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News and insights in the world of DNA and genetics for paternity, immigration and forensics

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On December 7, 1941 the Japanese struck Pearl Harbor in a surprise attack that decimated the US Pacific Fleet. Of the ships that were attacked few sank as fast or as completely as the Oklahoma, which listed and capsized within minutes after a rapid series of direct torpedo strikes.

Survivors from the Oklahoma described a surreal scene below deck of sloshing water and fuel oil, men trying to climb from the darkness through hatches, beating their way out with tools. Hundreds remained trapped in interior compartments. Of the dead on the Oklahoma, 36 were easily recovered and identified. The remainder were not able to be identified and were interred in communal caskets.

Approximately 74,000 soldiers from World War II still remain unaccounted for. About one-quarter of those are considered recoverable by the military’s Joint POW/MIA Accounting Command, the Hawaii organization that has relied on scientific and geopolitical changes to identify more than 600 long-lost MIAs since 2003.

The Joint POW/MIA Accounting Command’s military and civilian teams have tracked down aircraft wrecks and burial sites in remote locations, exhumed remains, and analyzed bone fragments and bits of material at the world’s largest forensic anthropology lab. They work with casualty offices from each branch to find survivors and collect DNA samples for matching. For each name, the military tries to locate at least two relatives who share a long-lasting form of DNA passed along maternal lines.

In Hawaii, Greg Berg, the forensic anthropologist who manages the joint command’s Central Identification Laboratory, cautions that the work to identify remains could take years, the process he warns is complicated by commingling of remains which is far more extensive than expected. Only five people have been definitively identified since 2003.

Still, “the commingling problems are not insurmountable, and [we are] confident in our abilities to eventually bring about case resolution,’’ Berg said by e-mail.

For more see: Boston Globe

In a move that seems deceptively futuristic, but is in fact a sign of the times, the Nazareth, Pennsylvania based Martin Guitar Company is making waves in their industry by including botanical genetic coding in the body of their instruments.

Generations of  the Martin family have been proudly making guitars since 1833.  The current management, headed by Chairman and CEO Christian Frederick Martin IV, recently decided that, in an attempt to continue to fight for their otherwise stellar reputation, they will implant each new instrument with a DNA tag designed to thwart counterfeiters and send a message that they will not watch their company’s reputation diluted by cheap knockoffs, coming predominately out of China.

Gregory Paul, the company’s vice president of operations said, ”"The Martin family has always been vocal about fighting overseas counterfeiters. They have had a particularly hard time persuading the Chinese Government to prosecute imitators who have been selling inferior products under the C.F. Martin name.” “The Internet makes it too easy for a counterfeiter or their distributor to offer even a handful of units to a very broad audience. Ads for these sites crop up every day.”

The genetic tagging was developed by Applied DNA Sciences a company from Stony Brook, N.Y., which pioneered the technology allowing manufacturers to mark their products with a unique trace of plant DNA. According to a spokesman for the company ”The DNA tag itself can be put into anything in the production process it can be put into ink, for labels on wine bottles. It can be put into glue or varnish or just about anything.”

Applied DNA is also working with the Department of Defense to put tags on microchip components that go into weapons systems in order to combat counterfeit chips that have been making their way into the military supply chain.

What we wonder is how, exactly, the instruments will be tested for authenticity and how much it will cost to do so. Furthermore, if DNA/genetic coding can be found in the guitar and used for genetic testing to confirm authenticity, then won’t counterfeiters be able to obtain and replicate the DNA from the instrument(s) and apply it to their own?

Big questions for a big future in genetics…

When President Obama announced Sunday evening, May 1st,  that Osama Bin Laden had been killed in a United States military operation, many wanted physical proof that the person killed and taken into custody was in fact Mr. Osama Bin Laden.

At this time reports are confirming 3 ways the remains were identified: 1) Facial recognition software was used to match the remains with facial photos of Osama Bin Laden. 2) There was apparently a personal identification of the body by someone inside the complex (exactly who identified the remains is unclear).  3) DNA testing of the remains took place within hours of death.

DNA Testing is now fast and accurate. It no longer takes weeks but can be done in the matter of hours and has a 99.9% or better accuracy rate.  At least one question remains – who, how or what did they test to confirm that it was Osama Bin Laden?  Did they test a family member against his DNA? There is speculation that they could they have tested the purported Osama Bin Laden sample against DNA from his sister, which (according to reports) had been held at Massachusetts General Hospital after her death in Boston last year. Or did they somehow already have Osama Bin Laden’s DNA on file and test against that?

According to Dr. M. Al Salih, who works at DNA Reference Laboratory in San Antonio, TX, he is sure that the results are accurate.  “You can come up with a very solid and absolute certainty that that is him and nobody else. If you identify that individual through those markers, and you can compare and you can say, ‘They match,’ or ‘They don’t match.’” Salih went on to state that the technology is very precise and results are 99.9 percent accurate.

However, on the other side is Dr. Greg Hampikian, a biology professor at Boise State University, says if they can get DNA from one of his kids and their mother then they do a reverse paternity test to confirm his identity and he suspects that is the type of DNA testing that was done. However even with a 99.9 percent identification Hampikian says that this case is not closed. As a scientist, Hampikian says 99.9 percent does not equal a positive identification.

As is the case with most major events such as this, skeptics speculate that we have not received enough proof and conspiracy abounds. One thing is for certain, we love conspiracies and we will never really know the truth.

That’s right April 25th is National DNA Day.  It was proclaimed by both the US Senate and the House of Representative in 2003 and while you might not have the day off you might want to stop and think about just what DNA has done for us.

DNA Day is a remembrance of the day in 1953 when a gound breaking article on the structure of DNA was published as well as the the day that the Human Genome Project was completed in 2003.

DNA has made big changes in our lives whether we know it or not.  So this April take some time to think about DNA and some of it’s many uses:

1. In archeology DNA helps record genetic information of life on earth many centuries ago. This creates a data base that can be used to learn more about our planets past.

2. Genetic testing is used to determine the paternity or maternity of a child.

3. DNA testing can be used to help create a family tree or genealogical chart. Through genetic data bases one can trace lost relatives or find ancestors. Using both the Y chromosome and Mitochondrial DNA people can use DNA testing to establish ancestral lines (both remain unchanged for generations).

4. Prenatal genetic tests can help doctors determine whether or not the unborn fetus will have certain health problems.

5. DNA tests are also used to help solve murders and other crimes. In recent years many unsolved mysteries have been solved due to new ways of analysis as well as clearing many people found guilty of crimes that the did not commit.

6. DNA testing finds great use in the health field as DNA sometimes is the cause of rare medical conditions or heritable diseases.

7. Genetic testing is used in healths checks. For example it can be used to help determine the presence of viruses or cells that have mutated (causing cancer).

8. DNA tests are often used to reunite lost siblings or families or identify remains of the unknown. The genetics of a person leaves an indelible mark and this is used by police, military and authorities as well as individuals to confirm relationships.

9. DNA tests on new species or on material from outer space help scientists and researchers determine the origins of a species and where they stand with reference to known living forms.

In 2009 a new laboratory was opened at the University of Otago it was expected to unlock secrets about the genetic heritage of Pacific people, animals and plants according to scientists and anthropologists.

The ancient DNA laboratory, allows scientists to extract DNA from bones, teeth and plant matter. The DNA will be analyzed using the latest technology, including the university’s $1 million gene sequencing machine which was purchased in 2008. The facility is a joint project between 3 departments.

Ancient DNA did not necessarily mean from antiquity, according to Professor Matisoo-Smith. In scientific terms, ancient means any DNA samples which were not taken from living subjects. Matisoo-Smith did go on to say that some of the samples the laboratory would handle would be thousands of years old.

Already, projects were planned with samples from many parts of New Zealand, several Pacific islands and from Chile.

Representatives of Maori iwi whose ancestors’ DNA will be analysed in the laboratory spoke of their initial reluctance to allow their ancestors’ remains to be analysed because of the intrusiveness of the process.  They did however agree to allow the DNA analysis after discussions with Prof Matisoo-Smith and her staff which allayed their fears.  Both sides are now hoping the laboratory would provide interesting information on how their ancestors lived, what they ate and what they looked like.

Respecting the remains of people from the past was paramount, said Prof Matisoo-Smith. An ultra-clean environment had to be preserved to ensure ancient DNA samples were not contaminated.

In just a year after opening, an international team of researchers, which includes University of Otago archaeologists Chris Jacomb and Richard Walter, successfully isolated ancient DNA from eggshells of extinct birds.

Previous attempts to recover DNA from fossil eggshell have been unsuccessful. Chris Jacomb said, “this new ability to isolate ancient DNA from moa eggshell opens up exciting new research possibilities not just for palaeobiologists, but also for archaeologists. Indeed, it was this potential to address important questions in New Zealand archaeology that drew Associate Professor Walter and me into this international collaboration.”

Using the DNA from the moa’s provides a powerful new tool in understanding how the demise of moa occurred. “Not only can we now match eggshell to particular moa species, we can develop detailed models of hunting practice by looking at the family relationships of individual birds. This will help us understand hunting and extinction processes.”

Ozzy Osbourne is the first rock star to give his DNA to science.  As reported in Scientific American in October 2010 Ozzy Osbourne has become one of the few to have their entire genome sequenced.  Osbourne’s DNA was sequenced and analyzed by  Cofactor Genomics and Knome Inc.  According to Knome’s analysis Ozzy Osbourne has some Neandertal in his DNA.

“For a long time we thought that Neandertals didn’t have any descendents today, but it turns out that Asians and Europeans have some evidence of Neandertal lineage—like a drop in the bucket,” Pearson told Scientific American. “We found a little segment on Ozzy’s chromosome 10 that very likely traces back to a Neandertal forebearer.”

Pearson went on to caution that we are very early on in this particular field and that it is going to be sometime before there is enough data to understand the human genome.

By Alex Blake

DNA testing is done for a variety of  reasons. DNA evidence can link an alleged criminal to a crime scene.  DNA paternity and maternity testing can identify a child’s father or mother. DNA relationship testing can determine if two individuals are from the same family. DNA ancestry testing can determine ethnic origins and genealogical roots.

How DNA testing is done depends on the what kind of results are desired and on what types of samples are available. DNA fingerprinting (or profiling as it’s also known) is the process of analyzing and comparing two different DNA samples. Only identical twins have the exact same DNA sequence, everyone else’s DNA is unique. This makes DNA the perfect way to link individuals to each other or to locations where they have been.

The entire DNA chain is incredibly long, much to long to examine all of it in one test. Human DNA is made up of about 3.3 billion pairs. The differences between DNA samples occur only in small segments of the DNA–the rest of the DNA is pretty much the same. DNA testing focuses on those segments that are known to differ from person to person.

As DNA testing has evolved over time, the testing methods have become more precise and are able to work with much smaller DNA samples. Early DNA testing was done using dime-size drops of blood. Today’s tests can extract DNA from a drinking container. The DNA is extracted from whatever sample is provided (some times there is not enough DNA to provide for testing). DNA must be isolated and purified before it can be compared. In essence, it has to be “unlocked” from the cell in which it exists. The cell walls are usually dissolved with a detergent. Proteins in the cell are digested by enzymes. After this process, the DNA is purified, concentrated, and then tested.

DNA testing is done most often today by using a process called “short tandem repeats,” or STR. Human DNA has several regions of repeated sequences. These regions are found in the same place on the DNA chain, but the repeated sequences are different for each individual. The “short” tandem repeats (repeated sequences of two to five base pairs in length) have been proven to provide excellent DNA profiling results. STR is highly accurate–the chance of misidentification being one in several billion.

By Alex Blake

DNA testing is done for many different reasons.  Sometimes DNA evidence can link an alleged criminal to a crime scene or DNA paternity and maternity testing can identify a child’s father or mother. While DNA relationship testing can determine if two individuals are full or half siblings and DNA ancestry testing can determine ethnic origins and genealogical roots.

How DNA testing is done depends on the results desired and the samples available. DNA profiling is the process of analyzing and comparing two DNA samples. Only identical twins have the exact same DNA sequence, everyone else’s DNA is unique. This makes DNA the perfect way to link individuals to each other or to locations where they have been.

The entire DNA chain is incredibly long, much to long to examine all of it. Human DNA is made up of about 3.3 billion base pairs. The differences between DNA samples occur only in small segments of the DNA–the rest of the DNA is very similar. DNA testing focuses on those segments that are known to differ from person to person.

As DNA testing has evolved over time, the testing methods have become more precise and are able to work with much smaller DNA samples. Early DNA testing was done using dime-size drops of blood. Today’s tests can extract DNA from the back of a licked stamp (in some cases) but is most often done by using cheek swabs.  These cheek swabs are easy to collect, painless and very accurate The DNA must be extracted from whatever sample is provided. DNA must be isolated and purified before it can be compared. In essence, it has to be “unlocked” from the cell in which it exists. The cell walls are usually dissolved with a detergent. Proteins in the cell are digested by enzymes. After this process, the DNA is purified, concentrated, and tested.

DNA testing is done most often today using a process called “short tandem repeats,” or STR. Human DNA has several regions of repeated sequences. These regions are found in the same place on the DNA chain, but the repeated sequences are different for each individual. The “short” tandem repeats (repeated sequences of two to five base pairs in length) have been proven to provide excellent DNA profiling results. STR is highly accurate–the chance of misidentification being one in several billion.

I just came across an article distributed by the Slate discussing the above topic. This brought my thinking to the use of DNA and the idea of anonymity in general.

DNA testing makes them easy to trace
By Rachel Lehmann-Haupt Last Updated Monday, March 1, 2010, at 9:36 AM ET

When Donor 3066 signed up with the California Cryobank, he offered some basic information about himself on a piece of paper: that he had a BA in theater; that his mother was a nurse and his father was in the Baseball Hall of Fame; that his birthday was Sept. 18, 1968. He made it clear that he didn’t want to be found by signing a waiver of anonymity…

Donor 3066 was being sought out by Michelle Jorgenson, a 39-year-old waitress from Sacramento, Calif., whose daughter, Cheyenne, was born in 1998.  When her daughter turned 5, Jorgenson joined the Donor Sibling Registry and began searching for other mothers and donor offspring who used Donor 3066. She was concerned because her daughter was sensitive to sounds and walked on her toes, and she wanted to know if other half-siblings were displaying similar behavior. Through the registry, she met a number of other mothers and half-siblings. She discovered that two had autism and two others showed similar signs of sensory disorder…

Jorgenson began her search by approaching a mother in her group with a son named Joshua and suggested he do a cheek swab so she could explore his paternal roots through a Y chromosome test. The mother agreed. Through the test, Michelle learned about some of Joshua’s genetic markers. A few weeks of searching on the Family Tree DNA Web site using these markers led to two families with matching DNA. Through one of the families, she met a woman who mentioned that she found the obit of a relative who was a former baseball manager, and three children were listed. Michelle suspected that this might be her donor’s father, so she looked up the phone number of his listed son. When Michelle called the number, the deceased man’s son answered the phone. She began to ask him questions: Was your father in the Baseball Hall of Fame? Were you born in Illinois? Did you ever donate sperm? When the man said yes, she asked him if his birthday was Sept. 18, 1968. When he answered yes, she burst into tears. “You’re the biological father of my daughter,” she said. He was shocked but agreed to talk to Cheyenne on the phone—and eventually allowed the two to come visit him in Los Angeles.

Although in this case there appears to be a happy out come for all parties this is not always the case.  What about the request for privacy that Donor’s sign up for when they choose to remain anonymous?  Is that even something that clinic should offer since there is no guarantee that the donor can’t be found?  What are the options for men who do become donors?  There are many questions that are raised in this article and very few answers, partly because technology is growing at such a fast rate and party because it appears in the article many clinics are ignoring this issue of privacy.  Let us know what you think about this issue.

Michelangelo Merisi da Caravaggio Baroque master’s death is surrounded in mystery, but that mystery may soon be solved thanks to DNA testing — as long as the right body can be found.

The caused of death for this famous painter in 1610 and the whereabouts of his corpse have always been unclear.  But a team of Italian anthropologists believe that what is left of Caravaggio’s body may be hidden among dozens of bodies buried in a crypt in Tuscany, thanks to recent historical clues.

The team using CAT scans and kits for carbon dating plan to study what they believe are the painter’s exhumed remains to discover how he died.  “If we are lucky enough to find Caravaggio’s skull, we will also be able to do a reconstruction of his face, just as we did in 2007 for Dante Alighieri,” Silvano Vinceti, head of the National Committee for Cultural Heritage, told Reuters.

The only images of the artist available until now have been self-portraits.  Scholars have put forward many theories about Caravaggio’s death. The most popular are that the painter was assassinated for religious reasons or collapsed with malaria on a deserted Tuscan beach.

However, in 2001 an Italian researcher claimed to have found the painter’s death certificate, which allegedly proved that he died in hospital.  “This historical document shows Caravaggio did not die alone on the beach but after three days in hospital, which means the body must have been buried in the San Sebastiano cemetery,” said Vinceti, referring to a Tuscan town near the city of Grosseto.

But in 1956, bodies buried at the tiny San Sebastiano graveyard were moved to a nearby town, Porto Ercole, and scholars hope that the remains of Caravaggio will be among them.

The team from the departments of Anthropology and Cultural Heritage Conservation at the universities of Ravenna and Bologna will have to examine the bones of between 30 and 40 people, selecting those that belong to young men who died at the beginning of the 17th century, to try and identify the painters remains.

“We will check the DNA extracted from the bones and teeth of possible matches against that of the painter’s male descendants,” Professor Giorgio Gruppioni, who will head the team, told Reuters.  “Sadly Caravaggio died childless,” said Gruppioni, “but his siblings had children whose relatives are still living in the northern Italian town that carries his name.”

Caravaggio, who pioneered the Baroque painting technique of contrasting light and dark known as chiaroscuro, is famed for his wild life. Legend has it that he was on his way to Rome to seek pardon for killing a man in a brawl when he died.

Based on the article by Ella Ide: DNA tests could solve mystery of Caravaggio’s death