Daily Archives: September 17, 2014

Craig Venter, Scientist - Reprogramming DNA to Create a More Information-Driven Species - Clip

By: zeitgeistminds

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Craig Venter, Scientist - Reprogramming DNA to Create a More Information-Driven Species - Clip - Video

Craig Venter, Scientist - Reprogramming DNA to Create a More Information-Driven Species

By: zeitgeistminds

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Craig Venter, Scientist - Reprogramming DNA to Create a More Information-Driven Species - Video

Your DNA TV Episode 5

By: Your DNA - The Creative Hub

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Your DNA TV Episode 5 - Video

A DNA sequencer the size of a cell phone could change where, and how, gene research occurs.

The DNA sequencer built by Oxford Nanopore draws power from a computers USB port.

One day in 1989, biophysicist David Deamer pulled his car off Californias Interstate 5 to hurriedly scribble down an idea. In a mental flash, he had pictured a strand of DNA threading its way through a microscopic pore. Grabbing a pen and a yellow pad, he sketched out a radical new way to study the molecule of life.

Twenty-five years later, the idea is now being commercialized as a gene sequencing machine thats no larger than a smartphone, and whose effects might eventually be similarly transformative.

Early versions of the instrument, called the MinION, have been reaching scientific labs over the past few months after long delays (see 10 Breakthrough Technologies 2012: Nanopore Sequencing). Its built by a U.K. company, Oxford Nanopore, that has raised $292 million and spent 10 years developing Deamers idea into a DNA sequencer unlike any other now available. It is four inches long and gets its power from a USB port on a computer. Unlike other commercial sequencing machines, which can be the size of a refrigerator and require jugs of pricey chemicals, this one measures DNA directly as the molecule is drawn through a tiny pore suspended in a membrane. Changes in electrical current are used to read off the chain of genetic letters, A, G, C, and T.

Scientists with early access to prototypes of the first commercial nanopore sequencer say its glitchy and error-prone but may still be the way scientists study DNA in the future. After testing it, Mick Watson, a bioinformatics researcher at the Roslin Institute, in Scotland, says nanopore sequencing is a disruptive technology that could, potentially, dominate the sequencing market for years to come.

Although researchers say the device is still desperately inaccurate, it can already carry out some unheard-of scientific feats. And then theres its size. A sequencer this small might one day let police read off a genome from a spot of blood at a crime scene, or permit doctors to pinpoint viruses in the midst of an epidemic. One scientist this month tweeted a picture of the sequencer on his dining room table, decoding DNA.

The MinION is the result of some very high-stakes R&D by Oxford, a 200-person company thats long has had its eye on the expanding market for high-speed DNA sequencers. Cracking that market wont be easy. About 90 percent of DNA data is produced on sequencing machines from a single company, Illumina of San Diego (see 50 Smartest Companies: Illumina). Its sequencers are so good that most of its competitors have ended up in Chapter 11 or retreated in ignominy.

David Deamer made this sketch in 1989 when the idea for nanopore sequencing came to him.

But now some big companies are betting that nanopores could be the technology to break Illuminas lucrative monopoly. Roche, which made a failed attempt to acquire Illumina in 2012, this year spent $125 million to buy Genia Technologies, a small nanopore company based in California, and invested in another, Stratos Genomics. Hitachi is also working on nanopore technology, as are startups like Electronic Biosciences.

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Radical New DNA Sequencer Finally Gets into Researchers Hands

By Sara Morrison

Boston.com Staff

September 16, 2014 7:42 AM

New DNA test technology that can distinguish between identical twins has linked one Dedham man to two 2004 rapes, the Suffolk County District Attorneys office announced on Monday.

Dwayne McNair, 33, and Anwar Thomas, 32, were accused of raping two women in 2004. Thomas pled guilty to the crimes in 2011 after a DNA test linked him to one of the rapes, but McNairs case was more complicated. The DNA test couldnt distinguish between McNair and his identical twin.

Now theres a new DNA test that claims it can detect genetic differences between identical twins. Prosecutors said the test did link McNair to the crime with a reasonable degree of certainty (hes two billion times more likely to be the source of the DNA than his brother, the DAs office said). He was arraigned in Suffolk Superior Court on Monday and held on $500,000 bail. He faces eight counts of aggravated rape and two counts of armed robbery.

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If the trial goes forward, it will be the first time the new DNA test, which was developed in late 2013, has been used in the state. Jake Wark, spokesperson for the Suffolk County DAs office, told Boston.com last week that the new test could be a breakthrough in prosecuting identical twins.

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Twin Linked to Rape Case With New DNA Test

By Sara Morrison

Boston.com Staff

September 16, 2014 7:42 AM

New DNA test technology that can distinguish between identical twins has linked one Dedham man to two 2004 rapes, the Suffolk County District Attorneys office announced on Monday.

Dwayne McNair, 33, and Anwar Thomas, 32, were accused of raping two women in 2004. Thomas pled guilty to the crimes in 2011 after a DNA test linked him to one of the rapes, but McNairs case was more complicated. The DNA test couldnt distinguish between McNair and his identical twin.

Now theres a new DNA test that claims it can detect genetic differences between identical twins. Prosecutors said the test did link McNair to the crime with a reasonable degree of certainty (hes two billion times more likely to be the source of the DNA than his brother, the DAs office said). He was arraigned in Suffolk Superior Court on Monday and held on $500,000 bail. He faces eight counts of aggravated rape and two counts of armed robbery.

Advertisement - Continue Reading Below

If the trial goes forward, it will be the first time the new DNA test, which was developed in late 2013, has been used in the state. Jake Wark, spokesperson for the Suffolk County DAs office, told Boston.com last week that the new test could be a breakthrough in prosecuting identical twins.

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Twin Linked to Rape Case Through New DNA Test

Researchers at Johns Hopkins have identified a highly sensitive means of analyzing very tiny amounts of DNA. The discovery, they say, could increase the ability of forensic scientists to match genetic material in some criminal investigations. It could also prevent the need for a painful, invasive test given to transplant patients at risk of rejecting their donor organs and replace it with a blood test that reveals traces of donor DNA.

In a report in the September issue of The Journal of Molecular Diagnostics, the research team says laboratory tests already show that the new analytical method compares favorably with a widely used DNA comparison technique. The researchers have applied for a patent.

The current method for comparing DNA to determine paternity and advance criminal investigations counts the number of repeats in certain highly repetitive blocks of DNA that are not part of genes. But, says James Eshleman, M.D., Ph.D., a professor of pathology at the Johns Hopkins University School of Medicine, "Repeat testing will only detect DNA that makes up at least 1 percent of a DNA sample, so it's not great for situations in which results depend on small amounts of material within a larger sample."

Making comparisons based on common "point mutations," or variations within actual genes, was long considered impractical because of the high costs of DNA sequence testing. But the cost of sequencing has fallen so low in recent years that Eshleman's team revisited the idea.

Choosing a block of DNA with 17 common point mutations in close proximity along the genome, Marija Debeljak, a technician in Eshleman's laboratory, looked for mismatches in various mixtures of lab-grown human cells. "We could detect cells when they made up just .01 percent of the mixture, which is a big improvement over the current method, which can only detect DNA that makes up 1 to 5 percent of a sample," Eshleman says.

In addition to forensic and paternity testing applications, the new method could also potentially be used to monitor the health of bone marrow transplant patients, Eshleman says. Testing transplant patients' blood for low levels of leukemia blood cells could theoretically be used as an early warning system, but current analysis based on the standard repeat testing is not sensitive enough to detect low levels of recurring leukemia DNA in blood.

In contrast, when the researchers tested bone marrow recipients' blood with their new system, they found that it could detect patient DNA. "If we're able to develop this test for commercial use, it could also free some solid-organ transplant recipients of the invasive biopsies that are currently used if rejection is suspected," Eshleman says. Other authors on the paper were Donald N. Freed, Jane A. Welch, Lisa Haley, Katie Beierl, Brian S. Iglehart, Aparna Pallavajjalla, Christopher D. Gocke, Mary S. Leffell, Ming-Tseh Lin, Jonathan Pevsner and Sarah J. Wheelan, all of The Johns Hopkins University.

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The above story is based on materials provided by Johns Hopkins Medicine. Note: Materials may be edited for content and length.

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Improved means of detecting mismatched DNA

BOSTON, Sept. 16 (UPI) -- A Boston-area man long suspected of two 2004 rapes was formally charged after a new DNA test linked him to the crimes and excluded his twin brother.

Dwayne McNair, 33, of Dedham pleaded not guilty Monday. His bail was set at $500,000.

McNair had been charged earlier and spent almost two years in jail. A judge ordered him released, and prosecutors dropped the charges while the new test, which can distinguish between identical twins, was conducted.

Prosecutors in Suffolk County said the test, used for the first time in Massachusetts, found there was only a 1 in 2 billion chance the DNA in the samples being tested could have come from McNair's brother, Dwight. McNair was indicted on eight counts of rape and two of armed robbery.

Another man, Anwar Thomas, 32, pleaded guilty in the case in 2011. But the prosecution of McNair was stymied by the possibility the DNA could have been his brother's.

2014 United Press International, Inc. All Rights Reserved. Any reproduction, republication, redistribution and/or modification of any UPI content is expressly prohibited without UPI's prior written consent.

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Identical twin linked to 2004 rapes by new DNA test