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Science Feature Articles</p>

An Open- and Shut- Case

English
(l-r) Prof. Eitan Reuveny, Ayelet Cooper, Liora Guy-David and Dr. Adi Raveh. Gear shift
 
 
 
The hero, as heroes do, is relaxing with friends or enjoying a meal, when a mortal threat – a giant wave, a monster or a blood thirsty criminal – appears with no prior warning, compelling the hero to jump up and run for his life. As he does so, his heart must speed up its beat drastically within seconds, pumping extra blood to his muscles to ensure his safe escape. How can the heart “shift gears” so quickly, from beating at a leisurely pace to thumping frantically? The drama of sudden danger is familiar – not only to motion picture heroes – so this question is relevant to all of us.


In a new study published in the prestigious journal Cell, Weizmann Institute researchers revealed a previously unknown mechanism responsible for the rapid and accurate control of signals transmitted by the nerves to muscle cells, among them the signals governing the rate of heart muscle contraction. The study helps explain how signal transmission is regulated in the heart and brain with exquisite precision. It was conducted by Adi Raveh with Ayelet Cooper and Liora Guy-David in the laboratory of Prof. Eitan Reuveny of the Biological Chemistry Department.

 
To convey electric signals that transmit messages between nerve cells or from nerve cells to muscle cells, ion channels in the cell membrane – through which the cell’s electrical activity is generated – open up for a moment to allow the flow of charged ions into or out of the cell. In this particular case, the opening occurs when a neurotransmitter – a chemical messenger – binds to a receptor in the cell membrane, activating an intracellular molecule called the G protein. This protein then opens up the ion channel by altering its structure – an action akin to releasing a door latch, allowing the door to open.
 
To prepare the cell for receiving the next signal, it’s obvious that the ion channel must close again after a while. This indeed happens very soon if the neurotransmitter is short-lived: With no signal from the cell membrane, the G protein is deactivated, resulting in the closing of the “door latch.” But if the neurotransmitter is long-lived, the cell has an additional mechanism that makes sure the ion channel doesn’t stay open continuously. This mechanism involves an internal “controller,” an enzyme known as GRK, which cancels the G protein’s activity: GRK causes these receptors to be drawn inside the cell, which means that they no longer respond to the neurotransmitter and consequently no opening of the channel occurs.
 
One example of GRK controller activity has to do with such long-lived neurotransmitters as morphine and other opioids, commonly used as painkillers. When given as drugs, these neurotransmitters lose their effectiveness after a while because the GRK removes all the G-protein-linked receptors from the cell membranes, thereby preventing the generation of the signal for ion channel opening; these painkillers can then no longer exert their action. Thus a mechanism so vital to normal cellular communication becomes an impediment to therapy. For this reason, it is recommended that opioids not be given continuously for too long, to prevent the patient losing sensitivity to these drugs.
 
This control function of GRK – drawing the receptors into the cell – is a relatively lengthy process that can take hours. But what happens if the opening and closing of ion channels needs to be controlled much more quickly? To adjust the heartbeat to a sudden change in the environment, the neurotransmitter that slows down the heart rate must be instantly turned off, closing down the ion channel to make room for adrenalin action, which makes the heart beat faster. In fact, scientists have known for some time that the ion channel can indeed shut down very quickly, even in the presence of a long-lived neurotransmitter. What causes this rapid shutdown?
 

 

The Second Mechanism

 

 
In their new study, Weizmann Institutes scientists have found the answer. They discovered that the GRK controller can terminate the action of the G protein in a previously unknown manner – one that is much faster than the lengthy drawing of the receptor into the cell. It turns out that within seconds, the GRK can simply rush to the door-latch control mechanism and, rather than bothering to relocate receptors, simply remove the G protein itself. Once the G protein has been pushed away from the “door handle,” the ion channel closes down.
 
To reveal this mechanism, the Weizmann team conducted elaborate studies using nerve and heart muscle cells. These studies involved measuring electric currents passed through the cell membrane, tracing the movement of proteins by labeling them with fluorescent markers and selectively disrupting selected molecules by genetic manipulation in order to elucidate their function.
 
The newly discovered mechanism helps explain how electric signals in the body can be turned off rapidly and precisely. This new understanding sheds fresh light on the functioning of ion channels throughout the body but particularly in the heart and brain, where rapid signal regulation is crucial. Thus, in an instant, the GRK controller can turn off the slow, steady heartbeat signal to make way for the adrenalin signal, which immediately makes the heart beat faster. In this way, the body’s muscles are quickly provided with the massive supply of blood needed for intensive activity, such as running – ensuring that the hero faced with sudden danger will survive until the end of the film.

Prof. Eitan Reuveny's research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the Nella and Leon Benoziyo Center for Neurological Diseases; the Clore Center for Biological Physics; the David and Fela Shapell Family Center for Genetic Disorders Research; the Yeda-Sela Center for Basic Research; and the Philip M. Klutznick Fund for Research.
 
 
G Proteins and opiates
 
One example of GRK controller activity has to do with such long-lived neurotransmitters as morphine and other opioids, commonly used as painkillers. When given as drugs, these neurotransmitters lose their effectiveness after a while because the GRK removes all the G-protein-linked receptors from the cell membranes, thereby preventing the generation of the signal for ion channel opening; these painkillers can then no longer exert their action. Thus a mechanism so vital to normal cellular communication becomes an impediment to therapy. For this reason, it is recommended that opioids not be given continuously for too long, to prevent the patient losing sensitivity to these drugs.
 
 
 
 
 

 

 

 

 
 
 
 
 
(l-r) Prof. Eitan Reuveny, Ayelet Cooper, Liora Guy-David and Dr. Adi Raveh. Gear shift
Life Sciences
English

Keeping Pace with the World’s Food Demand

English
 
 
(l-r) Drs. Olga Davydov and Nardy Lampl, Prof. Robert Fluhr, Drs. Ofra Budai-Hadrian and Thomas Roberts. Secrets to growth

 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
When a heat wave sent tomato prices soaring this past summer, before the High Holidays, Israelis got a taste of the precarious nature of our food supply: Any climate upheaval can instantly create dire shortages of food staples. Even in the absence of natural disasters, securing the world’s food supply in the 21st century promises to be a tall order: Global population continues to grow while the areas of cultivated land tend to remain stable – a situation that is bound to lead to food shortages, and will be further aggravated by global warming.
 
“It’s vitally important to keep up the green revolution,” says Prof. Robert Fluhr, referring to the increases in yields that in the second half of the 20th century saved much of the world from starvation. “Adapting agriculture to meeting the world’s needs is a continuous battle. We must stay on our toes in order to win.”
 
Feeding the world is all the more challenging because a staggering proportion of crop yields worldwide – above 30 percent – is regularly lost to pests, disease and weather. Prof. Fluhr’s laboratory in the Weizmann Institute’s Plant Sciences Department focuses on research that can help increase yields by reducing these losses. In particular, the lab’s research is aimed at understanding – and ultimately enhancing – the plant’s natural defenses against a variety of ills.
 
In a recent collaborative study with researchers from Australia, Fluhr’s team has taken an important step in this direction. The scientists have unraveled the control switch for a crucial plant growth- and survival- mechanism: the killing of individual plant cells by activating enzymes called proteases that chop up essential proteins. These enzymes come into play when the plant is trying to control the spread of a disease or needs to recover nutrients from old unused leaves. It’s crucially important, however, that the proteases work at precisely the pace needed to ensure the plant’s survival: fast enough to contain a disease, for example, but not so fast as to cause this rescue operation to kill the entire plant.
 
 
Precarious supply? Photo: Böhringer Friedrich, Wikimedia Commons

 

The new study led by Prof. Fluhr has defined a potential “pace-setter” that can determine the rate at which proteases perform their “constructive destruction”: a molecule belonging to the family of proteins called serpins. The molecule, referred to as AtSerpin1, functions like a molecular mousetrap, latching onto a specific protease and inactivating it when the destruction must be slowed down. In this manner, AtSerpin1 determines the pace at which cell death will occur in the plant. The study, published in the Journal of Biological Chemistry, was performed by former graduate student Dr. Nardy Lampl, and Drs. Ofra Budai-Hadrian and Olga Davydov of the Weizmann Institute’s Plant Sciences Department, in collaboration with Australian researchers: Tom V. Joss and Dr. Thomas H. Roberts of Macquarie University and Dr. Stephen J. Harrop and Prof. Paul M. G. Curmi of the University of New South Wales, in Sydney.

The serpin “pace-setter” must be an unusually effective mechanism, for it has been in use for at least a billion years – a sure sign of evolutionary success. In fact, it exists both in plants and in animals and can be traced back to their common ancestors, single-celled eukaryotes (that is, cells possessing a nucleus) that in Earth’s distant past gave rise to plant and animal kingdoms alike. In mammals, including humans, serpin-controlled proteases perform a variety of functions in immunity, blood clotting and development.

The fact that in animals many protease activities are regulated by serpins has been known for a number of years, but the Weizmann Institute-led study represents the first time the serpin “pace-setter” and the specific protease with which it interacts have been identified in plants. The study was performed on Arabidopsis, a convenient model plant related to mustard; but genome analysis suggests that the findings are applicable to the entire plant kingdom. These findings open up a new avenue of research that can identify additional “pace-setters,” that is, other serpin molecules regulating the activity of different proteases. The ultimate goal: an in-depth understanding of plant defenses that can help create hardier plants, minimizing loss in the face of adversity.

Fluhr says that achieving this goal has a special urgency: “As a country where overcrowding, water shortage and the scarcity of arable land make agriculture particularly vulnerable to environmental impact, Israel can set an example for increasing crop productivity worldwide.”
 
Prof. Robert Fluhr's research is supported by Joel Jacob, Bloomfield, MI. Prof. Fluhr is the incumbent of the Sir Siegmund Warburg Professorial Chair of Agricultural Molecular Biology.

 
 

 

 
(l-r) Drs. Olga Davydov and Nardy Lampl, Prof. Robert Fluhr, Drs. Ofra Budai-Hadrian and Thomas Roberts. Secrets to growth
Environment
English

Fat Chance for Health

English

Dr. Karina Yaniv. New growth

 


We all care about having healthy levels of cholesterol and other fats in our blood, but our blood vessels themselves don’t seem to care. Even when plaques of fat threaten to block the flow of blood, the vessels fail to respond to the danger, when they might, for instance, sprout new branches. Conventional wisdom has it that the vessels don’t “know” the fat is there. But don’t they? And wouldn’t it be wonderful if they did sense the danger and branched out to bypass the blockage, thus preventing heart attacks?

Exploring the relationship between blood vessels and fat is one of the two major projects in the lab of Dr. Karina Yaniv, who recently joined the Biological Regulation Department as a senior scientist. She addresses this question as part of a more general theme: clarifying how blood vessels form in the embryo.
 
The cells that form blood vessels, called endothelial cells, have long been known to be sensitive to blood oxygen levels: If these levels drop, new vessels grow in the vicinity to ensure the surrounding tissue gets an adequate oxygen supply. As for fat, until now scientists believed that the vessels didn’t “feel” its presence. Yet during her postdoctoral studies at the National Institutes of Health in the United States, Yaniv provided the first experimental evidence for a new hypothesis according to which endothelial cells are attuned to the fat availability in their environment and respond accordingly. Using zebrafish as a model, her research revealed that when fat supply is low, developing zebrafish embryos grow extra blood vessels, probably to ensure adequate levels of vital nutrients. After all, the embryo is nourished mainly by fat molecules, such as those in egg yolk. When fat is plentiful, vessel growth in the embryo comes to a halt.

In adulthood, this biochemical dialogue between fat and blood vessel walls could be misfiring: High cholesterol levels in the blood might be preventing collateral vessels from growing, even though such growth is precisely what’s needed to prevent blood vessel blockage. In her new lab at the Weizmann Institute, Yaniv seeks to identify the molecular signals exchanged between fats and the endothelial cells of the blood vessel walls.
 
Understanding how blood vessel growth is regulated could have important implications for human health, possibly even enabling the regulation of such growth on demand. Helping the body grow new vasculature could be beneficial after a heart attack or stroke, or in preventing these events. Conversely, in cancer, selectively blocking the formation of new blood vessels that feed the tumor could help in treating malignancy.
 
 

Zebrafish Vessel Formation in vivo

 


This movie shows timelapse multiphoton confocal images of vessel dynamics in fli-EGFP transgenic zebrafish. Elongating angiogenic sprouts migrate between the somites to give rise to a dorsal branch. Highly dynamic behavior involving extension and retraction of numerous filopodia can be seen as the sprouts extend dorsally.

 
 
 

Zebrafish do have a lymphatic system


When not studying the development of blood vessels in the embryo,  Yaniv focuses on the lymphatic system, which is essential for the immune response, fluid metabolism and fat absorption. During her postdoctoral research, she showed that, contrary to common belief, zebrafish do have a lymphatic system. Thanks to her research, several labs in the United States and Europe have started using zebrafish in their studies of the lymphatic system. Yaniv also provided the first in vivo evidence in support of a century-old hypothesis concerning the origin of the lymphatic system: Her studies showed that in the vertebrate embryo, the lymph vessels originate in the veins. Because the lymphatic system is involved in numerous disease processes, this research, too, could help in the treatment of disease. In particular, metastatic cells use the lymphatic network to migrate to distant organs; knowing in greater detail how lymph vessels form during embryonic development might make it possible to block their growth around a malignant tumor, preventing the spread of metastasis.

Yaniv has chosen to conduct her studies on zebrafish because they offer an excellent model for her genetic research. Their small size allows her to keep a staggering 12,000 fish in 400 one-foot-high aquaria in an average-size lab. In the transparent embryos, blood and lymph vessels are easily visualized. Moreover, their genes are convenient to manipulate: Though all the fish swimming merrily in Yaniv’s aquaria look identical, sporting the same “zebra” stripes, some are transgenic, their genomes containing “reporter” genes that emit a glow marking particular DNA segments, while others are mutant, missing certain genes. The range of mutants prepared by Yaniv’s lab promises to help reveal numerous genetic secrets vital for human health.
 
 
 

Development of the Lymphatic Vascular System in Zebrafish

 

This movie shows two-photon time-lapse images of transgenic zebrafish expressing GFP in the nuclei of endothelial cells. Two lymphatic endothelial progenitors and their daughters have been highlighted in yellow and red for ease of tracking. Endothelial nuclei in the midline of the embryo migrate rostrally and then ventrally. Just ventral to the dorsal aorta they divide and the daughter cells incorporate into the wall of the newly formed thoracic duct - the main lymphatic vessel of the fish.
 
 


Creative time management

 
Born in Cordoba, Argentina, Dr. Karina Yaniv immigrated to Israel in 1989 as part of a Zionist youth movement program. After a year on Kibbutz Magal, she enrolled in the Hebrew University of Jerusalem, earning a Ph.D. in developmental biology from Hadassah Medical School in 2005. She then conducted postdoctoral research at the National Institutes of Health in Bethesda, Maryland, and joined the Weizmann Institute faculty in the summer of 2009. Yaniv is married to Ram, a software engineer, and is a mother of three: Yotam, 12, Nitay, 9 and Eylon, 4. She says combining motherhood with scientific research takes creative time management, such as taking a break from work in the afternoon and resuming it late at night. Working hard is part of her nature: “If you do something you love, you want to do it well,” she says.
 

Dr. Karina Yaniv's research is supported by the Willner Family Center for Vascular Biology; the Carolito Stiftung; the Abraham and Sonia Rochlin Foundation; Lois Rosen, Los Angeles, CA; the estate of David Arthur Barton; the estate of Paul Ourieff; and the estate of George Talis.

 
Dr. Karina Yaniv. New growth
Life Sciences
English

The Nano-Surgeon Always Signals Twice

English

Prof. Roy Bar-Ziv and Dr. Lior Nissim. Identifying cancer

 

The search for effective cancer therapies is a lengthy journey fraught with ups and downs: great hopes alternate with disappointing downturns. Research at the Weizmann Institute of Science that is currently in its initial stages might pave the way to a new treatment approach using a miniature genetic device. “We have succeeded in presenting the idea in a test tube,” says Prof. Roy Bar-Ziv of Weizmann’s Materials and Interfaces Department, who headed the research team. “Of course, the human body is so complex compared with isolated cells in a laboratory dish that prolonged studies will be required before this idea can be tested in human beings.”
 
To save the life of a cancer patient, the surgeon must remove the cancerous tumor without harming the surrounding tissue – often a challenging task. Cancer drugs, ideally, must also kill only the tumor cells while sparing the cells that are healthy. Yet, unfortunately, most conventional drugs, along with eliminating the cancer, destroy non-cancerous tissue, producing severe side effects. A new generation of therapies is being designed to kill cancer cells in a targeted, selective manner, reducing unwanted side effects to a minimum.

 
In a study published recently in Molecular Systems Biology, Weizmann Institute researchers synthesized a tiny genetic sensor that identifies cancer cells with great precision and destroys them effectively. The device, a three-gene DNA circuit called a “dual-promoter integrator,” or DPI, performs impressively well in a laboratory dish. Not only does it reliably identify and kill various cancerous cells, it can even assess the “degree” of malignancy, distinguishing between premalignant and full-blown cancerous cells.

 
Yeda Research & Development Company, the Weizmann Institute’s technology transfer arm, has patented the nano-device. Says Bar-Ziv: “We have a long road ahead of us before the genetic sensor can be tried in patients. Our ultimate future vision is for this synthetic sensor to serve as an independent ‘nano-surgeon’ that makes its own decisions, patrolling the body’s tissues, and entering and destroying cancerous cells on the spot.”

 
The DPI “nano-surgeon” identifies the cell as cancerous with the help of two DNA sequences in its circuit. These are two “promoters,” so called because they promote a gene’s activity, determining its timing and levels. For example, some promoters of growth are implicated in cancer: when such promoters are abnormally switched to the ON position more often or with a greater intensity than necessary, the cell turns cancerous. Accordingly, the DPI was designed to measure the activity levels of two such promoters and identify a cell as cancerous when both of them are overly active.

 
When the DPI is inserted into a cell, it responds to its surroundings, mimicking the behavior of the cell’s own genes. If the cell is cancerous and its own promoters are ON, the two promoters in the sensor also switch into an ON position. And once the cell has thus been identified as cancerous, the sensor sends a signal to its third gene – the “killer” gene, which releases a toxic substance eliminating the cell.

 
This relatively simple nano-device has major advantages over existing molecular approaches to the selective destruction of cancer cells. In most cancer gene therapies, malignant cells are identified by only one genetic feature, which often causes healthy cells to be mistakenly targeted for destruction. Using two genetic features makes it possible to identify cancer cells with much greater precision. Moreover, the new synthetic sensor can be “tuned” so that its “killer” gene responds only to signals above a certain level: If even one of the promoters exhibits only weak activity, the sensor will not respond. That in fact is what allowed the scientists to distinguish premalignant cells from cancerous ones: the growth signal in the latter was significantly stronger. Since the difference in growth signal levels between cancerous cells and healthy ones is even greater, this “tuning” can help the “nano-surgeon” to operate efficiently, zeroing in on the cancerous tumor without harming “innocently” growing healthy cells.

 
The research was performed in the laboratory of Prof. Roy Bar-Ziv by Dr. Lior Nissim for his Ph.D. dissertation. Nissim had previously earned a master’s degree in the molecular biology of cancer under the guidance of Weizmann Institute’s Prof. Varda Rotter. Even though the current study focused on cancer, the three-gene sensor, which is built from replaceable modules, might in the future be adapted for the treatment of other diseases or for such screening tasks as the sorting of various stem cells.
 

Prof. Roy Bar Ziv's research is supported by the Phyllis and Joseph Gurwin Fund for Scientific Advancement; and the Carolito Stiftung.

 


 
Prof. Roy Bar-Ziv and Dr. Lior Nissim. Identifying cancer
Life Sciences
English

A Sense of Size

English

 

Dr. Ida Rishal and Prof. Michael Fainzilber. Ping-Pong signals

 

How does a cell sense its own size? That question becomes especially significant when the cell is large: a human peripheral neuron, for example, which can grow extensions reaching up to a meter in length – some 20,000 times the cell body’s diameter. Without some basic information on the distance involved, just getting the building materials out to the growing end could be a logistical nightmare, exposing the cell to logjams in the supply line. These cells most probably assess their dimensions on an ongoing basis in order to direct further growth, but until now, no one was quite sure how they accomplished this feat.


Dr. Ida Rishal and Prof. Michael Fainzilber of the Weizmann Institute’s Biological Chemistry Department and their collaborators have now provided the answer for large cells such as neurons. Among other things, their findings may have relevance for understanding how to accelerate the repair of damaged nerves.
 

Fainzilber and Rishal, together with Dr. Naaman Kam and Rotem Ben-Tov Perry of the Biological Chemistry Department, Dr. Vera Shinder of the Chemical Research Support Department, Prof. Elizabeth Fisher of University College London and Prof. Giampietro Schiavo of Cancer Resesarch UK London Research Institute, thought the solution might lie in the motorized transport system that runs up and down the length of the nerve cell. This system consists of tracks called microtubules and two families of motors known as kinesin and dynein. One, the kinesin, travels only from the cell center to the end of the extension; the other, the dynein, goes only in the other direction, toward the center. Could these two, in addition to hauling cargo of various sorts up and down the tracks, be measuring distance?


The researchers began by constructing computer models of possible mechanisms by which these cellular motors might measure length. In the first model, dynein motors moving toward the cell center would carry signals that would gradually be lost along the way, like breadcrumbs dropping at a constant rate. The amount of signal left at the end of their journey would reveal the distance traveled. In this model, if the number of dynein motors was smaller than normal, the lowered signal would make the cell seem larger than it is, and thus the extensions would grow more slowly and end up shorter.


A second proposed mechanism involved a feedback loop between the two motors. When the signal on one motor reached the end of the line, it would activate a signal on the second, sending it back in the other direction. The second signal would then terminate the activity of the first at the opposite endpoint. The measurement in this case would be based on timing – more specifically, on the frequency of the interactions at the terminal points. This frequency is something like a game of Ping-Pong: When played in a small area close to the net, the “pings” are rapid; bounces off the table’s far edges, by contrast, produce longer pauses between hits. As opposed to the first model, this one predicted that reducing the levels of either motor would actually result in faster-growing, longer nerve cell extensions, because the signal frequency would drop more slowly.


The team then conducted experiments, first in nerve cells grown in culture and then in mice, in which the levels of the dynein motor were reduced. In all instances, the extensions grew longer than usual, ruling out the first model and supporting the second one.
 

Neurons from wild type (left) and dynein mutant (right) mice grown in culture. The mutant neurons with lower dynein levels show longer axon growth

 

Finally, the team asked whether this mechanism is specific to nerve cells, or whether other large cell types might use similar methods to sense their size. Repeating their experiment in connective tissue cells called fibroblasts, they again found evidence for motor-based frequency signals.


In addition to providing the answer to a long-standing question about size-sensing in large cells, these findings may be relevant to research on the regeneration of nerve cells. Cells in the peripheral nervous system can grow back after injury, but the process is extremely slow – sometimes taking years in the case of the longest nerve extensions. This is in part because once a growing nerve cell connects with its target – usually sometime during embryonic development – it stops elongating from the end and, instead, grows along with the body by stretching throughout its length. Understanding the precise signals the cell uses to not only measure itself but then to direct the embryonic growth process accordingly might point to new directions in boosting nerve regeneration.    

 

Prof. Michael Fainzilber's research is supported by the Sylvia Schaefer Alzheimer's Research Fund; the Kahn Family Research Center for Systems Biology of the Human Cell; the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation; the Legacy Heritage Fund Program of the Israel Science Foundation; the Nella and Leon Benoziyo Center for Neurological Diseases; the Yeda-Sela Center for Basic Research; the estate of Raymond Lapon; the Irwin Green Alzheimer's Research Fund; and the estate of Florence Cuevas. Prof. Fainzilber is the incumbent of the Chaya Professorial Chair in Molecular Neuroscience.


 

 

 

Dr. Ida Rishal and Prof. Michael Fainzilber. Ping-Pong signals
Life Sciences
English

PAIRS

English
 
 Yonatan Herzig and Dr. Maya Schuldiner
                  

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Imagine sorting a pile of thousands of unmatched socks into pairs. Now imagine those pairs are microscopic. That begins to approach the challenge faced by Dr. Maya Schuldiner of the Molecular Genetics Department and her colleagues and students when they set out to identify pairs of proteins – proteins that get transported out of a cellular organelle coupled with the proteins that escort them to their rides. But Schuldiner and her team had some help: They adapted the robotic equipment in her lab to develop a system they call PAIRS, which prepares and sifts through thousands of samples to identify matches.
socks
Scientists have been searching for such pairs for the past 20 years, with only partial success. But the issue is vital: The proteins that the escorts match up with are hormones, growth factors and various other signaling molecules that are produced for export to other cells or organs, and their activities are implicated in many diseases, from autoimmune syndromes to cancer. A better understanding of the escorts’ functions could point to possible drug targets for treating these diseases.

The first way station for all proteins that need to either make it out of the cell or end up displayed on the cell’s outer surface is the endoplasmic reticulum (ER) – a maze-like organelle composed of folded internal membranes. The proteins entering the ER must get folded into shape as well as undergo quality-control testing before exiting the maze. But leaving for the next way station – the Golgi apparatus – for final sorting and routing is a much more complex affair than entering. The now functional, folded protein must be enclosed in a bubble of membrane that buds off from the ER, creating a vesicle – a sort of private taxi that delivers its passenger to the Golgi apparatus without letting it come in contact with the cell’s interior. This is where the escorts come into play. They sort and package the proteins – ensuring that only mature proteins leave the ER, and in the right vesicles.
 
Until now, identifying escorts and finding their matches had been something like trying to sort through all those socks by hand, one at a time. That is why only 10 escorts had been identified, and these had been matched to only a handful of proteins. And that, says Schuldiner, is not enough to begin to understand the rules of protein trafficking.
"Liquid Handling" robotic setup performs experiments in 96 wells in parallel

 
 
To remedy the situation, she and her team – including research student Yonatan Herzig and Dr. Yael Elbaz, together with Prof. Sean Munro and Hayley Sharpe of the MRC Laboratory of Molecular Biology, Cambridge, UK – decided a more systematic approach was called for. In the PAIRS method they developed, a lab robot prepared and cultured yeast cells. The samples – grown in rows of tiny wells – each contained a yeast strain that had been genetically engineered so that one of 400 different proteins would glow fluorescent green, while one of the 10 known escorts was rendered inactive. Producing all the possible combinations – just finding matches for the known escorts – required 4,000 different samples. Then, a second robot automatically scanned images of the cells, looking for the tell-tale green glow showing that a particular protein was building up in the cell rather than being exported – a sure sign of a match.
 
 
For each escort, new passenger proteins were identified. At that point, says Schuldiner, the team could begin to formulate some rules about the ER transport system. For instance, the scientists found that the escorts worked mainly with relatively small sets of proteins, each commited to using that particular escort. In some cases, the group of proteins tied to and escort had similar functions; in others, a shared chemical “password” gave them access.

Even more interesting was the one escort protein that seemed to be an exception to the rule: The scientists noted that Erv14 paired up with an unusually large number of proteins that apparently had nothing in common. After a series of experiments ruled out all sorts of possible factors, the team hit upon the one thing they all shared – an extra-long domain that is required for them to be displayed on the outer plasma membrane of the cell.
 
"Colony Arrayer" robot enables the production of tailor-made yeast libraries for screening
 
Because versions of this escort are found in everything from yeast to fruit flies to mammals, the same rule should apply to human Erv14 and the proteins it pairs with. One of those using the Erv14 escort is EGF receptor protein, a protein required for proper embryonic development that also plays a well-studied role in cancer growth. A better understanding of the requirements for EGF receptor trafficking is essential for developing models of both development and tumor progression.

In addition to the matches the researchers managed to identify, there were many proteins that didn’t pair with any of the known escorts. Do these forgo the help, or do they use other, as-yet-undiscovered escorts? Schuldiner and her team plan to continue investigating. Their eventual goal is to produce a “traffickome” that will map out transportation systems for all the proteins in the cell.
 
Dr. Maya Schuldiner's research is supported by the European Research Council; the Minna James Heineman Stiftung; the Enoch Foundation; Roberto and Renata Ruhman, Brazil; the Karen Siem Fellowship for Women in Science; Miel de Botton, UK; James  and Ilene Nathan, Beverly Hills, CA; and the Kahn Family Research Center for Systems Biology of the Human Cell.
 
 
 
 
socks
Life Sciences
English

Between the Lines

English

Old newsprint /Shironeko Euro. History behind the print

 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Some of the history preserved in old tomes and newspapers may be hiding in between the lines of print. A Weizmann Institute scientist has found that the paper in such collections contains a record of atmospheric conditions at the time the trees that went into making it were growing. By analyzing the carbon isotopes in bits of paper clipped from old magazines, Prof. Dan Yakir of the Environmental Sciences and Energy Research Department in the Faculty of Chemistry has traced the rising effects of atmospheric pollution from burning fossil fuel going back to the beginnings of the industrial revolution.

Scientists generally reconstruct the record of past climate change from such sources as ice cores or tree rings. But a reliable tree ring history, says Yakir, requires an analysis of quite a few trees. “Rather than going to forests all over the world to sample trees,” says Yakir, “we went to the local library.” In the Weizmann library’s archives, Yakir found issues of three scientific journals, Science, Nature and the Journal of the Royal Chemical Society going back over a hundred years, to the late 19th century. After removing small samples from the margins of successive volumes, he took them back to the lab for analysis.
 
Prof. Dan Yakir. Paper records
 
The analysis was based on a finding that the proportion of a carbon isotope – carbon 13 (13C) – to its lighter counterpart – carbon 12 (12C) – could provide information on the CO2 added to the atmosphere from burning fossil fuel. This is based on a cycle that begins with plants taking up CO2 in photosynthesis. All plants prefer to use CO2 made with the more common version of carbon, 12C, rather than the slightly heavier 13C. Every summer, when photosynthesis is intensive, many tons of 13C-poor biomass is formed. Millions of years ago, similar biomass was transformed into reservoirs of oil, gas and coal, and these are naturally low in 13C as well. When we started to burn those reservoirs following the industrial revolution, we began returning the 13C-poor CO2 to the atmosphere. Now, the atmospheric 13C content has become increasingly diluted, and many of the trees that absorbed this diluted CO2 over the past 150 years have been milled for pulp and paper. Thus the paper that eventually ends up in library archives exhibits varying levels of 13C dilution. Yakir’s work shows that this continuing dilution is indeed clearly recorded in the archival paper and, plotted over time, it demonstrates the increasing intensity of our fossil fuel burning in the past 150 years.
 
This project has been ongoing for about 14 years, with figures from new issues added over time. In the process, says Yakir, he has had to learn something about the paper industry. Some early issues, for instance, had been printed on rag paper (made of cotton, flax, etc.) rather than wood pulp, while blips in the data around the time of WWII led Yakir to suspect that the paper was either recycled or again supplemented with rag content to make up for wartime shortages.

Anomalies aside, 13C levels in the paper, especially for two of the journals, were a good match for existing atmospheric records and even revealed some local phenomena, including differences between American and European records. In addition to alerting climate scientists to a very well organized, untapped source of global change records, says Yakir, the technique could be used to authenticate samples of supposedly antique paper.
 
Prof. Dan Yakir’s research is supported by the Cathy Wills and Robert Lewis Program in Environmental Science; and the estate of Sanford Kaplan.
 
Prof. Dan Yakir and his team recently dedicated a new mobile research lab. Read about it here.

 

 
Old newsprint /Shironeko Euro. History behind the print
Environment
English

Universal Immunity

English
 
Prof. Zelig Eshhar. New approach to fighting cancer
 
Our immune system has ample weapons for fighting cancer, but of course nobody can win all the battles all the time. As we know only too well, it is often the tumor that gains the upper hand, outsmarting the body’s anti-cancer defenses.
One of the latest attempts to boost these defenses is the so-called adoptive cell transfer, in which patients receive a therapeutic injection of their own immune cells.
 
This therapy, currently being tested in early clinical trials of melanoma and neuroblastoma, has its limitations: Removing immune cells from a patient, not to mention growing these cells outside the body for future reinjection, is extremely expensive and not always technically feasible.
 

Weizmann Institute scientists have now tested in mice a new form of adoptive cell transfer that overcomes these limitations while enhancing the tumor-fighting ability of the transferred cells. The research, reported recently in Blood, was performed in the lab of Prof. Zelig Eshhar of the Institute’s Immunology Department by graduate student Assaf Marcus and lab technician Tova Waks.

The new approach should be more readily applicable than the existing adoptive cell transfer treatments because it relies on a donor pool of immune T cells, prepared in advance, rather than on the patient’s own cells. Moreover, using a method pioneered by Prof. Eshhar more than two decades ago, these T cells are outfitted with receptors that specifically seek out and identify the tumor, thereby promoting its destruction.

In the study, the scientists first suppressed the immune system of mice by a relatively mild dose of radiation; they then administered a controlled dose of the modified donor T cells. The mild suppression temporarily prevented the donor T cells from being rejected by the recipient, but it didn’t prevent the cells themselves from attacking the recipient’s body, particularly the tumor. This attack was precisely what rendered the therapy so effective: while the rejection of the donor T cells was being delayed, these cells had sufficient opportunity to destroy the tumor.

If this method works in humans as well as it did in mice, it could lead to an affordable cell transfer therapy for a wide variety of cancers. Such therapy would rely on an off-the-shelf pool of donor T cells equipped with receptors for zeroing in on different types of cancerous cells.



Proof of Concept



In August 2011, University of Pennsylvania researchers reported in The New England Journal of Medicine that they had successfully used Prof. Zelig Eshhar’s original, adoptive cell transfer approach in a pilot trial of patients with chronic lymphocytic leukemia. The patients were treated with T bodies – genetically engineered versions of their own T cells. “This study has provided a proof of concept for the potency of our T-body therapy: previously shown to work in mice, it has now proved beneficial in cancer patients,” Prof. Eshhar said. “Within three weeks, the tumors had been blown away, in a way that was much more violent than we ever expected,” said senior author Carl June, MD, professor of Pathology and Laboratory Medicine in the University of Pennsylvania’s Abramson Cancer Center, who led the trial. “It worked much better than we thought it would. ”

Encouraged by this initial success, Dr. June and colleagues plan to apply the method to the treatment of other malignancies, including non-Hodgkin lymphoma, acute lymphocytic leukemia and childhood leukemia that is not alleviated by standard family. They also consider using the T bodies in patients with solid tumors, such as ovarian and pancreatic cancer.

 
Prof. Zelig Eshhar’s research is supported by the M.D. Moross Institute for Cancer Research; the Leona M. and Harry B. Helmsley Charitable Trust; the Kirk Center for Childhood Cancer and Immunological Disorders; and the estate of Raymond Lapon.



 
Prof. Zelig Eshhar. New approach to fighting cancer
Life Sciences
English

Versatile Nanoparticles

English

“If you break a piece of gold in half,” says Dr. Dan Oron of the Institute’s Physics of Complex Systems Department, “Each of the halves will have the same basic properties as the original. But the same won’t be true if that piece of gold is just a few thousand atoms in size: Among other things, the color of the halves will be different.”
Dr. Dan Oron. Gold and crystal nanoparticles
 
 
We see color when light waves are absorbed or reflected from objects, and once the size of those objects gets down to the length of light waves or smaller, strange things begin to happen. In fact, many of the properties of familiar materials change dramatically at the nanometer scale (a billionth of a meter).
 
 
Oron has been investigating the characteristics of nanocrystals – seeking to understand the rules governing bits of matter around the size of protein molecules, and learning how to put those rules and properties to use. “Conventional inorganic chemistry gives us one kind of mechanism for creating materials – one with a limited set of ‘knobs.’ Nanoparticles could give us radically new machinery that could help us realize previously unattainable material properties.”

 
Just how versatile nanoparticles are can be seen in two of Oron’s recent research projects: In one, unique nanoparticles he is working on might be used to light up molecules under the microscope; in the other, they might power a new kind of solar collector.


Oron’s nanoparticles are semiconductors. When they’re disturbed – say by a photon (a light particle) striking them – an electron is briefly excited, leaving behind a positively charged hole. When the excited electron and the hole recombine, light is re-emitted. What happens when two electrons are excited in a single nanoparticle? Do the electrical charges occupying the nanocrystal interact, repelling or attracting each other? Oron has found that he can induce strong repulsion between the two holes by adding just a few atoms of a different element to the nanoparticles. This creates a cage that traps a single positive charge, repelling the second one as it does so and causing the light to be re-emitted from the particle in a different color.
 

In microscopes, such color-altering nanoparticles could be used as markers. Some of today’s advanced microscopes fire two photons at the same spot in rapid succession, causing the material to emit a brief flash of light. But light from tiny nanoparticles attached to cells or proteins could prove to be more stable and reliable. In addition, a nanoparticle could be designed to emit one color the first time it was struck by a photon and another color the second; or, to enhance resolution, it might scatter light only after being struck by two photons simultaneously. The challenge in creating such ultra-tiny markers, says Oron, lies on the one hand in controlling their fabrication to attain the desired structure and on the other hand in detecting extremely weak optical signals. The ability of nanoparticles to scatter light, for example, drops drastically as they shrink. These challenges, however, can be overcome. "We have recently succeeded in creating the smallest nonlinear light-scattering nanoparticle yet – less than 15 nanometers across. We managed to find a ‘sweet spot’ – one that works about ten times better than the equivalent bulk material,” he says.

 
Two-photon autofluorescence image of a live cell incubated with gold nanoparticles, superimposed on a simple transmission image of the cell
 
 
Oron’s solar collector research relies not on the nanoparticles’ light-emitting skills but rather on their ability to absorb light. The organic light absorbers in dye-based solar cells have a tough job: They must absorb quantities of light of a wide range of wavelengths, separate the electron from the “hole” it leaves, and then accept an electron back, over and over again. Oron and Dr. Arie Zaban of Bar-Ilan University knew that semiconductor nanoparticles could absorb sunlight much more easily almost across the entire visible spectrum but were much less efficient at splitting the charges. Many organic dyes, on the other hand, can separate charges reliably but are limited in the wavelengths of light they can take in, as well as in their long-term stability. Oron and Zaban had an idea: Why not divide the workload? The researchers created microscopic devices in which nanoparticles act as antennae, funneling the sun’s energy to dye molecules, where the charge separation takes place. Oron believes that with some tweaking, such combination solar collectors could be highly efficient.
 

Rehovot born and bred


Dr. Dan Oron was born in Rehovot in 1974 and grew up right around the corner from the Weizmann Institute. “I was at the Institute all the time and participated in many extracurricular activities here; my first was at age 11,” he recalls. He completed his B.Sc. and M.Sc. through the elite Talpiot army study program, the latter at Ben-Gurion University of the Negev, where he investigated the physics of turbulence. His doctoral research on spectroscopy using ultra-fast pulses of light was conducted at the Weizmann Institute in the group of Prof. Yaron Silberberg. Oron began working with nanoparticles during his postdoctoral research in the lab of Prof. Uri Banin at the Hebrew University of Jerusalem. He joined the Weizmann Institute in 2007.

Dan is married to Ruti; they have a daughter, Hila.
 
Dr. Dan Oron's research is supported by the Phyllis and Joseph Gurwin Fund for Scientific Advancement; the Wolfson Family Charitable Trust; Yossie Hollander, Israel; and Daniel S. Shapiro, UK.




 
 
Two-photon autofluorescence image of a live cell incubated with gold nanoparticles, superimposed on a simple transmission image of the cell
Chemistry
English

Micro Control for Insulin

English
(l-r) Standing: Sharon Kredo, Dr. Tali Melkman Zehavi, Roni Oren. Sitting: Dr. Eran Hornstein, Natali Rivkin, Amitai Mandelbaum

 
 
The water came and extinguished the fire that burned the stick that beat the dog that bit the cat that ate the goat that father bought for two zuzim. – Had Gadya (from the Passover Haggada)



 
According to Dr. Eran Hornstein of the Molecular Genetics Department, a Had-Gadya-like scenario takes place daily in the pancreas, and it goes something like this: The microRNA slew the negative transcription factor that inhibited the gene that codes for insulin that regulates sugar in the body.
 
The focus of Hornstein’s research is on one of those players: microRNAs – short bits of genetic material that don’t code for proteins. Nonetheless, these tiny sequences of code perform all sorts of regulatory functions in the cells, and they may be involved in a number of complex diseases. In a series of experiments over the past four years, Hornstein and his research team have been examining the role of microRNAs in the pancreatic beta cells – the producers of insulin. Their findings not only shed new light on the way that insulin production is controlled – they may aid, in the future, in the diagnosis and treatment of diabetes.
 

The team included Dr. Tali Melkman Zehavi, students Roni Oren, Sharon Kredo, Amitai Mandelbaum and Tirosh Shapira, and lab technician Natali Rivkin. To begin, the researchers first checked to see whether microRNAs were involved in any way in pancreatic function. Using advanced genetic techniques to prevent microRNA from forming in the pancreases of mice, they came up with a clear answer: Without microRNA, the mice did not produce insulin, and they soon developed the symptoms of diabetes.
 

Next, as the team probed further, they identified the step in the gene-to-protein process that is dependent on microRNA control. That step is transcription – the stage in which the information encoded in the genes is copied out for use in protein production. But this finding left them with further questions. “It’s not obvious that microRNAs would be involved in the control of insulin transcription, as they are more often known to regulate post-transcriptional events in the cell,” says Hornstein. “We had to sit down and come up with a hypothesis that would include another intermediate – a so-called negative transcription factor.”
 

All cells carry the genetic information needed to produce insulin, but only beta cells actually do so. One of the reasons for this is that other cells actively repress insulin production; negative transcription factors keep the genetic information from ever getting transcribed. Beta cells, in contrast, normally maintain a profusion of the transcription factors that bind to genes and initiate insulin production, and very few of the negative factors that inhibit this process. Further testing showed that microRNA affects only the negative transcription factors in beta cells, squelching them so that insulin production can proceed.
 

Finally, Hornstein and his team identified four specific microRNA genes that appear to promote insulin synthesis.
 

This research recently appeared in the EMBO Journal. By showing how microRNA affects insulin production, Hornstein and his team have added a new layer to our understanding of the mechanisms involved in diabetes. Their findings may pave the way, in the future, to better tools for diagnosing the disease and eventually to better treatment.

 
Dr. Eran Hornstein's research is supported by the Nella and Leon Benoziyo Center for Neurological Diseases; the Women's Health Research Center funded by the Bennett-Pritzker Endowment Fund, the Marvelle Koffler Program for Breast Cancer Research, the Harry and Jeanette Weinberg Women's Health Research Endowment, and the Oprah Winfrey Biomedical Research Fund;the Nathan, Shirley, Philip and Charlene Vener New Scientist Fund; the Legacy Heritage Fund; and the Wolfson Family Charitable Trust. Dr. Hornstein is the incumbent of the Helen and Milton A. Kimmelman Career Development Chair.
 

 
(l-r) Standing: Sharon Kredo, Dr. Tali Melkman Zehavi, Roni Oren. Sitting: Dr. Eran Hornstein, Natali Rivkin, Amitai Mandelbaum
Life Sciences
English

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