(l-r) Prof. Antoine Kahn, Dr. Oliver Seitz, Prof. David Cahen and Dr. Ayelet Vilan. Changing chemical bonds
The world runs on impurity. Impurities in the colorless mineral beryl turn it to emerald. A bit of carbon tossed into pure iron hardens it into steel. And the ubiquitous silicon chips that form the basis of everything from our computers and electronic devices to musical birthday cards must contain impurities to work. In a process called doping, small amounts of other materials are introduced into pure silicon, and these impurities are what enable electricity to flow through the semiconductor and allow designers to control the electronic properties of the material.
Dr. Hagai Cohen
Scientists at the Weizmann Institute are working on substitutes for the silicon that most of the electronics industry relies on today. Molecular electronics is based on single organic (carbon-based) molecules or thin layers the thickness of a single molecule. Semiconductors based on organic molecules might be inexpensive, biodegradable, versatile and easy to manipulate, and the wide variety of these molecules might open up all sorts of possibilities for new applications. But, like today's silicon semiconductors, organic monolayers would need to be doped to work efficiently.
The question facing scientists working in the field is whether such molecular systems, which tend to be delicate and hard to manipulate, can be properly doped. That is, can these materials first be purified and then impurities added to order? Prof. David Cahen and postdoctoral fellow Dr. Oliver Seitz of the Weizmann Institute's Materials and Interfaces Department, together with Drs. Ayelet Vilan and Hagai Cohen of Chemical Research Support, all of the Faculty of Chemistry of the Weizmann Institute, and Prof. Antoine Kahn, from Princeton University (a regular visitor to the Institute), showed for the first time that such doping of molecular electronic systems is, indeed, possible.
First they succeeded in purifying the molecular layer to such an extent that the remaining impurities did not affect the system's electrical behavior. The scientists then doped the clean monolayers by irradiating the surface with UV light or weak electron beams. In this case, the impurities were not a second kind of molecule but a change in the chemical bonds between the carbon atoms that make up the molecular layer. These bonds ultimately influenced electronic transport through the molecules.
This achievement was recently described in the Journal of the American Chemical Society (JACS). The researchers foresee that this method may enable scientists and electronics engineers to substantially broaden the use of organic monolayers in the field of nano-electronics. Cahen: "After establishing an ideal system (a uniform layer of 'pure' molecules), we can dope it, introducing impurities that will allow us to control electron transport properties according to specific needs." Seitz: "If I am permitted to dream a little, it could be that this method will allow us to create types of electronics that are different, and maybe even more environmentally friendly, than the standard ones that are available today."
Prof. David Cahen's research is supported by the Nancy and Stephen Grand Research Center for Sensors and Security; the Philip M. Klutznick Fund for Research; Mr. Yehuda Bronicki, Israel; and Mr. and Mrs. Yossie Hollander, Israel. Prof. Cahen is the incumbent of the Rowland and Sylvia Schaefer Professorial Chair in Energy Research.
Smart. Flexible. Copes well with stress. Adjusts quickly to new situations. Sound like a candidate applying for a demanding job? Indeed, except that the "candidate" is an unusual ceramic material capable of adapting to changing and stressful conditions.
Like discovering that your next-door neighbor, whom you supposed for years to possess average intelligence, is in fact a genius, a common ceramic material has been found to possess a hidden talent. Scientists at the Weizmann Institute, led by Prof. Igor Lubomirsky of the Materials and Interfaces Department, have discovered that under certain conditions, cerium gadolinium oxide behaves more like rubber than a regular ceramic: Much like a squeezed rubber ball, it adjusts to an externally imposed shape but regains its original shape once released from its constraints. The scientists designed a drum-like structure in which a "drumhead" – a thin film of the ceramic less than 1 micron thick – was tethered to a frame. At room temperature, the film was flat and perfectly fit the frame. When heated gradually, rather than buckling, as an average ceramic would, the "smart" ceramic remained steadfastly flat, even when the temperature was raised to 180°C. And when cooled back slowly, it still retained its original shape and showed no signs of cracks.
Instant heating and cooling, however, produced buckling and cracking – just like your run-of-the-mill ceramic. Apparently, the time factor played a crucial role. A rubber ball offers a perfect analogy for the two scenarios: When squeezed relatively slowly, it deforms to adjust to the stress and regains its shape when released. In contrast, upon fast impact – as, for example, when thrown against the floor – the ball bounces without altering its shape.
What mechanism makes the ceramic so "smart" and adjustable? The secret lies in the two types of so-called point defects the material contains: atoms of gadolinium that had been introduced into cerium oxide and vacant spots left where oxygen had been pushed out by the gadolinium atoms. These latter "vacancies" allowed the defects to move about in the material – something like movie viewers changing seats in a half-empty cinema. As the ceramic cools, the loss of energy drives the two types of defects closer together into a more "economical" state, and the material's volume shrinks gradually, without cracking.
Additional materials might possess a similar stress-coping ability, says Lubomirsky. Together with Anna Kossoy of the Materials and Interfaces Department, Dr. Yishay Feldman and Dr. Ellen Wachtel of Weizmann's Chemical Research Support, as well as Prof. Joachim Maier of the Max Planck Institute for Solid State Research in Stuttgart, Germany, he developed the theoretical framework for the ceramic's rubber-like behavior and supported it experimentally.
A material's ability to retain its original shape at all temperatures could be extremely useful, for example, in devices that undergo repetitive warming and cooling, such as fuel cells that convert chemical energy directly to electricity. The clever ceramic could also help in the manufacture of sophisticated microscopic devices that need to perform highly reproducible measurements, such as micro-sensors or miniature pumps.
Prof. Igor Lubomirsky's research is supported by Mr. and Mrs. Yossie Hollander, Israel.
(l-r) Keren Ziv, Vicki Plaks, Prof. Michal Neeman and Dr. Batya Cohen.
Reporters broadcast news about current events, trends and people "live" from the scene. Today's viewers need only tune in to this news, wherever and whenever it is taking place, to find out what's going on in the world.
Molecular biologists are faced with the much more difficult task of trying to keep abreast of events occurring within the world of an organism. In humans, for example, scientists need to keep tabs on the activities of the estimated 20,000 – 30,000 genes that code for proteins. To complicate things further, these thousands of genes can be expressed (i.e., converted into functional proteins) in many different combinations.
Gene expression, in turn, controls many events in the body: the structure and function of a cell, various processes such as blood flow and even the progression of certain diseases such as cancer.
Scientists need ways of getting an up-close look at events in which genes are controlled by the different regulatory mechanisms. To make their job easier, they employ reporter genes – genes that code for an easily detectable protein. The popular green fluorescent protein (GFP) reporter gene, for example, is widely used by scientists for this purpose. This gene "broadcasts" its reports by giving off light when it is expressed. Researchers insert the reporter DNA into a specific region of a gene they want to study, and it flashes its message back, filling them in on how this gene is regulated, where the regulation occurs and what the activity leads to in the end. But not all reporter genes are ideal for every situation. In particular, it is difficult to detect the location and intensity of fluorescent proteins in animals or people, especially when expression of the intended gene is localized deep within the body.
Alternatives have been suggested. In particular, considerable effort has been invested in developing reporter genes whose signals can be detected by magnetic resonance imaging (MRI), a non-invasive technique that is already widely used on humans and animals. Unfortunately, most of the candidate reporters proposed so far require the administration of additional substances, called reporter probes, before the MRI can detect their signals. Such substances are shut out of many cellular events – such as fetal development or those events taking place within the central nervous system, as both present barriers that the reporter probes can't cross.
In searching for a new reporter gene that would circumvent this problem, Weizmann Institute scientists have come across a promising candidate: ferritin. According to its resume, ferritin works by chemically neutralizing iron. This protein normally minimizes iron toxicity in the cell, but when it's overexpressed, it also causes signal changes in the surrounding environment that are strong enough to be detected by MRI; no additional substrate is needed.
Prof. Michal Neeman and Dr. Batya Cohen of the Biological Regulation Department, along with research students Keren Ziv and Vicki Plaks and their colleagues, decided to give ferritin a chance to show its stuff. The scientists sent it "on assignment" by inserting the ferritin gene into a circular piece of DNA, which was in turn introduced into a special mouse strain they had developed that allows the introduced ferritin gene to be expressed in a controlled manner. They also sent along the old hand – the GFP reporter gene – which they inserted next to the ferritin gene to check independently whether it was reporting events accurately. In a further test of the method, the scientists introduced an additional gene, one that acts like a switch – it can turn both reporters either "on" or "off" simultaneously – to make sure that the signals detected actually come from the reporters themselves, and not from another source.
So far, their results, which were published in the journal Nature Medicine, show that ferritin can function as a reporter, broadcasting its reports live, via MRI detection, from the liver, endothelial cells and even during fetal development in the pregnant mouse, all without help from other materials.
Cohen: "These new results have shown that the use of ferritin as a reporter of gene expression and biological activity, especially in live animals, is not only feasible but more efficient than that of other MRI reporter genes tested so far. This approach could open many additional possibilities for studying the activation of genes during different stages of development, or detailed studies of various disease models in strains of mice bred for this purpose."
This method grew out of a joint vision that originated 10 years ago in collaboration with the late Dr. Yoav Citri.
Top row: MRI images of a pregnant mouse, showing the embryonic liver, heart, brain and placenta. Bottom: Embryos genetically engineered to overexpress the ferritin reporter gene in the blood vessels (r) show higher ferritin induced contrast of the heart and liver compared with siblings that don't overexpress the gene (l)
MRI virtual sections of adult mouse brains expressing the ferritin reporter gene in the cells lining the blood vessels (bottom row) show high ferritin-induced contrast (red hues) compared with that in brains of sibling mice, in which expression of this gene is silent (top)
A(l-r) Prof. Irit Sagi, Barak Akabayov and Ariel Solomon. Real-time action
Enzymes are shape-shifters – their intricate molecular structures take on a variety of different arrangements as they go about their work. The ability to trace in real time the dynamic changes an enzyme molecule's structure undergoes has been a holy grail of molecular biology – one that scientists thought would only be attained many years down the road. But reality has overtaken the predictions: Prof. Irit Sagi of the Structural Biology Department in the Chemistry Faculty and her research team have developed a method of recording an enzyme's movements down to the scale of single atoms, and this technique is now being used as a tool for designing new drugs.
The complex molecular machines known as enzymes are involved in nearly all the functions of our bodies. Changes in enzyme structure take place at dizzying speeds – tiny fractions of a second – and this dynamic action makes them extremely efficient. To understand how enzymes work, scientists generally use a variety of techniques, such as crystallization, to determine the three-dimensional structure of the resting molecule. Although much information is revealed in these studies, they often can't give scientists a satisfactory picture of the steps involved in shifting an enzyme's shape. Yet a precise understanding of each step in enzyme activity can be especially important to drug makers, who aim to create new drugs that can tightly focus on a target protein or prevent a single type of action from taking place.
The Weizmann team's method allows them to identify the movement of single atoms residing within the active site of an enzyme molecule. The scientists freeze the process at various stages and then apply cutting-edge techniques borrowed from the field of X-ray spectroscopy and structural chemical analysis to determine the configuration of the molecule at each of those stages
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One of the enzymes tested by the team's method is an enzyme called TNF alpha convertase, which is suspected of involvement in many diseases, from multiple sclerosis to cancer. TNF alpha convertase is a protease – part of an enzyme family that cleaves other proteins and prepares them for specific actions. Among other functions, TNF alpha convertase cleaves a protein called PRO-TNF alpha, slicing through the part of its structure that attaches it to the inside of the cell wall. The released PRO-TNF is then free to act in the cell. These proteins perform some crucial functions, but if too many are released at once, problems can start to occur and diseases can develop. For this reason, scientists in labs around the world have pinpointed TNF alpha convertase as a target for drugs that will damp down PRO-TNF activity.
The only problem is that drugs that block TNF alpha convertase activity tend to have disastrous, sometimes even fatal, side effects. The reason for this is the familial resemblance between the structure of this enzyme and that of other protease family members. It turns out that these drugs are not overly discriminating about which protease they block, and they end up hindering some vital functions in the cell. Identifying the real-time structural and biophysical events taking place during enzyme action could therefore be a real boon to drug research.
At this point, Sagi and her team, together with Dr. Marcos Milla of Roche Palo Alto, LLC, in California, entered the picture. With the dynamic observation method they had developed, they succeeded in recording every change in the molecule at intervals of a few thousandths of a second. In the first stage of their research, they were able to put an end to a scientific debate that had gone on for years by pinpointing a specific response mechanism the enzyme employs.
Clockwise from top: Steps in the cleaving of a peptide bond in the PRO-TNF alpha protein by the TNF alpha convertase enzyme. The dot in the middle of the enzyme represents the zinc ion in the enzyme's active site, and changes in its color show the ion's charge at each step
Next, they discovered that when the enzyme closes in on the protein that it's preparing to cleave, it begins to get "excited." As it makes contact with the surface of the protein, the dynamic structural transformations pick up their pace. This is especially evident in the electrons belonging to the lone zinc atom sitting squarely in the active site of the enzyme molecule. The changes they observed appear to be uniquely characteristic of TNF alpha convertase; if drugs could be designed to target this particular action, they might avoid affecting other proteases and thus prevent unwanted side effects. The results of this study appeared recently in the Proceedings of the National Academy of Sciences (PNAS), USA.
This technique might be applied to a great many of the enzymes that are involved in various disease processes. The ability to observe enzyme activities in fine detail may turn out to be a powerful tool that could lead to new approaches in drug design and new drugs that are more efficient and less likely to cause side effects. Various pharmaceutical companies have already expressed interest in the Institute team's new technique.
Prof. Irit Sagi's research is supported by the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly; the Avron-Wilstaetter Minerva Center; Mr. and Mrs. Michael Ambach, Boca Raton, FL; and the estate of David Turner. Prof. Sagi is the incumbent of the Maurizio Pontecorvo Professorial Chair.
Like the old-time telephone networks run by switchboard operators, our cells have their very own "switchboard operators" that allow external signals to place a "call" to various cell centers such as the nucleus and other cellular organelles.
These "switchboard operators" are receptors – proteins that sit on the outer membrane of the cell wall. When they receive "incoming calls" – in the form of chemical molecules, such as insulin, or physical stimuli, such as heat – they become activated, transferring the message to the nucleus inside the cell. The cell then responds to these external stimuli, initiating cellular functions according to the specific message received. These functions include proliferation, differentiation, survival and even cell death.
t was as a postdoctoral fellow working in the laboratory of Nobel laureate Edwin Krebs that Prof. Rony Seger of the Weizmann Institute's Biological Regulation Department first encountered these messages being passed on once the receptor was activated. Signaling pathways – the cells' version of telephone lines – comprise about five to eight proteins each. These proteins, like runners in a relay race, activate the next protein in line until the last one crosses the finish line – in this case, the nuclear membrane.
Rather than electrical signals, as in telephones, the proteins use chemical signals, adding a phosphorus molecule to each "runner" in turn.
Through the Human Genome Project, it was discovered that cells employ only 100-200 "operators" at a time to receive hundreds of incoming calls. Each call requires an individual response, but just 10-12 main "telephone lines" are available to transfer messages. "How are all these different signals transmitted and responded to with such specificity?" wondered Seger.
Over the years, Seger has managed to identify various ways in which specificity is achieved; the most recent findings were published in the Journal of Cell Biology. Together with postdoctoral fellow Dr. Yoav Shaul, he has now shown that the main signaling pathways can branch out and subdivide – something like extension numbers in automated answering systems that prompt "Please press 1 for…, 2 for..."
This discovery came about when they were studying one of the main signaling pathways, called ERK, and noticed that it had various "extension numbers" – namely, ERK1, ERK1b, ERK1c and ERK1d. "The question was whether these extensions are redundant, dealing with the same 'queries' as the main ERK pathway, or whether they handle different messages of their own," explains Seger.
It turns out that the extensions do indeed have very specific functions. One role of the ERK signaling pathway is the regulation of cell division. During cell division, one of the cell's components – the Golgi apparatus – splits into thousands of tiny fragments that are doled out among the daughter cells for later reassembly. Seger found that only one of the ERK branch lines, ERK1c, was capable of transmitting the message to carry out this process.
Because breakdown in communication can lead to malfunction in cellular processes, discovering how specific messages are delivered may prove to be of major importance. For example, ERK signaling inhibitors are currently used to try to modulate the excessive cell growth of cancer, but because ERK is a main pathway involved in many cellular functions, jamming the signal may interfere with some necessary ones as well. The ability to target a specific pathway could lead to a more effective treatment and cause fewer side effects in the process.
Prof. Rony Seger's research is supported by the M.D. Moross Institute for Cancer Research; the Phyllis and Joseph Gurwin Fund for Scientific Advancement; and La Fondation Raphael et Regina Levy. Prof. Seger is the incumbent of the Yale S. Lewine and Ella Miller Lewine Professorial Chair for Cancer Research.
Cell to Cell
A surprising discovery in the lab of Prof. Rony Seger has shown that the body's cells appear to be able to "answer" calls made by cell phones. Our cells apparently pick up the radiation signals transmitted from cell phones and respond to the messages they are receiving.
Seger and Dr. Joseph Friedman, working part-time in Seger's lab, exposed living cells grown in lab dishes to cell phone radiation emissions in the range of frequencies and intensities used by cell phone networks for up to 45 minutes – well within the range of the average teenage phone conversation.
The researchers found that the "calls" placed by cell phone radiation were transmitted to the human cells via the ERK line – one of the more prominent intracellular telephone lines described here. Once the ERK line was activated, the cells were able to respond, providing various "answers" – adjusting cellular activity depending on the radiation frequency and intensity they were exposed to.
Do these findings suggest that cell phones "connect" to the central ERK line directly? Seger and Friedman suspect that cell phone radiation emissions first "call up" another set of molecules, known as free radicals. Free radicals are highly reactive molecules that are created in cells and may, under specific conditions, participate in the regulation of normal cellular processes such as proliferation, or pathological processes such as cancer. These, in turn, might activate the ERK telephone line.
The implications for human health are unknown at this point. To investigate further, Seger and Friedman intend to move their research up a step, from living cells to living organisms. This may lead to a better understanding of the effects of cellular phone radiation on living cells and help in assessing its effects on the human body.
(l-r) Dr. Eugenia Klein, Chen Luxenburg, Prof. Benjamin Geiger, Dafna Geblinger and Prof. Lia Addadi. All join hands
Breaking down bone is a tough job. Yet our bones undergo remodeling every day of our lives, and old material must be cleared away so that new bone can form. The heavyweights of the breakdown team are cells called osteoclasts that specialize in digesting bone. In diseases such as osteoporosis, an imbalance in this process is responsible for the characteristic bone loss.
Osteoclasts have some unique features. They move around the bone until they sense that their services are required, at which point they undergo a transformation called polarization. The polarized osteoclast sticks itself tightly to the bone, while an impermeable ring forms around the cell perimeter. This ring functions to keep the bone-eating acids and enzymes produced between the cell and the bone confined to the demolition site. New research at the Weizmann Institute of Science, which recently appeared in the on-line journal PLoS ONE, has revealed, in unprecedented detail, how these roving, bone-dissolving cells seal off their work area as they get down to business.
Prof. Benjamin Geiger, Dean of Biology, and Prof. Lia Addadi of the Structural Biology Department, together with doctoral students Chen Luxenburg and Dafna Geblinger, and with the assistance of Dr. Eugenia Klein of the Electron Microscopy Unit, and Prof. Dorit Hanein and Karen Anderson of the Burnham Institute, San Diego, applied two different observation methods to samples of stripped-down, polarized osteoclasts: electron microscope imaging that allowed them to see fine details of the ring structure, and a light microscope method in which specific features were induced to glow. Because each method captures a different type of information and on a different scale, combining them was tricky, but the two together gave them a uniquely extensive picture.
The team found that the ring is composed of dot-like structures called podosomes anchored to the cell membrane. When the osteoclast is on the move, these little dots amble randomly around the cell, but when the cell prepares to dissolve bone, they make a beeline for the edge. Scientists had been unsure of the podosomes’ role in ring formation. The research team’s findings showed clearly that the ring is made up of individual podosomes held together by interconnecting protein filaments they throw out to each other. “The podosomes are like folk-dancers,” says Geiger. “As soon as the music starts, they join hands and form a tight circle. From afar, a circle of dancers looks like a blur, but now we have managed to make out the individual dancers.”
Addadi points out that isolated podosomes look, from above, like big-top tents with “ropes” radiating out from a central pole. She says: “The podosomes may be more than just seals. They appear to act as highly connected nodes of communication between the inside and outside of the cell, enabling the cell to adjust its activity according to the condition of the bone underneath.”
Prof. Lia Addadi’s research is supported by the M. D. Moross Institute for Cancer Research; the Clore Center for Biological Physics; the Ilse Katz Institute for Material Sciences and Magnetic Resonance Research; the Helen and Martin Kimmel Center for Nanoscale Science; and the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly. Prof. Addadi is the incumbent of the Dorothy and Patrick Gorman Professorial Chair.
Prof. Benjamin Geiger’s research is supported by the Clore Center for Biological Physics; the Leo and Julia Forchheimer Center for Molecular Genetics; the Mario Negri Institute for Pharmacological Research - Weizmann Institute of Science Exchange Program; the Edith C. Blum Foundation Inc.; and the estate of Lore. F. Leder, Manchester, VT. Prof. Geiger is the incumbent of the Professor Erwin Neter Professorial Chair of Cell and Tumor Biology.
(l-r) Lior Segev, Onit Srur-Lavi, Dr. Ernesto Joselevich, Tzahi Cohen-Karni (on screen) and Dr. Sidney Cohen. Let’s twist again
Doing the twist may have faded away along with other fads of the 1960s, but the twist promises to make a comeback in the world of tiny molecular structures. As described recently in the first issue of the new journal Nature Nanotechnology, Dr. Ernesto Joselevich and his team in the Weizmann Institute’s Materials and Interfaces Department have managed to manipulate the properties of carbon nanotubes by twisting.
Carbon nanotubes are strong, flexible molecular wires that are harder than diamond and conduct electricity better than copper. Thanks to their unusual characteristics, they are ideal candidates to be components of tiny electronic and mechanical devices. Since their discovery more than a decade ago, scientists have been exerting great efforts toward understanding their properties, mainly in order to use them for building all sorts of specialized, highly structured instruments.
One of the traits of carbon nanotubes is their “split personality” when it comes to electrical conductivity. They can behave either like a metal, which is characterized by excellent conductivity, or like a semiconductor – such as the silicon in electronic chips – which, under different conditions, can be either a conductor or an insulator. Whether carbon nanotubes behave like conductors or semiconductors depends on their diameter and the way they form a spiral – a property known as chirality – the direction in which the carbon surface “rolls up” to create the tube. The chirality phenomenon generates molecules that have identical chemical compositions but differ from one another in their spatial structure, so that one molecule is a mirror image of the other – just as the right and left hand both resemble and differ from each other (hence the name: chiros means “hand” in Greek). Therefore, despite their identical chemical makeup, these molecules cannot overlap with one another, just as the right hand cannot overlap with the left.
Chirality had always been considered a basic property that could not be changed, but Joselevich asked himself whether it could be altered by twisting the nanotube – thereby turning a conductor into a semiconductor, or vice versa. The team, in addition to Joselevich, included research students Tzahi Cohen-Karni, Lior Segev and Onit Srur-Lavi, as well as Dr. Sidney Cohen of Chemical Research Support.
To twist nanotubes, the scientists created a unique device: a nanotube connected to two electrical contacts, with a pedal in the middle. Pressing the pedal with the tiny tip of an atomic force microscope caused the tube to twist, and the change in conductivity produced by the twisting was measured by the electrical contacts.
They found that gradual twisting of the nanotube led to periodic increases and decreases in conductivity. A check of the electron distribution in the nanotube during the twisting showed that what was taking place was indeed a periodic transition from a conductor to a semiconductor. The scientists then proposed a mathematical model that makes it possible to calculate and predict the oscillations in conductivity as a function of twisting.
These findings might in the future help in the design and production of tiny smart springs capable of measuring their own twisting by monitoring the changes in the electric current passing through them. Such springs could form the basis for a variety of nano-electromechanical devices, such as chemical or biological sensors, or gyroscopes for guiding miniature aircraft.
Dr. Ernesto Joselevich’s research is supported by the Helen and Martin Kimmel Center for Nanoscale Science; and the Asher and Jeannette Alhadeff Research Award. Dr. Joselevich is the incumbent of the Dr. Victor L. Ehrlich Career Development Chair.
An enzyme in the blood might be used to prevent brain damage
Prof. vivian Teichberg. Moving glutamate out of the brain
The brain is our most carefully guarded organ, protected by a thick layer of bone and an internal barrier that prevents many substances from getting into brain cells. But when injury does strike – from head trauma, stroke or disease – the consequences can be devastating. This is because a substance called glutamate inundates the surrounding areas, overloading the cells in its path and setting off a chain reaction that damages whole swathes of tissue. Glutamate is always present in the brain, where it carries nerve impulses across the gaps between cells. But when this chemical is released by damaged or dying brain cells, the result is a flood that overexcites nearby cells and kills them.
A new method for ridding the brain of excess glutamate – one that takes a completely new approach to the problem – has been developed at the Weizmann Institute of Science. Previous attempts to treat glutamate damage have been based on drugs that must enter the brain in an attempt to prevent glutamate from acting. However, many drugs can’t cross the blood-brain barrier, while other promising treatments have proved ineffective in clinical trials. Prof. Vivian Teichberg of the Institute’s Neurobiology Department, working together with Prof. Yoram Shapira and Dr. Alexander Zlotnik of the Soroka Medical Center and Ben-Gurion University of the Negev, has shown that in rats, an enzyme in the blood can be activated to “mop up” toxic glutamate spills in the brain and prevent much of the damage. This method may soon be entering clinical trials to see if it can do the same for humans.
Though the brain has its own means of recycling glutamate, thus keeping this substance in balance, injury causes the system to malfunction, allowing glutamate to build up to dangerous levels. Teichberg reasoned that this problem could be circumvented by passing the glutamate from the fluid surrounding brain cells into the bloodstream. But he first had to have a clear understanding of the existing mechanism for moving glutamate from the brain to the blood. Glutamate concentrations in the blood are several times higher than in the brain, and the body must be able to pump the chemical “upstream,” from an area of low concentration to one of high concentration. Glutamate pumps, called transporters, are found on cells on the outside of blood vessels that come into contact with the brain. Transporters collect glutamate from between brain cells, creating small zones of high concentration that facilitate the release of glutamate into the bloodstream.
Basic chemistry told Teichberg that he could affect transporter activity by manipulating the glutamate levels in the blood. When the blood’s glutamate levels are low, the increased difference in concentrations causes the brain to release more glutamate into the bloodstream. Using an enzyme called GOT that is normally present in blood to bind glutamate chemically and inactivate it, he effectively lowered glutamate levels in the blood and kicked transporter activity into high gear. In their experiments, the scientists used this method to scavenge blood glutamate in rats with simulated traumatic brain injury. They found that glutamate was effectively cleared out of the animals’ brains, and damage was prevented.
Yeda, the technology transfer arm of the Weizmann Institute, now holds a patent for this method, and a new company based on this patent, called Braintact Ltd., has been set up in Kiryat Shmona in northern Israel. It is currently operating within the framework of Meytav’s Technological Incubator. The USFDA has assured the company of a fast track to approval. If all goes well, clinical trials are planned for the near future.
Sections of injured rat brain: left column: untreated, right: after treatment with blood glutamate scavengers. Top: Violet stain reveals normal cell nuclei in treated tissue at right; these are all but missing in the left-hand image. Bottom: The brown line in the treated tissue shows healthy cells, absent in the untreated tissue at left. Photo: Courtesy of Prof. Vivian I. Teichberg of the Weizmann Institute and Dr. Joseph Burda of the Slovak Academy of Sciences
The method could potentially be used to treat such acute brain insults as head traumas and stroke, and prevent brain and nerve damage from bacterial meningitis or nerve gas. It may also have an impact on such chronic diseases as glaucoma, amyotrophic lateral sclerosis (ALS) and HIV dementia. Teichberg: “Our method may work where others have failed, because rather than temporarily blocking the glutamate’s toxic action with drugs inside the brain, it clears the chemical away from the brain into the blood, where it can’t do any more harm.”
Prof. Vivian Teichberg’s research is supported by the M. D. Moross Institute for Cancer Research; the Nella and Leon Benoziyo Center for Neurosciences; the Carl and Micaela Einhorn-Dominic Brain Research Institute; the Mario Negri Institute for Pharmacological Research - Weizmann Institute of Science Exchange Program; Mr. and Mrs. Irwin Green, Boca Raton, FL; and the estate of Anne Kinston, UK. Prof. Teichberg is the incumbent of the Louis and Florence Katz-Cohen Professorial Chair of Neuropharmacology.
Profs. Ronen Basri (l) and Achi Brandt. Find the glasses
Can computers see? Can they be taught to discern a polar bear on white snow? To tell where one spotted Dalmatian ends and another begins? To recognize a woman’s profile after viewing her face-on? Seemingly simple visual tasks that a human being takes for granted pose an enormous challenge to a computer: Every minor variation in lighting or angle interferes with the computer’s ability to perceive and identify objects. Living brains solve these problems thanks to amazing powers; computer scientists are working hard to endow machines with similar abilities.
A unique, innovative approach enabling computers to identify and recognize objects was developed by Dr. Eitan Sharon when he was a graduate student under the guidance of Profs. Ronen Basri and Achi Brandt of the Weizmann Institute’s Computer Science and Applied Mathematics Department, in collaboration with departmental colleague Dr. Meirav Galun and Dr. Dahlia Sharon of the Massachusetts General Hospital. The approach involves a multi-stage process that works from the bottom up.
The computer starts by comparing the individual pixels in an image and divides them into groups according to the degree of light intensity. The resulting groups go through a series of additional comparisons using such properties as texture, shape and so on. Groups that share common features are combined into increasingly larger segments, and at each stage the parameters for comparison become more numerous and complex. At the end of this process, known as segmentation, the computer can distinguish an object from its background.
After obtaining good results at this stage, the scientists moved on to the next challenge – object recognition. As in a children’s “find the hidden object” game, the computer was instructed to scan through a large database and pick out an image of a pair of glasses identical to a pair it was shown. To perform this task, the computer divided a picture of the glasses into segments and compared these with all the glasses segments in the database, searching for examples whose features matched those of the original pair. At the end of the process, it succeeded in finding the identical glasses, even when these appeared at a different angle or in a slightly different way from the original pair. The method was recently described in the journal Nature.
Now that the computer is capable of recognizing objects, can it be put to medical use – recognizing signs of disease? To test this idea, which has been explored by researchers around the world in a variety of ways, the Institute scientists defined a goal: identifying lesions in the brains of patients with multiple sclerosis. In these patients, the protective myelin sheath covering the nerve fibers is damaged, and this damage shows up in magnetic resonance imaging (MRI). The imaging provides the physician with a series of brain sections, which today must all be reviewed by a human being. “In the distant future, we hope that a computer program will be able to recognize the damaged areas independently,” says Basri. “In the more immediate future, the system should be able to help the physician identify these areas and provide information about their location and size, so as to be able to evaluate the patient’s condition or the effectiveness of treatment.”
With the help of Prof. Moshe Gomori, a radiologist from Hadassah University Hospital in Jerusalem, the scientists made a number of adjustments to the computer program, enabling it to analyze a three-dimensional image constructed from all the MRI section scans. Data processing then followed the same stages as object recognition: The picture of the brain was divided into segments, and each segment was characterized by a set of features defined by expert radiologists: light intensity, texture, shape and location in the brain. Then followed classification: The computer examined different segments and decided whether an area was healthy or damaged. Decision making involved a learning process: The computer reviewed pictures of brain areas affected by multiple sclerosis and gradually learned to characterize them.
The first experiments have produced encouraging results: 60 to 70 percent of areas labeled by the computer as affected matched the physician’s assessment – a percentage similar to the degree of agreement between two physicians. Results of the study, performed by Ayelet Akselrod-Ballin, a graduate student of Basri and Brandt, in collaboration with Italian colleagues, were published in the Proceedings of the 2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition.
The Weizmann Institute method has great potential for the diagnosis of any disease or disorder that produces signs visible through MRI or computed tomography scanning. The scientists are already working on additional applications, including the development of a program to identify liver tumors.
Now that they’ve taught the computer to see, Institute scientists hope to turn it into a multidisciplinary doctor’s aide that will be found in every clinic, assisting in the diagnosis and follow-up of a variety of ills. Once this vision is realized, they will only need to teach the computer to show a little empathy and tell the patient to say “Ah!”
Prof. Ronen Basri’s research is supported by the A.M.N. Fund for the Promotion of Science, Culture and Arts in Israel.
Prof. Achi Brandt’s research is supported by the Philip M. Klutznick Fund for Research. Prof. Brandt is the incumbent of the Elaine and Bram Goldsmith Professorial Chair of Applied Mathematics.
Profs. Eitan Bibi and Deborah Fass. Working in the wet
Even in the most thoroughly researched fields, surprises can still turn up. Once in a while these surprises challenge the accepted wisdom, even when that wisdom is well founded in fact. For instance, scientists studying the family of enzymes known as proteases recently found a new type of protease that seemed to stand the body of knowledge about these enzymes’ actions on its head.
Proteases (literally: protein cutters) are a large collection of enzymes responsible for clipping proteins. Because they are found in every life form and play key roles in numerous basic life processes, proteases are some of the best-studied enzymes around. But recent research turned up evidence of another long-lost branch of the family. While their well-known cousins are to be found floating in fluids inside or around the cell, these proteases are hidden away, embedded in the cell membrane. It was the enzymes’ location inside the membrane that created a paradox for the researchers: The proteases they had studied require water molecules to help them cleave proteins. The interior of the cell is hydrophilic – water-loving – and the enzymes have no trouble finding water molecules to use there. By contrast, the cell’s outer wall – the cell membrane – is made of fatty molecules that are water-repellent. How, then, could a protease function in this environment?
At first, scientists, steeped in the common wisdom, doubted the evidence hinting at the existence of membrane-bound proteases. Findings, however, continued to mount showing that they not only exist, but are involved in a range of important activities in the cell. These activities include intercellular communication, signaling inside the cell, regulating programmed cell suicide and preventing invasion by parasites. Membrane proteases also play a role in the formation of beta-amyloid protein segments such as those that accumulate in the brain in Alzheimer’s disease.
Yet the central question re-mained: How does protease activity, dependent as it is on water, take place in a water-repellent environment such as the cell membrane? To answer this question, Prof. Eitan Bibi and postdoctoral fellow Dr. Adam Ben-Shem of the Biological Chemistry Department, together with Prof. Deborah Fass of the Structural Biology Department, succeeded in solving the three-dimensional structure of a protease found in the cell membrane of the bacterium E. coli. The study, which recently appeared in the Proceedings of the National Academy of Sciences (PNAS), points to a possible mode of action for this enzyme – one that suggests an answer to the paradox.
The enzyme is made up of six coils joined together by loops. Five of the six coils form a sort of cylinder that transverses the membrane, extending out past the membrane surface on either side. Inside this tube, the sixth coil, shorter than the others, harbors the protease’s active site – where the actual cutting is performed. Situated right above the active site, supported by the ring of coils, is a sac-like structure that’s padded with amino acids. These amino acids carry electrical charges on their ends that attract water, and the sac’s position implies that the water molecules are then funneled down to the active site to create a hydrophilic mini-environment in which the enzyme can work.
GlpG protease structure and position in the cell membrane
In solving one mystery, however, the scientists stumbled on another: How does the protein that’s cut by the protease gain access to the active site, which is set deep within the enzyme structure and surrounded by closely packed protein coils? The research team’s findings suggest a number of possibilities. In one place, the structure showed evidence that one of the loops binding two of the outer coils together might act as a gate that opens to let in the protein molecule. Alternately, a V-shaped opening that showed up between another two coils might give the protein access. But both openings are far from the active site, and the scientists believe that protein, protease or both probably need to undergo a change in shape for cleavage to take place. “A change in the structure of the substrate protein might allow it to access the enzyme’s active site and also expose the spot that needs cutting,” says Bibi.
The next stage of inquiry poses a challenge to the researchers. The enzyme’s location makes it hard to study, and they are currently searching for ways to observe the changes it undergoes as it cuts proteins deep inside the cell membrane. Because membrane proteases are so widespread and are vital to so many of the cell’s functions, this research is likely to have an impact on a wide range of biological and medical research.
Prof. Eitan Bibi’s research is supported by La Fondation Raphael et Regina Levy.
Prof. Deborah Fass’s research is supported by the Clore Center for Biological Physics; and the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly.
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Introducing Impurity