Difference between revisions of "Anuvarsh Week 11"

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=Outline of Paper=
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*Introduction
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**Burkholderia cenocepacia is a known cystic fibrosis pathogen.
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***It appeared in 1980 when CF patients experienced several symptoms that resulted in early death.
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***The resulting decline in health was then on referred to as “cepacia syndrome”.
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***The specific strain associated with the “cepacia syndrome” is the ET12 strain.
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**B. cenocepecia J2315 is part the ET12 ancestral linage.
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**The researchers sequenced the J2315 strain in order to find information regarding the how the ET12 linage adapted to result in the previously mentioned clinical symptoms.
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***The sequence of the J2315 strain would also give insight on the performance of the J2315 strain in patients with CF.
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*Materials and Methods
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**Bacterial strains
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***B. cenocepacia was first isolated in 1989 in the UK.
 +
***J2315 is resistant to several different drugs
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***In addition to J2315, 7 other previously sequenced strains were also used in this study.
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**Genome sequencing
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***Whole genome sequencing
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****DNA was extracted from J2315 and sequence data was obtained.
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****Sequence was annotated using the Artemis software.
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****Initial coding sequences were identified using Orpheus.
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****The CDSs were verified using protein databases in conjunction with BLAST and the DNA sequence was verified through all 6.
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***Comparative genomics
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****Comparisons of genome sequences were run using Artemis Comparison Tool
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***B. cenocepecia strain J2315 was compared to several other burkholderia species
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**PCR screening
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***CRP amplification was done using Platinum Pfx DNA polymerase with suppliers protocols.
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Revision as of 05:15, 16 November 2015

Burkholderia cenocepacia Genome Paper

Holden, M. T., Seth-Smith, H. M., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., ... & Parkhill, J. (2009). The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. Journal of bacteriology, 191(1), 261-277.

Biological Terms and Definitions

Outline of Paper

  • Introduction
    • Burkholderia cenocepacia is a known cystic fibrosis pathogen.
      • It appeared in 1980 when CF patients experienced several symptoms that resulted in early death.
      • The resulting decline in health was then on referred to as “cepacia syndrome”.
      • The specific strain associated with the “cepacia syndrome” is the ET12 strain.
    • B. cenocepecia J2315 is part the ET12 ancestral linage.
    • The researchers sequenced the J2315 strain in order to find information regarding the how the ET12 linage adapted to result in the previously mentioned clinical symptoms.
      • The sequence of the J2315 strain would also give insight on the performance of the J2315 strain in patients with CF.
  • Materials and Methods
    • Bacterial strains
      • B. cenocepacia was first isolated in 1989 in the UK.
      • J2315 is resistant to several different drugs
      • In addition to J2315, 7 other previously sequenced strains were also used in this study.
    • Genome sequencing
      • Whole genome sequencing
        • DNA was extracted from J2315 and sequence data was obtained.
        • Sequence was annotated using the Artemis software.
        • Initial coding sequences were identified using Orpheus.
        • The CDSs were verified using protein databases in conjunction with BLAST and the DNA sequence was verified through all 6.
      • Comparative genomics
        • Comparisons of genome sequences were run using Artemis Comparison Tool
      • B. cenocepecia strain J2315 was compared to several other burkholderia species
    • PCR screening
      • CRP amplification was done using Platinum Pfx DNA polymerase with suppliers protocols.


Other Links

User Page: Anindita Varshneya
Class Page: BIOL/CMSI 367: Biological Databases, Fall 2015
Group Page: GÉNialOMICS

Assignment Pages

Week 1 Assignment
Week 2 Assignment
Week 3 Assignment
Week 4 Assignment
Week 5 Assignment
Week 6 Assignment
Week 7 Assignment
Week 8 Assignment
Week 9 Assignment
Week 10 Assignment
Week 11 Assignment
Week 12 Assignment
No Week 13 Assignment
Week 14 Assignment
Week 15 Assignment

Individual Journals

Individual Journal Week 2
Individual Journal Week 3
Individual Journal Week 4
Individual Journal Week 5
Individual Journal Week 6
Individual Journal Week 7
Individual Journal Week 8
Individual Journal Week 9
Individual Journal Week 10
Individual Journal Week 11
Individual Journal Week 12
Individual Journal Week 14
Individual Journal Week 15

Shared Journals

Class Journal Week 1
Class Journal Week 2
Class Journal Week 3
Class Journal Week 4
Class Journal Week 5
Class Journal Week 6
Class Journal Week 7
Class Journal Week 8
Class Journal Week 9
GÉNialOMICS Journal Week 10
GÉNialOMICS Journal Week 11
GÉNialOMICS Journal Week 12
GÉNialOMICS Journal Week 14
GÉNialOMICS Journal Week 15

Weekly Group Assignments Shared Group Journals Project Links Team Members
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