Monthly Archives: April 2013

DNA samples will help solve crimes

Posted: April 16, 2013 at 2:46 pm

Colorado in 2010 began requiring DNA testing of all felons and for a small list of criminal misdemeanors, a move that began providing matches to unsolved sexual assaults, robberies, burglaries and other crimes within months.

Now, Rep. Dan Pabon, D-Denver, is proposing the state go further by requiring DNA testing for all criminal misdemeanor convictions. We strongly support this idea and believe it could help catch rapists, burglars and even murderers going forward.

We especially support the idea now that House Bill 1251 has been considerably narrowed from its original version, which would have required DNA testing for all misdemeanor convictions, including a long list of minor violations hardly predictive of additional criminal behavior.

First, consider the results that have occurred since Colorado began requiring DNA testing for felony arrests and for six misdemeanor offenses. According to the Denver District Attorney's office, from December 2010 to March 2013, just in Denver, there were 187 DNA hits on samples taken upon arrest, and of those, 29 have been matched to sexual assaults and four to murders.

One of those cases included the March 21 charging of Eddie Simon on suspicion of kidnapping and raping a 20-year-old woman in 2001. Simon had been arrested earlier this year on felony drug charges and his DNA was taken at that time, leading to the potential break in the cold case.

But it's clear that expanding the DNA testing to serious misdemeanors will catch dangerous criminals as well. In New York, which in 2006 expanded the testing to certain misdemeanors such as shoplifting, assault and trespassing, DNA samples of people convicted of petty larceny were linked to some 48 murders and 220 sexual assaults, according to the Manhattan District Attorney's office.

Some critics of Pabon's bill say it would create an indiscriminate dragnet that would invade the privacy of many people convicted of extremely low-level offenses. Yet we think Pabon has largely addressed this concern by first limiting the bill only to Class 1 misdemeanors and then further winnowing that list to only certain Class 1 misdemeanors.

This list includes more serious offenses such as third-degree assault, various sexual assault offenses, forgery, indecent exposure, wiretapping, possession of an illegal weapon and various other crimes that could indicate future criminal behavior.

No doubt, some critics will point to certain other offenses included on this narrowed list, such as videotaping a movie inside a theater, and say they shouldn't necessitate a DNA sample. But we think these cases will be relatively rare, and the far greater number of more serious offenses justifies taking the DNA.

The bill should be passed into law.

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DNA samples will help solve crimes

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Junk DNA may be behind devastating neurological diseases

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Washington, April 16 (ANI): UC San Francisco scientists have revealed that specific DNA once dismissed as junk plays an important role in brain development and might be involved in several devastating neurological diseases.

Their discovery in mice is likely to further fuel a recent scramble by researchers to identify roles for long-neglected bits of DNA within the genomes of mice and humans alike.

While researchers have been busy exploring the roles of proteins encoded by the genes identified in various genome projects, most DNA is not in genes. This so-called junk DNA has largely been pushed aside and neglected in the wake of genomic gene discoveries, the UCSF scientists said.

In their own research, the UCSF team studies molecules called long noncoding RNA (lncRNA, often pronounced as "link" RNA), which are made from DNA templates in the same way as RNA from genes.

"The function of these mysterious RNA molecules in the brain is only beginning to be discovered," said Daniel Lim, MD, PhD, assistant professor of neurological surgery, a member of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF, and the senior author of the study.

Alexander Ramos, a student enrolled in the MD/PhD program at UCSF and first author of the study, conducted extensive computational analysis to establish guilt by association, linking lncRNAs within cells to the activation of genes.

Ramos looked specifically at patterns associated with particular developmental pathways or with the progression of certain diseases. He found an association between a set of 88 long noncoding RNAs and Huntington's disease, a deadly neurodegenerative disorder. He also found weaker associations between specific groups of long noncoding RNAs and Alzheimer's disease, convulsive seizures, major depressive disorder and various cancers.

Unlike messenger RNA, which is transcribed from the DNA in genes and guides the production of proteins, lncRNA molecules do not carry the blueprints for proteins. Because of this fact, they were long thought to not influence a cell's fate or actions.

Nonetheless, lncRNAs also are transcribed from DNA in the same way as messenger RNA, and they, too, consist of unique sequences of nucleic acid building blocks.

Evidence indicates that lncRNAs can tether structural proteins to the DNA-containing chromosomes, and in so doing indirectly affect gene activation and cellular physiology without altering the genetic code. In other words, within the cell, lncRNA molecules act "epigenetically" - beyond genes - not through changes in DNA.

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UPDATE 3-France tops EU DNA tests for horsemeat in beef

Posted: at 2:46 pm

* Horse DNA found in 1 in 8 beef products tested in France

* Results show 4.6 pct of tests positive across the EU

* Britain finds illegal drug residues in horsemeat

* EU experts say levels seen unlikely to pose health risk

By Charlie Dunmore

BRUSSELS, April 16 (Reuters) - France found more cases of illegal horsemeat in beef products than any other European Union country, results of official DNA tests ordered in the wake of the scandal showed, with more than 1 in every 8 samples testing positive.

Announcing the results on Tuesday, the European Commission said that for the EU as a whole, just less than 5 percent of all beef products tested had come back positive for horse DNA.

But the figures showed that of 353 tests carried out in France, 47 tested positive for horse DNA, giving a rate of more than 13 percent.

"In terms of image it's not good. It risks delaying our attempt to regain consumer confidence to get out of the crisis, because it is not over yet," Jean-Rene Buisson, chairman of the French food industry group ANIA, told Reuters.

Buisson said it would be important to know how much horsemeat was detected in each positive sample, as tiny traces could be the result of accidental contamination at processing plants rather than deliberate substitution. The Commission did not provide that information.

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UPDATE 3-France tops EU DNA tests for horsemeat in beef

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Brain development is guided by junk DNA that isn't really junk

Posted: at 2:46 pm

Apr. 15, 2013 Specific DNA once dismissed as junk plays an important role in brain development and might be involved in several devastating neurological diseases, UC San Francisco scientists have found.

Their discovery in mice is likely to further fuel a recent scramble by researchers to identify roles for long-neglected bits of DNA within the genomes of mice and humans alike.

While researchers have been busy exploring the roles of proteins encoded by the genes identified in various genome projects, most DNA is not in genes. This so-called junk DNA has largely been pushed aside and neglected in the wake of genomic gene discoveries, the UCSF scientists said.

In their own research, the UCSF team studies molecules called long noncoding RNA (lncRNA, often pronounced as "link" RNA), which are made from DNA templates in the same way as RNA from genes.

"The function of these mysterious RNA molecules in the brain is only beginning to be discovered," said Daniel Lim, assistant professor of neurological surgery, a member of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF, and the senior author of the study, published online April 11 in the journal Cell Stem Cell.

Alexander Ramos, a student enrolled in the MD/PhD program at UCSF and first author of the study, conducted extensive computational analysis to establish guilt by association, linking lncRNAs within cells to the activation of genes.

Ramos looked specifically at patterns associated with particular developmental pathways or with the progression of certain diseases. He found an association between a set of 88 long noncoding RNAs and Huntington's disease, a deadly neurodegenerative disorder. He also found weaker associations between specific groups of long noncoding RNAs and Alzheimer's disease, convulsive seizures, major depressive disorder and various cancers.

"Alex was the team member who developed this new research direction, did most of the experiments, and connected results to the lab's ongoing work," Lim said. The study was mostly funded through Lim's grant - a National Institutes of Health (NIH) Director's New Innovator Award, a competitive award for innovative projects that have the potential for unusually high impact.

Unlike messenger RNA, which is transcribed from the DNA in genes and guides the production of proteins, lncRNA molecules do not carry the blueprints for proteins. Because of this fact, they were long thought to not influence a cell's fate or actions.

Nonetheless, lncRNAs also are transcribed from DNA in the same way as messenger RNA, and they, too, consist of unique sequences of nucleic acid building blocks.

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Brain development is guided by junk DNA that isn't really junk

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DNA Tests Offer Quicker Results for Beach Bacteria

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Just in time for swimsuit season, federal researchers are touting a faster, more accurate water-quality test to keep beaches open and people healthy. But its expensive

By Brian Bienkowski and Environmental Health News

Just in time for swimsuit season, federal researchers are touting a faster, more accurate water-quality test to keep beaches open and people healthy. Image: Flickr/David Dufresne

Just in time for swimsuit season, federal researchers are touting a faster, more accurate water-quality test to keep beaches open and people healthy.

But its expensive, and most of the nations cash-strapped cities and counties can afford it.

Local officials traditionally check for bacteria in ocean and lake water with tests that take about 24 hours to complete. Now the U.S. Environmental Protection Agency is recommending testing at the molecular level tagging DNA and counting bacteria which provides results within hours.

Water quality can change significantly in 24 hours. This way were identifying threats to human health almost immediately,said Meredith Nevers, a research ecologist with the U.S. Geological Survey who is studying theEPAs new DNA test.

An estimated 3.5 million people get sick every year after a trip to the beach because of E. coli or other pathogens from sewage overflows, spills and polluted runoff, according to the EPA. Exposure can cause gastrointestinal illness, skin rashes and infections.

About 43 percent of beaches along the East and West coasts and the Great Lakes had at least one water-quality advisory in 2011, according to EPA data.

Counties and cities test beaches routinely often weekly but depending on the location and season. Beaches also are tested after spills to determine when they can be reopened.

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DNA Tests Offer Quicker Results for Beach Bacteria

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DNA matches victim's fiance in old Wyo. rape case

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By The Associated Press Tuesday, April 16, 2013

Additional DNA testing in a 24-year-old Wyoming rape case shows a match to the man who was the victim's fiance at the time, rather than the man who is in prison serving a life sentence for the crime.

A state district judge in Cheyenne will hold a hearing Tuesday to consider 63-year-old Andrew J. Johnson's request to receive a new trial based on DNA evidence. Johnson has maintained his innocence while serving a life sentence for the 1989 rape in Cheyenne.

In February, a judge granted Johnson's request for the first DNA testing in his case. Last month, initial results ruled out Johnson as the source of male DNA found in samples taken from the victim.

Relatives hope Johnson will get a new trial and possibly be released on bond.

"I cannot wait to finally see him walk free," his stepdaughter, Angela Johnson, 28, of Denver, said Monday.

The rape happened after Johnson and the victim spent an evening together visiting bars in Cheyenne. Johnson told police he walked back to his home after the victim drove home to hers without him. The victim told police Johnson later broke in to her apartment and raped her in the dark, according to court documents.

Now, additional testing shows a match between DNA taken from the victim's ex-fiance and DNA in a sample taken from the victim after the attack.

Laramie County District Attorney Scott Homar requested the additional testing after receiving the initial results. The victim had told police that only one man attacked her and that she didn't have sexual intercourse with anybody else the night she was raped.

Homar said the DNA match with the victim's ex-fiance wasn't surprising.

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DNA matches victim's fiance in old Wyo. rape case

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Horse DNA in 5% of EU tested beef

Posted: at 2:46 pm

16 April 2013 Last updated at 10:46 ET

Horse DNA has been found in up to 5% of beef products randomly tested across the EU, according to results from the European Commission.

Inspectors also found the banned anti-inflammatory horse drug phenylbutazone, or "bute", in 0.5% of horsemeat tested.

The EU said it was "a matter of food fraud and not of food safety".

The three-month programme of checks was agreed by the 27 EU member states in February after horsemeat had been found in a batch of Findus frozen lasagne.

"Restoring the trust and confidence of European consumers and trading partners in our food chain following this fraudulent labelling scandal is now of vital importance for the European economy," said EU Commissioner for Health and Consumers Tonio Borg.

He said the Commission would "propose to strengthen the controls along the food chain in line with lessons learned."

Of the 4,144 tests carried out across the EU for the presence of horsemeat DNA, 193 were positive (4.66%).

There were 3,115 tests for bute, of which 16 were positive (0.51%).

In addition, member states reported another 7,951 tests for horse DNA performed by food business operators; of these 110 were positive (1.38%).

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France tops EU DNA tests for horsemeat in beef

Posted: at 2:46 pm

By Charlie Dunmore

BRUSSELS (Reuters) - France found more cases of illegal horsemeat in beef products than any other European Union country, results of official DNA tests ordered in the wake of the scandal showed, with more than 1 in every 8 samples testing positive.

Announcing the results on Tuesday, the European Commission said that for the EU as a whole, just less than 5 percent of all beef products tested had come back positive for horse DNA.

But the figures showed that of 353 tests carried out in France, 47 tested positive for horse DNA, giving a rate of more than 13 percent.

"In terms of image it's not good. It risks delaying our attempt to regain consumer confidence to get out of the crisis, because it is not over yet," Jean-Rene Buisson, chairman of the French food industry group ANIA, told Reuters.

Buisson said it would be important to know how much horsemeat was detected in each positive sample, as tiny traces could be the result of accidental contamination at processing plants rather than deliberate substitution. The Commission did not provide that information.

Europe's horsemeat scandal has damaged confidence in parts of the continent's food industry, hitting sales of processed ready-meals and boosting demand for organic produce.

The program of EU-funded DNA tests was approved by member governments in February in a bid to gauge the extent of the problem and restore consumer confidence in the bloc's food safety controls.

The results revealed a mixed picture across the EU. Greece had the second-highest level of positive results with 288 tests yielding 36 positive results, a rate of 12.5 percent. About 1 in every 10 tests also returned positive in Latvia, Denmark and Estonia.

By contrast, Germany found horse DNA in just 3.3 percent of samples, and in the Netherlands the rate was less than 1 percent.

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Human Genome Project is 10 years old, what’s next?

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This past Sunday marked the 10th anniversary of the sequencing of the human genome. Many remember the peaceable celebration between two rivals on the project, Francis Collins, who ran the government-backed component of the project, and Craig Venter, whose private venture threatened to embarrass the whole effort by doing things much faster with his shotgun sequencing approach. Both men have now moved on to other projects. Venter among other pursuits, likes to sail around the world sampling the waters for new life forms to sequence, while Collins is now tasked with running the new BRAIN Initiative for Obama.

Now that a little time has passed, it makes sense to take stock of what the project has done for us. For the average person, probably not a whole lot. Having an example DNA sequence on file for analysis has slowly trickled out blips of insight for those who look at things like, for example, subtle varieties of various functional genes, or tracing the remnant repeats of viruses that have integrated into the sequence over time. Of particular interest has been how many times they have copied themselves, and spread throughout the genome. However, the main area that sequence technology gives its greatest benefit is medicine in particular, cancer treatment.

When Steve Jobs was diagnosed with pancreatic cancer, he paid around $100,000 to have his genome sequenced in an effort to gain any information he could about his cancer, and possible treatments for it. Unfortunately there wasnt a whole lot that could be done with that information even just a few years ago. Today however, depending on the type of cancer you have, everything from the invasiveness of your particular brand of tumor, its response to any of a host of drugs in your treatment cocktail, and even how your body metabolizes, excretes, or otherwise unravels in allergic response to those drugs, can be assessed.

Regrettably, at the moment at least, the tests for those various factors are still given piecemeal, kind of like paying $32 to read a journal article for 24 hours when a years subscription is only $120. With the cost of sequencing a genome shrinking to $1000 or less, it will soon make sense for everyone to subscribe.

Nowhere has genetic analysis of cancer patients become more of an issue than for breast cancer. This week the courts began deliberations on the right of one company, Myriad Genetics, to patent your genes in particular a gene known as BRCA-1. A better way to put that, may be to say that the courts began deliberations on your right to pursue genetically-informed treatments in a timely and affordable manner without the now present monopoly on information that should be in the public domain, regardless of efforts spent to obtain it. It is absurd to live under a system that says just because someone spends resource to solve a problem you happen to have, you have no right to seek relief from any other source. Right now if woman wants to know if she has mutations in two common breast cancer genes, she has little or no choice of where she can be tested, for her own gene. Myriad controls that, and virtually the entire market with it.

Immediate issues aside, we have a long way to go towards learning the function of all the genes we have now sequenced. Even more important than knowing these functions, is how all of the genome is organized in the nucleus to define each of our cells, and by implication, our entire organism. The neat pictures of chromosomes packaged into neat little x-shapes is not a picture of a nucleus as it normally exists. The operational structure of nucleus is what we want to understand now.

Beyond that, having a fully-clickable genome, not only for the fertilized egg from which we were conceived, but from any important cell in our bodies at the time it was sequenced, would would be invaluable towards understanding our current health and future prognosis. Each major hit of radiation, or of any of a host of other natural insults we receive in the course of life, leaves its mark. Depending on the health of repair mechanisms, faults might be repaired, or they can slip away unnoticed to cause problems at a latter date.

The legacy of the understanding of our genomes has just begun. As more people arm themselves with knowledge of their genes, this information will continue to grow in collective value. To share this information openly with others and learn from them in response is a privilege. To fear sharing that knowledge on the weak pretense of abuse will be seen looking back not only as cowardice, but ingratitude.

Now read: Your complete genome can now be sequenced from a single cell

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Tulip tree reveals mitochondrial genome of ancestral flowering plant

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Apr. 15, 2013 The extraordinary level of conservation of the tulip tree (Liriodendron tulipifera) mitochondrial genome has redefined our interpretation of evolution of the angiosperms (flowering plants), finds research in biomed Central's open access journal BMC Biology. This beautiful 'molecular fossil' has a remarkably slow mutation rate meaning that its mitochondrial genome has remained largely unchanged since the dinosaurs were roaming the Earth.

Evolutionary studies make used of mitochondrial (powerhouse) genomes to identify maternal lineages, for example the human mitochondrial Eve. Among plants, the lack of genomic data from lineages which split away from the main evolutionary branch early on has prevented researchers from reconstructing patterns of genome evolution.

L. tulipifera is native to North America. It belongs to a more unusual group of dicotyledons (plants with two seed leaves) known as magnoliids, which are thought to have diverged early in the evolution of flowing plants.

By sequencing the mitochondrial genome of L. tulipifera, researchers from Indiana University and University of Arkansas discovered that its mitochondrial genome has one of the slowest silent mutation rates (ones which do not affect gene function) of any known genome. Compared to humans the rate is 2000 times slower -- the amount of genomic change in a single human generation would take 50,000 years for the tulip tree. The rate is even slower for magnolia trees, taking 130,000 years for the same amount of mitochondrial genomic change.

Ancestral gene clusters and tRNA genes have been preserved and L. tulipifera still contains many genes lost during the subsequent 200 million years of evolution of flowering plants. In fact one tRNA gene is no longer present in any other sequenced angiosperm.

Prof Jeffrey Palmer who led this study explained, "By using the tulip tree as a guide we are able to estimate that the ancestral angiosperm mitochondrial genome contained 41 protein genes, 14 tRNA genes, seven tRNA genes sequestered from chloroplasts, and more than 700 sites of protein editing. Based on this, it appears that the genome has been more-or-less frozen in time for millions and millions of years."

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The above story is reprinted from materials provided by BioMed Central Limited, via AlphaGalileo.

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