IIP Placements in the Czech Republic
Academy of Sciences of the Czech Republic (ASCR): Institute of Nanobiology and Structural Biology, Department of Structure and Function of Proteins
Location: Nové Hrady, Czech Republic
The Laboratory of Structural Biology was founded in 2002 as a joint laboratory of the Institute of Systems Biology and Ecology of the Academy of Sciences and the Institute of Physical Biology of the University of South Bohemia named Laboratory of High Performance Computing. The laboratory today combines methods ranging from computational and spectroscopic to molecular biological and biochemical--and, in collaboration with the Kuta Smatanova, lab protein crystallization. With its focus on molecular systems biology, the relationship between structure and function of proteins, dynamic changes related to functional processes on the level of proteins, and the mutual interaction of co-factors and subunits in protein complexes, the laboratory is an integral part of the new research concept of the Institute. IIP interns will be introduced to the computational methods for building and investigation of biological systems and will be able to analyze dynamical changes in systems and learn how to interpret generated data. IIP interns will use special software for modeling biological systems and carrying out molecular dynamics simulations, partly using massive parallel calculations on a beowulf-computer cluster. The underlying experimental basis of all structural information comes from protein crystallography done in house. After getting intense training during the first weeks, IIP interns will each be responsible for a sub-project that leads to a clear outcome/prediction that can be experimentally verified. Possible sub-projects include a computational project and an experimental project. The IIP interns may also have the opportunity to participate in a symposium on Structure Systems Biology in Bratislava, Slovakia, and/or the opportunity to visit biomedical institutes of the Academy of Sciences in Prague. Each IIP intern will be assigned to one of the following two projects:
- Computational Project: Modeling interactions in and between biomolecules and complex biologically relevant systems. The intern will mainly work with computational tools on data, that are produced in house. The IIP intern will get insight into how experimental data, such as X-ray structures, are generated and will collaborate directly with the scientists working in that area.
- Experimental Project: The experimental basis for modeling interactions in and between biomolecules and complex biologically relevant systems for the restriction modification system EcoR124I. The IIP intern will not repeat something somebody has done already, but would use a unique mutant that should alter the functionality of either the DNA translocation or the endonuclease activity. The project would involve: 1) Polymerase chain reaction using primers that would introduce the mutation, amplification of the DNA; 2) Growing of e.coli cells used later for over-expression; 3) Over-expression of protein in e.coli cells; 4) French pressing the cells to disrupt them; 5) isolation of protein from the crude extract using gel filtration and affinity and ion exchange chromatography; 6) Malachite green assay to monitor ATPase activity of your protein; 7) In vitro assay of DNA cleavage; 8) Limited proteoplysis. In nearly all steps SDS-phage electrophoresis is used to monitor either the successful amplification, the over-expression, the protein purity or the fragments after cleavage. In parallel the theoretical work would include: 1) Generation of a homology model of point mutation, 2) Docking of ATP into the system, 3) Molecular dynamics simulation of the system in simple-point water, and 4) calculation of the ATP binding energy.
IIP candidates should have academic interest in life sciences, an understanding of biologically relevant systems and how they can be understood by computational modeling, a good background in physics and mathematics;, and a good relation to computers as a scientific tool. General UNIX knowledge is welcome, but no programming is required. Two placements have been created for International Internship Program (IIP) interns.
Previous work responsibilities (in the words of the previous IIP intern): Intern 1: Learning basic Unix commands; Learning a number of types of simulation software (VMD, GROMACS, YASARA, PYMOL) ; Studying the model system of interest ; Performing the necessary modifications to the structures; Determining what sort of simulations to run and how to vary system parameters; Analyzing simulation results; Learning to use various tools to complement the analysis. Intern 2: Worked on project focused on determining the structure and function of HsdR's C-terminal domain.
University of South Bohemia, Institute of Physical Biology
Location: South Bohemia, Czech Republic
This project is part of the Biological Engineering Group in the Institute of Physical Biology. IIP interns may choose from a few existing projects. In addition, projects that align with the IIP intern's own interests may be arranged. Here is some brief background on the Group's main project: Frontiers of biology lie now in exact evaluation of biological processes, whether the field is called Systems Biology, Biological Engineering, or another name. There is currently discrepancy between processes observed in living cells, for example by microscopy, and models that are based mainly on biochemical observations--that is, interactions of proteins and metabolites extracted from the cell culture and examined in the test tube. There are many examples of non-homogeneous behavior in cells that have essential functional meaning and may be crucial for discrimination between living and non-living matter. In contrast to the prevalent approach the Group examines the macroscopic properties of cells and uses a stochastic systems approach from control engineering for model building. For that a new mathematical method of point information contribution and point information entropy hsa been developed, which is implemented into software used for evaluation of processes in living cells. IIP intern responsibilities will include work in one or more of the following areas: 1) cell monolayer cultivation, cell time-lapse microscopy, simple data evaluation all with relation to cancer research, implantology, intestinal tract diseases, etc. 2) software testing, participation in image analysis or chromatography data analysis software development, building of data storage systems; 3) mathematical modeling of biological processes, fluid flow description in bioreactors by CFD (Computational Fluid Dynamics) codes, laboratory Couette-Taylor bioreactor testing, design of experiments to identify model parameters, proposal of new experimental protocols for essential biotechnology processes. At the end of the summer, the IIP interns will participate in a project presentation. IIP candidates should have an academic background in experimental or theoretical physics, chemistry, biology, mathematics, informatics, or mechanical, chemical, or electrical engineering. Basic chemical or biological laboratory skills, teamwork skills and computer knowledge are recommended. Skills in Spanish, Czech, German, or Swedish would be an asset but are not required. Three placements have been established for International Internship Program (IIP) interns.
Previous work responsibilities (in the words of the previous IIP intern): Tested and calibrated microscope equipment to determine its optimal functional limits; analyzed data from these tests using the lab's computational analysis protocols; and made a final poster and presentation.