Monday, December 8, 2008

The DNA Network

The DNA Network

Aphid-bacterial symbiosis in more detail, and in the New York Times [The Tree of Life]

Posted: 08 Dec 2008 07:41 PM CST

Nice little bit in the New York Times tomorrow about aphids and their symbionts. Henry Fountain writes (Observatory - How Tiny Insects, With a Little Help, Survive on Plant Sap - about a new article by Angela Douglas, one of the true pioneers of endosymbiont research. In her study she dissects in fine scale detail which essential amino acids are missing from the aphid sap only diet and which ones are made by the symbionts. Interestingly, the research apparently shows that the aphids may have figured out how to make methionine by themselves. I say apparently since I have been unable to track down the paper which I assume is coming out soon.

I should note, in one of the symbioses like this that I have studied with Nancy Moran we found that there were two symbionts contributing to the nutrition of the host. We found that one of the symbionts was likely making amino acids for the host (an insect called the glassy winged sharpshooter which eats only xylem sap) and the other symbiont was likley making vitamins. Nancy showed later with John McCutcheon that the symbiont that was making vitamins also was predicted to be making methionine for the host. So it seems possible there might be a missing symbiont in the aphid study? Although it would be cool if the aphid has figured out how to make an amino acid most animals are not able to make.

Hat tip to Max Lambert for pointing this out.

Nils Reinton (SciPhu) relaunches site: BIOpinionated [Think Gene]

Posted: 08 Dec 2008 06:23 PM CST

Nils Reinton has relaunched his site, SciPhu, as BIOpinionated. Nils is a molecular biology scientist working in medical diagnostics, and his blog is consistently interesting and insightful. Check it out!

Tree of Life Gift Recommendation - Climate Kits [The Tree of Life]

Posted: 08 Dec 2008 05:33 PM CST

Just a quick recommendations for a gift for this holiday seasons that seems cool (metaphorically and literally). It is the climate kit. It comes from a friend of mine from college, Kathy Washienko and this is some of their text:
Kits are convenient collections of tools and tips that will help your family and friends reduce your environmental impact. By grouping what you need in one handy package, a kit makes it easy and fun to take energy-saving steps. Each kit is ultimately a gift to our environment, but will also save you money in reduced energy costs.* And every kit comes with our innovative "rebate." Check them out!
Sounds good to me. And given that I am trying here to promote trees (albeit phylogenetic ones, not real ones) I like that they are planting a tree and trying to be green.

Save babies, break the law. [Think Gene]

Posted: 08 Dec 2008 04:52 PM CST

This was such a “good idea” that I had to share. Maybe some radical Ivy grad student can pick up the ball here.

If you want to put your money where you mouth is, email Josh here at Think Gene, and maybe he’ll tell you how to buy the supplies and make the primers to do these tests for free / at cost. You could drive around in a van providing free genetic tests to save babies —”liberating the science”— for probably less than a few thousand dollars US. It sounds like a good trustafarian grad student project. Fight the man, save babies, hide behind the family trust when your antics piss off powerful people who would crush you otherwise… yah. Much better than “saving the Earth” by smoking organic pot or whatever.

Originally posted as a comment by Andrew Yates on Think Gene using Disqus.

The genetic architecture of metabolic traits: a data explosion [Genetic Future]

Posted: 08 Dec 2008 03:07 PM CST

Nature Genetics has just released six advance online manuscripts on the genetic architecture of complex metabolic traits. The amount of data in the manuscripts is overwhelming, so this post is really just a first impression; I suspect I'll have more to say once I've had time to dig into the juicy marrow of the supplementary data.

The general approach of exploring the genetic architecture of quantitative disease-associated traits (often called intermediate phenotypes or endophenotypes) rather than categorical case-control analyses of disease status raises some interesting questions, but I'm going to save those for another time and focus instead on the results.

Executive summary
For those who don't want to wade through the details, here's the gist: these papers use genome-wide association data from very large numbers of individuals to analyse the genetic architecture of disease-associated traits like blood lipid and glucose levels (rather than looking for associations with disease status itself). They find a bewildering array of new variants associated with these traits, and indications of many more genes still to come as sample sizes increase. However, for most traits, despite very large sample sizes the majority of the variance is not explained by the identified variants.

For those who are interested in more details, I've tucked them below the fold:

Chiara Sabatti, Susan K Service, Anna-Liisa Hartikainen, Anneli Pouta, Samuli Ripatti, Jae Brodsky, Chris G Jones, Noah A Zaitlen, Teppo Varilo, Marika Kaakinen, Ulla Sovio, Aimo Ruokonen, Jaana Laitinen, Eveliina Jakkula, Lachlan Coin, Clive Hoggart, Andrew Collins, Hannu Turunen, Stacey Gabriel, Paul Elliot, Mark I McCarthy, Mark J Daly, Marjo-Riitta Järvelin, Nelson B Freimer, Leena Peltonen (2008). Genome-wide association analysis of metabolic traits in a birth cohort from a founder population Nature Genetics DOI: 10.1038/ng.271

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TripAnswers or Twitter? [ScienceRoll]

Posted: 08 Dec 2008 03:00 PM CST

Twitter is a microblogging tool that allows us to post 140 charachter-long messages and we do have a huge medical community there so it’s quite easy to ask medical questions and get relevant answers from doctors from around the world.

TripAnswers is a site where clinicians can ask questions.

TRIPanswers is a repository of clinical questions and answers drawn from a wide number of sources around the world and builds on TRIP's ten years experience of answering clinical questions.  Ultimately, we want to create a resource where clinicians can easily find answers to their question and, who knows, create a clinical Q&A 'space' where users can share their own Q&As (it's always struck us as wasteful that clinicians around the globe answer questions and this effort is never shared!)


Which one would you use to ask questions?

Futher reading:


National physician group MDVIP partners with Navigenics [The Navigator - Navigenics Blog]

Posted: 08 Dec 2008 03:00 PM CST

Vance Vanier, M.D.

imageNavigenics is pleased to announce a new relationship with a national network of physicians who practice proactive, personalized medicine. Through the collaboration, the Navigenics genetic testing service will be made available to their patients, who number more than 100,000 nationwide. I'd like to share some of the information about this collaboration, as described in a news release issued today:

National Physician Group MDVIP Partners with Navigenics to Provide Personal Genetic Tests for Preventive Medicine Practice

Boca Raton, FL and Redwood Shores, CA – December 8 2008 – MDVIP, Inc., a leading national network of physicians dedicated to preventive and personalized healthcare, and Navigenics, Inc., a leading personal genomics testing company, today announced a first of its kind collaborative effort to integrate genomic-based preventive healthcare in physician offices. Through this initiative, Navigenics' genomic testing service will be available to MDVIP affiliated physicians to help patients understand their genetic risk factors for disease and work with their doctors to develop individualized prevention plans.

Navigenics will provide MDVIP patients and their affiliated physicians with insight into their personal genetic predisposition for developing certain medical conditions where primary or secondary prevention could improve health outcomes. The Navigenics test will identify individuals' genetic markers for developing such conditions as type 2 diabetes, cancer, heart attack, and celiac disease. Working with their personal MDVIP physician and Navigenics' board-certified Genetic Counselors, individuals can chart and implement a personalized wellness course to help decrease their overall risk, delay disease onset or prevent it altogether.

"We have for many years been closely watching the field of genomic testing evolve into a tool that can enhance and inform the practice of preventive medicine," said Edward Goldman, M.D., CEO of MDVIP. "We believe that Navigenics' preventive genomics service has the potential to be an innovation that could significantly enhance patient care."

Next-Generation Sequencing Statistics [ScienceRoll]

Posted: 08 Dec 2008 02:52 PM CST

Have you ever wondered about the typical run time of a next-generation genome sequencer? PolITiGenomics has the answers:


Read more about next-generation sequencing in the Trends in Genetics article: The impact of next-generation sequencing technology on genetics.


Salary prospects for biology majors [Bayblab]

Posted: 08 Dec 2008 01:08 PM CST

This may or may not surprise you, but who do you think has the highest median starting salary and mid-career salary between those three: History graduate, philosophy graduate, biology graduate? When it comes to salary you're actually better off with an undergrad in history, philosophy, geography, any engineering, or any science other than biology. If it makes you feel better, it still beats drama and is about equivalent to an English major with $38.8K starting and $64.8K mid-career. Why is that? I'm not sure, but It probably is a consequence of supply and demand. Not much demand for biologists, and way too many graduates.

Leaf Camouflage Pictures and Videos [Bayblab]

Posted: 08 Dec 2008 12:59 PM CST

I ran into a collection of awesome leaf mimicry pictures and videos I origonally ran into on boing boing. Definitely worth checking it out. The blog that is hosting these pictures, The Conservation Report, seems to have an ongoing thing with pictures of impressive animal camouflage. While I would love to get some of the leaf mimicing fish for my aquarium, looks like they'd eat my neon tetras!

Finnish population structure won't persist much longer [Genetic Future]

Posted: 08 Dec 2008 12:45 PM CST

In my previous post on Finnish population clustering I should have emphasised that the map was constructed only from individuals who had both parents from the same geographic/linguistic region; this obviously provides a lot more power to detect a correlation.

The close match between genetic and geographic ancestry in these selected individuals indicates that there hasn't been a huge amount of long-range admixture between Finnish populations over quite a long period of time - if there had been, there would be no reason to expect much correlation between the two maps. However, data in the supplementary section of the paper show that there has been substantial mixing over more recent history:


This graph shows the number of individuals from the cohort that had both parents from a single region. You can see immediately that the single largest category is the "mixed" category indicating parentage that crosses region boundaries. It seems likely that many of these individuals come from border areas between the regions (in which case excluding them from the map will have resulted in a rather artificial increase in the separation between clusters), but no doubt there are also many examples of long-range admixture resulting from increases in population mobility during the 20th century.

As mobility continues to increase the correlation between geographical location and genetic ancestry will decline rapidly. We really are in a brief and privileged moment in time: a moment when we have the tools to perform genome-scale analyses of ancestry, but before globalisation [and urbanisation] begins to erase information about historical population structure.

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Chiara Sabatti, Susan K Service, Anna-Liisa Hartikainen, Anneli Pouta, Samuli Ripatti, Jae Brodsky, Chris G Jones, Noah A Zaitlen, Teppo Varilo, Marika Kaakinen, Ulla Sovio, Aimo Ruokonen, Jaana Laitinen, Eveliina Jakkula, Lachlan Coin, Clive Hoggart, Andrew Collins, Hannu Turunen, Stacey Gabriel, Paul Elliot, Mark I McCarthy, Mark J Daly, Marjo-Riitta Järvelin, Nelson B Freimer, Leena Peltonen (2008). Genome-wide association analysis of metabolic traits in a birth cohort from a founder population Nature Genetics DOI: 10.1038/ng.271

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Congrats to Pamela Ronald et al. for Award for Flood Resistant Rice [The Tree of Life]

Posted: 08 Dec 2008 11:00 AM CST

Congrats to Pam Ronald, colleague, Davis faculty member, and fellow science blogger for receiving a USDA Discovery Award for helping develop a flood resistant rice variety. For more on this see

deCODE to Integrate New Genetic Risk Factor for Type 2 Diabetes into its deCODEme™ Personal Genome Scan Service [deCODE You]

Posted: 08 Dec 2008 10:25 AM CST

Prince Joachim of Denmark and Princess Marie of Denmark along with deCODE scientist Unnur Thorsteinsdottir during an official visit to deCODE laboratories earlier this year

Prince Joachim of Denmark and Princess Marie of Denmark along with deCODE scientist Unnur Thorsteinsdottir during an official visit to deCODE laboratories earlier this year.

Reykjavik, ICELAND, December 8, 2008 – deCODE genetics (Nasdaq:DCGN) today announced the discovery by an international consortium of scientists from deCODE and major European and US academic institutions of a single letter variation in the human genome (SNP) that is associated with increased fasting glucose levels and risk of type 2 diabetes (T2D). deCODE will employ its CLIA-registered genotyping laboratory and existing testing platform to swiftly integrate the finding into its deCODEme™ personal genome scan, and to assess the addition of this new variant to the company's deCODE T2™ reference laboratory test for assessing individual risk of type 2 diabetes.

The multinational study analyzed a number of SNPs that had been suggestively linked with fasting glucose levels in several major studies involving some 36,000 individuals from Europe and the United States.The analysis identified a version of single SNP within the gene encoding melatonin receptor IB (MTNR1B) that was associated with notable increase in fasting glucose levels. The deCODE team then demonstrated in its Icelandic cohort that this SNP also associated with an increased risk of T2D, a finding that was then replicated in a meta-analysis of data from more than 80,000 cases and controls from Europe and the US. Approximately 10% of the participants in this study carry two copies of the at-risk version of this SNP, putting them at more than 15 percent greater risk of type 2 diabetes than individuals who carry no copies. The paper, entitled "Variants in MTNR1B influence fasting glucose levels," is published today in the online edition of Nature Genetics, and will appear in an upcoming print edition of the journal.

"This finding is another step towards rounding out our understanding of the genetic factors that underpin glucose regulation and risk of type 2 diabetes. This variant does not confer sufficient risk to be of clinical utility on its own. But when measured in addition to our TCF7L2 variant that is the anchor of the deCODE T2™ test, it may, like other common variants conferring modest risk, enable the test to capture an even larger proportion of inherited risk. We are currently evaluating its integration into deCODE T2™, because understanding genetic risk of T2D enables individuals and their physicians to focus, personalize and improve prevention. In the meantime, we will be enabling our deCODEme subscribers to check their profiles for this new variant, keeping them at the cutting edge of human genetics" said Kari Stefansson, CEO of deCODE.

Type 2 diabetes: A major public health problem
T2D is a chronic condition that develops when the body either becomes resistant to or doesn't secrete enough insulin. Diabetes affects nearly 200 million people worldwide and, according to the American Diabetes Association, some 21 million in the United States. The vast majority of these have T2D, and as many as one third of Americans with diabetes may not even be aware that they have the disease. More than 50 million Americans have pre-diabetes, a condition characterized by elevated blood glucose levels and which puts these individuals at high risk for developing T2D. T2D can be managed and – most importantly – prevented. If losing weight, eating better and getting adequate exercise aren’t enough, there are also medications that can help to manage blood sugar levels and insulin response to reduce the likelihood of developing diabetes. For more information on T2D and how to prevent it, you can go to the American Diabetes Association's website.

23andMe offers family discount, just in time for Christmas [Genetic Future]

Posted: 08 Dec 2008 09:45 AM CST

Personal genomics company 23andMe is now offering a discount of $200 for customers who buy three or more kits before December 31st.

In a press release the company explains the reasoning behind the price cut:

By offering this discount, 23andMe hopes to encourage families, in particular, to explore the unique features of the 23andMe Personal Genome Service™ that are of special interest to people who are related. These features allow family members to learn how genetically similar they are and how genes were passed down from grandparents to grandchildren.

Still unconvinced? Just imagine the heart-warming sound of your entire family spitting into plastic tubes on Christmas morning. Now that is the sound of the 21st century Christmas...


Example photo only. Results of buying a 23andMe kit for your children may vary from the scenario depicted.

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Genetics and geography in Finland [Genetic Future]

Posted: 08 Dec 2008 08:35 AM CST

Here's a figure from a brand new paper on the genetics of metabolic traits in a large Finnish cohort (which I'll be posting about in more detail shortly):
On the left is a map of the counties the samples were collected from, colour-coded by geographical/linguistic group; on the right is the genetic clustering of the samples using the same colour scheme. For anyone who's been reading Razib's posts on genetic maps of Europe and East Asia, the clear message here won't come as a surprise: once you have a sufficiently large sample of markers, genes correlate with geographic ancestry with satisfying precision even within countries. And of course this precision will continue to improve with analyses that involve markers with lower frequencies (using large-scale sequencing data), which are likely to be much more informative about fine-scale geographic ancestry.

The Finns are an interesting group, being clear genetic outliers relative to most of the rest of Europe. No doubt Razib will have more to say about this map given his notorious attitudes towards the Finnish people.

Added in edit: It's worth emphasising that the individuals plotted here were only those who had both parents from the same region; see my follow-up post.

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Chiara Sabatti, Susan K Service, Anna-Liisa Hartikainen, Anneli Pouta, Samuli Ripatti, Jae Brodsky, Chris G Jones, Noah A Zaitlen, Teppo Varilo, Marika Kaakinen, Ulla Sovio, Aimo Ruokonen, Jaana Laitinen, Eveliina Jakkula, Lachlan Coin, Clive Hoggart, Andrew Collins, Hannu Turunen, Stacey Gabriel, Paul Elliot, Mark I McCarthy, Mark J Daly, Marjo-Riitta Järvelin, Nelson B Freimer, Leena Peltonen (2008). Genome-wide association analysis of metabolic traits in a birth cohort from a founder population Nature Genetics DOI: 10.1038/ng.271

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I'll be hosting the 4th Molecular and Cell Biology Carnival on December 14th [The Daily Transcript]

Posted: 08 Dec 2008 08:18 AM CST

Send in your entries before the weekend using this form or by emailing me directly.

You can visit the MCB Carnival homepage by clicking on the badge/button:

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Advice for doctors on dealing with personal genomics customers [Genetic Future]

Posted: 08 Dec 2008 06:52 AM CST

Think Gene's Andrew Yates has posted generic responses for medical professionals to use when dealing with patients who come armed with their results from 23andMe or Navigenics.

They're probably quite useful little tools for busy doctors without the time to brush up on the field of personal genomics, but - seeing as this is Andrew Yates - they're also a dig at the careful "medicine but not medicine" stance of personal genomics companies.

An excerpt:

Thus, applying 23andMe to your health care would be a violation of the 23andMe terms of service and, as stated, it "cannot be relied upon at this point for diagnostic purposes." We think 23andMe is a great educational tool, and we are excited about its future potential, but we cannot use the test results to provide any medical services. Further, you consented to "not change your health behaviors on the basis of [23andMe]," so for us to counsel otherwise would be unethical.

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Calling fellow bloggers! [Genomicron]

Posted: 08 Dec 2008 06:40 AM CST

Calling fellow bio bloggers -- help get the word out for the special issue of Evolution: Education and Outreach all about eye evolution. The content is free to access online and the authors include many of the world's top eye evolution researchers. A handy table of contents with links is provided below for easy copy and paste maneuvers.

Evolution: Education and Outreach
Volume 1 Issue 4


351. Editorial by Gregory Eldredge and Niles Eldredge (PDF)

352-354. Introduction by T. Ryan Gregory (PDF)

355-357. Casting an Eye on Complexity by Niles Eldredge (PDF)

Original science / evolution reviews

358-389. The Evolution of Complex Organs by T. Ryan Gregory (PDF)
(Blog: Genomicron)

390-402. Opening the "Black Box": The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF)
(Blog: Evolutionary Novelties)

403-414. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky (PDF)

415-426. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin (PDF)

427-438. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young (PDF)

439-447. Charting Evolution's Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse (PDF)

448-462. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich (PDF)

463-475. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter (PDF)

476-486. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris (PDF)

487-492. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer (PDF)
(Blog: The Loom)

493-497. Suboptimal Optics: Vision Problems as Scars of Evolutionary History by Steven Novella (PDF)
(Blog: NeuroLogica)

Curriculum articles

498-504. Bringing Homologies Into Focus by Anastasia Thanukos (PDF)
(Website: Understanding Evolution)

505-508. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead (PDF)
(Website: NCSE)

509-516. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa (PDF)

Book reviews

548-551. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley (PDF)

Genetics of gene expression in African-Americans: ominous news for personal genomics? [Genetic Future]

Posted: 08 Dec 2008 06:00 AM CST

I was planning to write a long article on this recent paper in PLoS Genetics, but p-ter at Gene Expression and G at Popgen ramblings have both covered the central message very well.

So if you haven't read those articles, already, go and do so now - when you come back, I want to talk about the potentially worrying implications of this paper for the future of personal genomics.

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