Category Archives: DNA

DNA: Analysis of New Delhi #39;s alarming air pollution level
"New Delhi is breathing the most polluted air in the world, according to WHO report. The WHO found that 13 of the 20 most polluted cities in the world are in India, with New Delhi #39;s air being...

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DNA: Analysis of New Delhi's alarming air pollution level - Video

DNA Attempt, Will I Get It? EP3
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DNA Attempt, Will I Get It? EP3 - Video

DNA on Tryhards AK-12 recovery #1vs7
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DNA on Tryhards AK-12 recovery #1vs7 - Video

Court documents show strong DNA link between Jesse Matthew, Fairfax rape
As Jesse Matthew awaits his trial in the killing University of Virginia student Hannah Graham, some court documents in an unrelated rape case against him were unsealed Monday. http://bit.ly/1KNeywO.

By: ABC7 WJLA

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Court documents show strong DNA link between Jesse Matthew, Fairfax rape - Video

In a new study, researchers have shown that an innovative technique the use of DNA microcircles has the potential to detect a broad range of cancers in the earliest stages by forcing tumors to create a unique protein.

The proof-of-principal study from Stanford University Medical School used DNA microcircles, a customized genetic construct consisting of tiny rings of DNA. After injecting the microcircles into mice, researchers used a blood test to show that mice with tumors produced a substance that tumor-free mice did not.

With this approach, researchers are reversing the typical laboratory method of detecting cancer, senior study author Sanjiv Sam Gambhir, professor and chair of radiology and director of the Canary Center at Stanford for Cancer Early Detection, told FoxNews.com. With blood and urine tests, doctors must depend on detecting biomarkers that the tumor itself makes.

The challenge for those kinds of biomarkers is that theyre rarely very specific and often not made in sufficient quantities, Gambhir said.

For example, early detection of prostate cancer using prostate-specific antigen (PSA) is controversial because the biomarker is made even in normal prostate cells. Also, small tumors of any kind in the body may generate quantities of biomarkers that are too low to detect in blood or urine.

On the other hand, DNA minicircles work by forcing tumors to make something a protein that it otherwise wouldnt to detect the presence of cancer.

We flip the problem around. [Youre] no longer dependent on nature to make a molecule thats unique to cancer. Youre given a pill that forces cancer cells to make the molecule for you, Gambhir said.

For the purposes of their animal trial, Gambhir noted that a cancerous tumor one cubic millimeter in size, equal to about a grain of rice, would be detectable. For context, when a woman feels a mass in her breast, by the time shes able to feel it, its about a cubic centimeter in size. While researchers have yet to conduct trials with human participants, Gambhir said he hopes minicircles will be able to help detect early and stage 1 cancer.

The DNA minicircles, which are comprised of tiny rings of DNA, work by going into a cancer cell and turning on the cells machinery to make RNA. The RNA then makes protein, which in this case is secreted embryonic alkaline phosphatase (SEAP), which then serves as a cancer biomarker. While the microcircles infiltrate all cells in the body, healthy cells do not make SEAP because researchers added a switch, called a surviving promotor, that only activates in cancer cells. After minicircles are introduced to the body, the surviving promoter activates within about 48 hours to create SEAP. Eventually, the minicircles degrade and in about two weeks are no longer in the body.

Researchers say the minicircles are advantageous because they dont integrate with the host genome, which means they wont tamper with a healthy cells DNA.

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DNA rings may detect early cancer, researchers find

Lake County prosecutors plan to exonerate a man who has spent 20 years in prison for rape and abduction, a move that would lengthen the list of the county's criminal convictions wiped away by DNA evidence.

State's Attorney Mike Nerheim said he will go to court Monday afternoon and ask a judge to throw out the conviction of Angel Gonzalez, who has been serving a 55-year sentence for a 1994 rape and abduction in Waukegan.

The crime involved two suspects, and DNA test results that arrived late last week showed the presence of bodily fluids from two men, both of whom remain unidentified, Nerheim said. The prosecutor said it was "very clear" that the evidence indicates that Gonzalez, now 41, is innocent and contradicts the confession he gave and the victim's identification of him as one of her rapists.

Gonzalez, who is incarcerated at Dixon Correctional Center in northwestern Illinois, was speechless at first when he learned last week that prosecutors planned to clear him, said Vanessa Potkin, an attorney from the Innocence Project in New York who has represented him with the help of the Illinois Innocence Project at the University of Illinois at Springfield. Barry Scheck, co-founder and co-director of the New York group, said Gonzalez voiced sympathy for the victim and said he hoped that the perpetrators would be caught.

Gonzalez has maintained his innocence for decades, Potkin said.

"He's obviously anxious and excited to see his family again," she said.

If Monday's court hearing proceeds as planned, Gonzalez's conviction would be the fifth major felony case to collapse in the last five years after DNA indicated Lake County authorities had put an innocent man behind bars. Gonzalez, who lived in Waukegan, was tried during the 22-year tenure of State's Attorney Michael Waller, who retired in 2012 following revelations that prosecutors had disregarded forensic evidence that contradicted their conclusions and worked to prevent men from walking free even after DNA had indicated their innocence.

It is not clear whether Gonzalez will be freed after his scheduled appearance in Lake County court. He is a Mexican national who had once obtained a visa, but that expired after he was arrested, Potkin said. Attorneys have been working to try to make sure Gonzalez can remain in the country if he's freed, Potkin said.

Deporting him upon his release would be "a huge travesty of justice," she said, since he planned to seek citizenship before he was imprisoned.

"It's only the wrongful conviction that makes his status in the country illegal at this point," Potkin said.

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DNA clears another Lake County man

Maxilla and mandible of one of the three 17th century skeletons from the Caribbean island of St. Martin showing a common type of African dental modification. PNAS/H. Schroeder et. al.

To better understand the complex history of slavery, it helps to know more about the origins of millions of individuals who were shipped from their homes in Africa to plantations in the Caribbean, South America and the United States.

Historians have a good idea that 12 million or so slaves came from West and West-Central Africa between 1500 and 1850. But incomplete and scarce historical records have made it difficult to offer crucial details about the slaves' ethnic origins and the regions from which they were taken.

Now, a team of researchers says they have for the first time used a new DNA technique to fill in these gaps, which could provide further insight into the slave trade.

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Sixteen years after hundreds of remains were found, a national monument opens to the public

Writing in Proceedings of the National Academy of Sciences (PNAS) Monday, researchers led by Hannes Schroeder of the Centre for GeoGenetics at the University of Copenhagen described how they used whole genome capture to retrieve the DNA from 400-year-old skeletal remains of three slaves, known as the Zoutsteeg Three.

"There are historical records - merchant ledgers, shipping records and the like - but they tend to refer to coastal shipping points rather than the slaves' actual ethnic or geographic origins. This is where the DNA comes in," Schroeder said. "It can provide new insights where historical information is missing. In that way, DNA is simply another type of archive that we can use to study the past."

Schroeder and his team analyzed the DNA from teeth recovered from a construction site on the Caribbean island of Saint Martin back in 2010. They then used a different technique known as principal component analysis to compare that DNA with 11 modern West African reference populations. From that, they were able to conclude the individuals most likely came from Bantu-speaking groups in northern Cameroon and non-Bantu-speaking communities living in present-day Nigeria and Ghana.

When they were first uncovered, the remains of the three slaves were dated back to the 17th century by way of shards of pottery and other artifacts found at the site. It was also determined they were most likely slaves, given the time period and the fact their teeth had been filed, a common custom among Africans then.

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DNA analysis traces African slaves back to their roots

Modern humans share about 95% of their genetic code with chimpanzees. Yet human brains, and what we do with them, are vastly different.

In the decade since the human genome was mapped, researchers have identified hundreds of small regions that differ between humans and fellow primates. Many show evidence of accelerated changes that might offer evolutionary clues to such fundamental differences as skeletal structure, motor skills and cognition since our human ancestors parted ways with chimpanzees some 6 million years ago.

A new study suggests that just 10 differences on one particular strand of human DNA lying near a brain-development gene could have been instrumental in the explosive growth in the human neocortex.

The DNA region, containing just 1,200 base pairs, is not a gene. But it lies near one that is known to affect early development of the human neocortex, according to the study, published online Thursday inCurrent Biology.

Researchers showed that the region, known as HARE5, acts as an enhancer of the gene FZD8. Embryos of mice altered with human HARE5 developed significantly larger brains and more neurons compared with embryos carrying the chimp version, according to the study.

"It could contribute to making us unique, and making our brains unique, said Duke University developmental neuroscientist Debra Silver, coauthor of the study. Were seeing the human enhancer turn on gene activity right at the onset of when a population of cells called neural stem cells are rapidly proliferating. They shift within a day or two to making neurons.

The type of neurons and the timing of their development are significant -- these excitatory neurons arise later in utero, which is consistent with human fetal brain development patterns driven by the gene in question.

So have they found the genetic missing link between chimp brains and human brains?

"We think its likely that theres many additional accelerated regions that are contributing to human brain development, and they may be impacting other aspects that make our brains unique, Silver said.

It still would be a pretty big gap to go all the way to: Oh, and thats why we have a spoken language, or different types of fine muscle movements or different cognitive abilities,'" said Katherine Pollard, an evolutionary genomics researcher at UC San Francisco's Gladstone Institutes, who was not involved in the study. "But this is certainly a big step in that direction."

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Small DNA changes separate chimp and human brains

Foodborne illnesses and food fraud are common, but rapid DNA sequencing can reveal hidden dangers

Tools to analyze DNA in meals, including fish, may soon help eliminate fraudulent claims as to what type of food is being sold or served. Credit: Michael Saechang

An apple can kill, a sprinkle of sprouts can send you to the hospital and your succulent, pan-seared red snapper may actually be tilefish. Despite rising concerns about food safety and authenticity, contamination rates by salmonella, campylobacter, Escherichia coli and other common pathogens have not fallen or are actually on the increase, depending on the microbe, according to a 2013 report from the U.S. Centers for Disease Control and Prevention. Each year foodborne illnesses caused by these microorganisms sicken 48 million Americans, hospitalize 128,000 and kill 3,000, according to the agency.

Food fraud is also increasing. In 2014 Oceana, an international conservation organization, published a two-year study of 1,215 seafood samples and 46 fish types from 674 retailers in 21 states. They found that a third of samples were mislabeled.

Tools to analyze DNA in food items may soon help eliminate these problems. Techniques ranging from whole genome sequencing to the ability to create artificial DNA labels that indicate points of origin are surprisingly affordable now, and have led to novel global collaborations and inventions. Scientists worldwide are working to create databases of foodborne microbial strains, sequence the most common pathogens and tag foods for immediate traceability. The new initiatives promise to speed investigations and reduce foodborne illnesses and deaths; the techniques could also spot food fakery by marketers.

Genome Trakr, a five-year collaboration between the University of California, Davis; Agilent Technologies; and the U.S. Food and Drug Administration, promises to perform whole genome sequencing on a total of 100,000 types of common foodborne pathogens. The technology maps the entire DNA sequence of a microbe, and allows scientists to distinguish one strain from another, allowing fast track-back and earlier elimination of outbreaks around the world. The project began in March 2012 and the database, hosted by the National Center for Biotechnology Information, will be available online and at no cost to researchers and public health officials. The zoom-in detail of a sequenced genome will make it possible to distinguish different strains of a microbe that are otherwise indistinguishable, and trace back a small cluster outbreak before it becomes widespread.

Right now that kind of trace-back is difficult without detailed epidemiologic exposure data. A recent study from Cornell University suggests the new technology is an effective and faster replacement. Using whole genome sequencing, researchers were able to double the number of cases associated with a known 2010 outbreak of a strain of salmonella called salmonella Heidelberg at a long-term care facility in New York City. They even found cases outside the metro region.

Whole genome sequencing has already proved successful in halting serious food outbreaks. In 2012 researchers isolated the specific strain in a salmonella outbreak in tuna sushi that sickened 258 individuals, and tracked it back to a processing plant in India. The U.S. Food and Drug Administration investigated the plant and found 10 sanitation slipups, including four outright violations of safety protocols. In 2014 the FDA was able to halt a U.S. Listeria outbreak that had killed one and sickened seven others. They genotyped and linked the strain to soft Hispanic-style cheeses manufactured by a company called Roos Foods, which ceased all manufacturing after being shut down by the FDA

The gigantic open-access Genome Trakr database should speed up this kind of detective work by providing an enormous volume of data that has already been analyzed. The projects director, U.C. Davis microbiologist Bart Weimer, says that Weve just extended the project to China, and they will map another 10,000 genomes and deposit them. We have other global collaborations pending.

Sequencing a whole genome is only one of the new approaches to food safety, however. Food fraud prevention is also benefitting from a large international project called The International Barcode of Life (iBOL), which is building a genetic library of all life on Earth. Initiated in 2003 by geneticist Paul Hebert at the University of Guelph in Ontario, it offers a global online database of DNA labels, akin to the bar codes on food packaging, for different species. These DNA bar codes are sequences from a small and stable region of the genome, which can reliably be used to identify a species.

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Quick DNA Scans Could Ensure Food Is Safe to Eat

FALL RIVER, Mass. Shortly before embarking on a journey that ended in an alleged murder of Odin Lloyd, Aaron Hernandez walked through his family room with a black object in his hands an object prosecutors claim was a pistol.

Jurors in Hernandezs murder trial got a view of that moment Monday when prosecutors played a number of clips from the video surveillance system in the former NFL stars home. And the one that garnered the most attention in the courtroom was captured shortly before 1 a.m. on June 17, 2013.

In it, Hernandez walks through his family room, past his fiance, Shayanna Jenkins, his young daughter and the couples babysitter, Jennifer Fortier.

As Hernandez moves the object from one hand to the other, one of his alleged accomplices, Carlos Ortiz, walks behind him.

A defense attorney suggested in his opening statement that the object was a remote control and lead prosecutor William McCauley tried to refute that while questioning Fortier.

This remote control did you ever see a remote control anywhere in the house that resembled a firearm, a gun? McCauley asked.

Defense attorney Michael Fee immediately objected, and Judge E. Susan Garsh sustained it.

OK, McCauley continued, describe any remote control that you saw in that house.

The only ones Ive ever seen are what I told you earlier, a rectangle, black or gray, she said.

It was impossible to tell from the clip played Monday exactly what Hernandez was holding. However, prosecutors have other shots they allege show Hernandez with the murder weapon, and Judge Garsh has ruled that they can call an official from Glock who has studied the video clips and concluded the object is, in fact, a handgun manufactured by the Swiss company.

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Hernandez's attorney continues to challenge DNA evidence