Brochure - Department of Physiology & Biophysics - Stony Brook

Physiologyand Biophysics

Graduate Studies

The Graduate Program in Physiol-ogy and Biophysics is a broadlybased program in which a stu-

dent is exposed to a variety of researchperspectives. We view our wide range ofresearch interests as an importantstrength. The faculty are activelyengaged in research from ion channelbiophysics and signal transduction toorgan systems physiology. The graduatefaculty include members of clinicaldepartments and members from facilities such as Brookhaven NationalLaboratory. The campus houses a number of other graduate programs in the

biomedical sciences, physicalsciences, and mathematics.There is continuous interactionbetween faculty and studentsfrom all of these programs,including our own. This kind ofenvironment gives the studentthe best possible opportunity togrow and learn along with thefaculty. If you are interested,please take the time to visit usand talk with the faculty andstudents about graduate train-ing in physiology and biophysics.There is no better way for you

Chair’s MessagePeter R. Brink, Ph.D.

PROGRAM DESCRIPTION, PAGE 2Graduate Student Marjorie Bon Homme uses a pressure generator.

FACULTY PROFILES, PAGE 7Dr. W. Todd Miller and Graduate Student Haoqun Qiu.

to obtain the necessary information in making what will be one of the mostimportant decisions of your life.

For more information, you may also visit our Web site atwww.pnb.sunysb.edu. The site features our faculty’s latest research, listsseminars and courses for the upcoming semester, provides more in-depthdetails about our facilities and newest equipment,

and details on what isneeded to apply to theprogram. You can findmore information andeven apply online byvisiting the GraduateSchool Web site atwww.grad.sunysb.edu.

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PROGRAM DESCRIPTION, PAGE 2

GRADUATE COURSES, PAGE 3

RESEARCH FACILITIES, PAGE 4

DISTINGUISHED FACULTY, PAGE 6

FACULTY PROFILES, PAGE 7

PERSPECTIVES, PAGE 25

SPOTLIGHT ON ALUMNI, PAGE 26

LIVING IN STONY BROOK, PAGE 28

APPLICATION AND ADMISSION, PAGE 30

HOW TO GET HERE, PAGE 31RESEARCH FACILITIES, PAGE 4Students are provided with everything they need toaccomplish their research goals.

GRADUATE COURSES, PAGE 3Graduate Students Louisa Dowal and Vijaya Narayanan.

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The diverse nature of the department’s research provides aunique environment for graduate study. The overall goal ofour program is to prepare students to investigate complexphysiological and biophysical problems that often bridge tra-ditional academic boundaries. This requires sound training ina broad range of biological disciplines, plus experience inusing the latest techniques in biochemistry, molecular biology,physics, applied mathematics, and computing.

To accomplish this goal, we recruit a relatively smallnumber of students with diverse undergraduate training in thephysical and biological sciences. Individual courses of study arethen designed that reflect the background and goals of each stu-dent. Consequently, our students pursue graduate studies thatrange from the strictly biochemical to the strictly biophysical.

First Year and BeyondDuring the first year, all students take courses in cellular andorgan systems physiology, graduate biochemistry, and bio-physical chemistry. During the second year, students selectfrom a variety of advanced courses that suit their scientificinterests, goals, and background. Students rotate through atleast three faculty laboratories to gain research experience inthe first two years. Students also participate, under facultysupervision, in the teaching of physiology. Upon completion ofthe qualifying examination and the selection of a faculty advisorfor their research, the students then devote essentially all oftheir time to dissertation research.

There are two research concentrations available to gradu-ate students: Cellular and Molecular Physiology or Biophysics.

Cellular and Molecular Physiology ProgramThe goal of the Cellular and Molecular Physiology Program isto train students to investigate significant problems in humanphysiology using modern techniques of molecular and cellularbiology. Students who choose this option generally haveundergraduate degrees in biochemistry or biology, and will takeadvanced graduate classes in cellular and molecular biologyand molecular genetics during their second year.

To increase the training and research opportunitiesavailable to our students, this program is affiliated with aninterdepartmental program in Molecular and Cellular Biology(MCB). The MCB Program consists of approximately 100 fac-ulty from 11 departments, as well as investigators at ColdSpring Harbor and Brookhaven National Laboratories. Theprogram offers several core courses taken by all graduatestudents in the biological sciences. Students admitted intoPhysiology and Biophysics are permitted, with prior approvalof the advisory committee, to do laboratory rotations and/orconduct their dissertation research with any MCB member.

During the first two years, students usually rotatethrough three laboratories in the department. The duration ofthese rotations may vary, but do not exceed six months. At theend of each rotation, students will submit a written report ofthe aims and results, as well as the difficulties with the project.

Biophysics Studies ProgramThe goal of the Biophysics Studies Program is to train stu-dents with strong backgrounds in physics and/or chemistry inmodern biophysics. The program is an interdepartmentaleffort, which consists of 42 Stony Brook faculty, as well as scientists at Cold Spring Harbor and Brookhaven NationalLaboratories. Students who choose this option generally takeadvanced courses in biophysical chemistry, electrophysiology,or advanced biochemistry. Biophysics students can do rotationsand dissertation research in the lab of any faculty memberaffiliated with the Biophysics Program. The Biophysics Stud-ies Program is supported by a Training Grant in MolecularBiophysics from the National Institutes of Health.

Teaching ExperienceStudents are required to serve as teaching assistants for twosemesters in course(s) offered by the Department. This willfulfill the Teaching Practicum required for doctoral degreesawarded by the State University of New York.

Seminars and Journal ClubThe department hosts an extensive series of seminars ontopics of direct and indirect relevance to research interestsof the faculty. Seminars are given by faculty and visitingscientists, as well as by postdoctoral fellows and students.Students are required to attend all departmental seminarsunless there is a conflict with a class. Students are alsorequired to participate in the student journal club, whichmeets weekly with a member of the faculty. Each week acurrent scientific publication will be presented by an individualstudent and discussed.

Program Description

Students Paxton Provitera and Finly Phillip (seated) review research results.

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Graduate Course OfferingsPHYSIOLOGY HBY 501, FALL

Introduces normal function of human tissues and organs andtheir regulation by nervous and endocrine systems. Empha-sizes the organization and function of physiological control sys-tems and the maintenance of a constant internal environment.

MEDICAL PHYSIOLOGY HBY 502, SPRING

A graduate-level approach to the physiology of the organsystems is addressed in a lecture format with emphasis onproblem solving. Relevant clinical correlations are addressedat the end of each block insofar as they illustrate how symp-toms and signs of disease result from disordered physiology.Organ Systems addresses the structure and function of thecardiovascular, respiratory, renal, gastrointestinal, endocrine,skeletal, reproductive, and integumenary systems.

INTRODUCTION TO BIOPHYSICAL CHEMISTRY HBY 511, SPRING OR FALL

Introduces the chemical principles and techniques needed forthe study of biological macromolecules. Topics covered includesolution chemistry, chemical thermodynamics, binding and dis-sociation equilibria, denaturation phenomena, spectroscopy,and hydrodynamics. This course is intended to prepare non-chemistry majors for more advanced work in biophysics.

CELLULAR PHYSIOLOGY AND BIOPHYSICS HBY 530, FALL

Cellular structure and function. Topics include ion channels,excitability, transport, energetics and metabolism, contraction,secretion, and communication within and between cells.Emphasizes quantitative analysis of cellular structure andfunction. Topics include ion channels, excitability, transport,energetics and metabolism, contraction, secretion, and commu-nication within and between cells. Emphasizes quantitativeanalysis of cellular processes.

ORGAN SYSTEMS HBY 531, SPRING

A graduate-level introduction to the physiology of the organsystems with ultrastructural correlations. Ultrastructuralcorrelations are demonstrated in a laboratory setting usinghistological preparations in conjunction with electron micro-graphs illustrating the relevant ultrastructure needed tounderstand the normal functioning of tissues and organs. Thephysiology of the major organ systems is addressed in a lectureformat with the emphasis on problem solving. Relevant clinicalcorrelations are addressed at the end of each block in so far asthey illustrate how symptoms and signs of disease result fromdisordered physiology. Organ Systems addresses the structureand function of the cardiovascular, respiratory, renal, gastroin-testinal, endocrine, skeletal, reproductive, and integumenarysystems. Prerequisites: Admission to medical or dental schooland permission of instructor. Eight-credit course.

PHYSIOLOGY OF EXCITABLE MEMBRANES HBY 552, FALL OR SPRING, ALTERNATE YEARS

Covers the resting potential, the basis of the action potential,linear cable properties, and synaptic transmission. Studiessquid axon, the neuromuscular junction, and the cardiacPurkinje fiber model systems.

SIGNAL TRANSDUCTION HBY 553, FALL OR SPRING, ALTERNATE YEARS

The course will emphasize fundamental concepts in signaltransduction (e.g., membrane-protein and protein-proteininteractions, amplification of signals), and individual lectureswill apply these concepts at each stage of cell signalling fromthe cell surface to the nucleus, where signal transductionleads to specific gene expression.

ADVANCED PHYSIOLOGY HBY 557, FALL

This course is designed to introduce students to integrativeapproaches in biomedical research. Emphasis will be placed onthe primary physiological concepts of control, communication,signal processing, metabolism, and replication.

STATISTICAL ANALYSIS OF PHYSIOLOGICAL DATA HBY 561, FALL

MODEL-BASED ANALYSIS OF PHYSIOLOGICAL DATA HBY 562, FALL

MEASUREMENT AND ANALYSIS IN PHYSIOLOGICAL DATA HBY 563, SPRING

These courses are designed as a series of mini-courses tointroduce the principles of experimental design relevant tomodern physiological research. Emphasis will be placed ondata acquisition, signal processing, and statistical analysisassociated with basil experimental approaches currently usedin physiological research.

STUDENT JOURNAL CLUB HBY 570, FALL AND SPRING

Graduate student presentation on a selected topic with facultyconsultation. Prerequisite: Limited to students of the Phys-iology and Biophysics program.

SPECIAL TOPICS IN PHYSIOLOGY AND BIOPHYSICS HBY 590,

FALL AND SPRING

Student seminars on topics to be arranged through consulta-tion with faculty members.

PHYSIOLOGY AND BIOPHYSICS RESEARCH HBY 591,

FALL, SPRING, AND SUMMER

Original investigation under staff supervision.

SEMINAR IN PHYSIOLOGY AND BIOPHYSICS HBY 690, FALL AND SPRING

Seminars and discussions on major topics in physiology andbiophysics by students, staff, and visiting scientists.

PRACTICUM IN TEACHING IN PHYSIOLOGY AND BIOPHYSICS HBY 695,

FALL AND SPRING

Practical experience and instruction in the teaching of physi-ology and biophysics carried out under faculty orientation and supervision.

THESIS RESEARCH IN PHYSIOLOGY AND BIOPHYSICS HBY 699, FALL,

SPRING, AND SUMMER

Original (thesis) research undertaken with the supervision ofa member of the staff.

FULL-TIME SUMMER RESEARCH HBY 800

Full-time laboratory research projects supervised by staff.

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The Department of Physiology and Biophysics is wellequipped with major research instrumentation for physiolog-ical, metabolic, and biochemical studies, including scintillationcounters for radioisotope work, ultracentrifuges, amino acidanalyzers, a gas-phase protein sequencer, DNA synthesizer,DNA sequencer, and instrumentation for measuring ORD andCD, plus a wide variety of chromatographic, electrophoretic,spectrophotometric, and electronic equipment. Also availableare a peptide synthesizer, mass spectrometer, and laboratoryfor chemical synthesis of low-molecular-weight compounds.Nuclear Magnetic Resonance (NMR) instrumentation isavailable through collaboration with other departments. Tissueculture services, including monoclonal antibody production,are also available. Specialized equipment used in studies ofmembrane physiology and biophysics (e.g., membrane poten-tials and patch-clamp studies on ion channels) are in routine usein several faculty laboratories. Department faculty membersare associated with a Health Sciences Center diabetes andmetabolism group and have collaborative arrangements withother basic science and clinical departments. Many of the facili-ties are located within the Basic Science Tower of Stony Brook’sHealth Sciences Center, the home base of the department.

Molecular Biology CoreThe molecular biology core was established to provide studentsand faculty ready access to DNA/RNA recombinant technology.Departmental facilities now include a 37-degree environmentalroom, large orbital shakers, an array of incubators, DNAsequencing gel set ups (IBI), electrophoretic apparatus andpower supplies, an IBI gel reader and a software package thatpermits the reading of DNA sequencing gels, a selection ofrestriction enzymes, and a number of cDNA expressionlibraries. A DNA synthesizer and an automatic DNAsequencer were recently added to this core.

Molecular ModelingComputational molecular modeling and visualization arevaluable tools for the study of signal transduction systemsand protein structure/function. Some current applicationsof faculty affiliated with our Biophysics Program includeexamining the physical factors involved in protein/membrane,protein/protein, protein/DNA interactions, studying thespecificity of ligand and substrate binding to enzymes, andbuilding models of proteins using domain structures fromhomologous proteins. The computational facilities are state-of-the-art: a network of Silicon Graphic Indy and Indigoworkstations provides fast, high-resolution, interactivegraphics and a 500 Mb, eight-processor Sun supercomputer isused for intensive numerical analysis. Several members of thedepartment have access to National Supercomputing Centers.

Computing FacilitiesThe department has more than 60 different computer systems,ranging from high-end PCs and Macintosh systems to UNIX-based workstations. The department maintains a computer cen-ter for general use by all students, faculty, and staff, whichincludes a number of high-end PCs, scanners, graphics work-stations, laser and color printers, and data archival facilities.In addition, first- and second-year graduate students haveexclusive use of two additional high-end PCs for word pro-cessing, data analysis, and network access. All computers areconnected directly, via Ethernet, to a local area network, whichin turn, is directly connected to the campus-wide network andthe Internet. Thus, each computer has high-speed access to anumber of file and print servers, campus mainframes, librarysystems for catalog and literature searches, campus adminis-trative systems, and, via the Internet, the World Wide Weband NSF-sponsored supercomputer facilities.

Biophysics Program Research FacilitiesAll of the faculty have independent research programs andwell-equipped laboratories to carry out these programs.There are major shared facilities for X-ray diffraction,nuclear magnetic resonance, electron microscopy, molecularmodeling, and molecular biology at Stony Brook and ColdSpring Harbor Laboratory. In addition, Brookhaven NationalLaboratory offers unique possibilities employing synchrotronradiation and neutron diffraction.

Research Facilities

Dr. Peter R. Brink, Professor and Chair.

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Top row (from left to right): Graduate students Vijaya Narayanan, Svetlana Favelyukis and Wanging Li , and Maggie Luk-Paszyc. Middle row (l. to r. ): Dr.William Van der Kloot, Dr. Todd Miller, and Dr. Leon Moore. Bottom row (l. to r. ) Dr. Irene C. Solomon and graduate student Dan Cardone, Dr. James Dilger,and graduate student Marvin O’Neal.

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The research interests of the facultyin the Department of Physiologyand Biophysics are very diverse,

including systems and cellular physiology,cell and molecular biology, biophysics,and structural biology. A common threadthat links our faculty is an emphasis onquantitative understanding of biologicalprocess on a physical level. The departmenthas particular strengths in membrane bio-physics, cellular signal transduction, inter-cell communication, lipidmetabolism, vision, cardiac electrophysiology, neuroscience, and theregulation of cell growth and differentiation.

On the following pages, we highlight the work of each professor.For more details on their research groups and ongoing projects,please visit our Web site at www.pnb.sunysb.edu.

Our Distinguished Faculty

Dr. Thomas White (left) and Dr. Nicolas Nassar.

Graduate students Jiyao Wang and Urszula Golebiewska with Dr. Stuart McLaughlin.

NADA ABUMRAD, ProfessorPh.D. 1978, State University of New York, SyracuseThe research focus of Nada Abumrad’s laboratory involves fatty acid transport inblood and across membranes, and the effects of fatty acid esterification inmacrophages. Fatty acids are the major energy substrate for many tissues. They areprecursors of membrane phospholipids and modulators of channels, receptors, andenzymes. Blood fatty acids are tightly bound to albumin, but despite this binding theyare taken up very rapidly by most cells. Abumrad’s research has led to the identificationof a membrane protein called FAT that acts as a high affinity receptor for fatty acid.She is working to define the physiological effects of the FAT protein and regulation ofthe FAT gene.

Another research area of Abumrad’s lab concerns mechanisms that regulate fattyacid esterification by human macrophages. This process is implicated in the developmentof artheromatous lesions and of vascular complications in conditions like diabetes, thenephrotic syndrome, or obesity. Glucocorticoids influence the esterification of fattyacids and their contribution to the consequent development of vascular lesions and ofcoronary heart disease is being investigated.

(631) 444-3489, [email protected]

PAUL R. ADAMS, ProfessorPh.D. 1974, University of LondonDepartment of Neurobiology and BehaviorPaul Adams is interested in the following question: How fast should learning takeplace at the synapses made or received by a neuron if the neocortex is to acquire newunderstanding without forgetting the old? Perhaps new information should only belearned if it is not confusing. This idea can be made precise by considering the possi-bility that when connections strengthen, new synapses are sometimes incorrectlyplaced. Such synaptic errors, or “mutations,” smear neural wiring and reduce theamount of information that can be stored depending on the sharpness of the correla-tions across a particular connection. The brute force way to increase storage is tolower error rates, but this requires larger, less densely packed synapses, which dimin-ishes storage. A more subtle approach would be to allow plasticity only at connectionsacross those correlations that are sharp. This suggests that the neocortex should havemachinery to measure correlation sharpness and to control plasticity. There are indi-cations that layer six plays these roles. It also implies that the neocortex must sleep.


WILLIAM BAUER, ProfessorPh.D. 1968, California Institute of TechnologyDepartment of Molecular Genetics and MicrobiologyWilliam Bauer’s laboratory group is researching three separate projects, all involvingthe structure and energetics of superhelical DNA. The group is investigating theproperties of the vaccinia virus concatemeric replication region, an imperfect invert-ed repeat, cloned into a superhelical plasmid; increases in supercoiling cause cruciformextrusion and formation of the virus telomer. This structure contains several bulgedbases, both singly and in groups. The Bauer lab has determined the complete energeticsof formation of these important structures. In further research, it is extending the gelelectrophoreses and statistical mechanical techniques used to study the vacciniatelomer to additional nonstandard duplex regions. Using two-dimensional NMR tech-niques, Bauer and his group are determining the structure of the principal unpairedregion in the vaccinia virus telomer. Using elasticity theory, combined with finite ele-ment analysis, the group has analyzed the properties of looped DNA regions, tetheredby DNA binding proteins, and containing internal bends. This research explores thethree-dimensional structure of DNA contained in loops as the twist of the DNAchanges, with implications for recombination and DNA splicing.


WILLIAM B. BENJAMIN, ProfessorM.D. 1959, Columbia UniversityHormone-regulated protein phosphorylation is an important mechanism for orderedcontrol of enzyme activity. The final state of protein phosphorylation is the result ofprotein kinase and protein phosphatase activities on the phospho-protein. WilliamBenjamin’s research deals primarily with one protein kinase, glycogen synthasekinase-3 (GSK-3), and one of its important enzyme-substrates, ATP-citrate lyase (CL).This enzyme is phosphorylated on three sites by three different protein kinases invitro. The phosphorylations of these three sites are regulated by hormones withinseconds in vivo.

Using a clone (in hand) for ATP-citrate lyase, Benjamin and his research groupplan to study the effects of selected phosphorylation(s) of its multisite phosphoylationson the actions of allosteric effectors on enzyme activity. The aim of this research is todemonstrate for the first time that ATP-citrate lyase lies at an important insulin-directed control point for the flow of carbon atoms from sugar to cholesterol and fattyacids. This research will also place GSK-3 as an important protein kinase in thepathway of insulin-directed control of metabolism.


PETER BRINK, Professor and ChairmanPh.D. 1976, University of IllinoisPeter Brink uses dual whole cell patch clamp and dual permeabilized patch clamp tomonitor gap junction channel gating/permselectivity under defined ionic conditions andmore relevant physiological conditions: the effects of various messenger molecules ongating of gap junction are studied in detail with these approaches. Any individual gapjunction channel is composed of 12 subunit proteins known as connexins. Because theprimary sequence of a number of connexins has been elucidated, this has allowed for thetransfection of cells devoid of gap junctions to be used to study pure populations ofspecific connexin-derived gap junctions, as well as mutants generated via site-directedmutagenesis. Brink uses N2A mouse neuroblastoma cells as host cells for the transfec-tion of wild-type and mutant connexins. Dual whole cell patch clamp is then used to mon-itor the gating and preselective properties of the various expressed connexins. In oneexample, Brink uses two models, which result in dry-eye in mice. These efforts centeron elucidating the mechanism of fluid transport across the epithelium that makes up thesecretory portion of these lacrimal glands. His results from patch clamping cells isolatedfrom these animals indicate that diseased mice lack the necessary number of K channelsand possess an increased number of Cl- and cation channels resulting in membrane depo-larization and compromised transepithelial transport.


CAROL A. CARTER, ProfessorPh.D. 1972, Yale UniversityDepartment of Molecular Genetics and MicrobiologyCarol Carter’s laboratory focuses on the assembly of the Human ImmunodeficiencyVirus (HIV), the causative agent of Acquired Immunodeficiency Syndrome (AIDS).Assembly of this virus is a multi-stage process that involves both viral and cellularproteins and takes place both in the cytoplasm and on the inner surface of the plasmamembrane. The virus may use, transport, and export trafficking cellular machineryabout which little is known. The potential of this stage of replication as a target foranti-viral drug design has not been exploited because the assembly process is not yetunderstood in molecular detail. Carter’s specific interests are elucidating the structureand function of the proteins involved and studying the required protein-membraneinteractions. The goal of these studies is to identify critical events feasible for thedesign of anti-viral agents.


CHRIS CLAUSEN, Associate ProfessorPh.D. 1979, University of California at Los AngelesChris Clausen’s laboratory group is studying the regulation of proton transport in renalepithelia, the role of endo- and exocytotic processes in altering rates of ion transport,and mechanisms involved in epithelial sodium, chloride, and glucose transport. Exper-imental techniques include analysis of epithelial electrical impedance, transepithelialand intracellular electrophysiological recordings, measurements of uptake and releaseof fluid-phase makers, fluorescence microscopy, whole-cell patch-clamp studies,morphometric analyses, and computer modeling.

The lab has also developed computer models of ionic currents in Purkinje fibers andventricular myocytes to compute space-clamped and propagating action potentials. Themodels are used to investigate antiarrhythmic drug action and to model arrhythmias,notably early-after depolarizations and re-entrant arrhythmias.


IRA S. COHEN, Leading ProfessorM.D., Ph.D. 1974, New York UniversityThe research in Ira Cohen’s laboratory focuses on cardiac electrical activity. Using acombination of biophysical (patch clamp) and molecular (message distribution) tech-niques, the laboratory investigates both normal and abnormal (arrhythmogenic) elec-trical activity. A major focus of the laboratory is to assign to each cardiac membranecurrent a molecular correlate and to understand how second messenger systemsregulate the properties of ion channels. Recent projects in the laboratory include thestudy of primary and secondary pacemakers and the membrane currents that controlthe action potential duration.


CARLOS DE LOS SANTOS, Assistant ProfessorPh.D. 1987, University of Buenos Aires, ArgentinaDepartment of Pharmacological Sciences, School of MedicineResearch performed in Carlos De Los Santos’s laboratory involves determining thestructural properties of DNA molecules damaged by endogenous and exogenousagents and establishing structure-function relationships relating to mutagenesis andDNA repair. Under the assumption that macromolecule structures determined withinthe walls of an NMR tube are relevant to understand their biological properties, DeLos Santos’s group uses high-resolution nuclear magnetic resonance and restrainedmolecular dynamics simulations to establish the structure of short, lesion-containingDNA duplexes in solution. The long-term goal of De Los Santos’s group is to identifythe structural determinants involved in the recognition of damaged DNA moleculesand to characterize the formation of DNA/protein complexes. Specific DNA lesionsunder current investigation in his laboratory include exocyclic DNA lesions (ethano,etheno, and acrolein adducts) endogenously formed byproducts of lipid peroxidation,abasic sites and clustered abasic site lesions that have been implicated in long-termcytotoxic effects of gamma radiation, and S6-thio-2’-dG, as well as alkyl lesions producedby chemotherapeutic agents.


JAMES P. DILGER, Associate ProfessorPh.D. 1980, Stony Brook UniversityJames Dilger is Associate Professor of Anesthesiology with a joint appointment inPhysiology and Biophysics. His research deals with ligand-gated ion channels in nerveand muscle cells. His laboratory studies the structure and function of channels usingpatch clamp current recording techniques. A method of rapidly perfusing excisedpatches on the submillisecond time scale was developed in his lab. This provides acontrolled way to examine channel activation as it occurs during rapid synaptictransmission. These tools are applied to questions of the molecular actions of anestheticand muscle-relaxant drugs. Although general anesthetics have been in clinical usefor more than 150 years, the ways in which they cause unconsciousness, analgesia,and amnesia remain unknown. Ligand-gated ion channels are likely targets of anes-thetics. Work in Dilger’s lab involves determining sites and mechanisms of action ofthese drugs.


NORMAN H. EDELMAN, Professor and Vice President for the Health Sciences CenterM.D. 1961, New York UniversityDepartment of Physiology and Biophysics and Department of MedicineNorman Edelman is a pulmonologist with research interests in the integrative aspectsof respiratory control. His work focuses on the role of central nervous system hypoxia inmodulating the output of the controller. The most recent emphasis has been on definingthe chemoreceptor characteristics of the putative respiratory pacemaker cells in thepre-Botzinger complex of the ventral medulla.

He has served on National Institutes of Health (NIH) study sections, NIH advisorycommittees, and editorial boards of major publications in his field. He has been arecipient of an NIH MERIT award.


MOISÉS EISENBERG, Associate ProfessorPh.D. 1972, California Institute of TechnologyDepartment of Pharmacological SciencesResearch interests in Moisés Eisenberg’s group revolve around computationalapproaches to structural biology. Elucidation of three-dimensional structures of bio-logical macromolecules whose primary structure is known using computer-assistedmolecular mechanics and dynamics is now possible if additional experimental data isavailable; for example, inter-atomic distances derived from nuclear magnetic reso-nance, or sequence analogy to previously known structures in genetically related fam-ilies, both of which were used in Eisenberg’s computer laboratory. By applying thesemethods, the group continues to build up a library of structures of DNA molecules con-taining a variety of well-defined chemical lesions of biomedical significance, and thoseof complexes between these damaged DNA molecules and the enzymes they bind to,involved in DNA repair and replication. Prediction of the precise docking conforma-tion between pairs of biomolecules of known structures has been partially validatedand continues to be investigated.


M. RAAFAT EL-MAGHRABI, Research Associate ProfessorPh.D. 1978, Wake Forest UniversityResearch in Raafat El-Maghrabi’s laboratory deals with two facets of metabolic regu-lation of gene expression. First, delineating the factors involved in regulating expressionof 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase genes; the products of thesegenes are responsible for modulating rates of glycolysis in almost all cell types. Forexample, a novel form of the enzyme is overexpressed in brain tumor cell lines, and thelab is investigating the factors responsible for the activation of the gene. The studiesinvolve mapping of the regulatory regions of the genes with respect to transcriptionfactor and hormonal binding sites. The lab also deals with the structure/functionrelationships of the products of these genes, the enzymes themselves, with respect toreciprocal regulation of the two opposing activities by phosphorylation, and theinteraction of the two domains. These studies involve expression of wild type andmutated forms of the enzyme using bacterial expression systems and kinetic andstructural analysis of the various forms.


ARTHUR P. GROLLMAN, ProfessorM.D. 1959, Johns Hopkins UniversityDepartment of Pharmacological Sciences, School of MedicineArthur Grollman’s Laboratory of Chemical Biology focuses on the biological conse-quences of DNA damage with particular reference to molecular mechanisms of DNAreplication, mutagenesis, and DNA repair. Site-specific methods are used to explorethe mutagenic potential of defined DNA lesions in mammalian cells. Shuttle plasmidvectors are used to establish the efficiency and fidelity of translesional synthesis.Reactions, catalyzed by DNA polymerases, permit mutational events to be studied invitro. The three-dimensional structure of damaged DNA is used to correlate molecularstructure and biological function. This multidisciplinary approach permits Grollmanand his students to elucidate the molecular basis of mutagenic specificity. OxidativeDNA damage is a major contributor to spontaneous mutagenesis, carcinogenesis, andthe aging process. Grollman’s lab has determined the miscoding effects of DNA damageproduced by reactive oxygen species and has defined an error-avoidance pathway thatprotects cells against mutations produced by 8-oxoguanine. DNA N-glycosylases andAP-lyases are central to this process. Genes for these enzymes have been cloned andthe lab uses gene knockout technology to analyze the effects of repair of oxidativelydamaged DNA in transgenic mice.


YAACOV HOD, Associate Professor of ResearchPh.D. 1977, Technion, Israel Institute of TechnologyDepartment of UrologyThe main research work of Yaacov Hod focuses on the control of gene expression atthe level of mRNA stability. As a model system, Hod uses the gene encoding the gluconeogenic enzyme P-enolpyruvate carboxykinase (PEPCK), whose expression isregulated by several hormones including glucagon (acting via cAMP), insulin, andglucocorticoids. In previous studies, Hod has demonstrated that cAMP enhancesPEPCK gene expression both by inducing the transcription rate of the gene, as wellas by stabilizing the mRNA against degradation. In an effort to elucidate the mechanismby which cAMP regulates mRNA stability, Hod has isolated a novel protein (RBP)with an RNA-binding activity whose activity is regulated via protein-protein interaction.Current studies focus on establishing the exact cellular role of the RBP and its regu-lation, employing a variety of approaches in molecular and cellular biology. Recentstudies have identified the gene in a chromosomal region showing a large number ofchromosomal aberrations in several tumors. The possible involvement of RBP in canceris another goal of Hod’s studies.


CHRIS JACOBSEN, Associate ProfessorPh.D. 1988, Stony Brook UniversityDepartment of Physics and AstronomyChris Jacobsen carries out research in X-ray optics and microscopy. This involves acollaboration with Bell Labs on soft X-ray zone plates that produce the finest focus ofelectromagnetic radiation of any wavelength and research at a soft X-ray undulatorbeamline at nearby Brookhaven National Laboratory for which he is the spokesperson.His interests include X-ray optics and imaging theory, X-ray instrumentation, andapplication of these methods, such as tomographic imaging and spectromicroscopy, toproblems in biology and environmental science. He is the recipient of a PresidentialFaculty Fellow Award (National Science Foundation/White House, 1992-1997), theInternational Dennis Gabor Award for research in optics, and the Outstanding YoungScientist Award of the Microbeam Analysis Society.


ROGER JOHNSON, ProfessorPh.D. 1968, University of Southern California The laboratory of Roger Johnson investigates the regulation of adenylyl cyclases by3'-nucleotides. This family of enzymes catalyzes the formation of adeno-sine 3':5'-monophosphate (cAMP) from 5'ATP and constitutes a major trans-membrane signaltransduction system. One approach of the laboratory has been to synthesize and usebiochemical probes to define structural characteristics of the inhibitory configurationof the enzyme. These are used in conjunction with molecular biological approaches tofacilitate the identification of nucleotide binding sites within native and recombinantwild type and mutated forms of the enzymes. Experiments use standard techniquesfor chemical and proteolytic fragmentation and sequence analysis as well as time-of-flight MALDI (Matrix-Assisted Laser Desorption Ionization) mass spectrometry thatallows sequencing of intact peptides. The overall intent of the research is to describestructure-function relationships within the adenylyl cyclase family and to define thenew regulatory links between this family of enzymes and nucleic acid metabolism.


LEEMOR JOSHUA-TOR, Associate ProfessorPh.D. 1991, The Weizmann Institute of ScienceCold Spring Harbor LaboratoryLeemor Joshua-Tor studies the molecular basis of cell regulatory processes in termsof molecular recognition. In her research, her lab uses tools of structural biology andbiochemistry in a combined approach to look at proteins, protein complexes, andprotein-nucleic acid complexes associated with these processes. Through X-ray crys-tallography, an accurate three-dimensional structure of individual proteins, their com-plexes, and the interactions in which they are involved are determined. The lab usesbiochemistry to study properties predicted by protein structure and use informationfrom molecular biology and genetics in collaborative efforts to study protein function. Joshua-Tor’s current efforts center on two distinct themes. The first involves structuralstudies of complexes involved in DNA regulatory processes (replication and tran-scription). The second is concerned with the regulation of proteolysis in processes,such as apoptosis and in an evolutionarily conserved family of self-compartmentalizingintracellular proteases, the bleomycin hydrolases. With the bleomycin hydrolases, thelab is also investigating the structural basis for tumor cell drug resistance tobleomycin and the link to Alzheimer’s disease.


JANOS KIRZ, Distinguished ProfessorPh.D. 1963, University of California at BerkeleyDepartment of Physics and AstronomyJanos Kirz is interested in soft X-ray optics, coherence properties, the physics of theinteraction of soft X-rays with matter, and the applications of these topics tomicroscopy and spectromicroscopy. He and his students were the first to create a finefocused probe of soft X-rays using zone plates and to use this probe to build a scanningmicroscope. Kirz started his professional life in high energy physics, with experimentsin Berkeley, Brookhaven National Laboratory (BNL), CERN, SLAC, and Fermilab.His more recent work with X-rays is centered on the X1 undulator at BNL’s NationalSynchrotron Light Source. He was the recipient of a Sloan and a Guggenheim Fellow-ship, as well as the Chancellor’s Award for Excellence in Teaching. Between 1998 and2001, Kirz served as Chair of the Department of Physics and Astronomy.


CAROLINE KISKER, Associate ProfessorPh.D. 1994, Free University of Berlin Department of Pharmacological SciencesCaroline Kisker’s lab is elucidating the structures of key molecules essential for humanhealth. Maintenance of the correct genetic information is crucial for all living organ-isms. Mutations are the primary cause of hereditary diseases, as well as cancer, andmay also be involved in aging. Excision repair by removal of damaged DNA throughdual incisions on both sides of the lesion allows this system to recognize a wide varietyof different defects. The lab focuses on the excision repair mediated by UvrABC andis characterizing the individual proteins of this system and their complexes both withand without their substrates to understand how substrate recognition is achieved.A second area of research focuses on the molybdenum-cofactor containing enzymes. Inhumans, genetic deficiencies of sulfite oxidase and xanthine dehydrogenase lead tosevere abnormalities. Kisker’s lab is characterizing both enzymes on the atomic levelto understand their catalytic mechanisms and to elucidate the structural changescaused by mutations, which lead to the described deficiencies.


IRVIN B. KRUKENKAMP, ProfessorM.D. 1982, University of MarylandDepartment of SurgeryIn 1997, Irvin Krukenkamp joined the Stony Brook faculty as professor of surgery andchief of cardiothoracic surgery. Coming from Harvard University, Krukenkamp nowdirects the Division of Cardiothoracic Surgery, and also co-directs the newly formedHeart Hospital. Performing the only open heart surgery in Suffolk County, he and histeam of cardiothoracic surgeons specialize in high-risk and tertiary care types of surgicalintervention. Krukenkamp’s special clinical interests also include coronary and valvesurgery in the octogenarian, and operative management and myocardial protection ofthe profoundly dysfunctional heart.

Krukenkamp’s research interests include myocardial mechanics and energetics,myocardial protection by cardioplegia, and new endogenous myoprotective strategiesutilizing preconditioning. He is currently the principal investigator or co-investigatorof three NIH-funded studies focusing on myocardial protection in the senescent heart,the electrophysiology of potassium channel opening, and the mechanics of ischemicmyocardial preconditioning.


SCOTT W. LOWE, ProfessorPh.D. 1994, Massachusetts Institute of TechnologyCold Spring Harbor LaboratoryScott Lowe’s research investigates the control of apoptosis and senescence, and howmutations that disrupt these processes impact tumor development and therapy.Lowe’s research has previously shown that p53 tumor suppressor is an importantregulator of apoptosis, and, as a result, that p53 mutations can promote oncogenictransformation, tumor progression, and resistance to cytotoxic agents. His laboratoryhas also demonstrated that oncogenic ras can activate p53 to promote cellularsenescence, and that escape from ras-induced cell cycle arrest provides a biologic basisfor transforming interactions between ras and immortalizing oncogenes. Finally, hislaboratory has exploited a mouse lymphoma model to identify genetic factors involvedin chemosensitivity in a physiological setting. Lowe’s current research focuses on fourinterrelated areas: oncogene activation of p53, p53 action in apoptosis, the initiationand maintenance of oncogene-induced senescence, and the molecular genetics of drugsensitivity and resistance in vivo.


ERWIN LONDON, ProfessorPh.D. 1980, Cornell UniversityDepartment of Biochemistry and Cell BiologyErwin London’s interests involve membrane structure and function. One focus isunderstanding how proteins translocate across membranes using diphtheria toxin. Thestructure of this toxin within membranes and its translocation is being studied usingsite-directed mutagenesis to introduce fluorescence labels within the toxin molecule.Understanding translocation should have important implications for the design oftherapeutic agents and vaccines for bacterial infections. In a second project, London isdetermining the relationship between amino acid sequence and structure using syn-thetic transmembrane helices. Their structure and location within the lipid bilayer isanalyzed using fluorescence quenching, circular dichroism, and other spectroscopictechniques. The aim is to reveal the rules governing membrane protein folding. London’sthird project involves exploring the function of lipid domains enriched in cholesteroland sphingolipid. These domains are believed to play a role in signal transduction, viraland toxin entry into cells, protein sorting among organelles, and prion formation. Hisaim is to determine the principles that induce formation of these domains and regulatetheir lipid and protein composition.


WILLIAM LENNARZ, Professor and ChairPh.D. 1959, University of IllinoisDepartment of Biochemistry and Cell BiologyWilliam Lennarz is interested in understanding several steps involved in glycoproteinsynthesis, including N-glycosylation and protein folding, as well as the functions of theglycan chains. He uses yeast, a simple eukaryotic organism that can be geneticallymanipulated, to study glycoprotein assembly. More specifically, he investigates theenzymatic processes of oligosaccharide addition and removal that occur in nascentpolypeptides and misfolded glycoproteins, respectively. In addition, Lennarz is studyingthe enzyme that catalyzes folding and disulfide bond formation in glycoproteins.


GARY G. MATTHEWS, ProfessorDepartment of Neurobiology and BehaviorPh.D. 1975, University of PennsylvaniaAfter postdoctoral research at the University of Colorado Medical School and StanfordUniversity, Gary Matthews came to the Department of Neurobiology and Behaviorat Stony Brook in 1981. The Matthews laboratory uses biophysical and molecularbiological techniques to study mechanisms of cellular communication.


DAVID MCKINNON, Associate ProfessorPh.D. 1987, Australian National UniversityDepartment of Neurobiology and BehaviorDavid McKinnon’s research focuses on how the electrophysiological phenotype ofexcitable cells is established and maintained in vivo. The electrophysiological phenotypeis actively maintained by a combination of physiological inputs and tropic signals andcan be modified by changes in the nature of these inputs. One aim of the lab is to identifythe physiological signals that regulate ion channel gene expression in vivo. Experi-mental work has concentrated on voltage-gated potassium channels since the primaryfunction of most of these channels is to control the firing properties of excitable cells.To identify which channels contribute to the final differentiation of firing properties,the McKinnon lab has combined two different techniques. Voltage-gated potassiumchannels have been studied using electrophysiological techniques. In addition, the labhas used molecular biology techniques to clone a large number of novel, mammalianpotassium-channel cDNAs. The research concentrates on two separate systems:sympathetic neurons and cardiac myocytes.


RICHARD MATHIAS, ProfessorPh.D. 1975, University of California at Los Angeles Many physiological properties of a tissue are the integrated result of the physicalproperties of structure, electrical and diffusional interconnection of cells within the tissue,and specific membrane properties of each cell type. Richard Mathias is interested in howthese three factors interact to produce the functional tissue properties. His laboratory isworking on various types of mammalian cardiac tissue, where the function is primarilyregulation of excitability and contraction. Mathias and his team are working on thelens of the eye, where function requires crystalline clarity. Experimental techniquesinclude the following: intracellular microelectrode studies of tissue impedance, voltageclamp; membrane patch-clamp; ion selective microelectrodes, digital video microscopy;cloning and expression of membrane transport proteins; and modeling of forces/flows(e.g., voltage/current, pressure/fluid flow, concentration/diffusion, etc.) in tissues ofcomplex anatomy.


HAROLD J. METCALF, Distinguished Teaching ProfessorPh.D. 1967, Brown UniversityDepartment of Physics and AnatomyHarold Metcalf’s early work included precision measurements of fundamental con-stants, quantum beat spectroscopy, and pioneering advances in laser techniques. Hewas one of the initiators of laser cooling and atom trapping and has concentrated onoptical and magnetic manipulation of atoms since then. Novel experiments lead tosuperposition states (Schroedinger’s Cat), exceedingly low temperatures, and opticalforces that exceed the normal limits. New types of microKelvin thermometry andatom manipulation techniques have recently emerged. The modern laboratories areequipped with five atomic beams, multitudinous lasers of many kinds, and associatedelectronics and computers. Among Metcalf’s teaching accomplishments are foundingthe Master of Science in Instrumentation Program for graduate students and theLaser Teaching Center for student projects; instituting several new courses in atomicphysics, lasers, biophysics, physics for non-scientists, and instrumentation; writingtwo books, Topics in Classical Biophysics and Laser Cooling and Trapping (graduatetexts in contemporary physics); and serving as Ph.D. advisor to 25 students.


LORNE M. MENDELL, Distinguished ProfessorPh.D. 1965, Massachusetts Institute of TechnologyDepartment of Neurobiology and BehaviorLorne Mendell’s research examines the cellular mechanisms of neuronal plasticity inthe mammalian spinal cord. He is currently investigating mechanisms by whichneurotrophin molecules, such as nerve growth factor (NGF), modify activity of neuralcircuits mediating transmission of nociceptive stimuli and muscle stretch. He is alsointerested in the application of neurotrophins to the recovery of function after neuralinjury. Mendell served as President of the Society for Neuroscience in 1997-1998, andis Chair of the Department of Neurobiology and Behavior.


STUART MCLAUGHLIN, ProfessorPh.D. 1968, University of British ColumbiaStuart McLaughlin is a biophysicist interested in signal tranduction. His laboratorystudies how physical factors (e.g., electrostatics, reduction of dimensionality) choreo-graph the diffusional dance of information through the calcium/phospholipid secondmessenger system. Both theoretical and experimental approaches are used. For example,single molecule enzymology studies are being conducted with a phospholipase C enzyme(PLC) of known structure by combining laser tweezers and microelectrophoresis. PLChydrolyzes the lipid phosphatidylinositol 4,5-bisphosphate (PIP2) to produce two secondmessengers that activate protein kinase C (PKC). The Poisson-Boltzmann equation issolved for realistic atomic models of phospholipid bilayer membranes and the majorPKC substrate, MARCKS, in an attempt to understand how MARCKS sequestersPIP2, then releases the lipid upon phosphorylation by PKC, a phenomenon known asthe myristoyl-electrostatic switch.


LEON C. MOORE, ProfessorPh.D. 1976, University of Southern CaliforniaThe major ongoing research interest of Leon Moore’s lab is the physiology andpathophysiology of the renal microcirculation. At present, the mechanisms responsiblefor vascular dysfunction and vascular and glomerular injury in chronic renal failure(CRF) are being investigated. Among the factors that may contribute to the loss ofnormal vascular reactivity in CRF are low bioavailability of insulin-like growth factor I, rarefaction of the perivascular sympathetic nerves, and abnormalities inendothelial cell nitric oxide production. This work involves long-term animal studies,perfusion of renal arterioles in vitro, histochemical studies, and electrochemical measurement of NO release from renal arteries. Moore’s lab is also interested in thenonlinear dynamics of the tubuloglomerular feedback system. This system is animportant controller of renal function. It displays periodic limit-cycle oscillations and,in some disease states, chaotic fluctuations. The work involves theoretical analyses,computer simulations, and experimental studies.


NICOLAS NASSAR, Assistant ProfessorPh.D. 1992, University Joseph FourierGTP-binding proteins play crucial roles in transmitting cellular signals that are initiatedat the plasma membrane by the activation of various receptors. The proper spatial andtemporal regulations of these proteins are essential for the good functioning of the cell,whereas mutations that impair GTP-hydrolysis lead to cellular pathways that areconstitutively activated. Ras, which serves as a prototype for the small GTP-bindingproteins, is found, for example, mutated at two hot spots in 30% of human cancers.

Current work in Nicolas Nassar’s laboratory focuses on the understanding of theprotein-protein and protein-phospholipid interactions that govern the regulation of theRas-like proteins. X-ray crystallography and other biophysical techniques are usedto unravel the molecular details of the protein complexes that are at the heart ofsignaling pathways. Atomic models are in turn used to design inhibitors that might bedeveloped as drugs to fight the proliferation of human cancers.


W. TODD MILLER, Associate ProfessorPh.D. 1989, Rockefeller UniversityDepartment of Physiology and BiophysicsThe focus of research in Todd Miller’s laboratory is the specificity of signaling by tyrosine kinases. These enzymes play a central role in regulating the growth of normal cells, and constitutive activation of tyrosine kinases can lead to the develop-ment and progression of cancer. The major research goals of the laboratory are: tounderstand how tyrosine kinases recognize their target proteins in cells, to determinehow these enzymes are regulated in normal cells, and to develop strategies to block theaction of oncogenic tyrosine kinases. The laboratory primarily uses biochemical strate-gies to investigate tyrosine kinase structure and function.


MICHAEL R. ROSEN, ProfessorM.D. 1964, SUNY Downstate Medical CenterDirector, Center for Molecular Therapeutics, Columbia Presbyterian Medical CenterMichael Rosen’s research involves three interdependent areas. In the first of theseareas, he studies the developmental changes that occur in the mechanisms that controlcardiac rhythm. His lab group performs research on animal models with a view towardunderstanding the changes in electrophysiologic properties and ionic fluxes that controlthe normal heartbeat, as well as the mechanisms responsible for developmentalchanges in the cardioactive agents.

Rosen also studies the interaction of the heart with elements of the nervous system.Here, he considers both mechanisms of neurohumor action on the heart and nerve cells,as well as the links between the biochemical and electrophysiologic control mechanism.In Rosen’s studies of cardiac arrhythmias and their prevention and treatment, he isinterested in the events that govern the initiation of the heartbeat in various patho-logical settings. The central goal of the work is to develop means for the identification,prevention, and treatment of arrhythmias that will be readily applicable to the patient.

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MARIO J. REBECCHI, Research Associate ProfessorPh.D. 1984, New York UniversityDepartments of Anesthesiology and Physiology and BiophysicsThe aim of Mario Rebecchi’s research is to understand how the catalytic activities ofintracellular phospholipases are controlled, particularly those that hydrolyze inositollipids. Artificial and biological membranes and soluble substrate analogs are employedin the study phosphoinositide-specific phospholipase C (PLC) and its regulatory proteins.The roles of lipid packing and surface potentials on PLC adsorption, penetration, andactivity are under investigation. A combination of physical, chemical, and molecularbiological techniques are employed to understand how these enzymes adsorb to mem-brane surfaces and to identify those features of the protein important to processivecatalysis at the membrane/solution interface. Of special interest are the distributionand dynamics of PLC and its substrate in living cells, which are studied by fluores-cence microscopy using the latest imaging technology.


DANIEL P. RALEIGH, ProfessorPh.D. 1988, Massachusetts Institute of TechnologyDepartment of ChemistryDaniel Raleigh’s research is centered on three complementary topics: studies of proteinfolding, the role of improper protein folding in human disease, and protein design. Anunderstanding of how proteins fold is one of the major unsolved problems of modernbiochemistry. The last few years have seen an explosion of interest in the protein-foldingproblem. New theoretical approaches and new experimental methods have beendeveloped and applied to a variety of interesting systems. These developments coupledwith the growing realization that protein misfolding plays an important role in a numberof human diseases has fueled continued interest in this area. His investigations ofprotein misfolding are directed towards understanding the basis for the pathologicalaggregation of polypeptide hormones in certain diseases. Work on protein design iscentered on methods to rationally improve the properties of proteins. Raleigh’sresearch involves a wide range of techniques, including but not limited to peptidesynthesis, protein chemistry and molecular biology, multidimensional NMR, rapidkinetic measurements, and computational studies.


SAMI I. SAID, ProfessorM.D. 1951, University of Cairo, EgyptDepartment of Medicine, Pulmonary and Critical Care Division, School of MedicineSami Said has a primary appointment in the Department of Medicine (Pulmonary andCritical Care Division) as well as joint appointments in the Departments of Physiologyand Pharmacology. He is also a physician at the Northport VA Medical Center, where heis Associate Chief of Staff, Research and Development. Said’s work with vasoactiveintestinal peptide (VAS) began with its discovery, first in the lung and intestine, thenin the brain and nerve cells. His overall objective is to define its physiological role, itsrelationship to disease, and its therapeutic potential. Disease conditions in which basicknowledge of this peptide may be highly relevant include bronchial asthma, acute lunginjury, inflammation and tissue injury, and neuronal cell death and degeneration (bothacute and chronic). Said and his colleagues employ physiological, pharmacological,biochemical, and molecular biological techniques, and include the use of cells in culture,tissue strips, isolated organ preparations, anesthetized animals, and, most recently,clinical trials in human subjects.


NICOLE S. SAMPSON, Associate ProfessorPh.D. 1990, University of California at BerkeleyDepartment of ChemistryNicole Sampson’s research combines the areas of bio-organic chemistry, biochemistry,and molecular and cellular biology. She is interested in enzyme mechanisms of confor-mational changes, and has focused on structure-function studies of steroid-binding andbarrelenzymes. She has developed experimental probes for testing how cholesteroloxidase interacts with the lipid membrane. These studies are important for investigationsof membrane structure with cholesterol oxidase and understanding its insecticidalproperties. She is also interested in the role of the ADAM family of cellular ligands inmammalian fertilization. Recently, her laboratory identified the receptor for oneADAM protein, fertilin, which is important for sperm-egg binding as _6_1 integrin.Peptido-mimetics of receptor-ADAM ligand interactions are being synthesized andtested to investigate the roles of other ADAM proteins.


CLINTON T. RUBIN, Director of the Program in Biomedical Engineering and Professor Ph.D. 1983, Bristol UniversityDepartments of Anatomy, Bioengineering, and OrthopaedicsThe focus of Clinton Rubin’s work is aimed at understanding the cellular mechanismsresponsible for the growth, healing, and homeostasis of bone. More specifically, he isinterested in how biophysical stimuli (i.e., mechanical, electrical, temperature, magnetic,pressure) mediate these responses. The clinical significance of this work is applicableto the inhibition of osteopenia, the promotion of bony ingrowth into prostheses orskeletal defects, and the acceleration of fracture healing. These goals are approachedvia interdisciplinary studies at the biochemical, molecular, cellular, tissue, organ,computational (e.g., FEM), and clinical levels.


RICHARD B. SETLOW, Senior BiophysicistPh.D. 1947, Yale University Biology Department, Brookhaven National Laboratory Richard Setlow is a member of the National Academy of Sciences. He is interested inthe quantitative effects of ionizing, ultraviolet, and sunlight radiations on moleculesand on living creatures. He showed, using back cross hybrid fish of the genusXiphophorus that have only one tumor suppresser gene for melanoma, that the mostimportant spectral region in sunlight responsible for inducing melanomas was in thelonger ultraviolet, the so-called UVA (320-400 nm). These wavelengths are notabsorbed by conventional sunscreens.

Setlow is now working on the use of the Japanese fish, Medaka, to investigate therisks of the high-energy, high-atomic-number cosmic rays that would be encountered byastronauts on trips beyond Earth’s orbit, by measuring germ cell mutations in exposedmales. Wild type males will be exposed to nuclei from a high-energy accelerator atBrookhaven National Laboratory and mated to females with five homozygous recessivecolor loci. The developing eggs are observed microscopically for dominant lethals and forcolor mutations so as to obtain mutation frequencies as a function of dose.


HERMANN SCHINDELIN, Associate ProfessorPh.D. 1994, Free University, Berlin Department of Biochemistry and Cell BiologyOne major goal of Herman Schindelin’s laboratory is to study the enzymes involved inthe biosynthesis of the Molybdenum Cofactor (Moco) by protein crystallography andbiochemical methods. Biosynthesis of the Moco is an evolutionary-conserved pathwayfound in organisms as diverse as bacteria and humans. Deficiencies in the enzymesresponsible for Moco biosynthesis in humans lead to severe health problems andpremature death. Schindelin is also interested in enzymes containing the Moco. He isinvestigating their catalytic properties and the role of the cofactor during the catalyticmechanism. A second focus of his group is to study the ubiquitin-dependent proteindegradation pathway, which is a highly complex, temporally controlled, and tightlyregulated pathway. Abnormalities in ubiquitin-mediated protein degradation havebeen shown to cause pathological conditions, including malignant transformations,abnormal immune and inflammatory responses, as well as genetic and neurodegenerativediseases. Schindelin’s group is focusing on the structure analysis of a ubiquitin-activating enzyme and a ubiquitin ligase in complex with its specific target.


SUZANNE F. SCARLATA, Associate ProfessorPh.D. 1984, University of IllinoisDepartment of Physiology and BiophysicsSuzanne Scarlata’s laboratory is interested in the role of lipid membranes in regulatingthe association and oligomerization of membrane proteins. The association of membraneproteins is viewed by several biochemical and biophysical techniques, the most prominentof which is fluorescence spectroscopy. Currently, both traditional and newly developedfluorescence methods are being used to study two different biochemical problems. Thefirst of these is the mechanism through which G protein subunits activate phospholipaseC effectors. These studies include the energetics and kinetics associated with these inter-actions and the role of modular domains in mediating associations and activation. Thesecond problem seeks to understand the specific molecular interactions that drive theassembly of HIV 1 proteins on the membrane surface of host proteins and the role ofdifferent cellular factors in assembly. These studies involve fluorescence techniques, aswell as light scattering, sedimentation, and molecular footprinting.


SANFORD SIMON, ProfessorPh.D. 1967, The Rockefeller UniversityDepartment of Biochemistry and Cell Biology Acute and chronic inflammatory responses are important host defenses against for-eign substances or pathogens. These responses are largely mediated by neutrophilsand macrophages, which release proteases, cytokines, and a number of other media-tors of inflammation in the course of defending the host. Sanford Simon’s laboratorystudies the mechanisms of action of serine proteases and metalloproteases from acti-vated neutrophils and develops specific inhibitors to control the tissue destruction thatmay otherwise injure the host during an inflammatory response. The lab’s methodsinclude biophysical probes of enzyme active sites and kinetic measurements. The lab alsoallows the smooth muscle cells to deposit their matrix on porous membrane filters,which we then use to study invasive migration of neutrophils and macrophages inresponse to chemotactic stimuli. To understand how inflammatory cells communicate,Simon studies paracrine mechanisms of activation by cytokines, using immunofluores-cence and flow cytometry to measure levels of expression of cell surface receptors andother marker proteins that are sensitive to the state of activation of the cells.


STEVEN O. SMITH, Professor and Director, Center for Structural BiologyPh.D. 1985, University of California at BerkeleyDepartment of Biochemistry and Cell BiologySteven Smith is the Director of Structural Biology in the Centers for Molecular Medicine.His research involves understanding in structural and chemical terms how membraneproteins function. His work focuses on the molecular mechanisms of signal transductionby G protein-coupled receptors and receptor tyrosine kinases, and the mechanism ofselectivity and gating by ion channel proteins. His research on signal transductionmechanisms mediated by protein conformational changes has involved the visual pigmentrhodopsin, a seven-transmembrane helix receptor in vertebrate rod cells responsible forvision in dim light, and CCR5, one of the co-receptors for entry of HIV into T-cells.Current projects involving signal transduction mediated by receptor oligomerizationfocus on two receptor proteins—the neu or erbB-2 receptor and the platelet-derivedgrowth factor (PDGF) receptor—that can be constitutively activated through inter-actions involving their transmembrane domains. Finally, structure-function studies are inprogress on phospholamban, a 52-residue ion channel protein found in cardiac sar-coplasmic reticulum (SR) that regulates calcium levels across the SR membrane.


S. MURRAY SHERMAN, ProfessorPh.D. 1969, University of PennsylvaniaDepartment of Neurobiology and BehaviorThe goal of Murray Sherman’s lab is to understand the role of the thalamus with a sec-ondary emphasis on the visual pathways. The thalamus plays a key role in two relatedways. First, thalamic circuitry controls the cellular properties of relay cells via effectson voltage-gated channels, and this has a dramatic effect on the nature of signalsrelayed to cortex. It also seems that differing behavioral states (e.g., attention levels,and sleep vs. wakefulness) affects this circuitry. Second, new evidence that this lab ispursuing indicates that most or all corticocortical communication is not passed alongvia direct corticocortical pathways as conventionally thought, but instead involvesre-entry circuits in the form of cortico-thalamo-cortical pathways. Major approachesinvolve in vitro recording from thalamic slices of mammals to investigate the physiologyand pharmacology of local thalamic circuits, electron microscopy to determine theanatomical basis for local thalamic circuits; and recording single thalamic neurons fromconscious, active monkeys to ascertain the effects of behavioral state on the functionalproperties of thalamic neurons.


CHARLES SPRINGER, ProfessorPh.D. 1967, Ohio State UniversityNuclear Medicine, Brookhaven National LaboratoryThe aim of Charles Springer’s work as a senior scientist at Brookhaven NationalLaboratory is to develop new, in vivo nuclear magnetic resonance (NMR) techniques.His research group has recently demonstrated a new form of magnetic resonanceimaging called Relaxographic Imaging. This involves the production of images of anobject based on the distribution of nuclear magnetization relaxation times. Thispowerful approach allows direct imaging of the distribution of diagnostic contrastagents. It can be used to form a map of the cytoplasm of muscle cells to provide ameans of discriminating between intracellular and extracellular edema. It also produceshigh-contrast, high-resolution images of tumor masses and may allow their detectionat a very early stage. Springer is also working in the area of Functional Imaging.This provides a non-invasive way to visualize changes in the level of paramagneticdeoxyhemoglobin in the blood during mentation that cause microscopic changes inbulk magnetic susceptibility. Springer’s group is actively involved in the theoreticalaspects of tissue NMR.


ILAN SPECTOR, Associate ProfessorPh.D. 1967, University of Paris, France A general research interest of Ilan Spector’s laboratory is the discovery of newpharmacological agents derived from marine organisms, which represents today therichest untapped reservoir of biologically active agents with unique structural featuresnot encountered in terrestrial natural products. The lab has identified an extensivebattery of marine natural products that target the actin cytoskeleton, a majordeterminant of cell shape, motility, and adhesion, which control important biologicalprocesses such as tissue morphogenesis, cell growth and differentiation, wound healing,and malignant transformation. Spector and his team are using these agents to specif-ically perturb cytoskeletal structures, to modulate the state of actin filament assembly,and to gain insight into the functions, organization, and dynamics of the actincytoskeleton. The group has also identified new classes of marine compounds that reg-ulate cellular growth and differentiation and are investigating their mechanism of action.


IRENE C. SOLOMON, Associate Professor

Ph.D. 1994, University of California at DavisIrene Solomon’s laboratory seeks to understand the mechanisms by which centralnervous system (CNS) neurons integrate peripheral and central inputs in respiratoryand cardiovascular control. Solomon is investigating CNS sites and neuropharmaco-logical mechanisms mediating hypoxic ventilatory and sympathetic responses. Severebrain hypoxia which may result from numerous cardiovascular and respiratory diseases(e.g., stroke, corpulmonale) results in a shift from respiratory depression excitation(gasping) and an increase in sympathetic output. Solomon’s lab examines the brainstemsites and neural mechanism(s) responsible for this shift in respiratory patterning, aswell as the synchronization of the central respiratory cycle with sympathetic activity.The experimental approach in the laboratory involves neuroanatomical mapping, electro-physiological recording, and neuropharmacology. Another focus of research examinesreflex and central neural control of the airways.


WILLIAM VAN DER KLOOT, Distinguished Professor EmeritusPh.D. 1952, Harvard UniversityDepartment of Physiology and BiophysicsWilliam Van der Kloot is interested in synaptic transmission, using the frog and mouseneuromuscular junctions as models. The transmitter, acetylcholine, is packaged invesicles in the nerve terminal. Transmitter is released by exocytosis, both sponta-neously and at a greatly increased rate following nerve stimulation. Van der Klootand his laboratory group study the mechanism for loading acetylcholine into thevesicles, the regulation of the quantity loaded by hormones, drugs, and other treatments.They are also investigating the kinetics of the release of transmitter quanta followingnerve stimulation.

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HSIEN-YU WANG, Research Associate ProfessorPh.D. 1989, Stony Brook UniversityHsien-yu Wang’s long-term goals are to study transmembrane signaling by heterotrimeric G-proteins, focusing on their role in mediating Frizzled receptors. TheFrizzled 1 gene structure has been solved and the cell-surface receptor for Wnt ligandsis heptihelical, suggestive of coupling by members of the heterotrimeric G-proteinfamily. Purification of active Wnt ligands has not been successful and the Wang lab hasnow succeeded in crafting a new strategy with which to study the signaling of Frizzledreceptors, creating chimeric receptors in which the cytoplasmic domains of Rfz1 andRfz2 are substituted into the beta-adrenergic receptor (b2AR). The b2AR/Rfz2 chimera,for example, signals with Rfz2 character to downstream effectors in Xenopus, zebrafish,and mammalian cells, although now fully activated by an agonist ligand for the b2AR.With this proof-of-concept, a b2AR/Rfz1 chimera has been created as a tool for study ofsignaling and biology of Rfz1 in F9 teratocarcinoma stem cells in culture. Preliminarydata demonstrate that activation of the b2AR/Rfz1 chimera with isoproterenol promotesstabilization of beta-catenin, JNK activation, and primitive endoderm formation in F9cells and expression of target gene (Siamois and Xnr3) in Xenopus.


PETER J. TONGE, Associate ProfessorPh.D. 1986, University of Birmingham, U.K.Department of ChemistryPeter Tonge’s research focuses on developing precise structure-reactivity correlationsfor enzyme-catalyzed reactions using spectroscopic techniques, such as vibrationalspectroscopy and NMR spectroscopy. Detailed information is obtained concerning thegeometry of the bound substrate, the energy of specific enzyme-substrate contacts, andthe changes that occur in the electronic structure of the substrate on binding. Thisapproach provides fundamental insight into the mechanism of enzyme catalysis andfacilitates the rational design of enzyme inhibitors for use as novel therapeutics. Drug-design efforts are focused on an enzyme from Mycobacterium tuberculosis, which is atarget for the antitubercular drug isoniazid. A recent highlight of this work has identifiedtriclosan, an additive in many personal care products such as toothpaste, as an inhibitorof this enzyme. Tonge is also investigating how proteins cause and stabilize chargerearrangement with emphasis on enzymes involved in fatty acid oxidation. Finally,research efforts on green fluorescent protein (GFP) are seeking to determine how the flu-orescent properties of the GFP chromophore are modulated by the protein environment.


RUI-MING XU, Associate ProfessorPh.D. 1990, Brandeis UniversityCold Spring Harbor Laboratory Rui-Ming Xu uses X-ray crystallography to study the structural basis of the protein-RNA interactions involved in pre-mRNA splicing—a fundamental biological processin eukaryotic cells—and the molecular basis of gene expression in general. Xu hasfound that, in many cases, alternative splicing plays important roles in regulating geneexpression during development and differentiation.

In the Xu lab, X-ray crystallography is an effective method for providing thethree-dimensional structure of biological macromolecules at an atomic resolution. Xu’sapproach is to determine the structure of individual proteins and protein-RNA com-plexes. He hopes to use this structural information to learn how these proteins achievetheir RNA-binding specificities. A long-term goal is to assemble this information ofindividual spliceosomal components into a global picture to aid in the understanding ofthe dynamic process of pre-mRNA splicing.


STANISLAUS S. WONG, Assistant ProfessorPh.D. 1999, Harvard UniversityStanislaus Wong and his group have wide-ranging interests in the science of nano-technology. The focus of the research is to understand intermolecular interactions atthe nanometer scale, critical in understanding problems such as friction and lubrication,binding energies on surfaces essential for the design of effective catalysts, as well asphenomena such as chemical and biological self-assembly. The Wong lab studiesfundamental structure-correlations in unique nanostructures (as low as 1 nm in dimen-sion), such as carbon nanotubes and oxide nanocrystals, with an intent on exploitingthem for novel applications in physics, chemistry, and biology. Some of Wong’s workhas been featured in a cover article in the international scientific journal Nature. Wongholds a joint appointment at Brookhaven National Laboratory.


THOMAS W. WHITE, Assistant ProfessorPh.D. 1994, Harvard UniversityIntercellular channels present in gap junctions allow cells to share small molecules andthus coordinate a wide range of behaviors. In vertebrates, a large family of genes knownas connexins encodes these gap junctional channels, and mutations in human connexinsunderlie a variety of diseases, including deafness, skin diseases (keraotdermas),demylinating neuropathies, and lens cataracts. In addition, gene targeting of connexinsin mice has provided new insights into connexin function and revealed a variety ofunexpected phenotypes. Thomas White is interested in how different members of theconnexin family fulfill unique functions in tissue homeostasis, and use genetically engi-neered mice to probe the unique communication requirements of different tissues. Healso uses electrophysiological assays to determine the alterations in channel functionthat arise from connexin mutations that cause human hereditary disease.


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Perspectives

Alumna Amy B. Hall, Ph.D.Postdoctoral Fellow, Department of Cell Biology, Harvard Medical SchoolI am currently a postdoctoralfellow in the Department of CellBiology at Harvard MedicalSchool. My experience as a grad-uate student in the Departmentof Physiology and Biophysics atStony Brook was incrediblyexciting and rewarding. Theinfrastructure created by thedepartment and my advisor hasallowed me to pursue my ownresearch interests. Furthermore,the wide variety of courses andlaboratories creates a compre-hensive learning environment.The accessibility of the facultymembers and the first-classresearch facilities at Stony Brookand its affiliated institutions,Brookhaven National Laboratory

and Cold Spring Harbor Laboratory, provided many uniqueresearch opportunities. In addition, the ability to focus on teach-ing, as a teaching assistant, was truly one of the most rewardingexperiences of my graduate career.

Alumnus Francisco J. Martinez-Wittinghan, Ph.D., Research Scientist, Stony Brook UniversityThe Graduate Program in Physiology and Biophysics is veryappealing since it is a highly interdisciplinary program withjoint appointments with several other departments andresearch facilities (i.e. Brookhaven National Laboratory).When I was looking for programs from my country (Colombia,

South America) I came across a number of interdisciplinaryprograms, but what made this program stand out was thepresence of many well-known and respected researchers.Once I came to the program, I also found a friendly environ-ment with faculty and staff who are always willing to helpand provide advice.

Whether you come focused or undecided about yourresearch interest, this program provides the opportunity todevelop your scientific knowledge and reach your goals. Icame with interest in ionic channels and electrophysiologybut throughout rotations in different laboratories I learnedother techniques beyond my primary focus; now I am able toapply them in my research. If you come undecided you havenumerous possibilities of rotations to choose from.

The program is flexible enough to accommodate theextensive range of research interests in the area of Physiologyand Biophysics. For me, the basic course work gave me abroad perspective of the different approaches to questions inphysiology and biophysics, and the electives were tailored tomy more specific research interests.

Lastly, the program has a very nice multiculturalatmosphere to the point that it hosts an International CuisineFestival every December where everybody is welcome tobring food representing their native culture.

Graduate students Marvin O’Neal (back to camera) and Zaher Nahle at theVan der Kloot Symposium Graduate Student Poster Session.

The accessibility ofthe faculty membersand the first-classresearch facilities at Stony Brook University and itsaffiliated institu-tions, BrookhavenNational Laboratory andCold Spring HarborLaboratory,provided manyunique researchopportunities.

Graduate student Deeptankar Demazumder discusses his research with Distinguished Professor William Van der Kloot at the annual Van der KlootSymposium.

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Spotlight on Alumni

1997 Loren Runnels, Assistant Professor, Rutgers University

Monique Van der Molen, HSC Communications (Harrison, Starr, Weiner & Biteler)

Jiying Wu, Post-Doctoral Fellow, Stony Brook University, Department of Physiology and Biophysics

1999 David Cullinan, Post-Doc, Harvard Medical School

John Elliott, National Research Council Associate, NIST, MD,Biotech Division

Shari Spector, Joint Post-Doctoral Fellow, Departments of Biologyand Chemistry, Massachusetts Institute of Technology

Tieli Wang, Post-Doctoral Associate, Fox Chase Cancer Center,Philadelphia, PA

Michael Ziebell, Post-Doctoral Fellow, Department of Neurobiology,Harvard University

2000 Christopher Coburn, Post-Doctoral Fellow, Stony Brook University

Patricia Pellicena, Post-Doctoral Fellow, Department of Chemistry,University of California at Berkeley

Amy Walsh, Post-Doctoral Fellow, Department of Cell Biology, Harvard Medical School

2001 Brenda Daniels, Post-Doctoral Fellow, Brookhaven National Laboratory

Hyun Kim, Post-Doctoral Fellow, Stockholm University

2002 Deeptankar Demazumder, Medical Student and ResearchAssociate, Medical College of Virginia

Francisco Martinez, Research Scientist, Stony Brook University

Lori Seischab, Research Scientist, Stony Brook University

Edward Tall, Post-Doctoral Fellow, Department of Anesthesiology,Stony Brook University

Jiyao Wang, Post-Doctoral Fellow, Cornell Medical University

Current Positions Held by Selected Program Alumni (Ph.D. unless noted)

1989 Shinn-Zong Lin, Department of Neurosurgery, Tri Services General Hospital and Medical School, Taiwan

Carlos Oliva, Researcher, McNeil Pharmaceuticals

1990 Fang Chang, Cardiologist, Cornell Medical Center

Wendy Gruner, Physics Teacher, New York City High School

Adam Rich, Senior Research Scientist, Bristol-Meyers-Squibb

Shan Ping Yu, Department of Neurology, Washington University, St. Louis

1992 Jianmin Cui, Assistant Professor, Bioengineering, Case Western University

Phillip Ortiz, Assistant Professor, Department of Biology, Skidmore College

Gerrard Sanacora, Resident, Department of Psychiatry, Yale New Haven Hospital

Susana Velasco, Researcher, MERCK Research Institute

1993 Jiann-Liang Chen (M.D./Ph.D.), Neurosurgeon,Tri Services General Hospital and Medical School, Taiwan

HanGang Yu, Assistant Professor, Physiology, New York Institute of Technology

1994 Maria Cifuentes, Research Scientist, Ford Hospital, Michigan

Junyuan Gao, Research Faculty, Department of Physiology and Biophysics, Stony Brook University

Jiyun Kim (M.D., Ph.D.), National Institutes of Health

Jingyi Shi, Research Associate, Case Western University

1995 Yong-Hwan Lee, Research Faculty, Department of Biochemistry, University of Minnesota

1996 Christopher Kushmerick, Faculty, UFMG-Federal Universityin Minas Gerais, Belo Horizonte, Brazil

James R. Tonra, Staff Scientist, Millennium Pharmaceuticals, Cambridge, MA

Dr. Nada Abumrad (left) assists Drs. Azzedine Ibrahimi (center) and Claire Bastie with their research.

27

This image from the lab of Irene C. Solomon shows excitation of phrenic motor output evoked by discrete focal hypoxia in the pre-Bötzinger complex demonstrating central hypoxic chemosensitivity of the respiratory rhythm generator.

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The University is located in one of the East Coast’s mostdesirable spots—the North Shore of Long Island, about 60miles east of New York City (midway between Montauk andManhattan). The tranquil waters of Long Island Sound arejust minutes away to the north, and the white sandy beachesof the Atlantic Ocean beckon southward.

North of the University, within easy bicycling distance,lies the historic village of Stony Brook. Its quaint shoppingarea was created by Ward Melville, heir to the Thom McAnshoe fortune. (Ward and his wife, Dorothy, donated the landwhere the campus now stands.) One of the best ways to expe-rience Stony Brook village is to pick up an ice cream conefrom the Brook House luncheonette, sit on the village green,and enjoy an unobstructed view of the sunset or the fisher-men trying their luck at the dock. Across the street is thelandmark Three Village Inn, dating back to pre-Revolution-ary days. The Stony Brook Grist Mill, built in 1751, is a work-ing mill open to the public for tours. Local cafes and book-stores make the Stony Brook Village area a great place tospend the day.

Cultural DiversityCulture abounds on Long Island. Although Manhattan is onlya train ride away, theatre lovers need travel no further thanthe Staller Center for the Arts. Located on the Stony Brookcampus, the Staller Center presents hundreds of plays, con-certs, and special events each year. It houses the 1,100-seatMain Stage Theatre and a 4,700-square-foot art gallery.Staller’s summer film festival is recognized as a “mini-Sun-dance.” For those who enjoy cultural events, the new CharlesB. Wang Center, Celebrating Asian and American Cultures,is a comprehensive conference facility and showcase for thearts, featuring exhibit spaces, interior and exterior pools,gardens, and a chapel. In Stony Brook village, the LongIsland Museum of American Art, History, and Carriages is amust-see for art and history lovers. The complex houses oneof the world’s largest collections of horse-drawn carriagesand the paintings of William Sidney Mount, a Stony Brooknative who became the nation’s first famous “genre” painter.

Just a 30-minute drive west, the village of Huntingtonoffers the Cinema Arts Center, where one can view the latest“indie” films. In recent years Long Island has developed areputation for its blues music scene, but a growing number ofcoffeehouses present other types of music as well; folk, blue-grass, and jazz are just a few of the styles you’ll find.

For sports and fitness enthusiasts, the University has a5,000-seat indoor Sports Complex complete with running trackand a pool. The new outdoor 8,500-seat stadium holds majorsporting events and concerts. The Paul Simons Memorial Bicy-cle Path—six miles of well-lit, paved trails that encompass thecampus—is used year-round by cyclists, skaters, and runners.The Student Activities Center houses the Eugene WeidmanWellness Center, which offers fitness classes in everything fromaerobics to yoga, and state-of-the-art exercise equipment. Ifprofessional sports are your thing, Long Island has its own icehockey team, the New York Islanders, and minor-league base-ball team, The Long Island Ducks. The excitement of MadisonSquare Garden, Yankee Stadium, and Shea Stadium (home ofthe New York Mets) is only 60 miles away.

Long Island is heaven for “foodies.” Just about every cuisine you might think of can be sampled here, from seafoodshacks to the latest in nouveau cuisine. The region’s growingreputation as a producer of excellent wines makes for a pleas-ant day’s tour of Long Island wineries.

For those who like to “shop till they drop,” Long Islanddoes not disappoint. It’s home to Roosevelt Field, the

Living in Stony Brook

The Academic Mall, a focal point of campus life, features a fountain, benches,and areas for students to unwind before class.

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Bridgeport, Connecticut, makes the area a convenient jump-ing-off point for trips to New England.

Life at Stony Brook has something for everyone, no matter where you’re from or what your goals may be. Thediversity of the people who live, study, and work here helpsour community thrive. There is the tranquil pace of the surrounding village, which has managed to preserve an old-fashioned, small-town atmosphere. At the same time, thereare the cutting-edge resources and the abundant internationalculture of the University itself.

nationally known shopping mall, and the Smithhaven Mall,which is just minutes from campus. Long Island offers everytype of store, from the nation’s first supermarket (KingKullen) to retail outlets, including the popular Tanger Outletin Riverhead, featuring more than 200 stores.

Family LifeStony Brook is a great place for families. The University strivesto provide students with everything they need to create a homeaway from home, from the Barnes & Noble bookstore, full-ser-vice deli, and health care facilities to the craft sales, seasonalfarmer’s markets, and DVD loans at the library. One- and two-bedroom apartments for couples and families, and three- andfour-bedroom apartment shares for single graduate studentsare available on campus at the University Apartments. The Off-Campus Housing Service office will also assist students in find-ing suitable arrangements close to campus. For families withyoung children, the Stony Brook Child Care Center offers daycare for children ages six weeks to five years old.

Nature’s BountyLong Island is rich in wild landscapes. The campus is close tothe Fire Island National Seashore. To the east lies the uniqueecosystem of the pine barrens, where The Nature Conser-vancy maintains a number of hiking trails and nature pre-serves. The area’s miles of seacoast make it paradise forboaters, anglers, and windsurfers. In fact, the campus is sur-rounded by Long Island maritime heritage. Port Jefferson,Setauket, and Stony Brook were once bustling shipbuildingcenters; today the ferry that links Port Jefferson to

of shopping areas, historical landmarks, beautiful parks and beaches, andBroadway-quality entertainment at the Staller Center on campus.

Situated between Manhattan and Montauk, Stony Brook offers the best of both worlds. Our central location provides students with access to a variety

From quaint flower shops to the popular Three Village Inn, Stony Brook village provides hours of shopping as well as several dining possibilities.

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Application and Admission

Application Materials and DeadlinesApplication materials can be obtained by calling the graduateprogram administrator, (631) 444-2299, or by writing to theDirector of Graduate Studies, Graduate Program in Physiologyand Biophysics, Stony Brook University, Stony Brook, NewYork 11794-8661. Students may request application materialsor apply online via the Graduate School Web site atwww.grad.sunysb.edu.

In addition to a completed application form, candidatesmust also provide the following: official transcripts of allundergraduate and, if applicable, graduate coursework; offi-cial Graduate Record Examination Scores (Stony Brook’s codefor score reporting is 0213); three letters of recommendation;and a nonrefundable $50 fee. Foreign students must addition-ally supply an official TOEFL (Test of English as a ForeignLanguage) score of at least 550.

All application materials should be sent directly to theGraduate Program in Physiology and Biophysics, Stony BrookUniversity, Stony Brook, New York 11794-8661, USA.

The deadline for receipt of these materials is generallyFebruary 1 for consideration for Fall admission.

AdmissionsIn addition to the above,applicants should have abaccalaureate degree withpreparation in mathemat-ics through calculus andone year each of biology,chemistry, and physics.Additional preparation inthe following subjects isstrongly recommended:organic chemistry, bio-chemistry, cell biology, andphysical chemistry. Defi-ciencies in specific areasmay have to be metthrough additional coursesduring the first two yearsof graduate study.

Financial Support and BenefitsStudents accepted to the department’s graduate studies program are offered a yearly stipend and full tuition waiver.After three semesters, students must choose a faculty member and laboratory with which to conduct their doctoralresearch. The student’s stipend is then usually providedthrough the faculty member’s individual research grants.Basic health insurance is available to all graduate students.All applicants are considered for financial aid; a separateapplication is not required.

Department and Program Web SitesProspective graduate students can also find useful informationabout Stony Brook on the University’s home page on theWorld Wide Web (www.stonybrook.edu). The first page of thissite directs the reader to information about the Stony Brookarea, campus events, libraries, and research programs. It alsolinks to a list of Web sites for every department and programon campus. The Department of Physiology and BiophysicsWeb site (www.pnb.sunysb.edu) is on this list, along with thoseof the Molecular and Cellular Biology, Biochemistry, Genetics,and Structural Biology departments, and other graduate pro-grams relevant to training and research in physiology and bio-physics. Our site offers more detailed information about theprogram, our faculty, and our research. In many cases, facultymembers have included information about the students whowork with them, photographs from their laboratories, andsummaries of current research and publications.

Dr. Thomas White works with Graduate Student Dwan Gerido.

The Health Sceinces Center is home toPhysiology and Biophysics.

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This is a publication of Stony Brook University, Office of Communications, Stony Brook, NY 11794-0605. Yvette St. Jacques,Assistant Vice President; Joanne Morici, Director of Editorial Services; Shelley Colwell Catalano, Project Manager and Editor;Karen Leibowitz, Art Director; Kim Anderson, Designer. Photos pro-vided by the Department of Physiology and Biochemistry and MedicalPhotography/Marylou Stewart. Photo on page 28 by Matthew Klein.

For more information about Stony Brook, visit us on the Web atwww.stonybrook.edu.

Stony Brook University is an affirmative action/equal opportunity educator and employer. This publication is available in alternative format on request.

On the cover: Ca2+-Calmodulin (upper molecule) prepares to bind toand translocate the effector domain of MARCKS from the membraneto the adjacent aqueous solution. Courtesy Stuart McLaughlin.

How to Get Here

Directions to Stony Brook University

By AutomobileTake the Long Island Expressway(Route 495) to exit 62 N; followNicolls Road (Route 97) north fornine miles.

By RailroadTake the Long Island Rail Road’sPort Jefferson line (631-231-LIRR) to Stony Brook.

By BusCall Suffolk County Transit (631-852-5200) for schedules, rates,and routes for buses to campusfrom many local towns.

By AirLand at Kennedy or LaGuardia Airport, 50 miles west of campus, orat Long Island MacArthur Airport(631-467-3210), ten miles south ofcampus. All airports offer limousineand taxi service to campus

Ferry ConnectionConnecticut car ferries run fromBridgeport to Port Jefferson (631--473-0286) and from New London to Orient Point (631-323-2525); call for schedules and information.

University Area

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Long Island

1) The structure of the catalytic active site of adenylyl cyclase. From the laboratory of Roger Johnson. 2) A ribbon diagram of the protein Trio solved by X-ray crystallography.Structure determined in the lab of Nicolas Nassar. 3) A mouse lens with genetically altered connexin expression develops a cataract. From the lab of Thomas White.

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2 3

Confocal image showing astrocytic expression of the gap junction protein connexin26 (green) in relation to tyrosine hydroxylase immunoreactive neuronalsoma and processes (red) in the rostral ventrolateral medulla from adult rat. From the lab of Irene C. Solomon.

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