Oregon Trail Survivors

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Oregon Trail Survivors

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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

Specie to Investigate

  • Shigella flexneri

Week 10 Goals

  1. Genome sequence paper
  2. Microarray data and paper that goes with it
  3. Compile team page to have these papers/data

Meeting Times

  • Thursday, November 5th at 8:00 pm

Microarray papers

Annotated Bibliography of Genomics Papers for your Species

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

  • On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
  • On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:

Overview of Genome Paper

  • Used the genome sequencing article to perform a prospective search in the ISI Web of Science/Knowledge 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.

Microarray Papers

    1. Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
      • The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
        • A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
        • The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
        • The control sample needs to be derived from mRNA and not genomic DNA.
        • The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
      • We recommend that you begin by searching for the data, and then by finding the journal article related to the data. 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.
      • Give an overview of the results of the search.
        • How many results did you get?
        • Give an assessment of how relevant the results were.
      • For each article, please provide all of the same information that you provided for the genome article above.
      • 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:
          1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
          2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
        • Remember, microarray data is not centrally located on the web. Some major sources are:
      • On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

Sample Bibliographic Entry

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167

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.

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: http://www.ncbi.nlm.nih.gov/pubmed/21483688
  • PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071730/
  • Publisher Full Text (HTML format): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018509 HTML version]
  • Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0018509&representation=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.
    • Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22800/samples/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
    • 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.

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

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 these are all technical replicates of each other.


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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