The Tree of Life

Cool bacterial art makes gizmodo #MicrobialArt

2013-05-20T19:45:00.001-07:00

Quick post - cool bacterial art project has made Gizmodo. See Bacteria Never Looked So Beautiful. From an Art of Science competition at Princeton. I wonder what Artologica - my favorite microbial art artist - thinks of this.

For some other posts about microbial art see:

Germophobia: wanna get people in the mood for "Contagion" movie about killer virus - grow harmless microbes in public #microbialart
My new microbial art for my office: salt evaporation ponds and goethermal spring stamps
Microbial art for the holidays from the J. Craig Venter Institute
Guest post on "The phone microbiome" from Georgia Barguil in Jack Gilbert's lab
Microbes, art and a bit of satire all in one place - Design Interactions at the RCA
Headline says it all "Opera singer grows algae on her face by feeding it w/ her breath & then the audience eats it"
What to do - what to do - cool microbial art w/ a #badomics word --- must resist purchasing -- must resist ...
My new microbe art corner w/ three works by @artologica
Microbial & Evolution art by @artologica has whole new meaning now that I met her at @scio12

Thoughts on Citizen Microbiology and upcoming session at #ASM2013

2013-05-19T11:24:00.003-07:00

I am sitting on a Southwest Airlines flight heading to Denver for the American Society for Microbiology 2013 meeting. At 3 PM today I am scheduled to co-chair (with David Coil from my lab) a session on “Citizen Microbiology” (well the full title is Citizen Microbiology: Enhancing Microbiology Education and Research with the Help of the Public). The schedule of the session is at the bottom of this post but it promises to be very interesting and exciting (no bias here at all).

As far as I know, this is the first session ever on “Citizen Microbiology” at a large meeting of any kind. We held a small workshop at UC Davis in January of 2012 on Citizen Microbiology but that was quite small. I note - I use a very broad definition for Citizen Microbiology including basically any project that engages the public in some way to participate in a research project relating to microbes. This is the perfect time to have such a session at a large meeting and the ASM General Meeting is an ideal setting. There are a series of converging forces that makes this timing ideal including:

There is a growing appreciation of microbes and the role they play on the planet. Some of this appreciation is broad - covering all microbes - all the time - everywhere. But much of it is due to a growing interest in the microbes closer to us - those that live in and on us (the human microbiome) - those that live in and on plants and animals and other organisms we care about - and those that live in the places where we spend much of our time (the microbes of the built environment). I mean - come on - everyone is talking about fecal transplants now in public - in cover stories of the NY Times Magazine and in Ted talks.

Technological and scientific advances have made it possible to better sample the microbes found in any particular location. Clearly, DNA sequencing technology and associated analytical tools are a central component of these advances, but other factors are important too.
The world is becoming more and more digital which makes the sharing of information (which is key to Citizen Science) easier and better. And social media has made it easier to communicate and discuss actions like Citizen Microbiology.
Citizen Science is growing by leaps and bounds in other areas (e.g., check out http://www.scistarter.com).
Crowdsourcing (not the same thing as Citizen Science - more on this another time perhaps) is also growing in leaps and bounds.
Crowdfunding is providing new ways to fund scientific activities.
Sensors of all kinds are getting cheaper and easier to use and are being deployed widely.
Many people are becoming more and more interesting in recording information about themselves and sharing it with others.
The “open science” movement is making the literature, software, methods and data and more available to everyone with no or few restrictions thus allowing for more people in diverse environments to become engaged in research.
Microbiology education and outreach is spreading with some great journalists and diverse other sources of information including hundreds of microbiology blogs and many other forms of social media being used.

These are but a few of the reasons why I believe the time is right for Citizen Microbiology. But there are also what I would call somewhat negative reasons why the time is right too. These include

Germophobia is rampant and fueled by media hype and marketing forces.
We have done, and continue to do, serious harm to our microbial world. Antibiotics are overused. Antimicrobials are in everything. More and more children and missing out on vaginal birth. And so on
Although our understanding of the importance of microbes is everywhere, there are also many who are overselling what we know - claiming that probiotics will cure all ailments for example.
Some information about microbes that is out there on the web is, well, less that ideal
The ethics of engaging the public in studies of microbes are not fully appreciated by some and not completely understood by most.

So this is both an exciting and a critical time for microbes and microbiology. And I hope that this session will not only help launch the field of Citizen Microbiology, but will help get everyone to think about the bigger issues and how to move the field forward in the right directions. For there is so much we need to do and think about including

Ethics
Funding
Openness and sharing
Visualization
Analysis tools
Communication
Outreach

And of course - the people at the session are not the only ones engaged in Citizen Microbiology or related activities (see a list we made a while back here). If you are doing a project please post something about it here. And if you are not doing a Citizen Microbiology project - well - why not? Get your act together.

Anyway - got to put away the computer as we land in Denver soon and I will rush off to the conference center, hopefully on time, to chair this exciting session. And I hope to see you there or have you follow online (check out the Twitter hash tag #ASM2013). And keep your eyes open for more excitement in this area.

-------------------------
Today’s session at ASM 2013:

(Division W Lecture) Authentic Research for Novice Scientists: Phage Discovery and Genomics by Undergraduate Students
Graham Hatfull;
Univ. of Pittsburgh, Pittsburgh, PA.

Understanding Human Influence on Microbial Distribution Patterns in the United States: A Citizen Science Approach
G. Barguil Colares1, J. Marcell1, D. Smith1,2, J. A. Eisen3, J. Gilbert1,2;
1Argonne Natl. Lab., Lemont, IL, 2Univ. of Chicago, IL, 3UC Davis, Davis, CA.

The Home MIcrobiome Project: Learning the Lessons of Citizen Science and Communication
J. A. Gilbert, D. Smith;
Argonne Natl. Lab., Lemont, IL.

The New National Lab: How Citizen Science is Transforming American Research
Darlene Cavalier;
Sci. Starter, Sci. Cheerleader, Philadelphia, PA.

Sequencing the Human Microbiome with Citizen Science
Z. Apte1, J. Richman2, W. Ludington3;
1uBiome, Inc, San Francisco, CA, 2Oxford Univ., Oxford, UNITED KINGDOM, 3Univ. of California, Berkeley, Berkeley, CA.

The American Gut Project: Challenges and opportunities for crowdsourcingmicrobial ecology
Antonio Gonzalez Peña;
Univ Colorado at Boulder, Boulder, CO.

Public Science in Private Places: A Study of the Microbial Ecology of One Thousand Houses in Fifty States and Five Countries
Rob Dunn;
NC State Univ., Raleigh, NC.

Excellent piece in the NY Times Magazine by @michaelpollan "Some of my best friends are germs" #ASM2013

2013-05-19T06:41:00.001-07:00

Quick post here. There is a really nice piece on in the New York Times Sunday Magazine by Michael Pollan on the human microbiome: Say Hello to the 100 Trillion Bacteria That Make Up Your Microbiome. In it he discusses how he had his microbiome typed by the American Gut Project and he discusses browsing through the output. He also discusses a diversity of issues in the microbiome and work of various folks. People featured include Justin Sonnenburg, Rob Knight, Burce German, Catherine Lozupone, Stanley Falkow, Jeffrey Gordon, Michael Fischback, Maria Gloria Dominguez-Bello, Martin Blaser, Ruth Ley, Andrew Gewirtz, Patrice Cani, Erica Sonnenburg, and Stephen O'Keefe. The article does a really good job of highlighting why the microbiome is important yet does not oversell what we know at this point.

I note - Pollan came to UC Davis as part of his research for the article a little while back. Below are some pics of him getting a tour of the UC Davis LEED Platinum brewing facility. Anyway the article is definitely worth a look. And just in time for the ASM 2013 Meeting which I am about to head to this AM.

Just in time for #ASM2013 - FDA adding regulations for fecal transplants #microbiome

2013-05-18T13:59:00.001-07:00

Well, I guess this could be good news or bad news or both. The FDA has sniffed the winds of microbiome studies and decided that it wants some more regulation on fecal transplants (aka fecal bacteriotherapy). See for example Fecal Transplant: FDA Wants Regulation. Fecal transplants are spreading like crazy these days and every where I go in real life and online I hear and see more about them. For more on fecal transplants see some of my previous posts such as More (you know you wanted it) on fecal transplants and the microbiome and Fecal transplants in the news and Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively.

I guess the FDA feels like they have to do something given the spread of FT. Given how many scam artists and oversellers of the microbiome are out there I think some sort of increased protection or regulation is probably a good thing. But I am not sure what the best way to do this is. Clearly some are unhappy with the FDA sticking their noses into fecal transplants (e.g., see here). But given how little we know about FTs other than as treatment for Clostridium dificile infections it seems like one could make a reasonable argument for more regulation or caution. It seems strange though that we can do just about anything and everything we want to kill all the microbes around us with very little regulation and yet attempting to manipulate the microbes in and on us or add a few here and there is being regulated more.

What do others think? Do we need more regulation from the FDA on fecal transplants?

UPDATE - some links to other discussions of this:

The kibosh (from Controversies in hospital infection prevention)
Fecal transplants to treat C. diff now need FDA approval
FDA halts US poop transplants pending further review (Raw Story).
FDA: Fecal Transplants Need Investigational New Drug Application ... (JWatch blog)
Oversight for Fecal Transplants | The Daily Scan | GenomeWeb
Many Years Young: Fecal Transplant: FDA Wants Regulation
FDA Declares Stool a Drug -- Not kidding! @ TigerDroppings.com
Fecal Transplant: FDA Wants Regulation - Digestive Health Center - Everyday Health - EverydayHealth.com

Thanks to Software Carpentry (@swcarpentry) for coming to #UCDavis

2013-05-18T01:08:00.001-07:00

Quick post here. Jenna Lang in my lab has a post at microBEnet about the recent workshop that the Software Carpentry folks ran at UC Davis: Software Carpentry comes to UC Davis! | microBEnet: The microbiology of the Built Environment network. It was a major success. For those who don't know Software Carpentry's mission is is to build basic computing skills among researchers. From their web site:

Software Carpentry helps researchers be more productive by teaching them basic computing skills. We run boot camps at dozens of sites around the world, and also provide open access material online for self-paced instruction. The benefits are more reliable results and higher productivity: a day a week is common, and a ten-fold improvement isn't rare.

A great idea and done really well. Others out there should consider hosting or attending one of their Boot Camps and checking out their materials on their web site. See for example their videos and their reading list and their lessons. They really do great things ...

ICG Europe starts w/ "Omics & the future of man" & sticks to men the rest of the time

2013-05-14T07:32:00.003-07:00

Fun. Another day. Another YAMMGM (yet another mostly male genomics meeting). This one is the International Conference on Genomics Europe 2013. I have copied the program as it is now here and then highlighted the men and women as far as I can tell. And, well, it is not very balanced. It starts off, ironically, with "Omics and the future of man" and then stays on both omics and alas, men, for most of the meeting. The first woman does not talk until 5 pm on the first day. Nothing against BGI per se. But they seem to be repeat offenders in having meetings with mostly male speakers. A difference between countries? Perhaps. But unfortunate and unpleasant nevertheless.

Sessions with speakers:

Plenary Session 1: Omics and the future of man

09:00-09:10: Opening ICG-Europe 2013 & Welcome: Hans Galjaard, Chairman of the Department of Clinical Genetics at Erasmus University
09:10-09:55: Talk 1: Huanming Yang, BGI, China
9:55-10:25: Talk 2: Jeremy Nicholsen, Head of the Department of Surgery and Cancer, Imperial College London, UK
Topic: Molecular Phenotyping and Systems Medicine Approaches in Personalised and Public Healthcare

Chairman: Prof.Huanming Yang, BGI, China

Plenary Session 2 :

11:00-11:30: Talk 1 (30 min): Jun Wang, CEO, BGI, China
11:30-12:00: Talk 2 (30 min): Karsten Kristiansen, Head of the Department of Biology, University of Copenhagen, Denmark
12:00-12:30: Talk 3 (30 min): Nils Brunner, Director of the Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Denmark
Topic: Docetaxel resistance in vitro: Known mechanisms and novel pathways in breast cancer
Chairman: Prof. Jun Wang, BGI, China

Plenary Session 3: Plant and Animal Genomics

13:30-13.55: Talk 1: Rajeev K. Varshney, Director-Centre of Excellence in Genomics, ICRISA, Hyderabad, India
Topic: “Little” is “more” for chickpea and pigeonpea
13.55-14.20: Talk 2: Michael Bevan, Genomics and Functional Genomics of Bread Wheat for Crop Improvement, John Innes Centre, Norwich, UK
Topic: Genomics and Functional Genomics of Bread Wheat for Crop Improvement
14.20-14.45: Talk 3: Michel Georges, Unit of Animal Genomics, University of Liège, Belgium
14.45-15.15: Talk 4: Tomas Marques, ICREA Research Professor, Universitat Pompeu Fabra, Spain
Topic: Great Ape genetic diversity
15.15-15.35: Talk 5: TBC
Chairman: Prof. Marc Van Montagu , VIB, Belgium

Session 4: Cancer genomics and Transcriptional Regulation

16:00-16:20: Talk 1(20 min): Stein Aerts, Heading the Laboratory of Computational Biology, K.U.Leuven, Belgium
Topic: Probing into the genome, transcriptome, and regulatory network of T-cell acute lymphoblastic leukemia
16:20-16:40: Talk 2(20 min): Lars Bullinger, Assistant Professor, University of Ulm, Germany
Topic: Genomics in acute myeloid leukemia (AML) – clinical translation of findings
16:40-17:00: Talk 3(20 min): Diether Lambrechts, Assistant Professor, K.U.Leuven & VIB, Belgium
Topic: Mutation signatures of mismatch repair deficiency in cancer genomes
17:00-17:20: Talk 4(20 min): Lynnette Fernandez-Cuesta, University of Cologne, Germany
Topic: Characterization of lung neuroendocrine tumors
17:20-17:40: Talk 5(20 min): Henrik Ditzel, University of Southern Denmark, Denmark
Chairman: Dr. Jan Cools (K.U.Leuven, VIB)

Workshop：Innovation-Entrepreneurship and Venture creation-1

14:30-14:50: Talk 1 (20 min): Boo Edgar, Program Director, Innovation and entrepreneurship; The Sahlgrenska Academy, University of Gothenburg
14:50-15:10: Talk 2 (20 min): Martin Bonde, Chairman of Danish Biotech association
15:10-15:30: Talk 3 (20 min): Søren Møller, Managing Investment Director, Novo Seeds
Chairman: Johan Cardoen
16:00-16:20: Talk 1(20 min): Johan Cardoen, Managing Director VIB
16:20-16:40: Talk 2(20 min): Patrick Van Beneden, GIMV
16:40-17:00: Talk 3(20 min): Ann De Beuckelaer, Flanders Bio

Session 5: Human Disease- Structural Genomic Variation and Function

09:00-09:30: Talk 1 (30 min): Wigard Kloosterman, UMC Utrecht, The Netherlands
Topic: Cause and Consequence of Complex Genomic Rearrangements
09:30-10:00: Talk 2 (30 min): Michael Talkowski, Instructor, MGH, Harvard University, USA
Topic: Sequencing unique human genomes reveals novel loci in autism and predictive phenotypes in prenatal diagnostics
10:00-10:30: Talk 3 (30 min): Thierry Voet, K.U.Leuven
Chairman: Prof. Edwin Cuppen , Hubrecht Institute

Session 6: Metagenomics

09:00-09:30: Talk 1 (30 min): Hui Wang, The Centre for Ecology & Hydrology, UK
Topic: Virus discovery by using deep sequencing data
09.30-10:00: Talk 2 (30 min): TBC
10:00-10:30: Talk 3 (30 min): Bjoern Textor, New England Biolabs GmbH
Topic: Direct Selection of Microbiome DNA from Host DNA
11:00-11:30: Talk 1 (30 min): Jeroen Raes, Scientific Collaborator, VUB&VIB
11:30-12:00: Talk 2 (30 min): Rob Knight, Associate Professor, Colorado University
Topic: Characterizing microbial effects of family structure, including our furry family members?
12:00-12:30: Talk 3 (30 min): Ruth Ley, Cornell University
Topic: Host control of the microbiome
Chairman: Dr. Jeroen Raes (VUB, VIB)

Session 7(3 talks: include Q&A 5 mins): Human Disease - Clinical Genetics

11:00-11:35: Talk 1(35 min): Han Brunner, Department of Human Genetics, Radboud University Nijmegen Medical Centre, The Netherlands
Topic: Clinical Genetic Diagnostics by Genome Sequencing.
11:35-12:05: Talk 2(30 min): Wang Wei, BGI Health, Shenzhen, China
Topic: Non-invasive prenatal testing (NIPT): Current clinical application and future outlook
12:05-12:45: Talk 3(30 min): Gabor Vajta, BGI Europe, Copenhagen, Denmark and Central Queensland University, Rockhampton, Australia in concert with Du Yutao, BGI Health, Shenzhen, China
Topic: Pre-implantation Diagnostics by Blastocyst Biopsy, Vitrification and Genome Sequencing
Chairman: Prof. Lars Bolund, Aarhus University

Session 8: Health and Translational Medicine-1

13:30-13:55: Talk 1(25 min): Vince Gao, BGI
Topic: Development of Clinical Service at BGI Health
13.55-14:20: Talk 2(25 min): Attila Lorincz, UK
Topic: Clinical Validation of Genomic and Epigenomic Biomarker Panels
14:20-14:45: Talk 3(25 min): Maurizio Ferrari, Director of Clinical Molecular Biology and Cytogenetics Laboratory, and Head of Genomic Unit for the Diagnosis of Human Pathologies, Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele, Milan, Italian
Topic: From bench to bedside: new advanced molecular techniques for genetic diagnosis
14:45-15:10: Talk 4(25 min): Carlos Simón Vallés, Board Certified and Full Professor of Obstetrics and Gynecology at the University of Valencia,Spain
Topic: Clinical Application of the endometrial receptivity array
15:10-15:35: Talk 5(20 min): To be selected from submitted abstracts
Chairman: Dr. Vince Gao , BGI

Session 9: Human disease

13:30-13:55: Talk 1(25 min): Lars Bolund, Professor of Clinical Genetics at Aarhus University, Denmark, and Adjunct Professor of Human Genetics at Copenhagen University, Denmark
Topic: Chronic Disorders, Rare Genetic Variants and Pig Models of Degenerative Disease Processes
13:55-14:20: Talk 2(25 min): Tao Dong, Head of anti-viral T cell immunology group, MRC Human Immunology Unit, Oxford University, UK
14:20-14:45: Talk 3(25 min): Hartmut Wekerle, Honorary Professor, Max Planck Institute of Neurobiology, Martinsried, Germany
14:45-15:10: Talk 4(20 min): Ramneek Gupta, The Technical University of Denmark, Danmark
15:10-15:30: Talk 5(20 min): Anders Børglum, Professor, Aarhus University, Denmark
Chairman: TBC

Session 10: Health and Translational Medicine-2

16:00-16:20: Talk 1(20 min): Diana M Eccles, Academic Vice President of the Clinical Genetics Society, Southampton General Hospital, UK
16:20-16:40: Talk 2(20 min): E. Gomez Garcia, Maastricht University, the Netherlands
16:40-17:00: Talk 3(20 min): Pascal Pujol , Chu Montpellier, France
17:00-17:20: Talk 4(20 min): Atocha Romero, Hospital Clinico San Carlos, Spain
17:20-17:40: Talk 5(20 min): Ian Campbell, Peter MacCallum Cancer Centre, Australia
Topic: Identification and validation of familial cancer susceptibility genes using massively parallel sequencing
Chairman: Prof. Yves-Jean Bignon, Centre Jean Perrin

Workshop: Ethical, Legal and Social Implications (ELSI)

16:00-16:20: Talk 1(20 min): Lone Frank, Denmark
16:20-16:40: Talk 2(20 min): Pascal Borry, K.U.Leuven, Belgium
16:40-17:00: Talk 3(20 min): TBC
Chairman: Prof. Huanming Yang, BGI

Session 11: Biobanks

08:00-08:30: Talk 1 (30 min): Zhang Yong, BGI, China
08:30-09:00: Talk 2 (30 min): Kristian Hveem, Chief Scientific Officer, Nord-Trondelag County, Norway
09:00-09:30: Talk 3 (30 min): Shaoliang Peng, National University of Defense Technology, China
Topic: Bioinformatics and Computational Biology on TianHe Supercomputer
Chairman: Dr. Zhang Yong, BGI

Workshop: Use of Omics Technology for Personalized Medicine

08:00-08:30: Talk 1 (30 min): Jenny Wei, R&D Information China, AstraZeneca global R&D
Topic: Genomics for Personalized Medicine: From Discovery to Clinic
08:30-09:00:Talk 2 (30 min):André Rosenthal, CEO, Signature Diagnostics AG
Topic: Next-Gen Sequencing Tests for Prognosis and Prediction of Response to Therapy of Patients with Colorectal Cancer Using Somatic Mutation Signatures
09:00-09:30: Talk 3 (30 min):Radoje Drmanac, Complete Genomics, Inc. Mountain View, California, U.S.A.
Topic: Accurate whole genome sequencing as the ultimate genetic test enabling personalized disease prevention and treatment
Chairman: TBC

Session 12: Bioinformatics

10:00-10:30: Talk 1 (30 min): Nathaniel Street, Assistant professor, Umea University
Topic: Sequencing the Norway spruce genome reveals a unique history of repeat expansion
10:30-11:00: Talk 2 (30 min): Sofie Van Landeghem, Ghent University, VIB, Belgium
Topic: Mining the literature to enhance integrative network biology
11:00-11:30: Talk 3 (30 min): Mario Caccamo, Acting Director at The Genome Analysis Centre, Norwich, UK
Topic: Next Generation Genomics for Complex Crops
Chairman: Prof. Yves Van De Peer (U.Ghent, VIB)

For related posts see

No need to oversell the human microbiome with studies like these ...

2013-05-14T02:10:00.001-07:00

I know I complain all the time about news stories and people "overselling the microbiome". Mind you, I believe microbial communities are likely to be found to have very very important roles in the biology of the plants and animals and other organisms on which they live, but I worry about overhyping the possibilities. But thankfully, there are some good researchers at work out there documenting just what the microbiome can and does do. And the results continue to be promising.

Here is the one that caught my eye most recently: BBC News - 'Weight loss gut bacterium' found about this PNAS paper. While the study is in mice and it is what one could call "limited" in some ways, it is really fascinating and has much promise. Basically, they isolated a new bacterium (with the awkward name of Akkermansia muciniphila, and did a series of experiments in mice looking at the role this bacterium can play in many mouse gut properties. But most interesting, treatment of mice with this bacterium (and only when the bacterium was alive) led to a reduction in high fat induced metabolic disorders and obesity. I am still re-reading the paper but the result seems solid. And exciting.

So - there is no need to oversell the microbiome when the results coming in sell themselves ...

UPDATE 30 minutes after posting

Of course, I should have checked to see if Ed Yong wrote anything about this. And he did: The Mucus-Lover that Stops Mice from Getting Fat. Read his post. It is excellent. With ALL sorts of links and background and other detail.

Twisted tree of life award #15: NBC News on "Junk DNA mystery"

2013-05-13T00:52:00.001-07:00

Oh for fu$*# sake. Really MSNBC? I mean, I know perhaps I should not expect much from some in the press but this is just awful: 'Junk' DNA mystery solved: It's not needed.

Brought to us by NBC News and LiveScience (which actually can have some pretty good science coverage). This article has some complete and utter crap:

Some parts that I have issues with:

The headline: "'Junk' DNA mystery solved: It's not needed." The headline is silly but alas it is consistent with what is in the article.
"So-called junk DNA, the vast majority of the genome that doesn't code for proteins". So - they have redefined junk DNA as all non coding DNA?
"For decades, scientists have known that the vast majority of the genome is made up of DNA that doesn't seem to contain genes or turn genes on or off." Apparently there is an entity out there known as "The Genome".

And then we get into the quoting of author and researcher Victor Albert with no comments or responses from anyone is painful too.

"At least for a plant, junk DNA really is just junk — it's not required." Except that they did not show this - they just showed that one plant can have a small genome and not have a lot of "junk" as they call it, which of course does not really say anything about what "junk" does or does not do in other organisms.
"Nobody's really known what junk DNA does or doesn't do" apparently calling into question the some 10,000 plus papers on the topic.

Apparently, from reading the rest the whole point of this article is that it turns out that people sequenced the genome of a bladderwort and it has a small genome but a lot of genes. Oh and the organism is complex. Therefore, apparently, it follows that

"The findings suggest junk DNA really isn't needed for healthy plants — and that may also hold for other organisms, such as humans."

And this leads us to 'Junk' DNA mystery solved: It's not needed.

So - basically - if ONE FUCKING ORGANISM DELETES SOME OF IT'S NON PROTEIN CODING PORTIONS OF ITS GENOME THEN THIS MEANS THAT ALL NON CODING DNA IS USELESS.

Aaaaaaaaaaaaaaaaaaargh.

And for this evolutionary logic, I am awarding NBC News, Tia Ghose (the author of the piece) and Victor Albert, the 15th coveted Twisted Tree of Life Award.

Past winners:

UPDATE 5/17/13

Some other discussions of this paper and related to my critique (though not always agreeing with me)

Knight School of Journalism: A Weird Little Plant is Nearly Free of Junk DNA. Big Contentions Underlie Seemingly Cute Story
From T. Ryan Gregory Genome reduction in bladderworts vs. leg loss in snakes ...
Deconstructing Nature's “plant without junk DNA” story | Genetic ...
From Dan Graur: The Logical Fallacy of Jonathan Eisen ‏(a.k.a. @phylogenomics) and the Theological Implications of the Bladderwort Genome

Crosspost: Woohoo – two more genome announcement papers from our undergraduate project on built environment reference genomes

2013-05-10T10:39:00.001-07:00

Crossposting this from the microBEnet blog.

Two new papers out from the microBEnet Undergraduate Research: Built Environment Reference Genomes project:

Coil DA, Doctor JI, Lang JM, Darling AE, Eisen JA. 2013. Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announc. 1(3):e00172-13. doi:10.1128/genomeA.00172-13.
Diep AL, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Dietzia sp. strain UCD-THP (phylum Actinobacteria). Genome Announc. 1(3):e00197-13. doi:10.1128/genomeA.00197-13.

These go with two previously published ones:

Lo JR, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of an actinobacterium, Brachybacterium muris strain UCD-AY4. Genome Announc. 1(2):e00086-13. doi:10.1128/genomeA.00086-13
Bendiks ZA, Lang JM, Darling AE, Eisen JA, Coil DA. 2013. Draft genome sequence of Microbacterium sp. strain UCD-TDU (phylum Actinobacteria). Genome Announc. 1(2):e00120-13. doi:10.1128/genomeA.00120-13.

And two more coming. So proud of the undergrads in my lab who did this work and David Coil for coordinating it with help from Jenna Lang and Aaron Darling. Undergrads at UC Davis sequencing genomes of organisms they isolated. So cool.

YAMMGM: Yet another mostly male genomics meeting #2: Beyond the Genome 2013

2013-05-10T10:13:00.001-07:00

Well, the "winner" of this months YAMMGM award is Beyond the Genome 2013 | Mission Bay | San Francisco

Alas, YAMMGM stands for "Yet another mostly male genomics meeting" so it is not an award to covet.

This meetings listed speakers are below with women highlighted in green.

Nicholas Navin -The University of Texas MD Anderson Cancer Center
Sunney Xie – Harvard
Xu Xun – BGI
James Hicks -CSHL
Fuchou Tang – Peking
Itai Yanai – Israel
Thierry Voet - Sanger
Jacob Kitzman – Plasma cell free DNA sequencing
Stephen Quake – Stanford and Fluidigm
Mario Caccamo – Genome Analysis Centre
Rob Martienssen – CSHL
Ryan Lister – University of Westerm Australia
Neelima Sinha – UC davis
Jorge Dubcovsky – UC Davis
Robert Schmitz (Salk) – 1001 Arabidopsis project and CHiP-Seq
Marja Timmermans (CSHL)
Magnus Nordborg
Chairs Alicia Oshlack, Yingrui Li and Michael Schatz to chair the bioinformatics challenge.
James Taylor – Emory and Galaxy
Chris Dagdigian – Bioteam
David Haussler -UC Santa Cruz
Janet Kelso – Max Planck Institute for Evolutionary Anthropology

That comes to 16.6% if you count all listed. If you exclude session chairs the numbers are a little different but still pretty low.

Certainly this does not prove any bias on the part of the meeting organizers. But it certainly suggests to me they might want to think about why the ratio is skewed.

A good thing: More and more biology papers showing up in arXiv

2013-05-08T07:28:00.001-07:00

Good to see some more papers in microbiology & genomics and related topics going to the preprint server arXiv.

If you are interested in population and evolutionary genetics a good place to keep up with papers on this topic in arXiv is Haldane's Sieve. The good folks there in essence make a separate post about each paper of interest and then people can comment there on the papers, since the commenting functions at arXiv are, well, challenged.

In areas related to this blog, here are some recent papers in arXiv:

Am hoping more and more biologists start depositing papers in arXiv. My brother has started doing it for all papers in his lab so I guess that means I should too. And so should everyone else ...

The need for a phylogeny driven genomic encyclopedia of eukaryotes

2013-05-01T20:47:00.001-07:00

Monday I gave a talk for the SMBE Eukaryotic Omics satellite meeting that has been going on at UC Davis. When Holly Bik, a post doc in my lab asked me to talk at the meeting, I said, basically "Well, OK, but I don't really do much work on eukaryotes." And then I came up with an idea - I could make my talk about how it might be good to have a better phylogenetic sampling of eukaryotic genome sequences. I have been a bit obsessed for many many years about phylogenetic sampling of genomes and, well, though I have avoided eukaryotes mostly in most of my genome sequencing work, I figured, I should still get on my soap box about how phylogenetic sampling is a good thing. So, well, I did. And I think we (i.e., the scientific community) really needs a better sampling of eukaryotic genomes.

I have posted my talk to Slideshare and I recorded audio of my talk in synch with the slides and posted that to Youtube. These are below.

I hereby am calling for those people interested in participating in such a phylogeny driven genomic encyclopedia of eukaryotes to make yourselves known. We NEED to do this.

The need for a phylogeny driven genomic encyclopedia of eukaryotes #SMBEEuks from Jonathan Eisen

I love this ... "Dr. Eleanor's Book of Common Ants" based in part on citizen science data

2013-05-01T17:51:00.001-07:00

This is really cool: Dr. Eleanor's Book of Common Ants. Free to download. With incredible pics from Alex Wild. And based in part on data from the School of Ants citizen science project. You can download the PDF or the iBook from iTunes. From the folks at "Your Wild Life" including Holly Menninger and Rob Dunn and others. Definitely worth checking out.

Yes, the human microbiome has truly arrived: on Wait Wait Don't Tell Me

2013-04-27T12:16:00.001-07:00

So cool. Yesterday on "wait wait ... don't tell me" Kai Penn (actor) was enticed to play the game "Ahhh! Get It Off Me!" in regard to microbes: Not My Job: Kal Penn Takes A Quiz On The Microbiome : NPR

Hat tip to Jenna Lang for pointing me to this.

Via @nprnews: Not My Job: Kal Penn Takes A Quiz On The Microbiome n.pr/10hVj0J @jessicaleegreen @phylogenomics
— Jenna Morgan Lang (@jennomics) April 27, 2013

Trying to sort out all the STEM and STEM related departments, graduate programs , at #UCDavis

2013-04-27T10:36:00.003-07:00

Well, I was in a meeting yesterday for the UC Davis ADVANCE program. This program is an NSF funded project to improve presence of women and underrepresented minorities on the faculty in Science, Technology, Engineering and Math (STEM). So I decided to see - how many departments at UC Davis might participate in such an initiative. And, well, wow. I knew there were a lot of STEM or STEM-related departments at UC Davis but I did not know there were this many.

Here is a list I compiled of UC Davis STEM or STEM-related Departments. I included medical departments here since many people in such departments do medical/science research. But clearly this is a broad definition of STEM. But nevertheless, this gives some picture of the scope of science and medicine and related departments at UC Davis.

Vet School departments in Yellow
Med School departments in Red
College of Biological Sciences Departments are In Green
College of Agricultural and Environmental Sciences in Orange
College of Letters and Science in Light Blue
College of Engineering in Grey

And then of course UC Davis has a TON of graduate groups and almost all of these are separate from departments. They do not hire faculty but they are a key part of the atmosphere and academics at UC Davis. And there are an enormous number of these in STEM or STEM-related fields. See below

Graduate Groups

Agricultural and Environmental Sciences Graduate Programs

Biological and Life Sciences Graduate Programs

Engineering Graduate Programs

Health Sciences Graduate Programs

Physical Sciences and Mathematics Graduate Programs

Social Sciences Graduate Programs

And then there are the Undergraduate Majors of which many are in STEM or STEM-related fields

So - lots and lots of STEM stuff at Davis and lots of chances / opportunities to improve the presence / treatment / life of women and underrepresented minorities.

Bad Ome-like word of the week: symbiome

2013-04-27T08:58:00.001-07:00

Well I got pointed to this paper: Transgenerational Transmission of the Glossina pallidipes Hytrosavirus Depends on the Presence of a Functional Symbiome

And as many might guess - the word "symbiome" did not sit well with me. Alas, they don't define it in the paper. So I can't really quibble with their definition. But I did find some other stuff out there that, well, at least helps see how other people are using the word:

I can't really tell from most of these if "symbiome" can be a useful term or not sometimes. Certainly the iPhylo example above has potential. But in general, the word seems awkward at best. Now - as far as I can tell, nobody is using it in the context of "genomics" so this does not fit in with my "badomics" obsession. But it still does not make me feel warm and fuzzy so I am going to give it a pseudo-award - the Bad Ome-like word award.

Storified tweets from the #UCDavisADVANCE Symposium on Increasing Diversity of STEM Faculty

2013-04-26T06:54:00.000-07:00

I live tweeted a symposium at UC Davis yesterday that was part of the UC Davis ADVANCE project to increase diversity of STEM Faculty. Here are the notes.

For more on the project see

So cool - NSF has a program to provide supplemental funds when CAREER PIs go on family leave

2013-04-25T12:14:00.001-07:00

Just got pointed to this by Siobhan Brady from UC Davis:

US NSF - Dear Colleague Letter: FY 2013 Career-Life Balance (CLB)-Faculty Early Career Development Program (CAREER) Supplemental Funding Requests (nsf13075)

It is an NSF program to

"The purpose of this DCL is to announce the continuation of the supplemental funding opportunity initiated in FY 2012 for PIs supported in the CAREER program. CAREER Principal Investigators (PIs) are invited to submit supplemental funding requests to support additional personnel (e.g., research technicians or equivalent) to sustain research when the PI is on family leave. These requests may include funding for up to 3 months of salary support, for a maximum of $12,000 in salary compensation. The fringe benefits and associated indirect costs may be in addition to the salary payment and therefore, the total supplemental funding request may exceed $12,000."

This is part of a larger program on Career-Life Balance:

Instituted in 2012, NSF’s Career-Life Balance (CLB) Initiative is an ambitious, ten-year initiative that will build on the best of family-friendly practices among individual NSF programs to expand them to activities NSF-wide. This agency-level approach will help attract, retain, and advance graduate students, postdoctoral students, and early-career researchers in STEM fields. This effort will help reduce the rate at which women depart from the STEM workforce. By the end of this ten-year initiative (2021), it is expected that women will represent 41 percent of newly tenured doctoral S&E faculty—the same percentage as the available pool of women S&E doctorate recipients in 2009; and that women of color will comprise 17 percent of newly tenured faculty, the same percentage of their PhD production rate in 2009. Further information on the CLB initiative may be found on the Foundation’s website.

The primary emphasis of NSF’s CLB initiative in FY 2012 was focused on opportunities such as dependent-care issues (child birth/adoption and elder care). These issues initially were addressed through NSF’s Faculty Early Career Development (CAREER) program, where career-life balance opportunities can help retain a significant fraction of early career STEM talent. In FY 2013, the Foundation intends to further integrate CLB opportunities through other programs such as the Graduate Research Fellowship and postdoctoral fellowship programs, as well as expand opportunities such as dual career-hiring through the Increasing the Participation and Advancement of Women in Academic Science and Engineering Careers (ADVANCE) program. Each of these opportunities will be described and implemented separately.

I am involved in the UC Davis ADVANCE program (minor advisory role) and am always on the lookout for ways that institutions and fundings agencies try to increase representation of women and minorities in STEM fields so if you know of other examples - please post details.

If you are into microbial diversity and use R this may be worth checking out: phyloseq

2013-04-25T11:00:00.000-07:00

Just got pointed (by the lead author) to this new paper: PLOS ONE: phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

Abstract:

Background
The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data.
Results
Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research.
Conclusions
The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

Seems similar in some ways to the WATERs Kepler Workflow that we released a few years ago. Anyway - if you use R and are into microbial diversity studies this may be worth checking out. As a bonus - it has a strong emphasis on reproducibility - which is a good thing.

Quick post: interesting article in Smithsonian on the human microbiome by Richard Conniff

2013-04-25T07:02:00.002-07:00

Just q quick post here. There is an interesting article about the human microbiome worth checking out: Microbes: The Trillions of Creatures Governing Your Health. By Richard Conniff in Smithsonian Magazine. It also comes with some related videos and pictures. See for example and And it references my "Overselling the microbiome" award ...

When a scientific team recently suggested that changes in gut bacteria could protect against stroke, Jonathan Eisen of the University of California at Davis lambasted them for “absurd, dangerous, self-serving claims that completely confuse the issue of correlation versus causation.” Eisen, a specialist in microbial genomics, now regularly presents “overselling the microbiome” awards on his blog. He says he doesn’t doubt the ultimate importance of the microbiome: “I believe the community of microbes that live in and on us is going to be shown to have major influences.” But believing that “is different from actually showing it, and showing it doesn’t mean that we have any idea what to do to treat it. There is danger here.”

And it even discusses a fecal transplant-like treatment called RePOOPulate. What could be better? Anyway - definitely worth checking out.

Announcement: Intntl. BioInformatics Workshop on Virus Evolution & Molecular Epidemiology

2013-04-24T13:47:00.001-07:00

This looks pretty good:

18th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
University of Florida, Emerging Pathogens Institute
Gainesville, Florida, USA.
August 25th - August 30th, 2013

Bioinformatics Methods Applied to Virology and Epidemiology

We are announcing the organization of the international workshop on Virus Evolution and Molecular Epidemiology (VEME) in 2013, hosted by the Emerging Pathogens Institute in the warm city of Gainsville and sponsored by several local partners.

We plan to organize a 'Phylogenetic Inference' module that offers the theoretical background and hands-on experience in phylogenetic analysis for those who have little or no prior expertise in sequence analysis. An 'Evolutionary Hypothesis Testing' is targeted to participants who are well familiar with alignments and phylogenetic trees, and would like to extend their expertise to likelihood and Bayesian inference in phylogenetics, coalescent and phylogeographic analyses ('phylodynamics') and molecular adaptation. A 'Large Dataset Analysis' module will cover the more complex analysis of full genomes, huge datasets of pathogens including Next Generation Sequencing data, and combined analyses of pathogen and host. Practical sessions in these modules will involve software like, PHYLIP, PAUP*, PHYML, MEGA, PAML or HYPHY, TREE-PUZZLE, SplitsTree, BEAST, MrBayes Simplot and RDP3.

We recommend participants to buy The Phylogenetic Handbook as a guide during the workshop, and to bring their own data set.

For further information and applications we refer to a dedicated website that will be announced here soon.
Abstract and application deadline is April 30th.
Selections will be made by end of May 2013.

The registration fee of 1000 USD covers attendance, lunches and coffee breaks.

Participation is limited to 25 scientists in each module and is dependent on a selection procedure based on the submitted abstract and statement of motivation. A limited number of grants are available for scientists who experience difficulties to attend because of financial reasons.

For further information and applications we refer this website: http://conferences.dce.ufl.edu/vemei/http://conferences.dce.ufl.edu/veme/

Guest post: Kevin Carpenter on his new microbial photo exhibit at the Exploratorium in SF #SoCool

2013-04-24T13:15:00.000-07:00

Special guest post from Kevin Carpenter who has microbe photos featured at the Exploratorium.

One of my colleagues who does research on the microbes that live in the hindguts of lower termites once remarked that interesting organisms can be found in the most unusual of places. And the lower termite hindgut, by almost anyone’s estimation, is certainly an unusual place. It is also a fascinating place for anyone interested in biology, ecology, evolution, biochemistry, or beautiful natural forms and patterns.

Since my undergraduate days in the early 90s, I have had a deep interest in the tree of life, especially eukaryote phylogeny. After a Ph.D. in Plant Biology at U.C. Davis, I headed off to the University of British Columbia to work in Patrick Keel in g's lab to pursue these interests. Anyone who has this peculiar obsession (actually, I think it's peculiar not to have this obsession!) knows that the eukaryote tree comprises mostly protists, and they arguably encompass greater structural, cell biological, biochemical, (and certainly evolutionary!) diversity than all plants, animals, and fungi combined.

In Patrick's lab I developed methods for SEM and TEM imaging of these microbes to investigate their phenotypic character evolution, functional morphology, and symbioses with bacteria in the light of molecular phylogenetic data. In addition to a number of publications (with more to come) and talks in Russia, Germany, Norway, etc. my electron micrographs have been featured on numerous journal covers, textbooks, and invited artistic presentations in Canada and Germany.

On 17 April 2013, a collection of 11 of my scanning electron micrographs of lower termite hindgut protists and their bacterial symbionts will go on permanent exhibit at the Exp loratorium mu seum as they open their new $300 million dollar location on Pier 15 in San Francisco. This is a large (12' x 4') installation in the East Gallery (overlooking the bay):

The waterfront location, the architecture, the exhibits, and sustainable technology (rooftop solar panels, etc) are all amazing, and I encourage anyone with any interest in science/biology, art, experimentation, tinkering, and beautiful views to come out for a visit. For more information on the exhibit, the organisms, additional images and other resources (including a blog!), please visit my website at: KevinJCarpenter.com

As for the organisms...

The hindgut of wood-feeding lower termites--comprising approximately 1000 species (out of a total of several thousand species of termites)--is densely packed with symbiotic protozoa (protists), many of which engulf and enzymatically degrade wood fragments making their way to the termite hindgut. Far from being parasites, numerous studies have shown this to be a mutualsitic symbiosis, by demonstrating that the termites will starve and die if deprived of their protist symbionts. The symbiosis between lower termites and their hindgut protists is one of the longest-studied and best-known examples of microbial symbiosis, dating back nearly a century and a half to the work by Joseph Leidy and others.

The protists are anaerobic flagellates belonging to Parabasalia or Oxymonadida--members of the Excavate eukaryotic supergroup (also including euglenids, trypanosomes, Giardia, and heterolobosean amoebas). There are numerous odd, interesting, beautiful, and instructive things about these protists.

First, they are endemic to termite hindguts and are found nowhere else. Most of the protist species are found only in association with a single species of termite. The termites pass their hindgut biota from adult to newly hatched nymphs and moulting adult termites (which lose their hindgut contents) via specialized feeding behaviors. It is thought that termites evolved social behavior and caste differentiation from their cockroach ancestors partly to pass hindgut protists between individuals.

Second, many of the protist species and lineages have attained large size (up to 300 microns in length), and enormous structural complexity. Some of the protists are estimated to bear up to 50,000 flagella, each associated with specialized proteinaceous structures (kinetosomes, parabasal fibers) inside the cell. Hence, these are likely among the most structurally complex cells known to science. This is in marked contrast to other symbiotic protist lineages such as microsporidia, apicomplexans, and the coral reef symbiont Cyanidioschyzon, all of which have undergone extreme structural reduction. When looking at these termite gut protists in all of their great structural complexity, dwarfing their numerous bacterial surface symbionts, it is is kind of mind-boggling in a sense to realize that this is a unicellular organism!

Third, the cell biology of these organisms is so different from what is taught in undergraduate cell biology (which is really mammalian, or at best, metazoan cell biology), that it may (hopefully) cause one to reflect on how truly diverse and unknown our biosphere really is. As one example of this, in parabasalid protists, mitochondria have become drastically reduced structurally (loss of cristae), functionally (loss of oxidative metabolism/Krebs cycle), and genomically, and their only known function is the conversion of pyruvate to acetate, with the production of hydrogen gas as a waste product. Hence, these relict mitochondria are called hydrogensomes. The oxymonads are among the least understood group of eukaryotes, and for many species it is unknown what they eat (some of the smaller species apparently do not eat wood), how they reproduce, or how they metabolize their food. Some even have a non-canonical genetic code.

The sitution becomes even more complex when we consider the bacteria in lower termite hindgut systems. In light of their importance in the human and other gut microbiomes, it is no surprise that the termite gut is swarming with innumerable bacteria, many of which are likely found only in one species of termite. What is surprising is that an estimated 90% of all bacterial cells in these systems live either on the surface of, or inside of a protist, and are not free-swimming. One study estimates that the large protist Pseudotrichonympha harbors about 100,000 bacterial cells. Microscopy reveals specialized attachment structures that help the bacteria anchor to the protist surface. Our research shows that the large protist Barbulanympha has not only vast numbers of rod-shaped bacteria on its cell surface and interior, but also bacteria surrounding extruded strands of cytoplasm. This is possibly a mechanism to increase the area available for exchange of nutrients.

Recent research on bacteria symbiotic with termite gut protists suggests that they are important in nitrogen metabolism--both in nitrogen fixation and synthesis of vitamins and amino acids. They are thought to transfer these compounds to their host protist (and to the termite) in return for sugars derived from breakdown of wood.

Just as the protists are generally endemic to a single species of termite, in many cases, bacteria found in symbiotic association with the protists are endemic to a single species of protist. Given this close, three-way association between termite, protist, and bacteria, it is perhaps not surprising that evidence of triplex speciation has been found in these organisms: both the bacteria and their protist hosts speciate in tandem in response to termite speciation events. This is one of only a handful of putative cases of triplex speciation.

The symbiosis between termites and protists is actually also present in a species of wood-feeding cockroach--Cryptocercus punctulatus. C. punctulatus is actually more closely related to termites than to other cockroaches (cockroaches are paraphyletic). It is believed that symbiotic protists were present in the hindgut of the ancestor of C. punctulatus and modern termites, which likely lived over 100 million years ago.

Thus, I consider these termite hindgut systems to be among the most unusual, beautiful, and instructive natural laboratories in evolution and ecology known to science. Nature indeed seems to enjoy tinkering, and in that spirit, I think this is well suited to representation in a place like the Exploratorium!

A few references (copied straight out of one of my manuscripts!) for those interested:

Brune, A. & Ohkuma, M. (2011). Role of the termite gut microbiota in symbiotic digestion. In Biology of Termites: A Modern Synthesis, Bignell, D. E., Roisin, Y. and Lo, N. (Eds.), pp. 439-475. London: Springer.

Carpenter, K.J., Chow, L. & Keeling, P.J. (2009). Morphology, phylogeny, and diversity of Trichonympha (Parabasalia: Hypermastigida) of the wood-feeding cockroach Cryptocercus punctulatus. J Eukaryot Microbiol 56(4), 305-313.

Carpenter, K.J., Horak, A., Chow, L. & Keeling, P.J. (2011). Symbiosis, Morphology, and Phylogeny of Hoplonymphidae (Parabasalia) of the Wood-Feeding Roach Cryptocercus punctulatus. Journal of Eukaryotic Microbiology 58(5), 426-436.

Carpenter, K.J., Horak, A. & Keeling, P.J. (2010). Phylogenetic position and morphology of spirotrichosomidae (parabasalia): new evidence from Leptospironympha of Cryptocercus punctulatus. Protist 161(1), 122-132.

Carpenter, K.J. & Keeling, P.J. (2007). Morphology and phylogenetic position of Eucomonympha imla (Parabasalia: Hypermastigida). J Eukaryot Microbiol 54(4), 325-332.

Carpenter, K.J., Waller, R.F. & Keeling, P.J. (2008). Surface morphology of Saccinobaculus (Oxymonadida): implications for character evolution and function in oxymonads. Protist 159(2), 209-221.

Hongoh, Y., Sharma, V.K., Prakash, T., Noda, S., Taylor, T.D., Kudo, T., Sakaki, Y., Toyoda, A., Hattori, M. & Ohkuma, M. (2008a). Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell. Proc Natl Acad Sci U S A 105(14), 5555-5560.

Hongoh, Y., Sharma, V.K., Prakash, T., Noda, S., Toh, H., Taylor, T.D., Kudo, T., Sakaki, Y., Toyoda, A., Hattori, M. & Ohkuma, M. (2008b). Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut. Science 322(5904), 1108-1109.

Ohkuma, M. & Brune, A. (2011). Diversity, structure, and evolution of the termite gut microbial community. In Biology of Termites: A Modern Synthesis, Bignell, D. E., Roisin, Y. and Lo, N. (Eds.), pp. 413-438. London: Springer.

YAMMGM: Yet another mostly male genomics meeting

2013-04-24T12:59:00.000-07:00

Just got an email from Illumina - key parts are below:

2013 Illumina Scientific Summit

Dear Jonathan,

Illumina's third annual Scientific Summit will be held June 3rd through 7th in charming New Orleans, Louisiana, at the Loews Hotel. Described by a past attendee as, "an upscale Gordon Conference", the Scientific Summit is an invitation-only meeting of 120 leading scientists and thought leaders plus the Illumina executive and R&D leadership teams.

Plenary sessions will be focused on the Genetic Etiology of Cancer and Genetic Diseases, The Changing Landscape of Medical Genetics, Microbial Detection, and Epigenetics. The formal presentations will be complemented by attendee-driven discussion sessions on a variety of topics ranging from workflow bottlenecks to future applications of Next Generation Sequencing in single cells and diagnostics.

The following distinguished scientists are scheduled to speak:

Dr. Mark Adams, Scientific Director, J. Craig Venter Institute

Dr. Kenneth J. Bloom, Chief Medical Officer, Clarient

Dr. David Craig, Deputy Director of Bioinformatics, Associate Professor and Director, Neurogenomics Division, Head Neurobehavioral Research Unit, TGen

Dr. Richard Gibbs, Wofford Cain Chair in Molecular and Human Genetics, Professor, Department of Molecular and Human Genetics, Professor, Programs in Translational Biology & Molecular Medicine, Baylor College of Medicine

Dr. David Goldstein, Director, Duke Medical Center for Human Genome Variation, Duke University

Dr. Steven Jones, Head of Bioinformatics and Associate Director, Michael Smith Genome Sciences Centre, BC Cancer Agency

Dr. Michael Katze, Professor, Microbiology, University of Washington

Dr. Jim Knowles, Professor and Associate Chair for Research and Psychiatry and the Behavioral Sciences, USC

Dr. Peter Laird, Director, USC Epigenome Center, Professor of Surgery,Biochemistry and Molecular Biology, Keck School of Medicine, USC

Neil Miller, Director of Informatics and Software Development, Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City

Dr. Steven Musser, Director, Office of Regulatory Science, FDA Center for Food Safety and Applied Nutrition

Dr. Charles Perou, Distinguished Professor of Genetics, Professor, Pathology & Lab Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine

Dr. Jonathan Sebat, Chief, Beyster Center for Genomics of Neuropsychiatric Diseases, Associate Professor, Department of Psychiatry & Cellular and Molecular Medicine, University of California, San Diego

Dr. George Weinstock, Professor of Genetics and Molecular Microbiology, Washington University

Dr. Liz Worthey, Director of Genomic Informatics, Medical College of Wisconsin

I love Illumina sequencing toys. I really do. No so impressed with the gender ratio of this meeting however. Would not have gone anyway ... but if I COULD have attended I would not have. I wonder -did they even think about whether there might be some bias here? There certainly are plenty of female candidates they could have invited. Maybe they did not invite women? Maybe all the women said no?

Do we need naming regulations for computer software?

2013-04-22T06:26:00.001-07:00

Well, just saw this new paper: BMC Bioinformatics | Full text | Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data. Seems potentially interesting. But one part of it struck me as very awkward. You see, there already is a Bellerophon software program used by many in my field: Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Seems like a very bad idea to have a new program with the same name as an existing (and still used) one in a similar general field (DNA sequence analysis).

This leads me to the following question - do we need some sort of naming guidelines or regulations for computer software? We have all sorts of naming regulations and conventions for genes, for species, for other groups of taxa, and more. Why not software tools? But seriously, I don't think we need such a thing - we just need people to use Google and to do a little searching before they invent / publish a software package in case it's name is, well, already used.

Cool #OpenAccess paper from McTavish et al. on Domestication of New World Cattle

2013-04-04T07:15:00.000-07:00

Sort of randomly bumped into this one via Google Scholar Alerts I have set up and being from UC Davis the title caught my eye: New World cattle show ancestry from multiple independent domestication events. Yes, we think about cows a lot here OK. And then the second thing that caught my eye were the authors - including David Hillis - who I did not know was working on cattle. I mean - I knew he lived in Texas - so maybe I should have guessed this was coming at some point.

And then I noticed the first author is someone I follow on Twitter. Ok - enough. I got the message. So I looked over the paper.

From the Abstract:

Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment.

There is some really fascinating stuff in here. And some great figures.

Definitely worth a look if you are interested in cattle, domestication, population genetics, and more ...