Category Archives: DNA

LOVE Island fans noticed Kem Cetinays homecoming bash had two very special guests of honour waiting to welcome him back.

During tonights reunion show, eagle eyed viewers spotted Britains Got Talent double act DNA loitering in the background during a clip of Kem and Amber Davies visiting his salon in Essex.

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Some fans couldnt believe their eyes as they saw Darren, 29, and Andrew,43, mingling with the barbers friends and family.

One tweeted: Wtf! Was it just me who just saw DNA in Kems barbers shop?

Another wrote: Anyone know why DNA were in @KemCetinay barber shop on Love Island?

Darren and Andrew, who made it to the final of Britains Got Talent earlier this year, stayed pretty low key during Kems arrival and didnt speak during the short clip.

It turns out the pair are pretty chummy with Kem, and actually hinted they would be performing with them at a later date.

They told their Twitter followers: Great seeing Kem and Amber! So happy for them, worthy #LoveIsland winners!! Video of us performing on them coming soon! #KemandAmber.

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Tonight's reunion show had it's far share of surprises, with Chyna Ellis left stunned when Jonny Mitchell appeared to dump her live on air.

She got her revenge and later branded him a p***k - filming him secretly on her phone and uploading it to Instagram.

In another shot, she wrote over the smiling reality stars face, What a little p***k.

Jonny and Chyna had jetted off on a romantic break away to Budapest, giving fans the impression they were dating.

When Caroline Flack asked them what was happening however, Jonny denied they were dating leaving Chyna looking stunned.

As Caroline told them it was the most awkward moment of the night so far, Chyna blushed and said the pair were just having fun.

Caroline then quizzed Jonny on why hed taken Chyna on holiday which he had boasted cost 100,000 to which he replied: I just like holidays.

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The show became more awkward when Montana Brown and Alex Beattie tried to persuade Caroline they were still dating.

Since leaving the villa, the pair have tried to convince fans theyre dating despite The Sun revealing the couple had broken up.

A source told The Sun: Montana is keen to follow her dreams as a TV presenter and has been attending meetings this week to get the wheels in motion.

She doesnt like partying and isnt a big drinker so personal appearances in nightclubs arent really her thing.

Instead she is ambitious and very much a career woman her relationship with Alex is going to take a back seat.

Got a story? email digishowbiz@the-sun.co.uk or call us direct on 02077824220.

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Love Island fans spot Britain's Got Talent stars DNA on reunion show but did you see them? - The Sun

A DNA-based sunscreen that not only stops harmful ultraviolet (UV) light, but also becomes more protective the longer you expose it to UV rays? Thats the dazzling premise behind a recent study published in the journal Science Reports.

While sunscreen isnt the only form of sun protection (theres always protective clothing and floppy hats), the reality is that most of us just skip it. A 2015 study in Journal of the American Academy of Dermatology found that only 14.3 percent of men and 29.9 percent of women routinely use sunscreen when they are in outside for more than an hour. This wouldnt be a problem, except, Ultraviolet light is a carcinogen, Guy German a biomedical researcher at Binghamton University in New York and an author on the study, tells PopSci. We know it can give you a tan, but it can also cause cancer as well.

While dermatoepidemiologists (scientists who study diseases of the skin) suspect that sunlight causes cancer because it damages DNA in our cells, German and his colleagues were looking at DNA in an entirely different way. They wondered what would happen if they exposed DNA film, essentially a thin sheet of the stuff, to the same kind of ultraviolet light we get from walking in sunshine.

If youve ever taken glue and spread it on a surface and then let it dry to create a sheet or film, then you understand the basics of the material the researchers made: They took a liquid solution of DNA, smeared it on a piece of glass, and let it dry to create the film. The DNA, in case you were wondering, comes from salmon sperm. It was not that we chose salmon sperm, says German. It's just one of the readily available DNA sources.

German, along with the lead author on the study, Alexandria Gasperini, then exposed the film to UVA and UVB light to see how much, if any, radiation the films would allow to pass. UVA light makes up around 95-percent of the suns radiative light; it can penetrate deep into the skin, has long-been thought to be a culprit in premature aging, and is increasingly believed to play a key role in the formation of skin cancer. UVB, the radiation that makes us tan (and burn), also plays a role in skin cancer.

This was a fundamental study to see how UV light interacts with DNA films," says German, "Also, you know subsequently how the UV light can actually alter DNA films.

To measure these effects, the team used a device called a spectrophotometer, which allows them to control the amount and wavelength of light that they put through the films. A receptor on the other side measured how much of the light passed made it through. The DNA film did not allow up to 90 percent of UVB light and 20-percent of UVA light to cross through. Perhaps even more amazing: The DNA film seemed to grow strongerthat is, it seemed to allow less light to pass through the longer it was exposed to UV light. German and his team, however, aren't sure if the films achieve this by absorbing light or reflecting it.

We discovered two possible mechanisms, says German to explain how the DNA cells appear to achieving this feat. One is called hypochromicity, that is the increased ability of DNA molecules to absorb UV light, but also we found that the results that we got suggest a crosslinking density of the cells themselves.

Under a microscope, the film's crystalline structure got denser, or developed more crosslinks, as it was exposed to more light. The results suggest that, if a film has more crosslinks, its potentially going to absorb or scatter more UV light.

As an added bonus, the team also found that when they coated the film on human skin samples procured from elective surgeries, it also helped the skin retain moisture.

To be clear, what German and his team tested is not sunscreen, at least not in the traditional sense of a liquid or paste smeared onto the skin. You cant pick this up at the supermarket, at least not anytime soon. But between the ecological and health concerns of chemical sunscreens, and the lack of efficacy of mineral sunscreens, what they uncovered, might make its way into products in the future. Who wouldnt want a sunscreen that you apply once? That grows stronger the longer you frolic in the sun? It would, in a sense, act as a sacrificial layer, taking one for the team and allowing your own skin to go unscathed.

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Sunscreen made from DNA would last forever - Popular Science

Five years ago, Alice Collins Plebuch made a decision that would alter her future or really, her past.

She sent away for a "just-for-fun DNA test." When the tube arrived, she spit and spit until she filled it up to the line, and then sent it off in the mail. She wanted to know what she was made of.

Plebuch, now 69, already had a rough idea of what she would find. Her parents, both deceased, were Irish-American Catholics who raised her and her six siblings with church Sundays and ethnic pride. But Plebuch, who had a long-standing interest in science and DNA, wanted to know more about her dad's side of the family. The son of Irish immigrants, Jim Collins had been raised in an orphanage from a young age, and his extended family tree was murky.

After a few weeks during which her saliva was analyzed, she got an email in the summer of 2012 with a link to her results. The report was confounding.

About half of Plebuch's DNA results presented the mixed British Isles bloodline she expected. The other half picked up an unexpected combination of European Jewish, Middle Eastern and Eastern European. Surely someone in the lab had messed up. It was the early days of direct-to-consumer DNA testing, and Ancestry.com's test was new. She wrote the company a nasty letter informing them they'd made a mistake.

But she talked to her sister, and they agreed she should test again. If the information Plebuch was seeing on her computer screen was correct, it posed a fundamental mystery about her very identity. It meant one of her parents wasn't who he or she was supposed to be and, by extension, neither was she.

Eventually, Plebuch would write to Ancestry again. You guys were right, she'd say. I was wrong.

We are only just beginning to grapple with what it means to cheaply and easily uncover our genetic heritage.

Over the past five years, as the price of DNA testing kits has dropped and their quality has improved, the phenomenon of "recreational genomics" has taken off. According to the International Society of Genetic Genealogy, nearly 8 million people worldwide, but mostly in the United States, have tested their DNA through kits, typically costing $99 or less, from such companies as 23andMe, Ancestry.com and Family Tree DNA.

The most popular DNA-deciphering approach, autosomal DNA testing, looks at genetic material inherited from both parents and can be used to connect customers to others in a database who share that material. The results can let you see exactly what stuff you're made from as well as offer the opportunity to find previously unknown relatives.

For adoptees, many of whom can't access information about their birthparents because of closed adoption laws, DNA testing can let them bypass years, even decades, of conventional research to find "DNA cousins" who may very well lead them to their families.

But DNA testing can also yield uncomfortable surprises. Some testers, looking for a little more information about a grandparent's origins, or to confirm a family legend about Native American heritage, may not be prepared for results that disrupt their sense of identity. Often, that means finding out their dad is not actually their dad, or discovering a relative that they never knew existed perhaps a baby conceived out of wedlock or given up for adoption.

In 2014, 23andMe estimated that 7,000 users of its service had discovered unexpected paternity or previously unknown siblings a relatively small fraction of overall users. The company no longer provides data on surprise results. However, its customer base has more than doubled since 2014, and now contains more than 2 million people and as more people get involved with recreational genomics, bloodline surprises are certain to become a more common experience. The 2020s may turn out to be the decade that killed family secrets, for better and for worse.

"We see it every day," says CeCe Moore, a genetic genealogist and consultant for the PBS series "Finding Your Roots." She runs a 54,000-person Facebook group, DNA Detectives, that helps people unravel their genetic ancestries. "You find out that a lot of things are not as they seem, and a lot of families are much more complex than you assume."

Alice Plebuch found herself in this place in the summer of 2012. To solve the mystery of her identity, she needed more help than any DNA testing company could offer. After all, genetic testing gives you the what, but not the why.

Plebuch would turn out to be uniquely suited to the role of private eye in her own detective story. Now living in the suburbs of Vancouver, Washington, she worked as an IT manager for the University of California before her retirement. "I did data processing most of my life, and at a fairly sophisticated level," she says. Computers do not intimidate her, and neither do big questions that require the organization and analysis of complex information. She likes to find patterns hidden in the chaos.

Just the skills necessary to solve a very old puzzle.

After the initial shock of her test results, Plebuch wondered if her mother might have had an affair. Or her grandmother, perhaps? So, she and her sister, Gerry Collins Wiggins, both ordered kits from DNA testing company 23andMe.

The affair scenario seemed unlikely certainly out of character for her mom, and besides, all seven Collins children had their father's hooded eyes. But she couldn't dismiss it. "My father, he was in the Army and he was all over the world, and it was just one of those fears that you have when you don't know," she says.

As they waited for their results, they wondered. If the Ancestry.com findings were right, it meant one of Plebuch's parents was at least partly Jewish. But which one?

They had a gut sense that it was unlikely to be their mother, who came from a large family, filled with cousins Plebuch and her siblings all knew well. Dad, who died in 1999, seemed the likelier candidate. Born in the Bronx, Jim Collins was a baby when his mother died. His longshoreman father, John Collins, was unable to care for his three children and sent them to live in orphanages. He died while Jim was still a child, and Jim had only limited contact with his extended family as an adult.

But still, the notion Jim could somehow be Jewish seemed far-fetched. His parents had come to the United States from Ireland, and that history was central to Jim's sense of himself. "He was raised in an orphanage; he didn't have anything else," Plebuch says. "He had his Irish identity."

She plunged into online genealogy forums, researching how other people had traced their DNA and educating herself about the science. She and her sister came up with a plan: They would persuade two of their first cousins to get tested their mother's nephew and their father's nephew. If one of those cousins was partly Jewish, they'd know for sure which side of the family was contributing the mysterious heritage.

The men agreed. The sisters sent their kits and waited.

Then Plebuch's own 23andMe results came back. They seemed consistent with her earlier Ancestry.com test, indicating lots of Ashkenazi Jewish ancestry from areas such as Belarus, Russia, Ukraine and Lithuania. She also discovered that her brother Bill had recently taken a 23andMe test. His results were a relief sort of.

"No hanky-panky," as Plebuch puts it. They were full siblings, sharing about 50 percent of the relevant DNA, including the same mysterious Jewish ancestry. This knocked out another theory they had considered that Plebuch might have been adopted.

Plebuch found a feature on 23andMe's website showing what segments along her chromosomes were associated with Ashkenazi Jews. Flipping back and forth, comparing her DNA to her brother's, she had a sudden insight.

There was a key difference between the images, lurking in the sex chromosomes. Along the X chromosome were blue segments indicating where she had Jewish ancestry, which could theoretically have come from either parent because females inherit one X from each. But males inherit only one X, from their mothers, along with a Y chromosome from their fathers, and when Plebuch looked at her brother's results, "darned if Bill's X chromosome wasn't lily white." Clearly, their mother had contributed no Jewish ancestry to her son.

"That was when I knew that my father was the one," Plebuch says.

The next day, her sister Gerry Wiggins's results came back: She, too, was a full sibling who also displayed significant Jewish ancestry. Then, Plebuch got an email from a retired professor known for his skill at interpreting ancestry tests, to whom she'd sent hers. "What you are is 50 percent Jewish," he wrote. "This is in fact as solid as DNA gets, which in this case is very solid indeed."

But how could their father have been Jewish? Could Jim Collins's parents have been secret Irish Jews? Or maybe Jews from Eastern Europe who passed themselves off as Irish when they came to the country as immigrants?

Now they really needed the data from the cousin on their father's side. If he also had Jewish ancestry, Plebuch figured, that could point to a family secret buried in Europe.

They waited for months, through a series of setbacks problems in the lab, problems with the mail. Meanwhile, the sisters emailed back and forth.

Plebuch asked her younger sister: Did this revelation about their father's ethnicity unnerve her? They'd been so certain of their family roots, and "now we know nothing," she wrote.

"It is the first thing I think about when I wake up in the morning," Wiggins replied, "and the last thing I think about as I drift off to sleep."

At last, Plebuch was alerted that her cousins' results were ready. The data from their mom's nephew revealed that he was a full first cousin, as expected sharing about 12.5 percent of his DNA with Plebuch.

But the results from her dad's nephew, Pete Nolan, whose mother was Jim Collins' sister, revealed him to be a total stranger, genetically speaking. No overlap whatsoever with Plebuch or, by extension, with her father.

In other words, Plebuch's cousin wasn't actually her cousin.

And her dad's sister wasn't actually his sister.

Plebuch was devastated. This finding knocked out the secret-Jews theory but if it put Plebuch closer to the truth, she still felt unmoored. She was deeply fond of Nolan, with whom she shared a birthday. "I was afraid he was going to reject me because we were no longer biological cousins."

She called Nolan to share the results of his DNA test. "He was sad," Plebuch says, "but he also told me I was the best cousin he ever had."

Plebuch and Wiggins came to the stunned conclusion that their dad was somehow not related to his own parents. John and Katie Collins were Irish Catholics, and their son was Jewish.

"I really lost all my identity," Plebuch says. "I felt adrift. I didn't know who I was you know, who I really was."

For Wiggins, the revelation confirmed a long, lingering sense that something was amiss with her father's story. Studying the family photographs on her wall, she'd thought for years that their paternal grandfather looked like no one in her immediate family. Visiting Ireland in 1990, she had searched the faces for any resemblance to her 5-foot-4, dark-haired father. "There was nobody that looked like my dad," Wiggins says.

The sisters set about methodically pursuing several theories. With Jim Collins and his parents long dead, Plebuch knew she needed to unravel his story through the living. She signed up to take a class in Seattle on how to use DNA to find her father's relatives.

If the woman Jim called his sister was not his sister, was there evidence of an actual sibling out there somewhere? Might that sibling have children? Might Plebuch and her siblings have first cousins they'd never known about?

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The dystopian novelistMargaret Atwood is fond of saying that all new technologies have a good side, a bad side, and a "stupid side you hadn't considered." Doing DNA testing for fun can carry consequences few of us might anticipate. It requires little investment at the outset, but it has the potential to utterly change our lives.

After researching her family history, Laurie Pratt decided five years ago to enhance her genealogical knowledge by testing herself and her parents. This was how she discovered that her dad was not related to her.

Pratt, 52, an airline ground operations supervisor in Orange County, California, went to her mother, who at first said the results were "impossible." But over time, her mother divulged hazy memories of a short-lived relationship during a period when she and her husband were briefly separated.

Her mother couldn't recall a name before she died. The man who raised Pratt also died; she never told him he was not, biologically speaking, her father.

She searched over several years, eventually identifying a potential candidate within the family tree of previously unknown cousins she found through DNA matching. She sent this man a letter and days later, in February of this year, he suddenly popped up in the Ancestry.com database, identified by a saliva test as her biological father.

The man called her, and they spoke briefly on the phone. Though he was unmarried when Pratt was conceived, he fretted over the idea that he had abandoned a baby without knowing it. Pratt asked if they could meet, and the man agreed, but asked if he could take some time first to process the news and tell his wife and daughter.

Two days later, Pratt logged onto Ancestry.com and discovered that the man's test had been deleted.

Reactions to DNA testing surprises vary dramatically. Moore, the genetic genealogist, says that, in her experience, even those who are initially dismayed end up glad that "they learned about the truth of themselves."

But seekers may be a self-selecting bunch, and those who find the truth thrust upon them by someone else's quest are not always happy about it. Gaye Sherman Tannenbaum, an adoptee who spent decades searching for her birthparents and now helps others on their quests, says in some instances, people are "outright hostile" when they learn of a newly discovered relative.

The reaction is understandable: DNA surprises often imply extramarital affairs, out-of-wedlock births and decades-old secrets.

Researchers from theUniversity of Leuven in Belgium recently examined the English-language websites of 43 direct-to-consumer DNA testing companies and found that few companies warn consumers about the possibility of discovering "misattributed paternity."

23andMe is unusual in offering multiple warnings. ("Unexpected relationships may be identified that could affect you and your family.") "We are as transparent as possible," says Kate Black, the privacy officer for 23andMe, brought on in 2015after the company was criticized for failing to prepare consumers for such surprises. "We try to educate and inform people in every tool."

Still, consumers may skim those warnings, or refuse to believe such surprises might lurk within their own families. Jennifer Utley, the director of research at Ancestry.com, says that even though she had seen many cases of surprise relatives in her work, she still found herself in "complete shock" when she tested her own DNA and discovered a first cousin she hadn't known existed.

"I had no idea who this person was," says Utley, who has since learned that her cousin was the product of a teenage relationship, raised by an adoptive family. Of her family, she now concludes: "We're the best secret-keepers on the planet."

Pratt says she doesn't regret testing her DNA. She found herself both "devastated and curious" after the initial discovery about her genetic heritage. But, of course, that discovery was not hers alone, because her genes are not hers alone. Cases of unexpected paternity and secret adoptions implicate other people.

"I think this jars him," she says of her biological father. "He goes to bed the good guy he's always been very religious, very Catholic. And he wakes up, he's Mick Jagger. He has a baby. It blew his mind a little bit."

In late April, Pratt sent the man another letter. She had "no desire to push myself into your family," she wrote, nor make a financial claim. What she sought were stories about him and his family, to help her build a sense of where she came from. Just one meeting, a few hours, was all she asked.

She still hasn't heard back.

By early 2013, the Collins children were hot on the trail of a hundred-year-old mystery.

They had their father's birth certificate, indicating that he'd been born on Sept. 23, 1913. They wrote to his orphanage and learned that their dad had been sent there by the New York Society for the Prevention of Cruelty to Children.

Plebuch wondered if Jim Collins, just a baby at the time, had somehow been confused with another child when he was taken from his father's home.

She found a forensic artist said to be skilled in understanding how faces change over time. She sent her a picture of her dad sitting on his father's lap when he was about 11 months, along with photos of him as an adult. Were these of the same person?

Probably, the forensic artist ruled. The ears hadn't changed, and the mouth, chin and facial proportions seemed the same.

If the mystery of their father didn't begin with his parents' life in Ireland, nor with his own time in the orphanage, Plebuch and her sister concluded it must have happened shortly after Jim was born. Unusually for the era, his mother gave birth not at home but at Fordham Hospital in the Bronx.

Could something have happened there?

Wurts Bros./Museum of the City of New York

By this time, the sisters were using techniques developed by Moore and others to help adoptees try to find relatives in a vast universe of strangers' spit. Every time a site like 23andMe informed them of what Plebuch calls a "DNA cousin" on their Jewish side someone whose results suggested a likely cousin relationship they would ask to see that person's genome. If the person agreed, the site would reveal any places where their chromosomes overlapped.

The idea, Plebuch explains, was to find patterns in the data. A group of people who share segments on the same chromosome probably share a common ancestor. If Plebuch could find a group of relatives who all shared the same segment, she might be able to use that along with their family trees, family surnames, and ancestors' home towns in the old country to trace a path into her father's biological family.

The work was slow and painstaking, complicated by the fact that Ashkenazi Jews frequently marry within the group and often are related in multiple ways. This can make distant relatives look like a closer match than they actually are. But the sisters forged on, sending at least 1,000 requests for genome-sharing to DNA cousins through 23andMe. It became Plebuch's full-time job.

Some ignored their overtures, while others were drawn in by the saga and devoted their own efforts to helping the sisters untangle it. It was as if the Collins sisters had plugged into a larger family, a web of strangers who wanted to help because generations before, their ancestors had shared soup, shared heartache, slept in the same bed.

One DNA cousin made a clever suggestion: Why not search for evidence of a baby born around the same time under a common Jewish surname, Cohen? He reasoned that the nurses, perhaps relying on an alphabetical system, might have confused a Collins baby with a Cohen baby. CeCe Moore was by now volunteering to advise Plebuch, and with additional help from Tannenbaum and the New York City Birth Index of 1913, Plebuch found a Seymour Cohen born in the Bronx on Sept. 23. DNA cousins fanned out on the Internet, tracking down a descendant of Seymour's sister.

Plebuch wrote to the woman, a professor in North Carolina, and offered to pay for her test kit if she'd contribute something completely free and absolutely priceless: her saliva. The woman agreed.

Weeks later, the results came back. No relation.

After that red herring, Plebuch decided to dive deeper into the 1913 birth index, to find babies who were in the hospital at the same time as her father. It was no easy task: The list of children born in the Bronx in 1913 ran 159 pages, was not ordered by date, and didn't distinguish hospital births from home births. But she manage to isolate all the male children born on Sept. 23, as well as the day after and the day before. She further narrowed the list to names that sounded either Jewish or ethnically neutral 30 babies in all.

Her hope was that one of those babies would share a surname with one of the people that the DNA matching sites identified as a likely relative. So she searched methodically.

"Appel" nothing. "Bain" nothing. "Bamson" nothing.

It was another dead end.

The sisters went back to the chromosome segment matching, both at 23andMe and Family Tree DNA, where they had also uploaded their genetic data. They bought at least 21 DNA test kits for themselves, relatives and strangers suspected of being relations. Plebuch found she and her siblings matched to 6,912 likely DNA relatives, with 311,467 "segment matches" among them segments along the chromosomes that overlapped with those of the Collins children. Which is to say, 311,467 potential clues.

The data they had kept on spreadsheets quickly became overwhelming, so their brother Jim, a retired software and systems engineer who had worked on NASA supercomputers, designed an iPad app called DNAMatch to help them and other seekers keep their data straight.

Plebuch was determined, and unusually well suited to the task of solving a puzzle hidden in big data. She and Wiggins searched this way for two and a half years. But she was having no luck finding someone closely related to her father's biological family they simply weren't in the system.

Perhaps they didn't know about DNA testing, or couldn't afford it, or weren't interested.

All the sisters could do was keep working and waiting, hoping the DNA testing revolution would make its way to strangers who shared their blood.

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Ultimately, the crack in the case came not through Plebuch's squad of helpful DNA cousins, but through a stranger with no genetic connection.

It was Jan. 18, 2015, a Sunday, and Plebuch was feeling down. She was writing an email to her cousin Pete Nolan the beloved relative it turned out she wasn't really related to to update him on her stalled search.

As administrator of his 23andMe account, she had permission to check the list of his DNA relatives yet rarely did so, since new relatives rarely showed up. But she decided to check it this day and this time, there was a new person. A stranger had just had her saliva processed, and she showed up as a close relative of Nolan.

Plebuch emailed the woman and asked if she would compare genomes with Nolan. The woman agreed, and Plebuch could see the segments where her cousin and the stranger overlapped. Plebuch thanked her, and asked if her results were what she expected.

"I was actually expecting to be much more Ashkenazi than I am," the woman wrote. Her name was Jessica Benson, a North Carolina resident who had taken the test on a whim, hoping to learn more about her Jewish ethnicity. Instead, she wrote, she had discovered "that I am actually Irish, which I had not expected at all."

Plebuch felt chills. She wrote back that her father had been born at Fordham Hospital on Sept. 23, 1913. Had anyone in the Benson family been born on that date?

Jessica replied. Her grandfather, Phillip Benson, might have been born around that date, she wrote.

Plebuch began to cry.

She started combing through her list of baby names from the 1913 Index. No "Benson" born that day in the Bronx. But then, well after midnight, she found it:

The New York City Birth Index had a "Philip Bamson," born Sept. 23 one of the names she had searched among her DNA cousins. This had to be Phillip Benson, his name misrecorded on his birth certificate.

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She thought she was Irish until a DNA test opened a 100-year-old mystery - Chicago Tribune

The Canaanites lived at the crossroads of the ancient world. They experienced wars, conquests and occupations for millennia, and as a result evolutionary geneticists expected that their DNA would become substantially mixed with incoming populations.

Astonishingly, new genetic analysis shows that scientists were wrong. According to a new study in the American Journal of Human Genetics, todays Lebanese share a whopping 93% of their DNA with the ancient Canaanites.

The study also found that the Bronze Age inhabitants of Sidon, a major Canaanite city-state in modern-day Lebanon, have the same genetic profile as people living 300 to 800 years earlier in present-day Jordan.

Later known as Phoenicians, the Canaanites have a murky past. Nearly all of their own records have been destroyed over the centuries, so their history has been mostly pieced together from archaeological records and the writings of other ancient peoples.

Archaeologists at the Sidon excavation site have been unearthing ancient Canaanite secrets for the last 19 years in the still-inhabited Lebanese port city. The team has uncovered 160 burials from the Canaanite period alone, said Claude Doumet-Serhal, director of the excavation. They have found people of all ages in these Canaanite burials, she said children were buried in jars and adults were placed in sand.

Claude Doumet-Serhal / The Sidon Excavation

An aerial view of the Sidon excavation site.

An aerial view of the Sidon excavation site. (Claude Doumet-Serhal / The Sidon Excavation)

Aided by new DNA sampling techniques, a team of evolutionary geneticists including Marc Haber and Chris Tyler-Smith from the Wellcome Trust Sanger Institute stepped in.

They sequenced the whole genomes of five individuals found in Sidon who lived about 3,700 years ago. The team then compared the genomes of these ancient Canaanites with those of 99 Lebanese people currently living in the country, along with the previously published genetic information from modern and ancient populations across Europe and Asia.

First, they investigated the genetic ancestry of the Canaanites themselves. They found that these Bronze Age inhabitants of Sidon shared about half their DNA with local Neolithic peoples and the other half with Chalcolithic Iranians. Interestingly, this genetic profile is nearly identical to the one evolutionary geneticist Iosif Lazaridis and his team found last year in Bronze Age villagers near Ain Ghazal in modern-day Jordan.

This suggests that Canaanite-related ancestry was spread across a wide region during the Bronze Age and was shared between urban societies on the coast and farming societies further inland. This evidence supports the idea that different Levantine cultural groups such as the Moabites, Israelites, and Phoenicians may have had a common genetic background, the authors said.

The researchers were also able to determine that the genetic mixing of the Levantine and Iranian peoples happened between 6,600 and 3,550 years ago, a range they would be able to narrow down with more ancient DNA samples from the region.

Claude Doumet-Serhal / The Sidon Excavation

The buried remains of a Canaanite adult whose DNA was sequenced in the study.

The buried remains of a Canaanite adult whose DNA was sequenced in the study. (Claude Doumet-Serhal / The Sidon Excavation)

Next, the team wanted to compare the Canaanite genome with the genetic makeup of the people who currently inhabit the ancient Canaanite cities. To do this, they collected DNA from 99 Lebanese people Druze, Muslim, and Christian alike.

As expected, they found some new additions to the modern Lebanese genome since the Bronze Age. About 7% of modern Lebanese DNA originates from eastern Steppe peoples found in what is now Russia, but wasnt represented in the Bronze Age Canaanites or their ancestors. What surprised the team was what was missing from their genetic data.

If you look at the history of Lebanon after the Bronze Age, especially it had a lot of conquests, Haber said. He and Tyler-Smith expected to see greater genetic contributions from multiple conquering peoples, and were surprised that as much as 93% of the Lebanese genome is shared with their Canaanite predecessors.

Though a 7% genetic influx from the Steppe seems very small, that number might be covering some hidden complexities, said Lazaridis, who worked on the Bronze Age Jordanian samples but was not involved in the new study.

Not much is known about the migrations of these eastern Steppe populations, he said. If the genomes of the incoming people were only half Steppe, for example, 14% of the Lebanese genome could have come from the new migrants.

Haber and Tyler-Smith said they want to explore this complexity further. Who were those eastern migrants? Where did they come from? And why did they migrate toward the Levant region? Haber asked. Analyzing more samples from different locations and periods could lead to an answer.

The team also wanted to know if the individuals from Sidon are more similar to modern-day Lebanese than to other modern Eurasian populations.

Despite small genetic variations between the three religious groups caused by preferential mating over time, the Lebanese genome is not widely varied. As a whole, the Lebanese people have more genetic overlap with the Canaanites from Sidon than do other modern Middle Eastern populations such as Jordanians, Syrians or Palestinians.

The difference is small, but its possible that the Lebanese population has remained more isolated over time from an influx of African DNA than other Levantine peoples, Lazaridis suggested.

Claude Doumet-Serhal - The Sidon Excavation

An archaeologist sorts pottery at the Sidon excavation site.

An archaeologist sorts pottery at the Sidon excavation site. (Claude Doumet-Serhal - The Sidon Excavation)

The findings have powerful cultural implications, Doumet-Serhal said. In a country struggling with the ramifications of war and a society fiercely divided along political and sectarian lines, religious groups have often looked to an uncertain history for their identities.

When Lebanon started in 1929, Doumet-Serhal said, the Christians said, We are Phoenician. The Muslims didnt accept that and they said, No, we are Arab.

But from this work comes a message of unity. We all belong to the same people, Doumet-Serhal said. We have always had a difficult past but we have a shared heritage we have to preserve.

mira.abed@latimes.com

Twitter: @mirakatherine

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Fake news about statins is discouraging the use of these life-saving drugs, expert warns

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The DNA of ancient Canaanites lives on in modern-day Lebanese, genetic analysis shows - Los Angeles Times

DNA is compressed in the nucleus in a disorderly way that allows flexibility in how genes are turned on and off, according to a study by scientists from the Salk Institute and University of California San Diego.

This discovery was made with a new imaging technology devised by Salk researchers led by Clodagh OShea and carried out by UCSD researchers led by Mark Ellisman.

Published in Science, the study is available at j.mp/salkdna. OShea is listed as senior author with Ellisman as collaborator. The first author was Horng Ou, a researcher in OSheas lab.

Understanding DNAs 3D structure is expected to yield a better understanding of how defects in that structure relate to senescence and diseases, according to a perspective piece published along with the study.

In the nucleus, DNA is bound to proteins called histones to make a complex called chromatin, which in turn forms chromosomes. The degree of compression is extreme. Stretched out to form a line, the DNA in a single cell would extend about two meters, or about 6 1/2 feet. It must all fit into a nucleus of about 10 millionths of a meter.

What that means is that not all your DNA is accessible, OShea said. So even though the same DNA sequence is in every cell in your body, its structure in any cell nucleus can be different, which determines whether those DNA sequences can be accessed and used.

The fundamental question then is, well what's the structure of DNA in the nucleus, she said.

Existing models envision DNA as being grouped in increasingly large fibers, one inside another. But determining whether these models are correct has been stymied by the lack of imaging technology that can visualize chromatin.

Electron microscopy, one of the common tools to visualize such minute structures, doesnt work well with chromatin, OShea said. Thats because the chemical elements in chromatin dont provide sufficient contrast.

The Salk team solved that problem by using a fluorescent dye to stain the chromatin. When the dye was illuminated, it caused a metal to coat the DNA and associated proteins so they can be more easily detected by electron microscopy. They call this method ChromEMT.

The dye was already known, but it was the Salk teams idea to use it for imaging chromatin. The actual imaging, called "multi-tilt electron tomography" was performed by colleagues at University of California San Diego.

They found that chromatin is packed in clusters of various densities. The denser clusters are not as accessible as the looser cluster, OShea said. This provides a mechanism for allowing selective access to genes.

Previous hierarchy-based models didnt fit the experimental evidence of gene activation and suppression, OShea said. These models suggested that access would be allowed or denied at predictable, periodic intervals. The trouble with that is that one error would cause the whole intricate structure to fail.

By allowing DNA to be compressed into many separate clusters, with no grand structure, gene regulation can be take place independently. Moreover, a defect in one cluster wouldnt affect other clusters.

bradley.fikes@sduniontribune.com

(619) 293-1020

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Salk Institute, UCSD scientists decode DNA's 3D shape - The San ... - The San Diego Union-Tribune

Ramazzottius varieornatus, a species of tardigrade, photographed with scanning electron microscope

smithsonian.com July 27, 2017

Despite their tiny stature and their adorable nicknamesmoss piglets, water bearsthe tenacious tardigrade has some tremendous capabilities.Well-known for beingone of the hardiest-known forms of life, tardigrates can survivedesiccation,deadly radiation, and even thevacuum of space. Now researchers may finally be starting to tease out the genetic basis of tardigrade superpowers.

In 2015, a study published in the Proceedings of the National Academy of Sciences, suggested that some of their superpowers could come from an another oddballaccomplishment of the microscopic creature:DNA theft. The researchers sequenced a tardigrade species' genome and found that roughly one-sixth of its DNA (around 6,600 genes) appeared to come from other organisms, mainly bacteria. These sections of DNA were thought to be picked up through the process of so-calledhorizontal gene transfers, which is a commoninbacteria and other microbes (scientists have only recently discovered some animals can also do this).

If they can acquire DNA from organisms already living in stressful environments, they may be able to pick up some of the same tricks, researcher Thomas Boothby,a Life Sciences postdoctoral fellow at the University of North Carolina, Chapel Hill,told Smithsonian.com in 2015.

But just a week after it was published, the studyfaced steep opposition. Another group of tardigrade researchers claimed that much of the supposedly "stolen" DNA likely came from contamination of the samples from bacteria that lived alongside the tardigrades. "There is no way, biologically, these can be part of the same genome," geneticistMarkBlaxter told Ed Yong of the Atlantic in 2015.

Now Blaxterand his team are back with a new analysis of the tardigrade genome, publishedin the journal PLOSBiology."I have been fascinated by these tiny, endearing animals for two decades," Blaxtersays in a statement. "It is wonderful to finally have their true genomes, and to begin to understand them."

This latest study compares the genomes of two tardigrade species:Hypsibius dujardini and Ramazzottius varieornatus. Though the research hints at some of the reasons behind tardigrade superpowers, italso sheds light on how little we know about this adaptable critter.

The main superpower the researchers focused on was how the creatures can dry out at years at a time. For most life, desiccationmeans death. So the team examined genes that are activated under dry conditions, discovering a set of proteins that appear to fill in for water lost in tardigrade cells. By taking the place of the missing water molecules, the proteins prevent the cells structures from collapsing and allows the tiny tardigrade to revive itself when water returns.

The latest study isalso providing clues into how tardigrades came to be. Scientistspreviously suspected that tardigrades may be closely related to the phylum of arthropods, which includes insects and spiders. But this latest study strongly suggeststhattardigradesare actually more closely related to nematodes, also known as roundworms. The researchers examined a set genes that determine the layout of an embryo called "HOXgenes." They found that, similar to nematodes,both species oftardigradelackfive commons genes from this set.

As for the controversy over how much gene transfer really takes place? It appears to be mostly settled now, reports Tina Hesman Saey from Science News."The authors' analysis methods, and their methods for getting clean DNA, are certainly an improvement over our own earlier methods," Bob Goldstein, who supervisedBoothby's 2015 research, tellsSaey.

But the debate about tardigrades amazing superpowers and where they belong on the tree of life is far from settled. Are tardigradesmoreclosely related to arthropods or nematodes? "Its still an open question," phylogeneticist Max Telford tellsSaey.

Even so, Blaxter hopes that his team's tardigrade genomes will continue to help tease out tardigrade'stangled relationships as well as assist in the development of useful applications for the creatures superpowers."This is just the start," Blaxter says in a statement. "With the DNA blueprint we can now find out how tardigrades resist extremes, and perhaps use their special proteins in biotechnology and medical applications."

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Why Are Tardigrades the World's Hardiest Creature? DNA Offers Clues - Smithsonian

Genomic infrastructure needs constant upkeep but still falls into disrepair, upkeep or no, if upkeep quality is compromised. In fact, if DNA repairs are poorly executed, they may not only fail to correct the mutations that are due to ordinary wear and tear, they may also introduce additional mutations. These additional mutations, which appear to be an important cause of cancer, have been associated with DNA repairs that are executed under the influence of alcohol. Other adverse influences on DNAs repair crews include sunlight and smoking.

Cancer is mostly caused by changes in the DNA of our cells that occur during our lifetime rather than those that we inherit from our parents. Identifying the causes of these mutations is a difficult challenge because many processes can result in an identical DNA sequence change in a genome.

Regardless, it is possible to determine which mutations may be attributable to impaired DNA repair mechanisms. What is required, say researchers at the Centre for Genomic Regulation (CRG) in Barcelona, is the right kind of inspection.

The researchers decided to focus on clusters of mutations while scrutinizing more than a thousand tumor genomes, meaning that they hunted for mutations that occur close together in the same part of the genome. Such clusters are highly unlikely to happen by chance. Ultimately, the researchers hoped to get a better picture of the mutagenic factors that affect human cells and that might cause cancer.

Details of the researchers work appeared July 27 in the journal Cell, in an article entitled, Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes. This article makes the case that if mutations occur in clusters, as opposed to being sprinkled randomly through the genome, genome inspectors should suspect DNA repair crews of doing shoddy work.

"Clustered mutations are likely to be generated at the same moment in time, so by looking at several neighboring mutations at once, we can have a better understanding of what has damaged the DNA," says Fran Supek, Ph.D., first author of the Cell article, CRG researcher, and group leader and 'Ramon y Cajal' fellow at the Institute for Research in Biomedicine.

Of nine clustered mutation signatures identified from >1,000 tumor genomes, three relate to variable APOBEC activity and three are associated with tobacco smoking, wrote the authors of the Cell article. An additional signature matches the spectrum of translesion DNA polymerase eta (POLH).

In lymphoid cells, these mutations target promoters, consistent with AID-initiated somatic hypermutation. In solid tumors, however, they are associated with UV exposure and alcohol consumption and target the H3K36me3 chromatin of active genes in a mismatch repair (MMR)-dependent manner.

These results revealed new major mutation-causing processes, including an unusual case of DNA repair which should normally safeguard the genome from damage, but is sometimes subverted and starts introducing clustered mutations.

"Our work provides information about new biological mechanisms underlying some types of cancers, asserted Dr. Supek. For example, the main oncogenes involved in melanoma are well-known, but it is not known what causes the exact mutations that activate these genes to cause cancer. While many mutations in melanoma are recognized to be a direct consequence of UV radiation, the origin of mutations affecting the most important oncogenes is still a mystery. We identified a mechanism that has the capacity to cause these oncogenic, cancer-driving mutations in melanoma."

One of these new mutational processes is highly unusual and it is most evident in active genes. These regions are usually protected by DNA repair mechanismsin other words, DNA repair is directed towards the places where it is needed most.

"Our results suggest that exposure to carcinogens, such as high amounts of alcohol, can shift the balance of the DNA repair machinery from a high-fidelity mode to an error-prone mode, causing the mutation rates to shoot up in the most important bits of the genome," explained Ben Lehner, Ph.D., ICREA research professor at the EMBL-CRG Systems Biology Research Unit and principal investigator of the current study. "This error-prone repair generates a large number of mutations overall and is likely to be a major mutation source in human cells."

DNA repair is extremely important because our bodies are constantly renewing their cells which involves copying more than two meters of DNA and errors inevitably get introduced. Moreover, mutagens in the environment like sunlight and tobacco smoke damage DNA and this damage has to be corrected. DNA repair is normally exquisitely accurate, but some types of damage can only be corrected using lower-fidelity "spellcheckers." It is the mistakes made by one of these less accurate spellcheckers that cause many of the mutations seen in different types of tumors, including liver, colon, stomach, esophagus, and lung cancer.

Alcohol is a well-known contributor to many types of cancer, but the reasons for this are surprisingly unclear. The current study suggests that one effect of alcohol, when consumed in large amounts, is to increase the use of low-fidelity DNA repair, thereby increasing the mutation rate in the most important regions of the genome. This finding provides a first glimpse into one mechanism by which alcohol may contribute to cancer risk. High exposure to sunlight seems to have a similar consequence.

As another part of the study the CRG scientists also found that cigarette smoking is associated with several different kinds of clustered mutations, further revealing the details of how smoking results in horrific damage to our DNA.

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DNA Repair Under the Influence May Raise Risk of Cancer - Genetic Engineering & Biotechnology News

July 28, 2017 by Luis Ceze And Karin Strauss, The Conversation The next frontier of data storage: DNA. Credit: ymgerman/Shutterstock.com

Humanity is producing data at an unimaginable rate, to the point that storage technologies can't keep up. Every five years, the amount of data we're producing increases 10-fold, including photos and videos. Not all of it needs to be stored, but manufacturers of data storage aren't making hard drives and flash chips fast enough to hold what we do want to keep. Since we're not going to stop taking pictures and recording movies, we need to develop new ways to save them.

Over millennia, nature has evolved an incredible information storage medium DNA. It evolved to store genetic information, blueprints for building proteins, but DNA can be used for many more purposes than just that. DNA is also much denser than modern storage media: The data on hundreds of thousands of DVDs could fit inside a matchbox-size package of DNA. DNA is also much more durable lasting thousands of years than today's hard drives, which may last years or decades. And while hard drive formats and connection standards become obsolete, DNA never will, at least so long as there's life.

The idea of storing digital data in DNA is several decades old, but recent work from Harvard and the European Bioinformatics Institute showed that progress in modern DNA manipulation methods could make it both possible and practical today. Many research groups, including at the ETH Zurich, the University of Illinois at Urbana-Champaign and Columbia University are working on this problem. Our own group at the University of Washington and Microsoft holds the world record for the amount of data successfully stored in and retrieved from DNA 200 megabytes.

Preparing bits to become atoms

Traditional media like hard drives, thumb drives or DVDs store digital data by changing either the magnetic, electrical or optical properties of a material to store 0s and 1s.

To store data in DNA, the concept is the same, but the process is different. DNA molecules are long sequences of smaller molecules, called nucleotides adenine, cytosine, thymine and guanine, usually designated as A, C, T and G. Rather than creating sequences of 0s and 1s, as in electronic media, DNA storage uses sequences of the nucleotides.

There are several ways to do this, but the general idea is to assign digital data patterns to DNA nucleotides. For instance, 00 could be equivalent to A, 01 to C, 10 to T and 11 to G. To store a picture, for example, we start with its encoding as a digital file, like a JPEG. That file is, in essence, a long string of 0s and 1s. Let's say the first eight bits of the file are 01111000; we break them into pairs 01 11 10 00 which correspond to C-G-T-A. That's the order in which we join the nucleotides to form a DNA strand.

Digital computer files can be quite large even terabytes in size for large databases. But individual DNA strands have to be much shorter holding only about 20 bytes each. That's because the longer a DNA strand is, the harder it is to build chemically.

So we need to break the data into smaller chunks, and add to each an indicator of where in the sequence it falls. When it's time to read the DNA-stored information, that indicator will ensure all the chunks of data stay in their proper order.

Now we have a plan for how to store the data. Next we have to actually do it.

Storing the data

After determining what order the letters should go in, the DNA sequences are manufactured letter by letter with chemical reactions. These reactions are driven by equipment that takes in bottles of A's, C's, G's and T's and mixes them in a liquid solution with other chemicals to control the reactions that specify the order of the physical DNA strands.

This process brings us another benefit of DNA storage: backup copies. Rather than making one strand at a time, the chemical reactions make many identical strands at once, before going on to make many copies of the next strand in the series.

Once the DNA strands are created, we need to protect them against damage from humidity and light. So we dry them out and put them in a container that keeps them cold and blocks water and light.

But stored data are useful only if we can retrieve them later.

Reading the data back

To read the data back out of storage, we use a sequencing machine exactly like those used for analysis of genomic DNA in cells. This identifies the molecules, generating a letter sequence per molecule, which we then decode into a binary sequence of 0s and 1s in order. This process can destroy the DNA as it is read but that's where those backup copies come into play: There are many copies of each sequence.

And if the backup copies get depleted, it is easy to make duplicate copies to refill the storage just as nature copies DNA all the time.

At the moment, most DNA retrieval systems require reading all of the information stored in a particular container, even if we want only a small amount of it. This is like reading an entire hard drive's worth of information just to find one email message. We have developed techniques based on well-studied biochemistry methods that let us identify and read only the specific pieces of information a user needs to retrieve from DNA storage.

Remaining challenges

At present, DNA storage is experimental. Before it becomes commonplace, it needs to be completely automated, and the processes of both building DNA and reading it must be improved. They are both prone to error and relatively slow. For example, today's DNA synthesis lets us write a few hundred bytes per second; a modern hard drive can write hundreds of millions of bytes per second. An average iPhone photo would take several hours to store in DNA, though it takes less than a second to save on the phone or transfer to a computer.

These are significant challenges, but we are optimistic because all the relevant technologies are improving rapidly. Further, DNA data storage doesn't need the perfect accuracy that biology requires, so researchers are likely to find even cheaper and faster ways to store information in nature's oldest data storage system.

Explore further: Researchers break record for DNA data storage

This article was originally published on The Conversation. Read the original article.

University of Washington and Microsoft researchers have broken what they believe is the world record for the amount of digital data successfully storedand retrievedin DNA molecules.

(Phys.org) -- A team of researchers in the US has successfully encoded a 5.27 megabit book using DNA microchips, and they then read the book using DNA sequencing. Their experiments show that DNA could be used for long-term ...

Humanity may soon generate more data than hard drives or magnetic tape can handle, a problem that has scientists turning to nature's age-old solution for information-storageDNA.

Hand-written letters and printed photos seem quaint in today's digital age. But there's one thing that traditional media have over hard drives: longevity. To address this modern shortcoming, scientists are turning to DNA ...

Technology companies routinely build sprawling data centers to store all the baby pictures, financial transactions, funny cat videos and email messages its users hoard.

We are producing more data than ever before, with more than 2.5 quintillion bytes produced every day, according to computer giant IBM. That's a staggering 2,500,000,000,000 gigabytes of data and it's growing fast.

(Phys.org)Researchers have designed an optical lens that exhibits two properties that so far have not been demonstrated together: self-focusing and an optical effect called the Talbot effect that creates repeating patterns ...

Researchers have taken an important step toward the long-sought goal of a quantum computer, which in theory should be capable of vastly faster computations than conventional computers, for certain kinds of problems. The new ...

Washington State University physicists have found a way to write an electrical circuit into a crystal, opening up the possibility of transparent, three-dimensional electronics that, like an Etch A Sketch, can be erased and ...

Researchers at the UAB have come up with a method to measure the strength of the superposition coherence in any given quantum state. The method, published in the journal Proceedings of the Royal Society A, is based on the ...

The inner workings of the human brain have always been a subject of great interest. Unfortunately, it is fairly difficult to view brain structures or intricate tissues due to the fact that the skull is not transparent by ...

The perfect performance of superconductors could revolutionize everything from grid-scale power infrastructure to consumer electronics, if only they could be coerced into operating above frigid temperatures. Even so-called ...

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

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Storing data in DNA brings nature into the digital universe - Phys.Org

(The Conversation is an independent and nonprofit source of news, analysis and commentary from academic experts.)

Luis Ceze, University of Washington and Karin Strauss, University of Washington

(THE CONVERSATION) Humanity is producing data at an unimaginable rate, to the point that storage technologies cant keep up. Every five years, the amount of data were producing increases 10-fold, including photos and videos. Not all of it needs to be stored, but manufacturers of data storage arent making hard drives and flash chips fast enough to hold what we do want to keep. Since were not going to stop taking pictures and recording movies, we need to develop new ways to save them.

Over millennia, nature has evolved an incredible information storage medium DNA. It evolved to store genetic information, blueprints for building proteins, but DNA can be used for many more purposes than just that. DNA is also much denser than modern storage media: The data on hundreds of thousands of DVDs could fit inside a matchbox-size package of DNA. DNA is also much more durable lasting thousands of years than todays hard drives, which may last years or decades. And while hard drive formats and connection standards become obsolete, DNA never will, at least so long as theres life.

The idea of storing digital data in DNA is several decades old, but recent work from Harvard and the European Bioinformatics Institute showed that progress in modern DNA manipulation methods could make it both possible and practical today. Many research groups, including at the ETH Zurich, the University of Illinois at Urbana-Champaign and Columbia University are working on this problem. Our own group at the University of Washington and Microsoft holds the world record for the amount of data successfully stored in and retrieved from DNA 200 megabytes.

Traditional media like hard drives, thumb drives or DVDs store digital data by changing either the magnetic, electrical or optical properties of a material to store 0s and 1s.

To store data in DNA, the concept is the same, but the process is different. DNA molecules are long sequences of smaller molecules, called nucleotides adenine, cytosine, thymine and guanine, usually designated as A, C, T and G. Rather than creating sequences of 0s and 1s, as in electronic media, DNA storage uses sequences of the nucleotides.

There are several ways to do this, but the general idea is to assign digital data patterns to DNA nucleotides. For instance, 00 could be equivalent to A, 01 to C, 10 to T and 11 to G. To store a picture, for example, we start with its encoding as a digital file, like a JPEG. That file is, in essence, a long string of 0s and 1s. Lets say the first eight bits of the file are 01111000; we break them into pairs 01 11 10 00 which correspond to C-G-T-A. Thats the order in which we join the nucleotides to form a DNA strand.

Digital computer files can be quite large even terabytes in size for large databases. But individual DNA strands have to be much shorter holding only about 20 bytes each. Thats because the longer a DNA strand is, the harder it is to build chemically.

So we need to break the data into smaller chunks, and add to each an indicator of where in the sequence it falls. When its time to read the DNA-stored information, that indicator will ensure all the chunks of data stay in their proper order.

Now we have a plan for how to store the data. Next we have to actually do it.

After determining what order the letters should go in, the DNA sequences are manufactured letter by letter with chemical reactions. These reactions are driven by equipment that takes in bottles of As, Cs, Gs and Ts and mixes them in a liquid solution with other chemicals to control the reactions that specify the order of the physical DNA strands.

This process brings us another benefit of DNA storage: backup copies. Rather than making one strand at a time, the chemical reactions make many identical strands at once, before going on to make many copies of the next strand in the series.

Once the DNA strands are created, we need to protect them against damage from humidity and light. So we dry them out and put them in a container that keeps them cold and blocks water and light.

But stored data are useful only if we can retrieve them later.

To read the data back out of storage, we use a sequencing machine exactly like those used for analysis of genomic DNA in cells. This identifies the molecules, generating a letter sequence per molecule, which we then decode into a binary sequence of 0s and 1s in order. This process can destroy the DNA as it is read but thats where those backup copies come into play: There are many copies of each sequence.

And if the backup copies get depleted, it is easy to make duplicate copies to refill the storage just as nature copies DNA all the time.

At the moment, most DNA retrieval systems require reading all of the information stored in a particular container, even if we want only a small amount of it. This is like reading an entire hard drives worth of information just to find one email message. We have developed techniques based on well-studied biochemistry methods that let us identify and read only the specific pieces of information a user needs to retrieve from DNA storage.

At present, DNA storage is experimental. Before it becomes commonplace, it needs to be completely automated, and the processes of both building DNA and reading it must be improved. They are both prone to error and relatively slow. For example, todays DNA synthesis lets us write a few hundred bytes per second; a modern hard drive can write hundreds of millions of bytes per second. An average iPhone photo would take several hours to store in DNA, though it takes less than a second to save on the phone or transfer to a computer.

These are significant challenges, but we are optimistic because all the relevant technologies are improving rapidly. Further, DNA data storage doesnt need the perfect accuracy that biology requires, so researchers are likely to find even cheaper and faster ways to store information in natures oldest data storage system.

This article was originally published on The Conversation. Read the original article here: http://theconversation.com/storing-data-in-dna-brings-nature-into-the-digital-universe-78226.

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Storing data in DNA brings nature into the digital universe - San ... - San Francisco Chronicle

"This thing has haunted me," Kurtz says. "I think of her almost every day."

The 'thing' Kurtz is talking about is the 1988 disappearance of 19-year-old Susan Swedell from a Lake Elmo gas station, which remains unsolved to this day.

Thousands of other Minnesotans have gone missing, before and since. But the case was a first for state officials in a big way.

Back when Kurtzwho as a deputy responded to the initial missing person call at the Swedell family hometook a fresh look at the case in 2002, he remembers talking to Swedell's mother, again. They'd just had a news conference announcing a $25,000 reward for any information on the young woman.

"That same day I took her mom and sister over to Regions Hospital (and) did a blood draw," Kurtz remembers.

Then they drove to the Minnesota Bureau of Criminal Apprehension headquarters in St. Paul. Kurtz remembers telling a technician he had a DNA sample from the family of a long-time missing person.

But the BCA, at that point, wasn't used to accepting such evidence; there was no "DNA database" for family members of the missing.

"They didn't have anything. The technician had to get his boss. ... He said, 'not sure what you want to do with this. Is this a case we're working?' " Kurtz said.

Kurtz told the tech he'd like the state to keep that blood, in case it was needed in the future. You never knew what might happen to the family.

The boss evidently agreed: BCA officials confirmed that the Swedell family's DNA was the first "Missing Person Relative" sample in state history they ever took into their custody.

"They said 'we'll do it,' no arguments at all," Kurtz said.

Ever since, the state has been upping its efforts to get more "samples" from family. Earlier this month, they made a highly publicized push for more family to come forward, noting they'd just dug up five unidentified bodies from graveyards in the East Metro, to add to the 100 or so they already have in their care.

KURTZ: MAKE IT COMMON PRACTICE

But Kurtz wants more. For years, off and on, he's been pushing for a policyperhaps a lawthat would make it common practice for officers to get missing person DNA samples immediately, as they take their initial reports. Bag a tooth or hair brush, and keep it on hand, just in case.

"If they (families) don't wanna do it, they don't wanna do it, but I guarantee 99 percent of them will do it," Kurtz said. "Because what are family members doing? They're cleaning up the (missing person's) room." And what they remove could later be helpful to locate a loved one, he explains.

Kurtz admits he's not familiar with the lobbyist labyrinth he'd need to navigate to turn such an idea into a law. After retiring in 2003, he worked as a private investigator for awhile, and now does security work at Twins games.

But he's got a tentative advocate in current Washington County Sheriff Dan Starry, who he helped train years ago.

"I think the sooner that there's DNA, the better," Starry said. "But it has to be permission based."

Starry said he intends to bring the idea up at an August meeting of the Minnesota Sheriffs' Association.

HOW CASES CURRENTLY HANDLED

The BCA noted that they already ask local agencies to request and submit such DNA if the missing persons case is still active at 30 days.

When asked about Starry's idea, BCA spokesman Jill Oliveira said, "Each case has unique characteristics that will inform a local agency decision about whether direct reference or family member DNA collection would be of value in the earliest stages of their investigation.

"The local agency is in the best position to make that determination," Oliveira added.

When it comes to the Swedell case, Kurtz said he wishes he would've gotten those samples earlier.

"It is still one of those cases that is in the forefront of the sheriff's office,' said Starry. "I, as sheriff, will not allow that case to sit idle."

SWEDELL'S LAST KNOWN MOMENTS

Susan Swedell went missing on Jan. 19, 1988, after leaving her overheated car at a Lake Elmo gas station, following her shift at a Kmart in Oak Park Heights. The gas station's attendant saw her get in another man's car, and a subsequent investigation of her car found that the radiator's "petcock" the plug on the bottom had been removed, draining the radiator of fluid.

The station where she was last seen was less than a mile from her home.

The BCA made a public plea last week for family members of missing persons to come forward and give their own DNA, to help identify some of the remains they were keeping in custody.

One public event remains this month, from 4:30 to 6:30 p.m. Thursday, July 27, at the Mankato Public Safety Center at 710 Front St.

In all, the BCA has roughly 100 sets of remains that have yet to be identified; there are approximately 225 Minnesotans who have been missing for more than a year.

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As state wants DNA from families of the missing, retired cop remembers the first to come forward - Brainerd Dispatch