Category Archives: DNA

Agents for the Federal Bureau of Investigation on Wednesday morning raided Proove Biosciences, an Irvine company that sells a DNA test it claims can determine whether a patient is at risk of addiction to opioid painkillers.

In a press conference, FBI spokeswoman Cathy Kramer said the raid was part of an ongoing investigation concerning healthcare fraud. No arrests were made.

Anonymous company employees told STAT News, a healthcare news site, that about 25 agents arrived with a search warrant and spent several hours hauling out boxes of documents. The employees had been told by Proove to stay home for the day.

Proove maintains that its test can determine a patients risk of addiction with 93% accuracy.

In December, an article published by STAT questioned the scientific basis for Prooves test. Rockefeller Universitys Dr. Mary Jeanne Kreek, who researches genetic links to addiction, told STAT that Prooves test was hogwash. In February, the site said Prooves method of paying physicians to participate in clinical trials might violate anti-kickback laws.

That article included a statement from CEO Brian Meshkin, who said that Proove is acting within the confines of the law [and intends] to follow both the letter and spirit of the law.

Meshkin could not be reached for comment regarding Wednesdays raid.

Proove had 2016 revenues of $28 million, according to STAT. The company was able to collect more than 100,000 DNA specimens, largely because of a regulatory loophole regarding laboratory-developed tests. Essentially, these tests are free from Food and Drug Administration regulation so long as theyre designed, manufactured and used within a single laboratory.

Last November, the Obama administration halted plans to close the loophole, and the FDA elected to leave the decision for the Trump administration.

On average, 91 Americans die each day of an opioid overdose. From 2000 to 2015, more than half a million people died from overdoses, according to the Centers for Disease Control and Prevention.

jack.flemming@latimes.com

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FBI raids controversial DNA testing company in Irvine - Los Angeles Times

Defective DNA kits affect criminal cases

Tanya Eiserer, WFAA 6:11 PM. CDT June 08, 2017

(Photo: WFAA, WFAA)

DALLAS -- The Dallas County District Attorneys Office has halted DNA testing for criminal cases after defects were found with the county crime labs new DNA test kits.

The problem will result in the DNA testing in dozens of cases having tobe redone.

County lab officials recently notified the DAs office of the issue. Lab officials are in the process of replacing the kits. For now, the lab has stopped all DNA testing for cases that were slated to go to trial.

Officials expect to resume DNA testing by September.

Its not fatally defective in any of the cases, said First Assistant DA Mike Snipes. Its a slowdown in the administration of justice. The upshot of this is that we cannot rely on any test results from the new kits that came online this year. It doesnt affect any cases where weve already gotten convictions.

The issue revolves around new kits that the countys crime lab began using in March. The kits were made by Qiagen, a German research company.

Because the FBI had expanded the requirements for DNA testing profiles, it required labs like Dallas County's Southwestern Institute of Forensic Sciences, or SWIFS, to get new DNA testing kits.

Lab officials quickly realized there was a problem with the kits. They were not distinguishing between human DNA and that from bacteria and fungus in some cases.

This is a technical issue, said Tim Sliter, a section chief with SWIFS.

Sliter says the lab sent over the DNA testing results of about 30 cases. In those cases, the anomaly did not occur.

However, in about 50 other cases, the anomaly did occur, so the lab did not report those results to prosecutors.

Sliter says that although testing for trials has been halted for now, the lab will continue to use the Qiagen kits for investigative work for the time being.

The state's Department of Public Safety labs had recently started using the Qiagen kits.

Catherine Bernhard, a Dallas defense attorney, said she had recently heard from a couple of prosecutors that they were having a tough time finding out from SWIFs when DNA testing would be completed or even started.

What they expressed was that they were being stonewalled, Bernhard said. They thought something was up but they didnt know what.

Bernhard has a client, who has been in jail for 14 months on a capital murder case.

Its probably going to cause us to approach the judge about letting him out on bond, she said. He didnt have a firm trial date because we were waiting on the DNA.

Toby Shook, a defense attorney and former prosecutor, said the crime labs quick action averted a potential disaster.

Since they caught it so soon, I dont think its going to be that big a deal, Shook said. I think the only thing youre going to see are some minor delays in cases. If this had gone on a long time and cases had been tried, yes thatd be a major problem.

2017 WFAA-TV

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DNA testing for criminal cases halted after defects found - WFAA

Drexel University and Georgia Institute of Technology researchers have discovered how the Rad52 protein is a crucial player in RNA-dependent DNA repair. The results of their study, published June 8 in the journal Molecular Cell, uncover a surprising function of the homologous recombination protein Rad52. They also may help to identify new therapeutic targets for cancer treatment.

Radiation and chemotherapy can cause a DNA double-strand break, one of the most harmful types of DNA damage. The process of homologous recombination which involves the exchange of genetic information between two DNA molecules plays an important role in DNA repair, but certain gene mutations can destabilize a genome. For example, mutations in the tumor suppressor BRCA2, which is involved in DNA repair by homologous recombination, can cause the deadliest form of breast and ovarian cancer.

Alexander Mazin, a professor at Drexel Universitys College of Medicine, and Francesca Storici, an associate professor at Georgia Techs School of Biological Sciences, have dedicated their research to studying mechanisms and proteins that promote DNA repair.

In 2014, Storici and Mazin made a major breakthrough when they discovered that RNA can serve as a template for the repair of a DNA double-strand break in budding yeast, and Rad52, a member of the homologous recombination pathway, is an important player in that process.

We provided evidence that RNA can be used as a donor template to repair DNA and that the protein Rad52 is involved in the process, said Mazin. But we did not know exactly how the protein is involved.

In their current study, the research team uncovered the unusual, important role of Rad52: It promotes inverse strand exchange between double-stranded DNA and RNA, meaning that the protein has a novel ability to bring together homologous DNA and RNA molecules. In this RNA-DNA hybrid, RNA can then be used as a template for accurate DNA repair.

It appeared that this ability of Rad52 is unique in eukaryotes, as otherwise similar proteins do not possess it.

Strikingly, such inverse strand exchange activity of Rad52 with RNA does not require extensive processing of the broken DNA ends, suggesting that RNA-templated repair could be a relatively fast mechanism to seal breaks in DNA, Storici said.

As a next step, the researchers hope to explore the role of Rad52 in human cells.

DNA breaks play a role in many degenerative diseases of humans, including cancer, Storici added. We need to understand how cells keep their genomes stable. These findings help bring us closer to a detailed understanding of the complex DNA repair mechanisms.

The research was supported by the National Institutes of Health, the National Science Foundation and the Howard Hughes Medical Institute.

These results offer a new perspective on the multifaceted relationship between RNA, DNA and genome stability. They also may help to identify new therapeutic targets for cancer treatment. It is known that active Rad52 is required for proliferation of BRCA-deficient breast cancer cells. Targeting this protein with small molecule inhibitors is a promising anticancer strategy. However, the critical activity of Rad52 required for cancer proliferation is currently unknown.

This new Rad52 activity in DNA repair, discovered by Mazin, Storici and their team, may represent this critical protein activity that can be targeted with inhibitors to develop more specific and less toxic anti-cancer drugs. Understanding of the mechanisms of RNA-directed DNA repair may also lead to development of new RNA-based mechanisms of genome engineering.

This research was supported by the National Institute of General Medical Sciences (NIGMS) of the NIH (grant GM115927), the National Science Foundation (grant 1615335), and the Howard Hughes Medical Institute Faculty Scholar Program (grant 55108574). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsoring agencies.

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Researchers Uncover New Instruction Manual to Repair Broken DNA - ScienceBlog.com (blog)

The Nebraska Department of Correctional Services is making progress on collecting DNA samples from 78 inmates who have refused to give samples over the past 20 years, the agency said Thursday in a news release.

The department had reduced that number from 78 in February to 13 as of Thursday.

State law says a person who had been convicted of a felony or other specified offense as of July 15, 2010, who did not have a sample in the state DNA Sample Bank, was required to have one collected at his or her own expense. The law also applied to people already serving a sentence.

In spite of the law, 78 inmates had refused.

In February, the department implemented changes to procedures for collecting DNA samples, and provided consequences when an inmate refused to provide one.

"I am committed to collecting DNA samples from every incarcerated person and believe the course we have charted will result in full compliance with state statute," said Corrections Director Scott Frakes. "In those cases where additional steps are necessary, we will take them as we did in these four cases from Douglas County."

Frakes was talking about four inmates who continued to refuse to give DNA samples, even with the policy change, until the department sought an order from a sentencing judge to use force to obtain the samples. Three of the inmates complied with the directive, said spokeswoman Dawn-Renee Smith.

"One did not and force was used," she said.

Smith said physical force was used, but no weapons or chemical agents.

Thirteen of the 78 who have refused received misconduct reports and sanctions according to the policy, Smith said.

The new policy on collecting samples specified that DNA will be collected within two business days of admission to a prison, if no sample was on file at the time.

The sample collection includes a swab from the inside of the inmate's cheek, a fingerprint and signature. It can also be done with a blood sample, if the person chooses.

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According to the policy, people who haven't provided a sample will be ordered to do so each month until they comply. A misconduct report will be issued for each refusal.

The first offense includes sanctions of 30 days of telephone, kiosk and canteen restriction. The second offense gets those restrictions plus 30 days loss of good time if they have good time to forfeit, or 30 days room restriction without being able to work if they don't.

The third refusal gets an additional loss of 90 days of good time, or another 30 days of room restriction without work if they have no good time.

Those refusing will be treated as a maximum custody offender when on a court or medical travel order, and will not be promoted to minimum or community custody.

And no inmates without a sample on file will be released prior to serving their maximum sentences, with no credit for good time, until they provide a sample.

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Corrections collects DNA samples with new policy covering inmates who refuse - Lincoln Journal Star

Free speech and protest are at the core of our political system, no matter if the words are yelled or whispered. But the First Amendment does not confer a right to violent protest.

The Bill of Rights sits behind a thick plate of glass on a raised platform inside the dimly lit rotunda of the National Archives in Washington, D.C. The document has faded so much the words are nearly indecipherable, but they retain their impact. When I saw what the archives call the Charters of Freedom while in Washington last week, I thought of recent events at The Evergreen State College.

Free speech and protest are at the core of our political system. Until my fellow Americans vote to give up their freedom of speech and protest, those faded words protect students rights to yell whatever they want at professors, the administration and their classmates.

But the First Amendment does not protect shoving others, menacing with baseball bats or other threats of violence. The students at this small, public liberal-arts school near the Washington state Capitol clearly have a right to protest institutional racism, as theyve been doing all year. Incidents of physical violence have been few, and it should stay that way. Physically attacking others because you disagree with their words or their approach is more likely to send you to jail than advance your political cause.

Evergreen President George Bridges told The Seattle Times editorial board he has spent many uncomfortable hours listening to students the past few weeks. Of course he has. Thats his job. Bridges said he was never afraid of the protesters, but some others on campus have reported feeling threatened. Bridges said the universitys student discipline system is being applied to those who broke the universitys conduct code.

Im perfectly fine with the student protesters making the college president uncomfortable. I dont have an issue with them getting in the face of a professor they disagree with. I am not OK with other students feeling threatened by people patrolling the campus carrying baseball bats. Protest is part of the DNA of Evergreen but violence and threats of violence are not.

Bridges says he did his share of yelling at administrators while an undergraduate at the University of Washington. He acknowledges he was mean-spirited and said some awful things, including blaming President Charles Odegaard for causing the Vietnam War, but violence was not in Bridges political playbook.

The violence on Evergreens campus, in which no one was seriously hurt, pales in comparison with anonymous threats of gun violence on the campus called in to police last week. But its time for the protest leaders to decry the threats and physical attacks and use their words to draw attention to their cause and broker any necessary changes at the university.

Hopefully, someday everyone at Evergreen will be able to look back on this time as a deciding moment in their understanding of American democracy and what free speech means.

Bridges and the other administrators and professors on that campus have some work to do, as do the students. Both need to listen as loudly as they speak. No one should be silenced, even if others dont agree with their tactics. Sometimes it takes some shouting and interrupting to be heard. The Bill of Rights is clear on this issue: it doesnt matter whether you or anyone else agrees, they almost always have a right to speak.

If you marched for civil rights or against the war during the 60s, please try to refrain from telling todays college students the correct way to protest. If the books and movies from that era hold any truth, you made as many mistakes and were just as uninterested in hearing advice from anyone over 30.

The same advice applies to the trolls on social media, who have screamed louder and meaner than most people at Evergreen. Feel free to tweet and email your vitriol in my direction. Give the students and their teachers a break. Its finals week, and they have schoolwork to finish.

Actually, everyone needs to take a break. There will be more time for debate and protest after the quarter is over. The problems of racism and inequity are not going away this week.

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Protest, but not violence, is part of the DNA of this nation and The Evergreen State College - Seattle Times

June 7, 2017 A new single-molecule tracking method based on fluorescence molecular imaging revealed nonrandom motion of DNA molecules. Credit: KAUST Anastasia Khrenova

A different approach to analyzing the motion of diffusing molecules has helped overturn the long-held assumption that DNA molecules move in a haphazard way. KAUST researchers reveal for the first time that DNA molecules move not by random Brownian motion but by a nonrandom walk related to polymer dynamics in a way that conserves overall Brownian characteristics.

"Brownian motion is a process whereby molecules move randomly in a fluid by colliding with other molecules," explained Dr. Maged Serag, a postdoctoral researcher in Bioscience at KAUST. "In living cells, Brownian motion allows molecules to move rapidly and efficiently between cell organelles and interact with other molecules."

For many decades, scientists have used a relatively simple test to determine whether molecular diffusion is Brownian: when the mean-square displacement (MSD) of a population of molecules increases linearly over time. In a uniform medium like pure water, this means that a drop of saline solution will expand at a rate that makes the MSD increase linearly with time.

DNA conforms to this macroscale diffusion behavior, and so it has been assumed that its motion is Brownian like other molecules. However, it is also known that DNA, being a long polymer molecule, writhes spontaneously due to intramolecular forces.

"The DNA molecule can be viewed as a semi-flexible chain," said Serag. "If we follow its motion at short timescales and in a space close to its size, we see worm-like motional behavior."

Serag and colleague Associate Professor Satoshi Habuchi set out to see whether this writhing motion could affect the diffusion of DNA.

"Dr. Serag came up with a unique idea to describe the motion of a molecule based on the probability of occupying lattice sites rather than by mean-square displacement," said Habuchi. "MSD has been the standard method to detect deviation from Brownian motion, but it does not reveal any nonrandom motion for DNA molecules. By using this probabilistic approach instead, we were able to detect and quantify hidden nonrandom motion."

By developing a new theoretical framework in which motion is modeled in a step-wise manner accounting for molecular flexing, DNA molecules were found to move nonrandomly with varied speed and molecular 'track' in a way that precisely conserved the Brownian linear MSD.

"The most important result of this study is that we have demonstrated that a linear MSD does not always indicate underlying Brownian motion," explained Habuchi. "With this new theoretical framework, we can detect the nonrandom motion of single molecules that cannot be captured by conventional MSD analysis."

Explore further: Researchers find the macroscopic Brownian motion phenomena of self-powered liquid metal motors

More information: Maged F. Serag et al, Conserved linear dynamics of single-molecule Brownian motion, Nature Communications (2017). DOI: 10.1038/ncomms15675

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The hidden order in DNA diffusion - Phys.org - Phys.Org

Daniel Rochat, left, is on trial in the killing of Barbara Vernieri in 2012.(Photo: TARIQ ZEHAWI/NorthJersey.com file photo)

HACKENSACK DNA was once again the focus in the trial of Daniel Rochat, the Wood-Ridge man accused of beating and lighting East Rutherford real estate agent Barbara Verniei on fire in September 2012.

The defense called DNA expert Heather Coyle, an associate professor at the University of New Haven in Connecticut.She criticized the methods of the Bergen County Prosecutor's Office detectives used to determine the presence of blood in Vernieri's home and the Van Winkle Street condoin East Rutherford.

According to Coyle, the test to determine the presence of blood was inconclusive.She saidthe leuco crystal violet [LCV] should not have been used to determine if blood was present and that a Kastle Meyers test should have been performed first. Coyle's argument was that a Kastle Meyes test confirms the presence of human blood while LCV can fluoresce at the presence of hemoglobin, plant material, animal blood or heavy metals.

"They did not test in the proper order," Coyle said, noting that was potentially the reasons for a negative Kastle Meyers test.

Assistant Prosecutor Danielle Grootenboer asked Coyle if the "absence of evidence was not the evidence of absence" and Coyle said it was possible but reiterated that she believed the tests were performed incorrectly.

Coyle also testified about the reproducibility and reliability of low copy number [LCN] DNA testing, a technique that brought some controversy to the case. Defense attorney Richard Potter argued that LCN testing is unreliable and not widely accepted by the scientific community. The Office of Chief Medical Examiners [OCME] in New York City was the only lab in the country that utilized LCN testing and results are currently not allowed to be entered into the FBIs DNA database.

From left, Daniel Rochat, accused in the killing of Barbara Vernieri in 2012, with his attorneys Jim Doyle and Richard Potter, before Superior Court Judge Margaret M. Foti.(Photo: Tariq Zehawi/NorthJersey.com)

According to Coyle, LCN testing is unreliable because it allows for more contamination of samples. Coyle said it is difficult to reproduce the results of the LCN test because trace amounts of DNA were being tested and several tests conducted on evidence found at Vernieris home and the condo on Van Winkle Street failed to detect Rochats DNA profile.

Potter focused on the fingernail clippings taken from Vernieri, where small amounts of DNA were found. A YSDR test was performed on the clippings, which is used in specific cases where there is a mix of male and female DNA and specifically targets male DNA. Coyle examined a summary chart of the YSDR tests and said that there were gaps in the data because of the small amounts of DNA found underneath Vernieris fingernails.

The test revealed that, statistically Rochat or any of his paternal relatives could be a match for the DNA, but it was a relatively low match and that one in 333 people would have the exact same result. When Coyle did her own testing, she said her results were one in 379 due her testing being done at a later date, therefore the database was updated.

Coyle testified that the potential for Rochat's DNA to be under Vernieri's fingernails could have been from skin cells or sweat that was transferred due to touch or shedding of skin cells.

Following Coyle's testimony, Rochat's former fiance Brooke Karwowski testified briefly about her relationship with him and how she met Vernieri. Karwowski said Vernieri set her up with Rochat and they dated for four years before getting engaged in 2009. The engagement broke off after Kaworwski decided to move back to Philadelphia. She said she was informed of Vernieri's death by receiving a phone call from detectives.

The final witness called was Manford Schenk, who was sworn in as an expert in historical cell site analysis and radio frequency with some objection by the prosecution. Schenk was called to testify to dispute the testimony of Special Agent Ajit David, an expert in historical cell site analysis and a member of the FBI'sCellular Analysis Survey Team. David testified last week that Rochat's phone was found to be in the area around Vernieri's apartment the day of the murder, despite him telling police he was asleep in his apartment over mile away. David said he used data provided by Verizon Wireless in order to make that determination.

Schenk argued that it is "preposterous" to determine the location of a person's cell by using only one source to find them. Schenk believes that the use of GPS and triangulation is more reliable source of locating a cellphone.

On Tuesday, Rochats father testified that Vernieri loved his son and a neighbor of Vernieri testified that she called the police on a man who appeared to be posing as a PSE&G employee while a coworker testified to Vernieris prowess as a real estate agent.

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Rochat defense expert criticizes DNA testing by prosecutor's office - NorthJersey.com

Alissa Widman Neese The Columbus Dispatch @AlissaWidman

The Columbus Zoo and Aquarium polar bear cubs aren't just cute and cuddly.

They're also helping the federal government fight crimes against their wild relatives in the Arctic,thanks to advancements in forensic science and DNA testing.

The U.S. Fish and Wildlife Service's Forensic Laboratory in Oregon often relies on zoos to maintain its database of DNA samples from protected animal species. But when the Columbus Zoo sent DNA from its six polar bears to the lab in March, it came with payoffs for both parties including a confirmation of whether the zoo's three newest cubs are male or female.

The lab's scientists analyze evidence during investigations of violations of federal wildlife protection laws, including poaching, illegal trading of animals, theft of rare plants and creating products from endangered species.

For example, the lab could use DNA to identify a decaying carcass as a protected animal or confirm that a business is selling items made with bald eagle feathers or elephant ivory.

Scientists are trying to perfect a new, more accurate DNA test for bears and benefited from the Columbus Zoo's controlled samples from a known family of animals. The reference data illustrate how genetic patterns change in a population over time. It could someday pin down criminals who harm polar bears, which are protected by the Marine Mammal Protection Act and the Endangered Species Act, on which the bears are listed as threatened.

Only an estimated 20,000 to 25,000 polar bears are living in the wild, and there are just 40 or so bears in 27 U.S. zoos that are members of the Association of Zoos and Aquariums.

"Our polar bear database is fairly small, so the more samples we can get, the better," senior forensic scientistMary Burnham Curtis said.

The zoo, meanwhile, was seeking a non-invasive way to determine the sexes of its baby bears. Because the 6-month-old animals are being raised by their mothers and not hand-reared by zookeepers, staffers would have had to put them under anesthesia to examine their genitals and make an official determination.

"That seemed like an unnecessary risk for something that was just curiosity, not critical," said Randy Junge, the zoo's vice president of animal health.

"Luckily, we were able to help each other out."

Junge sent emails to diagnostic labs across the country seeking options, including the Fish and Wildlife forensic lab. Zoos work with the lab frequently to provide DNA samples to use as reference data the Columbus Zoo has provided samples of rhinoceros horn in the past, for example and some zoos serve as holding facilities for living animals that are considered evidence in ongoing criminal investigations.

Although the lab doesn't perform sex determination tests as a service to the public, its scientists are usually willing to work with zoos that provide DNA samples, Curtis said.

Columbus Zoo staff provided hair clippings and saliva swabs from all six of its bears.

Ultimately, test results confirmed what keepers suspected based on their observations: mother bear Anana's cub is female and mother bear Aurora's twin cubs are male and female.

Anana's cub was recently named Amelia Gray in an online naming contest. The twins were named Nuniq and Neva by zoo staff. Nuniq is a derivative of Nanuq, the name of all three cubs' father, who died in late April from liver cancer at age 29.

awidmaneese@dispatch.com

@AlissaWidman

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Columbus Zoo's polar bear cubs fight crime with their DNA - News ... - The Columbus Dispatch

CHESTERFIELD COUNTY, Va. (WRIC) On Friday, 18-year-old Quaseer Carter pled no contest to the 2015 rape and beating of a 47-year-old woman. The states DNA database connected Carter as a suspect.

Its the latest success story involving DNA, which is why many have called for the database to be expanded.

A few months ago, the parents of murdered UVaA student Hannah Graham urged lawmakers to study expanding the number of misdemeanor crimes that require DNA collection. They say their daughter would still be alive had Jesse Matthew, the man convicted in her death, had his DNA collected for trespassing in 2010.

Hannah would never have met him and he would not have abducted and murdered her and simply put she would be alive today, said Hannahs mother, Sue Graham back in January.

While a measure requiring studying expansion failed, the states crime commission decided a few days ago it would study the issue. Effective July 1, 2015, nine misdemeanors were added to the list of crimes that require DNA collection.

The state has more than 415,000 DNA samples currently in its database. Thats up from the almost 6,000 the state had in 1995.

While supporters argue more DNA would help solve more crimes, some lawmakers and groups like the ACLU continue to cite concerns over personal privacy. They say there has to be a balance between protecting the public and civil liberties.

Meanwhile, Carter will face sentencing in September.

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8News takes a closer look at state's DNA database in light of Chesterfield conviction - WRIC

WUSA 2:39 PM. EDT June 05, 2017

DNA data is being increasingly sold by private companies. (Photo: PhotoDisc)

CHESTERFIELD, VA. (AP) - Virginia's DNA databank has identified a teen as the suspect of an October 2015 rape and beating of a 47-year-old woman.

Richmond Times-Dispatch reports the 18-year-old man pleaded no contest to the attack in Chesterfield Circuit Court on Friday.

The prosecution and defense reached a plea agreement after the teen's first trial on the rape and sodomy charges ended with a hung jury.

Chesterfield prosecutor Stephen Sharpe says the victim was walking and only a few houses away from the home of her ex-husband she'd been helping pack for a trip when a man asked her for a cigarette before sexually assaulting her.

The teen's sentencing is in September and he faces up to five years in prison. He's free on bond but remains electronically monitored with an ankle bracelet.

___

Information from: Richmond Times-Dispatch, http://www.timesdispatch.com

2017 Associated Press

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Virginia teen identified as rape suspect through DNA - W*USA 9