Daily Archives: May 14, 2013

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