Category Archives: DNA

Public release date: 24-Feb-2013 [ | E-mail | Share ]

Contact: Robert Perkins perkinsr@usc.edu 213-740-9226 University of Southern California

Two USC scientists have developed an algorithm that could help make DNA sequencing affordable enough for clinics and could be useful to researchers of all stripes.

Andrew Smith, a computational biologist at the USC Dornsife College of Letters, Arts and Sciences, developed the algorithm along with USC graduate student Timothy Daley to help predict the value of sequencing more DNA, to be published in Nature Methods on February 24.

Extracting information from the DNA means deciding how much to sequence: sequencing too little and you may not get the answers you are looking for, but sequence too much and you will waste both time and money. That expensive gamble is a big part of what keeps DNA sequencing out of the hands of clinicians. But not for long, according to Smith.

"It seems likely that some clinical applications of DNA sequencing will become routine in the next five to 10 years," Smith said. "For example, diagnostic sequencing to understand the properties of a tumor will be much more effective if the right mathematical methods are in place."

The beauty of Smith and Daley's algorithm, which predicts the size and composition of an unseen population based on a small sample, lies in its broad applicability.

"This is one of those great instances where a specific challenge in our research led us to uncover a powerful algorithm that has surprisingly broad applications," Smith said.

Think of it: how often do scientists need to predict what they haven't seen based on what they have? Public health officials could use the algorithm to estimate the population of HIV positive individuals; astronomers could use it to determine how many exoplanets exist in our galaxy based on the ones they have already discovered; and biologists could use it to estimate the diversity of antibodies in an individual.

The mathematical underpinnings of the algorithm rely on a model of sampling from ecology known as capture-recapture. In this model, individuals are captured and tagged so that a recapture of the same individual will be known and the number of times each individual was captured can be used to make inferences about the population as a whole.

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Taking the gamble out of DNA sequencing

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Frozen food maker Birds Eye on Friday said it would withdraw some products in Britain and Ireland after it found traces of horse DNA in one of its ready meals sold in Belgium.

"Regrettably, we have found one product, chili con carne, produced for us by Frigilunch N.V. and sold in Belgium, that has tested positive for horse DNA at 2 percent," Birds Eye said in a statement.

"As a precautionary measure in the UK and Ireland we will withdraw all other products produced by the same supplier, namely traditional spaghetti bolognese (340g), shepherd's pie (400g) and beef lasagne (400g)."

Birds Eye, which is owned by Pinnacle Foods in North America and by private equity group Permira in Europe, said it would also immediately withdraw the chili con carne product from sale in Belgium.

The discovery of horse meat in food labeled as beef has triggered product recalls and damaged confidence in Europe's vast and complex food industry. The scandal erupted last month when tests carried out in Ireland revealed that some beef products also contained horse meat.

Birds Eye added that the withdrawn products would not be replaced on supermarkets shelves until it had completed an investigation into the issue and had complete confidence in Frigilunch N.V.

It said tests showed its beef burgers, beef pies and beef platters sold in Britain and Ireland did not contain horse DNA.

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Birds Eye recalls UK products after horse DNA find in Belgium

By JESSICA GRESKO Associated Press

WASHINGTON (AP) A Maryland DNA law being challenged in the U.S. Supreme Court helped lead to 43 convictions over the past four years, but state data shows the majority of the convictions could eventually have happened even without the new law.

For years, Maryland required people convicted of serious crimes to provide a DNA sample. The sample, taken from a swab of saliva, was then compared against a database of DNA evidence from crime scenes, and some old cases were able to be solved. Maryland changed its law in 2009, however, so that people had to provide the saliva sample when they were arrested on charges of committing certain violent crimes before going to trial.

The change is at the center of a U.S. Supreme Court case being argued Tuesday. Opponents say the law violates a persons constitutional right to be free from unreasonable searches and seizures. But supporters of the law, including Maryland Gov. Martin OMalley and Attorney General Douglas Gansler, say taking DNA from arrestees is an important law enforcement tool used by 27 other states and the federal government. They say it is no more invasive than taking a persons fingerprints.

Law enforcement has been taking fingerprints forever, Gansler said in a telephone interview Friday.

The state has now taken more than 33,000 DNA samples as a result of the expansion. Those samples have led to 73 arrests and 43 convictions, with sentences ranging from probation to life in prison. The majority of the convictions were for burglary or theft; seven were for rape or sex offenses.

But 29 of the convictions could have happened even if Maryland hadnt extended its law to arrestees, according to state data. Thats because those people were ultimately convicted of the offense for which their DNA was taken. Their DNA would have been collected even under the old law, though law enforcement would have had to wait until after their conviction.

For example, William Edward Burton III was arrested after being accused of attempted murder and rape. Officials took DNA and matched it to a rape that happened in Massachusetts from 1995. But because Burton ultimately pleaded guilty in the first case, his DNA would have been collected and would have ultimately led officials to the Massachusetts rape.

The attorney who prosecuted Burtons case, Elizabeth Ireland, said taking DNA from arrestees is still important because many cases dont end like Burtons.

Not all arrestees are convicted, especially when its a crime like a rape. Rape is one of the most under-reported and under-charged crimes, said Ireland, who also prosecuted the case that is before the Supreme Court.

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Md. DNA Law In Front Of SCOTUS Aided 43 Cases

ROME/ZURICH (Reuters) - Italy's Health Ministry said on Saturday that tests had found no trace of horse DNA in minced beef meals by Swiss food giant Nestle that were removed from sale on Monday.

Nestle removed the ready-made beef ravioli and tortellini sold under its Buitoni brand from shelves in Italy and Spain and halted production of the meals after its own tests had found more than 1 percent horse DNA in the products.

Italian authorities seized 26 tons of affected beef products on Thursday after Nestle withdrew the meals - the latest company to become embroiled in the scandal that has highlighted the complexities of Europe's food chain.

"No trace of horse DNA has been found in Nestle cooked and frozen minced beef," the ministry said in a statement.

It was not immediately clear what the outcome was of the tests of the food seized in Spain.

The Italian tests were carried out on beef products that had been stored at the Safim plant near Turin, the ministry said.

Meanwhile, Italy also ordered the seizure on Saturday of about 6 tons of frozen beef lasagne made by Italian group PRIMIA after tests showed the presence of horse meat, an official with Italy's NAS, a police unit that monitors health and safety standards, told Reuters.

A Nestle spokesman welcomed the ministry's decision to release its products.

"We are happy the ministry's tests came back negative," spokesman Chris Hogg said in an email to Reuters.

"Our focus now though is on restarting production of these products today and tomorrow with a new supplier, using beef we have tested to ensure it contains no horse DNA."

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Italy finds no trace of horse DNA in Nestle mince meals

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A skull found a year ago by hunters in the woods is that of a disabled girl who was killed and dismembered by her stepmother, North Carolina police said Thursday.

DNA tests show it was Zahra Baker's, but Hickory Police Chief Tom Adkins said investigators are still unable to say how the 10-year-old died. Adkins said he and other law enforcement officers who spent many months searching for the girl had "mixed emotions" about knowing for certain that it was her remains.

"It brings up the tragedy of Zahra's death and the life she lived before she was killed but it also gives us and the community a sense of finally bringing her home."

Said Caldwell County Sheriff Alan Jones: "She will be in our memories for the rest of our lives."

The Zahra Baker case captivated the attention of communities here and in Australia, where she had lived before her father, Adam Baker, moved to the United States to marry Elisa Baker.

Elisa Baker is serving up to 18 years in prison. She pleaded guilty in 2011 to second-degree murder with aggravating factors that included desecrating Zahra Baker's body.

Zahra Baker, who wore a prosthetic leg and hearing aids after a struggle with bone cancer, was reported missing in October 2010 from her home in the western North Carolina town of Hickory.

Parts of her remains were found in multiple sites around Hickory shortly after her reported disappearance. But her skull wasn't found until last year.

It was examined by investigators with the N.C. State Bureau of Investigation and N.C. Medical Examiner's Office using a DNA profile used for the prosecution of Elisa Baker.

Zahra's death was caused by "undetermined homicidal violence," medical examiners said.

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DNA confirms skull that of NC disabled girl

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