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During a routine experiment, Pitt researcher Simon Watkins encounters something unusual. Now, he and his equally unusual imaging center are part of a national initiative to reveal the hidden lives of cells. Plenty of scientists want to take a look.


Cara J. Hayden

  Simon Watkins (Harry Giglio photo)

Underneath the glow of green lasers, Simon Watkins squirts
bacteria into a dish. He’s perched in a dim lab, surrounded by boxy cameras, joysticks, ribbed hoses, and other electronics that are part of his specialized microscope
system. A computer monitor displays the contents of the dish: cells that turn from purple to yellow when they sense invading bacteria. Watkins is investigating how immune cells communicate with each other about an enemy assault.

The experiment is going well until he tries to add more bacteria. The tiny dropper clogs. As he fusses with it, he inadvertently jabs one of the cells with the tip. Suddenly, purple cells on the other side of the dish flare yellow, even though they’re nowhere near the poke or any bacteria. He pokes it again and gets the same result. Clearly, something unusual is happening. Wide-eyed, Watkins unclips his cell phone from his belt and calls his research partner, Russell Salter.

This serendipitous moment leads to something better than any plan could have produced. As Watkins and Salter explore the unexplained flare-up in further experiments, they uncover tiny tunnel networks that the cells use to communicate. Only months before, German researchers had published a paper identifying these tunnels, but no one had figured out their function and many thought the tunnel-strands were useless cell debris.

Using his imaging system with three-dimensional and real-time capabilities, Watkins—a professor of cell biology, physiology, and immunology in Pitt’s School of Medicine—could see more clearly than most researchers worldwide. He and Salter, an associate professor of immunology, were able to describe how the tunnel system works. Their discovery challenged long-held theories that immune cells share information only through chemical interactions and not through physical networks.

The two reported their findings in last September’s issue of the international journal Immunity, causing a flare-up of their own in the global science community. Now, the imaging system set up by Watkins at Pitt is attracting even more attention. The University of Pittsburgh’s Center for Biologic Imaging (CBI), which Watkins directs, is involved in a new national effort to decode the still-mysterious lives of cells. Thanks to the CBI’s powerful and unusual imaging technology, a whole new way of seeing will likely open a window on troves of hidden life.

At the helm of his microscope, Watkins torques a joystick, drums several buttons, and peers into the binocular lenses. Spinning robotic plates purr mechanically as he zooms toward a glowing object. Suddenly, fluorescent green spots flash on the screen, glaring in the darkness.

“Wow,” blurts cancer researcher Brooke McCartney in amazement. She leans over Watkins’ command post to get a better look at the bulbous shapes connected by finger-like strands.

“I guess we should take some pictures,” suggests Watkins, who is also vice chair of cell biology and physiology in the medical school. The green globs are clumps of DNA in a fruit fly embryo, a common lab specimen. The genetic material is dividing and looks like pieces of chewing gum being pulled apart.

After saving some pictures on the microscope computer, Watkins steers his chair around the closeted workstation with a few pushes of his hiking boots. He nonchalantly adjusts the super-scope, preparing to use a cutting-edge microscopy technique, called total internal reflection fluorescence microscopy (TIRF), so he and McCartney can examine the embryo’s surface.

McCartney, an assistant professor of biological sciences at Carnegie Mellon University, is using fruit flies to investigate a protein that, when mutated, causes colon cancer. One of the protein’s normal jobs is to control the microtubules that pull DNA apart during the division process. McCartney’s hypothesis is that the mutated protein causes something to go awry with the microtubules near the embryo’s membrane, eventually leading to tumors. Other scientists have suggested this theory, too, but none has actually witnessed what happens to the microtubules at the embryo’s surface.

As Watkins shifts to TIRF mode, the green spots recede and a web of microtubules appears, looking like a game of glowing pick-up sticks. It’s the first time this technique is being used on a fruit fly embryo. Today, Watkins and McCartney are using a dead embryo, but soon they’ll record what happens to the microtubules while DNA is dividing in a live embryo, making them the first observers of that biological process at the cell’s surface. McCartney is pleased. She knows this imaging technology is bound to give her new insights that will benefit her research in unprecedented ways. She’s not alone.

As McCartney studies the magnified microtubules, another researcher zips past Watkins’ imaging room, carrying papers and a beaker. On his way to one of more than 25 specialized imaging systems, he passes under a row of colorful flags representing the homelands of the scientists working at the CBI, a mini United Nations. In addition to 20 staff members, more than 150 research teams from across the University use the center’s equipment. Most are from the medical school, School of Health and Rehabilitation Sciences, and the School of Arts and Sciences. Nationally, scientists from Chicago, Boston, Philadelphia, and other major research hubs seek access to the center, and researchers from abroad have mailed live tissue samples to the CBI for imaging.

Watkins founded the CBI soon after arriving at Pitt in 1991. He had just completed a research fellowship at Harvard, and he also had received postdoctoral training at the Pasteur Institute in Paris. He earned his PhD from Newcastle University in his native England. While establishing the CBI, he cut back on his research hours for several years to hire staff, develop lab procedures, and amass the best microscopes, computers, and cameras available. He made connections with companies developing innovative imaging equipment, and he now tests many new technologies before they’re commercially available. In 2000, he was the first U.S. scientist to obtain a confocal endomicroscope, an imaging system that can observe cells functioning within living animals and humans. It’s an Australian invention, and the center now has two.

These days, CBI researchers produce more than 35 scientific papers every year. Watkins can’t even count the papers written by the hundreds of outside researchers who use the center’s equipment.
Linda G. Griffith, a professor of biological engineering and mechanical engineering at the Massachusetts Institute of Technology, has published findings that resulted from working with the CBI. For the past five years, Watkins and his team have been helping her to develop imaging techniques for her liver tissue engineering research.

“Simon Watkins is a resource to the whole country on difficult imaging problems,” she says. “CBI does a tremendous service by making sure the things they do reach out to the community.”

Now that the center is running successfully, Watkins has time to pursue bench work again, in between teaching microscopy imaging courses at Pitt and other top institutions in North America, Europe, and Australia. His hands-on work generated that stir in the research world last fall and opened a new chapter in the book of immunology.

Watkins’ and Salter’s discovery of the tunnel communication between immune system cells is the type of research the National Institutes of Health (NIH) is bolstering through a monumental initiative to accelerate 21st-century medical research. Scientists nationwide, Pitt researchers included, have been charged with discovering more about human biology than ever before. The latest NIH initiative, dubbed the Roadmap for Medical Research, calls for developing better research tools to understand more about complex biological systems. The research will subsequently build a stronger foundation for diagnosing, treating, and preventing diseases. The initiative also focuses on fostering interdisciplinary research, training new researchers, and revamping clinical research practices.

The NIH endeavor springs, in part, from the Human Genome Project, a large-scale undertaking by six nations to identify all of the roughly 25,000 genes in human DNA, determine gene-sequencing patterns, and create a complete human-genetics library. Along the way, scientists invented new tools and technologies to speed their process and collaboratively gained a storehouse of new knowledge. It was an enormous success, ending ahead of schedule in 2003 and producing a new approach to national research.

“What the Human Genome Project did was show the value of discovery research,” says John S. Lazo, the Allegheny Foundation Professor of Pharmacology in Pitt’s medical school. “Until it was completed, there was this tremendous emphasis on hypothesis-driven research.”
Discovery research culls data that can be used to investigate a wide range of biologic processes, helping researchers make connections across ideas, disciplines, and areas of expertise. Traditional hypothesis-based research focuses on testing a specific theory with narrow, controlled experiments. Ideally, both approaches should be used so that discovery researchers can generate information for further analysis by hypothesis researchers.

The NIH wants to build on the Human Genome Project’s approach and results. It launched the discovery-based Roadmap initiative in 2004, and Pitt immediately began to participate. The University was awarded funding for several projects, including the $14 million Multidisciplinary Clinical Research Scholars Program, which trains postgraduate health professionals in clinical research methods, and the $9 million Pittsburgh Molecular Libraries Screening Center, codirected by Lazo and chemistry professor Peter Wipf. The molecular library center places Pitt as one of the first universities in the country to have sophisticated screening capabilities, and it’s one of 10 national centers that are rapidly assessing small molecules for their potential to be unique biologic research tools or targets for future drug development programs. By next year, the center expects to process 100,000 molecules every week; a decade ago, success amounted to screening just 10 compounds in one year.

The newest NIH Roadmap center here is the National Technology Center for Networks and Pathways, initiated in April as a joint venture of Pitt and Carnegie Mellon University—another endorsement, among many, of the effective partnerships between the two institutions. Codirected by Watkins and funded by a $13.3 million grant, it’s one of five centers across the country that are developing tools to study the interactions of proteins in living cells. This is one of the next steps in building on the Human Genome Project, because genes determine the function of proteins. Often, diseases manifest themselves at the protein level, so understanding protein networks and pathways ultimately will lead to new treatments for many illnesses.

At the new Center for Networks and Pathways, codirector Alan Waggoner—a professor of biological sciences at Carnegie Mellon—coordinates efforts to design new dyes to attach to proteins. His center partner, Watkins, adapts the CBI’s imaging instruments to record, in three dimensions and real time, the colored proteins in motion. “Simon’s outfit at the CBI has many different kinds of fluorescence-detection instruments and is, in my view, the most powerful imaging center in the country,” says Waggoner, who has frequently collaborated with Watkins during the past decade.

Essentially, this new NIH Roadmap center in Pittsburgh is creating ways to observe daily life in a big city: Biologyland. Proteins populate the place like typical urbanites, performing different activities in different places, sometimes with others, sometimes not. It’s Waggoner’s job to tag a few of the proteins with, say, green dyes. Then Watkins’ sophisticated imaging systems can track the greenies as they travel, interact, and communicate. This will tell scientists a lot about the life of the tagged proteins, and the process will be used to investigate other proteins, too. The complexities are daunting, but the new tools will allow scientists to decipher protein life, bit by bit.

Watkins and Waggoner are applying the technologies to several protein research projects, including McCartney’s colon cancer studies with fruit flies. Lazo and scientists from Stanford University and the University of California, Berkeley, are also participating. They’re likely to unravel some lingering mysteries about cell behavior and will probably encounter some surprises, too.

In the CBI, Watkins leads McCartney from the microscope’s workstation into a hallway that doubles as a gallery of vibrant cell images. More than 50 science journals have published CBI images on their front covers and Watkins has framed most of them, showcasing the artistic beauty of his work. At the end of the hall, he veers past benches where scientists are working with traditional beakers and cell cultures and then introduces McCartney to the computer laboratory, where several researchers are studying colorful cell images on widescreen monitors. Here, she can conduct an in-depth analysis of the fruit fly microtubules with software that’s not available on her lab’s computers. It’s just one more way that Watkins is helping colleagues to see the unknown up close.

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