Kzebrows Week 10

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.