Module S3.01 - Biological microscopy

Coordinator

Prof. Dr. Christoph Biskup

Lecturers

Biomolecular Photonics Group: Prof. Dr. Christoph Biskup, Dr. Kathrin Groeneveld, Dr. Birgit Hoffmann
Single-Molecule Microscopy Group: Prof. Dr. Michael Börsch, Dr. Hendrik Sielaff
BioImaging Group: Prof. Dr. Knut Holthoff, PD Dr. Knut Kirmse
Institute of Molecular Cell Biology: Prof. Dr. Carsten Hoffmann
Institute of Physiology II: Dr. Ralf Schmauder

Schedule

Lectures: every Friday 14.15 - 15.45 (Lecture hall Humangenetik), starting on Oct 19th.
Exercise: every second Friday 16.00 - 17.30 (location will be announced in the lectures)

Contents

Week	Lecturer	Content	Download
1 19.10.2018 14.15-15.45	Biskup	Introduction Microscopy of living cells, biological model systems
2 26.10.2018 14.15-15.45	Biskup	Techniques in fluorescence microscopy I Epifluorescence microscopy, TIRF, confocal laser scanning microscopy, fluorescence lifetime measurements (FLIM), fluorescence anisotropy measurements	Part1 Part2
16.00-17.30	Biskup Hoffmann	Practical exercises: Fluorescence microscopy Demonstration of epifluorescence and confocal fluorescence measurements
3 2.11.2018 14.15-15.45	Biskup	Techniques in fluorescence microscopy II Fluorescence lifetime measurements (FLIM), fluorescence anisotropy measurements	Slides
4 09.11.2018 14.15-15.45	Biskup	Fluorophores I Organic fluorophores for biological imaging, labelling techniques	Part1 Part2
5 16.11.2018 14.15-15.45	Biskup	Fluorophores II Genetically encoded fluorescence proteins	Part1 Part2
6 23.11.2018 14.15-15.45	Börsch	Förster Resonance Energy Transfer (FRET) Principles & methods used to measure FRET: acceptor photobleaching, donor fluorescenece lifetime	Slides
16.00-17.30	Biskup, Hoffmann	Practical exercises: Fluorescence intensity based FRET measurements
7 30.11..2018 14.15-15.45	Börsch	Superresolution techniques SIM, STORM, STED	Slides
16.00-17.30	Biskup, Hoffmann	Practical exercises: Fluorescence lifetime based FRET measurements
8 7.12.2018 14.15-15.54	Börsch	Single molecule measurements Single photon counting, single molecule measurements setups, ABEL trap, single molecule FRET	Slides
9 14.12.2018 14.15-15.45	Schmauder	Illuminating molecular processes FRAP, FLIP, FCS	Slides
10 21.12.2018 14.15-15.45		Lecture is postponed to Feb 1st!
11 11.01.2019 14.15-15.45	Holthoff, Kirmse	Fluorescent indicators Organic indicators for pH, ion concentrations and membrane potential	Slides
12 18.01.2019 14.15-15.45	Holthoff, Kirmse	Manipulation of cells and tissues with optical tools Caged compounds, photochromic switches, optogenetics Please note: The lecture will take place in Lobeda (Forschungszentrum Lobeda, seminar room 012, ground floor. Take the hallway to your left after entering the building. The seminar room is the second room on the left side.)	Slides
16.00-17.30	Holthoff, Kirmse	Measurements in neuronal tissue Please note: The practical part of the course will take place in the lab of Prof. Holthoff (Forschungszentrum Lobeda)
13 25.01.2019 14.15-15.45	Hoffmann	Applications I - GPCRs Measurement of receptor activation
14 01.02.2019 14.15-15.45	Biskup, Groeneveld	Applications II - Receptor channels Measurement of ligand binding and receptor activation	Slides
16.00-17.30	Biskup	Evaluation of the FRET measurements
15 08.02.2019 14.15-15.45	Holthoff, Kirmse	Application III - Measurements in slices and living animals Please note: The lecture will take place in Lobeda (Forschungszentrum Lobeda, seminar room 012, ground floor)
16.00-17.30	Holthoff, Kirmse	Discussion of the experiments of Jan 18th Please note: The practical part of the course will take place in the lab of Prof. Holthoff (Forschungszentrum Lobeda)
1.03.2019 10.00-11.30	Biskup	Exam	Trainingquestions

Requirements to complete the module:

Evaluation of demonstration experiments executed during the course.
Written exam at the end of the semeseter.

Exam:

March, 1st 10.00 a.m., Lecture Hall Humangenetik
Some training questions can be found here.

Recommended literature

On this page you can find links to further resources (textbooks & websites) about topics covered in the course. Publications, which you should have read before the respective lectures starts, are highlighted in red.
Please note: Linked pdfs are only accessible from computers directly connected to the computer network of the Friedrich-Schiller-University Jena.

	Link
Optics
*Books* Eugene Hecht Optics, 4th ed. Addison-Wesley Longman, Amsterdam 2003. B.E.A. Saleh, M.C. Teich Fundamentals of Photonics, 2nd ed. John Wiley & Sons, New York, Chichester, Brisbane, Toronto, Singapore 2007
Microscopy
*Review articles* J. Lichtman, J.A. Conchello: Fluorescence microscopy. Nat. Methods 2, 910-919 (2005)	Link
Books James B. Pawley (Ed.) Handbook of biological confocal microscopy, 3rd ed. Springer, Singapore 2006.
World Wide Web Tutorials of microscope companies (in alphabetical order)	Leica Nikon Olympus Zeiss
Fluorescence
Books J. R. Lakowicz Principles of fluorescence spectroscopy. 3rd ed. Springer, Singapore 2006.
Fluorescence lifetime imaging
*Review articles* K. Suhling, P.W.M. French, D. Phillips: Time resolved fluorescence microscopy. Photochem. Photobiol. Sci. 4, 13-22 (2005)
Books A. Periasamy, R.M. Clegg FLIM Microscopy in biology and medicine. CRC Press, Boca Raton, London, New York 2009.
Organic fluorophores and labelling techniques
*Review articles on labelling techniques and green fluorescent proteins* Introduction into labelling techniques: B.N.G. Giepmans, S.R. Adams, M.H. Ellisman, R.Y.Tsien: The fluorescent toolbox for accessing protein location and function. Science 312, 217-224 (2006)
Genetically encoded fluorescent proteins
Overview about GFPs: N.C. Shaner, P.A. Steinbach, R.Y. Tsien: A guide to choosing fluorescent proteins. Nat. Meth. 2, 905-909 (2005). Discovery of GFPs: O. Shimomura: A short story of aequorin Biol. Bull. 189, 1-5 (1995) O. Shimomura: Discovery of green fluorescent protein (GFP) (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 48, 5590-5602 (2009) R.Y. Tsien: Nobel lecture: constructing and exploiting the fluorescent protein paintbox. Integr. Biol. 2, 77-93 (2010) See also the website of the Nobel Prize committee But see also B. Lieff Benderly: The man who wasn't there. Science-Website
FRET
*Review articles* A. Kenworthy: Imaging protein-protein interactions using fluorescence resonance energy transfer microscopy. Methods 24, 289-296 (2001) C. Biskup et. al.: Multi-dimensional fluorescence lifetime and FRET measurements. Microsc Res Tech. 70, 442-451 (2007)	Link Link