Revision as of 00:49, 11 November 2015

The Class Whoopers Crew Page

The_Class_Whoopers

• Species: Bordetella pertussis

Crew Members

• Coder and Project Manager: Nicole Anguiano
• Quality Assurance: Brandon Klein
• GenMAPP Users: Lena Olufson & Mahrad Saeedi

Team Goals for the Week of 11/3

• For all:
  • Make an annotated bibliography of 1-2 articles (preferably 2) on Bordetella pertussis following the instructions here, and post them on your individual journal page!
  • Once everyone has done their bibliographies, we'll discuss a ranking of which we think are the best ones and list them below in ranked order. Try to find different articles from everyone else so we have the maximum number of options.

Meetings!

• Monday, November 9, 8pm, Seaver 120

Annotated Bibliography

• Week 10 Creation of page and combined annotated bibliography (midnight 11/10)

Project Progress

Week 11

Include "Executive Summaries" for each individual's progress here.

Genome Sequencing Paper

Neither of these papers is the first to report the genome sequence of B. pertussis. The paper that you will want to use is this one. I found it by looking at the introduction and references of the Zhang et. al (2011) paper. For your Week 11 assignment, please remove your annotated bibliography entries for the two papers below and create one for this new paper by Parkhill et al. (2003). You will use the Parkhill paper for your project. — Kdahlquist (talk) 09:54, 10 November 2015 (PST)

• Zhang, S., Xu, Y., Zhou, Z., Wang, S., Yang, R., Wang, J., & Wang, L. (2011). Complete Genome Sequence of Bordetella Pertussis CS, a Chinese Pertussis Vaccine Strain. Journal of Bacteriology, 193(15), 4017-4018. doi: 10.1128/JB.05184-11
• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21622744
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147532/
• Publisher Full Text (HTML): http://jb.asm.org/content/193/15/4017.long
• Publisher Full Text (PDF): http://jb.asm.org/content/193/15/4017.full.pdf+html
• Copyright: © 2011, American Society for Microbiology (information found on PDF version of article). This article is not Open Access, but it is freely available 6 months after publication.
• Publisher: American Society for Microbiology (scientific society)
• Availability: in print and online
• Did LMU pay a fee for this article: no

(Note: The below paper is very similar to the genome sequencing paper listed above but more recent. We were unsure how to designate which of the two would be a better paper. If possible, feedback regarding which to choose would be appreciated. Otherwise, we would like to use the above genome sequencing paper.)

• Boinett, C. J., Harris, S. R., Langridge, G. C., Trainor, E. A., Merkel, T. J., & Parkhill, J. (2015). Complete genome sequence of Bordetella pertussis D420. Genome announcements, 3(3), e00657-15.
• The link to the abstract: http://www.ncbi.nlm.nih.gov/pubmed/26067980
• The link to the full text of the article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463544/
• The link to the full text of the article (HTML format): http://genomea.asm.org/content/3/3/e00657-15.long
• The link to the full PDF version of the article from the publisher web site: http://genomea.asm.org/content/3/3/e00657-15.full.pdf+html
• The authors won't he right of the copyright under a Creative Commons license.
• The article is available "Open Access".
• Published by the American Society for Microbiology online.
• Article is available online only and LMU has paid a subscription for access to this article.

Microarray Paper

This paper is suitable for your project. — Kdahlquist (talk) 10:04, 10 November 2015 (PST)

Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE, 9(12):e115243. doi: 10.1371/journal.pone.0115243

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25501560
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264864/
• Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243
• Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0115243&representation=PDF
• Copyright: © 2014 Hoo 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. (info found here)
• Publisher: PLOS ONE (respected open access organization)
• Availability: online only
• Did LMU pay a fee for this article: no
• Web site where the data resides: NCBI GEO data

Deliverables

• GenMAPP Gene Database for assigned species (.gdb)
• ReadMe file to accompany the Gene Database (.pdf)
• Sample ReadMe in Word format: ReadMe_Vc-Std_External_20131122.zip
• Include Gene Database Schema diagram in ReadMe
• Sample schema in Adobe Illustrator format: Vibrio_schema_20101022.zip
• Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file)
• Processed and analyzed DNA microarray dataset (.xls)
• GenMAPP Expression Dataset file (.gex)
• Filtered MAPPFinder Results (.xls)
• Sample MAPP file of a relevant biological pathway for your species (.mapp)
• Group Report describing the creation of the Gene Database and the biological analysis of the data (.doc or .pdf)
• PowerPoint presentation (.ppt, given on Tuesday, December 15)

Links

GenMAPP Analysis of Bordetella pertussis Microarray Data

Journal Entries

Group Members

• Project Manager & Coder: Brandon Klein
• Quality Assurance: Mahrad Saeedi
• GenMAPP User: Lena Olufson
• Team Page

Team Weekly Assignments

• Week 10 Creation of page and combined annotated bibliography (midnight 11/10)
• Week 11 (midnight 11/17)
• Week 12 (midnight 11/24)
• Week 14 (midnight 12/8)
• Week 15 (midnight 12/15)

Individual Journal Entries