Friday, December 5, 2008

The DNA Network

The DNA Network

If only I’d commissioned a tango on the RET proto-oncogene… []

Posted: 05 Dec 2008 04:24 PM CST

Maybe I’m a sucker for methylation, but when it comes to interpretive dance as a means of explaining one’s dissertation, my vote goes to “The role of folate in epigenetic regulation of colon carcinogenesis” by Lara Park of Tufts University.

You can see the rest here.

My First Twitter Interview [ScienceRoll]

Posted: 05 Dec 2008 02:22 PM CST, a Spanish medical site, kindly asked me to do an interview through Twitter. 15 short questions, 15 fast answers in the well-known 140 character-long format.

It will take place on the 10th of November (Wednesday) at 12:00 EST.

You can check it out if you visit my Twitter page.

Feel free to follow me, join the health 2.0 discussions or just check the links I publish on Twitter.



Radical Sharing Transforming Science [ScienceRoll]

Posted: 05 Dec 2008 02:16 PM CST

Cameron Neylon published another unique slideshow. The main question: Does science need transforming?


Healthcare in Second Life: Youtube Playlist [ScienceRoll]

Posted: 05 Dec 2008 02:13 PM CST

I just found a playlist on Youtube that is dedicated to healthcare in Second Life, the virtual world. Numerous videos about tools for medical education and sites for patient support.

An example:


When physicists try to talk genetics... [adaptivecomplexity's blog]

Posted: 05 Dec 2008 01:09 PM CST

...the result is never pretty. I made this point in a comment, but I've hoisted it up here because this issue deserves more visibility.

Physics professor Steve Hsu makes this argument:

read more

Overview of NGS platforms [Next Generation Sequencing]

Posted: 05 Dec 2008 09:10 AM CST

David Dooling over at PolITiGenomics has compiled a nice table with some important metrics of the three most prevalent NGS platforms - go check it out!

CNN Shuts Down its Science Journalism Department [The Daily Transcript]

Posted: 05 Dec 2008 08:54 AM CST

CNN, like most other MSM outfits have been sacrificing reporters, foreign correspondents in favor of pundits (aka political operatives), fancy gizmos (verging on a reenactment of Star Wars) and fluff. The canceling of their science journalism department is just the latest decision that underscores the decay of private-sponsored journalism in this country. Is it the MSM's fault or does it say something about the whims and wishes of the general public?

Sad. PZ says it best.

Read the comments on this post...

Flu Structure, Mp3s, and Magnetic Minestrone [Sciencebase Science Blog]

Posted: 05 Dec 2008 07:00 AM CST

You can read my latest science news updates in

One flu over - X-ray studies have revealed details of the structure of a protein used by the avian influenza, H5N1, that allows it to hide its RNA from the infected host’s immune system. The structure could provide a new target for the development of antiviral drugs against this potentially lethal virus

Minestrone and magnetic resonance - Researchers in the US and France may have overturned decades of theory in magnetic resonance studies by spotting a discrepancy in the way nuclear spins behave. Their new mathematical model of the process improves our understanding of atomic behaviour and could lead to better NMR spectra, sharper magnetic resonance images, and perhaps one day a fully portable MRI machine.

Organic soil matters - Could the earth beneath our feet hold the key to climate change? According to scientists at the University of Toronto Scarborough their NMR results show that global warming is changing the molecular structure of organic matter in soil.

Battery capacity is full of holes - Researchers in Korea have developed a novel material for the anode in rechargeable batteries, which they say could make them much more efficient and extend significantly the length of time between charges.

And on ChemWeb for science news with a chemical element:

First on the list in this week’s Alchemist, more on the new anode material, which is potentially good news for the iPod generation. In analytical research, HPLC has been used to spot dummy tequila and in medical chemistry US radiologists suggest that a dose of modified vitamin D could protect citizens from a dirty bomb attack. Next up, a new approach to addressing qubits allows for faster measurements that could take us a step closer to a quantum computer, while Yorkshire chemists are working out the best mix of starting materials to get the maximum height yield on their tasty products. Finally, this week’s award is a record breaker in the State where big is everything.

Flu Structure, Mp3s, and Magnetic Minestrone

Top Ten SNPs [Sciencebase Science Blog]

Posted: 05 Dec 2008 07:00 AM CST

dna-testIf you ever thought genetics was only about disease, then check out the popular SNPs list on SNPedia. A SNP (pronounced “snip”) is a single nucleotide polymorphism, which in BradSpeak(TM) is basically a difference in a bit of your DNA that makes you different from the rest.

Anyway, here’s the Top Five SNPs that might be described as having no obvious direct medical importance.

  • rs1815739 sprinters vs endurance athletes (I reckon I lack both)
  • rs7495174 green eye color and rs12913832 for blue eye color
  • rs6152 can prevent baldness (this was discovered far too late for me)
  • rs1805009 determines red hair (some “comedians” might suggest this be swapped to the second list below)
  • rs17822931 determines earwax (and presumably how well your ears stay clear of insect infestation)

And, here’s the more sober list of SNPs that could have serious medical implications should you happen to discover you have one of these when you have your genome read by the likes of 23andMe.

  • rs9939609 triggers obesity (not a genetic excuse for eating too much)
  • rs662799 prevents weight gain from high fat diets (ditto)
  • rs4420638 and rs429358 can raise the risk of Alzheimer’s disease by tenfold or more
  • rs7903146 and rs12255372 linked to type-2 diabetes, the latter also to breast cancer
  • rs324650 influences alcohol dependence, rs1799971 makes alcohol cravings stronger (it would not be funny to say, “Mine’s a pint, with a whisky chaser”, right now)

It was a twitter discussion between SNP experts mza and attilacsordas that led me to the SNP list.

Top Ten SNPs

Portuguese DNA database gets green light [My Biotech Life]

Posted: 05 Dec 2008 06:18 AM CST

Trying to keep up with the rest of Europe, Portugal is now ready to setup a DNA database of convicted criminals that receive sentences of 3 years or more. Basically the bad guys get booked and swabbed and the database should allow authorities to solve more crimes and convict the right people.

As I had stated a few months ago, the 3 years penalty rule is an iffy situation because there are some crimes like copyright infringement that can land you up to 3 years in jail.

The 3 year sentence aka "serious crime" rule is an obvious attempt to avoid the abusive DNA indexing of every criminal infraction. Sort of contrary to what takes place in the UK where anything except traffic infractions get you "tagged".

Keep in mind that the penal system in Portugal is way more bland than that of the US. Here, the maximum prison sentence is 25 years (No such thing as life in prison or death penalty).

The Portuguese authorities are doing their best to keep things as transparent as possible and have ensured that all will be done to guarantee the privacy of the data. Moreover, unlike the UK, criminal suspects will not be included in the DNA database and those that are acquitted will be immediately removed.

Not only criminal DNA information will be stored in the database. Anyone that wishes to be included in the database can do so. This can and has been found to be helpful in identifying missing persons and unidentified corpses.

Other countries like Spain and Greece have also recently began to maintain DNA databases.

[Image: Wikipedia:DNA]

Portuguese DNA database gets green light

Around the Blogs [Bitesize Bio]

Posted: 05 Dec 2008 04:58 AM CST

Three story highlights from related blogs:

All Graduate Student Supervisors Take Note
“This lovely piece has been circulating of late, but Sonke has been kind enough to allow the SCQ to present his “Advice for Potential Graduate Students” as a handy dandy pin-up, suitable for pinning up in some visible area of your lab.”

FDA Interested in Collaborating with Personal Genomics Companies
“[Genetic Future] describes an intriguing twist in the ongoing struggle between the nascent personal genomics industry and regulatory bodies: apparently the FDA is exploring the possibility of collaborating with consumer genomics providers to track adverse drug reactions”…

Increased Secretion in Senescent Cells, and Chris Patil on the Campisi Lab’s New PLoS Biology Paper: Cellular Senescence, Protein Secretion, and the Aging/Cancer Paradox
Chris Patil (Ouroboros) co-authors an interesting new paper in PLoS Biology, and bloggers discuss.

Gate Keepers for Genetic Information [The Gene Sherpa: Personalized Medicine and You]

Posted: 05 Dec 2008 04:48 AM CST

A recent set of comments came to me from a Genetic Counselor. They were well thought out, but I think she may have misinterpreted me... I pray that your attitude changes before you have a practice of...

[[ This is a content summary only. Visit my website for full links, other content, and more! ]]

Stock Response to “How 23andMe May Be Used In Medicine” [Think Gene]

Posted: 04 Dec 2008 10:56 PM CST

For your own use —at your practice, institution, or otherwise.

Regarding 23andMe and our genetic medical services, please note the following excepts from the 23andMe Terms of Service and the 23andMe Consent Form to which you agreed while purchasing your 23andMe test:

23andMe Terms of Service
“23andMe Service Is For Research and Educational Use Only. We Do Not Provide Medical Advice, And The Services Cannot Be Used For Health Ascertainment or Disease Purposes”
…”cannot be relied upon at this point for diagnostic purposes”

23andMe Consent Form
“You should not change your health behaviors on the basis of this information.”

Thus, applying 23andMe to your health care would be a violation of the 23andMe terms of service and, as stated, it “cannot be relied upon at this point for diagnostic purposes.” We think 23andMe is a great educational tool, and we are excited about its future potential, but we cannot use the test results to provide any medical services. Further, you consented to “not change your health behaviors on the basis of [23andMe],” so for us to counsel otherwise would be unethical.

Again, we would be honored to be caring for you, but any medical advice or genetic counseling services that we would provide would be exactly the same as for a patient without the 23andMe test.

Cancer Research Blog Carnival #16 [Bayblab]

Posted: 04 Dec 2008 10:47 PM CST

Welcome to the 16th Edition of the Cancer Research Blog Carnival, the monthly carnival of cancer-related blogging. This month's edition has a healthy dose of cancer stem cell news, and we'll kick it off right here at the Bayblab with a post from Rob on that very topic.

Rob describes a recent paper in Nature that casts some doubt on the cancer stem cell hypothesis - or at least the scarcity of these cells - though he doesn't think it's that serious a blow.
Part of the evidence for the cancer stem cell hypothesis is that when human tumour cells are implanted into an immunocompromised host mouse only a small percentage of these cells are capable of reproducing a tumour. This new paper demonstrates that if the host is more immunocompromised then a larger number of cells are capable of reproducing a tumour, instead of only as low as one in a million cells to as many as one in four.
Alexey at Hematopoiesis follows that up with a pair of research blogging posts also about stem cells and cancer. First off, he describes the complexity of the cell cycle and stem cell self-renewal, how disruptions in these processes can lead to hematological malignancies and how the complexity adds a layer of protection
So, on one hand, downregulation of those genes promotes stem cells to exit from a quiescent state and enter into cell cycle, leading to their expansion, exhaustion and cancer development, but on the another hand, the involvement of multiple genes could protect them from it.
This is followed with a post about age related changes in gene expression. Cancer is fairly well recognized as a disease of aging, but Alexey takes a closer look at specifics
Now, let's get close to cancer. Bmi-1 is known as a tumor promotor, and genes that it repress - Ink4a/Arf are tumor suppressors. Hmga2 is anti-aging, but is a tumor promotor. So, aging of adult stem cell system actually protects us from cancer.
Abel Pharmboy at Terra Sigillata has another piece about the link between aging and cancer. This one focuses on a recent PLoS Biology paper discussing senescence-associated secretory phenotype and how it may complicated therapies taking advantage of the senescence pathways.
Cells induced to undergo senescence with DNA-damaging agents exhibit a secretory phenotype, termed the senescence-associated secretory phenotype (SASP), whereby molecules involved in inflammation and metastasis are released into the local environment. In younger individuals, this
mechanism could prevent the development of cancer but in older individuals could increase the risk of cancer. In cancer, for example, therapies that causes cellular growth arrest and senescence may be of limited utility unless those senescent cells are removed. My takehome message from this paper is that we may have to rethink the benefit of cancer therapies that are cytostatic.
Abel Pharmboy was also able to talk to one of the authors directly about the significance of the paper.

While on the topic of unintended consequences, Philip Smith has sent us a story by dsantore at Sociology Eye. The brief piece describes the story of a New York Times editor taking testosterone suppressants as cancer treatment and found them gender blurring.
Among the more notable side effects are Jennings' shrinking testicles, hot flashes, and potentially enlarged breasts. The gendered implications of these bodily changes are not lost on Jennings
The original story in the NYT is an interesting cap on the month of Movember, and a reminder of some of the lesser thought of aspects of prostate cancer.

With that concludes the 16th edition of the Cancer Research Blog Carnival. The next one will appear Jan 2, but is still in need of a host. If you're sick of seeing it here at the Bayblab all the time, send us an email and we'll set you up as a future host. In the meantime, start writing posts for the next edition and submit them here. You can check out previous editions here.

Body-Swapping with a Mannequin [adaptivecomplexity's blog]

Posted: 04 Dec 2008 10:22 PM CST

If you need more proof of how easy the human brain is to fool, hop over to Scientific American's 60 second science and read about how a group of mad scientists used virtual reality goggle to get subjects to 'body-swap' with a mannequin.

I'm waiting for the Wii version.

read more

European ancestry associated with higher breast cancer risk? [Yann Klimentidis' Weblog]

Posted: 04 Dec 2008 09:28 PM CST

Latinas have been found to have a lower incidence of breast cancer than other ethnic groups. Indigenous Americans have the lowest incidence. This meta-review paper from a few months ago finds that ethnic disparities in breast cancer can be explained by SES, except for the lower incidence among African Americans.

So what do they find in this new paper (see abstract below)? It's a case control study with a pretty large sample size (440 cases and 597 controls, matched for age) of Latinas in the SF Bay area to determine whether genetic differences between groups account for differences in breast cancer incidence. They used 106 AIMs (ancestry informative markers). Interestingly:
"Breast cancer among Latinas presents a particularly
interesting case because the main ancestral components of the Latino population (European and Indigenous American) have the highest and lowest breast cancer incidence (1)."
They control for a suite of known breast cancer risk factors
(including education, but unfortunately, not income). Surprisingly the cases and controls differed significantly for many of the measured risk factors.

The main findings:
"In unadjusted models, we found a strong association between genetic ancestry (continuous) and breast cancer risk. Higher European ancestry was associated with increased risk, with an odds ratio (OR) of 1.79 [95% confidence intervals (95% CI), 1.28–2.79; P less than 0.001] for every 25% increase in European ancestry. When known risk factors and place of birth were adjusted for (Table 2), the association with European ancestry was somewhat attenuated but remained statistically significant (OR, 1.39; 95% CI, 1.06–2.11; P = 0.013). When African ancestry was included in the adjusted model, the association with European ancestry became stronger [OR for European ancestry, 1.54 (95% CI, 1.11–2.52; P = 0.004), and OR for African ancestry, 2.05 (95% CI, 1.00–7.56; P = 0.055)]."
They also looked at the association using genetic admixture and "using parent/grandparent European origin instead of genetic ancestry."
"We observed a significant association between the number of European-born parents/grandparents and breast cancer risk, with higher number of European ancestors being associated with increased risk (OR, 1.21; 95% CI, 1.02–1.44; P = 0.025, adjusted model)."
Although their results suggest that there may be some genetic risk factor specific to individuals with higher European ancestry, they are careful to acknowledge the possibility for residual confounders. It's too bad they didn't control for income and/or some other SES variables.

Genetic Ancestry and Risk of Breast Cancer among U.S. Latinas
Laura Fejerman, Esther M. John, Scott Huntsman, Kenny Beckman, Shweta Choudhry, Eliseo Perez-Stable, Esteban González Burchard and Elad Ziv
Cancer Research 2008;68(23):9723–8
Abstract: U.S. Latinas have a lower incidence of breast cancer compared with non-Latina White women. This difference is partially explained by differences in the prevalence of known risk factors. Genetic factors may also contribute to this difference in incidence. Latinas are an admixed population with most of their genetic ancestry from Europeans and Indigenous Americans. We used genetic markers to estimate the ancestry of Latina breast cancer cases and controls and assessed the association with genetic ancestry, adjusting for reproductive and other risk factors. We typed a set of 106 ancestry informative markers in 440 Latina women with breast cancer and 597 Latina controls from the San Francisco Bay area and estimated genetic ancestry using a maximum likelihood method. Odds ratios (OR) and 95% confidence intervals (95% CI) for ancestry modeled as a continuous variable were estimated using logistic regression with known risk factors included as covariates. Higher European ancestry was associated with increased breast cancer risk. The OR for a 25% increase in European ancestry was 1.79 (95% CI, 1.28–2.79; P less than 0.001). When known risk factors and place of birth were adjusted for, the association with European ancestry was attenuated but remained statistically significant (OR, 1.39; 95% CI, 1.06–2.11; P = 0.013). Further work is needed to determine if the association is due to genetic differences between populations or possibly due to environmental factors not measured.

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