Category Archives: Genome

Public release date: 15-May-2013 [ | E-mail | Share ]

Contact: David Gilbert degilbert@lbl.gov DOE/Joint Genome Institute

With the publication last year of its strategic plan, "Forging the Future A Ten-Year Strategic Vision" the U.S. Department of Energy Joint Genome Institute (DOE JGI) has positioned itself to provide the most current technology and expertise to their users so that they can address pressing energy and environmental scientific challenges.

An important early step in this process is the launch of the Emerging Technologies Opportunity Program (ETOP). The primary purpose of the ETOP is to develop and support selected new technologies that DOE JGI could establish to add value to the high throughput sequencing it currently carries out for its users. The program was one of several recommendations that emerged from the DOE JGI's strategic planning as well as a complementary process carried out by DOE's Office of Biological and Environmental Research. Now, a new set of partnerships is taking shape in response to the ETOP's first call for proposals. These span the development of new scalable DNA synthesis technologies to the latest approaches to high throughput sequencing and characterization of single microbial cells from complex environmental samples.

"A core philosophy of the DOE JGI is that our suite of technical and analytical capabilities needs to evolve continuously so that the scientific achievements of our users can be maximized," said Jim Bristow, who oversees the ETOP as DOE JGI's Deputy Director of Science Programs. "This occurs by building new scientific capabilities at the DOE JGI itself, and by enlisting partners, like the ones we've identified through this program, to develop and deploy highly-specialized technologies that complement activities at our Walnut Creek facility. While state-of-the art massive-scale sequencing remains a critical component of the DOE JGI, other large-scale capabilities particularly those that will help link sequence to function will be provided to JGI users in the future," Bristow said.

When the DOE JGI was founded back in 1997 to help accelerate the Human Genome Project (HGP) effort, the partnership consisted of DOE National Laboratory and university partners. After completing the DOE's commitment to the HGP in 2004, the DOE JGI opened its doors as a national user facility advancing the frontiers of genomics for energy and environmental applications. In 2012 alone, the Institute completed over 2,600 projects.

For the first cycle of the ETOP, the DOE JGI has selected these six new partnerships:

The DOE JGI expects to commit approximately $3.5 million over the next two years to the new ETOP initiatives.

"The DOE JGI strives to integrate these expanded activities in innovative and effective ways," said Bristow. "This is critical if the biological sciences are to realize the full benefits and promise of genome sequencing."

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The DOE Joint Genome Institute expands capabilities via new partnerships

PARIS - The head of a body set up by the G20 economic powers to help avert food crises urged governments on Tuesday to fund a map of wheat's unusually complex genetic code to help boost crop yields and feed growing world demand.

Five times bigger than the human genome, the mysteries of the world's most widely sown crop could be fully sequenced by late 2016 with financing of just $20 million, said Helene Lucas, coordinator of the Wheat Initiative, which meets in Paris on Wednesday to discuss the plan to counter stagnant wheat yields.

"We have reached a plateau in output, we now have to make a further step to produce more, produce better, by using all the tools available to us," Lucas, a scientist at France's National Institute for Agricultural Research (INRA), told Reuters.

"If we pool our financing now we can achieve a high-quality sequencing at the end of 2016 that will be available to everyone," she said in an interview, noting that this would mean her international agency's 14 state-funded members putting up a modest $1.4 million each over three years. "That's peanuts."

Flagging growth in harvest yields of wheat has raised concern countries will not be able to achieve the 60-percent rise in output by 2050 that the United Nations says is needed to meet rising demand from a growing population and a shift in appetites toward Western-style bread, cakes and biscuits.

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Full wheat genome within reach, at little cost

May 14, 2013

Image Caption: Texas A&M researchers have been studying Scarlet macaws for many years. Credit: Tambopata Research Center

redOrbit Staff & Wire Reports Your Universe Online

In what is being hailed as a groundbreaking advancement in the fields of avian evolution, biology and conservationism, researchers from the Texas A&M University (TAMU) College of Veterinary Medicine & Biomedical Sciences have successfully sequenced the complete genome of a Scarlet macaw.

Dr. Christopher Seabury and Dr. Ian Tizard of the College Station, Texas-based universitys Schubot Exotic Bird Health Center are the first scientists to successfully sequence the complete genome of the South American parrot. The results of their work are detailed in the current edition of the open-access, peer-reviewed journal PLOS One.

According to the researchers, they used a female macaw from the Blank Park Zoo in Des Moines, Iowa known as Neblina. The parrot is believed to have come from Brazil, and was confiscated during a 1995 US Fish and Wildlife Service (FWS) raid on illegally imported exotic birds. Tizard said he and his colleagues took a blood sample and extracted DNA from Neblina in order to complete the steps required for the sequencing process.

The final analysis showed that there are about one billion DNA bases in the genome, which is about one-third of that found in mammals. Birds have much less DNA than mammals primarily because they do not possess nearly as much repetitive DNA, he explained in a statement. While the final genome is similar to that of the chicken, Tizard said there are significant differences at both the genome and biological level.

Macaws can fly great distances, while chickens cant, he said. In addition, brain development and volume are very different in macaws, which is unsurprising since they are very intelligent birds compared to chickens. Likewise, macaws can live many years, while chickens usually do not, and therefore, our macaw genome sequence may help shed light on the genetic factors that influence longevity and intelligence.

Tizard explained the researchers selected a Scarlet macaw for the sequencing effort because researchers at Texas A&M had been studying the species for several years analyzing macaw diseases, behavior, and genetics at the Tambopata Research Center in Peru. He and his colleagues report that their work will also enhance the research-related possibilities surrounding the Scarlet Macaw.

There are 23 different species of macaws, some of which have become extinct and several others of which are currently endangered, the researchers said. The birds, which are typically found in Central and South America, have been targeted by trappers and negatively affected by deforestation in their natural habitats.

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Texas Researchers Sequence Entire Genome Of Scarlet Macaw

Image Caption: Nelumbo nucifera from China, more commonly known as the 'sacred lotus'. Credit: Jane Shen-Miller / UCLA

Lawrence LeBlond for redOrbit.com Your Universe Online

A team of international scientists report today that they have sequenced and annotated the genome of the sacred lotus (Nelumbo nucifera), which is thought to have a powerful genetic system. The team, which includes researchers from the US, China, Australia and Japan, have sequenced nearly 90 percent of the plants 27,000 genes.

The sacred lotus, which is a symbol of spiritual purity and longevity, has the ability to repair genetic defects, and may hold a key to the secrets of aging; the seeds of the lotus can survive up to 1,300 years. The petals and leaves of the plant also repel dirt and water and the flower can generate its own heat to attract pollinators.

Through sequencing, the researchers have found that the lotus bears the closest resemblance to the ancestor of all eudicots, than of any other plant that has been successfully sequenced to date. Eudicots are a group of flowering plants that include apple, coffee, peanut, soybean, tobacco, tomato, and countless others.

Publishing the paper in the journal Genome Biology, the team noted that the results of the sequencing offer insight into the heart of many of the plants mysteries.

The research was co-led by Ray Ming, a plant biology professor at University of Illinois Institute for Genomic Biology (IGB); Jane Shen-Miller, a plant biology professor at UCLA; and Shaohua Li, director of the Wuhan Botanical Garden (WBG) at the Chinese Academy of Sciences.

The lotus genome is an ancient one, and we now know its ABCs, said Shen-Miller, who works out of the UCLAs Center for the Study of Evolution and the Origin of Life. Molecular biologists can now more easily study how its genes are turned on and off during times of stress and why this plants seeds can live for 1,300 years. This is a step toward learning what anti-aging secrets the sacred lotus plant may offer.

Shen-Miller said the plants genetic repair mechanisms could be very useful if researchers could find a way to transfer them to crops that have seeds that generally only have life spans of a few years. They could even prove significant if transferable to human health.

If our genes could repair disease as well as the lotus genes, we would have healthier aging. We need to learn about its repair mechanisms, and about its biochemical, physiological and molecular properties, but the lotus genome is now open to everybody, she said.

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Sacred Lotus Genome May Hold Key To The Secrets Of Aging

Washington, May 14 (ANI): Researchers at Texas A and M University have successfully sequenced the complete genome of a Scarlet macaw for the first time.

This is a groundbreaking move that could provide new insight into avian evolution, biology and conservation.

The team was led by Drs. Christopher Seabury and Ian Tizard at the Schubot Exotic Bird Health Center in the College of Veterinary Medicine and Biomedical Sciences at Texas A 'n' M.

Macaws are found in tropical Central and South America, from southern Mexico to northern Argentina. Trapping of the birds for the pet trade, plus loss of habitat due to deforestation in their native lands, has severely decreased their numbers since the 1960s.

There are 23 species of macaws, and some of these have already become extinct while others are endangered.

Macaws can live 50 to 75 years and often outlive their owners.

"They are considered to be among the most intelligent of all birds and also one of the most affectionate - it is believed they are sensitive to human emotions," stated Tizard.

The bird selected for the sequencing was a female named "Neblina" who lives in the Blank Park Zoo in Des Moines, Iowa. Neblina is believed to be from Brazil. She was confiscated during a raid on illegally imported exotic birds by the U.S. Fish and Wildlife Service in 1995.

Tizard said that a blood sample was taken from Neblina, DNA was extracted for sequencing, and after a series of steps, the sequence of the genome was assembled by Seabury and his team.

"The final analysis showed that there are about one billion DNA bases in the genome, which is about one-third of that found in mammals," Tizard explained.

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Genome sequencing may shed light on parrots' longevity and intelligence

May 14, 2013 The toxin that causes botulism is the most potent that we know of. Eating an amount of toxin just 1000th the weight of a grain of salt can be fatal, which is why so much effort has been put into keeping Clostridium botulinum, which produces the toxin, out of our food.

The Institute of Food Research on the Norwich Research Park has been part of that effort through studying the bacteria and the way they survive, multiply and cause such harm. In new research, IFR scientists have been mining the genome of C. botulinum to uncover new information about the toxin genes.

There are seven distinct, but similar, types of botulinum neurotoxin, produced by different strains of C. botulinum bacteria. Different sub-types of the neurotoxin appear to be associated with different strains of the bacteria. Genetic analysis of these genes will give us information about how they evolved.

Dr Andy Carter, working in Professor Mike Peck's research group, used data generated from sequencing efforts at The Genome Analysis Centre, on the Norwich Research Park. Andy compared the genome sequence of five different C. botulinum strains, all from the same group and all producing the same sub-type of neurotoxin.

An initial finding was that the five strains were remarkably similar in the area of the genome containing the neurotoxin gene. This suggests that the bacteria picked up the gene cluster in a single event, sometime in the past. Bacteria commonly acquire genes, or gene clusters, from other bacteria through this horizontal gene transfer. It is a way that bacteria have evolved to share 'weapons', such as antibiotic activity or the ability to produce toxins. To find out more about how C. botulinum acquired its own deadly weapon, Andy delved deeper into the genome sequence.

Like fossils of long lost organisms, Andy found, in the same region of the genome, evidence of two other genes for producing two of the other types of neurotoxin. Although these gene fragments are completely non-functional, finding them in the same place in the genome as the functional neurotoxin gene cluster is significant as it suggests that this region of the genome could be a 'hotspot' for gene transfer.

Looking to either side of the neurotoxin gene cluster uncovered more evidence supporting the hotspot idea. When the gene cluster inserted into the C. botulinum genome, it cut in two another gene. This gene is essential for the bacteria to replicate its DNA, so why does destroying it not prove fatal? C. botulinum was unaffected by this because contained in the segment of imported DNA was another version of the chopped-up gene.

Perhaps this is pointing us to the way C. botulinum first picks up its lethal weapon. This should help us prepare against the emergence of new strains, and may even one day help us disarm this deadly foe.

The research was funded by the Biotechnology and Biological Sciences Research Council and published in the journal Genome Biology and Evolution Advance.

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Mining the botulinum genome

Texas A M Bird Expert Explains Importance Of Macaw Genome Sequencing
In groundbreaking research that could save future generations of parrots from becoming extinct, researchers at Texas A M University have for the first time s...

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Alessandro Parisi - Homo Saurus Genome Manipulation
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Alessandro Parisi - Homo Saurus Genome Manipulation - Video

Public release date: 10-May-2013 [ | E-mail | Share ]

Contact: Stuart Wolpert swolpert@support.ucla.edu 310-206-0511 University of California - Los Angeles

A team of 70 scientists from the U.S., China, Australia and Japan today reports having sequenced and annotated the genome of the "sacred lotus," which is believed to have a powerful genetic system that repairs genetic defects, and may hold secrets about aging successfully. The scientists sequenced more than 86 percent of the nearly 27,000 genes of the plant, Nelumbo nucifera, which is revered in China and elsewhere as a symbol of spiritual purity and longevity.

"The lotus genome is an ancient one, and we now know its ABCs," said Jane Shen-Miller, one of three corresponding authors of the research and a senior scientist with UCLA's Center for the Study of Evolution and the Origin of Life. "Molecular biologists can now more easily study how its genes are turned on and off during times of stress and why this plant's seeds can live for 1,300 years. This is a step toward learning what anti-aging secrets the sacred lotus plant may offer."

The research was published today in the journal Genome Biology.

Shen-Miller said the lotus' genetic repair mechanisms could be very useful if they could be transferred to humans or to crops such as rice, corn and wheat whose seeds have life spans of only a few years. "If our genes could repair disease as well as the lotus' genes, we would have healthier aging. We need to learn about its repair mechanisms, and about its biochemical, physiological and molecular properties, but the lotus genome is now open to everybody."

In the early 1990s, Shen-Miller led a UCLA research team that recovered a viable lotus seed that was almost 1,300 years old from a lake bed in northeastern China. It was a remarkable discovery, given that many other plant seeds are known to remain viable for just 20 years or less.

In 1996, Shen-Miller led another visit to China. Working in Liaoning province, her team collected about 100 lotus seeds most were approximately 450 to 500 years old with help from local farmers. To the researchers' surprise, more than 80 percent of the lotus seeds that were tested for viability germinated. That indicated that the plant must have a powerful genetic system capable of repairing germination defects arising from hundreds of years of aging, Shen-Miller said.

Understanding how the lotus repair mechanism works and its possible implications for human health is essentially a three-step process, said Crysten Blaby-Haas, a UCLA postdoctoral scholar in chemistry and biochemistry and co-author of the research. "Knowing the genome sequence was step one. Step two would be identifying which of these genes contributes to longevity and repairing genetic damage. Step three would be potential applications for human health, if we find and characterize those genes. The genome sequence will aid in future analysis.

"The next question is what are these genes doing, and the biggest question is how they contribute to the longevity of the lotus plant and its other interesting attributes," Blaby-Haas said. "Before this, when scientists studied the lotus, it's almost as if they were blind; now they can see. Once you know the repertoire of genes, you have a foundation to study their functions."

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Scientists sequence genome of 'sacred lotus,' which likely holds anti-aging secrets

Prof. Eric Lander Secrets of the Human Genome II Medicine - Technion Lecture
"Secrets of the Human Genome II - Medicine" by Prof. Eric S. Lander at Technion-Israel Institute of Technology, Rappaport Faculty of Medicine. April 30, 2013...

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Prof. Eric Lander Secrets of the Human Genome II Medicine - Technion Lecture - Video