Sunday, November 9, 2008

The DNA Network

The DNA Network

Molecular and Cell Biology Carnival #4 [the skeptical alchemist]

Posted: 09 Nov 2008 02:22 PM CST

Welcome to the fourth edition of the Molecular and Cell Biology Carnival! Let's get down to business right away...

FParrish presents Fly Flight Simulators: Science Videos - Science News - ScienCentral posted at Flies Playing Video Games...Could Lead To New Flying Robots. This is hands-down the most interesting submission of today's carnival, so I suggest you watch their YouTube video to find out more.

Phil B. presents Evolution is Dead posted at Phil for Humanity. This might be considered a controversial post, but I wanted to include it in this edition. Phil does not usually write strictly about science, but it is great to see that people who are not "in the works" take interest in these topics.

Larry Moran also contributed to this edition with his Gene Wiki posted over at Sandwalk.

GrrlScientist is the biggest contributor to today's edition (and I would like to invite her to become a host for one of the next editions). Her contributions are:

For the ones who think it's time for protein-interaction talk, 96well presents just another protein-interaction model, posted at Reportergene.

Cellular metabolism

Dr Shock presents Facts about Chocolate and Health posted at Dr Shock MD PhD, giving us an overview of what is known about the mechanism of action of cocoa polyphenols including clinical, pre-clinical and in vitro studies consistently show changes in biomarkers related to oxidative status and/or vascular function.


SciPhu presents Use of polyethylene glycol for drying polyacrylamide gels to avoid cracking posted at SciPhu.


In this section, we have a submission regardin career options for biologists, and a funny letter by a human-created organism:Khan presents Byte-Savvy Biologists, while Paras Chopra gives voice to the new organism in This is Synthia talking.

That concludes this edition. Submit your blog article to the next edition of molecular and cell biology carnival using our carnival submission form, or sending me an e-mail (address in the right column of this blog). Past posts and future hosts can be found on our blog carnival index page. We are still looking for hosts -- so if you are interested in hosting this blog on one of the second Sundays of the next few months, give me a shout!

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Crankishness. [Genomicron]

Posted: 09 Nov 2008 12:51 PM CST

As a brief follow up to the post about Dr. Andras Pellionisz's Google seminar, I cannot help but quote from his website:
Since a US Government-mandated (and taxpayer paid) 4-year study (ENCODE, led by Dr. Collins) established the scientific fact that (at the least a significant part of) formerly "written off" so-called "non-coding DNA" is massively involved in genome function, US government-supported professionals who after the release of ENCODE (reversal of the Establishment in 2007) neglect to to follow Dr. Collins' mandate that "the scientific community will have to re-think long-held beliefs" are actually liable for a hefty Class Action Lawsuit for Negligence when they disregard the established reversal of protocol and e.g. continue to "write off" investigation of 98.7% of the DNA in cases of grave genomic syndromes.
I really try to be fair with people like this, but woah. Can researchers be charged with negligence for what they don't study? (Assuming, that is, that there actually was a total dismissal of non-coding DNA, which there wasn't).

A Sunday with the Tardigrades [Discovering Biology in a Digital World]

Posted: 09 Nov 2008 10:36 AM CST

It was a wet and rainy day yesterday, and we have a dissecting microscope, so I decided to see if I could find some tardigrades.

Tardigrade photo by nebarnix

Reposted from Nov. 2006

Read the rest of this post... | Read the comments on this post...

A Lecture by Spencer Wells [The Genetic Genealogist]

Posted: 09 Nov 2008 10:04 AM CST

image Last week I had the opportunity to attend a lecture by Spencer Wells, director of the Genographic Project from National Geographic and IBM.

The talk was a Syracuse Symposium event, and the first big event ever to be held in Syracuse University’s new $110 million Life Sciences Center.  I thought it was fitting that the first event to celebrate the future of the new life sciences building was a lecture that examined the collective genetic journey of mankind.

Dr. Wells began by giving the audience a very brief introduction about DNA and genetic genealogy.  He included a great quote that “The question of origin is actually a question about genealogy.”  For those that are not familiar with the Genographic Project, it was launched in 2005 and includes three primary missions:

  1. Global DNA sampling from indigenous and traditional cultures which retain a geographic link with their current location;
  2. Public participation; and
  3. The legacy fund, which is funded by the public participation aspect of the project and aims to “empower indigenous and traditional peoples by supporting locally-led efforts.”

Dr. Wells is a great speaker and the hour-long lecture went by extremely quickly.  Some of the more interesting information he shared is not readily available on the Genographic Project’s website:

  • According to current projections, the project is about halfway finished and is predicted to end in 2011.
  • So far, 41,000 samples have been collected from indigenous populations, and 270,000 kits have been purchased by public participants in 130 countries (currently at about 800 kits ordered per week!).
  • The indigenous DNA samples are stored for future analysis - this will undoubtedly be an irreplaceable asset as indigenous populations continue to decline (although it does raise issues of informed consent; do indigenous people really understand the information?).
  • Eventually, the Genographic Project’s database will be searchable.

Valuable Research

He also highlighted the previous papers that resulted in party from the Genographic Project, including:

A new paper, soon to be released, will examine the genetic ancestry of the Toubou people indigenous to northern Chad in Saharan Africa.  The Toubou people have a rich and interesting history, but their actual genetic roots are unclear.  According to Sougoui, a Toubou:

"The Genographic Project is a great opportunity for us, the Toubou, because we are a people who are extremely interested in our origins… According to Toubou legend, we are a people who came from different places. This is a question that we continually talk about. We are anxiously waiting for the results of this study to answer this question for us. It is important for us as Toubou to know where we came from, how we got separated from other peoples, and how we actually fit into the world God created."

Dr. Wells showed a short clip of a new documentary that is being made about the Genographic Project.  In the clip, we were shown the challenges of collecting DNA from the Toubou; looks like it will be another very interesting documentary.  See more about the Toubou project here and here.

The Q&A Session

During the Q&A session, someone asked what regions are missing from the database.  Perhaps unsurprisingly, the answer was the Americas and Australia.  Apparently the Project has had a very difficult time getting permission to take samples from these populations.

Many of the questions reflected the fact that many people are confused about the inheritance of Y-DNA and mtDNA.  Half the them were about whether a child or a sibling would have the same or different Y-DNA or mtDNA.


Dr. Wells is a great lecturer, and I highly recommend watching him speak if you are ever able to do so.  I learned a great deal about the Genographic Project, and I look forward to the information that will continue to be released from this valuable endeavor.

Burrill and Company Personalized Medicine Meeting [The Gene Sherpa: Personalized Medicine and You]

Posted: 09 Nov 2008 09:09 AM CST

For all those people "In the Know" The Burrill Meeting is THE meeting to attend if you want to gain insight into the future of where Personalized Medicine is heading. Last year I was unable to attend...

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Rehabilitation in Modern Era: WiiHab and GestureTek [ScienceRoll]

Posted: 09 Nov 2008 07:30 AM CST

In the modern era of the history of rehabilitation, we have Nintendo Wii:

Nintendo Wii Fit:

Second Life, Virtual Ability:

And now Gesturetek:


MyFamilyHealth: Genetics and Personal Health Records [ScienceRoll]

Posted: 09 Nov 2008 07:19 AM CST

I’ve just come across MyFamilyHealth, an interesting genetic/PHR service:

MyFamilyHealth is a web-based service provided by Genseq Ltd., a privately-held personal genomics and health analytics company offering you the opportunity to learn about your genes and health. Through MyFamilyHealth services you can discover the disease risk and health conditions that run in your family. The company was founded in April 2007 by two successful entrepreneurs Jean-Yves Sireau and Jim Mellon.



  • create a family tree
  • record the family’s health history
  • review their health risks


  • their patients share family health history
  • identify and stratify risks based on the latest scientific guidelines
  • make more informed choices about diagnosis and treatment

But they are open to health organizations as well.


PRWeb: Webicina goes forward [ScienceRoll]

Posted: 09 Nov 2008 06:12 AM CST

PrWeb just published a press release about


The mission of Webicina is to build a bridge between medical professionals and e-patients by providing e-learning tools, personalized packages and online image building solutions. Webicina aims to help physicians make their online activity as efficient as possible and help patients how to find reliable medical information online.

Budapest, Hungary (PRWEB) November 6, 2008 — “Web 2.0 for physicians and patients”, that is the motto of Webicina, an online service focusing on how medical professionals of the 21st century can meet the expectations of e-patients and how patients can find reliable information and web 2.0 services about a specific medical condition.

E-patients are patients who try to find relevant medical information on the web; want to communicate with their doctors via e-mail or IM; share health stories in patient community sites and store their medical files online. They will change the way medicine is practiced and most of physicians are not ready for this challenge.

Webicina offers personalized medicine 2.0 packages that provide patients and physicians with all the web 2.0 tools they need to know about a medical specialty or medical condition. Patients who are interested in diabetes receive all the selected, quality blogs, blog carnivals, community sites, videos, slideshows, etc. focusing on diabetes in a digestible format.

It also helps doctors how to build a proper online reputation and the e-learning tools were designed to let them learn how to launch a successful medical blog; how to organize medical meetings in the virtual world of Second Life; and how to follow the medical literature more easily. Free e-courses are accessible without registration.

“We are sure web 2.0 can change the way healthcare is delivered and while the number of e-patients is growing rapidly, the number of web-savvy doctors is not, so we must help them to understand each other and be ready for the challenges web 2.0 sets up.” said Bertalan Mesko, founder of

For more information, or to schedule an interview, please contact Bertalan Mesko.


FDA approval for non-invasive brain stimulation [biomarker-driven mental health 2.0]

Posted: 08 Nov 2008 12:59 PM CST


Image via Wikipedia

re-posting from NARSAD news ... FDA approves an amazing new form of non-invasive magnetic brain stimulation for treatment resistant depression.

Great video demonstrates the methodology and its ability to interfere with neural processing with a high degree of temporal and spatial specificity. A new treatment that one day might be guided by genomic markers ? Perhaps.

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My Promethease Unbound [biomarker-driven mental health 2.0]

Posted: 07 Nov 2008 02:39 PM CST

Vulcan Chaining Prometheus, Rijksmuseum, Amsterdam

Image via Wikipedia

Thanks so very much to the folks at SNPedia for developing and sharing the Promethease analysis tool. What a delight to delve into my 23andMe profile ! I stumbled onto the usual dreary risks for this and that, and yes, I know I'm at risk for baldness, but did come up with a few bonus IQ points and moreover an allele that protects me from cannabis dependence (will have to return to Nijmegen sooner than later I suppose).

Just a sampling from the report ... what's in YOUR genome ?

rs2165241(T;T) >10x increased risk of exfoliation glaucoma (LOXL1)
rs2180439(T;T) 2x increased risk of baldness
rs1136287(T;T) 3.9x increased risk of wet age related macular degeneration (PEDF)
rs1426654(A;A) probably light-skinned, European ancestry
rs601338(A;A) resistance to Norwalk virus infection
rs324650(A;T) somewhat higher IQ (CHRM2)
rs1815739(C;T) mix of sprinting & endurance muscles (ACTN3)
rs16891982(C;G) if European, 7x more likely to have black hair (SLC45A2)
rs806368(C;C) lower risk of the development of substance dependence
rs1954787(T;T) ~10% less likely to respond to citalopram (HTR2A)
rs17822931(C;T) wet earwax
rs237025(A;A) MET/MET increased diabetes susceptibility
rs6449213(T;T) ~4x higher risk for hyperuracemia
rs1015362(C;C) 2-4x higher risk of sun sensitivity if part of risk haplotype (ASIP)
rs1800497(G;G) A2/A2 bupropion effective (DRD2)
rs363039(A;G) 2+ IQ points (SNAP25)
rs2383207(A;G) increased risk for heart disease
rs2987983(G;G) increased risk for prostate cancer
rs1800955(C;C) increased susceptibility to novelty seeking (DRD4)
rs2279744(G;G) generally more cancer prone (MDM2)
rs10260404(C;C) rs10239794(C;C) haplotype strongly associated with ALS
rs283413(A;C) 3.2x higher risk for PD (ADH1C)
rs1024611(G;G) increased risk of exercise induced ischemia (CCL2)
rs1328674(T;T) higher risk for RA (HTR2A)
rs2107301(A;A) 2.47x higher risk for prostate cancer
rs1801270(A;C) increased risk for lung cancer
rs1571801(T;T) >1.36x risk for prostate cancer
rs1799724(C;T) weak risk for Alzheimer's Disease
rs733618(C;T) 1.87x risk for myasthenia gravis (CTLA4)
rs7480010(G;G) increased susceptibility to Type II Diabetes
rs3018362(A;A) increases susceptibility to Osteoporotic fractures
rs4870044(T;T) increases susceptibility to Bone mineral density variations
rs806380(G;G) protection from cannabis dependence
rs17696736(G;G) associated with type-1 diabetes

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"sintinaptoo" is a nonword that makes it hard to read nonwords [biomarker-driven mental health 2.0]

Posted: 07 Nov 2008 06:04 AM CST


Image by Maproom Systems via Flickr

Like "Joe the Plumber" (whose real name is Samuel), CNTNAP2 (whose real name is CASPR2) has achieved a bit of fame lately. While recently appearing almost everywhere (here, here, here) except FOX News, CNTNAP2 (not Joe the Plumber) is apparently a transcriptional target of the infamous FOXP2 "language gene" - so says Sonja C. Vernes & colleagues [doi: 10.1056/NEJMoa0802828] who precipitated DNA-protein complexes using anti-FOXP2 antibodies from a cell line transiently expressing FOXP2. The team later evaluated measures of expressive and receptive language abilities and nonsense-word repetition and found that a series of snps - most significantly rs17236239 - were associated with performance of children from a consortium of families at risk for language impairment. This adds to several previous reports of CNTNAP2 and risk for autism, a disorder where language ability is severely impaired.

So what's all the fuss ? How can something so insignificant (rs17236239 not Joe the Plumber) stir up so much trouble ? Well, as reported in a previous post, the expression of CNTNAP2 in the developing superior temporal cortex may be a relevant clue since this brain region is activated by language tasks. Also, this gene encodes a rather massive protein which (as reported by Coman et al.,) seems to participate in the establishment of myelination and "nodes" that permit rapid neural transmission and long-range coordination across neural structures in the brain. Interestingly, this gene shows evidence for recent positive selection in humans (as posted on here and here) although the newly derived G-allele at rs17236239 seems to be the allele that is causing the language difficulties. My own 23andMe profile shows a middling A/G here which makes it slightly hard to recall and repeat "Samuel Wurzelbacher".

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