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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Calif. DNA Collection From Arrestees Challenged

STONY BROOK, NY--(Marketwire - Sep 17, 2012) - The Textile Center of Excellence at Huddersfield, United Kingdom (TCOE), and Applied DNA Sciences, Inc. ( OTCBB : APDN ) (Twitter: @APDN), a provider of DNA-based anti-counterfeiting technology and product authentication solutions, announced today the roll out of a new platform for protecting textile brands, under the SigNature DNA brand. The services, which the two organizations call "revolutionary," aim to protect textiles from a wave of counterfeiting which has struck the industry.

The platform includes applications which protect a wide range of textile, apparel and accessory products, including impregnation and authentication of DNA-marked:

The platform will be unveiled at the world-famous Premire Vision Pluriel, opening at Paris Nord Villepinte Parc d'Expositions (exhibition center) at Booth #5C18, from September 19-21, 2012. At the show, APDN and TCOE will feature demonstrations, samples, and technical experts, all showing the "unique, uncopyable, and uncompromising" abilities of the technology in protecting brands from counterfeiting.

In a joint statement, the two organizations said that their technology "offers our industry a unique and powerful means to mark and authenticate original items marked with DNA."

The two organizations described SigNature DNA as "a leading anti-counterfeiting technology that can be incorporated at any point in the textile supply chain as a means to link a genuine product to its original source of manufacture." Botanical SigNature DNA markers are authenticated in a laboratory and help to provide forensic evidence that can be used in a court of law.

The Textile Centre of Excellence has partnered with some of the most prestigious mills in the United Kingdom, including Bower Roebuck, Dormeuil, Holland and Sherry, Taylor and Lodge, and John Foster. Collectively, these fabric designers and weavers supply fabric to many of the most famous designer lines of Europe and America. Its botanical SigNature DNA-based technology protects historic and high-value Yorkshire Wool. APDN has separately partnered with Supima, a promotional organization of American growers of American Pima cotton.

Bill Macbeth, Managing Director of the Textile Centre of Excellence, commented: "SigNature DNA technology offers textile and clothing manufacturers a fool-proof and affordable solution to the growing menace of product counterfeiting. We are ready and willing to help brand owners and manufacturers to boost their brand values and revenues by incorporating this unique protection into their products."

Said Dr. James A Hayward, President and CEO, Applied DNA Sciences: "We believe that the Textile Centre's new platform is a powerful demonstration of the versatility and effectiveness of our SigNature DNA product. We urge visitors to Premiere Vision to visit the TCOE booth and see for themselves how DNA marking and authentication can add great value to their product lines."

About The Textile Centre of Excellence, and the Huddersfield and District Textile Training Company

The Huddersfield and District Textile Training Company was established in 1976 to unite the local textile industry in a shared approach to professional, equitable and high-quality training. In 1999 the company established the Textile Centre of Excellence, a 2 million development located in Leeds Road Huddersfield, providing a wide range of 'state of the art' textile and clothing research and development, training and production facilities including:

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Applied DNA Sciences, Textile Centre of Excellence Unveil Textiles Anti-Counterfeiting Platform

SAN FRANCISCO -- On a March day three years ago in San Francisco's Civic Center Plaza, Elizabeth "Lily" Haskell was arrested during a rally against the Iraq war, cuffed on a felony allegation that she tried to spring another protester who had been taken into custody.

But once hauled off to jail, Haskell found herself in the legal crosshairs for more than just civic rabble-rousing. Sheriff's deputies ordered her to submit to DNA testing under a then-new provision of California law, giving her the choice of letting them swab the inside of her cheek or face an additional misdemeanor charge and sit in a jail cell for two days.

Haskell relented and took the DNA test. But now the Oakland woman is at the center of an American Civil Liberties Union legal challenge to a state law that allows law enforcement to collect DNA samples from anyone arrested for a felony, regardless of whether they are later charged or convicted. In Haskell's case, prosecutors never followed up the 2009 arrest with a criminal charge.

"My DNA was taken without any kind of due process," Haskell said last week. "I believe people should have the right to refuse to give their DNA."

On Wednesday, a special 11-judge panel of the 9th U.S. Circuit Court of Appeals will hear arguments in the latest round in the case, which has highlighted a legal issue that appears bound for the U.S. Supreme Court. In fact, in a brief order earlier this year, Chief Justice John Roberts said

At the request of civil liberties lawyers, the 9th Circuit agreed to take a second look at the Haskell case after a three-judge panel, in a 2-1 ruling, earlier this year upheld a voter-approved 2004 California law allowing DNA collection. The 9th Circuit rejected arguments that the law, which went into effect in 2009, tramples on the constitutional rights of those arrested for felonies, saying "government's compelling interests far outweigh arrestees' privacy concerns."

In court papers, lawyers for Haskell and others arrested but never charged with felonies argue that the California law "is an unprecedented expansion of the government's power to collect DNA evidence and to DNA profile individuals who have never been convicted of any crime."

To the ACLU, there is no reason someone's DNA should wind up in the state's DNA database if the person has never appeared in court, much less in front of a jury.

"People who haven't been convicted of anything shouldn't be treated like criminals," ACLU attorney Michael Risher said.

Law enforcement officials argue that the DNA collection law is a crucial tool in solving crimes. They liken taking a DNA swab at the time of arrest to fingerprinting.

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Federal appeals court to hear challenge to California DNA collection law

The Irish Times - Monday, September 17, 2012

MATTHEW HOLMES

LEGAL OPINION: This legislation will strengthen the ability of the Garda to detect and prevent crime and, in particular, to snare repeat offenders

A DNA DATABASE is one of the most effective crime-fighting tools ever devised. Thanks to DNA databases, crimes that were previously unsolvable are now being solved and miscarriages of justice are being corrected.

Such databases save valuable time in investigations by quickly eliminating suspects or pinning them to a crime scene. They are particularly effective in sex crimes and in catching repeat offenders such as burglars. They also have uses beyond the criminal sphere in terms of identifying bodies and helping to locate missing persons. In February 2000, the then government announced a plan to establish a DNA database in Ireland. More than a decade has passed and this has still not been done. The lack of relevant legislation is hampering criminal investigations.

To date, three Bills have been drafted which seek to establish a DNA database in Ireland the Criminal Justice (Forensic Sampling and Evidence) Bill 2007, the Criminal Justice (Forensic Evidence and DNA Database System) Bill 2010 and the Criminal Justice (Forensic Evidence and DNA Database System) Bill, currently before the Dil.

The first had to be dropped after the decision of the European Court of Human Rights in Marper v the United Kingdom, which led to European-level change in the law on DNA databases; the second lapsed following the change of government last year. In April 2011, Minister for Justice Alan Shatter told a conference of Garda sergeants and inspectors he hoped to publish a new Bill before the end of that year and to progress its speedy enactment. This was postponed to the middle of this year and it has been pushed back again to the end of the year.

There is currently an ad-hoc Irish DNA database which contains a representative sample of DNA profiles from 300 Irish citizens. To put this in context, the British database contained the profiles of 3.1 million people at the end of 2005. Clearly the scope for accuracy and effectiveness of results is exponentially higher in their system than in ours. In the UK, using the database has resulted in a 50 per cent hit rate. One in two samples on the databanks result in information regarding suspects being provided to the police. At one stage the hit rate was 74 per cent.

When he was in opposition, Mr Shatter said it was almost beyond belief that more than a decade had passed and this important legislation had still not been passed. Speaking in January 2011, he said: It is completely outrageous important issue hasnt been prioritised, and extraordinary lethargy has been displayed; the legislation is on the back burner. If there was any sense of urgency about it, this legislation would have been implemented last Easter considering it was published last January.

Over a year has passed since Mr Shatter became Minister for Justice, and legislation has yet to be enacted.

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Lack of DNA database is a national disgrace

Forensic experts have failed to find crucial DNA evidence in the sexual assault case against Julian Assange, a British newspaper reports.

In a 100-page document shown to lawyers for the Australian WikiLeaks founder, Swedish police outlined their basis for seeking the 41-year-old's extradition to Stockholm to face questioning.

The report said staff at two forensic laboratories were unable to find conclusive evidence of Mr Assange's DNA on a torn condom provided by one of two women who claim to have been assaulted in August 2010.

However, the same analysts have found DNA believed to belong to Mr Assange on a condom provided by a second woman, The Mail on Sunday reported.

Mr Assange denies any wrongdoing and says sex with the two women was consensual.

He remains holed up in London's Ecuadorian embassy in a bid to avoid Swedish extradition, which he insists would lead to him being handed to authorities in the United States, where the actions of his secret-leaking website are under investigation.

The Swedish police report said that one woman, now aged 33, claims she was repeatedly molested by Mr Assange at her flat in Stockholm, adding on one occasion he deliberately broke a condom before wearing it to have unprotected sex with her against her will.

Scientists were unable to find traces of Mr Assange's DNA on the condom and his lawyers suggest that is because a fake one may have been submitted, the tabloid reports.

Mr Assange, who has been granted asylum by Ecuador, is yet to be formally charged with any offence by Swedish authorities.

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Missing DNA evidence in Assange case

Forensic experts have failed to find crucial DNA evidence in the sexual assault case against Julian Assange, a British newspaper reports.

In a 100-page document shown to lawyers for the Australian WikiLeaks founder, Swedish police outlined their basis for seeking the 41-year-old's extradition to Stockholm to face questioning.

The report said staff at two forensic laboratories were unable to find conclusive evidence of Mr Assange's DNA on a torn condom provided by one of two women who claim to have been assaulted in August 2010.

However, the same analysts have found DNA believed to belong to Mr Assange on a condom provided by a second woman, The Mail on Sunday reported.

Mr Assange denies any wrongdoing and says sex with the two women was consensual.

He remains holed up in London's Ecuadorian embassy in a bid to avoid Swedish extradition, which he insists would lead to him being handed to authorities in the United States, where the actions of his secret-leaking website are under investigation.

The Swedish police report said that one woman, now aged 33, claims she was repeatedly molested by Mr Assange at her flat in Stockholm, adding on one occasion he deliberately broke a condom before wearing it to have unprotected sex with her against her will.

Scientists were unable to find traces of Mr Assange's DNA on the condom and his lawyers suggest that is because a fake one may have been submitted, the tabloid reports.

Mr Assange, who has been granted asylum by Ecuador, is yet to be formally charged with any offence by Swedish authorities.

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DNA evidence missing in Assange case

The Irish Times - Monday, September 17, 2012

INNOVATION PROFILE:Teagascs Animal Bioscience facility, Grange, Co Meath

TEAGASCS NEWLY opened Animal Bioscience Facility in Grange, Co Meath, will use the latest DNA-based approaches to assist Irish farmers produce better quality and healthier livestock and ultimately improve Irish food production.

The publication of the genome sequence for cattle in 2009 has opened up the possibility to use these approaches to study commercially important traits. These include milk and meat production, immunity and disease, nutrition and reproduction, explains Teagasc director Prof Gerry Boyle.

The new facility was developed as part of the Teagasc vision programme which was initiated in 2006 with the objective of establishing centres of excellence in the key sciences that underpin Irish agriculture. Animal bioscience is a key component of the organisations Animal and Grassland, Research and Innovation Programme which integrates applied and strategic research across the main livestock species in Ireland namely dairy cattle, beef cattle and sheep.

The Animal and Bioscience Department carries out research in the areas of animal breeding and genomics, animal health and welfare, infection and disease, computational and systems biology, fertility and reproduction, feed efficiency and product quality. The new technologies being developed have the potential to accelerate the rate of gain in efficiency and quality.

Using the new areas of science such as genomics, proteomics, and systems biology, we are seeking to develop tools to more accurately identify the most profitable animals for current and future production systems, says Dr Richard Dewhurst, head of the Teagasc animal and bioscience department.

We are developing the optimal breeding programmes to maximise genetic gain in the long term. Our main research activities include the development of multi-breed genetic and genomic evaluations, breeding objectives and breeding programmes for dairy cattle, beef cattle and sheep. We also aim to identify genes, pathways and biological processes mediating resistance to infectious diseases in cattle and sheep and how these genes interact with pathogens and the environment.

While we are not quite at the stage of designer animals the use of these new DNA techniques could have a dramatic impact on Irish agriculture. If we take the DNA sequence of a bull, for example, we can use that to more accurately predict the characteristics that will be passed on to his progeny, Dewhurst explains. And the rate at which we can get the information is accelerating so we will soon be able to get the DNA sequence for individual animals. Its all about analysing the data and relating it to the traits we want to predict.

This highly scientific data led approach is a revolution in terms of the practices which obtained just 25 years ago. Over the past 25 years genetics has become much more statistics-based, before that it was an art, says Dewhurst. We have been using statistical models to predict traits in animals for the past while but now with the genome we will be able to identify good quality animals with the desired traits even before they reach maturity.

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DNA research key for Irish agriculture

For 30 years, Peggy Sue Houser was listed as a missing person. For nearly the same time, the Piqua womans unidentified corpse lay buried in Hillsborough County, Fla.

Last year, DNA brought the two cases together, something that may happen more frequently as local detectives submit genetic samples to the Center for Human Identification at the University of North Texas Health Science Center.

Funded by a National Institute of Justice grant, the Center is taking DNA samples from law enforcement agencies and coroners offices across the country, in an effort to match missing persons cases with unidentified remains.

Dayton Detective Patricia Tackett, who is assigned to cold cases, said she has collected DNA from the family members of nearly all of the eight open missing person cases she has, even the ones where the missing person has been declared dead.

Just because theyre declared dead doesnt mean weve recovered their bodies, and there are plenty of bodies out there, said Tackett.

Cold cases, by nature, are tough if they were easy cases, they would have been solved, police said. But missing persons cases offer a unique set of challenges. There is no body, no crime scene. Sometimes its not exactly clear when the person disappeared. Often police cant even prove a crime has been committed.

But in recent years, the federal government has taken steps to help match the cases of unidentified bodies estimated at more than 40,000 nationwide to those missing persons.

The National Missing and Unidentified Persons System (NamUs), an online tool administered by the National Institute of Justice, is now fully searchable by the public with databases of information from both missing person cases and those of human remains. NamUS is also administrated at the University of North Texas Health Science Center, like the DNA collection program.

Under the DNA program, law enforcement officials are given free collection kits to obtain the DNA from the close relatives of missing people. The kits are processed at the Center for Human Identification, also for free. The samples are then uploaded into the FBIs Combined DNA Index System (CODIS), so that it can be compared to those of unidentified remains. If relatives are not available, then police sometimes can get a genetic profile from the missing persons property, such as a hairbrush or toothbrush.

The Center claims to have assisted with more than 180 identifications made from Hawaii to New York.

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Police hope DNA will help solve cold cases

For 30 years, Peggy Sue Houser was listed as a missing person. For nearly the same time, the Ohio womans unidentified corpse lay buried in Hillsborough County, Fla.

Last year, DNA brought the two cases together, something that may happen more frequently as local detectives submit genetic samples to the Center for Human Identification at the University of North Texas Health Science Center.

Funded by a National Institute of Justice grant, the Center is taking DNA samples from law enforcement agencies and coroners offices across the country, in an effort to match missing persons cases with unidentified remains.

Cold cases, by nature, are tough if they were easy cases, they would have been solved, police said. But missing persons cases offer a unique set of challenges. There is no body, no crime scene. Sometimes its not exactly clear when the person disappeared. Often police cant even prove a crime has been committed.

In Butler County, missing cases involving Alana Laney Gwinner of Fairfield, Katelyn Markham of Fairfield, Ronald Tammen Jr. of Oxford and William DiSilvestro of Hamilton have went unsolved for years.

But in recent years, the federal government has taken steps to help match the cases of unidentified bodies estimated at more than 40,000 nationwide to those missing persons.

The National Missing and Unidentified Persons System (NamUs), an online tool administered by the National Institute of Justice, is now fully searchable by the public with databases of information from both missing person cases and those of human remains. NamUS is also administrated at the University of North Texas Health Science Center, like the DNA collection program.

Under the DNA program, law enforcement officials are given free collection kits to obtain the DNA from the close relatives of missing people. The kits are processed at the Center for Human Identification, also for free. The samples are then uploaded into the FBIs Combined DNA Index System (CODIS), so that it can be compared to those of unidentified remains. If relatives are not available, then police sometimes can get a genetic profile from the missing persons property, such as a hairbrush or toothbrush.

Bill Hagmaier, Executive Director of the International Homicide Investigators Association and a former FBI crime profiler, said the recent changes are long overdue. His group helped develop the DNA initiative a few years back, which he said he wanted to do 20 years ago.

He said the military has long done a far better job of matching bodies to those reported missing in action, just so much more than what were doing for our civilians here.

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DNA may help solve cold cases

Artistic impression of the dynamics of DNA supercoils. A person manipulates a long DNA molecule. Loops in the DNA molecule are created by winding up the DNA. For the first time ever, the research by Van Loenhout, Grunt and Dekker revealed how these DNA loops dynamically move along the DNA strand.

If you take hold of a DNA molecule and twist it, this creates 'supercoils', which are a bit like those annoying loops and twists you get in earphone cables. Research carried out by TU Delft, The Netherlands, has found that in the DNA molecule these coils can make their way surprisingly quickly along the length of the DNA. This newly discovered 'hopping' mechanism - which takes places in a matter of milliseconds - could have important biological implications, because cells use the coils to bring specific pieces of DNA into contact with one another. The researchers from Cees Dekker's group at the Kavli Institute of Nanoscience in Delft will be publishing their results in Science this week.

Supercoiling

A DNA molecule in a cell is not simply a loose wire; it is completely wound up in a tangle of loops ('DNA supercoils'). These supercoils in a DNA molecule (see the illustration on the right) are similar to those annoying loops and twists you often get in earphone cables.

In living cells, the DNA supercoils form and unravel and move along the DNA molecule. They are vital to the regulation of DNA activity, in determining which genes are switched on or off for example. One of the ways in which cells use the supercoils is to bring pieces of DNA into contact with one another.

Dynamic

Static images of the DNA supercoils have been studied in detail in the past, but their dynamics remained unknown up till now. PhD student Marijn van Loenhout from the Kavli Institute of Nanoscience at Delft developed a new technique that enabled him to observe how the coils travel along a DNA molecule for the first time. The research was led by Professor Cees Dekker, head of the Bionanoscience Department.

The TU Delft team used magnetic tweezers to stretch out a small section of a DNA molecule and were then able to observe the movement of the DNA coils using fluorescence microscopy (see movies at the website). They succeeded in showing these movements in real time, at the level of the individual DNA molecule.

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Van Loenhout: "We have discovered that the coils can move slowly along the DNA via diffusion. But what we also saw - and this was totally unexpected - that they can 'hop' along relatively long distances (micrometres). In such a movement a loop disappears in one spot, while simultaneously another loop appears in another spot, much further away. This information enables us to test theories about the mechanics of DNA, testing how you tie a knot in DNA, as it were."

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Research: Hopping DNA supercoils

ScienceDaily (Sep. 13, 2012) Scientists at Karolinska Institutet in Sweden describe in a new study how so-called DNA origami can enhance the effect of certain cytostatics used in the treatment of cancer. With the aid of modern nanotechnology, scientists can target drugs direct to the tumour while leaving surrounding healthy tissue untouched.

The drug doxorubicin has long been used as a cytostatic (toxin) for cancer treatment but can cause serious adverse reactions such as myocardial disease and severe nausea. Because of this, scientists have been trying to find a means of delivering the drug to the morbid tumour cells without affecting healthy cells. A possible solution that many are pinning their hopes on is to use different types of nanoparticles as 'projectiles' primed with the active substance.

In the present study, which is published in the scientific journal ACS Nano, scientists at Karolinska Institutet show how DNA origami can be used as such a projectile (or carrier) of doxorubicin. DNA origami is a new technique for building nanostrucutres from DNA, the hereditary material found in the cell nucleus. Using this technique, researchers can produce highly complex nanostrucutres with surfaces to which complex patterns of proteins and many other molecules can easily be attached.

What the researchers did on this occasion was to package the doxorubicin in a DNA origami configuration designed in such a way that relaxed the degree of twist of the DNA double helix. This allowed the drug to be released more slowly and operate more effectively on the cancer cells at lower concentrations than is otherwise possible.

"When the DNA has a lower degree of twist, there's more room for the doxorubicin to become attached, which leads to its slower release," says group leader Dr Bjrn Hgberg. "Another advantage to using DNA origami is that we will quickly be able to develop the targeted protein system. This will enable us to deliver drugs in a way that is even more sparing of healthy cells."

The study has been financed with grants from several bodies, including the Swedish research Council, Vinnova (the Swedish governmental agency for innovation systems), the Royal Swedish Academy of Sciences, the Falk Foundation, the Jeansson foundations, Carl Bennet AB and the Axel and Eva Wallstrm Foundation.

Publication: 'A DNA Origami Delivery System for Cancer Therapy with Tunable Release Properties', Yong-Xing Zhao, Alan Shaw, Xianghui Zeng, Erik Benson, Andreas M. Nystrm & Bjrn Hgberg, ACS Nano, online first 5 September 2012.

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Under-twisted DNA origami delivers cancer drugs to tumors

Sequenom has appointed Myla Lai-Goldman to its board of directors and to the board's science committee. Lai-Goldman is a managing partner at Personalized Science and CEO of GeneCentric Diagnostics. Previously, she served as executive vice president, chief medical officer, and chief scientific officer at Laboratory Corporation of America.

Aushon BioSystems has appointed Martin Verhoef to be company CEO and to serve on its board of directors. Verhoef takes over the position from company Founder Peter Honkanen, who will assume the post of COO and will continue as a board director.

Verhoef has spent 25 years in the life science research tools and molecular diagnostics business. He formerly was CEO at MiraDx and PrimeraDx, he led Ciphergen's Biosystems Division, and he held senior management jobs at Agilent in Germany and in the US.

The New York Genome Center has appointed Dirk Evers and Kevin Shianna to its leadership team. Evers, who will serve as senior vice president of bioinformatics, joins NYGC from Illumina, where he led the company's computational biology efforts in the UK. Previously, he served as managing director of the International Graduate School in Bioinformatics and Genome Research at the Center for Biotechnology at Bielefeld University. Shianna will serve as senior vice president of sequencing operations at the NYGC. He joins from Duke University, where he was an assistant professor in the School of Medicine, director of operations for the Center for Human Genome Variation, and founding director for the Genomic Analysis Facility.

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LBNL Seeks Licensees for Highly Specific and Sensitive DNA Extraction Method

Among the many mysteries of human biology is why complex diseases such as diabetes, high blood pressure and psychiatric disorders are so difficult to predict and, often, to treat. An equally perplexing puzzle is why one individual gets a disease such as cancer or depression, while an identical twin remains perfectly healthy.

Now scientists have discovered a vital clue to unraveling these riddles.

The human genome is packed with at least 4 million gene switches that reside in bits of DNA that once were dismissed as junk but that turn out to play critical roles in controlling how cells, organs and other tissues behave.

The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches.

The findings are the fruit of an immense federal project, involving 440 scientists from 32 labs around the world.

As they delved into the junk parts of the DNA that are not actual genes containing instructions for proteins they discovered it's not junk at all. At least 80 percent of it is active and needed.

The result is an annotated road map of much of this DNA, noting what it's doing and how.

It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.

The findings have immediate applications for understanding how alterations in the nongene parts of DNA contribute to human diseases, which may in turn lead to new drugs.

They also can help explain how the environment can affect disease risk.

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DNA ‘junk' contains a treasure of information about disease

ENCODE (Image: Ed Yong)

The recent dustup over the ENCODE project and its confusing finding that 80% of DNA is functional surprises me greatly. What surprises me especially is that people are surprised by junk DNA. Unfortunately this time the scientists are also culpable since, while the publicity surrounding ENCODE has been a media disaster, the 80% claim originated in the scientific papers themselves. There is no doubt that the project itself which represents a triumph of teamwork, dogged pursuit, technological mastery and first-rate science has produced enormously useful data, and there is no doubt it will continue to do so. What is in doubt is how long it will take for the public damage to be repaired.

Theres a lot written about the various misleading statements about the project made by both scientists and journalists and I cannot add much to it. All I can do is to point to some excellent articles:Larry Moran has waged a longstanding effort to spread the true wisdom about junk DNA for years on his blog. Ed Yong exhaustively summarizes a long list of opinions, links and analysis. T. Ryan Gregory has some great posts dispelling the myth of the myth of junk DNA. And John Timmer has the best popular account of the matter. The biggest mistake on the part of the scientists was to define functional so loosely that it could mean pretty much all of DNA. The second big mistake was not in clarifying what functional means to the public.

But what I found astonishing was why its so hard for people to accept that much of DNA must indeed be junk. Even to someone like me who is not an expert, the existence of junk DNA appeared perfectly normal. I think that junk DNA shouldnt shock us at all if we accept the standard evolutionary picture.

The standard evolutionary picture tells us that evolution is messy, incomplete and inefficient. DNA consists of many kinds of sequences. Some sequences have a bonafide biological function in that they are transcribed and then translated into proteins that have a clear physiological role. Then there are sequences which are only transcribed into RNA which doesnt do anything. There are also sequences which are only bound by DNA-binding proteins (which was one of the definitions of functional the ENCODE scientists subscribed to). Finally, there are sequences which dont do anything at all. Many of these sequences consist of pseudogenes and transposons and are defective and dysfunctional genes from viruses and other genetic flotsam, inserted into our genome through our long, imperfect and promiscuous genetic history. If we can appreciate that evolution is a flawed, piecemeal, inefficient and patchwork process, we should not be surprised to find this diversity of sequences with varying degrees of function or with no function in our genome.

The reason why most of these useless pieces have not been weeded out is simply because there was no need to. We should remember that evolution does not work toward a best possible outcome, it can only do the best with what it already has. Its too much of a risk and too much work to get rid of all these defective and non-functional sequences if they arent a burden; the work of simply duplicating these sequences is much lesser than that of getting rid of them. Thus the sequences hung around in our long evolutionary history and got passed on. The fact that they may not serve any function at all would be perfectively consistent with a haphazard natural mechanism depending on chance and the tacking on of non-functionality to useful functions simply as extra baggage.

There are two other facts in my view which should make it very easy for us to accept the existence of junk DNA. Consider that the salamander genome is ten times the size of the human genome. Now this implies two possibilities; either salamanders have ten times functional DNA than we do, or that the main difference between us and salamanders is that they have much more junk DNA. Wouldnt the complexity of salamander anatomy of physiology be vastly different if they really had so much more functional DNA? On the contrary, wouldnt the relative simplicity of salamanders compared to humans be much more consistent with just varying degrees of junk DNA? Which explanation sounds more plausible?

The third reason for accepting the reality of junk DNA is to simply think about mutational load. Our genomes, as of other organisms, have undergone lots of mutations during evolution. What would be the consequences if 90% of our genome were really functional and had undergone mutations? How would we have survived and flourished with such a high mutation rate? On the other hand, its much simpler to understand our survival if we assume that most mutations that happen in our genome happen in junk DNA.

As a summary then, we should be surprised to find someone who says they are surprised by junk DNA. Even someone like me who is not an expert can think of at least three simple reasons to like junk DNA:

1. The understanding that evolution is an inherently messy and inefficient process that often produces junk. This junk may be retained if its not causing trouble.

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Three reasons why junk DNA makes evolutionary sense

Researchers show that DNA supercoils are dynamic structures that can hop long distances, a phenomenon that could affect gene regulation.

Scientists understanding of how long strings of DNA are packaged into tiny spaces just got a little more complicated. New research on single molecules of DNA show that supercoilssegments of extra-twisted loops of DNAcan moving by jumping along a DNA strand. The results, published today (September 13) in Science, give researchers new insights into DNA organization and point to a surprisingly speedy mechanism of gene regulation inside cells.

This is the first study that addresses the dynamics of DNA supercoils, said Ralf Seidel, who studies movement of molecular motor proteins along DNA at the University of Technology Dresden, but was not involved in the research. This supercoil hopping motion allows DNA strands to transmit supercoiling, bringing sites together in very fast manner.

DNA, being a double helix, is naturally twisted. In vivo, its packaged with proteins called histones that help condense the millions or billions of nucleotides into the small space of a cells nucleus. Constant interaction with proteins moving along the strand, like transcription factors that need to open the helix to read the DNA sequence, can affect both the double helixs twist, and the strands writhethe coiling of the strand around itself. These extra-twisted coils, called plectonemes or supercoils, form not unlike coils in phone cords. By bringing together distant segments of DNA, such as regulatory elements and the genes they control, supercoiling can affect expression.

In order to get a better sense of how supercoils behave, Cees Dekker at Delft University of Technology and his colleagues induced supercoils in single strands of DNA molecules, labeled with fluorescent dye. One end of the DNA was anchored to the side of a glass capillary tube and a magnetic bead was attached to the other end. This allowed the researchers to use miniscule magnets to twist the DNA and induce supercoils, and watch their movement using fluorescence microscopy.

Unexpectedly, the team found that supercoils move along DNA strands in one of two ways. Sometimes they slowly diffuse along the strand; other times, the supercoils hoppeddisappearing suddenly from one location while simultaneously appearing at a distant location further down the strand.

This is far more complicated than diffusion of supercoils down the DNAs length, said Prashant Purohit, who studies DNA behavior at the University of Pennsylvania, but was not involved in the study. The DNA is behaving non-locally, he noted. It shows that writhethe coiling of the DNA strandis a global, not local quantity [of the strand].

So far the intriguing phenomenon has only been observed on single strands of naked DNA, Seidel cautioned, so its unclear how supercoils might act in vivo, when the DNA is well-packaged and studded with proteins. It may be that such behavior is more important for DNA in prokaryotic cells, which have less packaged DNA than eukaryotic cells, noted Bryan Daniels, who models biological systems at the Wisconsin Institutes for Discovery at the University of Wisconsin-Madison.

The ionic environment of the cell is also likely to influence supercoiling behavior. DNA is more likely to condense in the presence of multivalent ions (3 or more positive charges), for example, than in an environment of singly-valent ions. And Dekker and his colleagues, who used singly-valent ions in their experiments, found that more supercoils formed at lower concentrations of ions.

Dekker and his team are now looking at how different DNA sequences and the presence of DNA-binding proteins can influence supercoil formation and motionthe first step toward understanding supercoil movement in vivo.

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DNA with a Twist

A London familys DNA could be the missing link in a centuries-long quest to find the remains of King Richard III.

A team of archeologists at the University of Leicester in England exhumed a skeleton believed to be Richards beneath one of the universitys parking lots Wednesday and are hoping DNA evidence from the London family will prove their suspicions true.

Richard was killed in 1485 during the Battle of Bosworth often cited as the deciding battle in the War of the Roses by Henry Tudor VII, father of the famed King Henry VIII.

Richards Machiavellian rise to power its believed he had his nephews murdered in order to seize the thrown and short two-year reign as king is chronicled in Shakespeares play Richard III.

In 2005, British historian John Ashdown-Hill traced Richards bloodline to Joy Ibsen, a retired journalist who moved to London, Ont., from England after the Second World War and raised a family.

Ashdown-Hill discovered Ibsen and Richard shared a maternal ancestor, Cecily Neville.

Though Ibsen died in 2008, she passed the gene on to her three children: Michael, who lives in the U..K; Jeff, who lives in Toronto; and Leslie on Vancouver Island.

Its pretty exciting, said Jeff, 49. I wasnt expecting the findings to be so concise ... Im hoping that if theres a proper funeral for him, well get invited and maybe get a chance to rub elbows with some royals.

The skeleton exhumed Wednesday was found in whats believed to be the choir of the lost Church of the Grey Friars, the same place historical records indicate Richard was buried. Initial examinations found trauma to the skull consistent with a battle injury and a barbed arrow through the skeletons upper back.

Especially telling is the spinal deformity found on the exhumed skeleton. Its believed Richard had severe scoliosis, a form of spinal curvature that caused his right shoulder to appear higher than the left, the same type of curvature found on the skeleton.

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DNA could help ID a king

Video will begin in 5 seconds.

Archaeologists from the University of Leicester uncover remains that could be those of England's 15th century King Richard III.

It seems a most unlikely resting place for a King of England.

Buried under a car park behind a block of council offices, the skeletal remains of a man were discovered in the British city of Leicester this week, with a metal arrow lodged in its back and wrapped simply in a shroud.

And a Canadian-born furniture maker could help prove what archaeologists are hoping is true - that this is the lost skeleton of King Richard III.

Heir in there? ... Canadian furniture maker Michael Ibsen takes a DNA test at the site of the archaeological discovery. Photo: ITV screengrab

For the past decade, University of Leicester archaeologists, dubbed the Time Tomb Team, have been leading a search for the lost grave of the much-maligned king.

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Richard III, who had a reputation as a murderous "hunchback" in medieval times, was killed in one of the most important clashes in English history, the Battle Of Bosworth, in 1485.

What is known is that his body was stripped and brought to Leicester, where he was buried in the church of the Franciscan Friary, known as the Grey Friars.

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DNA to test heir claim

DNA on a cigarette butt found outside Lloyd Rayney's home around the time of his wife's murder matched a person 'well known to police', murder trial told.

Lloyd Rayney dodges witches hats to get to court for day 31 of his murder trial. PICTURE: Kerris Berrington Source: PerthNow

Sen-Const Warren Wheatley. Source: PerthNow

LAWYERS acting for barrister Lloyd Rayney today told the Supreme Court that DNA on a cigarette butt found by police outside the family home in Como matched that of a person "well known to police" as other witnesses told of "blood curdling" screams coming from Kings Park on the night Mr Rayney's wife Corryn disappeared.

In a new twist in the long-running trial, defence lawyer David Edwardson, QC, told trial judge Justice Brian Martin that the person whose DNA was found on the cigarette butt had the same surname - Eades - as the driver of a car which was stopped by Kensington police in Manning at about 9.10pm on August 7, 2007, the night Mrs Rayney was last seen alive.

"Your honour will hear evidence shortly that a cigarette butt was retrieved and that the DNA on that cigarette matched a person well known to police by the name of Eades," he said.

The cigarette butt was among items collected by police from the footpath and verge of the Rayney home on August 22, 2007.

Mr Edwardson's comments came as a former police officer, Darrel McLeod, gave evidence at Mr Rayney's murder trial today.

It has been alleged Mr Rayney killed his wife at the family home after she arrived home from a boot scooting class in Bentley.

He has pleaded not guilty to the charge and also to an alternative charge of manslaughter.

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DNA cigarette butt twist in Rayney trial

There was an extremely strong chance DNA found inside the underpants of a five-year-old girl came from the man accused of abusing her, a court has heard.

But the ACT Supreme Court has been told tests for saliva turned up nothing, despite the girls allegation her step-grandfather licked her vagina.

And the court has heard tests werent carried out on other items of clothing and bedding because they were likely to be covered in his DNA and have no probative value.

The underpants were also placed in the same bag as another item of clothing, prompting the defence to suggest the DNA might have transferred from one to the other.

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The 61-year-old man, who cannot be named, is on trial in front of Justice Richard Refshauge accused of two counts of having sexual intercourse with a child.

He has pleaded not guilty, and also denies two alternative charges of committing acts of indecency on the girl.

It is alleged he licked the girls vagina twice when he was babysitting her in April 2009.

The allegations came to light after the girls mother picked her up, when the girl asked her mother if she could tell her the secret she shared with poppy.

The accused man entered the witness box this afternoon and denied any wrongdoing, describing his shock when police confronted him with the allegations.

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Court hears DNA findings in child sex case

By Jen Wieczner

Now that scientists have revealed that the huge swaths of genetic code once dismissed as junk DNA are not so worthless, investors may wonder if theres similar hidden value in the biotech sector. The short answer: maybe.

Though analysts say its too soon to tell what impact the discovery will have on stocks, the recent breakthrough may eventually lead to new techniques for the early detection of diseases and to the development of new drugs. And that could be a boon to firms at the forefront of biotechnology and molecular diagnostics.

Even before the findings from the project known as Encode emerged, the biotechnology sector was already on the cutting edge, at least in terms of market performance: The iShares Nasdaq Biotechnology Index ETF /quotes/zigman/85342/quotes/nls/ibb IBB -0.0072% is up more than 47% over the past 12 months, with double the returns of the broader S&P Healthcare Index. But this latest discovery suggests there could be even more promising returns ahead. The new understanding of junk DNA may help science-driven pharmaceutical companies figure out which genetic proteins can be treated with drugs, lead diagnostics companies to which genetic variations are red flags for certain diseases and help other firms evaluate the effectiveness of their treatments, says Dr. Thomas Gingeras, the head of functional genomics at Cold Spring Harbor Laboratory and one of the principal investigators for the Encode project.

This junk DNA is just another layer of complexity, but it also brings us a little bit closer to having a more full set of therapies that we can bring to patients, says Karen Andersen, a Morningstar biotechnology analyst.

It wouldnt be the first time that what scientists once considered genetic trash turned into corporate treasure. Regulus Therapeutics, a joint venture between drug companies Alnylam Pharmaceuticals /quotes/zigman/92224/quotes/nls/alny ALNY +5.00% and Isis Pharmaceuticals /quotes/zigman/74162/quotes/nls/isis ISIS +0.34% that last month began SEC proceedings to go public, focuses entirely on treating diseases through microRNAbut a decade ago, that part of the genome was also considered junk. (Regulus declined to comment.)

The new research may also bring business to Alnylam, which uses a technique known as RNA Interference to basically turn off disease-causing genes; the data could help the company identify new disease markers for which it could develop therapies, says Barry Greene, Alnylams chief operating officer. It opens up a world of biologic insight that will be helpful, says Greene. While it may take a while for companies to apply the results, the research is a step forward that might eventually lead to companies like Regulus being formed to pursue new genetic therapies: Weve never written aspects of the genome off, Greene says.

The new insight may also have positive implications for molecular diagnostics companies that are already using genomic information to test for diseases, such as Myriad Genetics /quotes/zigman/58124/quotes/nls/mygn MYGN +0.86% , which makes tests for evaluating how likely a person is to develop various types of cancer. Knowing more about the junk DNA might help the company develop more sophisticated tests to detect a disease even before it forms, says Andersen. Myriad declined to comment.

Pharmaceutical companies are also increasingly interested in harnessing our genes to create better drugs and to assess whether those drugs will work for a patient or cause side effects. A large part of the strategy at Roche /quotes/zigman/137625/quotes/nls/rhhby RHHBY -0.68% , for example, is genetic research, which the company uses to create diagnostic tests to go along with each of its drugs, in an effort to deliver more personalized health care. Sixty percent of the drugs in the firms pipeline are now paired with a test, including treatments it is developing for schizophrenia and Alzheimers disease. Roche was not available to comment before press time.

Another type of genetic science known as epigeneticswhich relates to how a gene is expressedis becoming popular with pharmaceutical companies, who are using the concept to create new drugs that can virtually alter a persons genetic instructions, says Andersen. Celgene /quotes/zigman/69584/quotes/nls/celg CELG +0.50% , for one, racked up about $700 million last year in sales of its drug Vidaza, which treats some forms of anemia and leukemia by helping bone marrow produce normal blood cells instead of unhealthy ones.

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Investing in ‘junk DNA’