Technut News

New platform enables rapid, cost-effective analysis of entire genomes, and a systems-biology approach to the study of organisms

FOSTER CITY, Calif. – October 1, 2008 – Applied Biosystems (NYSE:ABI) today announced a new genomic analysis platform, the SOLiD™ 3 System, that is expected to enable scientists to sequence a human genome for approximately $10,000. Significant cost-reduction and productivity enhancements have been built into the company’s latest ultra-high-throughput genomic analysis platform, enabling researchers to dramatically drive down the cost of sequencing entire genomes of all organisms, and expand applications for RNA and epigenetic analysis. Use of this system is expected to help life science researchers move one step closer to the mainstream use of genomic data for clinical research and personalized medicine.

Earlier this year, Applied Biosystems used the SOLiD 3 System’s underlying oligonucleotide ligation and detection technology to sequence a human genome for less than $60,000. Technical enhancements to the new platform that enable higher sample and data throughput are expected to further decrease the cost of genomic sequencing. For example, the availability of lower cost genomic data is expected to accelerate disease association and biomarker discovery studies to improve diagnostics and disease management, support clinical trials that successfully match the right treatments for individuals, and help the general population to better understand their individual genetic makeup.

Jesse M. Gray, Ph.D., postdoctoral research fellow in the laboratory of Dr. Michael E. Greenberg, Ph.D., director of the F. M. Kirby Neurobiology Center at Children’s Hospital Boston, has been using the SOLiD Small RNA Expression Kit with multiplexing capability to investigate gene expression changes in response to nerve cell activation. He believes that the inherent scalability and sensitivity of the SOLiD technology has advantages for many sequencing-based and tag counting applications.

“The $10,000 genome represents yet another striking decrease in the cost per base for sequencing projects,” said Dr. Gray. “The reduced cost of sequencing will allow us to include more experimental time-points in our studies and run more experiments overall. This significant cost decrease will also allow for higher throughput across all types of sequencing experiments, not just for sequencing human genomes.”

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A drug that combines four different medicines and could halve deaths from heart attacks and stroke around the globe will enter human trials this week in London.

The once-a-day polypill has been the dream of doctors for many years, but because the drugs it contains, including aspirin, are cheap, there has been no financial incentive for the pharmaceutical industry to get involved.

Now, however, international teams of researchers, with the backing in the UK of the Wellcome Trust and the British Heart Foundation, are just a few years away from making the polypill an accessible reality.

Difficulties in combining four drugs in one tablet have been overcome and the Red Heart pill, as it has been christened, has been manufactured by the Indian generic drug company Dr Reddy’s. Volunteers are now being recruited for a 12-week pilot trial which will involve up to 700 people in six countries. If all goes well, the main trial with 5,000 to 7,000 volunteers will begin at the end of next year.

Anthony Rodgers, co-director of the clinical trials unit at the University of Auckland, leader of the project, said it had been a struggle to get the polypill this far. “The chances of mainstream pharmaceutical industry taking this on are slim.

“We spent a few years around about 2000-2002 trying to persuade a number of companies to do this, but got nowhere. Basically, their whole business model is around people paying a few hundred pounds a year for the latest blockbuster drug. A pill with established medicines that halved cardiovascular risk and could be available for £20 a year could be seen as a threat.”

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Yeah, let’s keep screwing around with health problems so people can make money off it.

The current greed based economy we have today just doesn’t have the right priorities…

In old movies we were going to improve society by making everything think like a computer. Now the goal is to make computers think like brains. Researchers at Missouri University of Science and Technology say they can make power network management more efficient by literally tapping brain cells grown on networks of electrodes.

The Missouri S&T group, working with researchers at Georgia Institute of Technology, plans to use the brain power to develop a new method for tracking and managing the constantly changing levels of power supply and demand.

Led by Dr. Ganesh Kumar Venayagamoorthy, associate professor of electrical and computer engineering, the researchers will use living neural networks composed of thousands of brain cells from laboratory rats to control simulated power grids in the lab. From those studies, the researchers hope to create a “biologically inspired” computer program to manage and control complex power grids in Mexico, Brazil, Nigeria and elsewhere.

“We want to develop a totally new architecture than what exists today,” says Venayagamoorthy, who also directs the Real-Time Power and Intelligent Systems Laboratory at Missouri S&T. “Power systems control is very complex, and the brain is a very flexible, very adaptable network. The brain is really good at handling uncertainties.”

Venayagamoorthy hopes to develop a system that is “inspired by the brain but not a replica. Nobody really understands completely how the brain works.”

The research is funded through a $2 million grant from the National Science Foundation’s Office of Emerging Frontiers in Research and Innovation.

The Missouri S&T team will work with researchers at Georgia Tech’s Laboratory for Neuroengineering, where the living neural networks have been developed and are housed and studied. A high-bandwidth Internet2 connection will connect those brain cells over 600 miles to Venayagamoorthy’s Real-Time Power and Intelligent Systems Laboratory. Missouri S&T researchers will transmit signals from that lab in Rolla, Mo., to the brain cells in the Atlanta lab, and will train those brain cells to recognize voltage signals and other information from Missouri S&T’s real-time simulator.

Venayagamoorthy’s lab is capable of simulating a power grid the size of Nigeria’s, or a portion of the combined New England and New York grid in the United States.

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In a surprise development that could have implications for powering electronics, cars and even the military, researchers at MIT have created the world’s first batteries constructed at the nano scale by microscopic viruses.

A much-buzzed-about paper published in the Proceedings of the National Academy of Sciences earlier this month details the team’s success in creating two of the three parts of a working battery—the positively charged anode and the electrolyte. But team leader Angela Belcher told PM Wednesday that the team has been seriously working on cathode technology for the past year, creating several complete prototypes.

“We haven’t published those yet, actually. We’re just getting ready to write them up and send them off,” says Belcher, who won a MacArthur genius grant for her work in 2004 and a Breakthrough Award from PM in 2006. “The cathode material has been a little more difficult, but we have several different candidates, and we have made full, working batteries.”

Instead of physically arranging the component parts, researchers genetically engineer viruses to attract individual molecules of materials they’re interested in, like cobalt oxide, from a solution, autonomously forming wires 17,000 times thinner than a sheet of paper that pack themselves together to form electrodes smaller than a human cell.

“Once you do the genetic engineering with the viruses themselves, you pour in the solution and they grow the right combination of these materials on them,” Belcher says.

The team is working on three main architectures: Filmlike structures—as small as a human cell—could form a clear film to power lab-on-a-chip applications to laminate into smart cards, or even to interface with implanted medical devices. Meshlike architectures—billions of tiny nano-components all interfaced together—might one day replace conventional batteries in larger applications such as laptops and cars. And fiberlike configurations—spun from liquid crystal like a spider’s silk—might one day be woven into textiles, providing a wearable power source for the military. “We definitely don’t have full batteries on those [fiber architectures]. We’ve only worked on single electrodes so far, but the idea is to try to make these fiber batteries that could be integrated into textiles and woven into lots of different shapes,” Belcher says.

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The next major advance in computer processors will likely be the move from today’s two-dimensional chips to three-dimensional circuits, and the first three-dimensional synchronization circuitry is now running at 1.4 gigahertz at the University of Rochester.

Unlike past attempts at 3-D chips, the Rochester chip is not simply a number of regular processors stacked on top of one another. It was designed and built specifically to optimize all key processing functions vertically, through multiple layers of processors, the same way ordinary chips optimize functions horizontally. The design means tasks such as synchronicity, power distribution, and long-distance signaling are all fully functioning in three dimensions for the first time.

“I call it a cube now, because it’s not just a chip anymore,” says Eby Friedman, Distinguished Professor of Electrical and Computer Engineering at Rochester and faculty director of the pro of the processor. “This is the way computing is going to have to be done in the future. When the chips are flush against each other, they can do things you could never do with a regular 2D chip.”

Friedman, working with engineering student Vasilis Pavlidis, says that many in the integrated circuit industry are talking about the limits of miniaturization, a point at which it will be impossible to pack more chips next to each other and thus limit the capabilities of future processors’. He says a number of integrated circuit designers anticipate someday expanding into the third dimension, stacking transistors on top of each other.

But with vertical expansion will come a host of difficulties, and Friedman says the key is to design a 3-D chip where all the layers interact like a single system. Friedman says getting all three levels of the 3-D chip to act in harmony is like trying to devise a traffic control system for the entire United States—and then layering two more United States above the first and somehow getting every bit of traffic from any point on any level to its destination on any other level—while simultaneously coordinating the traffic of millions of other drivers.

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A beloved pet bulldog has been fitted with a £10,000 bionic leg, which will help advance prosthetic techniques used to help bombing victims.

Coal, an eight-and-a-half year old hound had his left paw amputated because of cancer last year. He faced being put down because his other legs would be too weak to carry him.

But his determined owner Reg Walker, shelled out thousands of pounds to fit him with a sophisticated bionic leg, which was designed to be compatible with Coal’s own tissue.

The titanium alloy used mimics animal hide, allowing the skin and the bone from above to seal the metal implant below without it being rejected by the body.

It is only the second time such an operation had been performed on an animal, using a technique performed on a survivor of the London 7/7 bombings.

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Bionic implants that promise to give 45-year-olds the vision of someone 20 years younger could be available in just five years.

The ’super lenses’ will correct both long and short-sightedness, allowing patients to throw away their glasses for good.

What is more, those who undergo the half-hour operation will not develop cataracts in old age, the British Association’s Festival of Science heard.

Professor James Wolffsohn said: ‘Everyone over 45 would benefit because it means they will be able to see distance and near absolutely naturally.

‘It is the true definition of a bionic eye. You are replacing something that has aged in the eye with a technological structure.’

The concept is based on existing technology - the tiny plastic lenses that have been implanted into the eye after cataract surgery for decades.

These are stiff, however, and while the operation makes vision clearer, it does nothing to treat short or long-sightedness.

More flexible lenses called accommodating intraocular lenses have recently hit the market but they, like laser surgery, only treat either long or short sight.

Scientists are now trying to create extra-flexible ’super lenses’ which could be squeezed by the eye’s muscles into the shapes needed to focus on both near and distant objects - and all points in between.

They would be inserted into the eye in a simple operation that replaces the existing lens.

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Those of you who read this blog for sometime, already know some of my views concerning psychology. I am an avid supporter of “hard science”. Science that is based on solid facts and follows the reductionist paradigm. Even though solid facts are not always the answer and reductionism could be replaced in the following decades by something else, such as a holistic approach that focuses on “systems” rather than “reduction” (read this for example: Sacred Science: Using Faith to Explain Anomalies in Physics from Scientific American), I believe that this paradigm has just started to show its strength in cognitive science. Take this post for example: Neurons, politics and economics

The reason I am writing today is that I found this exciting article in Seed Magazine: A New State of Mind

The article speaks of Read Montague, director of the Human Neuroimaging Lab at Baylor College of Medicine in downtown Houston. He has participated in something very interesting researches which I was aware of. I was surprised, because I had forgotten his name, despite the fact that he was the mind behind some recent papers. However, what really suprised me was how all these researches are connected, what this man is studying and how his view on neuroscience coincides with mine. I am going to present the article and then I’ll make a few comments. If you are bored just skip the article.

Read Montague studies the actions of dopamine in the brain. However, his methodology is not an experimental (even though he is a researcher), but rather a theoritical one.

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Personalized genomics just got a lot more accessible. Until tonight, the cheapest genome scan was available for just under a thousand dollars. Thanks to improvements in microarray technology, 23andMe has been able to cut that cost by more than half — to $399 — well within the reach of cash-strapped grad students, frugal genealogy buffs and other not-so-early adopters.

“By taking advantage of continuing innovation we are able to introduce a new chip that will give people more relevant data at a lower price,” said Anne Wojcicki, co-founder of 23andMe. ”We are excited that we are opening doors for more people to learn about their health and ancestry and for more people to be able to participate in advancing research. It is important to democratize personal genetics and make it more accessible.”

On The Spittoon blog, Wojcicki mentioned that her company has also implemented a major technology upgrade. Among other things, their new chip can check people for a condition that makes taking some drugs extremely dangerous. If you are G6PD deficient, and unwittingly take the malaria drug primaquine, you’ll have a horrible reaction that may include hemolytic anemia and death.

By checking your genetic makeup before taking a new medication, you might be able to avoid that sort of nasty situation. In other words, the new test could give you a lifesaving warning.

Predicting how someone will respond to a drug before they ever take it, just by looking at their genes, is called pharmacogenetics. It is a rather new field, and not ready for prime-time yet, but I have a feeling that services like the one offered by 23andMe will greatly accelerate its development.

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Claudia Mitchell may look like your average 20-something college student. She is anything but.

As a result of an experimental surgery, Mitchell has become the first real “Bionic Woman”: part human, part computer.

Mitchell’s bionic life began in 2004 with a ride on a friend’s motorcycle. The bike suddenly spun out of control, and Mitchell’s left arm was severed by a highway divider. After her doctor’s attempts to reattach the arm proved unsuccessful, she was outfitted with a standard prosthetic arm.

Mitchell thought that her new prosthesis would make her life return to normal. But it didn’t work. Her amputation was almost at her shoulder, which made the prosthetic arm all but impossible for her to control.

“It just sat on the shelf. It didn’t do anything,” Mitchell said.

She grew depressed, thinking she would have to spend the rest of her life with one arm, unable to perform even the most basic tasks. What saved her was a tiny article about an experimental nerve surgery.

The “targeted reinnervation” surgery was developed by Dr. Todd Kuiken of the Rehabilitation Institute of Chicago. It was a radical idea: a robotic arm controlled not by a patient’s stump or shoulder, but by a patient’s thoughts.

Mitchell, a U.S. Marine, was ready to try anything to have a second functioning arm. She volunteered for the surgery.

During the six-hour procedure in 2006, doctors took the severed and dormant nerves in Mitchell’s shoulder, nerves that are used to control the movement of her arm, and put them under the muscle in her chest.

They wanted the nerves to reawaken and work her chest muscle. The doctors eventually used the electrical nerve signals from that chest muscle to power a new bionic arm.

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