Difference between revisions of "Oregon Trail Survivors"
From LMU BioDB 2015
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* Did LMU pay a fee for this article: no | * Did LMU pay a fee for this article: no | ||
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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. | ||
| − | + | ||
====Jake==== | ====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).) | + | 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).) --> |
| − | + | ||
| − | The link to the | + | 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 | + | *The link to the [http://www.ncbi.nlm.nih.gov/pubmed/22428000 abstract] |
| − | + | *The link to the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299763/ full text of the article] in PubMed Central | |
| − | + | *The link to the [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 full text of the article] (HTML format) from the publisher web site. | |
| − | *http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 | + | *The link to the [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF full PDF version] of the article from the publisher web site. |
| − | + | ||
| − | *http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF | + | |
| − | + | ||
*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. | *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? | + | *Does the journal own the copyright? NO |
| − | + | *Do the authors own the copyright? Yes | |
| − | Do the authors own the copyright? | + | *Do the authors own the rights under a Creative Commons license? Yes |
| − | * | + | *Is the article available “Open Access”? Yes |
| − | Do the authors own the rights under a Creative Commons license? | + | *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 |
| − | Is the article available “Open Access”? | + | *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. |
| − | * | + | |
| − | What organization is the publisher of the article? What type of organization is it? | + | |
| − | + | ||
| − | Is this article available in print or online only? | + | |
| − | + | ||
| − | Has LMU paid a subscription or other fee for your access to this article? | + | |
| − | + | ||
| − | 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? | + | **How many articles does this article cite? 25 cited references |
| − | + | **How many articles cite this article? 0 articles cite this article | |
| − | How many 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? |
| − | + | ||
| − | 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. | + | *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" |
| − | State what you used as search terms and what type of search terms they were. | + | *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 overview of the results of the search. | + | **Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable. |
| − | *7 results returned with 6 viable options due to the number assays. | + | *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? |
| − | Give an assessment of how relevant the results were | + | **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. | |
| − | + | ||
| − | + | ||
| − | What experiment was performed? What was the "treatment" and what was the "control" in the experiment? | + | |
| − | * | + | |
| − | 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. | + | |
Revision as of 22:26, 12 November 2015
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 | |||
Contents
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.
- 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
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.
- 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.
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 | |||
| 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 | |||
