Difference between revisions of "Heavy Metal HaterZ"

Revision as of 02:24, 10 November 2015

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 Files

Our Deliverables

Week 10 Assignment : Annotated Bibliography

Individual Biographies

• Mary's Bibliography
• Ron's Bibliography
• Josh's Bibliography
• Emily's Bibliography

Our 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.

Our Microarray Papers

• Datasets can be found at this link.
• The beginning of the headers given to the bibliography entries correspond to the data set results found when clicking the above link.

E-GEOD-15334 - Emily

E-GEOD-21044: Lassak et. al (2010)

Lassak J, Henche AL, Binnenkade L, Thormann KM. (2010). ArcS is the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1. Applied and Environmental Microbiology, 76(10), 3263-3274.

• • PubMed
  • PMC
  • Full Text
  • PDF Version
  • 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 76 citations.
  • According to the Web of Science, this article is cited by 35 other articles.
  • Looking at the titles of the other articles, it seems like most research has been focused on a two-component system present in shewanella oneidensis as well as anaerobic and aerobic respiration.
  • Raw microarray data
  • Processed microarray data
  • The experiment looked to find more information about the Arc two-component system of shewanella oneidensis by shifting oxygen levels. The treatment in the experiment was the changing levels of oxygen. The control were strains of shewanella oneidensis MR-1 wild type cells.
  • Expression profiles of three independent replicates of Shewanella oneidensis MR-1 delta-arcS were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells.

E-GEOD-15657 - Ron

Ranking of Microarray Papers