Difference between revisions of "Anuvarsh Week 11"

From LMU BioDB 2015
Jump to: navigation, search
(→‎Outline of Paper: first two parts of paper copied over)
(→‎Outline of Paper: finished results)
Line 30: Line 30:
 
**PCR screening
 
**PCR screening
 
***CRP amplification was done using Platinum Pfx DNA polymerase with suppliers protocols.
 
***CRP amplification was done using Platinum Pfx DNA polymerase with suppliers protocols.
 +
*Results
 +
**Fig. 1: Genome contained 3 circular chromosomes and a plasmid. The figure features diagrams of each of the chromosome and plasmid that are color coded according to CDSs.
 +
**Table 1: This table contained general features of the plasmid and each of the chromosomes in the B. cenocapacia J2315 genome. Chromosome 1 has the greatest number of base pairs, CDSs, and pseudogenes and partial genes while the plasmid has the fewest of each of those categories
 +
**Fig. 2: The general distributions of CDSs among chromosomes and the functional classes they are associated with.
 +
***Chromosome 1 has more CDSs that are involved with core functions of the cell (cell division, metabolism, etc.). Chromosome 2 and 3 have more CDSs that are involved with accessory functions (protective responses, gene transfer), and other unknown functions.
 +
**Fig 3: The orthologs associated with B. cenocepacia J2315 include B. cenocepacia HI2424, B. cenocepacia AU1054, B. contaminans 383, B. ambifaria AMMD, B. vietnamiensis G4, B. xenovorans LB400, B. pseudomallei K96243, B. thailandensis H264 and Ralstonia solanacearum GM11000.
 +
***B. cenocepacia was compared to 5 other Burkholderia cenocepacia complex (BCC) genomes in the public database as well as 4 other strains of B. cenocepacia known to cause melioidosis and glanders. The largest number of orthologs (found using FASTA) were found in the BCCs and Ralstonia solanacearum.
 +
**Table 2: RODs exist in the B. cenocepacia J21315 genome.
 +
***Comparison between B. cenocepacia strains found regions of difference (RODs) indicating that 21% of J2315 contains RODs.
 +
****These include genomic islands that appeared most likely due to horizontal gene transfer.
 +
****Genomic islands were defined as regions displaying irregular %G+C content or other indications of recent horizontal transfer of genes. Genes associated with mobile genetic elements (MGEs) were also identified (bacteriophages, transposons, and plasmids).
 +
****Other RODs in J2315: indel regions representing lineage specific DNA insertions or deletions ad allelic variants that have divergent sequences at the same locus.
 +
*****RODs not including at least one complete CDS were not considered in this analysis
 +
***ET12 linage of B. cenocepacia emerged recently and spread between patients readily, thereby causing disease. This may be attributed to 14 genomic islands in J2315 strain.
 +
**Table 3: 9 special functions encoded in the J2315 genome were identified that may have added effects to the virulence of J2315. These functions include exoproteins, secretion, LPS and capsule, adhesins, fimbriae and pili, quorum sensing, siderophores, intracellular stress, and motility.
 +
***Each of these functions are specific to J2315, and do not appear in other strains in the BCC.
 +
**Table 4: J2315 exhibits incredible drug resistance, which has been attributed to specific functions and products of each chromosome.
 +
***Chromosome 2 has the largest number of products that result in drug resistance.
 +
Some drugs J2315 is known to be resistant to include: Fosmidomycin, aminoglycosides, trimethoprim, tetracycline, and others.
 +
 +
  
  
 
{{Template:Anuvarsh}}
 
{{Template:Anuvarsh}}
 
{{Template:GÉNialOMICS}}
 
{{Template:GÉNialOMICS}}

Revision as of 05:19, 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.
  • Results
    • Fig. 1: Genome contained 3 circular chromosomes and a plasmid. The figure features diagrams of each of the chromosome and plasmid that are color coded according to CDSs.
    • Table 1: This table contained general features of the plasmid and each of the chromosomes in the B. cenocapacia J2315 genome. Chromosome 1 has the greatest number of base pairs, CDSs, and pseudogenes and partial genes while the plasmid has the fewest of each of those categories
    • Fig. 2: The general distributions of CDSs among chromosomes and the functional classes they are associated with.
      • Chromosome 1 has more CDSs that are involved with core functions of the cell (cell division, metabolism, etc.). Chromosome 2 and 3 have more CDSs that are involved with accessory functions (protective responses, gene transfer), and other unknown functions.
    • Fig 3: The orthologs associated with B. cenocepacia J2315 include B. cenocepacia HI2424, B. cenocepacia AU1054, B. contaminans 383, B. ambifaria AMMD, B. vietnamiensis G4, B. xenovorans LB400, B. pseudomallei K96243, B. thailandensis H264 and Ralstonia solanacearum GM11000.
      • B. cenocepacia was compared to 5 other Burkholderia cenocepacia complex (BCC) genomes in the public database as well as 4 other strains of B. cenocepacia known to cause melioidosis and glanders. The largest number of orthologs (found using FASTA) were found in the BCCs and Ralstonia solanacearum.
    • Table 2: RODs exist in the B. cenocepacia J21315 genome.
      • Comparison between B. cenocepacia strains found regions of difference (RODs) indicating that 21% of J2315 contains RODs.
        • These include genomic islands that appeared most likely due to horizontal gene transfer.
        • Genomic islands were defined as regions displaying irregular %G+C content or other indications of recent horizontal transfer of genes. Genes associated with mobile genetic elements (MGEs) were also identified (bacteriophages, transposons, and plasmids).
        • Other RODs in J2315: indel regions representing lineage specific DNA insertions or deletions ad allelic variants that have divergent sequences at the same locus.
          • RODs not including at least one complete CDS were not considered in this analysis
      • ET12 linage of B. cenocepacia emerged recently and spread between patients readily, thereby causing disease. This may be attributed to 14 genomic islands in J2315 strain.
    • Table 3: 9 special functions encoded in the J2315 genome were identified that may have added effects to the virulence of J2315. These functions include exoproteins, secretion, LPS and capsule, adhesins, fimbriae and pili, quorum sensing, siderophores, intracellular stress, and motility.
      • Each of these functions are specific to J2315, and do not appear in other strains in the BCC.
    • Table 4: J2315 exhibits incredible drug resistance, which has been attributed to specific functions and products of each chromosome.
      • Chromosome 2 has the largest number of products that result in drug resistance.

Some drugs J2315 is known to be resistant to include: Fosmidomycin, aminoglycosides, trimethoprim, tetracycline, and others.



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
Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Anuvarsh_Week_11&oldid=6244"