Category Archives: DNA

Earlier this year, a 17-year-old French woman arrived at her ophthalmologist with pain and redness in her left eye. She woman had been using tap water to dilute the cleaning solution for her contact lenses, and even though they were meant to be replaced every month, she would wear them for three. As a result, the fluid in her contact lens case had become contaminated with three species of bacteria, an amoeba called Acanthamoeba polyphaga that can caused inflamed eyes.

The mystery of the womans inflamed eyes was solved, but Bernard La Scola and Christelle Desnues looked inside the amoeba, they found more surprises.

It was carrying two species of bacteria, and a giant virus that no one had seen beforethey called it Lentille virus. Inside that, they found a virophagean virus that infects other viruseswhich they called Sputnik 2. And in both Lentille virus and Sputnik 2, they found even smaller genetic parasites tiny chunks of DNA that can hop around the genomes of the virus, and stow away inside the virophage. They called these transpovirons.

So, the poor red eyes of the French patient were carrying an entire world of parasites, nested within one another like Russian Matryoshka nesting dolls. The transpovirons were hidden in the virophage, which infected the giant virus, which infected the amoeba, which infected the womans eyes.

Rise of the virophages

The same team found the first virophage Sputnik back in 2008, under similar circumstances. In dirty water from a Parisian cooling tower, they had isolated an amoeba that contained a new giant virus mamavirus which was infected by Sputnik (named after the Russian for fellow traveller). Mamavirus a virus as big as some bacteria creates large viral factories inside the amoeba, where it makes new copies of itself. Sputnik hijacks these factories to replicate itself at mamavirus expense. It was a groundbreaking discoveryproof that viruses themselves can get sick. Just as they infect cells, virophages can infect them.

The world of virophages continued to grow. Last year, Matthias Fischer and Curtis Suttle discovered a second one Mavirus inside another giant virus called CroV. Weeks later, Sheree Yau announced a third virophage OLV infecting the giant viruses of Antarcticas Organic Lake. Yau also searched through genetic databases for sequences that looked like OLV, and found matches from the Galapagos Islands, Panama, the USA and elsewhere in Antarctica. An entire world of virophages lay waiting to be found.

In Sputnik 2, La Scola and Desnues have discovered the fourth virophage. More importantly, they found its DNA inside that of its Lentille virus host. This proves that, just as other viruses such as HIV and herpes can insert their DNA into animal genomes, Sputnik 2 can insert its DNA into viral ones. This could explain why distantly related giant viruses often carry similar genes. By hopping in and out of their genomes, virophages could be acting as vehicles that transfer genes from one giant virus to another.

Transpovirons

Next, the team did scoured the DNA they recovered from Lentille virus for fragments that didnt belong into either Lentilles or Sputnik 2s genomes. Its a process that team leader Didier Raoult describes as looking in the trash. He says, If you want to see something really bizarre, you have to look where you didnt know to look in the first place. And he was right.

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Jumping DNA rides aboard a virus, which infects a giant virus, which infects an amoeba, which infected a woman’s eye ...

LEXINGTON, Mass. & CORALVILLE, Iowa--(BUSINESS WIRE)--

RainDance Technologies, Inc., the Digital Biology Company, and Integrated DNA Technologies (IDT) Inc., the world leader in oligonucleotide synthesis, today announced a collaboration focused on consumables specifically tailored to perform the fast-growing application of digital PCR. Under the terms of the agreement, the companies will work together on the development of reagents compatible with the RainDrop Digital PCR System. Financial terms of the agreement were not disclosed.

The RainDrop Digital PCR System is a breakthrough research platform that is transforming the performance of molecular assays by enabling digital answers across a number of important applications including low-frequency tumor allele detection, gene expression, copy number variation, and SNP measurement. Built using RainDances proven RainStorm picodroplet technology, the RainDrop System generates up to 10 million picoliter-sized droplets per sample. Since each droplet encapsulates no more than a single molecule, researchers can quickly determine the absolute number of droplets containing specific target DNA and compare that to the number of droplets with background, wild-type DNA.

We have achieved a new gold standard in sensitivity, quantitation and multiplexing through enhancements in every aspect of system and reagent refinement, said Rena McClory, Ph.D., Marketing Director for Digital PCR at RainDance Technologies. We are pleased to be working with market leaders such as IDT on the development and broad availability of best-in-class reagents in support of our new RainDrop Digital PCR System.

IDT is a leader in manufacturing and developing custom oligonucleotideproductsfor use in the research and diagnostic life science markets.This includesdesign and synthesis ofdual-labeled probes for gene expression and genotyping as part of the PrimeTime qPCR product family. Founded by Dr. Joseph Walder in 1987, IDTs development has been guided by an uncompromising approach to quality, a belief in the value of good service, and a determination to minimize consumer costs.

We are pleased to be working with RainDance in supporting scientists who are seeking to apply the powerful attributes of digital PCR to their research projects, said Stephen Gunstream, Senior Vice President of Marketing and Strategy at IDT. Digital PCR is redefining the science of directly quantifying and amplifying nucleic acids and will open the doors to an exciting era of new discoveries.

For more information about the RainDrop Digital PCR System, please visit http://www.RainDanceTech.com.

About RainDance Technologies

RainDance Technologies, the Digital Biology Company, is pioneering the use of high-throughput picodroplet-based analysis in human health and life science research. The company's core RainStorm technology generates millions of discrete droplets that can encapsulate a single molecule, cell or reaction and be digitally analyzed and sorted one at a time. The power, precision and simplicity of picodroplets enable researchers to answer complex questions with unprecedented sensitivity and quantitation. The complete RainDance solution includes automated instrumentation, customizable bioinformatics and high-value consumables and reagents for applications including targeted next-generation DNA sequencing, methylation, digital PCR. Based in Lexington, Massachusetts, the company supports scientists around the world through its international sales and support operations and a global network of distributors and service providers. For more information, please visitwww.RainDanceTech.com.

For research use only. Not for use in diagnostics procedures.

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RainDance Technologies and Integrated DNA Technologies to Develop Reagents and Consumables for Digital PCR

Using tools he often had made himself, Leonard Lerman took great care in making precise measurements during experiments he performed to further the understanding of DNA.

A simple way to state it is that he was a deeply quantitative man, said Tom Maniatis, chairman of the biochemistry and molecular biophysics department at Columbia University, who had worked with Dr. Lerman as a graduate student at Vanderbilt University.

Discoveries he made about what can unwind the strands of DNA, and other research throughout his career, helped Dr. Lerman become a key figure in the field of molecular biology.

He was both a deep and brilliant man, and also a clever man, in the sense that he always had great ideas and techniques, Maniatis said.

Dr. Lerman, formerly a senior lecturer at the Massachusetts Institute of Technology, died Sept. 19 in his Cambridge home of a chronic neurological disease. He was 87.

He did lots of things that served for the increased understanding of the structure of DNA and the things that interacted with DNA, said Maurice Fox, a professor emeritus of molecular biology at MIT.

Dr. Lerman, Maniatis said, saw the world through mathematics and could use mathematical and physical properties of molecules to predict what would occur.

As a graduate student at the California Institute of Technology, Dr. Lerman worked with Linus Pauling, who in 1954 was awarded the Nobel Prize for chemistry and has often been referred to as one of the founders of molecular biology.

Dr. Lerman set out to prove his hunch that antibodies have two binding sites to bond with antigens, which are any foreign substances that prompt an immune response. After achieving that goal, he graduated from Cal Tech with a doctorate in chemistry in 1950 and went on to join the faculty of the University of Colorado.

The 1950s were an active time for DNA research. Dr. Lerman was determined to find out more about chemicals that attach to DNA strands and make them unwind, often causing mutations. The way certain chemicals attach to the strands is called intercalation, and it occurs between adjacent base pairs in double-stranded DNA.

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Leonard Lerman, 87; senior lecturer at MIT researched DNA

The Irish Times - Monday, October 15, 2012

PETER CLUSKEY in The Hague

DUTCH police have carried out the biggest DNA sweep in the history of the Netherlands, taking samples from more than 6,500 men in 12 separate villages, in a renewed attempt to solve the countrys most infamous murder that of 16-year-old schoolgirl Marianne Vaatstra, in 1999.

The DNA sampling was completed on Thursday, and police said at the weekend that they had successfully collected samples from 89 per cent of the 7,300 men still living within a five-mile radius of the meadow where Vaatstras body was dumped 14 years ago.

The schoolgirls age and the particularly gruesome nature of the murder she was raped, strangled and had her throat cut caused revulsion in the Netherlands. As a result there have been repeated attempts over the years to find her killer, most recently in 2007 using 3D technology.

The department of justice has refused on a number of occasions to give permission for such a wide sweep, but in June it relented on the grounds that DNA testing has become much more sophisticated and that police say they may have some of the killers DNA, which was discovered at the scene.

Hopes of a breakthrough now centre on a Playboy cigarette lighter found in the grass near the victims body in the field in Veenklooster, in the northern province of Friesland.

DNA found on the lighter, which was bought in a local shop, matches DNA found on the dead girls body and police hope it may still lead them to someone closely related to the killer.

One of the most controversial aspects of this murder case in 1999 was that, because the body was found near a centre for asylum seekers, the focus of the investigation and of local anger rapidly became the refugees.

An Iraqi who had recently left the camp was detained in the UK, while an Afghan was detained in Turkey. Both voluntarily gave DNA samples and were ruled out.

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New DNA hunt for killer of Dutch schoolgirl

THE owner of Argentina's powerful Clarin media group wants kidnapping charges dropped after DNA tests failed to link her adopted children to those stolen during the country's 1976-1983 "dirty war," her newspaper has reported.

The request, filed on Friday, comes after DNA samples submitted by the two adult children of Ernestina Herrera de Noble showed no matches with a DNA data bank of relatives of those who disappeared during the dictatorship.

Some 30,000 people vanished during the military's war on leftist activists.

The Grandmothers of the Plaza de Mayo, which represents female relatives of dictatorship-era victims, alleges that some 500 babies were stolen from those who disappeared - and then were adopted by pro-junta families.

Of those, only 107 have been identified.

The kidnapping case against Herrera de Noble was originally filed in 2001, and, after years of legal manoeuvering, a court ordered Marcela and Felipe Noble Herrera to submit to the DNA testing.

"There is no more cross-checking to do," attorney Gabriel Cavallo told the daily Clarin.

The case should be closed because "the experts have already determined that neither Felipe nor Marcela are the children of people who disappeared during the dictatorship," Mr Cavallo said.

But the Grandmothers of the Plaza de Mayo were not ready to admit defeat.

The group has long suspected the Noble Herrera children, both born in 1976, were kidnapped. It says the data bank is being still being updated because many people did not know that their daughters or daughters-in-law were pregnant at the time they vanished.

Continued here:
DNA 'clears magnate of kidnapping'

A retrial is expected in a San Francisco cold case murder in which DNA evidence failed to lead to a conviction Tuesday.

Just three of the 12 jurors believed there was enough evidence even after matching DNA samples to convict 48-year-old William Payne of strangling to death 41-year-old Nikolaus Crumbley while raping him in a car in John McLaren Park on Nov. 16, 1983.

On Wednesday, Deputy Public Defender Kwixuan Maloof, who represents Payne, said the hung jury proves that despite what we see on television, the presence of DNA does not prove a person is guilty of a crime.

But prosecutors appear determined to prove otherwise. Motions in Paynes retrial begin today, the Public Defenders Office said, with opening arguments scheduled for Oct. 22.

DNA evidence and independent corroborating testimony linked the defendant to the brutal rape and murder of Mr. Crumbely, District Attorney George Gascn said following Tuesdays outcome.

Payne was 19 years old when Crumbleys body was found facedown at the intersection of John Shelley Drive and Mansell Street. Prosecutors said Crumbleys pants and underwear were pulled down to his ankles.

Prosecutors believe Payne killed Crumbley while the two were having sex in Crumbleys rental car, which was later found in Oaklands Lake Merritt.

Three years ago, cold case investigators tied DNA found in Crumbleys rectum to Payne, whose DNA had been entered in a criminal database after he assaulted a woman in 1984.

In January, Payne was charged with first-degree murder during the course of sodomy.

But the DNA evidence wasnt enough to convince nine jurors of Paynes guilt.

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DNA evidence fails to convince jury of man’s guilt in 1983 killing

NEW YORK, NY--(Marketwire - Oct 11, 2012) - TriMarkPublications.com cites in its newly published "DNA Sequencing and PCR Markets" report that the next-generation DNA sequencing platforms market will more than double, reaching $3.2 billion by 2017. For more information, visit: http://www.trimarkpublications.com/products/DNA-Sequencing-and-PCR-Markets.html.

DNA sequencing has a number of applications, including: full-genome resequencing, targeted discovery of mutations or polymorphisms, mapping of structural rearrangements, large-scale analysis of DNA methylation, RNA-Seq and ChIP-Seq. The U.S. and Europe exhibit the highest market penetration for DNA sequencing, but other parts of the world are projected to see higher compound annual growth rates (CAGRs) of up to 13%. As DNA sequencing platforms become increasingly affordable, the cost of sequencing a human genome will soon fall below the $1,000 price point.

The "DNA Sequencing and PCR Markets" report covers:

The "DNA Sequencing and PCR Markets" report examines companies manufacturing DNA sequencing and PCR equipment and supplies in the world. Companies covered include: Abbott, Affymetrix, Agilent, AgriGen, Avesthagen Gengraine, BD, BGI Life, bioMerieux, Bioneer, Bio-Rad, BioServe, Caliper LifeSciences, Cepheid, Cogenics, CombiMatrix, Commonwealthnologies, Complete, Comprehensive Biomarker, CuraGen, Cytocell, DiaDexus, DNA LandMarks, DNAVision, DNASTAR, ELITech, Enigma, Enzo Biochem, Eppendorf, Eurofins Medigenomix, Exiqon, FASMAC, GE Healthcare, GeneticTechnologies, GeneWorks, Genia, Genisphere, Genovoxx, Gen-Probeorporated, Genset, GnuBIOorporated, GVK, Helicos, High Throughput, Hokkaido, Hy, Illumina, Inqabanical Industries, IntegenX, Integrated DNA, Intelligent Biosystems, Kreatech, LaserGen, LI-COR, Life, Lucigen, Luminex, Meridian, Microsynth, MilleGen SA, MWG, NanoString, NobleGen, Orchid Cellmark, Oxford Nanopore, Pacific, PamGene, PPD, PrimmBiotech, Promega, QIAGEN, RainDance, Research Biolabs, Roche, Rubicon, Saturn, SeeGene, Sequenom, Sequetech, SeqWright, Shanghai Sangon, Shimadzu, Siemens, SolGent, Stratos, TATAA Biocenter, Thermo Fisher, Third Wave, Wellcome Trust Sanger, ZS Genetics and ZyGEM.

Detailed charts with sales forecasts and marketshare data are included. For more information, visit: http://www.trimarkpublications.com/products/DNA-Sequencing-and-PCR-Markets.html.

About TriMarkPublications.com

TriMarkPublications.com is a global leader in the biotechnology, healthcare and life sciences market research publishing. For more information, please visit http://www.trimarkpublications.com.

Important Notice

The statements contained in this news release that are forward-looking are based on current expectations that are subject to a number of uncertainties and risks, and actual results may differ materially.

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Next-Generation DNA Sequencing Platforms Market to More Than Double to $3.2 Billion by 2017

The DNA of Idelfonso Velez was discovered on the kitchen knife authorities say was used to stab Trisha Bennett and Angel Ortiz to death in 2010.

Velez, 29, of Framingham, is on trial in Middlesex Superior Court on two counts of first-degree murder in the deaths of Bennett and Ortiz, who were found stabbed to death inside their Hudson apartment in May 2010.

Andrea Borchardt-Gardner, a senior DNA analyst with Bode Technology in Virginia, told jurors Thursday she tested several DNA samples from the handle, tip and the recasso, the portion of the knife where the handle meets the blade. She found the samples matched Velezs DNA.

The probability of a randomly selected, unrelated person matching the DNA from the profile on the handle, tip and recasso is 1 in 2.8 quintillion, said Borchardt-Gardner.

The current world population is estimated to be about 7 billion, said Borchardt-Gardner.

"I can say to a reasonable degree of scientific certainty that Mr. Velez is the source of that DNA profile," said Borchardt-Gardner.

Borchardt-Gardner also testified Thursday that Bennetts DNA was found on the recasso portion of the knife. The probability of a randomly selected, unrelated person matching Bennetts DNA from the recasso section of the knife is 1 in 3.1 trillion.

Earlier this week, Massachusetts State Police Trooper Kevin Murphy said Velez told him that he entered Ortiz and Bennetts bedroom the night of the murders after hearing Bennett scream "baby, baby, baby."

Velez told Murphy that a man with a knife was standing over Ortiz and then attacked him before dropping the knife as he was running from the apartment. Velez then picked up the knife for his safety and placed it in the kitchen sink, said Murphy.

Alanna Frederick, a chemist with the Massachusetts State Police, also told jurors that DNA tested from a swab of blood spatter on the left thigh of the jeans Velez wore the night of the murders matched the DNA of both Velez and Bennett.

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Prosecution: Velez' DNA found on knife used in Hudson murders

12 October 2012 Last updated at 12:42 ET

A legal challenge to the retention of DNA samples by police in Northern Ireland could have repercussions across Europe, Belfast High Court has heard.

The test case has been brought by convicted drink driver Fergus Gaughran.

His lawyers argued DNA profiles and fingerprints of those found guilty of lesser offences should not be retained.

They want a European ruling which found it was unlawful to hold samples from people arrested but later acquitted to be extended to cases like Gaughran's.

Our case is that the collection of this information and the indefinite retention on the police computer systems is unlawful

Newry-based solicitor Paul Fitzsimons predicted potentially huge consequences if the judicial review challenge succeeds.

He said: "If there is a judgment upholding our client's position it could lead to the destruction of vast amounts of police records built up in Northern Ireland, the United Kingdom and throughout Europe."

Mr Fitzsimons issued legal proceedings on behalf of Gaughran, who was stopped at a police checkpoint in Camlough, County Armagh three years ago.

Gaughran failed a breath test and was subsequently convicted and disqualified from driving for a year.

Continued here:
Challenge to European DNA records

Scientists have finally found out how long DNA lasts in fossils. Alas, their discovery puts dreams of real life Jurassic Parks to rest for good.

[More from Mashable: Liquid Nitrogen + Ping Pong Balls = Crazy Science Fun]

As it turns out, DNA has a half-life of 521 years, according to researchers who studied fossils of extinct giant birds found in New Zealand. Previously, nobody knew exactly how long DNA lasted before decaying, which meant that technically it was possible to extract and read DNA from ancient fossils. A theory which was the premise of the movie Jurassic Park and which allegedly prompted a billionaire to try cloning a dinosaur.

[More from Mashable: Sound Waves Make Liquids Levitate, Develop Better Drugs [VIDEO]]

This confirms the widely held suspicion that claims of DNA from dinosaurs and ancient insects trapped in amber are incorrect, said Simon Ho, a computational evolutionary biologist at the University of Sydney in Australia. Sorry, Jurassic Park fans, you're never going to see a breathing Tyrannosaurus rex.

To find out more about why one of our childhood dreams has been just a delusion, and about this important scientific discovery check out the video above.

This story originally published on Mashable here.

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DNA Half Life Discovery Rules Out Real Life Jurassic Parks [VIDEO]