Category Archives: Genome

Bethesda, Maryland, USA (PRWEB) January 06, 2015

Physical maps are the foundation to obtain a complete reference sequence of the bread wheat genome, expected by 2017-18 if funding is available. As part of its roadmap, the IWGSC is currently working on establishing physical maps of the 21 chromosomes of bread wheat. The results announced today concern the chromosome arms 2BL, 2BS, 4BL, 4BS, 5DL and 5BL, which complement the physical maps already available for 12 chromosomes.

IWGSC adopted the Keygene Whole Genome Profiling (WGP) technology as its standard since it provides a robust framework for physical mapping and sequencing individual chromosomes of the highly complex and repetitive wheat genome. Edwin van der Vossen, Vice President Field Crops at KeyGene comments: "Together with the IWGSC, we are convinced that the physical maps that we generated using the KeyGene's WGP sequence based method provide a sound foundation for the reference quality genome sequence of hexaploid wheat, irrespective of the sequencing platform and strategy used. I am confident that these results will play an important role in increasing wheat production for future generations."

This achievement was made possible by a 1 million contribution from Bayer Crop Science. "With this new piece of information now available to us we can speed up our breeding efforts and map based cloning projects for trait improvement, says Catherine Feuillet, head of trait R&D at Bayer Crop Sciences.

We would not have been able to achieve this milestone without the financial support of Bayer CropScience and the scientific leadership of KeyGene. We were faced with a difficult challenge of completing these physical maps in a short time period and KeyGene stepped up and delivered high quality physical maps that can now serve as a substrate for reference sequencing, says Kellye Eversole, IWGSC executive director.

The next step is to obtain a high quality reference sequence for each bread wheat chromosome. This will provide an accurate representation of the structure and organization of sequences along individual chromosomes and enable the precise locations of genes, regulatory elements, repetitive elements and sequence-based markers of different kinds to be identified. With a chromosome-based full sequence in hand, plant breeders will have high quality information at their disposal to accelerate breeding programs and to determine how genes control complex traits such as quality, yield, drought tolerance or durable disease resistance.

Wheat is the most widely grown cereal crop in the world, with almost 700 millions tons produced on over 210 million hectares. Each year, nearly US $50 billion-worth of wheat is traded globally. The worlds top producers are the European Union, followed by China, India and the USA. Wheat is currently the staple food for more than 35% of the global human population. With the worlds population estimated to reach 9.6 billion by 2050, the World Bank has estimated that global wheat production would need to increase by 60 % by 2050. To meet this rising demand, plant scientists will need new tools such as a reference genome sequence to produce a new generation of wheat varieties with higher yields and improved sustainability.

About the IWGSC: The IWGSC, with more than 1,000 members in 57 countries, is an international, collaborative consortium, established in 2005 by a group of wheat growers, plant scientists, and public and private breeders. The goal of the IWGSC is to make a high quality genome sequence of bread wheat publicly available, in order to lay a foundation for basic research that will enable breeders to develop improved varieties. http://www.wheatgenome.org

About Keygene: KeyGene is a privately owned, innovative molecular genetics Ag Biotech company with a primary focus on the improvement of 6F (Food, Feed, Fiber, Fuel, Flowers and Fun) crops. KeyGenes passion is to explore and exploit natural genetic variation in vegetable and other 6F crops. KeyGene delivers sustainable responses to the worlds needs for yield stability & quality of vegetable and field crops. KeyGene supports its strategic partners with cutting edge breeding technologies and plant-based trait platforms, with more than 135 employees from all over the world, with state of the art facilities and equipment. KeyGene has its headquarters in Wageningen, the Netherlands, a subsidiary in Rockville, USA and a Joint Lab with the Shanghai Institute of Biological Sciences in Shanghai, China. http://www.keygene.com

See original here:
Wheat Genome Sequencing on Track

IMAGE:New grants fund research on how the genes and switches in the genome fit together as networks. view more

Credit: Darryl Leja, NHGRI

The National Institutes of Health has awarded grants of more than $28 million aimed at deciphering the language of how and when genes are turned on and off. These awards emanate from the recently launched Genomics of Gene Regulation (GGR) program of the National Human Genome Research Institute (NHGRI), part of NIH.

"There is a growing realization that the ways genes are regulated to work together can be important for understanding disease," said Mike Pazin, Ph.D., a program director in the Functional Analysis Program in NHGRI's Division of Genome Sciences. "The GGR program aims to develop new ways for understanding how the genes and switches in the genome fit together as networks. Such knowledge is important for defining the role of genomic differences in human health and disease."

With these new grants, researchers will study gene networks and pathways in different systems in the body, such as skin, immune cells and lung. The resulting insights into the mechanisms controlling gene expression may ultimately lead to new avenues for developing treatments for diseases affected by faulty gene regulation, such as cancer, diabetes and Parkinson's disease.

Over the past decade, numerous studies have suggested that genomic regions outside of protein-coding regions harbor variants that play a role in disease. Such regions likely contain gene-control elements that are altered by these variants, which increase the risk for a disease.

"Knowing the interconnections of these regulatory elements is critical for understanding the genomic basis of disease," Dr. Pazin said. "We do not have a good way to predict whether particular regulatory elements are turning genes off or activating them, or whether these elements make genes responsive to a condition, such as infection. We expect these new projects will develop better methods to answer these types of questions using genomic data."

Recipients of the new GGR three-year grants (pending available funds) are:

The body's immune system can cause inflammation, which plays a central role in some diseases. The investigators will use a mouse model to study genomic mechanisms underlying immune system activity during inflammation. They will determine what and when genes are turned on and off, and how they are controlled, in the development and activation of two different types of immune cells with opposite functions. One cell type promotes the immune system's response and inflammation; the other dampens these functions.

Researchers will characterize how human lung epithelial cells respond to anti-inflammatory drugs called glucocorticoids (a type of steroid hormone). They will determine what and when genes are turned on and off, and how this process is controlled. They hope to create a model for this type of response, and detail the gene regulation patterns involved. This may allow the researchers to understand how glucocorticoids control both anti-inflammatory and metabolic responses.

Go here to see the original:
NIH grants aim to decipher the language of gene regulation

Steve Gschmeissner/SPL

Ovarian cancer is one of a few tumour types that will continue to be intensively sequenced after the end of a massive US cancer-genomics effort.

A mammoth US effort to genetically profile 10,000 tumours has officially come to an end. Started in 2006 as a US$100-million pilot, The Cancer Genome Atlas (TCGA) is now the biggest component of the International Cancer Genome Consortium, a collaboration of scientists from 16 nations that has discovered nearly 10million cancer-related mutations.

The question is what to do next. Some researchers want to continue the focus on sequencing; others would rather expand their work to explore how the mutations that have been identified influence the development and progression of cancer.

TCGA should be completed and declared a victory, says Bruce Stillman, president of Cold Spring Harbor Laboratory in New York. There will always be new mutations found that are associated with a particular cancer. The question is: what is the costbenefit ratio?

Stillman was an early advocate for the project, even as some researchers feared that it would drain funds away from individual grants. Initially a three-year project, it was extended for five more years. In 2009, it received an additional $100 million from the US National Institutes of Health plus $175 million from stimulus funding that was intended to spur the US economy during the global economic recession.

The project initially struggled. At the time, the sequencing technology worked only on fresh tissue that had been frozen rapidly. Yet most clinical biopsies are fixed in paraffin and stained for examination by pathologists. Finding and paying for fresh tissue samples became the programmes largest expense, says Louis Staudt, director of the Office for Cancer Genomics at the National Cancer Institute (NCI) in Bethesda, Maryland.

Also a problem was the complexity of the data. Although a few drivers stood out as likely contributors to the development of cancer, most of the mutations formed a bewildering hodgepodge of genetic oddities, with little commonality between tumours. Tests of drugs that targeted the drivers soon revealed another problem: cancers are often quick to become resistant, typically by activating different genes to bypass whatever cellular process is blocked by the treatment.

Despite those difficulties, nearly every aspect of cancer research has benefited from TCGA, says Bert Vogelstein, a cancer geneticist at Johns Hopkins University in Baltimore, Maryland. The data have yielded new ways to classify tumours and pointed to previously unrecognized drug targets and carcinogens. But some researchers think that sequencing still has a lot to offer. In January, a statistical analysis of the mutation data for 21 cancers showed that sequencing still has the potential to find clinically useful mutations (M.S.Lawrence etal. Nature 505, 495501; 2014).

On 2 December, Staudt announced that once TCGA is completed, the NCI will continue to intensively sequence tumours in three cancers: ovarian, colorectal and lung adenocarcinoma. It then plans to evaluate the fruits of this extra effort before deciding whether to add back more cancers.

Original post:
End of cancer-genome project prompts rethink

Scientists hope the secret to longevity and disease-resistance could be hidden within the now-sequenced genome of the bowhead whale the longest living mammal. Photo by Olga Shpak

The secret to giving humanity a longer life and protection from age-related illnesses could be hidden within the genome of the longest living mammal.

Scientists have sequenced the complete genome of the bowhead whale, an animal that has been known to live more than 200 years and resist many of the diseases associated with old age. While comparing the creatures genes with other mammals, the research team discovered key alterations related to cell division, DNA repair, cancer, and aging a possible explanation for why the whales not only live so long, but are also resistant to cancer and other diseases in its old age.

My view is that species evolved different tricks to have a longer lifespan, and by discovering the tricks used by the bowhead we may be able to apply those findings to humans in order to fight age-related diseases, Dr. Joo Pedro de Magalhes, senior author of the study published Monday in Cell Reports, said.

The genome data of the whale, the second heaviest whale after the blue whale with around 1,000 times more cells than humans, may also hold clues to explaining physiological differences between animals of different sizes. One example given was that whale cells have a lower metabolic rate compared to smaller mammals, with the explanation possibly being found in a difference within a specific gene related to body temperature regulation.

The complete genome data has been made available by the researchers for free online.

Continued here:
Can protection from aging be found in a whale genome?

Scientists at the University of Liverpool have sequenced the genome of the bowhead whale, estimated to live for more than 200 years with low incidence of disease.

Published in the journal Cell Reports, the research could offer new insight into how animals and humans could achieve a long and healthy life.

Scientists compared the genome with those from other shorter-lived mammals to discover genetic differences unique to the bowhead whale.

It is thought that large mammals, such as whales, with over 1000 times more cells than humans, have a lower risk of developing cancer, suggesting that these creatures have natural mechanisms that can suppress disease more effectively than those of other animals.

Sequencing of the bowhead whale showed changes in genetic information that related to cell division, DNA repair, disease and ageing that with further analysis, could help inform future studies in longevity and cancer resistance.

Dr Joo Pedro de Magalhes, from the University of Liverpool's Institute of Integrative Biology, explains: "Our understanding of species' differences in longevity is very poor, and thus our findings provide novel candidate genes for future studies.

"We believe that different species evolved different 'tricks' to have a long lifespan, and by discovering those used by the bowhead whale we may be able to apply these findings to humans in order to fight age-related diseases."

The research may also provide clues into why there is significant variance in the size of some mammals.

Dr Magalhes added: "The bowhead's genome is the first among large whales to be sequenced, so this new information may help reveal physiological adaptations related to size that we have not been able to study in any great detail before.

"Whale cells have a much lower metabolic rate than those of smaller mammals, and we found changes in one specific gene involved in thermoregulation (UCP1) that may be related to metabolic differences in whale cells. This might allow us to see how and why bowhead whales and other similar creatures have sustained such an enormous size."

Link:
Scientists sequence genome of longest-lived mammal

[241 pp] Tsunumaru - Daidai Genome
omfg finally damn -- Watch live at http://www.twitch.tv/shintany.

By: Irchad1K

See the original post:
[241 pp] Tsunumaru - Daidai Genome - Video

Orange genome - Hatsune Miku ger sub
Da ich diese Lied stndig in Osu! gespielt habe musste ich es unbedingt bersetzen Song: Orange genome - Daidai genome - "" Snger: Hatsune Miku.

By: Himari

Link:
Orange genome - Hatsune Miku ger sub - Video

Published December 30, 2014

Doctors expect soon to begin sequencing the genomes of healthy newborn babies as part of a government-funded research program that could have wide implications for genetic science.

The research, to be conducted at major hospitals around the country, stems from a growing recognition that genome sequencing could someday be part of routine testing done on every baby. Such testing could provide doctors and parents a vast pool of data likely to reveal a wider range of potential medical risks than the traditional heel-prick test, in which a small sample of newborns blood is taken to check for more than two dozen possible conditions.

Genome sequencing of infants also someday could provide people with a genetic blueprint to carry through life. The data could be used years later to help develop personalized medical treatment, such as choosing the most effective asthma medication.

We are entering an era where all of medicine is genomic medicine, says Robert C. Green, a geneticist and researcher at Brigham and Womens Hospital in Boston, which is participating in the research program. In the next five to 10 years, as costs come down and interpretation is more established, it will increasingly be to everyones advantage to have sequencing information integrated into their care, he says.

Early identification of diseases can save a childs life or lead to interventions that change the course of the disorder. Whole genome sequencing or whole exome sequencing, which focuses on the 1% to 2% of the genome believed to be responsible for most genetic disorders, can help identify mutations associated with some diseases. Some hospitals already perform sequencing on a small number of newborns who show signs of illness or developmental disorders. Those experiences so far suggest the procedure can help doctors identify the underlying problems.

Click for more from The Wall Street Journal.

View post:
Genome sequencing in babies to begin as part of study

December 24th - Brian Cox - Cosmic Genome Science Advent Calendar
Professor Brian Cox on the art of explaining physics. Every day a new free science clip from the good people at Cosmic Genome. Head to cosmicgenome.com/adven...

By: The Incomplete Map of the Cosmic Genome

Go here to read the rest:
December 24th - Brian Cox - Cosmic Genome Science Advent Calendar - Video

Lubbock, TX /PRNewswire-USNewswire/ - A significant accomplishment has been made in the sequencing of the cotton genome by a Texas Tech research team in collaboration with Bayer CropScience and the National Center for Genome Resources (NGCR), which will fuel multi-disciplinary basic and applied research to help increase cotton productivity.

"This information will significantly advance cotton research worldwide," said Dr. Mike Galyean, Dean of Texas Tech's College of Agricultural Sciences and Natural Resources. "The genome sequence will eventually lead to improved cotton varieties containing environmentally friendly traits, which are preferred by producers, processors, manufacturers, and consumers."

The annotated draft genome assembly being released is from Gossypium arboreum. This species is an extant representative of the cotton A-genome lineage, which is paired with the D-genome lineage making up present day cultivated cottons. The A-genome species gave rise to spinnable fiber eventually leading to what is today the modern-day textile industry.

This approach to unravel the genetic mystery of this African/Asian cotton species was led by Dr. Thea Wilkins, former Professor of Cotton Genomics in Texas Tech'sDepartment of Plant and Soil Sciences in close collaboration with scientists at Bayer CropScience and next-generation genomic sequencing technology and biocomputing providers, KeyGene and NCGR. This team's delivery of this annotated draft genome sequence adds to other recent efforts to present an unprecedented view into the structure of the A-genome, which will accelerate research efforts for improving cultivated cotton.

Cotton production contributes substantially to economies around the globe. Collaborative research projects such as this will help to increase that contribution. Dr.Don Jones, Director of Agricultural Research at Cotton Incorporated, said this sequence knowledge is another tool for improving commercial cotton. "This accomplishment is another cornerstone in understanding the biology that leads to higher yield, improved fiber quality, and better stress tolerance while reducing inputs used in producing the crop."

This research was completed under a public-private partnership between the State of Texas, Texas Tech University, and Bayer CropScience. Dr. Mike Gilbert, Vice President of Global Breeding and Trait Development at Bayer CropScience, stated that this accomplishment is another great example of the synergy that can be created to deliver innovation in cotton that will improve the sustainability and economic value from the farm to the consumer: "Through our collaborative cotton research program, Bayer CropScience and Texas Tech University under the umbrella of the Texas Research Incentive Program have partnered to create cutting-edge programs in fiber science and genomics to advance cotton knowledge and products. Together we are committed to providing long-lasting solutions for growers and the global cotton community."

The draft sequence of G. arboreum is currently deposited in Genbank and is scheduled to be released to the public on December 2, 2014.

Continue reading here:
Draft Sequence Of A Diploid A-Genome Cotton Generated & Released To Public By Texas Tech University, Bayer CropScience ...