A semen protein that helps HIV

An atomic-level look at an HIV accomplice:
[Via Eureka! Science News - Popular science news]

Since the discovery in 2007 that a component of human semen called SEVI boosts infectivity of the virus that causes AIDS, researchers have been trying to learn more about SEVI and how it works, in hopes of thwarting its infection-promoting activity.

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Getting some structural understanding of how this peptide helps HIV enter a cell provides some greater understanding of the opportunistic aspects of the virus.

SEVI stands for semen-derived enhancer of virus infection and was found when researchers looks for inhibitors and enhancers of HIV in human semen. While it costs $30 to read the whole paper, the abstract provides a lot of info, including a picture of the protein SEVI is derived from.

Perhaps one of these inhibitors of HIV entry found in the blood will be useful. VIRIP could be very interesting. The gp41 protein of HIV is involved in the actions of both VIRIP and SEVI.

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Get ready for a maize of puns

corn by shaferlens
Amaizing: Corn genome decoded:
[Via Eureka! Science News - Popular science news]

In recent years, scientists have decoded the DNA of humans and a menagerie of creatures but none with genes as complex as a stalk of corn, the latest genome to be unraveled.

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Sweet corn story begins in UW-Madison lab:
[Via Eureka! Science News - Popular science news]

This week, scientists are revealing the genetic instructions inside corn, one of the big three cereal crops. Corn, or maize, has one of the most complex sequences of DNA ever analyzed, says University of Wisconsin-Madison genomicist David Schwartz, who was one of more than 100 authors in the article in the journal Science.

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New maize map to aid plant breeding efforts:
[Via Eureka! Science News - Popular science news]

In a massive survey of genetic diversity in maize, also known as corn, researchers across the United States, have developed a gene map that should pave the way to significant improvements in a plant that is a major source of food, fuel, animal feed and fiber around the world.

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New map of variation in maize genetics holds promise for developing new varieties:
[Via Eureka! Science News - Popular science news]

A new study of maize has identified thousands of diverse genes in genetically inaccessible portions of the genome. New techniques may allow breeders and researchers to use this genetic variation to identify desirable traits and create new varieties that were not easily possible before.

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Lots of corn stories today because Science published a major paper on the maize genome. This is of real interest because corn, probably more than any other domesticated food, is highly altered from its natural form. Mankind has spent thousands of years modifying this grain.

So we have several major papers. The B73 Maize Genome: Complexity, Diversity, and Dynamics. A First-Generation Haplotype Map of Maize. Paternal Dominance of Trans-eQTL Influences Gene Expression Patterns in Maize Hybrids. The Palomero Genome Suggests Metal Effects on Domestication.

So it will interesting to see what genetic effects have been made during this domestication.The last paper looks at some of the changes that occurred.

Looks like I have lots to read this weekend.

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Something we can all agree on

goldman sachs by dandeluca
Goldman: Flu Fear Spurs Donation!:
[Via The Big Picture]

(Reuters) New York: Having inoculated its employees with H1N1 vaccine dosages usurped from pregnant women and children, Goldman Sachs has increased its vigilance against the contagious virus by banning employee contact with spare change.

An internal memo outlines steps staff should take to avoid becoming ill, starting with the eradication of the potentially infected currency that may have lodged itself under the seats of their automobiles. The hazardous materials are being collected and sent to Small Business for disposal.

The memo also advised employees to “resist the urge to open your own car door ; let your driver do it.”

-Richard Ambrose

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I really hope that this is just a spoof. There is no direct link to the Reuter item. But it is so good that it should be on the Onion. I’m sure this could go viral without any problem, it is so unbelievably believable. Goldman really could be that stupid!

It does not matter what your political affiliations are, Goldman should simply be broken up until it is actually run by people who give a crap.

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Overcoming the gut

fossil by kevinzim
The amateur scientist (that’s us)
[Via Seth's Blog]

Many people buy a car (probably their single biggest discretionary purchase) based on slamming a door, kicking a tire and judging the handshake of a salesperson.

We choose a surgeon based on the carpeting in his office and a politician by his hair cut.

During the first week of swine flu vaccines in New York, most parents (more than half!) chose to keep their kids out of the program.

Interviewed parents said things like, “I’m not sure it’s safe,” and “I wanted to see if it affected other kids…”

No mention of longitudinal studies or long-term side effects. No science at all, really, just rumors and hunches and gut instincts.

This gut-instinct approach served people well for hundreds of thousands of years, but it’s pretty clear that it doesn’t work in a complex world. Eating salmon at a wedding feels ‘safe’ because we always have, but of course any professional scientist will tell you that farmed salmon is an ecological disaster. You can’t see the problem, so you ignore it.

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I mentioned this the other day. Most people make decisions based on gut instinct, their own personal rules of thumb. Because of this, they are not very accessible through direct intellectual processes.

Marketing professionals use this all the time. But scientists are not only loathe to cloak their understanding of the real world in marketing lingo, they usually see that as as a direct assault on the science itself (I guess this is one of their own rules of thumb.)

That is why scientists who ARE quite good at connecting with regular people and making direct connections are often viewed with suspicion by other scientists. Carl Sagan, who surely did research of the level to get appointed to the National Academy of Sciences, was rebuffed, mainly due to the negative efforts of other members not in his scientific discipline. That is, the ones who were least able to really judge his science kept him out:

In the early 1990s the national academy of Sciences held its annual election to membership. Richard Feynman had already become so exasperated that he resigned his membership, saying that he saw no point in belonging to an organization that spent most of its time deciding who to let in.

But this time the best known astronomer in the world was nominated. Each section of the Academy votes separately on all candidates, and the astronomy division voted the fellow in. But there were negative votes from other divisions, notably the particle physicists. They disliked his public persona, some said. They complained that he was arrogant and an egomaniac, and said he was really not up to caliber, despite his fame. Clearly, envy played some role. Rumors flew.

This served as an object lesson for many other scientists. Do not invade the public realm or you will be flung out of the group.

In my opinion, the real reason for the snub had little to do with his science and much to do with his apparent steps into public policy.

As a young scientist, I was horrified by this event. I had a tremendous respect for Sagan, not only for his Cosmos series but for his current scientific work. He published, in Science, THE key paper on nuclear winter, helping coin the term. He is the ‘S’ in what became know as TTAPS, the first real attempt to model what would happen to our atmosphere in the event of massive nuclear explosions. It was published in December 1983. But not many remember that he had two papers in the same issue of Science, something very seldom seen.

Immediately following the TTAPS paper was one entitled Long-term biological consequences of nuclear war. Here is the abstract:

Subfreezing temperatures, low light levels, and high doses of ionizing and ultraviolet radiation extending for many months after a large-scale nuclear war could destroy the biological support systems of civilization, at least in the Northern Hemisphere. Productivity in natural and agricultural ecosystems could be severely restricted for a year or more. Postwar survivors would face starvation as well as freezing conditions in the dark and be exposed to near-lethal doses of radiation. If, as now seems possible, the Southern Hemisphere were affected also, global disruption of the biosphere could ensue. In any event, there would be severe consequences, even in the areas not affected directly, because of the interdependence of the world economy. In either case the extinction of a large fraction of the Earth’s animals, plants, and microorganisms seems possible. The population size of Homo sapiens conceivably could be reduced to prehistoric levels or below, and extinction of the human species itself cannot be excluded.

The idea of nuclear winter emerged due to the ideas of extinction first promulgated by the Alvarezes just 3 years earlier. If the dinosaurs became extinct because of an impact, one that resulted in the blockage of sunlight by the material blasted into the atmosphere, what would happen with the tons of material blasted into the atmosphere by nuclear warheads. The abstract to their paper, published in Science in 1980, had this to say:

Impact of a large earth-crossing asteroid would inject about 60 times the object’s mass into the atmosphere as pulverized rock; a fraction of this dust would stay in the stratosphere for several years and be distributed worldwide. The resulting darkness would suppress photosynthesis, and the expected biological consequences match quite closely the extinctions observed in the paleontological record.

The nuclear winter papers were derived from solid scientific principles. ‘If the dinosaurs were driven to extinction by the reduction in solar energy by the impact, what would happen today if a similar event occurred through nuclear explosions?’ They used one of the first primitive global models to examine the question. It was a classic science investigation.

The results had severe policy implications, and stirred fierce political debate. I think Sagan’s snub came more from the feeling that he was entering the public realm of policy not just education. In the heat of the final years of the Cold War, writing a paper about nuclear winter seemed more political than scientific.

Too many fellow scientists did not like his popularity. But I also think many did not like the idea of researchers entering the arena of public policy. Maybe they feared that funding would be cut off if the policy conflicted with government leaders. Maybe they just wanted to be left alone in their ivory towers.

Only recently has this old view been changing. Many scientists are now making connections to the community, are advocating policy decisions. But it always has to be in the service of science, of real data. Because if we lose the connection to the world around us, if we do not accurately use our tools to describe Nature to the rest of the community, we fail to remain scientists.</P.

So, how do we market that?

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