Jellyfish Eyes Solve Optical Origin Mystery

Eyes are one of evolution’s marvels, described by Darwin as “an organ of extreme perfection.” But whether the animal kingdom’s kaleidoscope of eyes evolved from a common structure, or separately in dozens of forms, is a nagging evolutionary question.

Now a study of optical genes in jellyfish, which are descended from creatures that swam Earth’s ancient seas, long before vertebrates and invertebrates took their separate paths, suggests a common optical origin.

“Eyes have evolved in parallel many times, but they all go back to one prototype,” said University of Basel cell biologist Walter Gehring.

In a study published July 27 in the Proceedings of the National Academy of Sciences, researchers led by Gehring describe genes isolated from Cladonema radiatum, a jellyfish with highly elaborate eyes. The genes belong to a family called Pax.

In earlier research, Gehring found that a gene called Pax-6 is a “master regulator” of optical development, controlling eye formation in creatures as simple as fruit flies and as complex as mice and men. That suggested a common origin — but Pax-6 couldn’t be found in jellyfish, leaving open the possibility that eyes evolved independently in higher animals.

In the jellyfish study, Gehring’s team found several other Pax genes. When they transplanted the genes into fruit flies, the flies formed extra eyes. It’s not Pax-6 that appears universal, but rather the whole Pax family.

“We’re convinced that the eye evolved in one phylum,” said Gehring. “All the higher animals have Pax-6. The jellyfish have Pax-a or Pax-b.”

The next question is where Pax genes and their resulting structures came from. According to Gehring, they could have arrived in jellyfish through symbiosis with dinoflagellates — a family of single-celled marine plankton, some with human-like eye structures inside their single cell.

Jellyfish absorbed dinoflagellates, speculates Gehring, after dinoflagellates absorbed Pax genes from red algae, which had absorbed light-sensitive cyanobacteria. Gehring describes this as his “wild Russian doll hypothesis.” His team is now searching jellyfish genomes for dinoflagellate genes.

“Evolution is very conservative. It uses the things that function well,” said Gehring.

Images: 1) Eyes formed in fruit flies after the insertion of Pax genes from jellyfish./PNAS.

2) A Cladonema jellyfish; arrow points to an eye structure./PNAS.

Oil Spill on Track to Reach Atlantic No Later Than October

BOULDER, Colorado — Oil gushing from the Deepwater Horizon site in the Gulf of Mexico will reach the Atlantic Ocean within six months, says oceanographer Synte Peacock. Exactly when is all down to an eddy that broke off of the infamous Loop Current southwest of Florida on June 12.

Peacock, of the National Center for Atmospheric Research in Boulder, Colorado, usually studies how the ocean’s water absorbs atmospheric gases. But after the Deepwater Horizon platform exploded April 20, she realized her computer models could be used to follow where the oil gushing from the seafloor might end up.

Her simulations, announced in a press release June 3, made headlines worldwide. No surprise: The simulations suggested that, once the oil became caught up in the Loop Current, it would be funneled into the Atlantic within weeks.

Talking with reporters at NCAR on June 14, Peacock explained how some news outlets misrepresented her work by glossing over a few major caveats. Most important, the work simulated the movement of dye (not viscous oil) injected in the upper layers of the ocean (not the deep seafloor) for a total of two months (not the ongoing no-end-in-sight disaster).

The simulations underscore how complicated it can be to track the movement of subsurface oil. “We saw large differences in details in how oil dispersed, depending on local eddies and currents in the gulf,” she says. Still, “no matter what you do it’s very, very hard in our model to find a scenario where dye is kept within the gulf for a period of longer than six months.”

The Loop Current circulates clockwise off the southwestern coast of Florida. About once or twice a year, it pinches off an eddy that either wanders around the gulf before dying out, or eventually reattaches with the main Loop Current.

The unusual thing about the Loop Current this year, Peacock says, is that it was located much more to the south and east than usual when it pinched off its new eddy. Eddies have popped off in this location twice before in recent years, she says. One of those times the eddy wandered to the west, toward Texas, before dissipating. The other time it reattached with the Loop.

Where the new eddy goes will strongly influence exactly where the oil ends up, she says. When it does reach the Atlantic, she notes, the oil will not necessarily wash ashore on beaches in a goopy mess. The oil might stay far out to sea, or be extremely diluted by the time it gets to the Atlantic.

Her team is now working on simulations of what will happen if the oil keeps gushing for months to come.

Image Courtesy: National Center for Atmospheric Research

Old memories may get the boot from new brain cells.

A new rodent study shows that newborn neurons destabilize established connections among existing brain cells in the hippocampus, a part of the brain involved in learning and memory.

Clearing old memories from the hippocampus makes way for new learning, researchers from Japan suggest in the November 13 Cell.

Other researchers had proposed the idea that neurogenesis, the birth of new neurons, could disrupt existing memories, but the Cell paper is the first to show evidence supporting the idea, says Paul Frankland, a neuroscientist at the Hospital for Sick Children in Toronto.

Scientists have known that memories first form in the hippocampus and are later transferred to long-term storage in other parts of the brain. For some amount of time the memory resides both in the hippocampus and elsewhere in the brain. What’s not been known is how, after a few months or years, the memory is gradually cleared from the hippocampus.

Researchers have also debated the role of neurogenesis in learning and memory. The hippocampus is one of only two places in the adult brain where scientists know that new neurons form. On the basis of previous studies, many researchers think new neurons stabilize memory circuits or are somehow otherwise necessary to form new memories.

The new study suggests the opposite: Newborn neurons weaken or disrupt connections that encode old memories in the hippocampus.

Kaoru Inokuchi, a neuroscientist at the University of Toyama in Japan, and his colleagues used radiation and some genetic tricks to block neurogenesis in rats and mice that had been trained to fear getting a mild electric shock when placed in a particular cage.

Control animals, with normal neurogenesis, eventually were able to bypass their hippocampi and retrieve the fear memory directly from long-term storage. But animals in which neurogenesis had been blocked still depended on the hippocampus to recall the fear memory, the researchers found.

Running on an exercise wheel, which boosts neurogenesis, also sped the rate at which old memories were cleared from the hippocampus.

But that doesn’t mean new neurons aren’t necessary to teach old brains new tricks, says Inokuchi.

“Our findings do not necessarily deny the important role of neurogenesis in memory acquisition,” Inokuchi says. “Hippocampal neurogenesis could have both of these roles, in erasing old memories and acquiring new memories.”

Essentially, the new neurons may aid formation of new memories by keeping the hippocampus from filling up with old ones.

Frankland adds, “This is about as novel as it gets in the field of neurogenesis and memory. It pretty much represents an entirely new framework that other researchers will chip away at for years to come.”

Image Courtesy: Hippocampal neuron/NIH

Frankenfood Gets Supersized...

For the first time, scientists have used genetic modification to increase the levels of multiple, rather than single, nutrients in a crop.

The first corn produced through the technique hasn’t yet been tested for dinner-table safety, but if it succeeds, it may signal the development of a new, super-nutritious generation of GM foods.

“The major message of the paper is that it’s possible to engineer crops with multiple nutrients,” said study co-author Paul Christou, a plant biochemist at Spain’s University of Lleida. “If you look at other nutritionally enhanced GM crops, up until now people have only been able to increase levels of one nutrient or vitamin.”

An estimated 40 to 50 percent of the world’s population suffers from nutrient deficiencies. The reasons for this are complex and sometimes political, but often involve reliance on a few staple crops that do not provide the nutrient balance common to mixed diets in the developed world.

Both conventional plant breeding and the high-tech activation of dormant genes are useful for adding some traits to crops, but they can’t provide a sufficient nutritional boost. Neither can traditional forms of genetic engineering. When researchers attempt to add more than one new nutrient pathway, the genes tend to become scrambled in subsequent generations.

The approach used by Christou’s group debuted last year in the Proceedings of the National Academy of Sciences, the same journal that published the latest corn research on Monday. It involves the bombardment of seed genomes with metal particles coated with desired nutrient-boosting genes. This produces a variety of different genomic configurations, some of which prove to be stable.

The researchers hope it will be more helpful than traditional techniques of nutritional genetic modification.

“We’re aiming to produce transgenic plants in which you can provide as many nutrients as possible in one and the same seed,” said Christou.

Christou’s team tested the technique on a variety of corn common in South Africa that’s known to produce low levels of beta carotene. Low levels of the nutrient can lead to blindness.

The resulting plants had double the usual amount of folate, sixfold levels of ascorbate and 169 times more beta carotene. At that level of expression, a single serving of corn can provide a recommended daily beta carotene intake.

The researchers are now experimenting with the addition of genes that enhance production of vitamin E, iron, zinc, calcium and other micronutrients, said Christou.

The study “shows the potential of this transgenic technology for accumulating genes that lead to micronutrient-enhanced crops,” said Rodomiro Ortiz, a researcher at the International Maize and Wheat Improvement Center.

Further studies are needed to see if the new nutrients are correctly metabolized by humans, and if the plant is environmentally and toxicologically safe.

According to Christou, the research was funded entirely by public money. The team is trying to convince holders of patented techniques used in their process to allow researchers in the developing world to freely develop the technology. A model for this is the intellectual property guidelines of beta-carotene–enhanced Golden Rice.

“This is not a commercial story,” said Christou. “This is aimed at people in developing countries.”

Citation: “Transgenic multivitamin corn through biofortification of endosperm with three vitamins representing three distinct metabolic pathways.” By Shaista Naqvi, Changfu Zhu, Gemma Farre, Koreen Ramessar, Ludovic Bassie, Jurgen Breitenbach, Dario Perez Cones, Gaspar Ros, Gerhard Sandmann, Teresa Capella and Paul Christou.

Proceedings of the National Academy of Sciences, Vol. 106, No. 17, April 27, 2009.
Image: The lower corn is transgenic; the upper is normal.

Image Courtesy: PNAS.

Secret Math of Fly Eyes Could Overhaul Robot Vision

By turning the brain cell activity underlying fly eyesight into mathematical equations, researchers have found an ultra-efficient method for pulling motion patterns from raw visual data.

Though they built the system, the researchers don’t quite understand how it works. But however mysterious the equations may be, they could still be used to program the vision systems of miniaturized battlefield drones, search-and-rescue robots, automobile navigation systems and other systems where computational power is at a premium.

“We can build a system that works perfectly well, inspired by biology, without having a complete understanding of how the components interact. It’s a non-linear system,” said David O’Carroll, a computational neuroscientist who studies insect vision at Australia’s University of Adelaide. “The number of computations involved is quite small. We can get an answer using tens of thousands of times less floating-point computations than in traditional ways.”

The best-known of these is the Lucas-Kanade method, which calculates yaw — up-and-down, side-to-side motion changes — by comparing, frame by frame, how every pixel in a visual field changes. It’s used for steering and guidance in many experimental unmanned vehicles, but its brute-force approach requires lots of processing power, making it impractical in smaller systems.

In order to make smaller flying robots, researchers would like to find a simpler way of processing motion. Inspiration has come from the lowly fly, which uses just a relative handful of neurons to maneuver with extraordinary dexterity. And for more than a decade, O’Carroll and other researchers researchers have painstakingly studied the optical flight circuits of flies, measuring their cell-by-cell activity and turning evolution’s solutions into a set of computational principles.

In a paper published Friday in Public Library of Science Computational Biology, O’Carroll and fellow University of Adelaide biologist Russell Brinkworth put these methods to the test.

“A laptop computer uses tens of watts of power. Implementing what we’ve developed can be done with chips that consume just a fraction of a milliwatt,” said O’Carroll.

The researchers’ algorithm is composed of a series of five equations through which data from cameras can be run. Each equation represents tricks used by fly circuits to handle changing levels of brightness, contrast and motion, and their parameters constantly shift in response to input. Unlike Lucas-Kanade, the algorithm doesn’t return a frame-by-frame comparison of every last pixel, but emphasizes large-scale patterns of change. In this sense, it works a bit like video-compression systems that ignore like-colored, unshifting areas.

To test the algorithm, O’Carroll and Brinkworth analyzed animated high-resolution images with a program of the sort that might operate in a robot. When they compared the results to the inputs, they found that it worked in a range of natural lighting conditions, varying in ways that usually baffle motion detectors.

“It’s amazing work,” said Sean Humbert, a University of Maryland aerospace engineer who builds miniaturized, autonomous flying robots, some of which run on earlier versions of O’Carroll’s algorithm. “For traditional navigational sensing, you need lots of payload to do the computation. But the payload on these robots is very small — a gram, a couple of Tic Tacs. You’re not going to stuff dual-core processors into a couple Tic Tacs. The algorithms that insects use are very simple compared to the stuff we design, and would scale down to small vehicles.”

Intriguingly, the algorithm doesn’t work nearly as well if any one operation is omitted. The sum is greater than the whole, and O’Carroll and Brinkworth don’t know why. Because the parameters are in constant feedback-driven flux, it produces a cascade of non-linear equations that are difficult to untangle in retrospect, and almost impossible to predict.

“We started with insect vision as an inspiration, and built a model that’s feasible for real-world use, but in doing so, we’ve built a system almost as complicated as the insect’s,” said O’Carroll. “That’s one of the fascinating things here. It doesn’t necessarily lead us to a complete understanding of how the system works, but to an appreciation that nature got it right.”

The researchers drew their algorithm from neural circuits attuned to side-to-side yaw, but O’Carroll said the same types of equations are probably used in computing other optical flows, such as those produced by moving forward and backwards through three-dimensional space.

“That’s more challenging,” said O’Carroll. “It may involve a few extra neurons.”

Image Courtesy: 1) Flickr/Tambako the Jaguar. 2) PLoS Computational Biology.

Happiness/Sadness, Spread Just Like a Disease

There may be a literal truth underlying the common-sense intuition that happiness and sadness are contagious.

A new study on the spread of emotions through social networks shows that these feelings circulate in patterns analogous to what’s seen from epidemiological models of disease.

Earlier studies raised the possibility, but had not mapped social networks against actual disease models.

“This is the first time this contagion has been measured in the way we think about traditional infectious disease,” said biophysicist Alison Hill of Harvard University.

Data in the research, in the July 7 Proceedings of the Royal Society, comes from the Framingham Heart Study, a one-of-a-kind project which since 1948 has regularly collected social and medical information from thousands of people in Framingham, Massachusetts.

Earlier analyses found that a variety of habits and feelings, including obesity, loneliness, smoking and happiness appear to be contagious.

In the current study, Hill’s team compared patterns of relationships and emotions measured in the study to those generated by a model designed to track SARS, foot-and-mouth disease and other traditional contagions. They discounted spontaneous or immediately shared emotion — friends or relatives undergoing a common experience — and focused on emotional changes that followed changes in others.

In the spread of happiness, the researchers found clusters of “infected” and “uninfected” people, a pattern considered a “hallmark of the infectious process,” said Hill. “For happiness, clustering is what you expect from contagion rates. Whereas for sadness, the clusters were much larger than we’d expect. Something else is going on.”

Happiness proved less social than sadness. Each happy friend increased an individual’s chances of personal happiness by 11 percent, while just one sad friend was needed to double an individual’s chance of becoming unhappy.

Patterns fit disease models in another way. “The more friends with flu that you have, the more likely you are to get it. But once you have the flu, how long it takes you to get better doesn’t depend on your contacts. The same thing is true of happiness and sadness,” said David Rand, an evolutionary dynamics researcher at Harvard. “It fits with the infectious disease framework.”

The findings still aren’t conclusive proof of contagion, but they provide parameters of transmission rates and network dynamics that will guide predictions tested against future Framingham results, said Hill and Rand. And whereas the Framingham study wasn’t originally designed with emotional information in mind, future studies tailored to test network contagion should provide more sophisticated information.

Both Hill and Rand warned that the findings illustrate broad, possible dynamics, and are not intended to guide personal decisions, such as withdrawing from friends who are having a hard time.

“The better solution is to make your sad friends happy,” said Rand.

Image courtesy: Morgan/Flickr.

Gene Makes Some Drink More When Other Boozers Are Around

Here’s some not-so-sobering news for party people, barhoppers and clubgoers. Individuals who inherit a particular gene variant that tweaks the brain’s reward system are especially likely to drink a lot of alcohol in the company of heavy-boozing peers.

That’s the preliminary indication of a new study directed by psychology graduate student Helle Larsen of Radboud University Nijmegen in the Netherlands. Adults carrying at least one copy of a long version of the dopamine D4 receptor gene, dubbed DRD4, imbibed substantially more alcohol around a heavy-drinking peer than did others who lacked that gene variant, Larsen’s group reports in a paper published online July 7 in Psychological Science.

“Carriers of the long gene may be more attuned to, and influenced by, another person’s heavy drinking than noncarriers are,” Larsen says.

Her study provides the first evidence that a gene influences human alcohol use in social situations.

Scientists have yet to decipher the precise brain effects of DRD4’s long form. Larsen hypothesizes that in the presence of heavy drinkers, the gene variant may increase dopamine activity in brain areas that amplify alcohol’s appeal as a rewarding social activity.

“If this gene-environment interaction stands, and I don’t see why it shouldn’t, there is every reason to expect the effect would extend to drugs besides alcohol, as well to many motivated pursuits,” remarks biopsychologist Kent Berridge of the University of Michigan in Ann Arbor, who was not involved with the new study.

Sociologist Michael Shanahan of the University of North Carolina in Chapel Hill lauds the new study for ruling out the possibility that carriers of the key gene simply like to drink a lot of booze and tend to do so with other heavy drinkers. Instead, alcohol use jumped among volunteers with a long DRD4 gene who happened to see a stranger imbibe heavily for a brief time.

Larsen and her colleagues asked 60 women and 53 men to evaluate advertisements for an alcohol-abuse prevention campaign. Each volunteer entered a room that had been furnished as a typical Dutch pub, accompanied by a person of the same sex who the volunteer thought was another participant but who was actually working with the researchers.

In between two 10-minute evaluation sessions, volunteers and the researchers’ confederates were given a break. An experimenter asked them to sit at a bar stocked with peanuts, beer, wine, soda and mineral water and to drink whatever they wanted.

As instructed, confederates took the initiative and drank either two sodas, one alcoholic drink and then one soda; or three alcoholic drinks for women and four alcoholic drinks for men over a 30-minute period.

DNA analyses of saliva identified 31 volunteers as carriers of the long DRD4 gene, which contains an amino acid sequence that repeats seven times.

When confederates stuck to sodas or drank one alcoholic beverage, long-gene carriers and noncarriers alike limited themselves to an average of less than half a glass of wine or half a bottle of beer.

When confederates quaffed multiple alcoholic drinks, carriers of the gene variant consumed an average of almost two wine or beer servings, versus almost one serving for noncarriers.

These results held for men and women, all of whom said they drink socially, regardless of how much alcohol they reported drinking weekly.

Deceptive research techniques can backfire if volunteers see through them and don’t admit it to researchers. But when interviewed after testing, none of the participants guessed the study’s real aim or the confederate’s agenda.

Other researchers need to confirm these findings, Larsen says. Some attempts to replicate findings from other studies of gene-environment interactions have yielded mixed results, including follow-up work on a study by researchers from Duke University in Durham, N.C., that found that another gene variant promotes depression in people who experience stress.

Image Courtesy: Flickr/Mourner