David Kirkpatrick

September 10, 2010

Graphene could speed up DNA sequencing

I’ve blogged on this topic before (and on this very news bit in the second post from the link), but this just reiterates the versatility of graphene and why the material has so many scientists, researchers and entrepreneurs so excited.

From the second link:

By drilling a tiny pore just a few-nanometers in diameter, called a , in the graphene membrane, they were able to measure exchange of ions through the pore and demonstrated that a long  can be pulled through the graphene nanopore just as a thread is pulled through the eye of a needle.

“By measuring the flow of ions passing through a nanopore drilled in graphene we have demonstrated that the thickness of graphene immersed in liquid is less then 1 nm thick, or many times thinner than the very thin membrane which separates a single animal or human cell from its surrounding environment,” says lead author Slaven Garaj, a Research Associate in the Department of Physics at Harvard. “This makes graphene the thinnest membrane able to separate two liquid compartments from each other. The thickness of the membrane was determined by its interaction with water molecules and ions.”

August 19, 2010

Graphene and DNA sequencing

News on potential applications of graphene is always interesting, but I’ll have to admit I’d like see more actual market-ready solutions. This news is both intriguing and promising, but the nut graf contains those dreaded words, “could help (insert the gist of any story here).” It’ll be a pretty exciting day when I blog about something that will help, instead of could help with graphene as the key helping element.

From the second link:

Layers of graphene that are only as thick as an atom could help make human DNA sequencing faster and cheaper. Harvard University and MIT researchers have shown that sheets of graphene could be a big improvement over membranes that are currently used for nanopore sequencing–a technique that promises to speed up and simplify the sequencing of long strands of DNA.

And:

The researchers create their membrane by placing a graphene flake over a 200-nanometer-wide opening in the middle of a silicon-nitride surface. Then they drill a few pores, just nanometers wide, in the graphene with an electron beam. The membrane is finally immersed in a salt solution that’s in contact with silver electrodes. The researchers observed dips in the current when a DNA strand passed through the pore, showing that the method could eventually be used to identify DNA bases.

May 28, 2010

Nanotech and DNA sequencing

Put the two together and you’ve got a solution for a major problem with the genome sequencing technique called nanopore translocation. And yet another application is found for graphene.

From the link:

But how do you measure the electrical properties of a single subunit among many tens or hundreds of thousands?

One of the most promising ideas is to make a tiny hole through a thin sheet of material and measure the amount of current that passes from one side of the sheet to another.

Next, pull a strand of DNA through this hole and measure the current again. Any difference must be caused by the nucleotide base that happens to blocking the hole at that moment.

So measuring the way the current changes as you pull the strand through the hole gives you a direct reading of the sequence of nucleotide bases in the strand.

Simple really. Except for one small problem. Even the thinnest films of semiconducting materials used for this process, such as silicon nitride, are between 10 and 100 times thicker than the distance between two nucleotide bases on a strand of DNA.

So when a strand of DNA passes through the hole, it’s not a single nucleotide base that blocks it but as many as 100. That makes it hard to determine the sequence from any change in the current.

Today, Grégory Schneider and buddies at the Kavli Institute of Nanoscience in The Netherlands present a solution to this problem. Instead of a conventional material, this team has used graphene, which is relatively easy to produce in sheets just a single atom thick.

Graphene is like a sheet of chicken wire made of carbon atoms. These guys have drilled holes of various diameters through just such a sheet using an electron beam to smash carbon atoms out of the structure.

November 5, 2009

Genome 10K Project

Filed under: Science, Technology — Tags: , , , , — David Kirkpatrick @ 2:59 pm

Via KurzweilAI.net — Interesting. And it is just amazing to think DNA sequencing costs are expected to go down by an order of magnitude or more over “the next couple of years.”

Genome 10K: A new ark
Science News, Nov. 4, 2009

The Genome 10K Project aims to collect tissues or cells from at least 10,000 vertebrate species, enough to catalog DNA sequences from about every vertebrate genus.

Its designers have decided to wait for sequencing costs to drop by a factor of 10 or more — probably in the next couple years — before launching their analytical program.

 

Read Original Article>>

September 13, 2008

Story ideas from the DoE’s Oak Ridge National Laboratory

Look for media on these stories in the coming weeks and months.

The press release:

September 2008 Story Tips

(Story Tips Archive)

Story ideas from the Department of Energy’s Oak Ridge National Laboratory. To arrange for an interview with a researcher, please contact the Communications and External Relations staff member identified at the end of each tip.

For more information on ORNL and its research and development activities, please refer to one of our Media Contacts. If you have a general media-related question or comment, you can send it to news@ornl.gov.

 

Transportation—New data available . . .

The Department of Energy has just released the 27th edition of the Transportation Energy Data Book. The book, available at http://cta.ornl.gov/data/index.shtml, is produced by Stacy Davis of Oak Ridge National Laboratory’s Center for Transportation Analysis. New data in this year’s edition include: transportation petroleum use by mode; ethanol consumption; number of vehicles per 1000 people in different regions of the world for 1996-2006 (China grew from 9.3 to 26.6); mpg for trucks as a function of speed; characteristics of daily driving; percent of housing units with a garage or carport; and more. The data book, created under the Office of Planning, Budget and Analysis in DOE’s Office of Energy Efficiency and Renewable Energy, draws together transportation data from diverse sources under a single, comprehensive document. It is a valuable tool for informing policymakers and analysts about activity in the transportation sector. Also available is http://www.fueleconomy.gov, maintained jointly by DOE’s Office of Energy Efficiency and the U.S. Environmental Protection Agency, which offers tips to help you reduce the amount of gas you use. [Contact: Mike Bradley; 865.576.9553; bradleymk@ornl.gov]

 

Energy—Microturbine magic . . .

Specialized skills and instruments at Oak Ridge National Laboratory are helping the world’s leading manufacturer of microturbines make products expected to set new standards for performance and reliability. Capstone Turbine Corp. of California credits ORNL and the High Temperature Materials Laboratory for playing a key role in developing the C200 microturbine with a generating capacity of 200 kilowatts. The unit boasts 33 percent efficiency and meets stringent California emissions requirements. While most of the microturbines sold by Capstone are used in land-based distributed generation applications, the company recently received a significant order for microturbines to be used in hybrid buses with double the fuel economy of a traditional diesel bus. This research has been funded by the Department of Energy’s Advanced Microturbines Program. [Contact: Ron Walli; 865.576.0226; wallira@ornl.gov]

 

Geology—Compelling evidence . . .

Fragments of tektites, natural glass objects, discovered by a team of geologists and geochemists help support a theory that a meteorite may be responsible for the sudden climate change that devastated large mammals in North America 11,000 years ago. While critics of such an extraterrestrial event have in the past noted the lack of evidence, the micro-tektites from the Clovis-age Murray Springs in Arizona could cause them to rethink their position. “These micro-tektites contain iron oxide spherules in a glassy iron-silica or silica matrix, which is one indicator of a possible meteorite impact,” said lead author Mostafa Fayek of the University of Manitoba in Winnipeg. “The spherules also contain elevated concentrations of vanadium and sulfur, and small amounts of titanium.” Colleague Larry Anovitz of the University of Tennessee noted that the chemistry of the spherules and matrix is consistent with that of tektites associated with other meteorite impact sites such as those found in Romania. [Contact: Ron Walli; 865.576.0226; wallira@ornl.gov]

 

Physics—Quadrupole DNA sequencing . . .

Research at Oak Ridge National Laboratory is exploring how a system of nanotubes, magnets and electrically charged particles could lead to a quicker, cheaper way to conduct DNA sequencing. The project headed by Predrag S. Krstic of ORNL’s Physics Division will use a nanoscale quadrupole Paul trap, a component of a mass spectrometer that captures ions in an electromagnetic field, to develop a high speed DNA sequencing device. Using the Paul trap to manipulate DNA between nanotube electrodes could result in a lower cost alternative to nanopore sequencing, which works by moving strands of DNA through a small hole in a membrane. Most of the work is being conducted in collaboration with the Mark A. Reed Research Group of Yale University. The research is funded by $722,000 from the National Human Genome Research Institute, part of the National Institutes of Health. The program seeks to cut the cost of whole-genome sequencing from millions of dollars to $1,000 or less, making individual genome sequencing cost-feasible for routine medical care. [Contact: Mike Bradley; 865.576.9553; bradleymk@ornl.gov]