Examination procedure
Oral exam
Prerequisites
Recommended for PhD students in Nanoscience, suggested for PhD students in Neurosciences, Chemistry, indicated also for PhD students in Physics.
Prerequisites: basic principles of Optics, of Organic and Inorganic Chemistry, and of Quantum Mechanics.
Syllabus
Measurements in microscopy and spectroscopy [1-4] (40 hours)
Noise in measurements, experimental uncertainties, basics of probability distributions, propagation of uncertainties.
Transmission, reflection and epifluorescence microscopy.
Magnification and resolution; contrast techniques; spherical and chromatic aberrations; hints on optical filters and dichroics.
Confocal microscopy: set-up, point spread function, hints on deconvolution, comparison with TIRF and 2-photon microscopy.
Light-matter interaction: fundamentals (also quantum mechanics) and setups for absorption, fluorescence, Raman, and multiphoton excitation. Jablonski diagrams and properties of fluorescence. Organic dyes: chemical structures and exploitation in fluorescence microscopy.
Hints on fluorescent quantum dots. Fluorescent proteins, GFP family.
Diffusion and Brownian motion. Techniques in fluorescence microscopy: colocalization, FRAP-like techniques, FRET, FLIM (fundamentals, instruments, phasors), FCS, super-resolution (RESOLFT, STED, F-PALM, SIM), single molecule spectroscopy and tracking.
Introduction to the structure of biological molecules [6]. Fluorescent proteins and their photophysics. [4]
Basis of molecular and cellular biology [5] (14 hours)
Prokaryotes vs eukaryotes. General organization of the eukaryotic cell. Cytoplasm: membrane structure and transport, intracellular compartments, cytoskeleton, cell signalling. The nucleus: chromosomal DNA and its organization, the Nuclear Pore Complex and nucleus-cytoplasmic transport. Cell cycle and cell division. Cell death. Biology laboratory techniques (Methods for cells growth and analysis; purification and analysis of proteins; DNA and RNA: methods for transfection; analysis of genes expression and function; labelling of molecules of interest: strategies and limits)
In-vivo microscopy and electrophysiology (6 hours)
Bibliographical references
[1] "An Introduction to Error Analysis", J. R. Taylor (Ch. 1-4, 9, 11)
[2] "Microscopy from the very beginning", Dr. H. G. Kapitza, © Carl Zeiss Jena GmbH, 1997, 2nd revised edition, on-line available
[3] "Introduction to Confocal Fluorescence Microscopy", Michiel Müller, edited by SPIE press (WA, USA), second edition (2006)
[4] "Fluorescence Applications in Biotechnology and Life Sciences", edited by Ewa M. Goldys (2009), published by John Wiley & Sons (Hoboken, NJ, USA), Ch. 1-6, 9-11, 16.
[5] "Molecular Biology of the cells", B. Alberts et al. (chosen parts)
[6] "Biophysical Chemistry", Cantor and Schlimmel; Part I