Whole genome analysis speeds up: 240 full genomes in 50 hours

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Although the time and cost of sequencing an entire human genome has plummeted, analyzing the resulting three billion base pairs of genetic information from a single genome can take many months.In the journal Bioinformatics, however, a University of Chicago-based team — working with Beagle, one of the world’s fastest supercomputers devoted to life sciences — reports that genome analysis can be radically accelerated. This computer, based at Argonne National Laboratory, is able to analyze 240 full genomes in about two days.”This is a resource that can change patient management and, over time, add depth to our understanding of the genetic causes of risk and disease,” said study author Elizabeth McNally, MD, PhD, the A. J. Carlson Professor of Medicine and Human Genetics and director of the Cardiovascular Genetics Clinic at the University of Chicago Medicine.”The supercomputer can process many genomes simultaneously rather than one at a time,” said first author Megan Puckelwartz, a graduate student in McNally’s laboratory. “It converts whole genome sequencing, which has primarily been used as a research tool, into something that is immediately valuable for patient care.”Because the genome is so vast, those involved in clinical genetics have turned to exome sequencing, which focuses on the two percent or less of the genome that codes for proteins. This approach is often useful. An estimated 85 percent of disease-causing mutations are located in coding regions. But the rest, about 15 percent of clinically significant mutations, come from non-coding regions, once referred to as “junk DNA” but now known to serve important functions. If not for the tremendous data-processing challenges of analysis, whole genome sequencing would be the method of choice.To test the system, McNally’s team used raw sequencing data from 61 human genomes and analyzed that data on Beagle. They used publicly available software packages and one quarter of the computer’s total capacity. …


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#Alzheimer, #Beagle, #Cancer, #Chicago, #Computing, #Gene, #Human, #Medicine, #Washington

Addicts and Disease

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Commentary.Former National Institute on Drug Abuse (NIDA) director Alan Leshner has been vilified by many for referring to addiction as a chronic, relapsing “brain disease.” What often goes unmentioned is Leshner’s far more interesting characterization of addiction as the “quintessential biobehavioral disorder.”Multifactorial illnesses present special challenges to our way of thinking about disease. Addiction and other biopsychosocial disorders often show symptoms at odds with disease, as people generally understand it. For patients and medical professionals alike, questions about the disease aspect of addiction tie into larger fears about the medicalization of human behavior.These confusions are mostly understandable. Everybody knows what cancer is—a disease of the cells. Schizophrenia? Some kind of brain illness. But addiction? Addiction strikes many people as too much a part …


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#Addiction-Disease, #Attractions, #Credit, #Drug, #Family-Disease, #Field, #Human, #King, #Psychiatry, #University

Zebrafish neurons may lead to understanding of birth defects like spina bifida

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The zebrafish, a tropical freshwater fish similar to a minnow and native to the southeastern Himalayan region, is well established as a key tool for researchers studying human diseases, including brain disorders. Using zebrafish, scientists can determine how individual neurons develop, mature and support basic functions like breathing, swallowing and jaw movement. Researchers at the University of Missouri say that learning about neuronal development and maturation in zebrafish could lead to a better understanding of birth defects such as spina bifida in humans.”We are studying how neurons move to their final destinations,” said Anand Chandrasekhar, professor of biological sciences and a researcher in the Bond Life Sciences Center at MU. “It’s especially critical in the nervous system because these neurons are generating circuits similar to what you might see in computers. If those circuits don’t form properly, and if different types of neurons don’t end up in the right locations, the behavior and survival of the animal will be compromised.”The scientists studied zebrafish embryos, which are nearly transparent, making internal processes easy to observe. Using modified zebrafish expressing green fluorescent jellyfish protein, Chandrasekhar and his team were able to track neuronal migration.”This approach is used extensively to visualize a group of cells,” Chandrasekhar said. “In our study, clusters of green cells glowed and indicated where motor neurons were located in the brain. Some groupings are shaped like sausages while others are round, but each cluster of 50 to150 cells sends out signals to different groups of jaw muscles.”These motor neurons that Chandrasekhar studied are located in the hindbrain, which corresponds to the human brainstem and controls gill and jaw movement in these tiny fish. Genes controlling the development and organization of these neurons in zebrafish are functionally similar to genes in higher vertebrates including mammals.Chandrasekhar’s work contributes to a better understanding of how neuronal networks are organized and “wired” during development. These studies also may provide insight into birth defects like spina bifida, which affects 1 in every 2,000 births, according to the National Institutes of Health.”One of the hallmarks of spina bifida is an open neural tube in the spinal cord,” Chandrasekhar said. …


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#Biology, #Birth, #Chandrasekhar, #Development, #Health, #Human, #National, #Process, #Researchers

Traditional Medicine: Environment change threatens indigenous know-how

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The way indigenous cultures around the globe use traditional medicines and pass on knowledge developed over centuries is directly linked to the natural environment, new research has found.This makes indigenous cultures susceptible to environmental change, a threat that comes on top of the challenges posed by globalisation.”Traditional medicine provides health care for more than half the world’s population, with 80 per cent of people in developing countries relying on these practices to maintain their livelihood. It is a very important part of traditional knowledge,” says Dr Haris Saslis-Lagoudakis, from The Australian National University’s (ANU) Research School of Biology.”This knowledge is typically passed down from generation to generation, or it is ‘borrowed’ from neighbours. Because of this borrowing, globalisation can homogenise medicinal practices of different communities, leading to loss of medicinal remedies.”But this is not the only challenge that indigenous cultures face.”Imminent changes in the environment also pose a threat to traditional knowledge,” explains Dr Saslis-Lagoudakis.”Traditional medicine utilises plants and animals to make natural remedies. Despite a lot of these species being under threat due to ongoing climatic changes and other human effects on the environment, the effect that these changes can have on traditional medicine is not thoroughly understood.”Dr Saslis-Lagoudakis and a team of international researchers led by the University of Reading (UK) investigated how the environment shapes medicinal plant use in indigenous cultures, specifically Nepal, a country in the Himalayans that has outstanding cultural, environmental and biological diversity.”By understanding the relationship between environment and traditional knowledge, we can then understand how cultures have responded to changes in the environment in the past,” he says.The team studied 12 ethnic groups from Nepal and recorded what plants different cultures use in traditional medicine. They calculated similarities in their medicinal floras and also calculated similarities in the floras these cultures are exposed to, how closely related they are, and their geographic separation.”We found that Nepalese cultures that are exposed to similar floras use similar plant medicines.”Although shared cultural history and borrowing of traditional knowledge among neighbouring cultures can lead to similarities in the plants used medicinally, we found that plant availability in the local environment has a stronger influence on the make-up of a culture’s medicinal floras.”Essentially, this means that the environment plays a huge role in shaping traditional knowledge. This is very important, especially when you think of the risks that these cultures are already facing.”Due to ongoing environmental changes we are observing across the globe, we might lose certain plant species which will lead to changed ecosystems, and an overall poorer natural environment. This will then affect what plants people can use around them.”We should be concerned about the fate of the traditional knowledge of these cultures. However, understanding the factors that shape traditional knowledge can provide the underpinnings to preserve this body of knowledge and predict its future.”Story Source:The above story is based on materials provided by Australian National University. Note: Materials may be edited for content and length.


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#Cancer, #Human, #International, #Knowledge, #National, #Nepal, #Nepalese, #Research, #Science, #World

Nanomotors are controlled, for the first time, inside living cells

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For the first time, a team of chemists and engineers at Penn State University have placed tiny synthetic motors inside live human cells, propelled them with ultrasonic waves and steered them magnetically. It’s not exactly “Fantastic Voyage,” but it’s close. The nanomotors, which are rocket-shaped metal particles, move around inside the cells, spinning and battering against the cell membrane.”As these nanomotors move around and bump into structures inside the cells, the live cells show internal mechanical responses that no one has seen before,” said Tom Mallouk, Evan Pugh Professor of Materials Chemistry and Physics at Penn State. “This research is a vivid demonstration that it may be possible to use synthetic nanomotors to study cell biology in new ways. We might be able to use nanomotors to treat cancer and other diseases by mechanically manipulating cells from the inside. Nanomotors could perform intracellular surgery and deliver drugs noninvasively to living tissues.”The researchers’ findings will be published in Angewandte Chemie International Edition on 10 February 2014. In addition to Mallouk, co-authors include Penn State researchers Wei Wang, Sixing Li, Suzanne Ahmed, and Tony Jun Huang, as well as Lamar Mair of Weinberg Medical Physics in Maryland U.S.A.Up until now, Mallouk said, nanomotors have been studied only “in vitro” in a laboratory apparatus, not in living human cells. Chemically powered nanomotors first were developed ten years ago at Penn State by a team that included chemist Ayusman Sen and physicist Vincent Crespi, in addition to Mallouk. “Our first-generation motors required toxic fuels and they would not move in biological fluid, so we couldn’t study them in human cells,” Mallouk said. “That limitation was a serious problem.” When Mallouk and French physicist Mauricio Hoyos discovered that nanomotors could be powered by ultrasonic waves, the door was open to studying the motors in living systems.For their experiments, the team uses HeLa cells, an immortal line of human cervical cancer cells that typically is used in research studies. …


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#Cancer, #Cell, #Fantastic, #French, #Human, #International, #Mallouk, #Physics, #State, #Story, #University