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Category Archives: Transhuman News

The Dark Corners of Our DNA Hold Clues about Disease

Posted: December 19, 2014 at 2:44 pm

A deep-learning algorithm shines a light on mutations in once obscure areas of the genome

The so-called "streetlight effect" has often fettered scientists who study complex hereditary diseases. Credit: Svisio/Thinkstock

The so-called streetlight effect has often fettered scientists who study complex hereditary diseases. The term refers to an old joke about a drunk searching for his lost keys under a streetlight. A cop asks, "Are you sure this is where you lost them?" The drunk says, "No, I lost them in the park, but the light is better here."

For researchers who study the genetic roots of human diseases, most of the light has shone down on the 2 percent of the human genome that includes protein-coding DNA sequences. Thats fine. Lots of diseases are caused by mutations there, but those mutations are low-hanging fruit, says University of Toronto (U.T.) professor Brendan Frey who studies genetic networks. Theyre easy to find because the mutation actually changes one amino acid to another one, and that very much changes the protein.

The trouble is, many disease-related mutations also happen in noncoding regions of the genomethe parts that do not directly make proteins but that still regulate how genes behave. Scientists have long been aware of how valuable it would be to analyze the other 98 percent but there has not been a practical way to do it.

Now Frey has developed a deep-learning machine algorithm that effectively shines a light on the entire genome. A paper appearing December 18 in Science describes how this algorithm can identify patterns of mutation across coding and noncoding DNA alike. The algorithm can also predict how likely each variant is to contribute to a given disease. Our method works very differently from existing methods, says Frey, the studys lead author. GWAS-, QTL- and ENCODE-type approaches can't figure out causal relationships. They can only correlate. Our system can predict whether or not a mutation will cause a change in RNA splicing that could lead to a disease phenotype.

RNA splicing is one of the major steps in turning genetic blueprints into living organisms. Splicing determines which bits of DNA code get included in the messenger-RNA strings that build proteins. Different configurations yield different proteins. Misregulated splicing contributes to an estimated 15 to 60 percent of human genetic diseases.

Frey, a computer engineer who has a cross appointment in the universitys Department of Medical Research, trained his algorithm using millions of data points: DNA sequences, genetic variations and RNA splicing patterns. The algorithm was then able to extrapolate how likely it was that any of tens of thousands of mutations could cause a splicing error associated with a particular disease.

The research team tested the method on spinal muscular atrophy as well as nonpolyposis colorectal cancer. Frey says the teams most ambitious case was its study of autism spectrum disorder; about 100 genes are known to be associated with it. In fact, many researchers think it is likely that autism comprises many disorders, each resulting from unique mutations but all resulting in common symptoms.

Working with U.T. autism researcher Stephen Scherer, Frey compared mutations in autism patients genomes with those of controls. Nothing unusual popped up. But when Frey and Scherer tested the genomes against the mutations flagged by Freys algorithm, they saw patterns emerge. According to Frey, Kids with autism are more likely to have these high-scoring mutations that change the meaning of the genome, and that are thought to be involved with brain functions and developmental functions.

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The Dark Corners of Our DNA Hold Clues about Disease

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Attorney: Worker linked to murder by tainted DNA

Posted: at 2:44 pm

SAN DIEGO - The DNA evidence linking a one-time San Diego police lab worker to the 1984 murder of a 14-year-old girl was likely the result of cross-contamination, an attorney for his family said Thursday.

Kevin Charles Brown, 62, was found dead of an apparent suicide at Cuyamaca State Park on Oct. 21. San Diego police said that at the time of Brown's death, preparations were being made to arrest him for allegedly taking part in the killing of 14-year-old Claire Hough.

RELATED: Deceased ex-SDPD criminalist named suspect in girl's murder in 1984

The teen was found dead at Torrey Pines State Beach on Aug. 24, 1984. She had been beaten, strangled and stabbed, and one of her breasts had been cut off, authorities said.

In November 2012, cold case homicide detectives uncovered DNA evidence that allegedly linked Brown and a second man, Ronald Clyde Tatro, to the slaying. Tatro was 67 when he died in a boating accident in Tennessee in 2011.

Brown worked in the police lab from 1982 until his retirement in 2002. He was not assigned to the Hough investigation, but attorney Eugene Iredale said Brown had been working while samples from the teen's body were in the lab.

It was also common practice in 1984 for lab workers to use their own blood or semen during examinations because commercial samples were unavailable, and to dry samples on swabs in the open air, Iredale said.

"His lab table was side-by-side with that of the analyst who was working on Claire Hough's case, and the fact is that it's highly likely that the result on the single swab of a tiny amount of Kevin Brown's DNA was not the result of it having been deposited on the body of Claire Hough at the time of her death, but as a result of cross-contamination," Iredale said.

Brown's widow, Rebecca Blakely Brown, describe her husband of 21 years as introverted, gentle and loving.

"He was not a rapist and a killer," she said. "He was a quiet good man who devoted his life to helping people -- and helping, he thought, by putting away bad guys and doing his job."

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Attorney: Worker linked to murder by tainted DNA

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Whole genome MLST: The Quality assessment window (BioNumerics 7.5) – Video

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Whole genome MLST: The Quality assessment window (BioNumerics 7.5)
In this video the Quality Assessment window is covered. This window summarizes the results obtained from the calculation engine (the quality of the output, t...

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DaiDai Genome DT – Video

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DaiDai Genome DT

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DaiDai Genome DT - Video

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~Smooches~ | 60 Seconds of Beauty | How To Winterize Your Face | Eczema Relief! – Video

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~Smooches~ | 60 Seconds of Beauty | How To Winterize Your Face | Eczema Relief!
PLEASE SUBSCRIBE...continuing with my series entitled, Smooches, 60 seconds of Beauty...I wanted to give u all an easy way to protect your face/skin from the harsh winter weather. It gets pretty...

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A*STAR scientists discover gene critical for proper brain development

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PUBLIC RELEASE DATE:

18-Dec-2014

Contact: Vithya Selvam vithya_selvam@a-star.edu.sg 656-826-6291 Biomedical Sciences Institutes (BMSI) @astarhq

Scientists at A*STAR's Institute of Medical Biology (IMB) and Institute of Molecular and Cellular Biology (IMCB) have identified a genetic pathway that accounts for the extraordinary size of the human brain. The team led by Dr Bruno Reversade from A*STAR in Singapore, together with collaborators from Harvard Medical School, have identified a gene, KATNB1, as an essential component in a genetic pathway responsible for central nervous system development in humans and other animals.

By sequencing the genome of individuals of normal height but with a very small head size, the international team revealed that these individuals had mutations in the KATNB1 gene, indicating that this gene is important for proper human brain development. Microcephaly (literally meaning "small head" in Latin) is a condition often associated with neurodevelopmental disorders. Measured at birth by calculating the baby's head circumference, a diagnosis of microcephaly is given if it is smaller than average.

Microcephaly may stem from a variety of conditions that cause abnormal growth of the brain during gestation or degenerative processes after birth, all resulting in a small head circumference. In general, individuals with microcephaly have a reduced life expectancy due to reduced brain function which is often associated with mental retardation.

The team also carried out further experiments to determine the function of KATNB1, whose exact mode of action was previously unknown in humans. Using organisms specifically designed to lack this gene, they realised that KATNB1 is crucial for the brain to reach its correct size. Zebrafish and mice embryos without this gene could not live past a certain stage and showed dramatic reduction in brain and head size, similar to the human patients. Their results were published in the 17 December 2014 online issue of Neuron, the most influential journal in the field of Neuroscience.

Sequencing and screening for this particular gene before birth or at birth might also help to detect future neurocognitive problems in the general population. Dr Reversade said, "We will continue to search for other genes important for brain development as they may unlock some of the secrets explaining how we, humans, have evolved such cognitive abilities."

Prof Birgit Lane, Executive Director of IMB, said, "This is one of a small number of genes that scientists have found to be vital for brain development. The work is therefore an important advance in understanding the human brain. The team's findings provide a new platform from which to look further into whether - and how - this gene can be used for targeted therapeutic applications."

Prof Hong Wanjin, Executive Director of IMCB, said, "This coordinated effort shows the increasingly collaborative nature of science. As the complexity and interdisciplinary nature of research evolves, so do the networks of collaborations between research institutes at A*STAR and across continents."

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UCLA launches revolutionary "big-data" research institute

Posted: at 2:43 pm

Provided by Stuart Wolpert, UCLA

A new research institute at UCLA may eventually provide doctors with tools to more accurately tailor medicines for individual patients, which could both improve quality of care and minimize the side effects associated with todays medicine.

TheInstitute for Quantitative and Computational Biosciences (QCB) will employ multidisciplinary researchto study how molecules and genes interact. Its goal: unlocking the biological basis of health and disease by tapping the power of big data and computational modeling.

UCLAs Institute for Quantitative and Computational Biosciences will have a major, positive impact on human health, said UCLA Chancellor Gene Block. It will engage exceptional faculty from the life sciences and physical sciences, and our David Geffen School of Medicine and Henry Samueli School of Engineering and Applied Science to ensure that UCLA is at the forefront of research that will help usher in a new era of personalized health care, and to transform research and education in the biosciences.

The institute is led by Alexander Hoffmann, professor of microbiology, immunology and molecular genetics in the UCLA College, whose research aims to understand how our genes interact to ensure health or produce disease and the roles played by such factors as food, environmental stresses, infectious agents and pharmaceuticals. Among the diseases for which Hoffmanns research may lead to significant progress are cancer and immune disorders, because they are caused by errors in cellular decision-making.

Hoffmann says that biologys million-dollar question is how genes and environment interact to ensure health or cause disease, he said. As UCLA researchers work to answer that question, they will collaborate with UCLA mathematicians who will create mathematical models that help them make sense of a tsunami of biological data.

Biology is entering a new phase, Hoffmann said. So far, biology has been much less math-based than the other sciences. Since the sequencing of the human genome in the early 2000s, there has been an irreversible change in the way biology and biomedical research are being done. At UCLA, we will lead research in that direction and connect basic and applied sciences in an unprecedentedly productive collaboration.

Victoria Sork, dean of the UCLA Division of Life Sciences, said the institutes approach represents the new life sciences and predicts that the new center will accelerate discovery and translational application in many areas, including medicine, the environment, energy, and food production and food safety.

Technological breakthroughs are enabling scientists to analyze not only one gene at a time, but how hundreds or thousands of genes work together, Sork said. Combined with big data, new knowledge of critical gene networks will lead us to a better understanding of what makes humans healthy.

The road to precision medicine

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THE CENSORSHIP OF PRO-ATHLETES – Video

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THE CENSORSHIP OF PRO-ATHLETES
When it comes to pro athletes #39; apparel, the rules may be written in stone, but they #39;re not always enforced.

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Face-sitting porn demonstrators protest against censorship laws outside Parliament – Video

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Face-sitting porn demonstrators protest against censorship laws outside Parliament
Dozens of protesters gathered outside the Houses of Parliament to participate in a mass face-sitting demonstration on 12 December to express their dismay at ...

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Rant: Hatred, Steam Greenlight, and Censorship (TF2 Gameplay) – Video

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Rant: Hatred, Steam Greenlight, and Censorship (TF2 Gameplay)
This is the first time I #39;ve ranted like this, but I really needed to let some stuff out after Valve #39;s recent decision making. I do have a Steam Curator Group that you can join for more game...

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