Dutch Elm Disease: Scientists map genome of fungus

Researchers from the University of Toronto and SickKids Research Institute announced today that they have successfully mapped the genes in the fungus that causes Dutch elm disease.

The researchers believe this is the first time the 30 million DNA letters for the fungus Ophiostoma ulmi have been mapped.

The findings, published in this week's online journal BMC Genomics, could help scientists figure out how to prevent the fungus from destroying elm trees in the future.

"Essentially, Dutch elm disease is caused by a fungus that prevents the normal distribution of nutrients in the tree by blocking the flow of sap," said Alan Moses, an Assistant Professor with the University of Toronto's department of Cell & Systems Biology, one of the authors of the study. "The tree wilts and eventually dies."

"Relatively little is known about the fungus that causes Dutch elm disease, and it's a very distant relative of the fungi that are more often studied by researchers, like bread mould or beer yeast. "

"We hope that the availability of the genome will encourage and speed-up research on this fungus -- it's only a matter of time before most the elm trees are gone."

Dutch elm disease is believed to have originated in the Himalayas, travelling to Europe from the Dutch East Indies in the late 1800s.

It emerged in Holland shortly after the First World War, earning the name Dutch elm disease.

It is the most destructive elm tree disease in North America, and typically kills most trees within two years of infection.

Dutch elm disease is a problem in many parts of the world, particularly Scotland, Spain, Italy, Western Canada and New Zealand.

The above story is reprinted from materials provided by University of Toronto

Scientists Nearer to Finding Solution for Age-Related Problems

A team of scientists from the Salk Institute, Ecole Polytechnique Federale De Lausanne (EPFL) and the University of Lausanne have created super strong mice by controlling its natural muscle growth.

This invention will help solve genetic muscular degeneration and other age-related problems.

The scientists changed the activity of certain genes by tweaking a genome regulator called NCOR1.

They suppressed a thyroid hormone which regulates growth in most mammals and created mice that were twice as strong as normal.

According to Johan Auwerx, the lead author from Ecole Polytechnique Fédérale de Lausanne (EPFL), "This could be used to combat muscle weakness in the elderly, which leads to falls and contributes to hospitalizations."

"In addition, we think that this could be used as a basis for developing a treatment for genetic muscular dystrophy."

"There are now ways to develop drugs for people who are unable to exercise due to obesity or other health complications, such as diabetes, immobility and frailty," said Ronald M Evans, a professor at the Salk Institute.

"We can now engineer specific gene networks in muscle to give the benefits of exercise to sedentary mice."

It may be recalled that cell biology expert Norman S Wolf dealt with muscular degeneration in his book 'Comparative Biology on Aging.' Wolf had argued that by restricting calories and doing regular exercise, humans could slow aging process and reduce muscular degeneration.

In the present case, the mice, which underwent genetic mutation, became true marathoners, running faster and longer before showing any signs of fatigue. They were able to cover almost twice the distance compared to the normal mice. They also exhibited better tolerance to cold.

Unlike "genetic accelerators," the new work shows that suppressing an inhibitor is a new way to build muscle, which in this experiment confirmed that the muscle fibers of the modified mice are denser, more massive, and the cells in the tissue contain higher numbers of mitochondria-cellular organelles that deliver energy to the muscles.

Auwerx said that if these results were confirmed in humans, the experiment would attract attention especially from the athletes and medical experts.

The Salk Institute conducts biological research on molecular biology, genetics, neuroscience and plant biology. Five scientists from here have won Nobel Prizes.

Recently, the institute discovered a safer way to cure asthma, allergies and arthritis. It has also done research on a drug that reduces baldness.

The EPFL (Switzerland) focuses on education, research, technology and has conducted several researches on subjects like microbiology and robotics.

$1,000 dollar genome by 2012

By 2012, sequencing the human genome will be done in two hours and will cost $1,000, Ion Torrent’s Jonathan Rothberg said at a recent conference.

As companies race to crack the $1,000 genome, contending DNA machines in the marketplace suggest an end is near.

Ion Torrent’s DNA machine reads sequences based on chemicals and electronic technology.

The technology is called the Personal Genome Machine and it has been used to determine the source of E. coli or mutations present in the genomes of patients’ cancers.

The Ion Personal Genome Machine, which is about the size of a desktop computer, uses chemistry and semiconductor technology to produce readouts of genetic information in a couple of hours.

Christopher Mims wrote in Technology Review:

“Right now don’t have very many correlations between those 3 billion base pairs [of the human genome] and outcomes or medicines,” says Rothberg.

He predicts it will take at least 10 years of clinical experiments with full genome sequencing to get us to the point where we can begin to unlock its value.

“And it will be 20 years before we understand cancer at same level as HIV and can come up with combinations of medicine [tailored] for each individual,” says Rothberg.

Human Genome Contains Viral DNA

WHEN, in 2001, the human genome was sequenced for the first time, we were confronted by several surprises.

One was the sheer lack of genes: where we had anticipated perhaps 100,000 there were actually as few as 20,000.

A bigger surprise came from analysis of the genetic sequences, which revealed that these genes made up a mere 1.5 per cent of the genome.

This is dwarfed by DNA deriving from viruses, which amounts to roughly 9 per cent.

On top of that, huge chunks of the genome are made up of mysterious virus-like entities called retrotransposons, pieces of selfish DNA that appear to serve no function other than to make copies of themselves. These account for no less than 34 per cent of our genome.

All in all, the virus-like components of the human genome amount to almost half of our DNA. This would once have been dismissed as mere "junk DNA", but we now know that some of it plays a critical role in our biology. As to the origins and function of the rest, we simply do not know.

The human genome therefore presents us with a paradox. How does this viral DNA come to be there? What role has it played in our evolution, and what is it doing to our physiology? To answer these questions we need to deconstruct the origins of the human genome - a story more fantastic than anything we previously imagined, with viruses playing a bigger part than you might care to believe.

Around 15 years ago, when I was researching my book Virus X, I came to the conclusion there was more to viruses than meets the eye. Viruses are often associated with plagues - epidemics accompanied by great mortality, such as smallpox, flu and AIDS.

I proposed that plague viruses also interact with their hosts in a more subtle way, through symbiosis, with important implications for the evolution of their hosts. Today we have growing evidence that this is true (New Scientist, 30 August 2008, p 38), and overwhelming evidence that viruses have significantly changed human evolution.

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CHINA: Panda genome resembles dog

A detailed genome map of the giant panda completed by Chinese scientists has shown that the notoriously shy animal is genetically similar to the dog, state media reported Sunday.

Scientists from the Beijing Genomics Institute finished sequencing the giant panda genome in October last year but a detailed genome map was only recently completed, Xinhua news agency said.

"The research found there is a high genomic similarity between giant panda and dog," the report said, but added that the research also supported the view of most scientists that the giant panda may be a subspecies of the bear family.

The detailed mapping showed that the giant panda has 21 pairs of chromosomes and more than 20,000 genes, Xinhua said.

The research is expected to provide scientific support for the conservation, disease prevention and artificial propagation of the endangered giant panda, researchers have said.

"We hope the genome map could help genetically explain why giant pandas have little reproductive capability so that scientists can help them deliver more cubs," Wang Jun, a scientist with the institute, was quoted in the state press as saying earlier.

Chinese experts say there are only about 1,600 wild pandas in China, mainly in the southwest, with another 200 or so raised in captivity in Chinese breeding centres.

The animals' notoriously low libidos have frustrated efforts to boost their numbers.

Breeders have resorted to tactics such as showing them "panda porn" videos of other pandas mating, and putting males through "sexercises" aimed at training up their pelvic and leg muscles for the rigours of copulation.

Scientists hope also to eventually gain a better understanding of why pandas subsist almost solely on bamboo, another factor viewed as inhibiting the species' range and adaptability.