Category Archives: Genome

XROMA - CHROMOSOME 11 - HD - THE HUMAN GENOME MUSIC PROJECT
Chromosome 11 from The Human Genome Music Project by UK Composer Stuart Mitchell - Real-time Genome Music - 3000 BPM.

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XROMA - CHROMOSOME 11 - HD - THE HUMAN GENOME MUSIC PROJECT - Video

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25-Apr-2014

Contact: Sue McGreevey smcgreevey@partners.org 617-724-2764 Massachusetts General Hospital

A next-generation genome editing system developed by Massachusetts General Hospital (MGH) investigators substantially decreases the risk of producing unwanted, off-target gene mutations. In a paper receiving online publication in Nature Biotechnology, the researchers report a new CRISPR-based RNA-guided nuclease technology that uses two guide RNAs, significantly reducing the chance of cutting through DNA strands at mismatched sites.

"This system combines the ease of use of the widely adopted CRISPR/Cas system with a dimerization-dependent nuclease activity that confers higher specificity of action," says J. Keith Joung, MD, PhD, associate chief for Research in the MGH Department of Pathology and senior author of the report. "Higher specificity will be essential for any future clinical use of these nucleases, and the new class of proteins we describe could provide an important option for therapeutic genome editing."

Engineered CRISPR-Cas nucleases genome-editing tools that combine a short RNA segment matching its DNA target with a DNA-cutting enzyme called Cas9 have been the subject of much investigation since their initial development in 2012. Easier to use than the earlier ZFN (zinc finger nuclease) and TALEN (transcription activator-like effector nuclease) systems, they have successfully induced genomic changes in several animal models systems and in human cells. But in a previous Nature Biotechnology paper published in June 2013, Joung's team reported that CRISPR-Cas nucleases could produce additional mutations in human cells, even at sites that differed from the DNA target by as much as five nucleotides.

To address this situation, the investigators developed a new platform in which the targeting function of Cas9 was fused to a nuclease derived from a well-characterized enzyme called Fokl, which only functions when two copies of the molecule are paired, a relationship called dimerization. This change essentially doubled the length of DNA that must be recognized for cleavage by these new CRISPR RNA-guided Fokl nucleases (RFNs), significantly increasing the precision of genome editing in human cells. Importantly, Joung and his colleagues also demonstrated that these new RFNs are as effective at on-target modification as existing Cas9 nucleases that target a shorter DNA sequence.

"By doubling the length of the recognized DNA sequence, we have developed a new class of genome -editing tools with substantially improved fidelity compared with existing wild-type Cas9 nucleases and nickases (enzymes that cleave a single DNA strand)," says Joung, an associate professor of Pathology at Harvard Medical School. The research team also has developed software enabling users to identify potential target sites for these RFNs and incorporated that capability into ZiFiT Targeter, a software package freely available at http://zifit.partners.org.

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Lead author of the Nature Biotechnology report is Shengdar Tsai, PhD, of the MGH Molecular Pathology Unit. Additional co-authors are Nicolas Wyvekens, Cyd Khayter, Jennifer Foden, Vishal Thapar, Deepak Reyon, PhD, Mathew Goodwin and Martin Aryee, PhD, all of MGH Molecular Pathology. The study was supported by National Institutes of Health Director's Pioneer Award DP1 GM105378; NIH grants R01 GM088040, P50 HG005550, and R01 AR063070; and by the Jim and Ann Orr Massachusetts General Hospital MGH Research Scholar Award. Joung is a co-founder of Editas Medicine, Inc., which has an exclusive option to license the new CRISPR RNA-guided Fokl nuclease technology for therapeutic applications.

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New genome-editing platform significantly increases accuracy of CRISPR-based systems

Large sections of the genome that were once referred to as "junk" DNA have been linked to human heart failure, according to research from Washington University School of Medicine in St. Louis.

So-called junk DNA was long thought to have no important role in heredity or disease because it doesn't code for proteins. But emerging research in recent years has revealed that many of these sections of the genome produce RNA molecules that, despite not being proteins, still have important functions in the body. RNA is a close chemical cousin to DNA.

Molecules now associated with these sections of the genome are called noncoding RNAs. They come in a variety of forms, some more widely studied than others. Of these, about 90 percent are called long noncoding RNAs, and exploration of their roles in health and disease is just beginning.

In a recent issue of the journal Circulation, Washington University investigators report results from the first comprehensive analysis of all RNA molecules expressed in the human heart. The researchers studied nonfailing hearts and failing hearts before and after patients received pump support from left ventricular assist devices (LVAD). The LVADs increased each heart's pumping capacity while patients waited for heart transplants.

"We took an unbiased approach to investigating which types of RNA might be linked to heart failure," said senior author Jeanne M. Nerbonne, PhD, the Alumni Endowed Professor of Molecular Biology and Pharmacology. "We were surprised to find that long noncoding RNAs stood out. In fact, the field is evolving so rapidly that when we did a slightly earlier, similar investigation in mice, we didn't even think to include long noncoding RNAs in the analysis."

Heart failure refers to a gradual loss of heart function. The left ventricle, the heart's main pumping chamber, becomes less efficient. Blood flow diminishes, and the body no longer receives the oxygen needed to go about daily tasks. Sometimes the condition develops after an obvious trigger such as a heart attack or infection, but other times the causes are less clear.

In the new study, the investigators found that unlike other RNA molecules, expression patterns of long noncoding RNAs could distinguish between two major types of heart failure and between failing hearts before and after they received LVAD support.

"We don't know whether these changes in long noncoding RNAs are a cause or an effect of heart failure," Nerbonne said. "But it seems likely they play some role in coordinating the regulation of multiple genes involved in heart function."

Nerbonne pointed out that all types of RNA molecules they examined could make the obvious distinction: telling the difference between failing and nonfailing hearts. But only expression of the long noncoding RNAs was measurably different between heart failure associated with a heart attack (ischemic) and heart failure without the obvious trigger of blocked arteries (nonischemic). Similarly, only long noncoding RNAs significantly changed expression patterns after implantation of left ventricular assist devices.

Because of the difficulty in obtaining human heart tissue, the study's sample size was relatively small, Nerbonne said. Her team analyzed eight nonfailing hearts, eight hearts in ischemic heart failure and eight hearts in nonischemic heart failure. Though small, the study is unique because each of the 16 failing hearts was sampled twice, once before and once after LVAD support.

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Genome regions once mislabeled 'junk' linked to heart failure

Pronounce Medical Words Genome
This video shows you how to say Genome. How would you pronounce Genome?

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Pronounce Medical Words Genome - Video

What are the benefits to society of the Human Genome Project?
Excerpts from New Wedding Planet #39;s Course Video Tutorial: #39;Wedding Entrepreneurship II #39; Learn how to identify the wedding coordinator duties demanded by different client groups in your local...

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What are the benefits to society of the Human Genome Project? - Video

April 25, 2014

Image Caption: This is a golden eagle. Credit: Todd Katzner

Purdue University

Purdue and West Virginia University researchers are the first to sequence the genome of the golden eagle, providing a birds-eye view of eagle features that could lead to more effective conservation strategies.

Their study calls into question long-held assumptions about golden eagle vision, indicating that the raptors may not be as sensitive to ultraviolet light as previously thought. The genome also suggests that golden eagles could have a sharper sense of smell than researchers realized.

Additionally, the genome provides thousands of genetic markers that will help researchers track populations and monitor eagle mortality.

Having the golden eagle genome in hand could directly affect the way we make conservation and management decisions, said Jacqueline Doyle, postdoctoral research associate and first author of the paper.

Though it is one of the most widespread avian species, the golden eagle is threatened throughout much of its range by poaching, shrinking habitats and fatal collisions with wind turbines. An estimated 67 golden eagles are killed annually at a single wind farm the Altamont Pass Wind Resource Area in central California a heavy toll on a species that reproduces slowly and can live up to 30 years, said J. Andrew DeWoody, professor of genetics and senior author of the study.

One recently proposed method of reducing turbine-related eagle deaths was to coat wind turbines with ultraviolet-reflective paint, thereby heightening their visibility to eagles, which were thought to be sensitive to ultraviolet light. But the golden eagle genome suggests that eagle vision is rooted in the violet spectrum like human sight rather than the ultraviolet.

We find little genomic evidence that golden eagles are sensitive to ultraviolet light, Doyle said. Painting wind turbines with ultraviolet-reflective paint is probably not going to prevent eagles from colliding with turbines.

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Genome Of Golden Eagle Could Lead To More Effective Conservation Strategies

Mining the genome of the disease-transmitting tsetse fly, researchers have revealed the genetic adaptions that allow it to have such unique biology and transmit disease to both humans and animals.

The tsetse fly spreads the parasitic diseases human African trypanosomiasis, known as sleeping sickness, and Nagana that infect humans and animals respectively. Throughout sub-Saharan Africa, 70 million people are currently at risk of deadly infection. Human African trypanosomiasis is on the World Health Organization's (WHO) list of neglected tropical diseases and since 2013 has become a target for eradication. Understanding the tsetse fly and interfering with its ability to transmit the disease is an essential arm of the campaign.

This disease-spreading fly has developed unique and unusual biological methods to source and infect its prey. Its advanced sensory system allows different tsetse fly species to track down potential hosts either through smell or by sight. This study lays out a list of parts responsible for the key processes and opens new doors to design prevention strategies to reduce the number of deaths and illness associated with human African trypanosomiasis and other diseases spread by the tsetse fly.

"Tsetse flies carry a potentially deadly disease and impose an enormous economic burden on countries that can least afford it by forcing farmers to rear less productive but more trypanosome-resistant cattle." says Dr Matthew Berriman, co-senior author from the Wellcome Trust Sanger Institute. "Our study will accelerate research aimed at exploiting the unusual biology of the tsetse fly. The more we understand, the better able we are to identify weaknesses, and use them to control the tsetse fly in regions where human African trypanosomiasis is endemic."

The team, composed of 146 scientists from 78 research institutes across 18 countries, analysed the genome of the tsetse fly and its 12,000 genes that control protein activity. The project, which has taken 10 years to complete, will provide the tsetse research community with a free-to-access resource that will accelerate the development of improved tsetse-control strategies in this neglected area of research.

The tsetse fly is related to the fruit fly -- a favoured subject of biologists for more than 100 years -- but its genome is twice as large. Within the genome are genes responsible for its unusual biology. The reproductive biology of the tsetse fly is particularly unconventional: unlike most insects that lay eggs, it gives birth to live young that have developed to a large size by feeding on specialised glands in the mother.

Researchers found a set of visual and odour proteins that seem to drive the fly's key behavioural responses such as searching for hosts or for mates. They also uncovered the photoreceptor gene rh5, the missing link that explains the tsetse fly's attraction to blue/black colours. This behaviour has already been widely exploited for the development of traps to reduce the spread of disease.

"Though human African trypanosomiasis affects thousands of people in sub-Saharan Africa, the absence of a genome-wide map of tsetse biology was a major hindrance for identifying vulnerabilities, says Dr Serap Aksoy, co-senior author from the University of Yale. "This community of researchers across Africa, Europe, North America and Asia has created a valuable research tool for tackling the devastating spread of sleeping sickness."

Tsetse flies have an armament of salivary molecules that are essential for feeding on blood. The team found one family of genes, the tsal genes, that are particularly active in the salivary glands of the tsetse fly. This allows the tsetse fly to counteract the responses from the host to stop bloodfeeding. This finding and several others are explored in more detail in eight research papers that accompany the publication of the tsetse fly genome in Science.

"This information will be very useful to help develop new tools that could reduce or even eradicate tsetse flies," says Dr John Reeder, Director of the Special Programme for Research Training in Tropical Diseases, at WHO. "African sleeping sickness is understudied, and we were very pleased to help bring together so many research groups to work collaboratively with the one shared goal in sight -- the elimination of this deadly disease."

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Tsetse fly genome reveals weaknesses: International 10-year project unravels biology of disease-causing fly

User Comments on Genome Compiler
A description of how to use the User Comments feature with Genome Compiler.

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User Comments on Genome Compiler - Video

Deciphering Nature #39;s Alphabet - 5. Impact of the Human Genome Project
This film describes the impact the Human Genome Project is having on basic research, medical advances and the application of genetic technologies to patients and families. Key inte

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Deciphering Nature's Alphabet - 5. Impact of the Human Genome Project - Video

Deciphering Nature #39;s Alphabet - 4. Imagining the Genome
This film describes the launch of the Human Genome Project, how the idea emerged from the growing genetic engineering capacity, the technologies, politics and finances of genomics. Key inte

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Deciphering Nature's Alphabet - 4. Imagining the Genome - Video