The Body Electric

English

Prof. Eitan Reuveny. Ion channels

 

 

A brilliant flash of lightning streaks across the evening sky followed by a sharp crack of thunder. As you rush upstairs to close the bedroom window, the millions of cells making up your heart muscle continue their endless task of contracting and relaxing in concert, guided by a small group of conductor cells. You then turn up the heater, relishing the wave of hot air as it meets your skin.


Electricity is everywhere: in nature, appliances and the human body. A steady heartbeat, mental processing, the perception of sounds, sights and temperatures - all depend on meticulously orchestrated cellular communication pathways linked up through electrochemical signaling.


One of the body’s primary communication pathways consists of a tiny pipe located in the cell membrane that opens to allow ions (electrically charged atoms) to flow into or out of the cells according to specific signals. These pipes, known as ion channels, are “motivated” to open by electrical differences existing between a cell’s internal and external environment.
Cells maintain an electric charge that is negative relative to their external environment. When these channels open, this difference in energy propels positively charged ions through the channel, triggering a variety of cellular processes.


Most channels allow the passage of only one type of ion. Yet how do different channels open and close? What enables them to act like bouncers at a club, selectively determining which ions (such as sodium, calcium or potassium) will enter or exit the cell?


Prof. Eitan Reuveny of the Institute’s Biological Chemistry Department is studying this cellular feat in potassium channels - key  ion channels affecting the electrical state of the heart, nerves and muscles.


Previous research had revealed that the potassium channel contains a selectivity filter that identifies and binds to potassium ions, filtering these ions from the intracellular solution. It does so with remarkable speed - tens of millions of ions are identified and travel through a single channel every second. The channel opens when an intracellular molecule, called a G protein, is activated, causing four of its subunits to rearrange themselves, thus permitting ion flow. The mechanism is similar to that of a door latch. Following activation, the G protein subunits bind to the channel, changing its formation in a way that essentially presses down a handle, pulling a door tongue inside and thus opening the channel.


To probe this “door-latch” mechanism, Reuveny is combining exciting new technologies from the worlds of biophysics and molecular genetics to do what was unthinkable just a few years ago: identify the tiny fluctuations of electric potential that occur within an individual cell. One of the technologies applied (which earned its developers, German cell physiologists Erwin Neher and Bert Sakmann, the 1991 Nobel Prize in Physiology or Medicine) is based on using microscopic glass pipettes a thousandth of a millimeter in diameter. By sucking in a tiny part of the cell membrane containing only one ion channel, the pipettes make it possible to measure the incredibly tiny current created as ions pass through.


Working with graduate students Rona Sadja, Karin Smadja, Noga Alagem and Inbal Riven, Reuveny began by introducing genetic modifications that in effect shortened the latch tongue, causing the channel to open even without G protein activation. Next, they tagged the channel with “reporter” proteins that lit up under certain optical conditions, making it possible to trace the actual movements of the channel latch.


Using this double strategy, the team succeeded in identifying the key molecular elements that open the potassium channel. Later research showed that these same elements also fulfill an important role in stabilizing the channel once it opens. The team’s findings were published in Neuron.


A better understanding of the rules governing potassium and other ion channels will clarify some of the most basic life processes. Insights into what goes wrong when cellular communication pathways break down may also lead to new therapies, from those targeting heart arrhythmia to diabetes and a range of neuronal disorders.

Opening the potassium channel

Potassium channels and diabetes


In related research, Prof.  Reuveny is studying how fluctuations in the electrical activity of potassium channels trigger a “shut-down” response that controls insulin release. Research in this field might lead to a new therapy for hypoglycemia - a complication of Type 1 diabetes occurring when elevated levels of insulin flow into the blood, causing glucose to drop to dangerously low levels.


Prof. Reuveny’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the Clore Center for Biological Physics; the Dr. Josef Cohn Minerva Center for Biomembrane Research; and the Buddy Taub Foundation.

 

 

Prof. Eitan Reuveny. Cell talk
Space & Physics
English

Live Footage of Enzymes

English

Thanks to a new method developed by the team of Prof. Irit Sagi of the Structural Biology Department, reality TV has reached enzyme molecules. They can now be viewed “live” in video clips. The clips’ resolution is so high that it is possible to see the movements of individual atoms within the molecule. Until now, scientists who studied the ultra-small enzymes had to rely on still photos. The pioneering method was published in Nature Structural Biology, where it was hailed as the first of its kind.

Apart from “putting enzymes on film,” the Weizmann Institute team was able to capture the step-by-step process an enzyme goes through as it performs its work. The entire process takes place in a fraction of a second. This new capability presents a huge step forward in the area of drug design, since it enables scientists to identify the precise parts of a molecule that are active in binding to a drug. Sagi’s team is doing just that for one enzyme family (called MMP), known to play a role in cancer metastasis. Using the knowledge gained by the new technique, the team has designed a molecule that blocks MMPs at a crucial phase. 

Prof. Sagi’s research is supported by the Avron-Wilstatter Minerva Center; the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly; the Ceil and Joseph Mazer Center for Structural Biology; the Cymerman-Jakubskind Prize; the Laub Fund for Oncogene Research; Prof. Clotilde Pontecorvo, Italy; and Verband der Chemischen Industrie.
Chemistry
English

Ancient Cast - New Production

English

Dr. Roy Bar-Ziv. Like an electrical circuit, but made of genes

 

Shaped through time, biological cells are the ultimate engineering systems, able to perform the most advanced information processing known. They also produce a wonderland of materials - from over 100,000 proteins to the materials they help build: skin, record-strong spiderwebs, horns and far more. The cell pulls off these feats in a tiny setting that engineers can only dream of. How do its systems work? Might they be harnessed to build superfast computers or advance new biotechnologies?


In a step that might help address these questions, a Weizmann scientist has now designed the first synthetic circuit able to process genetic input to produce proteins. The circuit works on the principles of a conventional electrical circuit - that of a flashlight, for instance - but is constructed entirely of genes, proteins and other biological molecules. “Our goal was to determine whether an assembly of these components could be made to operate outside the context of a living cell,” says Dr. Roy Bar-Ziv, of the Institute’s Materials and Interfaces Department, who performed the work with Prof. Albert Libchaber and Dr. Vincent Noireaux of Rockefeller University in New York.


The circuit built by the scientists floats in a biochemical “soup” containing the necessary ingredients and machinery for processing genetic information to produce proteins. The circuit inputs are genes (DNA molecules coding for proteins) which are “wired-up” so that the protein encoded by one gene can either activate or depress the production of neighboring proteins. The circuit design also uses an external sugar molecule that, functioning much like a biochemical switch, turns on the protein synthesis.


While other scientists have developed single-gene systems, this is the first time researchers have rigged up a multiple-gene circuit outside the cell. Though rudimentary, this synthetic circuit offers an isolated and thus highly controllable environment in which to explore the workings of the cell. Moreover, it may represent the first step to streamlined protein production plants or advanced biocomputers. Unlike conventional computer systems, in which information is processed through a rigid digital 0-or-1, yes-or-no framework, biological networks are able to plod toward their goal using the multi-branched routes characteristic of parallel processing. This inherent property, researchers believe, might significantly fast-forward computer processing.


But this won’t happen any time soon. The system’s DNA-to-protein reactions can take an hour or more, and it takes time until enough of the first material is produced to initiate the next stage. When too many stages are added to the sequence, the reactions tend to fizzle out as available resources are used up.


The next step, says Bar-Ziv, is to try to introduce circuitries of this sort into different materials. Once it is possible to create positive and negative feedback systems to turn things on and off, one could potentially design artificial circuits that mimic transistors, sensors, memory elements and clocks. “The gene is hardware and software all rolled up into one, and we need to learn to work with its unique properties,” says Bar-Ziv. “Scientists are busy trying to invent self-replicating nanotechnology, but why not use what already exists?”

 

Steps in the gene circuit

 


A different type of building


Dr. Bar-Ziv credits his current career track to his background in both theoretical and experimental physics (through M.Sc. and Ph.D. degrees completed at the Institute under Profs. Sam Safran and Elisha Moses, respectively), followed by a 3-year postdoc at Rockefeller University under Prof. Libchaber, where he focused on biological systems. The lab, says Bar-Ziv, is the best kind of work/playground he can imagine - where he can combine his fascination with the abstract questions of physics with his dream of building artificial biological circuits.


* Prof. Libchaber received an honorary doctorate from the Weizmann Institute in 2003.


Dr. Bar Ziv’s research is supported by the Clore Center for Biological Physics; the Sir Charles Clore Prize - the Clore Foundation; Sir Harry Djanogly, CBE, U.K.; the Philip M. Klutznick Fund for Research; the Levy-Markus Foundation; and the Lord Sieff of Brimpton Memorial Fund. He is the incumbent of the Beracha Foundation Career Development Chair.

 


 

Dr. Roy Bar-Ziv. Gene circuits
Space & Physics
English

Malaria's Achilles' Heel

English

 

Years of basic research into how crystals form have now proven relevant to probing the anti-malarial properties of common drugs.

 

Malaria is a leading killer. While mostly confined to sub-Saharan Africa, regions in Asia, and Central and South America, it infects an estimated 300 to 500 million people every year and kills between one and three million, most of them children under the age of five.

 

The new study, conducted by Dr. Ronit Buller and Prof. Leiserowitz of the Institute's Materials and Interfaces Department, as well as Dr. Matthew Peterson and Dr. Orn Almarsson of Boston-based Transform Pharmaceuticals Inc., has uncovered the precise mechanism by which common anti-malarial drugs zero in on their parasitic target. Like most living organisms, malaria parasites require amino acids and iron. They obtain them by penetrating the host's red blood cells, where they munch on the readily available hemoglobin (see box). The problem is that one of the byproducts of hemoglobin breakdown -  heme -  is toxic to the parasite. The parasite overcomes this by chemically modifying the heme and neatly packaging it into non-toxic crystals called hemozoin.

Prof. Leslie Leiserowitz. Drug action

 

Anti-malarial quinoline drugs function by inhibiting the growth of the hemozoin crystals, causing heme to accumulate in toxic amounts that ultimately kill the parasite. Although numerous studies have focused on this interaction, the crystal's micron-sized dimensions and poorly shaped surfaces impeded all efforts to determine the drug's precise mechanism of action.

 

Ronit Buller, at the time completing her doctorate at the Institute, came upon a key article by researchers who had succeeded in determining the structure of the hemozoin crystal, yet they too were unable to show how the drugs inhibit crystal growth. "She realized that this was an ideal project for our lab," says Leiserowitz. "The challenge also excited me for a personal reason -  I grew up in South Africa, where for years I witnessed firsthand the effect of quinine on my father, who took the drug on his work trips to the jungles of Central Africa."

 

 

Binding site revealed

 

Using computer software to calculate the shape of the hemozoin crystal, the team was able to identify the crystal's fastest-growing faces. One of these faces had a corrugated shape with a "tailored," nearly lock-and-key fit for docking quinoline drugs. The team then demonstrated that these drugs bind strongly to this face, inhibiting crystal growth.

 

Having unraveled the crystal's shape and its target binding site, the researchers were able to show why certain malarial drugs are more effective than others. Moreover, their study, published in Crystal Growth and Design, has provided a blueprint for designing improved drug therapies. One central idea is to increase the number of binding sites between the target crystal and each drug.

 

Commenting on the study, Dr. Robert Rubin of Harvard Medical School remarked: "Over the last decade, malaria has reemerged as one of the most widespread infectious diseases due to its resistance to the quinoline drug family. These findings are critical in providing us with better information on current drugs and the emerging resistance to them, as well as offering help in developing new drugs."

 

OUTSMARTING THE IMMUNE PATROL

 

The difficulty in combating the malaria parasite lies in its constantly changing form, which keeps it one step ahead of the human immune system. When an infected mosquito bites a human, it introduces the parasite, which spends only 30 minutes on average in the bloodstream before penetrating the liver – hardly enough time for the body to mount an effective antibody response. Once in the liver, each parasite invades a separate cell and begins to divide, producing thousands of parasites. The body’s immune T cells go to work at this point, but their response takes around 10 to 12 days, while the parasites are way ahead, taking only a week before they burst out of each liver cell, destroying it in the process. They then quickly invade red blood cells (which are not protected by killer T cells), where they start to break down the cell’s hemoglobin, gobbling up its amino acids. They continue to invade new cells and multiply furiously, resulting in millions of parasites.

Dr. Ronit Buller. Inspired by an article

 

Prof. Leiserowitz's research was supported by the Helen & Milton A. Kimmelman Center for Biomolecular Structure & Assembly; and the Joseph and Ceil Mazer Center for Structural Biology.

 

 
Prof. Leslie Leiserowitz
Chemistry
English

Blood Test for Smokers

English

Prof. Zvi Livneh and his research team. Low enzyme activity

 

Lung cancer is one of the most deadly malignancies, responsible for 30 percent of all cancer deaths. Most sufferers from the disease – about 90 percent – are smokers. Weizmann research has now yielded a new blood test that can detect smokers who are at especially high risk of developing the cancer.

 

Our DNA is damaged about 20,000 times a day by such factors as sunlight, smoke and reactions within the body. If left unrepaired, damaged DNA can lead to cancer. Fortunately, the body has a stock of enzymes whose function is to repair DNA. Upon detecting the damage, the enzymes "operate" on the DNA, replacing the damaged parts with new ones. The efficiency of these repair enzymes is thus critical for preventing cancer.

 

After years of research into DNA repair systems, Prof. Zvi Livneh and Dr. Tamar Paz-Elizur of the Biological Chemistry Department decided to concentrate on a specific DNA repair enzyme called OGG1 (8-oxoguanine DNA glycosylase 1). This repair enzyme deletes DNA parts damaged by toxic molecules (called oxygen radicals) found in tobacco smoke. By developing a new blood test that enables them to measure the level of OGG1 activity, the researchers found that 40 percent of lung cancer patients have low levels of OGG1 activity. This, in contrast to only 4 percent of the general population. "Only 10 percent of heavy smokers develop lung cancer," says Livneh, "and that suggested to us the involvement of a personal genetic susceptibility." In collaboration with Dr. Meir Krupsky of the Chaim Sheba Medical Center in Tel Hashomer, the scientists tested this theory in lung cancer patients.

 

Smokers still have higher risk

 

The findings, published in the Journal of the National Cancer Institute, show that smokers who carry a genetic marker signifying low OGG1 activity are around 5-10 times more likely to get lung cancer than smokers whose OGG1 activity is normal – and 120 times more likely than non-smokers who have normal OGG1 activity. (Smoking increases the risk, since it results in more damage to the DNA, and thus more work for the repair enzymes.)

 

Screening smokers for low OGG1 activity will help them make more informed decisions about smoking. Of course, even smokers with normal OGG1 activity are at greater risk of getting lung cancer than the general population, and the blood test will not ensure that they don't get the disease. In addition, smoking causes other types of cancer and cardiovascular diseases, whose relation to OGG1 activity is still unknown.

 

The Weizmann team also included Dr. Sara Blumenstein and Dalia Elinger. Statistical analysis was conducted by Dr. Edna Schechtman from Ben-Gurion University of the Negev.

 

 

 

Prof. Livneh's research was supported by the M.D. Moross Institute for Cancer Research; the Dolfi and Lola Ebner Center for Biomedical Research; the Levine Institute of Applied Science; and the Josef Cohn Minerva center for Biomembrane Research. He is the incumbent ot the Maxwell Ellis Professorial Chair in biomedical Research.

 

LUNG CANCER STATS

According to the American Lung Association:

  •  Lung cancer is the leading cancer killer in both men and women.

 

  • There were an estimated 164,100 new cases of lung cancer and an estimated 156,900 deaths from lung cancer in the United States in 2000.

 

  •  In most cases, the disease might have been prevented - nearly 90 percent of lung cancer cases are caused by smoking.

 

  •  Secondhand smoking is responsible for approximately 3,000 lung cancer deaths and as many as 62,000 deaths from heart disease annually.

 

  • When a person quits smoking, the risk of lung cancer decreases each year. Ten years later, the risk drops to one-third to one-half the risk for smokers.

 

  •  In addition, quitting smoking greatly reduces the risk of developing other smoking-related maladies, such as heart disease, stroke, emphysema and chronic bronchitis.

 

  •  Radon is considered the second leading cause of lung cancer in the U.S. today, with 12 percent of all lung cancer deaths linked to radon. The EPA estimates that nearly one out of every 15 homes in the U.S. has indoor radon levels at or above the level at which homeowners should take action - 4 picocuries per liter of air (pCi/L) on a yearly average. Exposure to radon in combination with cigarette smoking greatly increases the risk of lung cancer.

 
Clockwise from bottom left: Dr. Meir Krupsky, Dalia Elinger, Dr. Edna Schechtman, Dr. Tamar Paz-Elizur, Dr. Sara Blumenstein, and Prof. Zvi Livneh. Calculated risks
Life Sciences
English

Lord of the Ring

English
 
Prof. Avi Minsky. The trick of survival
 
Solving a longstanding mystery, Weizmann Institute scientists have found what makes a certain bacterium the most radiation-resistant organism in the world. The microbe’s DNA is packed tightly in a unique ring-like structure, which keeps pieces of DNA broken by radiation in close enough proximity for repair to occur.
 
The red-colored bacterium Deinococcus radiodurans can withstand 1.5 million rads – 3,000 times more than humans. Its healthy appetite has made it a reliable worker at waste sites, where it eats up nuclear waste, transforming it into safer derivatives. The ability to withstand other extreme stresses, such as dehydration and low temperatures, makes the microbe one of the few life forms found on the North Pole. It’s not surprising, then, that it has been the source of much curiosity worldwide, with Russian scientists proposing that it originated on Mars, where radiation levels are higher.
 
DNA is the first part of a cell to be damaged by radiation. The most lethal damage is the breakage of both DNA strands. While most cells, including human cells, can mend only a few such breaks in their DNA, D. radiodurans can fix more than 200. This outstanding performance caused scientists to believe that the microbe must possess uniquely effective DNA repair enzymes; yet a series of experiments found that the microbe’s repair enzymes were very similar to those in ordinary bacteria.
 
Using an assortment of optical and electron microscopy methods, Prof. Avi Minsky of the Institute’s Organic Chemistry Department has now shown that the microbe’s resilience lies in the unique ring-like structure containing its DNA, which, following radiation damage, holds severed pieces of DNA closely together, allowing for repair. This is in contrast to most other organisms, where radiation breaks the DNA into fragments that float off into the cell’s liquids and are lost. 
 
“Exciting as these findings may be, I don’t expect them to boost the protection of humans from radiation. Our DNA is structured in a fundamentally different manner,” says Minsky. “The results may, however, lead to a better understanding of DNA protection in sperm cells, where a ring-like DNA structure has also been observed.”
 

More survival tricks

 

Minsky’s team also found that the microbe undergoes two phases of DNA repair. During the first phase the DNA repairs itself within the ring as described. It then performs an even more unusual stunt.
 
The bacterium is composed of four compartments, each containing one complete copy of DNA. Minsky’s group found two small passages between the compartments. After roughly 90 minutes of repair within the ring, the DNA unfolds and migrates to an adjacent compartment – where it mingles with the copy of DNA residing there. At this point, “regular” DNA repair enzymes, common in humans and bacteria alike, kick in. To complete the mending process, the enzymes compare the two copies of DNA, using each as a template to repair the other. 
 

…and a backup system

 

Their finding of a tightly packed ring made the team wonder how the bacterium manages its everyday tasks – including protein production, for which its DNA must first unfold. How, they asked, can the microbe do this if its DNA can barely budge? This question led to the uncovering of yet another of the microbe’s survival strategies: Of the four copies of DNA, there are always two (or sometimes three) tightly packed in a ring while the other copies are free to move about. Thus at any given moment, there are copies of DNA that drive protein production and others that are inactive but continuously protected.
 

Deinococcus radiodurans. rings give protection

D. radiodurans was discovered decades ago in canned food sterilized by using radiation – setting off questions as to how it could have survived. Though these questions have now been answered, the tide of speculation as to how these defense mechanisms evolved – and where – is likely to continue.
 
Minsky, along with other scientists, believes that the bacterium’s answer to acute stresses evolved on Earth in response to a harsh environment. The very same mechanism enabling it to fight dehydration and thus survive in some of the planet’s most inhospitable deserts also protects it from the destructive effects of radiation.
 
Prof. Abraham Minsky is the incumbent of the Professor T. Reichstein Professorial Chair. His research is supported by the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly; TEVA Pharmaceutical Industries Ltd.; and the Verband der Chemischen Industrie.
 
Deinococcus radiodurans
Chemistry
English

Sperm on the Egghunt

English
 
Left to right: Ph.D. students Anna Gakamsky and Anat Bahat, Prof. Michael Eisenbach. Obstacle course
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Sperm have much in common with the heat-guided missiles used to track down planes and other military targets, a new Weizmann Institute study suggests.
 
The site where the egg lies is slightly warmer than the place where sperm pause during their journey through the female reproductive tract. This temperature difference apparently guides sperm in their navigation. The study, headed by Prof. Michael Eisenbach of the Institute’s Biological Chemistry Department and reported in Nature Medicine, may improve future IVF treatments for couples finding it difficult to conceive.
 
After passing through the womb, sperm cells enter the fallopian tubes. Once inside a tube, they attach themselves to the tube’s wall and pause for “storage,” during which they go through a maturation process that prepares them for penetrating the egg. A sperm cell that has completed this maturation process detaches itself from the wall and leaves the storage site.
If ovulation has taken place in the preceding 24 hours, releasing an egg ready to be fertilized, the mature sperm embarks on a long, complicated journey through the tube to the site of potential fertilization.
Egg and sperm meet in the middle of the fallopian tube
How does the sperm steer a course through the fallopian tube? In earlier studies, Prof. Eisenbach discovered that the egg “calls” the mature sperm by releasing a chemical substance. However, the chemical signal can attract the sperm only across a short range; since the tube normally moves in a wavelike fashion, the chemical apparently cannot spread effectively through the entire tube and therefore cannot signal the sperm over longer distances. This chemical attraction mechanism, known as chemotaxis, cannot therefore explain the sperm’s entire journey.
 

Some like it hot

 

Guided by the knowledge that the sperm storage site is about 2 degrees C cooler than the site of fertilization, Eisenbach and his team – Ph.D. students Anat Bahat and Anna Gakamsky, Dr. Ilan Tur-Kaspa from the Barzilai Medical Center in Ashkelon and visiting Argentinean scientist Dr. Laura C. Giojalas – hypothesized that sperm may be attracted to the fertilization site by a difference in temperature. The technical term for such attraction is thermotaxis.
 
To test this theory, the team built a model of the fertilization process consisting of the sperm storage site, the area where fertilization takes place and the tube in between. They then heated the sperm storage site to a temperature of 37 degrees C (98.6 degrees F) and the fertilization site to the slightly warmer temperature of 39 degrees C (102.2 degrees F), and checked the effect of this setup on the behavior of rabbit sperm. 
 
The findings were clear: The rabbit sperm were indeed sensitive to heat and moved quickly to the warmer fertilization area. On gradually reducing the difference in temperature, the scientists found that even a half-degree difference was enough to attract the sperm. Moreover, they found that only mature sperm – those most likely to penetrate the egg – are heat sensitive.
 
“Apparently, sperm are guided by temperature in their travels through most of the fallopian tube,” says Eisenbach. “Only when they near the fertilization site do they navigate by tuning in to the egg’s chemical call.”
 
The team’s findings were replicated in further research with human sperm, conducted in collaboration with Prof. Haim Breitbart of Bar-Ilan University.
 
Prof. Michael Eisenbach is the incumbent of the Jack and Simon Djanogly Chair of Carbohydrate Biochemistry.
 
 
Left to right: Ph.D. students Anna Gakamsky and Anat Bahat, Prof. Michael Eisenbach. Obstacle course
Life Sciences
English

Letters to the Genetic Editor

English
Profs. Ruth and Joseph Sperling. Stop and cut signs
 
 

 

Editors are a ruthless breed. They take a text the writer worked hard to produce, then heartlessly cut and paste, sometimes taking out entire paragraphs. All this is done for "editorial reasons"that no one can quite define. But the truth is, the editors are not to blame. They are simply following rules similar to those found in the most fundamental processes of nature, such as the transfer of genetic information from the cell's nucleus to other parts of the cell, where it is put to use.

For many years, biologists believed such information was meticulously preserved. With time, however, it became clear that on its way from the genes to the ribosome (the cellular structure that reads the information and uses it to manufacture proteins) the genetic text undergoes comprehensive editing. An understanding of this "editorial process"may help to clarify the factors involved in the development of various genetic diseases.

In the early 1960s, scientists believed that protein manufacture began when the closely intertwined double strands of DNA in the cell's nucleus unfurled, leading to the production of a new single strand (messenger RNA), which contained a "photocopy"of the genetic code. This strand traveled from the nucleus to the ribosomes in the cell, which then read the code and created proteins.
 
While this chain of events is true for bacteria, the picture is much more complicated in higher organisms. The American scientist Phillip Sharp and his British counterpart Richard Roberts discovered the existence of intermediate processes that resemble the way texts are edited and proofread before appearing in print. They found that the messenger RNA molecule was not a faithful copy of the DNA from which it was derived. There is a "pre-messenger" RNA molecule that indeed copies the DNA precisely, but some of its parts are cut out. The remaining parts come together and cling to one another, creating a "new genetic order," the messenger RNA molecule.

It later became clear that the removed parts, called introns -  those tossed to the "cutting room floor"-  carry no information for building proteins. The remaining parts, called exons, are the ones that, by connecting to one another, create the "real" genetic sequence that encodes the information needed to build the protein. Sharp and Roberts were awarded the 1993 Nobel Prize in Physiology or Medicine for their work.


End quote


But how can nature tell apart the exons, which contain the genetic information, from the introns, which carry irrelevant text? A once prevalent view was that each intron begins with a sequence of eight genetic letters, a command saying "end quote"or simply, "cut here!  "Later, however, it became clear that many such commands -  the same eight letters in the same order -  appear inside the introns themselves as well. In other words, the genetic "cut!" command also appears in many places where a cut would cause the creation of a defective, potentially toxic, protein. How then does nature distinguish between the "cut! "commands that must be executed and the "cut!" commands that should be ignored?

This is where Prof. Joseph Sperling of the Weizmann Institute of Science's Organic Chemistry Department and his wife and colleague Prof. Ruth Sperling of the Hebrew University of Jerusalem's Genetics Department enter the picture. Together with their teams, the Sperlings discovered that the undesirable "cut!" command is preceded by one of three three-letter genetic sequences: TAA, TAG, or TGA. These sequences function as genetic "stop signs." The scientists propose that the appearance of one of these stop signs, together with an eight-letter "end-of-quote" sequence, cancels the cut command. The scientists tested their hypothesis in a computer model using 446 human genes and found that in the vast majority of cases (98%) one of the stop signs appears before the eight-letter end-of-quote sign in places where cutting would lead to the production of toxic proteins.

In a series of experiments conducted to test this discovery in human tissue culture, the scientists placed one of the stop signs in various locations in the genetic code before a natural end-of-quote sequence. By so doing, they prevented the cutting that would have normally taken place. In a complementary series of experiments, they managed to perform the opposite process: They removed the natural stop sign, causing cuts to occur in places where they would not normally have taken place. Their findings were published in the Proceedings of the National Academy of Sciences (PNAS). The research team included postdoctoral fellow Dr. Binghui Li and graduate students Chaim Wachtel and Elana Miriami of the Hebrew University and graduate student Galit Yahalom of the Weizmann Institute.

Until now, most scientists believed that systems capable of deciding where to begin reading a strip of genetic information (such as the ribosome) existed only outside the nucleus. The Sperlings'findings, however, suggest that this kind of discretion (called the recognition of a "reading frame") takes place inside the nucleus as well. They have shown that the decision where to cut and paste introns and exons in pre-messenger RNA relies on an earlier choice regarding where the reading process begins. These unexpected findings are becoming the focus of numerous new studies in this field.
 

Finding the "stop" sign

Prof. Joseph Sperling's research is supported by Ms. Lois Zoller, Chicago, IL; Ms. Ruth Simon, Wilmette, IL; the Oscar and Emma Getz Trust, Chicago, IL; the Joseph and Ceil Mazer Center for Structural Biology; and the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly. He holds the Hilda Pomeraniec Chair of Organic Chemistry.

 
Life Sciences
English

DNA Trafficking

English

Dr. Ziv Reich. Gene smuggling

 

 

 

Though one thousand warrior-filled ships were sent to the ancient city of Troy, the city's layout and impregnable walls saved it from conquest. The turning point, as related in Homer's Iliad, was the famous scheme devised by a shrewd Greek strategist.


The task of gene therapists is no less challenging. Armed with beneficial genes, the tools for the potential recovery of ailing patients, gene therapists must navigate them to the appropriate cells within a ten-trillion-cell body. The scientists then have to pass two barriers: They must smuggle the genes first into these cells, and then into the cell's inner sanctum, the nucleus, which houses the genetic material. Having tackled the first barrier, scientists are now pondering how to overcome the second. The nucleus's "walls"are lined with "sentries"that keep a watchful eye out for anything peculiar. 


At first, viruses seemed well suited to the task because that is exactly what they have been doing for billions of years - penetrating the walls of the cell nuclei to maintain and propagate their genetic material. By replacing the harmful parts of their genetic material with genes intended to help treat a disease, scientists had hoped to use engineered viruses as delivery vehicles.  


However, this method proved problematic: The viruses were sometimes toxic, induced immune and inflammatory responses, and even turned off healthy genes, including genes that suppress tumor growth. And as if that weren't enough, these engineered viruses sometimes underwent mutations that equipped them with additional damaging properties.


As a result, scientists began to experiment with synthetic systems, which are safer than viruses and provide better control. But while scientists could sneak DNA into the cell using these methods, they were usually unable to effectively transport DNA into the nucleus. Past attempts succeeded only in slipping an "unreadable,"and therefore ineffective, form of DNA into the nucleus. (DNA contains genes, which must be "read"to produce the proteins they encode.) And even those attempts were too costly to render gene therapy practicable.


This is where Dr. Ziv Reich of the Weizmann Institute's Biological Chemistry Department and his team came in. They crafted a method for smuggling DNA through the walls of the nucleus under the very noses of the cell's guardians. The method bears an uncanny resemblance to the Trojan horse.


Finding a camouflage


There are two main routes into the nucleus. Molecules less than 8-9 nanometers (one nanometer is a billionth of a meter) in diameter can pass freely through its large pores. Larger molecules, however, must possess special "papers"-  called nuclear localization signals (NLSs) -  which DNA molecules, around 10 nanometers in diameter, don't carry.


To overcome this problem, Reich's team devised an approach in which DNA hitchhikes on a protein that does possess NLS. Reich modifies DNA to include specific binding sites for these proteins, which then transport the DNA into the nucleus, where it is "read."The bound proteins pose no obstacle to the reading process since their natural function is to bind to DNA inside the nucleus. Such modifications can be made readily, accurately, and inexpensively.


In addition, this study contains an unexpected twist. Since a variety of proteins in the cell possess NLS, Reich's group had to decide which family of proteins would play host to the hitchhiking DNA. "We chose the NFkB family,"says Reich, "because they bind strongly to DNA and are inducible, meaning that we can control their entry into the nucleus by sending special signals to the cell."


The NFkB family of proteins proved even more promising than anticipated. While Reich was studying their potential as DNA transportation vehicles, these proteins were discovered to play a central role in several autoimmune diseases, such as asthma and atherosclerosis, as well as in certain types of blood cancers -  especially Hodgkin's disease, a common lymphoma. Whereas NFkB proteins normally enter the nucleus only when an appropriate signal is received, in Hodgkin's cells, they continually shuttle back and forth between the diseased cell's nucleus and its cytoplasm.


This distinction, believes Adi Mesika, one of Reich's doctoral students, could be used to induce Hodgkin's cells to destroythemselves. DNA that contains instructions for self-destruction could infiltrate the nucleus, piggybacking on aberrant NFkB proteins. Since NFkB proteins would not enter the nucleus of healthy cells, onlydiseased cells would self-destruct. This ability to preferentially destroy Hodgkin's cells will soon be investigated in collaboration with physicians on cells obtained from patients diagnosed with this disease.


In parallel to the NFkB approach, another of Reich's students, Saroj Shekhawat, is looking for other proteins that can do the job. The aim, explains Shekhawat, is to find proteins that are specific to certain tissues or organs, or proteins that are active in disease, allowing the targeting of DNA to ailing cells. "We are also looking for proteins that will condense the DNA, making it smaller and therefore easier to import through the nucleus's channels,"he says.


If successful, Reich's special delivery service might be an important factor in developing future gene therapies.

Come into my cell

 

Dr. Reich's research is supported by the Levine Institute of Applied Science; the Clore Center for Biological Physics; the Kekst Family Center for Medical Genetics; the Avron-Wilstaetter Minerva Center for Research in Photosynthesis; the Molecular Imaging Corporation, Phoenix, AZ; Ms. Lois Rosen, Los Angeles, CA; and Teva Pharmaceuticals, Israel. He holds the Abraham and Jennie Fialkow Career Development Chair.

 

 

 
 
 
Dr. Ziv Reich.
Life Sciences
English

Natural Selection in the Lab

English
Dr. Dan Tawfik. Evolution in the making
 
 

 

Closely watching over a complex soup consisting mainly of genes, Dr. Dan Tawfik adds a generous dose of oil. What emerges is a vast array of tiny suspended water droplets. It is in these droplets -  holding one gene each -  that he hopes to find answers to some of the most fundamental questions of life.

"What dictates natural selection and evolution?"asks Tawfik, of the Weizmann Institute's Biological Chemistry Department. "Take proteins, the basic building blocks of our body. In theory, there could exist 2050 variations of the shortest proteins we know of, not to mention the longer ones. If all possibilities were realized, the proteins would weigh more than our entire planet. How does nature choose a select few?"

The answers to these questions had been sought by scientists long before Tawfik came on the scene. Their research, however, was conducted with living cells, which posed many problems. Cells contain countless factors that could influence research results. In addition, the kinds of forces driving selection that can be tested in living cells are limited.

Tawfik, who studies enzymes (proteins that catalyze critical processes in the body), found an original solution: He constructed simplified cell models in which the only unknown is the selection process. His method, developed in collaboration with Dr. Andrew Griffiths of the Laboratory of Molecular Biology in Cambridge, England, promises to revolutionize research in this field. It enables researchers to scrutinize many billions of samples in a single experiment, compared to a mere one thousand to a million using standard techniques.


The recipe

 
How is this done? Tawfik: First, decide what new traits your evolved enzyme should have. Then, for raw material, take an existing enzyme (without the desired traits). Make myriad copies of the gene behind the production of that enzyme, deliberately causing many mutations in the process. The logic behind this step is that at least one of the mutated genes will produce an enzyme with the desired traits. Add the supplies the genes would need to produce an enzyme and, mixing them with oil, create an emulsion (the droplets -  or simplified "artificial cells"-  each contain one gene and the essential supplies needed to produce an enzyme). Use a chemical process, also crafted by Tawfik, to ensure that the only genes surviving the emulsion are those that undergo mutations leading to the creation of the desired new enzyme. The others will be destroyed or washed away.

The next step is to see how the selected genes evolve. Choose the most efficient genes surviving the emulsion process and again make many copies of them, adding the supplies they need to produce an enzyme. Add oil, again producing an emulsion. Repeat the whole process of mutation and selection of the efficient genes. After many such cycles, highly evolved genes will emerge. These can direct the manufacture of fast, effective enzymes. The improvement in rate can be by a factor of many millions.


Evolution in takes


"Since this is a multistage process,"says Tawfik, "we can see evolution in the making, which is very important. Take two photos -  one of a baby and another of that person as an adult -  and you may not be able to tell that they are both the same person. However, if you have a series of pictures in between -  of the baby developing into a young boy and then into a young man -  you can link one to another and gain an understanding of how the outcome was reached."


Flexibility pays off


Some of Tawfik's findings point to a possible answer to the original question -  why certain proteins are chosen over others -  as it pertains to enzymes. It seems that nature may prefer enzymes that have the capacity to be jacks-of-all-trades.

Enzymes are known for their specificity -  they bind to specific materials to make a product. Tawfik found, however, that some enzymes can inadvertently perform other tasks. "The tasks may not be performed with great efficiency and might not even be apparent under normal conditions, but the fact that the capability exists and could, if needed, help the organism survive, makes these enzymes preferable and provides a vital springboard for the evolution of new enzymes."

In the years to come, Tawfik's method, which mimics the great driving force of evolution, might offer the opportunity to harness nature to yield a wide range of valuable new enzymes with important applications in chemistry, biotechnology, and medicine. And, equally captivating, it might also reveal the story of evolution, enhancing our understanding of how nature's expert machinery has evolved.
 

Emulsion for rapid gene analysis

Dr. Tawfik's research is supported by the Henry S. and Anne Reich Family Foundation, Washington, DC; the Estelle Funk Foundation, South El Monte, CA; Yad Hanadiv, Israel; the Harry and Jeanette Weinberg Fund for the Molecular Genetics of Cancer; and the Dolfi and Lola Ebner Center for Biomedical Research. He holds the Elaine Blond Career Development Chair.

 

 
Emulsion for rapid gene analysis
Life Sciences
English

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