郑少群博客

2013年7月2日星期二

Scientists help explain visual system's remarkable ability to recognize complex objects

July 2, 2013 — How is it possible for a human eye to figure out letters that are twisted and looped in crazy directions, like those in the little security test internet users are often given on websites?

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It seems easy to us -- the human brain just does it. But the apparent simplicity of this task is an illusion. The task is actually so complex, no one has been able to write computer code that translates these distorted letters the same way that neural networks can. That's why this test, called a CAPTCHA, is used to distinguish a human response from computer bots that try to steal sensitive information.

Now, a team of neuroscientists at the Salk Institute for Biological Studies has taken on the challenge of exploring how the brain accomplishes this remarkable task. Two studies published within days of each other demonstrate how complex a visual task decoding a CAPTCHA, or any image made of simple and intricate elements, actually is to the brain.

The findings of the two studies, published June 19 in Neuron and June 24 in the Proceedings of the National Academy of Sciences (PNAS), take two important steps forward in understanding vision, and rewrite what was believed to be established science. The results show that what neuroscientists thought they knew about one piece of the puzzle was too simple to be true.

Their deep and detailed research -- -involving recordings from hundreds of neurons -- -may also have future clinical and practical implications, says the study's senior co-authors, Salk neuroscientists Tatyana Sharpee and John Reynolds.

"Understanding how the brain creates a visual image can help humans whose brains are malfunctioning in various different ways -- -such as people who have lost the ability to see," says Sharpee, an associate professor in the Computational Neurobiology Laboratory. "One way of solving that problem is to figure out how the brain -- -not the eye, but the cortex -- -- processes information about the world. If you have that code then you can directly stimulate neurons in the cortex and allow people to see."

Reynolds, a professor in the Systems Neurobiology Laboratory, says an indirect benefit of understanding the way the brain works is the possibility of building computer systems that can act like humans.

"The reason that machines are limited in their capacity to recognize things in the world around us is that we don't really understand how the brain does it as well as it does," he says.

The scientists emphasize that these are long-term goals that they are striving to reach, a step at a time.

Integrating parts into wholes

In these studies, Salk neurobiologists sought to figure out how a part of the visual cortex known as area V4 is able to distinguish between different visual stimuli even as the stimuli move around in space. V4 is responsible for an intermediate step in neural processing of images.

"Neurons in the visual system are sensitive to regions of space -- -- they are like little windows into the world," says Reynolds. "In the earliest stages of processing, these windows -- -known as receptive fields -- -are small. They only have access to information within a restricted region of space. Each of these neurons sends brain signals that encode the contents of a little region of space -- -they respond to tiny, simple elements of an object such as edge oriented in space, or a little patch of color."

Neurons in V4 have a larger receptive field that can also compute more complex shapes such as contours. They accomplishes this by integrating inputs from earlier visual areas in the cortex -- -that is, areas nearer the retina, which provides the input to the visual system, which have small receptive fields, and sends on that information for higher level processing that allow us to see complex images, such as faces, he says.

Both new studies investigated the issue of translation invariance -- -- the ability of a neuron to recognize the same stimulus within its receptive field no matter where it is in space, where it happens to fall within the receptive field.

The Neuron paper looked at translation invariance by analyzing the response of 93 individual neurons in V4 to images of lines and shapes like curves, while the PNAS study looked at responses of V4 neurons to natural scenes full of complex contours.

Dogma in the field is that V4 neurons all exhibit translation invariance.

"The accepted understanding is that individuals neurons are tuned to recognize the same stimulus no matter where it was in their receptive field," says Sharpee.

For example, a neuron might respond to a bit of the curve in the number 5 in a CAPTCHA image, no matter how the 5 is situated within its receptive field. Researchers believed that neuronal translation invariance -- -the ability to recognize any stimulus, no matter where it is in space -- -increases as an image moves up through the visual processing hierarchy.

"But what both studies show is that there is more to the story," she says. "There is a trade off between the complexity of the stimulus and the degree to which the cell can recognize it as it moves from place to place."

A deeper mystery to be solved

The Salk researchers found that neurons that respond to more complicated shapes -- -like the curve in 5 or in a rock -- -- demonstrated decreased translation invariance. "They need that complicated curve to be in a more restricted range for them to detect it and understand its meaning," Reynolds says. "Cells that prefer that complex shape don't yet have the capacity to recognize that shape everywhere."

On the other hand, neurons in V4 tuned to recognize simpler shapes, like a straight line in the number 5, have increased translation invariance. "They don't care where the stimuli they are tuned to is, as long as it is within their receptive field," Sharpee says.

"Previous studies of object recognition have assumed that neuronal responses at later stages in visual processing remain the same regardless of basic visual transformations to the object's image. Our study highlights where this assumption breaks down, and suggests simple mechanisms that could give rise to object selectivity," says Jude Mitchell, a Salk research scientist who was the senior author on the Neuron paper.

"It is important that results from the two studies are quite compatible with one another, that what we find studying just lines and curves in one first experiment matches what we see when the brain experiences the real world," says Sharpee, who is well known for developing a computational method to extract neural responses from natural images.

"What this tells us is that there is a deeper mystery here to be solved," Reynolds says. "We have not figured out how translation invariance is achieved. What we have done is unpacked part of the machinery for achieving integration of parts into wholes."

Minjoon Kouh, a former postdoctoral fellow at Salk, participated in the PNAS study. Salk postdoctoral researcher Anirvan Nandy and senior staff scientist Jude Mitchell, of the Salk Systems Neurobiology Laboratory, were co-authors of the Neuron paper.

Both studies were funded by grants from the National Institutes of Health (R01EY019493), the McKnight Scholarship and the Ray Thomas Edwards and W. M. Keck Foundations. In addition, the PNAS study received a grant from the Searle Funds. The Neuron study was additionally funded by grants from the Alfred P. Sloan Foundation, the National Institutes of Health (EY0113802), the Gatsby Charitable Foundation and the Schwartz Foundation, and a Pioneer Fund postdoctoral fellowship.

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Vitamin C helps control gene activity in stem cells

July 1, 2013 — Vitamin C affects whether genes are switched on or off inside mouse stem cells, and may thereby play a previously unknown and fundamental role in helping to guide normal development in mice, humans and other animals, a scientific team led by UC San Francisco researchers has discovered.

The researchers found that vitamin C assists enzymes that play a crucial role in releasing the brakes that keep certain genes from becoming activated in the embryo soon after fertilization, when egg and sperm fuse.

The discovery might eventually lead to the use of vitamin C to improve results of in vitro fertilization, in which early embryos now are typically grown without the vitamin, and also to treat cancer, in which tumor cells abnormally engage or release these brakes on gene activation, the researchers concluded in a study published June 30, 2013 in the journal Nature.

In the near term, stem-cell scientists may begin incorporating vitamin C more systematically into their procedures for growing the most healthy and useful stem cells, according to UCSF stem-cell scientist Miguel Ramalho-Santos, PhD, who led the study. In fact, the unanticipated discovery emerged from an effort to compare different formulations of the growth medium, a kind of nutrient broth used to grow mouse embryonic stem cells in the lab.

Rather than building on any previous body of scientific work, the identification of the link between vitamin C and the activation of genes that should be turned on in early development was serendipitous, Ramalho-Santos said. "We bumped into this result," he said.

Working in Ramalho-Santos' lab, graduate student Kathryn Blaschke and postdoctoral fellow Kevin Ebata, PhD, were comparing different commercial growth media for mouse stem cells. The researchers began exploring how certain ingredients altered gene activity within the stem cells. Eventually they discovered that adding vitamin C led to increased activity of key enzymes that release the brakes that can prevent activation of an array of genes.

The brakes on gene activation that vitamin C helps release are molecules called methyl groups. These methyl groups are added to DNA at specific points along the genome to prevent specific genes from getting turned on.

During the development of multicellular organisms, humans among them, different patterns of methylation arise in different cells as methyl groups are biochemically attached to DNA at specific points along the genome during successive cell divisions. Normally this gradual methylation, a key part of the developmental program, is not reversible.

But after fertilization and during early development, a class of enzymes called "Tet" acts on a wide array of the methyl groups on the DNA to remove these brakes, so that genes can be activated as needed.

The UCSF researchers demonstrated that Tet enzymes require vitamin C for optimal activity as they act to remove the methyl groups from the DNA and to stimulate gene activity that more faithfully mimics in cultured stem cells what occurs at early stages of development in the mouse embryo.

"Potential roles for vitamin C in the clinic -- including in embryo culture media used during in vitro fertilization, which currently do not contain vitamin C, and in cancers driven by aberrant DNA methylation -- deserve exploration," Ramalho-Santos, said.

In addition, scientists previously have found that many adult tissues also have stem cells, which can generate a variety of cell types found within a specific tissue. This raises the possibility that vitamin C might help maintain healthy stem cell populations in the adult, according to Ramalho-Santos.

"Although we did not in this paper address the function of Vitamin C in adult tissues, given the roles that Tet enzymes are now known to play in adult tissues, we anticipate that Vitamin C might also regulate Tet function in the adult," Ramalho-Santos said. "This remains to be determined."

Vitamin C already has become a popular supplement in recent decades, and potential health benefits of vitamin C supplementation continue to be investigated in clinical trials. It has been more than 80 years since vitamin C was first recognized as vital to prevent scurvy, a now rare connective-tissue disease caused by the failure of another enzyme that also relies on vitamin C.

The function of vitamin C as an antioxidant to prevent chemical damage is the likely reason why some commercial suppliers of growth media have included it in their products, Ramalho-Santos said, but other antioxidant molecules cannot replace Vitamin C in the enhancement of the activity of Tet enzymes.

Despite its importance, humans, unlike most animals and plants, cannot synthesize their own Vitamin C and must obtain it through their diet. The mouse makes vitamin C, but that fact does not diminish the expectation that the new findings will also apply to human development, according to Ramalho-Santos. Only adult liver cells in the mouse make vitamin C, he said.

Ramalho-Santos now aims to explore the newly discovered phenomenon in the living mouse. "The next step is to study vitamin C and gene expression in vivo," he said.

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Inactivation of taste genes causes male sterility

"This paper highlights a connection between the taste system and male reproduction," said lead author Bedrich Mosinger, MD, PhD, a molecular biologist at Monell. "It is one more demonstration that components of the taste system also play important roles in other organ systems."

While breeding mice for taste-related studies, the researchers discovered that they were unable to produce offspring that were simultaneously missing two taste-signaling proteins.

As reported online in advance of print in the Proceedings of the National Academy of Sciences, the critical proteins were TAS1R3, a component of both the sweet and umami (amino acid) taste receptors, and GNAT3, a molecule needed to convert the oral taste receptor signal into a nerve cell response.

Breeding experiments determined that fertility was affected only in males. Both taste proteins had previously been found in testes and sperm, but until now, their function there was unknown.

In order to explore the reproductive function of the two proteins, the research team engineered mice that were missing genes for the mouse versions of TAS1R3 and GNAT3 but expressed the human form of the TAS1R3 receptor. These mice were fertile.

However, when the human TAS1R3 receptor was blocked in the engineered mice by adding the drug clofibrate to the rodents' diet, thus leaving the mice without any functional TAS1R3 or GNAT3 proteins, the males became sterile due to malformed and fewer sperm. The sterility was quickly reversed after clofibrate was removed from the diet.

Clofibrate belongs to a class of drugs called fibrates that frequently are prescribed to treat lipid disorders such as high blood cholesterol or triglycerides. Previous studies from the Monell team had revealed that it is a potent inhibitor of the human, but not mouse, TAS1R3 receptor.

Noting the common use of fibrates in modern medicine and also the widespread use in modern agriculture of the structurally-related phenoxy-herbicides, which also block the human TAS1R3 receptor, Mosinger speculates that these compounds could be negatively affecting human fertility, an increasing problem worldwide.

He in turn notes positive implications related to the research. "If our pharmacological findings are indeed related to the global increase in the incidence of male infertility, we now have knowledge to help us devise treatments to reduce or reverse the effects of fibrates and phenoxy-compounds on sperm production and quality. This knowledge could further be used to design a male non-hormonal contraceptive."

Previous work from Monell and other groups has shown that some taste genes can be found in other parts of the body, including stomach, intestines, pancreas, lungs, and brain, where they are increasingly thought to have important physiological functions.

"Like much good science, our current findings pose more questions than answers," comments Monell molecular neurobiologist Robert Margolskee, MD, PhD, also an author on the paper. "We now need to identify the pathways and mechanisms in testes that utilize these taste genes so we can understand how their loss leads to infertility."

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Hearing loss from loud blasts may be treatable

Using a mouse model, the study found that loud blasts actually cause hair-cell and nerve-cell damage, rather than structural damage, to the cochlea, which is the auditory portion of the inner ear. This could be good news for the millions of soldiers and civilians who, after surviving these often devastating bombs, suffer long-term hearing damage.

"It means we could potentially try to reduce this damage," said John Oghalai, MD, associate professor of otolaryngology and senior author of the study, published July 1 in PLOS ONE. If the cochlea, an extremely delicate structure, had been shredded and ripped apart by a large blast, as earlier studies have asserted, the damage would be irreversible. (Researchers presume that the damage seen in these previous studies may have been due to the use of older, less sophisticated imaging techniques.)

"The most common issue we see veterans for is hearing loss," said Oghalai, a scientist and clinician who treats patients at Stanford Hospital & Clinics and directs the hearing center at Lucile Packard Children's Hospital.

The increasingly common use of improvised explosive devices, or IEDs, around the world provided the impetus for the new study, which was primarily funded by the U.S. Department of Defense. Among veterans with service-connected disabilities, tinnitus -- a constant ringing in the ears -- is the most prevalent condition. Hearing loss is the second-most-prevalent condition. But the results of the study would prove true for anyone who is exposed to loud blasts from other sources, such as jet engines, air bags or gunfire.

More than 60 percent of wounded-in-action service members have eardrum injuries, tinnitus or hearing loss, or some combination of these, the study says. Twenty-eight percent of all military personnel experience some degree of hearing loss post-deployment. The most devastating effect of blast injury to the ear is permanent hearing loss due to trauma to the cochlea. But exactly how this damage is caused has not been well understood.

The ears are extremely fragile instruments. Sound waves enter the ear, causing the eardrums to vibrate. These vibrations get sent to the cochlea in the inner ear, where fluid carries them to rows of hair cells, which in turn stimulate auditory nerve fibers. These impulses are then sent to the brain via the auditory nerve, where they get interpreted as sounds.

Permanent hearing loss from loud noise begins at about 85 decibels, typical of a hair dryer or a food blender. IEDs have noise levels approaching 170 decibels.

Damage to the eardrum is known to be common after large blasts, but this is easily detected during a clinical exam and usually can heal itself -- or is surgically repairable -- and is thus not typically the cause of long-term hearing loss.

In order to determine exactly what is causing the permanent hearing loss, Stanford researchers created a mouse model to study the effects of noise blasts on the ear.

After exposing anesthetized mice to loud blasts, researchers examined the inner workings of the mouse ear from the eardrum to the cochlea. The ears were examined from day one through three months. A micro-CT scanner was used to image the workings of the ear after dissection.

"When we looked inside the cochlea, we saw the hair-cell loss and auditory-nerve-cell loss," Oghalai said.

"With one loud blast, you lose a huge number of these cells. What's nice is that the hair cells and nerve cells are not immediately gone. The theory now is that if the ear could be treated with certain medications right after the blast, that might limit the damage."

Previous studies on larger animals had found that the cochlea was torn apart and shredded after exposure to a loud blast. Stanford scientists did not find this in the mouse model and speculate that the use of older research techniques may have caused the damage.

"We found that the blast trauma is similar to what we see from more lower noise exposure over time," said Oghalai. "We lose the sensory hair cells that convert sound vibrations into electrical signals, and also the auditory nerve cells."

Much of the resulting hearing loss after such blast damage to the ear is actually caused by the body's immune response to the injured cells, Oghalai said. The creation of scar tissue to help heal the injury is a particular problem in the ear because the organ needs to vibrate to allow the hearing mechanism to work. Scar tissue damages that ability.

"There is going to be a window where we could stop whatever the body's inflammatory response would be right after the blast," Oghalai said. "We might be able to stop the damage. This will determine future research."

In addition to the Department of Defense, the study was funded by the National Institutes of Health (grants K08DC006671 and P30DC010363) and Chosun University in South Korea.

The first author of the study, Sung-Il Cho, MD, assistant professor at Chosun University, was working at Stanford during the study. Other Stanford authors were graduate students Simon Gao, Jongmin Baek and David Jacobs; senior research scientist Anping Xia, MD, PhD; research technician Rosalie Wang; research associate Felipe Salles, PhD; computer programmer Patrick Raphael; and research coordinator Homer Abaya.

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Superconductor created from solvent

July 1, 2013 — A study led by Washington State University researchers has turned a fairly common non-metallic solvent into a superconductor capable of transmitting electrical current with none of the resistance seen in conventional conductors.

"It is an important discovery that will attract a lot of attention from many scientific communities -- physics, chemistry, and materials science," said Choong-Shik Yoo, a professor of chemistry and Institute for Shock Physics. The National Science Foundation-funded discovery, which grows out of research by Yoo doctoral student Ranga Dias, appears in the Proceedings of the National Academy of Sciences.

The field of superconductivity has a wide variety of potentially revolutionary applications, including powerful electromagnets, vehicle propulsion, power storage and vastly more efficient power transmission.

Three years ago, Yoo used super-high pressures similar to those found deep in Earth to turn a white crystal into a "super battery," or what he called "the most condensed form of energy storage outside of nuclear energy."

This time, Yoo saw how carbon disulfide subjected to high pressure and cold started to act like a metal, taking on properties like magnetism, a high energy density, and superhardness as its molecules reassembled in three-dimensional structures like those found in diamonds.

Typically, non-metallic molecules are too far apart from each other-three times farther apart than metal molecules -- for electrical energy to move across them. But Yoo and his colleagues, including researchers at the Carnegie Institution of

Washington, compressed the compound in the small, compact space of a diamond anvil cell to 50,000 atmospheres, a pressure equivalent to that found 600 miles into Earth. They also chilled the compound to 6.5 degrees Kelvin, or nearly -447 F.

The pressure and temperature not only brought the carbon disulfide molecules together but rearranged them into a lattice structure in which the natural vibrations of the molecules can help electrons move so well the material becomes a resistance-free superconductor.

Yoo's research provides new insight into how superconductivity works in unconventional materials, an area that has intrigued scientists for several decades, he says. These unconventional materials are typically made of atoms with lower atomic weights that let them vibrate at higher frequencies, increasing their potential as superconductors at higher temperatures.

Yoo acknowledges that electronic materials are not about to be cooled to near absolute zero or subjected to extreme pressures. But he said this work could point the way to creating similar properties under more ordinary conditions, much as science paved the way to make synthetic diamonds at lower temperatures and pressures.

"This research will provide the vehicle for people to be clever in developing superconductors by understanding the fundamentals that guide them," said Yoo.

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Altitude sickness may hinder ethnic integration in the world's highest places

Research from Princeton University published in the journal Applied Geography suggests that people native to low-lying areas can be naturally barred from regions such as the Tibetan Plateau, the Andes or the Himalayas by altitude sickness, which is caused by low oxygen concentration in the air and can be life-threatening. As a result, the homogeny of the local population can increase with elevation. In nations shared by people of high- and lowland extractions, this separation can potentially increase ethnic tension.

The researchers studied Tibet and found that elevation has heavily influenced the location of the surrounding region's population of Han Chinese, who make up 92 percent of China's population and originate from the country's eastern plains. Tibet has an average elevation of roughly 14,370 feet (4,380 meters) above sea level. The number of settlements with a large Han Chinese population peaks at around 8,900 feet (2,700 meters), while Tibetan settlements only begin to peter out beyond 17,000 feet (5,200 meters), the researchers found. The researchers attribute the sudden drop in the Han Chinese population to altitude sickness, and cite existing research showing that Han Chinese are indeed susceptible to altitude sickness in areas in which Tibetans thrive.

First author Christopher Paik, who undertook the study as a postdoctoral research scholar in the Empirical Studies of Conflict Project in Princeton's Woodrow Wilson School of Public and International Affairs, said that the research adds a new dimension to the study of how terrain influences demographic patterns. The field already explores the role of factors such as soil quality and access to the sea. The biological effects of elevation make altitude a particularly objective and reliable measurement for helping determine and understand how populations around the world's highest areas form, he said.

"There is very little research about the effect of altitude on migration patterns," said Paik, who is now an assistant professor of politics at New York University Abu Dhabi. "One of the nice things about using this geographical indicator as an independent variable is that there isn't any human intervention in determining the altitude of the region because it's established by nature.

"Rather than saying there is merely a correlation between settlement patterns and altitude, our research takes it one step further and suggests that altitude can directly determine the settlement patterns we see today. There's a causal story here," Paik said.

The separation that results from these settlement patterns could result in greater ethnic friction, Paik said. He initiated the current study in the wake of the 2008 unrest in Tibet, a series of protests that lead to imprisonment, detainment and clashes with Chinese security forces. Paik noticed that the most violent outbreaks occurred in areas of Tibet with the lowest relative concentrations of Han Chinese -- regions that also have the highest elevations. (Paik is currently working on a paper that correlates lower levels of violence during the 2008 unrest with lower elevation and greater Tibetan/Han integration.)

Paik and co-author Tsering Shawa, who heads the Digital Map and Geospatial Information Center in Princeton's Lewis Library, used 2000 Chinese census data to determine the Han population in settlements within the traditional Tibetan homeland, which includes the Tibetan Autonomous Region as well as portions of the Chinese provinces Qinghai, Gansu, Sichuan and Yunnan. They also gauged past Han Chinese presence through maps and a database developed by Shawa that indicate whether the official name of the 1,960 settlements in this area is Han Chinese, Tibetan or both.

The researchers found a similar distribution pattern of towns where at least one-third of the population are Han Chinese and traditional Han settlements (most of which date as far back as the 13th century) -- the bulk are located lower than 8,900 feet above sea level. No towns with a Chinese name exist above 15,000 feet (4,600 meters). Meanwhile, the greatest number of settlements with a Tibetan name stands at an only slightly lower elevation of 14,760 feet (4,500 meters), an area that the census shows has a minimum of Han Chinese inhabitants.

"What the outcome suggests is that there is a direct effect of altitude now as well as in historical settlement patterns," Paik said. "On the one hand there are settlements where Han Chinese came 1,000 years ago and established roots in that region, which makes it easier for migrants to come in. That provides a channel through which more Chinese live there today because their ancestors lived there as well.

"But if historical settlement is the only channel through which altitude influenced current settlement patterns, then there wouldn't be the direct influence of elevation through altitude sickness that we still see," Paik said. "Han Chinese still suffer from altitude sickness and the influence on settlement seems to persist today."

Paik and Shawa reference at least 10 studies that delve into the genetic adaption of Tibetans' blood cells and lung tissue to the low-oxygen conditions of a life on high -- a tolerance research suggests they share with Andes dwellers in countries such as Bolivia.

Han Chinese do not enjoy this predisposition even in modern times. The researchers cite a 2009 paper in the journal Clinica Chimica Acta that explored the genetic susceptibility of Han Chinese laborers to the pulmonary edema -- potentially fatal fluid buildup in the lungs -- they experienced during construction of the Qinghai-Tibet railway completed in 2005.

"The main contribution of this research is to point out geography does matter in ethnic demographic patterns," said Enze Han, an assistant professor of politics and international studies at the University of London. Han, who had no role in the research but is familiar with it, agrees with the researchers when they write that modern technology and transportation makes migration into high-altitude lands easier.

But, Paik said, the population distributions he and Shawa document show that geography -- via altitude sickness -- continues to play a strong role in regional diversity despite modern trappings such as the Qinghai-Tibet railway and government initiatives such as China's Western Development Program.

"Ethnic integration policy seems to work in the long run, but it will be harder to implement in the higher altitude regions," Paik said. "There seems to be a strong enough influence of altitude on settlement patterns such that even if you try to have integration happening there, nature works against those initiatives."

This work was supported by a grant from the Air Force Office of Scientific Research (AFOSR) award number FA9550-09-1-0314.

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Improving crop yields in a world of extreme weather events

July 1, 2013 — When plants encounter drought, they naturally produce abscisic acid (ABA), a stress hormone that helps them cope with the drought conditions. Specifically, the hormone turns on receptors in the plants. Botanists have identified an inexpensive synthetic chemical, quinabactin, that mimics ABA. Spraying ABA on plants improves their water use and stress tolerance, but the procedure is expensive. Quinabactin now offers a cheaper solution.

Farmers in the United States witnessed record-breaking extremes in temperature and drought during the last two summers, causing worldwide increases in the costs of food, feed and fiber. Indeed, many climate scientists caution that extreme weather events resulting from climate change is the new normal for farmers in North America and elsewhere, requiring novel agricultural strategies to prevent crop losses.

Now a research team led by Sean Cutler, a plant cell biologist at the University of California, Riverside, has found a new drought-protecting chemical that shows high potential for becoming a powerful tool for crop protection in the new world of extreme weather.

Named "quinabactin" by the researchers, the chemical mimics a naturally occurring stress hormone in plants that helps the plants cope with drought conditions.

Study results appear online this week in the Proceedings of the National Academy of Sciences.

All land plants have intricate water sensing and drought response systems that are tuned to maximize their fitness in the environments they live in. For example, plants in environments with low water grow slowly so that they do not consume more water than is available.

"But since farmers have always desired fast-growing varieties, their most valued strains did not always originate from drought-tolerant progenitors," explained Cutler, an associate professor of plant cell biology. "As a result, we have crops today that perform very well in years of plentiful water but poorly in years with little water. This dilemma has spawned an active hunt for both new drought-tolerant crops and chemicals that farmers might use for improving crop yield under adverse conditions."

Working on Arabidopsis, a model plant used widely in plant biology labs, Cutler and his colleagues focused their efforts on tinkering with one of the plant endogenous systems involved in drought responses. Plant leaves are lined with tiny pores, called stomata, which dynamically open and close to control the amount of water lost to the environment by evaporation. So that the plants can acquire carbon dioxide from the atmosphere, the pores need to be open some of the time, resulting in some loss of water.

During drought the stomata close firmly to limit water loss. Behind the scenes, a small hormone called abscisic acid (ABA) orchestrates the opening and closing of the pores. Cells throughout the plant produce increasing amounts of ABA as water levels decrease. ABA then moves throughout the plant to signal the stressful conditions and close the stomata. Inside plant cells, ABA does its job by turning on a special class of proteins called receptors. The discovery in 2009 of ABA receptors by the same team behind the current breakthrough was heralded by Science magazine as one of the top breakthroughs of 2009 because of its relevance to the drought problem.

"If you can control the receptors the way ABA does, then you have a way to control water loss and drought-tolerance," Cutler said. "It has been known for many years that simply spraying ABA on plants improves their water use and stress tolerance, but ABA itself is much too expensive for practical use in the field by farmers."

To address this problem, Cutler and his team searched through many thousands of molecules to identify inexpensive synthetic chemicals that could activate the receptors by mimicking ABA. The team found and named quinabactin, a molecule they show is almost indistinguishable from ABA in its effects, but much simpler chemically and therefore easier to make than ABA. By studying how the new molecule activates the ABA receptors that are involved in drought tolerance, the team also has learned more about the underlying control logic of the stress response system and provided new information that can be used for others interested in developing similar molecules,

"This is a competitive arena that includes agrichemical giants who are busily working to bring similar drought-protecting molecules to market, so this is a landmark discovery because quinabactin is the first-in-class synthetic molecule of its kind," Cutler said.

The work reported this week is the first in a multistep process of bringing a new agricultural product to market. Given the complexity and costs of such a process, the UCR Office of Technology Commercialization (OTC) is working with an agricultural leader, Syngenta Biotechnology, Inc., to develop the technology.

Joyce Patrona, a licensing officer in OTC, is coordinating UCR's licensing efforts for quinabactin.

"It has become very apparent to industry engaged in this area of technology of the robustness of Dr. Cutler's research," she said. "This is a credit to Dr. Cutler and his team as well as to UCR for its commitment to bring innovative research to the marketplace."

Cutler's collaborators on the research project are Brian Volkman and Francis Peterson at the Medical College of Wisconsin, who helped unravel the mechanism by which quinabactin mimics ABA by determining the atomic structure of the new molecule bound to one of its cellular receptors. Others who worked with them are Masanori Okamoto (first author of the research paper), Andrew Defries and Sang-Youl Park at UCR; and Akira Endo and Eiji Nambara at the University of Toronto, Canada.

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Mapping the benefits of our ecosystems

Two ecologists at the University of Wisconsin-Madison report this week (July 1) in the Proceedings of the National Academy of Sciences a novel approach to analyzing the production and location of 10 different ecosystem services across a landscape, opening the door to being able to identify factors governing their synergies and tradeoffs.

Monica Turner, the Eugene P. Odum Professor of Zoology, and graduate student Jiangxiao Qiu mapped the production, distribution, and interactions of the services in three main categories: provisioning (providing resources like food, fiber, or fresh water), cultural (such as aesthetics and hunting), and regulating (including improving ground and surface water quality, handling floodwater, preventing erosion, and storing carbon). They focused on the Yahara River watershed, which covers much of central portion of Dane County and parts of Columbia and Rock Counties in southern Wisconsin and includes the chain of Madison lakes.

"We found that the main ecosystem services are not independent of each other. They interact spatially in very complex ways," says Qiu, lead author of the new study.

Some of those interactions were not surprising -- for example, higher levels of crop production were generally associated with poorer surface and ground water quality. However, two other sets of services showed positive associations: flood regulation, pasture and freshwater supply all went together, as did forest recreation, soil retention, carbon storage and surface water quality.

"If you manage for one of these services, you can probably enhance others, as well," says Turner. "It also means that you can't take a narrow view of the landscape. You have to consider all of the things that it produces for us and recognize that we have to manage it very holistically."

Even in the expected tradeoff between crop production and water quality, the researchers found something unexpected.

"There is a strong tradeoff between crop production and surface and groundwater quality," Qiu says. "But despite this, there are still some locations that can be high for all three services -- exceptions that can produce high crop yield and good water quality in general."

Preliminary analysis of these "win-win" areas suggests that factors like flat topography, a deep water table, less field runoff, soil with high water-holding capacity, more adjoining wetlands and proximity to streams with riparian vegetation may contribute to maintaining both crop production and good water quality.

The results also show that nearly all of the land in the watershed provides a high level of at least one of the measured services but that they are not uniformly distributed. Most areas offer a high level of just one or two services. But a few, termed "hotspots" and making up just three percent of the watershed (largely parks and protected areas), provide high levels of at least six of the measured services.

"A single piece of land can provide different kinds of services simultaneously but you cannot expect that this land can provide all of the benefits," Qiu says.

The work was undertaken as part of a larger project to improve water sustainability in a mixed urban and agricultural landscape, supported by the Water Sustainability and Climate Program of the National Science Foundation (NSF).

"This paper is an initial assessment that gives us a picture of the spatial distribution of ecosystem services in contemporary times, a starting point for comparison," says Chris Kucharik, a UW-Madison professor of agronomy and environmental studies and principal investigator of the overall NSF project. The project aims to use a combination of contemporary and historical data to understand how the watershed may change over the next 50 to 60 years.

"We ultimately want to be able to look at future scenarios for this watershed," Turner says. "If climate changes or land use changes, what's going to happen to the values that we care about?"

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Astronomer uncovers the hidden identity of an exoplanet

July 1, 2013 — Hovering about 70 light-years from Earth -- that's "next door" by astronomical standards -- is a star astronomers call HD 97658, which is almost bright enough to see with the naked eye. But the real "star" is the planet HD 97658b, not much more than twice Earth's diameter and a little less than eight times its mass. HD 97658b is a super-Earth, a class of planet for which there is no example in our home solar system.

While the discovery of this particular exoplanet is not new, determining its true size and mass is, thanks to Diana Dragomir, a postdoctoral astronomer with UC Santa Barbara's Las Cumbres Observatory Global Telescope (LCOGT). As part of her research, Dragomir looked for transits of this exoplanet with Canada's Microvariability & Oscillations of Stars (MOST) space telescope. The telescope was launched in 2003 to a pole-over-pole orbit about 510 miles high. Dragomir analyzed the data using code written by LCOGT postdoctoral fellow Jason Eastman. The results were published online today in the Astrophysical Journal Letters.

A super-Earth is an exoplanet with a mass and radius between those of Earth and Neptune. Don't be fooled by the moniker though. Super-Earth refers to the planet's mass and does not imply similar temperature, composition, or environment to Earth. The brightness of HD 97658 means astronomers can study this star and planet in ways not possible for most of the exoplanet systems that have been discovered around fainter stars.

HD 97658b was discovered in 2011 by a team of astronomers using the Keck Observatory and a technique sometimes called Doppler wobble. But only a lower limit could be set on the planet's mass, and nothing was known about its size.

Transits, such as those observed by Dragomir, occur when a planet's orbit carries it in front of its parent star and reduces the amount of light we see from the star ever so slightly. Dips in brightness happen every orbit, if the orbit happens to be almost exactly aligned with our line of sight from Earth. For a planet not much bigger than our Earth around a star almost as big as our Sun, the dip in light is tiny but detectable by the ultraprecise MOST space telescope.

The first report of transits in the HD 97658 system in 2011 turned out to be a false alarm. That might have been the end of the story, but Dragomir knew that the ephemeris of the planet's orbit (a timetable to predict when the planet might pass in front of the star) was not exact. She convinced the MOST team to widen the search parameters, and during the last possible observing window for this star last year, the data showed tantalizing signs of a transit -- tantalizing, but not certain beyond doubt. A year later, MOST revisited HD 97658 and found clear evidence of the planet's transits, allowing Dragomir and the MOST team to estimate the planet's true size and mass for the first time.

"Measuring an exoplanet's size and mass leads to a determination of its density, which in turn allows astronomers to say something about its composition," Dragomir said. "Measuring the properties of super-Earths in particular tells us whether they are mainly rocky, water-rich, mini gas giants, or something entirely different."

The average density of HD 97658b is about four grams per cubic centimeter, a third of the density of lead but denser than most rocks. Astronomers see great significance in that value -- about 70 percent of the average density of Earth -- since the surface gravity of HD 97658b could hold onto a thick atmosphere. But there's unlikely to be alien life breathing those gases. The planet orbits its sun every 9.5 days, at a distance a dozen times closer than we are from our Sun, which is too close to be in the Habitable Zone, nicknamed The Goldilocks Zone. The Goldilocks nickname is apropos: If a planet is too close to its star, it's too hot; if it's too far away, it's too cold, but if it's in the zone, it's "just right" for liquid water oceans, one condition that was necessary for life here on Earth.

Over the past few years, systems with massive planets at very small orbital radii have proved to be quite common despite being generally unexpected. The current number of confirmed exoplanets exceeds 600, with the vast majority having been discovered by radial velocity surveys. These are severely biased toward the detection of systems with massive planets (roughly the mass of Jupiter) in small orbits. Bucking that trend is HD 97658b, which orbits its star at a distance farther than many of the currently known exoplanets. HD 97658b is only the second super-Earth known to transit a very bright star.

"This discovery adds to the still small sample of transiting super-Earths around bright stars," said Dragomir. "In addition, it has a longer period than many known transiting exoplanets around bright stars, including 55 Cnc e, the only other super-Earth in this category. The longer period means it is cooler than many closer-in exoplanets, so studying HD 97658b's properties is part of the progression toward understanding what exoplanets in the habitable zone might be like."

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