Rationale

OK, this is the main event.

Why 'What is a Gene'? Why codons? Why BioBIKE? All of that so that you could be prepared for the analysis of mycobacterial phage genomes, a project that will consume most of the remainder of the semester. The goal of this unit is to give you an introduction to bacteriophage genome analysis and the specific areas of analysis that will be of most interest to us.

There's too much to learn about genome analysis. There's WAY too much to learn. Never mind you, there's too much for ME to learn, or any other human for that matter. Fortunately, humans have made significant progress despite the fact that no single human is an expert in all areas. The strategy for your research project is similar to the strategy for all large research projects: each person becomes expert in a small slice of the pie and conversent about other people's slices. Each person contributes to the whole, even though the whole is too big for any single person.

Readings, Tours, and Investigations
    Tour:
        Search for FMRP in Drosophila.
        Hatfull GF, Cresawn SG, Hendrix RW (2008). Research in Microbiology 159:332-339.

    Reading and Tour:
        Comparative genomics of the mycobacteriophages: Insights into bacteriophage evolution.
        The flavors of BLAST and their nature
        Tour: Part I and Part II

    Reading and Tour:
        The phage proteomic tree: A genome-based taxonomy for phage.
        Rohwer F, Edwards R (2002). Journal of Bacteriology 184:4529-4535. (+ tour)

    Reading and Tour:
        In silico analysis of mycobacteriophage Che12 genome: Characterization of genes
        required to lysogenise Mycobacterium tuberculosis.
        Gomathi NS, Sameer H, Kumar V, Balaji S, Azger Dustackeer VN, Narayana PR (2007).
        Computational Biology and Chemistry 31:82-91. (+ tour)

    Reading and Tour:
        Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
        Karlin S (2001).
        Trends in Microbiology 9:335-343. (+ tour)

    Tour:
        Was Mendel Right? (Part I and Part II )

Problem Sets
    Problem Set 4: Loops and Mapping (Target date March 5)
    Problem Set 5: Genome Analysis (Target date March 12)
    Problem Set 6: Statistics (Target date March 24)

Analysis Groups
Each group is defined by a core focus, which comes with a suggested article. Group members may use this article as inspiration, a starting point to find other pertinent articles, and an aid in defining and subdividing the project. A group is under no obligation to stick to any predetermined agenda, so long as it goes in a direction that is even more interesting than the original.

• Phylogeny Group/Charlie (Daniela, James, Ranya, Sophie, Stephanie)
      (TUE 11 AM / WED 9AM, Life Sci computer lab) Apr 6, Apr 14, Apr 20, Apr 28
  How do we draw connections between different bacteriophage?
  What family tree can be developed that incorporates the new phage genomes?
          The phage proteomic tree: A genome-based taxonomy for phage.
          Rohwer F, Edwards R (2002). Journal of Bacteriology 184:4529-4535.
   
• Mosaicism Group/Cornelius (Kevin, Mike, Muna, Rashonda) (TUE 12 noon, Life Sci computer lab)
  How can the different sources of a phage genome be recognized?
  Where do the parts of the new phage genomes come from?
          Genomic characterization of Mycobacteriophage Giles: Evidence for phage acquisition of host DNA
          by illegitimate recombination..
          Morris P, Marinelli LJ, Jacobs-Sera D, Hendrix RW, Hatfull GF (2008). Journal of Bacteriology 190:2172-2182.
   
• Sequence Bias Group/Theia (Christian, Jeri, Jesus, Katherine, Pratik)
      (Wed 9 AM / TUE 5 PM, Life Sci computer lab) Apr 7, Apr 13, Apr 21, Apr 27
  Do the new genomes exhibit oligonucleotide frequencies (e.g. codon frequencies) that can't be explained by chance?
  Do the phage sequence biases match those of their presumed bacterial hosts?
          Codon usages in different gene classes of the Escherichia coli genome..
          Karlin S, Mrázek J, Campbell AM (1998). Molecular Microbiology 29:1341-1355.
   
• Mobile Element Group/Trixie (Alex, Kanika, Kelly, Robel, Tara) (MON 2 PM, Life Sci computer lab)
  Do the new phages have sequences that appear to have inserted into their genomes?
  Are the insertions found in other genomes as well?
          Mycobacteriophages BPs, Angel and Halo: Comparative genomics reveals a novel class of ultra-small
          mobile genetic elements..
          Sampson T and 8 others (2008). Microbiology 155:2962-2977.
   
• Phage Integration Group/Wile (Amy, Erik, Lame, Shivanthi, Steven) (WED 10 AM, Life Sci computer lab)
  Do the new phage have protein indicative of a lysogenic life style?
  Can the sites of integration and repression of lytic expression be identified?
          In silico analysis of mycobacteriophage Che12 genome: Characterization of genes required to lysogenise
          Mycobacterium tuberculosis..
          Gomathi NS, Sameer H, Kumar Vanaja, Balaji S, Azger Dustackeer VN, Narayana PR (2007).
          Computational Biology and Chemistry 31:82-91.