The DNA Network |
| not just some chick... [the skeptical alchemist] Posted: 01 May 2008 07:15 PM CDT  Fabulous comic with a temper from marriedtothesea.com, found through Homosecular Gaytheist. Carnival update: the next Molecular and Cell Biology Carnival will be hosted on May 11 over at cotch dot net. We are still looking for hosts for future editions - if you are interested, check out the carnival's website and drop me a comment/e-mail. And the latest edition of Tangled Bank, which incidentally is celebrating its 4th birthday, is up over at Dammit Jim! View blog reactions |
| Posted: 01 May 2008 04:06 PM CDT
Here’s an interesting GMO crop angle: Transgenic corn that expresses very specific proteins toxic to borer worms. Bonus: no broader impact on soil microorganisms. It’s getting harder to be a pest these days. |
| Posted: 01 May 2008 03:51 PM CDT Good news! Good news! Last week the Senate passed the Genetic Nondiscrimination Act (GINA). This week it was passed by the House. It only needs one signature and GINA will become law. For years, those of us who teach genetics have had to caution students about genetic testing. The biggest reason was the fear that having a genetic test would cause them to lose their health insurance. Read the rest of this post... | Read the comments on this post... |
| GINA in da House! [genomeboy.com] Posted: 01 May 2008 03:17 PM CDT NEW YORK (GenomeWeb News) – A little less than a week after its passage by the US Senate, the Genetic Information Nondiscrimination Act has been passed by the US House of Representatives by a vote of 414 to 1.The bill is the closest it has ever come to being signed into law after being considered in various iterations by both chambers of Congress over the past decade. GINA, which would protect Americans from discrimination based on information from genetic tests, had previously passed in the House twice before — most recently last year, when the vote was 420 to 3 in favor of its passage. And by the way, we’ll miss you Ron Paul, you ornery cuss. |
| The snake rescuer [Discovering Biology in a Digital World] Posted: 01 May 2008 02:07 PM CDT Yesterday morning I was sitting at conference table, downing coffee to keep my eyes open, when I heard someone say that it's springtime now and the snakes are waking up. Well, those kinds of statements at the breakfast table do have a way of getting my attention. Read the rest of this post... | Read the comments on this post... |
| Posted: 01 May 2008 02:07 PM CDT I hope everyone who reads this will subscribe to Genome Technology Online (This is not a paid advertisement this is my opinion). Why? If you are asking this, it is likely because you have never... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| Health News in Second Life: Virtual Conference [ScienceRoll] Posted: 01 May 2008 01:39 PM CDT Second Life is a virtual world with more and more educational resources and in this series, I try to keep you up-to-date about these.
Why 3D? Web conferencing: 2D vs. 3D (or both), or 'Why conduct events and meetings in Second Life?'         |
| The Mission of Navigenics: Interview [ScienceRoll] Posted: 01 May 2008 01:16 PM CDT Navigenics is a company focusing on personalized genetics and it launched its service just weeks ago. Dr. Dietrich Stephan, a human geneticist at Navigenics, agreed to answer some of my questions.
My mother died of breast cancer when she was in her early 30’s due to a missed lump. This shaped my career and guided me toward developing effective early diagnostics and new knowledge-based therapies for human disease. I have been working in academia for the last 15 years to identify gene variants that cause human disease. My group has been involved in identifying the gentic basis of a dozen monogenic diseases that now allows early genetic testing following the established principles of medical genetics and genetic counseling. While crucial to the families afflicted with these diseases, they remain rare on a population-wide basis. Approximately 5 years ago my charged into the field of deciphering complex genetic disorders using ultra-high density SNP genotyping arrays and case-control study designs. We published the first paper using more than 500,000 SNPs (in Science), established new risk alleles for Alzheimer’s disease, amyotrophic lateral sclerosis, progressive supranuclear palsy, and have dozens more projects ongoing. I believe we are still the only group that makes our raw genotype data freely available on-line for any scientist to download and use . These risk alleles that we have been finding have effect sizes that are on exactly the same order of magnitude scale as the environmental risk factors that we, as a community, accept as robust and communicate to members of our community on a daily basis (for example “you are obese so you are going to get a heart attack”, or “you smole so you are going to get lung cancer”). The risk communication for environmental risk factors does not require a testing lab because we can see or sense the exposures in most cases, and the method of communication is quick crude in that we do not communicate effect sizes or interactive models between risk factors. As my group continued to define allelic imbalances that predisposed to human disease, I looked for a place where we could genotype individuals to assess their risk. There were no monogenic testing facilities that felt comfortable performing the genotyping tests and interpreting the results. Additionally, there were no genetic counselors or physicians who felt comfortable in using genetic risk information to work with their patients proactively to prevent disease based on a holistic understanding of their risk. It is critical to remember that all human disease has a genetic component. I started Navigenics with my partner David Agus, who is a clinical oncologist, to build the appropriate infrastructure to allow widespread assessment of genetic risks so that we, as a global community, could have a chance at effective prevention strategies to stave off a global health-care crisis in the next 50 years. The concept revolved around encouraging focused prevention, early screening, and early intervention to compress the burden of morbidity to the end of like and balance it with lifespan.
We will perform both - starting with genotyping for common variants for common disease and ending with whole-genome resequencing. You will see an exciting product line evolution over the coming year.
The SNPs we are reporting on are valid associations (based on thorough validation) and are independent risk factors in population-wide studies. Most of our interpretations are based on studies for which a whole-genome scan has been performed and we know that there are no other large effect size SNPs lurking in the genome. We are making the assumption that independent risk factors when present so not cancel each other out, rather they compound risk. We have seen no validated exceptions to this assumption in the literature. As we become aware of exceptions to this assumption we can modify our reporting. We are providing the current state-of-the-art and informing members that their risks may refine themselves over time. Take the example again of environmental risk factors - the more you have the higher your likelyhood of disease - but we know that we can’t predict with certainty an outcome.
Web2.0 features will be employed primarily to ensure data privacy, but also to assist in visualizing very complex data sets and results so they are understandable to members and physicians.
Quality. Data will be complete with all risk genotypes being called. Genotypes will be generated in a CLIA-certified diagnostic environment. On staff genetic counselors assist in interpreting this information any time of the day or night. We will not give risk information on associations that are wrong. Our ethics, policy, clinical, scientific, and business advisory boards are experienced and made up of individuals who want to ensure this type of sensitive information is used correctly and accurately. For example we are sponsoring an industry standard-setting meeting in conjunction with the personalized medicine coalition this fall. When making health decisions you need to be able to trust the quality of the information you base those decisons on.
Full resequencing of the genome, copy number analysis, and methylation status assessment where all of that data is run through the Navigenics interpretation engine to provide a rank-ordered list of health risks so that a focused prevention plan can be devised along with the physician, and a focused biomarker monitoring program for early detection is implemented. Early intervention equals better outcomes. Further reading:         |
| A molecule for May [Discovering Biology in a Digital World] Posted: 01 May 2008 08:42 AM CDT APRIL was so much fun, that I thought I should find a molecule for May. I searched both the Gene database, the structure database, everywhere, without any luck.
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| Phylogenetic Fallacies: Branching From a Main Line [T Ryan Gregory's column] Posted: 01 May 2008 07:14 AM CDT In Phylogenetic Fallacies: Early Branching Must Mean Primitive I focused on the misconception that an "early branching" lineage was necessarily "primitive" (i.e., very similar to a distant ancestor). This time, I want to discuss something slightly more subtle, but nonetheless important, with regard to interpreting phylogenies. Specifically, I want to note a problem with the very concept of one lineage "branching off from" another lineage. There can be a tendency to consider evolutionary trees as reflecting a main line with a series of "side branches". This is especially true when the tree is "unbalanced" (lineages are depicted with uneven amounts of diversity) and "ladderized" (the more diverse branches are placed on the same side of each node). The following is a general unbalanced, right-ladderized tree. |
| Low technical error rates for personal genomics companies [Genetic Future] Posted: 01 May 2008 06:26 AM CDT Antonio Oliveira from Longa Vista has compared the results of his genome scans from both 23andMe and deCODEme. Of the 560,299 sites analysed by both companies, just 23 showed a different result between the two scans - a discrepancy rate of just 0.004%! This fits with the low discrepancy rate reported by Ann Turner back in January. The take-home message: by all means worry about the interpretation of your personal genomics result, but it's likely that your actual genotype data are extremely accurate. Via The Quantified Self.  Subscribe to Genetic Future. |
| RSS Awareness Day [Sciencebase Science Blog] Posted: 01 May 2008 03:44 AM CDT |
| Enduring Grant Writing Edits [Bitesize Bio] Posted: 01 May 2008 03:35 AM CDT
That’s one of my main gripes with creationist simpletons who imply that scientists are uncritical of their peers, and that criticism is directed solely at those who refuse to take their claims at face value. They have no clue whatsoever what they’re talking about. Every scientific claim, as it’s actually being formulated, must be paved with meticulous attention to detail. The scientist advancing some newly-considered possibility must endure a constant barrage of critiquing, on both the grant application and results publication stages. It’s for a darn good reason - people, even scientists, are prone to error. The scientific method is a winnowing process, and the writing process is ripe with revisions and the repeated phrase “it’s not good enough.” Competition of ideas with the tangible results as the decider is how science inevitably moves forward. For the individual researcher however, it is humbling. It IS frustrating. But it’s what we do. Curiosity and enthusiasm began our careers in science, and a driving need to maintain an income reminds us to stick to it. The human frailty in me craves nothing more than the pat on the back, the kind appraisal, and the reassurance that I know what I’m doing. It doesn’t matter what career you’re in, science or otherwise, but you simply won’t get that form of condescension AND a competitive place in the job market. The only solution is to pay attention to detail, learn how to be thick-skinned, and learn how to write persuasively to grant foundations and scientific journals.
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| The most natural drug [Think Gene] Posted: 01 May 2008 02:03 AM CDT In the fight against infection, the human immune system isn't ready for a war. Vaccines push the immune system to create defenses against illness, but they take time to work. A new process developed by scientists at the Oklahoma Medical Research Foundation (OMRF) and Emory University stands to revolutionize the process. In an advance online publication in [...] |
| Press Release From The Newly-Created DNA Fund [The Genetic Genealogist] Posted: 01 May 2008 02:00 AM CDT Last week I received a press release announcing the creation of a non-profit organization to raise and disseminate funds to increase original research in genetic genealogy testing (some of which will undoubtedly be reported in the open-source Journal of Genetic Genealogy). The DNA Fund also has a blog, available here. Following is the press release:
Some of the projects proposed by The DNA Fund for funding include:
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| 8 new human genome projects offer large-scale picture of genetic difference [Think Gene] Posted: 01 May 2008 01:58 AM CDT A nationwide consortium led by the University of Washington in Seattle has completed the first sequence-based map of structural variations in the human genome, giving scientists an overall picture of the large-scale differences in DNA between individuals. The project gives researchers a guide for further research into these structural differences, which are believed to play [...] |
| USC researcher reveals new model for embryonic limb development [Think Gene] Posted: 01 May 2008 01:56 AM CDT A study led by a researcher at the University of Southern California has found a new model to explain how signals between cells in the embryo control limb development. The study, which will be published in the May issue of the journal Nature and now available online, found that secreted growth factors at the distal tip [...] |
| Turning on cell-cell communication wipes out staph biofilms [Think Gene] Posted: 01 May 2008 01:55 AM CDT University of Iowa researchers have succeeded in wiping out established biofilms of Staphylococcus aureus (staph) by hijacking one of the bacteria’s own regulatory systems. Although the discovery is not ready for clinical application, the findings offer insight into a dispersal mechanism for staph biofilms and might help identify therapeutic targets. Biofilms are communities of bacteria that [...] |
| Researchers discover molecular basis of a form of muscular dystrophy [Think Gene] Posted: 01 May 2008 01:54 AM CDT A team of French and German researchers report in the May 2008 print issue of The FASEB Journal (http://www.fasebj.org) that people with limb-girdle muscular dystrophy are missing a protein called c-FLIP, which the body uses to prevent the loss of muscle tissue. By targeting the cellular and molecular mechanisms responsible for creating this protein, scientists [...] |
| What is a genome? [Mailund on the Internet] Posted: 01 May 2008 12:07 AM CDT At Genomicron there is an interesting discussion about the definition of a genome. The main point is two different definitions: the genome of a species — the uniqueness of the species compared to other species’ genomes — and the genome of an individual — the unique sequence(s) of an individual including within species variation. Definition one, the “species genome”, is a reference or “average” genome of the individuals in the species, the genomes in definition two. It is an interesting read, I suggest you have a look. |
| SearchMe [Mailund on the Internet] Posted: 30 Apr 2008 10:48 PM CDT Check out the new search engine SearchMe.
It is no way near as good as Google for actual searching, but I really like the interface. For playing with, anyway. I am not sure it is that useful for everyday use. The simple and elegant Google interface is something that really appeals to me. On the other hand, the “cover flow” view of search results is a neat way of quickly scanning through results. |
| Visualization of My Genetic Similarity to People Around the World [BUZZYEAH » My Genome] Posted: 30 Apr 2008 10:02 PM CDT Here is a cool visualization of my genetic similarity to groups of people from around the globe. The longer the bar the greater my genetic similarity to people from that region.
As you can see, I'm most similar to people from Northern Europe in the 23andMe visualization.
Here is how my genetic similarity to different global regions stacks up:
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| A complexity complex [genomeboy.com] Posted: 30 Apr 2008 09:55 PM CDT In April 1986 Nancy Wexler appeared on 60 Minutes to talk about Huntington’s. “I’ve always believed in knowledge for its own sake,” she said. “And it is ironic that after working for precisely that, I’m finding it much more complex than I ever thought it would be.” - From Blood Matters by Masha Gessen |
Finally, I decided to change the search and use the date instead of the name of the month. And here we have it, straight from PubChem. A molecule for May. 05012008 is the 
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