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Science Feature Articles</p>

Gateway to the Brain

English
Immunostaining of brain section in which the epithelial choroid plexus expresses TGF-β (green), hanging in the brain ventricle, the keyhole-like structure delineated by the ependymal lining (red). In the box, monocytes (green) entering via the choroidal vasculature. The composition reflects the immune-educative nature of the choroid plexus as a gatekeeper of the route to the injured parenchyma
 
As we get older, our memory tends to get creaky. According to new research, this “rusty brain” could be tied to an aging immune system. Two recent studies in the lab of Prof. Michal Schwartz of the Institute’s Neurobiology Department reveal how certain immune cells – located in an unusual site, right on the edges of the brain – benefit the central nervous system (CNS), among other things, in healing injury. But they also suggest that a shift in the border’s gateway over time can contribute to declining mental function and neurodegenerative disease. These studies contain clues as to how we might, in the future, be able to slow or prevent cognitive decline and fight neurodegenerative conditions.

Following their discovery over a decade ago that circulating immune cells play a role in brain and CNS function, Schwartz and her group have been investigating the underlying mechanism. This research has often challenged the conventional wisdom: It was believed that immune cells were not allowed to infiltrate the brain, and if they did, their entry was considered to take place through fractures in the brain’s barrier system.
 
 
The results of the first study, which appeared recently in Immunity, showed that when healing immune cells are summoned to the brain following trauma, they do not need to breach barriers. Schwartz’s team discovered that the healing cells enter through structures within the brain called choroid plexi, which form the so-called cerebrospinal-fluid barrier. These structures – one choroid plexus in each quarter of the brain – have finger-like projections that exchange cerebrospinal fluid with the surrounding brain on the one hand and blood plasma and waste products with the blood vessels on the other.

To their surprise, the researchers found that cells needed for the repair of a distant spinal cord injury travel though this remote gateway, rather than drifting across breaches in the blood-brain barrier. The healing immune cells were found to cross the cerebrospinal-fluid barrier between the blood circulation and brain tissue and, from there, make their way to the injury site in the CNS. In other words, the cerebrospinal-fluid barrier, which was assumed to be as impenetrable as the blood-brain barrier, suddenly appeared to be quite porous. “It is more of a filter or a gate,” says Schwartz. “It sends immune cells through that gate when they are needed, though it first performs a security check and ‘educates’ them, so as to ensure that the right cells – with the right training – enter the system at the right time.”
 
The choroid plexus (CP) of young (3 months) and aged (22 months) mice immunostained for Claudin-1 (tight-junction marker; green), Arginase-1 (red), and Hoechst nuclear staining (blue), showing elevation of araginase-1 on the CP epithelium during aging
 

 

 
In the second study, which appeared in the Proceedings of the National Academy of Sciences (PNAS), the team wanted to find the immune cell “gatekeepers” controlling this newly discovered compartment of the immune system. The research team identified the resident immune cells in the choroid plexus as a type of T cell that is specially adapted to the CNS, and found that these cells are kept permanently within the choroid plexus structures. A careful examination of cell fate from youth to old age revealed that changes in certain substances produced by these cells affected the gateway’s properties. One of these substances, interleukin-4 (IL-4), was known to control inflammation and help keep the brain healthy.
 
Paradoxically, however, it was also known to be involved elsewhere in the body in the production of a biochemical known as CCL11, which, among other things, has been implicated in cognitive decline. Further experiments in mice and cell cultures revealed that IL-4 generally exists in this compartment in equilibrium with another substance, interferon gamma. In the aging animal brain, changes in the general T cell populations shift the ratio in favor of IL-4, and this imbalance leads to inflammation similar to that seen in an asthmatic lung. The result is the production of CCL11 by the choroid plexus; from there, it enters the cerebrospinal fluid, where it accumulates and impairs cognitive ability in aged mice, and also in humans.
 
The research team managed to partially reverse the cognitive decline of the aged mice by applying a somewhat drastic treatment: They “reset” the mice’s immune system by irradiating their bone marrow from the neck down and transplanting new bone marrow. But Schwartz believes the findings contain hints that less radical means of restoring the immune balance in the brain may be feasible in the future. For one thing, the inflammation-causing T cells found in the aging choroid plexus are also present in elevated levels in the blood of the elderly, which suggests that a general strategy for targeting these cells might be helpful. For another, the intriguing similarities between the inflammatory process in the brain and asthma – which, says Schwartz, “is another disease of a filter, in this case, the airways”– suggesting further possibilities for treatment. And, as these findings make clear, the “barriers” separating the brain from the rest of the immune system are by no means impermeable if the right approach to the gate can be found.
 
In other words, rather than an inevitable side effect of aging, cognitive decline and age-related neurodegenerative diseases might one day be considered treatable conditions, like any other disease of the immune system.  
 
Prof. Michal Schwartz’s research is supported by the Adelis Foundation; and the European Research Council. Prof. Schwartz is the incumbent of the Maurice and Ilse Katz Professorial Chair of Neuroimmunology.
 
Immunostaining of brain section in which the epithelial choroid plexus expresses TGF-β (green), hanging in the brain ventricle, the keyhole-like structure delineated by the ependymal lining (red). In the box, monocytes (green) entering via the choroidal vasculature. The composition reflects the immune-educative nature of the choroid plexus as a gatekeeper of the route to the injured parenchyma
Life Sciences
English

The Path Taken

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 Tslil Ast and Dr. Maya Schuldiner

                

 

 
 
 
 
 
 
 
 
 
 
 
 
“Biologists live in hope of discovering 'textbook examples’,” says Dr. Maya Schuldiner of the Molecular Genetics Department. To demonstrate, she opens a biology textbook and points to a diagram of a molecular pathway – a series of molecular interactions for getting a cellular protein or process from point A to point B. Since many proteins tend to use the same general molecular pathways, a textbook example should ideally reveal important insights into the working of a cell, and it may often generate reams of further study and discovery.

But textbook examples, says Schuldiner, are hiding a much more complex reality: “Generally, the pathways that are discovered first are assumed to be the most important. When we start finding proteins using other pathways, we call these ‘exceptions to the rule.’ Often, no one stops to ask how many proteins actually use one pathway or another.”

Schuldiner and research student Tslil Ast decided the time had come to ask that question. It was time, in part, because new technology would enable them to check many proteins at once: The high-throughput microscopy equipment and computational techniques used in Schuldiner’s lab are able to reveal the pathways of hundreds of cellular proteins in a fraction of the time formerly required to study just one or two.  
 
 
Endoplasmic reticulum. Image: Nicolle Rager, National Science Foundation
 
Schuldiner and Ast investigated the pathways taken by proteins to get into an organelle called the endoplasmic reticulum (ER), a maze-like series of folded membranes where the proteins undergo folding, quality control and routing to their next destination. The many and varied proteins passing through the ER are those that will eventually make their way out of the cell – hormones and external signaling molecules, as well as proteins that only make it as far as the outer face of the cell membrane. The well-studied pathway by which proteins enter the ER, discovered in the 1970s, is known as the SRP (signal recognition particle) pathway. The other pathways identified since are considered to be so insignificant that they are simply known as SRP-independent.

Is SRP truly the main pathway into the ER? The researchers surveyed all the ER-bound proteins in a baker’s yeast cell – some 1300 proteins. The answer was clear: Only about half of them strictly require the SRP pathway to get there. The rest can use other pathways; some of these pathways were partly known, but the findings hinted at undiscovered others, as well. The scientists found that, at least in yeast, there is a fairly clear-cut division: Proteins using the SRP pathway are those bound for the cell membrane. Because these pathways have been preserved throughout evolution, Schuldiner expects that a similar division exists in human cells. This means that the group of proteins using alternate pathways is likely to include many important hormones and signaling molecules.

The team is now working on developing a fuller picture of the parallel pathways. The ultimate goal is to identify all the molecular pathways for all of the cell’s exportable proteins. Rather than an ideal model, they expect to produce a complex picture that will better reflect actual protein behavior.

That may be bad news for the publishers of biology textbooks, but it’s good news for our understanding of living cells. “In the end,” says Schuldiner, “what we want to accomplish is a completely new image of how the cell works. We want researchers to stop looking ‘under the lamppost’ of the accepted models and broaden their scope to include all the possibilities.”
 
 
Dr. Maya Schuldiner's research is supported by the European Research Council; the Berlin Family Foundation; James and Ilene Nathan, Beverly Hills, CA; the Minna James Heineman Stiftung; the Enoch Foundation; Roberto and Renata Ruhman, Brazil; Karen Siem, UK; and the Kahn Family Research Center for Systems Biology of the Human Cell.
 
Endoplasmic reticulum. Image: Nicolle Rager, National Science Foundation
Life Sciences
English

Two Tests Are Better Than One

English
 
One of the best ways to fight a disease is to find risk factors and learn how to identify them early on, before the disease can take hold. Even if the disease does develop, early treatment can improve chances for a cure. For instance, the steep drop in heart disease in recent decades can be attributed to the discovery of a major risk factor – high cholesterol – and its prevention. With cancer, in contrast, things are not so clear-cut. Nevertheless, many groups around the world are looking for the biological signs that can point to a heightened cancer risk.

Prof. Zvi Livneh and Dr. Tamar Paz-Elizur of the Biological Chemistry Department have made progress in identifying certain markers – tiny cellular “machines” whose function is to keep the genetic material in good working condition. These have their work cut out for them: The DNA in our cells gets injured thousands of times a day from radiation, the side effects of our metabolism and exposure to harmful substances. To prevent this disarray (mutations) in the DNA from developing into such diseases as cancer, the cell maintains a a large store of molecular machines to locate the damage in the genetic material and fix it.
 
 (l-r) Prof. Zvi Livneh, Drs. Tamar Paz-Elizur, Ziv Sevilya and Yael Leitner-Dagan, and Dalia Elinger
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
“Our working assumption,” says Livneh, “has been that small differences in the efficiency of those DNA repair mechanisms can affect individuals’ tendencies to get cancer. The combination of two factors – exposure to carcinogens and a lowered ability to repair DNA damage – will elevate the risk of developing the disease.”  

Around a decade ago, Livneh and Paz-Elizur proved this assumption by discovering a biological marker that signals a higher risk of lung cancer. Lung cancer is one of the most common cancers in the world, and the most lethal: It is responsible for some 30% of cancer deaths. Yet, although the primary risk factor for lung cancer is smoking, “only” 10%-15% of heavy smokers develop the disease, while about 15% of those with lung cancer are not smokers. In other words, a majority of humans have the means to overcome the DNA damage from cigarette smoke (though other problems can still ensue), but a minority have something that increases their genetic sensitivity to smoke damage and thus are more likely to get cancer.
    
Livneh and Paz-Elizur developed a method to measure the activity of one repair machine – an enzyme called OGG1 – and discovered that unusually low levels of OGG1 activity increased the risk of lung cancer fivefold.
 
 
Lung cancer. Image: Lange 123 on Wikimedia commons
 
In the present study, Livneh, Paz-Elizur and Dr. Yael Leitner-Dagan set out to improve the accuracy of their predictions. They developed a method to measure the activities of a second repair machine, known as MPG. Like OGG1, MPG fixes oxidative damage, but unlike that enzyme, it deals with a broad range of injuries, among them those caused by chemotherapy. Together with Prof. Gad Rennert of the Technion and the Carmel Medical Center, and Dr. Ran Kramer of Rambam Medical Center, the scientists collected blood samples from 100 lung cancer patients and compared them, in a blinded test, with samples from 100 healthy people.

They found that there is, indeed, a correlation between MPG activity and the tendency to develop lung cancer, but this correlation was the opposite of what they expected: MPG was more active in the lung cancer patients. How could their results be explained? “There is a price to pay for the fact that MPG acts on a wide range of problems. It doesn’t always manage to cut out the injured bit,” says Livneh. “It can get ‘stuck’ to the DNA strand and block access for the repair machinery that is more specialized. So, high levels of this enzyme can be ‘too much of a good thing.’”

Using the activity levels of both enzymes to evaluate the lung cancer risk factor enabled them to better predict who would get the disease. The findings were recently published in the Journal of the National Cancer Institute.

The scientists hope their findings will not only result in a better test for lung cancer risk, but that they may aid in the development of ways to reduce the genetic sensitivity to carcinogen damage. For instance, a cocktail of drugs – one to raise OGG1 activity and another to lower that of MPG – could possibly restore the balance. Another avenue might be to find a common regulatory mechanism that controls the levels of both and adjust its function. Livneh and his team plan to check these possibilities using new equipment recently installed in the Israel National Center for Personalized Medicine at the Weizmann Institute.

Participating in the research were Dr. Ziv Sevilya and Dalia Elinger in Livneh’s group, and Mila Pinchev and Hedy Rennert in Rennert’s group. The statistical analyses were done by Prof. Laurence Freedman of the Gertner Institute for Epidemiology and Health Policy Research at Chaim Sheba Medical Center, and Prof. Edna Schechtman of Ben-Gurion University of the Negev.
 
Prof. Zvi Livneh's research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine, which he heads; the Leona M. and Harry B. Helmsley Charitable Trust; Dana and Yossie Hollander, Israel; and the estate of Alice Schwarz-Gardos. Prof. Livneh is the incumbent of the Maxwell Ellis Professorial Chair of Biomedical Research.

 

 
 
Lung cancer. Image: Lange 123 on Wikimedia commons
Space & Physics
English

Double Trouble

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Chromosome pairs: Does doubling them help or hurt? Image: Wikimedia commons
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
When we are under heavy stress, our reactions can sometimes be excessive, even if we know our actions carry a price. Once we have the time to stop and reflect, we are likely to come up with a more moderate solution. When a cell is exposed to harsh stress, it can also engage in a radical response involving the wholesale doubling of chromosomes. This mechanism is quick and effective, but it also comes at a heavy price for the cell. Recent Weizmann Institute research on yeast shows that stressed cells can behave like people: Given time, they are likely to adopt a different coping mechanism that is more specific, carries a lower cost and is more effective in the long run.

The change in chromosome numbers called aneuploidy has been well studied. In general, it results from an error taking place during cell division; when that mistake turns out to be to the cell’s advantage, it can be passed on to future generations. This “fast and dirty” response to environmental stress boosts the expression of most of the genes in the duplicated chromosome – including those that help the cell cope with stress. But there is also a great deal of waste: Cells must expend extra energy and resources on the extra genes, and so they develop more slowly and exhibit imbalances in their protein production schedules. In humans, aneuploidy in developing embryos can lead to miscarriages or, in the case of chromosome 21, to Down syndrome. Many tumor cells also have irregular numbers of chromosomes.

So is a non-standard number of chromosomes a “Dr. Jekyll” that helps cells survive stress or a “Mr. Hyde” that destroys them? This question, known as the aneuploidy paradox, is the subject of a long-standing scientific controversy.
 
 
(l-r) Dr. Orna Dahan, Avihu Yona and Prof. Yitzhak Pilpel
 
To approach the question, Prof. Yitzhak Pilpel and his team in the Molecular Genetics Department, including Avihu Yona and Dr. Orna Dahan, created an evolutionary process in the lab: For over a year, they grew baker’s yeast cells and followed their progress over thousands of generations. Though a year may seem a long time to watch yeast grow, it is a quick flash compared to the millions it takes for an organism to evolve in nature. The controlled experiment enabled the team to speed things up enough to observe the process of evolution instead of just viewing the end results. As the cells were exposed to heat or acidity – stress factors that acted as means of “natural” selection – the yeast adapted to survive. Every few generations, the researchers checked the genomes of their yeast, hoping to pinpoint the changes that contributed to their adaptation to the harsh conditions.

The results showed that the yeast adapted to heat by adding another copy of a certain chromosome. Growth in acidic conditions led to the doubling of a different chromosome. Clearly, the extra chromosomes were helping the yeast cells to improve their coping abilities in the face of the various stress factors. When the scientists tested cells with artificially inserted extra chromosomes and then exposed them to stress, these fared as well as the yeast that had evolved to do so in the lab.

But the scientists did not stop there: They continued to follow the evolution of the yeast cells as they kept growing and dividing. This persistence led the team to a surprising discovery: As time passed, the extra chromosome tended to disappear. In its place, new mechanisms arose that took longer to develop but were more focused and carried a lower cost to the cell. In particular, the expression of the genes for dealing with the stress remained as high as it had been with the extra chromosome. “The quick solution is not optimal, but in sudden, overwhelming stress conditions, it is worthwhile to the cell to pay the price,” says Pilpel. “When there is time to adapt, the cell will exchange that solution for another that is more precise.”

The research team demonstrated this principle by applying “gradual evolution” – worsening the yeast’s conditions slowly rather than all at once. Now, there was no aneuploidy, apparently because the yeast cells could take their time to adapt. In other words, says Pilpel, “The outcome depends on the pace of the evolutionary regime.”

The scientists believe that their findings may be relevant to understanding cancer, especially the ways in which cancer cells rid themselves of genetic mechanisms that suppress unchecked growth. For example, a cancer cell with a mutation in a tumor suppressor gene might double the damaged chromosome and then usurp the intact one, thus removing the “brakes” holding back cell division. Also, understanding how the coping ability of a cell is affected by extreme versus gradual environmental challenges might help doctors and biomedical researchers plan chemotherapy protocols in a way that will not encourage cancer cells to develop resistance.  
 
Prof.  Yitzhak Pilpel's research is supported by the Sharon Zuckerman Laboratory for Research in Systems Biology; the Braginsky Center for the Interface between Science and Humanities; and the European Research Council. Prof. Pilpel is the incumbent of the Ben May Professorial Chair.


 
 
Chromosome pairs: Does doubling them help or hurt? Image: Wikimedia commons
Life Sciences
English

Safer Stem Cell Scenario

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Chromosomal analysis of a polyploid stem cell: This cell does not turn malignant despite having three or four copies of most chromosomes
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Any virtue taken to an extreme can become a flaw. Take, for instance, stem cells. They hold tremendous promise for repairing or even replacing diseased tissues, by virtue of being flexible and ready to grow. But left unchecked, this same growth can become a hazard: It can lead to cancer.

A new Weizmann Institute study might help avoid this danger. As reported recently in Cancer Research, the scientists, in collaboration with researchers from the Chaim Sheba Medical Center, have identified genetic markers that, for a certain type of stem cell, make it possible to predict the risk of any particular cell turning cancerous.
 
 
(l-r) Dr. Ofer Shoshani and Prof. Dov Zipori
 
These cells, called mesenchymal stromal stem cells, or MSCs, are particularly attractive for use in therapy. They are almost as versatile as embryonic cells but much more readily available: Found in adults in the bone marrow, skin, fat, muscle and other tissues, they can be removed in large numbers with relative ease. Precisely for these reasons, MSCs are already widely used in clinical trials; for example, they have been transplanted into fetuses to correct a congenital bone disorder. Results have been mixed, partly because the cells fail to survive for a long time after the transplant. But in the future, when scientists learn to improve their survival, a major concern will be to prevent MSCs from causing cancer.

When examining the cancer-causing potential of MSCs in the new study, the scientists were in for a surprise. Overall, cancer-causing MSCs were rare. However, diploid MSCs – that is, those with the normal number of chromosomes – were much more prone to turning cancerous than the polyploid ones – cells that have three or four copies of each chromosome instead of the usual two and that traditionally have been associated with cancer.

The scientists have identified a genetic marker that could be used to distinguish diploid cells from polyploid – a gene called H19: Its activity was more than a thousand times greater in diploid than in polyploid cells. H19 was also found to be a good indicator of a cell’s cancer-causing potential. In fact, when the scientists artificially prompted a diploid cell to become polyploid, its H19 levels dropped – and so did its tendency to turn malignant. H19 measurements can therefore serve as a means of selecting “safe” MSCs, ones with the lowest risk of causing cancer.

The idea that an abnormal number of chromosomes actually leads to less cancer goes against prevalent scientific thinking: How is it possible that the study’s findings run so counter to existing views on polyploidy and cancer?
 
Polyploid stem cells under a fluorescent microscope, in two stages of cell division: (Left): The centrosomes (red dots) – small organelles that help the DNA ( blue) to separate into two during cell division – begin to cluster on either side of the nucleus (Right): The centrosomes are grouped into two clusters (large red dots), allowing the DNA (blue) to be divided equally between the two daughter cells. As a result, the cell divides normally, without turning malignant
 
 
 
“Polyploidy is not a direct cause of cancer – on the contrary, it’s probably one of the many strategies used by cells to avoid cancer under stress,” says lead study author Prof. Dov Zipori of the Molecular Cell Biology Department, a pioneer of adult stem cell research. He and his colleagues propose the following explanation: When exposed to environmental stress, such as UV radiation or exposure to chemical carcinogens that can cause mutations in its DNA, the cell responds by duplicating its chromosomes. If the duplication occurs before the mutation, polyploidy has a protective effect: The cell now has much more DNA than before, so that the effect of the mutation is “diluted” by the newly created mass of genetic material. If, on the other hand, the duplication takes place after the mutation has been introduced, the protective strategy fails: The mutation is multiplied together with polyploidy and can lead to cancer.

In any event, what emerges from the study is that polyploidy in itself is not a predictor of cancer. Rather, the opposite is true: It is a sign that a cell has confronted stress and in some cases, though not all, successfully avoided malignancy.

The study was performed in mice in Zipori’s laboratory by Dr. Ofer Shoshani with the Weizmann Institute’s Hassan Massalha, Dr. Nir Shani, Sivan Kagan, Drs. Orly Ravid, Shalom Madar and Dena Leshkowitz, together with Prof. Gideon Rechavi and Dr. Luba Trakhtenbrot of the Sheba Medical Center.

If confirmed in further studies, this research could increase the safety of stem cell use in a variety of therapies, as well as giving scientists a better understanding of the cellular events that might lead to cancer.
 
Prof. Dov Zipori's research is supprted by the Helen and Martin Kimmel Institute for Stem Cell Research, which he heads; the Leona M. and Harry B. Helmsley Charitable Trust; David and Molly Bloom, Canada; and Roberto and Renata Ruhman, Brazil.  Prof. Zipori is the incumbent of the Joe and Celia Weinstein Professorial Chair.
 
 



 
(l-r) Dr. Ofer Shoshani and Prof. Dov Zipori
Life Sciences
English

Bringing Down Barriers

English
 
 
Blood brain barrier. Image: Ben Brahim Mohammed via Wikimedia Commons
 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Our brains are well protected, and for a good reason. Most of the proteins present at high levels in the blood, such as antibodies or the regulatory molecule albumin, are kept out of the brain because they could damage it or disturb its exquisitely organized functioning. Only essential nutrients are allowed entry from the circulation.
Prof. Matityahu Fridkin
 

 

This tight control is imposed by the blood-brain barrier. The barrier is both physical – the cells lining the blood capillaries in the brain are tightly attached to one another – and chemical: The brain’s lining chemically repels potentially damaging substances. When essential nutrients are needed, the barrier creates “openings” called physiological gates – chemical and physical changes in the lining that permit these nutrients to enter.
 
Although this barrier is vital for health, it poses a major problem for treating brain disorders. For instance, since most drugs cannot get across this barrier, malignant brain tumors cannot be treated efficiently by regular anti-cancer chemotherapy. Scientists have attempted to overcome this problem by “smuggling” drugs into the brain with the help of “shuttle” proteins capable of passing through physiological gates. But unfortunately, these gates are relatively few in number, so that insufficient quantities of the drug are delivered to the brain using this strategy.
 
A potential solution might come from an unexpected direction: the study of HIV, the virus that causes AIDS. HIV is a master of penetration: It gets into mammalian cells – particularly immune T cells – with great ease and can even migrate from cell to cell. Not only that, in 1996, scientists discovered that HIV can cross the blood-brain barrier, penetrating the central nervous system – the brain and spinal cord. This was a surprising discovery because the two receptors known to help the virus infect T cells are not found on cells lining the brain’s protective barrier. The mystery was later resolved when the scientists found that the virus manufactures its own “opener” for the barrier: a molecule called HIV-1-TAT-protein, which contains unusual sequences of amino acids in two of its regions. Even when purified from the virus, the HIV-1-TAT-protein maintained its barrier-opening capacity.
Prof. Yoram Shechter
 

 

It is precisely this capacity that drew the attention of Weizmann Institute scientists. Prof. Yoram Shechter of the Biological Chemistry Department, Prof. Matityahu Fridkin of the Organic Chemistry Department in the Chemistry Faculty and Dr. Itzik Cooper of the Neurobiology Department decided to test the possibility that the blood-brain barrier could be opened by short peptides based on the unusual sequence of amino acids in the HIV-1-TAT protein.
 
To perform their test, they used an experimental system developed in the laboratory of the late Prof. Vivian Teichberg of Weizmann’s Neurobiology Department, which uniquely simulates the blood-brain barrier in a laboratory dish. This system consists of a layer of tightly linked cells drawn from the lining of pig brains and grown in culture. The tightness of the layer is measured by an evaluation of its electrical resistance. When this tightness drops, the permeability of the layer is further quantified with the help of radioactively labeled proteins.
Dr. Itzik Cooper
 
The scientists found that their HIV-1-TAT peptides were indeed able to weaken the blood-brain barrier, permitting the entry of therapeutic proteins and other drugs. Most important, as reported recently in the Journal of Biological Chemistry, the drugs penetrated the barrier in quantities sufficient for the treatment of major brain disorders. Further studies are being conducted at the Weizmann Institute in collaboration with Prof. Yosef Yarden of Weizmann’s  Biological Regulation Department and Prof. Yael Mardor of the Chaim Sheba Medical Center at Tel Hashomer.

Obviously, destabilizing the blood-brain barrier is undesirable in healthy people, but in cancer patients this approach could represent the least of all evils. In fact, in certain non-fatal diseases, this barrier is markedly disrupted, suggesting that such a disruption poses no immediate threat to a person’s life. The new Weizmann Institute approach could therefore be valid for treating brain tumors and other neurological disorders.
 
Prof. Matityahu Fridkin’s research is supported by the Adelis Foundation.

Prof. Yoram Shechter’s research is supported by the Adelis Foundation.
 
 
 
Life Sciences
English

A Proofreader for DNA

English

The device library consists of (1) an input module containing many different variants of the same gene (green) and (2) a selection module (blue) integrated within an Amp resistance gene (gray). The selection module contains a loop on its coding strand which frame-shifts (dark gray) and stops the translation (red stop codon) of the Amp gene

 

A synthetic device made of biological molecules can be programmed to search for and identify exact DNA sequences inside living cells – and reject any of those sequences that contain errors, however tiny. The Weizmann Institute researchers who invented the device believe that the concept behind it may lead to the development of new, highly sensitive diagnostic techniques, as well as enhanced methods for creating interfaces between natural and synthetic biological molecules.


Dr. Tuval Ben Yehezkel and Tamir Biezuner in the lab of Prof. Ehud Shapiro of the Biological Chemistry, and Computer Science and Applied Mathematics Departments created numerous copies of the DNA-based devices – each containing an identical, preprogrammed genetic sequence hooked up to a different target gene – and inserted them into bacterial cells. Inside the cells, the synthetic infiltrators, like tiny moles, recruited the cell’s “proofreaders”: internal repair mechanisms that normally, during cell replication, check for mismatches between the genetic “letters” A,T,G and C in a new DNA strand and those in the parallel sequence of the double strand. Normally, these proofreaders would snip out any offending letters on one strand and call on the paired strand of DNA to try substituting the information. The synthetic device, however, picked up on the error-correction activity and co-opted this mechanism, using it instead to reprogram itself to destroy the cell. Thus only cells containing the complete, correct sequence remained at the end of the process.
 
 
(l-r) Dr. Tuval Ben Yehezkel, Prof. Ehud Shapiro and Tamir Biezuner
 
In the experiment, the devices were programmed to preserve a DNA sequence that does not confer any selective advantage in E. coli cells. This ability to work with any DNA segment, regardless of its use in the cell, highlights its advantage over other methods: The other methods often rely on a gene’s functionality to select for it using classical Darwinian selection, or are liable to miss tiny errors in the sequence. In the future, slightly more sophisticated versions of the device could be used by researchers working with artificial genetic sequences to ensure their accuracy. The researchers think that future devices based on their concept could be employed in medicine to seek out hard-to-detect genes – for example harmful mutations in fetal cells in the mother’s blood or cancer-causing mutations that appear in just a few cells.

The findings, which appeared recently in PLoS One, incorporate aspects of two fairly new fields of research: synthetic biology and biological computing. They have demonstrated how a man-made genetic sequence can be inserted into a living cell and interface there with the cell’s natural mechanisms – a feat that has been a major, ongoing challenge for synthetic biologists. And with the help of those mechanisms, this synthetic construct performs like a simple computing device, in which DNA inputs – sequences that may or may not contain errors – are processed to arrive at an output – in this case the preservation or elimination of those sequences.  Shapiro says: “Future work in this direction may bring about the integration of synthetic DNA devices into ever more complex cellular environments. This, in turn, could lead to a wide variety of applications.”
 
Prof. Ehud Shapiro’s research is supported by the Paul Sparr Foundation; and the European Research Council. Prof. Shapiro is the incumbent of the Harry Weinrebe Professorial Chair of Computer Science and Biology.
 
(l-r) Dr. Tuval Ben Yehezkel, Prof. Ehud Shapiro and Tamir Biezuner
Math & Computer Science
English

A Question of Upbringing

English
 
 
The behavior (gene expression) of immune cells in the colon (l-r): 1) monocytes before arrival in the colon; 2) “delinquent” uneducated cells; 3) “educated” immune cells; 4) resident immune cells
 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Failure to educate the young generation properly can have devastating consequences – not only among human beings, but among cells too. Uneducated immune cells, it turns out, might be at least partly responsible for the notorious flare-ups that occasionally occur in chronic inflammatory diseases of the digestive tract.

Our digestive tract is teeming with bacteria – some inhabiting it permanently and assisting in digestion, others introduced with food and drink. Keeping such a dynamic system in balance requires ongoing maintenance. A central role in this process is played by immune cells called macrophages, or "big eaters," believed to play an important role in clearing debris and keeping tissues healthy. Macrophages are generated from precursor cells, the monocytes, which arrive from the blood and settle in the lining of the gut.  

A collaborative study led by Weizmann Institute researchers has revealed that for about ten days, all newly recruited monocytes are taught – probably by signals originating in the gut lining – to express the same genes as do the more veteran immune cells. Once their education is complete, these cells start dutifully contributing to the proper maintenance of the lining.
 
 
(l-r) Prof. Steffen Jung, and Drs. Ehud Zigmond and Chen Varol
 
But if the gut lining is already inflamed – for example, as a result of bacterial infection – the newly arrived monocytes display a strikingly different behavior. Like teenagers giving in to peer pressure, these cells, on landing in a bad environment, turn bad themselves. They fail to undergo the proper education, so that their gene expression follows an abnormal pattern. As a result, instead of helping to maintain the gut, they start promoting inflammation, making it even worse than it was when they arrived.

Such misbehaving immune cells might help explain what happens during flare-ups of inflammatory bowel disease: Even a slight disruption resulting from exposure to bacteria or certain foods, which would normally be quickly corrected in a healthy person, leads to lasting inflammation. And once such inflammation is in place, the newly arriving monocytes, acting like juvenile delinquents who refuse to be educated, apparently keep aggravating this inflammation instead of correcting it.

The study, reported recently in Immunity, was led by Prof. Steffen Jung of the Weizmann Institute’s Immunology Department and performed in transgenic mice developed in his laboratory. The research was conducted by Dr. Ehud Zigmond, a physician and Ph.D. student, and Dr. Chen Varol of the Tel Aviv Sourasky Medical Center, in collaboration with departmental colleagues Dr. Guy Shakhar and Julia Farache, as well as Dr. Gilgi Friedlander of  Biological Services. Reagents were provided by Dr.  Kenneth M. Murphy of Washington University School of Medicine, Dr. Matthias Mack of the University of Regensburg in Germany, Dr. Nahum Shpigel of the Hebrew University of Jerusalem and Dr. Ivo G. Boneca of the Pasteur Institute and INSERM in France.

The findings point to new ways of treating inflammatory bowel disease. One approach would be to temporarily interrupt the recruitment of new monocytes to the gut once inflammation has begun, to prevent its further aggravation. In their studies in mice, Jung and his team indeed showed that antibodies blocking the arrival of new monocytes to the colon alleviated the symptoms of inflammation.

But in the longer term, as in many other areas of life, it is education that holds the real promise for the future. Once scientists understand in greater detail how monocyte education takes place in the gut lining, they should be able to ensure that it runs its proper course, so that the monocyte “kids” behave themselves, contributing to health rather than disease.
 
Prof.Steffen Jung’s research is supported by the Jeanne and Joseph Nissim Foundation for Life Sciences Research; the Leir Charitable Foundations; the Leona M. and Harry B. Helmsley Charitable Trust; the Adelis Foundation; Lord David Alliance, CBE; the Wolfson Family Charitable Trust; the estate of Olga Klein Astrachan; and the estate of Florence Cuevas.

Dr. Guy Shakhar’s research is supported by the Clore Center for Biological Physics; the Yeda-Sela Center for Basic Research; the Jeanne and Joseph Nissim Foundation for Life Sciences Research; the Leona M. and Harry B. Helmsley Charitable Trust; the Dr. Dvora and Haim Teitelbaum Endowment Fund; Simone Pastor, Monaco; Lord David Alliance, CBE; Paul and Tina Gardner, Austin, TX; the Steven and Beverly Rubenstein Charitable Foundation; and the Paul Sparr Foundation.


 
 
Life Sciences
English

How Good Cells Turn Bad

English

(l-r) Amir Bar, Dr. Amos Tanay, Netta Mendelson-Cohen, Prof. Varda Rotter, Dr. Zohar Mukamel, Naomi Goldfinger, Gilad Landan and Dr. Alina Molchadsky

 

 

 

 

 

 

 

 

 

 

 

 

How does a cell turn “bad” – from a well-behaved individual that respects boundaries and only divides when necessary, into a cancerous one whose reproduction is out of control? Is this antisocial conduct simply a product of bad genes, or does something else push it into the life of a cancer cell?
 

Until recently, genes were assumed to play the sole driving role in this scenario. Indeed, for cancer to develop, a number of genetic mutations that accumulate as cells live and divide are necessary. But researchers have realized that mutations are not the whole story: They cannot fully explain how a cell makes the transition from average good citizen to cancer.
 
One idea that has been gaining ground in recent years is that epigenetic (literally, “above the genes”) changes taking place in parallel with mutations can play an important role in the initiation and development of cancer. Epigenetic modifications affect the genes and can be passed on to further generations of cancer cells. One important epigenetic mechanism is the DNA methylation system, in which biochemical groups are attached to various genes, thereby “disabling” them. In normal cells, this system helps prevent genes from being expressed in the wrong time or place.
 
Methylation has been well studied – mostly focusing on its role in embryogenesis. It is commonly believed that the majority of changes in methylation take place before and during embryonic development, after which cells and their descendents become locked into a pattern. Yet it was also known that cancer cells tend to have different methylation patterns from healthy ones. How do these changes come about? Dr. Amos Tanay of the Computer Science and Applied Mathematics, and Biological Regulation Departments, and Prof. Varda Rotter of the Molecular Cell Biology Department decided to explore the methylation of genes in healthy cells as they age and divide, to see if they could learn something about changes that might promote cancer.
 
 
(l-r) Dr. Amos Tanay and Prof. Varda Rotter
 
The two scientists and their groups combined methods and techniques from a number of different fields: Tanay is a computational biologist who has been developing computer-based methods of extracting significant information from huge quantities of genetic data, and Rotter is a cancer cell biologist who has developed original lab methods to investigate the genetics of cancer. Gilad Landan, a joint Ph.D. student with Tanay and Rotter, together with Dr. Zohar Mukamel, Netta Mendelson Cohen and Amir Bar from Tanay’s group, Naomi Goldfinger and Dr. Alina Molchadsky from Rotter’s group, and Dr. Einav Nili Gal-Yam, an oncologist in the Talpiot program at the Sheba Medical Center, created cultures of healthy, “immortal” cells that kept dividing past extreme old age – up to 300 rounds of cell division. The team developed new techniques that permitted the follow-up and analysis of methylation in the genomes of the cultured cells as they evolved over that period.

Among other things, their observations challenged the notion that methylation in cells is fixed early on and more or less maintained in a stable state throughout life. Patterns of methylation in the healthy cells accumulated changes almost from the onset of the experiment. The alterations were basically random, so that the methylation sites in cells that started out identical diverged more and more as division continued. In general, however, the number of genes that had methyl groups attached to them increased dramatically over time. By the 300th division, the cells had highly abnormal methylation patterns and many were on the verge of becoming cancerous. These findings appeared recently in Nature Genetics.

Tanay says that an older cell or one that has undergone too many rounds of division may still mostly function because certain genes that are in active, day-to-day use have mechanisms that prevent methylation. But it might find itself unable to react properly to the kinds of DNA damage or mutation that can initiate cancer growth because many other genes – for instance those that are activated only in emergencies – are disabled by random epigenetic markers. In other words, creeping epigenetic changes may aid and abet the cells’ transition to a cancerous lifestyle because they can have a “calcifying” effect on the genome: Like an aging joint, the genome may lose its flexibility as added methyl groups slow it down.

Tanay and Rotter and their teams are currently exploring the implications of these findings in cancer patients. They want to know more about methylation patterns in the tumor cells taken from those patients, to see if the shifts they identified in the lab match up. They also  suspect that the epigenetic changes may also help the cells keep up their bad behavior on their way down the cancerous path. Among other things, the researchers are now asking how the different methylation patterns might affect tumor cells’ response to chemotherapy.
 
Prof. Varda Rotter's research is supported by the Adelis Foundation; the Leir Charitable Foundations; and the Women's Health Research Center, which she heads. Prof. Rotter is the incumbent of the Norman and Helen Asher Professorial Chair of Cancer Research.

Dr. Amos Tanay's research is supported by Pascal and Ilana Mantoux, Israel/France; the Wolfson Family Charitable Trust; the Rachel and Shaul Peles Fund for Hormone Research; and the estate of Evelyn Wellner. Dr. Tanay is the incumbent of the Robert Edward and Roselyn Rich Manson Career Development Chair in Perpetuity.
 
 
(l-r) Amir Bar, Dr. Amos Tanay, Netta Mendelson-Cohen, Prof. Varda Rotter, Dr. Zohar Mukamel, Naomi Goldfinger, Gilad Landan and Dr. Alina Molchadsky
Life Sciences
English

Circular Reasoning

English
 
Polonius: What do you read, my lord?
Hamlet: Words, words, words.
Polonius: What is the matter, my lord?
Hamlet: Between who?
Polonius: I mean, the matter that you read, my lord.
~ Hamlet, act II, scene 2
 
(l-r) Prof. Elisha Moses and Dr. Tsvi Tlusty
 
 
Humans, according to the language theoretician Noam Chomsky, are born with a universal, “internal grammar,” which enables verbal communication. Although this idea is still controversial, it has received some support from genetic research: Certain mutations in a gene called FOXP2 significantly impair the ability to form sentences. If language is indeed a natural phenomenon stemming from the genes and the structure of the brain, then the tools of the natural sciences might be applied to discover where the roots of language lie.

The dictionary, as a particular example, is a collection of words defined by other words, and it can be probed methodically to reveal universal laws governing human language. Prof. Elisha Moses and Dr. Tsvi Tlusty of the Institute’s Physics of Complex Systems Department undertook this challenge. Together with Jean-Pierre Eckmann of the University of Geneva and summer student David Levary from Harvard University, they looked at the connections between the words – the network of relationships that arises when the words used in a definition are linked to the defined word. So for each word in their study, they drew lines connecting it to the words used to define it, as well as to those in the quotations demonstrating usage. This creates a complex graph with as many nodes as there are words in the dictionary, and if a word has multiple meanings then each one of them gets a node of its own.
 
For example, the Even-Shushan Hebrew dictionary defines the word love (ahava) thus: "strong affection, feeling of great or desirous attraction for someone or something.” To begin mapping a network with “love” at its center, one would draw a straight line from the word “love” to the words “strong,” “affection,” “feeling,” “desire,” “attraction,” and so on. Then, new sets of lines are drawn from the connected words to all the words in their definitions. Soon, a dense network of connections is generated between the words in the dictionary, with related words more likely to be found in proximity to each other.

Because even a large dictionary is not infinitely large, a full network of all the words contained within it is theoretically possible. This large network will typically resolve into smaller, partial networks, composed of words that tie in to a specific subject of the same area of content.
 
ouroboros love
 

Closing a loop


Following the interconnecting lines of the dictionary network will often bring one back to one’s starting point. In other words (no pun intended), the network closes in on itself, and a word, by extent, becomes a part of its own definition. Though it appears to be a tautology, such cyclical connections may be deeply rooted in the fundamentals of language. The researchers found that in a dictionary containing around 100,000 words, some 6,000 of them will circle, through the network, back on themselves. Moses and Tlusty investigated further, discovering that many of the words that close in on themselves belong to the relatively small subset of the dictionary that is considered “basic vocabulary.” (Basic vocabulary size varies with the definition: Ogden chose 850 for his Basic English, Jōyō Kanji in Japanese covered 2,136 symbols.)

Kurt Gödel famously dealt with the paradox of circular logic in his incompleteness theorem, which states that in a closed number system, there will always be true statements that cannot be proved within the system. A dictionary is also a sort of closed system, and upon consideration one realizes that it is impossible to create a set of definitions that never repeats back on itself. Circularity appeared historically with the Ouroboros - the image of a serpent biting on its own tail, which probably showed up first in Egypt and has played a role ever since in philosophy, religion, alchemy and psychology.
 
 
Nature has no problem with circularity: DNA, for instance, encodes the information needed to make proteins, but those very proteins activate DNA and regulate its activities. So if language is a natural phenomenon, arising from the basic patterns of living structures, it might not be so surprising to discover closed cycles that loop back on themselves, concepts that are explained by referring back to the concept itself.

The scientists say that this basic structure is so fundamental to the dictionary network that every time a new concept is added a loop will form to bring its definition back around. They found that when words are connected to one another on the same loop, these were significantly more likely to either be coined or their meaning updated in the same era. So the dictionary network turns out to reveal “peer relationships” among words.
 
dictionary
 

The dictionary


In June, 1857, three gentlemen named Richard Trench, Herbert Coleridge and Frederick Furnivall met in London to establish the Unregistered Words Committee. The idea was to produce a comprehensive English dictionary, a project they estimated would take around 10 years. It would eventually take 72 years to compile the first edition of the Oxford English Dictionary, which encompassed 10 volumes and included some 400,000 words and phrases, and 1,800,000 quotations. Hundreds of volunteers would participate in the project by sending quotations to demonstrate usage.

One of the best-known contributors was William Minor, who was later discovered to be a murderer. Minor was an army doctor who had suffered shellshock in the American Civil War. He later moved to England, where one night he killed a man in a manic fit and was confined to the Broadmoor Asylum. He spent the latter part of his life there, during which he started sending quotations to OED’s editor, Sir James Murray, who even visited Minor at Broadmoor. The unusual relationship between the editor and his prolific contributor has been described by Simon Winchester in his book The Professor and the Madman.

 
Prof. Elisha Moses's research is supported by the Murray H. & Meyer Grodetsky Center for Research of Higher Brain Functions; and the J & R Center for Scientific Research.


 
 
ouroboros love
Space & Physics
English

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