Daily Archives: May 8, 2013

From Britain to the Balkans, Europeans are part of one big family, scientists have learned.

Despite being separated by thousands of miles, they have shared ancestors dating back little more than a dozen generations.

Researchers compared the DNA of more than 2,000 individuals from all over Europe and found surprising levels of kinship between them.

As expected, the genetic relatedness of any two people diminished the further apart they lived. But even a pair of individuals in the UK and Turkey, separated by a distance of 2,000 miles, were likely to have relations in common who lived 1,000 years ago.

Italians turned out to be one of the most diverse groups, according to the findings. They tended to have lower levels of relatedness to one another and to other Europeans, possibly because of the long history of distinct cultures within the Italian peninsular.

In contrast, many eastern European showed subtly higher levels of relatedness. This may reflect the expansion of Slavic peoples into Europe more than 1,000 years ago.

"What's remarkable about this is how closely everyone is related to each other," said study leader Professor Graham Coop, from the University of California at Davis, US. "On a genealogical level, everyone in Europe traces back to nearly the same set of ancestors within a thousand years. This was predicted by theory over a decade ago, and we now have concrete evidence from DNA data."

Although the research focused on Europe, the same pattern is likely to apply to the rest of the world, he added.

Demographic shifts, historic migrations, physical barriers such as mountain ranges, and language differences all helped to separate people, said the scientists. However, the differences were relatively small.

"The overall picture is that everybody is related, and we are looking at only subtle differences between regions," said Prof Coop. The findings are published in the online journal Public Library of Science Biology.

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DNA data shows close family links

(File photo | The Associated Press) Sen. Orrin Hatch, R-Utah, wants an amendment to the immigration bill that would require the collection and filing of DNA samples from those seeking legal residency.

Washington Immigrants in the United States illegally who would seek permanent residency under an immigration reform bill before Congress would have to submit a DNA sample to be kept on file if Sen. Orrin Hatch has his way.

Hatch has submitted 24 amendments to the immigration package that he says will improve the bill, including one that would require the DNA test to be checked against criminal databases for anyone over the age of 18 who wants to gain provisional resident status.

"Inclusion of a DNA profile as part of any background check will ensure that decisions regarding residency status are made with fullest search of criminal activity and identification available," Hatchs office said in a memo describing his amendments.

The Senate reform bill, drafted by a bipartisan group of senators, would create a decade-or-longer pathway to citizenship for those in the country illegally as long as they pass through a series of hurdles and Americas borders are strengthened.

The bills first stop is the Senate Judiciary Committee, and its members have submitted hundreds of changes theyd like to see in the bill. Hatchs proposal would be the first to require DNA testing as part of the process to gain legal status, the initial step in seeking full citizenship.

The amendment quickly brought concerns from advocates for immigrants.

"Its a big difference to go from name and birth certificate to fingerprints and DNA," says Ali Noorani, executive director of the National Immigration Forum. "Its a slope that we have to be really careful with before we walk down it. ... To have a DNA database for people who the only thing they want to do is become Americans, seems a big step."

Gregory Chen, the director of advocacy for the American Immigration Lawyers Association, notes that the current bill already requires biographical information, including photos and fingerprints, for those applying for permanent status and Hatchs amendment would add significant burden and cost to the process.

"Why would they want to add this additional step when all those things would already be done," Chen said.

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Hatch bill seeks immigrants’ DNA

The history of Europe is written in its people's DNA.

The Huns and the Slavs made incursions into Eastern Europe about 1,500 years ago. Migrants moved from Ireland to England in recent centuries. Populations in Italy and Spain have been comparatively stable.

None of this is breaking news. But scientists were able to see it anew by examining the patterns of genes in 2,257 people now living in 40 countries on the continent.

It's surprising "how much past history was still evident in the patterns we've seen," said Peter Ralph, a computational biologist at USC who reported the findings Tuesday in the journal PLOS Biology.

Ralph and his former postdoctoral advisor, Graham Coop, a geneticist at UC Davis, conducted their analysis by looking at the Population Reference Sample data. The data include language and country-of-origin information for several thousand European people, along with DNA sequences covering 500,000 locations on the genome that are known to vary from person to person.

Coop and Ralph used computer programs to ferret out sequences that were identical or nearly identical and used the matches to figure out who was related to whom.

Following the DNA trails they encountered, the researchers were able to confirm that Europeans living near one another were more closely related than Europeans living farther apart.

They were also able to put a time frame on the genetic relatedness they saw, by examining the length of the DNA segments the people shared.

The DNA sequences you have in common with each of your parents are quite long, the chunks you share with each of your four grandparents are half as long, and the bits you share with each of your eight great-grandparents are half as long again.

"The longer ago an ancestor is, the shorter the chunk is likely to be," Ralph said.

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European migration evident in DNA patterns

The history of Europe is written in its people's DNA.

The Huns and the Slavs made incursions into Eastern Europe about 1,500 years ago. Migrants moved from Ireland to England in recent centuries. Populations in Italy and Spain have been comparatively stable.

None of this is breaking news. But scientists were able to see it anew by examining the patterns of genes in 2,257 people now living in 40 countries on the continent.

It's surprising "how much past history was still evident in the patterns we've seen," said Peter Ralph, a computational biologist at USC who reported the findings Tuesday in the journal PLOS Biology.

Ralph and his former postdoctoral advisor, Graham Coop, a geneticist at UC Davis, conducted their analysis by looking at the Population Reference Sample data. The data include language and country-of-origin information for several thousand European people, along with DNA sequences covering 500,000 locations on the genome that are known to vary from person to person.

Coop and Ralph used computer programs to ferret out sequences that were identical or nearly identical and used the matches to figure out who was related to whom.

Following the DNA trails they encountered, the researchers were able to confirm that Europeans living near one another were more closely related than Europeans living farther apart.

They were also able to put a time frame on the genetic relatedness they saw, by examining the length of the DNA segments the people shared.

The DNA sequences you have in common with each of your parents are quite long, the chunks you share with each of your four grandparents are half as long, and the bits you share with each of your eight great-grandparents are half as long again.

"The longer ago an ancestor is, the shorter the chunk is likely to be," Ralph said.

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Everyone on Earth is related to everyone else, DNA shows

DNA tests needed to identify river body

Wednesday, May 08, 2013

By Jimmy Woulfe, Mid-West Correspondent

DNA samples from people whose family members disappeared without trace in Limerick over 20 years will be used to try and identify skeletal human remains found by the river Shannon in Limerick yesterday.

Supt Frank OBrien said garda had no reason to suspect foul play but were keeping all options open in the investigation.

Deputy state pathologist Dr Michael Curtis will visit the scene this morning.

Garda have also called in forensic anthropologists to try and identify the remains.

Supt OBrien said: The remains... were exposed and not buried. We cannot say if the remains are that or a male of female at this stage. We do not know how long they have been there or what this person died from.

While we are treating the death as suspicious, we have no indication at this point to indicate any foul play.

It is understood some of the remains have been removed to another location to help in the forensic examination.

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DNA tests needed to identify river body

Artist Heather Dewey-Hagborg collects gum, hair, and cigarette butts from public places to extract DNA data and create 3D portraits based on genetics.

See anybody you know?

We can't help but leave our DNA all over the place. If you drop a chewed piece of gum or a cigarette butt, it might get picked up by artist Heather Dewey-Hagborg. She may mine it for DNA, analyze the results, and generate a portrait based on the data. That's either really spooky, really cool, or a bit of both.

Dewey-Hagborg's Stranger Visions project combines artistry and science while raising questions about genetic privacy. She starts by collecting genetic material from public places. She then analyzes it at a lab, mining the DNA for information like gender, ethnicity, and eye color.

The data is then fed into a custom computer program that translates the information into a 3D model of a face. That model is printed out in color using a ZCorp 3D printer. The results are disembodied faces, but they aren't exact copies of the person who dropped the DNA. Dewey-Hagborg describes it as a "family resemblance."

Stranger Visions all began with Dewey-Hagborg contemplating a stranger's stray hair. Combined with her viewing of forensics television programs like "CSI," and an interest in the issue of genetic surveillance, the artist decided to create the 3D portraits. It's a particularly unusual version of found art.

"Working with the traces strangers unwittingly leave behind, Dewey-Hagborg calls attention to the impulse toward genetic determinism and the potential for a culture of genetic surveillance," reads the project description. It's enough to make you think twice about brushing your hair in public.

Dewey-Hagborg has been working on the Stranger Visions project for over a year. She will be giving a talk at New York City community biolab Genspace on June 13 and showing her work at QF Gallery on Long Island starting on June 29. If you stop by, take a good look. You just might get a sense of familiarity about some of those portraits.

Heather Dewey-Hagborg stands with her DNA self-portrait.

(Via Colossal)

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Artist 3D-prints portraits from DNA left in public places

IPSWICH, Mass., May 8, 2013 /PRNewswire/ -- New England Biolabs (NEB) announces the release of the NEBNext Microbiome DNA Enrichment Kit, which uses a novel method to separate microbial DNA fromhost DNA, thereby reducing the high cost of sequencing microbiome DNA to a more practical level.

(Logo: http://photos.prnewswire.com/prnh/20090921/NE79207LOGO-b )

Microbiome samples are commonly dominated by host DNA (up to 99%). This complicates the genetic analyses of these samples, particularly total microbiome DNA sequencing studies. Since only a small percentage of sequencing reads pertain to the microbes of interest, obtaining sufficient sequence coverage of the microbiome DNA can become cost-prohibitive or even technically infeasible.

The NEBNext Microbiome DNA Enrichment Kit utilizes the MBD2-Fc protein, which binds to CpG-methylated DNA (including human genomic DNA) with very high specificity. The MDB2-Fc protein is attached to Protein A-coated magnetic beads, enabling quick and easy removal of the contaminating host DNA in about 30 minutes. The microbial DNA-enriched sample is then ready to be processed for multiple downstream applications, including next generation sequencing, qPCR and endpoint PCR.

"Although microbiome whole genome sequencing provides more information than other methods, such as 16S analysis, this method has proven difficult for many samples, due to the presence of contaminating host genomic DNA," says Fiona Stewart, Product Marketing Manager, Next Generation Sequencing at NEB. "The NEBNext Microbiome DNA Enrichment Kit makes it possible to substantially enrich samples for non-host, microbial DNA, while retaining microbial diversity, thereby improving the quality and cost-effectiveness of downstream analyses."

For more information, visit http://www.neb.com/microbiome

About New England BiolabsEstablished in the mid 1970's, New England Biolabs, Inc. is the industry leader in the discovery and production of enzymes for molecular biology applications and now offers the largest selection of recombinant and native enzymes for genomic research. NEB continues to expand its product offerings into areas related to PCR, gene expression, library preparation for next generation sequencing, cellular analysis, epigenetics and RNA analysis. Additionally, NEB is focused on strengthening alliances that enable new technologies to reach key market sectors. New England Biolabs is a privately held company, headquartered in Ipswich, MA, and has extensive worldwide distribution through a network of exclusive distributors, agents and seven subsidiaries located in Canada, China, France, Germany, Japan, Singapore and the UK. For more information about New England Biolabs visitwww.neb.com.

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New England Biolabs Releases the NEBNext Microbiome DNA Enrichment Kit

STONY BROOK, NY--(Marketwired - May 7, 2013) - Applied DNA Sciences, Inc. (OTCBB: APDN), (Twitter: @APDN), a provider of DNA-based anti-counterfeiting technology and product authentication solutions today issued its latest progress update to its program for SigNature DNA-marking of electronics supplied to the U.S. Defense Logistics Agency (DLA).APDN lists forty-two electronics companies that are either under contract, have entered into contract negotiation, or have requested and received a SigNature DNA quotation.The companies include Original Equipment Manufacturers (OEMs), Original Component Manufacturers (OCMs), and as designated by DLA, Qualified Manufacturers (QML), including both qualified independent and authorized distributors.

DLA announced in late January that it would subsidize costs for companies implementing SigNature DNA marks.Once the reimbursement policy was instituted, and initial DNA-marking customers trained and certified, APDN began incremental DNA shipments in March.

APDN noted that both the number and rate of contract signings have increased since the reimbursement policy was announced.The accelerated sales cycle is a sign of additional momentum in the DNA-compliant electronics vertical.Other developments include the recruitment of a second company providing third party SigNature DNA marking services and increased efficiency in the certification times for onboarding customers.

APDN stated that 10 companies have now signed contracts to provide SigNature DNA marking on parts provided to DLA, while 9 more have contracts under negotiation, and 23 possess requested quotations for DNA.(APDN noted that the negotiation process does not guarantee or automatically lead to a signed agreement.) These suppliers also support U.S. Department of Defense prime contractors and other military/aerospace companies.Many are looking to expand their SigNature DNA-marking capabilities beyond DLA and offer the forensically secured supply-chain platform to their existing and new OEM and Contract Manufacturer (CM) customers.

Manufacturers using the SigNature DNA platform will use an Authentication Mark, forensically verifying originality of a component anywhere along the supply chain.Distributors are assigned a SigNature DNA Provenance Mark, verifying the immediate source of the part.The Provenance Mark assures the identity of the distributor and verifies that the distributor possesses original component manufacturer traceability or test method paperwork using the widely accepted anti-counterfeiting standard SAE AS6081.

The company notes that SigNature DNA is approved only for companies certified by DLA as trusted sources.As such, the APDN platform is closely linked to DLA quality programs, and is one piece in the effort to prevent counterfeit parts from entering the supply chain.Certifications of the DNA-compliance include the Qualified Manufacturers List (QML), the Qualified Products List (QPL), and the Qualified Testing Suppliers List (QTSL.)In order to qualify for QTSL, companies are required by DLA to implement SigNature DNA marking on designated parts.

Some members of the electronics industry resisted the requirement for DNA marking due to concerns over increased costs or process impact. Early adopters are seeing a rapid return on their investment, with increasing sales to DLA. APDN views the contract increment as evidence of increasing industry acceptance.

Dr. James A. Hayward, CEO and President of Applied DNA Sciences, stated, "I believe that our company's significant commitment of resources to aid the military electronics program is bearing fruit.Our road map for implementation began with the independent distributors, and continues systematically through authorized distributors, OCMs and the prime contractors. We are seeing steady progress in all categories."

Janice Meraglia, APDN Vice President for Military and Government Programs, stated, "We are now strongly branded in the electronics industry, and that brand is recognized and bringing more companies to us.We believe there is a large potential for this technology to transition to other high reliability supply, beyond defense, such as medical and automotive equipment."

About Applied DNA Sciences

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Applied DNA Sciences Expands Base for Signature DNA Marking of Electronics: Forty-Two Companies Rally to DNA Mark