The DNA Network |
| Posted: 24 Jun 2008 07:11 PM CDT Oxford University Press has posted a conversation on their blog between Robert Paarlberg (who recently published Starved For Science) and I (co-author of Tomorrow's Table). We debate how to best ensure a safe food supply with the least amount of damage to the environment. This is a series that OUP will be publishing all week. Please check it out! |
| Hero Sighting [The Gene Sherpa: Personalized Medicine and You] Posted: 24 Jun 2008 05:08 PM CDT I met one of my heroes today. I am honored and in awe! They told me not to gloat!!! From now on I will never, ever, EVER gloat! I promise.....And I will play better with those who risked before... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| Females in families of homosexual men have higher fertility [Yann Klimentidis' Weblog] Posted: 24 Jun 2008 02:38 PM CDT Sexually Antagonistic Selection in Human Male Homosexuality Andrea Camperio Ciani, Paolo Cermelli, Giovanni Zanzotto PLoS ONE 3(6): e2282 Abstract Several lines of evidence indicate the existence of genetic factors influencing male homosexuality and bisexuality. In spite of its relatively low frequency, the stable permanence in all human populations of this apparently detrimental trait constitutes a puzzling 'Darwinian paradox'. Furthermore, several studies have pointed out relevant asymmetries in the distribution of both male homosexuality and of female fecundity in the parental lines of homosexual vs. heterosexual males. A number of hypotheses have attempted to give an evolutionary explanation for the long-standing persistence of this trait, and for its asymmetric distribution in family lines; however a satisfactory understanding of the population genetics of male homosexuality is lacking at present. We perform a systematic mathematical analysis of the propagation and equilibrium of the putative genetic factors for male homosexuality in the population, based on the selection equation for one or two diallelic loci and Bayesian statistics for pedigree investigation. We show that only the two-locus genetic model with at least one locus on the X chromosome, and in which gene expression is sexually antagonistic (increasing female fitness but decreasing male fitness), accounts for all known empirical data. Our results help clarify the basic evolutionary dynamics of male homosexuality, establishing this as a clearly ascertained sexually antagonistic human trait. |
| Genetic testing impacts life insurance policies [Microarray and bioinformatics] Posted: 24 Jun 2008 01:50 PM CDT The Association of British Insurers (ABI) has suspended the use of predictive genetic testing until the year 2014. allowing consumers to continue taking out cover without disclosing the adverse results of tests to predict a predisposition to cancer or heart disease. Does that mean they will discriminate us later Did they never heard of Genetic Information Nondiscrimination Act (GINA) the rule signed by US prsident with the intention of that will protect Americans against discrimination based on their genetic information when it comes to health insurance and employment. Stephen Haddrill, the ABI's Director General, said: "The moratorium on the use of predictive genetic test results works well for consumers. It means people can insure themselves and their families, even if they have had an adverse result from a predictive genetic test. The moratorium has proved effective since its introduction in 2001 and can now continue The moratorium was established in 2001 and covers policies worth up to £500,000 for life insurance, £300,000 for critical illness insurance and £30,000 a year for income protection insurance. The extension leaves consumers free to apply for cover up to these levels without advising an insurance company of the adverse results of any predictive genetic test they have taken. According to the ABI, around 3% of policies sold in the UK are above these limits and in these cases, insurers can request predictive genetic tests but only if the tests are approved by an independent Government committee. So far, the only test that has been approved in this way is for Huntington's disease, for life cover over £500,000.The ABI has updated its consumer guide "Insurance and genetics: what you need to know", which can be downloaded from its website. It will commence the next review of the moratorium in 2011         |
| Posted: 24 Jun 2008 01:45 PM CDT In my blog I give out some snarky awards for things that annoy me including the Genomics by Press Release Award and the Adaptationomics Award and the Overselling Genomics Award. Sometimes I really want to give something an award but I am not sure what it should get. That is the case here. There is what I find to be a painful press release on "Selfish Genes" in honeybees put out by University of Western Ontario. This press release relates to a paper being published in Genetics. on QTL mapping in honeybees and searching for alleles/genes that suppress the reproductive activity in worker bees. This suppression is a form of altruistic behavior in a way and has been the subject of a good deal of research. Basically, the ended up mapping some of the suppression to a few regions of the genome. The press release however, goes way way overboard in interpreting their results and claiming "New Discovery Proves 'Selfish Gene' Exists." They imply throughout the press release that prior work simply suggested that selfish genes were theoretically possible in this case and that now with their results they have been proven. For example they quote the lead author Graham Thompson: This means that the 'selfish' gene does exist, not just in theory but in reality.This is way beyond an overstatement. Their results are nice and interesting but they are part of a continuum of work on bees (and other selfish systems) and do not in any obvious way suddenly prove the existence of this selfish gene compared to prior work that they imply was just guesswork. I am personally baffled by the extent of this claim -- basically ignoring work by many others as well as work in a variety of systems outside of bees. They end the press release with the following: "This basically provides a validation for a huge body of socio-biology," says Thompson, who adds the completion of Honey Bee Genome Project in 2006 was crucial to this discovery.For that last statement, I am thus giving them my "Overselling genomics award" #4. But they easily could have gotten a few others. Hat tip to T. Ryan Gregory for pointing this out. And you should check out his new Genomics by press release "award" at his blog Genomicron. I will probably be writing about the same story soon. |
| Thompson Scientific has a closed science search engine. [Synthesis] Posted: 24 Jun 2008 01:35 PM CDT They sent me a survey and asked me some simple questions, but I don’t think they asked me the right ones, so I’m going to give a free-form review here. I think it’s a great idea, and presents some features not available anywhere else, but it’s missing some important content, and like everything Thompson does, it suffers from some useability issues. The search engine is called Thompson Scientific WebPlus, and you can only access it through their Web of Knowledge service, which they should really link to from the page telling you so. It’s also closed in the sense of being a somewhat curated list, with Thompson-selected authoritative sources ranked highest, but to their credit they do have a “suggest a site” button. If you can get to it, it’s actually a pretty standard Google-like interface, but with Tabs for Topic, Author/Person, Organism, Drug, and Gene, instead of the normal Web, Images, Maps, News tabs at google.com. The search results returned are then presented as normal search results, with separate tabs for only News articles, Blog posts, or Repository links. I really like the idea of institutional repositories having their own tab, so you can search for a gene and get only links pointing to pages in a repository. I also like the idea of blogs having their own tab, so you can see what people are talking about, and having the News on a separate tab helps you scan for press releases and see how (badly) science is covered in major media. Once you’ve executed the search, you can narrow it by TLD, to pick out only results from .com, .org, .net, etc. I tried a sample search that I’m familiar with in each one, just to see how this would work in practice. A topic search for “multiple myeloma” has multiplemyeloma.org and myeloma.org at the top of the list, as with a standard Google search for the same. The notable difference is that wikipedia is dead last in the WebPlus results. News and Blog tabs are present, but no repository tab is available. A Person/Author search for “William Gunn” looks much like it does on regular Google, again with Wikipedia being conspicuously absent. I’m pleased to see that my blog is the first in the results, as it should be for my name, and other results from the same domain are grouped. There’s even a link, which is dead, to my Nature Precedings account on the repository tab. Where things get strange are on the blog tab. They only list my other, infrequently updated, nonscience blogs, including a link to a development site on which I had a robots.txt containing An organism search for “mus musculus” gives results similar to standard Google’s results, again trashing wikipedia, but it’s the repository tab fails this time, not including links to Jackson’s MPD or MGI, though they are in the regular web results. A drug search for Velcade works like the organism search, presenting some good links up front and strangely lacking a repository tab. The blog tab works more or less as expected. A gene search for DKK1 works similarly as well. If there’s anywhere I would have expected a repository tab, it would be here, but no such luck. However, this is where the blog tab really comes in handy, allowing you to see who’s talking about your favorite gene. Given the incompleteness of the results in the blog tab, I’m concerned about coverage here, but they do have scientificblogging.org, scienceblogs.com, blogs.nature.com, and even friendfeed, as well as some really weird french splog results. So let’s summarize: Overall, it’s a strong first effort, and I expect the results to improve as they tweak things. I do think it’s a mistake to all but exclude wikipedia from results. For all it’s flaws, wikipedia still does a decent job on most things, and usually provides authoritative links for further reading. As I was finishing the survey about the service, they asked some questions about ResearcherID.com and about something that seemed to be referring to a search portal. I wouldn’t be surprised in the slightest if someone at Thompson thinks a 90’s Yahoo style search portal would be a good idea, but search isn’t about being a portal anymore. It’s about helping people find the best information from the millions of results for any given term. I would not like to see an igoogle or yahoo search portal, but rather a open search that widely syndicates results so existing filtering systems such as social networks can help promote the more relevant results. Other improvements I’d like to see: and, of course … .gif) This post is about ISI, publishing, search, Thompson, WebPlusRelated posts |
| Helicos will test single molecule sequencing in cancer model system [Next Generation Sequencing] Posted: 24 Jun 2008 01:26 PM CDT Helicos Biosciences have announced a partnership with the Children’s Oncology Group (COG) where Helicos will use their NGS platform to experimentally characterize different tissue types from patients with Ewing’s sarcoma, a rare cancer. In their press release they state that: These samples include a normal bone marrow sample and tumor cell lines derived from a Ewing’s sarcoma [...] |
| Deadline for Personal Genomics Companies [Microarray and bioinformatics] Posted: 24 Jun 2008 01:24 PM CDT State of New York has issues warning against Personal genomics companies , after they have received many complaints. Now the State of California Department of Helath (CDPH) is trying to keep consumer genetic testing companies from offering their services to the state's residents and last week sent letters to 13 firms saying they are violating state law. The companies have time till today June 24 to respond to the notice. While New York State warned several companies that genome tests could not be performed on samples from New York residents without formal state approval. CDPH requirements mandate that
The 3rd part of the requirements mean the end of DIY genetic testing and more headches for companies in coming weeks. Google-backed 23andMe and Navigenics are also included in the list of companies that received the notice The major companies, including 23andMe, Navigenics, and Decode Genetics have issued statements confirming that theya re using CLIA registered laboraotries for the testing DNA genotyping. 23andMe partners with Illumina, while Navigenics collaborates with Affymetrix. Steven Murphy compared these companies to napster check out his blog post1 post2 on this subjetcs. He is certainly not likely to be excited to learn that 23andMe has launched a wiki page called 23andWe to recruit its customers to participate in studies trying to shed additional light on genetic predispositions for certain diseases and adverse drug reactions. 23andMe has maintained that it is not selling a medical service but rather giving people access to their genetic information. They company prefers to call its 23andWe study participants "customers" and not "patients," . Smart move but lets see if CDPH is going to buy that argument. But today 23andMe shot back to CDPH that they’ll be doing neither cease nor desist. We believe we are in compliance with California law and are continuing to operate in California at this time,” the company said in a statement released to Wired.com The company has has argued that the testing they provide isn’t a prevention aid, but merely offers “individuals contextual information about their genetic makeup, including ancestry and applicable scientific research.”         |
| Who needs Dr. 90210? [Mary Meets Dolly] Posted: 24 Jun 2008 12:15 PM CDT According to this article from LiveScience, stem cells, your own stem cells, could replace plastic surgery:
Sorry, went on a tangent there. Let us get back to the article: While these applications are still a ways out, plastic surgeons in Europe and Asia are already using stem cells to get better results for their patients. To do this, they're harvesting stem cells from an unlikely place — human fat. Wait," all you need is liposuction?" No eggs, no embryos, no cloning? It seems as though our friends in "Europe and Asia" are a bit quicker on the uptake than we are. We are still too busy arguing over whether or not a human embryo is actually human life and whether therapeutic cloning is actually cloning. |
| Why do people believe scientists about evolution? [T Ryan Gregory's column] Posted: 24 Jun 2008 12:07 PM CDT Apparently Gordy Slack, author of a book o |
| 23andMe in Second Life: LIVE [ScienceRoll] Posted: 24 Jun 2008 11:34 AM CDT 23andMe, one of the (if not the) most famous companies focusing on personalized genetics, presented a slideshow today in Second Life in the latest session of the Scifoo Lives On series. The speakers were Erin Davis (science writer) and Joyce Tung (human geneticist). The title was 23andMe and 23andWe. Details here.
Live coverage starts (Pacific Time):
Welcome on Second Nature island! Today’s Scifoo lives on session will feature 23andMe, a privately held biotech company focusing on personalized genetics. Two members of their editorial board will present a slideshow about their service, research and the future plans. Please welcome Erin Cline Davis, Ph.D. (SL: Luttibelle Eames ) who received her Ph.D. in Molecular and Cellular Physiology at the Stanford University School of Medicine. and Joyce Tung, Ph.D., Human Geneticist (SL: Joyce Footman ) who pursued a Ph.D. in Genetics at the University of California, San Francisco. Please feel free to ask them questions after the presentation. Thank you!
Live coverage ends…         |
| It’s my duck in a box! [genomeboy.com] Posted: 24 Jun 2008 10:55 AM CDT I have tried to keep my big fat pie-hole shut about the ongoing battle over regulation of personal genomics companies and instead ply you all (my seven readers!) with genomic fluff because 1) I selfishly want to save a lot of the corporate personal genomics stuff for my book; 2) plenty of other folks have weighed in; and 3) I keep waiting for the curtain to fall on this theater of the absurd. Apparently the latter is not going to happen anytime soon:
Hoo wee! Really fills one with confidence, don’t it? I only wish I’d stuck around Beyond Genome long enough to see the show. |
| Posted: 24 Jun 2008 09:55 AM CDT  Penguins are a recognizable bird and a symbol of cold temperatures and frigid climates. However, penguins aren't restricted to Antarctica, nor even cold climes. The African (or Black-footed) Penguin is classified as 'vulnerable' on the endangered species list and can be found on the south-western African coast (South Africa and Namibia). In this region, the average summer daytime temperatures range from 20-34oC, but in the winter temperatures can drop below freezing at night.Closely related to the African Penguin is the endangered Galapagos Penguin. This equatorial penguin is native to the Galapagos Islands, and is the only penguin species to cross into the Northern Hemisphere. The temperature on the islands ranges from 15-30oC year-round. Maybe it's time to rethink our 'do not freeze' labels.  |
| Is it crazy to consider community curation? [Discovering Biology in a Digital World] Posted: 24 Jun 2008 09:37 AM CDT or is it just an idea that's ahead of the curve? Read the rest of this post... | Read the comments on this post... |
| Industry Watching: Pharma and open data [business|bytes|genes|molecules] Posted: 24 Jun 2008 08:48 AM CDT GTO points to the announcement by GSK that it is making molecular profiling data from a number of cancer cell lines available via NCI’s caBIG. IMO, this is another example of pharma making data that on its own is not a competitive advantage available freely. In the next few years you will see pharma sponsored GWAS studies, molecular profiling data and safety markers being made available in some form of another. Hopefully not only will the data be made available, but it will be done in the public domain, so that others can take advantage of it, both for better science and for commercial purposes. There is only so much a single company can do or even look into. Technorati Tags: GSK, caBIG, Open Data, Molecular Profiling  |
| The market for personal genetic testing [Genetic Future] Posted: 24 Jun 2008 08:48 AM CDT Helix Health's Steve Murphy argues, on the basis of a recent poll of 550 "upscale business professionals": Only [those who respond that they are "very likely"to get a genetic test for disease risk "in the next few years"] will get the test [...] So, I remain certain, the market for these tests is 5%Right now, public awareness of direct-to-consumer genetic testing is pretty minimal. That's changing fast, though: anyone tracking Google news alerts will have seen the recent spikes in mainstream media coverage of the genetic testing industry, particularly 23andMe. As people hear more and more about genetic testing it will cease being scary and new, and (like IVF or screening for Down syndrome) become familiar and legitimised. Meanwhile, over the next five years two things will happen: (1) the massive decrease in the cost of sequencing will bring large-scale genetic analysis within the grasp of the average upper middle-class consumer; and (2) our understanding of the genetics of common disease will increase exponentially, rapidly increasing the clinical (and recreational) value of genome sequence data. Thus the cost-to-benefit ratio of personal genomics will shrink incredibly quickly,even as frequent media coverage creates wider familiarity with the concepts and jargon of genetic testing, and simultaneously a host of influential early adopters publicly discusses their genetic testing experiences. Basically, the medical and social benefits of having your genome sequenced will make this option steadily more attractive while declining costs will make it steadily more affordable. That's a recipe for a market explosion. So, let's grant Steve's argument that the true size of the market right now is 5% of "upscale business professionals". That's going to be a pretty damn healthy market once Oprah starts talking about how 23andMe changed her life and the guy two cubicles down from you is bragging about his new genome sequence. Steve isn't getting this, though, I suspect because he keeps seeing it through his clinician prism. For instance, he claims: It is just like a referral to see another doctor.....if you aren't feeling ill, only the very likely will ever go see that specialist.....It is called the attrition rate and is commonly understood in medical care......only 20% of your "presymptomatic ill" ever go see the referral.That's because standard medical testing is so incredibly boring. Genome scans and sequences, on the other hand, are cool. They're based on fancy new technology; you've read about them in Wired; and they tell you interesting things about yourself. People will want to take these tests. And, if the medical establishment gets its act together and starts proving that clinicians can actually value-add to genetic health data (rather than pissing potential clients off with regressive regulations), people will want to take their test results to their doctor to put them in a broader health context. That's win-win - but only if doctors do things the right way.  Subscribe to Genetic Future. |
| Things I do not care for: science press releases. [T Ryan Gregory's column] Posted: 24 Jun 2008 07:13 AM CDT Many scientists are frustrated by the way scientific studies are reported in the media. |
| 23andMe in Second Life: Today! [ScienceRoll] Posted: 24 Jun 2008 06:45 AM CDT Just a quick reminder. 23andMe, one of the (if not the) most famous companies focusing on personalized genetics, will present a slideshow in Second Life in the next session of the Scifoo Lives On series.
If you would like to participate, here is the teleport link and some details as well. I already set the poster up:
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| Napster of Medicine [Think Gene] Posted: 24 Jun 2008 04:13 AM CDT This decade, genomic health care is for people with thousands of dollars of disposable income. Let’s not mince words: experimental health care is for the rich. But genomics is an information technology, and information technologies scale. A sequenced genome is a mere CD’s worth of data — data that can be freely transferred over the internet. No doctors or insurance middle-men required. Outrageous? An album of music is also a mere CD’s worth of data. Remember Napster? The music industry does. But will there be a Napster of medicine? Indie medicine is quackery, not creativity, and sticking it to the man in a medical context seems… unwise. It’s not only coming, it’s here. We’re in the hobby kit stage of personal genomics now, and you can do your own crude genomic test if you buy a $1000 SNP array from a company like 23andMe. I’ve done one myself (here’s how). Like the first personal computers, for some time, personal genomics will seem erudite and absurd — until it’s not. Let’s pretend that I’m building the Napster of medicine. If I want to compile my own genomic database from public information and run tests on genome sequences submitted over the Internet, who’s going to stop me? Nobody. Data is data, and having an MD or PhD doesn’t magically make a computer run better [1]. SNPedia is a start, but I can scrape patents, public research, and services like 23andMe, too. And if I wanted to run my own genetic tests, what would I need?
Will patent lawyers or legislative orders deter some self-righteous geek running, say, illegal at-cost BRCA tests? Here’s how successful the music industry has been prosecuting music sharing sites. And here’s a question, one that I’d like to pose to a patient advocate like Jessica Queller. If I could save a life from breast cancer with an illegal but perfectly valid free genetic test that was otherwise unobtainable, am I morally obligated to run that test? It’s still too expensive for amateurs to sequence entire genomes or run SNP chip tests, but like mainframe computers, that technology is rapidly approaching, and single gene tests are already achievable. Genetic testing isn’t magic, and it will be everywhere. I’m not advocating some trainspotter anarchist genomic revolution, I’m being realistic. The best way to get this technology to doctors to help patients is to help nurture responsible startups like 23andMe and Helix Health, not crush them under legislation and certification. The law only hurts those with something to lose, and draconian enforcement will spawn a digital black market, setting back the genomic industry ten years, if not forever. The entertainment industry is STILL paying for its Napster mistake, because despite services like iTunes, people have tasted the forbidden fruit of free, infinite media. Today, users are deeply reluctant to pay for any media on the Internet. They’ll be deeply reluctant to trust or pay for genomic medicine, too, if you nuke the market and leave the cockroaches to rule. Medical Industry: don’t piss off computer nerds. You don’t want to fight vaporous, smart people whose religion, hobby, and self-appointed career is to destroy you… especially if they can get venture capital to do it. [1] Unless you’re Navigenics. Their doctors make computers run 250% better. |
| Burrill Report....deCoded [The Gene Sherpa: Personalized Medicine and You] Posted: 24 Jun 2008 04:00 AM CDT Consumers are worried about developing genetic based diseases, but remain reluctant to use genetic tests that will provide early warning signs. That is the lead statement in the executive... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| Voices of the Infertile in the NY Times [DNA and You] Posted: 24 Jun 2008 03:08 AM CDT Infertility, which in some cases can have a genetic cause, is a challenging obstacle for many couples. A recent article by Karen Barrow, in the NY Times, focuses on the challenges faced by couples unable to conceive. An interactive feature associated with the article features the voices of several of women interviewed. |
| New paradigm for cell-specific gene delivery [Think Gene] Posted: 24 Jun 2008 03:06 AM CDT Researchers from Northwestern University and Texas A & M University have discovered a new way to limit gene transfer and expression to specific tissues in animals. In studies to determine how plasmids enter the nuclei of non-dividing cells, the group previously identified a region of a smooth muscle cell-specific promoter that was able to mediate nuclear targeting of any plasmid carrying this sequence uniquely in cultured smooth muscle cells but in no other cell type. In their current study to appear in the July 08 issue of Experimental Biology and Medicine, the team, led by Drs. David Dean and Jennifer Young from the Department of Medicine at Northwestern University, in collaboration with Warren Zimmer from Texas A & M University, now demonstrate that such restriction of nuclear entry using this specific DNA sequence can be used in blood vessels of living animals to direct gene transfer and expression specifically to smooth muscle cells. They have also developed a novel gene delivery approach for the vasculature that uses an electric field to transiently permeabilize the plasma membrane of cells to allow entry of DNA. Thus, this work establishes the control of nuclear entry of gene therapy vectors as a novel approach to target genes and gene expression to desired cell types in the body. Vascular smooth muscle proliferative diseases, including atherosclerosis and restenosis, are among the leading causes of morbidity and mortality in the US. Gene therapy may represent an important alternative for the treatment and prevention of these proliferative diseases of the vasculature. It can be highly cell-specific, mimic or restore normal in vivo function, and can be permanent or transient depending on vector design. Currently, a number of gene delivery systems for use on the arterial wall are being studied, but as yet their low efficiency in gene transfer and lack of cell-specific targeting and expression are major limitations. According to Dr. David Dean, “The benefit of our newly described approach is that it can target specific cell types. One of the most commonly envisioned treatments for these proliferative disorders is to deliver genes that kill or inhibit the dividing smooth muscle cells, but we need to target only these muscle cells and not any other cell in the vessel wall and this approach will enable us to do just that”. The goal of the team is to design more effective gene therapy vectors for use in the vasculature by understanding the molecular mechanisms by which DNA and DNA-protein complexes are actively transported into the nucleus. Dr. Warren Zimmer states “these results set the stage for our future use of this technology to deliver therapeutic genes to lessen the severity of restenosis which is the most common issue following angioplasty and placement of stents”. Dr. Dean continues, “Now that we have demonstrated proof of principle for this approach we can look for DNA sequences that act in other tissues and develop cell-specific treatments for any number of organs”. Dr. Steven R. Goodman, Editor-in-Chief of Experimental Biology and Medicine, stated “The exciting studies reported here are the first to demonstrate that non-viral gene delivery can be made cell-specific by controlling the nuclear entry of plasmid DNA, and as such, establishes a new paradigm for cell-selective gene delivery. Drs. Dean, Young, and Zimmer are to be congratulated on this ground-breaking study”. Source: Society for Experimental Biology and Medicine Josh says: Gene therapy will finally become a reality once we can have a safe, specific delivery system. Specificity can sometimes be achieved with certain viruses as vectors, but this has the tendency to sometimes cause cancer. I’m not sure if this method has the same risks with cancer development, but I would guess if it did, the liklihood is significantly reduced. |
| Drug reverses mental retardation caused by genetic disorder [Think Gene] Posted: 24 Jun 2008 03:01 AM CDT UCLA researchers discovered that an FDA-approved drug reverses the brain dysfunction inflicted by a genetic disease called tuberous sclerosis complex (TSC). Because half of TSC patients also suffer from autism, the findings offer new hope for addressing learning disorders due to autism. Nature Medicine publishes the findings in its online June 22 edition. Using a mouse model for TSC, the scientists tested rapamycin, a drug approved by the FDA to fight tissue rejection following organ transplants. Rapamycin is well-known for targeting an enzyme involved in making proteins needed for memory. The UCLA team chose it because the same enzyme is also regulated by TSC proteins. “This is the first study to demonstrate that the drug rapamycin can repair learning deficits related to a genetic mutation that causes autism in humans. The same mutation in animals produces learning disorders, which we were able to eliminate in adult mice,” explained principal investigator Dr. Alcino Silva, professor of neurobiology and psychiatry at the David Geffen School of Medicine at UCLA. “Our work and other recent studies suggest that some forms of mental retardation can be reversed, even in the adult brain.” “These findings challenge the theory that abnormal brain development is to blame for mental impairment in tuberous sclerosis,” added first author Dan Ehninger, postgraduate researcher in neurobiology. “Our research shows that the disease’s learning problems are caused by reversible changes in brain function — not by permanent damage to the developing brain.” TSC is a devastating genetic disorder that disrupts how the brain works, often causing severe mental retardation. Even in mild cases, learning disabilities and short-term memory probrapamycinlems are common. Half of all TSC patients also suffer from autism and epilepsy. The disorder strikes one in 6,000 people, making it twice as common as Huntington’s or Lou Gehrig’s disease. Silva and Ehninger studied mice bred with TSC and verified that the animals suffered from the same severe learning difficulties as human patients. Next, the UCLA team traced the source of the learning problems to biochemical changes sparking abnormal function of the hippocampus, a brain structure that plays a key role in memory. “Memory is as much about discarding trivial details as it is about storing useful information,” said Silva, a member of the UCLA Department of Psychology and UCLA Brain Research Institute. “Our findings suggest that mice with the mutation cannot distinguish between important and unimportant data. We suspect that their brains are filled with meaningless noise that interferes with learning.” “After only three days of treatment, the TSC mice learned as quickly as the healthy mice,” said Ehninger. “The rapamycin corrected the biochemistry, reversed the learning deficits and restored normal hippocampal function, allowing the mice’s brains to store memories properly.” In January, Silva presented his study at the National Institute of Neurological Disorders and Stroke meeting, where he was approached by Dr. Petrus de Vries, who studies TSC patients and leads rapamycin clinical trials at the University of Cambridge. After discussing their respective findings, the two researchers began collaborating on a clinical trial currently taking place at Cambridge to examine whether rapamycin can restore short-term memory in TSC patients. “The United States spends roughly $90 billion a year on remedial programs to address learning disorders,” noted Silva. “Our research offers hope to patients affected by tuberous sclerosis and to their families. The new findings suggest that rapamycin could provide therapeutic value in treating similar symptoms in people affected by the disorder.”‘ Source: University of California - Los Angeles Josh says: While it enables the mice to learn, I think the article is a bit misleading by implying that if someone started taking this drug they would suddenly be fine. The brain is very adaptive, so deficiencies in this pathway would cause the brain to develop abnormally. While memory functions normally on the drug, it won’t be as though the person was fine all along, since the brain would have developed differently. |
| Rett Syndrome on Fox Show: "So You Think You Can Dance" [DNA and You] Posted: 24 Jun 2008 02:50 AM CDT Tara Parker-Pope of the NY Times writes about an episode of the Fox reality show, "So You Think You Can Dance," in which Rett syndrome was featured. For more on Rett Syndrome: Rett Syndrome (MECP2-Related Disorders) GeneReview |
| 23andMe hosts first customer party! [Think Gene] Posted: 24 Jun 2008 02:16 AM CDT At last! My pleas for expensive social validation has been noted!
Yet, God must frown on my genomic shanagans because I will be visiting my family this week back east and I’ll be unable to attend. I tried to tell my mother: “Mom, I have to go to this company party! It’s for genomics, you know, DNA. It’s really cool. There will be light refreshments!” but I think she just rolled her eyes and asked me if I had a girlfriend. |
| Calculate your Fudge Ratio, Manage Lab Time Better [Bitesize Bio] Posted: 24 Jun 2008 12:54 AM CDT Efficient time management is essential if you are to get the most out of your time in the lab. Breaking down projects into individual tasks and planning out when to do them is relatively easy. But the thing I find most difficult is accurately estimating the amount of time to allocate for each task. I tend to be ridiculously optimistic with my estimates, so experiments and other tasks always take longer than I expect, resulting in a mad rush to get things finished at the end of the day. But (as is often the case) Steve Pavlina has the solution. According to Steve, the proportion by which you over/underestimate the amount of time you will take to complete any task is fairly constant. He calls it your “Fudge Ratio”. He suggests that you note down your expected and actual time taken to complete the tasks on your “to do” list for a couple of days. From this you can calculate your fudge ratio (e.g. expected time=2hr, actual time=3hr, fudge ratio=(3/2)=1.5). You can then use your fudge ratio to improve the accuracy of your future time estimates for a task by just taking your instinctive estimate and multiplying it by your fudge ratio. This is a remarkably simple and accurate approach. I tried it and found that my fudge factor is consistently somewhere between 1.8 and 2.0, which is pretty poor really and definitely explains the un-ticked boxes on my task list. So now armed with my fudge ratio I go forward with renewed confidence in my ability to finish my work by the end of the day. Steve’s original post, which contains other useful tips on making time estimates, can be found here. |
| Taking action [business|bytes|genes|molecules] Posted: 24 Jun 2008 12:45 AM CDT The other day I was playing around with the Operator Toolbar in Firefox (for those who don’t use that, or for that matter Blue Organizer should give them a shot). The preferences allow you to look at information in two ways This first screenshot shows actions
The second shows the data type
This reminded me of some thoughts I had when I was a young product manager. Do your users care about the data type, or do they care about the actions they can take on the data returned to them? It quickly became clear that they care about the actions, at least the bulk of customers do. So when we build software for scientists, we should think about what they would do with the returned information. That’s where context is really important as well. I’ve seen too many examples where the user is offered options that make no sense for what you want to achieve. Of course, this is not an easy problem to solve. One approach is the 37Signals approach. Just implement functionality that you believe address the problems of a certain percentage of your user base. Unfortunately, in the scientific realm, where people are always looking to explore, do things just a little bit differently. The challenge becomes recognizing the core set of actions that your target users share, and the scenarios that are the most common. Then you have to make a decision. Do you want to target a set of users who are happy being given tools that fill most of their basic needs and are easy to use, or do you want to add a layer of flexibility that empowers power users at the cost of some of a broader user base. Unfortunately, too many software providers try to make both groups happy with the same piece of software, which rarely works. That is one place where workflow engines shine. The best part here, is that a small group of power users/developers can implement methods that can then be accessed by a broader group of users who would not have to worry about implementation details but about performing actions that fit their goals and needs. The ability to distribute these workflows as web apps available on an intranet makes them very effective for certain applications. Software as a service is still not too common in the life science, at least not in the Web 2 sense of the word (companies like NextBio are exceptions). It will be interesting to see how SaaS-based offerings change the thinking around how scientific software is made available. Will there be APIs that allow people to modify or repurpose the services and integrate them into various workflows? What kinds of actions will people take on the information being provided? What kinds of information will people want to take actions on? Further reading  |
| Eating is Bad For the Environment [Bayblab] Posted: 23 Jun 2008 10:33 PM CDT I was just patrolling TheGoogle for statistics on some official Bayblab-sanctioned research when I came across an interesting stat cited in a CNN article. As Rob recently pointed out in his comments to a previous post, industrial food production relies heavily on energy input from fossil fuels; this number kind of puts things in perspective: production of a 2kg box of cereal requires the equivalent 1.9L of gasoline. That's probably what one person would easily eat in a week, and according to my calculations it's equivalent to the gasoline needed to drive a 2008 Honda civic 33km or so on the highway. On one hand, this doesn't seem like a lot - at least it's fairly insignificant compared to what the average North American puts into her car. The average commuter might reasonably burn 10 times as much gasoline than this in her car each week. On the other hand, when you think about how much heavier and therefore harder to move cars are than people, 33km is looking pretty good. It's clear that cars are making much better use of fossil fuels than humans are. So maybe we should stop "eating" fossil fuel energy and just feed it to our cars and other machines. That would make living difficult though, wouldn't it? And besides, aren't the machines just there to make life better/easier for us in the first place? (Follow-up Bayblab bonus homework: With the manufacturing processes in use right now, how much ethanol fuel can you get out of the grain in a box of 2kg cereal? How far could you drive that 2008 Honda civic on this ethanol? How much additional fossil fuel input is needed to convert the cereal grain into ethanol? How far could you drive a Honda civic on that extra fossil fuel?) |
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