By Rob Mitchum

Treating a brain tumor in a lab dish is easy. Scientists have developed a full arsenal of treatments to kill tumor cells, using natural toxins, chemotherapeutic drugs, and even gene therapy to send them to an early grave. But making those therapies work in the actual setting of the brain is a much different ballgame. The first major challenge is even delivering the therapy to the right place, as any drug must get past the brain’s defense systems and navigate the organ’s complex architecture. In addition, the therapy must be a picky killer, eradicating tumor cells while leaving the healthy brain cells intact.

Researchers are therefore searching for a smarter delivery system that can maximize the effectiveness of these brain tumor therapies, collaborating with experts in the world of chemistry, materials science, and engineering. Bakhtiar Yamini, an assistant professor of surgery at the University of Chicago Medicine, is collaborating on one such effort with a biotechnology company in Nebraska, targeting the most difficult malignant brain tumors Yamini sees in his neurosurgery practice. By designing a new nanoparticle “shell” capable of selectively targeting therapeutics to brain tumor cells — and capable of being watched as it travels through the brain — the research team hopes to make eradicating these cells in their native environment as simple as killing them in a dish.

“Even though new therapies are being developed that can kill cells in culture, getting them into the brain tumor is a big problem, so development of a vehicle is an important step,” Yamini said. “People have previously used both targeting and image guidance in the treatment of other cancers, but bringing these two strategies together in one vehicle is something that would be really useful.”

In Phase I of their NIH-funded project, Yamini and collaborators at LNKChemsolutions developed a nanoparticle made from materials such as polylactic acid and polycaprolactone. Despite the complicated chemical names, these materials are commonly used in biodegradable products — a feature that offers an advantage over other nanoparticles made from gold, titanium, and other metals. The nanoparticles are also customizable, able to carry a variety of therapeutics and different targeting signals, and incorporate a metal, iron oxide, that allows doctors to visualize the nanoparticles’ travels using MRI technology.

For Phase II of the project, funded late last year, the team is taking their technology to animal models. A nanoparticle designed to target a protein called the EGF receptor (often overexpressed by tumor cells) and deliver the chemotherapy drug temozolomide will be tested in mice and rats that have brain tumors. If those experiments are a success, the team will try the therapy on a larger animal model: dogs. Partnering with veterinary clinics in Chicago and Minnesota, the researchers will offer the treatment to pet owners willing to volunteer their sick dog for a cutting-edge therapy.

“That’s how we will develop the treatment, but at the same time it should be effective at helping the dogs,” Yamini said. “It’s essentially a clinical trial for dogs that have brain tumors, and because their tumors are very similar to human ones, the results in the dogs will have relevance to humans.”

Because of the blood-brain barrier, which prevents most molecules from passing from the body’s blood supply into the brain, just injecting the nanoparticles into a vein won’t work. Directly infusing particles into the brain during surgery to remove the tumor is possible, but the spread of particles by that method can be unpredictable and may miss the target. Instead, Yamini will use a method known as convection enhanced delivery to push the nanoparticles very slowly into the desired area of the brain, squeezing them through the space between brain cells. The iron oxide tags will allow surgeons to monitor the path of the nanoparticles by MRI as they are being infused through the brain.

“The image guidance is a big factor, because ‘blind’ infusion of the nanoparticles can be problematic,” Yamini said. “If you plan to treat the upper right corner and you see, on MRI, that the infusion actually went to the lower left, you can put your catheter back in and try again. This paradigm of ‘adaptive image guidance’ allows you to adjust subsequent treatments to target the areas that were missed on the original injection.”

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Roughly 30 million Americans suffer from migraines, and as you might expect, there’s a large pharmaceutical market to prevent or stop these debilitating headaches. Drugs such as Imitrex and Verapamil employ different pharmacological modes of action, reducing migraines by adjusting neurotransmitter levels, blocking ion channels, or simulating the body’s natural painkillers. There’s also a less pharmaceutical migraine treatment strategy, recommended by many headache specialists, that follows the old adage: “Active Body, Active Mind.” One recent study even found that 40 minutes of exercise three times a week can be as effective at preventing migraines as popular anti-migraine medications.

Still, prescribing exercise or environmental enrichment (keeping the mind busy through activities such as reading, crossword puzzles, exercise, or socialization) can strike some doctors and patients as frustratingly vague. Understanding the biological mechanism that makes these activities protective against migraines could help convince doctors and patients of their utility, while also giving researchers the opportunity to translate the factors associated with environmental enrichment into highly effective treatments.  In the laboratory of Richard Kraig, William D. Mabie Professor in the Neurosciences at University of Chicago Medicine, that very effort is underway.

“We are interested in environmental enrichment as a way to stop cognitive decline from aging, injury after stroke, Parkinson’s disease, and cell death after seizures.  With our new work, we apply this search for how the brain protects itself against disease to include migraines,” Kraig said.  ”The ‘why’ of it has sometimes been left in the realm of holistic medicine, with little scientific support.  So establishing the hard science makes it more credible to the psychologists, physiologists, physiatrists, because here’s the chemistry.”

Working with graduate students Yelena Grinberg and Aya Pusic as well as senior technician Heidi Mitchell, Kraig discovered three different natural signals elevated by exercise and environmental enrichment: insulin-like growth factor-1 (IGF-1), interleukin-11 (IL-11), and interferon gamma (IFN-γ). When these “cytokines” are applied to brain slices, they reduce the probability of triggering a spreading depression — a transient wave of reduced brain activity associated with migraines. Understanding how those cytokines stop spreading depression — and the nasal route by which they might be delivered — may revolutionize how migraines and other neurological conditions are treated.

A spreading depression of brain is a chain reaction of dramatic events. After an initial burst of increased neuronal activity, a subsequent ripple of absent activity slowly spreads across involved brain at a rate of about 3 mm per minute — lasting a few minutes overall.  While the event sounds brief, the consequences can last from hours to days, causing harmful oxidative stress, elevated inflammatory factors, moving microglia, and significant pain and discomfort for the migraine sufferer.

Paradoxically, the way to stop this chain reaction may not be to simply reduce or block the byproducts of a spreading depression, but to expose the brain to moderate levels of inflammatory factors, which include the cytokines described above. To interrupt the cycle of repeated migraines, treatments could take place before the process begins or in small steps after the recurrent spreading depression that underlies chronic migraine. While these factors may have negative effects in the short-term, in the long-term they prime the neurons to make antioxidants that are protective against oxidative stress.

“Spreading depression increases oxidative stress in a big fashion — it depolarizes all the brain cells. It’s like an engine kicking out a lot of exhaust, and the exhaust makes the brain hyper-excitable,” Kraig said. “But you have to let the engine run. The engine is running with stimuli that include cytokines that are initially irritative, but then adapt to stop spreading depression.”

The trick, Kraig said, is to mimic the natural cycles of cytokine levels the brain would experience during healthy, active behavior, rather than drowning the system in abnormally high concentrations of the factors that can occur with disease. The cytokines would be delivered to the brain in an on/off pattern rather than chronically, theoretically recreating the rise and fall of natural cytokines during a person’s sleep/wake cycle. By giving just a little bit of a factor normally considered harmful, the treatment could strengthen the brain’s resistance to spreading depression and migraines via the principle of hormesis, or “what doesn’t kill me makes me stronger.”

“The treatment is unique in that it’s the opposite of putting a Band-Aid on something,” Grinberg said. “It’s triggering cells to produce their own antioxidants instead of just providing the antioxidants exogenously. In that way it’s really unique and the opposite of how a lot of people think about medical treatment.”

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All of the animal life on Earth, including human beings, can be traced back to a unicellular ancestor somewhat similar to the modern-day protozoa. In one sense, the hundreds of millions of years of evolution is the story of how organisms became more and more complex, growing from a single cell to trillions of highly specialized cells forming different organs and tissues in a single body. Yet while you could easily tell a protozoa from a human in a police lineup, cells from the two species are made up of many of the same proteins, performing similar jobs. What changed to produce these profound differences in complexity?

One potential area where this complexity may have bloomed is tyrosine phosphorylation, a key cellular signal for pathways that control cell growth, proliferation, and structure. Enzymes called tyrosine kinases add a phosphate group to a wide range of cellular targets, which can act like a light switch, turning their function on or off. The phosphorylated proteins are recognized by another group of proteins with a special “sensor” called the SH2 domain. Because tyrosine kinases will promiscuously phosphorylate many targets in the cell, the very picky SH2 domain proteins are responsible for sorting out the noise.

“Tyrosine kinases tend to be not that selective,” said Piers Nash, assistant professor in the Ben May Department of Cancer Research at the University of Chicago who studies this system. “They’ll phosphorylate a lot of things, and that creates all of these docking sites for SH2-domain-containing proteins. It’s really up to the SH2 domains to interpret those signals and convert them into downstream signaling pathways.”

The more complex the cell, the more unique types of SH2 domains that are needed to perform this important sorting function. In the unicellular cousins of animals, organisms can get by with just a single SH2 domain. But in humans, some 121 SH2 domains are known to exist, managing many different pathways in many different cells. In two recent papers, Nash’s laboratory studied how these SH2 domains manage their impressive selectivity and the evolutionary pathway that they took from simple protozoa to complicated human.

It’s essential that SH2 domains only bind to the right phosphorylated protein — repeatedly screwing up and activating the wrong pathway could lead to diabetes, cancer, or worse. But scientists have struggled to figure out how SH2 domains choose their appropriate target, with some even concluding that they aren’t so selective at all, merely in the right part of the cell at the right time to only bind the correct protein. However, that wasn’t what a research team led Bernard Liu from Nash’s laboratory found when they looked at how SH2 domains bind actual cell targets such as the insulin receptor.

“It turned out that the SH2 domains were exquisitely selective, much more selective than the general motifs for the SH2 domains that had previously been mapped,” Nash said. “So it was clear there was additional information encoded in the peptide that the SH2 domain makes use of.”

The researchers then deduced that the SH2 domains select their target through a kind of language, looking for the exact sequence of amino acids - or “word” - that marks the appropriate match. Because each amino acid (akin to the letters of the word) will either attract a particular SH2 domain or reject its peers, changing only one amino acid can completely change the meaning, like altering the word “light” to “fight.”

“For SH2 domains, that makes all the difference in the world. They can sense incredibly subtle differences,” Nash said. “It’s looking at the entire peptide and seeing both the permissive and the non-permissive residues, integrating that and making this collective decision about what to bind.”

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When scientists picture the miniature machines that live inside cells, they often have to settle for indirect evidence and a bit of imagination. Proteins on the nanoscale - one million times smaller than a millimeter - can’t be seen with your typical microscope, so scientists turn to electrical measurements, genetic mutations, and chemical assays to deduce a rough sketch of their target’s structure. More recently, tools such as X-ray crystallography and electron microscopes have allowed scientists to see cellular proteins. But both techniques require steps that change the natural environment of the protein, and can only offer a single photograph rather than a “movie” of its dynamic changes in shape.

So when Joanna Gemel, a research associate assistant professor in the laboratory of Eric Beyer, decided to look at the structure of cellular proteins called connexins and the channels they form, she wanted a different option. Connexins are found within the membrane of a cell in groups of 6, called connexons or hemichannels. When two cells come into contact, their connexons “dock” with each other to form a pathway between the two cells called a gap junction channel. In organs such as the heart or smooth muscle, gap junctions play an important role by facilitating the rapid passage of ions and small molecules from cell to cell.

“Gap junctions are critical for the propagation of electrical impulses in the heart. Abnormalities or mutations in them can cause a lot of problems, such as arrhythmias and atrial fibrillation,” said Gemel, author of a recent paper in The Journal of Biological Chemistry. “We decided that we would like to do something different. Since we never see channels, we asked what would be the best way to see channels and learn more about them?”

The question led them to the Center for Nanomedicine, a laboratory run by Michael Allen, a research associate assistant professor in the Department of Medicine. Allen’s tool of choice is atomic force microscopy, a technology invented in the mid-1980’s that remains useful for the visualization of the very, very small. The method, known as AFM for short, uses a strategy similar to an old record player: an extremely tiny needle (2 nanometers at its tip) moves slowly across the surface of a sample, creating a topographic map of the molecular landscape.

“AFM is really good at measuring height, the resolution in the z-axis,” Allen said. “With AFM we can look at 3-dimensional architecture, and in the z-axis the resolution is a tenth of a nanometer.”

But before tapping the potential of AFM, Gemel had to first create a stretch of membrane containing only the connexin she wanted to study, a form called connexin40 that is expressed in certain regions of the heart. Through painstaking transfection, purification, and reconstitution, Gemel produced a layer as thin as a cell membrane, swarming with connexin proteins. After imaging with the microscope, the researchers produced images (like the one posted above) that resembled dense mountain ranges viewed from an airplane, bumps floating in a dark field. Remarkably, the individual subjects and even the channel opening - narrow enough to pass individual atoms - were visible, not unlike the cartoon representation of gap junctions seen in textbooks.

With the extremely fine resolution of the AFM needle, Allen and Gemel set about measuring the heights of individual objects in their sample. Even though they knew that connexin40 was the only protein present in the membrane, their images contained particles of two different heights: some “bumps” were roughly 2.5 nanometers tall, and others were approximately 4 nanometers in height. They subsequently showed that the two different-sized bumps corresponded to whether the asymmetric hemichannels were facing inward or outward in the membrane.

“While it was something that we did not expect, it was an accomplishment to be able to monitor channels from both sides,” Gemel said.

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Many of the most interesting processes in nature are so fast, they can make “a blink of an eye” look like a millennium. Cellular proteins undergo elaborate transformations in as little as a picosecond - one millionth of one millionth of a second. That astonishing time scale presents an enormous challenge to scientists who would like to study the structure and behavior of those proteins. To catch the extremely fleeting moments of transition between different structural states of one such protein, a University of Chicago laboratory used a strategy straight out of science fiction: freezing time.

Xiaojing Yang, a senior research professional in the laboratory of Keith Moffat, wanted to look at a particular protein called a bacteriophytochrome, a red light photoreceptor from bacteria related to phytochromes in plants. Photoreceptors are found everywhere in nature, from plants to eyes, and are activated by light to change their shape and transform a light signal into a biological signal.  Yang was interested in the contortions a photoreceptor makes when changing from the “dark” state to the “light” state, and chose a particular phytochrome from the bacterial species Pseudomonas aeruginosa.

Yang started with a method called X-ray crystallography, where proteins are maneuvered into crystal formation and then imaged at the atomic level using an X-ray beam. With traditional X-ray crystallography, Yang could determine the structure of the P. aeruginosa phytochrome in the dark state, before activation with the light signal - data she reported in a 2008 PNAS paper. But in order to see the transition between dark and light in finer detail, the researchers needed to develop a new trick.

“We applied an innovative application of crystallography called temperature-scanning cryocrystallography, where we use temperature to mimic time,” Yang said of the work, published this week in Nature. “So this is a new way of doing dynamic crystallography.”

Cryocrystallography, or “cryotrapping,” involves performing the method at a very low temperature to freeze the target molecule in a particular conformation. The temperature-scan aspect that Yang and colleagues added was to hold the crystal at an escalating series of temperatures (from -279° F to -135° F), each one moving the super-fast structural changes the slightest bit forward. The researchers could then do an X-ray scan at each temperature level to capture those normally-fleeting in-between stages.

“We shine the light at different temperatures, higher and higher,” Yang said. “The reaction progresses further as the temperature rises, and then you have a different mixture of reaction intermediates.”

“It’s a cunning way of slowing things down from picoseconds to minutes or even tens of minutes,” said Moffat, Louis Block Professor of Biochemistry & Molecular Biology at UChicago.

The experiments, using ten temperature levels in all, revealed three predominant intermediate states, called L1, L2, and L3. Transitions between states resemble a “molecular earthquake,” Moffat said, with the changes initially appearing at one corner of the light-sensitive chromophore of the phytochrome before spreading outwards until the entire structure is in flux. And as dramatic as the motion is, it’s only the initial steps of the phytochrome’s dance. Moffat uses the analogy of filming a sprint to describe the action they captured - the flash of light that starts the reaction is the starting gun - and says that they are so far only able to observe the first 15 meters of a 100 meter dash.

“We’re not in a position to observe the rest of the race,” Moffat said. “Yes, we would like to see the entire race going all the way to the finish, but we believe that the overall reaction from beginning to end involves quite a large molecular convulsion, which is probably not compatible with the crystals.”

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Like a basement in a flood plain, a cell needs a good pump. Cells must maintain a particular mix of ions inside their membrane walls, with low concentrations of sodium and high concentrations of potassium. The only problem is that cells are leaky, and sodium constantly rushes into the cell while potassium rushes out. To fight against this tide, the cell uses a very important and peculiar membrane protein called the sodium-potassium pump.

Since its discovery in the 1970’s, cell biologists have been baffled by the strange features of this powerful pump. Rather than an even one-to-one swap of potassium for sodium, in each cycle the pump transports three sodium ions out for every two potassium ions it takes in. Later, scientists discovered that both sodium and potassium could bind to the same locations on the pump, a fickle temperament that is unusual among membrane proteins typically very picky about the type of ion they bind. That presented an intriguing molecular engineering problem — how could the pump modify itself to bind sodium when it’s accessible to one side of the membrane and potassium when it’s accessible to the other?

Some biologists have suggested that this riddle could only be answered by analyzing the highly precise geometry of the binding sites. Thus, many predicted that the model could not be solved until the most minute details of the structure of the sodium-potassium pump was fully captured in both its sodium-bound and potassium-bound states. So far, only the latter pictures (taken by X-ray crystallography) exist. But Benoit Roux, professor of biochemistry and molecular biophysics, decided that half the information was good enough to form a new theory of how the pump pulls double duty.

“Biologists have swept this under the rug, saying we need to know the structure of both the sodium and potassium bound forms with a sub-angstrom accuracy to address this issue,” Roux said. “Our point of view is that proteins are flexible macromolecules and that the mechanism of ion selectivity ought to be fairly robust, even when there are small sub-angstrom thermal fluctuations.”

Roux’s group, which included Haibo Yu of UChicago and Ian Ratheal and Pablo Artigas from Texas Tech, applied a computational method called molecular dynamics to the two existing crystal structures of the pump - isolated, strangely, from the rectal gland of a shark. For a paper published in Nature Structural & Molecular Biology last week, the team ran computer simulations that tested the possibilities of how four important amino acids in the binding sites mediate the pump’s change in selectivity under normal conditions. Instead of a complicated transformation from sodium-binding to potassium-binding mode, Roux’s model identified a small change that could account for the pump’s changed loyalties.

Protonation is a chemical reaction that adds a single hydrogen atom to a molecule. The four binding site amino acids of interest happen to carry negatively-charged acidic side chains that may or may not bind an extra proton. Roux’s group found that when the four acidic residues lose that extra proton (called deprotonation), they strongly prefer sodium to potassium. In their protonated state, the preference reverses to potassium over sodium.

“At this point it’s speculation because we do not know the structure of the sodium-bound state. But perhaps protonation and deprotonation play a more active role on modulating selectivity of these sites during the functional cycle of the pump,” Roux said. “It’s a provocative idea, nobody has ever proposed something like that to the best of our knowledge. Some people might be a bit shocked.”

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by Meghan Sullivan

It would be easy to mistake the images in Harry Noller’s presentation last Thursday for shards of gemstones or modern art. “This part of the talk was influenced by our visit to the Art Institute,” he quipped, advancing through a gallery of slides that showed off a variety of crystals, ranging in color and shape. This was not, however, a geology talk. Noller, professor of molecular cell & developmental biology at the University of California, Santa Cruz, was this year’s invited speaker for the 6th annual Haselkorn Lecture, a seminar series named for UChicago molecular biologist Robert Haselkorn that invites leading researchers to the University for several days to interact with young scientists. His visit drew to a close with a lecture on the molecule he’s spent most of his life studying, the ribosome.

Every living thing possesses ribosomes. It makes sense, then, that ribosomes are fundamentally necessary for life, and may predate proteins and even DNA in the history of life on Earth. Since the identification of DNA, an overarching rule of life has emerged called the Central Dogma, which states that an organism’s DNA is transcribed into RNA, which is then translated into proteins. It’s as if you’re copying instructions from a cookbook. The cookbook - in this case, DNA - holds all the recipes, and you can copy out only the individual recipe you need - the RNA. The copied recipe can then be used as a reference to make the final product, proteins. But as with cooking, you can’t simply turn words on a page into chocolate chip cookies. Like a baker might hold a recipe with one hand and mix the ingredients together with the other, the ribosome is the stepping stone between RNA and proteins.

“Going from DNA to RNA is something like going from Spanish to Portuguese - they’re similar types of molecules,” Noller pointed out, “But going from RNA to protein is like going from Portuguese to Chinese - they’re two totally unrelated languages. In this case, the ribosome is the Rosetta stone.”

The ribosome, which can be found in the fossil record going back 3.5 billion years, is a molecular machine that reads RNA and assembles the protein it encodes. Unlike many of our enzymes, it is composed mostly of RNA, not proteins. Its unusual composition and the fact that it lies at the heart of a process fundamental to life has made it a frequent subject of research.

Noller’s laboratory focuses on the structure and function of the ribosome. This is where the gallery of crystals comes in. Ribosomes, while relatively large cellular structures, are small enough that microscopy can’t provide the kind of detail necessary to understand the nuances of their structure. To get around this, scientists use a method called X-ray crystallography. In essence, Noller’s lab tries a variety of conditions to coax ribosomes into forming microscopic crystals, made up of repeating units, which forces the ribosomes to form symmetrical, 3D structures. At low power on the microscope, researchers can see angular crystals. However, when placed in the path of a X-ray, the crystal breaks up the X-ray beam into a complex scatter, which is caught and recorded. Using a mathematical operation called a Fourier transformation, the scatter of dots, each of which represents a single atom in the molecule, is resolved into a 3D model.

The problem with crystallography is that it only gives us a snapshot of its target. By forcing the ribosomes into crystals, they lose all ability to move. It’s well established that ribosomes, which must deal with growing proteins and move along the RNA, are dynamic molecules, moving and changing conformation as they work. Thus, still images don’t tell the whole story, a limitation Noller described with the parable of the cavemen and the Ferrari.

“The caveman and his cave-buddies are having beers and telling stories and they come out of the cave and see this.” Noller showed an image of a vintage Ferrari.

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Cells are often described as factories, a metaphor that adequately describes the swarm of specialized tasks constantly underway in each of the human body’s 100 trillion cells. The factory floor of the cell is so busy and complex that scientists are still discovering new machinery responsible for important jobs, with no clear end in sight. The neurons of the brain have been especially difficult to analyze given their role as communicators, ceaselessly sending and receiving chemical messages called neurotransmitters. Many different proteins are needed to release these signals, and when just one is missing, it can cause disaster.

The CLC family is a group of ion channel proteins known by such disasters. When these channels are missing or not working properly, motor disorders such as myotonia can result, suggesting how important their normal function is to the nervous system. Through the use of genetically-modified mice, where the gene for a single protein can be switched off, scientists can determine what a protein’s job is in the cell’s factory. But the process requires working methodically backwards, analyzing the big problems caused by a defective factory and retracing the steps back to where the target protein should have been working.

Yesterday in Nature Neuroscience, the laboratory of Deborah Nelson, professor of neurobiology, pharmacology and cell physiology, reported on one such investigation of a CLC family member. CLC-3 has not been tied as of yet to any human disease, but when it is deleted in mice, there’s no missing the consequences. Without CLC-3, the hippocampus, a region of the brain involved in learning and memory, slowly degenerates over the first months of a mouse’s life until it has completely vanished by the end of their first year. The retinas of the eye also degenerate in CLC-3 knockout mice, causing blindness during their first month of life. What could CLC-3, a humble ion channel that allows chloride ions to pass through its gate when activated, be doing in normal circumstances to avert such neurological catastrophe?

Vladimir Riazanski and Ludmila Deriy, research associates in Nelson’s laboratory, started with a clue about where CLC-3 lives in the cells of the hippocampus. Before they are released, neurotransmitters must be concentrated into packages called synaptic vesicles, sort of like a car being filled up at a gas station. A 2001 study of CLC-3 found that the protein is located on these synaptic vesicles in hippocampal neurons, suggesting a role for the ion channel in this packaging process. Experiments recording electrical activity from hippocampal regions of CLC-3 knockout and normal mice indicated that something was wrong with the transmission of GABA, the inhibitory neurotransmitter, when CLC-3 went missing.

So Riazanski and his collaborators zeroed in on the process of filling vesicles with GABA in the neurons of the hippocampus. By isolating those extremely small vesicles (on the scale of nanometers), the researchers could look very closely at what CLC-3 is doing to package GABA. The vesicles lacking the ion channel acidified more slowly, researchers discovered - a logical result of losing a channel that allows for the influx of acidifying chloride ions. But without acidification, the GABA vesicles can not be filled as efficiently, leaving vesicles with lower amounts of GABA or no GABA at all. It’s as though the gas station inside GABA neurons is missing its attendants - there’s plenty of fuel, but nobody around to properly fill up the vesicles.

Without sufficient inhibitory GABA being released, surrounding neurons can become over-excited to the point of death, Nelson said, which may explain the hippocampal and retinal damage seen in knockout mice.

“This is the first study to show any effect of CLC-3 on inhibitory transmission,” Nelson said. “It’s this loss of GABA transmission that probably contributes to the imbalance between excitatory and inhibitory signals within the mouse hippocampus, and eventually gives rise to excitotoxicity and cellular loss.”

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I’ve said it before, but the AAAS Meeting is my favorite scientific conference, a cross-disciplinary feast of research that’s perfect for omnivores of science. As I wait for the meeting to return to Chicago (2014!), I spent the week attending from afar through the many online recaps. Depending on your preferences, you can get your AAAS download from The Economist (writing about alchemy, of all things), Science News, in podcast form from Scientific American, The Scientist, the inside-baseball view of the Knight Science Journalism Tracker, or AAAS itself. Or you can read more focused recaps of a study that suggests being bilingual can protect against Alzheimer’s disease, the debate over how to effectively communicate climate change to a skeptical public, or monkey video-game self-awareness.

The University of Chicago was represented at the meeting by two talks on very different subjects: the future of health care spending, and the history of human evolution. David Meltzer, associate professor of medicine, argued that cost-effectiveness studies must be performed to control surging health care costs in the United States and other countries. Runaway costs can be partially explained by the flood of new technologies and therapies that are dropped into the healthcare market each year, Meltzer argued. While the FDA makes sure that these new technologies are safe for patients, there is less oversight on whether they actually will offer enough clinical value for their often high price tags. Even old methods, such as pap smears to screen women for cervical cancer, have rarely been assessed from an economic perspective, Meltzer said. Yearly pap smear exams are three times as expensive as exams every three years, but increase life expectancy by only 32 hours compared to less regular screening.

“The value of scientific advance and the resources available for it are greatest when we use scientific advances wisely,” Meltzer said.

On the other end of the spectrum from the future of medicine, Anna Di Rienzo, professor of human genetics, spoke about the history of man. Expanding upon her PNAS study from 2010, Di Rienzo presented genetic data found by her method of using environmental differences to find regional variation. In this case, the search ended in sweat: a gene called keratin 77, expressed in the sweat glands of the body, that has a variant more prevalent in hotter regions of the world. That variant may have become popular in tropical populations due its role in cooling off the body, but in the modern world, such environmental adaptations may be counter-productive.

“We know for sure that a lot of these differences are due to environmental risk factors that differ,” Di Rienzo said, according to Science News. “But there’s also a growing consensus that genetic factors may also contribute to these differences in disease or trait prevalence.”

Elsewhere…

Last May, we told you about Zoltan Takacs, who spends half his year chasing venomous animals around the world and the other half studying their poisons in the University of Chicago laboratory of Steve Goldstein, professor of biophysics. The good people at PBS’ Nova series got wind of Zoltan’s exciting adventures, and featured him in an episode this week on the potential of deadly venoms to be re-cast as life-saving medications for diseases such as cancer and heart disease. That’s one of his snake photographs up top.

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The immune system relies heavily on memory and recognition, with its success dependent on marshaling defenses against only the right infectious invaders. Scientists are finding that this memory requires a lot of moving parts, including molecules that grab pieces of bacteria and viruses, specialized cells that can determine whether those pieces are dangerous or not, and cells that attack and kill those microbes if they are ruled to be a threat. The key at each step of this complex system is specificity; if each component only binds or attacks certain types of molecules, it makes the process of remembering the correct response that much easier. As with a condo building, having the right locksmith can make all the difference.

Bacteria are largely made up of proteins and lipids, and when they first get inside a cell, the initial defense system strips them down to these parts. For proteins broken up into smaller pieces called peptides, the MHC molecules are the designated grabbers, binding the molecules and bringing them to the cell surface for recognition. But for lipids, a different group of molecules, the CD1 family, performs this task. Because lipids make up the bacterial cell wall - the critical outer barrier of the microbe - they are good, reliable candidates for jogging the immune system’s memory and initiating a response.

“It’s a really excellent way of recognizing a bacterial lipid, because they look a lot different than what they look like in us,” said Erin Adams, assistant professor of biochemistry & molecular biophysics at the University of Chicago. “If you are a bacteria, you can mutate your protein to evade the immune response and not be recognized any more, but it’s really difficult to change the structure of a lipid. If you screw it up too much, then the bacteria doesn’t survive.”

Understanding more about how these CD1 molecules function could be helpful in building better vaccines or treatments against bacteria and viruses. But the traditional scientific approach of taking a snapshot of these molecules (through the method of X-ray crystallography) was frustratingly difficult. So a multi-disciplinary team led by Louise Scharf in Adams’ laboratory set about using some molecular engineering to solve that problem, and their work was published last month in the journal Immunity.

The mission was to catch one of the CD1 family, CD1c, in the act of binding with a bacterial lipid; in this case, a component of the bacteria that causes tuberculosis called mannosyl-ß1-phosphomycoketide (MPM, for much-needed short). The protein was normally too unstable for crystallography, so Scharf and colleagues meticulously changed pieces of CD1c to create a more stable structure, without betraying the molecule’s original function.

“We did a lot of tests to make sure that the protein that we made, our Frankenstein protein, was only Frankenstein in the bits that didn’t count, the structural parts of the protein,” Adams said. “We had to keep validating along the way, step by step, to make sure we weren’t creating a monster.”

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Artist's rendering of the new Eckhardt Center (Courtesy of HOK/JCDA/AJSNY)

Today, the University of Chicago announced plans to construct the William Eckhardt Research Center, an innovative new building along Ellis Avenue that will be home to many researchers in the physical sciences.

But just as newsworthy as the new building is one of its prominent tenants: the Institute for Molecular Engineering, the largest new department launched at the University since the Harris School of Public Policy in 1988. The Institute, called the IME for short, will serve as a bridge between the Physical Sciences Division and the Biological Sciences Division for shared goals in research and education.

But what exactly is molecular engineering? The specific mission of the IME will be set next year when a director is named, but the general direction of this exciting new discipline was summarized last year by a faculty committee appointed to evaluate the IME’s creation. ScienceLife talked to a few of those committee members to learn about what molecular engineering is, what kinds of problems it might solve, and what kind of students it will create.

Biology and medicine is increasingly focused on how small scale interactions are important for both normal function and disease. Simultaneously, engineers grounded in physics and chemistry are looking toward biological systems for ideas and solutions. Increasingly, physical and biological sciences are speaking the same language, said Raphael Lee, Paul and Ailene Russell Professor of Surgery, Medicine, and Organismal Biology & Anatomy.

“On the molecular scale, behavior is described by laws of physics and chemistry,” Lee said “The rules of biology and physics are identical at the molecule scale. That’s where the fields boundaries blur and overlap.”

At this common ground, molecular engineering provides a skill set for the next generation of scientists to address the world’s biggest problems. The knowledge gathered through basic science in biology, chemistry, and physics laboratories can be combined and applied to major issues, such as providing clean water to undeveloped countries, or developing more efficient energy sources.

“This is making the science much more applied: we know how it works, so let’s try to make it better. How do we apply that knowledge to these problems that we see,” said Erin Adams, Assistant Professor of Biochemistry and Molecular Biophysics.

Molecular engineering innovation may also lead to the development of new technologies for medical care. Scaffolds for stem cell treatment might be designed through engineering, chemistry, and biology collaboration. Animals that have evolved natural self-healing abilities could inform the design of materials that repair themselves, which could in turn be used for the design of industrial products and medical devices.

“I think it’s entirely possible that new kinds of tools could be generated in molecular engineering that would have therapeutic implications,” said Julian Solway, Professor of Medicine and Pediatrics. “The problems that we’re addressing are the same problems, and the solutions that we want to find are well-suited to be approached by both camps.”

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The structure of the agitoxin-Shaker channel complex (from Benoit Roux lab webpage)

Scientific grants are usually given out one investigator at a time, funding a single laboratory’s research. But as the questions of science grow larger, and the technology needed to answer those questions grows ever more specialized and expensive, funding collaborative grants becomes increasingly common practice. One type of multi-investigator grant has been dubbed a “glue” grant, so named because it sticks together researchers from several different institutions for the common pursuit of one important science goal.

Today, the National Institute of General Medical Sciences announced a glue grant on the topic of membrane proteins, an effort that will be led from right here on the University of Chicago campus. The grant formally creates the Membrane Protein Structural Dynamics Consortium, a team of nearly 30 scientists from 14 institutions in the United States, Germany, Canada, and the Netherlands.

“We have been able to put together almost a dream team of people currently involved in this type of research,” said Eduardo Perozo, PhD, Professor of Biochemistry and Molecular Biophysics at the University of Chicago Medical Center and the leader of the team. “There has been nothing like this project before.”

Membrane proteins are the machines on the factory floor of the cell’s surface, tasked with letting materials in and out of the cell, responding to signals from other cells, and even producing energy. The family includes ion channels that Perozo (and fellow team member Benoit Roux) study, the receptors for neurotransmitters and hormones, and various other pumps, transporters, and exchangers. Figuring out how these miniature machines function will be extremely helpful in designing new drugs, both to treat diseases caused by defective membrane proteins and for improving drugs that rely upon membrane proteins to get to their target.

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Last month, we discussed the garage doors of the body’s ion channels, the millions of microscopic machines that control the heart’s beat and the nervous system’s communication. Benoît Roux and his colleagues employed 25 million computational hours to model the potassium channel voltage sensor, a kind of garage door control box that determines when the channel opens its gate. But the metaphor breaks down a bit when the channel is open, as the potassium channel does more than just wait to close again. Instead, there’s an in-between phase that keeps excessive potassium from stampeding through the open gate while the door prepares to close, a state called inactivation.

Determining the mechanism for inactivation has befuddled scientists for the same reason as the voltage sensor: how do you reverse-engineer a biological machine that works at the  nanoscale level, moving less than one-billionth of a meter at a time? One solution is to take pictures of the channel in motion, but doing so in the channel’s native habitat of the cell is beyond current technical means. Scientists have therefore resorted to a method called X-ray crystallography, a trick of chemistry and physics where the atomic structure of a protein can be determined.

X-ray crystallography has been used on potassium channels before - one such experiment even won the Nobel Prize for Chemistry in 2003. But each crystallographic portrait only catches the channel frozen at one particular moment of time, leaving scientists to make (educated) guesses about the movements that take place between each laboriously-obtained picture. The more pictures available, the less guesswork required.

More pictures and better theory are the result of two papers appearing in Nature today from the laboratory of Eduardo Perozo, professor of biochemistry and molecular biology at the University of Chicago Medical Center. Perozo’s group added to the potassium channel crystallography gallery by using a slightly mutated channel to keep the gate locked open and expose the elusive inactivation state to portraiture. From experiments conducted at Argonne National Laboratory, they hoped to get a new snapshot portraying a form of inactivation known as the C-type. But to their surprise and delight, they got 15 slightly different structures for the channel, which were determined to represent sequential stages between the open and inactivated state.

“By sheer luck, we happened to trap the channel in the process of opening, just like a movie,” Perozo said.

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An EEG recording of a seizure.

The electrical symphony of the human brain, with billions of neurons firing at different rates, up to hundreds of times per second, likely looks like chaos to any outside observer. But there are patterns in the ongoing brain activity seen, for instance, on an EEG: slow oscillations, rhythmic coordination, and purposeful ripples of communication. The importance of this intricate harmony is best displayed when it is disrupted by an epileptic seizure, which turns the fascinating complexity of the EEG into an angry scrawl.

You don’t have to be a neurologist to see the difference between a brain’s normal behavior and a seizure, but the causes of those seizures are much less obvious. Current antiepileptic drugs have shown success in treating some forms of epilepsy, but in many cases therapeutic success or failure is poorly understood and positive results are almost accidental - doctors are not entirely sure how medications suppress seizures, but are happy when they do. But for roughly a third of patients with epilepsy, those with intractable epilepsy, there remain no such happy accidents. Understanding what sparks a seizure would provide a rational basis for scientists to develop new drugs to treat the untreatable, as well as to reduce the side-effects of the existing treatments.

“Nothing has moved in the last 20 to 25 years,” said Wim van Drongelen, professor of neurology at the University of Chicago Medical Center. “There have been a lot of new anti-convulsant medications, but that one-third of patients who do not respond to medication has remained the same. My conclusion from that is that apparently all the new medications that have been developed address more or less the same type of epilepsy. In this context, epilepsy is comparable to cancer - there’s not just one type of cancer, and there’s not just one type of epilepsy, there are multiple types.”

To understand the different ways a seizure can form, scientists need a model. Experimentalists have recorded EEGs or used higher-resolution methods such as electrophysiology to measure cellular activity in a slice of animal or human brain tissue (obtained during surgery). But to truly model the brain’s rhythms - both normal and abnormal - requires nothing less than the most powerful computers currently available, a task that van Drongelen’s lab has undertaken.

“It’s a lot easier to do an experiment with a computer model than in a real slice,” van Drongelen said. “In a real slice, you have drugs to affect a certain channel, but these drugs are dirty, they also affect other things. In a model you can really very purely see what the effects are of certain manipulations and components. An additional huge advantage is that this approach gives you simultaneous access to what the population on the whole is doing, and what the individual agents are doing.”

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The Kv1.2 channel (image courtesy Fatemeh Khalili-Araghi/Theoretical and Computational Biophysics Group at UIUC)

Inside the human body are millions of miniature machines, the gatekeepers of the electrical impulses that keep our hearts beating and our minds thinking. They’re called ion channels; portals that allow small ions such as sodium, potassium, calcium, and chloride, to pass in or out of cells. A simple responsibility, with a complex and crucial outcome, as the flow of ions allows muscles to contract and action potentials to fire along the length of neurons.

While the job of an ion channel may seem straightforward, their design is anything but. Because the channels are awfully tiny, scientists have been forced to determine their workings through indirect experiments. A handful of pictures of the channels have also been taken, via the method of X-ray crystallography, but the photos can only capture an ion channel at rest - imagine trying to figure out how a car engine works from a single photograph.

But what if you could take the volumes of indirect information about an ion channel and instruct a computer to fill in the blanks? That was the approach taken recently by a team of scientists from the University of Illinois and the University of Chicago to tackle a target at the top of the list for ion channel researchers: the potassium channel voltage sensor.

“A potassium channel is a switch that opens and lets ions flow,” said Benoît Roux, professor of biochemistry and molecular biophysics at the University of Chicago and an author of the paper. “And that voltage dependence switch is necessary to understand how the nerve impulse works.”

Think of the ion channel as a garage door, and the voltage sensor as the control box. The channel only opens at a particular voltage, so it needs a way of both detecting voltage changes and powering the transition from closed to open states. It does so with the voltage sensor, a group of positively-charged amino-acids that can be pushed a small distance inward or outward by changes in voltage.

Scientists have a fuzzy idea of how that voltage sensor works from electrophysiological experiments, but the fine points of the mechanism are still unclear. As with any unknown territory in science, competing theories with colorful names like the paddle model, the helical-screw model and the transporter model attempt to fill the void. But Roux and his colleagues decided to test the movement of the voltage sensor with a complex computer simulation of one particular potassium channel, called Kv1.2, found in the heart and brain.

“This is not something you can do on a desktop computer,” Roux said. “Other people have had access to big computers, but it’s the strategy to compute that quantity that has never been done. This shows that it’s possible to address this kind of question at the most quantitative level with an atomistic model, and that has never been shown before.”

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