From Pre-Gut Cells to Glory

Caltech researchers discover a genomic control system that regulates gut formation in sea-urchin embryos

PASADENA, Calif.—For all animals, development begins with the embryo. It is here that uniform cells divide and diversify, and blueprints are laid for future structures, like skeletal and digestive systems. Although biologists have known for some time that signaling processes—messages that tell a cell to express certain genes so as to become certain parts of these structures—exist at this stage, there has not been a clear framework explanation of how it all comes together.

Now, a research team at the California Institute of Technology (Caltech) has outlined exactly how specific sets of cells in sea-urchin embryos differentiate to become the endoderm, the early domain of the embryo that eventually forms the gut. Their findings were reported in a paper entitled "A gene regulatory network controlling the embryonic specification of endoderm," published by the journal Nature online on May 29, in advance of the print version.

"If you only look at the genetic information of cells in an embryo, they all have the same genome and they all start from the single-cell zygote," says Isabelle S. Peter, a senior postdoctoral scholar at Caltech and coauthor of the study. "But then cells start to divide and, at some point, these cells are no longer identical in the genes that they express. We wanted to know how this process is achieved—how differences are established in cells in the right place and at the right time."

In order for undifferentiated cells to change their state and become a specific part of the body, the right genes need to be expressed, and the wrong ones repressed. The most important genes are regulatory genes, which control the expression of other genes, and form a gene regulatory network (GRN) that doles out differentiation instructions by turning genes on or off at specific times during embryonic development.

In the work described in the Nature paper, Peter and Eric H. Davidson, the Norman Chandler Professor of Cell Biology at Caltech and the other coauthor on the study, were able to analyze systematically the specification process controlled by the GRN and map out a master plan that, for the first time, shows the relationships between all the regulatory genes in specific parts of the embryo.

They studied sea-urchin embryos over a 24-hour period, beginning at hour eight of the embryo's existence. During this period, different physical domains exist in the embryo, each of which represents a future structure in the body, like the gut. All the regulatory genes known to exist in the sea-urchin genome and to be expressed in the embryo have been studied, and it was found that certain regulatory genes are expressed in the cells of each domain. Some of the domains will express certain regulatory genes in common, but the combination of genes found in each domain is unique. In addition, they found that this process is dynamic—where the genes are expressed changes over time. For example, two genes that are coexpressed in one domain at an early stage of the process may then be expressed in different domains at a later stage.

"It's like you are building a complicated edifice," explains Davidson. "And before anything is actually there, the building instructions have already been handed to all the workers. They all know what they are going to have to do once the bulldozer comes in and starts moving earth around."

The team focused on pinning down the precise regulatory genes in the progression of pre-gut cells (which eventually form the gut), following them from their initial stage as undifferentiated cells, to the point of gastrulation. During gastrulation the endoderm cells reorganize from a single layer into an internal tube with three regions that serve as the foundation for the future foregut, midgut, and hindgut structures. The researchers were able to pinpoint which regulatory genes were expressed at which specific times in the 24-hour period, and how those genes interacted over time to turn each other on and off.

"The instructions for development have to be in the genome somewhere, but you would be surprised how fragmentary the information about how that works was until we did this system-level analysis," says Davidson. "You can never understand it by looking at one gene. You can never understand it by looking at a third of the genes. You really have to get the whole system mapped out—and that's what we did."

In 2008, Davidson—who has been studying the biological processes of sea urchins for many years—led a research team that sketched a rough outline, for the first time, of how the GRN works to produce the sea urchin's skeletal system. "We are light-years beyond that with this new study," he says. "That was about solving network subcircuits, but now we have a framework that causally explains the far more complex process of development required for gut formation in terms of the genome's regulatory instruction code." This advance opens a much larger range of developmental scenarios to causal network analysis.

Sea urchins' gene regulatory systems, Davidson points out, are the closest—among the thoroughly studied invertebrate systems—to those of mammals, in terms of evolutionary relationships. This means the mechanisms the team uncovered in their work are likely to illuminate our own developmental regulatory systems. This could have implications for human health.

"If you believe that medicine consists of putting Band-Aids on things, then we have no relevance to that," says Davidson. "But if you believe that we should understand how life works before trying to find a cure when something goes wrong, then understanding biological processes from their initial stages comes first."

The team would next like to take their framework analysis and apply it to later stages in development—to when the gut is actually present. "We would like to understand how the different compartments in the gut are established, which would also make the work more directly informative to the development of the human gut," says Peter.

They would also like to extend the analysis to as much of the sea-urchin embryo as they can, says Davidson, as well as to formalize their findings to make an abstract computer model of how the gene regulatory system works. This will allow them to validate this particular network and to eventually do experiments that involve manipulating the cells to produce different results.

"Basically everything that happens in us, or in any animal during development, is encoded in genomic regulatory instructions," says Davidson. "Now we have an explanation as to how that works, which is very exciting. We can only move forward from here."

The work was funded by the Swiss National Science Foundation and the National Institutes of Health.

Writer: 
Katie Neith
Writer: 

Learning to Tolerate Our Microbial Self

PASADENA, Calif.—The human gut is filled with 100 trillion symbiotic bacteria—ten times more microbial cells than our own cells—representing close to one thousand different species. "And yet, if you were to eat a piece of chicken with just a few Salmonella, your immune system would mount a potent inflammatory response," says Sarkis K. Mazmanian, assistant professor of biology at the California Institute of Technology (Caltech).

Salmonella and its pathogenic bacterial kin don't look that much different from the legion of bacteria in our gut that we blissfully ignore, which raises the question: What decides whether we react or don't? Researchers have pondered this paradox for decades.

In the case of a common "friendly" gut bacterium, Bacteroides fragilis, Mazmanian and his colleagues have figured out the surprising answer: "The decision is not made by us," he says. "It's made by the bacteria. Since we are their home, they hold the key to our immune system."

What's more, the bacteria enforce their "decision" by hijacking cells of the immune system, say Mazmanian and his colleagues, who have figured out the mechanism by which the bacteria accomplish this feat—and revealed an explanation for how the immune system distinguishes between beneficial and pathogenic organisms.

In addition, the work, described in the April 21 issue of Science Express, "suggests that it's time to reconsider how we define self versus non-self," Mazmanian says.

Like other commensal gut bacteria—those that provide nutrients and other benefits to their hosts, without causing harm—B. fragilis was thought to live within the interior of the gut (the lumen), and thus far away from the immune system. "The dogma is that the immune system doesn't respond to symbiotic bacteria because of immunological ignorance," Mazmanian explains. "If we can't see them, we won't react to them."

But using a technique called whole-mount confocal microscopy to study the intestines of mice, he and his colleagues found that the bacteria actually live in a unique ecological niche, deep within the crypts of the colon, "and thus in intimate contact with the gut mucosal immune system," he says.

"The closeness of this association highlights that an active communication is occurring between the bacteria and their host," says Caltech postdoctoral scholar June L. Round.

From that vantage point, the bacteria are able to orchestrate control over the immune system—and, specifically, over the behavior of immune cells known as regulatory T cells, or Treg cells. The normal function of Treg cells is to prevent the immune system from reacting against our own tissues, by shutting down certain immune responses; they therefore prevent autoimmune reactions (which, when uncontrolled, can lead to diseases such as multiple sclerosis, type 1 diabetes, lupus, psoriasis, and Crohn's disease).

Bacteroides fragilis has evolved to produce a molecule that tricks the immune system into activating Treg cells in the gut, but in this case, Mazmanian says, "the purpose is to keep the cells from attacking the bugs. Beautiful, right?"

In their Science paper, Mazmanian and colleagues describe the entire molecular pathway that produces this effect. It starts with the bacteria producing a complex sugar molecule called polysaccharide A (PSA). PSA is sensed by particular receptors, known as Toll-like receptors, on the surfaces of Treg cells, thus activating those cells specifically. In response, Treg cells suppress yet another type of cell, the T helper 17 (Th17) cells. Normally, Th17 cells induce pro-inflammatory responses—those that would result, for example, in the elimination of foreign bacteria or other pathogens from the body. By shutting those cells down, B. fragilis gets a free pass to colonize the gut. "Up until now, we have thought that triggering of Toll-like receptors resulted solely in the induction of pathways that eliminate bacteria," says Round. "However, our studies suggest that multiple yet undiscovered host pathways allow us to coexist with our microbial partners."

When Mazmanian and his colleagues blocked this mechanism—by removing the PSA molecule, by removing the Toll-like receptor for PSA, or by eliminating the Treg cells themselves—the bacteria were attacked by the immune system and expelled. "They can no longer co-opt the immune system into inducing an anti-inflammatory response, so the formerly benign bacterium now looks like a pathogen," he says, "although the bug itself is exactly the same."

"Our immune system arose in the face of commensal colonization and thus likely evolved specialized molecules to recognize good bacteria," says Round. Mazmanian suspects that genetic mutations in these pathways could be responsible for certain types of immune disorders, including inflammatory bowel disease: "The question is, do patients get sick because they are rejecting bacteria they shouldn't reject?"

On a more philosophical level, Mazmanian says, the findings suggest that our concept of "self" should be broadened to include our many trillions of microbial residents. "These bacteria live inside us for our entire lives, and they've evolved to look and act like us, as part of us," he says. "As far as our immune system is concerned, the molecules made by gut bacteria should be tolerated similarly to our own molecules. Except in this case, the bacteria 'teaches' us to tolerate them, for both our benefit and theirs."

The other coauthors on the paper, "The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota," are S. Melanie Lee, Jennifer Li, and Gloria Tran of Caltech; Bana Jabri of the University of Chicago; and Talal A. Chatila of the David Geffen School of Medicine at UCLA. June L. Round was supported by a Jane Coffin Childs Memorial Fund postdoctoral fellowship. The work was supported by the National Institutes of Health, the Damon Runyon Cancer Research Foundation, and the Crohn's and Colitis Foundation of America.

Writer: 
Kathy Svitil
Writer: 

Caltech Biologist Recognized for Cellular Noise Research

Nearly ten years ago, Michael Elowitz, Caltech Bren Scholar and professor of biology, bioengineering, and applied physics, first amplified the idea that stochasticity—or noise—plays an important role in the process of gene expression. Prior to his work, such cellular noise was treated as a mysterious property.

For his pioneering work on gene expression noise, Elowitz has been named the winner of the 2011 Human Frontier Science Program (HFSP) Nakasone Award. The HFSP is a program that funds frontier research in the life sciences and the award is for breakthrough contributions at the frontier of the life sciences, either conceptual or methodological, that have had a major impact on basic biological research.

Elowitz's work introduced conceptual and experimental tools to detect gene expression noise, to quantify its level, and to evaluate its effect on cellular function. Genetic noise is now considered a core aspect of biology–one that functions actively in diverse cellular functions, including differentiation, regulation, and evolution.

Because of Elowitz's findings, noise has gone from being considered a curiosity of cellular life to being recognized as a key process whose effects must be considered in almost any analysis of biological systems. Stochastic processes are thought to enable stem cell differentiation and reprogramming, and developmental cell fates are controlled by noise. Thanks to Elowitz's work, noise is now recognized as an essential and functional element that distinguishes and enables the core cellular behaviors of life. 

Elowitz will give the HFSP Nakasone Lecture at the annual meeting of HFSP awardees to be held in Montreal, Canada in June

Writer: 
Katie Neith
Writer: 
Exclude from News Hub: 
Yes

Pamela Bjorkman Named Among Most Powerful Moms

When Working Mother magazine recently compiled its list of the Most Powerful Moms in STEM (Science, Technology, Engineering, and Math), it included Caltech's Pamela Bjorkman—a pioneer in the study of cell-surface recognition in the immune system, and a mother of two—among its 10 honorees.

"I'm honored to be included among the very accomplished other women in this list," says Bjorkman, who is Caltech's Max Delbruck Professor of Biology and a Howard Hughes Medical Institute investigator.

"I think it's great to publicize that women can combine a career in science with having children. The more we can communicate this message to young women, the more likely we will be to keep women in the pipeline for STEM careers."

Working Mother says that the women on its list—which also includes Xerox Chairman and CEO Ursula Burns and Padmasree Warrior, Cisco's Chief Technology Officer—are all "shattering the illusion that women can't succeed in STEM fields."

"For all of the bunk that women aren't interested in careers in math or science," writes Leah Bourne in the magazine's introduction to the profiles of its selectees, "the numbers of women entering STEM careers has been quietly growing."

In its profile of Bjorkman, the magazine points to her "many awards," including election to the National Academy of Sciences in 2001, the L'Oreal-UNESCO Women in Science North American Laureate for her discovery of how the immune system recognizes targets in 2006 and a National Institute of Health Director's Pioneer Award in 2010. 

Despite her feeling of pride at being recognized by the magazine—"I can't wait to tell my kids that I'm one of the most powerful moms," she laughed when told of her inclusion on the list—Bjorkman says there is still a way to go in terms of women's parity in such traditionally male-dominated fields.

Working Mother agrees, noting that US Bureau of Labor Statistics show women hold only 14 percent of engineering positions, and a quarter of mathematics positions.

"Women are not so much deliberately excluded as they are not thought about," Bjorkman told the magazine. "It's human nature for people to have friends like themselves, and when a question comes up of who to invite to a meeting or who should give a talk, you tend to think of your friends. If all your friends are white males, then you'll tend to invite a white male. It's the same thing for minorities in science. It's this vicious circle. It's almost impossible to create a normal atmosphere for women in science when they are in such low numbers."

Writer: 
Lori Oliwenstein
Images: 
Tags: 
Writer: 
Exclude from News Hub: 
No
News Type: 
In Our Community

Caltech-Led Team Pinpoints Aggression Neurons in the Brain

Finding could lead to new treatments for impulsive violence

PASADENA, Calif.—Where does violence live in the brain? And where, precisely, does it lay down its biological roots? With the help of a new genetic tool that uses light to turn nerve cells on and off, a team led by researchers at the California Institute of Technology (Caltech) has tracked down the specific location of the neurons that elicit attack behaviors in mice, and defined the relationship of those cells to the brain circuits that play a key role in mating behaviors.

The researchers’ hope is that these insights might lead to treatments that can specifically address impulsive violence, a category of behavior that has been historically difficult to grapple with from a medical or psychological perspective.

In a study published in this week's issue of the journal Nature, the researchers were not only able to localize the neuronal circuits mediating attack behavior in mice, but were able to determine that these circuits are "intimately associated, deeply intertwined," with another basic social-behavioral drive—mating—according to David J. Anderson, the Benzer Professor of Biology at Caltech and a Howard Hughes Medical Institute investigator.

Indeed, the neurons for violence and mating live so close together, in a brain region known as the ventrolateral subdivision of the ventromedial hypothalamus (VMH), that "they are like a salt-and-pepper mixture," says Anderson.

And if you think of the brain as the world and the hypothalamus as a country, he adds, then the ventromedial hypothalamus is like a state and the ventrolateral subdivision is like a city within that state. "We've found that these 'mating' and 'fighting' neurons are not only located in the same city, but potentially in the same neighborhood," he says.

To determine whether aggression and mating involve the same—or, rather, distinct but intermingled—neurons, Dayu Lin, a former postdoctoral fellow in Anderson's lab and now an assistant professor at New York University, carried out a series of challenging electrophysiological recording experiments in the VMH. Because the VMH is located deep within the brain, it is exceedingly difficult to target accurately. But by inserting a bundle of 16 wire electrodes into this region, Lin was able to get recordings from multiple neurons during repeated episodes of fighting or mating. "It's the first time in which it's been possible to record electrical activity from deep-brain hypothalamic structures in animals while they are engaging in aggressive and mating behaviors," says Anderson.

Using software developed by Allen E. Puckett Professor of Electrical Engineering Pietro Perona and senior postdoctoral scholar Piotr Dollar—and with the help of several Caltech undergraduates—the researchers annotated behavioral changes on a frame-by-frame basis from video taken at the same time as the electrical recordings were performed. This annotation allowed them to make correlations between neuronal activity and behavior with a temporal resolution of approximately 30 milliseconds.

These experiments indicated that while there is some overlap between "mating" neurons and "fighting" neurons, the majority of these cells are distinct, despite their close proximity. Perhaps most surprising, Anderson notes, is the way that the neurons responsible for aggression and mating communicate—or, rather, how they shut each other up. Sex and violence, it seems, are actually at odds: a neuron that is turned on during aggressive behavior will turn off during mating, and vice versa. "We found that they talk to each other in an inhibitory way," he says.

But a correlation between neuronal activity and fighting behavior doesn't indicate whether the activity causes the behavior or the behavior causes the activity. And so Lin, Anderson, and colleagues carried out experiments to activate or inhibit VMH neurons, to distinguish between those alternatives and to determine the effect of such manipulations on behavior.

In order to activate neurons in the VMH, they used a technique known as optogenetic stimulation. Using a disabled virus as a kind of "disposable molecular syringe," Lin injected VMH neurons with DNA that carries the code for channelrhodopsin-2, a protein from blue-green algae that increases neuronal activity in response to blue light. The sensitized neurons could then be turned on or off with the literal flip of a light switch, allowing the scientists to watch what happens to the behavior of an individual mouse.

Remarkably, says Anderson, for mice in which the injection was targeted to the correct location, blue light induced an attack—even toward an inanimate object such as an inflated latex glove. Conversely, using a technique developed by Caltech’s Bren Professor of Biology Henry A. Lester that allowed the scientists to genetically inhibit neuronal activity, Lin and colleagues were able to show that neuronal activity in the VMH was necessary for normal aggressive behavior, as well.

"This answers an important, long-standing question in the field," says Anderson. "Are regions of the brain that can evoke aggression when artificially stimulated actually necessary for normal aggressive behavior? In this case, the answer is clearly 'yes.'"

The researchers also found that stimulating a male to be aggressive toward a female became more difficult as a mating encounter progressed to its consummatory phase. This result was consistent with the observation that neurons activated during fighting appear to become inhibited in the presence of a female. "The question," says Anderson, "is how that inhibition is achieved."

The answer may lead to new areas of research—and, perhaps, to new treatments for impulsive, violent behaviors. Specifically, notes Anderson, scientists can begin thinking about treatments that target violence-begetting neurons while sparing those involved in normal sexual behavior.

"For the last 500 years, we've really had no viable treatments for pathological violence other than execution or imprisonment," says Anderson. "And part of the reason is that we haven't understood enough about the basic neurobiology of aggression. The new studies are an important step in that direction."

In addition, he says, "mapping out the brain circuitry of aggression will provide a framework for understanding where and how in the brain genetic and environmental influences—nature vs. nurture—exert their influences on aggressive behavior."

The other authors on the Nature paper, "Functional identification of an aggression locus in the mouse hypothalamus," in addition to Anderson, Lin, Dollar, and Perona, are Caltech postdoctoral scholar Hyosang Lee and Maureen Boyle and Ed Lein from the Allen Institute for Brain Science in Seattle.

Their work was funded by the Weston-Havens Foundation, the Jane Coffin Childs Foundation, and the Howard Hughes Medical Institute.

 

Writer: 
Lori Oliwenstein
Writer: 

Neurobiologists Find that Weak Electrical Fields in the Brain Help Neurons Fire Together

Coordinated behavior occurs whether or not neurons are actually connected via synapses

Pasadena, Calif.—The brain—awake and sleeping—is awash in electrical activity, and not just from the individual pings of single neurons communicating with each other. In fact, the brain is enveloped in countless overlapping electric fields, generated by the neural circuits of scores of communicating neurons. The fields were once thought to be an "epiphenomenon" similar to the sound the heart makes—which is useful to the cardiologist diagnosing a faulty heart beat, but doesn't serve any purpose to the body, says Christof Koch, the Lois and Victor Troendle Professor of Cognitive and Behavioral Biology and professor of computation and neural systems at the California Institute of Technology (Caltech).

New work by Koch and neuroscientist Costas Anastassiou, a postdoctoral scholar in biology, and his colleagues, however, suggests that the fields do much more—and that they may, in fact, represent an additional form of neural communication.

"In other words," says Anastassiou, the lead author of a paper about the work appearing in the journal Nature Neuroscience, "while active neurons give rise to extracellular fields, the same fields feed back to the neurons and alter their behavior," even though the neurons are not physically connected—a phenomenon known as ephaptic (or field) coupling. "So far, neural communication has been thought to occur almost entirely via traffic involving synapses, the junctions where one neuron connects to the next one. Our work suggests an additional means of neural communication through the extracellular space independent of synapses."

Extracellular electric fields exist throughout the living brain. Their distant echoes can be measured outside the skull as EEG waves. These fields are particularly strong and robustly repetitive in specific brain regions such as the hippocampus, which is involved in memory formation, and the neocortex, the area where long-term memories are held. "The perpetual fluctuations of these extracellular fields are the hallmark of the living and behaving brain in all organisms, and their absence is a strong indicator of a deeply comatose, or even dead, brain," Anastassiou explains.

Previously, neurobiologists assumed that the fields were capable of affecting—and even controlling—neural activity only during severe pathological conditions such as epileptic seizures, which induce very strong fields. Few studies, however, had actually assessed the impact of far weaker—but very common—non-epileptic fields. "The reason is simple," Anastassiou says. "It is very hard to conduct an in vivo experiment in the absence of extracellular fields," to observe what changes when the fields are not around.

To tease out those effects, Anastassiou and his colleagues focused on strong but slowly oscillating fields, called local field potentials (LFP), that arise from neural circuits composed of just a few rat brain cells. Measuring those fields and their effects required positioning a cluster of tiny electrodes within a volume equivalent to that of a single cell body—and at distances of less than 50 millionths of a meter from one another; this is approximately the width of a human hair.

"Because it had been so hard to position that many electrodes within such a small volume of brain tissue, the findings of our research are truly novel," Anastassiou says. Previously, he explains, "nobody had been able to attain this level of spatial and temporal resolution."

An "unexpected and surprising finding was how already very weak extracellular fields can alter neural activity," he says. "For example, we observed that fields as weak as one volt per meter robustly alter the spiking activity [firing] of individual neurons, and increase the so-called 'spike-field coherence'"—the synchronicity with which neurons fire. "Inside the mammalian brain, we know that extracellular fields may easily exceed two to three volts per meter. Our findings suggest that under such conditions, this effect becomes significant."

What does that mean for brain computation? At this point we can only speculate, Koch says, "but such field effects increase the synchrony with which neurons become active together. This, by itself, enhances the ability of these neurons to influence their target and is probably an important communication and computation strategy used by the brain."

Can external electric fields have similar effects on the brain? "This is an interesting question," Anastassiou says. "Indeed, physics dictates that any external field will impact the neural membrane. Importantly, though, the effect of externally imposed fields will also depend on the brain state. One could think of the brain as a distributed computer—not all brain areas show the same level of activation at all times.

"Whether an externally imposed field will impact the brain also depends on which brain area is targeted," he says. "During epileptic seizures, the hypersynchronized activity of neurons can generate field as strong as 100 volts per meter, and such fields have been shown to strongly entrain neural firing and give rise to super-synchronized states." And that suggests that electric field activity—even from external fields—in certain brain areas, during specific brain states, may have strong cognitive and behavioral effects.

Ultimately, Anastassiou, Koch, and their colleagues would like to test whether ephaptic coupling affects human cognitive processing, and under which circumstances. "I firmly believe that understanding the origin and functionality of endogenous brain fields will lead to several revelations regarding information processing at the circuit level, which, in my opinion, is the level at which percepts and concepts arise," Anastassiou says. "This, in turn, will lead us to address how biophysics gives rise to cognition in a mechanistic manner—and that, I think, is the holy grail of neuroscience."

The work in the paper, "Ephaptic coupling of cortical neurons," published January 16 in the advance online edition of the journal, was supported by the Engineering Physical Sciences Research Council, the Sloan-Swartz Foundation, the Swiss National Science Foundation, EU Synapse, the National Science Foundation, the Mathers Foundation, and the National Research Foundation of Korea.

Writer: 
Kathy Svitil
Writer: 

Why Do We Sleep?

While we can more or less abstain from some basic biological urges—for food, drink, and sex—we can’t do the same for sleep. At some point, no matter how much espresso we drink, we just crash. And every animal that’s been studied, from the fruit fly to the frog, also exhibits some sort of sleep-like behavior. (Paul Sternberg, Morgan Professor of Biology, was one of the first to show that even a millimeter-long worm called a nematode falls into some sort of somnolent state.) But why do we—and the rest of the animal kingdom—sleep in the first place?

“We spend so much of our time sleeping that it must be doing something important,” says David Prober, assistant professor of biology and an expert on how genes and neurons regulate sleep. Yes, we snooze in order to rest and recuperate, but what that means at the molecular, genetic, or even cellular level remains a mystery. “Saying that we sleep because we’re tired is like saying we eat because we’re hungry,” Prober says. “That doesn’t explain why it’s better to eat some foods rather than others and what those different kinds of foods do for us.”

No one knows exactly why we slumber, Prober says, but there are four main hypotheses. The first is that sleeping allows the body to repair cells damaged by metabolic byproducts called free radicals. The production of these highly reactive substances increases during the day, when metabolism is faster. Indeed, scientists have found that the expression of genes involved in fixing cells gets kicked up a notch during sleep. This hypothesis is consistent with the fact that smaller animals, which tend to have higher metabolic rates (and therefore produce more free radicals), tend to sleep more. For example, some mice sleep for 20 hours a day, while giraffes and elephants only need two- to three-hour power naps.

Another idea is that sleep helps replenish fuel, which is burned while awake. One possible fuel is ATP, the all-purpose energy-carrying molecule, which creates an end product called adenosine when burned. So when ATP is low, adenosine is high, which tells the body that it’s time to sleep. While a postdoc at Harvard, Prober helped lead some experiments in which zebrafish were given drugs that prevented adenosine from latching onto receptor molecules, causing the fish to sleep less. But when given drugs with the opposite effect, they slept more. He has since expanded on these studies at Caltech.

Sleep might also be a time for your brain to do a little housekeeping. As you learn and absorb information throughout the day, you’re constantly generating new synapses, the junctions between neurons through which brain signals travel. But your skull has limited space, so bedtime might be when superfluous synapses are cleaned out.

And finally, during your daily slumber, your brain might be replaying the events of the day, reinforcing memory and learning. Thanos Siapas, associate professor of computation and neural systems, is one of several scientists who have done experiments that suggest this explanation for sleep. He and his colleagues looked at the brain activity of rats while the rodents ran through a maze and then again while they slept. The patterns were similar, suggesting the rats were reliving their day while asleep.

Of course, the real reason for sleep could be any combination of these four ideas, Prober says. Or perhaps only one of these hypotheses might have been true in the evolutionary past, but as organisms evolved, they developed additional uses for sleep.

Researchers in Prober’s lab look for the genetic and neural systems that affect zebrafish sleeping patterns by tweaking their genes and watching them doze off. An overhead camera records hundreds of tiny zebrafish larvae as they swim in an array of shallow square dishes. A computer automatically determines whether the fish are awake or not based on whether they’re moving or still, and whether they respond to various stimuli. Prober has identified about 500 drugs that affect their sleeping patterns, and now his lab is searching for the relevant genetic pathways. By studying the fish, the researchers hope to better understand sleep in more complex organisms like humans. “Even if we find only a few new genes, that’ll really open up the field,” he says. The future is promising, he adds, and for that, it’ll be well worth staying awake. 

Writer: 
Marcus Woo
Writer: 

David Anderson, Christof Koch Named Allen Distinguished Investigators

Two Caltech researchers have been named by the Paul G. Allen Family Foundation among the inaugural group of Allen Distinguished Investigators.

Caltech's David Anderson and Christof Koch are two of the seven investigators who were honored by the foundation as it launched a new program to advance important research in neuroscience and cellular engineering.

"A year ago, I started searching for programs with potential for major breakthroughs but which had struggled to find funding through traditional sources," says Paul G. Allen. "The inaugural Distinguished Investigators are working on some of the most exciting research in biology and neurology and I'm proud to be able to help keep that work going."

David Anderson, the Benzer Professor of Biology at Caltech and a Howard Hughes Medical Institute investigator, was granted $1.6 million over three years for a project designed to localize, identify, characterize, and turn on neurons in the hypothalamus associated with attack, and bring the study of aggression into the modern molecular era.

More specifically, Anderson's project will use powerful genetic tools to try to identify specific classes of neurons that control emotional behaviors. Identifying such neurons will greatly facilitate the study of how they are wired into the brain's circuitry, and how this circuitry is affected by genetic and environmental factors that influence emotional behavior. Such studies could potentially lead to the development of new treatments for emotional disorders.

Christof Koch, the Lois and Victor Troendle Professor of Cognitive and Behavioral Biology and professor of computation and neural systems at Caltech, will use his three-year, $600,000 award for a project entitled "Evaluating Connectomes Using Measures of Complexity and Synergy." A connectome is the complete set of connections among all processing elements of a particular nervous system. Koch's group will specifically analyze the locomotion network in the roundworm, Caenorhabditis elegans, with an eye toward assessing the information flow in the neural network that leads to a clearly measurable behavior.

Overall, Koch's group seeks to characterize the complexity of the connectome and its ability to integrate information using a combination of analysis and computation. The team proposes that integrated information—a measure that uses variables such as conditional entropy from information theory—is a critical property of nervous systems, and believes that evolution by natural selection gives rise to a systematic increase in the integrated information of brains. Koch and his colleagues propose to demonstrate this for both simulated artificial networks that evolve and/or learn as well as for extant neurobiological networks, such as the known locomotion network of C. elegans.

"One of the Foundation's goals is to support projects that create new knowledge about ourselves and our universe," says Susan M. Coliton, vice president of the Paul G. Allen Family Foundation. "Making investments in early stage, cutting-edge research leverages both our funding and the intellectual capital of talented scientists. We couldn't be more thrilled about the potential of this inaugural group of Allen Distinguished Investigators."

Writer: 
Lori Oliwenstein
Writer: 
Exclude from News Hub: 
No
News Type: 
In Our Community

Caltech Scientists Describe the Delicate Balance in the Brain that Controls Fear

Two different neural subtypes act like a seesaw to control the level of fear output from the brain's amygdala

PASADENA, Calif.—The eerie music in the movie theater swells; the roller coaster crests and begins its descent; something goes bump in the night. Suddenly, you're scared: your heart thumps, your stomach clenches, your throat tightens, your muscles freeze you in place. But fear doesn't come from your heart, your stomach, your throat, or your muscles. Fear begins in your brain, and it is there—specifically in an almond-shaped structure called the amygdala—that it is controlled, processed, and let out of the gate to kick off the rest of the fear response.

In this week's issue of the journal Nature, a research team led by scientists at the California Institute of Technology (Caltech) has taken an important step toward understanding just how this kickoff occurs by beginning to dissect the neural circuitry of fear. In their paper, these scientists—led by David J. Anderson, the Benzer Professor of Biology at Caltech and a Howard Hughes Medical Institute investigator—describe a microcircuit in the amygdala that controls, or "gates," the outflow of fear from that region of the brain.

The microcircuit in question, Anderson explains, contains two subtypes of neurons that are antagonistic—have opposing functions—and that control the level of fear output from the amygdala by acting like a seesaw.

"Imagine that one end of a seesaw is weighted and normally sits on a garden hose, preventing water—in this analogy, the fear impulse—from flowing through it," says Anderson. "When a signal that triggers a fear response arrives, it presses down on the opposite end of the seesaw, lifting the first end off the hose and allowing fear, like water, to flow." Once the flow of fear has begun, that impulse can be transmitted to other regions of the brain that control fearful behavior, such as freezing in place.

"Now that we know about this 'seesaw' mechanism," he adds, "it may someday provide a new target for developing more specific drugs for treating fear-based psychiatric illnesses like post-traumatic stress disorder, phobias, or anxiety disorders."

The key to understanding this delicate mechanism, Anderson says, was in uncovering "markers"—genes that would identify and allow for the scientists to discriminate between the different neuronal cell types in the amygdala. Anderson's group, led by postdoctoral fellow Wulf Haubensak, found its marker in a gene that encodes an enzyme known as protein kinase C-delta (PKCδ). PKCδ is expressed in about half the neurons within a subdivision of the amygdala's central nucleus, the part of the amygdala that controls fear output. 

Along with fellow postdocs Prabhat Kunwar and Haijiang Cai, Haubensak was able to fluorescently tag neurons in which the protein kinase is expressed; this allowed the researchers to map the connections of these neurons, as well as to monitor and manipulate their electrical activity. 

The studies, Anderson says, "revealed that PKCδ+ neurons form one end of a seesaw, by making connections with another population of neurons in the central nucleus that do not express the enzyme, which are called PKCδ- neurons." They also showed that the kinase-positive neurons inhibit outflow from the amygdala—proving that they act as the end of the seesaw that rests on the garden hose.

Still, a key question remained: What happens to the seesaw during exposure to a fear-eliciting signal? Anderson and his colleagues hypothesized that the fear signal would push down on the opposite end of the seesaw from the one formed by the PKCδ+ neurons, removing the crimp from the garden hose and allowing the fear signal to flow. But how to test this idea?

Enter neurophysiologist Andreas Lüthi and his student Stephane Ciocchi, from the Friedrich Miescher Institute in Basel, Switzerland. In work done independently from that of the Anderson lab, Lüthi and Ciocchi had managed to record electrical signals from the amygdala during exposure to fear-inducing stimuli. Interestingly, they had found two types of neurons that responded in opposite ways to the fear-inducing stimulus: one type increased its activity, while the other type decreased its activity. Like Anderson, they had begun to think that these neurons formed a seesaw that controls fear output from the amygdala.

And so the two teams joined forces to determine whether the cells Lüthi had been studying corresponded to the PKCδ+ and PKCδ- cells Anderson's lab had isolated. In what Anderson refers to as a "sophisticated experiment," the two teams performed electrophysiological recordings while simultaneously turning the PKCδ+ neurons on or off using a genetic method developed by Henry Lester, Caltech's Bren Professor of Biology.

The results of the experiment were "gratifyingly clear," says Anderson. The cells that decreased their activity in the face of fear-inducing stimuli clearly corresponded to the PKCδ+ neurons Anderson's lab had isolated, while those that increased their activity corresponded to the PKCδ-  neurons.

"These results supported the hypothesis that PKCδ+ neurons were indeed at the opposite end of the seesaw from the one that the fear signal 'presses down' on, consistent with the finding that PKCδ+ neurons crimp the 'fear hose,'" says Anderson.

The marriage of molecular biology and electrophysiology created by the collaboration between Anderson's and Lüthi's laboratories has revealed properties of the fear circuit that could not have been discovered in any other way, Anderson says. "The functional geography of the brain is organized like that of the world," he notes. "It's divided into continents, countries, states, towns and cities, neighborhoods and houses; the houses are analogous to the different types of neurons. Previously, it had only been possible to dissect the amygdala at the level of different towns, or of neighborhoods at best. Now, using these new genetic techniques, we are finally down to the level of the houses."

And that, he adds, is what will make it possible for us to fully understand the networks of communication that exist between neurons within a subdivision of the brain, as well as between subdivisions and different areas. "While these studies shed light on only a small part of the picture, they are an important step in that direction," Anderson says.

In addition to those previously mentioned, the other authors of the Nature paper, "Genetic dissection of an amygdala microcircuit that gates conditioned fear," are Nicholas Wall and Edward Callaway from the Salk Institute for Biological Studies; Ravikumar Ponnusamy, Michael Fanselow, Jonathan Biag, and Hong-Wei Dong from the University of California, Los Angeles; and Karl Deisseroth from Stanford University. Their work was funded by grants from the National Institutes of Health, Caltech, the Novartis Research Foundation, and the Howard Hughes Medical Institute, and by fellowships from the Human Frontier Science Program and the Jane Coffin Childs Memorial Fund for Medical Research.

Writer: 
Lori Oliwenstein
Writer: 
Exclude from News Hub: 
No
News Type: 
Research News

Controlling Individual Cortical Nerve Cells by Human Thought

PASADENA, Calif.—Five years ago, neuroscientist Christof Koch of the California Institute of Technology (Caltech), neurosurgeon Itzhak Fried of UCLA, and their colleagues discovered that a single neuron in the human brain can function much like a sophisticated computer and recognize people, landmarks, and objects, suggesting that a consistent and explicit code may help transform complex visual representations into long-term and more abstract memories.

Now Koch and Fried, along with former Caltech graduate student and current postdoctoral fellow Moran Cerf, have found that individuals can exert conscious control over the firing of these single neurons—despite the neurons' location in an area of the brain previously thought inaccessible to conscious control—and, in doing so, manipulate the behavior of an image on a computer screen.

The work, which appears in a paper in the October 28 issue of the journal Nature, shows that "individuals can rapidly, consciously, and voluntarily control neurons deep inside their head," says Koch, the Lois and Victor Troendle Professor of Cognitive and Behavioral Biology and professor of computation and neural systems at Caltech.

The study was conducted on 12 epilepsy patients at the David Geffen School of Medicine at UCLA, where Fried directs the Epilepsy Surgery Program. All of the patients suffered from seizures that could not be controlled by medication. To help localize where their seizures were originating in preparation for possible later surgery, the patients were surgically implanted with electrodes deep within the centers of their brains. Cerf used these electrodes to record the activity, as indicated by spikes on a computer screen, of individual neurons in parts of the medial temporal lobe—a brain region that plays a major role in human memory and emotion.

Prior to recording the activity of the neurons, Cerf interviewed each of the patients to learn about their interests. "I wanted to see what they like—say, the band Guns N' Roses, the TV show House, and the Red Sox," he says. Using that information, he created for each patient a data set of around 100 images reflecting the things he or she cares about. The patients then viewed those images, one after another, as Cerf monitored their brain activity to look for the targeted firing of single neurons. "Of 100 pictures, maybe 10 will have a strong correlation to a neuron," he says. "Those images might represent cached memories—things the patient has recently seen."

The four most strongly responding neurons, representing four different images, were selected for further investigation. "The goal was to get patients to control things with their minds," Cerf says. By thinking about the individual images—a picture of Marilyn Monroe, for example—the patients triggered the activity of their corresponding neurons, which was translated first into the movement of a cursor on a computer screen. In this way, patients trained themselves to move that cursor up and down, or even play a computer game.

But, says Cerf, "we wanted to take it one step further than just brain–machine interfaces and tap into the competition for attention between thoughts that race through our mind."

To do that, the team arranged for a situation in which two concepts competed for dominance in the mind of the patient. "We had patients sit in front of a blank screen and asked them to think of one of the target images," Cerf explains. As they thought of the image, and the related neuron fired, "we made the image appear on the screen," he says. That image is the "target." Then one of the other three images is introduced, to serve as the "distractor."

"The patient starts with a 50/50 image, a hybrid, representing the 'marriage' of the two images," Cerf says, and then has to make the target image fade in—just using his or her mind—and the distractor fade out. During the tests, the patients came up with their own personal strategies for making the right images appear; some simply thought of the picture, while others repeated the name of the image out loud or focused their gaze on a particular aspect of the image. Regardless of their tactics, the subjects quickly got the hang of the task, and they were successful in around 70 percent of trials.

"The patients clearly found this task to be incredibly fun as they started to feel that they control things in the environment purely with their thought," says Cerf. "They were highly enthusiastic to try new things and see the boundaries of 'thoughts' that still allow them to activate things in the environment."

Notably, even in cases where the patients were on the verge of failure—with, say, the distractor image representing 90 percent of the composite picture, so that it was essentially all the patients saw—"they were able to pull it back," Cerf says. Imagine, for example, that the target image is Bill Clinton and the distractor George Bush. When the patient is "failing" the task, the George Bush image will dominate. "The patient will see George Bush, but they're supposed to be thinking about Bill Clinton. So they shut off Bush—somehow figuring out how to control the flow of that information in their brain—and make other information appear. The imagery in their brain," he says, "is stronger than the hybrid image on the screen."

According to Koch, what is most exciting "is the discovery that the part of the brain that stores the instruction 'think of Clinton' reaches into the medial temporal lobe and excites the set of neurons responding to Clinton, simultaneously suppressing the population of neurons representing Bush, while leaving the vast majority of cells representing other concepts or familiar person untouched."

The work in the paper, "On-line voluntary control of human temporal lobe neurons," is part of a decade-long collaboration between the Fried and Koch groups, funded by the National Institute of Neurological Disorders and Stroke, the National Institute of Mental Health, the G. Harold & Leila Y. Mathers Charitable Foundation, and Korea's World Class University program.

Writer: 
Kathy Svitil
Writer: 
Exclude from News Hub: 
No
News Type: 
Research News

Pages

Subscribe to RSS - BBE