Summer Semester 2017

Raz Zarivach (Ben-Gurion University, Israel -- guest at MPIKG)
Title: Protein purification and characterization

Description: In the course we will learn the main techniques for protein isolation and characterization. The course purpose is to establish the connection between the protein structure and composition to its purification and characterization methodologies. The course is present and discusses several subjects: Internet databases and their importance for purification protocol design. Protein extraction and concentration from extract. Purification methodologies for membranal proteins, the use of detergents and the cleaning of inclusion bodies. The main methodologies to determine protein concentration, BCA, Bradford and UV spectroscopy. The use of native and denaturative gels for protein characteriazation and purification. The use of mass spectrometry for protein characterization. 
Place: MPIKG, Biomaterials seminar room
Duration: Every Thursday from July 6th to August 31st, from 1pm to 3pm.

Livnat Landau (MPIKG)
Title: Hands-on Matlab-based image analysis tutorial

Description:  Image analysis can help us extract meaningful information from images and is widely used in research and industry. This tutorial will cover basic image analysis techniques with an emphasis on applications on visual experimental data. The course will cover topics such as interactive measuring tools, image enhancement, detecting objects using image segmentation, time-lapse and video analysis, and applications of Fourier transform in image processing. No previous Matlab knowledge is required.
Place: MPIKG, Biomaterials seminar room
Duration: Tuesdays and Thursdays at 10:30 am, from June 20 to August 8.


Damien Faivre, Sara Ghaisari, Melis Goktas, Elisa Donate (MPIKG)
Title: A review of biomaterials characterization methods

Place: UP, 2.25.D1.02
Duration: Every Friday, from 2:15 pm to 3:45 pm, start April 21


Carsten Beta (UP)
Title: Cellular biophysics

Description:  Biophysics is an interdisciplinary field that combines the classical disciplines of physics and biology. While biology examines all forms of life in its diversity and complexity, physics concentrates on the mathematical laws and quantitative descriptions of simple, often idealized systems. The central challenge of biophysics is to build a bridge between the basic physical principles on the one hand and the complexity of living nature on the other. The lecture gives an introduction to the basic concepts of cellular biophysics. In addition to general principles, we will the focus on processes on the micro- and nanometer scale. Covered topics include cytoskeletal dynamics, membrane biophysics, and the basics of neural signaling.

Place: University of Potsdam, Institute of Physics and Astronomy, Room
Duration: Wednesday, 12:15 pm to 1:45 pm

Joao Robalo (MPIKG)
Title: Introduction to Molecular Dynamics simulations in biological systems

Description: Biological systems are typically comprised of structural domains spanning several length scales. The shortest-scale domains are those in which molecular-level interactions occur. These interactions, though intimately related to the macroscopic properties of the systems, are rarely directly accessible via experimental techniques. Therefore, atomistic molecular dynamics (MD) simulations are an invaluable tool to gain insight into the molecular-scale properties of biological systems. This workshop will focus on an intensive, "hands-on", introduction to MD simulations. The necessary theoretical and technical background will be given in order to proceed to the set-up, simulation and analysis of two systems, one consisting of a hydrated lipid bilayer, the other of a solvated protein. By the end of the workshop the students should be able to perform basic simulation and analysis of biological systems as well as having enough understanding to delve further into more advanced techniques.

Place: MPIKG, seminar room above the library
Duration: Monday to Friday, from 10 am to 5 pm, start March 20
Info Meeting: Wednesday March 8, 11 a.m. in the theory seminar room


Joachim Heberle (FU)
Title: Advanced biophysics

Description: This module will present and substantiate biophysical methods and concepts. Selected methods like spectroscopy and diffraction and their application to proteins, nucleic acids and biomembranes are of particular relevance. The lecture series will cover a selection of the following methods: absorption spectroscopy in the UV, visible and IR region; fluorescence spectroscopy, time-resolved approaches; spectroscopy with linear and circular polarized light; vibrational spectroscopy: Fourier-transform infrared (FTIR), resonance Raman, surfance-enhanced Raman and IR; diffraction with X-rays, Neutrons and electrons; crystallization and protein crystallography; nuclear magnetic resonance (NMR); light scattering; single molecule spectroscopy; optical tweezer; atomic force microscopy; theoretical methods: MD simulations, Poisson-Boltzmann, QM/MM. The lecture series is accompanied by a practical course of 8 biophysical experiments.

Place: FU Berlin, FB Physik, 1.3.14 Hörsaal A
Duration: Every Tuesdays and Fridays, noon to 2 p.m.
Contact: (link)

Ralph Graef (UP)
Title: Cell biology for life scientists

Location: Uni-Potsdam, Campus Golm, Haus 25 B0.01
Duration: Every Thursday starting April 20, at 4 pm to 5:30 pm


Salvo Chiantia (UP)
Title: Physical methods in live cell imaging

Description: The aim of this course is to illustrate the application of mathematical methods (e.g. fluctuation analysis, signal correlation) in the context of quantitative fluorescence microscopy of biological molecules in living cells. Such cutting-edge methods are capable of providing precise information about protein-protein interaction in complex biological systems. The lecture covers the most modern approaches in the field of quantitative fluorescence microscopy including single molecule approaches (e.g. single molecule FRET, tracking), image correlation methods (e.g. k-space microscopy) as well as super-resolution microscopy (e.g. STED, STORM). A special aim is set on introducing computer programming methods related to the analysis of imaging data (e.g. Montecarlo simulations, Fast-Fourier transformation for correlation analysis) using Matlab. The laboratory classes will provide the chance to deepen the practical knowledge of the students in a selection of the above mentioned microscopy and programming techniques. The students will actively participate in the seminars with one presentation, which will foster their ability to critically read and present scientific literature. In the experimental courses the students will learn to apply various quantitative microscopy methods to   study protein dynamics and protein-protein interactions directly in cells. The experimental part is carried out as a small, independent research projects, which allows developing skills to independently design and plan scientific experiments and to work in a team. Registration for the laboratory classes is compulsory.

Place: UP
Duration: TBA

Stefanie Barbirz, Joerg Fettke (UP)
Title: Modern aspects of biochemistry and analytics of carbohydrates

Description: Recent developments in molecular biology and modern analytical methods have increased the knowledge about the ubiquitous role of carbohydrates in animals, plants, and bacteria. Aim of this course is an insight into the interdisciplinary field of glycobiology. It will present an actual survey of the biochemistry of sugar building blocks, oligo- and polysaccharides in pro- and eukaryotic systems. Moreover, qualitative and quantitative carbohydrate analytics will be covered as well as the fundamental biophysical principles underpinning interactions of carbohydrates with proteins. Subject areas: Fundamentals on glycoconjugates. Structural and functional principles of the glycan conformational space. N-and O-linked glycosylation. Glycan analysis. Lectins and carbohydrate binding modules. Physicochemical principles of protein-carbohydrate interactions. Glycan arrays. Microbial glycobiology and pathogenesis.

Location: Uni-Potsdam, Campus Golm, Haus 25 F0.01
Duration: Every Tuesday starting April 18, from 12:12 to 1:45 pm


Agnese Codutti (MPIKG)
Title: Introduction to data analysis

Description: The course is an introduction to data anaylis, from defyining basic concepts as errors, weighted mean and distribution, to more complex topics as chi squared test, maximum likelihood and fitting. The course will be theoretical but practical applications and examples will be provided.

Location: MPIKG, theory seminar room
Duration: Monday and Wednesday at 10:30 am, from June 7 to July 26