Friday, 8 January 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge

Human Genome Is Part Bornavirus

Posted: 07 Jan 2010 02:11 PM PST


People may not be quite the humans they think they are. Or so suggests new research showing that the human genome is part bornavirus.

sciencenewsBornaviruses, a type of RNA virus that causes disease in horses and sheep, can insert their genetic material into human DNA and first did so at least 40 million years ago, the study shows. The findings, published January 7 in Nature, provide the first evidence that RNA viruses other than retroviruses (such as HIV) can stably integrate genes into host DNA. The new work may help reveal more about the evolution of RNA viruses as well as their mammalian hosts.

"Our whole notion of ourselves as a species is slightly misconceived," says Robert Gifford, a paleovirologist at the Aaron Diamond AIDS Research Center, affiliated with Rockefeller University in New York City. Human DNA includes genetic contributions from bacteria and other organisms, and humans have even come to rely on some of these genes for basic functions like fighting infections.

In the new study, Japanese researchers found copies of the bornavirus N (for nucleoprotein) gene inserted in at least four separate locations in the human genome. Searches of other mammalian genomes also showed that the gene has hitched rides in a wide variety of species for millions of years.

"Clearly they provide a fossil record of bornavirus that was previously only available for retroviruses," says John Coffin, a virologist at Tufts University School of Medicine in Boston who coauthored the study. "It tells us that virus evolution doesn't proceed the way many people have viewed it."

Scientists have long had direct evidence of retroviruses' ancient origins: Molecular fossils of those viruses persist in the genomes of species infected long ago.

Other RNA "viruses all look like they are relatively young, which doesn't make any sense," says Michael Emerman, a virologist at the Fred Hutchinson Cancer Research Center in Seattle.

Estimations of viral ages are calculated from mutation rates. RNA viruses' high mutation rates make it seem as if the viruses' molecular clocks are ticking faster than those of other viruses. "The high mutation rate doesn't allow us to see far into the past," Emerman says.

Many virologists suspected that RNA viruses were much older than molecular clock estimates suggested, "but it's nice to see direct evidence," he says.

In the new study, researchers led by Keizo Tomonaga of Osaka University found that two human genes are similar to the bornavirus N gene. These two genes, now called EBLN-1 and EBLN-2 for endogenous Borna-like N, are molecular fossils of an ancient bornavirus.

Retroviruses make up about 8 percent of the human genome. When these viruses insert into the genome, the result is usually bad for the host. But not always: Some retrovirus proteins can help fight off infection with other retroviruses. And at least twice in primate evolution retrovirus insertions have added genes to the host genome that aid in making the placenta. Now those proteins are essential for placenta development, says C├ędric Feschotte, an evolutionary geneticist at the University of Texas at Arlington. It is not clear what role, if any, the EBLN-1 and EBLN-2 genes play in humans.

Other mammals, including chimpanzees, gorillas, orangutans, macaques, mouse lemur, African elephant, Cape hyrax and 13-lined ground squirrels all carry N gene insertions in their genomes, Tomonaga and colleagues found. The insertion in the ground squirrel genome was probably a relatively recent event, occurring not more than 10 million years ago, the researchers report.

But bornavirus insertion isn't all ancient history. In laboratory experiments, Tomonaga's team found that modern bornavirus can integrate into the DNA of human, monkey, rat and dog cells. And mice with bornavirus infections were shown to have new insertions in brain cell DNA.

Modern bornaviruses are known to infect nerve cells, but the new study shows that the viruses are capable of infecting and inserting genes into many other types of cells. For the inserted virus sequences to pass to the next generation, the ancient infection must have happened in tissues that give rise to eggs or sperm. Scientists call these tissues the germ line.

"The fact that these viruses were able to get into the germ line, which requires many chance events, implies that they may insert at some appreciable frequency," Gifford says.

Feschotte agrees. "That, to me, is a revelation," he says.

He speculates that bornavirus could be another source of human mutations, especially in neurons. Some studies have linked infection with the virus to psychiatric disorders such as schizophrenia. Feschotte thinks modern bornaviruses may worm their way into human DNA in the neurons, creating mutations in genes that could lead to schizophrenia.

Tomonaga says the schizophrenia link is "not likely." Because bornavirus genes insert randomly in the genome, "it is not conceivable that mutations [caused] by the integration lead to the specific brain disorders, such as schizophrenia," he says.

Images: 1) Wikimedia Commons/M.Eickmann. 2) CDC.

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TigerCam: First-Ever Video of Sumatran Tigress and Cubs in the Wild

Posted: 07 Jan 2010 11:23 AM PST


A Sumatran tigress and her cubs took a special interest in a World Wildlife Federation camera, sniffing and possibly licking it during a brief sequence released in late December.

The video was released as a prelude to the WWF's Tx2: Double or Nothing campaign to call attention to plight of the tiger species. There are as few as 400 Sumatran tigers left in the wild, and they remain vulnerable to poachers and the destruction of their habitat on the Indonesian island.

WWF's field crew has been using the "wildlife-activated" cameras for five years, but this is the first time that a mother and her cubs have been recorded.

Tiger cubs sniff WWF camera trap from WWF on Vimeo.

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WiSci 2.0: Alexis Madrigal's Twitter, Google Reader feed, and green tech history research site; Wired Science on Twitter and Facebook.

Chinese Coal Formed During Earth’s Greatest Extinction Is Deadly

Posted: 07 Jan 2010 11:00 AM PST


A seam of coal formed 250 million years ago during the worst extinction event on record appears to be responsible for the anomalously high lung cancer death rates among women in the rural Chinese county of Xuan Wei in Yunnan Province.

It's long been known that the lung cancer mortality rates in the region were the worst in the world among female nonsmokers and some anomaly in the coal had been suspected. Lung cancer mortality in the region is up to 20 times the Chinese average. But it's only in recent years that scientists have focused in on silica in the form of very fine quartz as the mineral that makes burning the stuff so deadly.

Now, in a paper publishedin December in Environmental Science and Technology, Chinese, British and American researchers have proposed a link between the silica in the coal and the massive event that nearly wiped out life at the Permian-Triassic boundary.

"What we're saying is that the geologic and climatic events that nearly extinguished life 250 million years ago is still having an impact because its imprint is in the coals that the people are using," said Bob Finkelman, a geologist at the University of Texas, Dallas. "They are inhaling this material with nanoquartz that was precipitated 250 million years ago and in a sense it's extinguishing life in the community."


Throughout the early 20th century, the inefficient combustion of soft, bituminous coals smoked up the emerging industrial cities of the world. Similar problems now plague the developing world, both in cities and the hinterlands, where the coal is often used for heating and cooking. The inhalation of the particulates, trace minerals and other substances contained in smoke can lead to a variety of health complications: The World Health Organization estimates that 1.6 million people die each year as a result of indoor air pollution.

The new study underscores the variability between coals in the world. Some coals are particularly smoky, sooty or otherwise undesirable, while others burn cleaner. Coals formed at different times in the earth's history, so even though the dominant component is carbon, each seam has a very particular chemistry.

"Even when you look at coal from a small region, there's enough variation in the properties that you can't just call it all coal and expect it to have the same health effects when you burn it," said Donald Lucas, a physical chemist at Lawrence Berkeley National Laboratory. Lucas co-authored a paper on the nanoquartz in Xuan Wei's coal with geologist Linwei Tian ofChinese University of Hong Kong who did pioneering work on the subject.

What Finkelman's work provides is a plausible account of why this particular coal may be enriched with silica. While there are several hypotheses for what caused the mass die-off at the Permian-Triassic boundary 250 million years ago,a majorvolcanic episodeis likely to have contributed to the phenomenon. Massive amounts of gases leaving Siberian basalts are believed to have radically altered the geochemistry of the atmosphere.

"It lead to highly acidic rain which denuded life on the surface of the earth and acidified the rivers and the oceans," Finkelman explained. "It was so intense that they believe it actually dissolved a lot of the rocks on the surface, mobilizing the silica."

That silica was carried by groundwater into peat that over geological time became the coal the Chinese residents in the region use as a fuel source for cooking. Coal from this time period is not known to be used for indoor cooking elsewhere.

In Xuan Wei, the direct combustion of coal for cooking has waned in recent years, but basic cookstoves, sometimes without ventilation, have long been employed. Epidemiological studies as far back as 1991 found that the more time you spent cooking, the more likely you were to get lung cancer (.pdf).

Now, residents have been getting better stoves or moving into apartments, where they have electricity, Finkelman said, but the local coal still presents a problem for thousands.

Public health biologist Joseph Bunnell of the U.S. Geological Survey, who was not involved with the work, said the next step will be to try to determine exactly how the tiny silica particles could combine with other carcinogens in coal smoke to be so deadly.

"What needs to be done from an epidemiological point of view is to establish biological plausibility," Bunnell said.

Image: 1) Pushing coal in Sichuan Province/AP. 2) BMC Public Health.

Citation: "Silica−Volatile Interaction and the Geological Cause of the Xuan Wei Lung Cancer Epidemic" by David J. Large, Shona Kelly, Baruch Spiro, Linwei Tian, Longyi Shao, Robert Finkelman, Mingquan Zhang, Chris Somerfield, Steve Plint, Yasmin Ali, and Yiping Zhou

WiSci 2.0: Alexis Madrigal's Twitter, Google Reader feed, and green tech history research site; Wired Science on Twitter and Facebook.

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