Caltech Biologists Pursue Promising New Approach in Treatment of HIV/AIDS and Cancer

PASADENA, Calif.—In response to the arduously slow progress in finding cures for AIDS and cancer, Caltech researchers are now investigating a promising new approach in the treatment of these diseases.

With a $1.5 million matching grant from the Skirball Foundation in New York, Caltech biologists have established the Engineering Immunity project, designed to create a novel immunological approach to treating–and even some day preventing–HIV infection and some cancers like melanoma.

The immune system provides humans with a powerful defense against infectious diseases–but sometimes, it fails. Utilizing an innovative, integrated approach, the Engineering Immunity project will combine gene therapy, stem cell biology, and immunotherapy to arm the immune system; this integrative methodology offers groundbreaking potential for treatment of these diseases and others for which the immune system currently fails to provide defense.

Caltech President David Baltimore, who won the Nobel Prize in 1975 for his work in virology and cancer research, stated, "The Engineering Immunity project advocates a new approach to therapy for AIDS and cancer with revolutionary implications for the treatment of these and many other diseases. It is an innovative research project that holds special significance for the future of biomedical sciences."

In the fight against HIV, the virus that causes AIDS, T-cell immunity and T-cell-focused therapies and vaccines have been methods widely investigated and pursued. However, antibodies often provide the best protection against viruses, and virtually all vaccines for other viral diseases are designed to elicit antibody-based immunity. Antibodies against HIV do appear during HIV infections, but heretofore, they had not been able to provide therapeutic advantage to most patients. Rare neutralizing antibodies have been identified, but have not proven valuable because a general way to elicit their production in all patients has not been found. Moreover, most of them are effective only at very high concentrations that are hard to maintain in a person by conventional means. Thus, early attempts to elicit antibody-based immunity against HIV have largely failed.

The Engineering Immunity integrated methodology involves utilizing retroviruses, which are natural carriers of genes. Retrovirus vectors will be produced that encode antibodies found to be effective against HIV. Utilizing retroviruses, the Baltimore Laboratory at Caltech, in collaboration with Caltech structural biologist Pamela Bjorkman, will introduce specific genes into stem cells. These genes will encode specificity molecules on the immune cells, thereby arming the immune cells to kill selected agents or cells, i.e., the cells that are growing HIV or particular cancer cells.

The Engineering Immunity initiative will provide a new route to the production of antibodies with therapeutic, and even protective, ability for a potential cure of AIDS, melanoma, and other diseases ultimately.

The Skirball Foundation, an independent foundation created in 1950 by Jack H. Skirball, is dedicated primarily to medical research and care, educational and social needs of disadvantaged children, and advancing the highest values of the Jewish heritage. Among the many institutions that the Foundation has supported are the Skirball Cultural Center, the Salk Institute, the Venice Family Clinic, the Jewish Childcare Association in New York City, and the Skirball Institute of Biomolecular Medicine at New York University.


Contact: Deborah Williams-Hedges (626) 395-3227

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Memory Lane in the Brain

PASADENA, Calif.- Biologist Erin Schuman is interested in how memories are formed--or forgotten. The landscape the professor of biology at the California Institute of Technology explores is the hippocampus, the part of the brain known to be crucial for memory in humans and other animals.

In 2002, Schuman and Miguel Remondes, her graduate student, published a paper in the journal Nature that suggested a possible role for a well-known but poorly understood part of the brain known as the temporoammonic (TA) pathway. Using rat hippocampal slices, they suggested two possible roles for the TA pathway that were not previously known: to serve as a memory gatekeeper that can either enhance or diminish memories, and to provide information to help animals know where they are in their environments.

The researchers' next step was to prove their theories by looking at a possible role for the TA in memory at a behavioral level. That is, says Remondes, now a postdoctoral fellow at MIT, "to do the real test."

To understand how memories are formed, many scientists have focused on the "trisynaptic circuit," which involves three areas of the hippocampus: input from the senses is first sent from the cortex to the dentate gyrus, where this signal is processed by two sets of synapses, then sent back to the cortex. That's the circuit. An often overlooked separate input to the hippocampus, though, is the TA pathway. It makes direct contact with the neurons that are at the last station in the trisynaptic circuit, thus short-circuiting the traditional trisynaptic pathway.

Reporting in the October 7 issue of the journal Nature, Remondes and Schuman, also an associate investigator for the Howard Hughes Medical Institute, now show they were correct in their belief that the TA Pathway is important in spatial or location memory. The scientists used rats as their experimental animal, and the Morris Water Maze, a standard test for location memory in rodents. The animals swim in a pool of opaque water until they find a hidden goal--a platform which allows them to escape the water. To find the platform, the animals rely on the geometrical relationships of cues away from the pool (e.g., on the walls of the maze). In other words, says Remondes, "they have to navigate and remember where the platform is in order to escape the water."

The researchers tested both short-term (24 hours) and long-term memory (four weeks). The TA pathway was lesioned (disabled) in one set of rats; another set was used as a control. Having learned the location of the platform, both sets of rats still remembered where it was 24 hours later. But when tested four weeks later, only the control rats remembered where it was. The lesioned rats forgot, which showed that the TA pathway played some role in the retention of long-term memories. But what was the role?

"It led to a second question," says Schuman. "Because long-term memories require something called consolidation, an exchange of information between the cortex and hippocampus, we wanted to know if the TA pathway was working in the acquisition phase of memory or in its consolidation."

Using two other groups of rats, the pair conducted a second set of tests. After confirming the rat's memory of the platform after 24 hours, one group was immediately lesioned. These animals lost their long-term memory when tested 4 weeks later, indicating to Schuman and Remondes that ongoing TA pathway activity was required on days after learning to stabilize or consolidate the long-term memory.

The second group of rats was also lesioned, but not until three weeks later. The researchers found that this group remembered the platform's location, showing their memory had already been adequately consolidated after three weeks. This proved the TA pathway is required to consolidate long-term location memory.

"These data indicate there must be a dialogue between the hippocampus and the cortex during long-term memory consolidation," says Schuman. "Clearly, the TA pathway plays an important role in this discussion." Further, she notes, "understanding the mechanisms of memory formation and retention may shed light on diseases like Alzheimers, where memory is impaired. "

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New Target for Future Therapeutic Drugs

PASADENA, Calif. - "Sometimes letting nature tell you what's important is the better way to go," says Raymond Deshaies, an associate professor of biology at the California Institute of Technology. Deshaies is referring to new work to come out of his lab and the lab of Randall King at Harvard that defies conventional thinking--they've discovered a chemical that stops a key cell function, but, more importantly, suggests a new possible target within a cell, once thought to be untenable, for future therapeutic drugs.

In a report in this week's issue of the journal Science, lead author Rati Verma, a Howard Hughes Medical Institute (HHMI) Research Specialist in the Deshaies lab, Deshaies, also an assistant investigator for the HHMI, and nine other authors report that a small molecule called ubistatin blocked an important step in the so-called cell cycle, a process fundamental to life where a cell makes duplicate copies of its own DNA for distribution to two daughter cells. Knowing how to stop cell duplication is critical in preventing diseases like cancer, when mutated cells go out of control and proliferate madly. Further, ubistatin blocked the cell cycle by preventing two proteins from interacting together. Prior to this, it was thought unlikely that a compound with low molecular weight like ubistatin--or any future drug--would have much impact on the interaction of proteins with each other.

While ubistatin has other properties that preclude it from being a drug candidate, its stoppage of the cell cycle provides an important clue for future drug development, says Deshaies. "We've found a chemical Achilles' heel in this cell pathway, at least from the viewpoint of these small molecules that comprise most therapeutic drugs."

Because the cell cycle is maddeningly complex, researchers usually pick a single pathway (a pathway is a series of chemical events within a cell that perform some task), then try to make a chemical to block it. They may find such a chemical, but often find it difficult to discover where in the pathway--the target--their drug hit. Finding the target is like finding the proverbial needle in a haystack.

Deshaies's colleague Rati Verma found the needle. Instead of using the typical "top down" approach of starting with a specific target, then looking for a drug to block it, the researchers took a "bottom up" approach of starting with a drug and then searching for the target it blocks. They decided to test a large number of molecules to see if any of them might block any step in one particular pathway called the ubiquitin-proteasome pathway (UP pathway): within the cell cycle, when a protein's job is done, another chain of proteins called ubiquitin attaches to it. That serves as a signal to yet another protein called proteasome. The proteasome, says Deshaies, is the biological equivalent of a Cuisinart. "It attaches to these ubiquitin-marked proteins, then ingests them and chews them up."

The researchers examined an entire cell, specifically that of a frog's egg. The King group decided to screen 110,000 molecules to see if any had an impact on the cell. First, they weeded out those molecules that had no effect on cellular function in the UP pathway. King attached a molecule of luciferase ("the stuff that makes a firefly light up," says Deshaies) to certain proteins that are normally destroyed during cell division. Next, he added this newly created protein (now a readily detectable biological "flashlight") to droplets of cellular material extracted from the frog's egg that had been placed in individual chambers. As the egg extract conducted its normal cell division, the luciferase flashlight was destroyed and the chambers went dark. That meant those proteins had been destroyed as part of the normal progress of the cell cycle. He then separately added the 110,000 small molecules to see if any of them would prevent the loss of the luciferase--essentially looking for a lit-up reaction chamber in a field of darkness.

Using this approach, the researchers eventually narrowed the molecules they were testing down to a few that were operating in a specific part of the pathway--downstream from where ubiquitin attaches to the soon-to-be doomed protein, but before the proteasome ingested and chewed it up. But given that numerous proteins are involved in this process, the question remained--where specifically was the molecule they were testing working? In short, where was the target?

To find out, Deshaies turned to work they had done over the last five years with ubiquitin, which examined how it interacted with various other proteins, including proteasome. Through a process of elimination, says Deshaies, "we figured out that these small molecules called ubistatins were blocking the recognition of the ubiquitin chain by the proteasome." Graphic evidence for how this occurs was provided by a 'picture' taken by David Fushman at the University of Maryland with a nuclear magnetic resonance spectrometer.

This step blocked by ubistatin involves a protein-protein interaction, a surprise to Deshaies. "One interesting thing about our discovery is that it is further evidence that you can affect a protein-protein interaction with a small molecule. The conventional thinking was that if you look at a footprint of a drug binding a protein, the drugs are small, but the footprint that corresponds to one protein binding to another is big. So most people thought that the idea of trying to block the huge footprint of protein-protein interaction with a tiny drug was extremely unlikely. So if I were asked to predict what we would find, I would never have proposed that a drug could prevent the ubiquitin chain from binding to the proteasome, because I was also influenced by this conventional wisdom."

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Caltech Bioinformatics Experts DevelopNew Literature Search Engine for Biologists

PASADENA, Calif.—When it comes to finding a used book on the Internet, one merely needs to Google the title, and a few suitable items for sale will soon be just a click away. But for the biologist or medical researcher looking for information on how two nematode genes interrelate in hopes of better understanding human disease, there is a clear need for a more focused search engine.

Bioinformatics experts from the California Institute of Technology are formally announcing today the Textpresso search engine, which they hope will revolutionize the way that genetic information is retrieved by researchers worldwide. The Textpresso search engine is specifically built to serve researchers who work on the small worm known as C. elegans, but the basic design should lead to the creation of new search engines for researchers who specialize in other living organisms that are intensively studied.

In the current issue of the journal PLOS, published by the Public Library of Science, Caltech biology professor Paul Sternberg and his colleagues--research associate Hans-Michael Muller and bioinformatics specialist Eimear Kenny--write that the new "text-mining system for scientific literature" will be invaluable to specialists trying to cope with the vast amount of information now available on C. elegans. This information has vastly increased in recent years due to the large-scale gene-sequencing initiative as well as the more traditional small-scale projects by individual researchers. As a result, the need for a way to scan the vast literature has become much more important.

"Textpresso gives me, as a researcher, more time to actually read papers because I don't have to skim papers anymore," says Sternberg, who is leader of the federally funded WormBase project that has already put online the entire genome sequence of C. elegans and the closely related organism C. briggsae, as well as genes for some 20 other nematode species.

The four-year-old WormBase project, a linchpin in the worldwide effort to better understand how genes interrelate, also makes a host of other information freely available in addition to the 100.2 million base-pairs that make up the millimeter-long worm's genome. There are now 28,000 gene-disruption experiments in WormBase, along with 2 million DNA expression ("chip") microarray observations, as well as detailed information on the expression of more than 1,700 of the worm's 20,000 genes. The Textpresso search engine is a logical product for the WormBase team to develop in the ongoing quest to put genetic information to work in curing and preventing human disease.

Lest anyone assume that the genes of a millimeter-long nematode have little to do with humans, it should be pointed out that the two organisms are similar in about 40 percent of their genes. A very realistic motivation for funding the genome sequencing of the fruit fly, the small mustardlike plant known as Arabidopsis, the chimp, and various other species, has been the expectation of finding underlying common mechanisms.

Thus, a cancer researcher who discovers that a certain gene is expressed in cancer cells can use the WormBase to see if the gene exists in nematodes, and if so, what is known about the gene's function. And now that Textpresso is available, the researcher can do so much more efficiently.

"The idea is distilling down the information so it can be extracted easier," says Muller, the lead author of the paper and codeveloper of Textpresso with Kenny. The idea for the name of the search engine, in fact, comes from its resemblance to "espresso," which is a process used to get the caffeine and flavor out of coffee in a minimal volume.

According to Kenny, the search engine is designed with a special kind of search in mind, which establishes categories of terms and organizes them as an ontology--that is, a catalog of types of objects and concepts and their relationships. For example, if the researcher wants to find out whether any other researcher has worked on the relationship between the nematode gene called "lin-12" and the anchor cell, then typing the two terms into a conventional search engine like Google results in more than 400 hits. And if the researcher wants to know which genes are important in the anchor cell, the task is even more arduous. But Textpresso is designed to get the information in a much simpler, more efficient, more straightforward way.

Textpresso is a text-processing system that splits research papers into sentences, and sentences into words or phrases. All words and phrases are labeled so that they are searchable, and the labels are then condensed into 33 ontological categories. So far, the database includes 4,420 scientific papers on C. elegans, as well as bibliographic information from WormBase, information on various scientific meetings, the "Worm Breeder's Gazette," and various other links and WormBase information. Therefore, the engine already searches through millions of sentences to allow researchers to find a paper of interest or information of interest with great efficiency.

Finally, the Textpresso search engine should be a useful prototype for search engines to serve other biological databases--some of which have even larger piles of data for the specialist to cope with. "Yeast currently has 25,000 papers," Kenny says.

Textpresso can be accessed at or via WormBase at

Robert Tindol

Research uncovers new facts about odor detection in insects; findings could lead to more effective repellents

PASADENA, Calif.--If you think it doesn't do much good to swipe the fly that's going after the potato salad, guess again. You may be discouraging the fly's colleagues from taking up the raid.

New evidence shows that a stressed fly emits an odor that makes other flies avoid the space in which the stressful event occurred. Reporting in an advance on-line publication of the September 15 issue of the journal Nature, California Institute of Technology professors David Anderson and Seymour Benzer, along with Professor Richard Axel of Columbia University, discuss their findings about how flies may communicate information about their internal state to one another.

According to the authors, the act of shaking or shocking flies causes a repellent odor to be emitted that contains carbon dioxide as one of its active components. The research involved the fruit fly, Drosophila melanogaster, which has been used for decades in genetics experiments. However, the mechanism could be more widespread.

"We showed that CO2 is itself a potent repellent for Drosophila," says Anderson, a professor of biology at Caltech and also a Howard Hughes Medical Institute investigator.

The researchers also succeeded in mapping the initial neural circuitry that leads to CO2 avoidance. The team, led by Caltech postdoctoral scholar Greg Suh, found that CO2 activates a single class of sensory neurons in the fruit flies, and that these neurons seem to be dedicated to the sole task of responding to this odor. By inhibiting the synapses of these neurons using fancy genetic trickery, the researchers were able to block the ability of flies to avoid CO2, in behavioral experiments.

"These results show that there is probably a genetically determined, or 'hard-wired' circuit mediating CO2 avoidance behavior in the fly," Anderson says.

But even though the research is primarily aimed at furthering the understanding of the neural circuitry underlying innate behaviors, there might also be practical results. For one, the fact that mosquitoes are attracted to their warm-blooded hosts by CO2 exhalations has been known for years.

Although fruit flies are repelled by CO2, while mosquitoes are attracted to it, "given the evolutionary conservation of olfactory mechanisms in insects, if we learn about the molecular details involved in CO2 sensing in fruit flies, it could potentially lead to repellents that act by interfering with the reception of CO2," Anderson adds.

Such a repellent could be of benefit in third-world countries where mosquitoes are vectors of diseases like malaria--or even in the United States, where the mosquito-borne West Nile virus has been a serious health concern this year.

Robert Tindol

Caltech Professor Awarded Stein and Moore Award for Insights Into the Life Cycle of Cells

PASADENA, Calif.-- Ubiquitin is a small protein that has a very big job. Or jobs, to be more accurate. Indeed, the ubiquitin system is central to--literally--just about everything significant that goes on inside cells, and to a lot of intercellular business as well. Once unknown and, until the 1980s, unheralded, the ubiquitin system is now one of the major areas of study in cell biology, biochemistry, and genetics, and the point of convergence for many disparate disciplines.

For their cofounding of the ubiquitin field, Alexander Varshavsky of the California Institute of Technology and Avram Hershko of the Technion-Israel Institute of Technology have been named corecipients of the Protein Society's 2005 Stein and Moore Award. Presented annually, the award was given to the pair in recognition of their "revolutionary work in discovering the ubiquitin system of protein degradation, its mechanisms, and its significance to living cells."

Varshavsky is the Smits Professor of Cell Biology at Caltech; Hershko is the distinguished professor of biochemistry at the Technion. The Stein and Moore Award is another in a long line of prestigious awards presented to the pair for their groundbreaking work.

"I am grateful to receive the Stein and Moore Award," says Varshavsky, "in part because the people who won it before us are such an illustrious company in our profession: Anfinsen, Neurath, Rossman, Fersht, Sigler, to cite just a few of them. The award is named after two great scientists, Stein and Moore, whose work in the 1950s and 1960s laid the foundations of modern protein chemistry."

The ubiquitin system is central to an incredible variety of biological processes: the cell cycle, cell growth and differentiation, embryogenesis and later development, programmed cell death, signal transmission, all kinds of DNA transactions (including DNA repair and replication), the immune response, the functions of the nervous system--the list goes on and on.

In addition, the ubiquitin system has become the cornerstone of cancer research. The relevance of the ubiquitin system to cancer cannot be overstated: a large number, if not a majority, of oncoproteins (proteins that, when mutated or overexpressed, can cause a normal cell to become cancerous) and tumor suppressors have been found to be either components or targets of the ubiquitin system. Studies by Varshavsky and coworkers in the 1980s, and particularly their discoveries of the first physiological functions of the ubiquitin system (in the cell cycle, DNA repair, transcriptional regulation, protein synthesis, and stress responses), eventually led, through the work by many laboratories, to the current preeminence of the ubiquitin system in cancer research.

By the late 1980s, the definitive and profoundly complementary advances by the laboratories of Hershko and Varshavsky transformed the realm of intracellular protein degradation from a relative backwater to a broad and dynamic subject of great importance.

Varshavsky is a member of the National Academy of Sciences, and has received a number of scientific awards, including the Gairdner Award, the Lasker Award, the Sloan Prize, the Hoppe-Seyler Award, the Merck Award, the Wolf Prize, the Horwitz Prize, the Max Planck Research Award for Biosciences and Medicine, the Pasarow Award, the Massry Prize, and the Wilson Medal.

The Protein Society is the leading international society devoted to furthering research and development in protein science. Varshavsky and Hershko will be presented their award at the society's annual symposium, to be held in Boston in 2005.-

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Fish, Frog, and Fly Share a Molecular Mechanism to Control Embryonic Growth

PASADENA, Calif. — Oriented cell division is a fundamental process in developing organisms, whether you are a worm, a fruit fly--or a human. As an embryo begins to grow, cells divide again and again, from the single fertilized egg to the countless cells present at birth. These cell divisions are not haphazard; instead, they are often precisely oriented, playing an important role in building an embryo of the right size and shape, and with the right body "parts"--the control of cell division also plays a central role in placing cells in the proper positions to build organs that will contain the correct cell types.

The orientation of cell divisions has been well studied in invertebrates, especially in Caenorhabditis elegans (worm) and Drosophila melanogaster (fruit fly), but relatively little has been known about oriented cell division in vertebrates. Now for the first time, researchers at the California Institute of Technology report that the molecular machinery that underlies oriented cell division in invertebrates serves a similar but twofold purpose in the development of the vertebrate embryo. For one, it is responsible for orienting cell division, or mitosis. For another, it's responsibile for the movements that elongate the round egg into the vertebrate body plan; that is, the shape of the particular animal. The research appears in the August 5 edition of the journal Nature (

The researchers are recent graduates Ying Gong '04 and Chunhui Mo '03, working with Scott Fraser, the Anna L. Rosen Professor of Biology and director of the Biological Imaging Center. Using the zebrafish, a card-carrying vertebrate, as their animal model, the researchers first marked certain cells with fluorescent proteins. Then, using a four-dimensional confocal microscope, they were able to follow the motions of these cells in real time, as the body plan of the zebrafish took shape during development, or gastrulation. The researchers found that cells in dorsal tissue divide in an oriented fashion, with one of the two daughter cells from each division moving towards the head, and the other towards the future tail. They were able to determine that such oriented cell division is a major driving force for the extension of the body axis--the growth of the embryo into the animal's final shape.

By combining their advanced imaging tools with molecular biological techniques, the researchers were able to show that the driving force for these oriented divisions is the Wnt "pathway," a ubiquitous cascade of specific proteins that trigger cellular function. Research over the past decade has shown that the Wnt pathway controls the patterns, fates, and movements of cells in both vertebrates and invertebrates. One major branch of this biochemical communication network is the planar cell polarity (PCP) pathway. In previous work from the Fraser lab and their collaborators, the PCP pathway has been shown to guide the tissue motions that convert the spherical frog embryo into the familiar shape of the elongated tadpole. This is a key process in the life of the frog, termed convergent extension. Each cell attempts to "elbow between" the row of cells to its left or its right. "This simple motion has a profound effect on the length and width of the embryo," says Fraser; "think of a band marching shoulder to shoulder on a football field. If half of the rows of marchers merged with the adjacent row, the band would be half as wide and twice as long."

The trio of researchers explored the effects in fish embryos of altering the many proteins in the Wnt-PCP signaling pathway, including some of the potential signals and co-receptors (proteins called Silberblick/Wnt11, Dishevelled, and Strabismus). They were expecting to see an alteration in the convergent-extension motions. Instead, what they found was a major alteration in the orientation of cell division. When they blocked the Wnt pathway, cell division did not take place along the head-tail axis, but randomly. In normal fish embryos, the oriented divisions lengthened the body axis by nearly twofold. With randomization, though, a short and squat embryo was created.

Given that the same PCP pathway is involved in controlling cell division in the invertebrates, C. elegans and D. melanogaster, and the vertebrate zebrafish, the results suggest that the pathway has an evolutionary conserved role. That is, that across a wide variety of animal species, such pathways share a common function, perhaps reflecting a common origin in the biological past.

"The amazing thing about these studies is that they show that the many varied mechanisms that can create the long and narrow body plan of a fish, frog, or fly come under a common molecular control mechanism," Fraser says. "Work in frog embryos from John Wallingford (formerly of UC Berkeley, currently at University of Texas, Austin) and Richard Harland (UC Berkeley) have established a link between these motions and neural tube defects (such as craniorachischisis and spina bifida). Our new experiments have already prompted a new round of collaborative experiments to determine if the same molecular pathway controls convergent extension, cell division, or both in mammals. The answers to these questions promise new insights into the underlying cause for some of the devastating birth defects seen in humans. "

MEDIA CONTACT: Mark Wheeler (626) 395-8733

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New Class of Reagents Developed by Caltech Chemical Biologists for In Vivo Protein Tracking

PASADENA, Calif.--One of the big problems in biology is keeping track of the proteins a cell makes, without having to kill the cell. Now, researchers from the California Institute of Technology have developed a general approach that measures protein production in living cells.

Reporting in the July 26 issue of the journal Chemistry and Biology, Caltech chemistry professor Richard Roberts and his collaborators describe their new method for examining "protein expression in vivo that does not require transfection, radiolabeling, or the prior choice of a candidate gene." According to Roberts, this work should have great impact on both cell biology and the new field of proteomics, which is the study of all the proteins that act in living systems.

"This work is a result of chemical biology—chemists, and biologists working together to gain new insights into a huge variety of applications, including cancer research and drug discovery," says Roberts.

"Generally, there is a lack of methods to determine if proteins are made in response to some cellular stimuli and what those specific proteins are," Roberts says. "These are two absolutely critical questions, because the behavior of a living cell is due to the cast of protein characters that the cell makes."

Facing this problem, the Roberts team tried to envision new methods that would enable them to decipher both how much and what particular protein a cell chooses to make at any given time. They devised a plan to trick the normal cellular machinery into labeling each newly made protein with a fluorescent tag.

The result is that cells actively making protein glow brightly on a microscope slide, much like a luminescent Frisbee on a dark summer night. Importantly, these tools can also be used to determine which particular protein is being made, in much the same way that a bar code identifies items at a supermarket checkout stand.

To demonstrate this method, the team used mouse white blood cells that are very similar to cells in the human immune system. These cells could be tagged to glow various colors, and the tagged proteins later separated for identification.

Over the next decade, scientists hope to better understand the 30,000 to 40,000 different proteins inside human cells. The authors say they are hopeful that this new approach will provide critical information for achieving that goal.

The title of the paper is "A General Approach to Detect Protein Expression In Vivo Using Fluorescent Puromycin Conjugates." For more information, contact Heidi Hardman at

Robert Tindol

Caltech Nobel Laureate Ed Lewis Dies

PASADENA—Edward Lewis, winner of the 1995 Nobel Prize for his groundbreaking studies of how genes regulate the development of specific regions of the body, died Wednesday, July 21, 2004, at Huntington Hospital in Pasadena after a long battle with cancer. He was 86.

A member of the California Institute of Technology faculty since 1946, Lewis spent his life working on the genetics of the fruit fly, with special attention to the fundamental ways in which the genes relate to embryonic development. The work had profound implications for a basic understanding of the genetic regulation of development in humans. At the time of his death he was the Morgan Professor of Biology, Emeritus, and until very recently maintained an active schedule in his campus laboratory.

In a book published on Lewis earlier this year, author and longtime collaborator Howard Lipshitz wrote that Lewis's scientific research was "the bridge linking experimental genetics as conducted in the first half of the 20th century, and the powerful molecular genetic approaches that revolutionized the field in its last quarter." Lipshitz also lauded Lewis's much less widely known work on the understanding of radiation and cancer, and the closely related issues concerning nuclear-weapons testing policy.

Born May 20, 1918, in Wilkes-Barre, Pennsylvania, Lewis as an adolescent became interested in the genetics of the fruit fly, Drosophila melanogaster, which was already being touted as an excellent animal for research by Caltech's Thomas Hunt Morgan. Lewis performed genetics experiments on Drosophila while just a freshman in high school, and after taking a bachelor's degree in 1939 at the University of Minnesota, came to Caltech for a doctorate and remained at the Institute for the rest of his life, save for four years in the U.S. Army Air Force during World War II, when he worked as a meteorologist.

Lewis published several research papers while still a college student, and soon after the war was a recognized expert in the field of fly genetics. Returning to Caltech in 1946 as an instructor, he was named an assistant professor in 1948, earned tenure the following year, and became a professor of biology in 1956. He was named the Thomas Hunt Morgan Professor of Biology in 1966 and retained the chair until his retirement from active faculty duties in 1988.

In a campus article appearing in 1957, Lewis described his success in causing the flies to mutate with four wings (they normally have two). "We now have a working model for picturing the genetic control of development," he said. His prognostication was indeed correct, and nearly four decades later the Nobel Committee, in awarding Lewis the Nobel Prize in physiology or medicine, cited his triumph in identifying and classifying "a small number of genes that are of key importance in determining the body plan and the formation of body segments." The Nobel Committee also lauded Lewis for his discovery of "how genes were arranged in the same order on the chromosomes as the body segments they controlled."

In the same article, Lewis discussed his good fortune in becoming an active geneticist at a revolutionary time in biology. After the war, the gene was still treated as an abstract entity because the techniques needed to ascertain its molecular nature were yet to be developed, he explained. "You could begin to try to see how a gene is constructed, even though DNA hadn't yet been determined to be the hereditary material. The laws of genetics had never depended upon knowing what the genes were chemically and would hold true even if they were made of green cheese."

Although the modern techniques of molecular biology were yet to be invented, Lewis was never reticent about using novel methods to better understand the genetics of the fly. He created his four-winged mutants by bombarding the flies with x-rays, thereby playing a key role in discovering and explaining the role of homeotic genes--that is, genes that influence how the undifferentiated cells in a fertilized embryo separate into a head and a tail end, and how the eyes, legs, antennae, and other organs all form in their correct positions. These genes are "highly conserved," as geneticists say, because the genes are similar in all organisms and play a role in the development of all animals, from fruit flies to mice to humans.

"Ed was the bridge between the pioneers of Drosophila work--Morgan, Bridges, and Sturtevant--to modern developmental biology," said David Baltimore, president of Caltech and also a Nobel Prize-winning biologist. "Ed saw that even a lowly fruit fly could be a key to understanding the mysterious process of how a fertilized egg turns into a fully developed organism."

Lewis became a legend on the Caltech campus, and when he returned home after his 1995 Nobel Prize was announced—he had been attending a scientific conference in Switzerland at the time—was celebrated for his 60 years of dedication to his work and his classical approach to individual research in an era when "big science" increasingly became the more prominent model.

Lewis is survived by his wife of 57 years, Pam Lewis; and two sons, Keith Lewis of Redwood City, California, and Hugh Lewis of Bellingham, Washington.

Robert Tindol

Neuroscientists Demonstrate New Way to Control Prosthetic Device with Brain Signals

PASADENA, Calif.—Another milestone has been achieved in the quest to create prosthetic devices operated by brain activity. In the July 9 issue of the journal Science, California Institute of Technology neuroscientists Sam Musallam, Brian Corneil, Bradley Greger, Hans Scherberger, and Richard Andersen report on the Andersen lab's success in getting monkeys to move the cursor on a computer screen by merely thinking about a goal they would like to achieve, and assigning a value to the goal.

The research holds significant promise for neural prosthetic devices, Andersen says, because the "goal signals" from the brain will permit paralyzed patients to operate computers, robots, motorized wheelchairs—and perhaps someday even automobiles. The "value signals" complement the goal signals by allowing the paralyzed patients' preferences and motivations to be monitored continuously.

According to Musallam, the work is exciting "because it shows that a variety of thoughts can be recorded and used to control an interface between the brain and a machine."

The Andersen lab's new approach departs from earlier work on the neural control of prosthetic devices in that most previous results have relied on signals from the motor cortex of the brain used for controlling the limb. Andersen says the new study demonstrates that higher-level signals, also referred to as cognitive signals, emanating from the posterior parietal cortex and the high-level premotor cortex (both involved in higher brain functions related to movement planning), can be decoded for control of prosthetic devices.

The study involved three monkeys that were each trained to operate a computer cursor by merely "thinking about it," Andersen explains. "We have him think about positioning a cursor at a particular goal location on a computer screen, and then decode his thoughts. He thinks about reaching there, but doesn't actually reach, and if he thinks about it accurately, he's rewarded."

Combined with the goal task, the monkey is also told what reward to expect for correctly performing the task. Examples of variation in the reward are the type of juice, the size of the reward, and how often it can be given, Andersen says. The researchers are able to predict what each monkey expects to get if he thinks about the task in the correct way. The monkey's expectation of the value of the reward provides a signal that can be employed in the control of neural prosthetics.

This type of signal processing may have great value in the operation of prosthetic devices because, once the patient's goals are decoded, then the devices' computational system can perform the lower-level calculations needed to run the devices. In other words, a "smart robot" that was provided a goal signal from the brain of a patient could use this signal to trigger the calculation of trajectory signals for movement to be accomplished.

Since the brain signals are high-level and abstract, they are versatile and can be used to operate a number of devices. As for the value signals, Andersen says these might be useful in the continuous monitoring of the patients to know their preferences and moods much more effectively than currently possible.

"These signals could also be rapidly adjusted by changing parameters of the task to expedite the learning that patients must do in order to use an external device," Andersen says. "The result suggests that a large variety of cognitive signals could be interpreted, which could lead, for instance, to voice devices that operate by the patients' merely thinking about the words they want to speak."

Andersen is the Boswell Professor of Neuroscience at Caltech. Musallam and Greger are both postdoctoral fellows in biology at Caltech; Corneil is a former researcher in Andersen's lab who is now at the University of Western Ontario; and Scherberger, a former Caltech researcher, is now at the Institute of Neuroinformatics in Zurich, Switzerland.

Robert Tindol