Category Archives: DNA

Up to two male DNA profiles were recovered during the investigation into Corryn Rayney's murder that could not be matched to people in a national database, the trial of her estranged husband Lloyd Rayney has heard.

Forensic scientist Laurance Webb told the WA Supreme Court trial on Wednesday that the DNA profiles, one of which was only partial, were found but could not be matched.

Mr Webb said the DNA profile was weak and there was only a 'low level' indication of a second person.

The court heard Rayney, a prominent Perth barrister, could not be 'included or excluded' as a potential source of the DNA found on a handkerchief at Ms Rayney's grave site.

Under cross-examination, Mr Webb agreed that DNA results from a street directory inside Ms Rayney's car indicated at least three people, although it was unclear if Rayney was one of them.

He also agreed that DNA recovered from the CD button in Ms Rayney's car and from her debit card indicated a male who was not Rayney.

Mr Webb also gave evidence about a cigarette butt found outside the Rayney's home, which the court previously heard was DNA matched to a person 'well known to police'.

A full DNA profile was recovered from the butt, indicating that it had not been there for a long time, Mr Webb said.

The cigarette butt was among items found on a footpath during a police search on August 22, 2007.

The prosecution alleges Rayney murdered his estranged wife at their home in August 7, 2007 and then dragged her across the front yard to her car before burying her body head-first in a bush grave at Kings Park.

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DNA recovered during Rayney probe

Posted: September 24 Updated: Today at 12:44 AM Samples from the body of Rita St. Peter match the DNA profile of Jay Mercier, an expert says.

By DOUG HARLOW/Morning Sentinel

SKOWHEGAN DNA samples taken from the body of Rita St. Peter in 1980 match the DNA profile of Jay Mercier of Industry, the man who is charged with sexually assaulting and killing her, a state witness said in court Monday.

click image to enlarge

Murder defendant Jay Mercier looks around the courtroom on Thursday, Sept. 20, 2012 during his trial in Somerset County Superior Court for the death of Rita St. Peter 32 years ago..

click image to enlarge

Rita St. Peter in an undated file photo. She was 20 at the time of her death when her body was found off the Campground Road in Anson on July 5, 1980.

"Unless you have an identical twin, there is no one else in the world with your DNA," Kathy MacMillan, a forensic DNA analyst with the state police crime lab, told the jury in Somerset County Superior Court.

MacMillan said the possibility that DNA samples taken from St. Peter's body didn't come from Mercier is one in a trillion.

MacMillan's testimony came on the third day of the murder trial for Mercier, who was 25 when St. Peter's body was found off Campground Road in Anson on July 5, 1980.

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DNA in 1980 Maine murder case shown to match defendant

NEW YORK, Sept. 25, 2012 /PRNewswire/ -- Reportlinker.com announces that a new market research report is available in its catalogue:

DNA Microarray 2012: A Focus on Sales Growth

http://www.reportlinker.com/p0980749/DNA-Microarray-2012-A-Focus-on-Sales-Growth.html#utm_source=prnewswire&utm_medium=pr&utm_campaign=Genetically_Modified_Organism,_GMO

Background

From the early use of miniaturised microarrays for the analysis of gene expression in the mid 1990s, this technique has established markets that are expected to reach $3 billion by 2015. However markets are also changing as new applications are developed and new instruments and competitive technologies such as PCR, are launched. Today, more than ever, developers and vendors in the microarray field are targeting their resources in those areas that best support their own sales and growth strategies.

Purpose

This report, based on an analysis of prevailing and emerging market conditions in the DNA microarray field, has been produced to assist marketing and sales, and the identification of new opportunities. It is the outcome of an extensive global study involving more than 200 experienced DNA microarray users. It's findings provide a "focus on sales growth" to developers and vendors in the microarray field, and the changes that are driving these developments.

Analysis

As part of this report, market areas outlined below have been analysed to provide information relevant to marketing and sales, new market opportunities, qualified sales leads, customer needs and future plans, competitive position, new and emerging applications, growing and declining areas and threats.

Market Areas

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DNA Microarray 2012: A Focus on Sales Growth

ScienceDaily (Sep. 24, 2012) Much like the checkout clerk uses a machine that scans the barcodes on packages to identify what customers bought at the store, scientists use powerful microscopes and their own kinds of barcodes to help them identify various parts of a cell, or types of molecules at a disease site. But their barcodes only come in a handful of "styles," limiting the number of objects scientists can study in a cell sample at any one time.

Researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University have created a new kind of barcode that could come in an almost limitless array of styles -- with the potential to enable scientists to gather vastly more vital information, at one given time, than ever before. The method harnesses the natural ability of DNA to self-assemble, as reported September 24 in the online issue of Nature Chemistry.

"We hope this new method will provide much-needed molecular tools for using fluorescence microscopy to study complex biological problems," says Peng Yin, Wyss core faculty member and study co-author who has been instrumental in the DNA origami technology at the heart of the new method.

Fluorescence microscopy has been a tour de force in biomedical imaging for the last several decades. In short, scientists couple fluorescent elements -- the barcodes -- to molecules they know will attach to the part of the cells they wanted to investigate. Illuminating the sample triggers each kind of barcode to fluoresce at a particular wavelength of light, such as red, blue, or green -- indicating where the molecules of interest are.

However, the method is limited by the number of colors available -- three or four -- and sometimes the colors get blurry. That's where the magic of the DNA barcode comes in: colored-dots can be arranged into geometric patterns or fluorescent linear barcodes, and the combinations are almost limitless -- substantially increasing the number of distinct molecules or cells scientists can observe in a sample, and the colors are easy to distinguish.

Here's how it works: DNA origami follows the basic principles of the double helix in which the molecular bases A (adenosine) only bind to T (thymine), and C (cytosine) bases only bind to G (guanine). With those "givens" in place, a long strand of DNA is programmed to self-assemble by folding in on itself with the help of shorter strands to create predetermined forms--much like a single sheet of paper is folded to create a variety of designs in the traditional Japanese art.

To these more structurally complex DNA nano-structures, researchers can then attach fluorescent molecules to the desired spots, and use origami technology to generate a large pool of barcodes out of only a few fluorescent molecules. That could add a lot to the cellular imaging "toolbox" because it enables scientists to potentially light up more cellular structures than ever possible before.

"The intrinsic rigidity of the engineered DNA nanostructures is this method's greatest advantage; it holds the fluorescent pattern in place without the use of external forces. It also holds great promise for using the method to study cells in their native environments," Yin says. As proof of concept, the team demonstrated that one of their new barcodes successfully attached to the surface of a yeast cell.

More research beckons, particularly to determine what happens when each of the fluorescent barcodes are mixed together in a cell sample, which is routine in real-life biological and medical imaging systems--but there's plenty of good news as a starting point. It's low-cost, easy to do, and more robust compared to current methods, says Yin.

"We're moving fast in our ability to manipulate DNA molecules using origami technology," says Wyss Institute Founding Director Don Ingber, M.D., Ph.D., "and the landscape of its potential is tremendous -- from helping us to develop targeted drug-delivery mechanisms to improving the scope of cellular and molecular activities we are able to observe at a disease site using the latest medical imaging techniques."

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Novel DNA barcode engineered: New technology could launch biomedical imaging to next level

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'

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

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

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

It's history being made -- the FBI just this month took acceptance of its first-ever "Rapid DNA" equipment for near-instant DNA analysis in the field. But use of this DNA analysis-in-a-box, which can be carried around and connected to the Internet, may be slowed because current law never envisioned such analysis being done for law-enforcement purposes outside an accredited lab.

RELATED: FBI eager to embrace 'Rapid DNA' testing

That realization, brought to light at the Biometric Consortium Conference on Wednesday, cast a shadow on what's a shining moment for the biometrics industry and its partnership with the FBI. The FBI has spent years working to build Rapid DNA equipment according to careful designs for ruggedness, security and usefulness in generating individual DNA profile data that police stations could use to share and match against the FBI's existing DNA Index System (NDIS) database. Such Rapid DNA gear can take in a cotton swab of an individual's saliva or blood in the field and within about 90 minutes, automatically spit out a human DNA profile.

Dr. Thomas Callaghan , senior biometric scientist in the biometric analysis section of the FBI Laboratory, just this month took delivery on the first two working models of Rapid DNA machines, the RapidHit 200 made by integenX, and the ANDE box made by NetBio. "It really is a remarkable achievement," says Callaghan. He and many others in the biometrics field this week at the conference recognized the historic significance of the technology breakthrough presented by the first commercially-viable equipment for Rapid DNA.

The U.S. Army has started evaluation of two ANDE System boxes it got from NetBio, says Jeff Salyards, chief scientist at the U.S. Army Criminal Investigative Laboratory. He reports that the Rapid DNA technology supplied by ANDE appears to work effectively.

Richard Selden, CEO of NetBio, assures that the ANDE System boxes for DNA analysis have undergone military-standard testing for ruggedness. However, Salyards says more testing is needed, and cautioned military buyers, eager to use Rapid DNA equipment in the field, to show patience as more testing is done.

It also could be a while until Rapid DNA can be used for U.S. law enforcement purposes. The National Institute of Standards and Technology (NIST), which is teaming with the FBI to test the NetBio and IntegenX systems, as well as possibly others, for use with law enforcement, expects a full evaluation that includes new processes to be followed to connect to federal databases. Such an evaluation could take upwards of a year.

What's more, the DNA Identification Act of 1994 passed by Congress gave the FBI the authority to establish its DNA index system, but didn't envision that DNA information would be uploaded to the FBI database from a police station using Internet-connected Rapid DNA equipment. The law covers only accredited DNA labs in use today, not the mobile Rapid DNA equipment that can be operated by non-technical personnel anywhere, according to Clark Jaw, an auditor at the FBI Laboratory for the Combined DNA Index System (CODIS). It appears there needs to be a change to the DNA Identification Act to accommodate use of the new technology, he says.

Other obstacles to achieve full-scale use in law enforcement include the need to build out CODIS software to accommodate Rapid DNA and create a quality-assurance process system. That all means Rapid DNA for law-enforcement purposes in the U.S. may take time. But the first Rapid DNA equipment is known to already be in use among secretive intelligence agencies.

"The ultimate goal is to have that technology available for law enforcement use at the police station," Jaw says, pointing out that one day law enforcement officials should be able to carry out real-time DNA-related searches using the Rapid DNA equipment to aid in fast investigation of crime suspects and crime scenes.

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Legal hurdles threaten to slow FBI's 'Rapid DNA' revolution

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