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Showing posts with label Mapping. Show all posts
Showing posts with label Mapping. Show all posts

Adrian Bird wins the Frontiers of Knowledge Award for mapping gene activation and introducing new prospects to cure neurological disorders

MADRID, Jan. 28, 2014 /PRNewswire/ -- The sixth annual BBVA Foundation Frontiers of Knowledge Award in the Biomedicine category goes to British biochemist Adrian Bird, "for his discoveries in the field of epigenetics." Bird's achievements includes mapping DNA regions where genes are activated by the addition of a type of molecule known as a methyl group, in a process known as methylation. This contribution is of a fundamental nature, since DNA methylation, as the jury explains, "plays a crucial role in many diseases and in the progression of nearly all types of cancer."

In the words of the award citation: "In a mammal, all cells have the same DNA sequence. However, cells involved in different functions express distinct subsets of genes. These different expression patterns are stabilized through epigenetic marks, of which DNA methylation was the first to be discovered and characterized. DNA methylation marks are inherited as cells divide, and in some cases inherited across generations."

His work on methylation would later lead Bird to a discovery which could prove game-changing in the neurosciences domain. In experiments with mice, he found that by correcting defects in a protein associated with a severe form of autism known as Rett syndrome, the symptoms of the condition disappeared. "This is the first time that a neurological disease has been reversed in an experimental context, and offers hope that this approach can be translated into the clinic," the citation continues.

This result, obtained in 2007, has refocused research efforts on this congenital condition, which affects girls – one in every 10,000 – and causes severe mental retardation and the progressive and persistent loss of cognitive and motor skills. Bird has since combined his basic research with an active involvement in the quest "to do in humans what we have done in mice," he explained on the phone yesterday. "I used to be quite content with myself just pursuing knowledge. But to see that your research can have such practical relevance in people's lives adds a new dimension, and makes the whole thing more exciting and engaging," he remarked during the same conversation, after stating his surprise and gratitude for the jury's decision.

Importance in cancer and aging

Epigenetic changes in the genome occur naturally during embryonic development and throughout life. They are also the mechanism through which the environment impacts our genes – smoking, for instance, affects DNA methylation. So understanding how these changes happen is a vital first step in order to understand diseases like Rett syndrome, and clarify the ways in which lifestyle and environmental factors influence cancer.

"DNA methylation is organized in a pattern, which is slightly different in each cell. And in the case of cancer cells, we know that these patterns are really messed up," Bird explains. "Although the relationship between DNA methylation and cancer is not fully understood, it seems pretty clear that certain genes in the tumor cell that depend on the absence of methylation become methylated and are shut down in consequence, which facilitates the development of cancer."

By the late seventies, scientists knew a relationship existed between methylation and gene activation, but not how it worked. Bird obtained the first ever DNA methylation map, defining the regions where the process unfolds.

New hope for Rett syndrome

Bird not only revealed the precise form of organization of "the regions within the genome marked by DNA methylation," the jury remarks, but also "identified proteins that read the DNA methylation signals, mutation of which leads to human diseases."

His discovery of the MeCP2 protein that detects methylation signals in the genome occurred in the early nineties, before the human genome was sequenced. It was therefore a "huge surprise" to me and everyone, recalls Bird;  once he was able to show, at the end of that decade, that it was a mutation in this protein that causes Rett syndrome.

Even more remarkable was his achievement in reversing the disorder in an animal model. In 2001, Bird switched research tactics and created a mouse with the Rett syndrome genetic defect, presenting all the symptoms of the disease. In 2007, he found a way to activate the correct protein in these laboratory animals, and the symptoms disappeared.

"We didn't expect it because it was assumed that once you have a neurological disorder, you have it forever. We thought we might, with luck, delay the animals' death or perhaps alleviate some of the symptoms," Bird reflects. "But what we got was a clear result, a spectacular improvement. It was one of those Eureka moments."

The new laureate explained at a press event this morning that his experiment to treat mice with Rett syndrome started from the fact that the disease is not accompanied by the death of neurons, so it was theoretically possible to restore them to a fully functional state. This characteristic is shared by fragile X syndrome, another disabling hereditary disorder.

"We are still far from finding a cure for these diseases, but our work provides a proof of concept that has got a lot of other research groups involved in the search for therapies."

Bird admits to feeling pressured by the thought of people waiting for a cure and "frustrated" at the failure, so far, to replicate his results in human subjects. He also warns that "we cannot be sure" if the same cure will work in humans. Nevertheless, the hope felt by many families is not, in his view, unfounded: "The parents know it will take time, and that their daughters might not benefit from the advances. But they also know that there are lots of labs around the world working on curing Rett syndrome, and that wasn't the case before."

Adrian Bird was nominated for the award by David Leach, Head of the School of Biological Sciences at the University of Edinburgh

Bio notes

Sir Adrian Peter Bird earned his PhD in biochemistry from the University of Edinburgh in 1972. He then went on to occupy post-doctoral positions at the universities of Yale (United States) and Zurich (Switzerland). On returning to Edinburgh in 1975, he joined the Mammalian Genome Unit (Medical Research Council) where he would remain for eleven years. His next move was to Vienna, where he worked as a senior scientist in the Research Institute for Molecular Pathology.

In 1990, he was appointed to the Buchanan Chair of Genetics at the University of Edinburgh, a position he still holds today and which he combined for a time with the directorship of the same institution's Wellcome Trust Centre for Cell Biology.

He is a former governor of the Wellcome Trust (among the world's leading funders of medical research), serving for three years as its Deputy Chairman.

Author of more than 150 publications in international science journals, he is a Commander of the British Empire (2005) and has received numerous awards and honors, including a knighthood in 2014.

The BBVA Foundation Frontiers of Knowledge Awards

The BBVA Foundation promotes, funds and disseminates world-class scientific research and artistic creation, in the conviction that science, culture and knowledge in its broadest sense hold the key to a better future for people. The Foundation designs and implements its programs in partnership with leading scientific and cultural organizations in Spain and abroad, seeking to identify and prioritize those projects with the power to move forward the frontiers of the known world.

The BBVA Foundation established its Frontiers of Knowledge Awards in 2008 to recognize the authors of outstanding contributions and radical advances in a broad range of scientific and technological areas congruent with the knowledge map of the late 20th and 21st centuries, and others that address central challenges, such as climate change and development cooperation, deserving of greater visibility and recognition. Their eight categories include classical areas like Basic Sciences (Physics, Chemistry and Mathematics) and Biomedicine, and other, more recent areas characteristic of our time, ranging from Information and Communication Technologies, Ecology and Conservation Biology, Climate Change and Economics, Finance and Management to Development Cooperation and the innovative realm of artistic creation that is Contemporary Music.

The juries in each category are made up of leading international experts in their respective fields, whose involvement endorses the rigor of the awards and has indeed been instrumental in consolidating their prestige. The BBVA Foundation is aided in the organization of the awards by the Spanish National Research Council (CSIC), the country's premier multidisciplinary research organization. As well as proposing each jury chair, the CSIC is responsible for appointing the Technical Evaluation Committees that undertake an initial assessment of candidates and draw up a reasoned shortlist for the consideration of the juries.

In the Biomedicine category, Committee members were Dolores Gonzalez-Pacanowska, research scientist at the Instituto de Parasitologia y Biomedicina "Lopez-Neyra" (IPBLN), and coordinator of the Council's Biology and Medicine Area; Rafael Giraldo, research scientist at the Biological Research Center (CIB); V?ctor de Lorenzo, research scientist at the Spanish National Center for Biotechnology (CNB), working with an ERC Advanced Grant; Sergio Moreno, research scientist at the Instituto de Biologia Funcional y Genomica (IBFG, a joint center of CSIC and the University of Salamanca); and Angela Nieto, research scientist at the Instituto de Neurociencias de Alicante (CSIC- Miguel Hernandez University).

Biomedicine jury

The jury in this category was chaired by Angelika Schnieke, Chair of Livestock Technology in the Department of Animal Science at Technische Universitat Munchen (TUM) (Germany). The secretary was Oscar Marin, Research Professor in the Department of Developmental Neurobiology at the Instituto de Neurociencias de Alicante, a joint center of CSIC and Miguel Hernandez University (Spain). Remaining members were Dario Alessi, Director of the Protein Phosphorylation Unit, a Medical Research Council unit in the College of Life Sciences at the University of Dundee (United Kingdom); Mariano Barbacid, leader of the Experimental Oncology Group at the Spanish National Cancer Research Centre (CNIO); Robin Lovell-Badge, Head of the Division of Stem Cell Biology and Developmental Genetics at the MRC National Institute for Medical Research (United Kingdom); Ursula Ravens, Head of the Department of Pharmacology and Toxicology in the Carl Gustav Carus Medical School of Technische Universitat Dresden (TU Dresden) (Germany); and Bruce Whitelaw, Head of the Developmental Biology Division at The Roslin Institute, a basic and translational research center belonging to the University of Edinburgh (United Kingdom).

Previous laureates

The award in the last edition was shared by chemist Douglas Coleman and physician Jeffrey Friedman for "revealing the existence of the genes involved in the regulation of appetite and body weight, a discovery crucial to our understanding of human pathologies such as obesity." In the fourth edition, the award went to Alexander Varshavsky for "discovering the mechanisms involved in protein degradation." Preceding him were Shinya Yamanaka for his achievements "showing that it is possible to reprogram differentiated cells back into a state that is characteristic of pluripotent cells," and Robert Lefkowitz for "his discoveries of the seven transmembrane receptors." Finally, the winner in the inaugural edition was Joan Massague for "developing novel approaches to identify genes involved in organ-specific metastasis."

UPCOMING AWARD ANNOUNCEMENTS

Ecology and Conservation Biology

Economics, Finance and Management

www.fbbva.es

SOURCE BBVA Foundation

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UC Davis Purchases Irys System From BioNano Genomics To Advance Genome Mapping And Assembly Of Wheat Relative

SAN DIEGO, Jan. 13, 2014 /PRNewswire/ -- BioNano Genomics announced today the purchase of an Irys™ System by UC Davis to assist, among other projects, in completing the genome assembly of Aegilops tauschii, one of three progenitors of today's bread wheat. The team of researchers at UC Davis, led by Dr. Jan Dvorak, will use the Irys System in their workflow as they determine the sequence, location, and orientation of all genes and transposable elements of the A. tauschii genome.  This information will be used to advance the assembly and analysis of the wheat genome sequence, which is known to be five times larger and significantly more complex than the human genome.

"Among the world's essential crops for human and animal food, the wheat genome has yet to be fully realized because of its complexity," said Erik Holmlin, president and CEO of BioNano Genomics. "The UC Davis team's research with A. tauschii will help determine how wheat genome is organized and contribute to the large international effort to decode the genome of one of the world's most important food crops."

"To date, very few high-quality assemblies are available for large and complex genomes, like wheat, because we have inaccurate, low-resolution physical maps on which to arrange DNA sequence information," stated Han Cao, Ph.D., founder and chief scientific officer of BioNano Genomics. "The Irys System provides a high-resolution genome map upon which DNA sequences can quickly and accurately be organized."

Ancestor Gives Clues to Today's Wheat

Bread wheat (Triticum aestivum L.) is a hexaploid species containing three different ancestral genomes (designated A, B, and D), each of which has seven pairs of chromosomes. In addition, approximately 90 percent of the wheat genome is made up of repetitive stretches of DNA, making the assembly of an accurate and complete genome map and genome sequence extremely difficult. As the progenitor to wheat's D genome, A. tauschii is a wild grass that spontaneously hybridized with cultivated tetraploid wheat 8,000 years ago, producing what we know today as bread wheat.

"In order to complete the sequence of a large genome, like that of wheat, we need to know how all the genes are organized within each chromosome and the length and location of the many long areas of repeats," said Ming-Cheng Luo, Ph.D., research geneticist in the Department of Plant Sciences at UC Davis and co-PI on the A. tauschii sequencing project. "Despite advances in high-throughput sequencing, accurate de novo assembly of a genome has previously been the weak link in genomics research."  

To assemble a genome de novo (from scratch), scientists must determine how the small lengths of DNA sequences generated from short-read next generation sequencing (NGS) methods are organized in the whole genome. BioNano's Irys System is a genome mapping technology that fills a void in de novo assemblies by providing a high-resolution physical genome map to anchor and organize DNA sequence information to dramatically improve the fidelity of the final genome assembly. 

"Last year, we worked with BioNano to generate Irys data that allowed us to quickly create and publish a high-resolution genome map of a particularly complex region of Aegilops tauschii genome," said Dr. Luo. "Based on the success of that collaboration, we have decided to acquire our own Irys system, and we will build upon that research to create an accurate draft of the entire D genome sequence. Once completed, the high-quality draft of A. tauschii D genome can be used by the global research community to predict gene locations and accelerate genome sequencing and assembly of wheat and its relatives."

New Technologies Are Reducing the Costs of Genome Research

Assembling a genome to completion has previously been an intractable problem because researchers have not been able to easily visualize repetitive elements and structural variations. All genomes contain structural variations, which include large sections of repeats, deletions, duplications, insertions, inversions, translocations, and copy-number variants.  

BioNano's Irys System is an automated, long-read technology that allows for precise and accurate visualization of the underlying organization and structural variation of extended stretches of DNA.

"NGS methods, where the DNA is cut into smaller pieces to be sequenced, loses structural information making genome assembly an inaccurate, labor-intensive and costly task," said Dr. Luo. "With BioNano's Irys System, we can actually retain the long-range contiguity of the DNA, which allows us to accurately assemble and finish genomes as well as compare the structural variations that exist among different genomes to learn how an organism has genetically adapted to changing environments."

Dr. Cao added, "The hidden costs in sequencing are assembly, analysis, and annotation of the genome.  Rapid and accurate de novo map assembly with BioNano's technology makes sequencing projects less expensive by streamlining the process and providing a genome map with unprecedented quality and accurate structural variation information.  Our technology actually reduces backend analysis costs so that researchers can expand the number of genomes that can be studied, thus supporting more comprehensive surveys and comparisons among genomes."

Safeguarding Wheat's Future

The United Nations has said that harvest yield of wheat will need to increase by 60 percent by 2050 to meet the dietary needs for our expected population growth. However, wheat output has recently plateaued causing alarm in the wheat research and production community. A more complete genomic map of wheat and ultimately genome sequence could provide important information on how wheat adapts to drought, disease, and temperature changes.

Dr. Luo concluded, "With our recent grant from the National Science Foundation and the integration of the Irys System and the new high-throughput V2 chips into our workflow, we will be able to quickly complete a high-quality draft of the A. tauschii genome. By decoding the sequences of all genes and determining their locations and orientations relative to each other, wheat geneticists will be able to identify changes in the wheat genome that are responsible for the high productivity of modern cultivars. This knowledge and more efficient breeding techniques based on an accurate wheat genome sequence will accelerate breeding of new, more productive varieties."

To learn more: BioNano Genomics will be hosting a workshop at the upcoming International Plant and Animal Genomes Conference held in San Diego on Tuesday, January 14, at 1:30PM. Presentations will include results generated with the Irys System on wheat and other crop plants.

About Irys

Irys makes it possible to routinely and accurately detect genomic structural variation and to finish genome assemblies. The fully automated Irys benchtop instrument uses the IrysChip to uncoil and confine long DNA molecules in proprietary Nanochannel Arrays™ where they are uniformly linearized in a highly parallel display for high-resolution, single-molecule imaging. Irys does not employ DNA fragmentation or amplification, which are typical with next-generation sequencing. The result is sequence information over extremely long "reads" ranging from hundreds of kilobases to a megabase, where the sample's valuable structural information is preserved. Irys makes it possible for researchers to directly observe structural variants including replications, deletions, translocations and inversions.

About BioNano Genomics

Headquartered in San Diego, BioNano Genomics is delivering an altogether better way of gaining a fully informed understanding of genomes. The Company's platform provides researchers and clinicians the most comprehensive, organized and actionable picture of a genome with unprecedented insights into how the individual components of genomes are ordered, arranged, and interact with each other. BioNano Genomics works with institutions in life science, translational research, molecular diagnostics and personalized medicine. The Company is supported by private investors and grant funding from genomics programs at federal agencies, including the NIH and NIST-ATP.

www.BioNanoGenomics.com

Notes: BioNano Genomics is a trademark of BioNano Genomics, Inc. Any other names of actual companies, organizations, entities, products or services may be the trademarks of their respective owners.

SOURCE BioNano Genomics

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