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| Guide to translating scientific papers into plain English. [T Ryan Gregory's column] Posted: 28 Apr 2008 08:25 PM CDT Believe it or not, scientists do not always take themselves too seriously. We can laugh at ourselves and the sometimes rigid conventions of our profession. Take, for example, this guide to translating the formal language of scientific articles into plain English. |
| The genetic basis of height [Yann Klimentidis' Weblog] Posted: 28 Apr 2008 08:22 PM CDT  Nature Genetics has a commentary piece and three research papers looking at genetic variants associated with variation in height. First of all, from the commentary piece, we learn that height has a heritability of 0.8, so 80% of variation in height is due to variation in genetics.The three studies look at hundreds of thousands of SNPs among a total of 63,000 people. Surprisingly they find little overlap in terms of variants that are associated with height in all three studies (variants in only three genes across all three studies, and 7 genes in 2 out of three studies), perhaps due to statistical issues having to do with testing so many variants at once. They find a total of 54 variants that are associated with variation in height, all of them with small effects. They find no differences between males and females, and no evidence of interaction between alleles. Throughout this article, the author breaks down the costs and benefits of the various approaches of getting at genotype-phenotype relationships, and discusses some of the other major hurdles in the process. |
| i am tired of this CRAP!!! [the skeptical alchemist] Posted: 28 Apr 2008 06:22 PM CDT I do not understand why most of the science research news that can be found in some major mainstream broadcasters' websites are absolute crap. In a world where people are working on endogenous retroviruses, artificial life, stem cell research, and trying to assess and conserve biodiversity...all they are able to come up with in their breaking news is something related to the magical properties of tomato paste. Maybe I am exaggerating, and I am sure that the study done on the...effects of 5 spoonful of tomato paste and olive oil given out to participants might be groundbreaking. Maybe, regardless of the fact that I am quite skeptical about whether testing tomato paste is a good use for research money (which is hard to come by these days), the science behind the study presented at the annual meeting of the British Society for Investigative Dermatology is sound and valid. But I still cannot see how this deserves a prime spot in the BBC Health section. Here is the summary of the report. Pizza and spaghetti bolognese could become new tools in the fight against sunburn and wrinkles, a study suggests. A team found adding five tablespoons of tomato paste to the daily diet of 10 volunteers improved the skin's ability to protect against harmful UV rays. Damage from these rays can lead to premature ageing and even skin cancer. The study, presented at the British Society for Investigative Dermatology, suggested the antioxidant lycopene was behind the apparent benefit. That's right. Forget the considerable amount of cholesterol that you can possibly find in pizza and spaghetti alla bolognese - go ahead and chug it down, because it might even make your skin look better! Anti-ageing paste? Nice. I think I just got a new business idea - injecting tomato paste extracts, you know, for cosmetic purposes. I will call it the ForeverRipe(c) treatment, all rights reserved. Not joking, I am dead serious. I am tired of Nisbet and Mooney and the other SciBlings arguing. Can somebody please do us a favor, and start writing a few decent articles for main broadcasters, send them out, and get hired part-time? Somebody who possibly knows better than to write about tomato paste, when we are in a time of fabulous advances in system biology, proteomics, synthetic biology, genomics, stem cell and regenerative research? Please? View blog reactions |
| ERV finally makes the big move. [T Ryan Gregory's column] Posted: 28 Apr 2008 05:07 PM CDT There was a disturbance in the force of the blogosphere earlier when it appeared that ERV was no longer accessible . But you know what they say, if you strike her down she will become more powerful than you can possibly imagine. It certainly took long enough for Seed to call her up to the big show. The new and improved ERV is now live so go on over and wish her a happy housewarming. |
| Biobanks for Breakfast [PredictER Blog] Posted: 28 Apr 2008 03:39 PM CDT On April 25, 2008, a collection of community leaders, top medical researchers, and statewide biotech industry leaders met to discuss the bioethical and legal issues surrounding biobanks in Indiana. Biobanks are a growing resource in biotech research. They contain samples of human biological specimens and are often linked in varying degrees to the personal health and demographic information of the donor. Biobanks range from the very small disease specific collections of tissue to the very large national sponsored banks of several million specimens incorporating several different types of biological material from persons both healthy and with known disease. Ownership and commercial involvement are among the most difficult ethical issues in developing successful biobanks. The Bioethics for Breakfast group considered these issues along with Indiana's role in future biobanking by asking attendees to think about the following questions: - Are you willing to donate your DNA to a biobank for medical research? - Are you comfortable allowing Indiana companies to profit by developing commercial products from your samples and donations? Guest speakers at the event included: David Flockhart, M.D., Ph.D. , Chief of the Division of Clinical Pharmacology at the Indiana University School of Medicine – Dr. Flockhart outlined the national and international status of biobanks. Mervin C. Yoder, Jr., M.D., Richard and Pauline Klingler Professor: Department of Pediatrics, Indiana University School of Medicine – Dr. Yoder discussed the therapeutic use of biobank samples. Andrew R. Klein, J.D., Paul E. Beam Professor of Law, Indiana University School of Law - Indianapolis – Prof. Klein led the group in discussion of the difficult ethical and legal issues. The Bioethics for Breakfast series is co-sponsored by the Indiana University Center for Bioethics and the law firm of Sommer Barnard. – Patrick Barrett |
| Reminder About the NIH Public Access Policy [The Tree of Life] Posted: 28 Apr 2008 03:27 PM CDT To all interested in Open Access publishing
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| The DNA Testing of the YFZ Polygamous Ranch Children: A Commentary [The DNA Testing Blog] Posted: 28 Apr 2008 02:39 PM CDT It has been recently reported in the media that cheek swabs have been taken from over 400 members of the Fundamentalist Church of Jesus Christ of Latter-Day Saints, most of whom were removed from the YFZ ranch in Eldorado, Texas, earlier this month. These swabs contain DNA that will be used for DNA testing [...] |
| New business models for life science content [business|bytes|genes|molecules] Posted: 28 Apr 2008 10:00 AM CDT
Now to the good stuff. I have blogged about NextBio in the past. A couple of weeks about I was on the site and noticed that I could use the search engine without having to log in and get some pretty interesting results fast (well presented, well laid out, etc). I also registered and got an account for enhancements to the search experience. So when I got an advance copy of a press release announcing the formal public launch of the NextBio search engine. From the release
The release offers more details. There are over a billion data points, tens of thousands of study results and millions of scientific articles. There is a really neat autocomplete feature. Perhaps most importantly one can make correlations across six species, comparing animal models to human data. Here are some screenshots. What I like most about the service is just the look and feel, very “Googley” if I might say.
For me the more interesting part is the business model. The NextBio model is essentially the freemium model that so many have advocated. They offer a quality free search engine, but revenues are going to be driven by commercial services, both hosted search and local installs. Transinsight, with GoPubMed, is doing something similar albeit not quite at this scale. I like the direction life science content is taking. It’s only going to be better for science and for the companies working in this space Hopefully I will get a chance to see the presentation tomorrow here at Bio-IT World. Check the site out, I would love to hear what all of you think. Further readingh Technorati Tags: NextBio, Search, Biological Content  |
| State-of-the-Art Geeky Coffee [Bayblab] Posted: 28 Apr 2008 09:19 AM CDT  The coffee-maker pictured above is known as a Japanese siphon bar (see the NY Times website to see a slide-show of the thing in action). It is the only one of its kind in the US, imported for a mere $20,000. Eleven dollar globes of the non-espresso coffee product are apparently all the rage on the San Fransisco hipster-blogger-academe coffee-shop scene. The Times recently reported on this new trend in high-end brewed coffee making. The siphon bar is found at the Blue Bottle Coffee Company. Owner James Freeman explains the concept:"Does coffee brewed from single-origin beans in a siphon or a Clover taste more yummy than, say, Folgers from a percolator? I believe it does. But it would be hubris to suggest that we're making better coffee than anyone ever has. My feeling is, there are already enough places where you can get a cinnamon latte and a muffin wrapped in plastic. Why would I want to build another one of those?" Supposedly this thing makes the greatest cup of coffee known to (wo)man. No less than Starbucks has bought the rights to similar technology (the mystical "Clover"). I'll admit, my curiosity has been aroused. But I'm sure as hell not going to pay that kind of cash for a taste (not to mention the plane ticket). So I fired up the YouTube and did a little commercial espionage (see video clip and watch the brewing process in action). Turns out these guys are a bunch of scientist wannabes! I figure it'd be pretty easy to rig one up with a bunsen burner, a couple of flasks, a Buchner funnel and a vacuum line. All easily found within your standard biomedical research lab...except for the Yo-Yo stunt man... |
| Oprah, Oprah, Oprah! [The Gene Sherpa: Personalized Medicine and You] Posted: 28 Apr 2008 09:06 AM CDT In a gut wrenching episode of Oprah the other day Randy Pausch spoke about pancreatic cancer. It is a scary disease as almost everyone dies from this cancer AND it is so difficult to detect. He is... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| The best of Genomicron. [T Ryan Gregory's column] Posted: 28 Apr 2008 08:07 AM CDT I have promised to move some "classic Genomicron" posts to this new page, but in the meantime here is a list of what I consider the most significant posts from the last year. For readers who have been following the blog, this may highlight anything you missed, or maybe will be a chance to revisit some older favourites1. (And please update your blogroll to http://www.scientificblogging.com/genomicron) For new readers, it provides a sense of what you can expect from this blog. Either way, please enjoy.
Basic concepts: |
| Incidents and Accidents [Sciencebase Science Blog] Posted: 28 Apr 2008 07:00 AM CDT
A friend of mine who worked in a biotech lab in Europe suffered a bout of what she thought was hayfever this year…snuffling and runny nose, itchy and sore eyes, the usual thing…except this was in February! She took a few days sick leave - it was that bad - and the symptoms subsided. Until she went back to work, where she started up again her earlier experiment - enzymatic chemical synthesis. The devastating result was far worse than the snuffles she had suffered before his sick leave - her neck and face went bright scarlet, she started shaking and collapsed gasping for air. Anaphylactic shock was the diagnosis. She had to leave her job although the lab in question has implemented very strict protein-powder handling control systems, it’s the kind of accident that is almost impossible to predict and potentially more common than ever. There are more unusual accidents. In December 1999, Emory University in Atlanta paid out $66,400 in fines and changed its procedures following the death two years earlier of primate researcher Elizabeth Griffin who contracted herpes B after being hit in the eye with fecal material, urine, or saliva while putting a rhesus monkey in a cage at the Yerkes Regional Primate Center. A small-scale lab accident may involve someone mixing something and getting an unexpected exothermic or explosive reaction. The results often reach the community by word of mouth and through a note in the literature. For instance, Toshi Nagata of the Institute for Molecular Science, Okazaki, Japan, recently reported an accident while following a literature procedure published ten years ago. The chemical preparation involved synthesising a brominated bipyridine (Can. J. Chem. [69, 1117 (1991)] but instead of using standard quantities Nagata’s team had scaled it down to a tenth. While they were purifying the product, the 100 ml reaction flask exploded violently injuring one of the team in the arm. Nagata suspects that the problem lay in the formation of a peroxide by-product that would have been less concentrated on a larger scale. Nagata, wrote to Chemical & Engineering News, the flagship journal of the American Chemical Society, saying, “I do not intend to blame the authors for not describing the danger, but all chemists should be aware that this procedure could be dangerous.” Guidelines and regulations are all well and good but what about insidious threats like this? Such incidents beggar the question of how might they be predicted. Should there be stricter guidelines for the way procedures are described in the literature? If so, what might they be and how would they be applied? In 1995, a seemingly small-scale spill of hydrofluoric acid killed a technician in Australia. He died from multi-organ failure two weeks after the incident. Several factors contributed to his unfortunate death, according to the official report - he was alone, wearing only rubber gloves and sleeve protectors but nothing covering his lap, He was working in a crowded fume hood. The lab had no emergency shower, nor any calcium gluconate gel antidote available. The lessons may be obvious. But, accidents happen The slow death that befell Dartmouth chemist Karen Wetterhahn when she was exposed to a few drops of the highly toxic dimethylmercury in August 1996 took several months to kill her. Although Wetterhahn was wearing latex gloves this compound rapidly penetrated them and was absorbed through her skin. Ironically, she was at the time using dimethylmercury to examine the effects of toxic metals, such as chromium, on human cells. While, in October this year, Michal Wilgocki of the University of Wroclaw in Poland, a chemistry professor of thirty years experience, died after an explosion in his laboratory. Fire-fighters have suggested the accident may have happened while Wilgocki was drying unstable perchlorates.
So, who ensures that rules and regulations are adhered to in order to prevent accidents? Who makes sure the fume-cupboards and filters are up to a high enough standard and the reagent bottles are stored safely? According to Jim Kaufman of the Laboratory Safety Institute (LSI), “There are three levels of responsibility. First is Management. Safety is their responsibility. Preventing accidents and injuries is their responsibility. If you manage others, you are responsible for their health and safety. You have to enforce the rules,” he explains. “Second is the Chemical Hygiene Officer and the lab’s safety committee. They are advisors and recommenders. Third is everyone. Everyone needs to be responsible for health and safety. Follow the rules, report accidents, injuries, and unsafe conditions.” Organizations such as LSI - formerly the Laboratory Safety Workshop a not-for-profit center providing a focus for safety in science education, work, and our everyday lives. The LSI makes several assumptions about the level of knowledge of those “in the know”, they say “You know the hazards, you know the worst things that could happen, you know what to do and how to do it if they should happen, you know and use the prudent practices, protective facilities, and protective equipment needed to minimize the risks.” But, when the pressure is on, there can always be a proverbial roller-skate left on a stair to wreck the best of intentions. With the ubiquity of the Internet, every lab now can have instant online access to its health and safety rules and guidelines. The Biological Safety Policy of Washington State University at Pullman is a typical example of the materials freely available. One aspect of safety that is often ignored is that while personal protective equipment (PPE), such as eye protection, lab coats and fume hoods are essentialeye protection, lab coats and fume hoods are essential, there is an alternative and that is to better design an experiment so that the hazards are controlled without resorting to PPE. If safer materials or processes are available or the whole experiment can be enclosed then that reduces risks. There are numerous career opportunities in the field of safety. And quite a few glamorously named positions available, many of which are fairly synonymous job description minutiae aside. There are process/equipment safety engineers and technicians, laboratory safety officers, environmental protection agents, industrial (and chemical) hygienists, environmental, safety and health specialists, occupational health specialists and many others. Most of these positions require at least a Bachelor’s degree in a technical subject, usually chemistry, biology, engineering, or physics, and it is, of course, possible to graduate in Industrial Hygiene or the related Occupational Safety too. One important aspect of many of these positions is that they usually require that the jobholder can physically wear appropriate personal protective equipment (PPE) and be capable of functioning while wearing respiratory protection. Which precludes some applicants on medical grounds. An experienced industrial hygienist might work within an institute’s Occupational and Environmental Safety Office, for instance, and be responsible for coordinating support for the various laboratories, and ensuring employees, students, visitors, (patients, if they are working in a hospital), and the surrounding environment are protected.
Jason Worden has just completed his first year as a Laboratory Safety Technician at the University of Idaho, and has enjoyed the experience so far. “I work at a University in the Environmental Health & Safety Office,” he says, “My job includes surveying/inspecting labs on campus and testing and maintaining safety equipment. Another part of my job includes Radiation Safety duties as well as responding to Hazardous Material Emergencies and general office duties.” There are important differences between the various job descriptions though, for instance, a safety engineer deals with protection of people and property from injury and damage investigating incidents. Whereas an industrial hygienist may be looking at protecting people from more insidious threats, injuries and illnesses that come about because of exposure to chemical agents or materials that may not be such an obvious hazard as a boiling vat of solvent outside a fume hood. Jay Jamali is Environmental Health & Safety Director at Enviro Safetech Incorporated, a San Jose based company http://www.envirosafetech.com. So, what routes are there into safety? “I have a client that went from researcher to safety specialist in a biotech company,’ says Jamali. “In other cases the safety staff have no background in biotech.” He adds that the position of “safety officer” is usually dependent on size of an organization or institute. “Smaller organizations assign safety to multiple site personnel,” he explains, “some doing chemical hygiene plan, same radiation safety, some bloodborne pathogen safety, some laser safety, some doing the personal protective equipment and some the lab safety.” On the other hand, outside contractors, such as Enviro Safetech, can take on the entire safety support operation on an as needed basis. Bill Paletski of the Pennsylvania Technical Assistance Program (PENNTAP) points out that “flexibility and diversification is your key to beginning a career and improving it in the field of safety.” He suggests that without, belittling education, “Degree after Degree will not help�getting your feet wet is a good start.” Many countries have regional safety departments that also inspect laboratories while every university should have a safety officer or section. Companies are bound by law to ensure the “The work is very addictive,” Jamali enthuses, “and very few leave the field after they get in because it gets under your skin.” He adds, that, “The key to success is to be a generalist, specialize in one of the three [main] fields and be an expert in at least two topics in your specialty.” There are many specific problems that have not previously been such a concern in lab safety. Bio and chemical terrorism. Post 9-11, safety issues have been brought into sharp relief. Although most institutions are carrying on essentially as normal, security will ultimately impact on working practices in laboratories around the world. According to a spokesperson for Cornell University, “We’re still discussing all of this at various levels and there aren’t any clear answers. The one place that’s definitely involved is the College of Veterinary Medicine, where research on anthrax has been ongoing for years.” Merle Schuh is a chemist at a small college - Davidson in North Carolina. He reckons in terms of the safety of faculty and students, “We have not instituted any new security measures or management procedures as a result of the increased threat of terrorism. We have always been conscious of safety considerations and lab and building security, and our present activities and procedures are deemed adequate,” he told me. “Since we are a small college, most students and faculty recognize each other, and any strangers to the chemistry building and other science buildings during daylight hours would generally be noticed.” Working down a mine or on the high-seas, one might anticipate a real sense of danger when applying for the job, it might even be one of the thrills of the chase, but perhaps with the exception of those delving into active volcanoes or deep beneath the waves most researchers do not actively seek out dangermost researchers do not actively seek out danger. Instructors at colleges and universities have a duty to emphasize and teach safety to their students. Proper education leads to awareness of safety issues and self motivation for their personal safety and the protection of others. “By the time science students graduate,” says Schuh, “ideally their conscientiousness about safety issues should be as well developed as their skills in doing laboratory work.” These days, not even the smallest or most ill-equipped lab has an excuse for failing to do its best to keep its researchers safe. But, still, in real life there is no safety net. A version of this feature article by David Bradley first appeared in his careers column on BioMedNet. A post from David Bradley Science Writer |
| Pimp Your Plasmid Growth Medium [Bitesize Bio] Posted: 28 Apr 2008 05:47 AM CDT
I suppose rational scientists have often irrational superstitions.
One example of an old method that could be improved is the growth media used for plasmid preparation. The majority of us, throughout our university careers, have used either SOC, LB or TB, for recombinant plasmid propagation, typically in E. coli. LB or Luria-Bertani broth has been in use for almost 60 years or thereabouts, while SOC has certainly been in use for 2 decades. But by adding in a few more ingredients or being more economical on others (especially yeast extract and tryptone) that you could get a higher plasmid yield, quicker and with less money. To counter the naysayers, nobody wants to make very complex with 15 ingredients requiring filter sterilisation, as this obviously defeats the object of economy of time and budget. Indeed, there are trade-offs between optimising for biomass, plasmid yield, quality, stability and cost with the difference between protein production and plasmid production being that plasmid production requires only cell growth, division, and plasmid stability. The good news is that Michael Danquah and Gareth Forde from Monash University down-under have devised a stoichiometrically optimised medium for plasmid production. PDM, supposedly yields under the conditions they tested, twice the amount of plasmid in both volumetric and specific yields compared to TB , LB is left in the dust. Better yet, because it uses less tryptone and yeast extract, the cost per mg of DNA is roughly one quarter compared to LB. The recipes for LB, TB, SOC and PDM are shown below. If you decide to break with tradition and give PDM a go, be sure to tell us how it goes.
Note – Autoclave glucose, KH2PO4 and Na2HPO4 separately
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| Epigenetic research uncovers new targets for modification enzymes [Think Gene] Posted: 28 Apr 2008 02:05 AM CDT Enzymes regulating genetic expression can be just as important as the genome itself, increasing evidence shows. The expanding field of epigenetics focuses on the multiple influences on DNA and surrounding molecules that determine whether genes are turned on or off during development and disease processes. A consortium of scientists, led by Albert Jeltsch at Jacobs University, [...] |
| Gene therapy improves vision in patients with congenital retinal disease [Think Gene] Posted: 28 Apr 2008 02:04 AM CDT In a clinical trial at The Children's Hospital of Philadelphia, researchers from The University of Pennsylvania have used gene therapy to safely restore vision in three young adults with a rare form of congenital blindness. Although the patients have not achieved normal eyesight, the preliminary results set the stage for further studies of an innovative [...] |
| Bizarre inanity from the financial analysis world [Omics! Omics!] Posted: 27 Apr 2008 08:55 PM CDT In general I try to ignore the various bleatings of stock pickers. Given the mountain of evidence in favor of the efficient market hypothesis, claims of successful stock picking should be generally lumped in with schemes for perpetual motion machines. However, sometimes something truly ludicrous crosses my eyes & keeps them crossed. I've previously http://omicsomics.blogspot.com/2007_06_01_archive.html, but now I get to pick on someone calling a stock a buy. The stock is (surprise!) Millennium, which Zacks.com is diligent to inform us is still a buy in their opinion. When I saw the headline I did a double-take, and then had to read the article. It's just as bizarre as I expected. The author describes a complex analysis leading to a target price of $25, miraculously the same as what Takeda is offering. They note all sorts of good news which might occur to Millennium. But that's irrelevant, as Takeda has set the price for MLNM: $25/share. Given that MLNM has accepted the offer, the price ain't going higher without another bidder -- and unlike eBay auctions bidders don't tend to swoop in at the last minute. Indeed, Zacks isn't saying "buy this because the price will go higher". Yes, MLNM is currently priced a bit south of $25, but that's because there is really a difference of getting $25 when the deal closes versus getting money today. The gap prices in the transactional costs, the time value of getting (or giving) money now, and the tiny risk the deal won't go through -- but Zacks doesn't comment on any of those. Nope, according to them you should buy because MLNM might have good news! It should be noted that Zacks in Feb called MLNM a buy with a target of $18. Either they got lucky or they really can pick. However, nowhere do they explain how the calculations really changed between then and now -- supposedly they plugged new numbers in and got a new value. But which numbers changed & why? No talk there. |
Let me start of by pointing everyone to the standard 
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