Posted: 16 Oct 2008 11:15 PM CDT
Elissa Levin, M.S., CGC
If you've received your Navigenics genetic test results, it may be time for "the talk."
Time to have a candid conversation with your physician about your DNA and what you can do to improve the future direction of your health.
And, as one of our satisfied customers relates, having that conversation can be one of the most important steps you can take along the path toward optimal wellness.
In Patrick’s case, it meant early detection and early treatment of a health condition that might otherwise have gone undetected for some time.
Posted: 16 Oct 2008 06:13 PM CDT
Previous research has found that African ancestry is associated with healthier lipid profiles, compared to European ancestry, and that people of African descent in the UK have lower coronary heart disease compared to whites. Since sex also mediates the risk of cardiovascular disease, this study investigates four variants on the Y-chromosome, in "579 men of different ethnic groups (blacks, South Asians, and whites) from UK and in 301 whites in Italy." All Black and South Asian men were first generation immigrants, so that might be why they don't do any kind of adjustment for differing admixture proportions. Given their conclusion:
"In our study, the men of black African origin carrying the A alleles of both TBL1Y and USP9Y had a more favorable lipoprotein profile, characterized by lower levels of serum triglycerides and higher levels of HDL-cholesterol, thus indicating the existence of a "cardio-protective haplotype." In contrast, in white men, both from the UK and Italy, and in people of South Asian origin, the lipoprotein profiles were not affected by these genotypes."...they then have a pretty good discussion of the weaknesses and alternative explanations of their findings. They don't really discuss any kind of adaptive or evolutionary explanation for the population differences, other than to mention, regarding which alleles are ancestral, that:
"The data presented here suggest that G allele of TBL1Y and T allele of USP9Y, reported as the wild-type alleles in whites (http://www.ncbi.nlm.nih.gov/SNP) may be derived from the A alleles of both genes, which are the most frequent in black people of African origin."Genetic Variants of Y Chromosome Are Associated With a Protective Lipid Profile in Black Men
Paola Russo; Alfonso Siani; Michelle A. Miller; Sharada Karanam; Teresa Esposito; Fernando Gianfrancesco; Gianvincenzo Barba; Fabio Lauria; Pasquale Strazzullo;Francesco P. Cappuccio
Arteriosclerosis, Thrombosis, and Vascular Biology. 2008;28:1569.
Abstract Objective— Gender and ethnicity modulate the phenotypic expression of cardiovascular risk factors. In particular, men are at higher risk of developing cardiovascular diseases compared to women, whereas black populations of African origin display reduced mortality from coronary heart disease (CHD) as compared to both whites and South Asians. Because the male-specific region (MSY) of the human Y chromosome is an obvious candidate for gender-related differences in the development of cardiovascular diseases, we aimed to identify genetic variants of MSY influencing cardiovascular risk profile in different ethnic groups. Methods and Results— We genotyped 4 polymorphisms of MSY (HindIII±, rs768983 of TBL1Y, rs3212292 of USP9Y, and rs9341273 of UTY genes) in 579 men of different ethnic groups (blacks, South Asians, and whites) from UK and in 301 whites in Italy. We found that the TBL1YA USP9YA haplotype, present only in blacks in whom it represents the most frequent allelic combinations (AA: n=125; all other combinations: n=45), was associated with lower levels of triglycerides (P=0.025) and higher levels of HDL-cholesterol (P=0.005) as compared to the other haplotypes. Conclusion— The TBL1YA USP9YA haplotype of the Y chromosome, present only in black people of African origin, attributes a favorable lipoprotein pattern, likely to contribute to their reduced susceptibility to coronary heart disease. The study evaluated the association of genetic variants of the male-specific region of the Y chromosome with cardiovascular risk factors in different ethnic groups. The most frequently observed haplotype in black people was associated with a favorable lipoprotein pattern, thus contributing to the lower rate of cardiovascular diseases in blacks.
Posted: 16 Oct 2008 06:11 PM CDT
This is the second in a series of debates carried out by students in the UC Davis class Genetics and Society.
"Genetic differences make our society unique and interesting" argued the team in support of a ban on genetic screening. Where do you draw the line between the medical and non-medical?"
And so the debate began.
Team 2 argued against the ban. They offered up as an example the financial advantages of preimplantation genetic diagnosis that allows for genetic screening of embryos derived from in vitro fertilization prior to its placement into the uterus. "Children are expensive. It is cheaper to go through PGD for $12k than to support a kids with a genetic disease"
They talked about cystic fibrosis, which is a serious genetic disease that affects the mucus glands. If a child inherits one copy of an abnormal gene from each parent, they will develop the disease. Many of these children will die young from lung failure. PGD offers the possibility to gentically screen for healthy embryos prior to its placement into the uterus. If two mutated CFTR genes are identified, the embryo is not used for embryo transfer. Instead an embryo with at least one normal gene is implanted.
The team in favor of the ban argued that genetic screening is "a slippery slope. Some parents may believe that blindness, deafness or shortness are genetic disorders. If we throw away these embryos then we are losing the potential that those embryos will develop into human beings who can contribute greatly to society."
The team opposed to the ban argued that ethics rules and laws can be developed to oversee the procedures. "PGD is just a way to keep children healthy"
Posted: 16 Oct 2008 01:28 PM CDT
The quotes below are all from Andrew.
Sometimes, I need to let off steam. Those who have ever shared an office with me, or been in an office close to mine will know this. I am pretty vocal about it, when something is annoying me.
I’m not being particularly rational about it. I just complain a lot.
I calm down again pretty quickly, once I’ve stopped screaming and hitting the walls, but when I am frustrated about something, I do need to let off steam.
On my blog, that “steam off letting” is tagged as Rants. Now you know, so consider yourself warned.
Now, complaining about Linux will annoy some people. A lot of people feel strongly about it.
Not that the comments on the Linux rant are unfair in any way. It is more that my actual rant was unfair, and the comments are actually quite fair!
Not long ago, I would would have defended Linux strongly against just about any criticism. I was a strong believer in Linux. And it has gotten better and better since I started using it.
Why, then, do I complain so much about it now?
Two reasons, probably.
First, I’ve had a lot of problems with using it as a desktop computer that I am just not having with my new Mac.
I got an iMac a few months back, and this is the first non-Linux OS I’ve done any serious work on since I started using Linux in 1995 and so far it has been a pleasant experience.
Not all pleasure, of course. It takes some getting use to, and quite often I get annoyed when it doesn’t work exactly like what I am used to on Linux. And don’t get me started about the problems I’ve had with Boost and Xcode.
Still, fighting with drivers and whatnot is something I avoid on the Mac. Probably a good thing, ’cause I wouldn’t know where to even start with that…
That’s the second point (about why I am complaining now).
I was just pissed off that I had to reboot my laptop twice the same morning.
If I had waited with my ranting until this evening, I probably wouldn’t have ranted at all.
Of course, then there wouldn’t have been this discussion, and that would have been a loss.
I really do appreciate all the comments.
Posted: 16 Oct 2008 12:36 PM CDT
Posted: 16 Oct 2008 11:17 AM CDT
Attitudes towards breast cancer have changed quite a lot over the past three decades, a fact evidenced by the outpouring of response when stars such as Olivia Newton-John, Kylie Minogue, and, most recently, Christina Applegate, went public with their personal struggles with the disease. But this change in attitude is also reflected in many other ways and not least in the adoption of a new name for the patient advocacy and support organization that until now called itself Y-ME? Tomorrow, a gala event held at the Fairmont Hotel in Chicago will celebrate Breast Cancer Awareness Month and the evolution of Y-ME, 30 years on, into the Breast Cancer Network of Strength-a change they hope that will better communicate the organization’s mission to promote a proactive, engaged and positive approach to fighting breast cancer.
Started in 1978 by librarian Mimi Kaplan and social worker Ann Marcou (both breast cancer patients hailing from Chicago), the newly named Breast Cancer Network of Strength includes a 24-hour hotline with interpreters in 150 languages, as well as an internet-based support system where breast cancer patients can share their stories. Breast Cancer Awareness Month (BCAM) has a slightly shorter history but the pink ribbons you have seen everywhere for the past two weeks (one of which you are hopefully wearing right now) are now a familiar sight worldwide.
Alongside a number of other organizations, deCODE genetics is working on the preventative side of matters via ongoing research into the genetic risk factors for breast cancer. Last week deCODE genetics launched deCODE BreastCancerTM, a new tool for assessing risk of the common forms of breast cancer (that are also the result of environmental and lifestyle factors) and for targeting intensive screening and early detection for women at high risk of the disease. deCODE BreastCancerTM aims to put the power of genetic risk assessment to work for the majority of women, complementing the use of tests for variants in the BRCA1&2 that cause rarer, highly familial forms of the disease.
Posted: 16 Oct 2008 10:45 AM CDT
I've recently been to a conference supposed to network endocrine disruptor (ED) research laboratories in Italy. I got a poster aimed at explaining the opportunities to use in vivo reporter animals to better study EDCs. I experienced odd abstract submission that was initially refused by the scientific secretary.
We cannot accept your abstract in the present form.
The problem was that I submitted an abstract written in English language.
Please send us your contribution in Italian language.
I wonder how can be possible to effectively communicate scientific ideas in other languages other than English. Moreover I discovered one speaker getting accepted one abstract (Italian) about politics instead of science. He claimed that "it make not sense to speak about science when science is compromised by law".
I recognize that scientists need to deal with political management of public money to get funded research. Anyway I hardly accepted that an english scientific abstract was refused and an italian political abstract was accepted in a so-called SCIENTIFIC meeting. But I'm a naive man.
I usually share the bench with foreigner students (from Chile, India and Poland). Do you guess they were surprised when they saw me getting back to reduce refine and replace the abstract and the poster? Actually not. They work every day with italian computers because the english license is not available in our University (ok, that's another disillusion story).
Disclaimer: even if I got again my yearly disillusion, I'm a satisfied italian scientist, the meeting was organized by the great "National Institute of Heath" of Italy and was finally helpful to network collaborations and expertise. Finally here it is a review I've been recently involved, that try to address why reporter animals may be important for environmental risk assessment as an alternative toxicology approach (written in english this time).
Posted: 16 Oct 2008 10:29 AM CDT
Coca Cola was invented in the 19th century as a patented medicine in the drug store of John Pemberton. It was initially known as coca wine, and contained cocaine extracts as one of its active ingredients. It was supposed to cure morphine addiction, dyspepsia, neurasthenia, headache, and impotence. Since 1904 coca-cola has been using dry coca leaves (1oo tons) which are imported from South America under a special permit and processed to extract to cocaine, which is resold for medical purposes while "spent" leaves are used for flavoring. While it is now cocaine-free (other than trace amounts) and primarily enjoyed as a caffeinated soft drink, it still does have some medical uses:
"The results indicate: (a) an increase in body weight in all treated animals; (b) a statistically significant increase of the incidence in females, both breeders and offspring, bearing malignant mammary tumors; (c) a statistically significant increase in the incidence of exocrine ademonas of the pancreas in both male and female breeders and offspring; and (d) an increased incidence, albeit not statistically significant, of pancreatic islet cell carcinomas in females, a malignant tumor which occurs very rarely in our historical controls."
However since the control was drinking water I'm not sure what you can conclude from this study other than it's probably not a good idea to substitute all drinking water to a sweet liquid.
Posted: 16 Oct 2008 08:28 AM CDT
We have been fortunate to gain a new and very skilled employee in Singapore, Mr Henry Wang, which means that we now have a native Chinese speaker in CLC bio. In this video Henry uses his mother tongue to explains how to assemble data from two different NGS platforms, Illumina Genome Analyzer and 454, in [...]
Posted: 16 Oct 2008 03:13 AM CDT
I’ve been working on my Ubuntu Linux laptop the last couple of days, and I f*cking hate it. It seems to me that whenever I start a memory intensive job, the very next thing I do is to reboot it using the power button. It takes it a millisecond to reach the point where it is absolutely hopeless to try to interact with it. It is a swapping hell.
Now, I have always had problems with Linux when I fill up the RAM. In my PhD work I did explicit state space exploration, so I used massive amounts of memory and rebooting wasn’t that unusual. Then again, I think I could crash most other operating systems as well ;-)
These days I don’t even have to try to crash the box. Compiling a complex enough program, or leaving firefox on for a few hours, should do the trick. I swear, I am rebooting Linux three or four times a day! Usually loosing a bit of work each time, of course.
Have I fucked something up on my box? It just didn’t use to be this way…
It is not really a problem I have on the other Linux boxes I use, to be fair. On my desktop Fedora, I won’t have time to fill up the RAM before it crashes. It doesn’t like my graphics card, you see, so it will typically crash within 5 minutes of me logging in. That is part of the reason I am working on my laptop.
As long as I don’t log into the box through X, but ssh in instead, it is pretty stable though.
Still, I am so fed up with Linux. I don’t have to reboot Windows every two-three ours, and I’ve only had to reboot my Mac a few times in all the time I’ve had it.
Linux is supposed to be stable. It is praised to be. Still, I am finding that it is growing increasingly unstable on me.
It might just be me, of course. I’m no wiz systems administrator. I’m sure some of my geeky friends can set up a system that wont crash all the time, but I don’t have time for this if I also want to do my science. I just install Linox out of the box and it works like shit on me.
Oh well, with the new MacBook out I will soon not have this problem any longer… I will have the UNIX tools I love but on a box I can actually manage to set up.
Posted: 15 Oct 2008 10:52 PM CDT
Image by Getty Images via DaylifeNick Carr points to an article by Andrew Sullivan that sheds some very interesting insights into blogging, points that are even more important for scientific writing and journalism
Some of the key points made
Quoting Matt Drudge, Sullivan writes
If you are serious about blogging, either as a writer, or just a casual blogger, you have to continuously be on top of your game, constantly being aware of what’s going on, of responding to comments or what others write. It’s not easy.
Yes blogs are superficial, but in their superficiality they have power
I think all of us have bemoaned the lack of depth in mainstream scientific coverage, in the shallowness of press releases. One of the roles we can play/should play is bringing reality to the science many of us love and breathe. To highlight the beauty and power of what we do and its fragility. To explain the potential of scientific discoveries, yet keep them real and not make them sound like a silver bullet to solve all ills (or conversely, the next coming of Skynet).
The next paragraph says it best, although Sullivan seems to forget that women blog too
To some extent it doesn’t matter if you blog or not, but there is a power to talking about things you care about, which are highlighted very well above.
I will end with one more snippet
We are all scientists in one way or another, some just happen to have more formal education and training that others, but we all have a voice and we can all teach each other. I should rephrase that, we can all learn from each other. A blog is just one superficial, yet very powerful, medium that allows us to do just that.
Posted: 15 Oct 2008 09:58 PM CDT
A striking characteristic of the Cambridge biotech scene is how it is concentrated in an urban setting. While there are a lot of biotechs elsewhere in Massachusetts, the Hub's hub is clearly a 2+ mile long zone. One challenge this offers is getting to work via Boston's transportation system.
Boston doesn't have an awful transportation network, but it isn't golden either. The transit system is decent, but the routes still largely follow a radial design, with routes that have changed little in the last half century (I kid not; I've seen a map that old & it takes a careful eye to find the differences). An extensive network of commuter rail feeds the downtown, but is split between two termini separated by a mile. The highway network has a number of gaping gaps, due to a mass cancellation of uncompleted highways in the early 1970's. However, this wasn't necessarily bad for biotech; I've spent half my career in offices that would literally be in the middle of the road should those highways have been built (for example, this very different vision for 640 Memorial Drive than a genomics-based pharmaceutical company).
The commuter rail option presents a particular challenge. One station, South Station, is connected to the Red Line subway which has two stops (Kendall & Central) proximal to many biotechs. The other station, North Station, has terrible connections to Cambridge, other than the perhaps future expansion of the zone into the Cambridge-Charlestown-Somerville interzone. But, if you live north of town it's either deal with getting from North Station to Cambridge or brave I-93. So, by multiple subway connections or a tortuous pedestrian path through Mass General's campus to the Red Line, a not tiny cohort of biotechies has made their commute this way.
Then about five years ago a new option appeared. Little blue buses promising a single seat ride from North Station to Cambridge, with a twisting route designed to be near nearly every major employer in the zone. Called EZRide, for $1 anyone can ride, but better yet the larger employers offer ride-all-year stickers.
The service was a bit slow starting up & went through a few hiccups, but over time it has been impressive. If memory serves, the initial frequency was every 30 minutes; this has been steadily dropped so that now a bus shows up every 8 minutes during commute time. However, demand has grown even faster; during core commuting times the bus is at its legal limit, with only ~30 seats and less than a dozen legal standees.
But a couple of weeks ago the announcement came out: a new vendor would be running full size buses on the route. And last week they showed up. On the one hand, there are more seats -- but not as many as one might think due to the layout. On another, more legal standees and less of the EZRide shuffle -- having to exit the bus at the early stops to let people off, as if you were standing you were a cork in aisle of the old buses. The longer buses don't handle the tight turns as well but do away with the most unpleasant aspect of the old buses: their short wheelbase combined with Cambridge's potholes yielded an amusement-park quality bumpy ride (particularly unpleasant if you made the mistake of leaning against the wheelchair lift).
EZRide isn't run by the transit system, but rather by a quasi-public entity called CRTMA which is charged with improving transit into Cambridge. The director, Jim Gascoigne, is energetic and personable and often on the scene, particularly when weather or accidents snarl require emergency re-routing.
In some ways the EZRide highlights issues in Boston. The T does an okay job, but it apparently never occurred to them in several decades that a market existed for a route from North Station to Cambridge. I've also seen the truly surreal quality of Boston from the blue bus: due to some construction, one Boston police officer directed the bus to stop in a new location, where the driver was promptly berated & ticketed by a second Boston officer. This is the town where the mayor had major apoplexy when a nearby airport added Boston to their name; transportation issues are about turf battles as much as moving people around. The planners also have a fondness for expensive megaprojects (the current shopping list can be found here). Several of these would have important benefits for the biotech zone -- for example, the proposed Urban Ring would run right through it & connect the zone to the Longwood Medical Area.
However, perhaps what is more realistic are more EZRide-like services, perhaps connecting to the south (Brookline, Brighton/Allston) that have surprisingly poor connections, or to the large transit hubs to the north (Wellington, Anderson). A direct connection to Charlestown wouldn't be a bad concept either.
In the meantime, I'll keep riding EZRide. And anxiously awaiting my train line(s) getting the free WiFi service a few lucky commuters have gotten to pilot. One more good reason to stay off the road and out of my car!
Posted: 15 Oct 2008 01:30 AM CDT
We are, the media tells us, either on the verge or diving head first into a global recession the likes of which we have never seen. Countless financial headlines have screamed Credit Crunch, which sadly isn’t a wholegrain breakfast cereal for day-traders, for a year now. Banks are borrowing billions from taxpayers to allow them to lend even more money to each other.
There has almost been not a thought for the millions of people out of work and out of a home the ruins of whose lives the apparent collapse of capitalism is built. Anyone who thought Freddie Mac and Fanny Mae were porn star names, or the Lehmann Brothers were a support act for Marx (as in Groucho and gang) surely now knows better. Stocks and share prices yo-yo between lower highs and increasingly depressing lows.
But, away from the cold-sweating of traders, the pinging of stripy braces, and the red screens of death, on the market floors of the so-called developed world, the old-school third world, the allegedly developing world continues in its grinding abject poverty. However, providing the developed world does not collapse into utter chaos, Jenifer Piesse of the Department of Management, at King’s College London and the University of Stellenbosch, RSA working with Colin Thirtle of the Centre for Environmental Policy, at Imperial College London, and the University of Pretoria, RSA, suggest in a recent issue of the IJBT that at least one product of modern capitalism, genetically modified (GM), herbicide tolerant (HT) white maize, developed in the USA to save labour might help ease poverty in the developing world too.
They report how HT white maize is now being grown by smallholders in KwaZulu Natal, South Africa, and elsewhere and use panel data for Africa, Asia and Latin America to investigate the effects of factor endowments and biased technological change on productivity growth, labour incomes and poverty reduction. Can GM produce a Green Revolution (GR) in Africa and would it be poverty
Their preliminary findings demonstrate that a simple absence of population pressure on the land slows yield growth, which itself largely explains labour productivity growth in agriculture. Labour productivity growth is the key determinant of wages, growth in GDP per capita and poverty reduction.
“Africa seems to have fared poorly in poverty reduction because many countries have abundant poor quality land,” the researchers explain, “There has been yield growth, but it has not led to growth in labour productivity, as it did during the Asian green revolution.” This finding suggests that GM technology that raises labour productivity could be enormously beneficial, so long as employment is maintained.
Their analysis reports that yield growth in Asia was about 2.6% per year, but that Africa was not far behind at 2.0%. However, labour productivity in Asia grew at 1.5% per annum, whereas Africa managed only 0.4%. Yields in Asia grew at 1.1% faster than labour productivity and there was substantial progress in poverty alleviation. In contrast, in Africa, yields grew 1.6% faster than labour productivity, but the impact on poverty has been less.
They explain that yield growth is in fact a main cause of labour productivity growth in both continents, but in Africa the impact is far weaker. The most obvious cause is that both yields and labour productivity grow less where land to labour ratios are low, which is particularly true in the countries of sub-saharan Africa, the researchers say.
Jenifer Piesse, Colin Thirtle (2008). Genetically modified crops, factor endowments, biased technological change, wages and poverty reduction International Journal of Biotechnology, 10 (2/3) DOI: 10.1504/IJBT.2008.018354
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