Difference between revisions of "Oregon Trail Survivors"

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(→‎Paper Rankings: paper 1 is suitable)
(→‎Annotated Bibliography: added comments for unnecessary info)
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===Microarray Papers===
 
===Microarray Papers===
  
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It would have been helpful for you to actually lit the papers in this ranked order.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:32, 10 November 2015 (PST)''
 
It would have been helpful for you to actually lit the papers in this ranked order.  ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 10:32, 10 November 2015 (PST)''
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#Peng J, Yang J, Jin Q (2011) An Integrated Approach for Finding Overlooked Genes in Shigella. PLoS ONE 6(4): e18509. doi: 10.1371/journal.pone.0018509
 
#Peng J, Yang J, Jin Q (2011) An Integrated Approach for Finding Overlooked Genes in Shigella. PLoS ONE 6(4): e18509. doi: 10.1371/journal.pone.0018509
 
#Waddell, C. D., Walter, T. J., Pacheco, S. A., Purdy, G. E., & Runyen-Janecky, L. J. (2014). NtrBC and Nac Contribute to Efficient Shigella flexneri Intracellular Replication. Journal of Bacteriology, 196(14), 2578–2586. http://doi.org/10.1128/JB.01613-14
 
#Waddell, C. D., Walter, T. J., Pacheco, S. A., Purdy, G. E., & Runyen-Janecky, L. J. (2014). NtrBC and Nac Contribute to Efficient Shigella flexneri Intracellular Replication. Journal of Bacteriology, 196(14), 2578–2586. http://doi.org/10.1128/JB.01613-14
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Peng J, Yang J, Jin Q (2011) An Integrated Approach for Finding Overlooked Genes in Shigella. PLoS ONE 6(4): e18509. doi: 10.1371/journal.pone.0018509
 
Peng J, Yang J, Jin Q (2011) An Integrated Approach for Finding Overlooked Genes in Shigella. PLoS ONE 6(4): e18509. doi: 10.1371/journal.pone.0018509
 
*PubMed Abstract: [http://www.ncbi.nlm.nih.gov/pubmed/21483688 Abstract]
 
*PubMed Abstract: [http://www.ncbi.nlm.nih.gov/pubmed/21483688 Abstract]
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* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
 
* 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.
 
** 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.
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Revision as of 22:19, 12 November 2015

Oregon Trail Survivors

Oregon-trail-dysentery 5 biodb.jpg

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

Group Members

  • Coder: Jake Woodlee
  • Quality Assurance: Trixie Roque
  • GenMAPP Users: Erich Yanoschik & Kristin Zebrowski
  • Project Manager: Kristin Zebrowski

Week 10 Goals

Over the upcoming weeks our group will be investigating Shigella flexneri.

  1. Find genome sequence paper
  2. Find 4-8 microarray data and paper that goes with the genome paper
  3. Compile team page to and create a ranked annotated bibliography

Group Meeting Times

  • Thursday, November 5th at 8:00 pm

Overview of Genome Paper

  • Used the genome sequencing article to perform a prospective search in the Web of Science database.
  • Overview of the search:
    • 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.

Annotated Bibliography

Genome Paper

Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (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.

Microarray Papers

Jake

The complete bibliographic reference in the APA style (see the Writing LibGuide) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)

  • Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in shigella flexneri. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

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?

  • Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Does the journal own the copyright?

  • NO

Do the authors own the copyright?

  • Yes

Do the authors own the rights under a Creative Commons license?

  • Yes

Is the article available “Open Access”?

  • Yes

What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here.

  • Plos One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)

Is this article available in print or online only?

  • Online only from what I can see.

Has LMU paid a subscription or other fee for your access to this article?

  • No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.

Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database. How many articles does this article cite?

  • 25 cited references

How many articles cite this article?

  • 0 articles cite this article

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?

  • Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.

State which database you used to find the data and article.

  • ArrayExpress

State what you used as search terms and what type of search terms they were.

  • "shigella flexneri" filtered by organism, experiment type:"rna assay", experiment type: "array assay"

Give an overview of the results of the search.

  • 7 results returned with 6 viable options due to the number assays.

How many results did you get?

  • 7

Give an assessment of how relevant the results were.

  • Very relevant, 6/7 results were viable.

In addition, you must also link to the web site where the microarray data resides.

For each of the microarray articles/datasets, answer the following: What experiment was performed? What was the "treatment" and what was the "control" in the experiment?

  • Drugs(RNA Polymerase Inhibitors) were added to Shigella flexneri in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.

Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?

  • There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.


Helpful Links

Team Links
Files Team Members Week 11 Assignment Week 12 Assignment Week 14 Assignment Week 15 Assignment
OTS Deliverables Trixie Week 11 Week 12 Week 14 Week 15
Jake Week 11 Week 12 Week 14 Week 15
Gene Database Testing Report Erich Week 11 Week 12 Week 14 Week 15
Kristin Week 11 Week 12 Week 14 Week 15
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
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
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