Daily Archives: June 8, 2017

Scientists sequenced DNA from mummies from the settlement of Abusir el-Meleq, south of Cairo, and were buried between 1380 B.C. and A.D. 425.

For the first time, researchers have successfully sequenced the DNA from Egyptian mummies. The findings reveal that these ancient people were more genetically similar to populations living in the eastern Mediterranean a region that today includes Syria, Lebanon, Israel, Jordan and Iraq than people living in modern-day Egypt.

"We were excited to have at hand the first genome-wide data of ancient Egyptian mummies," said Stephan Schiffels, leader of the Population Genetics Group at the Max Planck Institute for the Science of Human History, in Jena, Germany. [24 Amazing Archaeological Discoveries]

Schiffels and a team of scientists from Poland, Germany, England and Australia led by Johannes Krause, a geneticist also at the Max Planck Institute for the Science of Human History, published their research in the May 30 issue of the journal Nature Communications.

Worldwide, the remains of thousands of mummies from ancient Egypt have been excavated, but obtaining intact, undamaged DNA from the bodies has proved challenging.

"Researchers were generally skeptical about DNA preservation in Egyptian mummies, due to the hot climate, the high humidity levels in tombs and some of the chemicals used during mummification, which are all factors that make it hard for DNA to survive for such a long time," Schiffels told Live Science.

Map of Egypt depicting the location of the archaeological site Abusir-el Meleq (marked by the orange "X") and the location of the modern Egyptian samples (marked by the orange circles).

Other research teams made at least two previous attempts to sequence DNA from mummies, but those efforts were met with intense skepticism. The first undertaking occurred in 1985 and was later shown to be flawed, because the samples had become contaminated with modern DNA. The second analysis, published in 2010, focused on King Tutankhamun's family, but it could not satisfy the critics either. Both studies used a technique called polymerase chain reaction (PCR), which can hone in on specific fragments of genetic information but can't distinguish ancient DNA from modern DNA, nor differentiate human DNA from other types that may be present.

In this latest study, Krause and his colleagues used a newer technique called next-generation sequencing, which can extract human DNA from other types and can tell whether a genetic fragment is very old or suspiciously new (an indication that it might be modern).

The scientists focused their efforts on the heads of 151 mummified individuals who lived in the settlement of Abusir el-Meleq, south of Cairo, and were buried between 1380 B.C. and A.D. 425.

To reduce the risk of contamination, the researchers extracted the DNA inside a laboratory clean room. There, they irradiated the surfaces of bone and soft tissue for 60 minutes using ultraviolet radiation, which destroyed any modern DNA. The scientists then removed samples from inside soft tissue, skull bones and the tooth pulp. [Photos: 1,700-Year-Old Egyptian Mummy Revealed]

Following these and numerous other rigorous steps, the researchers found that the soft tissues had no viable DNA. However, the bone and tooth samples for 90 individuals contained ample amounts of DNA from mitochondria, the organelles inside a cell that convert oxygen and nutrients into energy. Mitochondrial DNA is passed down from mother to child and so contains genetic information from only the mother's side of the family.

To get a more complete picture of a person's genetic history, the researchers needed DNA from the cell's nucleus, which contains DNA from the father's side of the family as well as the mother's. But that DNA was very poorly preserved, Schiffels said.

"We were only able to generate three nuclear genomic data sets," he said.

After extracting the DNA, the researchers enriched it and made copies for analysis. They then compared it with the DNA of other populations, both ancient and modern, that lived in Egypt and Ethiopia.

The researchers found that over the 1,300-year time span, the genetics of the people in the sample remained consistent a remarkable finding, the researchers said, because ancient Egypt had been conquered several times in those years, including by the Greeks and Romans, and through it all, served as a trading crossroads for many different people.

Yet when the scientists compared their samples to genetic data from modern-day Egyptians, they found a difference. The DNA from the ancient Egyptians contained little DNA from sub-Saharan Africa, yet 15 percent to 20 percent of mitochondrial DNA in modern Egyptians shows a sub-Saharan ancestry, the researchers said.

Schiffels said the scientists can only speculate on why the genetic changes showed up later. "One possible cause could be increased mobility down the Nile and increased long-distance commerce between sub-Saharan Africa and Egypt," he said.

These changes could have been related to slave trading, which reached its height in the 19th century, he said.

He added that the team hopes to continue building on this research by analyzing more mummies from more time periods and more sites in Egypt.

Original article on Live Science.

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Surprising Find: Ancient Mummy DNA Sequenced in First - Live Science

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

Twitter: @jflem94

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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