Difference between revisions of "Oregon Trail Survivors"
From LMU BioDB 2015
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**Number of times this article has been cited: 0 | **Number of times this article has been cited: 0 | ||
**What research directions have been taken since this article has been published? This article has not been cited at all. It was published in July 2014 (pretty recently), which may contribute to this. | **What research directions have been taken since this article has been published? This article has not been cited at all. It was published in July 2014 (pretty recently), which may contribute to this. | ||
| − | **[https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-49939/samples/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= | + | **link to [https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-49939/samples/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data] |
**What experiment was performed? What was the "treatment" and the "control"? | **What experiment was performed? What was the "treatment" and the "control"? | ||
***The experimenters examined 12 two-component regulatory systems in ''Shigella flexneri'' for their abilities to sense changes in environmental conditions and regulate gene expression in response. Virulence was testing by infecting Henle cells with wild type and mutant TCRS. They found four systems required for the formation of plaque in wild-type and microarray analysis was performed to identify which genes were regulated differently by the NtrBC system or by Nac. | ***The experimenters examined 12 two-component regulatory systems in ''Shigella flexneri'' for their abilities to sense changes in environmental conditions and regulate gene expression in response. Virulence was testing by infecting Henle cells with wild type and mutant TCRS. They found four systems required for the formation of plaque in wild-type and microarray analysis was performed to identify which genes were regulated differently by the NtrBC system or by Nac. | ||
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* Availability: in print and online | * Availability: in print and online | ||
* Did LMU pay a fee for this article: no | * Did LMU pay a fee for this article: no | ||
| − | + | *The publisher is a sceintific society. The Journal of Proteome Research publishes content encompassing all aspects of global protein analysis and function, including the dynamic aspects of genomics, spatio-temporal proteomics, metabonomics and metabolomics, clinical and agricultural proteomics, as well as advances in methodology including bioinformatics. The theme and emphasis is on a multidisciplinary approach to the life sciences through the synergy between the different types of "omics". -quote from the about section http://pubs.acs.org/page/jprobs/about.html | |
| − | + | *Used the ISI Web of Science/Knowledge database to search this article | |
| − | + | ** The article has 28 cited references | |
| − | + | ** The article is cited 4 times | |
| − | + | ** Directions of research has been focused towards profiling which parts of the shigella flexneri genome is responsible for virulence and pathogenicity factors along with chromosomal inactivation. | |
# Global patterns of '''''gene expression''''' of a virulence cured plasmid strain compared with the wild-type strain were analyzed using 2-DE combined with MALDI-TOF MS. | # Global patterns of '''''gene expression''''' of a virulence cured plasmid strain compared with the wild-type strain were analyzed using 2-DE combined with MALDI-TOF MS. | ||
#* There are 6 biological replicates total. | #* There are 6 biological replicates total. | ||
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*Is this article available in print or online only? Online only | *Is this article available in print or online only? Online only | ||
*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. | *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. | *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 does this article cite? 25 cited references | ||
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**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? | **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. | *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 which database you used to find the data and article | + | *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" |
| − | *State what you used as search terms and what type of search terms they were | + | |
*Give an overview of the results of the search. | *Give an overview of the results of the search. | ||
**How many results did you get? 7 results returned with 6 viable options due to the number assays. | **How many results did you get? 7 results returned with 6 viable options due to the number assays. | ||
**Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable. | **Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable. | ||
*Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data] | *Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data] | ||
| − | |||
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment? | *What experiment was performed? What was the "treatment" and what was the "control" in the experiment? | ||
**Antibiotics (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. | **Antibiotics (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. | ||
Revision as of 23:11, 12 November 2015
Oregon Trail Survivors
Contents
Group Members
- Coder: Jake Woodlee
- Quality Assurance: Trixie Roque
- GenMAPP Users: Erich Yanoschik & Kristin Zebrowski
- Project Manager: Kristin Zebrowski
Group Meeting Times
Thursday, November 5th at 8:00 pm
Goals
Over the upcoming weeks our group will be investigating Shigella flexneri.
Week 10
- Find genome sequence paper
- Find 4-8 microarray data and paper that goes with the genome paper
- Compile team page to and create a ranked annotated bibliography
Week 11
- Prepare for journal club presentations in Weeks 12 and 13
- Begin initial tasks on research project
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.
- PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
- PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
- Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
- Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
- Copyright: 2002 Oxford University Press
- Publisher: Oxford University Press
- Availability: in print and online
- Did LMU pay a fee for this article: no
Microarray Paper
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
- The link to the full text of the article in PubMed Central
- 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.
- 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? 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
- 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.
- How many results did you get? 7 results returned with 6 viable options due to the number assays.
- Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable.
- Link to microarray data
- What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
- Antibiotics (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.
Executive Summaries for Week 11
Click on links for more information regarding each team member's contributions for the week.
Jake
Trixie
Erich
Kristin
Helpful Links
| 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 | |||
