Neuroscientists Uncover Brain Region Involved in Voluntary Behavior

PASADENA, Calif.-Scientists at the California Institute of Technology have deciphered the activity of an area of the brain that could one day prove vital in the development of neural prostheses--within-the-brain implants that would translate thought into movement in paralyzed patients. The results of this study were published as the featured article in the November 8 issue of Neuron.

Richard A. Andersen, the James G. Boswell Professor of Neuroscience at Caltech, and his postdoctoral fellow, He Cui, looked in particular at the posterior parietal cortex (PPC), a higher brain region where sensory stimuli are transformed into movement.

To tease out the functions of two subregions of the PPC, the parietal reach region (PRR) and the lateral intraparietal area (LIP), Cui and Andersen designed an experiment in which rhesus monkeys were allowed to freely chose one of two actions, an eye movement or an arm movement, to acquire a visual target. Prior to the monkeys' selection, a computer program "guessed" which of those two actions would be performed by the monkeys, and picked the opposite movement as the choice to be rewarded. (The monkeys were essentially playing a matching game.) The computer's choices were biased by the previous choices made by the monkeys, which gave the monkeys an incentive to mix up their choices. Without it, they would invariably opt for the eye movement, which is the less energetically taxing of the two.

When the monkeys chose the arm movement, the PRR showed the most activity; when the monkeys opted for the eye movement, the LIP was most active.

The experiment shows that it is "the monkey's own choice that activates these areas," says Cui, and not the sensory stimuli provided by the visual target it sees on the computer screen. This finding is significant, Andersen says, because "this is the earliest stage in the brain found so far that is actively related to movement plans."

The research in Andersen's laboratory is focused on understanding the neurobiological underpinnings of brain processes, including the senses of sight, hearing, balance, and touch, and the neural mechanisms of action. The lab is working toward the development of implanted neural prosthetic devices that would serve as an interface between severely paralyzed individuals' brain signals and their artificial limbs--allowing thoughts to control movement. To assist in designing a more optimal prosthetic, they are now examining whether the decision to make a reaching motion is first made in PRR, or is made in another area of the brain and then transferred to PRR to form the movement plan.

"These areas are prime targets for neural prosthetics. The better we understand these areas, the better we can design prosthetics to decide the subjects' intent," Andersen says.

Kathy Svitil

Brain Imaging Aids in Defense against Genetic Disease

Pasadena, Calif.--Children born with a rare genetic disorder that can lead to debilitating and irreversible brain injury may find protection with the aid of brain imaging and a modified diet.

Caltech researchers joined scientists at Penn State College of Medicine to study the signs of glutaric aciduria type I (GA-I), a disorder arising from a gene defect that blocks a child's ability to break down the amino acids lysine and tryptophan. Lysine in the blood stream goes straight to the brain, where acids concentrate and damage the mitochondria, the brain's energy producers. The team made two significant discoveries: all the mice fed a tailored diet survived the disorder symptom-free, and signs of impending brain injury could be detected with brain imaging techniques.

The findings are available online this week in the latest issue of Journal of Clinical Investigation.

A rare disorder in the general population, GA-I affects around 1 in 35,000 children in the United States. However, 1 in 400 Amish children are born with GA-I-sometimes called "Amish cerebral palsy"-because in their small communities, chances are higher that two carriers of the recessive gene will marry. Not all children with the disorder will develop symptoms, but when a GA-I-affected child gets an inflammation from a mainstream illness like the flu, they can suffer a stroke. Despite current treatments, GA-I can lead to severe brain damage, painful crippling, or death in 25 to 30 percent of children who have it.

Jelena Lazovic, a postdoctoral scholar in biology, specializes in imaging brain injuries. She had spent the six months prior to her 2004 arrival at Caltech working in a clinic specializing in genetic disorders like GA-I. So when Penn State biologists Keith Chang and William Zinnanti--her husband and the study's lead author--asked her to lend her expertise to studying the disease in mice, she was happy to get on board.

Lazovic and Russell Jacobs, a researcher at Caltech's Biological Imaging Resource Center, began with magnetic resonance imaging (MRI) of mice that Zinnanti fed with a high-lysine diet, in order to pinpoint the regions of the brain affected by GA-I. Zinnanti used a "knockout" mouse model that lacked the functional gene that is disrupted in children with the disease. He discovered that increasing the level of lysine in the mouse diet could trigger a brain injury that was strikingly similar to those caused by GA-I in human patients.

The disease affects a region of the brain called the striatum in a manner similar to Huntington's disease. "We first thought we need to image the mice to see what areas of the brain will get damaged when we give them a lysine diet," says Lazovic. Other approaches to the problem are invasive, she says, but "imaging seemed to be the most convenient; it's in vivo and the findings can translate to humans." At the imaging center, Lazovic and Jacobs put the mice in an MRI machine first to get a brain image, and then to run proton nuclear magnetic resonance spectroscopy. The peaks of the spectroscopic reading reveal different compounds, called metabolites, which aid in growth and development. "Each peak is like a fingerprint with its own frequency," says Lazovic, and the area under a peak shows how much of the metabolite is present. The team found that one of the brain's more important metabolites, a neural transmitter called glutamate, is actually reduced just before brain injury occurs

One aspect of the disease that puzzled the scientists was the appearance of symptoms primarily in children younger than age three. Zinnanti found the same age-dependent brain-damage susceptibility in his mice. The scientists think that young mice are more susceptible to GA-I because their immature brains metabolize and accumulate more lysine than an adult brain does. The young mice were also seen to develop hypoglycemia just as patients with GA-I do.

Using a dietary intervention strategy, Zinnanti and colleagues showed that a combination of homoarginine, which limits lysine accumulation in the brain, and glucose, which prevents hypoglycemia and reduces lysine breakdown in the brain, can prevent brain injury in 100 percent of susceptible young mice. Lazovic's and Jacobs's spectroscopic analyses may also provide a means to monitor children with GA-I for impending brain injury, something that has previously been impossible. Children who test positive for the genetic deficiency at birth could be monitored on a monthly basis.

"We had no pointers as to what was happening with these kids," says Lazovic. "Now we think we have a method where you can do spectroscopy on the children, and you can measure decreased glutamates, and you can tell that energy production in the brain is suppressed." The technique may also help with other genetic disorders that inhibit amino-acid metabolism, like maple syrup urine disease (so called because of the sweet smell it gives infants' urine), propionic acidemia, and methylmalonic academia. Each of these affects children at about the same rate as GA-I, and is more prevalent in tight-knit communities.

"This disease is certainly a major concern in the Amish community, so it's something they know to be on the lookout for," Zinnanti says. "But it also affects children around the world, and it's ten times worse when you're not expecting it and don't know what to look for. We hope our work begins to offer tools for these patients and their caregivers to diagnose and treat this disorder before it causes irreversible damage."

Other authors of the paper are Cathy Housman, Kathryn LaNoue, Ian Simpson, James Connor, and Keith Cheng of Penn State; James O'Callaghan of the Centers for Disease Control and Prevention; and Michael Woontner and Stephen Goodman of the University of Colorado at Denver.

Elisabeth Nadin

Caltech Neuroscientist Named to Institute of Medicine

PASADENA, Calif.-- Richard A. Andersen, the James G. Boswell Professor of Neuroscience at the California Institute of Technology, has been elected as a member of the Institute of Medicine (IOM). Andersen is one of 65 new individuals to be admitted to the elite organization, which was established in 1970 by the National Academy of Sciences and now has 1,538 active members. It is recognized as a national resource for independent, scientifically informed analysis and recommendations on human health issues. By their membership, inductees agree to volunteer their time on IOM committees examining health policy issues.

Andersen studies the neurobiological underpinnings of brain processes, including the senses of sight, hearing, balance, and touch, and the neural mechanisms of action and is a pioneer in the development of implanted neural prosthetic devices that would serve as an interface between severely paralyzed individuals' brain signals and their artificial limbs--allowing thoughts to control movement. Andersen says, "It's a very exciting time in neuroscience. After decades of study, our basic research is finally yielding findings we are able to translate into clinical advancements to help paralyzed people. Caltech has provided a unique environment for such study, as we in our lab have enjoyed close collaboration with bioengineers, electrical engineers, economists, and physicists as well as clinicians toward developing a neural prosthesis. The next step is to move our studies into clinical trials with human patients, an endeavor we will enter jointly with the medical community."

Andersen received his PhD from the University of California, San Francisco, in 1979, and was a postdoctoral fellow at Johns Hopkins Medical School. He was on the faculties of the Salk Institute and MIT before joining Caltech in 1993. He is a member of the National Academy of Sciences, and a fellow of the American Academy of Arts and Sciences and the American Association for the Advancement of Science. He is the recipient of a McKnight Foundation Scholars Award, a Sloan Foundation Fellowship, the Spencer Award from Columbia University, a McKnight Technical Innovation in Neuroscience Award, and a McKnight Neuroscience Brain Disorders Award. The new members of the IOM will be formally inducted during the annual meeting, which is scheduled for October 12-13, 2008.

Kathy Svitil
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Researchers Discover Link Between Schizophrenia, Autism and Maternal Flu

PASADENA, Calif.- A team of California Institute of Technology researchers has found an unexpected link connecting schizophrenia and autism to the importance of covering your mouth whenever you sneeze.

It has been known for some time that schizophrenia is more common among people born in the winter and spring months, as well as in people born following influenza epidemics. Recent studies suggest that if a woman suffers even one respiratory infection during her second trimester, her offspring's risk of schizophrenia rises by three to seven times.

Since schizophrenia and autism have a strong (though elusive) genetic component, there is no absolute certainty that infection will cause the disorders in a given case, but it is believed that as many as 21 percent of known cases of schizophrenia may have been triggered in this way. The conclusion is that susceptibility to these disorders is increased by something that occurs to mother or fetus during a bout with the flu.

Now, researchers have isolated a protein that plays a pivotal role in that dire chain of events. A paper containing their results, "Maternal immune activation alters fetal brain development through interleukin-6," will be published in the Oct. 3 issue of the Journal of Neuroscience.

Surprisingly, the finger of blame does not point at the virus itself. Since influenza infection is generally restricted to the mother's respiratory tract, the team speculated that what acts as the mediator is not the mother's infection per se but something in her immune response to it.

To prove this, they triggered an artificial immune response in pregnant mice--giving them a faux case of the flu. The trigger they used was a snippet of double-stranded RNA called poly(I:C), which fools the immune system into thinking there has been an infection by an RNA virus.

A single, mid-gestation injection of poly(I:C) creates a strong immune response in a pregnant mouse. When her offspring reach adulthood, they display behavioral and tissue abnormalities similar to those seen in schizophrenia in humans.

Though there might be some disagreement over what it means for a mouse to be schizophrenic, these abnormalities are generally marked by inappropriateness of response and difficulty in coping. For instance, afflicted mice often show antisocial tendencies, have trouble internalizing basic cause-and-effect connections, and are anxious about entering wide-open spaces or interacting with novel objects. Moreover, some of these abnormal behaviors are corrected by antipsychotic drug treatment.

These behaviors then pose a new question, what in the mother's immune response caused the abnormalities?

At the cellular level, the innate immune response is driven by proteins called cytokines, which are produced by the body in response to infection. The researchers speculated that something was being transmitted to the fetus by one or more cytokines produced by the mother in response to her infection.

"It's known that humans that are treated--say, for cancer--with an experimental cytokine treatment can display very significant changes in behavior," says Paul H. Patterson, Biaggini Professor of Biological Sciences and senior author of the paper. "So we know cytokines can have dramatic effects, of the kind you see in schizophrenia."

The team tried injecting the pregnant mice with individual cytokines, rather than with poly(I:C). It turned out that after a single dose of a specific cytokine known as interleukin-6 (or IL-6), a mouse would give birth to offspring who, at maturity, exhibited the familiar schizophrenia- and autism-like behaviors.

To confirm the role of IL-6, Steve Smith, the lead researcher, gave fake colds (poly(I:C)) to two groups of pregnant, IL-6-free mice. One group had received anti-IL-6 antibodies which blocked IL-6; the other consisted of so-called IL-6 knockout mice (mice whose genetic makeup prevents them from synthesizing IL-6). In both groups, offspring grew up normal, showing that IL-6 is necessary for the maternal poly(I:C) treatment to alter fetal brain development and subsequent behavior in the offspring.

The decision to try injecting IL-6 was a long shot. "It is really unexpected that a single injection of a single cytokine would exert such a powerful effect," says Patterson.

The scientists are still unsure what it is about increasing IL-6 levels in the mother that causes undesirable effects in her offspring. "The most obvious possibility is that IL-6 acts directly on the fetal brain," the paper's authors say, but they acknowledge that the cytokine might also alter the transfer of materials across the placenta or might even alter the maternal immune system that gave rise to it, in effect triggering a low-grade rejection of the developing fetal tissue by the mother's body.

Once the exact role of IL-6 has been nailed down, there will still be more work to be done. The researchers are hunting for ways of preventing cytokines like IL-6 from inflicting their damage on the developing or maturing brain--perhaps via mechanisms involving other cytokines.

"We could certainly imagine that there would be anti-inflammatory cytokines that would be involved, that would be acting in the opposite direction," suggests Patterson. "We haven't tested those yet, but we would like to. We also want to test anti-inflammatory drugs in the postnatal offspring to see if we can normalize their behavior."

The paper's authors are Patterson and Stephen Smith, a graduate student in biology at Caltech; Jennifer Li, now a graduate student at the University of California Medical Center, San Francisco, who participated in the project as part of a Caltech Summer Undergraduate Research Fellowship; and Drs. Krassimira Garbett and Karoly Mirnics, both of the Department of Psychiatry and the Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University.

The research was supported by the National Institute of Mental Health and by the McKnight, Cure Autism Now, and Autism Speaks foundations.

David Zobel

MacArthur Foundation Names Two New Caltech "Geniuses"

PASADENA, Calif.--Two California Institute of Technology faculty members were named MacArthur Fellows today, each winning a five-year, $500,000 grant awarded to creative, original individuals that is often referred to as the "genius grant."

Michael Elowitz, Bren Scholar and assistant professor of biology and applied physics, and Paul W. Rothemund, a senior research fellow in computation and neural systems and computer science, are two of 24 MacArthur Fellows honored today. The accomplishments of both of this year's winners highlight the interdisciplinary nature of Caltech's research endeavors.

Michael Elowitz is a molecular biologist who combines mathematical and computational modeling with experiments on individual living cells to understand how genes and proteins interact to form circuits. These circuits allow the cells to interact with their environments, communicate with one another, and develop into multicellular organisms. He uses two different approaches; in the first, he tracks changes in proteins in natural genetic circuits with time-lapse movies, and in the second, he engineers new circuits that provoke alternative cellular behaviors. In one demonstration of new cell behavior, Elowitz created a simple synthetic genetic clock by programming cells to show oscillations in the level of a fluorescent protein as the cells grew.

More recently, Elowitz tackled the long-standing question of how cells reliably control their own behavior when the intracellular environment they depend on is so complex and unpredictable. He used fluorescence again; in this case, differences between how much of a red protein and how much of a green protein the cell made allowed him to see to what extent the expression of genes is intrinsically random. Currently, his lab investigates how cells make decisions about differentiating into different cell types.

"I was just dumbfounded, befuddled," Elowitz says about the phone call that told him he was a MacArthur Fellowship recipient. "It's amazing, it's very hard to believe. It just wasn't something I had thought about, and it was out of the blue." He stresses that his research is very collaborative, and says that "by far the greatest pleasure has been working with and learning from a spectacularly talented and fun group of scientists." He has no plans yet for the cash award.

After earning degrees from UC Berkeley and Princeton University, Elowitz joined the Caltech faculty in 2003.

Paul Rothemund's work, which he began over a decade ago, borrows tools from molecular biology to show that DNA can be used to perform the tasks of a computer.

Recently, he's used computers to design large DNA molecules that reliably self-assemble into microscopic shapes and patterns, like a map of the Americas or a pair of smiley faces 100 nanometers wide and two nanometers thick. He calls his technique "scaffolded DNA origami" because it involves folding a very long strand of DNA dozens of times, into different designs. Rothemund says this kind of DNA technology might eventually be used to build smaller, faster computers. He also envisions far more fantastical potentials, like building whole organisms from self-assembling biological bits.

Rothemund considers himself lucky to be working at a moment in history that has provided his detail-oriented personality with something to do. "I really like to make intricate things with lots of little parts. In a different age I'd probably be a watchmaker, although I am not that mechanically inclined." He has yet to decide what he'll do with the grant money, besides travel for future collaborations.

In keeping with the MacArthur tradition, the Caltech nominees did not know they were being considered. "It is amazing that such a thing exists," says Rothemund. "That one can pursue beautiful or meaningful or societally redeeming things with no interest in doing it for money, and then out of the blue, someone walks in and says 'Surprise, we're going to give you half a million dollars to keep doing whatever you think is beautiful or meaningful or important, and there are no strings attached and we aren't going to keep track of you or bother you again ever. . . bye!'"

After receiving degrees from the California Institute of Technology and from the University of Southern California, Rothemund returned to Caltech as a Beckman Fellow in 2001. He joins ranks with the director of his lab, Associate Professor of Computer Science and Computation and Neural Systems Erik Winfree, who was named a MacArthur Fellow in 2000.

Elisabeth Nadin

Two Nicotine Addiction Puzzles Explained

PASADENA, Calif.--The stranglehold of nicotine addiction leads to more than four million smoking-related deaths each year. Scientists at the California Institute of Technology have now explained two roots of that addiction. The discoveries may offer new hope not just for smokers, but eventually also for sufferers of Parkinson's disease, a debilitating movement disorder that affects some 40 million people worldwide.

Researchers have known for decades that chronic exposure to nicotine increases the number of nicotine receptors--molecules that are activated by binding to the drug--on nerve cells. The binding of nicotine to these receptors, and in particular to one specific subunit known as alpha4, enhances the release of a pleasure-causing neurotransmitter called dopamine.

But "this increase is confusing," says Henry A. Lester, the Bren Professor of Biology at Caltech, "because for opioid addiction, and for many other classes of addictions and of drugs in general, the body attempts homeostasis and adjusts the number of receptors downward if there is a constant stimulus." Understanding this paradox--how it is possible that smokers become tolerant to the pleasurable effects of nicotine despite the fact that their brains produce new nicotine receptors in response to the chemical--is crucial for defeating nicotine's addictive power.

Lester, his postdoctoral researcher Raad Nashmi, and their colleagues at Caltech, the University of Colorado at Boulder, and the University of Pennsylvania School of Medicine, have now solved the mystery, by developing a special mouse strain with fluorescent nicotine receptors. These fluorescent tags allowed the scientists to monitor the effects of the nicotine throughout the brain, down to the level of individual neurons.

"We find that alpha4 containing receptors, those with some of the highest sensitivity to nicotine, are upregulated"--or increased in number--"by chronic nicotine in a cell-specific fashion," Lester explains. "In particular, the alpha4-containing receptors are indeed upregulated in the dopamine-producing portions of the brain, but not in the dopamine neurons themselves." Instead, the increase in receptor number occurs only in neurons that inhibit dopamine neurons--a group called the GABAergic neurons.

This surprising result led the researchers to conduct experiments with delicate electrical probes. In chronic nicotine-treated mice (and presumably in chronic smokers), the dopamine neurons are chronically inhibited from firing in the absence of nicotine. And nicotine itself still excites the dopamine neurons, leading to pleasure, but much less than expected.

"This research explains tolerance during nicotine addiction," Lester says. "Once in a while, an important piece of a puzzle does fall into place."

"This is outstanding work that will open the door to further studies of nicotinic receptor upregulation in the cognitive and rewarding effects of nicotine," comments Daniel S. McGehee of the University of Chicago, who studies the neurobiology of nicotine addiction. McGehee was not involved in the present research.

But there's more. In the special Caltech mice, the largest number of new nicotine receptors appeared in the mouse forebrain. This is the part of the brain involved in cognition. Electrical measurements showed that these new receptors also helped to boost synaptic transmission. The result may explain why many smokers claim that cigarettes actually help them think better--and why 44 percent of the cigarettes smoked in the United States are consumed by people with mental health problems.

"People may attempt to medicate themselves with nicotine, and my research is also aimed at trying to understand the mechanism behind that," Lester says.

"We now think that we need to concentrate on drugs that manipulate upregulation." Lester adds. His lab is currently developing simpler cell-based systems using the fluorescently labeled nicotine receptors. Using special microscopes, the effect of particular drugs on those receptors can be monitored.

One long-term benefit of the research could be the development of better therapies for Parkinson's disease, the chronic neurological condition that gradually destroys some dopamine cells. Although the cause of Parkinson's disease is unknown in most patients, one curious observation is that few smokers are ever affected. In fact, they seem to be protected against the condition. The reason, researchers suspect, is nicotine--and the new brain studies reveal that the reason may be those cell-specific differences in the regulation of nicotine receptors.

Previously, animal models of Parkinson's have shown that the excessive activity of dopamine neurons, firing in hysterical bursts, can lead to the death of those neurons. The affected neurons are located in a brain region called the substantia nigra, which is a center of voluntary movement control.

"These dopamine cells are actually persuaded by chronic nicotine to fire less, which may help them to live longer," says Lester, who hopes the research will lead to the development of drugs that act "very specifically" on these nicotine receptors and prevent cell death, "so people with the early stages of Parkinson's disease get the protection that they need."

The paper, "Chronic Nicotine Cell Specifically Upregulates Functional alpha4* Nicotinic Receptors: Basis for Both Tolerance in Midbrain and Enhanced Long-Term Potentiation in Perforant Path," was published in the August 1 issue of the Journal of Neuroscience. The research was supported by the National Institutes of Health and the National Alliance for Research on Schizophrenia and Depression, and by previous grants from the California Tobacco-Related Disease Research Project, Philip Morris USA/International, the Elizabeth Ross Foundation, and the W. M. Keck and Plum Foundations.

Kathy Svitil

Caltech Scientists Create Breakthrough Sensor Capable of Detecting Individual Molecules

PASADENA, Calif.- Applied physicists at the California Institute of Technology have figured out a way to detect single biological molecules with a microscopic optical device. The method has already proven effective for detecting the signaling proteins called cytokines that indicate the function of the immune system, and it could be used in numerous medical applications, such as the extremely early detection of cancer and other diseases, as well as in basic biological research.

According to Kerry Vahala, the Jenkins Professor of Information Science and Technology and professor of applied physics, this new detection technology revolves around a previous invention from his lab called an "ultra-high-Q microtoroid resonator." This is a donut-shaped glass device that is narrower than the width of a human hair and that is able to hold on to light very efficiently. Vahala explains that "the detector relies upon this feature to boost sensitivity to the single molecule level, albeit in a surprising way." He notes that the original idea was to detect an optical response elicited directly by molecules landing on the donut-shaped device. "As work proceeded, however, we were able to observe single molecule detection events with far greater ease than was originally expected." This pleasant surprise was traced to minute amounts of heat generated when molecules interact with the light stored within the microtoroid resonator. "This thermo-optic response boosts the sensitivity a millionfold," explains Vahala. Andrea Armani, who works in Vahala's laboratory and developed the detector as part of her thesis research, notes that besides being extremely sensitive, the device is also programmable by coating its surface with substances that react to a specific biological molecule. "The molecule which the device is targeting, whether it is a growth factor or a chemical like TNT, is determined by the surface treatment of the glass microtoroid. Fortunately, the biology and chemistry communities have developed very effective techniques for attaching proteins to glass surfaces, because most microscope slides are glass. All we had to do was adopt those techniques to fit our structure," explains Armani.

Vahala notes that "this combination of single-molecule sensitivity and programmable detection, that is, without labeling of the target molecule, has not been demonstrated before, and enables new kinds of tests and measurement."

Scott Fraser, the Rosen Professor of Biology, professor of bioengineering, and collaborator on the project, explains further that "this technology should lead to many applications for biological experiments, medical tests, and even medical treatments. The advantages are its ability to detect extremely small numbers of molecules, and the fact that there's no need to label target molecules. At this sensitivity level, it is possible even to study growth factors being emitted in real time from a single cell." Fraser adds, "This is the only sensor that currently has the requisite sensitivity and rapidity."

This type of experiment is important in monitoring how environmental changes, such as pH or temperature, can influence a cell's behavior. Currently, these types of experiments must be performed with populations of millions of cells, which often blurs results because it is like trying to pick out a single voice in a choir.

In the July 5 issue of the online journal Science Express, the team reports on its success in detecting a series of different molecules, including one immune response signaling protein, interleukin-2 (IL-2). For the latter, the targeting molecule the devices were coated with was a specific antibody that recognized IL-2. This surface preparation allowed the detector surface to bind the IL-2, while the thermo-optic mechanism provided the sensitivity required to detect the IL-2 at the single molecule level, even in serum (blood with the clotting factors and red blood cells removed).

"What is most exciting about this device is its ability to get single molecule results in real time without labeling. Because it can be programmed to detect almost any biological molecule, it is a universal detector, and as such opens the door to a whole field of new experiments," adds Armani.

The work was supported by the Defense Advanced Research Projects Agency-funded Center for Optofluidic Integration at Caltech.

The coauthors of the paper are Armani, a Clare Boothe Luce postdoctoral fellow; Vahala; Fraser; Richard Flagan, the McCollum-Corcoran Professor of Chemical Engineering and professor of environmental science and engineering; and Rajan Kulkarni, a recent Caltech biology doctoral graduate.

Robert Tindol
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Engineering Populations of Wild Insects to Fight Disease

PASADENA, Calif.-- Malaria infects more than half a billion people every year, and kills more than one million, mostly children. Despite decades of effort, no effective vaccine exists for the disease, caused by single-celled Plasmodium parasites. The parasites are transmitted to humans via the bite of infected mosquitoes.

One way to stop malaria is to make the mosquitoes that carry the disease themselves resistant to the pathogen. Getting disease-fighting genes into the mosquito population can be tricky, however, because bugs carrying disease-resistance genes are likely to be less reproductively fit than their wild counterparts, and thus less likely to spread their genes naturally.

Associate Professor of Biology Bruce Hay of the California Institute of Technology, postdoctoral fellow Chun-Hong Chen, and their colleagues at Caltech and the University of California, Los Angeles, have come up with a novel method for introducing such genes into insect populations. The work, published recently in the journal Science, involves the creation of a selfish genetic element that is uniquely adapted to spread itself quickly throughout the population.

"This spread is essential," says Hay, "because people who live in areas affected by malaria and other mosquito-borne diseases are bitten often, so there will be little benefit unless most of the mosquito population is disease resistant."

"What we need," says Chen, the first author of the study, "is some way of forcing, or helping, these disease-resistance genes to spread rapidly throughout the wild population."

The technique Chen, Hay, and their colleagues have come up with uses a maternal-effect dominant embryonic arrest--or Medea--genetic element, a particularly spiteful selfish genetic element.

"Selfish genetic elements (single genes or clusters of genes) are basically units of genetic information that are more successful than your average gene at passing themselves from generation to generation," says Chen, even if their presence makes an organism less fit. "Our idea was to create a selfish genetic element that could be linked with a specific cargo, the disease-resistance gene, as a way of rapidly carrying this gene through the population."

Medea elements were first described in 1992 by Richard Beeman and colleagues at Kansas State University, who found the entity in populations of the common flour beetle Tribolium castaneum.

Beeman and his colleagues do not yet know the molecular nature of Tribolium Medea, but their work suggests that Medea consists of two linked genes. One gene, whose expression is activated in the mother, encodes a toxin that is deposited into all oocytes, or eggs. Embryos that do not inherit a Medea element die because of the toxin. Embryos that inherit Medea from either their mother's or their father's genome, however, will survive because they produce an antidote that neutralizes the toxin. As a result, chromosomes that carry Medea end up in offspring more often than those that do not, and Medea can spread rapidly through a population.

"We spent several years trying to create a selfish genetic element based on these principles," says Chen, "but it was difficult to get the insects to produce just the right amount of toxin; enough to kill the embryo, but not so much that the toxin couldn't be inhibited by the antidote." The researchers eventually switched to a system in which the toxin caused the loss of an essential function, and the antidote restored that function. "We generated flies in which maternal expression of small noncoding RNAs, known as microRNAs, were used to silence a gene known as myd88, which is crucial for embryonic development. Embryos from mothers expressing these microRNAs all died, unless they also expressed a microRNA-insensitive version of the myd88 gene: the antidote," said Chen.

Fruit flies carrying this synthetic Medea element spread quickly throughout a laboratory population of wild-type flies. After just a few generations, all of the flies in the population carried at least one copy of Medea. "To our knowledge this work represents the first de novo synthesis of a selfish genetic element able to drive itself into a population. It provides a simple proof-of-principle experiment demonstrating that, at least in a highly controlled laboratory environment, in a model organism, we can change the genetic makeup of a population," says Hay.

The team now plans to use the technique to transmit a real payload--a disease-resistance gene--into the mosquito.

Says Hay: "Mosquitoes with a decreased capacity to transmit malaria and other mosquito-borne diseases have already been identified in the wild and created in the laboratory by other researchers. These observations tell us that we can manipulate the mosquito immune system and thereby, at least in principal, stop this and other mosquito-borne diseases at their source in the mosquito. When combined with a mechanism such as Medea that helps to spread these resistance genes through the wild population, there is a real possibility that disease transmission can be suppressed in an environmentally friendly way that does not involve the wholesale use of insecticides or modification of the environment; the mosquitoes will still be there but with one or two tiny genetic changes that make them unable to transmit these dreadful diseases."

"This work is a prime example of how fundamental research can lead to breakthroughs that have huge implications for bettering human health," says Marion Zatz, chief of the Developmental and Cellular Processes Branch at the National Institute of General Medical Sciences, which partially supported the research. "Dr. Hay's work on how microRNAs regulate cell death in the innocuous fruit fly has 'borne fruit' in potential applications for limiting the spread of malaria."

This work was supported by National Institutes of Health grants GM057422 and GM70956 to Bruce Hay, and NS042580 and NS048396 to Ming Guo, assistant professor in the departments of neurology and pharmacology at UCLA's Brain Research Institute, David Geffen School of Medicine.


Contact: Kathy Svitil (626) 395-8022

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Researchers Stimulate Growth of Neural Stem Cells in Adult Brain for Treatment of Neurological Disorders

PASADENA, Calif.—In a development that could potentially benefit victims of degenerative neurological diseases, researchers have succeeded in stimulating the growth of adult neural stem cells. Such cells could then be directed towards repairing one's own brain.

In the November 15 issue of the Journal of Neuroscience, California Institute of Technology neuroscientists report that they have discovered a way to stimulate an area of the brain where adult stem cells normally exist. As a result, there is a significant increase in stem cell production—up to six times the normal amount of adult neural stem cells found there.

According to Paul Patterson, the Biaggini Professor of Biological Sciences at Caltech and senior author of the paper, the good news is that these stem cells represent a large pool of precursor cells that future work may direct into pathways for replacement of dying cells in disorders such as Parkinson's and Alzhiemer's diseases and multiple sclerosis.

"Basically, what my colleague Sylvian Bauer has done is take a natural protein in the body called leukemia inhibitory factor, or LIF, and inject it into the brains of adult mice," Patterson explains. "The results show that you can stimulate the subventricular zone to produce a much larger pool of adult neural stem cells."

The idea then is to direct the stem cells to form the necessary specialized neurons or glia in the part of the brain that is damaged by disease or injury, Patterson says.

"Neuroscientists have known for some time that the adult brain possesses neural stem cells that could be used to regenerate neurons, and in fact, the brains of neurodegenerative disease patients show evidence that their neural stem cells do attempt to replace dying cells.

"However, the contribution of these cells to brain repair is currently very limited," he says. "Our approach may overcome the limitation of cell numbers, and the approach of using one's own cells offers the further advantage of avoiding the transplantation of immunologically foreign stem cells, thereby eliminating the problems of rejection."

This development in no way renders the use of embryonic stem cells obsolete, or argues against further research with embryonic stem cells, Patterson says. Embryonic stem cells have the potential to become any cell in the body, whereas his process uses adult neural stem cells for brain disorders only.

Although this stimulation of neural stem cell growth has been done in laboratory mice, Patterson says that humans also have neural stem cells in the adult brain.

The next step is to see if the adult neural stem cells can be directed to replace cells in mice with brains that are damaged in ways similar to humans with Parkinson's, Alzheimer's, and multiple sclerosis.

Bauer, the lead author of the paper, is a former postdoctoral researcher in Patterson's lab who recently moved to the Université Paul Cézanne, Aix-Marseille III, in France.

Robert Tindol

California Purple Sea-Urchin Genome Sequenced by International Team

PASADENA, Calif.—A group of 240 researchers from more than 70 institutions has announced the sequencing of the male California purple sea urchin. An animal frequently used in experiments, its genome has been studied intensely for years at Caltech's Kerckhoff Marine Biological Laboratory (KML), and will contribute significantly to biomedical advances of the future.

Reporting in the November 10 issue of the journal Science, the researchers are announcing that the high-quality "draft" sequence covers more than 90 percent of the sea-urchin genome. In addition to the primary results in Science, 41 companion manuscripts will appear in Science and a special issue of the December 1 issue of Developmental Biology.

The project was led by Erica Sodergren and George Weinstock, a husband-and-wife team at the Baylor College of Medicine-Human Genome Sequencing Center (BCM-HGSC), along with Richard Gibbs, director of the BCM-HGSC, and Eric Davidson and Andrew Cameron of the California Institute of Technology. The National Human Genome Research Institute of the National Institutes of Health provided most of the funding for the sequencing and annotation.

According to the researchers, the sea-urchin genome contains more than 814 million letters, spelling out 23,300 genes. To date, nearly 10,000 of the genes have been scrutinized by the international consortium.

The results are the outcome of work begun at Caltech more than 30 years ago, when Davidson and Roy Britten, a scientist working at Caltech's Kerckhoff Marine Biological Laboratory, began to exploit the utility of the sea urchin as an experimental animal and decided to develop it as a model system in the then emerging field of molecular biology. In the ensuing years many advances in cell and developmental biology derived from this decision.

"Roy Britten and Eric Davidson offered a comprehensive theory of gene regulation in higher organisms, and the sea urchin has been the premier model for testing these predictions," says Gibbs. "The complete sequence is now available to further these studies."

More recently, Davidson and Cameron have coordinated efforts to have the sea-urchin genome sequenced. Starting with a special grant from the Stowers Institute for Medical Research in Kansas City, they assembled the research materials that would be needed to sequence the genome at the Sea Urchin Genome Facility in Caltech's Beckman Institute and at the KML.

A culture system at KML in which the purple sea urchin is grown through the life cycle continues to provide the essential infrastructure. When the Human Genome Research Institute announced a way to propose additional genome sequencing to support the human genome information, the team at the BCM-HGSC was poised to take action. From these roots grew the Sea Urchin Genome Sequencing Consortium.

Sea urchins are echinoderms (Greek for spiny skin), marine animals that originated over 540 million years ago and that include starfish, brittle stars, sea lilies, and sea cucumbers. Following the great extinction of animals 250 million years ago, the modern sea urchins emerged as the dominant echinoderm species. The purple sea urchin emerged in the North Pacific Ocean during a rapid burst of speciation and diversification 15-20 million years ago.

There was great interest in the sea urchin as a target for genome sequencing because these animals share a common ancestor with humans. That ancestor lived over 540 million years ago and gave rise to the Deuterostomes, the superphylum of animals that includes phyla such as echinoderms and chordates, the phylum to which humans and other vertebrates belong. All Deuterostomes are more closely related to each other than they are to any other animals not included in the Deuterostome superphylum. For example, among sequenced genomes, the genomes of fruit flies and worms are more distant from the sea urchin genome than is the human genome. "Each genome that we sequence brings new surprises. This analysis shows that sea urchins share substantially more genes and biological pathways with humans than previously suspected," says Francis S. Collins, director of the National Human Genome Research Institute. "Comparing the genome of the sea urchin with that of the human and other model organisms will provide scientists with novel insights into the structure and function of our own genome, deepening our understanding of the human body in health and disease." To discover how sea urchins and humans can be so different, yet be related by descent from an ancient relative, their genomes were compared. The sea urchin is an invertebrate and the first example of sequencing a Deuterostome genome outside the chordates. Most previous invertebrate genomes that were sequenced, such as insects and nematodes, were animals outside the Deuterostome superphylum, although one genome of a chordate invertebrate, the sea squirt, has been sequenced. The sea urchin lies evolutionarily in a large niche between the chordate branch of the Deuterostomes and the non-Deuterostome superphyla. "The sea urchin fills a large evolutionary gap in sequenced genomes," says Weinstock, co-director of Baylor's Human Genome Sequencing Center. "It allows us to see what went on in evolution after the split between the ancestors that gave rise to humans and insects. The sea urchin genome provided plenty of unexpected rewards and was a great choice for sequencing." The comparison of the genes of the sea urchin to the human gene list shows which human genes are likely to be recent innovations in human evolution and which are ancient. It also shows which human genes have changed slowly in the lineage from the ancestral Deuterostome animal and which genes are evolving rapidly in response to natural selection. This will make it possible one day to know the history of every human gene-and build a picture of what the extinct ancestors that gave rise to animal life ranging from worms to humans looked like. Although invertebrate sea urchins have a radically different morphology from humans and other vertebrates, their embryonic development displays basic similarities, an important shared property of Deuterostome animals. This distinguishes them from Protostomes, which have a different pattern of embryonic development. This makes the sea urchin, with its many useful properties such as transparent embryos and ease of isolation of eggs and sperm, a valuable model for studying the process of development and helping us to understand human development. The development of the animal occurs through a complex network of genes, making the sea urchin one of the main models for systems biology, which describes how the building blocks of an animal interact in time and space. Sea urchins provide a rapid and efficient gene transfer system. By injecting DNA into the egg, researchers can determine which letters spell instructions for turning genes on and off. The series of genetic switches leading to the ordered cascade of expression of genes after fertilization in the sea urchin is among the best understood developmental systems among animal models. Now, with the genome sequence in hand, a more complete set of components of development are known, and this process can be studied exhaustively.

Because of its evolutionary position, the sea-urchin genome sequence was a sample of unknown biological territory. Some of the notable surprises and discoveries were that: —The sea urchin has most of the same gene families found in human beings. These gene families make up the Deuterostome tool kit used to create animals in this superphylum. However, the size of gene families is often larger in humans, reflecting, in part, two whole genome duplication events during vertebrate evolution after the separation of the sea urchin and human evolutionary lines. —One unexpected exception to this size rule is the immune system. Humans have innate and acquired immune systems. The sea urchin has some of the genes of the acquired immune system, but its innate immune branch is greatly expanded with ten- to twenty times as many genes as in humans. —Innate immunity is the set of proteins that are "hard wired" to detect unique molecules within bacteria, such as their cell walls, and to signal that there is an intruder. This rich repertoire of sea urchin proteins could turn out to provide new reagents in the fight against infectious diseases. —The sea urchin has genes for sensory proteins that are involved in human vision and hearing. Yet the sea urchin has no eyes and ears, at least as we know them. Some of the visual sensory proteins are localized within an appendage known as the tube foot, and likely function in sensory processes there. It is remarkable that the same sensory proteins are used in organs with such different structures in sea urchins and humans. "The sea urchin reminds us of the underlying unity of all life on earth," notes Sodergren. "It is a similar set of genes and proteins being reused in different ways, different numbers, and at different times in the life cycle to create the diversity of living forms." The sea-urchin genome was one of the most challenging to sequence to date at Baylor. The genome is highly polymorphic, meaning that the two copies of the genome in the diploid organism vary from each other by about 4 percent, or one difference in spelling every 25 letters. This posed a formidable challenge in assembling the nine million separate short sequences produced by DNA sequencing. A new approach was used, emphasizing the use of BAC clones as a framework. Each BAC clone represents only one version of the genome spelling, and thus provides a consistent sequence on which to build the genome. To sequence the 8,000 BAC clones covering the genome, another new technique was used. The process, CAPSS (clone-array pooled shotgun sequencing), sequences mixtures of BAC clones, rather than individual ones, and then assigns portions of the mixture of sequences to the proper clone. This reduces the cost and time to do the genome by an order of magnitude. The sea-urchin project was thus a test bed for innovations in whole genome sequencing. The sea-urchin project is one of more than 20 projects involving animal genomes that Baylor's Human Genome Sequencing Center has undertaken, including the human genome and those of primates like the rhesus monkey, other mammals like the cow and wallaby, insects such as the honey bee, beetle, and wasp, and most recently the dolphin. In addition, numerous microbes have been sequenced, with a focus on infectious diseases. Other projects include studying the genetic basis of human disease, and this will be the major emphasis of future work.

Robert Tindol