Revision as of 04:51, 10 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)

Genome Sequencing Paper

• 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 Papers

1

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 2014;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

2

• Brickman, T. J., Cummings, C. A., Liew, S.-Y., Relman, D. A., & Armstrong, S. K. (2011). Transcriptional Profiling of the Iron Starvation Response in Bordetella pertussis Provides New Insights into Siderophore Utilization and Virulence Gene Expression . Journal of Bacteriology, 193(18), 4798–4812. http://doi.org/10.1128/JB.05136-11
• ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Transcriptional+Profiling+of+the+Iron+Starvation+Response+in+Bordetella+pertussis+Provides+New+Insights+into+Siderophore+Utilization+and+Virulence+Gene+Expression
• Publisher Full Text (HTML): http://jb.asm.org/content/193/18/4798.full
• Publisher Full Text (PDF): http://jb.asm.org/content/193/18/4798.full.pdf+html
• Copyright: 2011 by the American Society for Microbiology
• Publisher: Journal of Bacteriology
• Availability: in print and online
• Did LMU pay a fee for this article: yes
• Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=

3

King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23776625
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679012/
• Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066150
• Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0066150&representation=PDF
• Copyright: © 2013 King 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: EBI ArrayExpress Data

4 (note, all of the papers from this point on involve additional species other than Bordetella pertussis)

• Cummings, C. A., Bootsma, H. J., Relman, D. A., & Miller, J. F. (2006). Species-and strain-specific control of a complex, flexible regulon by Bordetella BvgAS. Journal of bacteriology, 188(5), 1775-1785.
• ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1426559/
• PubMed Abstract:http://www.ncbi.nlm.nih.gov/pubmed/?term=Species-+and+Strain-Specific+Control+of+a+Complex%2C+Flexible+Regulon+by+Bordetella+BvgAS
• Publisher Full Text (HTML): http://jb.asm.org/content/188/5/1775.full
• Publisher Full Text (PDF): http://jb.asm.org/content/188/5/1775.full.pdf+html
• Copyright: 2006 by the American Society for Microbiology
• Publisher: Journal of Bacteriology
• Availability: in print and online
• Did LMU pay a fee for this article: yes
• Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=

5

• Brinig, M., Register, K., Ackermann, M., & Relman, D. (2006). Genomic features of Bordetella parapertussis clades with distinct host species specificity. Genome Biology, 7(9). doi:doi:10.1186/gb-2006-7-9-r81
• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/16956413?dopt=Abstract&holding=f1000,f1000m,isrctn
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794550/
• Publisher Full Text (HTML): http://www.genomebiology.com/2006/7/9/R81
• Publisher Full Text (PDF): http://www.genomebiology.com/content/pdf/gb-2006-7-9-r81.pdf
• Copyright: Brinig et al.; licensee BioMed Central Ltd. (information found on the article); open access
• Publisher: BioMed Central Ltd (for-profit publisher)
• Availability: online
• Did LMU pay a fee for this article: no

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?

• Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-95/

6

• Cummings, C., Bootsma, H., Relman, D., & Miller, J. (2006). Species- and Strain-Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS. Journal of Bacteriology, 188(5), 1775-1785. doi:doi: 10.1128/JB.188.5.1775-1785.2006
• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/16484188?dopt=Abstract
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1426559/
• Publisher Full Text (HTML): http://jb.asm.org/content/188/5/1775.full
• Publisher Full Text (PDF): http://jb.asm.org/content/188/5/1775.full.pdf
• Copyright: American Society for Microbiology; open access
• Publisher: American Society for Microbiology (professional organization for scientists)
• Availability: online and in print
• Did LMU pay a fee for this article: no

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?

• Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/

7

• King, Audrey J et al. “Comparative Genomic Profiling of Dutch Clinical Bordetella Pertussis isolates Using DNA Microarrays: Identification of Genes Absent from Epidemic Strains.” BMC Genomics 9 (2008): 311. PMC. Web. 10 Nov. 2015.
• PubMed Abstract: http://www.biomedcentral.com/1471-2164/9/311#abs
• PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/>
• Publisher Full Text (HTML): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/
• Publisher Full Text (PDF): <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/pdf/1471-2164-9-311.pdf>
• Copyright: © 2008 King et al; licensee BioMed Central Ltd.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
• Publisher: BMC Genomics
• Availability: online access
• Did LMU pay a fee for this article: no

8

• Nakamura, Mari M. et al. “Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella Pertussis .” Infection and Immunity 74.10 (2006): 5537–5548. PMC. Web. 10 Nov. 2015.
• PubMed Abstract: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/?report=reader#__abstractid499869title>
• PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/>
• Publisher Full Text (HTML): <http://iai.asm.org/content/74/10/5537.full>
• Publisher Full Text (PDF): <http://iai.asm.org/content/74/10/5537.full.pdf+html>
• Copyright: © 2006, American Society for Microbiology
• Publisher: Infection and Immunity
• Availability: online access
• Did LMU pay a fee for this article: no

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)