Monthly Archives: April 2017

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smithsonian.com April 26, 2017 1:07PM

Researchers recently extracted DNA from the remains of 24 sailors from the doomed Franklin Expedition to find the Northwest Passage, reports Megan Gannon at LiveScience. The new DNA database will allow the team to learn more about the sailors and possibly identify the remains by connecting them to living descendants.

The Franklin Expeditionset sail fromthe United Kingdom in 1845 with a crew of 134 sailors aboardtwo ships, the H.M.S. Erebus and the H.M.S. Terror.They headedto Arctic Canada to look for the fabled route between the Atlantic and the Pacific. But by 1846, Franklin and his129 crewmembers (five sailorshad earlier been discharged and sent back home) were iced in. Though the expedition was stocked with enough food to last for several years, a note discovered over a decade later indicated that Franklin and 23 crew members died of unknown causes by 1847. The other 105 sailors abandoned the ships in 1848. None of them survived.

It wasnt until the 1980s that researchers started finding remains of the sailors, reports Gannon. Corpses were found on Beechey Island and remains of other individuals were found at various sites. According to the study in theJournal of Archaeological Science: Reports,Nunavut's Department of Culture and Heritage conducted DNA testing on 39 bone and teeth fragments from around Erebus Bay as well as samples from Booth Point, King William Island, Todd Island as well as Wilmot and Crampton Bay. The were able to get results from 37 of the fragments, determining that they came from 24 different individuals.

One of the most interesting findings was that four of the remains may have come from European women, which is surprising since the crew was reported as all male. The researchers ruled out the possibility that the remains came from local Inuit women. While degraded DNA can give false female readings, the researchers say its not out of the realm of possibility that women were on the expedition and that there are records of women sneaking onboard British ships. Some of these women were smuggled onboard [the] ship, and others disguised themselves as men and worked alongside the crew for months or years before being detected or intentionally revealing themselves to be female, they write in the study.

They hope that the DNA will allow them to positively identify some of the remains. We have been in touch with several descendants who have expressed interest in participating in further research, Douglas Stenton, lead author of the study, tells Gannon. We hope that the publication of our initial study will encourage other descendants to also consider participating.

These findings are part of a renaissance of Franklin Expedition discoveries taking place recently, which are finally piecing together what went so wrong. In 2014, after 180 years of of looking, searchers found the shipwreck of the Erebus and last September they located the Terror. A study released in December which examined the toenails of one of the mummies found on Beechey Island showed that he suffered from a zinc deficiency, which may mean the canned food onboard the ships spoiled or the crew was unable to find fresh meat in the Arctic.

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Jason Daley is a Madison, Wisconsin-based writer specializing in natural history, science, travel, and the environment. His work has appeared in Discover, Popular Science, Outside, Mens Journal, and other magazines.

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DNA Could Identify the Sailors (Including Women) of the Doomed Franklin Expedition - Smithsonian

Mapping the relationships between different dog breeds is rough (get it?), but ateam of scientists at the National Institutes of Health did just that using the DNA of 1,346 dogs from 161 breeds. Their analysis, which appears April 25 in Cell Reports, offers a lot to chew on.

Here are five key findings from the work:

As human lifestyles shifted from hunting and gathering to herding to agriculture and finally urbanization, humans bred dogs (Canis familiaris) accordingly.Then over the last 200 years, more and more breeds emerged within those categories. Humans crossed breeds to create hybrids based on appearance and temperament, and those hybrids eventually became new breeds.

Genetic backtracking indicates that, for example, mixing between bulldogs and terriers traces back to Ireland between 1860 and 1870. That timeframe and location coincides with historical records indicating a dog-fighting fad thats linked with crossing breeds to make better fighters.

While herderdog breeds showed a lot of genetic diversity, they fallinto two general groups from the rural United Kingdom and the Mediterranean on the breed family tree. When humans switched from hunting to farming, herding breeds may have emerged independently in different areas. Geography could also explain why these two groups use different herding tactics.

A genetic legacy of America's early canine inhabitants lives on in some of today's breeds. Dogs trekked to the Americas from Asia with peoplemore than 10,000 years ago, but when European groups started to colonize the Americas, they brought European dog breeds with them. Past studies suggestthat outside breeds largely replaced New World dogs, but the new dataset shows New World dog DNA actually does persist in a few modern New World breeds, such as Chihuahuas.

European mastiffs and Mediterranean sheepdogs dont share recent changes in their DNA, meaning their size traits arose separately and for different reasons. While both breed groups specialize in guarding things, mastiffs use their size to intimidate humans, while sheepdogs use their size to overpower animal predators. Larger size may have been one of the first traits that human breeders zeroed in on, the researchers suspect.

Read more from the original source:
Dog DNA study maps breeds across the world - Science News (blog)

Eileen Rapley, who joined the trial after being diagnosed with lung cancer a year ago. She hopes the new test might lead to the kinds of improvements that screening techniques like mammograms have brought about for breast cancer. Photograph: Graeme Robertson for the Guardian

A revolutionary blood test has been shown to diagnose the recurrence of cancer up to a year in advance of conventional scans in a major lung cancer trial.

The test, known as a liquid biopsy, could buy crucial time for doctors by indicating that cancer is growing in the body when tumours are not yet detectable on CT scans and long before the patient becomes aware of physical symptoms.

It works by detecting free-floating mutated DNA, released into the bloodstream by dying cancer cells. In the trial of 100 lung cancer patients, scientists saw precipitous rises in tumour DNA in the blood of patients who would go on to relapse months, or even a year, later.

The findings add to building anticipation that the technology, which is already in widespread use in non-invasive prenatal tests for Downs syndrome, will have a major impact in cancer medicine.

Nitzan Rosenfeld of the Cancer Research UK Cambridge Institute, who was not involved in the latest trial, predicts that most if not all cancer patients will be given the DNA-based tests in future.

Even if only a fraction of cancers that are currently detected at a lethal stage will in future be detected at an early curable stage this will represent a great benefit in lives saved, he said.

In the latest trial, reported in the journal Nature, 100 patients with non-small cell lung cancer were followed from diagnosis through surgery and chemotherapy, having blood tests every six to eight weeks.

By analysing the patchwork of genetic faults in cells across each tumour, scientists created personalised genomic templates for each patient. This was then compared to the DNA floating in their blood, to assess whether a fraction of it matched that seen in their tumour.

Prof Charlie Swanton, a cancer geneticist at the Francis Crick Institute who led the work, described how circulating tumour DNA tracked the patients disease status with remarkable precision. Of patients who would remain in remission, he said that Within 48 hours of surgery, the DNA drops down to undetectable.

By contrast, rising tumour DNA levels were seen in patients whose disease would later recur, indicating that cancer remained in the lungs or had migrated to other organs, where it was lying dormant.

When the tests of 24 patients were analysed in detail, the scientists could say with 92% accuracy who would relapse.

I think this is going to be very useful clinically, said Swanton. This allows us to identify high risk patients. We have predictive value of 92% that your cancer is going to recur within 350 days.

The tests even revealed an apparent outlier, a patient whose cancer had not yet resurfaced, but whose blood test showed high levels of circulating tumour DNA.

We said either theres something wrong with our assay or this patients got recurring disease, said Swanton. Almost a year later, cancer showed up on a CT scan.

The liquid biopsies also showed whether chemotherapy was working or if the disease had evolved resistance, as happens in the majority of stage 2 and 3 cancers. In future, this could allow doctors to switch to a more effective drug and spare patients gruelling but futile treatment.

Were giving all this toxic chemotherapy on the basis that only 1 in 20 patients will ever benefit, said Swanton. We could say this patient is not benefiting from chemotherapy so we should stop it. Or this patients disease is coming back but we cant see it on a CT scan so we should give more treatment.

This has got real, clear practical relevance now in lung cancer, he added.

Eileen Rapley, 74, a retired art teacher from London, entered the trial after being diagnosed with lung cancer a year ago. Since treatment, doctors discovered that Rapley had also developed a brain tumour, for which she has also been treated. Although the liquid biopsy did not guide her own care, she hopes the new test might lead to the kinds of improvements that screening techniques like mammograms have brought about for breast cancer.

That sort of research has helped so many, she said. Friends of mine with breast cancer, I cant think of any for years and years who have died, because there were early tests and early diagnosis.

The test used in the study relied on building a bespoke genetic template for each patient based on detailed analysis of tumour samples, with an estimated cost of over 1,300 per patient. However, Swanton predicts the same kind of profile could be built using computational methods from just an initial blood test, making the technology viable outside a purely research setting.

Were not a million miles away from that; it will probably happen in the next 2-3 years, he said.

Lung cancer causes more than one in five of all cancer deaths in the UK and, although incidence of the disease is falling, survival has only improved fractionally in the past 40 years.

Read more from the original source:
DNA-based test can spot cancer recurrence a year before conventional scans - The Guardian

S

ome human stem cells growing in labs that researchers have used in experiments to treat serious diseases contain serious cancer-causing mutations, scientists reported on Wednesday. The discovery raised alarms that patients could be treated for one disease, such as macular degeneration, only to develop another, cancer.

Harvard scientists obtained samples of most of the human embryonic stem cell lines registered with the National Institutes of Health for use in both basic research and in developing therapies for patients with diseases including diabetes, Parkinsons, and macular degeneration. They found that five of the 140 lineshad cells with a cancer-causing mutation.

At least two of the fivelines have been used in experimental treatments testedin clinical trials in an unknown number of patients. None is known to have developed cancer.

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Youre probably asking:

Actually, a 2011 studyfound the same cancer-causing mutation, in a gene called TP53. But the study examined a single embryonic stem cell line, said biologist Jeanne Loring of the Scripps Research Institute, who led that research.

Three patients blinded by stem cell procedure, physicians say

You start with cells from a days-old human embryo, a hollow ball of 200 or so cells. You remove the stem cells, which are genetically identical, and grow them in lab dishes. The cells divide and proliferate. All of these progeny constitute a cell line. In 2009, President Obama approvedthe use of federal funds to create such lines from embryos that were going to be discarded by fertility clinics or were donated by couples and met ethical criteria.

Scientists led by Kevin Eggan and Steven McCarroll of Harvard University zeroed in on the 182 supposedly healthy human embryonic stem cell lines that meet Obamas criteria and were registered with the NIH, they reported in Nature online. They obtained those they could (the NIH registry is just a list; you have to get the actual cells from the labs that made and own them) and did DNA sequencing on 114. They also did DNA sequencing on another 26 lines that had been prepared for human experiments. Of these 140, five had cancer-causing mutations in the TP53 gene.

Patients do not receive embryonic stem cells; they get cells that those stem cells turn into, like pancreas cells or neurons or heart cells. The problem, Eggan said, is that as stem cells grow in lab dishes they have a propensity to acquire the same kind of genetic mutations found in human cancers. The final type of cell liver, lung, pancreas, and anything else will inherit the mutations, conferring a very real risk of causing cancer in the patient who received the cells.

You might think otherwise if you received cells from any of the five. In fact, some cell lines have been used more than others, so five out of 140 might understate the risk. Two of the lines most widely used in research, called H1 and H9, both have thecancer-causing mutations. H1 was used in a famous clinical trial by the biotech company Geron for spinal cord injury. That study was abandoned in 2011, after five patients received cells, but picked upin 2014 by Asterias Biotherapeutics. H9 is the source of cells in a clinical trialfor macular degeneration. Other stem cell lines with TP53 mutations are in line for use in other trials. No one knows how many patients have received cells from lines with TP53 mutations.

A spokesman for Asterias told STAT that Geron and now Asterias have followed the original five patients and have seen no evidence of tumor formation. Asterias is giving all participants in the ongoing trial frequent MRIs to look for tumors. WiCell, a nonprofit associated with the University of Wisconsin that owns and supplies the H1 line, said it was unaware of the new findings. We always want to do what is best for the research community, said Robert Drape, executive director of WiCell. Once we have an opportunity to review [the] publication, we will consult leading researchers in the field and determine the appropriate next steps.

They started seeing cancer-causing mutations in stem cells about 10 months ago, McCarroll said, and we shared the results ahead of publication, including telling stem cell scientists about the problem at a meeting last fall. Scientists who control some of the lines have begun their own DNA testing, he said.

Scrippss Loring said there was no reason to say the sky is falling. There are ways to ensure cells are healthy before theyre implanted in patients. But NIH cancer geneticist Dr. Stephen Chanock suggested that TP53 mutations might be just the tip of the iceberg: We cannot rule out the possibility of additional, less frequent acquired [mutations] in other cancer genes, he wrote in Nature in a commentary.

Drive to get more patients experimental stem cell treatments stirs concern

Those are called induced pluripotent stem cells; they come from the cells of already-born people. Unfortunately, any such cells that grow in the lab long enough can accumulate cancer-causing mutations, Loring said. Perversely, cells that do acquire cancer mutations survive better than cells that dont.

Neither the Harvard scientists, nor Loring nor Chanock, believe the discovery of cancer-causing mutations in stem cells should derail stem cell therapies. But the Food and Drug Administration does not require researchers to sequence the DNA of cells before putting them into people, mandatingonly testing for abnormal chromosomes. Thats a mistake, Loring said. We need to use the tools we have to make sure we dont screw up somebody were trying to cure, by giving them cancer. In her own research testing iPS cells as a treatment for Parkinsons disease, we are doing tons of quality control to be sure nothing bad slips into people, she said. You have to check your cells even though the FDA does not require it.

DNAsequencing to catch cancer-causing mutations in stem cells costs about $1,000 per genome. Regulators in both Europe and the US are considering making that mandatory, said Pete Coffey of University College London, who is studying the use of stem cells to treat eye diseases. Although a 5-in-140 risk may seem small, regulators are going to ask [researchers who propose clinical trials] what are you going to do when it goes wrong, not if.

McCarroll and others think not.There is something very different about the environment of cells growing in a lab dish versus the body, he said. But suddenly discovering cancer-causing mutations in cell lines that have been around for nearly two decades is nevertheless enough of a surprise to underscore the need for regenerative medicine to proceed with care, Eggan said.

Sharon Begley can be reached at sharon.begley@statnews.com Follow Sharon on Twitter @sxbegle

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Cancer-causing DNA is found in some stem cells being used in patients - STAT

New hope for victims after DNA links accused sexual attacker to crime. Image from Boynton Beach Police Department.

A Palm Beach County judge denied Bond Wednesday for a man charged with sexually assaulting a teenage girl in 2015.

Boynton Beach Police say Miguel Antonio Guzman, 41, was arrested this week in Boynton Beach by U.S. Marshals.

Guzman was arrested for the September 23, 2015 home invasion and sexual assault of a teenage girl.

Police said DNA evidence proves Guzman is the attacker.

It was very significant, said Thomas McKinlay, a Crime Scene Investigator with Boynton Beach Police Department.

Investigators say the unidentified teenage girl was home alone September 23, 2015 when she heard noise in her house. When she went to check out what the sound was, officers say the girl was then confronted and assaulted by a man now identified as Guzman.

Once he finds there is a young lady there on her own, he then obviously seized the opportunity to try to sexually assault her, McKinlay said. In the struggle, he partly undresses her and in her struggle with him, she scratched him in the groin.

McKinlay said the act of scratching and fighting back produced just enough blood from the suspect for police to test, a crucial piece of evidence that eventually led this week to Guzmans arrest.

It does give victims hope, theres no two ways about it, victims have to be rest assured, in this particular case, this is a young girl, as opposed to an adult whose more experienced with life, this must have been exceptionally terrifying for her, as a result it must make her feel better that her assailant has now been apprehended and will answer for a despicable attack on her, McKinlay said.

Investigators say after initial analysis of the DNA, the information was put into a law enforcement database. In July 2016, Palm Beach County Sheriffs Office got a confirmed hit, a link to an identity. Police tracked down Miguel Antonio Guzman, who in October 2016 provided a DNA sample and his version of what happened.

Guzman stated that he never broke into anyones home, a Probable Cause report states. I showed Guzman a picture of (redacted) and he stated that he knew the girl but never met her. He stated that he used to smoke weed with her father. Guzman knew the house that the victim lived at bus said he was never in the home.

Police say after taking a direct DNA sample from Guzman at that time, results came back April 6, 2017 confirming Guzman is the man who attacked the teenage girl.

It is an arrest a year and a half in the making. McKinlay said despite the time it takes to analyze and wait for results, it should allow victims to keep hope that no matter the days and months that may pass, that there is still hope for them to find peace and justice.

It does give victims hope, theres no two ways about it, McKinlay said. Victims have to be rest assured, and in this particular case, this is a young girlthis must have been exceptionally terrifying for her, and as a result it must make her feel better that her assailant has now been apprehended and will answer for a despicable attack on her.

Read more from the original source:
New hope for victims after DNA links accused sexual attacker to crime - WPEC

During and after the war, he used alcohol to numb the pain; as Presley grew up, so did she.

"I've always felt like I inherited this sadness that wasn't my own," said Presley, 38, now a teacher in Atlanta.

Presley was diagnosed with PTSD in 2010, and the idea that trauma can be passed down generations has long hit close to home.

For those who develop PTSD, the fear and stress of trauma doesn't go away.

"But I have not put all my eggs in the genetic basket," she said.

While the vast majority of the people in the study had experienced trauma, only a quarter of them had been diagnosed with PTSD.

Using common genetic markers, the study found evidence of a genetic risk for PTSD, but Koenen said she would need an even bigger group of people to identify the specific genes involved.

Her goal for the next study is to include up to 75,000 people, with roughly a third carrying a diagnosis of PTSD.

"Were looking at millions of places along the genome," Koenen said. "You need a lot of people" to see a clear signal for individual genes.

But for white men and all African-Americans, the researchers were unable to tease out statistically significant results from their DNA -- even though African-Americans comprised roughly half of the people in the study. This may be because prior research has largely focused on white populations, the authors noted.

The difference between men and women in this study may not be entirely explained by gender, Koenen said.

Many men in the study, but very few women, came from the military -- where service members may have experienced very different types of trauma from the general population, she said.

"Is it a military-civilian difference, or is it a male-female difference?" Koenen asked.

By unraveling the link between genetics and mental illness, researchers hope to find new ways to diagnose, prevent and treat disorders like PTSD, Koenen said.

While the research is still in its early stages, Koenen and her colleagues -- some of whom hold patents and have ties to pharmaceutical companies -- hope that they might one day identify new targets for drug development. Because of the potential genetic overlap with other psychiatric conditions, like schizophrenia, researchers are also on the lookout for shared pathways.

They also hope to find molecules that might allow doctors to measure and track the progress of mental illness. These molecules are known as biomarkers.

"Everybody has been searching for biomarkers for PTSD, but maybe the inability to find a single biomarker is because you have to stratify people according to their genetics," said Yehuda.

But looking at genetic risk has not been without some controversy, she said.

"People criticized me like you can't imagine," Yehuda said. "The minute you throw in that it's not about the trauma, (people worry that) we're jeopardizing veterans' benefits, torts cases, victims' rights -- it has to be about the event."

"You couldn't stay on that perch too long," she added. "There's too many individual differences in responses (to trauma)."

"Maybe genetics can help us clean that up a bit," said Yehuda.

However, some experts caution that focusing too much on common genetic variants may not have the therapeutic payoff these researchers are hoping for.

Willsey's research at UCSF focuses instead on rare genes, not common ones. While common genes as a group may have a greater impact on our health, he said, some researchers suspect that each rare variant holds more weight by itself.

"Rare variants are not going to be present in every patient, but the effect is going to be higher," he said, adding that neither set of genes tells the whole story by itself.

"At the end of the day ... what is really necessary is a complete picture of both common and rare variants so that we can have an integrated understanding of the biology."

After she published the book, responses from veterans' families came pouring in.

"It was such a huge epiphany to me that I wasn't alone," Presley said. "There has been such a focus on veterans and PTSD in the media, which is great, but somehow the missing piece is how that PTSD also affects a person's family."

Presley said that, through her difficult experiences, there have been additional positives. As a schoolteacher, for example, she said that her "hypersensitivity" has allowed her to read her students and be a more effective educator.

"It was like I was born with that," she said. "I have worked in some of the most challenging schools in Georgia, and I do not have classroom management problems because of my ability to read situations before they happen. That's been a huge positive that has come out of this."

Harvard's Koenen also comes from a military family. Her grandfather served in World War II, and her father served in Vietnam. Her cousin entered the military right out of high school and was sent to Iraq, where he developed PTSD.

"He never thought he'd be deployed," Koenen said. "It really changed the course of his life."

But Koenen's cousin has found some hope in her research, she said.

"It just makes him feel really encouraged that perhaps future generations of soldiers and veterans won't have to suffer as much as he has," she said.

More here:
PTSD risk may be passed down through our DNA - CNN

A man suspected of breaking into a Boynton Beach home and assaulting a 15-year-old girl in 2015 has been tracked down and arrested, Boynton Beach police say.

The alleged victim reported the crime Sept. 23, 2015. She said a man with a knife broke into the residence, intended to rob it and ended up molesting her. She said during the encounter she struggled and thought she scratched him a few times.

After police arrived, investigators collected DNA evidence.

Results were later sent to a database to see if there was a match.

Several months later police said that they learned the DNA matched Frank Williams, an alias for Miguel Guzman.

In late 2016, police eventually found Guzman and obtained his DNA through a search warrant.

In April 2017 police said that they learned the sample from Guzman and the DNA recovered at the scene of the home invasion were a match.

The U.S. Marshal's South Florida Fugitive Task Force arrested Guzman Tuesday.

Police have charged him with burglary while armed and lewd or lascivious battery on a person under 16-years-old. He's being held without bond in the Palm Beach County Jail.

See more here:
DNA leads to suspected molester's arrest, Boynton Beach police say - WPTV.com