ComBio 2006 Day 1

A very brief round-up.

The day did not start well. The conference centre is loaded with wireless access points (Linux tip of the day: ‘iwlist eth0 scanning’), but the opening pages of the conference program tell me:

BCEC provides user-pays internet access…

Too right the user pays. Ten dollars for 30 minutes, to be exact. No thank you. This is a major national/international meeting with no free internet access for delegates? Get real, ASBMB. You’ll be hearing from me in the suggestion box.

No choice but to listen to the talks then. Here’s what I heard today.

  • Invasion, remodelling and disease – malaria in humans. This had the potential to be really interesting – it’s all about how the malaria parasite modifies erythrocytes for its own ends. Here’s a reference if you’re interested. Unfortunately, rather too much background information and too little actual data made it rather hard to follow for me.
  • Discovery and design of biological networks. Much more interesting – a talk on synthetic biology. Included the “bacterial digital camera”, if you recall that from Nature a few months ago.
  • Bulged epitopes and MHC restriction. Immunology isn’t really my thing, but quite interesting nonetheless – presented some MCH-peptide structures that exhibit, you guessed it, bulged epitopes.
  • GATA-1 and PU.1 interaction. Some structural insights into transcription factor interactions. Way too specific to be of much interest to me.
  • Decoding the vertebrate regulome. This is much more like it – a great talk by Tim Hughes. They aim to define the targets of every vertebrate DNA-binding domain – and it’s not as crazy as it sounds.
  • Regulatory events in neural crest induction and migration. I like developmental biology talks as they always have lots of pretty pictures (GFP-labelled proteins migrating around and that sort of thing). This was no exception, if a little hard-core embryology for me.
  • Ser/Thr protein kinase signaling in tuberculosis. Only talk today in my current area. Emphasised that prokaryotes really do have functional eukaryote-like protein kinases. They’re fewer in number and that might be because they exert global changes via environmental sensing and direct action on transcription. Should try and chat to this guy sometime.
  • Mitochondrial protein import and TIM9.10. So TIM9 and 10 are these dinky little 2-alpha helix hydrophobic proteins that bind to proteins destined for the mitochondrial inner membrane and guide them on their way.
  • Protein recruitment by Lsm rings. Lsm/Sm proteins bind various RNAs on their processing journey through the cell. They occur as rings of 6, 7 or 8 subunits. Noone has reconstituted a mixed ring with much success to date. Archaea to the rescue! They form a simpler, homo-heptameric ring structure. Once again an illustration that analogous processes in Archaea are of use in understanding Eukarya if you can get over your single-cell snobbery. Oh and this work is by friends of mine.

There was much more. I paced myself, it’s only day 1 after all. I’m not convinced yet that this meeting is of great value for me – it’s rather large, diverse and most of the bioinformatics is by people from the IMB which I’ve heard already. Still, it’s a break from the daily grind and a chance to broaden my biological education. There are worse places to be than Brisbane’s South Bank in spring.

3 thoughts on “ComBio 2006 Day 1

  1. Pedro Beltrao

    Do you happen to have one or two references for Ser/Thr in prokaryotes. I have been thiking about an idea regarding specificity of binding and cellular complexity/cellular size and I actually though the there were no Ser/Thr kinases in prokaryotes. The idea goes along the lines of smaller less complex cells have to use more specific components and an example is the use of His kinases instead of Ser/Thr kinases.

  2. nsaunders Post author

    Try “Alber T[AU]” or “Kennelly PJ[AU]” in PubMed. Those two are the main guys in the prokaryote protein S/T/Y kinase field.

    Here are some slightly dated reviews to start you off:
    Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry

    Protein kinases and protein phosphatases in prokaryotes: a genomic perspective

    You might also like to try the “experiment” yourself, if you have the hmmer package installed:

    1. Get file ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.faa.tar.gz (246 057 858 bytes), or from your local BioMirror
    2. gunzip all.faa.tar.gz – creates about 384 directories, one per genome, containing .faa files
    3. Browse to http://pfam.wustl.edu/cgi-bin/gethmm?name=Pkinase&type=ls and save page as “Pkinase.hmm”, plain text
    4. find ./ -name “*.faa” -exec hmmsearch --cut_tc Pkinase.hmm {} > genomes.hmmer \; (wait patiently)

    Parsing the hmmsearch report is left as an exercise for the reader :)

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