Difference between revisions of "Heavy Metal HaterZ"

Revision as of 17:41, 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.)
  • I am not sure what you mean by the HTML version not being available. This link is to the HTML version. — Kdahlquist (talk) 09:19, 10 November 2015 (PST)
• 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-15657: Charania et. al (2009)

This paper is not suitable because they only do two replicates for each condition and we will not be able to do statistics. — Kdahlquist (talk) 09:40, 10 November 2015 (PST)

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.

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

This paper is not suitable because they do not use two-color microarray chips. — Kdahlquist (talk) 09:41, 10 November 2015 (PST)

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-15334: Yang et. al (2009)

Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., ... & Zhou, J. (2009). Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC genomics, 10(1), 131.

• The link to the abstract from PubMed.
• The link to the full text of the article in PubMedCentral
• The link to the full text of the article (HTML format) from the publisher web site.
• The link to the full PDF version of the article from the publisher web site.
• Who owns the rights to the article?
  • The article is Open Access and the authors own the rights under a Creative Commons license.
• What organization is the publisher of the article? What type of organization is it?
  • BMC Genomics is the publisher, which is a scientific society
• Is this article available in print or online only?
  • It is online only
• Has LMU paid a subscription or other fee for your access to this article?
  • No
• How many articles does this article cite?
  • This paper sites 48 other articles
• How many articles cite this article?
  • 3
    • Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction
    • Global transcriptional response of Caulobacter crescentus to iron availability
    • Molecular ecological network analysis
• 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?
  • This article has mostly been used to look at the iron response of other strains or organisms. It may have been used for comparison's sake or to modify the original methodology to fit the new experiment.
• Link to microarray data
  • Found it on ArrayExpress
  • This contains the raw data that we will use for our research
• What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
  • Strains of Shewanella oneidensis were put under iron depletion and repletion conditions. The control would be a regular strain of the organism, while the treatments would be either increasing or decreasing the iron levels.
• Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
  • 4 biological replicates of each treatment condition were performed

Ranking of Microarray Papers

1. Yang et. al (2009)
2. Lassak et. al (2010)
3. Charania et. al (2009)