Month: November 2009

And the sling jaw wrasse makes it to ESPN

OK – now this is really going viral. The slingjaw wrasse video from Peter Wainwright’s lab at UC Davis (which I wrote about here) has now made it to ESPN.

See the SportsNation web site:

Weird Web Stories: Monday, Nov. 16 – SportsNation – ESPN

And on Twitter SportsNation says

The slingjaw wrasse has officially replaced the waiter monkeys as our favorite animals: http://bit.ly/34mMzE


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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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ASM – launches new Open Access journal – w/ some aspects of #PLoS One and PNAS

Just got this in an email announcement from the President of ASM

ASM’s first broad-scope, online-only, open access journal, mBio™ will begin accepting submissions in January 2010 in preparation for launch in May 2010. mBio™ will offer rapid review and publication of the best research in microbiology and allied fields. The scope of mBio™ will reflect the enormity of the microbial world, highly interconnected biosphere where microbes interact with living and non-living matter to produce outcomes that range from mutualism to parasitism, energy acquisition and conversion, climate change, geologic change, food and drug production, and behavioral change. “We will encourage authors to explain how their findings fit into the larger picture,” says Editor in Chief Arturo Casadevall. Find out more at http://mbio.asm.org.
Seems like they are trying to become a PLoS One for Microbiology. Actually, they are going one interpretation of their description is that they are going even further than PLoS One in terms of making review more streamlined (see below).

mBio™ will offer authors streamlined decisions. mBio™ editors will either accept or reject manuscripts, and will request only minor revisions; editors generally will not require authors to make extensive modifications or perform additional experiments. The philosophy behind this decision is a desire to break away from the current publication model where authors are often uncertain of whether their work will ultimately be acceptable when additional work is required. Authors of a manuscript rejected by mBio™ who choose to do additional experiments will have the option of resubmitting the paper to mBio™ or another ASM journal one additional time. The resubmission must be accompanied by a response to the prior decision letter. A rejection from mBio™ does not disqualify a manuscript from subsequent submission to another ASM journal.

NOTE – THERE ARE MULTIPLE INTERPRETATIONS OF THIS STATEMENT – COULD MEAN THAT EVERYTHING WILL BE SENT OUT FOR REVIEW AND THEN EDITORS WILL MAKE SIMPLE DECISIONS. ALTERNATIVELY EDITORS COULD JUST ACCEPT OR REJECT PAPERS WITHOUT SENDING THEM OUT. THE LATTER IS HOW I INTERPRETED THE ANNOUNCEMENT.

Not sure everyone is going to like the policy here of allowing editors to just accept papers. Also – seems like they are adopting a policy like PNAS where Fellows can submit their own papers. I note PNAS just ditched this policy, in part due to the problems with peer review of some such papers.

AAM Fellows also will be entitled to submit one paper per calendar year via a special, accelerated submission path. This path will require Fellows to obtain two reviews (from reviewers who are not recent collaborators, trainees, etc.) prior to submission, make any necessary modifications in response to the reviewers’ comments, and communicate the paper plus reviewer feedback and author responses to mBio™. After the manuscript is received by the journal it will be assigned to a member of the Editorial Board (EB) for disposition. Although we anticipate that most manuscripts submitted by Fellows will be approved, the EB member will have the option of recommending modification, additional review, or rejection.

One other things to note – which I do not like by the way – ASM has created their own version of Open Access that they call ASM Access

The term “open access” can mean different things depending on the publisher. ASM has coined the term “ASM Access™” to describe the specific form of open access that applies to mBio™. Full text of mBio™ articles and supplemental materials will be freely available on the mBio™ website immediately upon publication. Full text of mBio™ articles also will be deposited in PubMed Central and will be freely available upon publication.

Authors of accepted papers will be asked to sign a license that grants ASM publishing rights and permits unrestricted non-commercial reuse. ASM will continue to require permission for commercial reuse of mBio™ content.

“ASM Access™” publications will fully meet the open access requirements of funding agencies such as NIH, HHMI, and the Wellcome Trust.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Worst new omics word award: material degradomics

And the bad omics words just keep getting worse. This one really takes the cake. A story from BBC News Online (Sniff test to preserve old books)
discusses how

“Researchers report in the journal Analytical Chemistry that a new “sniff test” can measure degradation of old books and historical documents.”

The work they are doing actually seems quite interesting. But alas, the way they describe it does not. They refer to this method as “material degradomics“. I fortunately do not have access to the paper at home but a google search reveals some text from their paper

Through similarities with metabolomics,(15) we propose to define a new field of material degradomics (and related terms, Table 1).

I literally dread what is in table 1. For creating a new omics term that seems thoroughly unnecessary and distracting, I am giving Matija Strli and colleagues one of my coveted “Worst New Omics Word Awards.” Hat tip to PaulBo who posted a comment about this on my “Fermentome” award post.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Day 2 on the pump

Well, Day 2 on the pump was better than Day 1. The night went well — was a little weird to have a thing attached to me all night but not so bad – slept in some nice big Livestrong sweatpants with big pockets where I put the pump.

Earl AM went fine – had some issues with the pump in mid day – not sure what exactly was going on but still fine tuning the dosing and all the parameters with trying to make the pump mimic a pancreas.

Anyway – enough about me. Most important thing to post today is that tomorrow is World Diabetes Day. Lots of events and activities and other things going on in the real and cyber world.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Holy Slingjaw Wrasse and the power of twitter

OK I am now a bit blown away by twitter.

“Peter Wainwright showed this crazy slingjaw wrasse video in our class at#UCDavis yesterday:http://tinyurl.com/ybqv429“

The video indeed is awesome:
And then a few others retweeted/commented on this.
Then Carl Zimmer blogged about it on “The Loom” in a post “The last thing the mosquitofish saw“.
And that is really when the fish hit that fan.
On Tuesday, Tom Chivers at the Telegraph wrote about it “Weird feeding habits of the slingjaw wrasse” saying

“Almost 6,000 people have watched the YouTube footage of Epibulus insidiator, a strange predator found in tropical waters in the Pacific and Indian Oceans.”

Little did he know what would happen next. It seems to have then gotten picked up by all sorts of web news sites around the world and KABOOM, like the fishes jaw, this video went crazy.
See for example
Now there have been 165,000 views. Completely deserving I must say. But pretty surprising too …
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And here are some more links:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Day 1 – Pumping Again

I was torn about whether to blog about this whole thing or not, but inspired by Lance Armstrong’s openness about this cancer treatments, I have decided that it might be useful to some people — so here goes….

Well, after a HORRENDOUS experience with the Insulin Pump last summer, I am trying it again. Last summer, I spent 2.5 weeks on the pump. Week 1 was freaky – getting used to the whole concept after 25 years on insulin. Week 2 was pretty nice – getting used to the whole thing. Week 3 was the worst – got a very bad infection at the pump insertion site. After a few days went off the pump and then spent 1.5 months dealing with something akin to MRSA. Never got the organism typed (which was really really dumb in retrospect) but when the third antibiotic I went on started to work it seemed like MRSA.

Anyway – more on the disaster later.

Today is for new beginnings. Starting on the Insulin Pump again. Got trained by the Medtronic specialist, which went much better this time than last time. And was up and running in ~ 2 hours. And then I went off with the pump connected, a cyborg again for the first time in over a year.

I went to work for a bit for my lab meeting (a student was presenting and I already delayed her presentation last week so could not ditch her again this week). And after talking to people a bit after lab meeting, I went home.

This time around, with a year to think about things, I feel much better being on the pump Of course I could still get an infection but hopefully that will not happen and things will go better this time.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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1000 Complete Bacterial and Archaea Genomes -wow


1000 Complete Bacterial and Archaeal Genomes in Genbank. Big MileStone. Good day for a microbial genome party. This whole thing is amazing to me. I moved to TIGR in 1998 in order to get in early on the “genome sequencing revolution” as we called it then. We were amazed when the 10th genome came out. We were then thrilled when TIGR sequenced its 20th genome. And now, there are 1000. Amazing.

And as Nikos Kyrpides just told me (he is sitting next to me right now) – actually if you go to GOLD (Genomes Online) (Nikos runs this DB) you can see there are actually a few more than 1K there. Even more amazing.

Posted using ShareThis

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Bay Area Bioinformatics Group

OK – so in the era of H1N1 it is definitely yucky to have REAL meetings with people, but this “Bay Area Bioinformatics” meetup group seems like a good idea. They have a meetup in Berkeley 11/14 at Cafe Strada. Folks can sign up here: BayBIFX (El Cerrito, CA) – Meetup.com

Seems like they are focused on East Bay but want to get Davis, and other people involved …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Bay Area Biosystematists Mtg 11/10, #UCDavis, on Community Phylogenetics

Bay Area Biosystematists Meeting: Tuesday, 10 November, 2009

at UC Davis, 1022 Life Sciences (LSA)

“Community Phylogenetics”

Featuring Jean H. Burns of the Center for Population Biology, UC Davis
Plus contributions from panel discussants:
Paul Fine, Integrative Biology, UC Berkeley
William Cornwell, Integrative Biology, UC Berkeley

Come and hear about this emerging synthesis of systematics and ecology that promises to transform the way we do both!

Schedule and venue:
5:30 – social gathering with beverages and informal pizza dinner:
cost ca. $12, to be collected at door, 1022 Life Sciences Bldg. (LSA),
UC Davis campus.
7:00 – talks followed by discussion, in same room.

Please email reservations to your host, Kristy Deiner, at alpinedna@gmail.com by Monday, Nov. 9th

All are welcome, members or not. If you want to join the Biosystematists, a venerable yet exceptionally lively group that provides the only inter-institutional seminar/discussion forum addressing evolutionary topics in the Bay Area, sign up for our mailing list at: https://calmail.berkeley.edu/manage/list/listinfo/babs-l@lists.berkeley.edu

For a map of this region of the UCD campus, use the link below.
http://www.cevs.ucdavis.edu/map/map_detail.cfm?centerTile=7_6

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Posting Notes from NAS Microbes and Health Meeting here on my blog

I am going to be posting notes on the NAS Meeting on Microbes and Health Here

http://friendfeed.com/treeoflife/9ab60359/dennis-kasper-from-harvard-brigham-is-now-up-at?embed=1

http://friendfeed.com/treeoflife/21a50e16/beta-version-of-qiime-software-from-rob-knight?embed=1

http://friendfeed.com/treeoflife/afe12ea8/now-speaking-at-nasmh-gunnar-hanson-on-mucus?embed=1

http://friendfeed.com/treeoflife/6dde23dc/getting-ready-for-david-mills-from-ucdavis-to?embed=1

http://friendfeed.com/treeoflife/501f92f3/ruth-ley-at-nasmh-talking-about-development-of?embed=1

http://friendfeed.com/treeoflife/4fee5fdd/karen-guillemin-from-u-orgeon-is-now-talking-at?embed=1

http://friendfeed.com/treeoflife/7e249d3d/michiel-kleerebezem-is-talking-at-nasmh-about?embed=1

http://friendfeed.com/treeoflife/07aae71d/david-relman-from-stanford-now-talking-about?embed=1

http://friendfeed.com/treeoflife/5f1eb001/forest-rohwer-now-talking-at-nasmh-meeting-on?embed=1

http://friendfeed.com/treeoflife/96b1c26d/may-shift-from-twitter-to-friendfeed-for?embed=1

Elaine Holmes at #NASMH studying metabolomics & microbes vs. human hypertension & BMI & type II diabetes – strong IDing signals

Vaughan at #NASMH using “Simulator of the Human Intestinal Microbial Ecosystem” aka SHIME Reactor

@DavidSela There goes my 30 minutes of twitter fame …

Vaughan at #NASMH performing human ‘intervention study’ using tea & grape/wine polyphenols – each person is their own control

Keijser at #NASMH using microarray to survey rRNAs from oral samples – calls this the “OC” chip

Elaine Holmes #NASMH “dosed up post docs w/ Chamomile tea” & compared metabolites & microbes (hard to prevent EToH consumption though)

Elaine Vaughan from UNILEVER at #NASMH discussing bioconversion of dietary polyphenols by gut microbiota

RT @Scitable Cucumber genome published http://www.eurekalert.org/pub_rel… Guide to pumpkin, melon and plant vascular system #UCDavis

Bart Keijser at #NASMH talking about exploring oral microbiota in kids – using traveling “dental bus” – every kids nightmare

Keijser at #NASMH – w/ array get correlations betw. oral health status & certain organisms – these may be new targets for intervention

Vaughan at #NASMH looking at polyphenol metabolites from grape/wine extract & black tea – steps by microbiota vary greatly

Elaine Holmes at #NASMH trying to correlate specific metabolites w/ specific organisms – very difficult

Keijser at #NASMH using 454 rRNA sequencing to compare oral microbiota over time in permanent vs. “deciduous” teeth

Elaine Holmes at #NASMH is talking about metabolomics of microbes – see here home page here http://www1.imperial.ac.uk/medicin…
Monday from Twitter – Comment – Share – Edit

Elaine Holmes at #NASMH is talking about metabolomics of microbes – see here home page here http://www1.imperial.ac.uk/medicin…

Elaine Holmes at #NASMH looking at metabolites & microbes in model of bariatric surgery in rats

Elaine Holmes at #NASMH looking at metabolic profiles in different ethnic groups re; obesity epidemic

Elaine Holmes at #NASMH – using metabolomics of faecal H20 to compare normal & vancomycin treated mice

Elaine Holmes at #NASMH discussing study infecting germ free mice with microbiota from human babies http://www.nature.com/msb…

Elaine Holmes at #NASMH – metabolomics of urine from rats gives insight into gut microbiota (very cool)

Elaine Holmes at #NASMH – metabolomics of gnotobiotic (aka germ free) mice w/ and w/o colonization by microbes

R. Knight #NASMH discussing ecological “convergence” in microbial communities species assemblages

R. Knight #NASMH showing amazing study of microbes all over people’s bodies (27 or so locations)

R. Knight #NASMH – comparison of mammal gut communities shows clustering by diet

R. Knight #NASMH “much as we love rRNA at Boulder we accept that we have to look at other parts of the genome”

R. Knight #NASMH – deep sequencing gives us samples of rare biosphere – though unclear what these rare organisms do

R. Knight #NASMH using 454 sequencing to survey microbial communities – expensive but saves money in long run

Knight #NASMH – UNIFRAC comparison of all communities suggests vertebrate gut communities are very unique

Getting reads for my talk at #NASMH

Knight at #NASMH says “hierarchical clustering as w/ microarrays” -good 2C my brother’s work referred this way http://www.pnas.org/content…

Rob Knight at #NASMH discussing how UNIFRAC uses tree of life as organizing theme http://bmf2.colorado.edu/unifrac…

N. Moran #NASMH – aphid defense against parasitoids by H. defensa due to phage encoded toxins

Rob Knight – microbiome is good for personalized medicine b/c there is much variation between people

Rob Knight #NASMH discussing how van Leeuwenkoek was first to look at “Human Microbiome” using tooth scrapings

N. Moran #NASMH – many symbionts on border between bacteria & organelle – though more on the bacteria side

N. Moran #NASMH aphid resistance to parasitoid wasps due to presence of facultative symbiont H. defensa http://www.pnas.org/content…

# Rob Knight from CU-Boulder talking at #NASMH on 16s rRNA “enlightenment”

R. Knight #NASMH – was a major need for methods to compare rRNA data from different microbial communities

N. Moran #NASMH summary: symbioses major force in evolution, source of adaptation in changing envir, source of host constraints

N. Moran #NASMH comparing symbiont DNA repair genes: all missing some, some missing all, leads to incr. mutation rate & DNA biases

N. Moran #NASMH – once endosymbionts lose genes – never coming back b/c no lateral transfer – has profound effects on host ecology

R. Knight at #NASMH says next generation sequencing helps saves toothpicks previously used for colony picking

N. Moran #NASMH – accidental selection in lab for symbionts to lose heat shock response – see #PLoS Bio http://www.plosbiology.org/article…)

N. Moran #NASMH: organisms w/ small genomes lose non essential genes & also useful genes by drift b/c population sizes low

N. Moran #NASMH aphid resistance to parasitoid wasps due to presence of facultative symbiont H. defensa http://www.pnas.org/content…

# Rob Knight from CU-Boulder talking at #NASMH on 16s rRNA “enlightenment”

R. Knight #NASMH – was a major need for methods to compare rRNA data from different microbial communities

N. Moran #NASMH summary: symbioses major force in evolution, source of adaptation in changing envir, source of host constraints

N. Moran #NASMH comparing symbiont DNA repair genes: all missing some, some missing all, leads to incr. mutation rate & DNA biases

N. Moran #NASMH – once endosymbionts lose genes – never coming back b/c no lateral transfer – has profound effects on host ecology

Watching Nancy Moran, 1 of my favorite scientists, talk on symbioses at NAS Microbes&Health mtg (#NASMH) http://www.nasonline.org/site…

Nancy Moran at #NASMH: bacteria are incredibly diverse & plastic whereas animals are not so plastic & need some metabolic help

N. Moran #NASMH: in many symbioses host & symbiont phylogenetic trees are congruent -must be due to ancient associations

Nancy Moran defines symbiosis as I do: “members of more than 1 genetic lineage associate closely, often for mutual benefit” #NASMH

Nancy Moran: studies of symbionts used to be very hard b/c most cannot be cultured – molecular methods have revolutionized studies #NASMH

Nancy Moran is talking about symbioses

SHowing rRNA tree of life

Bacteria very diverse – in many ways – and very plastic and dynamic

Animals do not do this much

Essential roles of symbionts in animals – many examples

Giving props to Paul Buchner who documented associated involving bacteria buyt had not molecular methods and no culturing

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–