Genetics

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 »

The ongoing debate about whether, what, when and how to feedback incidental findings (IFs) from whole genome sequencing continues to rage on both sides of the Atlantic following the American College of Medical Genetics and Genomics’ controversial recommendations on reporting IFs released last month. In an unexpected twist, the authors of the guidance have now written “a clarification” in response to the many criticisms that have been raised including here on GenomesUnzipped. The clarification covers five points – autonomy, children, labs, communication and interpretation.Read the rest of this entry | Read comments

Researchers claim to have created the first ever viable human pluripotent embryonic stem cells (ESCs) using somatic cell nuclear transfer (SCNT), the same ‘cloning’ technique used to produce Dolly the sheep. The work published in Cell says it identified the key factors that thwarted prev ...

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 a

A new Target Discovery Institute based at the University of Oxford aims to identify better targets for drugs to tackle common diseases such as cancer, diabetes and Alzheimer’s disease. Eight international pharmaceutical companies - including Pfizer, GlaxoSmithKline and Novartis - have each con ...

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 bac