The DNA Network |
| I’ve opened the friendfeed info-torrent! [Synthesis] Posted: 03 Jun 2008 06:25 PM CDT I was never much for twitter, but I finally signed up for friendfeed, because it seems like everyone’s got their twitters and blogs and bookmarking fed into there, and commenting on the friendfeed works just as well. I’ve been meaning to switch from Plaxo given their somewhat shady tactics, but I did like their activity aggregation, so I made do with simply not giving them access to my contacts. However, now that Comcast has bought them, it was time to find another service, and friendfeed looked like just the thing. It was easy to hook up my various sites to my feed(a little too easy - since they only require a username), and immediately was able to find the same crowd of people from Nature Network and SciLink, due to the handy recommendation feature. Once I subscribed to Attila and Deepak, the recommendation feature brought up Neil and Pedro and JC Bradley and the whole rest of the early-adopter lot. Hi Guys! .gif) This post is about friendfeed, Mr. Gunn, plaxo, Science 2.0, social networking, twitterRelated posts |
| Posted: 03 Jun 2008 06:08 PM CDT A little over ten years ago, Dr. Elaine Johnson obtained funding from the National Science Foundation to start Bio-Link, an Advanced Technology Education center, focused on biotechnology. Since that time, Dr. Johnson has become a national leader in biotech education, enlisting the country's top educators and industry captains to ensure that community college students receive a quality education and the best preparation possible for entering the workforce. In this radio interview from Tech Nation, Dr. Johnson talks with Dr. Moira Gunn about the easiest way to a biotech career. A Career in Biotech Tech Nation 23 minutes, 10.7mb, recorded 2008-05-21 |
| How Much Does a DNA Paternity Test Cost? [The DNA Testing Blog] Posted: 03 Jun 2008 04:42 PM CDT One of the most common questions DDC's client care team receives is regarding cost. Understandably, our clients want to be sure they are receiving a high-quality, accurate and reliable DNA test that is right for them, at a price they can afford. A standard DNA paternity test from DNA Diagnostics Center costs between $400-500. This standard [...] |
| Scholarz.net: For better research and academic writing [ScienceRoll] Posted: 03 Jun 2008 04:39 PM CDT Scholarz.net, as stated on their website, is an online-software for better research and academic writing. It offers reference management, knowledge organisation, social knowledge and research community. I’m pretty sure this video will explain it all:
You can:
It seems to be a useful tool but I have to use it for more to see whether it’s better than Connotea or 2collab. Here are some other similar sites.         |
| Will your next poster session be in Second Life? [ScienceRoll] Posted: 03 Jun 2008 04:22 PM CDT Stephen T Huang, Maged N Kamel Boulos and Robert P Dellavalle published an article in EMBO Reports about Second Life, the virtual world under the title, Scientific discourse 2.0. Will your next poster session be in Second Life? Some excerpts:
Some of my posts dedicated to the educational opportunities of Second Life:
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| Second SOLiD Publication: Stem cell transcriptome profiling [SEQanswers.com] Posted: 03 Jun 2008 11:29 AM CDT Just caught this last night. The good folks at The University of Queensland in collaboration with ABI have used SOLiD to take a close look at the transcriptome of mouse embryonic stem cells and embryoid bodies. Read more and join the community... |
| This Week’s Best of the Kit [Bitesize Bio] Posted: 03 Jun 2008 10:12 AM CDT Lazy DNA ligation, low carbon footprint bunsens and back-to-basics E.coli… they’re among our top picks of the kit (molecular/Cell bio kits, reagents, services and other stuff) for this week. A lower carbon footprint alternative to bunsens. A bare bones competent E.coli strain
If you have a favorite piece of equipment, kit, service (or anything else) that you’d like us to include in our pick of the kit, let us know. |
| Journals, shmournals [genomeboy.com] Posted: 03 Jun 2008 08:31 AM CDT “Senior scientists running labs don’t read journals; they say the younger people will tell them about anything important that gets published—if they haven’t heard about it beforehand anyway…” |
| Science Tuesday: Lies on the Motel TV [chrisdellavedova.com » Science] Posted: 03 Jun 2008 07:12 AM CDT
A paper published in the latest issue of PLoS Medicine quantifies what most of us already know - that U.S. journalists are doing a poor job of accurately reporting on science, particularly in the field of medicine. The PLoS study was carried out by Gary Schwitzer, a journalism professor at the University of Minnesota. Schwitzer established HealthNewsReview.org, a website that publishes reviews of medical new stories, two years ago based on similar sites in Australia and Canada. The study that he’s published in PLoS reports the results of two years of analysis of the mainstream media’s treatment of health news. Schwitzer’s group monitors science news by the biggest newspapers in the U.S. and watch the morning and evening news programs of the three major networks on a daily basis. (If you think you’re job sucks, imagine if you had to watch all three morning shows every single day. Good god.) The researchers then assign a rating based on how well the story covers a number of criteria.
Schwitzer’s conclusions are basically that he’s doing good work - and that is true. Take a look at his site - the “0 Star Stories” are particularly fun. Schwitzer places the bulk of the blame on the news outlets themselves rather than the journalists. He recognizes that in the era of media consolidation many newsrooms have eliminated trained science journalists. He urges the reader to check out his site for the best health care news analysis. The problem is that not very many people know about Schwitzer’s site. I frequently rant about how shabby and corrupt the mainstream media has become and am a scientist and I hadn’t heard of it. The problem is that most people still get their science news from the mainstream media and they are being misled most of the time. With the continued consolidiation of media outlets, most of whom are owned by conglomerates who also have interests in pharmaceuitical companies, it’s not outlandish to believe that this is intentional. I know that I’m preaching to the choir - if you’re reading a blog then you’ve already discovered the new media. But if you’re still getting your science news from the Today Show then the best case scenario is that you’re not getting all the facts. The worst case scenario is that you’re being lied to. Here are links to a few good “new media” alternatives: Also check out some of the sites on my “Science” blogroll. This posting includes an audio/video/photo media file: Download Now |
| Join our NGS sessions in Asia [Next Generation Sequencing] Posted: 03 Jun 2008 07:05 AM CDT Abstract With Next Generation Sequencing (NGS) technologies, High Throughput Sequencing has become accessible to a much larger group of researchers. NGS technologies therefore have the potential to transform biomedical research and eventually also health care areas such as molecular diagnostics and personalized medicine. However, High Throughput Analysis has not become commonly accessible yet, and therefore data [...] |
| DNA 11 Introduces GenePak Genome Analysis [Eye on DNA] Posted: 03 Jun 2008 04:22 AM CDT
Co-founder Nazim Ahmed:
GenePack is available for an additional $99 with any DNA portrait as an upgrade. NB: DNA 11 was recently mentioned in this Clarion-Ledger article - Getting personal: Products touting individuality appeal to the masses. |
| Henry Louis Gates, Jr. Interviews James Watson at The Root [DNA and You] Posted: 03 Jun 2008 03:37 AM CDT Kudos to my girlfriend for pointing me in the direction of this one. It's worth a look:
What do you all think? |
| TGG Interview Series IV - Alastair Greenshields [The Genetic Genealogist] Posted: 03 Jun 2008 02:00 AM CDT Today’s interview is with Alastair Greenshields, founder of the genetic genealogy testing company DNA Heritage. Alastair is also the founder of Ybase, a Y-DNA database. I recently wrote about a helpful and informative video series by Alastair for DNA newbies (see “New Videos for Genetic Genealogists“). In today’s interview, I ask Alastair about his introduction to genetic genealogy, some of the ethical issues raised by the recent launches of personal genomics companies, and about the future of genetic genealogy. TGG: How long have you been involved in genetic genealogy, and how did you become interested in the field? Have you undergone genetic genealogy testing yourself? Were you surprised with the results? Did the results help you break through any of your brick walls or solve a family mystery? You founded DNA Heritage in 2003. What led you to create the company? Can you also tell us a little bit about Ybase? Alastair Greenshields: I got started in genetic genealogy back in 2002. My mother had been researching the family line for many years and this new DNA thing looked promising in connecting lineages up, untangling them, and proving if the paper trails were correct. After so much invested in paper research it was a sensible idea to check using a different method. A company in the UK was contacted, swabs were sent out and samples sent in. Results came back but it was very hard to work out how people were related. As the scientist in the family I tried my best in interpreting them but came to the conclusion that the 10 markers that we were tested upon weren’t enough for any accurate comparison. I looked around at the current research at that time and came to the conclusion that the test could be made far more accurate. Working alongside a university research lab, I developed a 21-marker Y-chromosome STR test and brought it to market. While the test was in development, I also created Ybase which helped people compare results more easily (at the time there were only in-house databases). That first year of Ybase allowed me to get fully-acquainted with the many different types of questions genealogists wanted answered and put me in good stead when DNA Heritage was officially launched. The testing into our own family line is ongoing… Have I been tested? Many times. My own DNA is often one of the guinea-pig samples for the tests that we do. Surprised by the results? I have an open mind undertaking any test - a better word would be intrigued. It’s a source of satisfaction when customers feel the same way; and if it gets people thinking how we are all connected and part of a bigger picture then I’m happy. TGG: In light of the recent ethical issues raised by the launch of companies like 23andMe and deCODEme, have you noticed any increase in concern by either European or American customers? AG: There is of course differentiation between genetic genealogy tests and medically informative tests. Companies providing direct-to-consumer health tests have been around for some time; 23andMe and deCODEme are simply getting a lot of media focus right now. The SNP chips used have been available for a while but when you have a lowering of cost, two competitors fuelling the media interest and combine that with a big marketing push, they are naturally being widely discussed about. I think the valid concern of most ethicists is the volume of potentially medically-informative genetic data provided vs. our current understanding of what it all means along with what impact it has on the individuals concerned. And then add to this the desire of many customers to want to share this data with others. Prevention is less expensive than treatment. An environment where people are more savvy about their health is obviously desirable. But we are still in our infancy of our understanding. When a journal comes out with ground-breaking research on a link between genetics and physical condition, it is often tempered with conflicting results months later. So there has to be a balance on the interpretation of results and expectation by the customer. Companies understand this but ethicists do an essential job of pointing out the need for this balance. One harder stance is taken by the State of New York in that a doctor is required as an intermediary for their residents, even for paternity testing. This view isn't shared by other states and so maybe this is the start of the trend, but more likely that NY will relax their own regulations. Incidentally, because of the nature of our own tests, no intermediary is required. In all, the genetic cat is out of the bag and people knowing more about their genetic selves will increase dramatically in the years to come. Personalized medicine will make a big impact. It’s the medical unknown of what it all means which raises doubt. The sharing of this data raises issues also. Do you share just the conclusions that e.g. you may have a pre-disposition to Celiac Disease, or do you share the hard data for which not everything is known? On the whole, the participants are self-selecting, do their homework and are quite aware that the data may reveal other genetic information later on. It's the sub-section who aren't fully aware that need protection. And this is the crux. In genetic genealogy, the picture is much clearer. The results aren't medically informative*. The results of a Y-chromosome or mtDNA test won't even identify you as an individual. They are good for known lineages and thus, to make sense of them it works best if results are shared, particularly the Y-chromosome STR test. *There are two exceptions; very rarely a DYS464 on the Y-chromosome is not present which may indicate infertility (although never encountered by us in several years of testing), and with whole mtDNA sequencing when you venture into genes you reveal medical information. Which is why we don't perform that full sequencing test. If there are any differences between American and European customers regarding their genetic data at all it has been on privacy and the perceived threat from insurance companies and employers. In the US, there was always the overhanging question of medical genetic data being used against them. With the (impending) passing of GINA, the basis for this worry will be minimal. And again, because of the tests that we do, any issue has been negligible. TGG: What do you think the future holds for genetic genealogy? AG: Always hard but as ever, genetic genealogy will continue to be more mainstream. We’re now seeing many more professional genealogists using it alongside their library research with great results. I’m sure that one day DAR and SAR will begin to accept lineage data as acceptable evidence for inclusion. TGG: Thank you, Alastair, for a great interview! Other posts in the TGG Interview Series:
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| More Education Decreases the Risk of Death [Highlight HEALTH] Posted: 02 Jun 2008 11:14 PM CDT
The study restricted the analyses to deaths among non-Hispanic whites and blacks. It also excluded deaths that occurred in seven states (Georgia, Kentucky, New York, Oklahoma, Rhode Island, South Dakota and West Virginia) because completeness of education on death certificates in these states was less than 80% in at least one of years considered in the study. The study found that between 1993 and 2001, the ratio of the all cause death rate in people with less than 12 years versus greater than or equal to 16 years of education significantly increased in white and black men, and in white women, indicating that those with a college education or better had an increased life expectancy. Contributing to the inequality was significant reductions in mortality for the most educated men (36% in black men and 25% in white men), largely due to decreases in death rates from HIV infection, cancer and heart disease. Interestingly, the decrease in all cause death rates among men became larger with each additional increment of educational attainment (i.e. 12 years of education vs. 13 — 15 years vs. greater than or equal to 16 years). In women, this affect was only observed with greater than or equal to 16 years of education. The study results support a previous investigation of county-level mortality published last month showing a steady increase in mortality inequality across the U.S. [2]. In that study, death rates between 1983 and 1999 increased for women in a large number of counties, principally due to chronic diseases related to smoking, overweight and diabetes, and high blood pressure. Most counties that showed a worsening of life expectancy were in the deep South, along the Mississippi River and in the Appalachia, extending into the southern portion of the Midwest and into Texas. Between 1961 and 1983, counties with increased or decreased life expectancy improvements had relatively similar levels of income. However, after 1983, gain in life expectancy was positively associated with county income. Thus, those who were disadvantaged did not benefit from the increase in life expectancy experienced by the advantaged, demonstrating a large health inequality. What does all this mean? It means those with less education are getting left behind and literally dying earlier as a result. ACS chief executive officer Dr. Otis W. Brawley, M.D. said that [3]:
Last year, the American Cancer Society launched the Access to Health Care campaign, a national initiative to raise awareness about the problem of true access to health care. The website shows what is being done to help those uninsured and underinsured and how you can help. Education is a marker of socioeconomic position. Lower educational attainment and thus a poorer socioeconomic position is associated with a variety of factors that affect health, including decreased financial resources, reduced access to health insurance and health literacy. Given that one of the CDC’s strategic imperatives is “all people, and especially those at greater risk of health disparities, will achieve their optimal lifespan with the best possible quality of health in every stage of life” [4], these results are troubling and highlight the growing problem with the U.S. healthcare system. References
.gif) Thank you for subscribing by RSS or email. I work hard to make the articles on Highlight HEALTH engaging and I truly appreciate your interest and readership!This article was published on Highlight HEALTH. Related articles |
| Absence of “High Penetrance” in SNP Genomic Services [Think Gene] Posted: 02 Jun 2008 11:00 PM CDT deCODEme, 23andMe, and Navigenics all offer services that only test for “low penetrance genes,” or genes which only sometimes produce an expected trait. Why do these services not test for high penetrance genes, which do produce an expected trait? The official line is that low penetrance genes are more common and thus more relevant. From Dr. Nierenberg of Navigenics:
“We make it clear in our literature?” that’s PR-speak for “we know you’re right, our service would be much more useful if we included those tests, but we can’t, so we pretend sour grapes.” The real reason is that many of the most important tests are patented or are not identified by SNPs (like deletions or repeating sequences). However, I can’t blame a company representative for a positive spin on the product. My problem is that the PR is confusing the public about the possibility of genetic testing. By telling consumers that they’re the best, the big three SNP services imply to consumers that they are the best that genetic testing has to offer. This is not true, and it’s making the industry as a whole look flaky. The reality is that except for a few enthusiasts (like anyone in the DNA Network, including myself), existing SNP genomic services just aren’t that useful. It’s not useful to know that one has a 7% lifetime risk rather than a 5%. I need to know risks of about 40% and higher. No test offered by deCODEme, 23andMe, and Navigenics gives me this information. Even Kari Stephansson of deCODE has admitted “we are marketing these tests without any claim that they will impact on people’s lives.” Myraid Genetics, unmentioned in the press recently, has a good selection of medically relevantly genetic tests not offered in SNP services and is a good example of the potential usefulness of genetic testing today: Myraid |
| House ATG.GAC. [Omics! Omics!] Posted: 02 Jun 2008 10:30 PM CDT I don't watch a lot of network television, but there are a handful of programs that have latched onto me. At the end of this season, there were just two and by accident rather than design (or perhaps it is the current plethora of such) they are both hospital-based. Last week I viewed the last of the new episodes off my PVR – so in place of a new episode this week, I'll try to sketch out my own House M.D. is an hourlong drama focusing on Dr. Gregory House, a brilliant diagnostician who is also an extremely difficult human being. He terrorizes his three junior colleagues, who are trapped in his orbit like the inner moons of Jupiter -- and subject to similar violent (though only psychologically) tidal forces. Three previous assistants have attained somewhat more distant orbits, though one has spiraled back in. His boss & a colleague attempt to be friends, but get much grief for their efforts. As with most series TV, there is a basic formula, a framework which the writers decorate or modify each week, rarely breaking it entirely. The scheme here generally starts with a patient arriving with some strange, dramatic set of symptoms (usually exposited prior to the opening credits). House is either intrigued or blackmailed by his boss into taking the case Lots of diagnostic dead ends follow (and new symptoms appear), accompanied by exorbitant amounts of testing. House's assistants provide the union of all high tech medicine & are capable of running any diagnostic under the sun (somehow, the hospital lacks lab techs!). By the end, the case is solved -- and more often than not the patient survives (a few lose the lottery). One thing you actually DON'T see much of is DNA testing -- once in a while, but it hardly shows up as much as on a CSI/Law & Order type police procedural. DNA testing just doesn't televise well; the best you can do is show someone drawing their own blood (what, no buccal swabs?). In contrast, the MRI room has lots of fun angles -- private conversations behind the console, bouts of claustrophobia, or dramatic races to reach the suddenly stricken patient. Sequencers just aren't very dramatic. So, I'm going to suggest an episode. Perhaps this qualifies as a "treatment" in Hollywood-speak. I have no desire for a career there, but if the writers take the idea I'd hardly turn down a walk-on. A patient arrives at Princeton-Plainsboro seeking House due to a mysterious set of symptoms which has afflicted her for years. As usual with such, House is disdainful -- until the patient tries to hand him a DVD but dramatically collapses instead with some interesting symptom along the way. When the patient regains conciousness in a hospital bed, they start asking about the DVD again -- and then deliver the trump card: the DVD has her genome sequence on it. House has no great interest in the DVD, and argues how useless it is. He's patently annoyed by it. One of the assistants makes the mistake of rising to the bait and proposing that perhaps a critical clue lies within -- and thereby gets assigned the task of cross-referencing EVERY polymorphism against the patient's symptoms. Several dead ends come from the DNA data, but nothing useful -- or in reality, just too many hypotheses which are too tenuous to do anything with. That doesn't stop the young assistants from batting some around and debating the now and future utility of such scans. Now, as an aside, the story really (in my opinion) needs a complete genome scan. However, if there is a desire to garner some product placement that would narrow the candidates to one (Knome) at this stage. SNP scans are quite as dramatic! At the end, the patient's puzzle is solved & they get to proceed in life knowing what they have & able to manage it. But, the kicker is that the assistant now cross-references the now known disease against the polymorphisms and comes up with an answer -- but it was buried deep within hundreds of other equally supported hypotheses. Finish the episode with some more back-and-forth amongst the characters about how this might play out the next time. How their careers might change. How well (or not so well) their training has prepared them for this. |
| Don't Complain About The Teaching At Research Universities [adaptivecomplexity's column] Posted: 02 Jun 2008 09:55 PM CDT Over at Cosmic Variance, Sean tells us that the purpose of Harvard is not to educate people. Lately, there has been a dustup between Harvard, with its fat endowment, and various groups, including the Massachusetts state government, which think that money could be better spent elsewhere. |
| The good news in our DNA: Defects you can fix with vitamins and minerals [Think Gene] Posted: 02 Jun 2008 09:28 PM CDT As the cost of sequencing a single human genome drops rapidly, with one company predicting a price of $100 per person in five years, soon the only reason not to look at your “personal genome” will be fear of what bad news lies in your genes. University of California, Berkeley, scientists, however, have found a welcome reason to delve into your genetic heritage: to find the slight genetic flaws that can be fixed with remedies as simple as vitamin or mineral supplements. “I’m looking for the good news in the human genome,” said Jasper Rine, UC Berkeley professor of molecular and cell biology. “Headlines for the last 20 years have really been about the triumph of biomedical research in finding disease genes, which is biologically interesting, genetically important and frightening to people who get this information,” Rine said. “I became obsessed with trying to decide if there is some other class of information that will make people want to look at their genome sequence.” What Rine and colleagues found and report this week in the online early edition of the journal Proceedings of the National Academy of Sciences (PNAS) is that there are many genetic differences that make people’s enzymes less efficient than normal, and that simple supplementation with vitamins can often restore some of these deficient enzymes to full working order. First author Nicholas Marini, a UC Berkeley research scientist, noted that physicians prescribe vitamins to “cure” many rare and potentially fatal metabolic defects caused by mutations in critical enzymes. But those affected by these metabolic diseases are people with two bad copies, or alleles, of an essential enzyme. Many others may be walking around with only one bad gene, or two copies of slightly defective genes, throwing their enzyme levels off slightly and causing subtle effects that also could be eliminated with vitamin supplements. “Our studies have convinced us that there is a lot of variation in the population in these enzymes, and a lot of it affects function, and a lot of it is responsive to vitamins,” Marini said. “I wouldn’t be surprised if everybody is going to require a different optimal dose of vitamins based on their genetic makeup, based upon the kind of variance they are harboring in vitamin-dependent enzymes.” Though this initial study tested the function of human gene variants by transplanting them into yeast cells, where the function of the variants can be accurately assessed, Rine and Marini are confident the results will hold up in humans. Their research, partially supported by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army, may enable them to employ U.S. soldiers to test the theory that vitamin supplementation can tune up defective enzymes. “Our soldiers, like top athletes, operate under extreme conditions that may well be limited by their physiology,” Rine said. “We’re now working with the defense department to identify variants of enzymes that are remediable, and ultimately hope to identify troops that have these variants and test whether performance can be enhanced by appropriate supplementation.” In the PNAS paper, Rine, Marini and their colleagues report on their initial analysis of variants of a human enzyme called methylenetetrahydrofolate reductase, or MTHFR. The enzyme, which requires the B vitamin folate to work properly, plays a key role in synthesizing molecules that go into the nucleotide building blocks of DNA. Some cancer drugs, such as methotrexate, target MTHFR to shut down DNA synthesis and prevent tumor growth. Using DNA samples from 564 individuals of many races and ethnicities, colleagues at Applied Biosystems of Foster City, Calif., sequenced for each person the two alleles that code for the MTHFR enzyme. Consistent with earlier studies, they found three common variants of the enzyme, but also 11 uncommon variants, each of the latter accounting for less than one percent of the sample. They then synthesized the gene for each variant of the enzyme, and Marini, Rine and their UC Berkeley colleagues inserted these genes into separate yeast cells in order to judge the activity of each variant. Yeast use many of the same enzymes and cofactor vitamins and minerals as humans and are an excellent model for human metabolism, Rine said. The researchers found that four different mutations affected the functioning of the human enzyme in yeast. One of these mutations is well known: Nearly 30 percent of the population has one copy, and nine percent has two copies. The researchers were able to supplement the diet of the cultured yeast with folate, however, and restore full functionality to the most common variant, and to all but one of the less common variants. Since this experiment, the researchers have found 30 other variants of the MTHFR enzyme and tested about 15 of them, “and more than half interfere with the function of the enzyme, producing a hundred-fold range of enzyme activity. The majority of these can be either partially or completely restored to normal activity by adding more folate. And that is a surprise,” Rine said. Most scientists think that harmful mutations are disfavored by evolution, but Rine pointed out that this applies only to mutations that affect reproductive fitness. Mutations that affect our health in later years are not efficiently removed by evolution and may remain in our genome forever. The health effects of tuning up this enzyme in humans are unclear, he said, but folate is already known to protect against birth defects and seems to protect against heart disease and cancer. At least one defect in the MTHFR enzyme produces elevated levels in the blood of the metabolite homocysteine, which is linked to an increased risk of heart disease and stroke, conditions that typically affect people in their post-reproductive years. “In those people, supplementation of folate in the diet can reduce levels of that metabolite and reduce disease risk,” Marini said. Marini and Rine estimate that the average person has five rare mutant enzymes, and perhaps other not-so-rare variants, that could be improved with vitamin or mineral supplements. “There are over 600 human enzymes that use vitamins or minerals as cofactors, and this study reports just what we found by studying one of them,” Rine said. “What this means is that, even if the odds of an individual having a defect in one gene is low, with 600 genes, we are all likely to have some mutations that limit one or more of our enzymes.” The subtle effects of variation in enzyme activity may well account for conflicting results of some clinical trials, including the confusing data on the effect of vitamin supplements, he noted. In the future, the enzyme profile of research subjects will have to be taken into account in analyzing the outcome of clinical trials. If one considers not just vitamin-dependent enzymes but all the 30,000 human proteins in the genome, “every individual would harbor approximately 250 deleterious substitutions considering only the low-frequency variants. These numbers suggest that the aggregate incidence of low-frequency variants could have a significant physiological impact,” the researchers wrote in their paper. All the more reason to poke around in one’s genome, Rine said. “If you don’t give people a reason to become interested in their genome and to become comfortable with their personal genomic information, then the benefits of much of the biomedical research, which is indexed to particular genetic states, won’t be embraced in a time frame that most people can benefit from,” Rine said. “So, my motivation is partly scientific, partly an education project and, in some ways, a partly political project.” Marini and Rine credit Bruce Ames, a UC Berkeley professor emeritus of molecular and cell biology now on the research staff at Children’s Hospital Oakland Research Institute, with the research that motivated them to look at enzyme variation. Ames found in the 1970s that many bacteria that could not produce a specific amino acid could do so if given more vitamin B6, and in recent years he has continued exploring the link between micronutrients and health. “Looked at in one way, Bruce found that you can cure a genetic disease in bacteria by treating it with vitamins,” Rine said. Because the human genome contains about 6 billion DNA base pairs, each one subject to mutation, there could be between 3 and 6 million DNA sequence differences between any two people. Given those numbers, he reasoned that, as in bacteria, “there should be people who are genetically different in terms of the amount of vitamin needed for optimal performance of their enzymes.” This touches on what Rine considers one of the key biomedical questions today. “Now that we have the complete genome sequences of all the common model organisms, including humans, it’s obvious that the defining challenge of biology in the 21st century is not what the genes are, but what the variation in the genes does,” he said. Rine, Marini and their colleagues are continuing to study variation in the human MTHFR gene as well as other folate utilizing enzymes, particularly with respect to how defects in these enzymes may lead to birth defects. Rine also is taking advantage of the 1,500 students in his Biology 1A lab course to investigate variants of a second vitamin B6-dependent enzyme, cystathionine beta-synthase. He also is investigating how enzyme cofactors like vitamins and minerals fix defective enzymes. He suspects that supplements work by acting as chaperones to stabilize the proper folding of the enzyme, which is critical to its catalytic activity. “That is a new principle that may be applicable to drug design,” Rine said. Source: University of California - Berkeley Josh says: The chaperone idea that’s mentioned at the end is intriguing. However, doctors have been treating these types of genetic deficiencies for a while. Most of them are in the pentose phosphate pathway, with the most common being glucose-6-phosphate dehydrogenase (G6PD). A “byproduct” of the pentose phosphate pathway is NADPH, which is also used as a cofactor by methylenetetrahydrofolate reductase (MTHFR). Certainly, there are little mutations in some of our enzymes that will affect their efficiency. I’m not sure how much it will help to target these minor ones, though it definitely won’t hurt. In the meantime, I’m going to continue to just take my daily multi-vitamin. The actual paper isn’t available yet online, but hopefully will be within 24 hours of posting. I’ll update this post with the actual citation. Note: for biochemistry, wikipedia is a surprisingly thorough resource. It doesn’t have as much when it comes to specific proteins for developmental biology or some aspects of molecular biology, but the biochemistry is exceptional. |
| Gotta love an airport with dinosaurs [The Tree of Life] Posted: 02 Jun 2008 08:27 PM CDT
More airports need these |
Play
In last week’s 
Epidemiologists at the 
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