Genetics

The methodology underpinning the PHG Foundation Health Needs Assessment Toolkit for Congenital Disorders has been published online in the Journal of Public Health.The eight page exposition of the Toolkit, its aims, development and purpose is written by the Toolkit developers, led by Luis Nacul and c ...

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 -------- 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. --------

The Wellcome Trust is to fund a ?2.7 million research programme to introduce a new patient pathway for access to genetic testing for cancer predisposition. ? The three-year Mainstreaming Cancer Genetics programme is a collaborative venture between the Institute of Cancer Research (ICR) ...

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

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. -------- 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. --------

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 -------- 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. --------

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 ... -------- 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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I've been thinking about this piece for a while, because I am a frequent presence on SEQAnswers.com and often dive into questions regarding de novo sequence assembly, particularly for small genomes.  It's good to help out and a way to feel like one is contributing to a broader community, but sometimes it can be very frustrating because the seekers (SEQers?) of help do not post their questions very well.  So, it would be helpful to have a post to point them to, though I'm sure there are considerations I either haven't thought of or will fail to remember to add.  So, those can either go into the comments or a future post, or perhaps something can go in the Wiki at SEQAnswers.But in general, think of it this way: you have some experienced hands in a field you wish to enter, who are willing to give detailed advice for free.  But, they can't give that advice unless you specify your question well, and if you don't get it right the first time they may not see (or may ignore) your second shot.Read more »