Monday, October 20, 2008

The DNA Network

The DNA Network

Don’t forget your B12 [The Navigator - Navigenics Blog]

Posted: 20 Oct 2008 08:10 PM CDT

Michael Nierenberg, M.D.

imageAs far as vitamins go, the popular belief has been that B – or B12, specifically – is for brain. Memory, cognition and brain size have all appeared to benefit from the dietary supplement.

A new study suggests, however, that vitamin B12 doesn't slow cognitive decline in patients already diagnosed with mild to moderate Alzheimer's disease. Symptoms did not improve in 202 patients put on high doses of the vitamin.

But don't throw away your bottle of B vitamins just yet.

While the new study raises questions about the vitamin's ability to treat Alzheimer's disease, there is still a growing body of evidence indicating that it may be useful in preventing it. A number of clinical trials have determined that sufficient levels of vitamin B12 may be needed to keep the brain from shrinking and mental cognition from declining. So, it is more important than ever to make sure you're getting enough of this nutrient.

Bio-Boosted Bouquet []

Posted: 20 Oct 2008 06:33 PM CDT


Food tastes better. Flowers smell fresher. Crops enjoy a pollination advantage. These are just some of the advantages plants plants enjoy with a transgenic boost to their odor, assert scientists at Hebrew University in Jerusalem. The same lab is “full of genetically engineered flowers whose architecture, color and scent the researchers are trying to alter.” We’ll be really excited when they figure out how to make a blue rose.

If I was sick, I would be pissed off. [Mary Meets Dolly]

Posted: 20 Oct 2008 06:19 PM CDT

If I had Parkinson's or diabetes or any other degenerative disease, I would be hopping mad.  Why?  Because of the insistence of the American media and some politicians that embryonic stem cell research is the only hope for regenerative medicine, when in other countries treatments with adult stem cells ARE ALREADY BEING USED WITH SUCCESS!!!!! 

One of the ads for Barack Obama says:

My name is Jody Montgomery and my daughter Maddy was diagnosed with type 1 juvenile diabetes at age 3. Six times a day, I take her blood. Six times a day, I pray for a cure. Researchers are working hard to do just that. Our best hope is stem cell research, and that's why we
support Barack Obama.

Unfortunately, it is politicians like Obama, who insist that embryonic stem cells are the best thing since sliced bread and are subsequently confusing the issue, that are slowing the cure that people like Maddy needs.  We are so obsessed with the stem cells contained in the embryo that we are ignoring the advances in treating disease going on in other countries where people are not so myopic.

Thanks to the Stell-Cell-Therapy blog, I found this website.  The Repair Stem Cell Institute states:

While the American news media continues to focus its attention on embryonic stem cells, Europe, Asia and Latin America have established the lead in Repair Stem Cell technology. Here is our list of the top seven stem cell treatment centers in the world. There are two in Latin America, two in Europe, one in Israel, one in China, and one in Thailand.

Now, I am not saying that the Repair Stem Cell Institute is curing people left and right (even they don't say that) or that they are 100% reputable.  What I am pointing out is they have a list of diseases that they are willing to treat that is enormous.  If I was sick, I would find more hope there, than in Senator Obama's empty rhetoric and the so-called cures from embryos that are decades away.

Wake up America!  Regenerative medicine is happening NOW, just not here.  If we can just get our heads out of our "you-know-whats" long enough, we may begin to see that arguing over left-over embryos is getting us nowhere!.

Would you let an astrologer evaluate your child's 6th grade earth science curriculum? [adaptivecomplexity's blog]

Posted: 20 Oct 2008 02:13 PM CDT

Of course not. Then why do we have advocates of intelligent design pseudoscience evaluating the Texas state science standards for evolution? Among the intelligent design proponents evaluating the Texas science curriculum is Stephen Meyer, an armchair non-scientist who has proven over and over that he doesn't grasp even the basics of the theory he claims to be so astutely criticizing.

read more

On voting pro-life [Mary Meets Dolly]

Posted: 20 Oct 2008 02:06 PM CDT

At the risk of being redundant here is the audio of my interview at Sacred Heart Radio.  This time I am discussing what it means to vote pro-life.  Thank-you to Sacred Heart Radio and the Son Rise morning show with Brian Patrick for letting me put in my two cents! 
I sure wish that I was more eloquent, but through all the bumbling and stumbling I think I made my point.

Revenge of the clones: the immunology movie [Discovering Biology in a Digital World]

Posted: 20 Oct 2008 01:29 PM CDT

What happens when a group of streptococci stick to cells in your throat and start to make toxins?

Your body fights back by making clones.

strep.gifThe animated video, Fighting Infection by Clonal Selection, from Etsuko Uno and Drew Berry is so good that if I didn't know better, I would almost think it's really capturing clonal selection on film.

What is clonal selection?

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

Cardiopulmonary resuscitation with Bee Gees! [ScienceRoll]

Posted: 20 Oct 2008 01:27 PM CDT

You know well how important it is to know the rules of cardiopulmonary resuscitation properly. Now the University of Illinois medical school suggested to use the rhytm (103 beats per minute) of Stayin Alive, the famous song of Bee Gees.

“Properly performed CPR can triple survival rates for cardiac arrest, but many people hesitate to jump in because they don’t feel confident about maintaining the proper rhythm,” Matlock says in a news release. “Our research subjects felt that listening to “Stayin’ Alive” improved their ability to perform chest compressions at the proper speed, and indeed their performance even five weeks later was excellent,” Matlock says.

First, how to perform adult CPR and save a life according to the British Red Cross:

And the well-known song:

Let’s practice…


Come one, come all, and witness the molecular MACHINE [The Daily Transcript]

Posted: 20 Oct 2008 12:00 PM CDT

Last week was a big one for the Rapoport lab.

Throughout my years here, I've come to realy apreciate how structure biology can realy lead to insight. In the latest issue of Nature, two papers describe how proteins are pumped out of cells by the SecA secretory protein.

You can divide proteins into three classes, those that stay inside the cell, those that are pumped out of the cell and those that must be incorporated into the membrane. The problem with the last two classes of proteins is that they must cross a membrane. This is accomplished by the translocon, a protein conducting channel that is conserved throughout life. In bacteria it is reffered to as SecY and in eukaryotes (that wuld be us), Sec61. Secreated proteins completly traverse the channel while membrane bound proteins enter the chanel and exit sideways through a lateral gate.

So how are secreated and membrane bound proteins translocated through the translocon?

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

deCODE Genetics Sinking Low [Eye on DNA]

Posted: 20 Oct 2008 10:52 AM CDT

Nasdaq and taxi by victoriapeckham.deCODE Genetics is still sinking after it laid off 15% of its workforce this past March. At the time, I was told that I misread CEO Kari Stefansson’s remarks on the potentially negative future of the personal genomics marketplace but now I wonder if I was on target after all.

According to Portfolio’s David Ewing Duncan, deCODE may have its stock delisted from the Nasdaq Stock Market if it can’t “raise its market cap over the $50 million minimum by October 30.” Recent negative publicity surrounding the launch of its breast cancer genetic test couldn’t have helped either. Duncan also says that other biotech companies may suffer if they can’t find more investors or credit. Some may even choose to sell out to Big Pharma.

Sounds bad.

With the global economic slowdown that could lead to a major recession, we are being warned to downsize our lifestyle and to downsize NOW before we lose our jobs, our homes, and who knows what else. As I’ve mentioned before, personal genomics companies rely on people having disposable income to spend on non-necessities.

Times are going to get rough and not just for deCODE.

Photo credit: Victoria Peckham

Satisfy your voyeuristic desires... [adaptivecomplexity's blog]

Posted: 20 Oct 2008 10:02 AM CDT

Your desires for genome voyeurism, that is.

read more

Heart attack and stroke prevention: measuring lifetime risk [deCODE You]

Posted: 20 Oct 2008 09:43 AM CDT

Amy Doneen, Director of the Heart Attack & Stroke Prevention Center, Spokane, WA.

Amy Doneen, Director of the Heart Attack & Stroke Prevention Center, Spokane, WA.

Amy Doneen at the Heart Attack and Stroke Prevention Clinic in Spokane, Washington, talks about an “exciting new time” for preventive health care. Amy, a nurse practitioner, has been using nutrigenomics (the response of genes to nutrition) as part of the program for more than a decade and with outstanding results. “The goal,” says Amy “is to find out what path a patient is on to developing certain diseases and kick them off that path.” Scanning for risk factor for common conditions (such as diabetes, heart attack, several types of cancer etc.) She emphasizes the importance of gauging lifetime risk as against clinical tests that usually concentrate on immediate high risk. According to Amy, some people walk away from the second kind with a negative result and think things are always going to be fine. Genetic testing is just arriving to the market place, but Americans currently spending nearly $50 billion on stroke care alone, the time is ripe to back all advances in preventive medicine.

To read more and watch parts of the interview with Amy Doneen visit the deCODEme Customer Stories.

Automated transgenic sorters? [Reportergene]

Posted: 20 Oct 2008 09:37 AM CDT

Fluorescence activated cell sorters (FACs) are well-established machines able to separate different cell populations on the basis of their inner fluorescence. Although technical challenging, new strategies strive to adopt FACs architecture to the automated isolation of fluorescent organisms, like worms (recently appeared on Nature Methods) and Xenopus tadpoles (recently patented by WatchFrog). To date, with mice we have still to run boring PCR or setup tedious Southern blots to get out our offspring genotype. Maybe in future we will have an automated mice sorter, to date I found only an automated rodent trap patented in 1920.

Check out Scientific Blogging's Makeover [adaptivecomplexity's blog]

Posted: 20 Oct 2008 08:56 AM CDT

If you've been reading this blog via feed, it's time to come pay the home page a visit. Scientific Blogging has received its long-awaited makeover, and the place looks great. And if you're been thinking of starting a science blog, now is a great time to come over and start writing.

Explosive News [Sciencebase Science Blog]

Posted: 20 Oct 2008 07:00 AM CDT

In my column this week: US researchers have used NMR to help them develop a new high explosive material that can be melt cast into a charge with any shape (and presumably whose explosions could be monitored by the blast-proof thermometer).

Nanotubes and geckos caught the eye of The Alchemist this week as US chemists describe a way to out-gecko the gecko by developing a new material that simulates the animal’s hairy feet but is ten times as sticky. Adhering with the theme of sticking, European researchers have found a way to tether prions to a model cell membrane that could open up new research into diseases such as Creutzfeldt-Jakob, BSE and scrapie.

explosive-newsIn environmental news, recent insights into dust from the Sahara could improve our understanding of climate change. Finally, dust of another kind is being used in an entirely different way, by British researchers to protect a new type of thermometer used to measure the 3000 Kelvin temperatures of an explosion.

The crystal structure of a cancer-killing virus has been revealed. The 3D structure of the recently discovered Seneca Valley Virus-001 shows that it is unlike any other known member of the Picornaviridae viral family (which includes the common cold viruses), and confirms its recent designation as a separate genus “Senecavirus”.

Morbid tales for Waco CSI reveals how cheminformatics forensic scientists might use spectroscopy on skeletal remains to determine post-mortem interval, how long the corpse has been dead, in other words.

Under the Spotlight, over on Intute:

Oily fungus helps reduce acid rain - Researchers in Iran have discovered a fungus that can metabolise and absorb sulfur from crude oil and so reduce one of the major sources of air pollution when petroleum products are burned…

Radio samples - More than 20 years after Chernobyl, US researchers have travelled to Sweden and Poland to gain insight into how radioactive elements spewed out by the reactor fire have undergone “downward migration” into the soil…

The dark energy illusion - What if Copernicus were wrong and the earth actually has a special place in the universe? Not some metaphysical, philosophical, supernatural special place, but just special in that the local environment is not the same as other local environments across the reaches of space?

Explosive News

More On Revealing Surnames Using Genetic Genealogy [The Genetic Genealogist]

Posted: 20 Oct 2008 06:40 AM CDT


Image by gravitywave via Flickr

Last week I wrote about using genetic genealogy databases to identify someone’s surname (see “DNA Could Reveal Your Surname, Of Course.”)  The article discussed results from researcher Dr. Turi King which suggested that there is a 24% to 50% chance that two men who share the same surname share a common ancestor through that name, with chances increasing if the surname is rare.

Somehow I completely missed “Adoptees use DNA to find surname“, an article at BBC News this June.  Men who were adopted as children are using genetic genealogy databases in an attempt to identify their biological surname.  This is Dr. King’s research in motion.  Family Tree DNA, for example, has a project for Adopted people that is over 2 years old, and has a success rate of more than 30%, thanks in large part to their database of over 130,000 records.  From Bennett Greenspan:

“We now have a growing number of people who are adopted, who have tested with us and have matched several individuals with a particular surname, and maybe they haven’t matched anyone else with a different surname. From that, they can get the idea that they have at least found the surname they need to start looking for in the town in which they were born.”

The BBC article ends with Mark Jobling predicting what will happen in the future as technology opens doors for adopted individuals, stating that “tests offering better resolution on the whole genome should be able to solve other familial puzzles.”

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Posted: 20 Oct 2008 03:41 AM CDT

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Waste from gut bacteria helps host control weight, UT Southwestern researchers report [Think Gene]

Posted: 19 Oct 2008 08:10 PM CDT

Josh: This is a rather interesting study. It will certainly be at least 5 years before we could hope to see any drugs available that block this receptor (Gpr41). I would be more interested to see if there are variations in the gene encoding Gpr41, causing people to be more or less sensitive to the ligands, which in this case are fatty acids.

A single molecule in the intestinal wall, activated by the waste products from gut bacteria, plays a large role in controlling whether the host animals are lean or fatty, a research team, including scientists from UT Southwestern Medical Center, has found in a mouse study.

When activated, the molecule slows the movement of food through the intestine, allowing the animal to absorb more nutrients and thus gain weight. Without this signal, the animals weigh less.

The study shows that the host can use bacterial byproducts not only as a source of nutrients, but also as chemical signals to regulate body functions. It also points the way to a potential method of controlling weight, the researchers said.

“It’s quite possible that blocking this receptor molecule in the intestine might fight a certain kind of obesity by blocking absorption of energy from the gut,” said Dr. Masashi Yanagisawa, professor of molecular genetics at UT Southwestern and a senior co-author of the study, which appears online in Proceedings of the National Academy of Sciences.

Humans, like other animals, have a large and varied population of beneficial bacteria that live in the intestines. The bacteria break up large molecules that the host cannot digest. The host in turn absorbs many of the resulting small molecules for energy and nutrients.

“The number of bacteria in our gut far exceeds the total number of cells in our bodies,” said Dr. Yanagisawa.

“It’s truly a mutually beneficial relationship. We provide the bacteria with food, and in return they supply energy and nutrients,” he explained.

Using mice, the researchers focused on two species of bacteria that break up dietary fibers from food into small molecules called short-chain fatty acids. Dr. Yanagisawa’s team previously had found that short-chain fatty acids bind to and activate a receptor molecule in the gut wall called Gpr41, although little was known about the physiological outcome of Gpr41 activation.

The researchers disrupted communication between the bacteria and the hosts in two ways: raising normal mice under germ-free conditions so they lacked the bacteria, and genetically engineering other mice to lack Gpr41 so they were unable to respond to the bacteria.

In both cases, the mice weighed less and had a leaner build than their normal counterparts even though they all ate the same amount.

The researchers also found that in mice without Gpr41, the intestines passed food more quickly. They hypothesized that one action of Gpr41 is to slow down the motion that propels food forward, so that more nutrients can be absorbed. Thus, if the receptor cannot be activated, food is expelled more quickly, and the animal gets less energy from it.

Because mice totally lacking Gpr41 were still healthy and had intestinal function, the receptor may be a likely target for drugs that can slow, but not stop, energy intake, Dr. Yanagisawa said.

Source: UT Southwestern Medical Center

Buck S. Samuel, Abdullah Shaito, Toshiyuki Motoike, Federico E. Rey, Fredrik Backhed, Jill K. Manchester, Robert E. Hammer, S. Clay Williams, Jan Crowley, Masashi Yanagisawa, and Jeffrey I. Gordon. Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. PNAS published October 17, 2008, doi:10.1073/pnas.0808567105

Top 10 Genomics News from [Think Gene]

Posted: 19 Oct 2008 03:22 AM CDT

Caltech engineers build first-ever multi-input ‘plug-and-play’ synthetic RNA device [Think Gene]

Posted: 19 Oct 2008 01:45 AM CDT

Kevin: Very cool. It’s going to be a while before this is ready for any sort of practical application, but it is another great tool for the cyborg scientists of the future to use.

Engineers from the California Institute of Technology  have created a “plug-and-play” synthetic RNA device–a sort of eminently customizable biological computer–that is capable of taking in and responding to more than one biological or environmental signal at a time.

In the future, such devices could have a multitude of potential medical applications, including being used as sensors to sniff out tumor cells or determine when to turn modified genes on or off during cancer therapy.

A synthetic RNA device is a biological device that uses engineered modular components made of RNA nucleotides to perform a specific function–for instance, to detect and respond to biochemical signals inside a cell or in its immediate environment.

Created by Caltech’s Christina Smolke, assistant professor of chemical engineering, and Maung Nyan Win, postdoctoral scholar in chemical engineering, the device is made up of modules comprising the RNA-based biological equivalents of engineering’s sensors, actuators, and information transmitters. These individual components can be combined in a variety of different ways to create a device that can both detect and respond to what could conceivably be an almost infinite number of environmental and cellular signals.

This modular device processes these inputs in a manner almost identical to the logic gates used in computing; it can perform AND, NOR, NAND, and OR computations, and can perform signal filtering and signal gain operations. Smolke and Win’s creation is the first RNA device that can handle more than one incoming piece of biological information. “There’s been a lot of work done in single-input devices,” notes Smolke. “But this is the first demonstration that a multi-input RNA device is possible.”

Their work was published in the October 17 issue of the journal Science.

The modular–or plug-and-play–nature of the device’s design also means that it can be easily modified to suit almost any need. “Scientists won’t have to redesign their system every time they want the RNA device to take on a new function,” Smolke explains. “This modular framework allows you to quickly put a device together, then just as easily swap out the components for other ones and get a completely different kind of computation. We could generate huge libraries of well-defined sensors and assemble many different tailored devices from such component libraries.”

Although the work in the Science paper was done in yeast cells, Smolke says they have already shown that they can translate to mammalian cells as well. This makes it possible to consider using these devices in a wide variety of medical applications.

For instance, ongoing work in Smolke’s laboratory is looking at the packaging of these RNA devices–configured with the appropriate sensor modules–in human T cells. The synthetic device would literally be placed within the cell to detect certain signals–say, one or more particular biochemical markers that are given off by tumor cells. If those biomarkers were present, the RNA device would signal the T cell to spring into action against the putative tumor cell.

Similarly, an RNA device could be bundled alongside a modified gene as part of a targeted gene therapy package. One of the problems gene therapy faces today is its lack of specificity–it’s hard to make sure a modified gene meant to fix a problem in the liver reaches or is inserted in only liver cells. But an RNA device, Smolke says, could be customized to detect the unique biomarkers of a liver cell–or, better yet, of a diseased liver cell–and only then give the modified gene the go-ahead to do its stuff.

Source: California Institute of Technology

Maung Nyan Win and Christina D. Smolke
Science 17 October 2008:
Vol. 322. no. 5900, pp. 456 - 460
DOI: 10.1126/science.1160311

Call for Moderators [Think Gene]

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