Bklein7 Week 10

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Researching Bordetella pertussis Genomics Papers in the Public Domain

Important Links:

Searching the Literature for a Genome Sequence Paper for Bordetella pertussis

Conducting Keyword Searches Using PubMed, Google Scholar, and the Web of Science.

  • PubMed
    • Original Keyword Search: Bordetella pertussis genome
      • Results: 757
    • Narrowing the Search
      • Added the keyword sequence
        • Search: Bordetella pertussis genome sequence; Results: 530
        • This addition was moderately helpful in narrowing the search results.
      • Added the keyword complete and sequence
        • Search: Bordetella pertussis complete genome sequence; Results: 36
        • This addition was very helpful in significantly narrowing the search results (much more so than the addition of just the keyword sequence).
        • The list of papers retrieved using this search was easy to manually review.
        • 5 Bordetella pertussis genome sequence papers were retrieved in the list of 36 results.
  • Google Scholar
    • Original Keyword Search: Bordetella pertussis genome
      • Results: 22,500
      • The number of results retrieved by Google Scholar was significantly larger than the number of results retrieved by PubMed for the same search, indicating the wider scope of Google Scholar searches.
    • Narrowing the Search
      • Added the keyword sequence
        • Search: Bordetella pertussis genome sequence; Results: 20,500
        • This adjustment to the search was not very helpful.
      • Added the keyword complete and sequence
        • Search: Bordetella pertussis complete genome sequence; Results: 17,700 results
        • This adjust to the search was also only somewhat helpful in narrowing down the results (like in PubMed, this keyword was a more helpful addition than sequence).
        • Most of the top search results included genome sequences for bacteria other then Bordetella pertussis, indicating the need for advanced search functions and filters to sort through this data.
          • Although Google Scholar casts a wide net, this is sometimes not useful, as it brings up junk results.
  • Web of Science
    • Original Keyword Search: Bordetella pertussis genome
      • Results: 415
      • Evidently, the Web of Science appears to be the smallest of the three databases in which I have been searching.
    • Narrowing the Search
      • Added the keyword sequence
        • Search: Bordetella pertussis genome sequence; Results: 285
        • This adjustment to the search was helpful in narrowing the search.
      • Added the keyword complete and sequence
        • Search: Bordetella pertussis complete genome sequence; Results: 50
        • As in the other databases, the keyword complete was a more helpful keyword in narrowing results than sequence.
        • The results from this search were able to be manually reviewed.
        • 7 Bordetella pertussis genome sequence papers were retrieved out of the 50 retrieved results.
          • Note: These 7 papers all occurred at the very end of the results list and were therefore were not the easiest to find. I think it would be more intuitive for these results to have been presented first, although there are filters I could play with to make this happen. It is just surprising to me that the default filter doesn't appear to be one based on relevance.

Conducting Advanced Searches Using PubMed, Google Scholar, and the Web of Science.

  • PubMed
    • I began with the original keyword search conducted on PubMed: Bordetella pertussis genome (Results: 757)
      • Originally, changing keywords narrowed the search down to 36 results.
    • This search was successfully narrowed down further than it had been during any keyword searches using advanced searches.
      • Searching for "Bordetella pertussis genome" only in the Title/Abstract of papers significantly narrowed down the search results
        • Search: Bordetella pertussis genome[Title/Abstract]
        • Results: 7
        • 2 Bordetella pertussis genome sequence papers were retrieved out of the 7 results.
          • I was surprised to find that, although a better ratio of relevant papers was retrieved, not all of the genome papers found in the original keyword searches were retrieved in this fashion.
    • By searching for the best keyword result of "Bordetella pertussis complete genome sequence" using the Title/Abstract advanced search, the most efficient search was conducted.
      • Search: Bordetella pertussis complete genome sequence[Title/Abstract]
      • Results: 9
        • Surprisingly, this more precise advanced search yielded more results, suggesting that keyword order is important to the advanced search algorithm.
        • 4 Bordetella pertussis genome sequence papers were retrieved out of the 9 results.
  • Google Scholar
    • Building off of the success of [Title/Abstract] searches in PubMed, I decided to try the Google Scholar advanced search where all keywords must occur in the title of retrieved articles.
      • Search 1: "allintitle: Bordetella pertussis genome"
        • Results: 40
        • This advanced search successfully narrowed down the Google Scholar search results for this keyword search from 22,500 to 40, a number that is easy to manually assess!
        • 8 Bordetella pertussis genome sequence papers were retrieved out of the 40 results.
      • Search 2: "allintitle: Bordetella pertussis complete genome"
      • Results: 5
        • I chose to add the most useful of the two keyword additions I had been using, complete, to the allintitle advanced search. This resulted in the most narrow search witnessed thus far in my investigation of the literature (5 results). This is particularly interesting because this narrow search occurred in the largest database.
        • 5 Bordetella pertussis genome sequence papers were retrieved out of the 5 results.
        • This 100% accuracy was tied for the best witnessed out of any advanced search.
  • Web of Science
    • As with PubMed and Google Scholar, I found title advanced searches to be the most useful in narrowing my results.
      • Search 1: "TITLE: (Bordetella pertussis genome)"
        • Results: 38
        • This search was better than the most narrow keyword search produced, which yielded 50 search results. However, I felt as though adding additional keywords to the title advanced search would be more effective than manually sorting through 38 records.
      • Search 2: "TITLE: (Bordetella pertussis complete genome)"
        • Results: 5
        • As in Google Scholar, adding the more successful keyword complete significantly narrowed down the search results to just 5 records!
        • 5 Bordetella pertussis genome sequence papers were retrieved out of the 5 results.
        • This 100% accuracy was tied for the best witnessed out of any advanced search.
        • It is impressive that this same result was yielded by the smallest database in addition to the largest database.
      • Note: I found the option to filter papers by the number of times they were cited in the Web of Science to be useful.

Genome Sequencing Article Citation:

Zhang, S., Xu, Y., Zhou, Z., Wang, S., Yang, R., Wang, J., & Wang, L. (2011). Complete Genome Sequence of Bordetella Pertussis CS, a Chinese Pertussis Vaccine Strain. Journal of Bacteriology, 193(15), 4017-4018. doi: 10.1128/JB.05184-11

Genome Sequencing Article Prospective Search:

  • This article cites 16 sources.
  • Since its publication in 2011, this article has been cited by 7 sources.
  • By assessing the titles of the 7 papers that cited this article using the Web of Science, I was able to determine the type of research directions that have been taken using the genome sequence for Bordetella pertussis:
    1. Assessment of proteins secreted by Bordetella pertussis such as Pertussis Toxin, and how genetic mutations effect the functions of these proteins.
    2. Evolution of virulence in pathogenic bacteria.
    3. Creating better vaccines.

Searching the Literature for Microarray Papers involving Bordetella pertussis

Searching directly for Bordetella pertussis microarray data using EBI ArrayExpress.

  • I performed an advanced search for "Bordetella pertussis".
    • Advanced Search Filters
      • Organism: Bordetella pertussis
      • Experiment Type: "Array assay" and "RNA assay"
    • Search Results
      • 13 experiments were retrieved.
        • This number of results of was easy to manually assess.
      • In assessing the result entries in the "Organism" column, I realized that over half of the retrieved experiments included "Bordetella pertussis" as only one of several species.
        • To address this, I filtered the results by Organism. Only 3 of the results pertained to experiments only using "Bordetella pertussis".
      • Overall, the results were moderately helpful. The immediate access to narrow search results was convenient and brought me to 3 data sets that were useful for consideration in our project (right kind of experiment and many arrays). However, the fact that over 75% of the search results included several organisms (particularly when I had specified only "Bordetella pertussis" as the organism to retrieve in the advanced search) was not helpful.
    • Selecting an Article from the Results
      • I chose to seek the original article for one of the three applicable data sets. By typing in the name of the data set in Google Scholar, I instantly was able to find the original paper (it was the first retrieved result). I confirmed that this was the correct paper by checking the authors, abstract, and publication date.
      • The citation for the article I found through EBI ArrayExpress is listed below:

King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150

Article Analysis:

  1. This article linked a recent resurgence of pertussis with an expansion of B. pertussis strains containing a novel allele for the pertussis toxin (ptx) promoter ptxP3 in place of the typical ptxP1 promoter. PtxP3 strains were noted to have better fitness due to higher expression rates of the pertussis toxin. In this experiment, a microarray analysis was conducting comparing several ptxP1 strains to several ptxP3 strains.
    • Treatment Group: PtxP3 strains (n=5)
    • Control Group: PtxP1 strains (n=9)
  2. Three or more biological replicates were conducted for each of the 14 "Bordetella pertussis" strains assessed in this paper, making for a total of 57 unique biological replicates. The data collected for all the replicates within each group was averaged and compared for the final microarray analysis.
    • Replicates, including strain names and the number of biological replicates per strain in parentheses:
      • 1949-B0558 (5)
      • 1967-B1213 (3)
      • 1982-B0689 (4)
      • 1988-B2973 (5)
      • 1995-B0602 (4)
      • 1995-B0607 (4)
      • 1996-B0777 (4)
      • 1999-B1834 (4)
      • 2000-B1878 (4)
      • 2000-B1917 (3)
      • 2007-B3104 (4)
      • 2008-B3183 (5)
      • 2008-B3234 (4)
      • 2008-B3265 (4)

Searching directly for Bordetella pertussis microarray data using NCBI GEO.

  • I performed an advanced search for "Bordetella pertussis".
    • Advanced Search Filters
      • Organism: Bordetella pertussis
      • Study Type: "Expression profiling by array"
    • Search Results
      • 2 experiments were retrieved.
      • Overall these search results were also moderately helpful. Both of the 2 retrieved results appeared to be data sets that I could use for our project. However, the limited number of search results was not ideal. As an aside, I was not a fan of this web sites user interface. The user interface on the ArrayExpress website was far superior.
    • Selecting an Article from the Results
      • I chose to seek the original article for one of the two applicable data sets. The GEO information page for the data set included a citation for the article in which the data was published. This made it very simple to find the original article using Google Scholar.
      • The citation for the article I found through NCBI GEO is listed below:

Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE, 9(12):e115243. doi: 10.1371/journal.pone.0115243

Article Analysis:

  1. This paper identified polysaccharide (PS) capsules as important virulence determinants for bacterial pathogens and and KpsT as a membrane protein involved in the transport of PS polymers across the cellular envelope in Bordetella pertussis. To determine the impact of PS capsules on the virulence of B. pertussis, a microarray experiment was run testing a ∆KpsT mutant against the wild-type.
    • Treatment Group: ∆KpsT Mutant
    • Control Group: Wild-type (BPSM)
  2. Biological replicates: 3 replicates of both the control and treatment groups; Technical replicates: 2 per biological replicate (dye-swapped)
    • Replicate Listings (taken from NCBI GEO):
      • GSM1519507 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 1
      • GSM1519509 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 1 by dye-swap color
      • GSM1519511 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 2
      • GSM1519514 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 2 by dye-swap color
      • GSM1519516 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 3
      • GSM1519519 Strain of Bordetella pertussis deleted of KpsT versus wild-type B. pertussis replicate 3 by dye-swap color

Annotated Bibliography

Genome Sequencing Paper:

Zhang, S., Xu, Y., Zhou, Z., Wang, S., Yang, R., Wang, J., & Wang, L. (2011). Complete Genome Sequence of Bordetella Pertussis CS, a Chinese Pertussis Vaccine Strain. Journal of Bacteriology, 193(15), 4017-4018. doi: 10.1128/JB.05184-11

Microarray Papers:

King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150

Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE, 9(12):e115243. doi: 10.1371/journal.pone.0115243

Links

Assignments Pages

Individual Journal Entries

Shared Journal Entries

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