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Science Feature Articles</p>

Alternate Endings

English
 
Drs. Keren Yacobi-Sharon and Eli Arama
          

 

 

 

 

 

 

 

 

 

 

 

 

To save lives, it is sometimes vital to know as much as possible about death, in particular, the death of cells. For example, cancer chemotherapy works by activating a cellular death program called apoptosis. But if the molecular machinery of apoptosis is defective, or if the cancer cells learn to avoid apoptosis, which indeed they often do, chemotherapy becomes ineffective. Therefore, the recent discovery at the Weizmann Institute of so-called germ cell death – an alternative cell death pathway – can be of great value for the development of future life-saving therapies.

 

In short

•    Some germ cells – sperm precursors – undergo a special form of cell death that ensures quality control.
•    Germ cell death differs from the main type – apoptosis – in a number of crucial ways.
•    These may point to new mechanisms for anti-cancer therapies.

In the study, which was reported in Developmental Cell, Dr. Eli Arama, senior intern Dr. Keren Yacobi-Sharon and graduate student Yuval Namdar, all of the Molecular Genetics Department, revealed a new mechanism that is responsible for the death of some male germ cells, the precursor cells that give rise to sperm, in the testis of the adult fruit fly.

Sperm cells are formed in a seemingly wasteful manner, which probably serves to ensure quality control: Germ cells are constantly created in large numbers, after which many of them die. By tracking the death of those cells in a living organism, the researchers were able to reveal its mechanics in great detail.
 
 
In an adult fruit fly testis, viewed under a confocal microscope, maturing germ cells (a nonapoptotic process) use active caspases (green); in contrast, dying germ cells (red) do not express activated caspases
 
First of all, the scientists confirmed that these germ cells do not die by apoptosis, the most common type of cell death. In particular, they showed that effector caspases, the destructive enzymes that execute apoptotic death, are not involved in germ cell death. Next, they defined the structural hallmarks of germ cell death. Like in apoptosis, the entire cell and its nucleus shrink, and the DNA becomes fragmented. However, many typical apoptotic features are missing in dying germ cells; moreover, unlike in apoptosis, these cells contain large degrading regions and their mitochondria, the energy-producing organelles, become distorted.  

The researchers discovered that a central role in germ cell death is played by the mitochondria: These organelles activate a particular gene, htrA2, which makes a destructive protease enzyme. HtrA2 has an equivalent in organisms ranging from bacteria to mammals, which suggests that the findings of the Weizmann fruit fly study are applicable to humans. Yet another major component of the germ cell death mechanism is the lysosome, the cell’s stomach-like organelle that is filled with enzymes for breaking down cellular waste and debris. Lysosomes contribute to cellular destruction by spilling out their contents.
 
Why do the cells need an alternative death pathway? One possible explanation is that germ cell death is the more ancient in evolutionary terms, while apoptosis, as well as the involvement of caspases in apoptotic death, may have evolved more recently. That could be why flowers and yeast lack conventional caspases and make use of a cell death pathway that is similar to germ cell death, whereas cell death is not the only function of the caspases in multicellular animals.
The tips of two adult fruit fly testes, viewed under a confocal microscope, are filled with dividing germ cells (green). About one quarter of these germ cells die by an alternative death pathway called germ cell death (pink and red)
 
Knowing the mechanism of germ cell death might have important implications for cancer research, among other things. It may, for instance, help explain the origins of testicular cancer, in which germ cells in the testes multiply uncontrollably. On a more general level, it may help in the development of anti-cancer drugs that could kill cells by an entirely new mechanism, helping to overcome the drug resistance that often emerges in response to more conventional chemotherapy.
 
Dr. Eli Arama’s research is supported by the Yeda-Sela Center for Basic Research; the Fritz Thyssen Stiftung; and the late Rudolfine Steindling. Dr. Arama is the incumbent of the Corinne S. Koshland Career Development Chair in Perpetuity.
 
The tips of two adult fruit fly testes, viewed under a confocal microscope, are filled with dividing germ cells (green). About one quarter of these germ cells die by an alternative death pathway called germ cell death (pink and red)
Life Sciences
English
  • Apoptosis
  • Cancer
  • Caspase
  • Cell suicide
  • Eli Arama
  • Fruit fly
  • Molecular Genetics

How to Prune a Nerve Cell

English
 
 
 
Sensory axons induced to prune by trophic withdrawal in vitro: While wild-type axons degenerate (left), axons that lack KIF2A remain intact
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Like a sprouting thicket, the cells of the developing nervous system extend long, thin branches called axons into all parts of the growing body. This thicket, at second glance, turns out to be a well-tended garden: As development progresses, quite a few extraneous nerve cells are weeded out and many of the axons are pruned back. This gardening activity remodels the nervous system even as it continues to spread and grow. It is the key to a well-functioning nervous system, and there is some evidence that certain neurological disorders, for instance autism, may be tied to imperfect remodeling.

Dr. Avraham Yaron and research student Maya Maor-Nof of the Weizmann Institute’s Biological Chemistry Department recently revealed a central player in the process of axon pruning. This is crucial, says Yaron: “Before we can understand the mechanisms involved in health or disease, we must be able to identify the various players involved. Until now, we have had very little idea of who or what these players are.”  

Pruning of axons takes place from the inside out: Long structural elements, called microtubules, that run down their length are first disassembled. Microtubules are both backbone and transport system: various payloads, including signaling molecules and other materials, are conveyed up and down the rail-like microtubule system. The researchers wanted to know what mechanism controls the breakdown of microtubule structures during axon pruning. Working with sensory nerve cells grown in culture, they used a process of elimination to identify the one – called KIF2A – that carries out the job. Interestingly enough, KIF2A is a member of the family of motor proteins that travel up and down the microtubules and transport various cargos.

To understand the role KIF2A plays in nervous system development and axonal pruning, the Weizmann researchers obtained knockout mice from scientists from the University of Tokyo, Japan, that were missing KIF2A. In the KIF2A-deficient mice, the axons grew normally but the pruning process was impeded as the microtubules and the axons remained intact.
 
Dr. Avraham Yaron
This confirmed that KIF2A is the crucial factor – one which must be present for pruning to occur. The KIF2A knockout mice were distinguished by the fact that their skin – a main destination for developing sensory nerve axons – was inundated with numerous nerve endings.   

How does the process work? The research findings suggest that KIF2A is controlled by molecules called neurotrophins that play the role of head gardener. Neurotrophins are found in the nerve’s target tissues (the skin, for example, in the case of the sensory nerve cells in the experiments), where they guide the growth of axons in the right direction and help them to survive. But neurotrophin numbers tend to be limited, and the axons end up competing for their signals. When an axon does not obtain a neurotrophin signal, its KIF2A, which is normally present in an inactive form, will become activated and the pruning procedure will be initiated.

This creates a process, according to Yaron, that at first appears to be somewhat random but is in reality quite orderly. Not only are the numbers of axons carefully regulated – leading to optimum configurations of nerve cells – but the pruning also proceeds step by step in a preset, genetically determined order. If the first step – microtubule disassembly – does not take place, the rest of the pruning process cannot follow.

Previous research in Yaron’s group, conducted together with Dr. Eli Arama of the Molecular Genetics Department, investigated another type of machinery that regulates nervous system remodeling –  the apoptotic (cell suicide) system . Taken together, this research is beginning to fill in the details of how the nervous system’s “garden” grows: exuberant growth and development alongside judicious thinning, weeding and pruning. Once researchers understand where the balance between them lies and how that balance is achieved, they can begin to understand diseases that arise out of an imbalance, says Yaron. There are some indications, for instance, that autistic brains may suffer from too little pruning – leading to an excess of nerve connections. Yaron thinks that a faulty KIF2A mechanism may play a role in the disorder.
 
Prof. Avraham Yaron's research is supported by the Nella and Leon Benoziyo Center for Neurosciences; the Wolfson Family Charitable Trust; the Koshland Family; the Rowland and Sylvia Schaefer Family Foundation; the Irving Harris Foundation; the estate of Lola Asseof; the estate of Nathan Baltor; and the Joseph D. Shane Fund for Neurosciences.
 
Sensory axons induced to prune by trophic withdrawal in vitro
Life Sciences
English
  • Autism
  • Avraham Yaron
  • Axon
  • Biological Chemistry
  • Brain research
  • Eli Arama
  • Nervous system

The Path to Personalized Prognosis

English

Doctors seeking to prescribe personalized therapy for a cancer patient face a great deal of uncertainty. How fast is the tumor growing? How aggressively should the cancer be treated? And which treatment approach is likely to be most effective?


Answers to these questions remain elusive, even though in the past decade or so scientists have accumulated mounds of data about the human genome in health and disease. In fact, this embarrassment of riches is itself part of the problem. Cancer is a disease of faulty genes, but since there are more than 20,000 human genes, a physician trying to define a particular tumor in terms of its genetic defects confronts a daunting challenge.

“Deregulation scores” of hundreds of brain tumor patients: Each row corresponds to a pathway (that is, a biochemical process), and each column to a sample taken from a patient. Every colored spot stands for a number – the value of the “deregulation score” of the corresponding pathway, as determined for a particular patient. Dark blue stands for the activity of the pathway in normal brain tissue, whereas dark red indicates a high level of deviation from normal behavior. The clearly distinct group of normal brain samples appears as the dark blue vertical stripe, TgS7, in the middle. The TgS15 stripe corresponds to the newly identified subgroup of patients with longer survival prospects
 
 
 
 
 
 
 
 
 
 
 
 
 
Weizmann Institute scientists propose an original and relatively simple method for making sense of the vast amounts of cancer-related genomic data. Prof. Eytan Domany and Dr. Yotam Drier of the Physics of Complex Systems Department have developed an algorithm called Pathifier that can help medical researchers and practicing physicians assess the prognosis of a given tumor based on its genetic profile. As reported in the Proceedings of the National Academy of Sciences (PNAS), the scientists, together with postdoctoral fellow Dr. Michal Sheffer, have already used Pathifier to identify previously unknown cancer subtypes that differ in their prognosis.

Pathifier, as its name suggests, analyzes pathways, the biochemical processes making up the life of the cell, each involving 20 to 30 genes. About 500 such pathways are known to science. In any given cancer, at least a few of them are abnormal. For example, if some of the pathways that govern growth are defective, the cell keeps dividing uncontrollably, leading to the formation and growth of a tumor. The extent of deregulation of different pathways varies from cancer to cancer and from patient to patient.
 
By comparing genomic data from cancerous and healthy cells, Pathifier assigns a “deregulation score” to each pathway. The set of these scores makes up the profile of the tumor.  The researchers believe it can help evaluate the cancer’s aggressiveness, assess its chances of responding to a particular therapy and perhaps even identify key biochemical processes that in the future may serve as targets for therapy.
 

pathways

 
Because the new method focuses on entire pathways, it gives a more accurate picture of the cancer’s properties, as opposed to monitoring individual genes. “It’s like analyzing what’s wrong with a car by observing the performance of its engine, brakes, steering and other systems, rather than dismantling it and looking at all the individual nuts and bolts,” Domany says. Moreover, the method is particularly reliable because it is based on the analysis of large sets of genomic data from hundreds of patients. Yet it is manageable because it focuses only on essential data, rather than trying to encompass the entirety of genomic details.

In the new study, the researchers applied Pathifier to a malignant brain tumor called glioblastoma. It was known from past genetic analyses that patients with a certain type of this tumor survive longer than others, but on the basis of the tumor profiles, the algorithm has allowed scientists to identify a smaller subtype of patients who are the truly longer survivors, as opposed to the rest of the patients with the same tumor type, who are not.  Furthermore, Pathifier has enabled the scientists to identify three pathways whose levels of deregulation are strongly indicative of the survival prospects of colon cancer patients.

Currently, Pathifier can be used as a research tool, offering medical researchers a reliable way of processing cancer-related genomic data. In the future, the algorithm can point to relevant biomarkers – that is, measurements of the levels of certain chemicals that are indicative of the activation of key pathways – that could help practicing physicians choose appropriate treatments for their patients. The physicians could rely on such biomarkers to evaluate a tumor’s deregulation profile.
 
Prof. Eytan Domany's research is supported by the Kahn Family Research Center for Systems Biology of the Human Cell, which he heads; the Mario Negri Institute for Pharmacological Research -Weizmann Institute of Science Exchange Program, the Leir Charitable Foundations; Mordechai Segal, Israel; and the
Louis and Fannie Tolz Collaborative Research Project.  Prof. Domany is the incumbent of the Henry J. Leir Professorial Chair.
 


 
 
“Deregulation scores” of hundreds of brain tumor patients: Each row corresponds to a pathway (that is, a biochemical process), and each column to a sample taken from a patient. Every colored spot stands for a number – the value of the “deregulation score” of the corresponding pathway, as determined for a particular patient. Dark blue stands for the activity of the pathway in normal brain tissue, whereas dark red indicates a high level of deviation from normal behavior. The clearly distinct group of normal b
Math & Computer Science
English
  • Algorithm
  • Cancer
  • Cancer genetics
  • Eytan Domany
  • Molecular pathways
  • Personalized medicine
  • Physics of Complex Systems

Mutations Trump Invasion

English

 

Dr. Ron Diskin
 
The human immunodeficiency virus (HIV) is a sly invader: It goes straight to the very immune cells meant to protect against infection, slips inside through the cells’ outer defenses and hijacks the cells’ machinery to make copies of itself. To seek out and infect those immune cells, the virus uses three-part protein complexes: the HIV spikes that are strategically placed around its outer envelope. This protein complex has been very well studied, says Dr. Ron Diskin, who recently joined the Weizmann Institute’s Structural Biology Department, but, surprisingly, no one has yet managed to solve the crystal structure of the entire complex. That is because the complex is almost entirely covered in flexible sugar molecules that hinder structural studies. One of the first tasks that Diskin is setting himself in his Weizmann lab is to find a way to reveal the atomic structure of the spike complex.
 
 
In his postdoctoral research at the California Institute of Technology, Diskin studied another aspect of HIV infection: antibodies to the virus that naturally occur in some people. These are called broadly neutralizing antibodies (bNAbs); some people whose bodies manage to produce bNAbs can be infected with HIV without developing the disease, AIDS. It is surprising that such antibodies exist at all: HIV is notorious for its ability to evade the immune system’s antiviral mechanisms. It does this, in part, by mutating rapidly, so that antibodies that are specific to one form may be useless against another. The bNAbs somehow manage to target conserved sites on the spike and remain effective against many different versions of the virus.
A model of bNAb showing the canonical antigen binding site in cyan and framework region mutations in magenta
 
 
In the research, which recently appeared in Cell, Diskin and his colleagues investigated what makes bNAbs unique. Their idea was to decipher the role of the various mutations that accumulate in bNAbs. In general, antibody production works a bit like fast evolution: Many different mutations are produced in germline antibodies, and these undergo natural selection so as to produce the ones that can best bind to an invading pathogen. In this way, as the immune system is exposed over time to a pathogen, it continues to hone its weaponry. The team was intrigued by the fact that, compared to the regular antibody repertoire, bNAbs carry a large number of mutations, including some surprising changes to the protein sequences in unexpected places on the antibody structures. Specifically, it was thought that these mutations mostly occur in variable regions that make contact with foreign invaders; but some of the mutations in bNAbs were in structural regions that give antibodies their shape and maintain their structural integrity.

To understand the role of these unusual mutations, the researchers reverse-engineered the antibodies, returning parts of them to a germline state and making comparisons. Diskin and his colleagues found that those changes gave the highly mutated bNAbs a clear advantage in fighting HIV. For example, a small mutation – a substitution of one amino acid for another – in a non-antigen-binding region reduced the structural stability of the antibody molecule, giving it a greater flexibility that the researchers think might enable it to conform to different virus shapes.
 
 
HIV: illustration from the National Institutes of Health
 
This research, says Diskin, is likely to have important implications for the design of HIV vaccines and vaccination strategies. But it has also revealed some vital principles of how these antibodies form. For instance, the researchers believe that just getting the right combination of so many different mutations should take at least several years, so even those people lucky enough to have bNAbs would develop them only a long time after they become infected. In addition, by refuting the scientific dogma and showing that useful mutations can occur far away from the main sites, the study has revealed new aspects of antibody production and function that may be relevant for other types of antibody and vaccine research.

Diskin is a crystallographer – that is, he reveals the structures of proteins by getting them to form crystals, bombarding them with X-ray radiation and creating a model of the structure based on the way the radiation scatters. In addition to revealing the HIV envelope protein complex structure in his Weizmann lab, he plans to investigate other proteins that interact with viruses, protein-protein interactions and the ways that individual proteins combine to form large protein complexes.  

Dr. Ron Diskin's research is supported by the Abramson Family Center for Young Scientists; and the Enoch Foundation.  Dr. Diskin is the incumbent of the Tauro Career Development Chair in Biomedical Research.


 
 
Space & Physics
English
  • Antibody
  • HIV
  • Protein structure
  • Ron Diskin
  • Structural Biology

The Spies Inside

English

Dr. Guy Shakhar

 

 

 
 
 
 
 
 
 
 
 
 
 
We do not live by bread alone. To digest the bread, as well as the rest of the food we consume, our bodies resort to the help of microbes that live in our gut. These number in the billions; their total weight adds up to nearly two kilograms. Most are friendly and, as noted, even vital for the normal functioning of digestion and other body systems. But occasionally, disease-causing microbes such as Salmonella sneak in among them.

In most cases, the immune system identifies and destroys the dangerous microbes so that we do not even know we’d been exposed to the risk. But how does the system tell the good microbes from the bad? How does it detect the danger? The task is far from trivial: The microbes are contained in the gut, whereas the immune cells are embedded in the gut lining, the epithelium. Complicating detection even further, the few harmful bacteria present in a healthy gut are vastly outnumbered by the rest of the gut flora.
 
 
Live two-photon microscopy of the small intestine
 
A team of Weizmann Institute scientists headed by Dr. Guy Shakhar of the Immunology Department recently shed light on this mystery. As reported in the journal Immunity, the scientists showed that the immune system sends its “spies,” so-called dendritic cells, to the surface of the gut lining. The research was performed by graduate student Julia Farache, along with her lab-mates Idan Koren, Idan Milo and Dr. Irina Gurevich; Drs. Ki-Wook Kim and Ehud Zigmond from Prof. Steffen Jung’s lab in the same department; and researchers from the Mt. Sinai School of Medicine in New York: Drs. Glaucia C. Furtado and Sergio A. Lira.

Using a two-photon microscope, the scientists created an innovative setup that enabled them to monitor in real time immune cells in the gut of a live mouse. It turns out that the moment Salmonella bacteria stick to the epithelium of the small intestine, the epithelial cells inform the immune system and, within half an hour, dendritic cells are recruited to the site of the infection. In video clips created under the microscope, these cells can be clearly seen squeezing through crowed tissue to reach the upper layer of the epithelium and sending their extensions – the dendrites for which they are named – to capture the bacteria.

Why do they respond in this manner to Salmonella but not to the millions of “good” bacteria in the same environment? While the beneficial bacteria don’t damage cells because they probably don’t stick to the gut lining, Salmonella signals its intent to harm by latching on to the epithelium.

Having swallowed the bacteria, the dendritic cells rush to report to the immune system. They start expressing receptors that guide them back into the intestinal tissue and through the lymph vessels. In the lymph nodes, they present fragments of Salmonella’s proteins – in other words, the bacterium’s “body parts” – to immune T cells, which turn on mechanisms that destroy the Salmonella, preventing poisoning.

This research may in the future help develop therapies against inflammatory bowel diseases, which are characterized by flare-ups of inflammation. Since dendritic cells are involved in igniting these flare-ups, possibly by overreacting to an infection, understanding their mechanism of action in the gut may help prevent their harmful activity.
 
Dendritic cells send their extensions (red arrows) between adjacent epithelial cells (blue) in the lining of the small intestine

The new findings may also help develop oral vaccines, which offer major advantages over conventional methods of vaccination; for one, it’s easier to convince people to take a pill than to get an injection. Vaccines consist of weakened microbes, but for them to be effective, the microbes must be weakened in such a manner that they are capable of activating the immune system, yet do not cause disease yet. Therefore, it’s important to understand how microbes communicate with the immune system in the intestines, which is precisely what the current study has helped achieve.
 
Dendritic cells (brown) capture Salmonella microbes (light blue), then rapidly retract their extensions (arrow)
 
Prof. Steffen Jung's research is supported by the Leir Charitable Foundations; the Leona M. and Harry B. Helmsley Charitable Trust; the Adelis Foundation; Lord David Alliance, CBE; The Wolfson Family Charitable Trust; and the estate of Olga Klein Astrachan.
 
Dr. Guy Shakhar's research is supported by the Clore Center for Biological Physics; the Yeda-Sela Center for Basic Research; the Leona M. and Harry B. Helmsley Charitable Trust; the Dr. Dvora and Haim Teitelbaum Endowment Fund; Simone Pastor, Monaco; Lord David Alliance, CBE; Paul and Tina Gardner, Austin, TX; the Steven and Beverly Rubenstein Charitable Foundation; and the Paul Sparr Foundation.

 
 
Live two-photon microscopy of the small intestine
Life Sciences
English
  • Bacteria
  • Guy Shakhar
  • Immune system
  • Immunology
  • Microscopy
  • Steffen Jung

Veto on Disease

English

 

Prof. Yair Reisner
 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
A little tolerance can go a long way. If the immune system, for instance, could be coaxed into tolerating foreign tissue rather than rejecting it outright, a variety of blood disorders could be treated by bone marrow transplants. Immune tolerance could also help extend these transplants to people who are currently too frail to receive them; in addition, it could facilitate the transplantation of kidneys, liver and other body organs.

An international team led by Weizmann Institute researchers has recently managed to induce a certain degree of immune tolerance by making use of so-called veto cells. These are naturally occurring immune cells that exert veto power over their own destruction: When attacked by the recipient’s immune cells, they launch a pre-emptive strike, destroying the attackers.

Lead study author Prof. Yair Reisner of the Institute’s Immunology Department  has been studying veto cells for more than a decade, focusing on certain types known as CD8+. These cells exhibit the most potent veto activity of all, but they may be toxic to the patient because they can induce a complication known as graft-versus-host disease, in which the transplant attacks the host. Reisner’s team has found a way of circumventing this problem by generating a line of less toxic CD8+ veto cells. In the new study, reported in Blood, he and colleagues have now prepared the ground for using these cells in patients.  According to the accompanying editorial entitled “Location, Location, Location,” the study has revealed the conditions in which the “promise of veto cells, as a cellular therapy, may finally be realized.”

As suggested in the editorial’s title, the scientists have determined the exact location in which veto cells exert their protective effect: the lymph nodes. The researchers have also revealed the mechanism of the cells’ action. It turns out that the cells cast their veto as soon as the recipient’s immune system T cells, which continuously patrol the body looking for foreign invaders, recognize the newly transplanted veto cells and latch onto them. That is precisely when the veto cells make their preemptive move: Equipped with ready-made poisons, they destroy the attackers, whose own poisons take longer to be produced. These details were revealed in collaboration with the lab of Dr. Guy Shakhar, also of the Immunology Department, thanks to an innovative two-photon microscopy system that made it possible to observe individual immune cells in a live mouse in real time.

The scientists further determined how to make sure veto cells reach their destination: Prior to transplantation, they must be grown in culture with the help of the biochemical interleukin-15, which preserves the “homing” receptor that guides them to the lymph nodes.
 
 
Anti-donor immune T cells (green) attach themselves (blue arrows) to the donor’s veto cells (red); this binding leads to their destruction by the veto cells. Viewed under a two-photon microscope

 
Indeed, in the study, veto cells successfully eliminated they type of recipient T cells that are responsible for much of the rejection. As a result, white mice tolerated skin grafts from black mice. Normally, such transplants require a drastic suppression of the recipient’s immune system with drugs and radiation to prevent rejection, but thanks to the tolerance induced by veto cells, the white mice did not reject the black patches even though their immune systems had been only mildly suppressed. Further research is needed to establish whether this approach can be as effective in humans as it is in laboratory animals.

Major and equal contributions to this study, conducted in Reisner’s lab, were made by graduate students Dr. Eran Ophir and Noga Or-Geva. In an earlier, preliminary study in Reisner’s lab, led by Ophir and Dr. Yaki Edelstein and published in Blood in 2010,  the concept of using veto cells to induce tolerance had been established in a more artificial mouse model for bone marrow graft rejection.  

Currently, bone marrow transplants are used only to treat disorders that are otherwise fatal because the treatment itself is risky. The major risk is infection, which stems from the suppression of the immune system in preparation for the transplant. But if the suppression can be mild, as was the case in the current study, bone marrow transplants could potentially be extended to such nonfatal disorders as sickle-cell anemia and thalassemia. They could also be made available to people who are presently unable to benefit from such transplants because they are too vulnerable to undergo a massive suppression of the immune system, such as elderly patients with leukemia or lymphoma. Moreover, the veto cell approach could be used to induce tolerance toward transplanted kidneys or other organs without the need for continuous immune suppression.
 
Prof. Yair Reisner's research is supported by the Belle S. and Irving E. Meller Center for the Biology of Aging, which he heads; the Leona M. and Harry B. Helmsley Charitable Trust; the Steven and Beverly Rubenstein Charitable Foundation; Roberto and Renata Ruhman, Brazil; the wstate of Samuel and Valerie Rodetsky; and the Estate of Lola Asseof. Prof. Reisner is the incumbent of the Henry H. Drake Professorial Chair in Immunology.
 
 
Life Sciences
English
  • Bone marrow
  • Immune cells
  • Immunology
  • Yair Reisner

Noncoding Sequences Get Equal Listing

English
New and improved GeneCards, over 100,000 separate entries: The orange arc shows GeneCards before the addition of the ncRNAs in the study, the blue those added in the study (with an overlap of around 14,000 entries)
 
Nowadays, to the familiar mRNA that ferries the genetic instructions for protein production out of the cell nucleus, we can now add thousands of microRNAs, long non-coding RNA, piRNA, antisense RNA and more. In fact, of the roughly 80% of the DNA in the human genome that is estimated to be copied out (transcribed) into RNA sequences, only around 2% gets translated into proteins. Though we still don’t know exactly how much of the rest is functional, it is already clear that a better understanding of the various kinds of non-protein-coding RNA sequences (ncRNAs) and the roles they play will have important consequences for research on health and disease. If the diverse and still growing collection of RNAs is bewildering, the various attempts to catalog them have created even more bafflement.
 
That is why the group of Prof. Doron Lancet of the Molecular Genetics Department decided to take on the challenge of fully incorporating these novel RNAs into GeneCards, their user-friendly, searchable, unified database of human genes. Initiated by Lancet and his team in 1996, GeneCards has become one of the world’s most popular genomic research tools. But until recently this database focused mainly on the 20,000-odd protein-encoding genes, while a handful of ncRNA genes were scantly represented. Their intent was to significantly enhance the representation of ncRNAs within the GeneCards framework – an improvement that could provide the scientific and medical community with an authoritative, fully annotated compendium of these varied, versatile and vital cellular components.
 
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Prof. Doron Lancet
 
The lead figure in this project was Dr. Frida Belinky, a postdoctoral fellow with Lancet, head of the Institute’s Crown Human Genome Center. The work was done in close collaboration with other members of the GeneCards development team headed by Marilyn Safran.

Belinky started out with 15 different ncRNA gene databases and developed computerized integration methods for bringing them together into a single one. Among other things, the sorting and assembling process involved finding genes that overlapped by more than 70% – suggesting they were the same gene – and separating sequences that apparently have some function from those that do not seem to be of use. For example, one gene group, called piRNAs, that was thought to contain over 30,000 genes, was eventually narrowed down to a mere 20,000.

By the time they had finished the project, they had expanded the GeneCards ncRNA content from about 15,000 to some 80,000 distinct genes. In addition to the sequences and their placement in the genome, the database contains information on where these genes are expressed and which other species contain their similes – highly useful features for unraveling their function. Since the team’s paper detailing the creation of this database appeared in January’s Bioinformatics, it has garnered considerable interest among researchers in various fields in the life sciences. Cancer researchers, for instance, can use it to find ncRNAs that may be active in initiating or promoting tumor growth. Many rare diseases are also thought to be tied to faulty ncRNAs, and the extended database could help researchers identify the sequences involved.

 

 
Dr. Frida Belinky
 
“This ‘grand unification’ of ncRNA genes will enable scientists to make new discoveries on biological and disease-related roles for genes belonging to this newly opened vista of the human genome,” says Lancet.


GeneCards and the Human Genome


When Interface magazine first reported on GeneCards in 1998, the web-based database included a mere 7,000 genes and averaged 22,000 hits a month. By the end of the Human Genome Project in 2003, GeneCards contained web cards for all of the roughly 20,000 well-documented human protein-coding genes, plus about the same number of predicted or suspected genes. In the decade since, a great deal of research has focused on the 97% of the genome that does not direct protein production, spearheaded by the world-wide ENCODE project. Views have come around from seeing it as “junk DNA” to realizing that ncRNA genes encompass a complex network of activities that complements and regulates that of the coding genes. This has led to the intense proliferation of knowledge in the new realm of ncRNA studies – and has necessitated the relevant, unified view now provided by GeneCards. There are now over 12 million page visits to the GeneCards site a year, and its users obtain what may prove to be the most updated, inclusive ncRNA view available.

The GeneCards project has a research grant from LifeMap Sciences, Inc., a subsidiary of the California-based biotech firm BioTime, Inc. LifeMap holds an exclusive worldwide license for GeneCards from Yeda Research and Development, Ltd., Weizmann’s technology transfer arm. LifeMap also recently helped Lancet’s lab establish MalaCards, a companion database of human diseases.
 
Prof. Doron Lancet's research is supported by the Crown Human Genome Center, which he heads; the Dr. Dvora and Haim Teitelbaum Endowment Fund; the Nella and Leon Benoziyo Center for Neurological Diseases; and the estate of Nathan Baltor. Prof. Lancet is the incumbent of the Ralph D. and Lois R. Silver Professorial Chair of Human Genomics.


 
 
 
Dr. Frida Belinky
Math & Computer Science
English
  • Doron Lancet
  • Gene code
  • MicroRNA›miRNA
  • Molecular Genetics
  • RNA

Bringing Down Walls

English
Cellulose fibers in the plant cell wall magnified 50,000 times by an atomic force microscope
 
Plant biomass can be converted into green fuel using clean, sustainable technologies, but the major challenge involved in producing biofuels from biomass on a large scale is the high cost. Visualizing the minutest details of biomass conversion down to the atomic level can help optimize the process, according to a study performed by researchers from the Weizmann Institute of Science and the National Renewable Energy Laboratory (NREL) in the United States.

The study, reported in Science, has confirmed the basic idea that one of the major obstacles to effective biomass conversion is lignin, the sturdy polymer that gives plants their strength. In fact, to facilitate the conversion of  the  polysaccharides – the complex sugar compounds in the plant cell wall – into the biofuel ethanol, the process usually starts with pretreatment in which the lignin gets mechanically chopped up or chemically destroyed. In the new study, the researchers devised innovative methods that for the first time made it possible to observe lignin destruction at the molecular and atomic resolution, using advanced laser microscopy. The images have revealed that lignin actually interferes with the ability of enzymes to digest polysaccharides. This understanding has enabled the scientists to define the parameters of an ideal pretreatment – one that focuses on removing the lignin without damaging the polysaccharides.
 
 
The team further compared two different methods for digesting the polysaccharides. One relied on individual enzymes derived from fungi; the other made use of cellulosomes – natural molecular complexes of several enzymes by means of which bacteria, fungi and other microorganisms degrade plant cellulose. The scientists discovered that the loose enzymes penetrated deeper inside plant cells than the cellulosomes, which acted mainly on the plant cell surface. This new understanding of the mechanisms involved in the deconstruction of cellulosic biomass may help scientists design more effective enzyme systems for bringing down plant cell walls.
Prof. Ed Bayer
 
Cellulosomes were discovered some three decades ago by Prof. Ed Bayer of the Weizmann Institute’s Biological Chemistry Department, together with his colleague Prof. Raphael Lamed of Tel Aviv University. In the current study, Bayer collaborated with researchers from the NREL, including Dr. Shi-You Ding, who had conducted postdoctoral research in Bayer’s laboratory in the late 1990s. Dr. Ding and Dr. Yu-San Liu of the NREL devised methods for visualizing the effects of different chemicals on the plant cell wall at an enormous range of resolutions, spanning a million-fold difference: from a millimeter to a nanometer (one millionth of a millimeter). Other members of the NREL team included Drs. Michael Himmel, Yining Zeng and John Baker.
 
The study’s findings can help researchers optimize biomass pretreatment and the activity of the enzymes used to degrade the biomass. Such improvements, in turn, could increase ethanol yields, lowering the cost of making biofuels.
 
A historic aside: The cellulosome in the study was derived from the microorganism Clostridium thermocellum, which belongs to the genus of bacteria historically linked to the Weizmann Institute and the State of Israel. Dr. Chaim Weizmann, the Institute’s founder and first President of Israel, had used a bacterium of the same genus, Clostridium acetobutylicum, now often called the Weizmann organism, to produce acetone during World War I. Following in Dr. Weizmann’s footsteps, Weizmann Institute researchers have recently established yet another tie between past and present science: Genetic studies have demonstrated that Weizmann’s bacterium, somewhat surprisingly, produces a cellulosome of its own.
 
Prof. Ed Bayer’s research is supported by the Leona M. and Harry B. Helmsley Charitable Trust; and the Brazilian Friends of the Weizmann Institute of Science. Prof. Bayer is the incumbent of the Maynard I. and Elaine Wishner Professorial Chair of Bio-Organic Chemistry.
 
Bright-field light microscopy images of plant cell walls, stripped of lignin, degraded by cellulosomes
 

 

Cellulose fibers in the plant cell wall magnified 50,000 times by an atomic force microscope
Life Sciences
English
  • Atomic force microscopy
  • Biological Chemistry
  • Ed Bayer
  • Enzyme

The Secret of the Smile

English

we all smile

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
At a very young age, babies learn to smile back. Soon after, they realize that if they themselves initiate the smiling, they will get a smile in return. As adults, too, we automatically correlate our own facial expressions with those of others: Being greeted with a scowl by someone at whom we have smiled feels completely different from a scowl prompted by our own hostile stare. In other words, the ability to identify the facial expressions of all participants, including ourselves, is crucial for interpreting complex social situations. In people with autism, this ability is obviously missing. Yet despite a large body of research into brain mechanisms dealing with the facial representation of emotions, virtually no studies have focused on ways by which the brain monitors one’s own behavior.

A study conducted in the laboratory of Dr. Rony Paz of the Weizmann Institute’s Neurobiology Department has for the first time revealed how the brain integrates self-monitoring with observations of others. These findings, reported in the Proceedings of the National Academy of Sciences (PNAS), also open new avenues of research into the faulty processing of emotional and social information, such as that which occurs in people with autism.
 
 
Dr. Rony Paz
 
Research student Uri Livneh, together with Jennifer Resnik and Yosef Shohat, created a unique experimental system in which two monkeys, separated by an opaque shutter, faced one another. Periodically, the shutter turned clear for a few seconds, enabling the monkeys to interact spontaneously, through nonvocal facial expressions, as they do in nature. The scientists identified three major expressions: a positive one, characterized by smacking the lips and contracting the surrounding muscles; a threatening one, characterized mainly by stretching the eyebrows and increasing the eyes’ movements; and a neutral one, observed when the shutter was closed and no interaction took place. In the course of the experiment, the scientists measured the electrical activity of individual neurons in the monkeys’ brains.

The scientists focused on two brain areas involved in processing emotional information and responding to positive and negative facial expressions: the amygdala and a certain portion of the cortex. They found that neurons in both these areas were responsible for two different activities: They both processed information about the individual’s own facial expressions and decoded the expressions of others.

The scientists were able to differentiate the electrical signals involved in the two types of decoding only by conducting extremely precise measurements, at a resolution of a few dozen milliseconds. They revealed that the amygdala actually knows about the smile before it occurs; it receives a neural signal directly from the part of the brain that controls the facial muscles as the smile is being created. This then provides the proper context for interpreting the facial expression of others. Thanks to this close overlap of the neural networks charged with interpreting one’s own and others’ behavior, the amygdala and cortex can quickly receive all the relevant information and create a complete and accurate picture of a social situation.

In follow-up research, the scientists plan to examine whether the same networks are involved in social learning – that is, learning through observing others. For example, if one monkey learns something by classic conditioning, can another monkey learn the same thing just by watching? Does the monkey brain have a neural network for learning by observation? And if so, what can this network teach us about human social learning?

Yet another potential future study concerns neuropsychiatric disorders characterized by defective social communication, as in autism. Autistic people have difficulty creating and interpreting emotional and social situations. Previous research had shown that the neural networks examined in the current study don’t function properly in these people, but appropriate models for studying these networks in depth were not available. “The unique experimental system we have developed can provide a basis for creating a natural model of autism,” says Paz. “The system enables researchers to observe natural and versatile social behavior unique to primates while at the same time analyzing the complex neural networks underlying this behavior.”
 

A connection with animals

Yosef Shohat
 
Yosef Shohat, lab technician and manager of Dr. Rony Paz’s laboratory, is an animal person. As a child, he used to go to the beach after storms to collect wounded seagulls to take care of at home. Birds, dogs, insects – all found shelter on his balcony in Kiryat Haim, much to the displeasure of his mother. At age 25, his dedication to animals led to a tragic incident: Yosef tried to restrain a camel that had gone wild while carrying children on its back, and he was attacked and nearly fatally wounded by the animal. He remained paralyzed for a long time; but following prolonged rehabilitation – and contrary to the prognosis of all the doctors – he regained control of his body. Yosef credits animals with this medical miracle: “I needed the connection to animals to overcome not only the physical difficulties but also my depressed mental state.” In the wake of his injury, he gave up on studies of animal behavior at Oranim College, but not on his connection with four-legged and flying creatures. The injury has also caused him to forget the foreign languages he once knew, English and Arabic (he is now learning them anew), but not his mother tongue, Hebrew, nor the nonverbal language in which he communicates with animals.

Yosef lives in Rehovot with his wife, Stavit, who works in the Hebrew University’s Faculty of Agriculture. They have two sons: Omer, 12, and Segev, 10.
 
Dr. Rony Paz's research is supported by the Sylvia Schaefer Alzheimer's Research Fund; the Ruth and Herman Albert Scholars Program for New Scientists; Pascal and Ilana Mantoux, Israel/ France; Katy and Gary Leff, Calabasas, CA; and the European Research Council. Dr. Paz is the incumbent of the Beracha Foundation Career Development Chair.
 

 

 
 
 
we all smile
Life Sciences
English
  • Amygdala
  • Autism
  • Learning and memory
  • Neuron
  • Rony Paz

An Atlas for Cells

English

 

Michal Breker and Dr. Maya Schuldiner
 
Where do proteins go when they move around the cell? Interested scientists will now be able to look up the answer. Dr. Maya Schuldiner and graduate student Michal Breker of the Molecular Genetics Department recently produced a comprehensive atlas of changes in yeast proteins’ localization and abundance under stress that presents a wealth of new information. This atlas, which they are making available online, is likely to become an important tool for the many scientists who use this model research organism to investigate the workings of living cells.

Schuldiner and Breker began with a different kind of reference work: a strain library. Strain libraries hold sets of cells with specific genetic alterations. Bakers’ yeast cells contain some 6000 different genes, each encoding a protein. In each “volume” of their library, one “bookmark” has been created – a gene has been modified such that a particular protein is tagged with a fluorescent “highlighter” molecule that glows under a special microscope. In Schuldiner’s lab, using a state-of-the-art, automated microscopy system, researchers can examine an entire strain library at once. Other types of libraries exist, as well, including those in which each gene, in turn, has been removed. Libraries can even be mixed and matched to create new combinations. A robotic search then scans the entire set to find out which proteins are active in any given experimental situation.  
 
 
This unique set-up enabled Schuldiner and Breker to track protein movement – one of the “big” questions in cell biology. Knowing where proteins go, says Schuldiner, can help to answer a number of important research questions: “How many of the cells’ proteins are mobile? Under what conditions? How does the cell use this protein mobility to remain healthy and divide under a variety of different conditions?”

Subjecting the yeast cell libraries to various conditions and putting them through the robotic system, the researchers were able to trace the movements of each protein in the yeast cell. The result: a complete, detailed map describing protein routes, as well as a record of the amounts of each protein produced in the different situations.

A bird's-eye view of the data presents a picture of constant bustle in the cells. At any one time, hundreds of proteins are in transit. But the numbers the researchers collected on protein amounts held some real surprises. In much of today’s research, protein levels are inferred from experiments that actually check the production of messenger RNA (the instructions sent to the cell’s protein factories) – something like using building plans rather than actual buildings to map a town, when those plans can be shelved or reused for the next housing development. In tracing the proteins themselves, Schuldiner and Breker revealed that messenger RNA and true protein quantities don’t always match. Schuldiner: “Many beautiful works have already shown that protein production is regulated in many different ways after the RNA leaves the nucleus. Our findings hint that some of the later stages may be more significant than we thought in determining protein levels.”
Yeast cell atlas: image by Michal Breker
 
The online atlas is named Loqate (LOcalzation and Quantization Atlas of the yeast proteome). Schuldiner: “The atlas can be used by those seeking answers to such specific questions as: Which proteins are involved in a particular cellular activity, and when and where do they act? In addition, those who want to integrate different kinds of information to attain a more comprehensive picture of the cell’s life will find the atlas an indispensible aid.”

 

Checking all possibilities


The latest research methods have advanced molecular biology beyond the standard ABCs of research – formulating a hypothesis and then testing it through experiments. Using fast, powerful, completely automated equipment, much of it assembled according to Schuldiner’s specifications, she and her research team can now check all of the possibilities and extract the significant data. “With these tools, our research can be totally unbiased,” she says. “If we once started with an educated guess – say, ‘A affects B’ – and then tried to confirm our conjecture experimentally, we can now ask: ‘Which proteins are involved in B’s activity?’ In this way, we might find that G, L and M also act on B. And if a doctoral student formerly spent the whole of his or her studies checking that hypothesis, he or she can now get answers in a matter of weeks.”

 
Dr. Maya Schuldiner's research is supported by the European Research Council; the Berlin Family Foundation; James and Ilene Nathan, Beverly Hills, CA; the Minna James Heineman Stiftung; the Enoch Foundation; Roberto and Renata Ruhman, Brazil; Karen Siem, UK; and the Kahn Family Research Center for Systems Biology of the Human Cell.


 

 
 
Yeast cell atlas: image by Michal Breker
Math & Computer Science
English
  • Cell
  • Maya Schuldiner
  • Microscopy
  • Molecular Genetics
  • Protein

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