Friday, 4 March 2011

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge

iPad Lets Scientists Drag, Pinch and Swipe Real Molecules

Posted: 03 Mar 2011 04:03 PM PST

Using laser beams to control individual molecules is a precise, difficult operation rendered nearly impossible by the limitations of the computer mouse.

Unless you have the right iPad app.

New software called iTweezers lets scientists drag molecules around the screen as easily as shooting angry birds at pigs.

"It's cool because it takes something that normally lives on a lab bench, and makes it so simple," said physicist Richard Bowman of Scotland's University of Glasgow, lead author of a paper in the March 4 Journal of Optics describing the new software. "We have visitors who have never seen an optical tweezer before in their lives, and they happily move particles around."

'You can learn stuff by physically connecting in a different way.'

The new app is an interface for controlling optical tweezers, an instrument that uses laser light to trap and move microscopic objects. It works a little like a sci-fi tractor beam: The radiation from a tightly focused beam of light applies enough pressure to tiny objects like cells or proteins to pin them to the spot or push them around.

The invention of optical tweezers won Secretary of Energy Steven Chu a Nobel Prize in Physics, and they have proven their worth in biology labs, where they have been used to trap and manipulate everything from viruses to DNA. They have helped measure some of the smallest forces ever recorded, detected how DNA's double helix unzips, and watched molecular motors move matter around inside cells.

But most of the early experiments with optical tweezers could only focus on one spot at a time.

"Up till now, people typically controlled things using a mouse," said physicist Gordon Love of Durham University in England, who was not involved in the new work. "A mouse is great for moving around one thing like a cursor on a screen, but it's no good for moving around multiple things."


The multitouch interface was born when Bowman's colleagues at England's University of Bristol struggled to control a tiny rod about 300 nanometers wide. To keep the rod from flipping over, the physicists needed to pin the rod down in several places at once.

In 2009, the team built a custom table that let them drag and drop microscopic glass beads just by swiping their fingers along a layer of paper coated with silicon rubber. The device was clunky and complicated, but it mostly worked.

But soon the team found a more elegant setup: the iPad.

"When the iPad came out we thought, well hey, this is just like the big table, except it's small and works really well," Bowman said.

The physicists shine laser light through a high-powered microscope onto a slide holding whatever objects the scientists are interested in. Bowman's lab usually uses glass beads about two microns across, which are used in many experiments as a handle for harder-to-grasp molecules.

Before entering the microscope, the laser beam bounces off a tiny LCD screen that splits the beam and steers it around to focus on several beads at once.

A computer tells the LCD screen to display specific holograms designed to bend the laser light in specific ways. The app Bowman and colleagues use to write the holograms is available on iTunes as iHologram.

"It's fun to use and quite visually attractive," Love said. "My young daughters play with it. They have no idea about optical tweezers, but they think it's fantastic."

The iPad displays the view through the microscope, and wirelessly sends the computer the information on where the user's fingers are. A user can select up to 11 different objects by tapping them, move them around by dragging them, and use the pinch-zoom feature to move the objects up and down in space.

Theoretically, scientists could be sitting on the couch with an iPad at home moving beads or molecules in the lab. But so far, the method hasn't made it out of the University of Glasgow physics lab. The researchers hope to bring it into other labs to help biologists and chemists run complicated experiments without stressing about the technology.

"The interface makes it really easy," Bowman said. "If somebody comes along and sees my computer program with about a bajillion controls on it, it's a bit off-putting. Whereas the iPad lets you get stuck right in there and move stuff around, without having to worry about setting up all the physics behind it."

Feeling like you can directly touch cells and molecules can also help build an intuitive sense of the microscopic world, Bowman says. His lab has also developed a way to manipulate molecules with a joystick that transmits the forces the molecule feels to the user's hand, like a video game with tactile feedback. Bowman says you can even feel water molecules jiggling around your trapped molecule.

"The interface stuff is fun, but I think you can learn stuff by physically connecting in a different way," he said. "You get a feel for how things work."

Video and image: Richard Bowman/University of Glasgow

Citation: "iTweezers: Optical micromanipulation controlled by an Apple iPad" (.pdf). R.W. Bowman, G. Gibson, D. Carberry, L. Picco, M. Miles and M.J. Padgett. Journal of Optics, Vol. 13, March 4, 2011.

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Deepwater Horizon’s Impacts Found in Bacteria

Posted: 03 Mar 2011 03:17 PM PST

Nobody's going to shed a tear for an oiled microbe, but the Deepwater Horizon's impacts include bacteria, underscoring just how subtle and fundamental the blowout's ecological consequences may be.

The findings, based on comparisons of microbial flux before and after oil washed ashore, are not a final analysis. It's too soon to say how long-lasting those fluctuations were, or what they meant to other creatures. Instead they're a starting point, an early observation in research that will continue for years, even decades.

"While visible damages are evident in the wildlife populations and marine estuaries, the most significant effect may be on the most basic level of the ecosystems: the bacterial and plankton populations," wrote researchers in a study Feb. 28 in Nature Precedings. "Abrupt and severe changes in the microbial metabolism can produce long-term effects on the entire ecosystem."

Led by biologist William Widger of the University of Houston, the researchers sequenced DNA from near-shore water and beach-soil samples gathered before and after oil arrived in Gulfport, Mississippi, and Grand Isle, Louisiana, following the blowout last spring.

By cross-referencing the DNA to microbe gene databases, they identified populations of bacteria and how they changed. Vibrio cholera, the bug that causes cholera, spiked upward after the spill. So did Rickettsiales, an order of bugs whose diseases include typhus and spotted fever.


Populations of Synechococcus, a typically ubiquitous photosynthesizing bug, collapsed. Communities of Archaea — the lesser-recognized microbial kingdom — also underwent radical makeovers.

The new analyses are not meant to be exhaustive. Most species of ocean-dwelling microbes have not yet been identified. Rather, they're a diagnostic snapshot that wouldn't have existed even a decade ago, before the advent of faster, cheaper gene sequencing and a rising appreciation of bacteria's ecological importance.

"Microbial communities are an essential but vulnerable part of any ecosystem. The basic metabolic activities of microbial communities represent the fundamental status of any environment," wrote Widger's team.

Andy Juhl, a Columbia University plankton ecologist who was not involved in the study, cautioned against drawing premature conclusions. "I would take the findings that oil resulted in these changes in microbial composition as a plausible hypothesis," he said. "Further work may support or refute that hypothesis."

Juhl's assessment is in keeping with scientific debate over a growing body of research into exactly what poured and bubbled from the Deepwater Horizon wellhead, and what it meant to the Gulf's already-troubled ecologies. The research is still in its early stages, painstakingly gathered and deliberated — as it will be for years to come — even as BP has reneged on restoration agreements, arguing that the damage wasn't so bad after all.

In mid-February, researchers led by University of Georgia biogeochemist Samantha Joye concluded that up to 40 percent of hydrocarbons released by the blowout came in the form of methane gas. Its fate remains unknown, and vast methane pockets could still be floating through the Gulf, they said.

Those findings were criticized as relying on outdated data by oceanographers John Kessler and David Valentine, who a month earlier said that the methane had been consumed by deep-sea bacteria.

The disagreement was a standard scientific back-and-forth, but much less debatable were seafloor movies subsequently shown by Joye at the American Association for the Advancement of Science meeting in Washington, D.C. Shot by a robotic submersible vehicle in December, the films showed a Gulf seafloor covered with oil and dead invertebrates.

What all this ultimately means for Gulf ecology is unknown. As for human impacts, the National Institutes of Health announced on March 1 that it's looking for 55,000 oil cleanup workers to participate in a long-term study of chemical impacts on health.

In the meantime, the oil industry and Gulf lawmakers continue to push for lifting restrictions on deepwater drilling. Kenneth Feinberg, administrator of the $20 billion claims fund established by BP, has said that Gulf ecosystems should be fully recovered by 2012.

"One viewpoint, which is what BP would want us to believe, is that this oil and gas had been naturally dispersed and had a relatively minor effect, and perhaps no long-term impact on the health of the Gulf of Mexico ecosystem. The other point of view is that it killed lots of animals, oiled wetlands and may have long-term ecological impacts, but it's too early to assess that," said Ian MacDonald, a Florida State University oceanographer and co-author with Joye of the methane estimates.

"We all hope the first one is correct, but we should try to be very objective about determining what really did happen," he said.

Widger's group concluded that "the long-term damage to the ecosystem including the basic food chain is uncertain and requires future research."

Images: 1) Geoff Livingston, Flickr. 2) Samantha Joye, University of Georgia.

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Citation: "Longitudinal Metagenomic Analysis of the Water and Soil from Gulf of Mexico Beaches Affected by the Deep Water Horizon Oil Spill." By William R. Widger, Georgiy Golovko, Antonio F. Martinez, Efren V. Ballesteros, Jesse J. Howard, Zhenkang Xu, Utpal Pandya, Viacheslav Y. Fofanov, Mark Rojas, Christopher Bradburne, Ted Hadfield, Nels A. Olson, Joshua L. Santarpia & Yuriy Fofanov. Nature Precedings, February 28, 2011.

Engineered Viruses Boost Memory Recall in Mice

Posted: 03 Mar 2011 12:19 PM PST

By John Timmer, Ars Technica

Memories fade with time, often to the annoyance of those who can't recall important details. But scientists have now found a way to boost the recall of memories even after they've started to fade. Unfortunately, the method involves injecting an engineered virus directly into the brain, so those of us who are bad with names may want to wait a bit for the technique to be refined.

The work was done in rats, and the memories in question are associations between a specific taste — saccharine, for example — and an unpleasant stimulus, caused by injection of a nausea-inducing drug (the approach is called "conditioned taste aversion"). Unless the unpleasant association is reinforced, the memories will slowly fade with time, although the aversion doesn't disappear entirely during the two-week period that the authors were looking at.

Two years ago, the same authors found that it was possible to radically accelerate this fading. By injecting a chemical that blocked a specific brain enzyme (protein kinase M ζ), the authors caused the rats to act as if they had never experienced the nausea, even if the memory manipulation took place 25 days after the conditioning. Most chemicals that interfere with memories tend to prevent them from being consolidated for long-term storage, but this chemical seemed to work even after the memory was firmly in place.

That's potentially helpful, since some people have formed negative associations with harmless or even helpful items. Still, for most of us, it would be nice to think that fading memories could be resuscitated. Apparently, they can. The researchers have now done what's effectively the converse experiment, and increased the activity of protein kinase M ζ. They did this by engineering a virus to express the gene for the kinase, and then infected specific areas of the brain involved in memory. All the infected cells had additional copies of the gene, and thus made more of its product.

The virus had exactly the effect that the authors would presumably have predicted. The virus was injected a week after the rats were given the aversion conditioning, when the memory would already be starting to fade, and the memory tests were done a week after that, yet rats showed a significantly improved retention of their memories. As the authors point out, the engineered virus boosted a memory that was formed before it was even present.


The memory molecule, PKMzeta, overexpressed in rat neurons. Red (left) shows PKMzeta while green (middle) is a fluorescent protein that shows nerve cells have been infected by viruses engineered to boost the memory molecule. Yellow (right) shows both the memory molecule and green fluorescent protein only overexpress at certain locations in the neuron. Weizmann Institute of Science/Science

Actually, you can make that memories, plural. The authors trained rats to avoid both saccharine and salty liquids over the course of three days, and then injected the virus a week after the last training. The memories of both of these trainings were enhanced by the presence of the viral protein kinase M ζ gene.

The authors can't tell exactly what protein kinase M ζ is doing to increase the recall of memories, and suggest it could be either enhancing the association between taste and the unpleasant experience, or simply enhancing recall in general. Although they don't mention it, their findings may also be limited to specific classes of memories, like the associations examined here.

That latter point makes the last sentence of the paper a bit over the top, as the authors suggest that a chemical that enhances protein kinase M ζ activity might make for a good treatment for memory disorders like amnesia and age-related decline. Until we have a clearer sense of how many types of memories it works for, that's a bit premature. Fortunately, there are lots of ways to test the recall abilities of animals, many of which don't involve negative associations. Hopefully, testing of the virus' more general impact on memory is already underway.

Image: HIV (green dots), a member of the lentivirus genus. (C. Goldsmith/P. Feorino/E. L. Palmer/W. R. McManus/CDC)

Citation: "Enhancement of Consolidated Long-Term Memory by Overexpression of Protein Kinase Mζ in the Neocortex." Reut Shema, Sharon Haramati, Shiri Ron, Shoshi Hazvi, Alon Chen,
Todd Charlton Sacktor and Yadin Dudai.
Science, Vol. 331, March 3, 2011. DOI: 10.1126/science.1200215

Source: Ars Technica

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4 New Species of Zombifying Ant Fungus Found

Posted: 03 Mar 2011 09:50 AM PST

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Four new species of brain-manipulating fungi that turn ants into "zombies" have been discovered in the Brazilian rain forest.

These fungi control ant behavior with mind-altering chemicals, then kill them. They're part of a large family of fungi that create chemicals that mess with animal nervous systems.

Usually scientists study these fungi as specimens preserved in a lab, said entomologist David Hughes of Pennsylvania State University, co-author of a study March 3 PLoS ONE. "By going into the forest to watch them, we found new micro-structures and behaviors."

Once infected by spores, the worker ants, normally dedicated to serving the colony, leave the nest, find a small shrub and start climbing. The fungi directs all ants to the same kind of leaf: about 25 centimeters above the ground and at a precise angle to the sun (though the favored angle varies between fungi). How the fungi do this is a mystery.

"It's related to the fungus that LSD comes from," Hughes said. "Obviously they are producing lots of interesting chemicals."

Before dying, ants anchor themselves to the leaf, clamping their jaws on the edge or a vein on the underside. The fungi then takes over, turning the ant's body into a spore-producing factory. It lives off the ant carcass, using it as a platform to launch spores, for up to a year.

"This is completely different from what we see in temperate zones where, if an insect dies from a fungal infection, the game's over in a few days," Hughes said. "The fungi rots the body of the insect and releases massive amounts of spores over two or three days. But in the tropics, where humidity and temperature are more stable, the fungi has this strategy for long-term release."

Of the four new species, two grow long, arrow-like spores which eject like missiles from the fungus, seeking to land on a passing ant. The other fungi propel shorter spores, which change shape in mid-air to become like boomerangs and land nearby. If these fail to land on an ant, the spores sprout stalks that can snag ants walking over them. Upon infecting the new ant, the cycle starts again.

Chemicals from this global group of fungi, known as Cordyceps, have been a part of traditional medicine for thousands years, and part of Western medicine for the last 50.

Organ transplant patients, for example, receive ciclosporin — a drug that suppresses the immune system, reducing the chance the body will reject the new tissue. Chemicals from this same fungal group are also used for antibiotic, antimalarial and anticancer drugs.

The fungi help the forest by keeping ant populations in check. "All of the problems with global ant infestations, for example the Argentine fire ant," Hughes said, "is because the ants have escaped their natural enemies. Then they become a pest."

These fungi need a precise level of humidity to survive. As global temperature changes, the forests where they live are drying. Hughes and his colleagues are now studying the decline these fungi.

"We're worried we'll see the extinction of a species we've only just managed to describe."

On the following pages are more photographs of zombifying fungi in action.

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All images: David Hughes, Pennsylvania State University

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Citation: "Hidden diversity behind the Zombie-Ant fungus Ophiocordyceps unilateralis: Four new species described from Carpenter ants in Minas Gerais, Brazil." By Harry C. Evans, Simon L. Elliot, David P. Hughes. PloS One, Vol. 6 No. 3, March 2011.

An Unknown Ocean: The Other Rhythms of Life

Posted: 02 Mar 2011 03:41 PM PST

Circadian rhythms are well known to biologists, with hundreds of studies analyzing fundamental links between sunlight, cellular clocks, hormones and metabolism function.

But for the first few billion years of Earthly life, it wasn't just solar cycles that mattered. Lunar and tidal cycles were just as important, and for modern marine creatures they still are. Yet these cycles have received only a smidgen of scientific attention.

"When you look at the literature of circadian and lunar rhythms, they were equally prominent in the literature" until the early 1980s, said evolutionary neurobiologist Kristin Tessmar-Raible of Austria's University of Vienna.

That's when the first circadian clock gene was cloned in a fruit fly, allowing scientists to manipulate its function in a common model organism, and focus shifted. "Everything switched in modern molecular biology to what you could look at in fruit flies and mice. Those only have circadian rhythms," she said.


In a research review published in the March Bioessay, Tessmar-Raible and Florian Raible, a molecular biologist at the University of Vienna, describe the ubiquity of lunar and tidal cycles in ocean creatures, and the still-embryonic understanding of how those cycles work.

Their own interest was sparked several years ago in work on Platyneereis dumerilii, a marine worm known to evolutionary biologists as a living fossil, last sharing a common ancestor with vertebrates 600 million years ago. They found a previously unknown, light-sensitive cell deep in the worms' brains, far from any light.

Mystified at its location, they researched the worm's natural history, and learned that their wild spawning cycles occurred in time with lunar cycles. At conferences with marine biologists, Raible and Tessmar-Raible learned of a vast literature on animal behavior and lunar cycles.

'How many different clocks can you have? It's an open question.'

From algae to jellyfish to worms to crustaceans to mollusks to fish, examples abound of behaviors that change according to moon and tide. Molecular research is just beginning now, and questions abound. Raible and Tessmar-Raible's most basic question is how the lunar clock mechanisms work — and, indeed, how many different clock mechanisms there are.

"How many different clocks can you have? It's an open question," said Raible. "You can imagine that the inputs could differ between species. It doesn't have to be light. It could be the pressure of the water. This is all up for investigation. It's going to be very interesting to see and compare between species. It may be the same system, or there may be several independent systems that have evolved."

Another question is how lunar clocks don't interfere with circadian clocks, and vice versa. Yet another is whether land-dwelling creatures still have lunar clocks. It's not uncommon for complex terrestrial vertebrates to share features with ancient marine ancestors; in humans, female reproductive cycles may correlate with lunar cycles, though evidence is mixed.

However, Raible and Tessmar-Raible note that many other animals' reproductive patterns show no connection to the moon, and warn against speculation.

To them, understanding lunar cycles is less about investigating potential terrestrial analogues than coming to a deeper understanding of ocean creatures, which — despite humanity's landed perspective — dominate Earthly life.

"First we want to understand how these things work in organisms that really have lunar clocks, and see which molecules are involved," said Tessmar-Raible. "And then, are they really involved in vertebrates? Do we have them, and what are they doing? Let's see."

Images: 1) Frank van de Velde/Flickr 2) Phylogenetic chart of animals with lunar cycles. (Bioessays)

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Citation: "Another place, another timer: Marine species and the rhythms of life." By Kristin Tessmar-Raible, Florian Raible and Enrique Arboleda. Bioessays, Vol. 33 No. 3, March 2011.