Difference between revisions of "Troque Week 10"

Latest revision as of 22:03, 9 November 2015

Searching through databases

Basic search:

• PubMed
  • Original keywords: "shigella flexneri": 4832 results
  • Keyword combinations: "shigella flexneri genome": 664 results, "shigella flexneri 2a": 609 results, "shigella flexneri complete genome": 46 results
  • Comments: Even though adding more specificity to the strain in question should have resulted in less results, and it did, adding the keyword "genome" actually was the better option in this case since it directed me to more relevant articles.

• Google Scholar
  • Original keywords: "shigella flexneri": 66,100 results
  • Keyword combinations: "shigella flexneri genome": 27,800 results, "shigella flexneri genome sequence": 25,300 results, "shigella flexneri genome sequence": 21,300 results, "shigella flexneri 2a genome sequence article": 18,100 results, "shigella flexneri genome cy3 cy5": 708 results
  • Comments: Since Google tends to have a rather broad database anyway, I didn't expect to get results lower than 1000. Adding the keywords for the name of the dyes used for creating microarrays did help in bringing the results to about 700, but most of the articles still seemed irrelevant to what we actually were looking for.

• Web of science
  • Original keywords: "shigella flexneri": 24,737 results
  • Keyword combinations: "shigella flexneri genome": 590, "shigella flexneri genome sequence": 460, "shigella flexneri complete genome sequence": 144 results
  • Comments: I was surprised that I wasn't able to narrow down my search even when I added the "complete genome sequence" at the end of my original keyword search. Compared to the results I got from PubMed, which was already pretty low after only adding "genome sequence", the results here were still relatively high and difficult to just sift through.

Advanced search:

• PubMed
  • Changing the "All fields" dropdown bar into "Title/Abstract" significantly narrowed down the results. From the basic search, when I typed "shigella flexneri genome", I would get 42. However, when I applied the advanced settings, those results were narrowed into 5, all of which only focused on S. flexneri and its genome. I would have also used the Boolean value options, but I felt that the results were already small enough that using the Booleans would just be insignificant.

• Google Scholar
  • I, at first, used the "Find articles with all of the words" function, but that didn't help as much since the basic search method already uses this function by default so I ended up with the same results. When I used the "Find articles with the exact phrase" with the phrase "shigella flexneri genome", it only showed me 31 results. (Note: these were the results when searching the terms anywhere in the article.
  • What actually worked best for me was actually switching the option to look for the terms "anywhere in the article" to "in the title of the article". This is similar to PubMed's search field option to only look for the terms within the titles instead of the body of the article. When I used both "Find articles with all of the words" with "in the title of the article", I only received 29 results, which was the lowest I've received from Google Scholar.

• Web of science
  • I mainly used the dropdown list next to the search bar (the one that lists "Topic", "Title", etc.) in order to focus my search. That was because I didn't realize that the option to switch into the Advanced search was actually the blue button next to the "Basic Search" term (it would have been easier to notice if they actually put the words "Advanced Search" in the button instead of making it an arrow that is pointed downwards -- for interaction design purposes :P). However, once I figured out where the actual Advanced search field was, it turned out that it functions exactly the same way and yields the same results as when I was doing my "Advanced" searches before (even though the results were presented slightly differently). In any case, I would basically change the "Topic" into "Title" so that I only get hits for the articles that actually focus on the organism in question.

Aside: We figured (with a little help from Dr. Dahlquist) that the best way to find the genome paper was to use the database in conjunction with each other. We actually searched for the phrase "shigella flexneri genome" in PubMed first, then copied and pasted the title of an article that seemed promising into Web of Science, visually/manually sifted through a couple of articles in that database by looking at their titles, and finally looked at the articles that they cited in the Citation Network feature of WoS. As a result, we ended up with 2 potential genome sequence papers once we entered the title of the article we found on PubMed into the Web of Science database. The paper cited 13 other articles so this seemed like a good enough point to sift through the ones with the actual complete genome sequence for our species. As a group, we then talked to each other in order to decide which paper to use as our genome sequence paper and base our microarray papers off of.
After all of these, the genome sequence paper that we ended up deciding was the one titled "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157".

Genome Paper

Bibliography

Jin, Q., et al. (2002). Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.

• PubMed Abstract: Abstract
• PubMed Central: PMC
• Publisher Full Text (HTML): Full Text (HTML)
• Publisher Full Text (PDF): Full Text (PDF)
• Copyright: 2002 Oxford University Press
• Publisher: Oxford University Press
• Availability: in print and online
• Did LMU pay a fee for this article: no

Comments/Answers to questions

• 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 finding our genome paper, we used the database ArrayExpress in order to find datasets related to our organism. In this database, when "Browse" is clicked, the filter option appears. I used this to search "By organism" - Shigella flexneri, and "By experiment type" - RNA assay, Array assay. This search yielded only 7 results. Most of these results were relevant to us, but there were ones that we immediately ignored: the articles that only had 2, 3 or 4 assays. Since the number of assays was too small, the variability and significance of the data in question was suspicious. Ignoring these two articles then left us with a maximum of 4 articles, which was actually the minimum number of articles we needed. These remaining ones seemed relevant enough to what our class is about that we decided to keep them.

Microarray Papers

Bibliography

Morris, Carolyn R, et al. ‘Characterization of Intracellular Growth Regulator IcgR by Utilizing Transcriptomics to Identify Mediators of Pathogenesis in Shigella Flexneri’. Infection and Immunity 81.9 (Sep. 2013): 3068–3076. 6 Nov. 2015.

• PubMed Abstract: Abstract
• PubMed Central: PMC
• Publisher Full Text (HTML): Full Text (HTML)
• Publisher Full Text (PDF): Full Text(PDF)
• Copyright: 2013, American Society for Microbiology. All Rights Reserved.
• Publisher: American Society for Microbiology
• Availability: only online
• Did LMU pay a fee for this article: no
• doi: 10.1128/IAI.00537-13

Comments/Answers to questions

• Link to microarray data: Microarray data
• How many articles does this article cite? 2
• How many articles cite this article? 52
• 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?
  • Since the organism's genome has been sequenced, new research about this specie now tends to focus more on its pathogenesis using bioinformatic methods with in vitro and in vivo microarray data. For example, the article "Analysis of the Proteome of Intracellular Shigella flexneri Reveals Pathways Important for Intracellular Growth" that cites this article analyzes the metabolic pathways that allow the organism to grow.
• What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
  • This experiment involved combining high-throughput bioinformatic methods with in vitro and in vivo assays to provide new insights into pathogenesis. The intracellular growth regulator was deleted in order to observe its effects and compare to the wild type, or the control in the experiment. The "treatment" involved culturing the strains in Luria broth or tryptic soy agar with Congo red (TSA/CR) medium supplemented with the appropriate antibiotics (15 μg/ml chloramphenicol, 50 μg/ml kanamycin, and 100 μg/ml ampicillin) and allowing them to invade colonic epithelial cells for a set period of time.
• Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
  • The experiment had both biological and technical replicates. Since the experiment involved analyzing the pathogenesis of the organism, the researchers tried deleting the gene they believe is involve in intracellular growth, which they called the icgR. In their documentation, they wrote that they compared the results of subjecting the ΔicgR strain (and its complement, ΔicgR(pSECicgR), or ΔicgR mutant transformed with pSECicgR) to certain conditions to the control, the wild type 2457T. In other words, the experiment involved 3 biological strains (namely the wild type, ΔicgR, and ΔicgR complement). 5 technical replicates were then conducted for each different strain, resulting in a grand total of 15 microarrays.

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