Article posted: 6/4/2012 12:27 PM

Daniel J. Olaska

Shaun Wild

Willie Hayes

The knife that prosecutors say killed schoolteacher Shaun Wild and injured two other men inside a Naperville nightclub can be tested for DNA, a judge ruled Monday.

DuPage County prosecutors said two bloodstains were found on the 5-inch blade seized by police after the Feb. 4 stabbings at Frankies Blue Room. DNA testing likely will destroy the stains and prevent further analysis, they said.

Defense attorney Brian Telander, who represents murder suspect Daniel Olaska of Naperville, did not object to the request, saying it isnt relevant to the issues in the case.

This isnt a whodunit, Telander said. Its a whydunit.

Prosecutors say security footage from several angles showed Olaska, 28, fatally stab Wild, 24, during a confrontation that allegedly began when another man, North Central College student and football player Willie Hayes, teased Olaska about drinking beer from a wineglass.

Prosecutors said Olaska stabbed Hayes in the chest, then stabbed Wild in the heart as the teacher tried to intervene. Olaska also is accused of stabbing bouncer Rafael Castaneda, who was injured holding the suspect until police arrived.

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DNA testing for knife that killed Naperville teacher

BINGHAMTON, NY and STONY BROOK, NY--(Marketwire -06/04/12)- The New York State Center of Excellence in Small Scale Systems Integration and Packaging at Binghamton University (S3IP), New York, and Applied DNA Sciences, Inc. (APDN) today announced the signing of a Memorandum of Understanding calling for collaboration on microelectronics research and commercialization, and other projects. The two organizations aim to embark on various projects, including further advancements in Applied DNA Sciences' forensic authentication and security technologies.

The partnership capitalizes on the skilled staff and advanced facilities at S3IP, combined with the technology, business experience and product lines of APDN. It comes at a time when the defense industry is searching for new ways to battle the increasing number of counterfeit electronics that have flooded both consumer and the military markets. The partners will aim to commercialize the resulting applications, with the potential to impact the estimated $3.1 billion annual flow of semiconductors to the U.S. military(1) and a global commercial market in semiconductors valued well in excess of $300 billion.

The new partnership was welcomed by United States Senator Kirsten Gillibrand (D-NY) who said, "New York is poised to lead in the high-tech economy of the future. When we partner our world class universities and research laboratories with cutting-edge businesses like S3IP in Binghamton and Applied DNA Sciences on Long Island, we can spark new innovation with the power to protect our defense technology, keep our country safe, and attract new businesses and new jobs to help grow our economy."

APDN, a leading security and authentication firm based in Long island, NY, and S3IP, which focuses on research and development in small scale systems, envisage accelerating APDN's commercial applications, filing new grant proposals, and advancing new research. The partners will develop a joint research program to develop new and ways to embed and authenticate DNA on various substrates. The advances are aimed at extending the company's botanically derived DNA technology to new verticals and to future needs. According to the Memorandum of Understanding signed by The Research Foundation for the State University of New York, whose office is located at Binghamton University Office of Sponsored Programs, and by APDN, the partners will aim to scale up new methods for SigNature DNA incorporation into and onto a variety of materials.

The program may also involve testing of marked packaging of microchips in coordination with APDN partners, and explore advances in rapid reading solutions for screening chips in varying scenarios.

"S3IP works in partnership with government, academia and industry to enable new electronics applications for energy, healthcare, telecommunications and consumer applications, and defense industries," said Bahgat Sammakia, interim vice president for research, and director of S3IP at Binghamton University. "We are excited about this partnership with Applied DNA Sciences, which will enable new research opportunities for our faculty, staff and students. This program is just one example of the benefits of working in collaboration with industry, the results of which will bridge our expertise in biotechnology and information technology to enable new opportunities for ensuring the security of our nation's electronic systems."

Said Dr. James A. Hayward, President and CEO of Applied DNA Sciences, "Our collaboration with Binghamton University extends our commitments to collaborative research with NYS universities, including our current work with Stony Brook University, and the College of Nanotechnology Science and Engineering at the University of Albany. Combined with Long Island's heritage in DNA science and in the defense industry, we could not be in a better strategic location to extend our biotechnologies for microelectronics."

About The New York State Center of Excellence in Small Scale Systems Integration and Packaging at Binghamton University (S3IP)

The Small Scale Systems Integration and Packaging (S3IP) Center is an academic research organization that enables new electronic applications and devices to improve the way people live and interact with their environment. The Integrated Electronics Engineering Center (IEEC), which a component of S3IP, is a New York State Center for Advanced Technology and is focused on electronic packaging.

Located at Binghamton University, these centers bring together partners from government, industry and academia to provide opportunities for collaborations that will advance microelectronics research and development. S3IP was designated as a New York State Center of Excellence in 2006.

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Binghamton University S3IP Center and Applied DNA Sciences Partner on DNA Authenticity Technologies for Microelectronics

DNA analyst: Andreas Sundquist cofounded DNAnexus, a company that uses cloud computing to analyze sequenced DNA. Technology Review

DNAnexus thinks cloud computing can help analyze sequenced DNA and push personalized medicine forward.

Since the completion of the Human Genome Project in 2003, a string of technological advances have made it faster and cheaper to sequence a human genome. But there's still a big problem: what do you do with all that data once you've unraveled it?

For Andreas Sundquist, the answer is to send it to the cloud. Sundquist is the CEO and cofounder of DNAnexus, a software startup that positions itself between DNA sequencing facilities and those who need to manage, and glean information from, sequenced genomesincluding academic researchers, doctors, and biotechnology and pharmaceutical companies.

"The more and more data you produce faster and cheaper, the more the bottleneckwhich used to be the DNA sequencing itselfis actually now the data management," he says.

Sundquist sees his company as an instant online genomics center, offering clients immediate access to vast stores of DNA data and to analysis tools so they can make sense of it alland potentially come up with better treatments for cancer and genetic diseases, as well as identify genetic links to diseases like autism and alcoholism.

Here's how it works: Your lab's data is uploaded to DNAnexus through a Web browser or sent via a DNA-sequencing machine connected to the Internet. It then sits in your cloud-based account (the company uses Amazon's and Google's cloud services). You log in to the account on your computer to see the data and use DNAnexus's tools to analyze it.

Eventually, Sundquist hopes DNAnexus will bring together lots of different genetic databases (which for now tend to exist on their own, without being linked to others), aiding research efforts, drug discoveries, and the creation of drug-targeting diagnostic tests.

And Sundquist expects the market for Mountain View, California-based DNAnexus's services will grow dramatically. He estimates that about 20,000 full genomes have already been sequenced worldwide, and predicts this will rise to a million in several years as the price and time required continue to fall (right now, he estimates the process takes about a day and costs roughly $4,000). All that data will amount to more than an exabyte of dataone billion gigabytesand hundreds of thousands of central processing units will be needed to analyze it all, he estimates.

DNAnexus isn't the only company betting on this growth. David Dooling, assistant director of the Genome Institute at Washington University in St. Louis, points out that several other companies are offering cloud-based DNA analysis services, too, including Illumina.

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A Startup Uses the Cloud to Unravel DNA

BY DAN ROZEK Staff Reporter drozek@suntimes.com June 4, 2012 11:46AM

Daniel Olaska

storyidforme: 31566953 tmspicid: 9212450 fileheaderid: 4208563

DNA testing can be done on two blood stains found on the knife authorities allege Daniel Olaska used to kill Naperville school teacher Shaun Wild, a DuPage County judge ruled Monday.

Prosecutors sought the genetic testing on the 5-inch-long folding knife to confirm it was the weapon used to kill Wild and wound two other men during a deadly Feb. 4 clash in a Naperville nightclub.

Judge Kathryn Creswell agreed to allow the testing after Olaska didnt object to testing the weapon, which was found by police in Frankies Blue Room after the late-night stabbings.

The DNA testing isnt crucial because security cameras captured the stabbings, which also were witnessed by other nightclub patrons, defense attorney Brian Telander said.

I dont think the results will be relevant. Its not a who-dunit, said Telander, who has hinted he will argue the stabbings occurred in self-defense during an altercation.

Olaska, 27, is charged with fatally stabbing the 24-year-old Wild, as well as wounding Wilds friend, 22-year-old William Hayes, and bar bouncer Rafael Castenada.

Olaska was arrested as he tried to leave the bar with other clubgoers after the 12:45 a.m. stabbings.

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DNA tests ordered on knife in stabbing death of Naperville teacher

After more than a decade of unsuccessful efforts to obtain DNA testing of evidence collected at the scene of a 1993 Pampa murder that sent him to death row, Henry Skinner won a major battle Friday when Texas Attorney General Greg Abbott recommended to a state appeals court that the testing take place.

In a filing with the Texas Court of Criminal Appeals, which is considering Skinner's latest request for the tests, Abbott said the state and Skinner's lawyers have reached a "preliminary understanding" to do the testing. The court still must approve the lawyers' agreed order.

Skinner, 50, was sentenced to die for the 1993 New Year's Eve murder of his girlfriend and her two adult sons. The convicted killer has argued that he had lost consciousness after consuming alcohol and codeine and, therefore, was not able to bludgeon the woman or stab her sons.

While some evidence had been subjected to DNA testing, clothing, knives and biological samples, including specimens from a rape examination, have not been tested.

Skinner has had at least two execution dates set. Last November, the appeals court issued a stay to ascertain how revised laws regarding such testing may apply to his case.

In his filing, Abbott said the state dropped its objections to testing "in the interest of justice." The attorney general also told the court the state will request testing of additional items submitted by prosecutors.

Skinner's lawyer, Rob Owen, visiting professor at Northwestern School of Law, said prosecutors had "squandered" an opportunity to test the items 12 years ago by barring defense counsel from a role in the deciding the issue.

"Texans expect accuracy in this death penalty case, and the procedures to be employed must ensure them confidence in the outcome," Owen said in an email. "To that end, all determinations about how and by whom the evidence will be handled and tested must be entirely transparent with both parties involved in every step."

allan.turner@chron.com

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AG agrees to DNA tests in convicted killer's case

9 hrs.

Devin Coldewey

When you think of robots in agriculture, you likelythink of automatic threshers, fruit picking machines and corn huskers. But a recent addition at an agricultural research center is doing fiddly lab work all day long -- at 100 times the rate of a full-time researcher.

There is much in science that requires a human touch: designing experiments, collecting field samples, and assessing the health of creatures in a study, for instance. But there are also many tedious portions, like running the same experiment on 50 different dishes of bacteria, and of course the inevitable sterilizing of lab equipment.

These tasks, more manual than intellectual labor (though no less critical to the end product), are beginning to be handed off to more capable, less error-prone hands. Hands that will work 24 hours a day, 7 days a week, no less.

What the Donald Danforth Plant Science Center is looking into is how certain plants, like wheat and rice, activate different genes encoded into their DNA. If they can learn how aplant, say, responds to cold weatherby flowering early, they can use that information to help producean improved plant with a shorter growth period. Dr. Todd Mockler's lab is working on improving biofuel plants like switchgrass, which may be critical to green energy in coming decades.

The experiment being performed is one that has a long history in biology, but has always been performed manually. It's called Yeast 1 hybridizing, and it consists of essentially copying and pasting short strands of plant DNA into yeast's well-known genetic code, and letting the yeast multiply. They can then test the effects of certain moleculeson just those bits of DNA.

It's a well-known technique, but not without its weaknesses. The main problem is that if you have a lot of material to check, you're looking at thousands upon thousands of experiments as you exhaust every possible combination of DNA snippet and activating molecule. This means months of mind-numbing work as lab technicians pipette substances from one test tube to another. On the other hand, as Dr. Mockler told me,it's very valuable when you get results, because they're not simulated; it's real DNA reacting as it would in the wild.

A perfect match for a tireless machine, then. A human researcher working 40 hours a week can perform the monotonous testing at a rate of about 2000 per week. But in April, they installed a robot arm and a number of other automated machines, which work together to perform 200,000 such tests weekly. Dr. Mockler said he hoped to bring about desired changes in plants, such as improved yield per plant or better resistance to drought, within a few years rather than a decade or two.

But although the robot is powerful and never sleeps, it's still just a robot. Even this highly sophisticated machine can only do what it's told. Dr. Mockler explains:

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DNA-wrangling robot performs 200,000 experiments a week

DNA samples recovered from a serious car collision in 2010 indicate that an off-duty Utica firefighter was behind the wheel at the time of the allegedly alcohol-related crash, prosecutors said Friday.

While prosecutors argue this is compelling evidence that Travis Maurine misled police when he initially said his unconscious girlfriend at the time, Kate Rizzo, was driving and not him, Maurines defense attorney said its no surprise that his DNA would be found in a vehicle they both used together.

The prosecutor, however, said that has nothing to do with DNA that was found on an airbag that deployed after the two-car collision on Route 233 in Rome on Dec. 18, 2010.

Once an airbag is deployed, its never used again, Assistant District Attorney Stacey Paolozzi said following a brief proceeding Friday in Oneida County Court.

Maurine, 25, of Waterville, was supposed to report whether he wanted to accept or reject a plea offer in connection to charges of second-degree and third-degree assault, second-degree vehicular assault, driving while intoxicated and failure to keep right.

But when Maurines attorney, George Aney, asked for more time to review Maurines hospital records and Rizzos blood results, Judge Michael L. Dwyer said Maurine will have until Tuesday, June 19, to make a final decision on the offer.

At this time, Aney said plea discussions have included the possibility of jail punishment.

Maurine is accused of moving his severely injured girlfriend into the drivers seat after the crash. Maurines blood alcohol level was not tested at the time, because first responders believed Rizzo had been driving, prosecutors said.

But once the near-fatal crash made the news, at least one person came forward to report that he or she might have seen the vehicle moments before the crash and that what they witnessed didnt coincide with what police were saying, Aney said.

Somebody may have called and said they might have observed something, and I think thats where the tide may have turned and police turned their investigation to both people in the vehicle, Aney said.

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DNA suggests Utica firefighter was driving in near-fatal crash

LEAMINGTON SPA, United Kingdom, May 31, 2012 /PRNewswire/ --DNA Dynamics, Inc. (OTC Pink: DNAD), a global developer and publisher of mobile videogames is delighted to announced that, through its wholly-owned subsidiary DNA Interactive Ltd, and in collaboration with Appbackr, Inc. and Bad Neighbors, Inc., THE NAKED GUN: I.C.U.P. is at long last now available for download on iOS devices.

Named as one of the most anticipated mobile games of 2012 by Pocket Gamer, THE NAKED GUN: I.C.U.P. was designed by DNA and Bad Neighbors as an uproarious adventure game that introduces a fresh twist to the venerable Paramount Pictures film franchise. Spoofing modern crime dramas and popular video gaming culture, THE NAKED GUN: I.C.U.P. features classic 2-D adventure gaming updated for today's modern audiences. Gameplay features include finger-numbing mini-games, collectible objects, upgradeable environments, completely arbitrary unlockable outfits and surprise cameos by some of the gaming world's most notoriously obnoxious characters.

Bob LoCash, the original film series writer/producer who penned the game's all-new storyline, stated, "Bringing this new chapter to life with the amazing and talented crew at DNA (I was held hostage for three days with a sack over my head until I agreed to the preceding statement) was a total pleasure. This game is something special - a funny and engaging piece of entertainment that will hopefully win the hearts of Naked Gun fans, gaming fans, and comedy fans alike. If not, there's always dinner theatre."

Channelling the hard-nosed, but dumb-witted characters brought to life in the film series, THE NAKED GUN: I.C.U.P tasks mobile gamers to follow Lt. Frank Drebin's son, Frank Drebin, Jr. along with his brand-new crime-fighting team to dispense justice on evil-doers which, let's face it, should be easier than finding morbidly obese people at a Renaissance Fair!

THE NAKED GUN: I.C.U.P. is available for $4.99 or about the same price as a gallon of milk for your needy family - from the App Store for iPad and iPhone.

About Bad Neighbors, Inc.Bad Neighbors Inc. is a multimedia company dedicated to returning the lost arts of narrative and twisted humor into video games, feature films, and television. THE NAKED GUN: I.C.U.P. is their first title. Other projects in development include the feature-film comedies THE NOBODY and STUDS, currently in pre-production with Stove Village Pictures.

About Appbackr Inc.Appbackr Inc. is a privately funded startup based in Palo Alto, CA. The first wholesale marketplace for apps, appbackr's approach revolutionizes the mobile industry by solving common funding and distribution problems. Appbackr enables app developers to raise cash without giving up equity in the company or product. Winner of the PayPal X Developer Challenge and SVASE/Cambridge West Ventures Seed Fund Award, the Company was also selected as an AlwaysOn Global 250 Company.

About DNA Interactive LtdEstablished in 2010, DNA Interactive, a wholly-owned subsidiary of DNA Dynamics, is a publisher of games and apps for mobile and tablet devices including iPhone, iPad and Android phones and tablets. At the present time, DNA Interactive's IP portfolio is comprised of proprietary game titles which include Quest of Legends, Jigsawium, Legacy: Mystery Mansion, Chess Crusade and Sudokium. Its licensed titles include The Naked Gunand Warheads: Medieval Tales. For more information, please visit http://www.dna-interactive.com.

About DNA Dynamics, Inc.Headquartered in Leamington Spa in the United Kingdom, DNA Dynamics is a worldwide developer and publisher of graphically rich, highly experiential interactive entertainment currently delivered on iOS, Android, Nintendo DS and Sony PSP platforms. Through its operating subsidiaries, DNA Studios and DNA Interactive, the Company has created, acquired or licensed a portfolio of highly recognizable or emerging brands that broadly appeal to its consumer demographics, ranging from children to adults and casual gamers to serious enthusiasts. For more information, please go to http://www.dnadynamics.net. You can also follow the Company on Facebook and Twitter.

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DNA Dynamics Announces Release Of THE NAKED GUN: I.C.U.P.® For iOS® Devices -- In Glorious 2-D

Public release date: 31-May-2012 [ | E-mail | Share ]

Contact: Yivsam Azgad news@weizmann.ac.il 972-893-43856 Weizmann Institute of Science

Our ability to "read" DNA has made tremendous progress in the past few decades, but the ability to understand and alter the genetic code, that is, to "rewrite" the DNA-encoded instructions, has lagged behind. A new Weizmann Institute study advances our understanding of the genetic code: It proposes a way of effectively introducing numerous carefully planned DNA segments into genomes of living cells and of testing the effects of these changes. The study is being reported in the June issues of Nature Biotechnology and Nature Genetics.

Until now, changing the DNA sequence has been a slow and labor-intensive process. It took several weeks to alter just one DNA region at a time; testing the effects of each of these changes took even longer. In the new study, Weizmann Institute scientists have developed a technology that makes it possible to simultaneously introduce tens of thousands of DNA regions into tens of thousands of living cells each region in a separate cell in a planned and systematic manner, and to measure the results of each such change with great precision and within a single experiment.

"This fast method will significantly advance our ability to understand the 'language' of DNA," says research team leader Prof. Eran Segal, of the Weizmann Institute's Computer Science and Applied Mathematics and Molecular Cell Biology Departments. "Reading out a person's entire genome is already a manageable task, but what exactly is written in that genome? After all, a genome looks like a lengthy string of letters whose meaning is for the most part obscure. Just deciphering the DNA letters is like trying to understand a foreign language by listening to it being spoken. Our method will help us identify DNA 'words' and understand their meaning."

Understanding what's written in the DNA might help us interpret, among other things, how genotypic differences among people generate observable differences among them, from the way we look to the way our cells function. Thus, for example, it might be possible to clarify which genetic differences are responsible for the development of various diseases in certain individuals. The Weizmann Institute technology can also lead to improved genetic therapies based on introducing new genes or improved regulatory sequences into cells in order to repair genetic defects.

In the present study, the scientists investigated a vital aspect of the DNA language: How the control of gene expression is encoded in the DNA that is, the instructions determining the level of activity of each gene in the genetic code. Since gene activity levels have crucial effects on cell function, this question, considered one of the central in molecular biology, has been studied for decades. The new technology has enabled the scientists to isolate and test the effects of various parameters on gene activity levels: For example, how a gene's activity level is affected by the gene's distance from its regulatory sequence. The researchers have managed to elucidate how various parameters define the regulatory "language" and to demonstrate how deliberate changes in the genetic sequence affect these parameters in a way that alters the level of a gene's activity in a predictable manner.

The new method consists of four steps that combine existing technologies in an innovative manner. The steps are: creation of 50,000 different genetic sequences on DNA chips; massive insertion of these sequences into cells at the same time; sorting the cells with the help of a sorting machine that senses the expression levels of a "reporter" gene; and high-throughput parallel DNA sequencing.

Taking part in the study were Weizmann Institute's graduate students Eilon Sharon, Tali Raveh-Sadka and Michal Levo, research assistant Dr. Yael Kalma and research associate Dr. Adina Weinberger, as well as Dr. Zohar Yakhini from the Technion Israel Institute of Technology and Agilent Laboratories, Santa Clara, California.

###

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Rewriting DNA to understand what it says

SAN DIEGO--(BUSINESS WIRE)--

Illumina (ILMN) today introduced the Nextera XT DNA Sample Preparation Kit, the easiest way for researchers to prepare and sequence small genomes, PCR amplicons, and plasmids. When paired with Illuminas MiSeq system, Nextera XT provides the fastest time to result of any next-generation sequencing technology currently available, enabling researchers to go from genomic DNA to analyzed data in less than 8 hours.

Nextera is the industrys fastest sequencing sample preparation technology, with a simple assay that fragments DNA and inserts sequencing adapters and barcodes, all in a single tube. Nextera XT builds on this foundation with its cost-effective and improved workflow. The kits innovative sample normalization procedure eliminates the need for library quantitation prior to sample pooling and sequencing.

Whether you are sequencing bacterial or viral genomes, plasmids, or PCR amplicons, the Nextera XT DNA Sample Preparation kit delivers the fastest time to answer, said Christian Henry, Senior Vice President and General Manager of Illuminas Genomic Solutions Business. Researchers will easily and cost-effectively be able to prepare a large number of amplicons by simultaneously pooling and preparing them with Nextera XT. Up to 96 samples can then be combined and rapidly sequenced to enable flexible and scalable study design.

Additionally, Nextera XT DNA Sample Preparation Kits offer unique benefits to researchers including:

Nextera XT made transitioning our targeted HIV amplicon sequencing experiments to the MiSeq system extremely easy, said Dr. Jacques Corbeil from the Infectious Disease Research Center in Quebec and Canada Research Chair in Medical Genomics. The output of the MiSeq system helps us screen many more samples rapidly, and its high-quality data enables us to detect low-frequency HIV variants.

Illuminas Nextera XT DNA Sample Preparation Kits are now shipping. For more information, visit http://www.illumina.com/xt.

About Illumina

Illumina (www.illumina.com) is a leading developer, manufacturer, and marketer of life science tools and integrated systems for the analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA, and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare.

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Illumina Introduces Nextera® XT DNA Sample Preparation Kits

LEGO, eat your heart out. Blocks of DNA have been programmed to automatically build themselves into nanoscopic structures. Eventually the DNA programmes will be sophisticated enough to churn out minuscule therapeutic devices that work inside the body.

Single-stranded DNA has already proved itself to be a useful addition to the nanotechnologist's toolbox. A very long strand can be intricately folded into complex 3D structures through a process known, appropriately, as DNA origami. These structures could be used to ferry drugs to specific sites in the human body.

But those long strands typically come from a virus, which raises the possibility that the body will attack the structures. Now, Peng Yin and colleagues at Harvard University have designed a similar technology that relies entirely on synthetic DNA. "Our structures could be made to be highly biocompatible," he says.

Instead of folding one long strand of viral DNA, Yin's team designed short synthetic DNA strands that can fold into a small tile, just 7 by 3 nanometres in size. "Each tile acts like a Lego block," he says. Tiles automatically interlock with neighbouring tiles that carry a complementary DNA sequence. This means that with a bit of forward planning, the team could design a complete set of tiles that lock together to create more than 100 shapes - including any letter of the alphabet.

The synthetic DNA shapes could dodge the immune system, buying them more time to shuttle drugs to the right tissue (Nature, DOI: 10.1038/nature11075).

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DNA origami: synthetic tiles can make over 100 shapes

B. Wei et al. / Wyss Institute, Harvard

This atomic-force microscopy shows 100 shapes, each created from tiles of DNA strands. Each shape takes up a space measuring 150 by 150 nanometers, or roughly one-thousandth the width of a human hair.

By Alan Boyle

The DNA molecule serves as the code of life, but it also serves as handy building material for nanoscale structures and newly published research shows how patterns as complex as letters, numbers and smiley faces can be created far more cheaply and quickly than previously thought.

Harvard researchers demonstrate the latest twists in this week's issue of the journal Nature. The process involves laying out short segmentsof DNA in a tile-shaped pattern determined by custom-designed chemical bonds. Those single-stranded tiles, in turn, can assemble themselves into larger shapes like Lego blocks, depending on how the bonds attach to one another. Different recipes for mixing the tiles together will produce different shapes.

The researchers Bryan Wei, Mingjie Dai and Peng Yinestimate that the process yielded the desired structure 12 to 17 percent of the time. That yield is far from perfect, but it could be perfectly acceptable for a process involving thousands upon thousands of self-assembling molecules.

The technique updates a construction strategy that was first pioneered in the 1980s. Back then, it took two years to create a 7-nanometer-wide cube from 10 strands of DNA, Caltech's Paul Rothemund and Aarhus University's Ebbe Sloth Andersen observed in a Nature commentary on the research. In contrast, the newly reported results suggest that far more complex shapes, measuring more than 100 nanometers across, could be churned out at an average rate of one per hour. (A human hair is roughly 100,000 nanometers wide.)

Another attractive factor has to do with the cost: An alternate method for creating nanoscale shapes, known as DNA origami, twists one long molecular strand into a desired shape rather than using lots of smaller tiles. But for each different shape, a new set of molecular "staples" has to be synthesized at a cost of roughly $1,000, according to the Nature commentary. The Harvard researchers' method involves creating a $7,000 set of tiles that could theoretically produce 2 X 10^93 shapes. That's a 2 followed by 93 zeros.

In their Nature paper, Wei and his colleagues showed off 100 shapes including the Roman alphabet, numerical digits, punctuation marks, the peace sign, Chinese characters and 10 kinds of emoticons. They made use of a custom-designed computer program to aid in the design of the shapes and control the liquid-handling robot that mixed the DNA ingredients.

"This advance truly brings DNA nanotechnology into the rapid-prototyping age, and enables DNA shapes to be tailored for every experiment," Rothemund and Andersen wrote in their commentary.

Link:
DNA designs done faster, cheaper

ScienceDaily (May 30, 2012) Researchers at the Wyss Institute have developed a method for building complex nanostructures out of short synthetic strands of DNA. Called single-stranded tiles (SSTs), these interlocking DNA "building blocks," akin to Legos, can be programmed to assemble themselves into precisely designed shapes, such as letters and emoticons. Further development of the technology could enable the creation of new nanoscale devices, such as those that deliver drugs directly to disease sites.

The technology, which is described in the May 30 online issue of Nature, was developed by a research team led by Wyss core faculty member Peng Yin, Ph.D., who is also an Assistant Professor of Systems Biology at Harvard Medical School. Other team members included Wyss Postdoctoral Fellow Bryan Wei, Ph.D., and graduate student Mingjie Dai.

DNA is best known as a keeper of genetic information. But in an emerging field of science known as DNA nanotechnology, it is being explored for use as a material with which to build tiny, programmable structures for diverse applications. To date, most research has focused on the use of a single long biological strand of DNA, which acts as a backbone along which smaller strands bind to its many different segments, to create shapes. This method, called DNA origami, is also being pursued at the Wyss Institute under the leadership of Core Faculty member William Shih, Ph.D. Shih is also an Associate Professor in the Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School and the Department of Cancer Biology at the Dana-Farber Cancer Institute.

In focusing on the use of short strands of synthetic DNA and avoiding the long scaffold strand, Yin's team developed an alternative building method. Each SST is a single, short strand of DNA. One tile will interlock with another tile, if it has a complementary sequence of DNA. If there are no complementary matches, the blocks do not connect. In this way, a collection of tiles can assemble itself into specific, predetermined shapes through a series of interlocking local connections.

In demonstrating the method, the researchers created just over one hundred different designs, including Chinese characters, numbers, and fonts, using hundreds of tiles for a single structure of 100 nanometers (billionths of a meter) in size. The approach is simple, robust, and versatile.

As synthetically based materials, the SSTs could have some important applications in medicine. SSTs could organize themselves into drug-delivery machines that maintain their structural integrity until they reach specific cell targets, and because they are synthetic, can be made highly biocompatible.

"Use of DNA nanotechnology to create programmable nanodevices is an important focus at the Wyss Institute, because we believe so strongly in its potential to produce a paradigm-shifting approach to development of new diagnostics and therapeutics," said Wyss Founding Director, Donald Ingber, M.D., Ph.D.

The research was supported by the Office of Naval Research, the National Science Foundation, the National Institutes of Health, and the Wyss Institute at Harvard University.

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Nanodevice manufacturing strategy using DNA 'Building blocks'

GRAND RAPIDS, Mich. (WOOD) - A murdered woman's family says a slow system cost their loved one her life.

DNA from a 2005 rape matched Christopher Wallace, but it took several weeks after initial confirmation for charges to be approved. During that time, a Muskegon-area mother of two was murdered in her home -- allegedly by Wallace.

Kalamazoo police investigating the rape pointed the finger at the slow process of getting the DNA analyzed -- a process that took place at the Michigan State Police Crime Lab in Grand Rapids.

MSP says its goal turnaround time on DNA evidence is 30 days.

That would have been enough to lock up Wallace, 34, before the murder, but it didn't happen in this case -- and the reason why boils down to a tight budget.

Police don't doubt now that Wallace should have been in prison for a 2005 rape, but they couldn't arrest him until it was too late for Jennifer Phillips.

"I believe that if they would have had him in prison where he should have been she would still be here," said Jennifer Phillips's sister Mary Phillips.

Jennifer, 37, was strangled to death in her home on Oct. 21, 2011, police say.

"I don't think she gave up until she couldn't try anymore," said Mary.

The holdup in the arrest, Kalamazoo police say, was in the confirmation process the DNA was going through to be checked for a match with the cold case rape.

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DNA match goal missed, woman murdered

Numbers, letters and symbols are some of the 100 or so self-assembled DNA shapes designed by Harvard scientists.

B. Wei, M. Dai, P. Yin/Wyss Inst. for Biologically Inspired Engineering/Harvard University

Scientists have developed a way to carve shapes from DNA canvases, including all the letters of the Roman alphabet, emoticons and an eagles head.

Bryan Wei, a postdoctoral scholar at Harvard Medical School in Boston, Massachusetts, and his colleagues make these shapes out of single strands of DNA just 42 letters long. Each strand is unique, and folds to form a rectangular tile. When mixed, neighbouring tiles stick to each other in a brick-wall pattern, and shorter boundary tiles lock the edges in place.

In their simplest configuration, the tiles produce a solid 64-by-103-nanometre rectangle, but Wei and his team can create more complex shapes by leaving out specific tiles. Using this strategy, they created 107 two-dimensional shapes, including letters, numbers, Chinese characters, geometric shapes and symbols. They also produced tubes and rectangles of different sizes, including one consisting of more than 1,000 tiles. Their work is published today in Nature1.

Weis work revitalizes a technique used by Ned Seeman a chemist at New York University and pioneer in the field of DNA nanotechnology. As early as 1991, Seeman moulded short strands of DNA into cubes, tubes and lattices. It was laborious work and limited to small and simple designs2.

In 2006, Paul Rothemund from the California Institute of Technology in Pasadena created bigger structures using a technique called DNA origami. He folded a 7,000-letter strand of DNA from the genome of the M13 virus into the right shape, and used around 200 smaller staple strands to hold it in place3.

Since then, long scaffolds have featured in all such work. Wei and his colleagues depart from this tradition. They show that small strands can be combined into large structures without the need for a scaffold, and with acceptable yields (the proportion of strands that assemble into shapes) of 1217%.

This approach clashes with the traditional thinking about tile-based assembly, says Kurt Gothelf, director of the Centre for DNA Nanotechnology at Aarhus University in Denmark. Many scientists assumed that small strands would need to be mixed in very precise ratios to avoid making fused or half-finished structures. It has long been assumed that this sets a limit for the size of structures that can efficiently be assembled in this way, he says.

Peng Yin, also from Harvard Medical School and leader of the study, thinks that the technique works because the strands are slow to assemble, but grow quickly once they start. This means that the shapes have a low probability of touching one another and fusing incorrectly as they begin to take shape.

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DNA drawing with an old twist

When cancer blooms in the body, tiny bits of tumor DNA can be found in the blood. Cancer specialists would love it if these DNA fragments could one day be used in noninvasive diagnostic tests -- liquid biopsies -- that are relatively inexpensive and sensitive. There's a lot of work going on in this area right now.

One team of researchers reported a step toward that goal in a paper published Wednesday in the journal Science Translational Medicine. They used a strategy that can detect many different mutations in some key genes known to be involved in cancer even though the pieces of DNA from them were present in the blood plasma at low levels. Such a test, they say, would not have to be tailor-made for each cancer patient because it can look at a lot of different mutations at once, and that would make it cheaper and more practical.

The researchers, of Cambridge, England, showed that their strategy could track the progression of disease in advanced ovarian and breast cancer patients fairly accurately. They could see when a patient responded to treatment (plasma levels of key DNA fragments fell) and when they stopped responding to treatment (plasma levels of the DNA fragments started to rise again).

In a case that illustrates how they think their technology could be used, the scientists described a patient whod had tumors in the bowel and ovary. She had surgery, and responded well to it. Five years later, however, she developed a mass in the pelvis and the doctors werent sure which tumor it had come from. It was not biopsied because that was deemed too dangerous, so doctors proceeded with their best bet for a course of treatment and the patient did, in fact, respond to it.

The authors of the paper did an after-the-fact genetic analysis of the patients plasma and tumors. They found that the bowel and ovarian tumors had different genetic mutations in them and that the patients plasma at the time of relapse contained the mutations corresponding to the bowel tumor, not the ovarian tumor. Had these results been available, uncertainty and treatment delays may have been avoided, as well as the risk of prescribing chemotherapy for an inappropriate tumor site, wrote Tim Forshew, of the Cancer Research UK Cambridge Research Institute, and his colleagues.

There are a variety of ways that such technology could be helpful one day in cancer treatment, the scientists say:

Doctors could see what mutations were behind a patients cancer and when new mutations were added as time went by and the cancer mutated further. Cancer, as its often been said, isnt a single disease: There are many different ways that cells of the body can go rogue and start growing out of control and spreading.

Whats more, analysis of plasma would offer a noninvasive whole body look at all the cancer growing in a persons body. Since cancers mutate and change over time, one tumor in the same body could contain mutations not present in another one. With a plasma screen, bits of DNA from all of them would be floating around and be detected.

Because a test like this could help cancer doctors know just which genes are responsible for Person As cancer versus Person Bs cancer, it might help them decide which drugs and therapies to give a patient. (Some drugs are helpful for some types of cancer and not others.) As new mutations arose, they could change the therapy if appropriate.

Doctors could track how well therapy was working, and test to see if the cancer was returning in patients who had been responding to treatment.

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Detecting cancers -- from tiny bits of tumor DNA in blood

NEW YORK, May 30, 2012 /PRNewswire/ -- Reportlinker.com announces that a new market research report is available in its catalogue:

DNA Sequencing: Emerging Technologies and Applications

http://www.reportlinker.com/p0254559/DNA-Sequencing-Emerging-Technologies-and-Applications.html#utm_source=prnewswire&utm_medium=pr&utm_campaign=Genomics

INTRODUCTION

STUDY OBJECTIVES

BCC's goal in conducting this study is to provide an overview of the current and future characteristics of the global market for industrial enzymes. The key objective is to present a comprehensive analysis of the current market and its future direction in the enzymes market as an important tool for increasing the efficiency and specificity of the products in which the enzymes are used.

This report is an update to the previous report on industrial enzymes and explores the present and future strategies within the industrial enzymes market, which includes the detergent, technical, food and beverages, and animal feed sectors. The improvisation of the market, the setbacks and the needs of the market are discussed in this report. The comparisons, usage, and the advantages and disadvantages of types of enzymes are also portrayed in this report.

A detailed analysis of the enzymes industry structure has been conducted. Revenues are broken down by region. Sales figures are estimated for the five-year period from 2011 through 2016.

Applications for industrial enzymes are also discussed separately in the report, with emphasis of the use in technical enzymes and the food and beverages enzymes. The report also covers significant patents and their allotments in each category.

REASONS FOR DOING THIS STUDY

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DNA Sequencing: Emerging Technologies and Applications

Even though police say Craig Ingersolls DNA links him to the body of a Utica woman who was killed more than five years ago, that doesnt necessarily mean he sexually assaulted and strangled her, his defense attorney said Wednesday.

As Ingersoll, 30, of Herkimer Road, spends the next month considering whether he will plead guilty in connection to the 2007 death of 29-year-old Jennifer Bennett, Assistant Public Defender Luke Nebush said the circumstances surrounding Ingersolls DNA will be open to discussion.

Where the DNA was found is also a critical issue in this case, Nebush said, without clarifying exactly where Ingersolls genetic material was located on either Bennetts body or clothing, or anywhere else.

Nebush also would not comment when asked whether the circumstances of Bennetts death leave any room to be interpreted as an innocent accident.

Ingersoll pleaded not guilty Wednesday morning in Oneida County Court after he was indicted last week on charges of second-degree murder and first-degree criminal sexual act.

He is due back in front of Judge Barry M. Donalty on Tuesday, June 26, to either accept or reject the prosecutions plea offer.

In the meantime, Nebush said he expects to further review additional evidence provided by Assistant District Attorney Laurie Lisi and to look further into Ingersolls psychiatric background.

Thats something were going to explore, to determine whether any psychiatric issues actually exist, Nebush said.

Ingersoll is accused of killing Bennett sometime between Jan. 7 and 9 in 2007 while using forcible compulsion during a sexual assault on the woman.

After Oneida County sheriffs investigators spent years trying to identify unknown Bennetts killer, Ingersoll unexpectedly became the prime suspect several months ago after a statewide DNA database for previously convicted criminals matched Ingersolls DNA with DNA that was found with Bennetts body behind a Deerfield Fire Department pavilion on Jan. 11, 2007.

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Defense to explore DNA, mental health in Utica woman’s death

Newswise DNA, deoxyribonucleic acid, forms a blueprint of life represented by billions of chemical "base-pairs." But mismatch just one of these complementary pairs, and the genetic code gets altered. While certain proteins can diffuse along DNA strands to search for damaged sites, how they find them -- and how quickly -- remain unanswered questions.

University of Illinois at Chicago physics professor Anjum Ansari hopes to find some answers, supported by a new five-year, $1.14 million National Science Foundation grant.

Ansari and her UIC laboratory team are studying two classes of DNA-bending proteins. One is a "damage recognition" protein that recognizes a mismatched base-pair, binds to that site, and then signals for helper proteins to gather and aid in the repair. The other protein is an enzyme that targets invader DNA, cutting it apart.

Ansari is collaborating with other researchers at UIC, University of Pittsburgh, Wesleyan University and Arizona State University to study different aspects of these proteins.

Ansari's lab is one of only a few equipped to monitor the dynamics of DNA bending in complex with these proteins on timescales ranging from several milliseconds down to as fast hundreds of nanoseconds -- or less than one-millionth of a second.

The instruments in her lab are designed to look at macromolecules as they change their shapes within this time window -- "which is precisely the time window in which proteins recognize their specific binding sites," she said.

Researchers have made measurements at the longer timescales on which proteins diffuse along DNA in search of target sites Ansari said, "but not much is known about the timescale of the recognition process, for virtually any protein."

Her lab's experiments "are designed to make time-resolved measurements of how a protein, when it reaches its target site, transforms the DNA from a conformation in which it is straight to one which is kinked and bent," Ansari said, and to "learn about the recognition mechanism by watching the dynamics -- or time scales -- on which this happens."

Many other biophysical questions about this protein-DNA interaction will be investigated by the team, including the presence of subtle kinks in DNA structure at the damage sites in the absence of a bound protein.

"Clearly, the kinked conformation of the DNA facilitates the [protein's] recognition that something is wrong at the site," Ansari said. "The question we're addressing is, 'Is it the protein that bends and kinks the DNA when it reaches that site?' Or does the DNA, on its own, have a propensity to adopt these locally bent conformations because there's a mismatch -- and the protein, when it is moving along on the DNA, recognizes that something is not right at certain spots?"

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Kinks, Bends & Repairs: DNA-Bending Protein Studied

DNA samples consistent with all three murdered Singh siblings were detected on a garden fork that police found hidden in their family home's garage, a court heard today.

In Supreme Court in Brisbane, Justin Anthony Howes, a DNA expert from Brisbane's John Tonge Centre, said various major and minor DNA profiles consistent with Neelma Singh, Kunal Singh and Sidhi Singh were found on the front and back of the garden fork's tines.

Mr Howes was giving evidence on the 60th day of a trial in which Max Sica, 42, has pleaded not guilty to murdering Neelma Singh, 24, Kunal Singh, 18, and Sidhi Singh, 12, at Bridgeman Downs, on April 21, 2003.

Follow the Max Sica trial day-by-day here

The trial has heard police found the fork behind a barbecue in the garage several days after the murders.

Mr Howes explained that in various samples there was a major profile for each sibling on at least one occasion.

But in some others the minor profile could have been either Neelma or Sidhi because they were sisters.

Scientists had been unable to get any identifiable DNA from the fork's handle.

Mr Howes told the court bleach could have a major impact on the collection of DNA at crime scenes.

The trial has heard police alleged whoever killed the Singhs had tried to sterilise parts of the house with bleach.

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Garden fork held DNA of all slain siblings