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Inside the toolbox

The School of Medicine’s core research facilities include imaging modalities that allow biological visualization on the atomic, molecular, and cellular scales. Hundreds of YSM investigators make use of the facilities to probe drug-target interactions, protein folding, and disease mechanisms; and the shared nature of the facilities means that collaboration and advances often go hand in hand. Here we describe the cutting-edge technology of the core imaging facilities and explain how this colorful science is being translated into medical treatments.


Magnetic resonance allows the study of systems-level processes in both brain and body by magnetically aligning and then tracking the relaxation properties of atoms in the body (usually those in water). Douglas Rothman, Ph.D., professor of diagnostic radiology and biomedical engineering and director of the Yale MR research center, uses MR spectroscopy to measure chemical pathways in the body, including liver metabolism, as well as brain neurotransmitter and energy cycling. Other studies at the Magnetic Resonance Research Center look at changes in blood flow (the primary measure of functional MR, or fMRI) or brain volume in cases of epilepsy and autism. Because MR is nonionizing and provides good contrast between soft tissues, it has applications from tracking the mechanisms of drug action in the brain to visualizing injury and noninvasively identifying tumors. Frontiers of MR involve combining it with other techniques like recording of electrical potentials, for even more precise understanding of the interplay between brain function and signaling.

Positron emission tomography

What imaging technique can be used to study drug addiction, Alzheimer disease, eating disorders, cancer, and diabetes? These diverse conditions can all be imaged using PET, which tracks radioactively labeled pharmacologic agents as they circulate through the body. Established in 2007, the Yale PET center does roughly 1,000 scans a year, many that focus on drug distribution and binding in the brain. A team of more than 50, led by professor of diagnostic radiology and biomedical engineering Richard E. Carson, Ph.D., develops new tracers; scans patients and disease model animals; and analyzes the flow and molecular mechanisms of administered treatments; as well as the metabolic processes of tumors and inflammation. New forays in PET research include imaging the action of cancer drugs and the presence of beta cells in the diabetic pancreas.

Confocal microscopy

Yale’s confocal microscopy facility, one of the first in the country, pushes the boundaries of what can be seen in living cells and tissues. Instead of flooding a sample with light, confocal microscopy uses point illumination and a pinhole to increase the depth resolution of an image, enabling the visualization of 3-D structures within cells. Now, the facility’s three microscopes, including a combination confocal/two-photon system, are being used by 70 different labs, says director Michael H. Nathanson, M.D., Ph.D., professor of medicine and cell biology. “The facility is a workhorse, giving people throughout the medical school access to state-of-the-art microscopy plus highly skilled technical support,” said Nathanson. Among the cellular mechanisms being probed with microscopy are signaling pathways in cell nuclei and cytoplasm. Another project has identified how human papilloma virus can enter cells. Among others, Joerg Bewersdorf, Ph.D., assistant professor of cell biology and biomedical engineering, is developing improved microscopy tools, ensuring that YSM faculty will always have access to the latest cutting-edge techniques.

Electron and cryo-electron microscopy

Since joining Yale at the end of 2011, electron microscopy (EM) facility director Xinran Liu, M.D., Ph.D., has brought biological and cryo-EM under one roof. The facility takes on about one new project per day, estimates Liu, including imaging animal and plant samples from nonmedical departments like forestry. With traditional EM, for example, the changing morphology of genetically manipulated cells can be tracked, and fluorescing agents can be introduced to localize proteins within cells. Cryo-EM uses frozen samples that are unadulterated by staining or fixation to get a clearer view of native protein structures. By tilting samples systematically as they are being bombarded with electrons, researchers can create volumetric reconstructions of samples that reveal 3-D structures of individual proteins and receptors, down to the resolution of ångstrõms.

X-ray crystallography

Using X-ray diffraction to visualize the structure of molecules is essential to modern drug discovery research, says macromolecular X-ray core facility director Ya Ha, Ph.D., associate professor of pharmacology. The interactions of drugs with cellular target sites are no longer a black-box process, as the diffraction pattern of a crystallized sample can reveal the atomic blueprint of how and where drugs bind with protein. Another facet of research involves looking at how molecular structure changes in cancer, Alzheimer disease, or cerebral cavernous malformations. Only about 1 percent of the protein structures in the human genome are known, so a substantial effort of X-ray crystallographers at Yale also goes toward the basic research needed to solve these structures. A fundamental life science discovery was solving the structure of the ribosome’s subunit using X-ray crystallography, a feat that earned Sterling Professor of Molecular Biophysics and Biochemistry and Professor of Chemistry Thomas Steitz, Ph.D. the Nobel Prize in chemistry in 2009.