Difference between revisions of "Eyanosch Week 10"

Revision as of 01:47, 10 November 2015

Website to genome sequence papers

http://iai.asm.org/content/69/5/3271.short

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 Check out who cited the paper and what articles the paper cited from

http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=Shigella+flexneri&organism=Shigella+flexneri&exptype[]=%22rna+assay%22&exptype[]=%22array+assay%22&array=

• Look under files, and use sample and data relationship, raw data, processed data, array design. ETC

Microarray : http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12535

Individual Journal Assignment

• Store this journal entry as "username Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
• Link from your user page to this Assignment page.
• Link to your journal entry from your user page.
• Link back from your journal entry to your user page.
• Don't forget to add the "Journal Entry" category to the end of your wiki page.
  • Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
• For your assignment this week, you will keep an electronic laboratory notebook on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.

Information regarding Annotated Bibliography of Shigella Flexneri

• 1. Regular search queries
     • PubMed
       • Original keyword(s) used and number of results:
         • The keywords used were 'shigella flexneri' and that produced 4832 results
       • Most successful terms used to narrow down the search and number of results:
         • To narrow the search down, tags such as 'genome' and 'genome sequencing' were used. The results were narrowed to 664 and 56 respectively.
     • Google Scholar
       • Original keyword(s) used and number of results:
         • The keywords used were 'shigella flexneri' and that produced 66,100 results
       • Most successful terms used to narrow down the search and number of results:
         • To narrow the search down, tags such as 'genome' and 'genome sequencing' were used. The results were narrowed to 27,800 and 25,200
     • Web of Science
       • Original keyword(s) used and number of results:
         • The keywords used were 'shigella flexneri' and that produced 24,737 results
       • Most successful terms used to narrow down the search and number of results:
         • To narrow the search down, tags such as 'genome' and 'genome sequencing' were used. The results were narrowed to 590 and 460
  2. Advanced search function queries
     • PubMed
       • Advanced search functions that proved useful and number of results:
         • Utilizing advanced search functions of publication dates ranging back 5 or 10 years and text availability
     • Google Scholar
       • Advanced search functions that proved useful and number of results:
         • The advanced options of including patents or citations, by unchecking the boxes narrows the search results down. The results can be sorted by relevance and sorted by date.
     • Web of Science
       • Advanced search functions that proved useful and number of results:
         • Changing the publication dates to show the order from oldest to newest. Checking the times the article has been cited and the citations of other articles within the chosen article. There are some options within research domain that will help narrow down the search results.

Bibliographic Entry

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

1. The publisher of the article Oxford University Press is apart of the University of Oxford and its purpose is to advance education and scientific research by publishing worldwide.
   • Is this article available in print or online only?
     • The article is available in both print and online
   • Has LMU paid a subscription or other fee for your access to this article?
     • No LMU has not paid a subscription for access to this article.
   • Used the genome sequencing article to perform a prospective search in the ISI Web of Science/Knowledge database.
2. 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.
3. Micro array data information
   • This micro array data provides 6 biological replicates.
   • 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 is derived from mRNA and not genomic DNA.
   • The database used to find the micro array was the NCBI Gene Expression Omnibus
     • We used the specific species of shigella flexneri 2a.
4. Overview of search results
   • Number of Results:
     • 5 results appeared
   • Relevant results:
     • There were 2, possibly 3, relevant results.
   • http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12535
   • Experiment performed with "treatment" and "control" explanation:
   • A virulence Plasmid cured Shigella flexneri and a wild type shigella flexneri 2a were both observed to see protein expression at 30°C and 37°C. The control would be the Wild type shigella flexneri 2a, and the treatment is the change in temperatures.
   • There were 12 biological replicates and 4 technical replicates of the experiment done.

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

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed?LinkName=gds_pubmed&from_uid=200012535
• PubMed Central: N/A
• Publisher Full Text (HTML): http://pubs.acs.org/doi/full/10.1021/pr9007514
• Publisher Full Text (PDF): http://pubs.acs.org/doi/pdf/10.1021/pr9007514
• Copyright: 2009 American Chemical Society
• Publisher: Journal of Proteome Research
• Availability: in print and online
• Did LMU pay a fee for this article: no

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.
     • The micro array data can be found http://pubs.acs.org/doi/abs/10.1021/pr9007514
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.