Moore Notes 9 18 12

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Group Call - Journal Club

  • Attending: Tom, Josh, Dongying, Stephen, Katie
  • Inconsistencies in SFams db (Tom)
    • 1st and 2nd rounds of clustering results disagree due to data encoding changes at IMG
    • How to handle future updates?
      • Just IMG or other data resources?
      • How to handle version control when IMG updates their annotations?
      • Hard to identify the problematic sequences
      • Hard to reinitialize the SFams if they become obsolete
    • Dongying and Tom will follow up
    • Keep it simple for future updates
  • Journal Club: Deepwater Horizon http://www.nature.com/ismej/journal/v6/n9/full/ismej201259a.html
    • Two plume communities and one distal community at similar depth
    • Comparisons of:
      • Taxonomic composition
      • Pathways in genomes
      • Pathways in transcriptomes
    • Single cells and filtrate (metagenome/metatranscriptome)
    • Timing of samples and progression of response to spikes of new metabolites and electron donors (waves over time as move through compounds from easiest to hardest to metabolize)
      • Bloom of oceanospirillales and metabolism of hydrocarbons
      • Maybe a rare organism is eating a little bit of benzene (could bloom later possibly), or common organism would shift onto it when other metabolites run out
    • Additional reading: http://www.nature.com/ismej/journal/v6/n9/full/ismej2011197a.html
      • DNA/RNA extraction techniques and library prep bias comparisons of metagenomes and metatranscriptomes
    • Our tools might be useful for annotation of single cell genomes and transcriptomes (growing approach)
    • Josh: good to think about limiting nutrients (alkanes in this study)
      • Who will take over the community?
    • More good work on bioremediation from JGI and others.
  • Next time: two weeks from now
    • Josh
    • Guillaume, Tom and Dongying will meet at JGI next week for SFams presentation/mtg