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Science Feature Articles</p>

The Double Life of a Cancer Gene

English

Without the c-Kit gene, colon cancer cells grow in a disorderly, aggregated manner and are invasive (A); when c-Kit expression is restored in these cells, they revert to a more normal organization (B)

 

 

A murderer turns out to be a saver of lives – this sounds like a plot twist in a thriller, but Weizmann Institute scientists have found that such a scenario can play out in cancer. In a study published recently in Cancer Research, they have discovered that a cancer-causing gene can prevent the deadly spread of a tumor at a later point in the progress of the malignancy.
 
The study’s goal was to identify genes involved in the metastatic spread of colorectal cancer. Working with mice injected with human colorectal cancer cells, the scientists unraveled a long chain of biochemical events that results in metastasis. This chain starts with a mutation present in over 80 percent of patients with malignant colorectal tumors that disrupts a cellular signaling mechanism. The scientists found that the disruption, in turn, increases the expression of a cellular adhesion gene called L1, which enhances the motility of cells at the invasive front of the tumor, facilitating their metastasis to distant organs, in particular the liver.
Prof. Avri Ben-Ze'ev
 

 

Moreover, the scientists discovered that L1 affects the expression of one of the targets in its signaling chain: a gene called c-Kit, which is essential for preventing metastasis. When the levels of expression of this gene were low, the tumors metastasized to the liver. But when normal c-Kit levels were restored, the metastasis stopped even in the presence of L1. The c-Kit gene prevents metastasis by prodding cells to stick together and behave in an orderly fashion, the way they do in normal tissue lining, rather than exhibiting the aggressive, “individualistic” properties of invasive cancer cells.

This finding was a major surprise: c-Kit is known to be an oncogene – that is, a cancer-causing gene. In other words, the same gene that promotes growth in the early stages of tumor development, including the growth of colon cancer cells, has been found to block their spread at later stages!
 
Further analysis suggested that the findings from the mouse study were relevant to humans. When the scientists examined the genomic profiles of tumors in 300 patients with colorectal cancer, they found that in all these patients, c-Kit’s levels were suppressed compared to its levels in the healthy colon.
 
 
infographic_Ben Zeev
 
 

The research team, headed by Prof. Avri Ben-Ze’ev of the Molecular Cell Biology Department, included Dr. Nancy Gavert, Anna Shvab, Dr. Amir Ben-Shmuel, Gal Haase and Eszter Bakos. The research was performed in collaboration with Dr. Michal Sheffer from the computational group of Prof. Eytan Domany of the Physics of Complex Systems Department.

In addition to revealing one of the molecular mechanisms by which colorectal tumors spread to the liver, the most common site of their metastasis, the study has exposed cancer in all its complexity: The same gene can be a “bad guy” at one stage of malignancy and a “good guy” at another.  Weizmann Institute researchers conclude that great caution is required in cancer therapies targeting specific oncogenes. In particular, if drugs are given to block c-Kit so as to stop the growth of colorectal cancer, care must be taken not to interfere with the function of this same gene in preventing metastasis. This conclusion is reinforced by recent studies conducted by other researchers. They had shown that another common oncogene, c-Myc, displays the same duality as c-Kit: while it enhances the growth of breast cancer cells, when overexpressed it prevents their metastatic spread.
 
Prof. Avri Ben-Ze'ev is the incumbent of the Samuel Lunenfeld-Reuben Kunin Chair of Genetics.
 
Prof. Eytan Domany's research is supported by the Kahn Family Research Center for Systems Biology of the Human Cell, which he heads; the Mario Negri Institute for Pharmacological Research -Weizmann Institute of Science Exchange Program; the Leir Charitable Foundations; Mordechai Segal, Israel; and the Louis and Fannie Tolz Collaborative Research Project. Prof. Domany is the incumbent of the Henry J. Leir Professorial Chair.


 
 
Without the c-Kit gene, colon cancer cells grow in a disorderly, aggregated manner and are invasive (A); when c-Kit expression is restored in these cells, they revert to a more normal organization (B)
Life Sciences
English

The 16th Problem

English

David Hilbert, probably the most prominent mathematician around the turn of the previous century, gave a talk at the 1900 International Mathematicians Congress in Paris in which he presented a list of outstanding math challenges for the new era. His full list included 23 problems. He explained to those in attendance: “For the close of a great epoch not only invites us to look back into the past but also directs our thoughts to the unknown future.” Hilbert expected that his 23 problems would be solved by the end of the 20th century. Indeed, most have been solved, but a few have resisted all efforts to find solutions.


Under number 16 on Hilbert’s list appears the “problem of the topology of algebraic curves and surfaces.” This is really a two-part problem: The first involves closed ovals defined by algebraic equations and the second planar problem concerns closed trajectories of differential equations.
 
(l-r) Profs. Dmitry Novikov and Sergei Yakovenko, and Dr. Gal Binyamini. Illustration: Gil Gibli
 

 

The solutions to planar differential equations are expressed as curved lines in a plane that do not intersect themselves. When such a line comes back around to its starting point, thus “closing,” it is called a cycle. Often the other solutions close to such a cycle spiral gradually inward toward it; the cycle is then called a “limit cycle,” and it becomes the limit of all the solutions around it. Such limit cycles are considered important not just for what they reveal about their own solutions, but because they can be used to reveal all the solutions adjoining them.
 
The second part of the problem had essentially been put forward earlier by Henri Poincaré, yet even today it is far from being solved. Despite the difficulty in resolving it, one can state the problem in somewhat simple terms: How many limit cycles can there be in a planar polynomial differential equation of a given order?”
 
A number of attempts to solve the Hilbert 16th problem had been proposed over the years, but these were eventually found to contain fatal flaws. The most significant progress was made by the mathematicians Yulij Ilyashenko and Jean Ecalle, who had each independently proved in the early 1990s that for every planar differential equation there is a finite number of limit cycles. Though it was a tremendous breakthrough, this finding was still far from a complete solution of the problem. At some point, the mathematical community realized that the problem, in its entirety, was resisting their best efforts to solve it; and they turned to intermediate, “weakened” problems in hopes of gaining insight through dealing with these simpler cases.
 
One such relaxed problem, put forward by Ilyashenko, was to focus on equations that are small perturbations of a particular case known as Hamiltonian equations. Hamiltonian equations, among other things, are often used to describe the physics of mechanical systems. They have been used to show, for instance, that when such a system is in perfect energetic balance, it contains no limit cycles.
 
But following a small change in the system, that perfect energy balance can be broken; when this happens, limit cycles arise in the system as if appearing out of nowhere. Ilyashenko proposed to investigate the question of how many cycles can be created this way from a Hamiltonian system and thus to determine the upper limit to this number. Though this problem has been known under a number of different names, today it is most commonly referred to as the “infinitesimal Hilbert 16th problem.”
 
equations
 

The sounds of cracking
 

 
Prof. Sergei Yakovenko, today head of the Weizmann Institute’s Mathematics Department, focused on a particular case of the infinitesimal Hilbert 16th problem in his Masters’ thesis work under Ilyashenko at Moscow University. “Since then,” he says, “I have returned to the question again and again. It is, for me, a sort of beacon pointing me in the most intriguing direction.” Years later, together with his then student Dmitry Novikov – now, himself, a professor in the Institute’s Mathematics Department – Yakovenko succeeded in obtaining several intermediate results. But a comprehensive solution remained elusive.
 
Fast forward eight years: A visitor poking his head into Yakovenko’s office would have encountered the silence of deep thought – and three pairs of feet propped up on the low table in the middle of the room. These feet belonged to Yakovenko, Novikov and research student Gal Binyamini. Or, as Yakovenko describes this scene: “We were banging our heads against a solid brick wall, and suddenly we heard the sounds of cracks appearing. It was an exciting period in my career, and one of the most turbulent.”
 
Binyamini says: “One day, as I was taking my usual walk around campus, I thought of the work of another of Prof. Yakovenko’s students, Dr. Alexei Grigoriev. Incidentally, it occurred to me that it might be possible to ‘rescale’ or ‘stretch’ the arguments he put forward in his thesis in various and different ways.”
 
Rounds of rescaling enabled the team to uncover new properties of a very classical object – linear differential equations with polynomial coefficients – which had previously gone unnoticed. As they built on the information they obtained, the three Institute mathematicians were able to determine an upper limit that represents a full solution to the infinitesimal Hilbert 16th problem.   
 
“That,” says Yakovenko, “is still a far cry from the complete solution to Hilbert’s 16th problem. But then, even the infinitesimal Hilbert 16th problem had stood open for 50 years, until we managed to find an explicit upper bound for the number of newborn limit cycles and thus solve the infinitesimal version. It appears to be one of the most significant advances in this field in the past few decades.”  
 

Prof. Sergei Yakovenko is the incumbent of the Gershon Kekst Professorial Chair.

 

 

 

 

 

 

 
(l-r) Profs. Dmitry Novikov and Sergei Yakovenko, and Dr. Gal Binyamini. Illustration: Gil Gibli
Math & Computer Science
English

The Second Genome

English
 SEM image of the dense microbial ecosystem overlying the 'hilly' gastrointestinal epithelial layer

 

 
 
Our bodies are alive – not just with muscles and nerves but with populations of bacteria and other single-celled organisms that are along for the ride. An estimated 1016 single-celled organisms – ten to a hundred times more than our own body’s cells – reside in each and every one of us. In recent years, we have been coming to understand the significance of these microorganisms – both for the healthy functioning of our bodies as well as for the role they play in such diseases as diabetes, obesity and cancer. If researchers once saw these organisms as “stowaways” that had a limited effect, mainly on the digestive system, today they are understood to be an integral part of who we are. Some even relate to the multicellular host and its population of single-celled organisms as a “super organism” with two genomes, the “second genome” being the combined genetic material of the microorganism population, which is a hundred to a thousand times larger than the “first genome.”

Dr. Eran Elinav, a medical doctor and researcher who recently joined the Institute’s Immunology Department, researches the complicated relationship between the host’s body and the population of microorganisms that call it home. In a series of papers published during his postdoctoral research, Elinav discovered a means of communication for passing messages between different cell types, in the process revealing clues as to how the single-celled population contributes to some of the most common diseases in the Western world: diabetes, cancer, arteriosclerosis and inflammatory bowel disease (IBD).
 
inflammasome infographic
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
The intimate relationship between microorganisms and their host transpires in a number of places, including the skin and such mucus membranes as the mouth and airways. The most dramatic encounters take place in the digestive system; the population density in the gut is one of the highest on the planet. And yet only the single layer of cells lining the gut – the epithelial cells – keeps the inner parts of our body free from this immense microbial population. In a study that appeared in Cell, Elinav found that this layer, which serves as the gut’s first line of defense against unwanted invaders, contains a sort of “snooping device” that helps the immune system keep tabs on the nearby bacteria. The sensor he discovered, called an inflammasome, is one of a group of factors identified in recent years that enable host and bacterial cells to communicate. (Related sensing systems – toll-like receptors – discovered in 1996, were the subject of the 2011 Nobel Prize in Medicine.) When Elinav disrupted the function of this inflammasome in mice, they developed inflammatory bowel disease, thus demonstrating the importance of this factor in keeping the gut healthy.

In further research, Elinav found that this inflammasome may also be involved in metabolic disease and cancer. In one study, which appeared in Nature, he created mice lacking the inflammasome in order to investigate a question about the progression of fatty liver disease: Why does this disorder, which affects up to 30% of the human population in the developed world, cause severe problems in only a minority of them? Most people with the disease do not suffer any serious problems, but around 20-30% progress to complications that include chronic liver inflammation, cirrhosis, tumors and even death. Elinav showed that a change in the composition of single-celled organisms in the gut can act as a “switch” that turns on the complications, and that such changes in the bacterial population may also be implicated in diabetes and obesity. Amazingly, in these instances, metabolic disease and obesity may be transferrable between individuals just by a transfer of these microbes between them. In additional research, he revealed a connection between these microbial changes and the propensity to develop cancer.
 
 
Dr. Eran Elinav
 
In his new lab at the Weizmann Institute, Elinav plans to continue this line of research, both in mouse models and in humans. Because this young field presents a variety of challenges, he has brought together in his group people with experience in different areas: immunology, microbiology, metabolics and bioinformatics; and he has established collaborative partnerships with research groups within the Institute and around the world. He also works closely with the Israel National Center for Personalized Medicine, on the Weizmann campus. “Everyone carries around their unique, personal population of microorganisms, and this, in turn, is affected by everything from diet to geography to environmental exposure. Revealing a person’s ‘second genome’ will give us precise tools, for example, to predict how certain diseases will develop or progress, as well as the ability to tailor individual treatments for such diseases as diabetes, atherosclerosis and cancer,” he says.


Pursuing Medicine and Research

 
Dr. Eran Elinav studied medicine at the Hebrew University of Jerusalem Medical School because, he says: “It is a fascinating profession that combines intellectual and emotional abilities.” During his residency at Hadassah Hospital, he began to take an interest in research. After finishing his residency, in parallel with his work as a doctor in the gastroenterology institute of Sourasky Medical Center in Tel Aviv, he undertook doctoral studies in the group of Prof. Zelig Eshhar at the Weizmann Institute. In 2012, after completing postdoctoral research in the group of Prof. Richard Flavell of the Yale School of Medicine, he joined the Immunology Department of the Weizmann Institute.

Eran is married to Hila, a medical doctor who directs the AIDS center at Hadassah-Hebrew University Medical Center. The couple has twins – Shira and Omri – age 13, and an 8-year-old daughter, Inbal. When he has free time, Eran enjoys water sports, biking and hiking.
 
Dr. Eran Elinav's research is supported by the Abisch Frenkel Foundation for the Promotion of Life Sciences; the Gurwin Family Fund for Scientific Research; the Leona M. and Harry B. Helmsley Charitable Trust; Yael and Rami Ungar, Israel; the estate of Jack Gitlitz; and the estate of Lydia Hershkovich.


 
 
 
 SEM image of the dense microbial ecosystem overlying the 'hilly' gastrointestinal epithelial layer
Life Sciences
English

Down to the Wire

English

 

Platinum wires attached to a single organic molecule (center) can be elongated into a chain a single atom thick

 

The never-ending trend of miniaturization in electronics hits the wall when things get down to the nanometer scale. At this point, it is not enough to make the same device but smaller; new technology is needed. That is why scientists investigate the use of single molecules for electronics. They already know how to get such molecules to conduct electricity, and even how to manipulate the structure of these molecules so as to control the electric current moving through them (in much the same way as a drug molecule’s structure will determine its actions in the body). For example, molecules have been designed to act as switches or one-way valves that regulate the direction of flow of current.

 

However, to use these molecules in electronic circuits, they must be able to connect with metal wires. Until now, such molecules have been held in place between electric wires before use, but even the smallest wires are several orders of magnitude larger than the molecules. Dr. Oren Tal and research students Tamar Yelin, Ran Vardimon and Natalia Kuritz of the Chemical Physics Department recently took a significant step toward bringing the wires into line with the molecules. They managed to connect a single organic molecule to the thinnest electric wire possible: a single-file string of platinum atoms.
 

 

Dr. Oren Tal

 

The scientists first trapped a single molecule between two much thicker platinum wires, and then, immediately afterward, they moved the wires away from each other until the platinum atoms in them were pulled into a chain of atoms that was connected to the molecule on one end and a standard metal wire on the other.

 
The research showed that the electrical conductance of the organic molecule-platinum wire setup was not significantly suppressed by elongating the chains with additional atoms. This implies that such systems might be useful for transferring electronic signals over distances without a significant reduction in intensity. The scientists also experimented with different molecules and molecular structures; they found that different molecules can be wired up in this way. Thus the method could potentially have a wide variety of applications.


Also participating in this research – and helping the group decipher the properties of the new system and the chemical nature of the connection between the atomic strings and the molecule – were the research groups of Prof. Leeor Kronik of the Weizmann Institute’s Materials and Interfaces Department and Prof. Ferdinand Evers of the Karlsruhe Technical Institute in Germany.


Tal’s group and others have already begun to investigate the behavior of electric current when it passes through single molecules connected to the ultra-thin platinum wires. Among other things, the contact points between two very different nanostructures – organic molecules and strings of metallic atoms – may provide new and unique ways of controlling electric current on the sub-nanometer scale.
 

Prof. Leeor Kronik's research is supported by the Wolfson Family Charitable Trust; the Carolito Stiftung; the European Research Council; the Leona M. and Harry B. Helmsley Charitable Trust; Antonio and Noga Villalon, Winnetka, IL; and the Philip M. Klutznick Fund for Research.

 

Dr. Oren Tal's research is supported by the Carolito Stiftung. Dr. Tal is the incumbent of the Alvin and Gertrude Levine Career Development Chair.
 

 
Platinum wires attached to a single organic molecule (center) can be elongated into a chain a single atom thick
Chemistry
English

Exchange Rates

English

 

Prof. Dan Yakir
We know that green plants are important for keeping our planet cool: Around the globe, they consume billions of tons of the greenhouse gas carbon dioxide (CO2), converting it, through photosynthesis, to sugars and ultimately to wood. But CO2 is also released back into the atmosphere in a process called respiration, both from living plants and from the decomposition of detritus. Thus the total amount of CO2 plants take out of the atmosphere equals the quantity they absorb for photosynthesis, minus the amount they return to the atmosphere through respiration. It sounds like a simple equation, but until now, measuring its components has been anything but simple; scientists have been stumped for years trying to come up with an accurate means to tease out the two components of the “simple equation” – an analysis that is critical to predicting the future impact of plants on our climate.

Recently, a research team in the lab of Prof. Dan Yakir of the Environmental Sciences and Energy Research Department demonstrated a new method for just measuring how much CO2 is taken up, independent of the amounts released back in respiration. This method, based on another chemical compound in the atmosphere – one found in extremely tiny amounts – should help scientists around the world clarify the picture of the ongoing exchange of carbon between plants and the atmosphere, hopefully leading to better climate models and predictions. Measuring the levels of this compound, COS, involved developing new, ultra-precise tools to reveal its presence.

In the commonly used methods for figuring carbon exchange, only the net difference between photosynthesis and respiration can be directly measured in the air above vegetation. But that doesn’t indicate specifically how much CO2 is lost or gained – information that is critical when trying to understand how patterns change daily or seasonally, across regions or in response to climate change. Researchers trying to tease apart CO2 fluxes have used various “tricks” – for example, measuring at night, when photosynthesis shuts down; but the results have still been only approximations.

Yakir and his team decided to act on an idea that had come up several years earlier but was considered too impractical to be of use: Measure the flux of another substance, carbonyl sulfide (COS) into the plant biosphere. COS is similar to CO2, except that instead of two oxygen atoms attached to the carbon, the molecule contains an oxygen and a sulfur atom. Plants absorb COS along with the CO2; but they don’t release it again in respiration, so measurements could serve as a good proxy for CO2 uptake. The only problem was that there is about a million times less COS in the atmosphere than CO2: If CO2 is measured in parts per million, COS must be measured in parts per trillion (that is one molecule of COS for every trillion molecules of gas in the atmosphere).
 
Yakir infographic
 
 
Though these figures were daunting, the researchers convinced a scientific instrument company in the US to build them a tool – called a quantum cascade laser (QCL) – capable of accurately measuring minute amounts of COS. Research student Keren Stimler then spent around five years testing the QCL with plants in the lab, “developing the ‘language’ of COS exchange, the instrument, and the analysis of its results,” says Yakir.

In the team’s recent work, which appeared in Nature Geoscience, Yakir and postdoctoral fellow Dr. David Asaf decided it was time to take the QCL on the road. They loaded it into the Biosphere-Atmosphere Mobile Research Lab (see below) and took it to various sites to see how well it works in real conditions – in pine forests in a variety of climate regions and in agricultural fields. Their results demonstrate that COS measurements based on the new QCL technology are able to provide the numbers on CO2 uptake that scientists have been seeking for years. Indeed, the team can now confirm their previous finding that pine forests in Israel are as effective in carbon storage (carbon sequestration) as European pine forests: While the semi-arid local forests take up much less CO2 in photosynthesis than European ones, they also lose much less CO2 in respiration, so the net carbon storage is the same in both forests.
 

Going mobile pays off

Biosphere-Atmosphere Mobile Research Lab
 
 
Two years ago, when Prof. Dan Yakir together with staff scientist Dr. Eyal Rotenberg and their team finally (after two years of development) started up the four-by-four, 12-ton truck that houses the Biosphere-Atmosphere Mobile Research Lab, they knew they were taking a bit of a risk. Although they had visions of the exciting contributions the one-of-a-kind transportable lab could be making to global research on the exchange of materials between forests and the atmosphere, there were no guarantees that the new approach would be widely endorsed or that other researchers in this field would be lining up on their doorstep.

This summer, any fears they may have had were laid to rest when research groups from the US, Spain, Austria and Germany all showed up to work together out of the Mobile Lab. The teams brought along their research tools – including large pieces of equipment that had to be carefully shipped halfway around the world. The idea was to combine the mobile platform, with its fully operational (and air-conditioned) laboratory, on the one hand, and, on the other hand, to make use of the mobile lab’s 28-meter-high telescopic mast, which, according to Yakir, reaches the critical layer “between the plant canopies and the airspace below the mixed atmosphere.” Each group planned to investigate one slice of the larger question: How do the volatile compounds released by trees (think of the terpenes that give pines their characteristic scent) link to CO2 exchange, and how does this affect atmospheric chemistry and ultimately cloud formation and climate?

One group, for example, took detailed measurements of the trees at ground level; another measured levels of the volatile compounds above the forest canopy; a third monitored the size of particles, which, above a certain diameter, can serve as nuclei for the condensation of water drops in clouds; and so on. Combining the data from all of the groups, says Yakir, “is beginning to give us an overall picture of the evolution of climate – from the trees to clouds and rain.”

“We were very excited by this campaign,” he says. “It was a great example of scientific collaboration in which different groups worked together out of one small traveling lab. It was a further test of our own instruments, including the new mobile platform and the QCL system, and it looks like the results will be really interesting. Most of all, it showed us that the investment in the Biosphere-Atmosphere Mobile Research Lab was worth the risk – it is clearly paying off.”
 
 

Prof. Dan Yakir's research is supported by the Cathy Wills and Robert Lewis Program in Environmental Science; the estate of Sanford Kaplan; and the
Carolito Stiftung.

 

 

 

 
Biosphere-Atmosphere Mobile Research Lab
Environment
English

Bacterial Booby Traps Revealed

English

Growth of bacteria when only antitoxin is induced (left), only toxin is induced (middle), and both are induced together (right)

 

 

 
 
 
 
 
 
 
 
 
 
 
 
Bacteria can be veritable poison factories. In addition to those that harm humans, such as tetanus and botulism, or the toxins they produce to compete with other microorganisms, we now know that bacteria can produce poisons especially for committing suicide. Indeed, many bacteria carry around a sort of “suicide pill,” which comes with its own antidote. To do itself in, the bacterium simply does away with the antidote. Recent Weizmann Institute research revealed many novel versions of these suicide pills in bacteria and showed that they help the bacteria resist viral attacks.

Suicide is most often a last-ditch response to one of the viruses that invade bacterial cells. If the cell cannot overcome the infection, it may take its own life to prevent the virus from spreading to neighboring bacteria. Understanding how the suicide pill mechanism works may, on the one hand, help protect useful bacteria like those in yogurt cultures from viral assault and, on the other, lead to the development of new antibiotic drugs against harmful bacteria. In addition, it could yield new insights into treating such scourges as tuberculosis.
 
Drs. Rotem Sorek and Azita Leavitt
 
Dr. Rotem Sorek and his team in the Institute’s Molecular Genetics Department, working with Dr. Udi Qimron of Tel Aviv University, discovered the suicide mechanism using a method for identifying toxic bacterial genes that he had developed several years ago, when he realized that a drawback of a common technique for sequencing bacterial genomes could be a unique research tool in disguise. The technique of genome sequencing involves cutting up the bacterial genome and inserting the pieces into another bacterium – E. coli – for duplication and further sequencing. But this method always left gaps in the sequence. Sorek understood that the missing genes encoded toxins that killed the host E. coli cells. Building on this insight, he developed a computerized method for identifying these killer genes. Recently, together with his research team, he created an online database called PanDaTox containing some 40,000 sequences for genes encoding bacterial toxins.

But some instances of cell-killing genes seemed to be less than clear-cut: While many of the toxins killed the host E.coli cells outright, others seemed to be more sporadic – destroying them only part of the time. This led Sorek and his team to surmise that certain suicide mechanisms involve pairs of genes – one for a toxin, the other for an antitoxin.
 
Hila Sberro
         
In their study, which appeared recently in Molecular Cell, Sorek and research students Hila Sberro and Dr. Azita Leavitt went looking for toxin-antitoxin pairs. Their quest involved analyzing the results after inserting over a million genes from hundreds of microbial genomes into E. coli cells. When only the toxin gene was present, the E. coli cells died, but when both toxin and antitoxin were present, the genes for both were cloned in the cells. The researchers tentatively sorted into different families all of the toxin-antitoxin pairs they identified and explained how they function.

The team found that the toxin-antitoxin mechanism works something like a booby trap. The toxin molecule – which, as they discovered, can come in many different forms – is highly stable. The antitoxin that fits it, however, is a sort of hair-trigger component that is fragile and easily destroyed, so the supply must be constantly renewed. So when a virus takes over the cell and attempts to hijack its DNA production machinery, the frail antitoxin is destroyed, leaving the toxin free to kill the cell and the viruses along with it.
 
sorek infographic
 
 
Among other things, the study may yield some important insights into such hard-to-treat diseases as tuberculosis. Not only are new strains of TB appearing that are increasingly resistant to known antibiotics, but even the common forms of the disease require many months of treatment to rid the body of all the pathogens. The research helps explain why. TB-causing bacteria contain unusually large numbers of toxic genes, and the team identified some new ones. Their findings support the idea that some of those toxin-antitoxin mechanisms merely cause the cells to fake their own suicides: Though they appear to be dead, these cells are actually only dormant. Since only active cells are killed by the antibiotic drugs, these must be administered until all the bacteria have come out of dormancy. In the future, says Sorek, methods to prevent dormancy could shorten and improve TB treatment.

The findings have also yielded a number of new insights into the strategies that bacteria use in their evolutionary battle with viruses, and these, in turn, may have implications for industry as well as biomedical research. For instance, food industries that rely on bacterial cultures have already shown interest in new methods for boosting bacterial resistance to viral infection. The same findings might, in the future, lead to the development of novel antibiotic drugs based either on the new types of toxin molecules the team discovered or on substances that can interfere with the toxin-antitoxin mechanism.
 
 
 

Dr. Rotem Sorek’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the Abisch Frenkel Foundation for the Promotion of Life Sciences; the European Research Council; the Leona M. and Harry B. Helmsley Charitable Trust; and the Hugo and Valerie Ramniceanu Foundation. Dr. Sorek is the incumbent of the Rowland and Sylvia Schaefer Career Development Chair in Perpetuity.

 
 
Life Sciences
English

Limits to Growth

English
 
 

Prof. Yuval Eshed

Elephants’ ears and those of humans may differ wildly in size, but nature provides each with a more-or-less fixed range and upper limit. Such evolutionary extremes are seen in the plant kingdom as well: Cabbage leaves, for instance, are ten times the size of those of a close relative, the inconspicuous mustard cress (Arabidopsis thaliana). What sets the ultimate size of an organ such as a leaf? Research in the lab of Prof. Yuval Eshed of the Plant Sciences Department has revealed a part of the answer, and the findings are something of a surprise: Most of the mechanisms involved in fixing leaf size are ones that put the brakes on growth, rather than ones for promoting growth.

These findings originated in previous research in Eshed’s lab. In the earlier study, the team was investigating a different question: What causes a leaf to begin growing? The onset of growth is not a preordained, automatic event. First the plant produces a leaf primordium, which, in order to grow, must undergo division into top and bottom sides. It is the interactions between the two sides of the primordium that initiate leaf growth. This type of interaction, interestingly enough, is also found in an unrelated two-dimensional organ – a developing fly wing. In the research, which was conducted by then research students Drs. Idan Efroni and Eyal Blum, and which appeared in The Plant Cell, the researchers wanted to understand the exact nature of this interaction. They used genetic engineering to create plants with leaves made up of a single cell type – either top or bottom – and compared them with normal plants.
 
The genetically engineered leaves did not grow; but the comparison enabled the scientists to discover dozens of proteins that were expressed in the normal plants but not in those with one-sided leaves. In further experiments, they looked for the functions of these proteins by creating a new series of genetically engineered plants, each producing a large quantity of one of the proteins. To their surprise, none of these proteins spurred leaf growth: Around half had no effect on leaf size, while the other half decreased it.
 
leaf size
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
This finding seemed to throw a large bucket of cold water on their basic assumption that the majority of factors in a developing leaf would be pro-growth. To understand where they had gone wrong, the team focused on a group of proteins that were implicated in reducing leaf size, a family called TCP that regulates gene expression. Using a combination of genetic methods, the researchers created plants that did not produce any of the eight members of the TCP family. The result: a major improvement in leaf growth.
 
This finding led the scientists to the conclusion that the logic behind leaf growth is quite different from what they had originally thought. Growing appears to be the “default” setting for the leaf, so it does not require much prompting or regulation for it to happen; putting the brakes on growth, on the other hand, entails a number of different factors. This is necessary, in part, because it can take weeks or months for a leaf to grow and, during that time, any number of environmental factors can change. Lack of water or a rise in temperature, for example, can activate the brakes on growth. (That is why, in arid, subtropical regions like those of Israel, many wild plants sprout big leaves in the winter and small leaves in the summer.)
 
Leaf from a genetically engineered plant that does not produce five members of the TCP family and another four similar factors. These leaves grow without stopping
 
In a follow-up study that appeared in Developmental Cell, Efroni and Eshed discovered how the orders to halt leaf growth are carried out. The scientists suspected that a plant hormone called cytokinin was involved. Cytokinin had previously been known to encourage cell division but hinder differentiation. The researchers sprayed the hormone on the leaves of plants that had been genetically engineered to produce a larger-than-normal amount of TCPs, and found that these leaves did not respond to the hormone and thus did not grow larger.

In other words, the TCPs reduced the sensitivity of the leaves to the growth-promoting hormone. How do they do this? In an experiment conducted together with a research group from Pennsylvania, Eshed and his team revealed the active mechanisms in detail. To carry out their duties, TCPs recruit the help of another protein – one that exposes certain areas of the genetic sequence so that the process of gene expression can begin. One gene that gets exposed in this way reduces the sensitivity of the plant to cytokinin; the TCP-protein partnership increases the expression of the gene. This system turns out to be quite flexible, enabling a range of leaf sizes within the proscribed limits. It can be activated at various stages in leaf development, so that the later the braking mechanism is deployed, the larger the leaf.

More than revealing a mechanism for regulating plant size, says Eshed, these studies have granted researchers a peek into the basic principles that guide development. They have shown that those principles can sometimes go against the instincts of even the most experienced scientific researchers.
 
Prof. Yuval Eshed is the incumbent of the Jacques Mimran Professorial Chair.
 
 
 
what determines how big a plant will grow
Environment
English

New Angle on Perception

English

 

How does the brain form a detailed, updated, accurate image of the world? The simple answer is that the sensory organs send electrical impulses though their nerve cells, which ultimately conduct those signals to the various “information-processing” centers in the brain. Recent research at the Weizmann Institute introduces a new wrinkle in that picture, however, showing that the information processing may begin in the sensory organs themselves, before the first neuron ever receives the incoming data.


This research, led by Prof. Ehud Ahissar of the Neurobiology Department, focused on a unique sensory organ: the whisker hair of a rat. Crucial to a rat’s sense of touch, each follicle at the base of a whisker hair contains around 2,000 receptors for sending information to the underlying nerve cells, which relay it on to the brain. As sensory organs go, whiskers are ideal for observation: They are, basically, long, thin, elastic rods that bend as they encounter an object.
 
whisking infographic
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
In the experiments, objects were placed in various positions near the rats’ heads. In the first series of trials, the rats were anesthetized and their whisker hairs activated by the electrical stimulation of their motor nerves. This gave the researchers precise control over the whiskers’ movements. The entire experiment was filmed on a high-speed camera, which enabled the scientists to precisely measure the changes in a whisker hair as it came into contact with the object. They identified four variables: global bending over the entire hair, the amount of bending at the base, the angle of the hair in relation to the rat’s head and the extent of angular movement that is blocked by the contact (angle absorption).
 
(l-r) David Deutsch, Dr. Knarik Bagdasarian and Prof. Ehud Ahissar
 
The research team – which included Dr. Knarik Bagdasarian, then research students Drs. Marcin Szwed, Per Magne Knutsen, Maciej Pietr and Erez Simony, and research student David Deutsch – discovered that just knowing the figures for each pair of angular and bending variables was sufficient to pinpoint exactly where the object was in relation to the rat’s head. The closer it was to the head, the greater the bending at the base and angle absorption, and the smaller the global bending and angle protraction. The combinations of bending and angular variables also revealed the angle of the object in relation to the nose-tail axis of the rat’s head. These two pieces of information – distance and angle – identified the object’s precise location. The scientists then observed the process in alert rats that were allowed to move their whiskers naturally; they found that the same relationships held true.

These results, which were published in Nature Neuroscience, imply that we may need to update the way we describe the process of perception. Today, we know that perception is both an active process and a cyclical one. For example, movement leads to interaction with an object (e.g., a finger alights on a tabletop), and receptors in the organ (finger) activate sensory nerves. These cells conduct information (finger is touching a surface) to the brain. Processing this information leads to the initiation of further movement (sliding the finger across the table’s surface to feel its texture). But, according to the present study, the morphology – physical form and structure – of the sensing organ are an integral part of the cycle, and they enter it at an early stage. In fact, morphological information – bending and angle in the case of the whiskers – appear to be processed mechanically in the follicle before being sent as electrical signals to nerve cells in the brain.

Although the experiment was conducted on rat whiskers, Ahissar believes that this absorption and processing of information arising from the physical properties of the organ may be relevant to other senses and other animals, including humans. Our sense of touch, for instance, is dependent on movement: how much pressure we exert, whether we move our fingers over an object quickly or slowly, and the morphology of our fingertips – all determine which receptors are activated and what signals will be sent to our brain. Even sight, which is still often misconstrued as a passive sense, depends on movement. When we look at faces, for instance, our focus jumps from feature to feature – eyes, nose, mouth – in a sort of visual “touching.” The properties of our eye movements, combined with the morphology of our eyeball, cornea, retina and other parts of the eye determine how accurately we perceive the world through our sense of sight. In other words, the divide between sensing and perception – the first thought to be a function of our external sensory organs, the second the result of processing the data from those sensory organs in the brain – may not be as clear cut as we thought.
 
Prof. Ehud Ahissar's research is supported by the Murray H. and Meyer Grodetsky Center for Research of Higher Brain Functions; the Jeanne and Joseph Nissim Foundation for Life Sciences Research' the Kahn Family Research Center for Systems Biology of the Human Cell; Lord David Alliance, CBE; the Berlin Family Foundation; Jack and Lenore Lowenthal, Brooklyn, NY; Research in Memory of Irving Bieber, M.D. and Toby Bieber, M.D.; the Harris Foundation for Brain Research; and the Joseph D. Shane Fund for Neurosciences. Prof. Ahissar is the incumbent of the Helen Diller Family Professorial Chair in Neurobiology.


 
 
Rats' whiskers
Life Sciences
English

A Viral “Crook” Cracks Many Locks

English
In short
    VSV is a useful virus – one that is used to insert therapeutic genes into cells, and that can selectively kill cancer cells.
    Scientists had assumed that VSV uses the LDL (“bad” cholesterol) receptor to break into cells, but it manages to get into cells without the receptor, as well.
    Experiments show that this virus can enter though a number of related receptors in the LDL family.
 
A master trickster virus called VSV has baffled scientists for quite some time. Because VSV is a true expert at sneaking into cells, it is widely used in gene therapy and might, in the future, help to treat cancer. Yet even though it’s been employed in research and in pre-clinical studies for over 30 years, how it gets into cells has remained a mystery. Weizmann Institute scientists have now solved this riddle, as reported in the Proceedings of the National Academy of Sciences (PNAS).
 
VSV is particularly suitable for research and therapeutic use because, although it causes disease in farm animals, it rarely does so in humans. Yet the virus is so good at penetrating human cells that scientists commonly use it in experimental gene therapy as a vehicle to deliver desired genes to cells. In addition, VSV holds promise for use in cancer therapy because it selectively kills cancer cells.
(l-r) Dr. Daniela Novick, Prof. Menachem Rubinstein, Dr. Danit Finkelshtein and Sara Barak
 
Some 20 years ago, Prof. Menachem Rubinstein and his colleagues in the Weizmann Institute’s Molecular Genetics Department discovered that virus-infected cells secrete a soluble protein that prevents further VSV infection. They then found that this soluble protein is identical to the extra-cellular portion of the receptor for LDL, the “bad” cholesterol. This observation led them to assume that VSV penetrates cells by binding to the cells’ surface receptor of LDL. But when they conducted experiments with cells that lacked LDL receptors, VSV was still able to get in.

In the new study, Rubinstein’s team – research student Danit Finkelshtein, working together with Dr. Ariel Werman, Dr. Daniela Novick and Sara Barak – revealed that VSV can indeed cheat its way into cells through the LDL receptor. The virus can do that because it is coated with a decoy molecule mimicking LDL: This decoy acts as a key that opens the LDL receptor “lock” on the cell’s surface.

 
But how does the virus infect cells lacking the LDL receptor? The researchers explored the hypothesis that VSV lets itself in through more than one receptor – that is, not only through LDL but also through alternative, structurally similar receptors that must all be members of what is known as the LDL receptor family. To test this hypothesis, they conducted experiments with a versatile protein called RAP, which blocks all family members of the LDL receptor (but, oddly, not the LDL receptor itself).
Top: Human cells light up with green fluorescenTop: Human cells light up with green fluorescent markers after being penetrated by a genetically engineered virus coated with the VSV envelope protein; Bottom: The decoy LDL-like structures on the surface of the virus have been blocked by the soluble fragment of the LDL receptor; as a result, the virus fails to infect the cells, hence the absence of the green markers. Cell nuclei are stained bluet markers after being penetrated by a genetically engineered virus coated with the VSV envelope protein; Bottom: The decoy LDL-like structures on the surface of the virus have been blocked by the soluble fragment of the LDL receptor; as a result, the virus fails to infect the cells, hence the absence of the green markers. Cell nuclei are stained blue
 
 
Indeed, when they pretreated cells lacking LDL receptors with the RAP protein, VSV was no longer able to penetrate these cells. In other words, the experiments bore out the hypothesis: VSV gets into cells mainly through the LDL receptor but also through other members of the LDL receptor family.
 
This new understanding may be of potential importance for the development of VSV-based cancer therapies. In particular, colon cancer cells have high levels of the LDL receptor on their surface, which suggests they could be selectively killed by VSV.
 
The new findings might also help improve gene therapy, by increasing the number of LDL receptors on the outer membranes of targeted cells – to facilitate the entry of viruses that carry a desired gene. This goal could, for example, be achieved by the anti-cholesterol drugs statins, which cause cells to display more LDL receptors on their surfaces.
 
Prof. Menachem Rubinstein’s research is supported by the Bernard and Audrey Jaffe Foundation; the Adelis Foundation; and the Florence Blau Charitable Trust. Prof. Rubinstein is the incumbent of the Maurice and Edna Weiss Professorial Chair of Cytokines Research.
 
Top: Live cells lacking LDL receptors. Middle: These cells are killed by a VSV infection. Bottom: Protected by the RAP protein, these cells survive a VSV infection
 
 
 
 
 
 
Human cells light up with green fluorescent markers after being penetrated by a genetically engineered virus coated with the VSV envelope protein
Life Sciences
English

Side Effects

English

(l-r) Dr. Sigalit Boura-Halfon, Hadas Shatz-Azoulay, Dr. Eytan Elhanan, Prof. Yehial Zick, Roi Isaac, Dr. Yaron Vinik, Prof. Sanford Simpson, Itai Efodi, Prof. Rivka Pollak and Sarina Striem

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
One of the known side effects of certain antidepressants and antianxiety drugs, including the popular drug Prozac, is weight gain. Research at the Weizmann Institute led by Prof. Yehiel Zick has now shown that this class of drugs can also contribute to the development of diabetes. The study’s findings hint that caution might need to be exercised in the use of these medications, especially in people with diabetes or those at risk for the disease.

The connection between these drugs, known as selective serotonin reuptake inhibitors (SSRIs), and weight gain is well known: They hinder the absorption of the neurotransmitter serotonin, so that its levels in the brain rise. Serotonin (which is also found in such foods as chocolate) is a natural “feel good” neurotransmitter, but it also increases appetite. If people using SSRIs overeat as a result, they can end up with that plague of recent decades – obesity – and they will be at risk for cancer, heart disease and diabetes.
 

In short

•    Antidepressants known as SSRIs have been known to cause weight gain.
    New Weizmann Institute research shows that SSRIs may also promote obesity and diabetes in much the same way as fatty acids do – by hindering insulin production.
    They can also initiate cell death in the insulin-producing cells.

But various scientific findings in recent years have suggested that the links between antidepressant use and diabetes go beyond hunger pangs. These drugs can cause insulin resistance, a condition in which the beta cells in the pancreas – the body’s insulin factories – cannot function properly. Normally, the beta cells produce insulin, the hormone responsible for getting sugar into the body’s cells, in response to a rise in blood sugar levels. But when the cells develop insulin resistance, more insulin is needed to overcome the resistance. Insulin resistance can eventually turn into diabetes – a breakdown in the body’s ability to regulate sugar levels. How, exactly, do SSRIs cause insulin resistance in beta cells?

To understand what happens, Zick and his team closely observed the chain of events that begins with the binding of insulin to a receptor on the beta cells. This receptor, whose action Zick had discovered in his postdoctoral research in the 1980s, activates another protein called IRS-2 by attaching a phosphorous-based chemical group to one of its amino acids. This phosphorylation then sets off a chain of biochemical events that facilitates insulin production and secretion, as well as maintaining the viability of the beta cells. Normally it is an amino acid called tyrosine that is phosphorylated; but following a rise in agents in the blood that induce insulin resistance, for instance, fatty acids, another amino acid in the IRS-2 protein – serine – is phosphorylated. This hinders the first step –  tyrosine phosphorylation by the insulin receptor. By breaking the connection between the first two links in the chain – between the receptor and IRS-2 – further activity is held up. When this happens, extra insulin is needed to get things moving again. At some point, if resistance builds up to very high levels, the pancreatic cells buckle under the non-stop demand for insulin and they begin to die.
 
 
Image: Thinkstock- fat guy pops a pill
In the new study, conducted on mouse and human pancreatic beta cells, the scientists discovered that SSRIs disrupt the chain of events that lead to insulin secretion in much the same way as the agents that induce insulin resistance – by hindering the insulin-induced tyrosine phosphorylation of IRS-2. In further experiments, the team discovered the exact mechanism by which antidepressants interfere with IRS-2, showing it is the same mechanism that is activated by fatty acids and other similar molecules.

If this were not enough to deal a fatal blow to the functioning of the beta cells, the researchers discovered that SSRIs can also kill them off more directly, by initiating a cellular suicide pathway (apoptosis). They do this by activating a series of enzymes in the cells’ endoplasmic reticulum – the cellular organelle in which proteins are processed before use. This leads to a buildup of defective proteins within the endoplasmic reticulum. When the buildup threatens to cause serious problems, the cell will sacrifice itself for the greater good of the organism. But if too many beta cells go the suicide route, the body’s capacity to produce insulin is impaired and it loses the ability to regulate sugar. The findings of this study appeared in the Journal of Biological Chemistry.

Says Zick: “SSRI medications not only promote obesity but, as we have shown, they directly contribute to insulin resistance and a drop in insulin secretion. Thus they can hasten the progression of insulin resistance into diabetes. This suggests that we may need to reevaluate the use of these drugs and possibly search for ways of preventing their negative side effects.”

The research was conducted by Roi Isaac, Dr. Sigalit Boura-Halfon and Diana Gurevitch in Zick’s group in the Molecular Cell Biology Department, together with Alla Shainskaya, of the Biological Services Unit and Prof. Yechiel Levkovitz of the Shalvata Mental Health Center and Tel Aviv University.
 
Prof. Yehiel Zick’s research is supported by the Adelis Foundation. Prof. Zick is the incumbent of the Marte R. Gomez Professorial Chair.
 
(l-r) Dr. Sigalit Boura-Halfon, Hadas Shatz-Azoulay, Dr. Eytan Elhanan, Prof. Yehial Zick, Roi Isaac, Dr. Yaron Vinik, Prof. Sanford Simpson, Itai Efodi, Prof. Rivka Pollak and Sarina Striem
Life Sciences
English

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