Troque Week 10

Bibliography

Basic search:

• PubMed
  • Original keywords: "shigella flexneri": 4832 results
  • Keyword combinations: "shigella flexneri genome": 5 results, "shigella flexneri 2a": 609 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": 7408 results
  • Keyword combinations: "shigella flexneri genome": 42, "shigella flexneri genome sequence": 33, "shigella flexneri complete genome sequence": 4 results
  • Comments: I was able to bring the search results down to just 4 articles and these all seem relevant to what we are looking for.

Advanced search:

• PubMed

• 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 worked best for me would have to be switching the option to look for the terms "anywhere in the article" to "in the title of the article". When I used both "Find articles with all of the words" with this, 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.

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. From WoS, we used the Citation Network feature in order to find the articles that were cited in the paper from PubMed. 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.

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

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
• 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.

Bibliography for Microarray Papers

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
• 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.