Daily Archives: February 7, 2017

February 7, 2017 by Mark Derewicz Credit: CC0 Public Domain

Day in and day out, in our bodies, the DNA in cells is damaged for a variety of reasons, and thus intercellular DNA-repair systems are fundamental to the maintenance of life. Now scientists from the UNC School of Medicine have confirmed and clarified key molecular details of one of these repair systems, known as nucleotide excision repair.

Using an advanced sequencing technique to map and analyze DNA damage, the scientists demonstrated the functions in bacterial cells of two important excision repair proteins: Mfd and UvrD.

"The biochemical mechanisms of these proteins have been known for years from experiments involving purified protein and DNA, and that's very important, but in this new work we've clarified these proteins' roles in living cells," said co-senior author Christopher P. Selby, PhD, research assistant professor of biochemistry and biophysics at UNC.

"Ultimately, this better understanding of bacterial DNA repair could be useful toward the development of antibacterial drugs," said co-senior author Aziz Sancar, MD, PhD, the Sarah Graham Kenan Professor of Biochemistry and Biophysics at UNC.

The research publishes this week in the Proceedings of the National Academy of Sciences.

Sancar was awarded the 2015 Nobel Prize for Chemistry for his research in the 1980s and early 1990s on excision repair in bacteria and in human cells. This repair process, which also occurs in animal cells, fixes one of the most common forms of DNA damage: the bulky adduct, an unwanted chemical modification of DNA typically caused by a toxin or ultraviolet (UV) radiation.

To study excision repair in cells, Sancar, Selby and colleagues recently developed a new technique, XR-seq, which allows investigators to isolate and sequence the small lengths of adduct-damaged DNA that are snipped from the genome during the excision repair process. Knowing the sequences of these DNA snippets allows their locations in the genome to be mapped precisely. They used this method first in 2015 to generate a UV repair map of the human genome, and in 2016 they used the XR-seq method to generate the damage and repair maps of the anticancer cisplatin drug for the entire human genome. Now they have applied this method to answer some fundamental questions about damage repair in E. coli with the potential of developing novel antibiotic drugs.

The un-sticker: Mfd

In this study, which was also led by postdoctoral research associate Ogun Adebali, PhD, the researchers focused largely on Mfd, a protein known from prior work by Sancar and Selby to have a special - and mechanistically unusual - role in excision repair in bacteria.

"I think Mfd is the most interesting protein in E. coli," Selby said. Here's why: When the DNA of a bacterial gene is being transcribed into RNA, and the molecular machinery of transcription gets stuck at a bulky adduct, Mfd appears on the scene, recruits other repair proteins that snip away the damaged section of DNA, and "un-sticks" the transcription machinery so that it can resume its work. This Mfd-guided process is called transcription-coupled repair, and it accounts for a much higher rate of excision repair on strands of DNA that are being actively transcribed.

Using XR-seq to map UV-induced damage in E. coli bacteria cells, the researchers found clear evidence of transcription-coupled repair in normal cells, but not in cells that lack Mfd, thus confirming the protein's role in the process.

The unwinder: UvrD

In further experiments, the researchers defined the role of an accessory excision repair protein in E. coli - UvrD, which helps clear away each excised segment of damaged DNA.

In the absence of UvrD, the excised piece of DNA remains bound to the chromosomal DNA, making it hard for cellular waste-disposal enzymes to chop it up. At the same time, the repair proteins that excised the strand tend to remain stuck to it, and are thus kept from moving on to excise other bits of damaged DNA. UvrD's job is to unwind these damaged and discarded strands from chromosomal DNA, so that they can be disposed of quickly and the associated repair proteins can go on to catalyze additional rounds of repair.

Using XR-seq on UV-damaged E. coli cells, the UNC team confirmed that without UvrD, excised DNA fragments remain stuck to chromosomal DNA, survive much longer in cells, and - by holding onto excision repair proteins - slow down the overall rate of excision repair in cells.

In addition to clarifying the roles of Mfd and UvrD, the research generally heralds the use of the new XR-seq technique in mapping and studying excision repair processes.

"XR-seq provides a new type of sequence data, and in this work we've provided for the first time a genome-wide map of excision repair in a bacterium," said Adebali. "We think this map will be broadly useful to the scientific community."

The researchers now plan further studies using XR-seq in bacterial cells, as well as in human and other mammalian cells where the process of excision repair is less understood.

Explore further: Researchers create DNA repair map of the entire human genome

More information: Ogun Adebali et al, Genome-wide transcription-coupled repair inis mediated by the Mfd translocase, Proceedings of the National Academy of Sciences (2017). DOI: 10.1073/pnas.1700230114

When the common chemotherapy drugs cisplatin or oxaliplatin hit cancer cells, they damage DNA so that the cells can't replicate. But the cells have ways to repair the DNA. The cancer drugs aren't as effective as patients ...

A key biochemical enables bacteria to repair otherwise fatal damage to their DNA, including that caused by antibiotics. That is the finding of a study led by researchers at NYU Langone Medical Center and published May 20 ...

(Medical Xpress)The results of two studies by two different teams studying the role that DNA repair plays in the production of mutation-prone sequencesprecursors to cancer, have been published in the journal Nature. ...

A recent study led by University of Kentucky researchers illuminates a new way that tobacco smoke may promote the development of lung cancer: inhibiting a DNA repair process called nucleotide excision repair (NER). The results ...

Researchers from the Institut Jacques Monod (CNRS/University of Paris Diderot), the Institute of Biology of the Ecole Normale Suprieure (ENS/CNRS/Inserm), and the University of Bristol, have described for the first time ...

If you have a soft spot for unsung heroes, you'll love a DNA repair protein called XPG. Scientists from the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) discovered that XPG plays a previously ...

Day in and day out, in our bodies, the DNA in cells is damaged for a variety of reasons, and thus intercellular DNA-repair systems are fundamental to the maintenance of life. Now scientists from the UNC School of Medicine ...

If you've ever been elbowed out of the way at the dinner table by older, stronger siblings, you'll identify with wolves competing with larger bears for food. A study by Utah State University ecologist Aimee Tallian and colleagues ...

Scientists have uncovered key processes in the healthy development of cells which line the human gut, furthering their understanding about the development of cancer.

While searching for a potential Achilles' heel in the insect responsible for spreading the bacterium that causes citrus greening disease, researchers have uncovered a protein that makes their bellies blue and may impact how ...

A study led by UC Santa Cruz researchers has found that drought dramatically increases the severity of West Nile virus epidemics in the United States, although populations affected by large outbreaks acquire immunity that ...

Few animals can match the humble hydra's resilience. The small, tentacled freshwater animals can be literally shredded into pieces and regrow into healthy animals. A study published February 7 in Cell Reports suggests that ...

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How life survives: Researchers confirm basic mechanism of DNA repair - Phys.Org

Legislation has passed in the state Senate that would allow New York to use familial DNA, a test that Karina Vetranos parents were pushing for in their effort to help solve her brutal rape and murder.

Familial DNA searching is a technique that compares DNA found at a crime scene, for example, to DNA already in the offender databank, providing near matches that could lead authorities to family members of the person who left the DNA sample.

It is unknown if familial DNA played a part in catching the suspect who is charged with killing Vetrano, state State Sen. Joseph Addabbo, Jr. said. The test is only legal in a handful of states, and New York is not one of them.

RELATED:Karina Vetranos family seeks ideas on donating reward money

The Queens Democrat co-sponsored the bill with Assemblywoman Stacey Pheffer Amato, a member of the DNA Subcommittee of the New York State Commission on Forensic Science.

I continue to believe that this type of search is an important resource in violent criminal investigations where the trail seems to be getting colder and colder, Addabbo said.

It took six long and painful months for the investigators to identify and arrest a suspect in Karinas case. Against great odds, our law enforcement agencies did a tremendous job in connecting the dots between the suspects earlier suspicious behavior, a 911 call, and the murder.

We know that familial DNA has been used in roughly 10 other states for almost 10 years, with success in finding felons, he added.

The DNA Subcommittee plans to create a report by the end of the year recommending best practices for the use of familial DNA searching.

There will be a public hearing on the issue on Friday. The senator said he will be testifying.

While there are legitimate questions regarding privacy rights and other issues surrounding the practice, I believe we can develop a policy that would address these concerns while giving our law enforcement community a powerful new tool to bring violent felons to justice, Addabbo said.

Excerpt from:
Familial DNA bill passes NY Senate - Metro.us

ST. LOUIS A first-degree murder charge filed here Tuesday says a DNA match and witness identification have linked a convicted drug dealer to a 2012 fatal shooting in St. Louis.

Charles Billingsley, 26, who is in federal prison for drug trafficking, was charged in the May 17, 2012, shooting death of 19-year-old Lamar E. Miller.

Millers body was found behind the wheel of a black Ford Mustang in the 5400 block of Beacon Avenue in the citys Walnut Park East neighborhood, police said. He suffered a gunshot to the head.

Charges say a witness told Detective Scott Sailor that he had been in the back of the Mustang and saw Billingsley shoot Miller while Miller was driving.

DNA found inside the car was a match to Billingsley, and Millers DNA was found on clothing worn by Billingsley the day of the killing, the charges say.

Billingsley had given his clothing to someone for safekeeping, charges say, and the recipient at some point turned over the clothes to police, and told them Billingsley admitted killing Miller.

Billinglsey has been serving an eight-year term in federal prison since 2013 for several counts of marijuana trafficking and illegal possession of a firearm. He also has drug convictions in St. Louis County in 2009 and 2013.

His address in court records is in the first block of Chambers Road in St. Louis County, near Riverview. He also was charged Tuesday with armed criminal action, and cash bail was set at $500,000.

Miller lived in the 2000 block of East Prairie Avenue.

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DNA, witness ID lead to charges against St. Louis drug dealer in 2012 killing - STLtoday.com

Directors influence each other with their work. Sometimes that influence is overt La La Land clearly evokes Singin in the Rain and Umbrellas of Cherbourg but other times it is more unexpected, hinging on storytelling choices or structure.

SEE MORE: Awards: The Contenders This story first appeared in the February 07, 2017 issue of Variety. Subscribe today.See more.

Variety asked this years directing nominees to help us trace the DNA of their movies, and all were happy to oblige.

Arrival Paramount In Villeneuves alien-invasion tale, humans eventually discover that the aliens want to help you help us.

Villeneuves choices: 2001: A Space Odyssey 1968: Definitely 2001, Villeneuve says, of Stanley Kubricks sci-fi classic in which Earthlings, searching for signs of intelligent life, are nearly outwitted by artificial intelligence. Jaws 1975: It was Spielbergs idea that you unveil slowly the entity, to create suspense, Villeneuve says. That very slow striptease is something I stole from Jaws.

Our choices: The Day the Earth Stood Still 1951: Aliens caution Earthlings not to destroy themselves with nuclear weapons in Robert Wises sci-fi classic. Starman 1984: A friendly interplanetary visitor gets a hostile reception from fearful humans in John Carpenters movie. The Miracle Worker 1962: Language is the bridge between two seemingly separate worlds in Arthur Penns Helen Keller biopic.

Hacksaw Ridge Lionsgate A deeply religious medic who refuses to carry a gun becomes an unlikely hero in Mel Gibsons brutal World War II saga.

Gibsons choices: Saving Private Ryan 1998: Its part of a great tradition of war films, Gibson says of Spielbergs D-Day drama, which raised the bar on graphic war carnage. Sergeant York 1941: That was kind of an inspiration, Gibson says of Howard Hawks movie, although that one is about a conscientious objector who actually picked up a gun and started shooting.

Our choices: The Longest Day 1962: A massive battle against impossible odds is fought with a giant all-star cast in Ken Annakins tale. From Here to Eternity 1953: A soldier receives unfair harsh treatment from officers in the run-up to Pearl Harbor in Fred Zinnemanns movie. Platoon 1986: Willem Dafoe suffers a Christ-like death, after being betrayed by a Judas among his own men in Oliver Stones Vietnam War movie.

La La Land Lionsgate Damien Chazelle traces his L.A. musicals lineage back to the silent era.

Chazelles choices: The Umbrellas of Cherbourg 1964: This film definitely, Chazelle says, citing Jacques Demys musical as an influence, and Lola, an earlier Demy film, also was very influential. Singin in the Rain 1952: Chazelle cites any of those great Gene Kelly musicals like Singin in the Rain or American in Paris, the former directed by Stanley Donen and the latter by Vincente Minnelli in 1951. Boogie Nights 1997, directed by Paul Thomas Anderson: I was influenced by some of those great L.A. movies, Chazelle says. I love Boogie Nights, Short Cuts, and a couple of others. 7th Heaven 1927: Chazelle cited Frank Borzages silent weepie in which a woman whose lover has died in WWI briefly imagines their entire life together, had he returned as the inspiration for his ending when accepting an award from the New York Film Critics Circle.

Our choice: A Star Is Born 1954: George Cukors film features the original show-business-tale trope: An established star discovers a rising talent, then suffers a decline.

Manchester by the Sea Amazon Studios Kenneth Lonergans wrenching drama revolves around the aftereffects of unspeakable tragedy.

Lonergans choices: Five Easy Pieces 1970: Lonergan cites Bob Rafelsons haunting tale of an estranged family dealing with its ghost as an influence. Coal Miners Daughter 1980: Its such a human story, Lonergan says of Michael Apteds bio of Loretta Lynn starring Sissy Spacek. Its got a personal scale and a universal scale. Its a very emotional story with a lot of love and a lot of loss. Bang the Drum Slowly 1973: Lonergan also took inspiration from John Hancocks tale of a dying baseball players final season.

Our choices: Ordinary People 1980: A suburban family begins to splinter after the eldest sons accidental death in Robert Redfords movie. Whos Afraid of Virginia Woolf 1966: Edward Albees play, adapted by Mike Nichols, focuses on a married couple whose great tragedy is either their dead son or their dead dream of having a child.

Moonlight A24 Barry Jenkins directed this coming-of-age tale about being young, black, poor, and gay in 80s Miami.

Jenkins choices: Happy Together 1997: This is one of three films I usually cite, Jenkins says of director Wong Kar-wais movie. It was the first film I saw that dealt with a relationship between two men. Beau Travail 1999: I love the way she deals with masculinity in a corrupt system, Jenkins says while saluting Claire Denis movie as an influence. Three Times 2005: Jenkins also mentioned Hou Hsiao-Hsiens film set in three separate time periods, with the same actors playing different characters who encounter each other in each section of the film.

Our choices: Boys Dont Cry 1999: A young transgender man runs afoul of small-town intolerance in Kimberly Peirces indie landmark. Boyhood 2014: A boys youth is thrown off-kilter by his moms personal drama in Richard Linklaters film.

Originally posted here:
Oscar Directing Nominees Help Us Trace Their DNA - Variety

February 7, 2017 A microfluidic chip used to fabricate nanoparticles that could be used to deliver therapeutic genes to specific organs of the body. Credit: Rob Felt, Georgia Tech

Using tiny snippets of DNA as "barcodes," researchers have developed a new technique for rapidly screening the ability of nanoparticles to selectively deliver therapeutic genes to specific organs of the body. The technique could accelerate the development and use of gene therapies for such killers as heart disease, cancer and Parkinson's disease.

Genetic therapies, such as those made from DNA or RNA, are hard to deliver into the right cells in the body. For the past 20 years, scientists have been developing nanoparticles made from a broad range of materials and adding compounds such as cholesterol to help carry these therapeutic agents into cells. But the rapid development of nanoparticle carriers has run into a major bottleneck: the nanoparticles have to be tested, first in cell culture, before a very small number of nanoparticles is tested in animals. With millions of possible combinations, identifying the optimal nanoparticle to target each organ was highly inefficient.

Using DNA strands just 58 nucleotides long, researchers from the University of Florida, Georgia Institute of Technology and Massachusetts Institute of Technology have developed a new testing technique that skips the cell culture testing altogetherand could allow hundreds of different types of nanoparticles to be tested simultaneously in just a handful of animals.

The original research was done in the laboratories of Robert Langer, the David H. Koch Institute Professor, and Daniel Anderson, the Samuel A. Goldsmith Professor of Applied Biology, at MIT. Supported by the National Institutes of Health, the research was reported February 6 in the journal Proceedings of the National Academy of Sciences.

"We want to understand at a very high level what factors affecting nanoparticle delivery are important," said James Dahlman, an assistant professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, one of Langer's former graduate students, lead author on the study, and one of the paper's corresponding authors. "This new technique not only allows us to understand what factors are important, but also how disease factors affect the process."

To prepare nanoparticles for testing, the researchers insert a snippet of DNA that is assigned to each type of nanoparticle. The nanoparticles are then injected into mice, whose organs are then examined for presence of the barcodes. By using the same technologies scientists use to sequence the genome, many nanoparticles can be tested simultaneously, each identified by its unique DNA barcode.

Researchers are interested not only in which nanoparticles deliver the therapeutics most effectively, but also which can deliver them selectively to specific organs. Therapeutics targeted to tumors, for example, should be delivered only to the tumor and not to surrounding tissues. Therapeutics for heart disease likewise should selectively accumulate in the heart.

While much of the study was devoted to demonstrating control strategies, the researchers did test how 30 different particles were distributed in eight different tissues of an animal model. This nanoparticle targeting 'heat map' showed that some particles were not taken up at all, while others entered multiple organs. The testing included nanoparticles previously shown to selectivity enter the lungs and liver, and the results of the new technique were consistent with what was already known about those nanoparticles.

The single-strand DNA barcode sequences are about the same size as antisense oligonucleotides, microRNA and siRNA being developed for possible therapeutic uses. Other gene-based therapeutics are larger, and additional research would be needed to determine if the technique could be used with them. In the research reported this week, the nanoparticles were not used to deliver active therapeutics, though that would be a near-term next step.

"In future work, we are hoping to make a thousand particles and instead of evaluating them three at a time, we would hope to test a few hundred simultaneously," Dahlman said. "Nanoparticles can be very complicated because for every biomaterial available, you could make several hundred nanoparticles of different sizes and with different components added."

Once promising nanoparticles are identified with the screening, they would be subjected to additional testing to verify their ability to deliver therapeutics. In addition to accelerating the screening, the new technique may require fewer animalsperhaps no more than three for each set of nanoparticles tested.

There are a few caveats with the technique. To avoid the possibility of nanoparticles merging, only structures that are stable in aqueous environments can be tested. Only nontoxic nanoparticles can be screened, and researchers must control for potential inflammation generated by the inserted DNA.

In Langer and Anderson's laboratory, Dahlman worked with Kevin Kauffman, who remains at MIT, and Eric Wang, now an assistant professor the University of Florida. Other co-authors of the paper included Yiping Xing, Taylor Shaw, Faryal Mir and Chloe Dlott, all of whom are at MIT.

"Nucleic acid therapies hold considerable promise for treating a range of serious diseases," said Dahlman. "We hope this technique will be used widely in the field, and that it will ultimately bring more clarity to how these drugs affect cellsand how we can get them to the right locations in the body."

Explore further: Making organs transparent to improve nanomedicine

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Scientists used one of the world's most powerful electron microscopes to map the precise location and chemical type of 23,000 atoms in an extremely small particle made of iron and platinum.

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DNA 'barcoding' allows rapid testing of nanoparticles for therapeutic ... - Phys.Org