Rlegaspi Week 10

Shewanella oneidensis

Our Gene Database Testing Report

Group Paper - File:Final Report 20151218 2 HMH.docx

Group Members

• Coder: Mary Alverson
• GenMAPP User & Project Manager: Ron Legaspi
• Quality Assurance: Josh Kuroda
• GenMAPP User: Emily Simso

Important Links

Our Deliverables

Gene Database Project Links
Overview	Deliverables	Reference Format	Guilds	Project Manager	GenMAPP User	Quality Assurance	Coder
			Teams	Heavy Metal HaterZ	The Class Whoopers	GÉNialOMICS	Oregon Trail Survivors

Individual Journal Entries
Mary Alverson	Week 11	Week 12	Week 14	Week 15
Emily Simso	Week 11	Week 12	Week 14	Week 15
Ron Legaspi	Week 11	Week 12	Week 14	Week 15
Josh Kuroda	Week 11	Week 12	Week 14	Week 15

Annotated Bibliography for Heavy Metal HaterZ species Shewanella oneidensis

Electronic Lab Notebook

• 1. Genome Paper Search
     • Used a keyword search for each of these databases/tools and answer the following:
       • PubMed
         • What original keyword(s) did I use? How many results did I get?
           • Original keywords used were "Shewanella oneidensis genome sequence"; number of results found was 128.
         • Which terms in which combinations were most useful to narrow down the search? How many results did I get after narrowing the search?
           • After original keyword search, (shewanella oneidensis[Title]) AND genome sequence was used to narrow down the search and the results were narrowed down to 74.
       • Google Scholar
         • What original keyword(s) did I use? How many results did I get?
           • Original keywords used were "Shewanella oneidensis genome sequence"; number of results found was 7,470.
         • Which terms in which combinations were most useful to narrow down the search? How many results did I get after narrowing the search?
           • After original keyword search, allintitle: genome OR sequence "Shewanella oneidensis" was used to narrow down the search and the results were narrowed down to 25.
       • Web of Science
         • What original keyword(s) did I use? How many results did I get?
           • Original keywords used were "Shewanella oneidensis genome sequence"; number of results found was 144.
         • Which terms in which combinations were most useful to narrow down the search? How many results did I get after narrowing the search?
           • After original keyword search, TITLE: (shewanella oneidensis) AND TOPIC: (shewanella oneidensis genome sequence) AND YEAR PUBLISHED: (2000-2015) was used to narrow down the search to 40.
     • Use the advanced search functions for each of these three databases/tools and answer the following:
       • PubMed
         • Which advanced search functions were most useful to narrow down the search? How many results did I get?
           • On PubMed, I used the advanced search function of [Title] to ensure that Shewanella oneidensis was in the title of the article; thus, the articles were a primary focus to the article. In addition, I limited the search to the last 5 years and the results were narrowed down to 29.
       • Google Scholar
         • Which advanced search functions were most useful to narrow down the search? How many results did I get?
           • The advanced search functions used were searching terms in the title where Shewanella oneidensis had to be in the title, whereas, the terms "genome" and "sequence" were optional terms within the title. In addition, having the result range be between the years 2000 to 2015 narrowed the results down to 16.
       • Web of Science
         • Which advanced search functions were most useful to narrow down the search? How many results did I get?
           • The advanced search functions used were searching the species name within the title of articles, the topic of "genome sequence" was covered, in addition to limiting the search to articles published within the last 15 years and articles covering Microbiology; the advanced search led to the limiting of search results down to 22.
  2. Microarray Paper Search
     • Microarray data is not centrally located on the web.
       • To find microarray data for Shewanella oneidensis, I used EBI ArrayExpress (recommended)
         • Clicked on the link to "Browse ArrayExpress"
         • Use the drop down "Filter Search Results" to filter datasets by my organism, by "RNA assay" and "Array assay" to narrow my search.
  3. On my team wiki page, my team compiled the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for our project. The instructors will have reviewed our results to make sure that the data are suitable for the project before we move forward with the analysis.

Ron's Annotated Bibliography

Genome Paper

Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, 20(11), 1118-1123. doi:10.1038/nbt749

• The abstract from PubMed.
• The full text of the article in PubMedCentral : Not available.
• The full text of the article from the publisher web site. (The HTML version was not available.)
• The full PDF version of the article from the publisher web site.
• Who owns the rights to the article?
  • The Nature Publishing Group, which is the publisher of this article, according to this site.
• Do the authors own the rights under a Creative Commons license?
  • Yes, according to this site.
• Is the article available “Open Access”?
  • According to this site, the article is available "Open Access".
• What organization is the publisher of the article? What type of organization is it?
  • According to the site above, this publisher is a "Professional OA Publisher (Large)".
• Is this article available in print or online only?
  • Online only. It was published online in November, 2002.
• Has LMU paid a subscription or other fee for your access to this article?
  • No.
• We performed a search in the ISI Web of Science/Knowledge database by typing in the title "Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis" to the search bar.
  • Three articles came up as results. The first two articles title's did not exactly match, and were cited under 15 times each. The third article was the article we were searching for.
• How many articles does this article cite?
  • This article has 41 cited references within the Web of Science Core Collection, according to this site.
• How many articles cite this article?
  • It has been cited 1079 times in all databases, and 426 within the Web of Science Core Collection, according to this site.
• 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?
  • Examples of titles that reference the genome paper:
    • Environmental genome shotgun sequencing of the Sargasso Sea
    • Deciphering the evolution and metabolism of an anammox bacterium from a community genome
    • Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments
    • More can be found by clicking this link.
  • These papers include studying within in the species, finding out the genomes of other species, as well as the metabolic versatility of microorganisms and metal ion reduction in environments. This shows that a sequenced genome can aide in experiments of many kinds.

Microarray Paper: E-GEOD-15657: Charania et. al (2009)

Charania, M. A., Brockman, K. L., Zhang, Y., Banerjee, A., Pinchuk, G. E., Fredrickson, J. K., Beliaev, A.S., Saffarini, D. A. (2009). Involvement of a Membrane-Bound Class III Adenylate Cyclase in Regulation of Anaerobic Respiration in Shewanella oneidensis MR-1 . Journal of Bacteriology, 191(13), 4298–4306. http://doi.org/10.1128/JB.01829-08

• Link to abstract on PubMed
• Link to full text of article on PMC
• Link to Full Text from publisher.
• Link to PDF Version from publisher.
• The American Society for Microbiology owns the copyright. The article is not open-access.
• The publisher is the American Society for Microbiology. It is a scientific society.
• This article is available in the printed and on-line journals.
• LMU has not paid for my access.
• This article has 39 citations.
• According to the Web of Science, this article is cited by 29 other articles.
• Looking at the titles of the other articles/abstracts, it seems like most research has been focused on catabolic and regulatory pathways of Shewanella oneidensis, along with the two-component system that regulates nitrogen (nitrite and nitrate) respiration.
• Link to Raw microarray data
• Link to Processed microarray data
• The experiment looked to find more information about the cyclic AMP receptor protein (CRP) within the membranes of Shewanella oneidensis that regulates the respiration of fumarate, dimethyl sulfoxide (DMSO), or Fe(III); thus, manipulation of the particular genes were done in order to observe how gene deletions would affect the anaerobic respiration.
• A total of six expression profiles of Shewanella oneidensis samples (wild-type and mutant strains); 2 wild-type, 2 CRP deletion mutants, cyaC deletion mutants.
• Datasets can be found at this link.