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Science Feature Articles</p>

Yeast Side Story

English
 
Yeast cells yearning for a “soul mate” have a problem: They lack the ability to move on their own. To get closer to a potential mate, all they can do is reach out with cellular extensions. This enables a pair of yeast cells to make contact, after which they fuse their membranes together and ultimately merge their genomes.
Cell Reports cover: Illustration by Dr. Rita Gelin-Licht showing yeast cells mating through extensions
 
Prof. Jeffrey Gerst of the Weizmann Institute’s Molecular Genetics Department has now discovered the mechanism that controls the growth of yeast cell extensions called shmoos in a particular direction, making sure the cells can engage in successful mating. This same control mechanism is predicted to govern the growth of cellular extensions in organisms other than yeast – for example, the growth of neurons towards attractive signals or away from repellent signals in the human brain.
 
The scientists found that when yeast cells ready for sexual reproduction receive a chemical signal from a prospective “mate,” they respond by sending specific messenger RNA (mRNA) molecules – whose job is to convey DNA-encoded information to be translated into proteins – to the point on their membrane where the mating signal has been received. This prompts the cells to start growing shmoos in the direction of the mate, a process called chemotropism. They also revealed how mRNA reaches this location: They identified a protein, called Scp160, that is activated by the mating signal and guides the needed mRNAs to the appropriate spot near the cell surface. When the scientists created a mutation in Scp160, disrupting its activity, yeast cells grew extensions in the wrong direction and failed to mate. Taking part in the study, published recently in Cell Reports, was Rita Gelin-Licht, then Gerst’s graduate student, as well as Saurabh Paliwal, Patrick Conlon and Andre Levchenko of Johns Hopkins University.
 
 
In earlier research, Gerst had already shown that mRNA movements around the cell are not random; rather, its protein-making information is targeted to the exact spot or spots where this protein will eventually be needed. In the present study, Gerst and his team showed for the first time that mRNA targeting is crucial for the cell to respond properly to external chemotropic signals.
Prof. Jeffrey Gerst
 
If these findings are found to be applicable to neurons, they might shed new light on the wiring of the human brain. They may help explain how the brain neurons grow the lengthy projections that link up into precise neural networks that transmit electric signals throughout the brain.
 
Prof. Jeffrey Gerst's research is supported by the Miles and Kelly Nadal and Family Laboratory for Research in Molecular Genetics; the Hugo and Valerie Ramniceanu Foundation; the Y. Leon Benoziyo Institute for Molecular Medicine; the Yeda-Sela Center for Basic Research; and the estate of Raymond Lapon. Prof. Gerst is the incumbent of the Besen-Brender Professorial Chair of Microbiology and Parasitology.
 
 
 
Cell Reports cover: Illustration by Dr. Rita Gelin-Licht showing yeast cells mating through extensions
Life Sciences
English

The Slings and Arrows of Outrageous Cellular Fortune

English

Anat Florentin and Dr. Eli Arama

 
 
To die or not to die: That is the question all living cells face at some point in their lives. How this dilemma is ultimately resolved can have crucial consequences for our health. When cancer cells refuse to die, having developed a resistance to drugs, chemotherapy becomes ineffective. On the other hand, Parkinson’s disease and other neurodegenerative disorders occur when certain neurons in the brain die too readily. Understanding the precise mechanics of the major cellular death program, called apoptosis, is therefore essential for developing treatments for a variety of diseases.

Crucial new information about apoptosis has emerged from a Weizmann Institute study published recently in the Journal of Cell Biology. Dr. Eli Arama of the Molecular Genetics Department and Ph.D. student Anat Florentin have found a mechanism that makes some cells more sensitive to apoptosis than others, and they have established, in great detail, how the final stage of the cellular death program works.

Apoptosis can be triggered by a variety of signal sequences, but the final link, the “weapon” that performs the actual killing of the cell, is always the same: It consists mainly of utterly destructive enzymes – the effector caspases – which kill the cell by chopping up hundreds of cellular proteins. Until recently it was known that in mammalian cells two such enzymes, caspase-3 and caspase-7, were intimately involved in apoptosis, but their distinct roles in this process were unknown. Working with fruit flies, which have enzymes similar to the human caspases – Drice and Dcp-1, respectively – Arama and Florentin have produced a series of findings that make it possible to draw conclusions about the two mammalian caspases.
 
Budding wing from irradiated fruit fly larvae, magnified about 80 times; various aspects of apoptosis in a regular fly (left column) are compared with the mutant fly lacking the drice gene (right column). Upper row: “reporter” proteins are highlighted with green fluorescent protein; middle row: the cutting up of these reporter proteins by caspases; bottom row: numerous cells die by apoptosis in the regular fruit fly (left), whereas almost no apoptosis occurs in the fly lacking the Drice caspase (right)
 
Their results suggest that Drice is the major killing machine: It can destroy a cell on its own, even though it does work more efficiently in the presence of Dcp-1. As for Dcp-1, its major role is to set the pace of the killing, determining how fast and how many cells will die. Dcp-1 can also finish off the cell on its own, but this will happen only if it is present in large amounts.

In fact, one of the study’s central findings is that both caspases can kill cells only when their activity exceeds a certain threshold. Below that threshold, the cell can survive, replenishing the proteins destroyed by the caspases. This finding also explains how certain cells manage to use enzymes such as caspases to promote vital cellular processes without bringing destruction upon themselves: With low or transient levels, the cells avoid apoptosis while employing the caspases for other purposes.  

Why are two caspases necessary to perform essentially the same function? The scientists believe that the availability of two “weapons” offers greater precision in controlling the process than would be provided by a single killing enzyme. Drice is more of a sledgehammer, suitable for coarse demolition jobs, whereas Dcp-1 is more of a chisel, best suited to fine-tuned cellular elimination.

The study has shown that the tendency to undergo apoptosis, which varies greatly among different types of cells, is determined by the amount of the caspases present in the cell. Cells less prone to apoptosis are likely to have lower levels of the destructive enzymes. Among these are the brain’s neurons, which are limited in number, and the sperm and eye cells, which would perish upon each contact with the environment if they weren’t so resistant to apoptosis. In contrast, cells that are relatively expendable because they regenerate are more prone to apoptosis and these should have more caspases. These include hair cells and those in the inner lining of the gut, which must be continuously replaced after being damaged by digestive acids.

Florentin and Arama were able to discover these details about the workings of the caspases because they observed their function in living animals – genetically engineered fruit flies – rather than in tissue culture. To locate and quantify the activity of the different caspases in the flies’ bodies under a microscope, the scientists first inserted “reporter” genes into the flies’ genomes, and then relied on these reporters to highlight the proteins to be destroyed with a fluorescent dye.

By showing that the function of caspases is far more complex than previously thought, the new Weizmann study may have important implications for cancer drug development. In particular, the study suggests that in designing drugs intended to enhance apoptosis, researchers must make sure these raise the activity of the caspases above a critical threshold so that cancerous cells are effectively destroyed.
 
Dr. Eli Arama's research is supported by the Fritz Thyssen Stiftung; the M.D. Moross Institute for Cancer Research; the Y. Leon Benoziyo Institute for Molecular Medicine; the Jeanne and Joseph Nissim Foundation for Life Sciences Research; and the Yeda-Sela Center for Basic Research. Dr. Arama is the incumbent of the Corinne S. Koshland Career Development Chair in Perpetuity.


 
 
 
Budding wing from irradiated fruit fly larvae, magnified about 80 times; various aspects of apoptosis in a regular fly (left column) are compared with the mutant fly lacking the drice gene (right column). Upper row: “reporter” proteins are highlighted with green fluorescent protein; middle row: the cutting up of these reporter proteins by caspases; bottom row: numerous cells die by apoptosis in the regular fruit fly (left), whereas almost no apoptosis occurs in the fly lacking the Drice caspase (right)
Life Sciences
English

Shine a Light

English
11-06-2012
(l-r) Rivka Levy, Shiri Ron, Dr. Ofer Yizhar, Lihi Gibor, Roy Degani, Tess Oram and Mathias Mahn
 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Dr. Ofer Yizhar, who recently joined the Weizmann Institute’s Neurobiology Department, plans to shed light – literally – on the workings of the brain. In his new lab, researchers will be able to turn specific types of brain cell on and off by flashing a tiny beam of light on them.

“Even small areas of the brain contain different kinds of neurons, often performing completely different functions, and as each of these can connect, through its synapses, to thousands of other cells, we have not been able to really understand the complex interactions between them,” he says. “That complexity is especially daunting when we look at a higher brain area like the cortex (the outer shell of the brain); it contains interconnected networks that are widely distributed, and we think that disorders like schizophrenia and autism might originate there.”

But the young field of optogenetics is giving scientists new tools for directly investigating neuron functions. (The term optogenetics refers to the genetic alterations in specific brain cells that enable them to sense and respond to light.) Until now, says Yizhar, brain researchers have had many tools for measuring brain activity but very few that allowed them to precisely control that activity and observe the results. Yizhar began working in this field in his postdoctoral work at Stanford University, and in his Weizmann lab, he is currently building and assembling the specialized setup he will need to continue his optogenetics research.
 
 
Mouse hippocampus containing two different types of channelrhodopsins. The green fluorescence marks axons entering into the hippocampal CA1 region, and the red fluorescence is expressed in the dentate gyrus part of the hippocampus (inverted V-shaped structure)
 
The idea of controlling the activities of individual brain cells originated with Francis Crick, one of the discoverers of the DNA double helix. Crick, who later in his life was involved in neurobiology research, predicted in the 1970s that scientists would find ways to actively manipulate brain cells, and even guessed it would be done with light. People have attempted to do this in various ways over the years, but it took the discovery, in 2001, of a light-sensitive protein in a microscopic alga to kick-start the field of optogenetics.

This protein is a member of a large family called rhodopsins, all of them built to absorb light. The algal rhodopsin, which helps the microorganism steer toward light, is unique in the way it works: Light prompts it to open channels in the cell membrane, letting various charged ions in or out and thus changing the cell’s internal chemistry. Since neurons fire off charged signals to one another through similar channels, scientists thought that these rhodopsins might finally give them the control they sought. Surprisingly, the algal rhodopsins functioned quite well in sophisticated mammalian nerve cells.

The first report on a marriage between an algal protein and a nerve cell was published in 2005, and it was this seminal paper that set Yizhar on his path. As he neared the end of his doctoral research at Tel Aviv University and was contemplating postdoctoral positions, he was searching for ideas in the pages of neuroscience journals. “I wanted a subject that would excite me,” he says. That seminal paper was the spark he was looking for, and Yizhar set off to do his postdoctoral research in the optogenetics lab of the paper’s lead author, Dr. Karl Deisseroth, at Stanford University.

There, Yizhar joined a group of young researchers in developing the toolkit for the nascent field. Beginning with nerve cells grown in culture and progressing to genetically engineered mice in which selected brain cells were activated by light pulses from tiny implanted optic fibers, the team continued to demonstrate the potential of the method. By now, says Yizhar, the toolkit has advanced to the point where different neurons can be made to respond to different colors of light, enabling scientists to work with more than one cell type at a time. The developers have made the toolkit available to other researchers and, so far, over a thousand labs worldwide have requested it.

In his Weizmann lab Yizhar intends, among other things, to continue research he began at Stanford in an area of the brain called the prefrontal cortex. This is where such higher functions as goal-directed behavior and working memory take place; faulty circuitry in this area is implicated in a number of psychiatric problems. Yizhar and the Stanford team tested a theory that both autism and schizophrenia might be tied to an imbalance in the activities of two types of neurons controlling these circuits. Indeed, when the researchers used their light-activated optogenetic tools to create such an imbalance in lab mouse brains, they saw behavior associated with autism.

Yizhar emphasizes that we will not be curing psychiatric disorders anytime in the near future with implanted optic cables. Rather, optogenetics will give researchers powerful tools that should enable them to pinpoint the sources of malfunctions and hopefully lead to the design of effective treatments.

Back to Rehovot

Dr. Ofer Yizhar grew up in Mazkeret Batya, near Rehovot, and attended the Israeli Arts and Science Academy high school in Jerusalem. He received his B.Sc. from the Hebrew University of Jerusalem, and his M.Sc. and Ph.D., in neurobiology, from Tel Aviv University.

He lives on campus with his wife Lital, a breast-feeding counselor, and their three children. In his spare time, Yizhar enjoys swimming, rock climbing and music.
 
Dr. Ofer Yizhar's research is supported by the Adelis Foundation; the Candice Appleton Family Trust; and the Clore Center for Biological Physics. Dr. Yizhar is the incumbent of the Gertrude and Philip Nollman Career Development Chair.
 
 
Mouse hippocampus containing two different types of channelrhodopsins. The green fluorescence marks axons entering into the hippocampal CA1 region, and the red fluorescence is expressed in the dentate gyrus part of the hippocampus (inverted V-shaped structure)
Life Sciences
English

Taking Stock of Calcium

English

 


(l-r) Ido Kaminsky, Prof. Eitan Reuveny, Ruth Meller, Raz Palty and Dr. Adi Raveh. Steady supply

 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Calcium is one of the most regulated minerals in the human body. That may be because so many important cellular processes rely on calcium ions: cell growth, neural signaling, muscle contraction, bone formation and fertilization, to name just a few. In fact, it is crucial that a low yet steady concentration of calcium ions be maintained within cells: There is growing evidence that disturbances in intracellular calcium levels may result in serious cellular dysfunction. For example, an excessive amount of calcium in nerve cells causes them to die, leading to neurodegenerative disease. Imbalances in calcium levels are also believed to be associated with various types of cancer as well as vascular and heart diseases.
 
Cells have evolved a unique “stocktaking” system to ensure their calcium supplies are tightly monitored and regulated. Prof. Eitan Reuveny of the Weizmann Institute’s Biological Chemistry Department has now discovered the role of a new protein that is involved in this process.

To make sure there is a plentiful supply of calcium on hand at all times – one that doesn’t jeopardize the carefully balanced concentration within the cell – calcium is stored in cellular “warehouses”: membrane-enclosed organelles known as mitochondria and the endoplasmic reticulum (ER). These immediately get restocked as soon as their supplies start to dwindle. How does the cell know exactly how much calcium to order? The process of acquiring more calcium is called store-operated calcium entry (SOCE), and up to now two players were known to be involved – STIM and Orai. STIM – a “stock-taker” protein – detects the depletion of calcium within the ER warehouses and makes its way to Orai – calcium-selective channels located in the cell’s plasma membrane – where it activates them to open. This results in an influx of calcium into the cell from the outside, which then gets taken up by the cellular warehouses.

 
SARAF1Fluorescent images of a HEK293-T cell expressing SARAF-GFP (green) and STIM1-mCherry (red). Third panel is an overlay
 

 

What scientists didn't know was what regulates the closing of these channels, preventing the cellular warehouses from overfilling and spilling out into the cell. Now, Reuveny, together with Raz Palty, Adi Raveh, Ido Kaminsky and Ruth Meller, have identified a new protein that helps regulate SOCE activity, as they reported in the journal Cell. They found that once the Orai channels have opened, the new protein, SARAF, is employed to slowly inactivate STIM, causing the channels to start closing. This prevents the rapid overfilling of cells with calcium and keeps levels under control.

As expected, disabling SARAF activity led to calcium overspill and cell hyperactivity. The added observation that SARAF travels with STIM to the plasma membrane, where the Orai channels are located, provides further evidence that SARAF is involved in regulating STIM deactivation.

Although there is no direct evidence linking mutations in SARAF to human diseases, studies have recently identified SARAF as a biomarker that is associated with prostate cancer, Alzheimer’s disease and dilated cardiomyopathy – disease states that are accompanied by abnormal intracellular calcium levels.

Reuveny: “SARAF is expressed in cells all over the body, but their levels are especially high in the immune system and brain. We still don’t know exactly what it does there or how it works, so this is what we are endeavoring to find out next.”
 
SARAF tagged with green fluorescent protein. The fluorescent signals get stronger as SARAF moves closer to the plasma membrane.
 
 
Prof. Eitan Reuveny’s research is supported by the Nella and Leon Benoziyo Center for Neurological Diseases; the Yeda-Sela Center for Basic Research; and the Hugo and Valerie Ramniceanu Foundation. Prof. Reuveny is the incumbent of the Charles H. Hollenberg Professorial Chair. 

 
 
 

 

 

 

 
(l-r) Ido Kaminsky, Prof. Eitan Reuveny, Ruth Meller, Raz Palty and Dr. Adi Raveh. Steady supply
Space & Physics
English

Matchmaker

English
Dr. Sarel Fleishman. Designed to fit
 
Does the perfect match exist? Despite the promises of numerous dating sites, finding the ideal mate is rarely a rational, systematic process. Until now, the same could be said for matches between protein molecules. We might be able to observe which proteins get together – which pairings initiate molecular processes and which block them – but we haven’t really been able to generate novel, “perfect” matches from scratch.

This situation is now changing, however, thanks to a new method, the first of its kind, for “fine tuning”  various physical features on the surface of a protein molecule. The method, developed by Dr. Sarel Fleishman – who recently joined the Institute’s Biological Chemistry Department – and his colleagues at the University of Washington, Seattle, enables researchers to redesign the surface of protein molecules so that they will match up with target proteins and strongly bind to them.
 
For instance, the scientists created new proteins that can bind to the active site on the surface of a flu virus, obstructing its activities. This particular site has been conserved throughout the evolution of the flu, so it is found in many strains including bird and swine flu. Thus a protein molecule like the one Sarel and his colleagues programmed to target that site could conceivably block a range of flu viruses. The therapeutic potential of these molecules is currently being investigated.

In addition to sophisticated computer analyses of the physical properties of protein molecules, the system makes use of a number of online databases of protein molecule structures (including pioneering databases developed at the Weizmann Institute). According to Fleishman, the process begins with a theoretical computation to determine the ideal molecular structure needed to perfectly bind to the active site of a target protein. The next step is to scan the protein structure databases to find natural molecules into which the programmed active site might feasibly be integrated.
 
 
In the case of the new flu-binding protein, several dozen proteins were altered to include the new binding site. Of these, five succeeded in the lab in binding to the targets. One of the five managed to block the ability of various flu viruses to spread.
 
The molecular structure of Spanish flu protein (hemagglutin) bound to a computationally designed protein (green). The designed protein binds the viral protein tightly and with high specificity, blocking the protein's function and neutralizing viral infectivity
 
“Basically,” says Fleishman, “by combining our computational tools with an experimental approach, we were able to create molecules that don’t exist in nature. Such programmed molecules could give us the ability to direct molecular activities, and they might have a wide range of uses in medicine, diagnostic tools and biotechnology.” In other words, nearly ideal matches – ones that don’t exist in nature – can now be produced with a computer and a biology lab. The method might be used, in the future, to design a variety of new drugs, including those to combat emerging diseases for which current drugs may be ineffective.
 
Dr. Sarel-Jacob Fleishman’s research is supported by Sam Switzer and family; the Geffen Trust; and the Yeda-Sela Center for Basic Research.

 
 
The molecular structure of Spanish flu protein (hemagglutin) bound to a computationally designed protein (green). The designed protein binds the viral protein tightly and with high specificity, blocking the protein's function and neutralizing viral infectivity
Life Sciences
English

Synthetic Cells Stand In for the Real Thing

English

(l-r) Profs. Benjamin Geiger and Joachim Spatz

 

 

 
What makes one cell stick to its home base and another cell detach and migrate? How do cells “sense” their physical environment and respond? These questions go to the core of what it means to be a living cell, but the answers are anything but simple. Indeed, some of the most complex cellular systems – from yeast to human cells – are those for adhesion and environmental sensing.

“Add to that the complexity of a dynamic environment,” says Prof. Benjamin Geiger of the Weizmann Institute's Molecular Cell Biology Department, “and you have something that is very difficult to even define, much less describe in any useful way.”

That is why Geiger and Prof. Joachim Spatz of the Max Planck Institute for Intelligent Systems, Germany, have launched a project that presents a new approach to understanding the ways in which cells reach out to their surroundings. Simply put, they plan to conduct experiments with a man-made system in which synthetic cells – in the form of vesicles consisting of a simple lipid membrane and a handful of protein molecules – sit on synthetic substrates. Experimenting with these simplified models, in which the researchers can control every aspect of their design, will hopefully yield new insights into how living cells work. While the plan is admittedly ambitious, the payoff could be great: Adhesion and sensing are crucial to everything, from growth and development, to cell migration and tissue architecture, to – when the process goes awry – cancer metastasis.

The idea falls within the new field of synthetic biology, in which scientists take an engineering approach to the cell and its components. Spatz is a materials scientist and Geiger, a biologist. For the past several years, the two have worked closely together to create unique substrates, and used them to test living cells’ sensing abilities. Synthetic cells are the logical next step in the research process.

The scientists’ method for creating artificial cells begins with blood platelets – simple cells that have the ability to adhere to biological as well as artificial surfaces. The researchers remove everything but the cell’s outer “skin” and adhesion-mediating proteins, called integrins, which perform the actual sticking. Then, these proteins are extracted and inserted into synthetic vesicles, and additional components of the adhesion site are gradually added, a few at a time, so that the researchers can test as they go. In parallel, they will experiment with the substrate – controlling its properties down to the placement and spacing of individual molecules. As they analyze the results obtained from the synthetic system, Spatz and Geiger plan to recheck their findings in living cells, to see how well their progressing model reflects the considerably more complex reality.
 
Prof. Geiger explains: Synthetic cells and substrates will be checked against their natural counterparts in all permutations and combinations
 

 

 
Even such comparatively simple synthetic cell models are quite complicated. “If we manage to find the right combination to get these cells to respond to environmental cues,” says Spatz, “we will consider that a great success.” Eventually, the scientists intend to move past the present understanding – a “grocery list” of hundreds of individual molecules that participate in the molecular cross-talk underlying a cell’s adhesion and sensing mechanisms – toward  understanding how those individual bits and pieces come together to make functional components.

This new undertaking has already demonstrated one considerable success: The European Research Council (ERC) recently awarded the project a grant of 3.5 million euros. Such ERC Advanced Grants are specifically “aimed to promote substantial advances at the frontiers of knowledge and to encourage new productive lines of enquiry, including unconventional approaches and investigations at the interface between established disciplines.”

In addition to advancing the understanding of how living cells sense and respond to their environment, the scientists think the project may yield some interesting insights into the origins of living cells. Even before cells started to stick together to form multicellular organisms, they probably had rudimentary adhesion mechanisms for sensing and grabbing onto food – the most basic need of all.
 

Prof. Benjamin Geiger’s research is supported by the Leona M. and Harry B. Helmsley Charitable Trust; the Adelis Foundation; the Mario Negri Institute for Pharmacological Research; the estate of Alice Schwarz-Gardos; IIMI, Inc.; and the European Research Council. Prof Geiger is the incumbent of the Professor Erwin Neter Professorial Chair of Cell and Tumor Biology.
 
(l-r) Profs. Benjamin Geiger and Joachim Spatz
Life Sciences
English

Skeletons (and other Organs) in the Cell Family Tree

English
 
Mouse cell lineage tree. Oocytes are in red, bone marrow stem cells in yellow, demonstrating that the two form separate clusters with only a distant relationship
 

 

 
 
 
 
 
 
 
 
 
 
 
 
In recent years, a number of controversial claims have been made about the female mammal’s egg supply – that it is renewed over her adult lifetime (as opposed to the conventional understanding that she is born with all of her eggs), and that the source of these eggs is stem cells that originate in the bone marrow. Now, Weizmann Institute scientists have disproved one of those claims and pointed in new directions toward resolving the other. Their findings, based on an original method for reconstructing lineage trees for cells, were published in the online journal PLoS Genetics.

The method, developed over several years in the lab of Prof. Ehud Shapiro of the Institute’s Biological Chemistry, and Computer Science and Applied Mathematics Departments, uses mutations in specific genetic markers to determine which cells are most closely related and how far back they share a common parent cell, to create a sort of family tree for cells. Shapiro and members of his lab, including Drs. Shalev Itzkovitz and Rivka Adar, together with Prof. Nava Dekel and research student Yitzhak Reizel of the Biological Regulation Department, used their method to see if ova could be descended from bone-marrow stem cells. Their findings indicated that any relationship between the two types was too distant for one to be an ancestor of the other.

These scientists also found, surprisingly, that the ova of older mice had undergone more cell divisions than those of younger mice. This could be the result of replenishment during adulthood; but an alternate theory holds that all eggs are created before birth, and those that undergo fewer divisions are simply selected earlier on for ovulation. Further experimentation, says Shapiro, will resolve the issue.
 
 
Top: Dr. Noa Chapal-Ilani and Yitzhak Reizel. Bottom: Drs. Rivka Adar and Shalev Itzkovitz, and Profs. Nava Dekel and Ehud Shapiro
 
Cell lineage trees are similar to modern evolutionary and taxonomic trees based on genome comparisons among organisms. Shapiro and his team used mutations in cells that are passed on to daughter cells over an organism’s lifetime (though not on to the next generation). By comparing a number of genetic sequences called microsatellites – areas where mutations occur like clockwork – they can place cells on trees to reveal their developmental history.

A number of papers published by Shapiro, his team and collaborators in recent months have demonstrated the power and versatility of this method. One study, for instance, lent support to the notion that the adult stem cells residing in tiny crypts in the lining of the colon do not harbor, as thought, “immortal DNA strands.” Immortal strands may be retained by dividing stem cells if they always relegate the newly synthesized DNA to the differentiating daughter cell and keep the original strand in the one that remains a stem cell.

A second study addressed an open question about developing muscle cells. Here they found that two kinds of progenitor cell – myogenic cells, which eventually give rise to muscle fiber, and non-myogenic cells – found within the same muscle are more closely related than similar cells in different muscles.

One immediate advantage of the cell lineage analysis method developed by Shapiro’s team is that it is non-invasive and retrospective, and as such can be applied to the study of human cell lineages. Most other studies of development rely on genetically engineered lab animals in which the stem cells are tagged with fluorescent markers. In addition to providing a powerful new research method that does not rely on such markers, Shapiro believes that it could one day be adapted as a diagnostic tool that might, for instance, reveal the history of an individual’s cancer and help doctors determine the best course of treatment.
 
Also participating in this research were Noa Chapal-Ilani, Adrian Jinich and Drs. Elad Segev, Eran Segal and Yosef Maruvka, of the Computer Science and Applied Mathematics Department; Zipora Marx, Inna Horovitz and Adam Wasserstrom of the Biological Chemistry Department; Drs. Judith Elbaz and Nava Nevo of the Biological Regulation Department; Dr. Avi Mayo of the Molecular Cell Biology Department; Drs. Gabi Shefer and Irena Shur, and Prof. Dafna Benayahu of Tel Aviv University; and Prof. Karl Skorecki of the Technion and Rambam Medical Center, Haifa.
 
Prof. Nava Dekel's research is supported by the Jeanne and Joseph Nissim Foundation for Life Sciences Research; the M.D. Moross Institute for Cancer Research; the Y. Leon Benoziyo Institute for Molecular Medicine; the Yeda-Sela Center for Basic Research; the Willner Family Center for Vascular Biology, which she heads; the Dwek Family Biomedical Research Fund; the J&R Foundation; the estate of John Hunter; and the Allyson Kaye Charitable Trust. Prof. Dekel is the incumbent of the Philip M. Klutznick Professorial Chair of Developmental Biology.

Dr. Eran Segal's research is supported by the Cecil and Hilda Lewis Charitable Trust; the Carolito Stiftung; the Kahn Family Research Center for Systems Biology of the Human Cell; and the European Research Council.

Prof. Ehud Shapiro's research is supported by the Paul Sparr Foundation; Miel de Botton, UK; the Carolito Stiftung; and the European Research Council. Prof. Shapiro is the incumbent of the Harry Weinrebe Professorial Chair of Computer Science and Biology.


 

 

 
Top: Dr. Noa Chapal-Ilani and Yitzhak Reizel. Bottom: Drs. Rivka Adar and Shalev Itzkovitz, and Profs. Nava Dekel and Ehud Shapiro
Math & Computer Science
English

Meeting Places

English

 

 

 

 

Our behavior is a product not just of who we are, but of where we are and who we’re with. That goes also for a protein called BID that plays a central role in our cells’ life cycles. Institute scientists studying this protein are finding that it can split its activities between two different sites in the cell, and its different actions in each can literally be a matter of life or death. Their findings may be important for understanding a number of disorders, from a rare genetic disease to such metabolic syndromes as obesity and diabetes.
The two faces of BID. When duty calls, it leaves the cell nucleus to initiate cell suicide. Illustration: Elite Avni
 
When Prof. Atan Gross and his research team in the Biological Regulation Department began investigating BID in lab dishes, they discovered that BID steers a cell that is in trouble – from damaged DNA, for instance – toward either altruistic suicide or survival. The critical factor was the connection to a second protein called ATM – a sort of “boss” molecule that oversees the actions of BID and a number of other proteins. The team discovered that when ATM interacts with BID, the cell stays alive. When ATM refrains from this interaction, BID attaches to proteins on the surface of organelles called mitochondria – the cell’s power plants – to initiate the series of events leading to cell death.

In research that appeared recently in Nature Cell Biology, Gross and his team set out to get a better picture of BID activity. Together with research students Maria Maryanovich and Galia Oberkovitz, and postdoctoral fellow Dr. Hagit Niv, he created and characterized mice in which the BID protein was mutated: It was unable to accept orders from ATM. After damaging the mice’s DNA, the team watched to see what would happen.

In studies led by Maryanovich, they found that BID is a regular multi-tasker. On the one hand, it does, as they had seen in the lab dishes, administer the cell’s decision to either commit suicide or keep things on hold while repairs are carried out. Unsurprisingly, the team found that cells with the mutated BID had a high suicide rate, especially in the bone marrow, which is highly sensitive to DNA damage. On the other hand, in a seemingly unrelated act, BID also directs the conversion of stem cells that reside in the bone marrow into functional blood cells. These blood stem cells, a kind of adult stem cell, are used to replace all types of blood cells over an organism’s lifetime, and their differentiation is a tightly controlled process. But when BID couldn’t communicate with ATM, the mice’s blood stem cells differentiated without restraint, soon depleting the supply.
 
 
To understand how BID does two jobs at once – directing both suicide and stem cell differentiation – the scientists had to find out where it was going and which proteins it was hooking up with. The cell nucleus, for instance, was where they found the meetings with ATM taking place. The experiments suggested that ATM brings along a physical restraining order telling the BID protein to stay where it is. Without ATM's restraining stamp, BID is free to wander off to its alternate site – the mitochondria – where it meets its other contact on the mitochondria’s outer surface. This is where things start to happen: The interaction spurs the creation of reactive oxygen species – the cells’ all-purpose stress molecules. The reactive oxygen species are like buckshot, tearing holes in the mitochondrion wall to release cell-killing toxins. But these molecules also work as SOS signals to the stem cells, calling on them to differentiate in a hurry.
Prof. Atan Gross
 
The scientists think that the ATM-BID partnership is a sort of control mechanism that senses the amount of DNA damage in a cell and adjusts reactive oxygen species levels accordingly. The findings, says Gross, are surprising – not just for the new function they have revealed for BID. They have yielded interesting insights into previously unsuspected connections between the mitochondria and the cell nucleus, as well as revealing tight coordination between two parts of the cellular life cycle – cell suicide and adult cell replenishment.

Gross and his team believe that these findings and insights may, in the future, have biomedical relevance. ATM mutations in humans cause a rare but devastating degenerative disease that appears in childhood and affects all parts of the body. Many of the worst effects seem to be tied to excess reactive oxygen species, and Gross thinks that finding ways to block BID could relieve symptoms and extend life. But there may be much broader applications: Recent research hints that the behavior of BID and the other proteins it interacts with may be linked to such metabolic syndromes as obesity and diabetes, as well as autoimmune diseases and even cancer. So it might be helpful to find ways of directing BID proteins to the right place and the proper meetings, at the right time.

Also participating in this research were Dr. Yehudit Zaltsman and Lidiya Vorobiyov of the Biological Regulation Department, Profs. Steffen Jung and Tsvee Lapidot of the Immunology Department, and Drs. Rebecca Haffner and Ori Brenner of the Veterinary Resources Department.
 
Prof. Atan Gross’s research is supported by the Jeanne and Joseph Nissim Foundation for Life Sciences Research; the Pearl Welinsky Merlo Foundation; the Helen and Martin Kimmel Institute for Stem Cell Research; the Clore Center for Biological Physics; the Yeda-Sela Center for Basic Research; and the Dr. Josef Cohn Minerva Center for Biomembrane Research.
 
 
 
 

 
 
The two faces of BID. When duty calls, it leaves the cell nucleus to initiate cell suicide. Illustration: Elite Avni
Life Sciences
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Darkness at Noon

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Work of art: A portion of a plant cell

 
The woman in the image has a gorgeous mane of hair that partly wraps her naked torso. This is not a newly discovered Modigliani. The “woman” is in fact a portion of a plant cell magnified more than twenty thousand times. (Above, top) In a project that won first prize in the Beauty of Science competition held recently in the Weizmann Institute’s Feinberg Graduate School, Onie Tsabari, a student in the lab of Prof. Ziv Reich of the Biological Chemistry Department, turned this image into a work of art. (Above, bottom)

Now in a new study published in the Proceedings of the National Academy of Sciences, USA, Reich and his colleagues from Washington State University have revealed why the “hair” in that image is so lush. It is in fact a network of tiny flattened vesicles called thylakoids which reside in the plant’s chloroplast and contain the machinery that carries out the primary steps of photosynthesis – the process by which plants, algae and certain bacteria use sunlight to produce chemical energy and, along the way, almost all of Earth’s oxygen. The new study – selected for the “Faculty of 1000” website of important articles on biology and medicine – has shown that the water-filled space within the thylakoids, called the lumen, nearly doubles in width when the leaves are exposed to light.

The expansion of the lumen facilitates photosynthesis by increasing the space available for the diffusion of a protein that transports electrons. These electrons are eventually used to convert carbon dioxide into sugars, and their flow is essential for the formation of ATP – the major energy molecule of living cells. The enlarging of the lumen also promotes the repair of damaged components of the photosynthetic apparatus – by facilitating their dismantling and shuttling of the components.

When light is replaced by darkness, the lumen shrinks, thus restricting the movement of proteins. This shrinkage is probably intended to prevent damage to the photosynthetic machinery at dawn or during rapid increases in light intensity (due to sudden changes in cloud cover, for instance). The gradually expanding lumen ensures that the rate of electron transport doesn’t rise too suddenly – such a rise could damage a key protein in the electron transport chain.
 
 
Prof. Ziv Reich
 
These findings overturn a long-standing belief that the thylakoid lumen contracts under light, which stemmed from the limitations of the research methods available in the early 1970s. The new study was performed with advanced techniques: A plant leaf was examined by cryo-electron microscopy after being rapidly vitrified at very high pressure in liquid nitrogen and cut up into ultra-thin slices, each only a few tens of nanometers (billionths of a meter) thick. The team, headed by the Institute’s Prof. Reich and Washington State University’s Prof. Helmut Kirchnoff included Washington State’s Chris Hall, Magnus Wood and Dr. Miroslava Hirbstova, and Weizmann’s Onie Tsabari, Dr. Reinat Nevo and Dr. Dana Charuvi of the Biological Chemistry Department, as well as Dr. Eyal Shimoni of the Electron Microscopy Unit.

In addition to revealing the beauty inside a common plant cell, the new findings provide crucial insights into the regulation of photosynthesis and into the ways by which plants adapt to changes in light conditions that occur throughout the day.
 
Prof. Ziv Reich’s research is supported by the Carolito Stiftung.
 
 
Work of art: A portion of a plant cell
Environment
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The Vitamin Map

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Improve speed on the Piccadilly Line, create delays on the track to Hyde Park Corner, route more trains through Kings Cross. These are not suggestions for baffling passengers of the London Underground. Rather, it’s a metaphor describing how plant scientists may one day breed new varieties: To enhance the breeding process, they may consult plant metabolism models that resemble the familiar map of the London Tube.
 

Tube map for plants
 
Creating such metabolic models, which simulate the network of biochemical reactions in the plant, is extremely challenging because plant metabolism involves thousands of enzymes and is extremely complex. A new plant metabolic model, the most complete to date, has recently been created by a team headed by scientists from the Weizmann Institute, the Technion – Israel Institute of Technology and Tel Aviv University. This computerized model, described in the Proceedings of the National Academy of Sciences, USA, focuses on Arabidopsis, a plant in the mustard family that is commonly used in research. The network of this plant’s metabolic reactions is so wide and branched that it indeed evokes the layout of an extensive underground system, in which the lines represent the pathways of metabolic reactions, the trains symbolize individual enzymes and the ends of the lines – the reactions’ end products.
 
 
Applied to the breeding of plants, the model might predict, for example, that the best way to increase the production of a desired nutrient, say vitamin E, is to close a particular “train line” – that is, block a certain biochemical reaction in the plant, or to increase “traffic” on another line – that is, speed up another reaction. Armed with such predictions – the technical term is “predictive metabolic engineering” – plant breeders should be able to produce desired new varieties more quickly and efficiently than by trial and error, as has been done in the past.
 
Prof. Asaph Aharoni
The new model has been created by Prof. Asaph Aharoni and Ph.D. student Shira Mintz-Oron of the Weizmann Institute’s Plant Sciences Department, Dr. Tomer Shlomi of the Technion and Prof. Eytan Ruppin of Tel Aviv University. The team also included the Institute’s Ph.D. student Sergey Malitsky and Aharoni’s lab assistant Dr. Sagit Meir.

Though the model was developed for Arabidopsis, it is applicable to many other plants as well. Among the projects to which Aharoni and his colleagues now intend to apply it is the breeding of new crops, such as rice that is rich in vitamin B1. Crops fortified in this way might in the future help prevent serious vitamin deficiencies that affect people in developing countries.

Prof. Asaph Aharoni’s research is supported by the Tom and Sondra Rykoff Family Foundation; Roberto and Renata Ruhman, Brazil; the Clore Center for Biological Physics; the Minna James Heineman Stiftung; and the Kahn Family Research Center for Systems Biology of the Human Cell. Prof. Aharoni is the incumbent of the Peter J. Cohn Professorial Chair.
 
Tube map for plants
Environment
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