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

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I just came across an article distributed by the National Public Radio (NPR) about a scientific beak though in DNA sequencing. This article just goes to show that DNA can answer current question about crimes, relationships and health but it can also help us look into our past.

Scientists have used DNA lurking inside the teeth of medieval Black Death victims to figure out the entire genetic code of the deadly bacterium that swept across Europe more than 600 years ago, killing an estimated half of the population…

People back then had no access to modern antibiotics and were likely weakened by other infections as well.

Poinar says the ancient Black Death DNA looks so similar to Yersinia pestis that still infects people today that researchers believe the medieval strain must be the ancestor of all modern strains.

The Natural History Museum of Denmark’s Thomas Gilbert says the insights that come from these studies will be of interest not only from a historical perspective, but also to help scientists understand how deadly epidemics have emerged in the past so that they can get ready for what might come in the future.

For the full story see: Decoded DNA Reveals Details Of Black Death

While this field of research might not seem very practical at first glance there is a wealth of knowledge about, diseases, bacteria and the ways we interact with them and how they spread and change.

I thought that the “Is It Local?” comedic skit on the television show, Portlandia, took local dining to a new extreme.  However,  I recently came across an article about consumers who are willing to pay for a DNA test to confirm the source of their meet. This demand has pushed DNA tested, traceable, meat onto restaurant menus.

DNA-traceable meat is not a new technology, as it has been used in Europe and other countries for decades, but has been slow to catch on in America. This is beginning to change  according to industry experts. These experts say that DNA-traceable meat can pay off in multiple ways, including boosting consumer confidence, upping the value of a dinner, and cutting the time needed to track recalled meats.

Tracy Tonning, executive chef at Blackstone restaurant in Iowa City, Iowa thinks that “People want to know where their food is coming from and this gives you a perfect avenue for you to go ahead and find out. You can trace it back to where it came from, where it was raised… It’s a security factor for the guest, as well as the chef.” Blackstone resturant is one of more than 11,000 locations being supplied with DNA-traceable beef by Richmond-based food distributor Performance Food Group. Performance Food Group is able to do DNA tracing because it is using smaller suppliers dedicated to producing meat for the company.

Performance Food Group tested their products in some of the steakhouses it supplies, as well as surveying outside other restaurants. These surveys and tests showed consumers were willing to pay $2 or $3 more for the same cut meat if various “pleasers” were added — a higher quality of meat, traceability, as well as how the animals were treated and fed. This value only came if the customer knew about it.

Phil Lempert, a food marketing expert says that DNA-traceable meat is ”really good marketing. The awareness in general is, in my opinion, at the highest level it’s ever been — from a health stand point, from a food safety standpoint. We really need to rebuild confidence in our food and technologies like this help that.”

The process work because workers take DNA samples at processing point as well as other places along the supply chain. The samples are gathered to determine the specific animals each product came from. In addition information kept by farmers and others involved in the raising and processing of the animals can be added to give a more complete history.

In addition to rebuilding confidence in our food chain DNA tracing would also provide a faster way to identify the source of contaminated meat in the event of a recall. This could speed up the process from weeks or months to just hours. For example, it can identify the multiple animals whose parts were used in ground beef. Ground beef can be made up of meat from 1,000 different animals in a 10-pound box. DNA-tracing could point to particular animals and could even reduce the amount of meat affected by recalls, which generally are tremendously costly for producers, suppliers and others.

Read more: VA-Based Food Distributor Using DNA To Track Beef

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.

Cocoa Plant BeansThe Cacao plant, that makes our beloved chocolate, has officially had it’s DNA sequenced. Oddly enough, more than one team of scientists, both of whom claim they were the first, has completed it.

In 2010, a team of researchers financed by MARS, the candy maker, announced that they had competed the sequencing of the Cacao plant. However, another candy maker, Hershey, also financed a group of scientists who completed and published their findings in the journal “Nature Genetics”. The Hershey team claims that they had completed the task first, yet they did not release their findings first as they wanted to go through the full peer review process before publishing.

Regardless of this Chocolate pioneering augment, the fact is that both teams were first since they sequenced different strains of the cacao plant. The Hershey team sequenced an ancient Mayan variety that was domesticated about 3000 years ago and team MARS sequenced the Matina chocolate plant which is supposed to represent the cultivar from which most cocoa in the world is cultivated.

So, why sequence this plant? Why sequence any plant? That topic is hotly debated. In theory, understanding and gaining genetic insights to cocoa can help aid in creating more disease resistant plants which can help farmers grow more cocoa since they would not be losing as many crops. And, crazy enough, it has been reported that they have also isolated the gene that determines the melting point of chocolate, which could help in a number of ways, including genetically modifying the plant so that scientists can change the melting point for whatever purpose suits a candy maker’s fancy.

Regardless of your feelings and thoughts about the sequencing of this fine plant, the truth is that every plant will eventually be sequenced and it’s no surprise that the chocolate plant was at the top of the list.

(Blog based on reports by the New York Times on December 27, 2010 and Genome Web Daily News on September 15, 2010.)

By Brooke Hayles

What do you think of when you hear about DNA testing? Is it specified testing that looks for DNA sequences? Your genetic information is inside every cells.

Deoxyribonucleic acid is the scientific name for DNA, and it determines each cells behavior, function, and structure. What is great about DNA is that not only can it tell the identity of a person, and their relationship to others, but it can also give information about thousands of genetic conditions and diseases. Because DNA testing is becoming cheaper, it is becoming more popular.

There are many uses of DNA testing, such as to establish paternity. Paternity can also be established in an unborn child. This is done with amniocentesis or CVS (Chorionic Villi Sampling). The CVS test is generally done in the early stages of a pregnancy between ten to thirteen weeks along. While the amniocentesis is generally done between the fourteenth and twenty-fourth weeks of pregnancy.

Breakthroughs with DNA testing happen often. One DNA tests that has been gaining in popularity is ancestry DNA testing. Our DNA comes from both of our parents. Most areas of our DNA go through changes. However, there are some areas of the DNA do not change at all or change very slowly. By looking at the changes and at the DNA that does not change, ancestry testing is able to link many generations together and reconstruct the history of families.

DNA testing has also become popular with people who have been adopted. DNA testing can allow them to trace their ancestors and find biological parents.

To perform most kinds of DNA testing, a cotton swab is rubbed on the inside of the clients’ mouth.  It is painless, easy, and quick, this means even a baby can undergo testing. The cheek swab contains skin cells that have the same DNA material that is in blood. Then the swab is sent to the laboratory to analyze the DNA in the cells, and determine if there is a match between the people participating in that test.

DNA is also used to solve crimes. DNA testing has been used to prove guilt or innocent in those that stand accused of crimes.

DNA testing has been used to conduct an evaluation of health risks and health. The tests can even aid a person in loss by defining foods they crave.

Scientist are now saying that, Humans may have originally caught malaria from gorillas.  This is based on research that examined malaria parasites in great ape feces.  It was originally thought that the human malaria parasite split off from a chimpanzee parasite when humans and chimpanzees last had a common ancestor.

Scientists have found that the DNA of malaria from western gorilla was the most similar to human malaria parasites.  Scientists had assumed that when the evolutionary tree of humans split off from that of chimpanzees – around five to seven million years ago the malaria parasite had already jumped species.  But new evidence suggests human malaria is much newer.

Malaria disease that is caused by a parasite called Plasmodium, this parasite is carried by mosquitoes and is contracted when a person is bit by a mosquito.  Over 800,000 people die from malaria each year in Africa.

To study the DNA of malaria in wild apes, you cannot use blood samples. So researchers collected 2,700 samples of faecal material from both western and eastern gorillas as well as from chimpanzees and bonobos.

They sequenced Plasmodium DNA from the faeces with techniques that use a large sample, and drew a genetic family tree to see which parasites were related.  ”When we did conventional sequencing, the tree didn’t make any sense, because each sample contained a mixture of parasites,” Said Dr Beatrice Hahn of the University of Birmingham, Alabama.

Researches diluted the DNA so to isolate one parasite’s genome which represented in a single sample  From there they amplified the DNA, meaning that they were able to separate the DNA from different species of the parasite much more effectively.

Comparing both methods they found that looking a the larger sampling tree method made much more sense.

They found that the human Plasmodium was not very closely related to chimpanzee Plasmodium,but that the human strain was very closely related to one out of three species of gorilla Plasmodium.  Specifically the strain from western gorillas in Central and West Africa.

Researchers discovered that there was more genetic variety in the gorilla parasites than in human parasites.

The study which was published in Nature, and while it provides a lot of answer researchers are going to investigate further.  They want to see exactly how different the gorilla and human parasites are and to determine if cross-infection between humans and gorillas may be going on currently.

Members of the research team are hunters and loggers in Cameroon, who spend a lot of time in the forests to determine whether these workers carry malaria parasites from the gorillas, which would suggest that new infections from other species can still happen.

In a study published on September 2nd in HealthDay News the question of why some people are more likely to become addicted to opioid painkillers (like morphine, codeine or oxycodone) has now been partially unraveled by the Geisinger Health System in Pennsylvania.

For the study, Geisinger Health System researchers interviewed and analyzed DNA from 705 patients with back pain who were prescribed some kind of opioid painkillers for more than 90 days.

Geisinger Health System researchers found that the group most vulnerable to addiction has four main risk factors in common: age (being younger than 65); a history of depression; prior drug abuse; and using psychiatric medications. Painkiller addiction rates among patients with these factors are as high as 26 percent.

The researchers also looked at a gene located at chromosome 15 that had been linked with alcohol, cocaine and nicotine addiction. This study indicates that genetic mutations on a gene cluster on chromosome 15 may also be associated with opioid addiction.

According to Joseph Boscarino, an epidemiologist and a senior investigator at Geising’s Center for Health Research, “these findings suggest that patients with pre-existing risk factors are more likely to become addicted to painkillers, providing the foundation for further clinical evaluation.”  He Added, “by assessing patients in chronic pain for these risk factors before prescribing painkillers, doctors will be better able to treat their patients’ pain without the potential for future drug addiction.”

Obesity has become such a large problem world wide that in Britain there are children listed on the British social services ”at risk” register because it was assumed their parents were abusing them with deliberate overfeeding.  ”In one case, one of the children had been taken into care,” said Stephen O’Rahilly, a world expert on the genetics of obesity at the University of Cambridge.

But then his research team discovered the problem. The obese children had a section of DNA missing in their genetic code – a fault that produced a very strong drive to eat. ”They are very hungry children and very hard to keep healthy,” said Professor O’Rahilly.

The research, published in December, is the latest discovery in understanding better why some people are more likely than others to become overweight and obese.  A food-on-tap environment had contributed to the obesity epidemic but telling people to eat less and exercise more would not solve it, Professor O’Rahilly said, when about 70 per cent of body size and shape was determined by genetic inheritance.

Professor O’Rahilly’s team found the first genetic fault linked to childhood obesity more than a decade ago and showed that giving children the protein they lacked, leptin, led to weight loss.  While big genetic mistakes such as this were responsible for a small number of cases, for most overweight and obese people it was the result of a combination of many genetic variations with small effects, he said.

More than 60 of these variations have been identified and most appear to be active in the brain and to influence hunger, appetite and and satiety.  ”Some of these genes will be affecting your weight by only a pound,” Professor O’Rahilly said.

Professor O’Rahilly said obesity should be regarded as a ”heritable neuro-behavioural disorder” and he hoped genetic research would lead to new treatments which, with societal and lifestyle changes, would make it as manageable as blood pressure.

Researchers may have discovered a genetic equivalent  of the Fountain of Youth hidden in the DNA of centenarians.

Only 1 in 6,000 people reaches the century mark and just 1 in 7 million lives to be a supercentenarian (someone who is 110 or older). A new study, published online in Science, suggests that more people may have the right genetic stuff for extreme longevity.Click here to find out more!

This new study, looked at genetic markers called single nucleotide polymorphisms (SNP), in 1,055 centenarians and 1,267 younger people, all of European descent. The researchers found 150 genetic SNP variants which were linked to extreme longevity.

At first, the team identified only 33 SNPs found more often in people aged 90 to 114 years but not in a control group made up of people who will presumably live an average lifespan.  Thomas Perls, a geriatrician at Boston University School of Medicine who coauthored the new study, the researchers felt that they were still missing part of the story.

Biostatistician Paola Sebastiani of the Boston University School of Public Health devised a different statistical method to identify additional SNPs that would improve the team’s ability to predict longevity. The team tested their predictions on a separate group of centenarians and controls. With the 150 SNPs, the researchers could correctly predict who was a centenarian 77 percent of the time.

“77 percent is a very high accuracy for a genetic model, which means that the traits that we are looking at have a very strong genetic base,” Sebastiani says. On the other hand, the 150 SNPs can’t explain why the remaining 23 percent of centenarians in the study have reached such ripe old ages. It could mean that those people have other, rare genetic variants or lifestyles responsible for their longevity or some combination of the two, she says.

Extrapolating these results to try to predict how long the average person will live would be a mistake, says Nicholas Schork, a statistical geneticist at the Scripps Translational Science Institute and the Scripps Research Institute, both in La Jolla, Calif.  “They’ve identified markers for something, but what that something is remains a mystery,” Schork says. How the combination of genetic markers work together to extend health and life “is the zillion-dollar question.”

Don’t expect the genetic data to lead to a Methuselah pill, Perls says.  “I look at the complexity of this puzzle and feel very strongly that this will not lead to treatments that will get a lot of people to become centenarians,” he says. But the research could conceivably lead to treatments that delay diseases such as Alzheimer’s.

Supercentenarians (someone who is 110 or older) had nearly all of the longevity markers. But most of the over-100 crowd carried different combinations of SNPs that fell into one or more of 19 different genetic profiles. These results indicate that there are many different genetic combinations to longevity and that many different biological processes are involved, Sebastiani says.

The researchers had expected that centenarians would lack disease-associated variants, but that isn’t the case. Some of the genetic profiles correlated with extreme delays in the onset of diseases such as dementia, heart disease or cancer. Others seem to allow centenarians to withstand the effects of such diseases.

About 15 percent of people in the general population may actually have what it takes genetically to reach 100, says Perls. “If they’re not hit by a bus, if they’re not in a war, if they haven’t had some other accident happen, maybe they get to fulfill that,” he says. “Now, a bunch of those people may also need to not smoke and not be obese and a number of important lifestyle factors as well.”

Sebastiani says, “One can conjecture that genetically we’re built to live longer,” and longer life expectancies associated with improved public health measures seem to bear that out.

Other studies have shown that genetics account for only 20 percent to 30 percent of a person’s chances of living beyond age 85. Environmental factors, including lifestyle choices such as diet, smoking and exercise habits, are still the most important determinants of longevity.

A new study failed to provide answers after pursuing a genetic explanation for why one identical twin developed multiple sclerosis while the other stayed healthy.  Researchers created complete genetic blueprints for a pair of  identical twins, looking for differences that might explain why one developed multiple sclerosis and the other did not. According to researchers there were no traces of a discrepancy in the twins’ DNA.  Scientists found no smoking gun when they compared amount of gene activity between the twin with multiple sclerosis and the twin without. The results appear in a study published on April 29 in Nature.

According to Stephen Kingsmore, a geneticist at the National Center for Genome Resources in Santa Fe, N.M., and leader of the new study, “We looked under a lot of rocks and we found no differences that we could replicate.” Kingsmore went on to say that the findings “points to some novel environmental trigger that must be very important to the disease. We don’t know what it is.”

This study was small; it examines only three pairs of identical twins and  one type of immune cell known to be involved in multiple sclerosis. A telling difference between sickness and health might be found in other types of cells, says Esteban Ballestar of the Bellvitge Biomedical Research Institute in Barcelona, Spain.  Ballestar went on to say, “They are closing a door here, but I think, perhaps, the door should be open.” Multiple sclerosis is a disease where the immune system attacks and damages the myelin sheath that helps speed electrical communication between nerves, this is the equivalent of scraping the coating away from an electrical wire. The damage results in pain and symptoms such as loss of coordination and vision.

In the study, Kingsmore and his colleagues determined the entire genetic makeup of the immune cells called T cells from the female twin who had developed multiple sclerosis at age 30 and from her twin who had remained healthy. It was important that the twins were now old enough that the healthy one is not likely to develop the disease.

Identical twins share the same genetic makeup (it is believed that they have identical DNA), and the researchers confirmed that both women carried variants of genes already known to increase the risk of getting multiple sclerosis. Scientists had thought that maybe the sick twin had developed an additional mutation in her DNA that finally triggered the disease. But the team found no such mutations.