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Tech Beat - October 2, 2012

Tech Beat Archives

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Editor: Michael Baum
Date created: October 2, 2012
Date Modified: October 2, 2012 
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NIST, Columbia Engineering Collaborate on Inexpensive DNA Sequencing Method

Rapid, accurate genetic sequencing soon may be within reach of every doctor's office if recent research from the National Institute of Standards and Technology (NIST) and Columbia University's School of Engineering and Applied Science can be commercialized effectively. The team has demonstrated a potentially low-cost, reliable way to obtain the complete DNA sequences of any individual using a sort of molecular ticker-tape reader, potentially enabling easy detection of disease markers in a patient's DNA.

polynuclease sequence
Schematic of an artificial membrane, across which a voltage forces an ionized fluid through the nanopore. Nucleotides on a strand of DNA are first tagged with different-sized polymers, and then the strand is passed near the nanopore opening, where a polymerase cleaves the polymers and passes them one by one through the nanopore. As they pass, the pore produces a unique ionic current blockade signature due to the tag’s distinct chemical structure, thereby determining DNA sequence.
Credit: NIST
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While sequencing the genome of an animal species for the first time is so common that it hardly makes news anymore, it is less well known that sequencing any single individual's DNA is an expensive affair, costing many thousands of dollars using today's technology. An individual's genome carries markers that can provide advance warning of the risk of disease, but you need a fast, reliable and economical way of sequencing each patient's genes to take full advantage of them. Equally important is the need to continually sequence an individual's DNA over his or her lifetime, because the genetic code can be modified by many factors.

The new method determines DNA sequences by attaching distinct molecular "tags" to each of the four chemical building blocks, or "bases," that comprise the genetic information in a strand of DNA—abbreviated as A, G, C and T. Each of these polymer tags can then be cut from the strand and passed, one by one, through a nanometer-size hole in a membrane. A steady stream of fluid and ions flows through this "nanopore," which is large enough to contain only one tag at a time. As the polymer tags are different sizes, the change in electrical current caused by altered fluid flow shows which of the four bases sits at each point on the DNA strand.

Nanopores and their interaction with polymer molecules have been a longtime research focus of NIST scientist John Kasianowicz. His group collaborated with a team led by Jingyue Ju, director of Columbia's Center for Genome Technology and Biomolecular Engineering, which came up with the idea for tagging DNA building blocks for single molecule sequencing by nanopore detection. The ability to discriminate between the polymer tags was demonstrated by Kasianowicz, his NIST colleague Joseph Robertson, and others. Columbia University has applied for patents for the commercialization of the technology.

Kasianowicz estimates that the technique could identify a DNA building block with extremely high accuracy at an error rate of less than one in 500 million, and the necessary equipment would be within the reach of any medical provider. "The heart of the sequencer would be an operational amplifier that would cost much less than $1,000 for a one-time purchase," he says, "and the cost of materials and software should be trivial."

Kasianowicz adds that a private company might create a large array of nanopores that can analyze a single individual's genome cut up into many short strands of DNA, each of which could be sequenced quickly. Such an array potentially could provide the low-cost sequencing needed for routine medical use.

* S. Kumar, C. Tao, M. Chien, B. Hellner, A. Balijepalli, J.W.F. Robertson, Z. Li, J.J. Russo, J.E. Reiner, J.J. Kasianowicz and J. Ju. PEG-labeled nucleotides and nanopore detection for single molecule DNA sequencing by synthesis. Scientific Reports (Nature Publication group). Sept. 21, 2012. doi:10.1038/srep00684.

Media Contact: Chad Boutin, boutin@nist.gov, 301-975-4261

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NIST Selects Winner of Secure Hash Algorithm (SHA-3) Competition

The National Institute of Standards and Technology (NIST) today announced the winner of its five-year competition to select a new cryptographic hash algorithm, one of the fundamental tools of modern information security.

hash algorithm collage
Credit: K. Talbott/NIST with Shutterstock images
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The winning algorithm, Keccak (pronounced “catch-ack”), was created by Guido Bertoni, Joan Daemen and Gilles Van Assche of STMicroelectronics and Michaël Peeters of NXP Semiconductors. The team’s entry beat out 63 other submissions that NIST received after its open call for candidate algorithms in 2007, when it was thought that SHA-2, the standard secure hash algorithm, might be threatened. Keccak will now become NIST’s SHA-3 hash algorithm.

Hash algorithms are used widely for cryptographic applications that ensure the authenticity of digital documents, such as digital signatures and message authentication codes. These algorithms take an electronic file and generate a short "digest," a sort of digital fingerprint of the content. A good hash algorithm has a few vital characteristics. Any change in the original message, however small, must cause a change in the digest, and for any given file and digest, it must be infeasible for a forger to create a different file with the same digest.

The NIST team praised the Keccak algorithm for its many admirable qualities, including its elegant design and its ability to run well on many different computing devices. The clarity of Keccak’s construction lends itself to easy analysis (during the competition all submitted algorithms were made available for public examination and criticism), and Keccak has higher performance in hardware implementations than SHA-2 or any of the other finalists.

“Keccak has the added advantage of not being vulnerable in the same ways SHA-2 might be,” says NIST computer security expert Tim Polk. “An attack that could work on SHA-2 most likely would not work on Keccak because the two algorithms are designed so differently.”

Polk says that the two algorithms will offer security designers more flexibility. Despite the attacks that broke other somewhat similar but simpler hash algorithms in 2005 and 2006, SHA-2 has held up well and NIST considers SHA-2 to be secure and suitable for general use.

What then will SHA-3 be good for? While Polk says it may take years to identify all the possibilities for Keccak, it immediately provides an essential insurance policy in case SHA-2 is ever broken. He also speculates that the relatively compact nature of Keccak may make it useful for so-called “embedded” or smart devices that connect to electronic networks but are not themselves full-fledged computers. Examples include sensors in a building-wide security system and home appliances that can be controlled remotely.

“The Internet as we know it is expanding to link devices that many people do not ordinarily think of as being part of a network,” Polk says. “SHA-3 provides a new security tool for system and protocol designers, and that may create opportunities for security in networks that did not exist before.”

For more on the SHA3 competition, see http://csrc.nist.gov/groups/ST/hash/sha-3/index.html.

Media Contact: Chad Boutin, boutin@nist.gov, 301-975-4261

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Oct. 18 Colorado Workshop to Explore Plans For National Network for Manufacturing Innovation

Boulder, Colo., will be the site of the fourth and final public workshop to gather input on the design of the proposed National Network for Manufacturing Innovation (NNMI), on Oct. 18, 2012, at the Millennium Harvest House Boulder.

"Designing for Impact IV: Workshop on Building the NNMI" is organized by the Advanced Manufacturing National Program Office (AMNPO), a federal interagency body launched in late 2011 to coordinate federal resources and to promote collaborations addressing key manufacturing technology challenges and opportunities. Area hosts include the Colorado Office of Economic Development and International Trade, the University of Colorado Boulder, Colorado State University, and the National Renewable Energy Laboratory.

The Boulder workshop will be seeking ideas on the technology focus, organization, operation, management, and other topics and activities relating to the proposed network. It will be held one week before the Oct. 25, 2012, deadline for submitting comments in response to a formal "request for information"* issued by the AMNPO and published in the Federal Register on May 4.

Conceived to address strategic gaps in national capabilities to translate innovations into products and processes, the NNMI is envisioned as a network of up to 15 regional hubs—Institutes for Manufacturing Innovation. These collaborative institutes will connect research discoveries and emerging ideas for tomorrow's technologies and products with current U.S. manufacturers, as well as aspiring start-up firms. The network is proposed as a public-private collaboration in the president's fiscal year 2013 budget.

Regional partnerships will bring together industry, universities and community colleges, federal agencies and states to accelerate innovation by investing in industrially relevant manufacturing technologies with broad applications and to support education and training of an advanced manufacturing workforce.

Boulder workshop participants will learn about the principles and concepts behind the NNMI and participate in interactive sessions designed to solicit ideas on how to best structure the network and the institutes.

Facilitated interactive discussions will focus on four areas key to the success of the institutes:

  • technologies with broad impact,
  • institute structure and governance,
  • strategies for sustainable institute operations, and
  • education and workforce development.

Advance online registration is now open and will close by Oct. 16. A $45 event fee, payable at the time of registration, is required and includes a working lunch and two breaks. For more information on the workshop and to access the registration site, go to: http://manufacturing.gov/event_101812.html

A meeting announcement was published in the Federal Register on Sept. 28. The notice can be accessed from the workshop web page at http://manufacturing.gov/event_101812.html.

AMNPO is hosted by the National Institute of Standards and Technology. Partner agencies include the departments of Commerce, Defense, Energy, and Labor; NASA; and the National Science Foundation. For more information on the NNMI, go to: http://manufacturing.gov/nnmi.html

* See https://www.federalregister.gov/articles/2012/05/04/2012-10809/request-for-information-on-proposed-new-program-national-network-for-manufacturing-innovation-nnmi

Media Contact: Mark Bello, mark.bello@nist.gov, 301-975-3776

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NIST Special Publications 1200: New Means of Disseminating Lab Procedures

When scientists and engineers at the National Institute of Standards and Technology (NIST) want to tell their peers about experimental methods they have “road-tested” for reliability and consistent results, they can now spread the word via a new agency publication series.

tio2 nanotubes
An electron micrograph of nanotubes made from titanium dioxide (TiO2). Three of the first five documents in the new NIST Special Publications 1200 series describe protocols for preparing TiO2 dispersions for laboratory tests. (Color added for clarity.)
Credit: Argonne National Laboratory
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Documents in the NIST Special Publications 1200 (SP-1200) protocol series are guidebooks for the design and implementation of experiments that facilitate successful replication of results by others. These may include detailed procedural “recipes,” lists of required equipment and instruments, information on safety precautions, methods for calculating results and strategies for reporting standards.

“The NIST SP-1200 series lets our researchers share what would be the ‘methods section’ of a journal paper when a procedure is successful—even before there is enough research to warrant publication of a full article,” says Leah Kauffman, a NIST communications specialist and one of the creators of the system. “In fact, these documents may have more procedural detail than would typically be accommodated in a journal article.”

Kauffman says that the SP-1200 series offers a number of advantages over traditional means of disseminating pre-journal methodologies such as private communications, self-publishing or simple sharing on peer websites. “The publications are approved by NIST’s internal scientific review board, are easily accessible through the NIST Research Library’s online catalog* or the WorldCat global catalog, are available on the NIST Publications Portal, and most importantly, have a citable, permanent DOI [digital object identifier],” she says.

While the NIST SP-1200 series is meant for methods and protocols of any type, the fast-moving field of nanotechnology has provided the subject matter for the first five documents published. All five describe protocols for the measurement, dispersion and characterization of engineered nanoparticles in different media as developed by NIST and collaborators at Duke University's Center for the Environmental Implications of NanoTechnology (CEINT). The partners hope that by broadly disseminating these methods, it will lead to their broader acceptance and use in studies assessing the environmental, health and safety (EHS) impacts of nanoparticles.

To find NIST SP-1200 volumes, go to the NIST Publications Portal at www.nist.gov/publication-portal.cfm, select “Special Publication (NIST SP)” in the “By series” search block and then type “1200” in the “By report number” search block.

* NIST Research Library’s online catalog: www.nist.gov/nvl/nist_publications.cfm; WorldCat global catalog: www.worldcat.org; NIST Publications Portal: www.nist.gov/publication-portal.cfm

Media Contact: Michael E. Newman, michael.newman@nist.gov, 301-975-3025

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November Symposium Focuses on Forensics at NIST

The link between the National Institute of Standards and Technology (NIST) and forensic science dates back to 1913 when the agency’s predecessor, the National Bureau of Standards, served as the nation’s de facto criminal forensics laboratory until the Federal Bureau of Investigation hired its first scientist in 1932. Since that time, NIST has continued to play an important role in improving the accuracy and reliability of forensic science by developing calibration methods and reference standards, advancing state-of-the-art measurement techniques, and helping establish performance and procedural criteria. To showcase how NIST currently serves the forensics community, the agency is hosting “Forensics@NIST 2012” on Nov. 28-30, 2012, at NIST headquarters in Gaithersburg, Md.

cartridge case mark
NIST engineer Alan Zheng points to the firing pin impression, one of three marks impressed on the surface of a cartridge case when a gun is fired. The marks, also known as signatures, can act like fingerprints to identify a specific firearm and are key elements in NIST’s standard casing, Standard Reference Material 2461.
Credit: NIST
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Attendees at the three-day symposium will learn how NIST’s world-class laboratories and staff support many branches of forensic science including DNA analysis, arson investigation, trace evidence analysis, fingerprint impression analysis, biometrics, and computer and cell phone forensics. The event will feature 45 lectures and 40 poster presentations by NIST scientists, engineers and collaborators.

Each day will highlight a specific set of disciplines:

  • Nov. 28: forensic biology/DNA, firearms/toolmark analysis and fire research
  • Nov. 29: trace analysis/collection
  • Nov. 30: computer forensics, fingerprints and biometrics, and multimedia forensics

Along with access to a limited number of forensics product and service exhibitors, attendees at “Forensics@NIST 2012” will have the opportunity to experience a deployable forensic laboratory on display by one of the exhibitors that demonstrates how sampling, collection and analysis of evidence can be executed outside a traditional crime laboratory environment.

NIST is hosting the symposium at no cost to attendees. However, to allow as many people as possible to benefit from the event, participants are asked to sign up for only the specific days they plan to be present.

For more information and to register online, go to http://www.nist.gov/oles/forensics-2012.cfm. To learn more about NIST forensic science research, activities and resources, see http://www.nist.gov/oles/forensics/index.cfm.

Interested persons also may want to check out a video featuring presentations from recent NIST meetings on forensic science. It covers the July 10-11, 2012, “Measurement Science and Standards in Forensics Firearms Analysis Conference,” and may be accessed at www.nist.gov/oles/forensics/measurement-science-and-standards-in-forensic-firearms-analysis-webcast.cfm. Presentation topics include the current state of firearms analysis, manufacturing processes and procedures, measurement advances, and innovations in image and statistical analysis. An industry panel discussion on automated ballistic search and identification systems also is featured.

*Edited to update text on 05/02/14.

Media Contact: Michael E. Newman, michael.newman@nist.gov, 301-975-3025

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Third Annual NICE Workshop Adds a Virtual Cyber Threat Training and Competition Track

The National Institute of Standards and Technology (NIST) is offering a strong finale to National Cybersecurity Awareness month with its the third annual National Initiative for Cybersecurity Education (NICE) Workshop, Oct. 30 through Nov. 1, at its Gaithersburg, Md., campus.

NIST coordinates NICE, an interagency initiative focused on enhancing cybersecurity in the United States by raising national awareness about risks in cyberspace; improving cyber behavior, skills and knowledge in general; and cultivating a globally competitive cybersecurity workforce.

The theme of the 2012 workshop is “Shaping the Future of Cybersecurity Education—Connecting the Dots in Cyberspace.” It will focus on making cyber connections between government, academia, industry and the public to help NICe achieve its goals.

The workshop will feature four tracks focused on those goals:

  • Raising Awareness: Online Safety Starts with You!,
  • Education, Professionalism and Certifications,
  • Training and Maintaining a Competitive Cybersecurity Workforce, and
  • The Role of Cybersecurity in Competitions.

For the first time, the workshop will include a cybersecurity competition track with sessions focused on the role of competitions in NICE. Workshop attendees will observe students competing in an event called the Cyber Elite Challenge.

Student competitors will “harden” a network to protect against potential threats, assess and identify potential network vulnerabilities, diagnose and fix common vulnerabilities, and identify threats from routine network traffic – all part of the day-to-day reality for IT security professionals. Hosts of the competition in addition to NICE are the Department of Homeland Security and the Department of State Bureau of Diplomatic Security.

More information on the workshop, including an agenda and registration form is available at csrc.nist.gov/nice/2012workshop.

Media Contact: Evelyn Brown, evelyn.brown@nist.gov, 301-975-5661

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Three Experts Named to Earthquake Advisory Board

Three earthquake authorities from academia and the private sector have been appointed by Patrick Gallagher, Under Secretary of Commerce for Standards and Technology and Director of the National Institute of Standards and Technology (NIST), to serve on the Advisory Committee on Earthquake Hazards Reduction (ACEHR) of the National Earthquake Hazards Reduction Program (NEHRP).

Established by the Earthquake Hazards Reduction Act of 1977, NEHRP is the federal government’s program to reduce the risks to life and property from earthquakes. NEHRP consists of four federal agencies: the Federal Emergency Management Agency (FEMA), the National Science Foundation (NSF), the United States Geological Survey (USGS) and NIST, which serves as lead agency.

The new ACEHR members, whose terms extend to July 31, 2015, are: Craig Davis, geotechnical engineering manager, Los Angeles Department of Water and Power, Los Angeles, Calif.; Robert Herrmann, Paul C. Reinert Chair of Natural Sciences, Saint Louis University, St. Louis, Mo.; and Mary Lou Zoback, seismologist and consulting professor, Stanford University, Stanford, Calif. They join a group of nine previously appointed academic, industry and government experts on the ACEHR.

The committee’s responsibilities include assessing:

  • trends and developments in the science and engineering of earthquake hazards reduction;
  • the effectiveness of NEHRP in performing its statutory activities (fostering improved design and construction methods and practices; land use controls and redevelopment; prediction techniques and early-warning systems; coordinated emergency preparedness plans; and public education and involvement programs);
  • any need to revise NEHRP; and
  • the management, coordination, implementation, and activities of NEHRP.

More information on NEHRP and the ACEHR can be found at http://www.nehrp.gov.

Media Contact: Mark Bello, mark.bello@nist.gov, 301-975-3776

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