Difference between revisions of "Oregon Trail Survivors"

From LMU BioDB 2015
Jump to: navigation, search
(title edit)
(formatting)
Line 1: Line 1:
−
= The Oregon Trail Survivors =
 
 
<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>
 
<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>
  

Revision as of 07:27, 10 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

Paper Rankings

  1. 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
  2. Morris, Carolyn R, et al. ‘Characterization of Intracellular Growth Regulator IcgR by Utilizing Transcriptomics to Identify Mediators of Pathogenesis in Shigella Flexneri’. Infection and Immunity 81.9 (Sep. 2013): 3068–3076. 6 Nov. 2015.
  3. Global analysis of a plasmid-cured Shigella flexneri strain: new insights into the interaction between the chromosome and a virulence plasmid. Li Zhu, Xiankai Liu, Xuexue Zheng, Xin Bu, Ge Zhao, Chaohua Xie, Jingfei Zhang, Na Li, Erling Feng, Jie Wang, Yongqiang Jiang, Peitang Huang, Hengliang Wang J Proteome Res. 2010 February 5; 9(2): 843–854. doi: 10.1021/pr9007514
  4. 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
  5. 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

Kristin

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: Abstract
  • PubMedCentral: PMC
  • Publisher Full Text (HTML format): HTML
  • Publisher Full Text (PDF): PDF
  • Copyright: 2011 Peng et al. Article is Open Access and the authors own the copyright, not the journal, under a Creative Commons license.
  • Publisher: PLOS One
    • Is the article available under "Open Access"? Yes
  • Availability: online only
  • Did LMU pay a fee for this article: no
  • Database used to find the data and article: ArrayExpress
  • Terms searched: Shigella flexneri
    • Filtered by organism: Shigella flexneri
    • Filtered by experiment type: RNA assay, array assay
  • Search overview
    • Results: 7
    • Assessment: All of the articles were relevant but not all had enough assays to be able to be used for this assignment. All involved transcription profiling by array but obviously the experiments differed. Expression analysis was used to examine an RNA polymerase inhibitor, comparing wild type to mutant Shigella, and virulence plasmid-cured strains amongst others.
  • Search in Web of Knowledge
    • Number of articles this article cites: 71
    • Number of times this article has been cited: 1
    • What research directions have been taken since this article has been published? The only article that cited this paper involved detecting infectious diarrheal diseases by chemiluminescence imaging.
    • Microarray data
    • What experiment was performed? What was the "treatment" and the "control"?
      • The experiment performed was to identify overlooked small RNAs (sRNAs) and small open reading frames (sORFs) in Shigella that were overlooked in the initial genome sequences. Microarrays were performed to search for sRNAs as well as RT-PCR and northern blots were used to identify sRNAs and regions for possible sRNAs. 64 sRNAs that were previously confirmed were used as controls. As a treatment, cells were harvested in the lag, log, and stationary phases at 37C in LB medium and then in the log and stationary phases at 37C in LB medium with 0.01% Congo red, a salt.
    • Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? Competitive hybridization was conducted three times for each condition. These were technical replicates because the conditions were different samples (treated differently) measured in different conditions.

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

  • PubMed Abstract: Abstract
  • PubMedCentral: PMC
  • Publisher Full Text (HTML format): HTML
  • Publisher Full Text (PDF): PDF
  • Copyright: 2014 American Society for Microbiology. The ASM is a non-profit organization with numerous publications, some of which are open access and some of which are not.
  • Publisher: American Society for Microbiology
    • Is the article available under "Open Access"? It is available open access after 6 months.
  • Availability: online and in print
  • Did LMU pay a fee for this article: no
  • Database used to find the data and article: ArrayExpress
  • Terms searched: Shigella flexneri
    • Filtered by organism: Shigella flexneri
    • Filtered by experiment type: RNA assay, array assay
  • Search overview
    • Results: 7
    • Assessment: All of the articles were relevant but not all had enough assays to be able to be used for this assignment. All involved transcription profiling by array but obviously the experiments differed. Expression analysis was used to examine an RNA polymerase inhibitor, comparing wild type to mutant Shigella, and virulence plasmid-cured strains amongst others.
  • Search in Web of Knowledge
    • Number of articles this article cites: 70
    • 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.
    • Microarray data
    • 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 treatment for this experiment was to create Shigella TCRS mutants using phages or transduction and to test their effectiveness in invading Henle cells. Assays were then done to compare gene expression in these mutants with wild type Shigella TCRS. The control for this experiment was DNA-ase treated RNA and assays performed with avirulent strains of Shigella.
    • Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? Assays were conducted three times. These were technical replicates because the conditions were different samples.

Erich Yanoschik

Global analysis of a plasmid-cured Shigella flexneri strain: new insights into the interaction between the chromosome and a virulence plasmid. Li Zhu, Xiankai Liu, Xuexue Zheng, Xin Bu, Ge Zhao, Chaohua Xie, Jingfei Zhang, Na Li, Erling Feng, Jie Wang, Yongqiang Jiang, Peitang Huang, Hengliang Wang J Proteome Res. 2010 February 5; 9(2): 843–854. doi: 10.1021/pr9007514

  1. 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
  2. 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.
  3. 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.
    • The control sample is derived from mRNA
  4. Overview of Search Results
    • The results of the search mainly consisted of E.coli and Shigella flexneri transcriptional profiling.
    • There are 178 results in the GEO DataSets Database and 22283 in GEO profiles database.
    • The results were mostly relevant, the first results were datasets. Anything related to the bacteria came up, the order was seemingly relevant.
  5. The experiment was contrasting the pathegenicity of a virulence cured plasmid strain versus a wild type shigella flexneri, a virulence plasmid cured strain was constructed through plasmid incompatibility. The control was the wild type Shigella flexneri strain in each experimental construct.
    • There were at least 3 biological replicates of each experiment conducted and 2 techincal replicates.

Trixie

Morris, Carolyn R, et al. ‘Characterization of Intracellular Growth Regulator IcgR by Utilizing Transcriptomics to Identify Mediators of Pathogenesis in Shigella Flexneri’. Infection and Immunity 81.9 (Sep. 2013): 3068–3076. 6 Nov. 2015.

Database used to find the data and article: ArrayExpress

  • Terms searched: Shigella flexneri
    • Filtered by organism: Shigella flexneri
    • Filtered by experiment type: RNA assay, array assay
  • Search overview
    • Results: 7
    • Assessment: Some of the results only used 2-4 assays so we immediately felt suspicious as to the accuracy of the results they would provide. Out of the 7 results, 5 had 9 or more assays so we decided to look at those data.

Web of Science:

  • Link to microarray data: Microarray data
  • How many articles does this article cite? 2
  • How many articles cite this article? 52
  • 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?
    • Since the organism's genome has been sequenced, new research about this specie now tends to focus more on its pathogenesis using bioinformatic methods with in vitro and in vivo microarray data. For example, the article "Analysis of the Proteome of Intracellular Shigella flexneri Reveals Pathways Important for Intracellular Growth" that cites this article analyzes the metabolic pathways that allow the organism to grow.
  • What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
    • This experiment involved combining high-throughput bioinformatic methods with in vitro and in vivo assays to provide new insights into pathogenesis. The intracellular growth regulator was deleted in order to observe its effects and compare to the wild type, or the control in the experiment. The "treatment" involved culturing the strains in Luria broth or tryptic soy agar with Congo red (TSA/CR) medium supplemented with the appropriate antibiotics (15 μg/ml chloramphenicol, 50 μg/ml kanamycin, and 100 μg/ml ampicillin) and allowing them to invade colonic epithelial cells for a set period of time.
  • 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.

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
Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Oregon_Trail_Survivors&oldid=5951"