Tag: Misc.

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.

——–

More on the PLoS Special Collection on the Genomic of Emerging Infectious Diseases

In case people have not seen in. There is a new collection out from PLoS on the Genomics of Emerging Infectious Diseases. The collection, edited by me and Catriona MacCalum, one of the PLoS Biology Editors. It was sponsored by Google.Org who have a growing interest in emerging infectious diseases. Also heavily involved were Carol Featherstone a freelance writer/editor and Maggie Brown the copy editor.


An Editorial by me and Catriona describing the collection is here: PLoS Biology: Genomics of Emerging Infectious Disease: A PLoS Collection

The papers in the collection are listed below. It truly is an amazing collection of papers all on genomics of emerging infectious diseases and all completely open. Take the material from these papers. Reprint it. Reuse us. Mash it up. Use the figures. And most of all, help in the fight against emerging infectious diseases. Thanks to all the authors, all the PLoS folks (especially Catriona) and all the Google.Org people for working on this. And also thanks to Dr. Kiki for handling the interview for the podcast about the series which is available here.

http://www.flickr.com/apps/slideshow/show.swf?v=71649

Some more on the series from the web:

Eisen, J., & MacCallum, C. (2009). Genomics of Emerging Infectious Disease: A PLoS Collection PLoS Biology, 7 (10) DOI: 10.1371/journal.pbio.1000224

——–
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.

——–

Genomics Faculty Jobs at the Joint Genome Institute


Just got an email from Eddy Rubin the Director of the Joint Genome Institute (JGI) advertising faculty jobs in genomics at the JGI. Looks like this could be very nice. I have an Adjunct Appointment at JGI and do a lot of work there and am hoping that some great people apply for these jobs …

Dear JGI User Community,
I would like to bring to you attention an elite early career faculty position presently available at the DOE Joint Genome Institute. The Divisional Fellow position that we are advertising (in Nature and Science, attached) is equivalent to a tenure-track faculty position at a university, and is appropriate for highly-qualified scientists with a Ph.D. or M.D. degree, who have completed post-doctoral training or equivalent experience. We are specifically seeking individuals to direct a genomics-based research program in the study of either plants, microbes, metagenomes or genome informatics. Divisional Fellows are appointed to five-year term, provided with research and salary support and an accelerated path for achieving promotion to Senior Scientist status at the end of this term.

I urge you to contact me directly if you have questions about the position while interested parties should submit CV, summary of research interests, and references to recruiter Bill Cannan: WRCannan@lbl.gov.

For more information see: http://jobs.lbl.gov/LBNLCareers/details.asp?jid=23646&p=1

——–
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.

——–

Personal Medicine Panel Discussion at American River College

Genetics as a Consumer Good: The Personal Side of Medicine, What It Means,
and Who Should Know?
You can obtain a scan of your personal genetic code with just the internet and a credit card—
for as low as $100! Consumer Genomics can be part of your medical care in the 21st century.

• Will this information enable us to take charge of our own health?
• Is it a form of medical “self-malpractice”?
• How will Consumer Genomics affect patient privacy?

Explore these issues with leading experts in the field:

FREE Public Forum at American River College
Date & Time: Saturday, November 7, 2009 * 2:00 – 4:00 PM
Location: ARC Main Theatre * 4700 College Oak Dr. Sacramento
Free Parking in Lot D – Corner of College Oak Dr. & Myrtle Ave.

Speakers Include:
• Andro Hsu Ph.D.: Science and Policy Liaison, 23andMe (a pioneering Direct to Consumer
Genomics Company)
• Lynn Dowling, MA, MBA: Consultant to El Camino Hospital’s Genomic Medicine Institute (one of
the first hospitals to incorporate genetic analysis with traditional medical practice)
• Kelly Ormond, MS CGE: Program Director, Human Genetics and Genetic Counseling MS
Program, Stanford University (one of only four genetic counseling programs in the Western US)

For more information contact the North Valley Biotechnology Center at: (916) 484-8660

——–
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.

——–

Job posting: Bodega Marine Reserve Manager #ecology #marine #UCDavis

Reserve Manager, Bodega Marine Reserve, Bodega Bay, California,
University of California – Davis

Principal Museum Scientist – Supervisor
Career position, 50% variable, full benefits
$4,024-$6,841/Mo. (minimum to midpoint of salary range)

For consideration, apply by November 10, 2009. Open until filled.

The Reserve Manager is responsible for all management of the University’s Bodega Marine Reserve and coordination and support of all field programs at the site. Facilitates and implements the research, education and public service missions of the Natural Reserve System and supports field programs of the Bodega Marine Laboratory. Reviews proposals, develops policies for use of both terrestrial and marine habitats, supervises staff, administers budgets, and develops management plans. Gives lectures and leads field trips for classes and the public. Develops monitoring programs and databases, initiates invasive species control and re-vegetation programs.

Seeks supplemental funding through grants and contracts. Coordinates with local, state and federal agencies in matters of permits, land management, conservation and land use policies. Represents the Reserve and the University at public meetings, government hearings, and scientific meetings at the local and national level.

Qualifications include:
Background in ecology or related field, experience in land stewardship, skills to make sound scientific decisions while developing Reserve use and management policies, skills to develop and maintain effective working relationships with neighboring landowners, resource agencies, campus departments, administrative offices, and faculty, staff and students, and knowledge of invasive plant species, control methods, and re-vegetation techniques. Supervisory experience, experience at a field station or marine lab and skills in writing, preparing proposals and verbal communication/presentation are preferred.

Application Procedure:
To view the position and to submit an application on-line visit
http://www.employment.ucdavis.edu/applicants/Central?quickFind=53986;
Requisition
Number #03001704

——–
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.

——–

Microbes, art, science all rolled into one – yum


A quick one here. Just got sent a link to this site – Microbial Art. It includes work art with microbes from “Dr. Niall Hamilton (New Zealand), Dr. T. Ryan Gregory and his students (Canada), Dr. Jeff Tabor and colleagues (USA), Dr. Ben Wise and his students (USA), Dr. Eshel Ben-Jacob (Israel), and various other contributors.”

It has some nice stuff. Definitely worth checking out.

——–
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.

——–

A field guide to the microbes?


Here is a link to an article in Microbe Magazine (Genomic Analyses Could Lead to “Field Guide to Microbes”) discussing in part a session from last years ASM Meeting on the “1$ Bacterial Genome”. The article includes a discussion of my proposal to create a “Field Guide to the Microbes.” Also the article has a link to an audio interview of me by the article author Jeffrey Fox.


Audio interview with Jonathan Eisen

The article does not quite capture what I mean by a Field Guide to the Microbes (not the authors fault – my talk did not capture this either). But I will be writing more on this soon. Very soon. Stay tuned. Also here are the slides from that talk, which I posted to slideshare

Jonathan Eisen talk on 1$ Genomehttp://static.slidesharecdn.com/swf/ssplayer2.swf?doc=eisen-1-091025210254-phpapp02&stripped_title=jonathan-eisen-talk-on-1-genome

Also see this talk I gave at the JGI User Meeting where I ended with my call for a Field Guide to the Microbes …

http://www.scivee.tv/flash/embedCast.swf

——–
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.

——–

CSI-Miami could be renamed CSI Microbiology

The CSI shows have certainly done a lot for science, from the point of view of getting people to talk about science as it relates to forensics. Sure, much of the science in the show is a bit off kilter, but the show would basically suck if it showed the real science (e.g., things work really quickly in all the shows — unlike much of science). But if we compare the science in CSI versus in the latest CNN/Fox yelling matches or the latest wife swapping show, CSI rules the day.

And all of the CSI-like shows (which can be viewed as a form of convergent evolution in ways), also have a decent chunk of science here and there (e.g., NCIS). What is most remarkable to me about all of this has been the number of shows with something about microbes. And the latest CSI- Miami is an example of this (see the recap here:CSI: Miami Recap: Bad Seed – CBS.com)

This episode had a mix of DNA based forensics of E. coli infections, as well as a smattering of microbe associated anti-GMO sentiment when an evil biotech company made some GMO corn that was designed to be carrying a cellulytic gene from a Clostridium species but instead some of the corn carried a toxin gene from Clostridium botulinum. And the winner from a microbial point of view was the brief mention of lateral gene transfer that was responsible for the cellulolytic species of Clostridium picking up some genes from the botulism bug.

No the science they showed was not perfect. But when a TV show starts discussing mechanisms of lateral gene transfer – they will get my attention.

——–
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.

——–

What a waste in #Davis – a whole election & associated material for one vote


Well, however you feel about the Wildhorse Ranch vote in Davis, this whole election just seems absurd. A whole election just to vote on this one thing? And do they really need a multi-page color sample ballot? So if I could, I would vote to require these “special” elections about rezoning to only happen if there already was another important election going on. Even if the pro-Ranch crown pays for the election, it just seems like a waste …

——–
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.

——–

Walkscore – software for walkability of communities goes open source

Just got this email (see below) from WalkScore that I thought might be of interest to Davisites. Walk Score is one of several types of “software for civic life” from Frontseat. This systems allows one to evaluate the walkability of a community or address. And now they are looking to release the software for WalkScore at Walkscore.Org as an open source development. And they are trying to get more people involved in this – including asking for what new developments they should make. I have suggested previously that they should incorporate bikability. And if you agree, you should vote for it here.

Dear Jonathan,

You deserve a break. Take a sec to:

Also, we’re thrilled to announce our Rockefeller Foundation grant (see below).

— The Front Seat Team

Vote on Walk Score improvements

We just launched WalkScore.org — a new website where you can vote on Walk Score improvements. We’re also releasing open source code for Walk Score on this site.

Friends with benefits

Can you help us get to 100 fans on Facebook so we can claim a URL for our Facebook page?

Let’s create a Facebook group of people who support walkable neighborhoods.

Rockefeller Foundation grant

We’re using our new grant from the Rockefeller Foundation to improve Walk Score and make it open source. Sign up on WalkScore.org to get notified when the code is available.

——–
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.

——–