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Here is a link to my FriendFeed notes from Day1 of the meeting - http://friendfeed.com/e...
Keynote: Craig Venter, JCVI - http://www.jcvi.org/
Jonathan Eisen and Ricardo Vidal liked this
Craig is here, and the room is basically full.
- Jason Stajich
Craig's talk entitled, "reading to writing the genetic code"
- Jason Stajich
in honor of Craig I am posting a link to an interesting story about him and sequencing the ocean http://homepage.mac.com/jonatha... that I distributed on APRIL 1 (hint hint) two years ago
- Jonathan Eisen
Jason beat me to the punch on the thread creation
- Thomas Sharpton
April 1, 2009 is just around the corner.....
- Thomas Sharpton
Eddy says Craig's science is marked by "punctuated revolution"
- Jonathan Eisen
"new revolution on how to write the genetic code after reading it"
- Jason Stajich
Craig gave a cool TED talk on this subject not too long ago for the less scientifically literate
- Thomas Sharpton
Showing a picture of my old haunting grounds (the JCVI / ex TIGR campus in MD)
- Jonathan Eisen
JCVI will be Designing and constructing the world's first zero-carbon facility
- Jason Stajich
Big questions - can we be reductionists to pare down life to bare minimum.
- Jason Stajich
Quote of the day "Plenty of people ask these types of big questions, usually after smoking something"
- Thomas Sharpton
His big questions: what is life (which he says you ask after smoking something), can we digitize life, how extensive is it, can we pare it down to basic components, can we regenerate it
- Jonathan Eisen
Talking about moving biology from analog to digital data
- Thomas Sharpton
"digitizing life" being important. 50M EST sequnces in dbEST - that seems low...
- Jason Stajich
1st genome was 14 years ago, 8 genomes per 454 run now (multiplexed)
- Jason Stajich
Many completed genomes, JGI has done more than any other institution (by NUMBER)
- Jason Stajich
tom - i dunno, "Sex with dead things is better than no sex at all" from peg riley is in competition
- val
JGI has done more genomes than any other institutions, but together, JCVI and JGI have sequenced half of those available across the world
- Thomas Sharpton
Says he JGI and JCVI have produced half the genomes in the world (left out TIGR there but he counts it as part of JCVI)
- Jonathan Eisen
citing genome paper of a diploid individual (PLoS Biology paper)
- Jason Stajich
see human genome paper in PLOS Bio http://biology.plosjournals.org/perlser...
- Jonathan Eisen
Moving onto Sargasso Sea sequencing project, understanding genetic makeup of the environment
- Thomas Sharpton
sorcerer II sampling around Europe.
- Jason Stajich
showing slide entitled Fragment recruitment SAR11 - indicating regions where there are differences, like a viral genome insertion.
- Jason Stajich
5 recuited taxa (37% of sequences sampled) are SAR11, SAR86, Prochlorococcus, alpha-Proteombacterium, Synechococcus
- Jason Stajich
20 Million gene set being worked on. trouble is "computational tools and on these sets get harder at each stage"
- Jason Stajich
With such a rapidly growing dataset, computational tools become taxed and present new challanges.
- Thomas Sharpton
Rate of new gene finding in mammals has plateaued, but still moving at linear stage of discovery.
- Jason Stajich
Shows this figure from Yooseph et al (http://biology.plosjournals.org/archive...)
- Jonathan Eisen
Mentions that we've pretty much discovered all of the mammalian genes, but we're still in linear phase of gene discovery in microbes
- Thomas Sharpton
not a fair comparison, though, given the phylogenetic distances that make up the groups he's considering with that argument
- Thomas Sharpton
switching from diversity to what is the minimal set of genes, looking at Mycobacterium genitalium. ~400 genes, to figure out which ones are essential. hard to do sequential KO, so easier to synthesize the genome instead.
- Jason Stajich
Raises question regarding which genes are essential and what's the small, or simplest, genome that can be synthesized
- Thomas Sharpton
showing PNAS paper on bacterial phage synthesis. (phi-X174)
- Jason Stajich
error rates are a fairly sizable problem in DNA synthesis when dealing with long fragments
- Thomas Sharpton
Turning the digitization concept on it's head, now he's taking digital data and turning it into analogous biological sequence
- Thomas Sharpton
Says that you can only synthesize something accurately if the database is accurate
- Jonathan Eisen
bermuda standards are untolerable for synthetic biology...
- Jason Stajich
"This software builds it's own hardware"
- Thomas Sharpton
describing bootstrapping "software building hardware" Isn't this basically RNA world?
- Jason Stajich
Bring back the RNA world
- Jonathan Eisen
well, it's central dogma too
- Thomas Sharpton
incorporated dna watermarks into their synthetic genome to ensure that what booted up in the cell was that which they synthesized
- Thomas Sharpton
says you can write all sorts of things in a genome and he is trying to write more clever thigns in this genome - maybe he should write "SARAHPALIN" http://phylogenomics.blogspot.com/2008...
- Jonathan Eisen
synthesizing genomes, troubles when get to 100kb.
- Jason Stajich
Hierarchical DNA assembly of synthetic fragments
- Thomas Sharpton
Referring to one of my favortie bugs - Deinococcus radiodurans - and using it to reassemble large DNA pieces b/c it can do this well
- Jonathan Eisen
D. radiodurans is a great model for genome assembly as it can reconsititute it's genome sequence after RAD attack
- Thomas Sharpton
Learning from Deinococcus radiodurans -- "Somehow it reassembles its genome"
- Jason Stajich
Reinventing YACs...?
- Jason Stajich
Bringing back YAC
- Thomas Sharpton
Says it works better in yeast
- Jonathan Eisen
Recombing YACs to make larger segments I guess.
- Jason Stajich
TS - Great Minds....
- Jason Stajich
100% what they designed
- Thomas Sharpton
He does a good job of referring to who did certain studies at JCVI --- even showing pictures of some of them ---
- Jonathan Eisen
I've just learned to think like you ;)
- Thomas Sharpton
583 kb synthesized genome.
- Jason Stajich
Singleshot assembly of 25 pieces accomplished in yeast
- Thomas Sharpton
Says the "genome transplantation paper" of his was one of the most profound that has come out of his group
- Jonathan Eisen
Talking about how changing the DNA in the cell (and only the DNA) changed one species in the lab into another
- Thomas Sharpton
Mentions recent paper to PNAS, but props that he also made it open access. http://dx.doi.org/10...
- Jason Stajich
I think he's genuinely interested in others picking up this technique - he made a call to young students at Berkeley to think big about what can be done with this technology
- Thomas Sharpton
Says he is still not certain what happened in the genome transplantation study
- Jonathan Eisen
Is this what one refers to as an "Oops!" discovery
- Thomas Sharpton
Genome transplants worked when going from bacteria to bacteria but not with the apparently the same DNA from yeast to bacteria
- Jonathan Eisen
Transplanting the same synthetic sequence into yeast did no recapitulate the results
- Thomas Sharpton
They think they now have a mechanism to take the DNA grown in yeas t and then in vitro convert it into somethign that can be taken up into a bacterium
- Jonathan Eisen
Has figured out how to create bacteria from prokaryotic genomes engineered in Yeast. This means that all conventional yeast genetic tools can now be used in this system
- Thomas Sharpton
Now is talking about "why do this"
- Jonathan Eisen
Brilliant strategy by the way by the organizers to have Craig give the last talk - it is completely full in here which is almost unheard of for a half day at the end of a meeting
- Jonathan Eisen
It seems like his vision for monetization of this is in the end products not the technology to get there?
- Jason Stajich
Ok, enough of what's going on, now on to the why we need to do this. Citing increasing population growth and declining energy reserves, CO2 emissions climbing, etc. Wants these tools to be used to solve these problmes
- Thomas Sharpton
genes as "design components"
- Jason Stajich
Jason - agreed. I'm thinking industrial application of the technology to change how and what we manufacture
- Thomas Sharpton
software to "design organisms". Lucy Shapiro getting mad props - like 4 mentions.
- Jason Stajich
Introducing the Synthetic Genomics Organism Designer. I played with it pre 1.0, this looks quite a bit cleaner than it did a while ago
- Thomas Sharpton
Says we need to know better how circuits work in organisms (and cross refs Lucy Shapiro's talk)
- Jonathan Eisen
Combinatorial Genomics - rapidly screen genes via cassette based contstruction of 1000 - Ms of genomes/day
- Thomas Sharpton
[me]what happens when we build organisms that become sentient? SchiNet [/me]
- Jason Stajich
Sounds similar (but different) to Church's MAGE method of rapidly identifying optimal protein sequence
- Thomas Sharpton
Many people are taking pictures of Craig and/or video --- I know I said George Church was a rockstar but I forgot Craig was coming to the meeting
- Jonathan Eisen
designer fuels showing picture of what I thought was chlamy, says they have made algae that make fuels.
- Jason Stajich
This really has been a meeting of the minds - great talks all around
- Thomas Sharpton
referring to methanogens now --- b/c they are autotrophs that take CO2 to CH4
- Jonathan Eisen
I have the tendency to dream when I hear a talk like this - the future is very exciting
- Thomas Sharpton
Says they have an anaerobic cell sorter to start to better characterize organisms that live off of coal
- Jonathan Eisen
Coal to methane production - does this help reduce CO2 emissions though? Just cleaner than burning coal.
- Jason Stajich
Wants to use these organims to convert deep earth coal into natural gas as they release methane
- Thomas Sharpton
Says they should be able to convert large collections of coal into natural gas using enzymes from some of these bugs
- Jonathan Eisen
Imagines people will be designing their own plant species in a few years ...
- Jonathan Eisen
Says the day of creating unique plants isn't very far away
- Thomas Sharpton
[me]Does it make sense to also look at the source of oil - is it purely chemical process from decomposed algae and pressure or is there a biochemical process facilitated by microorganisms? I thought we don't really know how oil is naturally made[/me]
- Jason Stajich
Ends with a picture of a whale and says "thats my tail and Im sticking to it"
- Jonathan Eisen
Part of the BP/EBI initiative is to look at this - they're going to sample oil wells and look for orgs that grow in them.
- Thomas Sharpton
After a quesion Craig admits to having made a mistake with mycoplasma since it grows so slowly
- Jonathan Eisen
I must say I don't like computer analogy to cells.
- Jason Stajich
"There's no intention of putting these into the environment; that would be ethically wrong"
- Thomas Sharpton
ethically wrong to put these (engineered) organisms into the environment. Nothing that can survive outside lab. 150 algae companies in last year?
- Jason Stajich
I'm surprised he didn't talk a bit more about the ethics board he established to deal with a lot of the concerns that arise regarding this technology.
- Thomas Sharpton
Craig says they are trying to work out laws, rules and regulations and that they are working to avoid this ... he even makes a comment about how some companies are planning to make and release genetically engineered algae --- nice criticism of the talk that he did not go to from two days ago that I had trouble with too
- Jonathan Eisen
by the way - the question about ethics came from Dawei Lin from the UC Davis Genome Center - I did not see him but I know his voice
- Jonathan Eisen
Even in answering questions Craig does a good job of referring to previous speakers (now he was referring to Jeff Miller)
- Jonathan Eisen
Question - do you think you can make a bacterial chromsome boot up in yeast - answer - no we are trying to prevent DNA from booting up in yeast
- Jonathan Eisen
We are not ready to release our software or our bugs because thesoftware has bugs
- Jonathan Eisen
Great talk, user meeting has ended.
- Thomas Sharpton
and we are done
- Jonathan Eisen
Well in a year lets see how much BGI has done
Epic trip around the world - was that to sequence the sea or to take an epic trip around the world?
- Thomas Sharpton
then mentions the GOS papers (also in PLoS Bio ... yay ... and I was a coauthor - ... http://collections.plos.org/plosbio...)
- Jonathan Eisen
Talking about improving the sampling frequency around the globe
- Thomas Sharpton
That was a great series, Jonathan
- Thomas Sharpton
He is making one somewhat misleading comment -- that they expected to have very few organisms in the Sargasso Sea --- I never expected that nor did many others (although Craig may have)
- Jonathan Eisen
Rod Wing - To Refseq or Reseq Oryza - That is the Question
Jonathan Eisen and Jason Stajich liked this
Jumping the gun a bit here, but Rod, who is coming up shortly, is the director of the Arizona Genomics Institute
- Thomas Sharpton
Title slide has a picture of a big bowl of rice. Now I'm hungry
- Thomas Sharpton
sushi?
- val
With all, due respect, would Shakespeare really ask that question? ;)
- Thomas Sharpton
Well at least it's different from quoting Darwin
- Chris Villalta
doesn't look like there's a lot of oryza out in arizona
- val
He's showing a slide about the global importance of rice. Woah, we need 40% more rice by 2030, and we'll have less land, water, labor and chemicals to meet this demand.
- Thomas Sharpton
2020 rice initiative to coordinate effort to characterize the rice genome. functional genomics to natural variation.
- Jason Stajich
Rice 2020: A call for an international coordinated effort in rice functional genomics
- Thomas Sharpton
showing tree with very small species names (from the back) -- genome size varies from 425 Mb to 1.2 Gb
- Jason Stajich
24 species total, wide habitat diversity
- Thomas Sharpton
24 total species widely distributed.
- Jason Stajich
Wild relatives contain a suite of useful trait compared to domesticated rice
- Thomas Sharpton
Generating BAC libraries for the 10 genome types.
- Jason Stajich
www.OMAP.org
- Thomas Sharpton
i wonder how close the "wild rice" relative Zizania is, and whether anybody's exploring that
- val
Chromosome 1 (used as an example) shows great colinearity across the 8 species, but exhibit expansions and contractions (looked like few inversions, but hard to tell)
- Thomas Sharpton
Constructed a rearrangement index to identify putative syntentic changes between species
- Thomas Sharpton
Expansions and contractions appear to account for a great deal of genome size variation across taxa - upwards of 37.9 Mb in additional sequence relative to the reference genome
- Thomas Sharpton
Developing a "rearrangement index" to identity putative rearrangements inferred indirectly through the BAC map data. This seems a little backwards from using sequence, but is required since they are only using the map data. Of course Rod has been one of the leaders in the BAC map building so it is in good hands.
- Jason Stajich
Val- Seems like looking at population genetics of zizania would be interesting also for exploring resistance genes - this seems to be important for wheat too.
- Jason Stajich
Percent identity plot across Oryza chromosome 3 begtween several of the species shows LOTS of divergence.
- Jason Stajich
Percent ID plots at the short arms of chr 3 shows an increase in snp rate as divergence time increases
- Thomas Sharpton
There is also a whole lot of unaligned (repetitive) sequence
- Jason Stajich
also a good deal of variation in gene content in this region
- Thomas Sharpton
1984 genes is being called the 'core gene content of chr 3 chromosomal arm'
- Thomas Sharpton
also, zizania is delicious. hm. according to wikipedia, a chinese zizania infected with ustilago is actually cultivated asexually for its stems, as a vegetable! ustilago as a value-added product...
- val
'it's not a bug, it's a feature'
- Thomas Sharpton
val: a hah, a plant-microbe project that is also edible, I like the sound of that.
- Jason Stajich
lost of gene family dynamics - lineage specific genes, lots of duplication, local duplications. Whether these are mediated by repeats is unclear, but is sort of invoked.
- Jason Stajich
I think a bullet point on a prior slide suggested that repeats play a role here, but I only got a brief look at it
- Thomas Sharpton
ugh, very small bullet points, shouldn't sit in the back if I want to read.
- Jason Stajich
conclusion is yes refseq?
- Jason Stajich
So the answer to the question? RefSeqs for all 8 genomes are needed
- Thomas Sharpton
yeah, tough to read that last slide, even if close
- Thomas Sharpton
Slide indicating that lost of genome sequences are needed to fully characterize a model organism
- Thomas Sharpton
talking about iplant circuitously?
- Jason Stajich
All I can say is that it is hard to live blog when people keep saying "can I talk to you for just one minute?" ....
- Jonathan Eisen
holograms are the answer
- Jason Stajich
what happened to the old-fashioned clone answer?
- val
speakers have done a fairly good job at staying on time at this conference
- Thomas Sharpton
Question being asked by a friend from Davis about the number of genes that are different between the varieties
- Jonathan Eisen
This guy spoke two years ago at the Student Microbio symposium I remember he mentioned Treponema, seemed to think tooth architecture had a lot to do with what grows in your mouth. - http://asiago.stanford.edu/RelmanL...
Finishing with a summary or DGR properties, too many to list here.
- Thomas Sharpton
So why are the DGRs enriched for A and not some other nucleotide?
- Thomas Sharpton
Jeffrey Miller - Diversity Generating Retroelements
Jonathan Eisen and Jason Stajich liked this
Story starts with bacteriaphage of Bordetella
- Thomas Sharpton
Virus is trophic of virulent phase of its host; recognizes a surface epitope expressed by host
- Thomas Sharpton
some recognize environmental state of host as well, tropism is determined by cell surface recognition - observed that the viruses can switch between virulent phase recognition and environment phase recognition
- Thomas Sharpton
Sequencing genomes from viruses with different tropisms identified differential SNPs in a particular gene (mtd). At the end of mtd is a VNTR that accumulates substitutions at paricular sites. Appears to modulate protein diversity at this locus
- Thomas Sharpton
down stream mtd is a Reverse Transcriptase called brd. Delta(btr) yields non tropism switching of the phage
- Thomas Sharpton
last meeting I was at where he talked, he gave by far and away the best talk ... hope this one compares
- Jonathan Eisen
Also, smaller repeat sequence just downstream mtd called TR. Knock out TR in phage and no tropism switching
- Thomas Sharpton
Appears that TR transfers information into the VNTR of mtd via the Reverse Transcriptase. Mutagenesis of TR supports this theory
- Thomas Sharpton
Calling TR a Diversity Generating Retroelement
- Thomas Sharpton
he has seen these across the tree of bacteria - and most are in chromosomal regions (although in some lineages most are in phage)
- Jonathan Eisen
DGRs are found in a wide variety of bacterial taxa, many are inserted directly into the host chromosome rather than sitting on phage or plasmid. Gram(+), however, most are found on phage
- Thomas Sharpton
Key point is RNA intermediate to move these -- I'm thinking about intron loss again -- they do this with self-splicing type I introns.
- Jason Stajich
For some reason I'm reminded of Austin Burt's homing endonuclease theory of mosquito eradication. Don't ask me why.
- Thomas Sharpton
Intron insertion into TR verifies RT nature of the element - intron is spliced properly from sequence
- Thomas Sharpton
This also reminds me a little of the Jef Boeke's experiment where an RNA intermediate is proven.
- Jason Stajich
Just a little plug for PLoS - he had a (what I thought was) cool paper in PLoS Bio last year on part of this story http://biology.plosjournals.org/perlser...
- Jonathan Eisen
Open access getting all sort of props at the conferences, and rightly so.
- Thomas Sharpton
reverse transcriptase -- it's not just for making cDNAs.
- Jason Stajich
Yes, openness has gotten some plugs but I am somewhat disappointed by how some people promote how open they are with data and then do not publish openly. Open Science should be open in every way.
- Jonathan Eisen
Looks like variation in mtd, modulated by TR, affects MTD protein properties (hydrophobicity, etc)
- Thomas Sharpton
He is comparing this system to the antibody diversity in a structural sense
- Jonathan Eisen
Enriched diversity in the Mtd variable region - they never find the same sequence twice
- Thomas Sharpton
Positive Selection? Where in the coding sequences are changes enriched?
- Thomas Sharpton
Although it is not clear how they have sampled viruses - it seems liek they are sampling not so closely related viruses and they see differences. I would be more interested in studying how this evolves in real time
- Jonathan Eisen
Domain architecture across taxa seems to be conserved, particularly the c-type lectin domain
- Thomas Sharpton
Those are some gnarly teeth on that slide
- Thomas Sharpton
talking about treponema and reminding everyone to brush and floss
- Jonathan Eisen
has somebody done the human oral metagenome?
- val
In Treponema, it looks like there is a family of homologs that share 1) the TR conversion site and 2) secretion signals at N-terminus
- Thomas Sharpton
That's part of the JCVI initiative, I believe.
- Thomas Sharpton
lots of work on oral microbiome and metagenome --- will post links in a bit
- Jonathan Eisen
Trichodesmium erytheraeum now, a marine filamentous cyanobacteria, also fix N2 in the ocean, contains what he calls a chromosomal diversity generator
- Thomas Sharpton
Peg Riley - Population Genomics and the Bacterial Species Concept
Jonathan Eisen liked this
She's starting by mentioning how the genomics era has reshaped our view of diversity
- Thomas Sharpton
Now she's introducing the challenging concept of a species - what are they, how are they identified. She argues that a species are a cluster of organisms, easy to recognize in non-microbes, but tougher in microbial taxa. Interbreed paradigm is invoked
- Thomas Sharpton
She notes that bacteria do actually have "sex" (recombine dna) - transformation, transduction, conjugation
- Thomas Sharpton
Leads into horizontal gene transfer - how important is HGT? Invoking Doolittle's 'web of life' and the idea of a pangenome. This presents a bacterial species problem, as the exchange across lineages may be high enough to destroy species boundaries
- Thomas Sharpton
So what do bacterial genomes look like? Pangenomes or co-evolved groups or clusters?
- Thomas Sharpton
She's not Jonathan Eisen, so she still uses MLST to type strains. 5-7 housekeeping genes, never 16S because it doesn't evolve fast enough (but markers shouldn't evolve too quickly....)
- Thomas Sharpton
Showing the Bennet et al 2007 tree - Neisseria Species
- Thomas Sharpton
There is a complicated webbing of genes across the genome when viewed at the species level, but this is expected. Zooming out past the species level shows clear clusters of groups that she argues are bacterial species.
- Thomas Sharpton
A phylogeny of Borrelia Species (in press) built from MLST shows species fall out into independent clusters quite clearly - very little in between the species clades
- Thomas Sharpton
Similar trend observed in Burkholderia Species. The theme is apparent here - great recombination withing a cluster, but between clusters there are relatively long branches, suggesting relative genetic isolation between groups
- Thomas Sharpton
she says medical microbiologists should never name things
- val
what if they are medical microbiological taxonomists?
- Thomas Sharpton
sounds like a mythical beast
- val
Now talking about MLST v. whole genome - does additional information change the pattern?
- Thomas Sharpton
Burkholderia MLST tree v. whole genome tree shows the same pattern - clustering exists at the whole genome level
- Thomas Sharpton
I promise you, val, they may be elusive, but they exist
- Thomas Sharpton
Same pattern observed in Clostridia
- Thomas Sharpton
Snipe against closed access journals - can't do a side by side comparison of figures in a talk arranged at the last minute
- Thomas Sharpton
Using array typing, data suggests that one can identify sub-species clusters in particular clades
- Thomas Sharpton
Bringing ecological considerations into play - ecological and phenotypic potential as well as their genetic discontinuity between strains should be the basis for a species definition
- Thomas Sharpton
The goal is to design a predictive species definition
- Thomas Sharpton
In Vibrio, there is a relationship between genotype and ecology, she's extending the observation to make the point that adaptation to a niche yields maintenance of genotype
- Thomas Sharpton
She mentions paradox of genomic stability and flux - these two opposing forces are ongoing and seemingly at odds, but must be balanced in nature
- Thomas Sharpton
predictive of what?
- val
Concept of core genome (Lan and Reeves 1993) - there exists a subset of genes that all members of a taxonomic group share. This differs from the auxiliary genome, which is the subset of genes that are shuffled around between groups and help organisms adapt to a local niche
- Thomas Sharpton
val -i think that's still unfolding in the talk
- Thomas Sharpton
Detecting gene transfer at the whole genome level - she looked for potential HGT evens between E. coli and S. enterica to identify the extent of the core and auxiliary genomes. Finds <5% of genome appears to come from outside of the species.
- Thomas Sharpton
But, what is core in one species may be auxiliary in another.
- Thomas Sharpton
Using Beta Lactamase Resistance Gene (bla-tre) as an example - looks and behaves like an auxiliary gene. However, a close relative of this gene, (bla-oxy), looks and behaves like a core gene. Here a resistance gene has evolved within a species and rarely exists outside of it.
- Thomas Sharpton
Lots of species concepts, but she prefers Mayr's 1942 view of the Biological Species Concept. Her modification of Mayr's view, fit to include bacteria: "Groups of strains that frequently exchange, or could exchange, core genes but that are relatively restricted from such exchange with other groups."
- Thomas Sharpton
Peg's Pet Peeve: The 16S is nothing for species and there should be a fine for anyone that uses it to identify species
- Thomas Sharpton
val - there it was, regarding the definition being predictive: her definition provides an assay to test whether two individuals are the same species or not
- Thomas Sharpton
Last slide: why bother with a bacterial species concept? 1) we have to name things, and we need to do it correctly. Names are important for even simple tasks like blast analysis. 2) we've hardly touched bacterial diversity - many lineages require naming and we should try to name given their evolutionary histories
- Thomas Sharpton
she's making a distinction between predicting evo history and pathogenicity or other phenotypes.
- val
Stuck in traffic ..,,dsmn
- Jonathan Eisen
Well, I'll do my best to keep you in the loop, Jonathan
- Thomas Sharpton
Goal - dive into a bug and understand the regulatory network and regulatory molecules that enable the bug to do what it does
- Thomas Sharpton
She says that the regulatory system is the brain that allows the cell to function. It determines when to move through the cell cycle, how to respond to environmental dangers, etc
- Thomas Sharpton
She focuses on the logic pathways involved in several key pathways. Today she will posit that another aspect of evolution is at the regulatory network level
- Thomas Sharpton
Transcriptional machinery isn't enough - there are multiple levels of control that need to be considered holistically
- Thomas Sharpton
Slide on Caulobacter - standard stalk/swarmer slide
- Thomas Sharpton
She notes utility of the system - cell cycle tightly controlled and 2 different types of cells are left behind. This cycle appears to occur irrespective of environment (really?). All of these points make this an interesting model of cell cycle study.
- Thomas Sharpton
DNA Methylation is key to differentiation between swarm and stalk cells. She notes that 4 master regulators control 200 cell cycle regulated genes.
- Thomas Sharpton
Microarray slide. Roughly 19% of Caulobacter gene vary as a functoin of the cell cycle. This is a nice slide - the induction of genes over time is clear cut and distinct.
- Thomas Sharpton
CtrA is a response regulator that controls 95 genes during various cell cycle events. Sits on the promoters of 95 genes (ChIP-Seq? didn't say how)
- Thomas Sharpton
Introducing the ClpX and ClpP complex and how RcdA/CtrA interacts with it. Because CtrA can inhibit progression into another cell cycle checkpoint, the Clp complex destroys CtrA to progress development
- Thomas Sharpton
she emphasized the cellular localization of the proteolytic complex.
- val
Introducing Phospho-regulation: CpdR-P is the inactive form of CpdR. Phosphorylation occurs via CckA, by transferring P from CtrA/CtrAp. CpdR localizes to the ClpXP protease to initiate degredation of CtrA.
- Thomas Sharpton
But when CpdR is in the P form, it localizes to the cell pole of the developing swarmer and is thus absent in the stalk, creating an asymmetry between the two morphologies
- Thomas Sharpton
GcrA is another global regulator that oscillates with cell cycle phase (missed details)
- Thomas Sharpton
Showing complicated slide of global regulator network during Caulobacter cell cycle.
- Thomas Sharpton
Building these circuits (as she calls them) enables identification of key nodes in circuit. DNA Methylation is one such key node.
- Thomas Sharpton
Back to CtrA and GtrA - GcrA silences CrtA by sitting on promoter. CtrA positive feedback on itself and also inhibits GcrA expression
- Thomas Sharpton
DnaA sits at inducer site of GcrA and opens the origin of replication
- Thomas Sharpton
Uh oh, battery going to die - feed might stop in a bit
- Thomas Sharpton
She's introducing a complicated model of chromosomal replication during this cell cycle, in such that replication and segregation occur simultaneously
- Thomas Sharpton
oh no! no charger?
- val
too far from plug atm - will get juice at break
- Thomas Sharpton
you can use this extension.
- val
showing a model for placement of the z-ring. mipz prevents polymerization of ftsz, and the mipz minimum is at the center of the cell.
- val
had a very clean slide showing the circuit of epigenetic control of master regulator transcription
- val
I guess if you are a medical microbiologist you are probably more interested in what can kill it and what antibiotic resistant genes it has?
i think her point is that medical doctors tend to regard human pathogenicity as a species-defining trait, but this doesn't necessarily fall out in phylogenies.
- val
Sabeeha Merchant - Chlamydomonas Transcriptomics
Jonathan Eisen, Jason Stajich and Neil Saunders liked this
The term reference organism seems to have really taken off. This talk is titles 'Chlamydomonas as a reference organism'
- Thomas Sharpton
I think every talk about a particular organism should start with a phylogenetic tree
- Thomas Sharpton
and a cross-section
- val
She's moving on to discuss why Chlamy is a good model/reference - interesting metabolism, genetically tractable, well understood biochemistry/mirobiology, a genome sequence (v3.1) and miRNA
- Thomas Sharpton
Copper nutrition-independent photosynthetic growth, interested in transcriptional activation in copper limited environment.
- Thomas Sharpton
compare + and - copper conditions, delta(crr1) to complement, and algal bloom experiments (which I don't fully understand)
- Thomas Sharpton
transcriptomics of the aforementioned comparisons: standard RNA isolation and quality control are applied, though she adds real time PCR of known transcripts as a control
- Thomas Sharpton
tell me if you spot the name Dudley Page in the acknowledgements - trying to track him down!
- Neil Saunders
Decided to use RNA-Seq - 500 Mb of 35-70 nt length reads, single and paired ends
- Thomas Sharpton
Neil, I'll keep an eye out for you
- Thomas Sharpton
SOAP used for read alignment, 2 mismatch threshold; aligned to both genome and transcripts, though transcripts harder here since transcriptome not well understood in Chlamy. 89% reads align to genome, 81% are unique
- Thomas Sharpton
Roughly 162 lanes of sequence have been generated across multiple labs (or are pending)
- Thomas Sharpton
reads map well to exons - but Jason's right - need statistics that clearly illustrate genome wide associations between datasets. I'm sure these exist, but they aren't being invoked
- Thomas Sharpton
issued corrections for length of gene model, read length, differences in sequencing depth and (hence) under-estimation of weakly expressed genes. The goal with said corrections is to enable reproducibility between individuals and other labs
- Thomas Sharpton
I wonder how the corrections work - the error introduced by the data handler at the time of sequencing is documented and the aforementioned lanes were run at myriad sites
- Thomas Sharpton
she says the distributions of counts/genes/genome across labs and handlers is highly reproducible post correction
- Thomas Sharpton
Comparing the + and - transcriptome and the delta(crr1) and complement show an overlap of 58 genes - these are the nutritional Cu transcriptome.
- Thomas Sharpton
~50% are redox proteins, ~25% are unknown, ~15% transport, then protease, transferase and other
- Thomas Sharpton
Looking at interesting genes now, many have been previously identified in this pathway via arrays
- Thomas Sharpton
CRR1 targets are expressed during the algal bloom (I still don't understand this method)
- Thomas Sharpton
RT-PCR v. RNA-Seq has r^2 or 0.95. Similar to other experiments using the same RPMS method for transcript counting
- Thomas Sharpton
aligning reads to genome identifies alternative transcripts that are regulated by copper nutrition
- Thomas Sharpton
i blinked there a bit, but i think they grow chlamy with adequate cu, then transfer to media without cu, then take some time points.
- val
now she's switching gears to RNA-Seq2Gene (genome annotation from RNA Seq)
- Thomas Sharpton
Paired end reads enabled prediction of 'new' exons relative to the gene model.
- Thomas Sharpton
can look at distribution of distance from paired ends to make predictions about intron/exon junctions de novo
- Thomas Sharpton
pairs within an exon cluster at a short distance relative to pairs separated by an intron
- Thomas Sharpton
over half of the automated models have an overlap score with gold standard genes greater than 0.8, but some overlaps are very poor. Believed to be due to reads coming from unfiltered introns.
- Thomas Sharpton
Seems that given the observation of alternative splicing, that could also explain this discrepancy.
- Thomas Sharpton
now she's discussing her annotation pipeline based on read data to improve gene prediction. would have liked more time on that slide.
- Thomas Sharpton
dudley page is not on the final slide, for anyone interested
- Thomas Sharpton
Gary Andersen - Phylochip analysis of microbial diversity
Jonathan Eisen and Jason Stajich liked this
Gary is from LBNL, works with Todd DeSantis on the Phylochip, which is based off of the Green Genes database
- Thomas Sharpton
various markers produce differential taxonomies - A Taxonomy in Flux
- Thomas Sharpton
He's saying that FASTA file isn't enough - need quality scores of each base. Thus now when they take sequences for GreenGenesDB, they import Phred Score as well
- Thomas Sharpton
This is because the probes on the chip are clusters of common sequences. 24 probe pairs on average for each of the probe sets (generation 2).
- Thomas Sharpton
He mentioned benefit of clusters - it enables multiple taxa to be identified simultaneously by targeting unique regions or combinations of sequence
- Thomas Sharpton
The phylochip is a high density Affy array. > 1M probes of the array. Included are mismatch probes that serves to control for cross hybridization. Because all DNA from community is probed, long tail can easily be identified (if it exists on the chip)
- Thomas Sharpton
Not sure if the phylochip approach has legs ... why wouldnt you just sequence the *#$# out of a rRNA sample?
- Jonathan Eisen
Eoin Brody's Iron remediation study is being featured on the current slide - Eoin looked at the temporal shift in diversity during remediation
- Thomas Sharpton
jonathan - agreed, but i think there's still an issue of depth of long tail coverage that the chip might be able to hit a bit better
- Thomas Sharpton
he's postulating the question: "What environmental factors determine the composition and structure of soil microbial communities"
- Thomas Sharpton
10m transects per ecosystem (6 total, I think) studied in triplicate
- Thomas Sharpton
Sure - dynamic range is important. But ease of data analysis is another. Sequence data is, well, easy. Compared to analyzing the phylochip at least
- Jonathan Eisen
3018 terminal bacterial taxa detected in soil, 347 families, 2 phyla (really? only 2?)
- Thomas Sharpton
83 Terminal Archeaa detected, 12 families, missed number of phyla
- Thomas Sharpton
does not make sense to have only two phyla
- Jonathan Eisen
agreed, also a bit more quantitative. plus sequencing enables consideration of novel taxa. just trying to play devil's advocate on gary's behalf :D
- Thomas Sharpton
I totally agree - is there a phylogenetic bias on the chip?
- Thomas Sharpton
goodness, geobacter is everywhere. here it is responding positively to soil moisture.
- Thomas Sharpton
51% of the taxa studied respond (in one way or another) to a change in soil moisture
- Thomas Sharpton
from what I know - this chip is really really good at picking up what you are looking for but not as good for picking up what you are not looking for - I prefer either sequencing or Pat Browns rRNA chip which took a different approach
- Jonathan Eisen
neat - overlaid correlation data onto a phylogenetic tree. Found a non-random association
- Thomas Sharpton
Here he's saying that spatial segretagion may be the source of differences between rates of diversification between wet/dry communities
- Thomas Sharpton
What organisms are on space craft. I know one answer: Penicillium
- Thomas Sharpton
Oh, here we go: 454 v. PhyloChip comparison.
- Thomas Sharpton
There are great ways to amplify without bias, especially for 454 and Solexa library prep
- Thomas Sharpton
Found substantial overlap between the two methods, each also detected a small number of unique calls
- Thomas Sharpton
He is arguing that 454 seq and phylochip are complementary
- Jonathan Eisen
But I am not sure I buy it
- Jonathan Eisen
Generation 3 is coming out - 1.1M probes. I'd like to know what the phylogenetic coverage looks like on G3 relative to G2
- Thomas Sharpton
could nasa just buy a pac sci machine?
- val
if they do, I'm moving into astrobiology
- Thomas Sharpton
you're too big to fit in a mars rover, you know.
- val
so - make a new one ---
- Jonathan Eisen
they can send it back like the space dust from the comet. Did that ever come back?
- Chris Villalta
Everyone is selling their technology today, but no one is talking price. I imagine this is one place the Chip can compete
- Thomas Sharpton
Mycochip only gets one slide? Awwwww
- Thomas Sharpton
Mycochip uses ITS for recent divergence discrimination, 28S for more diverged diffentiation
- Thomas Sharpton
Pavel Pevzner - Short Read Assembly
Jonathan Eisen liked this
Dealing with repeats in short read assembly is a pain - can artificially collapse a long region into a relatively short one (or vise versa)
- Thomas Sharpton
He's showing a complicated network of repeat/non-repeat regions in a graphic called a repeat graph
- Thomas Sharpton
the genome can be translated into a repeat graph easily, but with the genome, moving in the other direction can be difficult
- Thomas Sharpton
error in previous comment - without the genome, this can be difficult
- Thomas Sharpton
Mass Spectra data can be used in a similar fashion to sequence proteins
- Thomas Sharpton
the eulerian approach of repeat graph assembly works well for error free reads, but deteriorates otherwise
- Thomas Sharpton
to assembly genome, then, must correct errors in reads. this is difficult to do a aprior (ie, without a genome!)
- Thomas Sharpton
Solexa reads highly accurate in early read, error prone near the end
- Thomas Sharpton
Can map error prone reads to a repeat graph: mapping with minimal number or mismatches
- Thomas Sharpton
this is implemented in EULER-USR algorithm
- Thomas Sharpton
for short reads, EULER-USR performs similarly to velvet
- Thomas Sharpton
but at long reads, it looks like euler-usr out performs - didn't get a good view at that slide
- Thomas Sharpton
dealing with paired end reads in euler-usr: map the ends to the repeat graph and fill in the gap with the corresponding sequence from repeat graph
- Thomas Sharpton
what happens when there are multiple paths that exist in said gap?
- Thomas Sharpton
Read length doesn't matter, span does (gap + each mate pair read length)
- Thomas Sharpton
ah, here we come back to multiple paths - if read length decreases, efficiency decreases because probability of placement on repeat map around multiple path gaps increases
- Thomas Sharpton
in this regard, a small drop in read length yields a dramatic drop in efficiency and N50
- Thomas Sharpton
Now he's discussing the problem of identifying the breakpoing for mammalian genomes. In yeast it is 45bp reads with span of 300bp
- Thomas Sharpton
Their simulations suggest that there is a relationship between span and read length in mate pair assembly accuracy (fix one and the other varies, vice versa) - can determine optimums from this type of analysis
- Thomas Sharpton
Breakpoints are thus the points on these cuves where N50 drops off because either 1) span is too short or 2) read length is too short
- Thomas Sharpton
did he mention the reasons for a certain breakpoint?
- val
damn - missed it ... glad you blogged it
- Jonathan Eisen
Pacific Biosciences Talk now - Steven Turner
Steve Koch and Jason Stajich liked this
DNA Polymerase is a Sequencing Machine (or engine)
- Thomas Sharpton
attach florescent labels to watch in real-time how DNA synthesis is going on.
- Jason Stajich
Single Molecule Real Time Sequencing - what Jason just described
- Thomas Sharpton
Says they are different in that they do "single molecule real time sequencing" as opposed to just "single molecule sequencing
- Jonathan Eisen
Background fluorescence is a significant challenge with this method
- Thomas Sharpton
other companies (Solexa, 454) deal with this by halting the synthesis, hence they are not real time.
- Thomas Sharpton
Says that one of the key things that his company has done is that rather than clearing out all the fluoresncent nucleotides and stopping the reaciton after every base in order to avoid noise - their company focuses on dealing with the noise and watching in real time
- Jonathan Eisen
Sounds like the competition point is the rate of sequencing - no halting means constant data acquisition
- Thomas Sharpton
Says that they are basically trying to match the polymerase in real time through a little pore by using a technology like that in the screen of a microwave oven which blocks most wavelengths from getting through ... they do the same thing at the nano level
- Jonathan Eisen
Says that another key innovation for their method is where they label the nucleotides
- Jonathan Eisen
another point of competition is in regards to how nucleotides are labeled - rather than being base-linked, they are phospholinked, meaning that DNA Poly can cleave the flour off during synthesis. No chemical removal of flours required.
- Thomas Sharpton
pacbio uses "natural" dna synthesis which allows for speed and accuracy, other methods have fluorophores that incorporate into the DNA which causes inhibition of polymerase enzyme.
- Jason Stajich
this also decreases read time.
- Thomas Sharpton
this is a polished talk - nice use of accurate rhetoric with clear cut animations.
- Thomas Sharpton
this method requires high throughput flourescence microscope to observe the incorporation.
- Jason Stajich
Compared to when I saw their firs talk at the Marco Island meeting - their cartoons, and little movies are much better and it really helps explain their technology
- Jonathan Eisen
you are watching the matrix
- Jason Stajich
showing a little movie of their system actually sequencing in real time
- Jonathan Eisen
movie reminds me of the matrix code
- Thomas Sharpton
showing movie of real time trace from a single polymerase
- Thomas Sharpton
Serious amount of information is being spit out such that they can only sample 1/3 and get good information - did I understand that correctly?
- Jason Stajich
now he is showing an actual trace of one polymerase
- Jonathan Eisen
by and large, peaks look pretty clean, though i'm guessing they have single poly-nt error problems (indels)(
- Thomas Sharpton
currently showing a trace in real-time that is probably generating sequence at couple bases per second reading from a polymerase.
- Jason Stajich
he said they can tell how long poly nts are because each base is read as a very short pulse
- Jonathan Eisen
talking about sample preparation.
- Jason Stajich
nice little gimmic - the sequence trace continues to read at the bottom of his slide
- Jonathan Eisen
thanks - missed that point jonathan
- Thomas Sharpton
workflow doesn't require any new technology for sample prep - that I could tell.
- Jason Stajich
Gbrowse graphic #2 today!
- Jason Stajich
talking about a Human BAC they sequenced in November
- Jonathan Eisen
99.99% repetitive DNA accuracy
- Jason Stajich
yes, i was thinking of you on that slide
- Thomas Sharpton
4.5Mb at high coverage (20X) Q61 (99.99992% accuracy)
- Jason Stajich
38X coverage of K12, 99.3% unambiguously covered - discussing statistics of this now
- Thomas Sharpton
Then in January sequenced E. coli K12 and the quality apparently is good - not sure if they published this or released the data
- Jonathan Eisen
they are also using R for these graphics
- Jason Stajich
Can show there is origin of replication bias where there is more DNA present!
- Jason Stajich
very slight GC bias in reads
- Thomas Sharpton
Says the sequencing if not very biased to particular regions of the genome
- Jonathan Eisen
accuracy of 1st base or last base should be the same, accuracy varies by < 5% from beginning or end bases.
- Jason Stajich
looks like diminishing returns ~24X coverage
- Thomas Sharpton
Low rate of systematic error.
- Jason Stajich
Neat: That real time poly DNA sequence read is still coming in at the bottom of this slides like a stock ticker
- Thomas Sharpton
Says one of the sources of error is that the fluors do not have uniform intensity
- Jonathan Eisen
3200 bp continuous read!
- Thomas Sharpton
SHowing a 3200 base pair single molecule read -- that straddles a repeat
- Jonathan Eisen
read length distribution goes from ~100 to 1600bp - it is an exponential.
- Jason Stajich
can modulate runs - select short reads for high throughput, or spend more time running long reads
- Thomas Sharpton
have exceeded sanger sequencing length. I hope no one is basiing their thesis on writing short-read assemblers - seems like we're going back to long reads before too long...
- Jason Stajich
Did a test to see if they can perfectly recover ratio of input sequence with 1 bp difference.
- Jason Stajich
on track for commercial delivery Q2/Q3 2010
- Thomas Sharpton
Summary 0- sequencing is ahead of plan - sequencing reactions takes minutes, long reads, 12 instruments in operation, on track to deliver in second half of 2010, thinks thy can get 20-50000 bases in read length
- Jonathan Eisen
30,000X faster than current technologies. Long read length. Machine is shipping sometime next year. 12 prototypes in operation.
- Jason Stajich
over 100 Gb/hour using this technology!
- Thomas Sharpton
[me] Okay so we're just to going to resequence all the genomes where there are any problems with pacbio, will be cheaper than finishing or any manual process... [/me]
- Jason Stajich
says with only some small modifications they should get 180 Gb/hour (estimates this might come by 2013)
- Jonathan Eisen
I wonder what the cost per run is - will these guys win the X prize?
- Thomas Sharpton
[me] let's make sure we buy some stock in computer hardware companies to handle all this data.[/me] >100 Gb/hr so human genome in 15 min. Faster than slowest technology at clinical diagnostic lab.
- Jason Stajich
q? in the trace there are gaps, because of pausing in polymerase.
- Jason Stajich
PacBio confident that Polymerase they're using will be able to read high GC biased genomes accurately
- Thomas Sharpton
"We are already seeing the beginnings of the genome based economy....this sector is the one place that seems to be untouched."
- Thomas Sharpton
Steve Turner was a friend of mine in grad school. I saw the zero-mode waveguide stuff when it was merely the cover of Science magazine (6 years ago?). Glad to see that their company seems to be succeeding!
- Steve Koch
George Church on Reading and Writing Genomes
Mackenzie Cowell, Ricardo Vidal and Neil Saunders liked this
First thing he says is that when he was in Wally Gilberts lab it was about $7000 for a few oligos and now for the same amount you can order 1.5 Mbp of DNA
- Jonathan Eisen
Says it is Moore's Law on steroids
- Jonathan Eisen
Some bozo on his cell phone in the back of the room talking - yuck
- Jonathan Eisen
Illumina tops Church's list of 'favorite companies'
- Thomas Sharpton
Put up a list of 14 ultra low cost sequencing platforms - Ullumina, CGI, Polonator, Enzymatics, Lightspeed, Roche, PacBio, Halcyon, Bionanomatrix, Helicos, etc
- Jonathan Eisen
nanopore sequencing can detect the 4 bases, plus methyl-C!
- Thomas Sharpton
That's Clarke, Bayley, Nature Nanotechnology 2009
- Thomas Sharpton
I like this slide - Why open-architecture hardware, software and wetware?
- Thomas Sharpton
Talking about why there is a need for an Open Architecture system for sequencing - Says there are certain companies that get the idea of open architecture (e.g., IBM, Google)
- Jonathan Eisen
Says "The revolution is not over just because some companies have developed cheap sequencing methods ..."
- Jonathan Eisen
Surprise surprise. The room if overpacked for George, one of the rock stars of genomics
- Jonathan Eisen
Selective genome sequencing - preferentially sequence template of interest
- Thomas Sharpton
3 ways to capture: 1) paired ends, 2) Hybridazation-Selection, 3) Gap filling and ligation
- Thomas Sharpton
Says they are developing methods for selective sequencing of regions where rearrangements have happened
- Jonathan Eisen
I wanted to look at that slide a bit longer - Array based selective sequencing
- Thomas Sharpton
Me too ...
- Jonathan Eisen
With targeted sequencing and cheap oligo synthesis if it cost $5000 to sequence a euk. genome for $50 you could sequence all the protein coding regions
- Jonathan Eisen
Bioweathermap: functional metagenomics (Dantas, Sommer Church
- Thomas Sharpton
...Science 2008 (don't hit enter too early!)
- Thomas Sharpton
Bioweathermap is the antibiotic consumption study he published last year. See http://bioweathermap.org/
- Jonathan Eisen
"One of the companies I founded, LS9" ... how many companies has Church started?
- Thomas Sharpton
he has been involved in many many companies ...
- Jonathan Eisen
He is now talking about "multiplex genome engineering". I do not know about others but he makes $&%# ridiculously complex stuff seem really easy to do
- Jonathan Eisen
Good - good scientists are needed to lead industry in the proper direction.
- Thomas Sharpton
Well, the method is called MAGE.... perhaps Church is a wizard
- Thomas Sharpton
Looks liek a wizard too
- Jonathan Eisen
Holy crap - his accelerated evolution of lycopene clearly demonstrates this technology's industrial utility
- Thomas Sharpton
and here i was, thinking the answer to 'what threatens all biological systems' was humans.
- Thomas Sharpton
Now he is talking about making a new genetic code for organisms - as a safety feature
- Jonathan Eisen
Pretty cool idea, but I can't help recall the line 'Nature finds a way'
- Thomas Sharpton
Yes, without a doubt - just using an alternative genetic code will not protect you from all threats
- Jonathan Eisen
In vitro translation applications: ribosome display, membrane protein drug receptor studies, personal cancer vaccines, label one protein specifically, new chemistry (mirror chirality)
- Thomas Sharpton
OK this is getting wild - he is talking about creating a "mirror world"
- Jonathan Eisen
He is now going to end on the personal genome project - http://www.personalgenomes.org/ - this is the ONLY open access database of this type of information
- Jonathan Eisen
Awesome - Personal Genome Project is the first (and only) open access gt/traits database
- Thomas Sharpton
Cool, the database will include microbiome data on sequenced individuals
- Thomas Sharpton
Says they have some 10,000 people so far
- Jonathan Eisen
10,000 volunteers so far, funding for 100,000, go to personalgenomes.org to sign up
- Thomas Sharpton
George Church just painted a vision of the future of genomics. Wonderful talk.
- Thomas Sharpton
Diatom comparative genomics. Ginger Armbrust, U. Washington - http://armbrustlab.ocean.washington.edu/node...
Jonathan Eisen liked this
Diatoms are important photosynthesizers. Eukaryotic. 20% global photo synth
- Jason Stajich
Iron limits phytoplankton growth. 30% of oceans. JGI sequencing many diatom genomes
- Jason Stajich
That iron limits diatom growth has led many to argue that we should 'seed' oceans with iron to increase global photosynthesis
- Thomas Sharpton
Showing pat keelings tree of eukaryotes. I see this one and sandy baldauff's in most talks about eukaryote groups
- Jason Stajich
secondary endosymbiosis is responsible for photosynthetic capabilities in diatoms - independent from plant photosynthetic origins
- Thomas Sharpton
As with most good genomicists - they are using the phylogeny of this group to guide genome sequencing --- systematics and genomics work hand in hand
- Jonathan Eisen
1st genome from group originated 100mya
- Jason Stajich
I missed that - 3 sequences from the 55MYA point and 1 from the 100MYA point?
- Thomas Sharpton
Enormous diversity. Genome size varies from 30 mb to 300 mb
- Jason Stajich
fragilariopsis - genus adapted to low temp, high salt, pseudo-nitzshia and phaeodactylum both bloom in response to iron, pseudo-nitzshia produces toxin harmful to most verts
- Thomas Sharpton
She says that genomic differences are greater than what you would see for animals separated by this amount of time
- Jonathan Eisen
'these organisms aren't like animals and plants, these organisms mix and match metabolic pathways'
- Thomas Sharpton
Surprise #1 genome has hybrid metabolic pathways. Photosyntetic organism with ureic cycle.
- Jason Stajich
jonathan - that seems to be a common theme among microbes in general. a function of generation time, perhaps?
- Thomas Sharpton
Is that really a surprise? She even says it should not have been a surprise
- Jonathan Eisen
Surprise #2 many bacterial genes -HGT invokation.
- Jason Stajich
Bowler 2008 nature
- Jason Stajich
Tom - I think it is completely unclear what causes the differences in genome evolution rates and patterns --- when you compare diatoms vs. animals there are 10000 other differences between them in addition to generation time ...
- Jonathan Eisen
ok, fair point :D
- Thomas Sharpton
She is showing a picture from "The birds" b/c Hitchcock may have seen birds behaviing weirdly due to consuming a diatom toxin
- Jonathan Eisen
Pseudo-nitzschia - birds eating domiic acid produced by diatom inspired Hitchcock
- Jason Stajich
don't yet know where, when and why the toxin is produced in nature
- Thomas Sharpton
ferritin, common iron storage protein found in a diverse array of lineages
- Thomas Sharpton
EST analysis revealed ferritin gene 1st found in brown algae lineage /supergroup.
- Jason Stajich
Says the phylogeny of the ferretin seems - bounces around in the tree
- Jonathan Eisen
Claims this might be due to lateral transfer but sounds to me more like this is just ambiguous --- why is it that whenever the result is ambiguous people want to claim LGT?
- Jonathan Eisen
Tree shows it is its own lineage so novel divergence. Alien insertion or HGT. But no clear origin.
- Jason Stajich
good question - it's become the default bin for genes whose evolution we don't understand well, some seemingly going so far as to treat it as the null hypothesis
- Thomas Sharpton
Tree did not show that Jason -- she said the gene bounced all over the place -- its position was ambiguous. If you ran a southern and you found hybridization all over the gel, would you say you knew which one was right?
- Jonathan Eisen
enrich a community with iron and pseudo-nitzschia dominates...perhaps credence for the iron seeding idea
- Thomas Sharpton
I guess lack of a supported position meant we can't say it's origin. I don't think the tree supports LGT since it wasn't embedded i'm any clade. I joke about alien. My words not hers.
- Jason Stajich
now she is talking about some population-genetics/genomics
- Jonathan Eisen
Says there is a region on Chromosome 1 with very few SNPs - consistent with a selective sweep
- Jonathan Eisen
sorry, but how many strains is she considering here?
- Thomas Sharpton
So they went ahead and did resequencing of other strains using ABI solid
- Jonathan Eisen
ABI solid on 6 strains
- Thomas Sharpton
Big chunk of genome with low SNP diversity. Resequencing to see if region has evidence for selective sweep.
- Jason Stajich
To come: transcriptomics of several strains at high and low physiological differences across strains
- Thomas Sharpton
Now she is talking about her dream - to use organisms as sensors to tell about the state of the oceans
- Jonathan Eisen
Her dream - using the swath of genomics data to create biosensors that track the state of the ocean
- Thomas Sharpton
Their vision is to use these genomes to build tools to make sensors for biological diversity.
- Jason Stajich
Genomic Analysis of Adaptation and Speciation in Mimulus guttatus. John Willis, Duke University. - http://www.biology.duke.edu/willisl...
Jonathan Eisen liked this
Oh boy. I think john didn't have coffee, usually he is jumping around. =)
- Jason Stajich
I love this system because it is ecology and evolutionary bio and genomics now.
- Jason Stajich
Prolly got to the coffee when all they had was decaf
- Thomas Sharpton
Slides says "Perfect time to develop new plant system for ecological genomics"
- Jonathan Eisen
Great time to study ecological genomics.
- Jason Stajich
This is John Willis from Duke talking
- Jonathan Eisen
Mimilus is so much cooler tha arabidopsis. Huge flower diversity and great study for speciation.
- Jason Stajich
There goes the coffee let's see what happens.
- Jason Stajich
last bullet of the slide: "BUT essentially no decent genetic/genomic resources"
- Thomas Sharpton
missed that but figured that was coming ...
- Jonathan Eisen
Here is his web page by the way http://fds.duke.edu/db...
- Jonathan Eisen
wow - am jealous of the beautiful phenotype he gets to study
- Thomas Sharpton
No genetic or genomic resources till recently. Wait for it - JGI sequencing.
- Jason Stajich
you always spoil the punchline ;)
- Thomas Sharpton
mimulusevolution.org
- Thomas Sharpton
Mimilus is first genome from the major Clade. Hmm what was the name of it. Not eudicots since poplar already done.
- Jason Stajich
lots of repeats: RepeatMasker hits 60% current assembly
- Thomas Sharpton
Trouble assembling genome because lots of repeats but chromosome assembly not done. 500k ESTs. Lots of gypsy elements. 60% repetitive according to rrpeatmasker
- Jason Stajich
what's vistis-mimulus divergence? did he say?
- Thomas Sharpton
Gbrowse screen shot of annotation.
- Jason Stajich
Some microsynteny with tomato and solanace
- Jason Stajich
OK - its cool that mimulus can grow in diverse environments as he is saying here - cold, warm, etc but not extreme in my world (grows at apparently 50C but you know, some archaea go a wee bit higher)
- Jonathan Eisen
Mimilus colonized copper mine tailings. AM fungi associated
- Jason Stajich
maybe extreme for a plant?
- Thomas Sharpton
I love western coast these pictures make me want to hike
- Jason Stajich
Yes, extreme for a plant ... just giving props to my bugs
- Jonathan Eisen
live fast and die young - mimulus is the james dean of plants
- Thomas Sharpton
speaking of bugs, i wonder if there's microflora associated with various mimulus clines
- Thomas Sharpton
Structure picture of dave lowrys sampling from coastal and inland sampling.
- Jason Stajich
He suggested he was looking at microbes --- probably to look along clines --- but not sure
- Jonathan Eisen
Went to grad school with these guys so it is so cool to see their data in basically complete stories
- Jason Stajich
I must say - I know this meeting is kind of JGI biased but JGI really is the key place to do ecological and evolutionary genomics -- sure other places do some (e.g., JCVI and Broad and inidivual labs) but JGI really has been the key to so many eco-evo-genomic studies ---
- Jonathan Eisen
QTL study showed 2 genomic loci that controlled flowering time and morphology, 3 major QTL that are responsible for salt tolerance.
- Jason Stajich
as jason pointed out earlier, this is a great time for eco-evo genomics, and JGI is a great contributor to this development
- Thomas Sharpton
inversion in chromosome appears to be responsible for adaptive trait
- Thomas Sharpton
interesting to see another good example of the role synteny plays in evolution
- Thomas Sharpton
Inversion between coastal and inland might have fixed a bunch of genes that are responsible for adaptation. Cool! Early stage in speciation by ecological adaptation?
- Jason Stajich
drought tolerance adaptations in mimulus as well, i would be really surprised if there weren't microbes associated with root structures of drought tolerant varieties
- Thomas Sharpton
Mapping water use efficiency. Related to stomatal density.
- Jason Stajich
OK - now the microbes must be involved - mimulus gorwing at copper mines - a single locus confers copper tolerance
- Jonathan Eisen
I think Jason just whispered the punchline to me again...he knows too much ;)
- Thomas Sharpton
Selfing lines are uniquely found in copper tailings. Fine mapping. Genome assembly not good enough in the region.
- Jason Stajich
This is really an amazing amount of work - they've really taken the genome and run into the eco-evo endzone here
- Thomas Sharpton
Also is looking at mimulus in serpentine ... seems like he studies a lot of mimulus in California even though he is at Duke ...
- Jonathan Eisen
Sign of the golden age: High throughput phenotype mapping!
- Thomas Sharpton
Building RILs to make tools which are part of collaborative cross.
- Jason Stajich
Room for population genomics and phylogeography to understand divergence times and dispersal.
- Jason Stajich
Fungal genomics. James Galagan, Broad Institute - http://www.broad.mit.edu/about...
Jonathan Eisen liked this
Um so he did bait and switch. Talk is on systems biology of TB.
- Jason Stajich
No fungi no genome evolution. =(
- Jason Stajich
Talking about latent TB infection and that it adapts to environmental niche (body).
- Jason Stajich
Aren't Actinobacteria honorary fungi b/c some used to call some of them fungi?
- Jonathan Eisen
I'm rather disappointed, was hoping for an update on Broad and FGI
- Mike Challen
Omics on TB I guess.
- Jason Stajich
Says they have an integrated TB database that is acollaborative effort to make TB data available to all - see http://www.tbdb.org/
- Jonathan Eisen
Says that they now have a TB Systems Biology Collaboration - then he listed 6-7 omics they are doing - and they are doing it in vitro and in macrophages
- Jonathan Eisen
JE that's right. Joke made at mtg last week is fungi are things studied by mycologists. So that lets us include oomycetes...
- Jason Stajich
So Streptomyces counts right?
- Jonathan Eisen
Myces gets you in the club but probably won't get you MSA membership card.
- Jason Stajich
I still remember reading this well regarded DNA repair book and seeing them say "Such and Such genes was found in Streptomyces and thus is the first time this has been seen in a fungi...."
- Jonathan Eisen
Is it considered meta-analysis when you analyze data in a different way from its initial collection?
- Jason Stajich
I would guess so --- but all I do is metagenomics so what do I know
- Jonathan Eisen
here is a link to their NAR paper on the TB database http://nar.oxfordjournals.org/cgi...
- Jonathan Eisen
Showing a somewhat cool figure that shows the goodness of fit of how well their predictions based on expression data matches actual utilizaiton of some nutrient
- Jonathan Eisen
I guess this is cool modeling but I'm not entirely sure how accurate their models really are
- Jason Stajich
Genome biologists love showing fancy figures that are too complicated to digest during a talk
- Thomas Sharpton
Yeah Tom you are right --- I was captivated by the colors ... but no longer sure what it meant
- Jonathan Eisen
Great for papers, but I think too much for a fast talk. I'm guilty of doing this too....
- Thomas Sharpton
Combining data from chipseq and rnaseq - but I am waiting for someone to really build a combined data analysis approach that includes statistics and uncertainty rather than just individual sites predicted from each dataset.
- Jason Stajich
I think that would help with the aforementioned point, jason - fancy images are often used to visually represent the association between data sets, whereas a nice statistical analysis can distill it into something easy to digest while remaining meaningful
- Thomas Sharpton
Phylogenetic footprinting ... Shooting fish in barrel based on the figure.
- Jason Stajich
Data rules! That is the systems biology drum I would say
- Jason Stajich
Whole Genome Comparisons of Bacillus subtilis. Ashlee Earl, Harvard University - http://staging.catalyst.harvard.edu/Profile...
Jonathan Eisen liked this
Genome gymnastics. Lots of strain specific islands when comparing genomes.
- Jason Stajich
Some islands contain NRPS and some of these produce compounds to out compete. Some contain killer toxins to out fight siblings. Strain specific islands contain these genes.
- Jason Stajich
Developmental pathways in bacillus and we know a lot about signaling and control of the pathways. Showing diagram of what is know. Compare flexibility of the network with genome variability among different strains.
- Jason Stajich
Too busy worrying about my talk to have blogger hers but all I can say is she showed why I wanted to hire her years ago ... good combination of genomics, genetics, etc
- Jonathan Eisen
Genomic Encyclopedia of Bacteria and Archaea (GEBA). Jonathan Eisen, UC Davis - http://phylogenomics.blogspot.com/
Who is this guy... =). Whyisnt he liveblogging his own talk.
- Jason Stajich
dan rokshar making joke about dobzansky's ghost hovering over jonathan's head at Davis since that is where he ended his career.
- Jason Stajich
Chuck D = Charles Darwn's 200 yr birthday
- Jason Stajich
rRNA tree of life was important starting point for species relationships ... but the tree isn't always so good (sad face)
- Jason Stajich
Genome sampling has not been even across the phyla (citing tree of Hugenholtz 2002) . Most genomes are from 3 phyla, though there are 40 major phyla. Some phyla only sparsely sampled.
- Jason Stajich
Tree based guidance to choose which genomes to sample.
- Jason Stajich
Tree of Life proposal to sequence unsampled lineages while at TIGR - thought it would lead to discovery of novelty. Showing paper on T. roseum (wu et al... PLoS One) - novel lineage so can learn a lot of from novel samplings.
- Jason Stajich
Diversity within phyla of bacteria is IMMENSE. Some have 100s of orders" (okay here we show that linnean doesn't really work to describe these). Phyla are like 2Bya in many. Enter JE's move to Davis and interaction with JGI which led to building an encyclopedia that is guided by the tree of life.
- Jason Stajich
GEBA - was a pilot project at JGI. 200 organisms at the outset. Sequence and finish 100. All data available -- not to guide any particular work in one species - but to get the data out there.
- Jason Stajich
Resources at JGI which make them well positioned for this. Genomes Online - GOLD being mention, Nikkos, Phil Hugenholtz, and Jonathan's lab to pick cases where there are cultured samples but no genomes. Took 200 and ranked them to pick ~100 that would be the targets.
- Jason Stajich
GEBA sequencing page lists the species are chosen and done/inprogress the JGI website.
- Jason Stajich
Jonathan giving major props to the Project Management team at JGI which makes this possible. Because of their pipeline of getting data in. Also important to have partnership from culture collection - getting DNA was going to be the bottleneck. DSMZ culture collection agreed to grow up and did it FOR FREE at probably $1000 per sample!!
- Jason Stajich
ATCC did a few, but for a fee
- Jason Stajich
Because this is also done from collections in a culture collection center then anyone can order the strains that were sequenced - takes responsibility from the JGI/labs.
- Jason Stajich
All data is open and available at JGI and the IMG-GEBA.
- Jason Stajich
Side project -- "adopt a microbe" so that people can use an organism in the curriculum of a class and basically work on a genomics project in a class for a really recent genome sequence.
- Jason Stajich
what is value of GEBA? (v56)
- Jason Stajich
How many species were phylogenetically novel -- since species were chosen by rRNA tree -- rebuilding tree with whole genome data (or lots of housekeeping genes) shows that these lineages are really phylogenetically diverse (ie rRNA tree did good enough to get this diversity for picking samples).
- Jason Stajich
Protein family rarefaction -- what are the rate of discovery of novel gene families when adding new genomes. (Pan genome hypothesis). See some increase in the number of protein families as new genomes added. When a family of bacteria added get a nice rate, an even greater rate of novel discovery when looking at many samples across orders & phyla. "We discover more of the new ones when sampling from truly diverse lineages"
- Jason Stajich
Structurally novel proteins being discovered as well from this diversity being sampled. So new families are showing up. In addition within known families there is some novelty within a family (paralogs basically).
- Jason Stajich
First bacterial actin homolog found - all the other rest are actin-like in bacteria. It is structurally closely related to eukaryotic actin - most closely related to ARP8 (actin-related protein).
- Jason Stajich
In addition to novelty, the use of these other genomes should help annotate other genomes. Does it help for bacteria and archeal - convert hypothetical "conserved hypothetical". Can link proteins into distantly related protein families. Can be used in phylogenetic profile construction. Showing data that linking of protein families improved and fusion based prediction of genomes.
- Jason Stajich
Increasing diversity will help be a phylogenetic scaffold where there isn't a reference genome to match metagenomic data. How do these data help in metagenomic analyses? GEBA genomes help (slightly) for compositional binning.
- Jason Stajich
metagenomic improvement isn't so great only because the diversity of bacteria is immense so only adding 56 genomes doesn't really do more than scratch the surface.
- Jason Stajich
Post-pilot, what's next. - big extrapolation curve of what is the diversity? How many more genomes from the culture collection -- 1000 more genomes to cover 1/2 of the cultured diversity.
- Jason Stajich
This graphic is really interesting - he should post it - basically x axis is number of genomes, y axis is total branch length. it goes up fast if you add more diverse lineages.
- Jason Stajich
q? were you surprised about anything from the trees when doing this work? Yes metagenomics metrics did not improve as much as he thought they would. MEGAN and phylogenetic binning didn't improve as much as he would have thought. The phylogenetic signal that emerges from sampling many more species shows how fast you discover new families - he didn't expect to see so many more as you cover phylogenetic tree rather than across ecological environments.
- Jason Stajich
I should have stopped in the middle and twittered like Shaq
- Jonathan Eisen
Here is a link to the IMG GEBA page http://img.jgi.doe.gov/cgi-bin...
- Jonathan Eisen
Back to live blogging - James Galagan from the Broad
Syas they have an integrated TB database that is acollaborative effort to make TB data available to all
- Jonathan Eisen
here is the db http://www.tbdb.org/
- Jonathan Eisen
Says that they now have a TB Systems Biology Collaboration
- Jonathan Eisen
Then he listed 6-7 omics they are doing - and they are doing it in vitro and in macrophages
- Jonathan Eisen
Live Blogging the JGI Users Meeting - http://phylogenomics.blogspot.com/2009...
Liveblogging JGI UserMeeting: Mike Mendez on algae energy - http://stajich.wordpress.com/2009...
Cameron Currie: ant farmers - http://stajich.wordpress.com/2009...
Liveblogging JGI UserMeeting: Joe Ecker - http://stajich.wordpress.com/2009...
To Refseq or Reseq Oryza - That is the Question. Rod Wing, U. Arizona. - http://ag.arizona.edu/pls...
Diversity Generating Retroelements. Jeffrey Miller, UCLA. - http://www.mimg.ucla.edu/faculty...
Systems biology in Caulobacter. Lucy Shapiro, Stanford University. - http://med.stanford.edu/profile...
Population Genomics and the Bacterial Species Concept. Peg Riley, U. Massachusetts - http://www.bio.umass.edu/biology...
Chlamydomonas Transcriptomics. Sabeeha Merchant, UCLA. - http://www.chem.ucla.edu/dept...
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