Final project

• Final project
  • Brief summmary of rules
    • Credit
    • Teams
    • Multimedia
  • 2007 theme
    • How the theme connects to topics covered in class
    • General idea of projects
    • Specific hints for starting points
    • Caveat
  • Dates

Brief summmary of rules

The idea of the final project is to expand on one of the homework exercises, labs or lectures. You will give a 5-minute presentation on this work in class.

Credit

The final presentation will be worth 25% of the final grade.

Teams

You are encouraged to form teams, in which case you will get 5 minutes per person in the team. You also need to clearly identify the separate contributions of team members.

Multimedia

The idea of the "elaboration" is to extend or riff on the original homework idea: to think about previously undiscussed algorithms or theory issues (or generalizations of the algorithm); to visualize it by showing some previously unseen pictures; or to do a Karaoke song or a standup routine or a videogame pitch... all of these are admissible (though bear in mind that you will be assessed on both scientific content as well as presentation, so do bear this in mind if you choose to go for a multimedia extravaganza...)

You will have full access to the class AV equipment (including speakers) and you can bring your laptop. The time limits will be strictly enforced, with 2- and 4-minute warnings.

2007 theme

A suggested theme (and this is just a suggestion -- you're free to pursue other ideas) is the following recent paper from JGI:

• Makarova KS et al.  Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.  PLoS ONE. 2007 Sep 26;2(9):e955.

How the theme connects to topics covered in class

This paper discusses the comparative genomics of radiation-tolerant extremophiles (Wikipedia) . The paper contains a lot of bioinformatics analysis and there are many opportunities for you to apply the ideas and algorithms in the class syllabus (alignment, phylogeny, ontologies, pathway mining, gene prediction, probabilistic analysis, protein structure visualization...)

General idea of projects

The suggestion here is that you describe, analyze, reconstruct or extend some small part of the analysis in this paper using the ideas that we have covered in class or lab. For example, you could use a program that you have written and compare the results to the ones shown here; or you could discuss an analysis from the paper, explaining the algorithms together with the biological implications of the results.

Specific hints for starting points

• Read papers (e.g. this one) on bioengineering Deinococcus geothermalis for bioremediation of hot nuclear waste dumps
• Download Genbank entries for Deinococcus geothermalis and Deinococcus radiodurans
  • Note that there may be multiple entries, e.g. the D.geothermalis genome spans several plasmids
• Make alignments and/or sequence logos for the palindromic "radiation/desiccation response motif" (RDRM) located in upstream regions of radiation-resistance genes
  • According to the paper, such genes include DR0326, DR0423, DRA0346, DR0070, DR0219, DR0906, DR1913, DR0659 ...
• Reproduce the part of the analysis where genes common to both thermophiles are identified
  • As above, try to identify genes common to both thermophiles, but restrict the search to genes that are implicated in radiation resistance in D.radiodurans
• Build phylogenetic trees for gene families of interest
  • e.g. one of the families in the gene-gains-and-losses figure (Fig 3) or the conserved-gene-alignments figure (Fig 5)
  • compare the "gene tree" to the "species tree" of the organisms from whence the genes were taken. Are they in agreement? (Sometimes, in bacteria, they aren't: for example, in the lactic acid bacteria, the phylogeny for proteins associated with the transcription/translation machinery is different from the phylogeny of the fermentation-related proteins, suggesting horizontal gene transfer possibly associated with an ecological adaptation)
• Look in each genome for genes connected to a particular Gene Ontology term, and make a prediction about the biology of the organisms based on the number of genes you find in that pathway
  • e.g. are there any genes for tryptophan biosynthesis? If not, the bacterium may be a tryptophan auxotroph (Wikipedia)
  • a starting point might be the metabolic or other processes referred to in the paper, e.g. GO:0005996 (monosaccharide metabolism), GO:0016491 (oxidoreductase activity), GO:0006281 (DNA repair) ...

Caveat

Note (again) that you are free to choose a different topic other than those listed.

Dates

Final presentations will take place during the last 3 lectures of the semester (Wednesday 12/5, Friday 12/7 and Monday 12/10).

Please sign up on the Final Presentation Schedule.