PNAS First Look Blog

Science journalists discuss a selection of new papers from PNAS

Recovering function after brain damage

Picture yourself driving home. Half way there, you find a huge tree in the middle of the road, blocking your normal route. Rather than abandoning hope, you turn around and go home by another way.

When our brain regains function after one region is damaged, this effectively is what it is doing. Though this plasticity of the brain has been observed for many years, how this happens is just starting to be understood.

In a new study life scientists from University of California, Los Angeles, and the Garvan Institute of Medical Research in Australia report one mechanism of brain compensation–recruitment of alternate circuits. These pathways, somewhat surprisingly, do not need to be near the damaged site.

“Most views of compensation following tissue loss (stroke for example) think of compensation occurring in adjacent tissue,” write the authors. “A unique finding here is that compensation can occur in regions that are not directly proximal to the site of injury.”

The hippocampus, a small seahorse-shaped structure deep in the brain, is the brain’s bedrock of learning and memory formation. It can be damaged by a lack of oxygen or a stroke, and its dysfunction is key in Alzheimer’s disease

To test the brain’s rewiring capacity, Moriel Zelikowsky and her colleagues taught lab rats to fear a tone, through conditioning with electrical shocks. Damage to the hippocampus removed this fear and slowed their ability to form memories post-injury. The animals were still able to learn, however, by bringing a section of the brain known for storing long-term memories, into action.

To find this, Zelikowsky traced early gene expression in the brain following injury to the hippocampus. She found dramatic rearrangement of cells in the frontal cortex, specifically in the infralimbic and prelimbic regions of the medial prefrontal cortex (mPFC).

The researchers believe the mPFC is playing a more general role in memory and context-sensitive learning, rather than the specific role it has been assigned in the past, of exciting and inhibiting fear.

Researchers hope this understanding will eventually direct them toward treatments for patients suffering degeneration or memory loss after a brain injury. Many have tried to simulate repair within the hippocampus, for instance, but these findings open new possible targets.

“Interestingly, previous studies had shown that these prefrontal cortex regions also light up in the brains of Alzheimer’s patients, suggesting that similar compensatory circuits develop in people,” co-author Bryce Vissel told UCLA.

“While it’s probable that the brains of Alzheimer’s sufferers are already compensating for damage, this discovery has significant potential for extending that compensation and improving the lives of many.”

Categories: Neuroscience | Leave a comment

Fewer animals, more money–a new model for grassland management?

Grazing on the Mongolian Plateau. Image: fao.org.

Grazing on the Mongolian Plateau. Image: fao.org.

Bayin Village sits high on the Mongolian Plateau, part of northwest China’s vast grasslands. This region is inhabited by ethic minorities who graze sheep, goats, and cattle, selling meat to southern and eastern China, where there is greater affluence.

Since the mid-20th century, when the Chinese government decided grasslands were an underutilized resource, overall livestock numbers have increased dramatically. “When we were young, we had trouble seeing the cattle in the grassland,” say older herders in the region.” Now we can see the mice.”

By some estimates, 90 percent of China’s grasslands have problems with too little ground cover, increased erosion and plant communities that are changing from more palatable to less palatable species. The quality of livestock is often poor, farmers have trouble putting weight on them, even in the summer. Household incomes are at or below the poverty levels, with many in the region make less than $2 per head per day.

A new study suggests it doesn’t have to be this way. A team of plant and animal scientists, policy economists, and others from China and Australia present a case study from Bayin Village, where it has been possible to boost household incomes by dramatically decreasing stocking levels. Their results appeared this week in PNAS Early Edition.

By grazing fewer animals, grasslands are recovering, livestock is healthier and fatter and farmers are receiving better prices. Based on early pilot studies, the local government of Siziwang Banner, which oversees the regions around Bayin, implemented a program in 2009 to encourage the reduction of stocking rates, with dramatic results. The 560 herders involved in the program report a net increase in income of approximately 50 percent, compared with control farms, by reducing their stocks by 45 to 65 percent.

Further work is needed to firmly quantify the net benefits, write the authors, nevertheless “recent interviews with herders indicate they do believe the strategy is working and they have no wish to return to former practices.” The herders are pleased, by and large, to run fewer livestock and believe the condition of their grassland is improving.

The authors are hopeful this strategy can be exported to other regions, where overgrazing has also become a major problem, such as in Central Asia and Africa.

Categories: Sustainability Science | Tagged | Leave a comment

Emotions link sound-color associations

kandinsky-sm

Composition VIII (1923) by Wassily Kandinsky. Image: ibiblio.org

Russian painter Wassily Kandinsky literally saw sounds and heard colors. The artist is believed to have had synaesthesia, a harmless condition where people experience sounds, colors, or words simultaneously through several senses. Kandinsky used this gift to create what many believe are the world’s first abstract paintings.

Most of us do not experience sound in this way. Evidence is mounting, however, that we do link our senses, and tie emotions, colors, and sounds together in predictable ways. Psychologists from the University of California, Berkeley and the University of Guadalajara report on these associations in a new PNAS Early Edition paper.

Other studies have found such associations before, for instance, music with major chords (often called “bright”) seems to go best with lighter colors than music with minor chords. Gray has been associated with “sadder” music, while reds, yellows, blues, and greens seem right with “happier” tunes.

To dive into these associations, Palmer and his colleagues conducted three experiments. In the first they explored how dimensions of color (such as saturation, lightness, and yellowness or blueness) associate with musical dimensions (tempo, major or minor chords).

They then explore how emotionally expressive faces are assigned colors, and finally how those emotions are associated with music. Each experiment was done twice: once with study subjects from the United States, once with subjects from Mexico. Despite slight differences (Mexican participants chose somewhat lighter, yellower, and greener colors than US participants) the patterns reported were the same in each country and may, the researchers suggest, be universal.

What do you hear? Image: PNAS.

What do you hear, feel? Image: PNAS.

In general, the faster tempoed Bach, Brahms and Mozart “went best” with more saturated, lighter, and yellower (warmer) colors. “By the same token,” they write, “slower tempi and music in the minor mode were associated with less saturated, darker/cooler colors. For major (but not minor) music, slow tempi were associated with greener colors than medium or faster tempi.”

When viewing faces, participants linked moderately light, slightly cool colors (light blues and greens) with neutral or calm faces. Sad faces looked darker and cooler (bluish or deep greenish gray). Happy faces seemed brightly colored and warm (yellows, oranges and reds, in both vivid and pastel colors). Angry faces were were associated with dark, rather reddish colors.

In the final experiment, researchers assumed if “music and color can be related through emotional associations and … color and faces can be related through the same emotional associations, it follows that music and faces should be analogously relatable.” They found the same strong correlations.

This, they believe, is evidence that color and music are linked through shared emotional associations, dubbed the “emotional mediation hypothesis.” An alternate theory, the “direct connection hypothesis” holds that there are direct, unmediated associations between colors and musical sounds.

“The fact that the pattern of cross-domain matching results is so clearly and consistently related to emotion in all three studies,” write the authors, “provides strong support for emotional mediation as a mechanism of at least some cross-modal associations.” However, they say, “It does not rule out the possibility that there might also be direct or other sorts of associations.”

The experiment opens a host intriguing questions. Where do cross-modal associations (“hearing color” for instance) come from? How are they processed in the brain? Do the results generalize beyond classical orchestral music to non-western music? Do music-color synesthetes have the same associations as the rest of us?

It may help if we knew what Kandinsky listened to as he painted.

Categories: Psychological and Cognitive Sciences | Tagged | Leave a comment

The brain biology of nicotine relapse

At the moment a former smoker catches a whiff of tobacco, glimpses the corner store where they used to buy cigarettes, or sees a stranger pull a pack of smokes out of their pocket, something happens in their brain that causes an intense craving, even years after they’ve quit. In a PNAS Early Edition paper published this week, scientists have now described the molecular events that happen in the brain at this precise moment that a former nicotine addict is faced with a cue to smoke.

“The big question is what’s the neurobiology of why people are vulnerable to relapse,” says Peter Kalivas of the Medical University of South Carolina. And in his latest work, Kavilas narrowed in on an area of the brain that he suspected might be involved in relapse based on previous knowledge on habits.

“We all go through life with a series of habits,” Kalivas explains. These habitual tasks are mediated by habit circuitry in the brain, which lets your brain go into a kind of auto-pilot to complete them. When a habit is disrupted, however–whether that means the road you normally drive home is closed or the coffee shop rearranges its milk and sugar–a part of the brain called the frontal cortex becomes involved, more actively planning out your actions. But if the frontal cortex repeatedly mediates this new behavior, it becomes a new habit, replacing the old one in the brain’s habit cortex and no longer requiring that active control.

For cigarette smokers, as well as cocaine and heroin addicts, the habit cortex doesn’t become reprogrammed when they quit, Kalivas says. “Unlike normal habits, where if you get enough new signals, it changes the behavior, they don’t seem to be able to change their smoking habit very effectively.”

The frontal cortexes of former smokers are fully functional, so Kalivas and his colleagues suspected that the signalling between the frontal cortex and the habit circuitry might be to blame for the stubborn cravings. To test their hypothesis, the scientists trained nicotine-addicted rats to associate a particular light and sound with receiving a dose of nicotine. Then, the animals were forced to quit nicotine, given no doses for two weeks–long enough that the drug would have fully left their body and a normal habit would have been reprogrammed in the brain.

Next, the scientists flashed the same light and sound that the rats had previously learned to associate with nicotine. The animals’ brains showed huge increases in activity, unlike any normal response to trained stimuli (they tested rats that had been trained to associate the same stimuli with sugar, and didn’t see the same massive response in the brain).

The researchers saw a rush of signalling molecules–one called glutamate, specifically–in an area of the brain called the nucleus accumbens, a key connection between the frontal cortex and the habit circuitry.

“Not only do you get this huge outpouring of signalling,” Kalivas says, “but the connection actually keeps getting stronger.” This overstimulation is likely what causes an intense craving when faced with a cue to smoke, he says.

The team went on to show that when they blocked the molecules in this part of the brain that respond to glutamate, the rats no longer wanted a dose of nicotine when faced with the sound and light (they chose not to press a lever in their cage that would give them the drug).

“Just these kinds of drug-associated stimuli alone are capable of producing very rapid changes in the brain that stimulate drug-seeking behavior,” says Kalivas. “By discovering what some of those changes are, I think we can find some very strong potential targets for treatments.”

The scientists are now moving toward an initial human clinical trial of a drug that can block the response to glutamate, hoping to see the same diminished nicotine craving observed in the mice.

Categories: Neuroscience | Leave a comment

Your brain is not that big, get over it

Image courtesy Flickr user _DJ_

Image courtesy Flickr user _DJ_

Humans are proud of their brains, and rightfully so. A new comparative analysis suggests however, that we should not be so obsessed with size when considering our smarts.

This week evolutionary anthropologists Robert Barton and Chris Venditti report the results of a wide analysis in PNAS Early Edition comparing human frontal lobe size to other brain structures. For an animal our size, our frontal lobes are not larger than expected.

This finding runs counter to conventional wisdom in the popular press and much scientific literature.

“One of the most pervasive assumptions about human brain evolution is that it involved relative enlargement of the frontal lobes,” the authors write. “We show that this assumption is without foundation.”

Prior studies cited as evidence for relative expansion of the frontal lobes, involved in higher-order functioning, have sometimes been based on unscaled measurements. These comparisons confuse selective enlargement with allometric scaling.

“In addition to this theoretical point,” write the authors, “unscaled measures of frontal cortex size give problematic empirical results when the comparative net is cast widely.” As an example they point to human frontal gray matter volume. In humans this volume is smaller as a proportion of total cortical volume than in several other nonhuman primates and two mustelid carnivores (members of the weasel family).

In terms of absolute size, humans have larger frontal cortexes than other measured animals. However sea lions, not considered terribly smart, exceed baboons and gibbons by this measure, animals that are noted for intelligence. And a llama’s frontal cortex is larger than a macaque monkey. Scaling must be taken into account, the authors write:

“Unless one is willing to take seriously the hypothesis that lemurs have more of the qualities bestowed by frontal cortices than do humans, or that llamas possess more than monkeys.”

The primary driver of intelligence, they suggest, is in distributed neural networks–systems coordinated between the neocortex, cerebellum, and basal ganglia, for example. “Experimental evidence now implicates such distributed networks in uniquely human cognitive capacities,” conclude the Barton and Venditti. “We suggest that natural selection selectively enlarged such distributed networks and that these–rather than more localized size change of frontal cortical regions–are likely to form the basis of human cognitive specialization.”

Categories: Anthropology | Evolution | Tagged | Leave a comment

New ruler for telomere length

It’s not just organisms that change as they grow old—individual cells age too.  Among myriad changes during cellular aging is the gradual shortening of telomeres, the protective ends of gene-containing chromosomes.  To study telomeres, their regulation, and their associations with health and disease, biologists have largely relied on collections of cells to measure average telomere length. Older groups of cells have, on average, shorter telomeres than younger groups of cells. Now, a team of researchers has developed a way to measure the telomeres in one individual cell at a time. The method, published in a PNAS Early Edition paper this week, can be used to uncover telomere heterogeneity between similar cells and to better understand the regulation and consequences of telomere length.

Older methods used to measure telomere length in cells were costly and time consuming, says Sherman Weissman, a Yale University School of Medicine genetics researcher who spearheaded the new work.  But the new technique, he says, “is very robust and quick and inexpensive.”

The biggest drawback to previous techniques is that, to measure telomeres, they required more DNA than a single cell contains. So cells had to be combined into groups to get large enough samples. To get around this problem, Weissman and his collaborators developed a method that, instead of measuring only the telomeres, compares the length of telomeres to the length of other genes that are more stable in length. One cell’s worth of DNA is sufficient for this comparison.

To perform the measurements, the researchers used quantitative real-time PCR (qPCR), an established method that determines the amount of DNA in a sample. They’ve dubbed their new approach single-cell telomere qPCR, or SCT-pqPCR. To illustrate its usefulness, the team measured telomere length in a variety of human cells, as well as mouse embryos.

“We discovered that during repeated cell divisions, telomeres not only become shorter, but also become more heterogenic,” says Xinghua Pan, a Yale genetics researcher who collaborated with Weissman.

It will take more work to understand the significance of this heterogeneity, and uncover molecular differences that impact it. To help speed up the experiments required to answer such questions, the team wants to develop a high-throughput version of SCT-pqPCR so that they can get many single-cell measurements at once.  But they expect the current version of the method to gain popularity even without these improvements—being able to measure single-cell telomere lengths will be a boon to researchers studying human fertility, stem cells, and cancers, Weissman says. And the method is easily adoptable by any lab that already performs other qPCR experiments.

And now that they can measure the telomeres of individual cells, Weissman’s team has set their sights even higher: “We would like to be able to measure the telomere length of individual chromosomes now,” Weismann says. Heterogeneity likely doesn’t end with at the cellular level, he says, and it’s important to know which chromosomes are wearing down the fastest and how this affects cells.

Categories: Cell Biology | Genetics | Leave a comment

Antifreeze found trapped inside ice crystals

A common antifreeze compound is methanol, the simplest kind of alcohol molecule. Now scientists find that even methanol can get trapped within ice-like cages, findings detailed in the Proceedings of the National Academy of Sciences that could influence what researchers think about the potential for life in Saturn’s moon Titan and other icy celestial bodies.

Methanol is a colorless, flammable, poisonous chemical also known as wood alcohol that can blind or kill if drunk. One of the best-known uses for it is as antifreeze, suppressing the formation of ice when temperatures drop below the normal freezing point of water. The potential existence of methanol on Titan lends credence to the idea that it harbors watery oceans under its icy shell. This in turn raises the possibility that life as we know it might dwell there, since life exists virtually everywhere there is liquid water on Earth.

“Both methanol and ammonia, when mixed with water in the right proportions, can stay liquid down to very low temperatures,” said physical chemist John Ripmeester at the National Research Council of Canada in Ottawa.

Methanol is often used by industry to prevent ice-like lattices known as clathrate hydrates from forming within oil and gas pipelines. Clathrates all serve as cages that entrap molecules — the ones that can block pipelines typically hold methane.

In the roughly 70 years of research of methanol in relation to clathrate hydrates, there was little or no direct evidence that clathrates might cage methanol. Now Ripmeester and his colleagues find methanol can indeed get trapped inside clathrate hydrate structures after all.

The scientists first experimented with clathrates not made of water ice, but rather clathrates made of organic compounds such as tetrahydrofuran hydrate. At temperatures near zero degrees C, X-ray diffraction and nuclear magnetic resonance (NMR) spectroscopy revealed methanol could get incorporated within such clathrate hydrate lattices.

Solutions consisting solely of water and methanol could not be frozen to form clathrate hydrates. However, experiments and molecular dynamics simulations hinted that solutions containing water, methanol and methane could form these ice-like lattices.

Unexpectedly, the researchers discovered that at low temperatures, methanol can actually promote the formation of solid clathrate hydrates instead of preventing it. These findings might influence whether and how methanol is used to help suppress clathrate formation in pipelines in the future, especially in the deep ocean and in polar climates.

“None of the models used to predict hydrate formation conditions in pipelines are accurate as they all assume that methanol will not go into a hydrate,” Ripmeester said.

By spurring the formation of methane clathrate hydrates on icy celestial bodies, methanol could also explain the relatively high concentrations of methane and other hydrocarbons seen on the surface of Saturn’s moon Enceladus, despite predictions that most hydrocarbons should have escaped from its atmosphere long ago. As temperatures fluctuate, clathrate hydrates on these bodies “may anneal giving different compositions, or even may disappear again,” Ripmeester said.

One intriguing aspect of these findings regarding the possibility of life on alien worlds is how clathrate hydrates can bring together key ingredients of life close together, such as water, methane, ammonia and methanol. “This closeness of these various molecules gives a favorable environment for producing more complex compounds as brought about, for instance, by radiation,” Ripmeester said.

Categories: Chemistry | Leave a comment

Challenges of comparative environmental analysis

Stratospheric ozone loss is on course to become a solved environmental problem, with all significant producing countries (including China and India) undertaking complete phase-outs of ozone-depleting substances. The universal concurrence and speed with which ozone loss has been addressed are sometimes heralded as signs that effective international agreements on other problems of the global commons are just around the corner. However, progress on many other issues has been strikingly limited. Is ozone the exception, rather than the rule, and if so why?

Read the full Opinion piece here.

 

Categories: Opinion | Leave a comment

Getting meaning out of the noise

What was that you said? Image courtesy Flickr/ marcokalmann.

What was that you said? Image courtesy Flickr/ marcokalmann.

As we go through the day, listening, reading, instant messaging with co-workers, we are constantly decoding sentences and constructing meaning from them. As we build meaning based on syntax and semantics, we are also, it seems, calculating how likely what we heard is what the other person meant.

A recent study by Edward Gibson, Leon Bergen, and Steven Piantadosi argues that we mentally compensate for noisy environments and producer or perceiver errors when we hear or read ambiguous sentences. After reading, “The mother gave the candle the daughter,” we might decide something more sensible like ,“The mother gave the candle to the daughter,” was intended.

In fact we seem “well designed” for “recovering intended meaning from noisy utterances,” say the authors. To date, most sentence processing theories assume that sentence transmission is error free. In reality though, if we are young or a non-native speaker or stressed, confused, or tired, our language can be rife with errors. We mishear people and misread sentences. People speak to us in noisy, crowded bars. People write us notes with sloppy, near-illegible handwriting.

“Given the prevalence of these noise sources,” the authors write, “it is plausible that language processing mechanisms are well adapted to handling noisy input, and so a complete model of language comprehension must allow for the existence of noise.”

Communication is counted a success, the say, when the meaning gleaned is the same as the meaning intended. We seem mentally optimized for decoding a person’s true meaning, acting, the authors write, as rational Bayesian decoders–able to assimilate new information into our prior knowledge and expectations.

The authors report evidence for each of four predictions they make based on their model. In the first, semantic cues pull us toward plausible interpretations, especially if the structural changes needed in the sentence are few. For example take, “The mother gave the candle the daughter” and “The mother gave the candle to the daughter.” We expect mothers to give things to their daughters. To candles? Not so much.

In the second prediction, deletions should be counted as more likely than insertions. While “a deletion only requires a particular word to be randomly selected from a sentence,” write the authors, “an insertion requires its selection from (a subset of) the producer’s vocabulary.” If a word is added to the original, intended sentence we’re more likely to assume the literal meaning.

As a third line of evidence, the authors predicted comprehenders would be more willing to infer non-literal, more plausible meanings in noisy environments. So, if you hear, “The ball kicked the girl” in a crowded room, you are more likely to assume your companion really meant, “The ball was kicked by the girl,” than if you are listening in a quiet place.

Lastly, Gibson and his colleagues find that if we listen to someone who speaks in many nonsensical sentences we start assuming they are not making errors, but they intend to speak or write that way. (We may also start assuming they’re crazy.)

This model–that we rationally integrate noise and expectations of sentence structure and meaning into our interpretations–helps explain some of the neural firing patterns observed in the event-related potential research. It may also, he says, help explain how people with agrammatic aphasia can understand language so well, even if their own speech is grammatically incorrect.

“More generally,” he says, “we think that noisy-channel models of language can help explain word-order origins and variation in human language.”

Language like Japanese, Turkish, or Hindi, he believes retain a more general, basic word order: subject – object – verb. Languages like English and Chinese, may have evolved in word order (to subject – verb – object) to minimize confusion when both the subject and object are animate. In the future work, the researchers plan to look for similar patterns of rational Bayesian inference across other languages.

Categories: Psychological and Cognitive Sciences | Tagged , | Leave a comment

Controlling drag with tunable bubble mattresses

Scanning electron microscopy image of a representative microfluidic device, showing two main microchannels for gas (Pg) and liquid (Qw) streams connected by gas-filled side channels.

Scanning electron microscopy image of a representative microfluidic device, showing two main microchannels for gas (Pg) and liquid (Qw) streams connected by gas-filled side channels.


Bubbles can reduce the drag that slows ships and submarines in the water. As such, researchers want to exploit cushions of air to help create faster torpedoes and attack vessels as well as drastically cut the enormous volumes of fuel needed to ship freight around worldwide. Novel devices that emit mattresses of bubbles reported this week in the Proceedings of the National Academy of Sciences now could help researchers find ways to make hulls even more slippery than ever.

Chemical engineer Rob Lammertink at the University of Twente in the Netherlands and his colleagues designed and fabricated microfluidic chips that could influence the flow of fluids much as microelectronic chips steer the flow of electricity. These devices consisted of two parallel microscopic channels, one for liquid, the other for gas, that were connected by side channels in between. By controlling the gas pressure, the researchers could easily and precisely control how much bubbles jutted into the channel filled with liquid. Particles scattered into the liquid could reveal how the liquid was flowing over this cushion of air.

The scientists experimented with how much the bubbles protruded into the liquid — the more the bubbles protruded, the more the walls of the bubbles were angled against the flowing liquid. They found the most slippery protrusion angle was about 10 degrees, corresponding to a 23 percent reduction in drag. These findings roughly matched computer simulations that suggested a 21 percent reduction in drag when the protrusion angle was in the range of -2 to 12 degrees.

“It is the first experimental proof that the geometry of a bubble has a strong influence on the hydrodynamics of the liquid flowing along it,” Lammertink said.

In the future, Lammertink and his colleagues want to see how bubble geometry might influence how liquids absorb gases. Such research can improve transport of gases through membranes into liquids — “think of artificial blood oxygenation, or soft drink carbonation,” Lammertink said.

Categories: Applied Physical Sciences | Leave a comment