James Jonkman, M.Sc.
Advanced Optical Microscopy Facility (AOMF)
University Health Network
Ontario Cancer Institute, Princess Margaret Hospital
610 University Ave., Room 7-319
Toronto, ON, M5G 2M9
Tel: (416) 946-4501 x5655

Email: jjonkman@uhnres.utoronto.ca

Research Interests

My goal is to establish the Advanced Optical Microscopy Facility (AOMF) at OCI/PMH as a leading center for optical microscopy in the Toronto area. The AOMF provides researchers with the latest in optical micro-imaging technology for the observation of cells and tissues. We also provide training and support on various instruments and teach users techniques of optical micro-imaging ranging from the basics of transmission and fluorescence microscopy to modern live-cell methods. Software and training for image processing are also available.

My work in the Light Microscopy Group at EMBL focused mainly on three aspects of advanced live-cell experiments using the Compact Confocal Camera (CCC), a confocal microscope originally developed in collaboration with Carl Zeiss Germany. First, I optimized the optical arrangement of the CCC for live-cell imaging by incorporating appropriate lasers, filters, and detectors for viewing Green Fluorescent Protein (GFP) and its wavelength-shifted variants (most notably CFP and YFP). Second, I developed macros for performing photobleaching, automatic refocus, online analysis and graphing of data during custom time-series acquisitions. Third, I participated in several collaborative investigations into dynamic cellular processes: the kinetics of cytoskeletal proteins during mitosis in the social amoeba Dictyostelium; the roles of actin, myosin, and tubulin during muscle tissue morphogenesis; mitotic spindle assembly in the worm C elegans; and the motility of nuclear proteins.

Additionally, I played a major role in the organization of the EMBO Practical Course on Live-Specimen Light Microscopy (May, 2002). Through lectures and practical, hands-on sessions, students were taught all relevant aspects of deriving important parameters from living specimens using optical techniques. Basic topics included transmission and fluorescence microscopy, confocal microscopy, multi-photon microscopy, image processing, and two- and three-dimensional time-lapse microscopy. Advanced topics included Fluorescence Correlation Spectroscopy (FCS), Fluorescence Recovery After Photobleaching (FRAP), Fluorescence Resonance Energy Transfer (FRET), Total Internal Reflection Fluorescence (TIRF) Microscopy, and extended-resolution microscopy.

Education and Experience

Research Technician, (2002 - present), Ontario Cancer Institute / Princess Margaret Hospital, Toronto, Canada.

Research Technician, (2000 - 2002), European Molecular Biology Laboratory, Heidelberg, Germany.

Staff Scientist, (1999 - 2000), Photonics Research Ontario, Biophotonics Facility, Toronto, Canada.

Technologist, (1998 - 1999), Photonics Research Ontario, Biophotonics Facility, Toronto, Canada.

M.Sc. Physics (1998), University of Waterloo, Waterloo, Canada.

B.Sc. Physics (1995), McMaster University, Hamilton, Canada.

Recent Publications

Bretschneider, T., Jonkman, J., Köhler, J., Medalia, O., Barisic, K., Weber, I., Stelzer, E.H.K., Baumeister, W., and Gerisch, G. Dynamic organization of the actin system in the motile cells of Dictyostelium. Journal of Muscle Research and Cell Motility, Special Issue: Dictyostelium. ed. D.J. Manstein (in press)

James E.N. Jonkman, Jim Swoger, Holger Kress, Alexander Rohrbach, and Ernst H.K. Stelzer, "Resolution in Optical Microscopy," in Methods in Enzymology, Vol 360: Biophotonics, eds. G. Marriott and I. Parker (2003)

James E.N. Jonkman and Ernst H.K. Stelzer, "Resolution and contrast in confocal and two-photon microscopy," in Confocal and Two-photon Microscopy: Foundations, Applications, and Advances, A. Diaspro Ed., Wiley-Liss, Inc., New York (2002)

Nicholas J. Salmon, James E.N. Jonkman, and Ernst H.K. Stelzer, "The Compact Confocal Camera: Instrument Control Software built around Databases, for Applications in Molecular Biology" in Proceedings of the 12th IEEE International Congress on Real Time for Nuclear and Plasma Sciences. (2001)


optical microscopy, light microscopy, confocal microscopy, fluorescence, optical design, live-cell imaging, FRAP, photobleaching, FRET, GFP.