Tuesday, September 16, 2008

Lake arrowhead notes - UPDATED

Well I gave my talk

Seemed to go ok except getting cutoff early because the chair ignored
that the session started late but that is ok

George Weinstock is now speaking using my laptop so I am trying to
post from my phone

He said one key thing I left out ... Big scale microbial sequencing
projects are now possible thanks to next gen sequencing in particular
454-Roche tools

More later
Sent from my iPhone


More now

George Weinstock gave a good overview of the "Human Microbiome Project" which is a NIH Roadmap initiative to catalogue the genomic content of the microbes associated with humans. He described some of the big picture of why do the project, of the different fundingin initiatives being done through NIH and he gave some detail on the "jumpstart" project going on at the big genome centers right now. He outlined how the current plan is to select a few hundred people and to survey their mcirobiomes from multiple sites using rRNA PCR and possibly metagenomics. In addition, he described how there is also an effort to sequence 100s if not a 1000 genomes of cultured organisms that have been isolated from human environments. He did say one thing I disagreed with which is that he thinks it is somewhat reasonable to treat the environment that microbes live in in essence as a big bag of genes. In other words, if you sequence from a community, he implied that one can focus just on the genes and their functions and not the organisms that they come from. On this I disagree (and pointed this out after the next talk). But overall George gave anice overview of the project and its goals.

Eric Wommack gave a good talk about viral metagenomics work he has been doing. He pointed out that a lot of the viral world is "unknown" but that does not mean it is unimportant. And this is consistent with what I and George Weinstock said which is that we need more genome data from viral isolates. Eric presented some very useful results on the challenges of using short read sequence data in metagenomics and he referenced a few papers on this. He also referred to a cool viral genome survey project that I was not aware of by Hatfull which involved undergraduates in sequencing and analyzing the genomes of phage that infect Mycobacterium smegmatis.

Jim Bristow on Biofuels. He is now giving a summary of some of the JGI work on the genomics of cellulolytic organisms and processes. He is focusing on the termite gut community and had some good one liners about this (e.g., he said many people want to kill termites but not JGI. They are our friends; he also said "it takes a village to sequence a termite gut").

Not sure exactly how to say this, but here goes. There was one talk in the AM I was not overly fond of. This was a talk by Bernard Palsson. Now I confess, I am not overly familiar with much of his work but what I know of it suggests he does some really solid, interesting and important work on metabolic network modeling and analysis. But his talk at this meeting was disappointing. His talk was about his use of genome sequencing to characterize "adaptive evolution" in E. coli. And the results he presented seemed solid enough. The problem I had was that it was a prime example of "overselling genomics". Why? Here is what they did. They took E. coli mutants. And the then took them through cycles of growth and then dilution. And then they looked at the populations after a certain number of generations and did a variety of analyses. Included in this was some whole genome sequencing that helped identify mutations arising in the cultures. And then they did some characterization of these mutations/mutants including some competition experiments and some pretty interesting gene expression studies of some RNA polymerase mutants. And he made some conclusions based on their results like that E. coli in the lab can find new adaptive peaks and that mutations differ in different replicates, and that different mutations confer different fitness, that they can monitor the appearance of mutations over time, and so on.

So what is the problem -- the problem is that he (1) presented this as though the serial cycling of E. coli was novel when in fact it is not and that (2) he presented the conclusions as though they were novel when they also are not. People have been doing this type of experiment for many decades (in fact, one person, Rich Lenski, has been doing an experiment like this for decades). And they get these exact results. But they have not sequenced genomes as part of their experiment. And thus, at least for this talk, they were not mentioned, and the rediscovery of many truisms in population genetics was presented as novel because it involved genome sequencing.

Trent Northen created a serious buzz during and after his talk with his presentation of some of the things one can do with Nanostructure Initiated Mass Spectrometry (NIMS). I confess - I want his toys.

Lynn Silver is now talking about the challenges in the development of new antibiotics. She argues that the focus by some on trying to find new targets for antibiotics has been a bit misguided.

Julian Parkhill gave a good talk about population genomics of Salmonella. He pointed out a few things people still ignore. For example, if you want to identify polymorphisms in a species to use for population genetics/genomics studies, you really need to do a survey to identify polymoprhisms from diverse members of the population. If you do not, and then you use a biased set of polymorphisms, your population inferences will be wrong. He also said, in response to a quesiton of mine, that at least for this species, they see very little variation in copy number in genes which is different than what people seem to see in humans.

Tiffany Williams from Baylor gave a talk about using high throughput sequencing in collaborations with developing countries. She outlined some of the challenges as well as the benefits from such collaborations.

Kim Lewis gave a very interesting talk on microbial biofilms and persister cells, of which I know vanishingly little. He showed some very cool experiments trying to "complement" unculturable organisms and get them to grow.

Jeffrey F. Miller gave a talk focusing on diversity generating retroelements in bacteria which appear to be a means by which bacteria can target particular regions of the genome for mutagenesis in a comparable way to VDJ mutagenesis in humans. This was perhaps my favorite talk so far at the meeting as it combined microbial genomics, evolvability, mutation processes and other things I tend to focus on.

Steven Benner gave a talk which I had to skip out on early because I was doing a radio interview. Benner said one thing that annoyed me at the beginning - he made a comment that was complaining about prior talks that referred to "Rosetta Stone" methods of predicting function (I was one of the people who mentioned this) because he thought that we were referring to blast searches. He clearly was not paying any attention as the Rosetta Stone method is a method to predict function for genes by finding connections between non homologous proteins based upon having other proteins that have domains found in both of the original proteins of interest. Oh well, glad I had to leave early because I was itching to jump up and correct him.

Heather Allen, from Jo Handelsman's gave a very good talk about doing functional metagenomic screens for antibiotic resistance encoding genes. She has been using DNA from multiple soil sites, including a pristine site in Alaska, and screening the DNA for antibiotic resistance genes in E. coli. These screens identify a wide diversity of genes, including some novel forms. This work helps highlight the need to not just sequence the snot out of the world but to also do some functional assays at the same time. In addition she mentioned that she was able to come to the meeting because Jo Handelsman set up a fund for mothers to pay for babysitters to come to a meeting with them. All I can say is Jo Handelsman was already one of my favorite people in science and this is just another brilliant and wonderful thing that she does.

David Relman gave a talk about two studies of the human microbiome that his lab has been doing: (1) studies of marine mammals to compare the microbial diversity in their surfaces with the diversity in the water and the diversity on their insides and (2) study the response of the human gut microbial community to antibiotic treatment. I am particularly fond of the antibitotic treatment study because they are treating it as an "ecological disturbance" study and analyzing it much like ecologists would analyze recovery of a forest after fires. I think we definitely need more ecologists to bring their techniques and skills to human microbiome studies and so this was exciting to see.

Ashlee Earl gave a talk about biofilm formation in Bacillus subtilis. Much like Kim Lamb's talk earlier, this talk was in an area I know little about and I guess you could say it kind of blew my mind. It seems that in B. subtilis and I guess in many other microbes biofilms are in essence analogous to multicellular organisms. Within a biofilm there are different types of cells that have different roles and the patterns are highly reproducible and organized. It seems to me that the boundary between multicellular and single-celled organisms is getting blurrier and blurrier. Ashlee reported on some cool experiments where she collected strains from around the world and then dod comparative genetics and genomics of their biofilm formation patterns.

Alas I missed Mary Lidstrom's talk which based upon prior experiences I am sure was fascinating. She has been working in studying processes inside single bacterial cells and has been developing a suite of techniques and tools to carry out such studies. Maybe someone else from the meeting can post details about her talk.

Unfortunately, I had a conference call during some of the next talks that I had to do so I do not have details for the blog. Then I returned and served as chair for a session. I did take some notes so here goes.

Byung-Kwan Cho gave a tour de force talk about reconstructing the transcriptional regulatory network in E. coli. He presented results from a dazzling and dizzying array of genome-scale methods (e.g., ChipChip, tiled arrays, sequencing, etc etc) to characterize transcription regulation. In addition he did some complex and big scale computational work to combine all of the data together to characterize networks. It was quite impressive stuff.

Ginger Armbrust talked about her favorite critters - diatoms and focused on how they used the genome data to characterize silicon deposition processes. She was convincing as to the importance of diatoms and to the value of having the genome sequences from some species. She did discuss some of the challenges of using the genome data including the challenges in gene prediction for microbial eukaryotes. She also discussed her dream of utilizing some of the new genomic information as part of real time sensors in the oceans.

Anthanasios Typas discussed work to build tools for carrying out genome-scale analyses of genetic and chemical-genetic interactions. For example they are working on taking two comprehensive gene KO libraries from E. coli and using them to create all possible double mutants and to then screen those mutants for whether they have the same or different phenotypes than the single mutants. This allows them to look for gene-gene interactions. They also are doing this type of analysis with chemical-gene interactions.

Devaki Bhaya gave a brief talk on what I think is the single most interesting thing in all of microbiology right now - CRISPRs. These are clustered regularly interspaced short palindromic repeats. She is studying them in cyanobacteria from Yellowstone hot springs

Good quotes from the meeting:

  • So we simply sequenced the genome of the different variants
  • Antibitoics do not kill things, they corrupt them
  • Dormancy is the default mode of most bacterial life
  • Who knows what a yoctomole is?
  • I am going to defend genomics
  • There comes a point in life when you have to bring chemists into the picture
  • Gosh, was that today or yesterday
  • The rectal swabs are here in tan color
  • I'll try to let the pictures do the talking and I will get out of the way
  • Our model system de jour
  • And there's Jeffrey Dahmer
  • And this is my cheesy analogy here
  • He could not be here so I am here. His loss. My gain. Hopefully not your loss.
  • We are the environment. We live the phenotype.
  • If I have time I will tell you about a dream
  • Every fifth breath - thank a diatom
  • While we still have poles
  • A paper came out next year

1 comment:

  1. Hey Jonathan,

    I'm catching up on reading while a validation script chews up most of my CPU cycles ... It sounds like the Lake Arrowhead meeting was, as usual, a great one. Sorry I missed it.

    Since you're adding links where possible, here's one for Heather Allen.

    I've known Jo Handelsman for ages -- we were classmates in grad school -- and yet I didn't know about the "Moms on the Go" fund until you mentioned it! BTW, I asked, and Dads are also eligible, which would have been handy back in the day ... Anyway, I've added it to my alumni giving list.

    One quick question: You awrote "Ashlee Earl gave a talk about biofilm formation in Bacillus subtilis. Much like Kim Lamb's talk" -- shouldn't that be Kim Lewis?