<p>
Science Feature Articles</p>

And Energy for All

English
Prof. Yitzhak Maron. Containing fusion
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
An ancient Greek myth relates that Prometheus, son of gods, stole fire from the heavens and gave it to the people on Earth. This gift and all its many applications catapulted humankind from a harsh, primitive existence toward civilization. Today, scientists in many parts of the world seek to perform a Prometheus-like act, granting human civilization a new energy source that will propel it forward once again. They are looking for ways to harness nuclear fusion, the process by which the sun and other stars generate their abundant energy. Formerly this process was used for destructive purposes: to fuel the explosion of the hydrogen bomb. Today’s researchers, however, pursue peaceful applications of nuclear fusion for its greatest potential benefit: a safe and abundant energy source for all humankind.
 
The existence of nuclear fusion was first hypothesized in the 1920s, and in the late 1930s it was described in quantitative terms by Hans Bethe and others. They discovered that light chemical elements appear to act in an “anti-holistic” manner: the whole is somehow smaller than the sum of its parts. For example, the overall mass of the nucleus of helium (which can be created by fusing two hydrogen atoms) is smaller than the joint mass of its components. What happens to the small mass missing from the helium nucleus? It turns out that when the helium nucleus is created by the fusion of its parts, this mass is converted into energy in accordance with Einstein’s famous equation, E=mc2 (energy = mass x the speed of light squared).
 
From this equation, one can see that a very small amount of matter can yield enormous amounts of energy. Indeed, calculations show that the energy released by fusing 25 grams of hydrogen into helium could provide all the energy needs of a person living in the Western world throughout his or her entire lifetime. And hydrogen is the most abundant element in the universe. Fusion for energy production is environmentally friendly, safe and clean: there is substantially less radioactive waste than with nuclear fission and no harmful byproducts such as the carbon dioxide associated with fossil fuels – a significant contributor to global warming. The catch is that building an installation to convert the energy of nuclear fusion into electricity is like trying to harness a raging tiger to a supermarket shopping cart. Nuclear fusion is a tumultuous event with huge, destructive potential; safely controlling the process is the biggest challenge facing fusion researchers today.
 
Nuclear fusion is the result of a sort of atomic train wreck: two stripped-down hydrogen isotopes speed toward each other, accelerating as they go, until they slam into each other with so much force they stick together, releasing “surplus” energy as heat. Because the isotopes – essentially positively charged nuclei – repel each other, their speed must be quite high to overcome the strong forces of electrical repulsion between them.
 

Cooking with plasma

 
For any kind of energy production to be feasible, one must get more energy out of the system than one puts in, over time. Though this may seem self-evident, fusion until now has demanded a colossal amount of energy to achieve the conditions required to get it up and running, and these still fall short of what’s needed to sustain it in a controlled manner: The hydrogen atoms must reach a temperature of at least 100 million degrees centigrade. (In comparison, the temperature at the center of the sun is “only” 15 million degrees centigrade.) This intense heat transforms the hydrogen gas into a plasma of hot, electrically charged ions. (Plasma is the fourth state of matter after solids, liquids and gases.)
 
Unfortunately, hot and dense plasma, the favored medium for fusion, seeks to expand, thereby losing its heat and reducing the chances for atom collision. The energy invested in containing the plasma and creating the right conditions for nuclear fusion has until now been much greater than the energy obtained. Today, intense research efforts are aimed at finding ways to increase the efficiency of the process and enable it to become “profitable.”
 
Several methods have been proposed to this end. For instance, giant, hollow donuts, the size of football fields, employ strong magnetic fields to keep plasma going for about one second. That’s an eternity compared to the life span of the plasma created in a second approach, where much hotter and denser plasma is formed in a mini-scule area, just a few millimeters in size, for only ten billionths of a second. In this method, there’s no need to contain the plasma – it’s so hot and the atoms are so close together, fusion takes place within that tiny instant.
 
One way to create the extremely hot and dense plasma needed for the second method involves compressing the plasma with powerful pulses of magnetic fields produced by strong electrical currents. In the past decade this approach has led to several breakthroughs, most of them achieved at the Sandia National Laboratories in the United States, which has close ties and an open exchange of ideas with the Weizmann Institute. Still, numerous basic questions need to be answered, calling for additional research. That’s where Prof. Yitzhak Maron and his plasma laboratory in the Particle Physics Department enter the picture.

 

Modest facility, international scale research

 
The Weizmann Institute of Science is one of only two research institutions outside the United States involved in the University Excellence Center – a prestigious initiative sponsored by the United States Department of Energy that promotes research into hot and dense plasma. Maron and the scientists who work with him in the relatively small system on the Weizmann Institute campus study the behavior of plasma created using the leading approach in this area, known as Z-pinch. (Z-pinch refers to the vertical, or Z, axis on a three-dimensional grid; in this method, magnetic pulses compress plasma in a vertical tube along the Z axis.) By investigating the behavior of Z-pinched plasma and the different processes by which this plasma’s kinetic energy is converted into heat and radiation, the scientists hope to identify those in which energy will undergo the most efficient conversion. In other words, they are looking for ways to get the most usable radiation energy output for the least input.
 
Capturing processes that take place within nanoseconds at blistering temperatures requires sophisticated methods. Maron’s group uses spectroscopy, the technique scientists employ to study the most remote and violent areas of the universe. Their equipment captures the spectra of radiation emitted from the plasma, translating light intensities and wavelengths into information about plasma components and their properties: temperature, density, electric and magnetic fields, and atomic velocities.
 
Expanding magnetic field in plasma
 
 
Researchers in Maron’s lab, in collaboration with scientists from the University of Jena and the GSI Laboratory in Germany, have recently come up with innovations in spectroscopy, making it possible to obtain better information about dynamic plasma processes. With these innovations, Dr. Eyal Kroupp and his team in the Institute’s plasma labmeasured and tracked very rapid changes in the energies of the plasma ions. A series of spectral images captured at increments of one per nanosecond (one billionth of a second), at ultrahigh spectral resolution, is what allowed them to see more clearly than ever what happens in plasma. The images revealed cases in which most of the compressed plasma energy is converted to radiation. The innovative methods developed by Maron’s team are now being employed in large laboratories in the United States and Europe.
 
In other experiments, Dr. Ramy Doron and a team of researchers in Maron’s laboratory were able to observe plasma phenomena never before seen in a lab, such as ions separating and electrons accelerating at the advancing edge of magnetic fields. Similar phenomena have recently been recorded by research satellites monitoring the plasma and magnetic activity of the sun, and the scientists are currently discovering what laboratory measurements can tell us about events observed from space. Thus out of one relatively modest laboratory comes research that contributes insights into the universe in which we live, as well as those that bring us closer to the use of controlled nuclear fusion for making our own world more livable.

 
Prof. Yitzhak Maron’s research is supported by the Monroe and Marjorie Burk Fund for Alternative Energy Studies; Sandia National Laboratories; and Dr. and Mrs. Robert Zaitlin, Los Angeles, CA. Prof. Maron is the incumbent of the Stephen and Mary Meadow Professorial Chair of Laser Photochemistry.
 

 

Prof. Yitzhak Maron. Creating a hot, dense plasma
Space & Physics
English

A Beautiful Magnetic Mind

English

 

Clinical depression and addiction can spin destructive realities – crushing careers, dreams, families, even life itself. Depression is considered a leading cause of disability in the Western world, affecting 120 million people, while some 90 million worldwide were diagnosed in 2003 with addictive disorders associated with alcohol and drug abuse. Recent studies show that these conditions share a common biological link in areas of the brain referred to collectively as the “reward system.”
 

Dr. Abraham Zangen of the Institute’s Neurobiology Department investigates the reward system's role in mitigating stress – one cause of depression. This part of the brain, he found in several experiments, produces chemical compounds in a number of stressful situations. For instance, rats pressing a lever received a mild electrical stimulus straight to their reward centers; when this pleasurable sensation was withheld, the brain released beta-endorphin – which has an effect much like a mild dose of morphine. This neurochemical response may be the reward system's way of coping – a sort of “consolation prize” to allow animals to adapt to a new situation and perhaps mitigate feelings of frustration and stress. Rats, humans and other mammals share a similar neurochemistry, suggesting that imbalances in these chemicals in the human brain’s reward system could be tied to depressive or addictive tendencies, in which stress is a key factor.
 

“In the black box of psycho-physics, the reward system is a small window to understanding how the mind and the brain relate,” says Zangen. He predicts that the several parallel paths of study he currently pursues will ultimately converge to improve understanding of the brain's reward system and its effects on behavior.

 

Another of his research paths targets chronic cocaine use, which can cause permanent changes to the network of neurons in the reward system, compromising its ability to mediate motivation and pleasure. Zangen wanted to see if stimulation to specific deep brain areas could reverse these neuro-logical changes. His team, which included Ph.D. student Dino Levy, found that rats treated with electrode stimulation of a specific reward-related brain region during cocaine detox exhibited 50% less cocaine-seeking behavior than the control group. There was also a measurable improvement in the treatment group’s brain chemistry: The electrode stimulation partly reversed cocaine-induced changes affecting glutamate, one of the reward system's key neuro-transmitters. Further study is in progress to elucidate the neurochemical effects of such electrode stimulation as well as the potential therapeutic benefits.
 

Could deep brain stimulation be applied to humans with problems related to reward system dysfunction? Zangen was interested in a non-invasive technique known as transcranial magnetic stimulation (TMS) – a method of triggering electrical responses in the brain through the use of external, rapidly alternating magnetic fields. TMS however, can penetrate only the outer layers of the brain – up to about 2 cm – whereas the reward system is buried much deeper. Efforts to increase its range by increasing the magnetic field intensity were unsuccessful, sometimes having an intolerably painful effect on subjects. Zangen conceived of a device that would produce low-level magnetic fields arranged radially so as to come together only at the desired deep brain region.

 

Dr. Abraham Zangen. Magnetic stimulation

 

In collaboration with Yiftach Roth, a graduate student at Tel Aviv University, he designed and perfected the device, using computer modeling techniques and a “phantom” brain – a spherical container of a solution with the same conductivity as the brain. Their final design, the “H-coil,” was patented in 2002 by the National Institutes of Health, USA. Zangen and his colleagues recently tested the device on healthy volunteers in the U.S. and found it attained depths of up to 6 cm – deep enough to reach reward system centers.
 

The H-coil may, in the future, enhance many areas of brain research and treatment. For depression, Zangen believes the H-coil may offer an effective alternative to electroconvulsive therapy. Variations in the design of the H-coil may potentially be useful for the treatment of addiction, neurological disorders such as epilepsy, and diseases such as Alzheimer's and Parkinson's.    

 

Joystick

There is a large genetic component to depression. To link specific genetic factors to behavior, Zangen has employed a number of rat testing methods, including the swimming test – widely used for analyzing levels of motivation. Zangen and Ph.D. student Roman Gersner recently developed a novel approach that improves diagnostic accuracy and objectivity in this swimming test. Instead of timing periods of activity with a stopwatch, they use a joystick to measure the swimming rat’s limb motion, which is recorded and plotted by computer. Zangen predicts this methodology will contribute to a better mathematical analysis of behavior and potential drug effectiveness.

 

A Promising Career

 

Dr. Abraham "Boomy" Zangen received a B.Sc. in pharmacology from the Hebrew University of Jerusalem in 1991, and from Bar Ilan University, an M.Sc. in biochemical pharmacology and a Ph.D. in psychopharmacology. In 1999, he travled to the US on fulbright and Fogarty scholarships to comlete postdoctoral research at the National Institutes of Health. In 2003 he returned to Israel to a position as senior scientist in the Weizmann Institute's Neurobiology Department. He has reiicved the annual proze of the Israel Society for Biological Psychiatry (twice), a Fellows Award for Research Excellence for the NIH and published over 25 papers in scientific journals.

 

Zangen lives in Jeruslaem with his wife, Rachel, and their four children.

 

Dr. Abraham Zangen’s research is supported by the Nella and Leon Benoziyo Center for Neurological Diseases; the Carl and Micaela Einhorn-Dominic Brain Research Institute; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the Charles and M.R. Shapiro Foundation Endowed Biomedical Research Fund; and the Lord Sieff of Brimpton Memorial Fund. Dr. Zangen is the incumbent of the Joseph and Celia Reskin Career Development Chair.

 
Dr. Abraham Zangen. Rewarding research
Life Sciences
English

Send in the Substitutes

English

If there were no bench for second-string players on a football team, who would substitute for tired or injured team members? Weizmann Institute scientists have found that, if the team were made up of genes, they might pull athletes who can play a little football in a pinch from nearby basketball or rugby teams.

 

Dr. Yitzhak (Tzachi) Pilpel and graduate students Ran Kafri and Arren Bar-Even, of the Institute’s Molecular Genetics Department, knew from previous studies that up to 80% of the genes in yeast, a common model for genetics research, have potential stand-ins in various spots around the genome. Though not identical to the original gene, they make a protein that is sufficiently similar to the one it produces to pass muster. Many scientists believed that both genetic substitutes and the main gene were expressed simultaneously so as to supply the organism with needed quantities of proteins. But Pilpel and his team showed in a study published in Nature Genetics that in fact when the original gene is up and running, the others are off playing at their own sports. Only when that gene is damaged or deleted do the substitutes get called onto the “football field,” where they play as best they can.

 

Dr. Yitzhak Pilpel. Similar enough

 

The scientists reached this conclusion after analyzing data from some 40 studies of yeast cells by different research teams around the world. Using the latest bioinformatics techniques to identify patterns and trends in the enormous flux of data supplied by these studies and by the sequencing of the yeast genome, they proposed a “football coach” mechanism that knows when to call up the substitute players.

 

This “coach” gets the lowdown on the players’ performance from the raw materials genes use to make proteins. When a gene is working at full capacity, it will use up most of the raw material available to it, leaving little in its original state. But if it’s not making sufficient quantities of protein, or producing defective proteins that are missing bits, a relatively larger amount of the raw material will be left over. Raw material that is sitting around activates a special set of proteins, called transcription factors, whose job is to turn on genes. The transcription factors then bind to, and activate, the substitute genes.

 

Why evolve genes to make proteins that are similar but not identical, and thus imperfect substitutes? Pilpel’s group proposed that the small variations between exchangeable genes, such as differences in the conditions that cause them to be activated, impart to each a unique function. These differences in function make them sufficiently vital to be preserved by evolution, yet allow them, when necessary, to step in for a gene on a different team as a substitute player.

 

Dr. Yitzhak Pilpel’s research is supported by the Leo and Julia Forchheimer Center for Molecular Genetics; Mr. Nathan Kahn, Riverdale, NY; the Ben May Charitable Trust; the Dr. Ernst Nathan Fund for Biomedical Research; the Rosenzweig-Coopersmith Foundation; the Samuel M. Soref and Helene K. Soref Foundation; and Mr. Walter Strauss, Switzerland.

 
Dr. Yitzhak Pilpel. Gene team
Life Sciences
English

Battle Hymn of the Immune System

English

Cohen and Domany. antigen chip developers

 

They volunteer in the largest army in the world. They don't get uniforms, or boots, or a paycheck, but they're heavily armed. They patrol, check identification, isolate and render harmless all suspicious objects, and fight every battle to the death. Their mission: to guard against invasion. Their unit name: the immune system.
 

As in any army, however, mistakes are made. Communication breaks down and casualties result from friendly fire. Physicians generally lack information about the immune system’s overall battle plan, relying instead on limited information obtained through the questioning of a few scouts. “Medical strategies could be more effective with global information about the system,” says Prof. Irun Cohen of the Immunology Department. Meanwhile, researchers at the Weizmann Institute have developed a way to eavesdrop on the immune system's communication network for clues about the battles being waged.

 

Immune system cartoon

 

Communications are critical, for instance, to antibodies, the specialized soldiers of the immune system. Antibodies fight against foreign agents (antigens), but they must be trained to distinguish antigens from normal parts of the body (self-antigens). One small breakdown in identification or communication can trigger an autoimmune response – a deadly attack on self-antigens.  Autoimmune diseases are typically chronic and range from slight allergies, to painful and disfiguring diseases like rheumatoid arthritis and multiple sclerosis, to potentially fatal diseases like diabetes. One’s susceptibility or resistance is dependent on the collective state of the immune system, which may be vulnerable for a number of reasons, ranging from inheritance to lifestyle.

Recognizing that an effective defense initiative requires cooperation, Cohen formed an alliance with Prof. Eytan Domany of the Physics of Complex Systems Department. Drawing upon their combined knowledge of biology, immunology, bioinformatics and physics, the two researchers teamed up to develop a comprehensive analysis of the immune system. They hoped to find patterns in an individual’s repertoire of antibodies that might make it possible to predict resistance or susceptibility to various diseases.

 

The team elected to study Type 1 diabetes. Prediction is particularly important for diabetes because most of the pancreatic cells producing insulin have already been destroyed by the disease by the time the patient experiences any symptoms. There is no cure, and the prognosis is lifelong insulin dependence, susceptibility to kidney damage, loss of eyesight, leg amputation, coma and death.  
    
In their first collaborative study, the two groups obtained the “immune fingerprints” of both diabetic and healthy subjects – finding each person’s unique complement of antibodies by testing blood samples for interaction with 80 different antigens. They were able to demonstrate that such fingerprints can be used to identify diabetic subjects. This type of trial, however, is very labor-intensive, making it impractical for large-scale, multiple-antigen testing.
 

Cohen’s lab, therefore, took the lead in developing a chip that would allow testing for a large number of antibodies. The antigen chip contains many hundreds of minuscule antigen dots. Each of these dots attracts a different antibody out of a blood sample, which will hook on to it, just as it would attach to a natural antigen in the body. Researchers from Domany's lab assisted in perfecting the chip for clear and consistent results – a process that took eight months to complete. In theory, data from this exercise could be used to create an extensive profile of an individual’s immune system and perhaps even enable a physician to predict susceptibility to various diseases before they develop.
 

Obtaining a reading entails shining a laser light on the chip, which gives researchers information not only about the presence of antibodies that bind to the antigens printed on each spot, but also about their relative concentrations. The chip yields unwieldy quantities of information, so to make sense of the numbers, Domany’s group used an algorithm they developed to detect clusters and patterns in large amounts of data. From the original hundreds of antigens, 27 could be used to predict into which of two groups tested mice would fall: those that would become diabetic in the future and those endowed with resistance to the disease.
 

The researchers credit their in-vention to the cross-fertilization of ideas between their respective scientific fields: “Our multi-disciplinary approach,” says Domany, “led to new questions and new methods for finding answers.”
 

“Solutions for many types of illnesses and diseases have their foundations in understanding the collective behavior of the immune system,” explains Cohen. Armed with antigen chips, immunologists may gain a new advantage in the fight against silent and deadly enemies. The possible applications range from treating autoimmune diseases to fighting bioterrorism.

 

A number of people were involved over several years in researching and developing the antigen chip; they include Francisco Quintana, Gaddy Getz, Gad Elizur, Ilan Tzafrir, Dafna Tzafrir and Peter Hagedorn.

 

Prof. Irun Cohen’s research is supported by the Minna James Heineman Stiftung; the Robert Koch Minerva Center for Research in Autoimmune Disease; and Mr. and Mrs. Samuel Theodore Cohen, Chicago, IL.  Prof. Cohen holds the Helen and Morris Mauerberger Professorial Chair in Immunology.

 

Prof. Eytan Domany’s research is supported by the M.D. Moross Institute for Cancer Research; the Yad Abraham Research Center for Cancer Diagnostics and Therapy; and the Ridgefield Foundation, New York, NY. Prof. Domany is the incumbent of the Henry J. Leir Professorial Chair.

 
(l-r) Prof. Irun Cohen and Prof. Eytan Domany. Profiling the immune system
Math & Computer Science
English

Splice of Life

English

 

Genes may contain the blueprint for life, but they’re written more like coded messages in a spy thriller: Short segments of DNA carrying instructions for protein formation are imbedded in a longer text, and interspersed with “filler” DNA that has no known function. The picture becomes still more complicated when one realizes that the useful “characters” in the genetic code may be pieced together, or spliced, in different combinations. “Alternative splicing” allows relatively few genes to give rise to a great number of protein structures.

 

Since the discovery of RNA splicing, around 25 years ago, scientists have worked to understand how the right sequences are lifted out and strung together to make a coherent set of instructions. Both straightforward and alternative splicing take place in the “spliceosome,” situated in the cell nucleus. A large complex of proteins and short strands of RNA, the spliceosome distinguishes the beginnings and ends of coded segments, precisely cutting and “stitching” them together.
 

A husband-and-wife team, Prof. Ruth Sperling of the Hebrew University of Jerusalem’s Genetics Department and Prof. Joseph Sperling of the Weizmann Institute’s Organic Chemistry Department, has produced the most detailed 3-D representation of the spliceosome’s structure to date. Rather than follow others’ attempts to observe spliceosomes created in test tubes, the Sperlings and team members Maia Azubel, Ruth’s graduate student, and Sharon Wolf of the Institute’s Chemical Research Support Department managed to take spliceosomes directly from living cells and examine them under an electron microscope. 
 

The living spliceosome presented them with a challenge. In cells they come packaged in sets of four identical modules strung together like beads on a strand of RNA, each a miniature spliceosome capable of splicing on its own. The connections between the modules tend to be flexible, allowing the position of the units to vary in relation to one another, and making pinning down a definitive shape and structure for the whole complex close to impossible.

 

Spliceosome, including internal tunnel

 

 

The team found a way to cut the RNA connections between the modules without harming the integral short strands of RNA that are essential to the splicing process, so they could study them individually. Split-second freezing at very low temperatures allowed the scientists to view the spliceosome units in a state as close to natural as possible. From thousands of images, each at a slightly different angle, a composite 3-D structure of the spliceosome was built up. 

 

The revealed structure has two distinct, unequal halves surrounding a tunnel. The larger part appears to contain proteins and the short segments of RNA, while the smaller half is made up solely of proteins. On one side the tunnel opens up into a cavity, which the researchers think functions as a holding space for fragile RNA waiting to be processed in the tunnel itself.

 

What they didn’t see may be as important as what they saw. Whereas researchers examining splicing in test tubes saw evidence of a complicated sequence of events in which the spliceosome machinery assembles itself anew for each splicing job, the team’s investigations of spliceosomes from live cells found splicing to take place in preformed machines. This fits in with what is known about the way cells optimize their workload.  “It’s much more efficient to have a machine on hand, ready to go, than to build a new one each time,” they noted.

 

Prof. Joseph Sperling’s research is supported by the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly; the J & R Center for Scientific Research; the Joseph and Ceil Mazer Center for Structural Biology; and Lois Zoller, Chicago, IL. Prof. Sperling is the incumbent of the Hilda Pomeraniec Memorial Chair of Organic Chemistry.

 
A view of the spliceosome showing internal details
Chemistry
English

Betting on the Side

English

There are gambles, and there are gambles. In a lottery, a modest investment buys a tiny chance of winning a fortune, while in Russian roulette, you run a fairly high risk of losing big-time. Evolution is a high-stakes game that combines features of both. Its instrument, mutation, carries a serious threat: mutations are hundreds of times more likely to be harmful than advantageous. But the right mutation at the right time can grant an all-important winning edge against competition or predators.
 

Recently a team of scientists, headed by Dr. Dan Tawfik in the Biological Chemistry Department, demonstrated how evolving organisms may be hedging their bets in the evolutionary game. In a paper published in Nature Genetics the scientists focused on a group of proteins that exhibit so-called “promiscuous” or “moonlighting” activity. Though evolved to perform a given function, these proteins are able to take on other, often completely unrelated, tasks as well. For example, the enzyme PON1 both removes cholesterol from artery walls and breaks up chemicals used in pesticides. Yet its main function is the removal of a completely different class of compounds. Tawfik believed promiscuity might provide nature with ready-made starting points for the evolution of new functions.
 

To investigate what advantage promiscuity offers, the team, which included Amir Aharoni, Leonid Gaidukov, Olga Khersonsky, Stephen McQ. Gould and Cintia Roodveldt, created a speeded-up version of evolution in the lab. They introduced random mutations into genes coding for a number of promiscuous proteins and selected those mutants with higher levels of activity in one specific promiscuous trait. After several rounds of mutation and selection, the scientists checked their enzymes to see what had changed. As expected, they had managed to increase the targeted activity a hundredfold or more. But did increasing one skill affect the others?

PON structure

 

 

 

 

 

 

 

 

 

 

 

Indeed, though the selection process was aimed at one promiscuous trait alone, any other “moonlighting” activities carried out by the protein also underwent drastic adjustment – some dropping to as low as a thousandth of their former activity, though a few showed a significant increase. However, the primary function for which the enzymes had originally evolved changed by a factor of only one or two at most. “This is particularly surprising when you consider that all of these activities take place at the exact same site on the enzyme,” says Tawfik.
 

“In evolution, two contradictory things are necessary for the survival of organisms,” he says. “First, an organism needs to be robust – that is to undergo as little change as possible in functioning in spite of mutations. But evolutionary adaptation requires some mutations to induce new traits. It appears that the organism can have it both ways: the main function remains robust while the promiscuous functions are extremely responsive to mutation.”
 

Promiscuity may be an intermediate phase for some evolving proteins, the “moonlighting” functions becoming full-time “professions.”  The protein line would then eventually split, diverging into two distinct genes.
 

Multi-tasking may also partly explain another phenomenon that has been puzzling biologists: Proteins both in the body and in bacteria rapidly become resistant to many drugs; and some enzymes, such as PON1, adapt to breaking down man-made chemicals that have been around for only 50-100 years.  But promiscuous functions, because they’re secondary, haven’t been under the selection pressure that drives “traditional” evolution. Such skills may be in the wings, ready to provide the evolutionary shortcut needed for rapid adaptation.   

 

Dr. Dan Tawfik’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the Dolfi and Lola Ebner Center for Biomedical Research; the Estelle Funk Foundation; the Dr. Ernst Nathan Fund for Biomedical Research; the Henry S. and Anne Reich Family Foundation; the Harry and Jeanette Weinberg Fund for Molecular Genetics of Cancer; and the Eugene and Delores Zemsky Charitable Foundation Inc. Dr. Tawfik is the incumbent of  the Elaine Blond Career Development Chair.

 
The 3-D structure of the PON1 enzyme. The main section, in red, is the scaffold of the enzyme and is responsible for PON1’s primary function, while the blue and gray segments can undergo mutation and endow PON1 with additional, promiscuous functions
Life Sciences
English

Billiard Ball Math

English

Your average billiards player down at the local hall might not be aware that the table he’s playing on represents a complex mathematical problem. Imagine a frictionless (and pocketless) billiard table on which a ball bounces endlessly from wall to wall. Though a seasoned billiards player or mathematician might be able to predict where the ball will hit the side once, possibly twice, soon even tiny differences in angle at each strike will add up and become magnified. Thus the further the time from the original bounce, the more impossible it becomes to predict how the ball will continue to move.

Prof. Vered Rom-Kedar of the Institute’s Computer Science and Applied Mathematics Department is one of a group of mathematicians who study the theoretical properties of billiards. More than just an interesting thought problem, billiard mathematics can describe the physics of everyday systems. It had its beginnings in the theories of such scientists as Ludwig Bolzmann, who in the late 19th century suggested that the molecules of gas in a closed container are similar to hard spheres in motion. Like the balls on a table, their constant bouncing off each other and the container walls results in pnpredictable, erratic trajectories. This insight led him to formulate his basic law of gases, which roughly states that gas molecules, on average, will scatter evenly throughout a space.

 

Prof. Vered Rom-Kedar. islands of stability

In a highly chaotic system such as Bolzmann’s gas, one cannot foresee where any one “ball” will go, but it’s possible to predict the average outcome for a large number of balls. On the other hand, on a perfectly round table with one ball bouncing off its circular boundary, one can predict the ball’s endlessly repeating course with precision. But what can be said about systems that have elements of both?

Rom-Kedar and Prof. Dmitry Turaev of Ben-Gurion University of the Negev investigate so-called “mixed systems,” in which “islands of stability” (areas of predictable, repeating orbits) can coexist with chaotic movement. They begin with the shape of the table, which strongly influences movement. The two work with a fancifully shaped group of tables that have inward-curving sides, making them look something like fat cartoon stars. Called Sinai or dispersing tables, these are variations on a well-studied model composed of two moving disks in a rectangle and they were proved to be inevitably chaotic. Rom-Kedar and Turaev have been demonstrating how, with the slightest of modifications, these highly chaotic systems can give way to mixed ones.

 

Painting by Prof. Vered Rom-Kedar. billiard balls

 

They suggest mixed systems might arise, for instance, if the balls resemble electrons or ions more than billiard balls. Unlike hard balls, these particles do not bang into one another because they carry repellent charges – the particles are deflected before they can make contact. Another way to think of the problem, says Rom-Kedar, is as a system with one ball and elastic walls. As opposed to a sharp impact, which not only changes a ball’s direction but jolts its energy potential, the potential energy of a deflected electron, or of a ball rebounding from an elastic wall, will change in an even, unbroken curve, termed “smooth” or “soft” potential.

Rom-Kedar and Turaev proved that smooth potential allows islands of stability to be created on dispersing tables; they found, furthermore, how the relative hardness or softness of the wall affects the island’s size. Islands of stability come into being, in this case, if a part of the ball’s path forms a tangent to one of the concave boundaries. In another collaborative paper, the two proved that hitting corners – as long as those corners have set, finite angles – can also send the ball on a non-chaotic, stable, repeating path.

The published billiards research relates to two-dimensional tables. Now, with graduate student Anna Rappaport, the mathematicians are working on a theory for smooth, billiard-type systems of higher dimensions. “If we accomplish that,” says Rom-Kedar, “we’ll be closing in on a mathematical understanding of Bolzmann’s hypothesis.”

 

Atomic Billiards

Prof. Nir Davidson of the Physics of Complex Systems Department has been working for the last few years on trapping atoms in what are arguably the world’s smallest “billiard tables.” These are so-called dark optical traps – a small number of atoms held in a dark space surrounded by a thin wall of laser beam light.  He and his team were working on refining the walls of their traps, changing the shapes and trying to thin down the width of the beams.

 

But the atoms bouncing off the experimental walls were behaving unpredictably. The laser walls were “spongy” – the atoms sank into them a little way before bouncing back, and the walls’ slopes, never exactly 90°, seemed to affect the way the atoms moved.

 

At this point Prof. Uzy Smilansky of the same department suggested that Rom-Kedar and Turaev’s work on soft-sided tables and islands of stability might hold answers to some of the physicists’ questions. Indeed, the billiards formulas were able to predict how changes in the thickness and slope of the laser enclosure would affect the motions of the entrapped atoms, giving Davidson’s group a solid mathematical basis for its observations.

 

Later, Davidson’s group noticed that atoms hitting the corners of the traps tended to come back to their starting points, and mentioned this to Rom-Kedar. This observation led her and Turaev to their mathematical study of the conditions needed to create islands of stability for corners.

 

Prof. Vered Rom-Kedar. Stability in chaos
Math & Computer Science
English

Making a Heart

English
 
Right from the beginning, life is all about choices. The decision to proceed down one path eliminates the possibility of taking others, and consequences can be lifelong.
 
Cells in a developing embryo must make such critical, final decisions. The thousands of different tissues that make up the body are all derived from one original cell type, and in the earliest stages of development the possibilities are wide open. A cell can decide to become any part of the body, such as heart or bone. But cells do not take the decision-making process lightly. A complex orchestration of events underlies each choice, and these “defining moments” are as yet poorly understood. Mistakes can cause innumerable problems, and if we understood how cells determine their fate during embryonic development, we could perhaps guide them to make better decisions.
 
Dr. Eldad Tzahor of the Biological Regulation Department heads a team of researchers working to identify the series of events occurring during normal embryo development that leads to the formation of heart or skeletal muscle tissue. Among the lab’s sophisticated equipment is a standard white refrigerator full of farm-fresh fertilized eggs. At early stages of development, all vertebrate embryos, from alligators to humans, share remarkable similarities, so the chick embryo, with its short gestation period and easy accessibility, is an ideal model to study developmental biology.
 
Eldad Tzahor. Element of choice
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Tzahor and members of his group are able to isolate so-called progenitor cells from a developing chick embryo and follow their development and differentiation into the various types of tissue. “When I started my research in this field, I tried to isolate cells that should normally develop into skeletal muscle. To my surprise, I saw beating heart cells in the culture dish. Suddenly we realized that the textbook definition of the developmental fate of a certain type of cell was no longer black and white but fairly gray,” says Tzahor. His research revealed a cell’s destiny is not only fate: there’s also an element of choice. The decision depends, in part, on its developmental context: its stage in development, the signals it receives from its neighboring cells and the sequence in which those signals are exchanged. Thus a cell’s proximity to other types of cells at critical stages in its development guides its developmental choices.
 
Tzahor unraveled some of the mystery of the decision-making process by identifying the role of a group of protein molecules called Wnt in managing cell fate decisions. Wnt are signaling molecules that instruct cells not to form a particular cell type - heart, for instance - causing them to follow a different path. Tzahor and his research team are now pursuing the identification and classification of other “general managers” of the differentiation program of embryonic heart cells. Their findings could be an important key to future progress in stem cell research seeking to generate specialized cell types for organ or tissue repair.
 
 
“Cells have to walk and talk together to make decisions that lead to their ultimately separate developmental paths,” says Tzahor. “The molecular crosstalk between cells leads to a perfect orchestration of events that results in the creation of our bodies, but it's in a language that we don't yet understand. Despite the wealth of information we have in the textbooks, the deeper, real-life dynamics of embryonic development are much more complicated.”
 

From Farm fields to Research Fields

 
Growing up on a kibbutz has its advantages: From a young age Tzahor made observations about the cycles of life. His childhood experiences and early interest in veterinary biology help explain why a successful career scientist changed paths to pursue embryonic development research. Tzahor says this career shift has been crucial to his development as a scientist, enabling him to apply and inject new themes and perspectives across a range of fields.
 
In 1988, Tzahor completed a Ph.D. in the Weizmann Institute's Molecular Cell Biology Department under Prof. Yosef Yarden. Following a postdoctoral fellowship at Harvard Medical School in boston, he returned to the Institute as a senior scientist in the biological Regulation Department in 2003.
 
Tzahor is married to Talia and the father of Noam (9) and Roy (4).


 
Dr. Eldad Tzahor’s research is supported by the Estelle Funk Foundation and Mr. and Mrs. Charles Stephens, Somers, NY. Dr. Tzahor is the incumbent of the Philip and Gertrude Nollman Career Development Chair.
 
Dr. Eldad Tzahor. Molecular crosstalk
Life Sciences
English

Reds

English
Each day, your blood travels 19,000 km (12,000 miles) on the circulatory highway. Throughout its journey, a red blood cell (RBC) rides bumper to bumper, enduring dense, merging traffic as it transports its precious load of oxygen or carbon dioxide waste. Like an armored car, the tough blood cell must safeguard the hemoglobin at its center that could damage organs if spilled, yet it must be flexible enough to fold and squeeze into the tiny capillaries where it delivers its load. When RBCs are flawed or malfunctioning, serious, sometimes fatal, illnesses can result.
 
Dr. Nir Gov. Fluctuations mean flexibility
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Dr. Nir Gov of the Chemical Physics Department approaches the puzzle of the red blood cell by studying the physics of its structure, building theoretical models that attempt to explain how this unique cell type’s construction makes it exceptionally well adapted to do its specialized work.
 
Recently, Gov added another, crucial piece to the puzzle. A normal RBC looks like a flattened oval depressed in the center. Helping the cell keep its shape is the cytoskeleton, resembling a springlike wire mesh attached to nodes in the cell's outer membrane. These connections create tension points that hold up the cell wall. It was previously thought that the cell's rigidity/flexibility could be calculated on the basis of the springy properties of the cytoskeleton, but the model developed from this formula wasn’t consistent with experimental results. Something was missing.
 
Working with Prof. Samuel Safran of the Materials and Interfaces Department, Gov found the key to the missing calculation when he took into account the properties of the connections at the nodes. He realized that the presence of ATP, a molecule that converts stored mechanical energy into kinetic motion in the cell, causes transient disassociations and re-associations between the cytoskeleton and the membrane nodes. As tension in the nodes is reduced, motion occurs in the outer membrane. Height fluctuations in the RBC membrane, originally thought to be a negligible effect of small changes in temperature, are instead the result of metabolic activity unique to the living system. This was a defining moment that for Gov highlighted the complexities of modeling dynamic living matter. He proceeded to develop a model linking the presence and concentration of ATP to its effects on cytoskeleton rigidity and, therefore, on RBC shape.
 
RBC models can illuminate important aspects of various diseases and immunities, and these may have vital  impacts on human health research. For example, excessive ATP results in cells that are too flexible, as is the case in some forms of anemia, so that ensuing collisions cause the vulnerable cytoskeleton to break down and the life-giving RBC functionality to be lost. When the ATP level is low, as occurs in some liver diseases, the node connections are too rigid, resulting in stiff, spiky shapes that do not travel smoothly and can block circulation. By modeling, for the first time, ATP’s role in determining the shape and rigidity of the RBC’s outer membrane, Gov has pointed to a completely unexplored avenue of treatment for a number of diseases.
 
In addition, accurate theoretical models might lead the way to creating viable artificial replacements for RBCs. Artificial blood cells could address several problems: rejection, infection and shortages, for example. Gov’s findings might provide a framework for further research in this direction.
 
 
Dr. Nir Gov’s research is supported by the Robert Rees Fund for Applied Research. Dr. Gov is the incumbent of the Alvin and Gertrude Levine Career Development Chair.
 
Dr. Nir Gov. Moving models
Chemistry
English

Dying to Live

English

 

Wallach and his research tem. Understanding the mechanisms of cell life and deathj

 

How does one define the borderline between life and death?” asks Prof. David Wallach of the Biological Chemistry Department. Most doctors agree that cessation of heartbeat or brainwaves is the standard indication of human death. For the body’s cells, too, scientists have clear ideas as to the signs that indicate death. For instance, they can point to specific molecules that are intimately associated with the cell death process. But, as Wallach and an international team of researchers have recently demonstrated, at least one of the molecules most closely linked to cell death may be just as necessary for maintaining cell life.
 

Caspase-8 is a member of the caspase family of enzymes, known to play a central role in the complex process leading to cell death, also called apoptosis. This enzyme’s activation is, in itself, taken as a sign that the cell is on an irreversible path to suicide.
 

In the 20 years that Wallach has been studying apoptosis, he has brought to light some of the more important biological molecules and processes involved, including caspases. Around six years ago, he and his research team used a technique called “gene knock-out” to create mice lacking the gene that produces caspase-8. However, rather than breeding mice with immortal cells, as would be the case if caspase-8 was merely a link in the cell-suicide chain, they found their mice didn’t make it past the embryo stage. Apparently, this “cell death” enzyme also had important roles to play in growth and development.
 

“Unfortunately, when knocking out a gene causes so much havoc in the organism, it's very hard to study its function,” says Wallach. But a recent advance in knock-out technology inspired the team to try once again to unravel caspase-8's role. Called conditional knock-out, it allowed the scientists to delete the gene in only one organ at a time or to turn it off at a specific time.
 

When the caspase-8 gene was knocked out from the liver, the result was, indeed, the creation of cells that refused to die, giving scientists further proof that caspases are crucial to apoptosis in living mammal cells. In contrast, knocking out the caspase gene from the circulatory system produced nearly opposite results. Cells did not grow and develop properly, and the fine capillary blood vessels failed to form as they should. Similarly, knocking out the caspase gene from the stem cells that become various types of blood cells resulted in the complete arrest of blood-cell generation, while deleting it in unformed macrophages (a type of white blood cell) kept them from maturing, showing the “death” gene may be a “life” gene after all.

 

While this study raised some new questions about the mechanisms that control life, another study recently published by Wallach and his team settled the long-standing question of how a protein they had previously discovered helps the cell resist death. Called NIK, this protein relays messages from the immune system outside the cell to an intracellular “messenger service” called NF-kB, which sparks the production of proteins that, among other effects, endow cells with death resistance. But NIK works only some of the time, and the circumstances of its employment were the subject of scientific controversy. Wallach’s team showed that NIK comes into play only if specific receptors on the cell membrane - those tied to the functioning of white blood cells known as lymphocytes - are activated. Because an accumulation of death-resistant lymphocytes is tied to such problems as graft rejection and various autoimmune diseases, NIK is a promising target for new drugs to treat a variety of conditions.

 

Prof. David Wallach’s research is supported by the Kekst Family Center for Medical Genetics; the Dr. Josef Cohn Minerva Center for Biomembrane Research; the David and Fela Shapell Family Center for Genetic Disorders; the Joseph and Bessie Feinberg Foundation; and the Alfred and Ann Goldstein Foundation.

(l-r) Parameswaran Ramakrishnan, Dr. Wangxia Wang, Prof. David Wallach, Tehila Ben Moshe and Dr. Tae Bong Kang. Resisting death
Life Sciences
English

Pages