A Glimpse Through the Microscope

Groundbreaking research. Revolutionary discoveries. Science at CUNY.

by Neil S. Rosenfeld


"I'm looking for ideas about water that no single person could have thought about." said Charles Vorosmarty, who will direct the ASRC environmental sensing lab.

What do chronic water shortages mean in a volatile and nuclearized region like South Asia? Or in our country when farmers, industry and city dwellers argue over finite water supplies?

These are some of the questions that drive Charles Vörösmarty and his research team to study the state and trajectory of freshwater resources. Hydrology, the study of water in the environment, "is no longer about small units of landscape called watersheds," he said. "It's now focused on big, strategic issues, and often those are dictated by humans attempting to control water supplies. We've got to be talking about the Northeast Corridor; the U.S. national water policy in light of climate change; and the overuse of water as you're growing biofuels while trying to feed a hungry world, or when water scarcity invokes national security issues."

Vörösmarty is the first of what will be five nationally known directors whom CUNY is recruiting to run the laboratories at the Advanced Science Research Center, the keystone of CUNY's Decade of Science (2005-2015). The $300 million, 200,000-square-foot center on the grounds of City College is slated to open in 2012. It will provide $50 million worth of sophisticated equipment to researchers from across the University, while becoming a crossroad for scientific creativity.

"I'm looking for ideas about water that no single person could have thought about," said Vörösmarty, who will direct the laboratory of water and environmental sensing, a field that uses computer analysis and instruments ranging from satellites to ocean buoys to collect data for earth, atmospheric, environmental and marine sciences.

Similar brainstorming is also the goal in the ASRC labs dedicated to the University's four other flagship areas of science: nanotechnology, neuroscience, photonics and structural biology. CUNY researchers in those fields are already laying the groundwork to stop the spread of cancer, halt or even reverse degenerative nerve diseases, produce clearer mammograms and miniaturize electronics via biological processes.

Chancellor Matthew Goldstein launched the Decade of Science to help position CUNY as a premier research institution. The plan includes more than $1 billion for science facilities on eight campuses; "cluster hires" of more than 80 faculty members so far in science, technology, engineering and math; restructuring Ph.D. programs in the sciences and engineering; boosting financial aid for doctoral students; and training more teachers of middle- and high-school science and math.

Vice Chancellor for Research Gillian Small, who has overseen the ASRC project almost from the start, said CUNY was thrilled to have recruited Vörösmarty from the University of New Hampshire's Institute for the Study of Earth, Oceans, and Space, where he founded and directed its Water Systems Analysis Group. "Dr. Vörösmarty comes with an international reputation for excellence in interdisciplinary environmental studies," she said. "He will bring CUNY's water and environmental sensing initiative to the forefront. We are delighted to have him at CUNY and the ASRC."

Vörösmarty joined the civil engineering faculty at the City College of New York's Grove School of Engineering in September. He brought a hydrology team that includes about a half-dozen postdoctoral researchers and administrative staff from New Hampshire. Plans are to hire three faculty members who will teach and conduct research with him.

His team develops computer models and geospatial data sets to analyze the interaction of the water cycle with climate, biogeochemistry and human activities (including water engineering projects) on scales ranging from local to global. "We have to study the policy of water, the economics of water and how humans are managing or mismanaging this resource," he said.

Hunter College associate professor of biotechnology Hiroshi Matsui works at building complex diagnostic devices in nanoscale.

Although the United States has yet to adopt a national approach to managing carbon and climate change, Vörösmarty believes in "regional ecomanagement, and the only way to do that coherently is to take a multistate perspective and make water a part of the dialogue."

His viewpoint is broader still. He has consulted for the 24-agency UN World Water Assessment Programme and represented the International Council of Scientific Unions at the U.N. Commission on Sustainable Development. "I've opened a dialogue with the U.N. on how to better manage water in the 21st century. Our CUNY initiative is perfectly poised, because of our location, to be a central force in that dialogue."

He looks forward to working with the many CUNY professors who study environmental issues, including "the powerhouse in remote sensing and geospatial data-set integration" that is NOAA-CREST (Cooperative Remote Sensing Science and Technology Center), a multidisciplinary consortium led by CCNY and sponsored by the National Oceanic and Atmospheric Administration. It includes four CUNY institutions (CCNY, Lehman College, Bronx Community College and New York City College of Technology); Bowie State University; Columbia University; Hampton University; the University of Maryland, Baltimore County; and the University of Puerto Rico at Mayaguez.

"I'm amazed at the strength here at CUNY, but that strength sits on many different campuses," Vörösmarty said. "Our intent is to use ASRC as a magnet to draw these otherwise disparate students and professors together in an interdisciplinary research framework, in particular in reaching out to our next generation of students."

He sees the ASRC lab as "an incubation vessel for ideas, for the gee-whiz stuff that we can turn on its ear and apply to the environment."

Here is a look at some of the other scientists working in each of the University's five flagship areas of science.


The collection of data about the atmosphere, earth and living creatures, often via remote devices.

For the public, the most familiar environmental sensing is visible, from pictures of melting glaciers to TV graphics of howling hurricanes. But it's the invisible—what's in the air— that interests Fred Moshary, a professor at City College's Grove School of Engineering.

"On the health side, the main thing we're looking for is pollution," he said. "On the environment side, aerosols [liquid or solid particles] figure into global warming because they represent a cooling, not a warming, effect. When you're studying global warming, you have to look at the overall energy balance."

Curtailing global warming or meeting prospective environmental regulations are "difficult, high-stakes issues; dealing with them will be disruptive and expensive," he said.

New York City, for instance, falls short of national ambient air quality standards, and it could prove prohibitively costly to meet them solely by capping local emissions. "You have to understand the makeup of pollution, what portion is produced locally and what portion is transported here." Gasses from an Ohio smokestack could change chemically by the time they arrive here; acid rain is an example. Sensors can point to polluters upwind that also need to control pollution.

Moshary and his colleagues belong to a consortium, the Mid-Infrared Technologies for Health and Environment, funded by the National Science Foundation and industry. MIRTHE is developing devices that can detect minute amounts of chemicals, yet are so cheap and easy to use that they will transform how doctors treat patients, states track illegal dumping and Homeland Security monitors against biological attack. CCNY focuses on remote gas and aerosol sensors for deployment in cities, while Johns Hopkins, Princeton, Rice and Texas A&M Universities explore related environmental and medical applications, and the University of Maryland, Baltimore County, studies advanced laser materials

Meanwhile, Moshary helps plan the rooftop sensing lab at the ASRC. "For astronomers, the atmosphere is a nuisance that they have to look through before they see the stars, but we're looking at the atmosphere, itself," he said. The CCNY team is designing and building instruments including a volume-imaging lidar, which emits laser beams that bounce back when they strike airborne molecules and particulates. Using invisible light, either ultraviolet or near-infrared, it won't distract pilots, enabling scientists to point it at many angles to get a three-dimensional picture of air.

Moshary also is part of NOAA-CREST, the CCNY-based Cooperative Remote Sensing Science and Technology Center. "Some of our instrumentation is developed and packaged in-house, from atmospheric sensors used in the region to coastal-water-sensing packages that are lowered into the water or placed on buoys. All of that is constructed here by students before our scientists take off into the field," he said.


Daniel Akins has discovered a way to create
infinitessimal sensors for medical and other uses.

Technology that controls matter at atomic or molecular scales of 1 to 100 nm (nanometers, or billionths of a meter).

Human beings develop from almost nothing. A single cell, some programming instructions and, generally speaking, you get a smoothly functioning and complex machine. Would it be possible, Hiroshi Matsui wondered, to mimic that process by using biological building blocks to construct nanoscale electronics?

"We work with peptides and antibodies," explained the associate professor of bionanotechnology in Hunter College's Chemistry and Biochemistry Department. Peptides, which are chains of two or more amino acids, assemble themselves and can be fashioned into nanoscale wires that function like regular electric wires. And antibodies naturally attach to specific receptors on the peptides.

"We can program it to build complex devices in nanoscale, so this wire goes to position A, this wire to position B, and this particle to position C." Matsui said. "If we use the right antibodies, the wires won't be misplaced."

This approach could overcome a weakness in nanotechnology today, the difficulty in aligning parts of the tiny machines. "You can't pick up a nanoscale device and put the wires in the right places, but if you direct this wire to go to this place and attach itself, then it will do it. It sounds difficult, but that's how humans are made," he said.

Matsui's team is exploring how to use this technology to create sensors that, depending on which antibody is attached, would spot a specific virus or bacterium. "You could have a simple tabletop diagnostic device that could quickly say if you are infected [via an electric signal]. This could be of tremendous value in remote places where you don't have sophisticated instruments," he said.

Beyond detection, "We're trying to make this a diagnostic system," he said. "We are finding that the electric signal depends on the strength of the viruses, so the signal level could tell us the strain. That's what we're hoping for."

Matsui trained as a physical chemist and stumbled into this research when a graduate student made a mistake in synthesizing a known molecule. Back then, Matsui was "interested in how nature assembles a molecule into a certain shape." His student quickly realized that the peptide he had made was something new, and Matsui discovered that it functioned like an electric wire and could absorb biomolecules. That sent him down a different path of research, one that required him to learn a good deal of biology and biochemistry.

"Before this, almost nobody was thinking about using biological molecules for electronics, so we were almost the sole investigators thinking that crazy way, thinking that the hard-core semiconductor industry could marry with biology. Now many people have that idea," Matsui said.

It's hard to conceive how small a nanometer is. Web definitions call it 1/80,000th the diameter of a human hair or, at 3 nm, imagine it as a three-inch by three-inch Post-It Note seen from halfway across the planet.

Things 1 to 100 nms are inconceivably tiny. Yet scientists like Daniel Akins have made nanomaterials with amazing abilities.

A distinguished service professor of chemistry at City College, Akins has patented an inexpensive way of turning a carbon source like methane into nanotubes, which are cylinders of carbon atoms that "have fantastic properties. They're stronger than steel, conduct electricity better than the best metal conductors and have chemical properties that allow one to attach things to them." Things like gold nanoparticles that can register minute electric currents, turning nanotubes into infinitesimal sensors.

With the right blood-sampling system, such sensors could alert people with diabetes to the presence of hydrogen peroxide, which indicates insulin deficiency.

Nanostructures build themselves when scientists create the right conditions. In nature, carbon atoms bond differently, creating familiar materials like graphite, coal and diamond; in the lab, scientists can induce carbon atoms to form tubes, lattices and spheres, each possessing unique properties.

Scientists, including Akins, have used nanotubes to improve fuel cells. A fuel cell generates electricity when a catalyst (like gold or platinum) promotes the burning of a fuel (like hydrogen) in the presence of an oxidant, thereby releasing electrons. Fuel cells were conceived in 1838 and were first used commercially in the Gemini space program in 1965. But their use as a nonpolluting alternative to the internal combustion engine has stalled because they are inefficient and catalytic metals are expensive.

Nanotechnology that requires far less of the costly metals may be the solution. "We use carbon nanotubes as catalyst-assist agents, or cocatlysts. We coat particles of platinum or palladium onto the nanotubes. This improves efficiency and lowers the potential required for the chemistry to occur," he said.

Akins foresees extending his research into biofuel cells, which would use natural body processes to generate power. Imagine keeping warm in arctic conditions with a heater powered by normal blood chemistry. "When you pedal a bicycle, you're extracting energy; but with a biofuel cell, instead of having your whole system involved in generating energy, you're using a much smaller part."

Since 1988, Akins' Center for the Analysis of Structures and Interfaces has recruited many minority-group members and helped them move into doctoral work. He also was a leader in creating a subdiscipline in nanotechnology in CUNY's chemistry doctoral program. In 2000 he received the

Presidential Award for Excellence in Science, Mathematics and Engineering Mentoring from the White House Office of Science and Technology Policy.


The study of the development, anatomy, functioning and pathology of the brain and nervous system.

If you cut a nerve in the spinal cord, it won't spontaneously regrow. Paralysis results. Scientists had long thought that scar tissue was to blame, and it certainly does play a role.

Marie Filbin discovered something else: Nerves try to regenerate, but are stopped by a protein in the myelin sheath that protects them. Then she found that a molecule in every cell can counteract that protein, opening the door to therapies that one day may enable people with spinal cord injuries to walk and physicians to treat nerve-killing conditions like Lou Gehrig's, Parkinson's and Alzheimer's diseases.

Filbin, a distinguished professor of biology at Hunter College, said myelin contains myelin-associated glycoprotein, or MAG. It is believed to prevent nerves from sprouting randomly and making the wrong connections. But when a nerve is severed, MAG and related proteins also inhibit desirable regrowth.

She discovered that when she increased the concentration of a common signaling molecule called cyclic adenosine monophosphate, or cyclic AMP, nerve axons (which carry outgoing messages from neurons) overcome the inhibitory effects of MAG and grow.

Her basic research explores how cyclic AMP "changes a neuron to enable it to grow in this inhibitory environment. We have identified what genes are turned on in response to cyclic AMP and know that the proteins that result from these genes are sufficient to overcome inhibition. We are systematically working through these different downstream effectors to see if they will allow neurons to grow, will they promote central nervous system regeneration in vivo, and how they work."

Preliminary animal research shows that "if you elevate cyclic AMP you will get the nerve to regenerate and will get some functioning back. My long-term dream is that we can artificially change the dynamics of the cytoskeleton, which is to nerves what bones are to the body, to get nerves to regenerate," she said.

Clinical trials, though, are still far off.

Despite the potential of her work and five patents either approved or pending, Filbin is frustrated that major pharmaceutical companies have dropped their research into nerve regeneration. Perhaps they don't see a big enough market in treating people with spinal cord injuries like the late actor Christopher Reeve, who helped secure state funding that supports her research. Or perhaps they just don't see the future evident in an aging population.

"My argument is that in motor neuron diseases, Parkinson's, Alzheimer's or multiple sclerosis, you have ongoing nerve death. You have to arrest the progression of those diseases and, if you want full functional recovery, you're going to have to replace those lost neurons in an inhibitory environment. Everything we find out about regeneration after injury could be applicable to neuron replacement in degenerative diseases," Filbin said.

Anxiety, rage, depression and brain cancer form an understandable quartet, but for Probal Banerjee they encompass two distinct research projects.

The first examines how the neurotransmitter serotonin governs emotions. "We have shown for the first time that the serotonin 1A receptor in the brain plays a varied role in the early postnatal stages," said Banerjee, a professor of chemistry, biochemistry and neuroscience at the College of Staten Island.

Queens College assistant professor Vinod Menon is
developing integrated circuits that could lead to
ultrafast optical computers.

"In the hippocampus, which controls memory, it helps cell division just before neuronal connections are made. Then it changes its mode of action to help build neuronal connections. We are working out the signal transduction cascade, which is the sequence of events inside the neuron that regulates its electrical activity, cell division and maturation," he said. The proteins created or activated "can be our therapeutic targets in treating depression and anxiety."

The amount of serotonin in the cerebral spinal fluid affects emotions. At normal levels, serotonin is a calming agent, but having too little can trigger aggression and emotional problems including depression and suicidal tendencies.

Banerjee's team determined that a common drug for schizophrenia, clozapine, works through the serotonin 1A receptor, leading him to speculate that "many emotional disorders which surface in puberty are related to serotonin disorder."

He also studies brain tumors, taking divergent approaches.

Normally, the body's defenses recognize and destroy cells with unfamiliar surfaces. But cancer cells can hide by changing their surfaces. "By doing genetic targeting, we would alter the surface of the cancer cells in such a prominent manner that the scavenger cells would eat them up," Banerjee said.

His other approach to brain cancer employs curcumin, the main ingredient in the Asian spice turmeric. "On the Indian subcontinent, there is practically no colon cancer, although some people there have bad lifestyles; a lot of people smoke," he said. Could the reason be this pungent yellow spice, used in India to anoint the foreheads of wedding couples and in cosmetics to slough off dead cells and make the skin glow?

"Curcumin is becoming a legendary molecule, and there is a huge amount of research into it. It blocks breast cancer, lung cancer, colon cancer, but there wasn't any research in brain cancer because, when eaten, it metabolizes before it can reach the brain."

So Banerjee developed an easily metabolized, soluble formulation of curcumin. When injected into the brain or blood of mice, it "blocks the formation of tumors and is completely harmless to normal brain cells. In fact, it protects against oxidative injuries."

Banerjee even coined a name for his curcumin therapy: "spicile," from spice and guided missile.


The study of the properties and applications of light, or energy whose basic unit is the photon.

Making photonic devices flexible and miniaturized opens many possibilities for research and practical applications, said Queens College assistant professor Vinod Menon, one of CUNY's "cluster hires" in photonics.

Take flexible display screens, which one day could rival the rigid flat screens that are now the high-definition rage. These solid-state displays are extremely thin, like the ultraviolet-absorbing films that are sometimes placed over windows, but they can emit light just like a television.

"They could be wrapped around buildings," or run up a wall or around columns. "You even could put them on clothes for identification purposes," Menon said. "And the technique of making these emitters is so simple that I even have high school students in my lab who make them."

He uses a fast-spinning machine to coat multiple layers of polymers onto a flexible base, creating an optical microcavity, which traps and amplifies light at specific frequencies, harnessing it for emission like a TV or transmission over fiber-optic lines. Microcavity lasers are used widely, such as to produce the narrow beams that read and write CDs and DVDs.

His microcavity light emitters are more efficient, controllable and cheaper than previous attempts at creating flexible photonic devices, he said. "The other big advantage is that you can cover the visible and near-infrared spectrum, depending on the materials you choose."

He predicted that microcavity devices that can emit single photons (which are to light what electrons are to electricity) will lead to practical quantum information processing and quantum encryption, in which data sit on individual photons. His group is developing materials to manipulate signals at the single photon level.

And they are working on photonic integrated circuits (similar to electronic chips) for ultrafast signal processing; that could lead to optical computers whose speed would surpass current silicon-based circuitry. This and the flexible emitter work are funded by the Army Research Office.

Turning to fundamental research, Menon explores three-dimensional photonic crystals, which can efficiently trap photons. He collaborates with City College chemical engineering assistant professor Ilona Kretzschmar, whose group constructs these crystals using directed self-assembly; Menon evaluates their ability to trap light. The CUNY collaborative program funds this research.

He also seeks to understand how light acts in a structure where light emitters are stacked periodically (imagine a display of oranges). This work is incollaboration with Queens College theorists Lev Deych and Alexander Lisyansky; it is funded by the Air Force Office of Scientific Research.

Could light provide more detailed mammograms than X-rays, making surgical biopsies obsolete for diagnosing breast cancer?

Swapan Gayen hopes so. A professor in the Department of Physics and the Institute for Ultrafast Spectroscopy and Lasers at the City College of New York, he is the principal investigator of a four-year, $1.36-million grant to evaluate whether near-infrared light (just beyond the visible spectrum) can not only detect and diagnose breast cancer, but also assess how rapidly tumors are growing.

His team includes CCNY professors Robert Alfano and Feng-Bao Lin, and Memorial Sloan-Kettering Cancer Center's Dr. Jason Koutcher. The U.S. Army Medical Research and Materiel Command Breast Cancer Research Program funds their work.

Current screening methods like X-ray mammography and ultrasound excel at detecting abnormalities, but they cannot diagnose whether they are malignant or benign. For that, physicians need to perform biopsies, anxiety-producing surgical procedures that in 80% of U.S. cases do not find cancer.

But using light for mammography is easier said than done.

"The main problem is that light does not go through human tissue as it goes through a glass of water," Gayen explained. "It's absorbed and scattered many times, so it's hard to get a direct image." However, since normal tissue has different optical and molecular properties than cancerous tissue, and since "we can model how light transits through breast tissues and can measure the different angular orientations and transit times of the light that comes out the other end, we should be able to get an interior map of the breast."

To learn how to do that, Gayen's team constructs model breasts using samples of tumors and healthy breast tissue. They compare their images made with light to the results of X-rays and MRIs.

Beyond detecting tumors, this research offers hope of diagnosing breast tumors without surgery. The researchers will try to measure the rate of tumor growth by monitoring the progress of cancer in animals using both conventional methods and near-infrared spectroscopy. If the studies prove successful, they will seek additional funding for in vivo research.

Gayen's work into how light behaves in a highly scattering medium has other potential uses. Under a grant from the Office of Naval Research, his team investigated technology that penetrates coastal water better than ordinary light. The Navy might use such technology to detect mines, while marine biologists could employ it to study ecosystems and environmental sensing scientists could use it to see through clouds.

Structural Biology

Brooklyn College chemistry professor Lesley Davenport seeks ways to prevent an abnormal body process that can trigger cancer.

The study of the architecture and functioning of macro-molecules, which work properly in cells only in specific three-dimensional shapes..

What if you could halt cancer in its tracks by stopping a key enzyme from working when it's not supposed to? Lesley Davenport, a chemistry professor at Brooklyn College, thinks the solution may lie in the protective four-stranded knots that may be found at the ends of chromosomes.

These knots—quadruplexes, they're called—have the potential to form in telomeric DNA located at the end of chromosomes. And quadruplexes, in the laboratory at least, inhibit the action of telomerase. In most cells, the enzyme shortens telomeres with each replication cycle as part of the normal process of cell aging and death. (The exception is in reproductive cells, which telomerase protects by lengthening telomeres.) But when this process goes awry, telomerase can trigger uncontrolled replication and cell immortality – cancer, in other words.

Davenport hopes that her basic research can lead to drugs that would lock the telomeres of cancer patients, shutting down the progress of the disease. "We ask simple questions: What drives quadruplex folding and what are the dynamics of its formation?"

Among researchers who study telomeres and telomerase, she stands out for her expertise in fluorescent spectroscopy. She maps model DNA quadruplex sequences with the help of specially synthesized, fluorescent probes made of guanine-like residues. (The nucleotide guanine is a building block of DNA and a main component of telomeres.) Because this guanine is fluorescent, it's easy to find with optical spectroscopy even at low concentrations.

"We've been asking: Are all guanine positions in the DNA quadruplex identical? We've found that they're not," Davenport said.

She and her research team designed sequences with fluorescent guanines at various points in the quadruplex and observed how minor changes affect their ability to form knots. In certain positions, the altered guanine makes the quadruplex fall part, indicating locations that are vital for quadruplex stabilization.

That's significant because before researchers can develop drugs to lock quadruplexes, they have to know where to attach the lock.

That brings Davenport to another question: the dynamics and thermodynamics of how it folds. "If we understand how the quadruplex folds up on itself, then maybe drugs can be designed to make it lock the closed quadruplex conformation and thereby prevent telomerase from binding."

Davenport hopes to develop, test and screen for potential drugs that could keep telomeres tied in their elegant knots in collaboration with Mary Hawkins of the National Cancer Institute, who prepared some of the early fluorescent DNA sequences that she used.

Working from the premise that molecular architecture can shed light on function, Ruth Stark parses tiny structures that operate within cells, like the pigment melanin that can develop in certain fungi.

Working from the premise that molecular architecture can shed light on function, Ruth Stark parses tiny structures that operate within cells, like the pigment melanin that can develop in certain fungi.

Melanin protects fungi, just as it colors and protects human skin. It also can make them virulent, a worry for AIDS patients with fungal infections, said Stark, a distinguished professor of structural biology in the City College Chemistry Department.

Her current projects include studying how fungi create melanin from amino acid derivatives and how melanin attaches itself to fungal cell walls. "In contrast to other ubiquitous pigments like chlorophyll and hemoglobin, little is known about the molecular basis for melanin's many biological functions," Stark said. "Melanins resist traditional structural analysis because they don't dissolve in water or crystallize."

Her tool of choice is nuclear magnetic resonance (NMR), which examines nuclei nondestructively, as solids or in solution, by aligning them with a magnetic field, then perturbing the alignment with radio waves. The high-resolution results show the response for each atom of a pigment or protein target, revealing molecular structures and flexibility, two keys to physiological function.

Stark, a physical chemist, also explores what happens to dietary fat within animal cells. "As fats are digested, one of the things that they're broken down into is fatty acids, which typically are shuttled to the cell membrane and the nucleus by protein chaperones. Some of these proteins are found in adipose [fatty] tissue, where they may facilitate signaling related to insulin tolerance," she said.

"We look at these proteins and the small molecules they grab or release, and how the three-dimensional shapes of the proteins are changed either to accommodate a foreign fatty acid that gets in or to push it out. Or one protein may collide with another to effect the fatty acid transfer. Ultimately, we want to understand the basic processes of a human cell in healthy and disease states."

Stark works with NMR equipment at CCNY and at the internationally known New York Structural Biology Center, where she is a principal investigator. She also directs CUNY's Institute for Macromolecular Assemblies. "We now have a virtual institute for structural biology and engineered assemblies with more than 30 faculty teams on seven campuses." she said. The goal is "to become a cutting-edge crossroads for scientists making biomedically important discoveries."