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Category Archives: Transhuman News

How long can DNA last? A million years

Posted: October 11, 2012 at 11:17 am

In "Jurassic Park," scientists extract 80-million-year-old dino DNA from the bellies of mosquitoes trapped in amber. Researchers may never be able to extract genetic material that old and bring a T. rex back to life, but a new study suggests DNA can survive in fossils longer than previously believed.

The oldest DNA samples ever recovered are from insects and plants in ice cores in Greenland up to 800,000 years old. But researchers had not been able to determine the oldest possible DNA they could get from the fossil record because DNA's rate of decay had remained a mystery.

Now scientists in Australia report they've been able to estimate this rate based on a comparison of DNA from 158 fossilized leg bones from three species of the moa, an extinct group of flightless birds that once lived in New Zealand. The bones date between 600 and 8,000 years old and importantly all come from the same region.

Science news from NBCNews.com

Science editor Alan Boyle's blog: Next year, the committee behind the Nobel Prize for physics could have a huge Higgs hassle on its hands. And maybe that's a good thing.

Temperatures, oxygenation and other environmental factors make it difficult to detect a basic rate of degradation, researcher Mike Bunce, from Murdoch University's Ancient DNA lab in Perth, explained in a statement.

"The moa bones however have allowed us to study the comparative DNA degradation because they come from different ages from a region where they have all experienced the same environmental conditions," Bunce said.

Based on this study, Bunce and his team put DNA's half-life at 521 years, meaning half of the DNA bonds would be broken down 521 years after death, and half of the remaining bonds would be decayed another 521 years after that, and so on. This rate is 400 times slower than simulation experiments predicted, the researchers said, and it would mean that under ideal conditions, all the DNA bonds would be completely destroyed in bone after about 6.8 million years.

"If the decay rate is accurate then we predict that DNA fragments of sufficient length will preserve in frozen fossil bone of around one million years in age," Bunce said.

But he cautioned that more research is needed to examine the other variables in the breakdown of DNA.

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DNA leads to arrest in sexual assault of Santa Ana girl

Posted: at 11:17 am

A man was arrested Wednesday after he was linked through DNA to the sexual assault of an 8-year-old Santa Ana girl in her bunk bed, police said. The assailant climbed in through an unlocked window of her home.

Damien Anthony Reyes was arrested at his home in the 1300 block of North King Street after detectives were told there was a positive match on the DNA left at the scene of the June attack.

Reyes was booked at the Santa Ana Jail on suspicion of burglary, child molestation by force with enhancements that could lead to a potential life sentence upon conviction. He is being held in lieu of $1 million bail.

Authorities did not say how Reyes' DNA got into the state or federal DNA database. In most cases an arrest or conviction leads to a DNA sample being taken.

The noise woke up the girl's 13-year-old sister, who was asleep on the bottom bed, police said. Both girls screamed and woke up their father, who ran to their aid.

Detectives said the man immediately fled the house through the same window and was last seen running south.

Man found with body bags, smoke grenade at LAX investigated

Hazing probe launched after Fresno State fraternity pledge dies

-- Richard Winton

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DNA leads to arrest in sexual assault of Santa Ana girl

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DNA decay rate makes 'Jurassic Park' impossible

Posted: at 11:17 am

Researchers in New Zealand found that DNA decays far quicker than previously considered, making it impossible to salvage usable genetic material from dinosaurs.

Don't worry, we won't have to worry about this scenario in the future.

Countless childhood dreams dissolved today upon the news that the calculated half-life of DNA figures out to around 521 years, all but invalidating the chances of a real-life "Jurassic Park."

The DNA fact-finding project involved a team of palaeogeneticists testing 158 leg bones belonging to three species of extinct giant moa birds ranging from 600 to 8,000 years old.

After running a series of comparisons between the age of the various bones and DNA degradation within each specimen, the researchers estimated that DNA's half-life works out to about 521 years after being kept in a swamp with an average temperature of 13.1 Celsius (55 Fahrenheit). Even a more ideal preservation temperature of minus 5 Celsius (23 Fahrenheit) would only result in readable DNA from specimens up to 1.5 million years old, meaning there is no possible way we can see a 65-million-year-old T-Rex waving its tiny arms about in this time frame.

DNA breaks down for a variety of reasons, including degradation from external influences such as temperature, water, soil chemistry, and so on. After half a millennium, the researchers assume that DNA continues to degrade as the nucleotide bonds within break in half. Each 521-year segment serves as another chapter of nucleotide structure breakdown and carries on until the bonds no longer exist. However, science has yet to determine the breakdown speed of DNA in environments that are more supportive of preservation, such as permafrost.

Morten Allentoft at the University of Copenhagen and Michael Bunce at Murdoch University in Perth, Australia, worked with a large team on the findings, which were published today in the Proceedings of the Royal Society B science journal.

(Via Nature)

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DNA decay rate makes 'Jurassic Park' impossible

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Murder accused's DNA 'on victim'

Posted: at 11:17 am

10 October 2012 Last updated at 12:37 ET

DNA representing a one-in-a-billion match to that of a retired teacher and the man accused of her murder was found on her hand, a court has heard.

A "full DNA profile" of Stephen Farrow, 48, was found on a swab taken from the back of Betty Yates's left hand following the discovery of her body.

Farrow denies the murders of Mrs Yates, in Worcestershire, and the Rev John Suddards, in South Gloucestershire.

He claims he saw 77-year-old Mrs Yates two days before she was killed.

She was found stabbed to death in her cottage, in Bewdley, on 4 January, having been killed two days earlier.

Farrow, of no fixed address, claims he saw Mrs Yates on 30 December, but Bristol Crown Court heard the location the DNA sample was found would make it "extremely rare" to get such a strong profile days later.

Forensic scientist Christopher McKenzie told the jury: "The DNA profile obtained showed a mixture of DNA from two people which matched the corresponding DNA profiles of Mrs Yates and Stephen Farrow.

"We found that it is a billion times more likely to have come from Betty Yates and Stephen Farrow than from Betty Yates and someone other than Stephen Farrow."

Mr McKenzie said given the strength of the DNA profile he would expect there to have been either direct physical contact between Mrs Yates and Farrow or for it to have come from a bodily fluid - potentially saliva or sweat.

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Citing privacy concerns, U.S. panel urges end to secret DNA testing

Posted: at 11:17 am

NEW YORK (Reuters) - They're called discreet DNA samples, and the Elk Grove, California, genetic-testing company easyDNA says it can handle many kinds, from toothpicks to tampons.

Blood stains from bandages and tampons? Ship them in a paper envelope for paternity, ancestry or health testing. EasyDNA also welcomes cigarette butts (two to four), dental floss ("do not touch the floss with your fingers"), razor clippings, gum, toothpicks, licked stamps and used tissues if the more standard cheek swab or tube of saliva isn't obtainable.

If the availability of such services seems like an invitation to mischief or worse - imagine a discarded tissue from a prospective employee being tested to determine whether she's at risk for an expensive disease, for instance - the Presidential Commission for the Study of Bioethical Issues agrees.

On Thursday it released a report on privacy concerns triggered by the advent of whole genome sequencing, determining someone's complete DNA make-up. Although sequencing "holds enormous promise for human health and medicine," commission chairwoman Amy Gutmann told reporters on Wednesday, there is a "potential for misuse of this very personal data."

"In many states someone can pick up your discarded coffee cup and send it for (DNA) testing," said Gutmann, who is the president of the University of Pennsylvania.

"It's not a fantasy to think about how, without baseline privacy protection, people could use this in a way that would be really detrimental," such as by denying someone with a gene that raises their risk of Alzheimer's disease long-term care insurance, or to jack up life insurance premiums for someone with an elevated genetic risk of a deadly cancer that strikes people in middle age.

"Those who are willing to share some of the most intimate information about themselves for the sake of medical progress should be assured appropriate confidentiality, for example, about any discovered genetic variations that link to increased likelihood of certain diseases, such as Alzheimer's, diabetes, heart disease and schizophrenia," Gutmann said.

The commission took on the issue because whole genome sequencing is poised to become part of mainstream medical care, especially by personalizing medical treatments based on a patient's DNA.

$1,000 GENOME

That has been driven in large part by dramatic cost reductions, from $2.5 billion per genome in the Human Genome Project of the 1990s and early 2000s to $1,000 soon. Several companies, including Illumina Inc. and Life Technology's Ion Torrent division, sell machines that can sequence a genome for a few hundred dollars, but that does not include the analysis to figure out what the string of 3 billion DNA "letters" means.

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Citing privacy concerns, U.S. panel urges end to secret DNA testing

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UConn Gets Grant For Genome Research

Posted: at 11:16 am

STORRS

In what could further bolster hopes of making the state a hub for genomics research, a University of Connecticut researcher has received a $9.3 million grant as part of the massive international effort to better understand the human genome.

With the four-year grant, Brenton Graveley, a professor of genetics and developmental biology at the UConn Health Center, will study the functions of the genome that essentially turn genes "on" and "off" at certain times and the role this has on disease.

It's one of 15 grants awarded by the National Institutes of Health as part of the Encyclopedia Of DNA Elements (ENCODE), a worldwide project that involves hundreds of scientists and is designed to catalog all the functional elements of the genome and learn more about the genetic origins of several diseases.

"It's a big grant," said Dr. Marc Lalande, director UConn's Stem Cell Institute, adding that it's one of the largest the Health Center has received. "But more important than the money, it really boosts our reputation in genomics around the country. The other institutes that were recipients are the best places in the country."

Graveley previously worked on the modENCODE project, an extension of ENCODE, in which researchers mapped the functional elements of the genomes of the fruit fly and roundworm.

The previous phase of the ENCODE project also featured a major contribution from a Connecticut researcher. Mark Gerstein, professor of biomedical informatics at Yale, had received three NIH grants to study the molecular interactions of the genome and the complex networks they form. His research also shed light on the degree to which a mother and father each contribute to a genome. His findings, along with those of the rest of the phase of ENCODE were released in September.

Work in genomics began in earnest in the state in the 1990s, when Connecticut resident Jonathan Rothberg founded CuraGen, one of the first genomics start-up companies. Researchers at Yale, UConn and Wesleyan have since produced several important studies in the field.

The possibility that the state could be a major player in the field gained further ground last year, when state officials announced that Maine-based Jackson Laboratory planned to build a research facility on UConn's campus.

One of the hopes for genomics research is that it will produce an accessible form of personalized medicine which will allow doctors to precisely and quickly diagnose patients and with little trial and error administer effective treatment. It would also give patients a better understanding of their genetic risks for certain diseases.

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Cheap genome sequences demand new rules on privacy

Posted: at 11:16 am

Peter Aldhous, San Francisco bureau chief In the era of the $1000 human genome, new rules will be needed to protect people's genetic privacy.

The US government and individual states should harmonize a mish-mash of laws to ensure a basic "floor" of genetic privacy protection across the nation, however the data information was obtained, the commission adds. For instance, if a volunteer has their genome sequenced for research, the information should have similar protection from prying eyes as if the analysis had been ordered by a doctor for diagnostic purposes.

Breaches in security of DNA sequence data held on computer systems are the most obvious threat. But in 2009, New Scientist pointed to another danger by simulating the surreptitious analysis of my genome: a colleague used commercially available services to extract DNA from a glass from which I had drunk, and analyse it for my genetic predispositions to disease.

We ordered a scan of about 1 million letters of my genetic code, but plummeting prices and advancing technology will soon make it feasible to obtain a full genome sequence in a similar way, at modest cost.

The new report comes down firmly against surreptitious genome sequencing:"[P]olicies should protect individual privacy by prohibiting unauthorized whole genome sequencing without the consent of the individual from whom the sample came."

This is part of a larger patchwork of regulation on genetic privacy that the bioethics commission wants to see overhauled.

Geneticists taking samples for research are not covered by HIPAA, but separate rules covering informed consent and the protection of research subjects. Researchers are usually careful to protect volunteers' privacy, but if breaches were to occur, those responsible would not be subject to the same criminal prosecution.

Without clear and consistent guidelines to protect personal genetic information, the bioethics commission fears that people could suffer harm - in part by keeping secret information that could help their doctors provide better treatment.

It was only when Grove developed a bout of pneumonia that she knew could lead to permanent lung damage for people with the condition that she broke down, explaining in a tearful phone call to a clinic why she needed an urgent prescription for antibiotics.

"If it's too difficult for those companies to operate, we may have a bottleneck in providing access to the patient who needs that information," she says.

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First whole genome sequencing of multiple pancreatic cancer patients has been outlined

Posted: at 11:16 am

ScienceDaily (Oct. 10, 2012) Whole genome sequencing -- spelling out all 3 billion letters in the human genome -- "is an obvious and powerful method for advancing our understanding of pancreatic cancer," according to a new study from TGen, Mayo Clinic and Scottsdale Healthcare published October 10.

The Translational Genomics Research Institute (TGen) demonstrated that the use of WGS "represents a compelling solution to obtaining detailed molecular information on tumor biopsies in order to provide guidance for therapeutic selection," concluded the study published by the journal PLOS ONE.

Examining three patients, the study spelled out the DNA of normal cells and compared that to the DNA of cells from biopsies of pancreatic adenocarcinoma (PAC), which makes up 95 percent of all pancreatic cancer tumors. Pancreatic cancer is the fourth leading cause of cancer death in the U.S.

Using next-generation sequencing, the study generated an average of 132 billion mappable bases, or data points, for each patient, resulting in the identification of 142 cellular genetic coding events, including mutations, insertions and deletions, and chromosomal copy number variants.

"This study is the first to report whole genome sequencing findings in paired tumor/normal samples collected from (three) separate PAC patients," said the report, which also was compiled with the collaboration of Mayo Clinic in Arizona, Arizona State University, and the Virginia G. Piper Cancer Center Clinical Trials at Scottsdale Healthcare, which is a partnership between TGen and Scottsdale Healthcare.

In all three case studies, the report found multiple potential therapeutic targets, highlighting the need to study the full spectrum of the genome and re-emphasizing the need to develop multiple avenues of therapeutics to match the specific medical challenges of each patient.

"Cancer, and specifically here pancreatic cancer, is a highly complex disease that ultimately will require a variety of treatment methods to control, and ultimately to cure," said Dr. Daniel Von Hoff, TGen's Physician-In-Chief, and Chief Scientific Officer for the Virginia G. Piper Cancer Center at Scottsdale Healthcare.

"This study shows that, as we continue to generate more information by sequencing the whole genomes of patients, we will continue to discover -- with ever more confidence -- the specific mechanisms that cause this cancer," said Dr. Von Hoff, one of the study's senior authors and one of the world's leading authorities on pancreatic cancer.

"We are very pleased to be working together with TGen in bringing hope and state of the art therapy to our patients at the Mayo Clinic Comprehensive Cancer Center," said Keith Stewart, M.B., Dean of Research at Mayo Clinic in Arizona, and the study's other senior author.

In the case of Patient 1, for example, genes previously associated with PAC were identified, including BRCA2, TP53, CDKN2A, MYC, SMAD4 and KRAS. But the study also made new discoveries. "Although BRCA2 mutations have been identified in PAC, the deletion we identify here in exon 10 of BRCA2 has not been previously reported," the study said.

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First whole genome sequencing of multiple pancreatic cancer patients has been outlined

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Research and Markets: Psoriasis – Thought Leader Panel 2012 – A Summary of Persepectives from 6 Key Opinion Leaders

Posted: at 11:16 am

DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/2r4sgn/psoriasis_thought) has announced the addition of the "Psoriasis Thought Leader Panel #22 2012-04" report to their offering.

Psoriasis Thought Leader Panel #22 summarizes the perspectives of 6 key opinion leaders who had attended Gene to Clinic (London), AAD, or both in 1Q2012, supplemented with comments from Panel #21 and publicly available data on key drugs in development.

The Panel Weighs in On:

- The pros and cons of sequencing IL23, IL17, JAK, other orals and topicals against their established 1st line biologicals.

- Increases and decreases in cardiovascular events associated with inhibitors of TNF, IL23, IL17 and IL12.

- Advantages/disadvantages of IL23/IL12 vs p19 inhibitors.

- Advantages of a pure IL12 inhibitor

- Advantages/drawbacks for broad vs subreceptor selective IL17 approaches.

- Combinations and immunosuppression

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High Levels of Blood-Based Protein Specific to Mesothelioma

Posted: at 11:16 am

Fibulin-3 Represents a Sensitive and Specific Marker for the Diagnosis of Mesothelioma, Offering a Potential Tool for Early Diagnosis, Monitoring

Newswise NEW YORK, October 11, 2012 Researchers at NYU School of Medicine have discovered the protein product of a little-known gene may one day prove useful in identifying and monitoring the development of mesothelioma in early stages, when aggressive treatment can have an impact on the progression of disease and patient prognosis.

This gene produces a protein, fibulin-3, that is present in levels four to five times higher in the plasma of patients with mesothelioma compared to levels in asbestos-exposed patients or patients with several other conditions that cause tumors in the chest, said lead investigator Harvey I. Pass, MD, the Stephen E. Banner Professor of Thoracic Oncology, vice chair of research for the Department of Cardiothoracic Surgery and division chief of General Thoracic Surgery at NYU Langone Medical Center. We didnt know anything about this proteins role in mesothelioma before this study, but it may be an extremely useful tool for monitoring patients under treatment and possibly even diagnosing the development of mesothelioma at early stages. This marker is as exciting as any biomarker in mesothelioma today and warrants further research and validation by the scientific community.

The study appears in the October 11 issue of the New England Journal of Medicine.

Malignant mesothelioma is a rare but aggressive thoracic cancer that can develop several decades after exposure to asbestos. Diagnosis is often delayed until patients begin to show symptoms, including shortness of breath, cough, chest pain and, in advanced stages, weight loss and night sweats.

Often, patients with mesothelioma seek treatment when the shortness of breath becomes a noticeable problem. At that point, an x-ray typically reveals fluid in the chest, but many doctors fail to inquire about asbestos exposure upon receiving this report. Rather, doctors initially associate fluid in the chest with pneumonia or other inflammatory conditions, further delaying diagnosis, Dr. Pass explained.

Despite advances in chemotherapy, radiation therapy, and surgical management for malignant mesothelioma, the median survival for patients diagnosed with mesothelioma remains 12 months.

There is a great need for something some marker or test that will heighten the alarm that a patient presenting with new onset chest fluid could have mesothelioma, Dr. Pass said. Our findings indicate that a simple blood test may lead physicians to ask questions about asbestos exposure and consider whether the medical history and symptoms are compatible with mesothelioma.

Dr. Pass and his team are dedicated to finding diagnostic biomarkers genes, proteins or other molecules that are not only different in people with mesothelioma compared with cancerfree individuals who have been exposed to asbestos, but also different when compared to individuals with a variety of conditions that could cause fluid in the chest other than mesothelioma.

Fibulin-3 is a protein that floats around outside cells, coating the cells and free floating in blood plasma and extracellular fluid. For the current study, the research team compared levels of fibulin-3 in two separate cohorts of patients who were exposed to asbestos through their jobs: a group of iron workers and other asbestos-exposed individuals in Detroit, and a group of insulators in New York. Both cohorts included individuals who had been exposed to asbestos but did not develop mesothelioma, as well as individuals with a confirmed mesothelioma diagnosis. The researchers found that fibulin-3 expression was markedly elevated in the plasma of the patients with mesothelioma compared with the plasma of patients without mesothelioma. But the researchers wondered if maybe the elevated fibulin-3 levels were associated with other conditions, in addition to mesothelioma, that are associated with the development of chest tumors.

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