IIP Internships in the Czech Republic
Academy of Sciences of the Czech Republic, Center for Nanobiology and Structural Biology
Location: Nové Hrady, Czech Republic
About: The Center for Nanobiology and 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 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 sub-units in protein complexes, the laboratory is an integral part of the new research concept of the Institute.
Intern Responsibilities: 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 receiving 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:
- Modeling interactions in and between biomolecules and complex biologically relevant systems - The IIP intern will mainly work with computational tools on data, that are produced by experimentalists in house. After getting intense training during the first weeks, she/he/they will be responsible for a sub-project that leads to a clear outcome/prediction that can be experimentally verified. The IIP intern will also get an insight how the experimental data, like the X-ray structures, are generated and will collaborate directly with the scientists working on that.
- Protein expression and purification, structural and functional characterization of protein systems - This project will focus on the experimental characterization of interactions in and between biomolecules and complex biologically relevant systems (like for example restriction modification system EcoR124I or the cation translocation system TrK1). The IIP intern would not repeat something somebody has done already, but would use a unique mutant, that should alter the functionality. In this sense this is a new and un-characterized protein, as we do not know its actual functionality unless the IIP intern will find out! This project involves: 1) Polymerase chain reaction using primers that would introduce the mutation, amplification of the DNA, 2) Growing of e.coli or yeast cells used later for over-expression, 3) Over-expression of protein in e.coli or yeast 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) In vitro assays to monitor protein activity , 7) Ligand-binding studies like ITC/SPR/fluorescence/microscale thermophoresis 8) limited proteolysis. In nearly all steps SDS-phage electrophoresis is used to monitor either the successful amplificiation, the overexpression, the protein purity or the fragments after cleavage.
- The experimental basis for modeling interactions in and between biomolecules - This would be a combined experimental and computational project focusing on protein crystallization and X-ray diffraction of mutants of type I restriction-modification systems to resolve the three-dimensional structure of these proteins. In parallel with the lab work the IIP intern would work computationally on: 1) Solving the X-ray structure and homology modeling 2) Ligand-docking 3) Molecular dynamics simulation of the system in simple-point water, 4) calculation of binding energy.
Qualifications: 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.
Previous work experiences (in the words of the past IIP interns): Intern 1: Learned basic Unix commands; Learned a number of types of simulation software (VMD, GROMACS, YASARA, PYMOL); Studied the model system of interest; Performed the necessary modifications to the structures; Determined what sort of simulations to run and how to vary system parameters; Analyzed simulation results; Learned to use various tools to complement the analysis. Intern 2: I worked on project focused on determining the structure and function of HsdR's C-terminal domain. Intern 3: I created a computational model of the S and M sub-units of the Type I Restriction Modification enzyme EcoR124I. This work involved a number of computational programs and algorithms including homology modeling, multiple sequence alignments, protein - protein docking, and molecular dynamics. I learned to work independently on a project and assume responsibility for research that other colleagues in the lab are depending on to get done. My work was important because I created the computational model of two key sub-units of the enzyme EcoR124I (of which there are three sub-units). My project was expanded to include simulations of the protein with different mutations along the helical chain. Once we ran simulations for up to 100 nanoseconds, we had to determine how the mutations were affecting the structure and integrity of the protein. This model will be published in the lab's next paper. Intern 5: I calculated the PMF for the permeation of CA through the human ORAI1 channel...I learned umbrella sampling simulation techniques.
View PowerPoint presentations by past IIP interns:
ASCR Intern #1
ASCR Intern #2
ASCR Intern #3
ASCR Intern #4
|For UPDATED information on SUMMER 2017 and TO APPLY, click here: Academy of Sciences, Czech Republic|
University of South Bohemia, Faculty of Fisheries and Protection of Waters Institute of Complex System
Location: South Bohemia, Czech Republic
About: This project is part of the Biological Engineering Group in the Institute of Physical Biology. 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.
Intern Responsibilities: IIP interns may choose from a few existing projects or projects that align with the intern’s own interests may be arranged. Projects will include work in one or more of the following areas:
- Reconstruction of the living cells using optical microscopy in transmitted light and atomic force microscopy- This project will help IIP interns become acquainted with such microscopy techniques like atomic force microscopy (AFM) and optical microscopy. IIP interns will prepare on their own samples with lving cells for AFM imaging. Partakers will have an opportunity to work in the force spectroscopy mode in order to get information about mechanical properties and topology of different cell lines and to work with an optical microscope to obtain information on the cell interior. Also, the IIP intern will be introduced to image processing techniques based on information entropy approach. The aim of this project is to cultivate and fix cells, get images, perform image processing and reconstruction.
- Testing microscopes and algorithms developed at the ICS, tracking organelles- Their lab has developed an algorithm for 3D modelling and tracking of cell organelles and their images by an optical system of a transmission light microscope. The goal of this project is to develop and use 3D polygraphy for printing mass models of these organelles and their images by the microscope and find the trajectory of organelles' movement. The project aim is to develop a method of 3D polygraphy for printing mass models of cell organelles and draw the trajectories of moveable organelles.
- Fish school behavior in five information dimensions- Fish behavior is a prototype for behavior of higher organism. Upon their analysis, numerous extrapolations are made for fields as distant as robotics and human psychology.
Qualifications: 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.
Previous work experiences (in the words of the past IIP interns): Intern #1: I 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. Intern #2: I worked on protein crystallization and atomic force microscopy (AFM) of living cells, particularly osteosarcoma cells, strain MG-62, and mice fibroblasts, strain L929. With protein crystallization, I prepared lysozyme crystals by trying out two different methods -- sitting drop and microseeding -- and successfully yielded crystals. I tried to find a way to adhere the crystals to the microscope slide so the sample does not move when it is being scanned. I contacted with a professor from NASA in order to figure out what materials he used so that I can replicate his experiment where he successfully held the protein in place. With atomic force microscopy, I was trained on using the machinery and how the images can be used to determine biochemical processes that are occurring within the cell. This can be used to determine whether or not a cell is at risk of certain diseases, especially cancer. I also learned to cultivate cells and immobilize them for scanning by AFM. I was trained in using the machinery and using it to take elasticity measurements of the cell. I used this information to determine which cells were most compatible with which substrate, which helped determine what material something should be made out of for permanent insertion into the body. In the end, I presented my project on a PowerPoint and created a poster for future displays.
View a PowerPoint presentation by a past intern:
University of South Bohemia Intern #1
University of South Bohemia Intern #2
|For UPDATED information on SUMMER 2017 and TO APPLY, click here: University of South Bohemia, Institute for Physical Biology|