Difference between revisions of "Bklein7 Week 11"

From LMU BioDB 2015
Jump to: navigation, search
(included methodology preface)
(wrote outline introduction)
Line 48: Line 48:
  
 
===''Comparative Analysis of the Genome Sequences of Bordetella Pertussis, Bordetella Parapertussis and Bordetella Bronchiseptica'' Outline===
 
===''Comparative Analysis of the Genome Sequences of Bordetella Pertussis, Bordetella Parapertussis and Bordetella Bronchiseptica'' Outline===
 +
The following outline was adapted from the original paper published by Parkhill et al. (2003) in ''Nature Genetics''.
 +
 +
====Introduction====
 +
*Establishing the Importance of ''B. pertussis'', ''B. parapertussis'', and ''B. bronchiseptica''
 +
**All three of these bacteria are pathogens that colonize the respiratory tracts of mammals.
 +
***''B. bronchiseptica''- infects a wide range of mammals.
 +
***''B. parapertussis''- infects both humans and sheep.
 +
***''B. pertussis''- specific to humans vectors.
 +
****''B. pertussis'' is the causative agent of whooping cough.
 +
****Despite vaccination programs, whooping cough is still endemic in some countries, causing hundreds of thousands of deaths every year.
 +
**Evidence suggests that ''B. pertussis'' and ''B. parapertussis'' may have evolved in the recent past from a common ancestor, possibly the more genetically diverse species  ''B. bronchiseptica''.
 +
***The species exhibit similar virulence factors.
 +
***Gene expression in these species is regulated by the two-component BvgA/S regulatory system.
 +
****Bvg-plus phase: vector detected. Virulence-activated genes (vags) up-regulated and virulence-repressed genes (vrgs) down-regulated.
 +
****Bvg-minus phase: in the environment. Standard gene expression occurs.
 +
 +
*Experimental Design: Sequencing ''B. pertussis'', ''B. parapertussis'', and ''B. bronchiseptica''
 +
**Specific strains of each Bordetella species were sequenced.
 +
**Genome sequences were compared to:
 +
#Compare genetic background.
 +
#Assess factors influencing variable disease severity.
 +
#Assess factors influencing variable host range.
 +
 +
====Results====
 +
 +
====Discussion====
 +
 +
====Methods====
  
 
==''Bordetella Pertussis'' Model Organism Database==
 
==''Bordetella Pertussis'' Model Organism Database==

Revision as of 03:45, 17 November 2015

Assessment of the Genome Sequencing Paper for Bordetella Pertussis

All of the content in this section discusses the following genome sequencing paper:

  • Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., et al. (2003). Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nature genetics, 35(1), 32-40. doi:10.1038/ng1227
  • PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/12910271
  • PubMed Central: Not available on PubMed Central.
  • Publisher Full Text (HTML): http://www.nature.com/ng/journal/v35/n1/full/ng1227.html
  • Publisher Full Text (PDF): http://www.nature.com/ng/journal/v35/n1/pdf/ng1227.pdf
  • Copyright: ©2003 Nature Publishing Group (information found on PDF version of article). This article is not Open Access, but it is freely available 6 months after publication.
  • Publisher: Nature Publishing Group (for-profit).
  • Availability: In print and online.
  • Did LMU pay a fee for this article: Yes, LMU pays a subscription fee for access to the journal Nature Genetics.

The Parkhill et al. (2003) paper was accessed using the link listed above as "Publisher Full Text (PDF)".

Defining Unknown Biological Terms from Parkhill et al.

Unknown terms from the Parkhill et al. (2003) paper were entered into search engines, and results were vetted until definitions for each were found in quality sources. Links to the sites from which the definitions were attained are included below.

  1. Pseudogenes
    • Pseudogenes are genomic DNA sequences similar to normal genes but non-functional; they are regarded as defunct relatives of functional genes.
    • Citation: http://pseudogene.org/background.php
  2. Fimbriae
    • Modern term for short, hair-like projections or appendages (organelles) on the outer surface of certain bacteria composed of protein subunits (pilin) extending outward from the surface that act as a virulence factor by promoting adherence; formerly known as pili.
    • Citation: http://www.life.umd.edu/classroom/bsci424/Definitions.htm
  3. Auxotrophy
  4. Ortholog
  5. Insertion Sequence Elements (ISEs)
    • Insertion sequences, or insertion-sequence (IS) elements, are now known to be segments of bacterial DNA that can move from one position on a chromosome to a different position on the same chromosome or on a different chromosome. When IS elements appear in the middle of genes, they interrupt the coding sequence and inactivate the expression of that gene.
    • Citation: http://www.ncbi.nlm.nih.gov/books/NBK21779/
  6. Horizontal Gene Transfer
  7. Prophage
  8. Autotransporter
    • The key feature of an autotransporter is that it contains all the information for secretion in the precursor of the secreted protein itself. Autotransporters comprise three functional domains: 1) an N-terminal targeting domain (amino-terminal leader sequence) that functions as a signal peptide to mediate targeting to and translocation across the inner membrane 2) a C-terminal translocation domain (carboxy-terminal) that forms a beta-barrel pore to allow the secretion of 3) the passenger domain, the secreted mature protein.
    • Citation: https://www.ebi.ac.uk/interpro/entry/IPR006315
  9. Type-III Secretion System
    • The protein Type III Secretion System (T3SS) is a supramolecular, organic nanomachine that injects bacterial virulence proteins into eukaryotic cells to modulate their physiology for the benefit of the pathogen.
    • Citation: http://lab.rockefeller.edu/stebbins/research/T3SS
  10. Constitutive Expression

Comparative Analysis of the Genome Sequences of Bordetella Pertussis, Bordetella Parapertussis and Bordetella Bronchiseptica Outline

The following outline was adapted from the original paper published by Parkhill et al. (2003) in Nature Genetics.

Introduction

  • Establishing the Importance of B. pertussis, B. parapertussis, and B. bronchiseptica
    • All three of these bacteria are pathogens that colonize the respiratory tracts of mammals.
      • B. bronchiseptica- infects a wide range of mammals.
      • B. parapertussis- infects both humans and sheep.
      • B. pertussis- specific to humans vectors.
        • B. pertussis is the causative agent of whooping cough.
        • Despite vaccination programs, whooping cough is still endemic in some countries, causing hundreds of thousands of deaths every year.
    • Evidence suggests that B. pertussis and B. parapertussis may have evolved in the recent past from a common ancestor, possibly the more genetically diverse species B. bronchiseptica.
      • The species exhibit similar virulence factors.
      • Gene expression in these species is regulated by the two-component BvgA/S regulatory system.
        • Bvg-plus phase: vector detected. Virulence-activated genes (vags) up-regulated and virulence-repressed genes (vrgs) down-regulated.
        • Bvg-minus phase: in the environment. Standard gene expression occurs.
  • Experimental Design: Sequencing B. pertussis, B. parapertussis, and B. bronchiseptica
    • Specific strains of each Bordetella species were sequenced.
    • Genome sequences were compared to:
  1. Compare genetic background.
  2. Assess factors influencing variable disease severity.
  3. Assess factors influencing variable host range.

Results

Discussion

Methods

Bordetella Pertussis Model Organism Database

Gene Database: http://www.genedb.org/Homepage/Bpertussis Example Link: http://www.genedb.org/gene/BP3783?actionName=%2FQuery%2FquickSearch&resultsSize=1&taxonNodeName=Root



Links

Assignments Pages

Individual Journal Entries

Shared Journal Entries

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Bklein7_Week_11&oldid=6319"