entire genome" gave me 15 results and adding the word "sequence" gave me only 11 results.
 +
*[https://scholar.google.com/ '''Google Scholar''']
 +
** What original keyword(s) did you use?  How many results did you get?
 +
***I searched "''Shigella flexneri'' genome and received 27,800 results.
 +
** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 +
***I then searched "''Shigella flexneri'' whole genome" and got 23,000 results, which is less but definitely not narrowed down enough. I tried "''Shigella flexneri'' entire genome sequence" and got 21,600. I then tried "''Shigella flexneri'' entire genome sequence RNA" and got 15,600 results. I then searched "''Shigella flexneri'' entire genome sequence cy3 and cy5" and got 676 results.
 +
*[https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= '''Web of Science''']
 +
** What original keyword(s) did you use?  How many results did you get?
 +
***I originally just searched "''Shigella flexneri''" and got 24,737 results.
 +
** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 +
***I used "''Shigella flexneri'' entire genome" and got 10 results. I then searched "''Shigella flexneri'' entire genome RNA" and received 1 result.  
  
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* On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
 
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* On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography.  Specifically, you need to search the literature/biological databases for the following:
 
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*# The journal article which describes the results of the whole genome sequencing for your species.  ''(Note that you will be giving a journal club presentation on this article for your [[Week 11]] assignment.)''
 
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*#* Use a keyword search for each of these databases/tools and answer the following: 
 
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*#** '''PubMed'''
 
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*#*** What original keyword(s) did you use?  How many results did you get?
 
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*#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 
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*#** '''Google Scholar'''
 
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*#*** What original keyword(s) did you use?  How many results did you get?
 
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*#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 
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*#** '''Web of Science'''
 
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*#*** What original keyword(s) did you use?  How many results did you get?
 
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*#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 
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*#* Use the advanced search functions for each of these three databases/tools and answer the following: 
 
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*#** '''PubMed'''
 
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
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*#** '''Google Scholar'''
 
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
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*#** '''Web of Science'''
 
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
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*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
 
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*#** The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide])  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).)
 
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*#** The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
 
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*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
 
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*#** The link to the full text of the article (HTML format) from the publisher web site.
 
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*#** The link to the full PDF version of the article from the publisher web site.
 
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*#** Who owns the rights to the article?
 
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*#*** Does the journal own the copyright?
 
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*#*** Do the authors own the copyright?
 
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*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license?
 
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*#*** Is the article available “Open Access”?
 
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*#** 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 [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.]
 
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*#** 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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*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
 
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*#* Give an overview of the results of the search.
 
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*#** How many articles does this article cite?
 
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*#** How many articles cite this article?
 
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*#** Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
 
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*# Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found.  Thus, each team should find 4-8 articles.  If you cannot find a minimum of four articles, please let the instructors know right away.
 
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*#* The experiments must be measuring '''''gene expression''''' aka '''''transcriptional profiling''''' or '''''transcription profiling by array'''''.  Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
 
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*#** A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
 
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*#** The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
 
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*#** The control sample needs to be derived from mRNA and not genomic DNA.
 
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*#** The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
 
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*#* We recommend that you begin by searching for the data, and then by finding the journal article related to the data.  State which database you used to find the data and article.
 
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*#* State what you used as search terms and what type of search terms they were.
 
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*#* Give an overview of the results of the search.
 
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*#** How many results did you get?
 
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*#** Give an assessment of how relevant the results were.
 
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*#* For each article, please provide all of the same information that you provided for the genome article above.
 
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*#* In addition, you must also link to the web site where the microarray data resides.
 
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*#** For each of the microarray articles/datasets, answer the following:
 
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*#**# What experiment was performed?  What was the "treatment" and what was the "control" in the experiment?
 
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*#**# Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
 
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*#** Remember, microarray data is not centrally located on the web.  Some major sources are:
 
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*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
 
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*#**** Click on the link to "Browse ArrayExpress"
 
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*#**** Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
 
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*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
 
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*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
 
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*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
 
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*#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
 
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*#* On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project.  The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.
 
  
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==== Sample Bibliographic Entry ====
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I then used the Advanced search functions for each of the databases/tools and answered the following questions.
 +
*'''PubMed'''
 +
** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 +
***To narrow it down, I went to the Advanced search as Dr. Dahlquist instructed us in class and searched "''Shigella flexneri'' genome" by Title/Abstract and received only 5 results.
 +
* '''Google Scholar'''
 +
** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 +
***Without checking the "patents" box I only got 550 results for "''Shigella flexneri'' entire genome sequence cy3 cy5". I then narrowed it down to the last 4 years (since 2011) and got 142 results. If I clicked on "Since 2015" without patents I received only 17 results.
 +
* '''Web of Science'''
 +
** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 +
***I searched "''Shigella flexneri''" as a topic and added "genome" and "RNA" as topics. This gave me 91 results. I added the topic "cy3 cy5" for the dyes and got 2 results.
  
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For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:
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===Overview of Genome Paper===
  
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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
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Dr. Dahlquist was very helpful in this portion of the assignment. First, in PubMed, I went to the [http://www.ncbi.nlm.nih.gov/pubmed/advanced Advanced Search]. Then I entered "''Shigella flexneri'' genome" and filtered by results with those keywords in the Title/Abstract. This gave me 5 results. I clicked on the first one ([https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=23&SID=1FSiDfIe2DsTtPPNrbx&page=1&doc=1 "Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence"]). I copied and pasted this into Web of Science and upon clicking on the article I saw that it had 13 cited references. I visited this reference list I found a paper called [https://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1FSiDfIe2DsTtPPNrbx&search_mode=CitedFullRecord&isickref=WOS:000182501500055 "Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T"] with 73 cited references, dated May 2003. To see if there was an older paper that this paper possibly got its original genome sequence from I visited its reference list. There was a paper dated from 2002 called [https://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1FSiDfIe2DsTtPPNrbx&search_mode=CitedFullRecord&isickref=WOS:000178826700021 "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157"] that looked promising and it was dated October 2002. Our group selected this paper as our genome paper as it was the oldest and most likely to be the basis for research in more recent papers.
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* 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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I then used the genome sequencing article found by the group to perform a prospective search in the ISI Web of Science/Knowledge database.
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* Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
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*Overview of the search:
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* Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
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**How many articles does this article cite? 37
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* 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
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**How many articles cite this article? 303
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* Publisher: American Society for Cell Biology (scientific society)
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**Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
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* Availability: in print and online
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***Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how ''S. flexneri'' has been able to develop resistance to multiple drugs. Furthermore, ''Shigella'' is suspected to have evolved from ''Escherichia coli'' so a lot of research has been done in how and when pathogenic ''Shigella'' split from ''E. coli'' on the evolutionary tree.
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* Did LMU pay a fee for this article: no
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 +
After locating the genome paper, each member of our group found a microarray paper using the database [https://www.ebi.ac.uk/arrayexpress/search.html?query=shigella+flexneri ArrayExpress]. I entered "''Shigella flexneri''" in the search bar and then applied the following filters:
 +
*By organism: ''Shigella flexneri''
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*By experiment type: RNA assay, array assay
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*By array: All arrays
 +
 
 +
This search yielded 7 results, but only 5 had above 3 assays and were considered viable candidates. Our group randomly assigned the data and corresponding papers to a different group member.
 +
 
 +
===Annotated Bibliography===
 +
 
 +
Peng J, Yang J, Jin Q (2011) An Integrated Approach for Finding Overlooked Genes in Shigella. PLoS ONE 6(4): e18509. doi: 10.1371/journal.pone.0018509
 +
*PubMed Abstract: [http://www.ncbi.nlm.nih.gov/pubmed/21483688 Abstract]
 +
*PubMedCentral: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071730/ PMC]
 +
*Publisher Full Text (HTML format): [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018509 HTML]
 +
*Publisher Full Text (PDF): [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0018509&representation=PDF PDF]
 +
*Copyright: 2011 Peng et al. Article is Open Access and the authors own the copyright, not the journal, under a Creative Commons license.
 +
*Publisher: PLOS One
 +
**Is the article available under "Open Access"? Yes
 +
*Availability: online only
 +
*Did LMU pay a fee for this article: no
 +
*Database used to find the data and article: ArrayExpress
 +
*Terms searched: ''Shigella flexneri''
 +
**Filtered by organism: ''Shigella flexneri''
 +
**Filtered by experiment type: RNA assay, array assay
 +
*Search overview
 +
**Results: 7
 +
**Assessment: All of the articles were relevant but not all had enough assays to be able to be used for this assignment. All involved transcription profiling by array but obviously the experiments differed. Expression analysis was used to examine an RNA polymerase inhibitor, comparing wild type to mutant ''Shigella'', and virulence plasmid-cured strains amongst others.
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*Search in Web of Knowledge
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**Number of articles this article cites: 71
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**Number of times this article has been cited: 1
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**What research directions have been taken since this article has been published? The only article that cited this paper involved detecting infectious diarrheal diseases by chemiluminescence imaging.
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**[https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22800/samples/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= Microarray data]
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**What experiment was performed? What was the "treatment" and the "control"?
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***The experiment performed was to identify overlooked small RNAs (sRNAs) and small open reading frames (sORFs) in ''Shigella'' that were overlooked in the initial genome sequences. Microarrays were performed to search for sRNAs as well as RT-PCR and northern blots were used to identify sRNAs and regions for possible sRNAs. 64 sRNAs that were previously confirmed were used as controls. As a treatment, cells were harvested in the lag, log, and stationary phases at 37C in LB medium and then in the log and stationary phases at 37C in LB medium with 0.01% Congo red, a salt.
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**Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? Competitive hybridization was conducted three times for each condition. These were technical replicates because the conditions were different samples (treated differently) measured in different conditions.
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Waddell, C. D., Walter, T. J., Pacheco, S. A., Purdy, G. E., & Runyen-Janecky, L. J. (2014). NtrBC and Nac Contribute to Efficient Shigella flexneri Intracellular Replication. Journal of Bacteriology, 196(14), 2578–2586. http://doi.org/10.1128/JB.01613-14
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*PubMed Abstract: [http://www.ncbi.nlm.nih.gov/pubmed/?term=Shigella+flexneri+ntrBC+and+nac+mutant+expression+analysis Abstract]
 +
*PubMedCentral: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097594/ PMC]
 +
*Publisher Full Text (HTML format): [http://jb.asm.org/content/196/14/2578.long HTML]
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*Publisher Full Text (PDF): [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097594/pdf/zjb2578.pdf PDF]
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*Copyright: 2014 American Society for Microbiology. The ASM is a non-profit organization with numerous publications, some of which are open access and some of which are not.
 +
*Publisher: American Society for Microbiology
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**Is the article available under "Open Access"? It is available open access after 6 months.
 +
*Availability: online and in print
 +
*Did LMU pay a fee for this article: no
 +
*Database used to find the data and article: ArrayExpress
 +
*Terms searched: ''Shigella flexneri''
 +
**Filtered by organism: ''Shigella flexneri''
 +
**Filtered by experiment type: RNA assay, array assay
 +
*Search overview
 +
**Results: 7
 +
**Assessment: All of the articles were relevant but not all had enough assays to be able to be used for this assignment. All involved transcription profiling by array but obviously the experiments differed. Expression analysis was used to examine an RNA polymerase inhibitor, comparing wild type to mutant ''Shigella'', and virulence plasmid-cured strains amongst others.
 +
*Search in Web of Knowledge
 +
**Number of articles this article cites: 70
 +
**Number of times this article has been cited: 0
 +
**What research directions have been taken since this article has been published? This article has not been cited at all. It was published in July 2014 (pretty recently), which may contribute to this.
 +
**[https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-49939/samples/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= Microarray data]
 +
**What experiment was performed? What was the "treatment" and the "control"?
 +
***The experimenters examined 12 two-component regulatory systems in ''Shigella flexneri'' for their abilities to sense changes in environmental conditions and regulate gene expression in response. Virulence was testing by infecting Henle cells with wild type and mutant TCRS. They found four systems required for the formation of plaque in wild-type and microarray analysis was performed to identify which genes were regulated differently by the NtrBC system or by Nac.
 +
***The treatment for this experiment was to create ''Shigella'' TCRS mutants using phages or transduction and to test their effectiveness in invading Henle cells. Assays were then done to compare gene expression in these mutants with wild type ''Shigella'' TCRS. The control for this experiment was DNA-ase treated RNA and assays performed with avirulent strains of ''Shigella''.
 +
**Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? Assays were conducted three times. These were technical replicates because the conditions were different samples.
 +
 
 +
{{Template : Kzebrows}}
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[[Category : Journal Entry]]

Latest revision as of 02:51, 10 November 2015

Electronic Lab Notebook

Information for this assignment can be found in the Week 10 assignment page.

Information was further compiled into the group page for the Oregon Trail Survivors Week 10.

Creating the Annotated Bibliography

In order to create an annotated bibliography of genomics papers for my team's species, Shigella flexneri, I visited the following databases/tools and answered the following questions using keyword searches.

  • PubMed
    • What original keyword(s) did you use? How many results did you get?
      • When I searched "Shigella flexneri" I got 4,832 results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I searched "Shigella flexneri genome" and got 664 results. "Shigella flexneri entire genome" gave me 15 results and adding the word "sequence" gave me only 11 results.
  • Google Scholar
    • What original keyword(s) did you use? How many results did you get?
      • I searched "Shigella flexneri genome and received 27,800 results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I then searched "Shigella flexneri whole genome" and got 23,000 results, which is less but definitely not narrowed down enough. I tried "Shigella flexneri entire genome sequence" and got 21,600. I then tried "Shigella flexneri entire genome sequence RNA" and got 15,600 results. I then searched "Shigella flexneri entire genome sequence cy3 and cy5" and got 676 results.
  • Web of Science
    • What original keyword(s) did you use? How many results did you get?
      • I originally just searched "Shigella flexneri" and got 24,737 results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I used "Shigella flexneri entire genome" and got 10 results. I then searched "Shigella flexneri entire genome RNA" and received 1 result.


I then used the Advanced search functions for each of the databases/tools and answered the following questions.

  • PubMed
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • To narrow it down, I went to the Advanced search as Dr. Dahlquist instructed us in class and searched "Shigella flexneri genome" by Title/Abstract and received only 5 results.
  • Google Scholar
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • Without checking the "patents" box I only got 550 results for "Shigella flexneri entire genome sequence cy3 cy5". I then narrowed it down to the last 4 years (since 2011) and got 142 results. If I clicked on "Since 2015" without patents I received only 17 results.
  • Web of Science
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • I searched "Shigella flexneri" as a topic and added "genome" and "RNA" as topics. This gave me 91 results. I added the topic "cy3 cy5" for the dyes and got 2 results.

Overview of Genome Paper

Dr. Dahlquist was very helpful in this portion of the assignment. First, in PubMed, I went to the Advanced Search. Then I entered "Shigella flexneri genome" and filtered by results with those keywords in the Title/Abstract. This gave me 5 results. I clicked on the first one ("Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence"). I copied and pasted this into Web of Science and upon clicking on the article I saw that it had 13 cited references. I visited this reference list I found a paper called "Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T" with 73 cited references, dated May 2003. To see if there was an older paper that this paper possibly got its original genome sequence from I visited its reference list. There was a paper dated from 2002 called "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157" that looked promising and it was dated October 2002. Our group selected this paper as our genome paper as it was the oldest and most likely to be the basis for research in more recent papers.

I then used the genome sequencing article found by the group to perform a prospective search in the ISI Web of Science/Knowledge database.

  • Overview of the search:
    • How many articles does this article cite? 37
    • How many articles cite this article? 303
    • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
      • Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how S. flexneri has been able to develop resistance to multiple drugs. Furthermore, Shigella is suspected to have evolved from Escherichia coli so a lot of research has been done in how and when pathogenic Shigella split from E. coli on the evolutionary tree.

After locating the genome paper, each member of our group found a microarray paper using the database ArrayExpress. I entered "Shigella flexneri" in the search bar and then applied the following filters:

  • By organism: Shigella flexneri
  • By experiment type: RNA assay, array assay
  • By array: All arrays

This search yielded 7 results, but only 5 had above 3 assays and were considered viable candidates. Our group randomly assigned the data and corresponding papers to a different group member.

Annotated Bibliography

Peng J, Yang J, Jin Q (2011) An Integrated Approach for Finding Overlooked Genes in Shigella. PLoS ONE 6(4): e18509. doi: 10.1371/journal.pone.0018509

  • PubMed Abstract: Abstract
  • PubMedCentral: PMC
  • Publisher Full Text (HTML format): HTML
  • Publisher Full Text (PDF): PDF
  • Copyright: 2011 Peng et al. Article is Open Access and the authors own the copyright, not the journal, under a Creative Commons license.
  • Publisher: PLOS One
    • Is the article available under "Open Access"? Yes
  • Availability: online only
  • Did LMU pay a fee for this article: no
  • Database used to find the data and article: ArrayExpress
  • Terms searched: Shigella flexneri
    • Filtered by organism: Shigella flexneri
    • Filtered by experiment type: RNA assay, array assay
  • Search overview
    • Results: 7
    • Assessment: All of the articles were relevant but not all had enough assays to be able to be used for this assignment. All involved transcription profiling by array but obviously the experiments differed. Expression analysis was used to examine an RNA polymerase inhibitor, comparing wild type to mutant Shigella, and virulence plasmid-cured strains amongst others.
  • Search in Web of Knowledge
    • Number of articles this article cites: 71
    • Number of times this article has been cited: 1
    • What research directions have been taken since this article has been published? The only article that cited this paper involved detecting infectious diarrheal diseases by chemiluminescence imaging.
    • Microarray data
    • What experiment was performed? What was the "treatment" and the "control"?
      • The experiment performed was to identify overlooked small RNAs (sRNAs) and small open reading frames (sORFs) in Shigella that were overlooked in the initial genome sequences. Microarrays were performed to search for sRNAs as well as RT-PCR and northern blots were used to identify sRNAs and regions for possible sRNAs. 64 sRNAs that were previously confirmed were used as controls. As a treatment, cells were harvested in the lag, log, and stationary phases at 37C in LB medium and then in the log and stationary phases at 37C in LB medium with 0.01% Congo red, a salt.
    • Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? Competitive hybridization was conducted three times for each condition. These were technical replicates because the conditions were different samples (treated differently) measured in different conditions.

Waddell, C. D., Walter, T. J., Pacheco, S. A., Purdy, G. E., & Runyen-Janecky, L. J. (2014). NtrBC and Nac Contribute to Efficient Shigella flexneri Intracellular Replication. Journal of Bacteriology, 196(14), 2578–2586. http://doi.org/10.1128/JB.01613-14

  • PubMed Abstract: Abstract
  • PubMedCentral: PMC
  • Publisher Full Text (HTML format): HTML
  • Publisher Full Text (PDF): PDF
  • Copyright: 2014 American Society for Microbiology. The ASM is a non-profit organization with numerous publications, some of which are open access and some of which are not.
  • Publisher: American Society for Microbiology
    • Is the article available under "Open Access"? It is available open access after 6 months.
  • Availability: online and in print
  • Did LMU pay a fee for this article: no
  • Database used to find the data and article: ArrayExpress
  • Terms searched: Shigella flexneri
    • Filtered by organism: Shigella flexneri
    • Filtered by experiment type: RNA assay, array assay
  • Search overview
    • Results: 7
    • Assessment: All of the articles were relevant but not all had enough assays to be able to be used for this assignment. All involved transcription profiling by array but obviously the experiments differed. Expression analysis was used to examine an RNA polymerase inhibitor, comparing wild type to mutant Shigella, and virulence plasmid-cured strains amongst others.
  • Search in Web of Knowledge
    • Number of articles this article cites: 70
    • Number of times this article has been cited: 0
    • What research directions have been taken since this article has been published? This article has not been cited at all. It was published in July 2014 (pretty recently), which may contribute to this.
    • Microarray data
    • What experiment was performed? What was the "treatment" and the "control"?
      • The experimenters examined 12 two-component regulatory systems in Shigella flexneri for their abilities to sense changes in environmental conditions and regulate gene expression in response. Virulence was testing by infecting Henle cells with wild type and mutant TCRS. They found four systems required for the formation of plaque in wild-type and microarray analysis was performed to identify which genes were regulated differently by the NtrBC system or by Nac.
      • The treatment for this experiment was to create Shigella TCRS mutants using phages or transduction and to test their effectiveness in invading Henle cells. Assays were then done to compare gene expression in these mutants with wild type Shigella TCRS. The control for this experiment was DNA-ase treated RNA and assays performed with avirulent strains of Shigella.
    • Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? Assays were conducted three times. These were technical replicates because the conditions were different samples.


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Additional Links

User Page: Kristin Zebrowski
Class Page: BIOL/CMSI 367-01
Team Page: Oregon Trail Survivors
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