Sunday, October 07, 2007

GME 2007 - Genomes, Medicine and the Environment

I am now at the "Genomes, Medicine and the Environment" conference in San Deigo. It looks to be quite good and diverse. Here is the schedule for Monday. I will try and post notes either as they happen or later tonight. First note --- my undergrad. advisor, Colleen Cavanaugh is showing some cool pictures of deep sea organisms and their symbionts that chemosynthesize for them. She says "genomics is literally like opening a window into our science, because we cannot culture any of these symbionts." And now she is talking about our paper on the symbionts of the giant clam, Calyptogena magnifica. It is really cool for me to see this -- Colleen was the person who got me interested in microbes and symbioses and even though I only worked in her lab for 1.5 years, it changed my life and scientific career.


Opening Remarks, J. Craig Venter, Ph.D., JCVI

Synthetic Biology

Colleen Cavanaugh, Ph.D., Harvard University - "Genomic Insights into Chemosynthetic Symbioses"

Nancy Moran, Ph.D., The University of Arizona - "Genomics of Symbiotic Bacterial Communities within Insects"

Hamilton Smith, M.D., J. Craig Venter Institute - "Toward a Minimal Cell"


Steve Briggs, Ph.D., University of California, San Diego - " Development and Application of Protein Profiling Methods"

Yuri Gorby, Ph.D., J. Craig Venter Institute - "Electromicrobiology: The Role of Bacterial Nanowires in Extracellular Electron Transfer"

Edward Bayer, Ph.D., Weizmann Institute of Science - "Bioengineering of Cellulosomes: Prospects for Conversion of Biomass to Bioenergy"

12:00-2:00 Lunch, Sunset Ballroom

Environmental Genomics

John Heidelberg, Ph.D., University of Southern California - "Genomic, Metagenomic and Functional Analyses of Cyanobacteria from Hot-Spring Microbial Mats"

Gene Tyson, Ph.D., Massachusetts Institute of Technology - "Metatranscriptomic Analysis of Microbial Communities in the North Pacific Subtropical Gyre"

Syed Hashsham, Ph.D., Michigan State University - "Understanding Microbial Community Succession in Response to Substrate Shock using Roche 454 GS FLX Sequencing System"

David Schwartz, M.D., National Heart, Lung & Blood Institute Toxicology Program - "Environmental Genomics and Human Health"

Human Metagenomics

Ren Bing, Ph.D., University of California, San Diego School of Medicine - " Annotating the Human Genome - a ChIP-chip Approach"

Russell M. Gordley, B.A., Scripps Research Institute - " Evolution of Programmable Zinc Finger-recombinases with Activity in Human Cells "


  1. Hi Jonathan - please post notes. (unfortunately, I had a poster but couldn't scrounge up any travel funds, so could not attend)

  2. Here are some quick notes

    Colleen Cavanaugh
    *introduced chemosynthetic symbioses
    * discussed the sequencing of the Ruthia magnifica genome
    * compared chemosynthetic genomes to those of insect symbionts
    * discussed the Sulfur metabolism in Ruthia and showed the Sox pathway which is similar to that in C. tepidum
    * had a RedSox hat next to the "Sox" pathway
    * discussed the multiple pathways for nitrogen assimilation in Ruthia
    * discussed how Ruthia is missing some key cell division proteins and how it is unclear what these bugs do to compensate
    * suggested the possibility that these bugs are becoming organelles and that there may be "sulfuroplasts" out there that we may not have recognized as organelles.
    * gave a good plug for the MBL Genomics Course

  3. Yuri Gorby is now talking about nanowires in bacteria. And he is showing some video of cool ROV based sampling of vents in Yellowstone.

    They are doing a metagenomics project using these samples to compare deep microbes in deep vs. shallow vents in the lake.

  4. Nancy Moran gave a good talk on small genomed symbionts. Her main theme for the talk was "understanding what is going on with such small genomes"

    Some key points
    * She says her work in this area is a good example of cross fertilization in science. She says she got interested in this area when Paul Baumann at UC Davis got in touch with her about the possibility of dating symbiont evolution. She gave props to Paul for being one of the first to recognize that PCR could be used to study symbionts. It is particularly useful in symbiont studied because symbionts can be VERY diverged in appearance and this molecular data is the only way to figre out who they are.

    *Mentioned that a key aspect of studying symbionts is the comparison of host and symbiont phylogenies which can tell one if they are coevolving and if so, for how long.

    * Says everything that feeds obligately on plant sap has symbionts to make up for deficiencies in nutrient.

    * Discussed Carsonella this symbiont with a 150 kb genome. One interesting thing she said here --- the proteins in this genome are very diverged and it is not clear how they function but they appear to.

    *Up to 40% of the genes cannot be matched using standard methods to homologs but they probably are orthologs of E. coli genes.

    * Suggests small symbiont genomes might have transfered genes to host genomes. But no evidence for this despite some attempts to look. Said that there is a genome being sequenced of the Buchnera host the pea aphid.

    * Then she discussed Sulcia and Baumannia, the symbionts of sharpshooters.

    * Says they have finished the Sulcia genome (which we started with her) using 454 sequencing. They were able to bin 454 reads based on depth of coverage which was very different between the different organisms in the sample.

    * Sulcia is 250 kb. First highly reduced non gamma proteobacterial genome. Sulcia are bacteroidetes relatives, by the way.

    * Discussed the amazing complementarity between the host and the two symbionts.

    * Suggested tiniest genomes are from maternally transmitted ones with ancient mutual dependence.

    * Many have lost genes that seem universally useful. Not clear what the bugs do to compensate.

  5. Edward Boyer from the Weizmann had a bit of an unusual introduction. He said "Lets start at the beginning" fr his talk on biofuels. And then he said "In the beginning, God made the trees and other plants, but they die and make waste. God also made the bacteria and fungi which decompose the plant matter. And this all worked well for hundreds of millions of years. And then make came along and messed things up"

  6. Boyer is describing his isolation and description and characterization of the "cellulosome." Suggests there are two systems for degrading cellulose - cellulosomes (mostly from anaerobic bacteria) and free cellulases (mostly from aerobic microbes). He is also spending a lot of time promoting the importance of the cellulosome, which is a bit unneeded. He showed a Wikipedia entry proving he was not making it up. And he showed a few journal covers and some detail about a cellulolytic conference. And then he switched to talking aboiut the need to produce cellulases economically. Suggested that for the cellulosome some engineering might be needed to make it work better for commercial cellulose degradation.

  7. Ham Smith gave an overview talk on minimal genomes including some of their results on "genome transplantation."

  8. Gene Tyson gave a interesting talk on some of the work in the Delong lab on "metatranscriptomics" of various ocean going microbes. Basically, what they did was collect samples of microbes, split the samples in two and then did DNA sequencing of one half and RNA sequencing of the other. He showed some methods for then deconvoluting this data that seemes to be reasonable.

    Some tidbits

    *They did the sequencing with a 454-Roche machine in Stephan Schuster's lab at PSU.

    *They made extensive use of the GOS sequence data for comparison

    *He said most of their results support the gene annotation of the GOS data

  9. Mary Ann Moran is now talking also about metatranscriptomics. Seems like this is the next big thing in environmental microbiology (last year it was metaProteomics from Jill Banfield's lab)

  10. Dave Stahl, one of the people who indirectly got me into the whole field of environmental microbiology, is now talking about ammonia oxidizing archaea. He gave a good overview of the history of studies of this type of organism and is now talking about some comparative genomics of Nitrosopumilus versus various genomics and metagenomic data.

  11. Shannon Williamson is giving a talk on viral communities in the deep sea. She showed a pretty cool sampling protocol for collecting samples off of vent sites. And then they took these samples and for some treated with mitomycin C to induce viruses in the microbes present in the sample and then did sequencing of both the microbes and the induced viruses. They also are comparing samples from different deep sea sites.

  12. George Church just gave an excellent talk on the personal genome project. He reviewed the methods/technologies they are using as well as some of the important issues. He also asked the audience how many would sign up to have their genome sequenced. A dozen or so raised their hands.