Monthly Archives: January 2015

DNA and RNA paper model lab directions part 3
Cutting and out and assembling a RNA model. Here we use the DNA as the template to make the RNA.

By: CuriousMoranland

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DNA and RNA paper model lab directions part 3 - Video

What Are DNA Tests Used For?

By: Top Nintendo Wii

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What Are DNA Tests Used For? - Video

3. Starting and Preparing Your DNA Assembly

By: synbiota

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3. Starting and Preparing Your DNA Assembly - Video

Cinnamon Bloss had part of her genetic makeup examined by 23andMe. She says the service can provide valuable information about potentially troublesome genes, and insight about how people could respond to certain medications.

SACRAMENTO In 1997s futuristic Gattaca, ones DNA determined ones destiny. Released a dozen years after the beginning of real-life genetic testing, the movie tracked a man conceived by love rather than in a lab, as Variety put it. Because his lousy genes limited his career, he went to a DNA broker who sells false identities to the genetically inferior.

As with all dystopian stories, Gattaca uses the future to explore trends in the present. Since the movies release, the genetic-data conundrum has become more pronounced. Testing offers great opportunities to cure disease and exonerate the innocent accused of crimes, but it also offers potential for government and private firms to invade privacy and misuse data.

A new bill, proposed by Assemblyman Mike Gatto, D-Glendale, attempts to create a balance by making it clear who owns the DNA samples already collected in California hospitals. A government repository of the DNA of all children born? It sounds like something out of 20th century dystopian fiction, Gattos office wrote, in a statement last week announcing the proposal.

As it further explains, newborns are tested via a blood sample taken from the heel of about a half-million babies born here each year and the information is sent to laboratories to screen for diseases and genetic disorders. Most parents dont even know about the test. All states do this, but California is one of a handful where the state owns and retains the information, and even sells it to private research companies.

Thats the problem, according to Gatto. In an interview last week, Gatto described potentially troubling scenarios. When hackers stole peoples credit-card data from a chain store, that created problems for consumers but imagine what can happen if hackers get into a database of genetic information? Right now, there are no real protections.

And then theres the potential for official misuses of the data. Technology is developing rapidly. Its not hard to envision a Gattaca-like scenario in which, as Gatto explains, eventually its possible to learn whether a person has a violent gene or is predisposed toward alcoholism. It gets kind of disturbing, he said. I dont mean to sound alarms, but it gets alarming.

Supporters of the current system say the information used for research is not attached to any persons name. But that may be a weak protection. The state screening programs de-identify newborn baby blood spots before loaning them out to research, but so far truly anonymizing DNA has proved impossible, according to a July Newsweek report that inspired the Gatto bill. Massachusetts researchers found the identities of anonymous DNA donors by cross-referencing their data with publicly available information.

AB 170 is a work in progress, but the parameters are simple: The bill would authorize a parent or guardian of a minor child and the newborn child, once he or she is legally an adult, to request that the department destroy, not use for research purposes, or both, the blood sample, and the department would be required to do so. It, in essence, gives the ownership right to its rightful owners. And it requires the state to provide various disclosures.

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DNA privacy bill strikes right balance

A boxer dog peeps out from its kennel. The breed was developed in Germany in the 19th century and imported to America after the first world war. Photograph: Matt Cardy/Getty

Humans began migrating to the Americas roughly 15,000 to 20,000 years ago. But domesticated canines likely didnt show up on American continents until 10,000 years ago, long after humans first arrived, according to a new analysis of ancient dog DNA by University of Illinois researchers. Their findings were published in the Journal of Human Evolution.

We were interested in seeing if we could see when dogs arrived in the Americas, said study author Kelsey Witt. Its assumed they came with humans, but no one has actually looked at it.

Dogs very likely were domesticated in Asia and then brought over to the Americas, Witt said. What we know about ancient dogs so far is that by the time Europeans arrived, they were pretty widely spread across the Americas. They were used to haul supplies, used as guards, had religious significance for some, used as a food source.

For this study, researchers analysed the remains of 84 dogs, including 34 from a single burial site in Illinois that dates back about 1,000 to 1,400 years. They specifically examined mitochondrial DNA, which is inherited maternally and allows a direct look back at a lineage. Previous studies only had access to about 40 such dog remains.

The genetic diversity of the dogs was only about 10,000 years old. And the newly studied dogs were closely related, which suggests that humans may have been breeding the animals, Witt said.

However, Witt said its possible their results were skewed because they were working with very old and disintegrated DNA. You cant always sequence as much as you might like, she said. Her next project involves working with a much longer stretch of DNA to see if she can replicate similar results.

The dogs arriving in the Americas were genetically similar to European wolves, and a prevalent theory is that some went on to breed with American wolves, Witt said.

Given that dogs have been an integral part of human life for so long, learning about their ancient history also means we are learning about our own. Witt said sequencing the DNA of ancient humans can be extremely challenging, especially when people dont want their ancestors remains destroyed or disturbed. Dogs can serve as a good proxy. Also, although humans in the American midwest were burying dogs about 1,000 years ago, they werent burying people.

The late arrival of dogs suggests that there may have been a second, major migration of humans as well. And once dogs arrived, they quickly spread, which tells us more about human movement.

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On the trail of the first dogs to put their paws in the Americas

IMAGE:Georgia Tech Associate Professor Francesca Storici (left), Graduate Student Kyung Duk Koh and collaborators have developed and tested a technique for identifying ribonucleotides in genomic DNA. view more

Credit: Credit: Rob Felt

Ribonucleotides, units of RNA, can become embedded in genomic DNA during processes such as DNA replication and repair, affecting the stability of the genome by contributing to DNA fragility and mutability. Scientists have known about the presence of ribonucleotides in DNA, but until now had not been able to determine exactly what they are and where they are located in the DNA sequences.

Now, researchers have developed and tested a new technique known as ribose-seq that allows them to determine the full profile of ribonucleotides embedded in genomic DNA. Using ribose-seq, they have found widespread but not random incorporation and "hotspots" where the RNA insertions accumulate in the nuclear and mitochondrial DNA of a commonly-studied species of budding yeast. Ribose-seq could be used to locate ribonucleotides in the DNA of a wide range of other organisms, including that of humans.

"Ribonucleotides are the most abundant non-standard nucleotides that can be found in DNA, but until now there has not been a system to determine where they are located in the DNA, or to identify specifically which type they are," said Francesca Storici, an associate professor in the School of Biology at the Georgia Institute of Technology. "Because they change the way that DNA works, in both its structure and function, it is important to know their identity and their sites of genomic incorporation."

A description of the ribose-seq method and what it discovered in the DNA of the budding yeast species Saccharomyces cerevisiae will be reported on January 26 in the journal Nature Methods. The findings resulted from collaboration between researchers in Storici's laboratory at Georgia Tech - with graduate students Kyung Duk Koh and Sathya Balachander - and at the University of Colorado Anschutz Medical School with assistant professor Jay Hesselberth.

The research was supported by the National Science Foundation, the Georgia Research Alliance, the American Cancer Society, the Damon Runyon Cancer Research Foundation, and the University of Colorado Golfers Against Cancer.

Because of the extra hydroxyl (OH) group in the ribonucleotides, their presence distorts the DNA and creates sensitive sites where reactions with other molecules can take place. Of particular interest are reactions between the OH and alkaline solutions, which can make the DNA more susceptible to cleavage.

Ribose-seq takes advantage of this reaction with the hydroxyl group to launch the process of identifying the genomic spectrum of ribonucleotide incorporation. Researchers first cleave the DNA samples at the ribonucleotides, then take the resulting fragments through a specialized process that concludes with generation of a library of DNA sequences that contain the sites of ribonucleotide incorporation and their upstream sequence. High-throughput sequencing of the library and alignment of sequencing reads to a reference genome identifies the profile of rNMP incorporation events.

"Ribose-seq is specific to directly capturing ribonucleotides embedded in DNA and does not capture RNA primers or Okazaki fragments formed during DNA replication, breaks or abasic sites in DNA," Storici noted.

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Ribose-seq identifies and locates ribonucleotides in genomic DNA