The DNA Network |
| Insurance and the Age of Personal Genetics [Bayblab] Posted: 29 Apr 2008 03:06 PM CDT In the age of the personal genome, companies like 23andMe are springing up, offering personal genetic profiling and ancestry tracing. While there are questions about the accuracy of their claims, the interpretation of the results (are we about to see a boom in genetic counsellors?) and other ethical and privacy considerations, the US Senate has made a pro-active move in passing a bill banning genetic discrimination. In short, the bill prohibits employers or insurers to use personal genetic information in decision making. Ars technica takes a closer look at the insurance angle, explaining why the bill is a good idea. From the article: Worse yet, the very concept [of insurance based on genetics] threatens to undermine another of the greatest potential benefits of the genome: personalized medicine. The goal of personalized medicine is to tailor treatments to a the unique genetic defects that have helped foster a disease, be it diabetes or cancer. But, if insurers can deny coverage based on those same genetic traits, the patient may never see the treatment. |
| Scientists make chemical cousin of DNA for use as new nanotechnology building block [Think Gene] Posted: 29 Apr 2008 03:06 PM CDT In the rapid and fast-growing world of nanotechnology, researchers are continually on the lookout for new building blocks to push innovation and discovery to scales much smaller than the tiniest speck of dust. In the Biodesign Institute at Arizona State University, researchers are using DNA to make intricate nano-sized objects. Working at this scale holds great [...] |
| Single-celled bacterium works 24-7 [Think Gene] Posted: 29 Apr 2008 02:49 PM CDT Researchers at Washington University in St. Louis have gained the first detailed insight into the way circadian rhythms govern global gene expression in Cyanothece, a type of cyanobacterium (blue-green alga) known to cycle between photosynthesis during the day and nitrogen fixation at night. In general, this study shows that during the day, Cyanothece increases expression of [...] |
| Research findings open new front in fight against AIDS virus [Think Gene] Posted: 29 Apr 2008 02:48 PM CDT A research group supported by the National Institutes of Health (NIH) has uncovered a new route for attacking the human immunodeficiency virus (HIV) that may offer a way to circumvent problems with drug resistance. In findings published today in the online edition of the Proceedings of the National Academy of Sciences, the researchers report that [...] |
| Cell-based therapy shows promise in patients with Parkinson’s disease [Think Gene] Posted: 29 Apr 2008 02:34 PM CDT A novel cell therapy using retinal pigment epithelial (RPE) cells attached to tiny gelatin bead microcarriers implanted in the brain can improve the symptoms of patients with moderate to advanced Parkinson's disease (PD). Rush University Medical Center neurosurgeon Dr. Roy A. E. Bakay and colleagues from Emory University, Atlanta found the therapy Spheramine was well-tolerated and [...] |
| Posted: 29 Apr 2008 02:32 PM CDT Imagine a technology that would not only provide a green and renewable source of electrical energy, but could also help scrub the atmosphere of excessive carbon dioxide resulting from the burning of fossil fuels. That's the promise of artificial versions of photosynthesis, the process by which green plants have been converting solar energy into electrochemical [...] |
| Anatomical Theatre [ScienceRoll] Posted: 29 Apr 2008 02:32 PM CDT I found this on BoingBoing:
Further reading:
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| How Not to Give a Presentation! [ScienceRoll] Posted: 29 Apr 2008 02:24 PM CDT This slideshow, I found at Clinical Cases and Images, is one of the best ones I’ve ever seen. It focuses on how not to give a presentation: I’m a medical student so I know exactly what it is like to sit and watch plenty of bad and long presentations while I still believe even the worst and most boring subjects could be visualized properly on a well-structured slideshow. I’ve given dozens of slideshows about web 2.0 and medicine and they changed a lot after my US trip this February. I realized the aim is not to transmit all the information you have, but to persuade your audience to search for your project or your work after your presentation. You can clearly see the difference if you take a look at my old and the new slideshows. Now I
What are your tips? Let’s finish with a funny video about the same topic:
Further reading:         |
| To buy or not to buy a NGS device.. [Next Generation Sequencing] Posted: 29 Apr 2008 02:04 PM CDT A lot of people are looking into buying a next generation sequencer these days and weighing the pros and cons. People are obviously attracted to the idea of expanding their research capacities with high throughput sequencing but at the same time they are worried about the skills and resources needed to run the instruments. As [...] |
| Online Gene Tests: Anyone purchased one of these tests? [ScienceRoll] Posted: 29 Apr 2008 01:31 PM CDT For an upcoming series on genetic testing, a major TV network would like to interview a person who has ordered an online gene test to assess their future risk of getting certain diseases, and would like to share their experience and reaction to their test results. Twelve complaints have been filed with the California Dept of Health, and the New York State Dept of Health has sent letters explaining the legal ramifications of testing New York residents without the proper clinical laboratory permit. Most of these complaints are anonymous. Would anyone speak on-camera to their issues and share their personal experience ordering one of these tests? Please e-mail: Gabrielle [at] caa.columbia.edu
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| Rewiring E. coli transcriptional network [The Seven Stones] Posted: 29 Apr 2008 12:52 PM CDT Research highlight by Kazuharu Arakawa and Masaru Tomita, Institute for Advanced Biosciences, Keio University, Japan
Since radical rewiring of the gene circuitry appears to have only a limited impact on expression levels, this work suggests that gene regulatory networks are highly dynamic and underscores the potential importance of post-transcriptional mechanisms for the robustness of transcriptional regulation. Moreover, this work illustrates the fundamental robustness and evolvability of gene regulatory networks, which is reassuring news for synthetic biology. Isalan M, Lemerle C, Michalodimitrakis K, Horn C, Beltrao P, Raineri E, Garriga-Canut M, Serrano L (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature 452:840 |
| GSK acquires Sirtris Pharmaceuticals [Bayblab] Posted: 29 Apr 2008 10:23 AM CDT Pharm giant GlaxoSmithKline acquired Sirtris Pharmaceuticals for the tidy sum of $720 million US last week. This story is interesting not because of the excitement of corporate deals and stock market fluctuations, but because Sirtris Pharmaceuticals specializes in developing small molecule activators of SirT1. And anything involving SirT1 - my protein of interest - is inherently fascinating. It's actually more interesting for other reasons. Previously on this blog, I've echoed a sentiment common in the skeptical blogosphere: There's no such thing as alternative medicine. Once a treatment has been shown to work, it becomes part of mainstream medicine. Resveratrol, a polyphenol, is a SirT1 activator. SirT1 (I told you it was interesting) has been shown to be involved in insulin signaling, energy metabolism and lifespan extension in model organisms. Other work has shown resveratrol to have cardioprotective and anti-cancer effects. Resveratrol has long been thought to be a molecule behind the 'drink red wine' wisdom. This all sounds great. And 'alties' probably feel vindicated: Resveratrol has been on sale in health food and dietary supplement stores for ages. Before many of the studies mentioned above had been done, in fact. But don't go reaching for your wineskin just yet. Studies have also shown that oral resveratrol has poor bioavailability. That's where Sirtris comes in. They develop compounds that are analogs of resveratrol to improve potency and bioavailability (and patentability), and test those compounds. And Big Pharma (GSK) has taken notice, decided this is viable science, and acquired Sirtris in the hopes of turning these compounds into diabetes, anti-obesity or anti-aging drugs. Like other examples we've discussed this is a case of a natural or alternative medicine becoming mainstream (or, rather, the beginning steps of that process). The moral of the story isn't that natural products work. In this case it doesn't - all resveratrol supplements will give you is expensive urine. The point is that if the science is there, the medicine will come. There's still a possibility that these compounds will fail for one reason or another. Perhaps they won't be effective in humans as in rodents. Maybe there will be toxicity issues. If this happens, no doubt that Big Pharma conspiracy theorists will jump up and down saying that GSK made the purchase to squash a promising natural medicine. An almost 1 billion dollar investment seems to be a bit much for such a petty goal. If I was the big, evil corporation, I'd sink that money into the supplement makers and keep it on the shelves. But shrewd companies know that a tested drug has more value than an untested one. The only reason not to get science onside is if you don't think it will support you. |
| RSS woes. [T Ryan Gregory's column] Posted: 29 Apr 2008 06:33 AM CDT We're working on connecting the feed from this new Genomicron to the Feedburner feed so that everyone gets counted, but obviously there's something funny going on in the meanwhile. Here is how my Feedburner subscriber totals have fared since the move. I had hoped that the transition would be smooth, but evidently there are lots of people who either a) bailed, b) were using the old Blogger feed (which no longer forwards on to Feedburner), or c) have subscribed to the feed from this site directly and it doesn't count at Feedburner. Anyway, this is the feed that will be counted: |
| Bio-IT World Day 1 - Visualization, the cloud and people [business|bytes|genes|molecules] Posted: 29 Apr 2008 05:49 AM CDT
Perhaps the highlight was the keynote by John Reynder from Johnson and Johnson PRD. He gave us a tour of his experiences through his career, including his time at Los Alamos. The talk was not in any great depth, but I left it very encouraged. Encouraged that the head of an IT organization at a large pharma company understood the value of collaboration, understood that innovation happens everywhere, and needs to be tapped appropriately and a lot of information is pre-competitive and should be shared across companies. Other things he talked about
Would have been nice to have open data mentioned explicitly, but he clearly said that pharma needs to appreciate data and information sharing. Bio-IT World means meeting old friends, especially from my Accelrys days as well as finally meeting people I admire from my online life, with a special shoutout to Michael Cariaso On tap on Day 2 - Electronic Data Capture, high throughput data management, supercomputing and a W3C lunch Image via Wikipedia Technorati Tags: Bio-IT World, BioIT, Visualization  |
| Gene Patents and Genetic Testing [Eye on DNA] Posted: 29 Apr 2008 04:32 AM CDT
Key points include:
Access to genetic testing can be impeded every step of the way from the discovery of new genes and mutations all the way up to availability of genetic tests. Right now, most of us concentrate on who has the right to have a genetic test and how. Another consideration clearly has to be who will develop the genetic tests and what intellectual property rights they have over their work. As Michael Crichton said in a New York Times op-ed against gene patents:
Should we prohibit the patenting of genes? Take the poll in this previous Eye on DNA post. |
| Biotechniques is 25 [Bitesize Bio] Posted: 29 Apr 2008 03:24 AM CDT Today’s issue of the Biotechniques journal is well worth a read. The journal celebrates 25 years of existence with a series of retrospective articles covering developments in various fields over the same period. Among the picks are: Twenty-five years of quantitative PCR for gene expression analysis Bacterial genetics: past achievements, present state of the field, and future challenges Over the rainbow: 25 years of confocal imaging Mass spectrometry: m/z 1983–2008 Kits and their unique role in molecular biology: a brief retrospective Remember that access to Biotechniques is free, but registration is required. Do you remember where you were 25 years ago? |
| Geeky DNA T-Shirts from the San Francisco Exploratorium [Eye on DNA] Posted: 29 Apr 2008 03:00 AM CDT For the 2007 National DNA Day, San Francisco’s Exploratorium Explainers mocked up some DNA t-shirts.
Seen any t-shirts for last week’s 2008 National DNA Day? |
| Posted: 29 Apr 2008 12:00 AM CDT Boston, USA — April 29, 2008 — Today at the Bio-IT World Conference & Expo in Boston, USA, CLC bio announced collaboration with Microsoft Corp. on integrating CLC bio’s extensive bioinformatics solutions with Microsoft’s software platform, for the benefit of companies, corporations, and institutions in the biotech, pharmaceutical, and life science sectors. CLC bio has [...] |
| Space, the final bio-frontier? [Omics! Omics!] Posted: 28 Apr 2008 11:13 PM CDT In case it hasn't been obvious from the occasional post, I am a spaceflight aficionado. As a very young child I watched some of the last moon landings. Many hours of play were spent imagining riding a rocket, playing with toy rockets, and building Lego spaceships. At some point I realized I really didn't quite have the Right Stuff. Clearly I was never going to cut it as a pilot (I carry scale models of Hubble's corrective lenses on my nose daily), and in the end my scientific interests weren't really going to support traveling to space. So it became purely an observational hobby, though the dream has been rekindled a bit by the notion of buying a rocket ticket (alas, 2001 has come-and-gone without the vision of 2001). When Millennium changed travel agents a few years back & we needed to fill out new travel preference forms, I put Virgin Galactic as my preferred carrier. A more inner struggle, one reflected in much of the space community, is the appropriate role of humans in space, or perhaps more pointedly, of government funding of humans in space. It is one thing for some gazillionaire to pay multi-millions to take a joy ride (anyone want to spot me $50M for a week PLUS a spacewalk?); it's another for governments to continue to spend billions to put people up there. Manned flight is thrilling, but robots tend to get more data. An item in The Scientist (free registration may be required) points to this debate again, and close to my scientific home. Lobbying is firing up again for biology research in orbit, and given that the company (Spacehab) lobbying for it builds manned research gear, they're pushing the manned angle. Space research has yielded many earthly benefits, but they're mostly in areas such as communications & remote sensing. It is difficult to really prove a case for very many other areas. Spaceflight remains rare, unpredicable & expensive, three qualities that few like to associate with their research programs. Two biotech claims are advanced to support space research. One is the long-standing issue of crystallography -- the claim is that crystals for X-ray diffraction studies can be grown in space that are either higher quality than ground samples or which simply can't be made on the ground. The other is a very new claim of vaccine research. If anyone knows of a good, balanced (not in the Fox News sense!) review of space-based crystallography, I'd love to have a pointer. I'm not in that community, but my general impression is that while useful data has been collected on space-grown crystals, it really hasn't taken that community by storm. Perhaps if flights were cheap & frequent it could, but other approaches such as high-throughput condition screening have had a bigger impact. The vaccine claims are based on a paper published last year in PNAS (also covered in The Scientist) which found that spaceflight changed some key gene expression programs in Salmonella and that the space-flown bugs were more virulent. A quick scan suggests that the paper is reasonably well done on the transcriptional profiling side (both biological & technical replicates). But, it also points to the challenge of space research -- when is the next flight opportunity to determine how general the effect is? I do believe there are a lot of fascinating fundamental questions to ask about biology in space. Many would be in the developmental & cellular world: to what degree does gravity influence various developmental processes. Some other research might be less about space & more about behavior: Skylab astronauts had spiders spin webs, and it took a number of trials for the spiders to learn to do it in Zero-G. It could be a fascinating way to study such behaviors & how an animal adapts to a changed environment. But, most space biology questions have an importance scaled to our commitment to manned presence in space. I'm a bit skeptical that the Salmonella experiments really help understand virulence on the ground (or more importantly, are going to be generally relevant -- but sometimes it doesn't hurt to be lucky!), but I'd sure want that line of work driven hard if I was going to spend months in space! |
| Getting Rejected! [adaptivecomplexity's column] Posted: 28 Apr 2008 10:51 PM CDT Interested in being a scientist? Then you had better get used to rejection and failure, because the truth is that most of your experiments will fail, most of your original ideas will be wrong, and most of your grant proposals and papers will be rejected on the first submission (especially if you submit to competitive journals). This doesn't mean you're a bad scientist - failure and rejection is a normal fact of life for most scientists (that is, all scientists except ones who aren't doing any science!). But this means that peer-review is a good thing, even when it affects you personally as your paper gets rejected (as mine was last week). How does peer review work in scientific publishing? One of the most important things you do as a scientist is produce publishable results, which generates not just in fame and glory, but hopefully progress in understanding an important question. When you have publishable results, you submit them to a professional journal. At the journal, an editor makes a triage decision (is there any hope at all that this paper will be accepted?), and either immediately rejects your paper, or sends it to 2-3 outside experts, who in all likelihood are people you know, even though they are technically anonymous (scientific communities are generally pretty small). These reviewers pass judgment on the significance of the work, as well as look for flaws in the reasoning or experiments. A paper is usually rejected, either before or after review, for one of three major reasons: |
| Height and hypertension genes in Nature Genetics [Genetic Future] Posted: 28 Apr 2008 10:47 PM CDT The advance online edition of Nature Genetics is stuffed with juicy complex human genetics goodness. Firstly, there are three massive genome-wide scans for genes involved in regulating human height, each of which analysed more than ten thousand individuals. As I've mentioned before, height appears to be one of those traits (like bipolar disease) that thumbs its nose at genome-wide association studies (GWAS). That's evidently clear from these studies, each of which - despite their unprecedented size (one of them scanned more than 25,000 individuals!) - managed to capture variants explaining less than 5% of variation in height. I note that a few previously identified height genes, like HMGA2 and GDF5, pop up in more than one of the three studies, while a new gene (ZBTB38) appears as the top candidate in all three of the studies. However, there doesn't seem to be a huge amount of overlap in the lower-ranked genes (although I need to read the articles more carefully to be sure). ScienceDaily puts a positive spin on the story ("Scientists are beginning to develop a clearer picture of what makes some people stand head and shoulders above the rest"), but the real story is this: despite the massive scale of these studies, they're still only capturing less than 5% of the total variance in a trait that is almost entirely (~80%) genetic. This is a powerful demonstration of the inability of current GWAS technology to access the genetic variants responsible for the vast majority of heritable variation in at least some complex traits, for reasons I've discussed recently. Researchers interested in the genetics of common diseases are no doubt experiencing a sinking feeling as they read these studies, since there's every reason to expect that what holds true for height will also apply in at least some of these conditions. If so, the number of patients required to characterise even a trivial proportion of the total genetic risk using GWAS will be astronomical. However, there is a light at the end of the tunnel: large-scale sequencing, once it drops in price, will provide researchers with access to the rare variants and structural variation currently missed by chip-based GWAS technologies, and should help to capture a substantial proportion of the missing variation. This leads into another Nature Genetics article, which used an interesting candidate gene resequencing strategy to detect variants linked with variation in blood pressure. Readers persistent enough to slog through yesterday's post on the genetics of bipolar disease might recall that hypertension is another disease in which the GWAS approach has yielded little success; in the comments to that post, G from Popgen ramblings notes that admixture mapping (an approach to gene identification using populations with mixed ancestry) has also failed to produce consistent signals, despite a profound difference in hypertension risk between populations. The Nature Genetics study took a different approach, sequencing the full coding regions of three genes associated with rare, serious hypertension conditions in previous family studies in more than 3,000 individuals from the Framingham Heart Study cohort. They found a scattering of rare variants - all present in a single copy in any given individual - with either inferred or biochemically verified effects on protein function. When the individuals carrying these rare mutations were analysed as a group they showed significantly lower blood pressure than non-carriers. This combination of targeted resequencing and functional analysis is a difficult road, but it's one that researchers will have to follow increasingly often as they attempt to characterise the rare variants that likely comprise a significant fraction of common disease risk. I'll have more to say about this in future posts.  Subscribe to Genetic Future. |
Gene duplications and mutations are central driving forces in the evolution of genomes. Genomes must be robust to such changes in order to be evolvable, and many studies have probed genome robustness using systematic gene knockouts or overexpression experiments. In a recent paper, 
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