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| Exercise helps keeps the heart on beat [The Navigator - Navigenics Blog] Posted: 14 Nov 2008 12:30 AM CST Michael Nierenberg, M.D.
For years, the prevailing wisdom has been that exercise – at least vigorous endurance training – increases a person's risk of atrial fibrillation, an irregular heart beat linked to the formation of blood clots that can potentially cause a stroke. By extension, many people feared the same might be true even for leisurely physical activity. But new research has determined that being inactive may be just as bad. Scientists recently found that light to moderate exercise appears to actually prevent this health condition from occurring in older adults. |
| Bits and bobs [A Free Man » Science] Posted: 13 Nov 2008 04:02 PM CST
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| It's the plastic, stupid! [Bayblab] Posted: 13 Nov 2008 03:26 PM CST  One of the original baybz alerted us of this paper in science which discusses contaminants found in plastic that can inhibit enzymes. We use disposable plastics a lot in the lab, from tips to eppies , without thinking too much about it. There are a few people who religiously believe that you should not change any of your plastic supplies (tips/tubes) when repeating an experiment. Well these people maybe on to something as this Canadian team from Alberta has shown as much as 40% inhibition of hMOA-B from coumpounds such as DiHEMDA and oleamide which leak into water or DMSO from tubes, tip, and TCware. And that's not even all. Apparently microbicides are added by manufacturers to the plastic along with other chemicals to prevent water from "sticking' to the sides:" Related slip agents such as erucamide and stearamide are endogenous molecules used routinely in plastic manufacturing (3), whereas quaternary ammonium compounds are included as biocides or antistatic agents. Many such biocides bind substantially to proteins and DNA and have recently been linked with fertility problems in mice (6). Our findings that processing agents leach from laboratory plasticware into biological media and solvents, particularly when liquids are stored in plastic vessels, identify a likely source of error in many assay systems." |
| Blogging from Bangladesh, part 4 [Tomorrow's Table] Posted: 13 Nov 2008 02:45 PM CST  November 5th This is the 4th in a series of posts describing my trip to Bangladesh and India. For part 3, see this post. After celebrating Obama's victory at our hotel in Kolkata, today we head out to visit the Rice Research Station in Chinsurah, India here in West Bengal.  The driving is not better in India than it was in Bangladesh. At least here, so far, we have not had any accidents. (In Bangladesh on the 6 hour drive from Dhaka, our driver hit a pedestrian and side swiped a bus. No injuries but a lot of screams from the passengers. The rice research station is housed in a 50 year-old buildings with a crumbling exterior, and sparsely furnished rooms. The fields, however, are well tended. Clearly this is where the effort of the Indian breeders has been spent. And it has paid off. The Swarna sub1 lines are flourishing. Ranjan Gosh, the Joint Director of Agriculture of the government of Wets Bengal, explained that the institute would soon release the Sub1 lines to farmers, who grow 3 crops in this region. First Swarna sub1 will be planted in the wet season (July through November), then potatoes or mustard (november though March) and then Boro rice, a variety that grows in the dry season (March through June). Out of the 4 million hectares of low-land rice planted in West Bengal, 20% is planted to deep-water rice and 80% to modern high yielding varieties. A full 80% of the modern varieties is planted to Swarna, He expects that within a few years, most of the Swarna rice will be replaced with Swarna-Sub1. The Indian government does not dictate what farmer's plant, although they do offer 20% subsidies on the rice purchase price. The subsidy encourages purchasing from certified seed agencies. Because farmers rotate their crops and because new varieties are introduced every few years, there is less of a risk of a disease epidemic that can afflict genetically uniform varieties.  Nitrogen is critical to the productivity of rice. The farmers here add 60kg/hectare of urea during the wet season and as much as 100kg/hectare during the dry season. The Indian government has developed a small organic program but it has not taken off for two main reasons. First, there is less land available for livestock so there is less manure available. Since the bird flu hit, there is not enough manure available from chickens. Indian researchers are now attempting a rabbit manure scheme. Second, because most farmers do not have vehicles, they do not have a way to transport and spread the heavy compost onto their fields. We finished the day with a cold drink of coconut milk and toasts to our new president elect. |
| Mister Doctor Prof. [Genomicron] Posted: 13 Nov 2008 02:16 PM CST I don't get too concerned about things such as titles, but I have noticed that this year a more substantial number of students has been sending emails addressed to "Mr. Gregory". I don't know if the students this year are unaware that most professors hold a Ph.D. and therefore are "Dr." and not "Mr." (or "Ms." as the case may be), but this seems to be much more common lately. Has anyone else noticed this? I know this can get a bit confusing, so let me try to explain it, at least as the terms are used in North America. The title "Doctor" and the abbreviated prefix "Dr." come from the Latin for "teacher", and are traditionally bestowed on those who have earned the highest academic degree attainable. The suffix Ph.D. is an abbreviation for Philosophiæ Doctor (L. "Teacher of philosophy"), with "philosophy" from the Greek for "love or pursuit of wisdom". The Ph.D. is awarded in most academic disciplines, including science. Medical professionals may also hold the title "Doctor" even though they may do little or no teaching, with common degrees being M.D. (Medicinae Doctor, or Doctor of Medicine), D.V.M. (Doctor of Veterinary Medicine), D.D.S. (Doctor of Dental Surgery), and so on. As a noun rather than a prefix, "Doctor" is usually reserved for medical doctors ("I'm not a doctor but I play one on TV"). Usually, the person teaching your course at a major university is a "Professor" and not a "Doctor" (noun) ("Are you really a mad scientist, professor?"). He or she does, however, use the prefix "Dr.". Get it? To make it more complex and Monty Python-ish, the prefix "Prof." is not used by all professors. "Professor" (noun) is the position, but there are also ranks. In North America, these would be "Assistant Professor", "Associate Professor", and "Professor" (or "Full Professor"). In many cases, only full professors use the prefix "Prof." in situations outside the university. I don't use "Prof. Gregory" in non-university settings because I am not a full professor. However, I am a professor, not a doctor, although I use Dr. Gregory instead of Prof. Gregory. Right. Perhaps that's all too complicated to bother about. Here is the short version: When addressing a professor*, just go with "Dear Dr. So-and-so" unless he or she asks you to call him or her something different. (*To clarify, this post is mostly for students) |
| Posted: 13 Nov 2008 01:12 PM CST |
| The ASHG Ancestry Testing Statement and Recommendations [The Genetic Genealogist] Posted: 13 Nov 2008 12:12 PM CST Today at 1:15PM, the American Society of Human Genetics released the “ASHG Ancestry Testing Statement and Recommendations (pdf)” during a press briefing session entitled “ASHG Ancestry Testing Statement and Recommendations: Guidelines for Understanding the Issues and Implications Involved." The briefing session, held from 1:15PM to 2:15PM, is part of the 58th annual ASHG meeting in Philadelphia. The paper was drafted by the recently-appointed ASHG Ancestry Testing Task Force Committee. Let me start my analysis by clearly pointing out my personal positions:
General Concerns: With those personal positions in mind, and after reviewing the paper, I have a number of general concerns with the paper's conclusions:
Specific Concerns: Now, onto a few specific criticisms of the paper: Limited Scope:
This paragraph largely deals with autosomal testing, but there is no clear distinction made. The questions that can be answered by genetic genealogy depend on the type of testing that is done. Additionally, there is no way to know for sure, short of testing, which ancestors contributed to your autosomal DNA (and even current testing is unable to do this, although it likely will be able to do so in the future). However, it is clear who contributed your Y-DNA and/or mtDNA (your father’s father’s father’s father contributed your Y-DNA, for example, even if their names are unknown). Accuracy:
I believe that the Task Force is aware of the GENEALOGY-DNA Mailing list, but I wonder if they are similarly aware that genetic genealogists often test the same markers with multiple companies. For example, test-takers were recently able to compare their results to the SNP results provided by new large-scale chip testing from 23andMe or deCODEme. Similarly, test-takers have also compared the results of SNP testing by 23andMe and deCODEme and found that the results were almost identical (see here). Many genetic genealogists, especially those associated with the GENEALOGY-DNA mailing list, are aware of and continue to explore accuracy issues. As a result, these individuals provide a market regulation mechanism that is much more robust that the authors imply, especially since some testing companies monitor and interact with these lists to address the concerns of customers. Group Identity:
Since I already discussed this above, I won’t add much here. Again I argue that any needed regulations should be established at the level of the group or organization rather than at the level of testing. The government should establish guidelines about how to use DNA testing results when filling out identity on government forms, and groups should determine how to use DNA testing results when addressing group rights or benefits. This is the most efficient and appropriate way to regulate these concerns. Emotional Distress:
I discussed this concern above, but I wanted to raise one more issue. While researching the ancestry of my great-grandmother, I discovered on a census return that she was ‘adopted’ as a child, and in fact I still don’t know the identity of her birth parents. Finding this unexpected result in this document caused a number of emotional responses over the ensuing years, including some anger and frustration. Should the government regulate access to census records, published family histories, or town records since finding unexpected results in these research sources can elicit emotional responses? Should I have to use the services of a professional genealogy counselor to share the results of the research with me? Based on my own anecdotal experience during 20+ years of traditional genealogy, I would argue that far more emotional distress is elicited by traditional genealogy than is elicited by genetic genealogy! Note, however, that I claim this information is anecdotal, not “well-documented.” Conclusion: If nothing else, I hope that his policy paper incites thoughtful conversation about these issues. I am genuinely interested in your thoughts and comments about both the paper and my response. This is a very important time for genetic genealogy, and I encourage you to join the conversation by leaving a comment here at TGG. And finally, in case you think that I am in complete disagreement with the paper, let me leave you with the group’s first recommendation which I consider to be sage advice:
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| Protein Expression and 3' Untranslated Regions [The Daily Transcript] Posted: 13 Nov 2008 10:20 AM CST Traditionally, gene expression patterns were seen as mostly dependent on transcription ... yes those nasty bits of DNA that seemed to be ignored by most "science journalists". But the picture that is imerging is that transcription is looking more and more sloppy, and this "sloppyness" is built into the system so that the act of transcription tends to influence the organization of that part of the genome, regardless of what is being transcribed. It also appears that processes upstream of transcription, (such as mRNA processing, mRNA export and translation) play a greater role in determining expression patterns. In a recent issue of Current Biology there's a nice example of post-transcriptional regulation of genes. In their manuscript, Merritt et al., demonstrate that in the ovaries of C. elegans (a nematode worm), the timing of expression of a given gene product at the protein level is largely determined by RNA elements found in the portion of the transcript that comes after the protein-coding region (also known as the 3' untranslated region or 3'UTR for short). Here's a remarkable figure from that paper showing the expression of GFP when fused to either the 3'UTR of an oocytes specific gene (left) or under the control of that same gene's promoter (right). Just to orient you, worm oocytes are a long sack that begin on the top left where the oocytes progenitors are found. As the oocytes mature they travel rightwards, then make a sharp U-turn and they finally endup at the bottom left where sperm is created (most C. elegans are hermaphrodites) : Read the rest of this post... | Read the comments on this post... |
| Family history misses cases......so what? [The Gene Sherpa: Personalized Medicine and You] Posted: 13 Nov 2008 06:09 AM CST In the last two days I have been fighting off false claims from certain employees of certain unnamed DTC genetic testing companies. Their claims/anecdotes....... "Family history is not that... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| Fast-track your Ampicillin Plasmid Transformations [Bitesize Bio] Posted: 13 Nov 2008 05:02 AM CST Most of us use pretty standard transformation protocols for E.coli. Yours probably goes something like this: - Thaw the competent cells on ice That 30-60 minute incubation can be pretty annoying, especially if you are performing the transformation late in the day. The good news is that if you are using ampicillin as your selection antibiotic, you can miss this step out without too much problem. The reason is that ampicillin acts differently from the other antibiotics commonly used for selection of E.coli in molecular biology (for a great summary, see this article). Antibiotics like chloramphenicol and kanamycin act by binding to the bacterial ribosome and inhibiting translation. This means that if you plated your transformation straight onto either of these antibiotics, translation of the antibiotic resistance enzyme would be suppressed, which would prevent the cells from acquiring resistance to the antibiotic. With these antibiotics, the 30-60 minute incubation allows the cells time to synthesise the antibiotic resistance enzyme so that they can survive when plated on the antibiotic. But ampicillin does not work in this way. Instead it prevents newly divided cells from synthesising the cell wall that they need for survival. Looking at it another way, this means that ampicillin does not kill cells unless they are dividing. So newly transformed cells plated straight onto ampicillin can synthesise the beta-lactamase enzyme required for resistance without any problem, thereby acquiring the means to inhibit ampicillin activity that will allow them to synthesise their cell wall normally when they divide. Ampicillin is not the greatest selection antibiotic in the world since it can allow satellite colony formation and plasmid loss (see this article) but this feature makes it a bit more convenient than others for transformations. Having said this, leaving the incubation step out might not be a great idea if you are performing a transformation that requires particularly high efficiency, for example if you are building a library or doing a particularly tricky ligation, because efficiency could be somewhat reduced. For example, individual cells that were close to dividing at the time of transformation might not have time to synthesise the beta-lactamase before the divide, so would not survive. This will only happen with a small portion of the cell population so will not be a problem for the majority of applications. What are your favorite shortcuts in the lab? |
| Blogging from Bangladesh, Part 3 [Tomorrow's Table] Posted: 13 Nov 2008 04:49 AM CST  November 3, 2008 This is the third in a series of posts describing my trip to Bangladesh and India. Part 2 is posted here. Today we visit Mostofa, a rice farmer in the village of Rajaharat in northern Bangladesh, a 2 hour drive from Rangpur. Mostofa has volunteered to test the submergence tolerant (Sub1) rice variety for the Bangladesh Rice Research Institute (BRRI).  He is pleased to show us the rice on his well-cared for farm. This year his young rice plants were hit with 15 days of submergence. Out of the 5 varieties he grew this year, only the new Sub1 lines survived the flood. Ample a grain will soon be ready for harvest. "What will you do with the grains?" I asked. I was curious if the grain would be consumed or not. He told us that this year he will save all the grain. He plans to use some for sowing in these fields next year and will give the rest to his neighbors, so that they can also benefit. The director general of BRRI told me that his generosity is unusual -other farmers who tested the Sub1 rice are planning to sell the grain to their neighbors, reaping the benefit of taking the risk of planting a new variety. Farmers here have this much in common with their fellow farmers in the wealthy developed world- they are entrepeneurs and business people. In Bangladesh, the national breeding stations distribute the improved varieties to government seed producers who currently can supply only 20% of the seeds needed by farmers. This seed is then inspected for quality and certified by another government agency. The certified seed processed this way is of high quality. Still, there is a need for more seed. This is the reason that several public-private partnerships and private seed companies have sprung up. The hope is that these groups will supply the seed production capacity that the national breeding programs lack. The danger is that some of these groups may not go through the proper seed certification and label the seed "Sub1", when in fact it is not. The Bangladeshi Director General of Agriculture, Elahi, predicts that within 3 years, Sub1 rice will be grown on 2 million hectares during the wet season. The farmers will have their choice of variety to plant, such as a popular Bangladeshi line favored for its non-sticky quality called BR11 or the shorter and more slender grain east Indians prefer, called Swarna. Given the positive performance of the Sub1 varieties its seems very likely that this trait will be bred into many more rice varieties that are grown during the monsoon season in Bangladesh.  Before I leave, I give away 2 soccer balls purchased from the savings of my children Audrey and Cliff. I brought them from Davis at the suggestion of my friend Leslie. She has started a program to distribute balls to children in less developed countries. My daughter Audrey did not hesitate to part with her savings- she was pleased to be able to give Bangladeshi children something she takes for granted. My son Cliff decided to donate only after some parental urging, and once he was resigned to the fact that he would not be allowed to spend the money in the Davis toy store.   |
| Plug of the week - Extreme 2008: A Deep-Sea Adventure: University of Delaware [The Tree of Life] Posted: 13 Nov 2008 02:41 AM CST Just a little plug here to suggest people might want to check out the web site for a Deep Sea Research Cruise going on right now (Extreme 2008: A Deep-Sea Adventure: University of Delaware). The focus of the cruise is summarized as follows: The scientists will focus on marine viruses and other tiny life called protists and their roles in the food chain. These organisms prey on bacteria, a primary food that sustains the vent ecosystem.Some friends/colleagues of mine are involved in this adventure and it sounds like some cool stuff could come out of it. Also you might want to check out the blog of Lisa Z (ExtremeVirus), who is posting about the cruise. |
| This press release deserves some sort of award ... [The Tree of Life] Posted: 13 Nov 2008 02:27 AM CST Just got pointed by Ruchira Datta to a new press release from Princeton (Princeton University - Evolution's new wrinkle: Proteins with cruise control provide new perspective) that makes some interesting claims about evolution. Ruchira asked if the press release made sense to me. And alas, it does not. It has all sorts of bizarre evolution claims in it including the following A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.It sounds like complete nonsense to me. But I am not sure. Anyone else out there know more? |
| The post election Tangled Bank [Discovering Biology in a Digital World] Posted: 12 Nov 2008 11:08 PM CST Is ready for reading at Submitted to a Candid World. I never thought I'd see the day when a Tangled Bank host would compare PZ Meyers to John McCain, but I admit, it was tastefully done. Read the comments on this post... |
| The Unusually High Standards of Genomics [Think Gene] Posted: 12 Nov 2008 08:52 PM CST Why do Navigenics, 23andMe, and other genomic companies incur so much scrutiny from the medical community when all sorts of flagrant quackery, mysticism, and crass marketeering seems to get a free pass to easy profit? Some genomic tests may not be as medically actionable as implied, yet we all endure billboards screaming crap like “scientifically proven: 30% more kick!”, and I don’t know of a serious organized effort in the medical community to regulate these industries out of existence. Pulp books about faith healing and horoscopes are sold at every grocery store checkout isle, yet a consumer website selling tests backed by well-cited genomic science (even if medically doubtful) is the worst public misinformation meriting the highest regulatory priority? Maybe the unusually high standards for genomics is because genomics can be held to high standards —it’s unusually scientific and unusually transparent compared to almost everything else the public labels as “health.” Fortunately, strong accountability to accurately and precisely describe reality is good science. Expect great, real results from genomics in the future. However, the focused scrutiny must be frustrating for well-meaning genomic companies their teams. Why must they endure the focused ire of ethicists, scientists, doctors, and the government when such other flagrant dishonesty is systemically dismissed? With few exceptions, the difference between “drugs and medicine” and “consumer products” seems to be about the same as the difference between “primitive magic” and “cultural diversity”: about one hundred years and a grandfathered license… assuming nobody seemed to die too quickly from its indulgence. An idea’s unremarkable past awards it some inscrutable permission to exist as it is, and that inscrutable permission is too easy to forget when a new idea like genomics seems so dubious by comparison. I always endorse the strictest scientific rigor, but we need some perspective. Genomic companies aren’t perfect, but both the petty condemnation and enthusiasm isn’t useful. For example, me mocking Navigenics for their apparent lack of customer endorsements might be funny for me, but that’s not a useful, rational contribution to our better understanding and application of medical genomics. What is useful to ask is if a company claims to be the agent of a “healthcare revolution” by providing “information about what actions to take to help them stay healthy,” then what physician endorses what action by what information, why, and how will that help people stay healthy? Is this too much to ask? Yes. In fact, I don’t think that there is just a problem regarding verifiable and actionable information about health, I don’t think that it hardly exists in the world of the average American consumer. I think that you could visit every supermarket in your city, watch 1000 hours of television news, and purchase every consumer product advertised as having anything to do with your health that’s not explicitly a drug —and not find one single scientifically verifiable and actionable claim about your health. What is useful to ask is if a company’s top investor states in a press release that it “ensures state-of-the-art medical advice and services” and the company very clearly advertising it’s product, “Health Compass,” as a medical advice service, then why is every webpage of the service branded with the statement “Navigenics does not provide medical advice, diagnosis or treatment.”? Is this too much to ask? Yes. In fact, I don’t think that there is just a problem regarding rational, consistent, honest, and transparent legal regulation of medical advice, I don’t think that it hardly exists in any American industry. I think that the failure of rational regulation of “insurance that is not called insurance” and “loans that are not called loans” cost Americans $700MMM+$200MMM ~= $1 Trillion in 2008. I challenge anybody to produce estimates of any other social liability that compares to social liability incurred by that great American tradition of selling “[blank] that is not [blank].” Yes, it is too much to ask, but I ask anyways. “How is this actionable?” “How is this legal?” This is my industry, my field, my passion I demand it, I expect better, and while I can’t fix the world, I can sure make every effort to make my little corner of it clinically sterile. I don’t care how aristocratic, rich, powerful, well-connected, and prodigiously educated you are, I can be understanding, I can be forgiving, I can be reasonable and professional, but I want a honest conversation and some real answers, not more feel-good marketing tripe. If nobody else has the mind, will, or balls to cite “IS X” and “IS NOT X” right next to each other and ask why they contradict while meanwhile everyone else milling about in some confused and imagined “deeply wise” “ongoing conversation” about how there should be “more regulation” or “more studies” or “more democracy” or “more empowerment” or “more awareness…” —then I guess it will have to be me. Me, in perspective. |
| How do you like them apples? [Bayblab] Posted: 12 Nov 2008 08:45 PM CST  As I'm typing this I'm snacking on a granny smith apple, one of my favourite varieties. Even though you'll typically find only a half dozen or so different varieties at the grocery store, there are over 7500 different cultivars (though not all are eating apples). The apple is a member of the rose family, and as one might expect they have a long history. They originated in Asia, and Alexander the Great is credited with bring dwarf apples back to Greece in 300 BC. The first apple orchard in North America is said to have been planted in the 1600s in Massecheusetts.AC wrote before about modern hybrid fruit. It should come as no surprise that having been around for centuries and being an important food crop, the apple has gone through several rounds of its own breeding to produce popular varieties we eat today. It can take 15-20 years to develop a new variety and promising cultivars are selected on the basis of appearance and flavour as well as ease of shipping, longevity in storage, and even length of stem to allow pesticides access to the top of fruit. The granny smith apple I mentioned above is originally an Australian fruit, but Canada is famous for apple varieties of its own. Every McIntosh apple can trace its lineage to a tree discovered in 1811 in Dundas County, Ontario. One of its offspring, the Spartan (another one of my favourites) was developed in BC in 1936 as part of Agri-food Canada's apple breeding program. It's widely described as a cross between McIntosh and Newton Pippin but recent DNA tests have put the Newton parentage in question. Over the past few weeks, I've been sampling several different apple types from the common Granny Smith (still my favourite) and McIntosh (which I find too soft) to less 'brandname' varieties such as Honeycrisp (which was almost unnaturally crisp and a bit too sweet) and Braeburn. Extensive lists of apples, their origins and descriptions can be found here and here. What's your favourite apple? |
| Not Exactly Rocket Science has a book out [Genetic Future] Posted: 12 Nov 2008 06:29 AM CST
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If you've been looking for excuses to skip exercise, a predisposition to 
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