Category Archives: Research

Image of Viral Coat

image of exterior of virus - made up of 5 million atoms

High-energy X-ray diffraction was used to pinpoint some 5 million atoms in the protective protein coat of the PsV-F virus. The coat’s symmetrical features are shared by hundreds of viruses. The red and yellow sections illustrate how building blocks of four proteins come together to form the spherical shell.

The image reveals the structure of a type of protein coat shared by hundreds of known viruses containing double-stranded RNA genomes. The image was painstakingly created from hundreds of high-energy X-ray diffraction images and paints the clearest picture yet of the viruses’ genome-encasing shell called a “capsid.”

Viruses can reproduce themselves only by invading a host cell and highjacking its biochemical machinery. But when they invade, viruses need to seal off their genetic payload to prevent it from being destroyed by the cell’s protective mechanisms. Though there are more than 5,000 known viruses, including whole families that are marked by wide variations in genetic payload and other characteristics, most of them use either a helical or a spherical capsid.

“Spherical viruses like this have symmetry like a soccer ball or geodesic dome,” Pan said. “The whole capsid contains exactly 120 copies of a single protein.” Previous studies had shown that spherical capsids contain dozens of copies of the capsid protein, or CP, in an interlocking arrangement. The new research identified the sphere’s basic building block, a four-piece arrangement of CP molecules called a tetramer, which could also be building blocks for other viruses’ protein coats.

Full press release

Continuing Bee Colony Collapse Disorder

Photo of a bee

‘I do everything… the bees still die’

The use of the term colony collapse disorder has been criticised by some scientists and other experts who say that it’s often an excuse for poor beekeeping. David sighs heavily.

“Well… I don’t abuse my bees, I kinda take offence at that, when we transport them we take great pains to make sure they arrive safely, to make sure they have water. It’s totally unexplained.

“That’s the frustrating part. There’s no reason that these bees here should be in this shape, just three months ago they were beautiful bees, they were large thriving colonies, and to have them dwindle down to one or two or frames of bees is beyond comprehension as far as I’m concerned.”

But despite the disappearance of his bees, and the lack of clarity about what’s causing it, David remains an optimist. He points to a small discreet emblem on the side of his pickup truck, a hieroglyph of an ancient bee.

“That little hieroglyph there is Egyptian it stands for a beekeeper or bees. It’s an ancient craft; it’s been around a long time. The bees will endure.”

Photo by Justin Hunter

Ozone Pollution Taking Toll on American Lives

Ozone Pollution Taking Toll on American Lives by Amanda Gardner

Thousands of Americans are dying each year from lung disease caused by atmospheric ozone, a new study finds.

The greatest risk may for those living be in hot, dry cities such as Los Angeles, which has one of the highest concentrations of ozone. Residents of Los Angeles may face a 25 percent to 30 percent higher annual risk of dying from a respiratory ailment versus people in low-ozone areas such as the Great Plains, the researchers said.
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An estimated 240,000 people in the United States and 7.7 million people worldwide die of respiratory disease each year, according to data from the World Health Organization. Efforts to reduce ground-level ozone have stalled in recent years, Jarrett said, and now one in three Americans lives in an area that exceeds the national standard for ozone levels.
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Ozone is also a powerful greenhouse gas, Jerrett said, so measures to improve health might have the added benefit of slowing climate change.

Very Cool Wearable Computing Gadget from MIT

Pattie Maes presentation at TED shows a very cool prototype for wearable, useful computing spearheaded by Pranav Mistry (who received a standing ovation at TED). It’s a wearable device with a projector that paves the way for profound interaction with our environment.

The prototype of the system cost only $350. The software, created by them, obviously is the key, but how amazing is that, $350 for the hardware used in the prototype! There is a useful web site on the Sixth Sense project.

The SixthSense prototype is comprised of a pocket projector, a mirror and a camera. The hardware components are coupled in a pendant like mobile wearable device. Both the projector and the camera are connected to the mobile computing device in the user’s pocket. The projector projects visual information enabling surfaces, walls and physical objects around us to be used as interfaces; while the camera recognizes and tracks user’s hand gestures and physical objects using computer-vision based techniques.

The software program processes the video stream data captured by the camera and tracks the locations of the colored markers (visual tracking fiducials) at the tip of the user’s fingers using simple computer-vision techniques. The movements and arrangements of these fiducials are interpreted into gestures that act as interaction instructions for the projected application interfaces. The maximum number of tracked fingers is only constrained by the number of unique fiducials, thus SixthSense also supports multi-touch and multi-user interaction.

Scientists Target Bacteria Where They Live

Scientists Learning to Target Bacteria Where They Live

Scientists have learned that bacteria that are vulnerable when floating around as individual cells in what is known as their “planktonic state” are much tougher to combat once they get established in a suitable place — whether the hull of a ship or inside the lungs — and come together in tightly bound biofilms. In that state, they can activate mechanisms like tiny pumps to expel antibiotics, share genes that confer protection against drugs, slow down their metabolism or become dormant, making them harder to kill.

The answer, say researchers, is to find substances that will break up biofilms.
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Melander said “a throwaway sentence in an obscure journal” — the Bulletin of the Chemical Society of Japan — gave them another clue. They isolated a compound from the sponge that disperses biofilms and figured out how to synthesize it quickly and cheaply.
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But dispersing biofilms without understanding all the ramifications could be a “double-edged sword,” Romeo warned, because some bacteria in a biofilm could wreak worse havoc once they disperse.

“Simply inducing biofilm dispersion without understanding exactly how it will impact the bacterium and host could be very dangerous, as it might lead to spread of a more damaging acute infection,” he said.

Resurrection of the Human IRGM Gene

Interesting open access paper on Death and Resurrection of the Human IRGM Gene. Author summary:

The IRG gene family plays an important role in defense against intracellular bacteria, and genome-wide association studies have implicated structural variants of the single-copy human IRGM locus as a risk factor for Crohn’s disease. We reconstruct the evolutionary history of this region among primates and show that the ancestral tandem gene family contracted to a single pseudogene within the ancestral lineage of apes and monkeys.

Phylogenetic analyses support a model where the gene has been “dead” for at least 25 million years of human primate evolution but whose ORF became restored in all human and great ape lineages. We suggest that the rebirth or restoration of the gene coincided with the insertion of an endogenous retrovirus, which now serves as the functional promoter driving human gene expression. We suggest that either the gene is not functional in humans or this represents one of the first documented examples of gene death and rebirth.

Rare Saharan Cheetahs Photographed

Â© Farid Belbachir/ZSL/OPNA

The first systematic camera trap survey across the central Sahara, identified four different Saharan cheetahs using spot patterns unique to each individual. ‘The Saharan cheetah is critically endangered, yet virtually nothing is known about the population, so this new evidence, and the ongoing research work, is hugely significant,’ said Dr Sarah Durant, Zoological Society of London Senior Research Fellow.

Farid Belbachir, who is implementing the field survey, adds: ‘This is an incredibly rare and elusive subspecies of cheetah and current population estimates, which stand at less than 250 mature individuals, are based on guesswork. This study is helping us to turn a corner in our understanding, providing us with information about population numbers, movement and ecology.’

The Northwest African cheetah is found over the Sahara desert and savannas of North and West Africa, respectively, including Algeria, Niger, Mali, Benin, Burkina-Faso and Togo. The populations are very fragmented and small, with the biggest thought to be found in Algeria.

Read the full press release

Update Dec 2010: Nighttime photos of Saharan cheetah and other Saharan cat photos.

Open Science: Explaining Spontaneous Knotting

Shedding light on why long strands tend to become knotted

Anyone who has ever put up Christmas lights knows the problem: Holiday strands so carefully packed away last year are now more knotty than nice. In fact, they have become an inextricable, inexplicable, seemingly inevitable mess. It happens every year, like some sort of universal law of physics.

Which, it turns out, it basically is. In October, two UCSD researchers published the first physical explanation of why knots seem to form magically, not just in strands of Christmas lights, but in pretty much anything stringy, from garden hoses to iPod earbud cords to DNA.
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“We’re not mathematicians,” Smith said. “We’re physicists. Physicists do experiments.”

UCSD researchers constructed a knot probability machine that involved placing a single length of string in a plastic box, sealing it, then rotating the box at a set speed for a brief period of time.
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The experiment involved placing a single length of floppy string into a plastic box, sealing it, then rotating the box at a set speed for a brief time. The researchers did this 3,415 times, sometimes changing variables such as box size and string length.

Open access research paper: Spontaneous knotting of an agitated string by Dorian M. Raymer and Douglas E. Smith.

Above a critical string length, the probability P of knotting at first increased sharply with length but then saturated below 100%. This behavior differs from that of mathematical self-avoiding random walks, where P has been proven to approach 100%. Finite agitation time and jamming of the string due to its stiffness result in lower probability, but P approaches 100% with long, flexible strings.
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As L [length] was increased from 0.46 to 1.5 m, P increased sharply. However, as L was increased from 1.5 to 6 m, P saturated at 50%.
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Tripling the agitation time caused a substantial increase in P, indicating that the knotting is kinetically limited. Decreasing the rotation rate by 3-fold while keeping the same number of rotations caused little change in P.
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We also did measurements with a stiffer string and observed a probability of finding a knot would approach 100% with an substantial drop in P.

Yet another interesting case of scientists explaining the world around us (and the value of open science).

John Conyers Against Open Science

Lawrence Lessig once again has written a good blog post: John Conyers and Open Access

Open access journals, such as, for example, those created by the Public Library of Science, have adopted a different publishing model, to guarantee that all all research is freely accessible online (under the freest Creative Commons license) immediately, to anyone around the world. This guarantee of access, however, is not purchased by any compromise in academic standards. There is still a peer-review process. There is still even a paper-based publication.

Pushed by scientists everywhere, the NIH and other government agencies were increasingly exploring this obviously better model for spreading knowledge. Proprietary publishers, however, didn’t like it. And so rather than competing in the traditional way, they’ve adopted the increasingly Washington way of competition — they’ve gone to Congress to get a law to ban the business model they don’t like. If H.R. 801 is passed, the government can’t even experiment with supporting publishing models that assure that the people who have paid for the research can actually access it. Instead, if Conyers has his way, we’ll pay for the research twice.
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The insanity in this proposal is brilliantly described by Jamie Boyle in this piece in the FT. But after you read his peace, you’ll be even more puzzled by this. For what possible reason could Conyers have for supporting a bill that 33 Nobel Prize Winners, and the current and former heads of the NIH say will actually hurt scientific research in America? More pointedly, what possible reason would a man from a district that insists on the government “Buying American” have for supporting a bill that basically subsidizes foreign publishers (for the biggest players in this publishing market are non-American firms, making HR 801 a kind of “Foreign Publishers Protection Act”)?
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the co-sponsors of this bill who sit on the Judiciary Committee received on average two-times the amount of money from publishing interests as those who haven’t co-sponsored the bill.

The damage done to science by dinosaurs fighting progress and corrupt or inept politicians is very disheartening. Thankfully we have been able to achieve great things in spite of politicians trying to favor their donors and harm the scientific community.

Problems Using Corn as Biofuel

The pluses and (mostly) minuses of biofuels by Robert Sanders

one ripple effect from the stampede to create more ethanol from corn in the United States. As corn prices skyrocketed several years ago, soybean fields were converted to corn, and the price of soy rose. As a result, farmers in Brazil, one of the main countries with the soil, climate and infrastructure to make up the difference, began to bulldoze rainforest to grow more soybeans.

“If reduced U.S. soybean production results in a parallel increase in Brazilian soybean production, a potential net release of 1,800 to 9,100 Tg (trillion grams) of CO2-equivalents of greenhouse gas emissions due to land-use change is possible,” Coe wrote in a summary of his talk. That is equivalent to more than 9 billion metric tons of carbon dioxide.