Category Archives: Genome

PUBLIC RELEASE DATE:

9-Dec-2014

Contact: Kevin Jiang kevin.jiang@uchospitals.edu 773-795-5227 University of Chicago Medical Center @UChicagoMed

The availability of a trace nutrient can cause genome-wide changes to how organisms encode proteins, report scientists from the University of Chicago in PLoS Biology on Dec. 9. The use of the nutrient - which is produced by bacteria and absorbed in the gut - appears to boost the speed and accuracy of protein production in specific ways.

"This is in some sense a 'you are what you eat' hypothesis,"' said senior study author D. Allan Drummond, PhD, assistant professor of biochemistry and molecular biology at the University of Chicago. "This nutrient that is absorbed through the gut looks like it can cause the recoding of an entire genome over evolutionary time."

All known organisms store the blueprint of life in their DNA, and use the information to produce proteins - the structural components and molecular engines for almost every function in a cell. To accomplish this, copies of relevant DNA regions must first be made. These copies are strings of chemical letters that serve as instructions, and are read three letters at a time by molecules known as transfer RNA (tRNA). Each tRNA has a preference for a specific three letter combination, or codon, and is attached to a single amino acid. As the instructions are read, tRNAs sequentially bind to their corresponding codon and deposit their amino acid, creating a protein.

tRNAs possess a special property known as "wobble" - a flexibility in one of the binding positions - that allows them to pair with multiple codons. This means that different spellings of genetic code can be used to create the exact same protein, similar to how sentences can be written using different synonyms. However, this flexibility comes with a cost. Some codons are less reliably read and can introduce more mistakes. As such, certain codons are thought to be favored by natural selection.

To investigate the mechanisms that underlie this process and the evolutionary consequences, Drummond, together with Tao Pan, PhD, professor of biochemistry and molecular biology, and colleagues from Cornell University, analyzed and compared thousands of genes in a dozen different species of fruit fly. They looked for the frequency at which certain codons were used to encode proteins, and how this affected the accuracy and speed of protein production.

To their surprise, they found that the availability of queuine - a trace nutrient produced by bacteria that is only available when absorbed through the gut - played a major role in determining which codons were optimal. Flies which had abundant queuine possessed a higher proportion of tRNAs with a specific modification: a portion of their wobble-binding sites was replaced with a queuine-derived molecule known as queuosine (Q).

The team found that these Q-tRNAs were able to read and process certain codons much faster and more accurately than unmodified tRNAs, and caused changes throughout the flies' genomes. Species with access to plentiful queuine favored codon spellings that were optimized for Q-tRNAs. Species with access to less queuine favored other codon spellings.

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Nutrient availability can cause whole-genome recoding

With the NantOmics Cancer Genome Browser, doctors can look up information about patients' genetic data.

IBM and Google aren't the only ones attempting to cure cancer: BlackBerry and NantHealth are partnering to give doctors simplified access to genetic data.

Specifically, the firms revealed a secure browser for the BlackBerry Passport, dubbed the NantOmics Cancer Genome Browser, which doctors can use to look up information about patients' genetic data, as well as relevant treatment options.

According to BlackBerry, doctors will be able to examine a patient's chromosomes at an individual base-pair level. The human genome contains approximately 3 billion of these base pairs.

"BlackBerry's partnership with NantHealth illustrates how the mobile security and collaboration technology we are known for can be reimagined to create revolutionary applications across a variety of industries," BlackBerry CEO John Chen said in a statement.

The Canadian manufacturer introduced its 4.5-inch square handset in September. It sports a physical QWERTY keyboard and 1,440-by-1,440 display.

"BlackBerry technology has proven itself secure, reliable and powerful enough to be counted on in life-and-death situations," Chen said. "Its innovative form and functionality make BlackBerry Passport an ideal addition to a doctor's medical kit."

The service works with NantHealth's Eviti treatment recommendation engine to help personalize protocols for individual patients.

"NantHealth has quietly built the unique capability of placing a supercomputer into the doctor's hand at point of care and in time of need," NantHealth CEO Patrick Soon-Shiong said. "Now with BlackBerry's partnership and through the power of the cloud and secure networks, the reality is we are now able to put dozens of supercomputers, through mobile devices, into doctor's hands on a global basis. Our goal is to extend this unique capability from doctor to patient, thereby establishing patient-empowered 21st century health."

The NantOmics Cancer Genome Browser will be on display at January's Consumer Electronics Show in Las Vegas, and will be preloaded on some BlackBerry Passport devices and available to professionals in early 2015.

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Deal Brings Genome Data to BlackBerry Passport

Viewing A Genome On A BlackBerry Passport
NantHealth CEO Patrick Soon-Shiong says his new app will let doctors view genomes on a secure phone. Subscribe to FORBES: http://www.youtube.com/forbes Check...

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Viewing A Genome On A BlackBerry Passport - Video

Download Owning the Genome A Moral Analysis of DNA Patenting PDF
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Download Owning the Genome A Moral Analysis of DNA Patenting PDF - Video

Dr Francis Collins Human Genome Project videos DNA National Institute of Health Brent Holland Show
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Dr Francis Collins Human Genome Project videos DNA National Institute of Health Brent Holland Show - Video

December 5th - Brenna Hassett - Cosmic Genome Science Advent Calendar
Brenna Hassett tells you how new, actual science suggests The Paleo Diet is not a brilliant idea after all... Every day a new free science clip from the good people at Cosmic Genome. Head...

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December 5th - Brenna Hassett - Cosmic Genome Science Advent Calendar - Video

osu Tsunamaru - Daidai Genome Insane
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osu Tsunamaru - Daidai Genome Insane - Video

December 6th - Baba Brinkman Dr Heather Berlin - Cosmic Genome Science Advent Calendar
As Baba Brinkman freestyle raps on the mean streets of Edinburgh, Dr Heather Berlin breaks down his brain function. Every day a new free science clip from the good people at Cosmic Genome....

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Scientists have been making rapid advances in studies of genetic variations in European and East Asian populations. Now, populations in Africa, the cradle of the human race, are getting the same treatment. The African Genome Variation Project set out to discover more about how variations in DNA can help in understanding patterns of disease, ultimately leading to better treatments. Working with other institutions, including partners throughout Africa, the Genome Variation Project has collected and analyzed genetic information from nearly 3,000 individuals representing the diversity of the African experience over many millennia.

Manjinder S. Sandhu of Britains Wellcome Trust Sanger Institute, senior author of an article on the project in the journal Nature, said in a telephone interview that DNA reveals traces of the movement of people who originated in Africa, migrated elsewhere, and returned. Its a mass population movement from out of Africa," Sandhu said. "Populations have returned over thousands of years and mixed with population groups. And you see vestiges of those signals in the human genomes of modern Africans today. For example, genetic characteristics of Eurasian people were found in todays West Africans. Sandhu said the Genome Variation Project might help explain why certain genetic variations make some people more likely than others to develop specific diseases. And ultimately, if we understand the biological processes underlying those diseases, we can start thinking about how we can develop new medicines, or use existing medicines, to help combat and control those diseases, he said. In a commentary also published in Nature, Raj Ramesar of the University of Cape Town said analyses of more African genomes would open a larger window into human diversity, evolution ... and disease susceptibility.

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African Genome Project Highlights Migration History

PKU and the Human Genome Project
via YouTube Capture.

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PKU and the Human Genome Project - Video