The DNA Network |
| Posted: 26 Apr 2008 06:09 PM CDT Some exciting news! After reflecting on the future of Genomicron, I have decided to move it to the Scientific Blogging network. Please update your links and keep reading!
Something you will undoubtedly note when you visit the new site is that I have simply copied the (booooooring) banner from the old site. There's only one thing to do to rectify this: BANNER DESIGN CONTEST! |
| America must rebuild, not destroy, agricultural research programs [Tomorrow's Table] Posted: 26 Apr 2008 04:47 PM CDT In an op-ed piece today, Nobel Peace Prize winner, Norman Borlaug, describes a new strain of stem rust, which could reduce world wheat production by 60 million tons, 10% of the world wheat harvest. "If millions of small-scale farmers see their wheat crops wiped out for want of new disease-resistant varieties, the problem will not be confined to any one country. Widespread failures in global wheat production will push the prices of all foods higher, causing new misery for the world's poor." Is there anything we can do to avoid a global crop failure of this magnitude? Yes. Borlaug argues that it is critical to continue American support for the international agricultural research centers (The State Department is recommending ending this support as well as support for important research centers, including the Department of Agriculture's essential rust research laboratory). If publicly financed international researchers move together aggressively and systematically, high-yielding replacement wheat varieties can be developed and made available to farmers before stem rust disease becomes a global epidemic. The story of papaya provides an excellent example of what plant biologists can do. In the 1950's, the entire papaya production on the Island of Oahu was decimated by papaya ringspot virus. Because there was no way to control the disease, the papaya farms moved to the island of Hawaii where the virus was not yet present. At the same time, Dennis Gonsalves, and coworkers initiated research to develop strategies to control the disease. In 1992, the virus was discovered in the papaya orchards and by 1995 the disease was widespread, creating a crisis for Hawaiian papaya farmers. By 1998 papaya production had dropped to 26 million pounds. Fortunately, Gonsalves' group was able to develop papayas resistant to the virus by using genetic engineering. Gonsalves' group spliced a small snippet of DNA from a mild strain into the papaya genome. Similar to human vaccinations against polio or small pox, this treatment immunized the papaya plant against further infection. The GE papaya were highly resistant to the viral strain. In May 1998, the GE seeds were distributed freely to local growers. After release of GE papaya to farmers, production rapidly increased with a peak of 40 million pounds in 2001. The story of the Hawaiian papaya is an example where GE was the most appropriate technology to address a specific agricultural problem. There was no other technology then to protect the papaya from this devastating disease, nor is there today. This brings us to the question, what if genetic engineering, the most promising method for controlling stem rust, is used to develop new high-yielding resistant wheat varieties? Will the public's anxiety about the process of GE, a technology that has been used in agriculture for 15 years (and in medicine even longer) without a single negative environmental or human health affect, paralyze us and prevent release of life-saving wheat varieties? Just as the public's embrace of the political strategy of "manufactured uncertainty" about global warming delayed much needed action, so can whispers of uncertainty about GE delay our focus on helping feed the poor and malnourished. |
| Welcome to the new Genomicron! [T Ryan Gregory's column] Posted: 26 Apr 2008 04:20 PM CDT Genomicron has recently moved to its new home here on the Scientific Blogging network from its original location. If you are a regular reader, I hope you will like the new look. If you're just finding the blog now, I hope you enjoy reading it! As always, my goal will be to post accessible and informative posts about evolution, genome biology, and the life sciences in general. Welcome to Genomicron 2.0.
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| Comparing mutant and wild type structures [Discovering Biology in a Digital World] Posted: 26 Apr 2008 01:21 PM CDT Over 2600 genetic diseases have been found where a change in a single gene is linked to the disease. One of the questions we might ask is how those mutations change the shape and possibly the function of a protein? If the structures of the mutant and wild type (normal) proteins have been solved, NCBI has a program called VAST that can be used to align those structures. I have an example here where you can see how a single amino acid change makes influenza resistant to Tamiflu®. This 4 minute movie below shows how we can obtain those aligned structures from VAST and view them with Cn3D. Read the rest of this post... | Read the comments on this post... |
| Personalized Genetics: Towards the 100$ Genome [ScienceRoll] Posted: 26 Apr 2008 01:13 PM CDT Please don’t forget to contribute to the database of real clinical examples I’m currently working on. Anyway, I should create something like an RSS feed for all the interesting news and announcement I usually find in the field of individualized medicine. But now I’m going to try to share some of them with you:
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| Medicine 2.0 Congress in Toronto [ScienceRoll] Posted: 26 Apr 2008 12:15 PM CDT I’m pretty sure one of the most interesting conferences this year will take place in Toronto, Canada between the 4th and 5th of September. I plan to attend it, that’s why I submitted an abstract (for oral presentation) and a panel abstract (with Canadian medical bloggers) as well.
The Medicine 2.0 Congress is organized by Gunther Eysenbach MD MPH, a Senior Scientist at the Centre for Global eHealth Innovation, Associate Professor at the Department of Health Policy, Management, and Evaluation at the University of Toronto, and a founding editor-in-chief and publisher of the Journal of Medical Internet Research. (More on the MaRS Blog) What is Medicine 2.0?
And you should also check out an extended article about this web-based aspect of medicine. I will keep you updated regarding the whole conference and our panel.         |
| Posted: 26 Apr 2008 10:39 AM CDT  Found on BoingBoing. "Science painter Cornelia Hesse-Honegger collects and paints mutant bugs in the vicinity of irradiated wastelands like Chernorbyl, around nuclear plants, and nuclear refining sites." Here is a link to the title page of this work. Awesome paintings of messed up bugs. Too bad that's pretty much all it is, and claims that the observed mutant phenotype of the insects has something to do with radiation from nuclear power plants is probably just to attract some attention to the great artwork. I love entomology and genetics so otherwise this would have been really cool with some statistics and some controls. |
| Rethinking software access [business|bytes|genes|molecules] Posted: 26 Apr 2008 10:25 AM CDT So today, I tried to download MODELLER which is free for academics and $$$ for commercial via Accelrys (Full Disclosure: While i did not directly manage MODELER at Accelrys, I had indirect responsibilities). I completely understand that part. The problem is that the MODELLER license does not seem to address what I want to do: hobby science. So I had to wait for my request to be approved, which it didn’t. There’s two thoughts that arise from this exercise, or maybe three. First, it’s clear that when the MODELLER license was written, personal research use was not considered. It harks back to the assumption that “real science” was either done in industry or at companies. Well folks, it might have been true some years ago, but it is an assumption that is a bit of a problem. I completely understand that they are trying to avoid the system from being gamed, but in my mind the old model (free for academic, $$$ for commercial via another entity) does not work as classically constructed in this case, for multiple reasons. The whole licensing model does not work for bursty science either, especially when one or more non-academics is installed (this is a question that I took a hard look at once for MD programs). Which leads me to thought #2. I come from an era when modeling software was local, either on a workstation or on a cluster somewhere. That’s how I always ran CHARMM, MODELLER, WHATIF, various threading packages, MOPAC, GAUSSIAN, various other QM packages. That is how most people run those codes today. Then think about a project that you might want to do, a bursty project spanning geeks across countries and continents. Yeah, modeling doesn’t live well on the programmable web. There are servers out there, especially for structure prediction, sequence alignment, etc, but they seem to belong to a different era of the web. We need to start thinking about the source hosted model, at least for academic code. Source code licenses that target developers and power users that like tinkering with the code, but that’s also better done by hosting all academic code at sourceforge, google code or github, so that collective intelligence comes into play, rather than people developing their own forks which no one else gets to see. Second, applications should be available on the web, ideally with APIs that make it possible to mash up solutions. Now, automating these tasks is not always trivial, neither is setup. All of us with hundreds of utility scripts know that, but lets think about the web when we develop code. Not just providing a web server, but how that server can be used as a powerful resource, not just a result submission and retrieval backend. I’d love to be able to get access to a NAMD server, run a series of utility tasks and then launch a compute job, where I could dial up a set of servers, etc. It’s also possible to attach utility based licensing and pricing to such a service. What I am arguing for is new ways to think about how we make software available, and how it is used. This can’t be done at the individual group level, but there is an opportunity here for universities and funding agencies to figure out how they can help facilitate this, and even companies that might want to commercialize some of these packages. Comments on this? What would you like to see? How might you access such tools? Would you want mashup APIs? Technorati Tags: molecular modeling, web services  |
| DNAPrint Genomics and a New Roots Television Video [The Genetic Genealogist] Posted: 26 Apr 2008 08:40 AM CDT Megan Smolenyak Smolenyak recently wrote “I’m a Euro-Mutt!” about the results of her AncestrybyDNA EuropeanDNA 2.0 test (from DNAPrint Genomics). Megan found that the results of her test were both expected and surprising! From DNAPrint Genomics’ website:
For the newbies, this test examines autosomal DNA, which is DNA other than the sex chromosomes and mtDNA. These types of tests will become much more popular as SNP testing and genomic sequencing become cheaper and more widespread. Roots Television Have you visited Roots Television lately? Don’t forget that the DNA Channel is available here at TGG (click the Roots Television - DNA Channel button above). Currently featured (under “DNA Testing”) is an interview with Rick Kittles, the co-founder of African Ancestry and a well-known name in the genetic genealogy field. |
| Phylogenetic Fallacies: Early Branching Must Mean Primitive [T Ryan Gregory's column] Posted: 26 Apr 2008 06:50 AM CDT Evolutionary trees, or "phylogenies", are a major part of modern evolutionary science. They depict hypotheses regarding the relationships among taxa, and are therefore important in reconstructions of the historical path of evolution (Gregory 2008a,b). Various approaches can be taken to formulating phylogenetic hypotheses, including analyses based on morphological, fossil, and/or molecular data. These methods often agree well, but sometimes one or another can throw up some surprises and challenge previous hypotheses about the relationships among groups of organisms. Reconstructing the tree of life is a difficult and complicated process, and one should expect there to be significant refinements and revisions along the way. This is especially true of the deepest branches of the tree, which are often the most difficult to resolve. Case in point, the Tree of Life Web Project gives the following summary of deep branches among major animal lineages: |
| Second Life Meeting Today: HPV vaccination [ScienceRoll] Posted: 26 Apr 2008 05:20 AM CDT There will be a meeting today at the Ann Myers Medical Center and it will be open to all!
Second Life, the virtual world and medical education:
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| DNA Video: Leah Sparks of DNA Direct [Eye on DNA] Posted: 26 Apr 2008 03:08 AM CDT
*I’m the Genetic Information Specialist at DNA Direct. |
| Genetic Information Nondiscrimination Act clears Senate [Think Gene] Posted: 26 Apr 2008 02:48 AM CDT The Senate passed the Genetic Information Nondiscrimination Act (GINA) on April 24, approving by unanimous consent an amended version of H.R. 493, which passed the House April 25, 2007 by a vote of 420-3. The House is expected to take up the measure again quickly before sending it to President Bush to sign the measure [...] |
| Anesthesia and Alzheimer’s [Think Gene] Posted: 26 Apr 2008 02:48 AM CDT In studies of human brain cells, the widely-used anesthetic desflurane does not contribute to increased production of amyloid-beta protein; however, when combined with low oxygen conditions, it can produce more of this Alzheimer's associated protein. Over 200 million people undergo surgery each year, and there has been concern that anesthetic use may contribute to Alzheimer's and [...] |
| Bypassing the insulin highway [Think Gene] Posted: 26 Apr 2008 02:47 AM CDT An immune cell known as a neutrophil releases a protein that can suppress glucose production in the liver –without targeting insulin, researchers have found. Neutrophils, a type of white blood cell, produce special immune proteins called defensins which seem to have a connection with glucose levels. During bacterial infection, defensin production can increase dramatically, a rise [...] |
| Yeast gives rise to new concept: cell fuel is ‘brains’ behind division [Think Gene] Posted: 25 Apr 2008 10:24 PM CDT With the cost of diesel and gasoline getting nearer to the hourly minimum wage, too bad the fuel doesn't do more work - like deciding what route to take and pressing the gas pedal. While that concept isn't likely to work for vehicle fuel, a new study has found that it is, in fact, what goes [...] |
| Viruses may play a role in lung cancer development [Think Gene] Posted: 25 Apr 2008 10:17 PM CDT Papers presented at the 1st European Lung Cancer Conference, jointly organized by the European Society for Medical Oncology (ESMO) and the International Association for the Study of Lung Cancer (IASLC) in Geneva, Switzerland highlight emerging evidence that common viruses may contribute to the development of lung cancer. Experts agree that smoking is by far the most [...] |
| Trojan horse of viruses revealed [Think Gene] Posted: 25 Apr 2008 10:16 PM CDT The vaccinia virus has a problem: it is a giant among viruses and needs a special strategy in order to infiltrate a cell and reproduce. Professor Ari Helenius and Postdoc Jason Mercer from ETH Zurich's Institute for Biochemistry have now discovered what this strategy is. In the process, they stumbled upon new and surprising findings. The [...] |
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