Monthly Archives: April 2013

Misdemeanor convictions in Colorado could call for DNA swab

Posted: April 11, 2013 at 6:50 am

Whether it's an assault or a relatively minor offense such as destroying a library book, Coloradans convicted of a misdemeanor would have to open wide and say "aaagh," should lawmakers pass a requirement that the state collect from them an oral DNA sample.

In what's billed as an ambitious effort to solve cold cases, exonerate those wrongfully convicted and quell future crimes, a Democratic state lawmaker wants to require that individuals convicted of Class 1, Class 2 or Class 3 misdemeanors must submit a DNA sample to be stored in a statewide database system.

But this effort to expand DNA collection to misdemeanor convictions has raised concerns about privacy issues and the rationale behind such a requirement.

"DNA is the 21st century fingerprint," said Rep. Dan Pabon, a Denver Democrat, who is the sponsor of the legislation that's set to be heard before a House committee Thursday. " We have become so sophisticated in our technology and science, we can without a shadow of a doubt link someone physically to a crime."

Already in Colorado, individuals arrested on a felony charge and some misdemeanors involving unlawful sexual conduct are required to provide the state with a DNA sample. And those convicted of a misdemeanor under the proposed legislation would have to pay a $128 fee to cover the costs of the sample.

Late Wednesday afternoon, after The Denver Post reported about Pabon's bill online, the sponsor said he would offer an amendment to the measure that would only require Class 1 misdemeanors be swabbed.

However, though Pabon is targeting most misdemeanor offenses, his legislation does not require those convicted of misdemeanor traffic offenses such as DUIs to submit oral samples.

"We don't have the statistics that demonstrate just because you're drinking and driving that you have a propensity to commit more serious crimes," Pabon said. "With respect to theft crimes, assault crimes, those involving the objectification of a person ... those types of crimes indicate that you're going to commit more serious crimes."

Denise Maes, public policy director at the American Civil Liberties Union of Colorado, said it's a false assumption to conclude that any person who commits a low-level misdemeanor will commit more serious crimes in the future.

"This encroaches on an individual's privacy," said Maes, who will offer testimony on Thursday in opposition to the bill. "Further, listen carefully to the rationale supporting this bill: 'Collecting DNA helps solve crime.' There is no end to this mission. One may facetiously say 'just chip us at birth,' but in reality this is precisely where the rationale of the proponents naturally leads us to."

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DNA discoverer's letter sells for more than $5M

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NEW YORK (AP) A letter that scientist Francis Crick wrote to his son about his Nobel Prize-winning DNA discovery was sold to anonymous buyer at a New York City auction on Wednesday for a record-breaking $5.3 million.

The price, which far exceeded the $1 million pre-sale estimate, topped $6 million when the commission is included, according to Christie's. The price was a record for a letter sold at auction, Christies said, eclipsing an Abraham Lincoln letter that sold in April 2008 for $3.4 million including commission.

On Thursday, the molecular biologists 1962 Nobel Prize medal in physiology or medicine will be offered by Heritage Auctions, which estimates it could fetch over $500,000.

The items are among a dozen artifacts Cricks heirs are selling to benefit scientific research.

In the March 19, 1953, handwritten letter to his 12-year-old son, Michael, Crick describes his discovery of the structure of DNA as something beautiful. The note tells his son how he and James Watson found the copying mechanism by which life comes from life. It includes a simple sketch of DNAs double helix structure, which Crick concedes he cant draw very well.

The seven-page letter, written to his son in boarding school, concludes: Read this carefully so that you will understand it. When you come home we will show you the model. Lots of love, Daddy.

Crick, who died in 2004 at age 88, was awarded the Nobel Prize along with Watson and Maurice Wilkins. He spent the latter decades of his career doing brain research at the Salk Institute, where he became a professor in 1977.

Michael Cricks daughter Kindra said the family decided to sell the medal and other items because they had been in storage for 50 years, first locked up in a room of her grandfathers La Jolla, Calif., home and later in a safe deposit box.

They chose to sell them now because it coincides with the 60th anniversary of the historic discovery and 50 years since he received the award, she said.

Half the proceeds from the Christies sale will benefit the Salk Institute for Biological Studies in La Jolla, the granddaughter said. Twenty percent of the proceeds from the Heritage Auctions sale will go to the new Francis Crick Institute in London, a medical research institute slated to open in 2015.

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DNA discoverer's letter sells for more than $5M

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Folded DNA templates allow researchers to precisely cut out graphene shapes which could be used in electronic circuits

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At left, metallized DNA (red) forms letters on a graphene surface. Treatment with oxygen plasma etches the shape of the letters into the graphene, right. Credit: ZHONG JIN

DNA's unique structure is ideal for carrying genetic information, but scientists have recently found ways to exploit this versatile molecule for other purposes: By controlling DNA sequences, they can manipulate the molecule to form many different nanoscale shapes.

Chemical and molecular engineers at MIT and Harvard University have now expanded this approach by using folded DNA to control the nanostructure of inorganic materials. After building DNA nanostructures of various shapes, they used the molecules as templates to create nanoscale patterns on sheets of graphene. This could be an important step toward large-scale production of electronic chips made of graphene, a one-atom-thick sheet of carbon with unique electronic properties.

"This gives us a chemical tool to program shapes and patterns at the nanometer scale, forming electronic circuits, for example," says Michael Strano, a professor of chemical engineering at MIT and a senior author of a paper describing the technique in the April 9 issue of Nature Communications.

Peng Yin, an assistant professor of systems biology at Harvard Medical School and a member of Harvard's Wyss Institute for Biologically Inspired Engineering, is also a senior author of the paper, and MIT postdoc Zhong Jin is the lead author. Other authors are Harvard postdocs Wei Sun and Yonggang Ke, MIT graduate students Chih-Jen Shih and Geraldine Paulus, and MIT postdocs Qing Hua Wang and Bin Mu.

Most of these DNA nanostructures are made using a novel approach developed in Yin's lab. Complex DNA nanostructures with precisely prescribed shapes are constructed using short synthetic DNA strands called single-stranded tiles. Each of these tiles acts like an interlocking toy brick and binds with four designated neighbors.

Using these single-stranded tiles, Yin's lab has created more than 100 distinct nanoscale shapes, including the full alphabet of capital English letters and many emoticons. These structures are designed using computer software and can be assembled in a simple reaction. Alternatively, such structures can be constructed using an approach called DNA origami, in which many short strands of DNA fold a long strand into a desired shape.

However, DNA tends to degrade when exposed to sunlight or oxygen, and can react with other molecules, so it is not ideal as a long-term building material. "We'd like to exploit the properties of more stable nanomaterials for structural applications or electronics," Strano says.

Instead, he and his colleagues transferred the precise structural information encoded in DNA to sturdier graphene. The chemical process involved is fairly straightforward, Strano says: First, the DNA is anchored onto a graphene surface using a molecule called aminopyrine, which is similar in structure to graphene. The DNA is then coated with small clusters of silver along the surface, which allows a subsequent layer of gold to be deposited on top of the silver.

Once the molecule is coated in gold, the stable metallized DNA can be used as a mask for a process called plasma lithography. Oxygen plasma, a very reactive "gas flow" of ionized molecules, is used to wear away any unprotected graphene, leaving behind a graphene structure identical to the original DNA shape. The metallized DNA is then washed away with sodium cyanide.

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Folded DNA templates allow researchers to precisely cut out graphene shapes which could be used in electronic circuits

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DNA discoverer's letter sells for $5.3M, a record

Posted: at 6:49 am

NEW YORK (AP) A letter that scientist Francis Crick wrote to his son about his Nobel Prize-winning DNA discovery was sold to anonymous buyer at a New York City auction on Wednesday for a record-breaking $5.3 million.

The price, which far exceeded the $1 million pre-sale estimate, topped $6 million when the commission is included, according to Christie's. The price was a record for a letter sold at auction, Christie's said, eclipsing an Abraham Lincoln letter that sold in April 2008 for $3.4 million including commission.

On Thursday, the molecular biologist's 1962 Nobel Prize medal in physiology or medicine will be offered by Heritage Auctions, which estimates it could fetch over $500,000.

The items are among a dozen artifacts Crick's heirs are selling to benefit scientific research.

In the March 19, 1953, handwritten letter to his 12-year-old son, Michael, Crick describes his discovery of the structure of DNA as something "beautiful." The note tells his son how he and James Watson found the copying mechanism "by which life comes from life." It includes a simple sketch of DNA's double helix structure, which Crick concedes he can't draw very well.

The seven-page letter, written to his son in boarding school, concludes: "Read this carefully so that you will understand it. When you come home we will show you the model. Lots of love, Daddy."

Crick, who died in 2004 at age 88, was awarded the Nobel Prize along with Watson and Maurice Wilkins. He spent the latter decades of his career doing brain research at the Salk Institute, where he became a professor in 1977.

Michael Crick's daughter Kindra said the family decided to sell the medal and other items because they had been in storage for 50 years, first locked up in a room of her grandfather's La Jolla, Calif., home and later in a safe deposit box.

They chose to sell them now because it "coincides with the 60th anniversary of the historic discovery and 50 years since he received the award," she said.

Half the proceeds from the Christie's sale will benefit the Salk Institute for Biological Studies in La Jolla, the granddaughter said. Twenty percent of the proceeds from the Heritage Auctions sale will go to the new Francis Crick Institute in London, a medical research institute slated to open in 2015.

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DNA discoverer's letter sells for $5.3M, a record

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DNA discoverer's items featured at 2 NYC auctions

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NEW YORK (AP) A letter that Francis Crick wrote to his young son about his DNA discovery and the scientist's Nobel Prize medal are among a dozen artifacts his heirs are selling at separate auctions to benefit scientific research.

On Wednesday, Christie's was offering the letter with a presale estimate of $1 million or more.

On Thursday, the molecular biologist's 1962 Nobel Prize medal in physiology or medicine will be sold by Heritage Auctions, which estimates it could fetch over $500,000. The medal is being sold with his Nobel diploma, a handsome two-page vellum document that contains an original hand-colored picture of a long-haired youth in a blue tunic holding the Rod of Asclepius.

In the March 19, 1953, handwritten letter to his 12-year-old son, Michael, Crick describes his discovery of the structure of DNA as something "beautiful." The note tells his son how he and James Watson found the copying mechanism "by which life comes from life." It includes a simple sketch of DNA's double helix structure, which Crick concedes he can't draw very well.

The seven-page letter, written to his son in boarding school, concludes: "Read this carefully so that you will understand it. When you come home we will show you the model. Lots of love, Daddy."

Crick, who died in 2004 at age 88, was awarded the Nobel Prize along with Watson and Maurice Wilkins. He spent the latter decades of his career doing brain research at the Salk Institute, where he became a professor in 1977.

Michael Crick's daughter Kindra said the family decided to sell the medal and other items because they had been in storage for 50 years, first locked up in a room of her grandfather's La Jolla, Calif., home and later in a safe deposit box.

They chose to sell them now because it "coincides with the 60th anniversary of the historic discovery and 50 years since he received the award," she said.

Half the proceeds from the Christie's sale will benefit the Salk Institute for Biological Studies in La Jolla, the granddaughter said. Twenty percent of the proceeds from the Heritage Auctions sale will go to the new Francis Crick Institute in London, a medical research institute slated to open in 2015.

Michael Crick, who was in New York to attend the auctions with his daughter, told The Associated Press that the family hoped the prospective buyers "will give people the opportunity to look at them and that they will be an inspiration for future scientists."

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DNA testing: Crack open your genetic code

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Peeking at your DNA is getting cheaper.

(Money Magazine)

You might also learn whether your genes raise your chances of getting diabetes -- but your doctor will still probably be more interested in other, more obvious risk factors, such as your family history and diet.

To avoid catching the attention of the IRS, beware of these pitfalls.

In short, although technology is quickly making it cheaper and easier to get data about yourself, it's not always clear which information is worth getting and which isn't.

Here's a guide to using, and paying for, genetic tests.

What you can find out -- and what you'll pay

Roughly, two kinds of tests are available.

The first is ordered by a doctor and will often involve finding all the variations in specific genes. Research has found some variations that point to a higher risk of diseases, including breast cancer and a kind of colon cancer.

A doctor might recommend a screen based on risk factors like family history or ethnic background. Other tests, says David Fleming, an internist and health ethicist at the University of Missouri, can provide clues to how you'll respond to certain drugs or treatments.

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NYC* 2013 – "How to analyze the human genome/DNA using Cassandra" by Sameer Farooqui – Video

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NYC* 2013 - "How to analyze the human genome/DNA using Cassandra" by Sameer Farooqui
Speaker: Sameer Farooqui, Freelance Big Data Consultant and Trainer "How to Analyze the Human Genome/DNA Using Cassandra" SlideShare: http://www.slideshare.n...

By: PlanetCassandra

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NYC* 2013 - "How to analyze the human genome/DNA using Cassandra" by Sameer Farooqui - Video

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Affymetrix and BioDiscovery Announce Software for Analysis of Whole Genome Copy Number Data Generated From FFPE Solid …

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SANTA CLARA, Calif.--(BUSINESS WIRE)--

Affymetrix, Inc. (AFFX) and BioDiscovery announce the availability of the Nexus for OncoScan Software for analysis of whole genome copy number data generated from formalin-fixed, paraffin-embedded (FFPE) solid tumor samples using the OncoScan FFPE Express 2.0 Service. Through a joint arrangement, this software, based on BioDiscoverys flagship Nexus Copy Number, is available to customers who are analyzing data generated using this service.

Obtaining high-quality copy number data using limited amounts of DNA from degraded FFPE samples is extremely challenging for cancer researchers. Utilizing Affymetrix unique Molecular Inversion Probe (MIP) technology, the OncoScan FFPE assay is capable of analyzing highly degraded DNA in FFPE tumor samples, even from less than 100 ng of starting DNA material, and is currently available as a service through Affymetrix Research Service Laboratory (ARSL) based in Santa Clara, California.

OncoScan FFPE Express 2.0 Service has been successfully used by more than 30 leading cancer research institutes, including M. D. Anderson Cancer Center, University of California San Francisco, and the Huntsman Cancer Institute at the University of Utah.

Cancer translational researchers have been able to quickly and easily analyze hundreds of degraded FFPE samples to correlate copy number aberrations with outcomes data, said Andy Last, Executive Vice President of the Genetic Analysis and Clinical Applications Business Unit at Affymetrix. Nexus for OncoScan Software is especially optimized for solid tumor copy number analysis and can generate whole genome copy number calls from raw data in minutes. We are very excited to continue to partner with BioDiscovery to bring this powerful and easy-to-use software to the cancer research community.

"The OncoScan FFPE assay is an amazing technology for cancer researchers allowing them to unlock DNA information from masses of archived FFPE samples to obtain high quality data," said Soheil Shams, President of BioDiscovery. Combining the powerful OncoScan FFPE technology with the proven power of Nexus Copy Number gives scientists a unique solution that is sure to accelerate cancer research, impact diagnosis, and ultimately lead to better patient care and treatment. We are very pleased to partner with Affymetrix in offering this powerful solution.

A next generation OncoScan FFPE product will be available in late 2013 enabling researchers to perform the assay and analysis in their own lab. Delivering results in about 48 hours, this new product will provide whole genome copy number coverage with high resolution in known cancer genes, loss of heterozygozity (LOH) as well as clinically relevant somatic mutation data - all from a single assay. An updated version of Nexus for OncoScan Software will be released in conjunction with the launch.

PLEASE NOTE: Affymetrix, the Affymetrix logo, and OncoScan trademarks are the property of Affymetrix, Inc. All other trademarks are the property of their respective owners.

Products mentioned in this release are for research use only. Not for diagnostic procedures.

Forward-looking statements

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Western Painted Turtle genome decoded: Scientist uncover evolutionary history behind common turtle's novel traits

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Western Painted Turtle. Credit: 2006 Don VandeBergh, Oregon Department of Fish & Wildlife

Scientists have recently decoded the genome of the Western Painted Turtle, Chrysemys picta bellii, one of the most widespread, abundant and well-studied turtles in North America. This freshwater turtle is only the second reptile species for which complete genome sequences have been assembled and analyzed, behind the green anole lizard.

"Turtles are an exceptionally old group of organisms, and they're also evolving very slowly," said University of Hawai'i at Mnoa Assistant Professor of Biology Robert C. Thomson, who has worked on the Western Painted Turtle project since 2008. Turtle genomes evolve at about one-third the rate seen in humans, and roughly one-fifth the rate of other reptiles such as the python.

Thomson led the analysis of the turtle's rate of evolution and phylogenetic relationshipsthe pattern of evolutionary divergence between turtles and other groups of organisms. These analyses indicate that turtles' closest living relatives are crocodiles and birds, not snakes and lizards as some previous studies have suggested.

Western Painted Turtle Hatchlings. Credit: 2006 Don VandeBergh, Oregon Department of Fish & Wildlife

"In many respects, turtles are a very strange group of animals," Thomson said. "They have a number of novel traits that we can learn from." For the Western Painted Turtle, these novel traits include the ability to hibernate through long winters by burying themselves in near-freezing mud beneath streams and ponds, surviving with almost no oxygen for up to four monthslonger than any other known tetrapod.

Comparative genomic information about animal species is often valuable for scientists working on certain human health-related problems. Understanding how turtles protect their vital organs during periods of oxygen deprivation may one day improve treatment for human victims of heart attack or strokes, researchers say. This majority of the turtle gene sequencing effort was completed at Washington University's Genome Institute, which is one of three National Institutes of Health (NIH)-funded sequencing centers in the United States.

No freshwater turtles are native to Hawai'i, although three species have been introduced, from the pet trade and for food. Five types of sea turtles occur in the Pacific waters off Hawai'i's coasts.

More information: Shaffer, H. et al. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology 14:R28 doi:10.1186/gb-2013-14-3-r28

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Genome mapping of koalas is promising start for understanding how koalas respond to infectious diseases

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Apr. 10, 2013 The "holy grail" for understanding how and why koalas respond to infectious diseases has been uncovered in an Australian-led, world-first genome mapping project.

The joint undertaking between QUT and The Australian Museum has unearthed a wealth of data, including the koala interferon gamma (IFN-g) gene -- a chemical messenger that plays a key role in the iconic marsupial's defence against cancer, viruses and intracellular bacteria.

Professor Peter Timms, from QUT's Institue of Health and Biomedical Innovation (IHBI), said the IFN-g gene was the key to finding a cure for diseases such as Chlamydia and Koala Retrovirus (KoRV), currently threatening the vulnerable species.

"We know koalas are infected with various strains of Chlamydia, but we do not know why some animals go on to get severe clinical disease and some do not," Professor Timms said.

"We also know that genes such as IFN-g are very important for controlling chlamydial infections in humans and other animals. Identifying these in the koala will be a major step forward in understanding and controlling diseases in this species. "

The research team -- made up of Professor Timms, Dr Adam Polkinghorne, Dr Ana Pavasovic and Dr Peter Prentis from QUT; The Australian Museum; veterinarians from Australia Zoo and the Port Macquarie Koala Hospital; and bioinformaticians from Ramaciotti Centre and UNSW -- have sequenced the complete transcriptome from several koala tissues.

Dr Polkinghorne from QUT's School of Biomedical Sciences said data sets from immune-related tissues of Birke, a koala who was euthanized following a dog attack, have revealed a wealth of information about the species' immune system including the sequences of at least 390 immune-related genes.

"Virtually nothing is known about the immune system of the koala and the absence of information has been a major hinderance to our efforts to understand how Chlamydia and KoRV infections lead to such debilitating disease in this native species," he said

Since finding the 'holy grail' the QUT team has developed a molecular test to measure IFN-g expression in the blood of healthy and diseased koalas, which has already been applied to a small group of wild koalas taken to the Australia Zoo Wildlife Hospital suffering ocular and reproductive tract disease.

The results will allow researchers to pull apart the complex immune response to better understand how to successfully treat and immunise the vulnerable koala population.

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