ScienceDaily (Sep. 21, 2012) DNA sequencing is the driving force behind key discoveries in medicine and biology. For instance, the complete sequence of an individual's genome provides important markers and guidelines for medical diagnostics and healthcare. Up to now, the major roadblock has been the cost and speed of obtaining highly accurate DNA sequences. While numerous advances have been made in the last 10 years, most current high-throughput sequencing instruments depend on optical techniques for the detection of the four building blocks of DNA: A, C, G and T. To further advance the measurement capability, electronic DNA sequencing of an ensemble of DNA templates has also been developed.

Recently, it has been shown that DNA can be threaded through protein nanoscale pores under an applied electric current to produce electronic signals at single molecule level. However, because the four nucleotides are very similar in their chemical structures, they cannot easily be distinguished using this technique. Thus, the research and development of a single-molecule electronic DNA sequencing platform is the most active area of investigation and has the potential to produce a hand-held DNA sequencer capable of deciphering the genome for personalized medicine and basic biomedical research.

A team of researchers at Columbia University, headed by Dr. Jingyue Ju (the Samuel Ruben-Peter G. Viele Professor of Engineering, Professor of Chemical Engineering and Pharmacology, Director of the Center for Genome Technology and Biomolecular Engineering), with colleagues at the National Institute of Standards and Technology (NIST) led by Dr. John Kasianowicz (Fellow of the American Physical Society), have developed a novel approach to potentially sequence DNA in nanopores electronically at single molecule level with single-base resolution. This work, entitled "PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis" is now available in the open access online journal Scientific Reports, from Nature Publishing Group.

The reported nanopore-based sequencing by synthesis (Nano-SBS) strategy can accurately distinguish four DNA bases by detecting 4 different sized tags released from 5'-phosphate-modified nucleotides at the single molecule level for sequence determination. The basic principle of the Nano-SBS strategy is described as follows. As each nucleotide analog is incorporated into the growing DNA strand during the polymerase reaction, its tag is released by phosphodiester bond formation. The tags will enter a nanopore in the order of their release, producing unique ionic current blockade signatures due to their distinct chemical structures, thereby determining DNA sequence electronically at single molecule level with single base resolution.

As proof-of-principle, the research team attached four different length polymer tags to the terminal phosphate of 2'-deoxyguanosine-5'-tetraphosphate (a modified DNA building block) and demonstrated efficient incorporation of the nucleotide analogs during the polymerase reaction, as well as better than baseline discrimination among the four tags at single molecule level based on their nanopore ionic current blockade signatures. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.

In previous work, the Center of Genome Technology & Biomolecular Engineering at Columbia University, led by Professor Ju and Dr. Nicholas J. Turro (William P. Schweitzer Professor of Chemistry), developed a four-color DNA sequencing by synthesis (SBS) platform using cleavable fluorescent nucleotide reversible terminators (NRT), which is licensed to Intelligent Bio-Systems, Inc., a QIAGEN company. SBS with cleavable fluorescent NRTs is the dominant approach used in the next generation DNA sequencing systems. Dr. Kasianowicz and his group at NIST pioneered the investigation of nanopores for single molecule analysis. They previously reported that different length polymers, polyethylene glycols (PEGs), could be distinguished by their unique effects on current readings in a -hemolysin protein nanopores at single molecule level and subsequently developed a theory for the method. Their results provide the proof-of-concept for single molecule mass spectrometry. The combination of the SBS concept with the distinct nanopore-detectable electronic tags to label DNA building blocks led to the development of the single-molecule electronic Nano-SBS approach described the current Scientific Reports article (09/21/2012).

As lead author Dr. Shiv Kumar points out, "The novelty of our approach lies in the design and use of four differently tagged nucleotides, which upon incorporation by DNA polymerase, release four different size tags that are distinguished from each other at the single molecule level when they pass through the nanopore. This approach overcomes any constraints imposed by the small differences among the four nucleotides, a challenge which most nanopore sequencing methods have faced for decades." Moreover, the technique is quite flexible; with PEG tags as prototypes, other chemical tags can be chosen to provide optimal separation in different nanopore systems.

With further development of this Nano-SBS approach, such as the use of large arrays of protein or solid nanopores, this system has the potential to accurately sequence an entire human genome rapidly and at low cost, thereby enabling it to be used in routine medical diagnoses.

The authors of the Scientific Reports article were Shiv Kumar, Chuanjuan Tao, Minchen Chien, Brittney Hellner, Arvind Balijepalli, Joseph W.F. Robertson, Zengmin Li, James J. Russo, Joseph E. Reiner, John J. Kasianowicz, and Jingyue Ju. The study was supported by a grant from the National Institutes of Health, a National Research Council/NIST/NIH Research Fellowship, and a grant from the NIST Office of Law Enforcement Standards.

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Novel approach for single molecule electronic DNA sequencing

A Middlesex Superior Court judge is allowing two samples of DNA to be used as evidence in the trial of a Framingham man accused of murdering a couple in Hudson in 2010.

Judge Sandra Hamlin denied defense attorney Thomas Fords request to dismiss a sample of Velezs DNA that was found underneath Trisha Bennetts fingernail and a blood spatter found on the jeans Velez wore the night of the murders, said Stephanie Chelf Guyotte, a spokeswoman for the Middlesex District Attorneys office.

During a pre-trial conference earlier this week, Ford argued that a report did not note which portion of Bennetts fingernail the DNA sample was taken from. Ford said DNA can be transmitted to the top of another persons fingernail through casual contact. However, DNA is normally transmitted underneath another persons fingernail if there is sexual or defensive contact.

Ford also expressed concerns that there was no defense expert present at the swabbing and testing of the DNA.

Assistant District Attorney Joseph Gentile said testimony at a previous hearing documented the DNA sample was found underneath Bennetts fingernail.

In the case of the blood spatter on Velezs jeans, Ford said a report did not identify which blood spot was extracted and tested for DNA. The number of spots tested was also not in the report, said Ford.

Citing a report, Gentile said the sample was taken from a defined section near the left thigh Velezs jeans near his thigh.

Jury selection began Friday and will continue on Monday, said Guyotte.

Velez, 29, is charged with first-degree murder in the stabbing deaths of Bennett, 20, and her boyfriend Angel Ortiz, 23. Bennett and Ortiz were found dead inside their Emerson Gardens condominium May 1, 2010.

Authorities arrested Velez nearly three months after he called 911 in the early morning of May 1, 2010, telling police he and two friends had been stabbed. Police found Velez, who was suffering from stab wounds, in the parking lot. Prosecutors say Velezs wounds were self-inflicted.

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Judge denies motions to dismiss DNA evidence in Hudson murder case

Schematic of single molecule DNA sequencing by a nanopore with phosphate-tagged nucleotides. Each of the four nucleotides will carry a different tag. During SBS, these tags, attached via the terminal-phosphate of the nucleotide, will be released into the nanopore one at a time where they will produce unique current blockade signatures for sequence determination. A large array of such nanopores will lead to high throughput DNA sequencing.

(Phys.org)DNA sequencing is the driving force behind key discoveries in medicine and biology. For instance, the complete sequence of an individual's genome provides important markers and guidelines for medical diagnostics and healthcare. Up to now, the major roadblock has been the cost and speed of obtaining highly accurate DNA sequences. While numerous advances have been made in the last 10 years, most current high-throughput sequencing instruments depend on optical techniques for the detection of the four building blocks of DNA: A, C, G and T. To further advance the measurement capability, electronic DNA sequencing of an ensemble of DNA templates has also been developed.

Recently, it has been shown that DNA can be threaded through protein nanoscale pores under an applied electric current to produce electronic signals at single molecule level. However, because the four nucleotides are very similar in their chemical structures, they cannot easily be distinguished using this technique. Thus, the research and development of a single-molecule electronic DNA sequencing platform is the most active area of investigation and has the potential to produce a hand-held DNA sequencer capable of deciphering the genome for personalized medicine and basic biomedical research.

A team of researchers at Columbia University, headed by Dr. Jingyue Ju (the Samuel Ruben-Peter G. Viele Professor of Engineering, Professor of Chemical Engineering and Pharmacology, Director of the Center for Genome Technology and Biomolecular Engineering), with colleagues at the National Institute of Standards and Technology (NIST) led by Dr. John Kasianowicz (Fellow of the American Physical Society), have developed a novel approach to potentially sequence DNA in nanopores electronically at single molecule level with single-base resolution. This work, entitled "PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis" is now available in the open access online journal, Scientific Reports, from the Nature Publication group.

The reported nanopore-based sequencing by synthesis (Nano-SBS) strategy can accurately distinguish four DNA bases by detecting 4 different sized tags released from 5'-phosphate-modified nucleotides at the single molecule level for sequence determination. The basic principle of the Nano-SBS strategy is described as follows. As each nucleotide analog is incorporated into the growing DNA strand during the polymerase reaction, its tag is released by phosphodiester bond formation. The tags will enter a nanopore in the order of their release, producing unique ionic current blockade signatures due to their distinct chemical structures, thereby determining DNA sequence electronically at single molecule level with single base resolution. As proof-of-principle, the research team attached four different length polymer tags to the terminal phosphate of 2'-deoxyguanosine-5'-tetraphosphate (a modified DNA building block) and demonstrated efficient incorporation of the nucleotide analogs during the polymerase reaction, as well as better than baseline discrimination among the four tags at single molecule level based on their nanopore ionic current blockade signatures. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.

In previous work, the Center of Genome Technology & Biomolecular Engineering at Columbia University, led by Professor Ju and Dr. Nicholas J. Turro (William P. Schweitzer Professor of Chemistry), developed a four-color DNA sequencing by synthesis (SBS) platform using cleavable fluorescent nucleotide reversible terminators (NRT), which is licensed to Intelligent Bio-Systems, Inc., a QIAGEN company. SBS with cleavable fluorescent NRTs is the dominant approach used in the next generation DNA sequencing systems. Dr. Kasianowicz and his group at NIST pioneered the investigation of nanopores for single molecule analysis. They previously reported that different length polymers, polyethylene glycols (PEGs), could be distinguished by their unique effects on current readings in a -hemolysin protein nanopores at single molecule level and subsequently developed a theory for the method. Their results provide the proof-of-concept for single molecule mass spectrometry. The combination of the SBS concept with the distinct nanopore-detectable electronic tags to label DNA building blocks led to the development of the single-molecule electronic Nano-SBS approach described the current Scientific Reports article.

As lead author Dr. Shiv Kumar points out, "The novelty of our approach lies in the design and use of four differently tagged nucleotides, which upon incorporation by DNA polymerase, release four different size tags that are distinguished from each other at the single molecule level when they pass through the nanopore. This approach overcomes any constraints imposed by the small differences among the four nucleotides, a challenge which most nanopore sequencing methods have faced for decades." Moreover, the technique is quite flexible; with PEG tags as prototypes, other chemical tags can be chosen to provide optimal separation in different nanopore systems.

With further development of this Nano-SBS approach, such as the use of large arrays of protein or solid nanopores, this system has the potential to accurately sequence an entire human genome rapidly and at low cost, thereby enabling it to be used in routine medical diagnoses.

More information: Scientific Reports, 2, 684 DOI:10.1038/srep00684, 2012

Journal reference: Scientific Reports

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Researchers report novel approach for single molecule electronic DNA sequencing

Public release date: 21-Sep-2012 [ | E-mail | Share ]

Contact: Beth Kwon beth.kwon@columbia.edu 212-854-6581 Columbia University

DNA sequencing is the driving force behind key discoveries in medicine and biology. For instance, the complete sequence of an individual's genome provides important markers and guidelines for medical diagnostics and healthcare. Up to now, the major roadblock has been the cost and speed of obtaining highly accurate DNA sequences. While numerous advances have been made in the last 10 years, most current high-throughput sequencing instruments depend on optical techniques for the detection of the four building blocks of DNA: A, C, G and T. To further advance the measurement capability, electronic DNA sequencing of an ensemble of DNA templates has also been developed. Recently, it has been shown that DNA can be threaded through protein nanoscale pores under an applied electric current to produce electronic signals at single molecule level. However, because the four nucleotides are very similar in their chemical structures, they cannot easily be distinguished using this technique. Thus, the research and development of a single-molecule electronic DNA sequencing platform is the most active area of investigation and has the potential to produce a hand-held DNA sequencer capable of deciphering the genome for personalized medicine and basic biomedical research.

A team of researchers at Columbia University, headed by Dr. Jingyue Ju (the Samuel Ruben-Peter G. Viele Professor of Engineering, Professor of Chemical Engineering and Pharmacology, Director of the Center for Genome Technology and Biomolecular Engineering), with colleagues at the National Institute of Standards and Technology (NIST) led by Dr. John Kasianowicz (Fellow of the American Physical Society), have developed a novel approach to potentially sequence DNA in nanopores electronically at single molecule level with single-base resolution. This work, entitled "PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis" is now available in the open access online journal, Scientific Reports (2, 684 DOI:10.1038/srep00684, 2012), from the Nature Publication group.

The reported nanopore-based sequencing by synthesis (Nano-SBS) strategy can accurately distinguish four DNA bases by detecting 4 different sized tags released from 5'-phosphate-modified nucleotides at the single molecule level for sequence determination. The basic principle of the Nano-SBS strategy is described as follows. As each nucleotide analog is incorporated into the growing DNA strand during the polymerase reaction, its tag is released by phosphodiester bond formation. The tags will enter a nanopore in the order of their release, producing unique ionic current blockade signatures due to their distinct chemical structures, thereby determining DNA sequence electronically at single molecule level with single base resolution. As proof-of-principle, the research team attached four different length polymer tags to the terminal phosphate of 2'-deoxyguanosine-5'-tetraphosphate (a modified DNA building block) and demonstrated efficient incorporation of the nucleotide analogs during the polymerase reaction, as well as better than baseline discrimination among the four tags at single molecule level based on their nanopore ionic current blockade signatures. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.

In previous work, the Center of Genome Technology & Biomolecular Engineering at Columbia University, led by Professor Ju and Dr. Nicholas J. Turro (William P. Schweitzer Professor of Chemistry), developed a four-color DNA sequencing by synthesis (SBS) platform using cleavable fluorescent nucleotide reversible terminators (NRT), which is licensed to Intelligent Bio-Systems, Inc., a QIAGEN company. SBS with cleavable fluorescent NRTs is the dominant approach used in the next generation DNA sequencing systems. Dr. Kasianowicz and his group at NIST pioneered the investigation of nanopores for single molecule analysis. They previously reported that different length polymers, polyethylene glycols (PEGs), could be distinguished by their unique effects on current readings in a -hemolysin protein nanopores at single molecule level and subsequently developed a theory for the method. Their results provide the proof-of-concept for single molecule mass spectrometry. The combination of the SBS concept with the distinct nanopore-detectable electronic tags to label DNA building blocks led to the development of the single-molecule electronic Nano-SBS approach described the current Scientific Reports article (09/21/2012).

As lead author Dr. Shiv Kumar points out, "The novelty of our approach lies in the design and use of four differently tagged nucleotides, which upon incorporation by DNA polymerase, release four different size tags that are distinguished from each other at the single molecule level when they pass through the nanopore. This approach overcomes any constraints imposed by the small differences among the four nucleotides, a challenge which most nanopore sequencing methods have faced for decades." Moreover, the technique is quite flexible; with PEG tags as prototypes, other chemical tags can be chosen to provide optimal separation in different nanopore systems.

With further development of this Nano-SBS approach, such as the use of large arrays of protein or solid nanopores, this system has the potential to accurately sequence an entire human genome rapidly and at low cost, thereby enabling it to be used in routine medical diagnoses.

###

The authors of the Scientific Reports article were Shiv Kumar, Chuanjuan Tao, Minchen Chien, Brittney Hellner, Arvind Balijepalli, Joseph W.F. Robertson, Zengmin Li, James J. Russo, Joseph E. Reiner, John J. Kasianowicz, and Jingyue Ju. The study was supported by a grant from the National Institutes of Health, a National Research Council/NIST/NIH Research Fellowship, and a grant from the NIST Office of Law Enforcement Standards.

Continue reading here:
Columbia researchers report novel approach for single molecule electronic DNA sequencing

WYCKOFF Police arrested a man known they called the "motorcycle burglar" this morning after matching him to DNA found at one of his victim's homes.

According to Wyckoff Chief Benjamin Fox, officers responded to a Nancy Lane residence in July 2011 after a homeowner reported that approximately $3,000 worth of jewelry had gone missing from her home.

A neighbor had observed a man activating an alarm system as he fled the home, and the man rode past the homeowner on a motorcycle as she was arriving home.

During an investigation, police found droplets of blood inside the home, along with a crowbar and a pair of latex gloves that had been discarded as the man rode away on the motorcycle, Fox said. They then matched DNA samples from the blood and gloves to 51-year-old Lee Malsch of Paterson, whose extensive criminal history included past burglaries.

Police obtained a warrant for Malsch's arrest on Sept. 11, but had trouble locating him. With the help of the Passaic County Sheriff's Department, however, they were able to find him this morning and take him into custody.

He was charged with burglary and theft, and is currently awaiting a bail hearing at the Bergen County Jail in Hackensack.

Fox praised the work of the investigating officers, saying that burglaries can often be difficult to solve.

"My guys don't solve every crime. No department does. But when they have evidence to works ith, they do everything that they can to apprehend those responsible," he said. "That's what they did here, and this community should be grateful."

Police were unable to recover any of the jewelry stolen from the home in 2011.

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DNA helps Wyckoff police nab 'motorcycle burglar'

Using DNA matches off a knife, San Luis Obispo police detectives were able to identify a suspect in an attempted murder case, and then arrested a Vallejo man for the alleged crime.

In a news release issued Thursday, police Lt. Jeff Smith said Austin Sarna, 21, was arrested Wednesday in Vallejo after the DNA evidence linked him to an attack that occurred in January.

Sarna was taken into custody without incident, and was transported to San Luis Obispo County Jail, where he remains on a no-bail warrant.

Smith said that at 12:30 a.m. on Jan. 20, police were called to the intersection of Broad and Monterey streets on the report of a man who had been stabbed and was bleeding profusely from his arm.

Police learned that several men got into an altercation with two or more others. Trevor Tice, 27, of Atascadero, was stabbed multiple times in the back and arm. Zachary Lerno, 26, was stabbed once in the head.

"During the investigation there were limited details regarding the suspect due to a lack of witnesses and levels of intoxication," Smith said. But the knife used in the attack was found by officers and taken as evidence.

The suspected weapon was sent to a state crime lab for analysis. One DNA sample matched Tice; another matched Sarna. Investigators then contacted the two male victims and witnesses, who identified Sarna as one of the men in the altercation.

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DNA evidence links Vallejo man to January stabbing in SLO, police say

ScienceDaily (Sep. 19, 2012) DNA barcoding developed by University of Guelph researchers has proven up to 88 per cent effective in authenticating natural health products, according to a new U of G study.

The study appears in the latest issue of Food Research International. It's a crucial finding because the health product industry is under-regulated worldwide and mislabelling poses economic, health, legal and environmental implications, says study author Mehrdad Hajibabaei.

"Currently there is no other broadly applicable tool that can identify the species used in both animal and plant natural health products as rapidly and cost-effectively," said Hajibabaei, a U of G integrative biology professor and director of technology development for the Guelph-based Biodiversity Institute of Ontario (BIO).

Up to about 80 per cent of people in developed countries use natural health products, including vitamins, minerals and herbal remedies. In Canada, these products have been regulated since 2004. But regulators face a backlog of licence applications, and thousands of products on the market lack a full product licence. In the U.S. and the U.K., regulatory problems involving natural health products have affected consistency and safety.

Authenticating natural product capsules or tablets -- containing dried fragments rather than whole specimens -- poses challenges.

DNA barcoding allows scientists to use short standardized regions of genetic material to identify species and compare them to reference genetic sequences, said Hajibabaei.

The technique works for all life stages and even for fragments of organisms, allowing scientists to ID even dried contents of a small pill.

"DNA barcoding provides a simple and efficient method for accurate identification and can play a key role in developing a more robust protocol for their regulation," Hajibabaei said.

For the study, researchers tested 95 plant and animal products bought in Toronto and New York City. Samples included capsules, tablets, roots, extracts, teas and shredded products. The researchers also sampled for products containing widely used shark tissue or ginseng.

Fully 81 per cent of natural health products made from animals correctly matched their commercial label. The rest contained everything from cheaper alternatives to fragments of protected species. One product labelled as tiger shark fins actually contained a catfish species.

Continued here:
DNA barcoding can ID natural health products

Public release date: 19-Sep-2012 [ | E-mail | Share ]

Contact: Prof. Mehrdad Hajibabaei Biodiversity Institute of Ontario mhajibab@uoguelph.ca 519-824-4120 x52487 University of Guelph

DNA barcoding developed by University of Guelph researchers has proven up to 88 per cent effective in authenticating natural health products, according to a new U of G study.

The study appears in the latest issue of Food Research International.

It's a crucial finding because the health product industry is under-regulated worldwide and mislabelling poses economic, health, legal and environmental implications, says study author Mehrdad Hajibabaei.

"Currently there is no other broadly applicable tool that can identify the species used in both animal and plant natural health products as rapidly and cost-effectively," said Hajibabaei, a U of G integrative biology professor and director of technology development for the Guelph-based Biodiversity Institute of Ontario (BIO).

Up to about 80 per cent of people in developed countries use natural health products, including vitamins, minerals and herbal remedies. In Canada, these products have been regulated since 2004. But regulators face a backlog of licence applications, and thousands of products on the market lack a full product licence. In the U.S. and the U.K., regulatory problems involving natural health products have affected consistency and safety.

Authenticating natural product capsules or tablets -- containing dried fragments rather than whole specimens -- poses challenges.

DNA barcoding allows scientists to use short standardized regions of genetic material to identify species and compare them to reference genetic sequences, said Hajibabaei.

The technique works for all life stages and even for fragments of organisms, allowing scientists to ID even dried contents of a small pill.

Go here to see the original:
Study: DNA barcoding can ID natural health products

DNA technology should dramatically cut the number of thefts from schools after being rolled out in Kapiti by Police Minister Anne Tolley.

SelectaDNA, an invisible liquid with a unique sequence of DNA including 60 chromosomes in every bottle, can be applied to laptops, musical instruments, trophies, or any other items at risk of being stolen from schools.

Police can identify the owner of a recovered item through a DNA test, or by looking at a microdot under a microscope.

At the Wellington region launch at Kapiti College, Mrs Tolley said schools were a traditional target of crime.

"As schools use technology more and more on a daily basis . . . these items are very saleable, so they have become a target. It's absolutely heartbreaking when these no-goods come in and steal it. All of that creates an enormous range of victims."

SelectaDNA director David Morrissey said the liquid had first been used in South Auckland, and had helped reduce crime there by about 60 per cent, which he described as "quite phenomenal".

It was also noticed during the trial that no crime, including tagging, had occurred at either of the three schools taking part.

Now 1600 schools have been given SelectaDNA, and 244 more schools in the Wellington region are being given deterrent kits this week.

By the end of the year, every school in the North Island will have a kit, and all South Island schools should have received one by term three of next year.

Early figures show crime decreasing by about 40 per cent at schools with SelectaDNA.

View original post here:
DNA tagging used to fight theft

State evidence released today in the George Zimmerman second-degree murder case shows new details from a state crime lab that found Zimmerman's DNA on Trayvon Martin, the teenager he shot to death, and Trayvon's DNA on him.

But the gun that Zimmerman used to kill Trayvon that night a gun that Zimmerman told police the teenager had reached for - revealed no evidence that Trayvon touched it.

State scientists checked several parts of the 9 mm handgun: its grip, trigger, slide and holster. They found Zimmerman's DNA and that belonging to other unidentifiable people but none that matched Trayvon, records show.

The gun evidence is important because Zimmerman told Sanford police he opened fire only after the 17-year-old pinned him to the ground and reached for the gun he wore holstered on his waist.

In a re-enactment for Sanford police the next day, Zimmerman did not say or show that the two had struggled over the gun, only that Trayvon had extended his hand toward it.

The 28-year-old Zimmerman killed Trayvon, a Miami Gardens high school junior, Feb. 26 in Sanford.

Zimmerman says he acted in self-defense. Prosecutors say Zimmerman, a Neighborhood Watch volunteer, spotted the black teenager, profiled him, assumed he was about to commit a crime, began following him then murdered him.

Prosecutors today released to the public several hundred pages of evidence. It included no bombshells.

The DNA evidence was among the most compelling because it confirmed that Zimmerman and Trayvon had been in extremely close contact.

Several neighbors reported seeing one on top of the other in a fight that left one of them screaming, Zimmerman with a broken nose and small gashes to his head and Trayvon dead from a gunshot wound to the heart.

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New George Zimmerman evidence: Details on Trayvon's DNA on Zimmerman and vice versa

Only DNA from George Zimmerman was found on the grip of the gun that was used in the fatal shooting of unarmed teenager Trayvon Martin, according to DNA test results released Wednesday.

The test results were in the latest batch of discovery material released by officials in the notorious murder case, which has become a national flashpoint in race relations and gun laws. Zimmerman, 28, is free on bail awaiting trial on charges of second-degree murder in the killing of Martin, an African American teenager, who was shot to death in a confrontation at a gated community in Sanford, Fla., on Feb. 26.

The tests on the gun and the holster were performed by the Florida Department of Law Enforcement. They found Zimmermans DNA on the gun but could not find any of Martin's. No determination could be made as to whether Martin's DNA was on the holster.

PHOTOS: Tense moments from Trayvon Martin case

Zimmerman has acknowledged shooting Martin, but insists he acted in self-defense in the wake of a confrontation that left him injured.

The DNA findings could play a role in the trial, allowing the prosecution to argue against self-defense since it now seems that Martin never touched the weapon. The defense could counter that Zimmerman shot before Martin could get to the gun.

Zimmerman was not arrested the night of the shooting. After weeks of protests about that fact, a special prosecutor charged Zimmerman, a neighborhood watch volunteer, with second-degree murder.

Among other material released Wednesday was an interview with a clerk of the convenience store where Martin had gone to buy a package of Skittles and a can of iced tea. Martin was returning from the store when the confrontation with Zimmerman took place. The unidentified clerk told authorities he had no recollection of serving Martin.

To be honest, I don't even remember that day, he said.

ALSO:

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George Zimmerman's DNA, not Trayvon Martin's, found on gun

George Zimmerman claims self defense in the killing of Trayvon Martin. But there's no DNA evidence that Trayvon Martin ever touched George Zimmerman's gun.

Forensic tests made public Wednesday show that George Zimmerman's was the only DNA that could be identified on the grip of the gun used to fatally shoot 17-year-old Trayvon Martin.

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The results rule out Martin's DNA from being on the gun's grip. Zimmerman's DNA also was identified on the gun's holster, but no determination could be made as to whether Martin's DNA was on the gun's holster, according to the report from the Florida Department of Law Enforcement.

Zimmerman is charged with second-degree murder for fatally shooting Martin during a confrontation in a gated community in Sanford in February. Zimmerman is pleading not guilty, claiming self-defense.

A delay in Zimmerman's arrest led to nationwide protests.

RECOMMENDED: How 5 black men view the Trayvon Martin case

The question of whose DNA is on the gun and holster could play a role in Zimmerman's defense.

Zimmerman says Martin had been on top of him, slamming his head against the ground and smothering his mouth and nose with his hand and arm when he grabbed his gun from a holster on his waist before Martin could get it. He shot the teenager once in the chest.

Originally posted here:
George Zimmerman: No DNA evidence of a struggle for his gun

SAN FRANCISCO -- A California law that allows law enforcement to collect DNA samples from anyone arrested for a felony appears to be on shaky legal ground.

During an hour of arguments Wednesday, an 11-judge panel of the 9th U.S. Circuit Court of Appeals was largely skeptical of the state's argument that government's public safety interest in collecting DNA from arrestees outweighs constitutional protections against unreasonable searches.

The majority of the judges expressed particular concern that the DNA is taken from people regardless of whether they are later charged or convicted of a crime. The arguments were the latest round in an American Civil Liberties Union challenge to the nine-year-old DNA collection law.

9th Circuit Judge N. Randy Smith grilled a deputy attorney general, insisting there is no reason California's law should permit DNA collection at the point of arrest.

"I don't see what the government loses by putting it off until conviction, or until a judge looks at it ... or at least the prosecutor looks at it, rather than just the police look at it," said Smith, a Republican appointee of former President George W. Bush.

9th Circuit Judge Raymond Fisher also expressed reservations about the government seizing a person's genetic map at the point of arrest. The ACLU case was filed on behalf of several people who were arrested and never charged with a crime, yet were forced to provide DNA samples.

"Now if I'm

The California legal battle over DNA collection is one of many unfolding around the country, with the U.S. Supreme Court poised to take up the issue as soon as this fall in a similar Maryland case.

California is one of more than 20 states with such laws, although the state's voter-approved law is broader than some, including Maryland's, because it allows police to collect the DNA at the time of arrest.

California law enforcement officials argue that the law's usefulness in solving murders, rapes and other crimes through DNA hits outweighs the privacy rights of those who give the DNA samples. Powell told the court on Wednesday that the tool serves "vital public safety and law enforcement interests."

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DNA sampling of arrestees draws skepticism in federal court hearing

ScienceDaily (Sep. 18, 2012) Human papillomavirus (HPV) DNA positivity alone, particularly when assessed using polymerase chain reaction methods, is a poor biomarker for HPV-driven head and neck cancers, according to two studies published in Cancer Research, a journal of the American Association for Cancer Research. These studies identified alternative potential markers including viral load, viral gene expression and the evaluation of HPV DNA in combination with certain HPV assays.

Prior research has established that HPV is a cause of some head and neck cancers, including oropharyngeal cancer, and that patients with HPV-associated disease tend to have a better clinical outcome. Consequently, the proper assessment of the clinical status of individual tumors has become a goal of clinicians treating this disease because HPV at the tumor site does not indicate causal involvement in the cancer.

In the first study, Dana Holzinger, Ph.D., of the division of genome modifications and carcinogenesis at the German Cancer Research Center in Heidelberg, Germany, and colleagues analyzed the potential of direct and indirect HPV markers to identify patients with HPV-driven tumors.

They analyzed 199 oropharyngeal squamous cell carcinoma specimens for HPV DNA, viral load, RNA expression patterns seen in cervical carcinomas and the p16 protein, which is associated with tumor suppression.

Results indicated that the cervical cancer RNA expression pattern and viral load were associated with the lowest risk for death from oropharyngeal cancer. In contrast, a weaker association was found for samples that were HPV DNA-positive or that expressed the p16 protein.

"We showed that high viral load and a cancer-specific pattern of viral gene expression are most suited to identify patients with HPV-driven tumors among patients with oropharyngeal cancer," Holzinger said. "Viral expression pattern is a completely new marker in this field and viral load has hardly been analyzed before."

In a second study, researchers evaluated several biomarkers individually and in combination for overall survival among head and neck cancers including polymerase chain reaction-based and serological HPV DNA testing, and p16 immunohistochemistry.

They found that the expression of two oncoproteins, E6 and E7, was associated with improved survival in oropharyngeal disease. In addition, HPV DNA positivity or p16 expression combined with E6 and E7 expression were also associated with enhanced survival. However, neither HPV DNA positivity nor expression of p16 alone yielded a similar result.

"Assessment of HPV DNA using polymerase chain reaction methods as a biomarker in individual head and neck cancers is a poor predictor of outcome and is also poorly associated with antibody response indicative of exposure and/or infection by HPV," said study author Karl T. Kelsey, M.D., professor in the department of epidemiology and the department of pathology and laboratory medicine at Brown University in Providence, R.I. "We may not be diagnosing these tumors as accurately and precisely as we need to for adjusting treatments."

The next step in this research is further validating the findings of these two studies using head-to-head comparisons and developing assays for direct clinical application of the markers.

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Assessment of HPV DNA Alone Insufficient to Identify HPV-Driven Head and Neck Cancers

18 September 2012 Last updated at 09:26 ET

A double rapist caught by chance years later through a DNA sample has been jailed for seven-and-a-half years.

Peter Hendry, 41, from Springburn in Glasgow, attacked the two women, who were working as prostitutes, in Rutherglen in 2004 and 2007.

He avoided capture until a former partner accused him of domestic abuse in 2011. DNA samples were taken which matched with both attacks.

Hendry, who denied the charges, was found guilty on a unanimous verdict.

Solicitor advocate Murray Macara QC, who represented the fork-lift truck driver, told the court that his client had "constantly and consistently maintained that he did not rape these two women".

Both women had told how Hendry picked them up and drove them to a deserted industrial estate.

A 33-year-old woman told the trial that he took her there in September 2004, pinned her down and raped her, before leaving her "like a bit of trash".

The woman reported the incident to police, but Hendry remained at large.

He carried out a similar attack on a 29-year-old woman in July 2007.

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Rapist caught by DNA test jailed

It's been the FBI's dream for years -- to do near-instant DNA analysis using mobile equipment in the field -- and now "Rapid DNA" gear is finally here.

The idea is that you simply drop into the system a cotton swab with a person's saliva, for example, and the "Rapid DNA" machine spits out the type of DNA data that's needed to pin down identity. Now that such equipment exists, the FBI is pushing to get it into the hands of law enforcement agencies as soon as possible. [Also see: "FBI building system that blows away fingerprinting"]

"DNA has emerged as the gold standard in forensics analysis," Steven Martinez, executive assistant director of the science and technology branch at the FBI, said in his keynote address to attendees of the Biometric Consortium Conference in Tampa on Tuesday.

RELATED: Biometrics scares people

Though the genetic information contained in an individual's DNA, which is in all human cells, has been used since the late 1980s to solve crime cases, analysis of DNA has remained frustratingly slow because DNA had to be sent to special labs to be analyzed. New "Rapid DNA" devices are now ready to be evaluated and the FBI has received two basic types.

One is called the RapidHIT, which is made by IntegenX, a Pleasanton, Calif.-based company whose CEO Stevan Jovanovich was in the exhibit hall to explain how the Rapid DNA device can spit out an individual's DNA data within 90 minutes.

Another company, NetBio, is also believed to have delivered its Rapid DNA-type equipment to the FBI, Jovanovich says, and the National Institute of Standards and Technology (NIST) is expected to play an important role in helping certify systems and processes for how these boxes will be used by the FBI and local police stations to collect DNA data on suspects.

Jovanovich notes that the networked IntegenX RapidHIT box, which is based on a hardened version of Windows and measures about 27-by-24-by-16 inches, costs about $245,000. RapidHIT boxes are already in use with intelligence agencies, says Jovanovich, who adds he's not at liberty to say which ones or what they're doing with them.

The FBI, which is believed to have upwards of 10 million DNA records on individuals already stored in databases, anticipates a significant expansion of DNA collection by means of Rapid DNA equipment.

The FBI has been known for pioneering a massive collection of fingerprint images and an online matching system that can be accessed remotely to help local law enforcement, as well as the Department of Defense and other law-enforcement agencies, nail down the identities of criminals and terrorists. Today, Dr. Alice Isenberg, chief of the biometrics analysis section at the FBI laboratory, explained in her presentation how the FBI hopes to expand the national DNA database used to investigate crime for DNA matches online as well.

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FBI eager to embrace mobile 'Rapid DNA' testing

Anyone arrested for a felony offense and all adults convicted of misdemeanor crimes would be required to provide a DNA sample to law enforcement under a proposal from the state Department of Justice.

Adults arrested for certain misdemeanor crimes such as fourth-degree sexual assault and prostitution also would need to provide DNA samples, which would be entered into a national database used to match DNA evidence collected at crime scenes to suspects.

Currently, state law allows DNA to be collected only from adults and juveniles convicted of felonies, with about 12,000 samples obtained each year.

Brian O'Keefe, administrator for the DOJ's Division of Law Enforcement Services, said the expected addition of about 68,000 DNA samples a year at least initially under the proposed expansion would help law enforcement solve more cases more quickly and get criminals off the street.

The number of new samples would eventually drop, he said, because DNA profiles of those reoffending would not have to be added to the system.

But Chris Ahmuty of the ACLU of Wisconsin said, "It seems like they've gone for the nuclear option when it comes to DNA on arrest."

Casting such a wide net raises concerns about cost, management and privacy and "turns the presumption of innocence on its head," Ahmuty said. He added that the DOJ proposal is more encompassing and costly than previous legislative proposals.

O'Keefe said the proposed expansion of DNA collection would begin in October 2014 and cost about $7 million in its first two years.

To cover those costs including the addition of 26 full-time positions DOJ is asking that everyone convicted of a felony be required to pay a $250 surcharge and that everyone convicted of a misdemeanor pay a $150 surcharge.

Currently, a DNA surcharge for people convicted of felonies is often waived by a judge.

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Proposal would expand DNA collection to more than just convicted felons

STONY BROOK, NY--(Marketwire - Sep 18, 2012) - Applied DNA Sciences, Inc. ( OTCBB : APDN ), (Twitter: @APDN), a provider of DNA-based anti-counterfeiting technology and product authentication solutions, announced today that it has entered into a Development Agreement with Inventionland Corporation.The two companies will collaborate on the development of innovative loss-prevention products, based upon APDN's botanical DNA-marking platform. Inventionland will participate in product development with APDN and take the resultant new products and applications to its customers.

The agreement between APDN and Inventionland follows closely the launch by APDN of smartDNA, a system designed to mark offenders and to prevent theft. The system has been deployed internationally to protect banks, retailers, jewelers and pharmacies. APDN also launched its digitalDNA platform this year that combines DNA-based security with secure-cloud technology, mobile computing and authentication on-the-fly.

Inventionland Corporation (www.Inventionland.com) is America's largest invention factory.Over 1,000 different retailers and on-line stores have sold its innovations.Inventionland builds 2,000-2,400 new product samples for corporations and retailers to review for their shelves each year.With some retailers facing large asset loss from their stores, Inventionland was asked to invent new products to help eliminate loss in a more innovative and effective manner.Inventionland's founder, George Davison, is an APDN stockholder.After Mr. Davison contacted APDN, both organizations began collaborating to offer a retailer solution that would help eliminate asset loss.

Mr. Davison, renowned for his novel approaches to product development, and himself the subject of a profile on the U.S. cable TV channel History (formerly The History Channel), stated: "I was a long-standing fan of Applied DNA Sciences' novel technology and enormous breadth of application, as well as Dr. Hayward's already-validated approach to managing biotechnology development.Inventionland is now pleased to be able to take this platform to our market-leading retailers."

Dr. Hayward commented: "Biotech companies can benefit from Inventionland's innovative approach and unmatchable speed-to-market. We are thrilled to partner with Inventionland on some very original and unique applications for DNA marking."

About Applied DNA Sciences

APDN is a provider of botanical-DNA based security and authentication solutions that can help protect products, brands and intellectual property of companies, governments and consumers from theft, counterfeiting, fraud and diversion. SigNature DNA and smartDNA, our principal anti-counterfeiting and product authentication solutions that essentially cannot be copied, provide a forensic chain of evidence and can be used to prosecute perpetrators.

The statements made by APDN may be forward-looking in nature.Forward-looking statements describe APDN's future plans, projections, strategies and expectations, and are based on assumptions and involve a number of risks and uncertainties, many of which are beyond the control of APDN. Actual results could differ materially from those projected due to our short operating history, limited financial resources, limited market acceptance, market competition and various other factors detailed from time to time in APDN's SEC reports and filings, including our Annual Report on Form 10-K, filed on December 8, 2011 and our subsequent quarterly reports on Form 10-Q.APDN undertakes no obligation to update publicly any forward-looking statements to reflect new information, events or circumstances after the date hereof to reflect the occurrence of unanticipated events.

About Inventionland Inventionland (http://www.inventionland.com) is America's largest invention factory, Inventionland, turns out 2,000-2,400 new inventions each year. Employees at Inventionland work in 16 unique themed sets, such as a shipwrecked pirate ship, a faux cave, a giant robot and a castle complete with turrets and drawbridge. The inspiring setting includes three running waterfalls, life-like trees and butterflies and chirping birds. In the rear of Inventionland is a red carpet that leads to a state-of-the art audio, video, and animation studio complete with sound room and one of the largest green screens in the tri-state area. Metalworking, woodworking, molding, laser cutting, prototyping, circuit board construction, and more take place in a state-of-the-art product sample construction facility. Hundreds of new ideas come to life every month at Inventionland, where Davison's award-winning team sets an example of America's can-do spirit and ingenuity.

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Applied DNA Sciences Contracts With Inventionland

SAN FRANCISCO An Alabama man was charged this month with the 1980 murder of an Oxnard teen. A Placerville man was arrested last month for a 1986 rape and murder of a San Mateo teen. A San Francisco man is currently on trial for the murder and robbery of a tourist two decades ago.

Technological advances in genetic research and computers in recent years have turned solving "cold cases" into near-routine police work. The California Attorney General reports that the state's DNA database of close to 2 million samples spits outs more than 425 "hits" a month, more than double the average monthly rate of 183 in 2008. More than 10,000 suspects have been identified in the last five years.

But on Wednesday, the American Civil Liberties Union will argue before a federal appellate court in San Francisco that California's DNA collection efforts have become unconstitutionally aggressive and that the spike in hits comes at the expense of civil liberties.

The ACLU is asking the 9th U.S. Circuit Court of Appeals to strike down California's Proposition 69, which authorized police to obtain a genetic sample from every person arrested on felony charges, not just those convicted. Some 25 other states have enacted similar laws since 62 percent of the California electorate passed the measure in 2004.

The issue of the warrantless swabbing of the cheek with a Q-tip of everyone arrested for a felony has sparked one of the hottest "search and seizure" debates in state and federal courts in decades.

The U.S. Supreme Court has already signaled its willingness to review Maryland's DNA collection law after a federal appeals court there ruled it unconstitutional in April. The California Supreme Court has agreed to review a lower court's overturning of the California law. Several other state and federal courts have already ruled or are weighing the issue throughout the country.

While the courts are sorting out the issue, California law enforcement officials are collecting more than 11,000 samples a month.

"Cold hit DNA is integral to bringing criminals to justice," said San Francisco District Attorney George Gascon, whose office is prosecuting William Payne for the 1983 strangulation murder of Nikolaus Crumbley. Crumbley's body was found in the city's McLaren Park along with DNA that was finally matched to Payne earlier this year. Payne denies killing Crumbley, saying his DNA was found at the scene because the two had had consensual sex. The match was made after Payne submitted a DNA sample after an unrelated assault conviction.

"Almost three decades later, we have charged the person responsible for this horrific murder," Gascon said.

The 9th Circuit itself has previously upheld the California law, which went into full effect in 2009. But underscoring the importance of the debate, a majority of the court's 24 judges voted to reconsider that divided ruling of three-judge panel. The matter now goes before a special "en banc" court of 11 judges.

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ACLU challenges California DNA collection practice

A week ago, a huge, painstakingly orchestrated PR campaign was timed to coincide with multiple publications of a long-term study by the ENCODE consortium in top-ranking journals. The ENCODE project (EP) is essentially the next stage after the Human Genome Project (HGP). The HGP sequenced all our DNA (actually a mixture of individual genomes); the EP is an attempt to define what all our DNA does by several circumstantial-evidence gathering and analysis techniques.

The EP results purportedly revolutionize our understanding of the genome by proving that DNA hitherto labeled junk is in fact functional and this knowledge will enable us to maintain individual wellbeing but also miraculously cure intractable diseases like cancer and diabetes.

Unlike the arsenic bacteria fiasco, the EP experiments were done carefully and thoroughly. The information unearthed and collated with this research is very useful, if only a foundation; as with the HGP, this cataloguing quest also contributed to development of techniques. What is way off are the claims, both proximal and distal.

A similar kind of theory of everything hype surrounded the HGP but in the case of the EP the hype has been ratcheted several fold, partly due to the increased capacity for rapid, saturating online dissemination. And science journalists who should know better (in Science, BBC, NY Times, The Guardian, Discover Magazine) made things worse by conflating junk, non-protein-coding and regulatory DNA.

Biologists particularly those of us involved in dissecting RNA regulation have known since the eighties that much of junk DNA has functions (to paraphrase Sydney Brenner, junk is not garbage). The EP results dont alter the current view of the genome, they just provide a basis for further investigation; their definition of functional is biochemically active two very different beasts; the functions (let alone any disease cures) will require exhaustive independent authentication of the EP batch results.

Additionally, the findings were embargoed for years to enable the PR blitz at minimum unseemly when public funds are involved. On the larger canvas, EP signals the increased siphoning of ever-scarcer funds into mega-projects that preempt imaginative, risky work. Last but not least, the PR phrasing choices put wind in the sails of creationists and intelligent design (ID) adherents, by implying that everything in the genome has a purpose under heaven.

What did the study actually do? The EP consortium labs systematically catalogued such things as DNAase I hypersensitive and methylated sites, transcription factor (TF) binding sites and transcribed regions in many cell types. Unmethylated nuclease-sensitive DNA is in the open configuration aka euchromatin, a state in which DNA can discharge its various roles. The TF sites mean little by themselves: to give you a sense of their predictive power, any synthetically made DNA stretch will contain several such sites. Whether they have a function depends on a whole slew of prerequisites. Ditto the transcripts, of which more anon.

Lets tackle junk DNA first, a term I find as ugly and misleading as the word slush for responses to open submission calls. Semantic baggage aside, the label junk was traditionally given to DNA segments with no apparent function. Back in the depths of time (well, circa 1970), all DNA that did not code for proteins or proximal regulatory elements (promoters and terminators) was tossed on the junk pile.

However, in the eighties the definition of functional DNA started shifting rapidly, though I suspect it will never reach the 80% used by the EP PR juggernaut. To show you how the definition has drifted, expanded, and had its meaning muddied as a term of art that is useful for everyone besides the workaday splicers et al who are abreast of trendy interpretations that may elude the laity, lets meander down the genome buffet table.

Protein-coding segments in the genome (called exons, which are interrupted by non-protein-coding segments called introns) account for about 2% of the total. That percentage increases a bit if non-protein-coding but clearly functional RNAs are factored in (structural RNAs: the U family, r- and tRNAs; regulatory miRNAs and their cousins).

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Junk DNA, Junky PR