Friday, August 21, 2009

MISSING LINK TO CLOUD FORMATION FOUND

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New chemical research shows how cloud seedlings form over forested areas. The discovery of an unknown hitherto chemical compound in the atmosphere may help to explain how and when clouds are formed. The discovery of the so called dihydroxyepoxides (an aerosol-precursor), is reported in Science by a team comprising of researchers from the California Institute of Technology (Caltech) and the University of Copenhagen (UoC).

Professor Henrik Kjærgaard from the Department of Chemistry at the UoC calls the new compounds a missing link in the formation of clouds.

"We know that aerosols are important in the formation of clouds but, we didn't know much about how the aerosols themselves were formed. This new compound may be just what we were looking for," says the professor who has recently moved from University of Otago, New Zealand to fill his new appointment in Copenhagen. The new compound was originally found when a team of researchers from Caltech mounted a measuring device known as a Chemical Ionization Mass Spectrometer (CIMS) on an aeroplane, and flew it over the oaken forests of Northern America.

Next to methane, deciduous plants and trees such as oak and maple, are known to be the largest source of hydrocarbons in the atmosphere; an important factor in climate-change. As a result, the researchers went into the lab to calculate what occurs to the tree-released hydrocarbon known as isoprene, when it meets other compounds in the atmosphere. Based on previous research, isoprene was expected to break down into smaller molecules. But previous research was done with air found over cities, where levels of the combustion by-product NOx are very high. And the chemicals formed when isoprene interacts with NOx do not easily form aerosols. However, when subjected to air as found over pristine stretches of forest, the fate of the tree-released hydrocarbons turned out to be a very different one. Without the NOx to skew the process, isoprene unexpectedly degraded into the new compound: dihydroxyepoxide. This new compound appears to be extremely reactive and likely to form aerosols.

The study detailed in this week's issue of Science, reports the laboratory measurement of the isoprene degradation by hydroxyl radicals "the vacuum cleaner of the atmosphere". The detection of these epoxides as a significant final product in the isoprene breakdown was supported by isotope and theoretical studies, and corroborated the field measurements. The theoretical studies from Kjaergaar's group at the University of Otago, improved the CIMS technique and supported the chemical degradation mechanisms proposed. Discovering a new and unexpected atmospheric compound in the air over forests is fundamental research. Nevertheless, with manmade climate-change looming on the horizon, the research might find applications sooner that expected. The new aerosol-precursor may be extremely important when researchers attempt to compute projected climate change.

"That means, that the new compound is a missing link in more than one sense", Professor Kjærgaard states. "Clouds can retain as well as block the heat of the sun, so, if we don't understand what drives the formation of clouds, our climate-models are bound to be less than exact".

(Photo: University of Copenhagen)

University of Copenhagen

STANFORD PROFESSOR SEQUENCES HIS ENTIRE GENOME AT LOW COST, WITH SMALL TEAM

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The first few times that scientists mapped out all the DNA in a human being in 2001, each effort cost hundreds of millions of dollars and involved more than 250 people. Even last year, when the lowest reported cost was $250,000, genome sequencing still required almost 200 people. In a paper published online Aug. 9 by Nature Biotechnology, a Stanford University professor reports sequencing his entire genome for less than $50,000 and with a team of just two other people.

In other words, a task that used to cost as much as a Boeing 747 airplane and required a team of people that would fill half the plane, now costs as much as a mid-priced luxury sedan and the personnel would fill only half of that car.

"This is the first demonstration that you don't need a genome center to sequence a human genome," said Stephen Quake, PhD, professor of bioengineering. "It's really democratizing the fruits of the genome revolution and saying that anybody can play in this game."

There are at least two reasons why lowering the cost and effort required to sequence all the genetic information of individuals is important. The more examples scientists have of the whole human genetic code, the more they can discern about how specific genes and mutations result in the traits that make us all different, the diseases that plague us and our response to medicines. As that understanding increases and costs drop, doctors could then sequence their patients' genomes and provide "personalized medicine" in which prevention and treatment of disease would be informed by the patient's exact genetic profile.

"This can now be done in one lab, with one machine, at a modest cost," said Quake, the Lee Otterson Professor in the School of Engineering and a member of Stanford's Cancer Center. "It's going to unleash an enormous amount of creativity and really broaden the field."

Quake's genome, one of less than a dozen sequenced so far because of the cost and resources needed, is now available to researchers worldwide. Quake's colleagues at Stanford's School of Medicine have been looking through it and sometimes examining Quake himself, mining the data for interesting connections between what they can observe about him, his DNA and his family history.

"Some of the doctors are starting to poke and prod me to see how they can couple my genome with medicine," he said.

To sequence his genome, Quake's team used a commercially available, refrigerator-sized instrument called the Helicos Biosciences SMS Heliscope. Quake, who pioneered the underlying technology in 2003, is a co-founder of the Cambridge, Mass.-based company and chairs its scientific advisory board.

The technology—the SMS in the instrument's name—is called single molecule sequencing. While many techniques require generating thousands of copies of a subject's DNA, the single molecule technique does not, reducing the cost and effort involved. Instead, the technique requires chopping the 3 billion or so fundamental units of DNA (called bases) into strands about 30 bases long. The four bases in DNA are adenine (abbreviated A), cytosine (C), guanine (G), and thymine (T).

Each base of DNA matches with a specific other base: For example, T only matches with A. The machine captures each of the millions of strands on a specially treated glass plate, holds them there and washes successive waves of fluorescently labeled "letters" over the plate. As each complementary letter sticks next to a strand, the machine can read out the sequence of each strand.

Assembling the strands back into a cohesive genome is then done by powerful computers, which compare it to the reference genomes that have been compiled before. The process is akin to assembling an enormous jigsaw puzzle by referring frequently to the picture on the box. The team said the sequencing process took about one month to complete.

Still, several tricky problems had to be solved before the machine could reliably sequence a whole human genome. Quake worked with Norma Neff, a research manager in Quake's lab, and physics doctoral student Dmitry Pushkarev to write a sophisticated algorithm that would enable them to determine how accurate the process is.

Overall, the genome is 95 percent complete, a rate comparable with other sequenced genomes, the team found. In the paper, the authors are careful to note that all genome-sequencing technologies, including the one they've demonstrated, have produced incomplete approximations of the actual genome. Still, it is enough to help produce genuine insights about a person's traits and health.

Quake's genome has already yielded a few interesting connections between his genetics and his health. One is that he carries a rare mutation associated with a heart disorder; the revelation, he said, sheds light on what members of his family have always wondered with regard to the health of prior generations. The good news, he said, is that he's also apparently genetically predisposed to respond well to common cholesterol-lowering statin medicines.

Quake said the information has also forced him to take heed of that history. "If you know your uncle had something, you kind of discount that you can get it, but to see you've inherited the mutation for that is another matter altogether," he said.

One amusing "revelation" is that Quake's code contains a form of a gene that has sometimes been associated with increased disagreeability, he said.

"Of course, you don't need my genome to tell you that," Quake acknowledged. "My wife could have told you that and certainly the dean could have as well."

Stanford University

AMAZONIAN TRIBE SHEDS LIGHT ON CAUSES OF HEART DISEASE IN DEVELOPED COUNTRIES

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Heart attacks and strokes — the leading causes of death in the United States and other developed countries — may have been rare for the vast majority of human history, suggests a study published in PLoS ONE on Tuesday, August 11.

"Understanding how physiological systems respond in [indigenous] populations helps us better understand conditions in countries like the United States at the beginning of the 20th century," said senior author Eileen Crimmins of the USC Davis School of Gerontology. "This also offers some insight into the worlds we evolved in."

Crimmins, lead author Michael Gurven (University of California, Santa Barbara) and an international team of scientists looked at a remote Amazonian tribe in Bolivia known as the Tsimane. They measured various predictors of heart disease such as hypertension, obesity, diet and smoking habits. (The Tsimane grow and harvest their own tobacco.)

"The Tsimane were chosen because they still live a relatively traditional lifestyle: fishing, hunting, engaged in horticulture, gathering, living in extended family clusters and without much access to modern amenities," Gurven explained. "There are other groups with similar lifestyles, but often those groups have very small population numbers. . . . The Tsimane population is large enough — about 9,000 — that we can study almost all of the adults over age 40."

With only limited access to medical services, half of documented deaths among the Tsimane are due to infectious or parasitic disease. About two-thirds of the population has intestinal worms, the researchers found.

"We looked at a lot of populations in both developed and developing countries, in urban and rural settings, but none live in the relatively isolated and infected conditions of the Tsimane," the researchers write.

Chronic inflammation, which may lead to damage of the arteries, is prevalent among the Tsimane. According to the study, the Tsimane also have unusually high levels of C-reactive protein, increasingly used in clinical settings to evaluate risk for cardiovascular disease.

Yet, despite these risk factors for heart attacks, the researchers found that the high levels of C-reactive protein were unrelated to risk of peripheral arterial disease (the hardening of plaque in the arteries).

In fact, peripheral arterial disease "increases with age in every investigated population except the Tsimane," according to the study. Among the Tsimane, not a single adult showed evidence for peripheral arterial disease (measured using the ankle-brachial blood pressure index).

"Neither demographic interviews nor the past 7 years of working with the Tsimane has turned up many overt cases of people dying from heart attacks," Gurven said. "The Tsimane data tell us that inflammation alone may not be destructive in terms of its effects on long-term health. However, that might only be true in the context of an active lifestyle, lean diet, and possibly (and this part is more controversial) with a history of parasitism."

The researchers note that the Tsimane may have a distinct genetic expression compared to people in developed countries. Specifically, there is overexpression of the human leukocyte antigen, which has been linked in cell studies to plaque erosion.

"We observed low levels of atherosclerosis and associated cardiovascular disease among Tsimane, suggesting that these conditions may have been rare throughout pre-industrial human history," Crimmins said. "We may not be built for the world we live in. The Tsimane are perhaps a better model for the world we are built for."

"We don't know for sure that as younger people today get older that [arterial disease] won't increase," Gurven said. "More heart disease may be on the horizon if lifestyles change rapidly."

(Photo: Roger Snider)

University of Southern California

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