technology

Nanopores as 'single molecule' sequencing candidates

Attila Csordas — Tue, 18 Nov 2008 03:14:53 -0800

Description

Nanopore sequencing is considered to be a next generation sequencing candidate enabling 'single molecule' sequencing using individual DNA fragments without amplification and the risk of introducing errors.

The biggest player in the field is Oxford Nanopore Technologies based in Oxford, UK, lead by Hagan Bayley, closest to making a working nanopore sequencer.

The principle is that DNA could be detected "as it passed through a pore by the interruption in the flow of ions through the aperture".

The pores, made from a ring of seven α-haemolysin membrane proteins, are the same as those that the infectious bacterium Staphylococcus aureus pushes into the membranes of other cells in order to create damaging holes.

Using the pores ion flow changes can be read out as electrical signals but the real challenge are: to come out with a method that gives distinguishable signals for all free nucleotides long enough.

Here Hagan Bayley's Oxford group might have the developed the proper hacks:

DNA cannot, for now, be run continuously through the nanopore, partly because of the need to hold each base in the pore long enough to disrupt the flow of ions. So, to do their sequence detection, Bayley's group has used genetic engineering and chemistry to make two alterations. At the pore's mouth, the team placed an exonuclease, an enzyme that grabs the ends of a DNA molecule from a solution running over the top. The enzyme then severs each base and directs it into the hole. At the other end of the pore, the group inserted a cyclodextrin plug, a ring-shaped molecule that narrows the neck. The passing bases have to squeeze through this plug and, as they do so, a phosphate group on the nucleotide briefly binds the cyclodextrin and blocks the pore. Because the bases are different sizes, they sit within the cyclodextrin for different lengths of time, and fill it to different extents, giving characteristic readouts for each base.

The nanopore efforts can be significant in the highly competitive race for faster and cheaper genome sequencing that might have a profound effect in medicine, agriculture, energy, biodiversity, evolutionary biology, genealogy and many other fields.

Biomedical Sciences and Biotechnology

Source

Personal genomes by Katharine Sanderson: Standard and pores Published online 5 November 2008 | Nature 456, 23-25 (2008) | doi:10.1038/456023a http://www.nature.com/news/2008/081105/full/456023a.html
http://www.nanoporetech.com/

The Internet Candidate Becomes the Internet President: Early Signs of the Importance of Technology to the Obama Administration

Jerry Sheehan — Mon, 17 Nov 2008 07:26:12 -0800

Description

Candidate Obama is widely recognized as having perfected the use of the Internet for the modern political campaign. From the use of the Web for fund-raising to marketing tax plans, Obama relied on the use of new media to help increase the breadth of his message.

President elect Obama has continued this trend with the transition team already making novel, and immediate, use of new information technologies. Obama launched Change.gov (http://www.change.gov) to detail the plans of his ambitious agenda and solicit input from citizens on how to improve this framework. Interestingly, the initial version of site contained an iteration of all of the campaign promises made by the candidate which was replaced within a week by a more general topical agenda. David All, of Slatecard.com, noted "I believe they were a bit out in front of themselves and realized after the fact that they didn't want to limit their agenda/priorities to what they put on the Web site before they had a clear picture of America's needs in a post-election environment."[1]

In addition to the use of the web, President Elect Obama has also embraced the use of Internet video. Obama announced that his weekly Presidential addresses will be made available not only on the radio, but also turned into YouTube videos. Barak made extensive use of YouTube during the campaign, uploading over 1800 videos that were viewed some 110 million times. Ellen Miller of the Sunlight Foundation, explains the potential importance of the use of this communication channel, "We're living, after all, in the Internet era. This is an individualized version of the 'fireside chats.' It's not delivered between 7 p.m. to 8 p.m. but whenever anyone wants to see it. I don't know if it necessarily creates transparency -- it's still a controlled, one-way message. But it creates the aura of a much more accessible presidency."[2]

Candidate Obama also made heavy use of personal communication technology, in particular the BlackBerry. This ubiquitous device allowed trusted colleagues and party officials to quickly, and most importantly privately communicate with the candidate. However, due to time constraints, security concerns, and public records act, it seems likely that this will be the one technology that gets eliminated as President Elect Obama transitions to the White House.[3] Not to worry though, aides have told reporters that Obama plans on being the first President to have a laptop on his desk in the Oval Office.[4]

Given how little has been done at the federal level to modernize rules regarding electronic communication for Executive Officials it will be important to watch Obama's technology efforts and the related interpretation of applicable laws on accessibility, record retention, etc. In a very real sense, the first Obama administration will likely write the rules for how these tools can, and should be, used by the President.

Science in the United States

Source

[1]"EXCLUSIVE: Agenda disappears from Obama Web", Stephen Dinan, Washington Times, November 11, 2008, http://www.washingtontimes.com/news/2008/nov/11/exclusive-obama-deletes-agenda-from-transition-web/
[2]"The YouTube Presidency", Jose Antonio Vargas, Washington Post, November 14, 2008, http://voices.washingtonpost.com/the-trail/2008/11/14/the_youtube_presidency.html
[3]"Lose the BlackBerry? Yes, He Can, Maybe", Jeff Zeleny, New York Times, November 15, 2008,http://www.nytimes.com/2008/11/16/us/politics/16blackberry.html
[4]"White House to cost Obama his 'BlackBerry'", ExpressIndia, November 16, 2008, http://www.expressindia.com/latest-news/White-House-to-cost-Obama-his---Blackberry--/386410/

Google Street View Captures The Damndest Things

Jerry Sheehan — Wed, 13 Aug 2008 17:33:00 -0700

NOTE: This content was aggregated from RSS feed. Original source is http://tech.einnews.com/news.php?fid=171649034

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E Recruits New Line's Greenwald as Programming VP

Jerry Sheehan — Wed, 13 Aug 2008 17:31:00 -0700

NOTE: This content was aggregated from RSS feed. Original source is http://tech.einnews.com/news.php?fid=171648264

E Recruits New Line's Greenwald as Programming VP ');" class=hotlink2>Television Wednesday named Beth Greenwald its vice president of original programming and series development, ...

Would-Be Linux Contributors May Get a Leg Up

Jerry Sheehan — Wed, 13 Aug 2008 17:29:00 -0700

NOTE: This content was aggregated from RSS feed. Original source is http://tech.einnews.com/news.php?fid=171647447

August 13, 2008 Would-Be Linux Contributors May Get a Leg Up By While Microsoft Windows is built by an army of the software giant' ...

Analyst: Apple to sell 4.47 million iPhones in quarter

Jerry Sheehan — Wed, 13 Aug 2008 17:29:00 -0700

NOTE: This content was aggregated from RSS feed. Original source is http://tech.einnews.com/news.php?fid=171647258

San Francisco - Apple will sell 4.47 million iPhone 3Gs in the current quarter, according a projection issued Wednesday by analyst Gene Munster of the ...

Magnetic RAM technology

Jerry Sheehan — Wed, 13 Aug 2008 17:29:00 -0700

NOTE: This content was aggregated from RSS feed. Original source is http://tech.einnews.com/news.php?fid=171647292

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Reflect Scientific to Present at 4th Annual Summer Technology Conference Hosted by Security Research Associates