1st year u/g students, 2nd year u/g students, 3rd year u/g students
Student Responsibilty with support from IIP and/or Host Organization
International Internship Program
University of South Bohemia, Faculty of Fisheries and Protection of Waters Institute of Complex System
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:
Testing microscopes and algorithms for 3D reconstruction of cell interior and tracking organelles developed at the ICS - 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. This project introduces image processing techniques based on information entropy approach. The results of the 3D reconstruction can be compared with the results obtained by atomic force microscopy. 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.
Fish barcoding - new method of fish labelling for ethological experiments Fish barcoding - This project aims to explore the possibility of “invisible” fish labelling for ethological experiments. This project is motivated by fish ethological experiments that are currently used for different areas of the research. The researches study the effects of micro pollutants water contamination (drugs, pharmaceutics, chemical), fish communication, group behaviour or fish cognition through the analysis of fish motion activity in fish school. The systems for fish trajectory estimation exist but the current problem is the difficulty to track individual fish within the group of many individuals. The researchers used the tags or visible colours for fish marking which influence marked fish behaviour and can influence group behaviour (the rest of the fish “see” the marks). The new method for invisible fish marking should be developed to solve the existing problem. The IIP intern will work on the development of new method for fish “invisible” marking. This project will consist from the design part and experimental part. At the design part the IIP intern will theoretically develop the approach of fish marking (one of the possibility is to use infra-red reflective colours, other is direct automated analysis of natural individual coloration and color pattern etc.) which will be then experimentally tested on the fish school activity monitoring. Several systems for fish activity monitoring were developed at the institute and can be used for the project.
Role of isozymes in metabolic regulation of Escherichia coli - This project is motivated by isozymes that are enzymes catalyzing the same reaction but have different kinetic properties. Furthermore, many organisms simultaneously express different isozymes. In the case of eukaryotic organisms, different organelles or tissues have different functions and thus require different kinetic properties of isozymes. On the other hand, it is not clear why there are two or even more isozymes catalyzing the same reaction within the same compartment in the case of prokaryotes. In their lab, a multi-level kinetic modeling approach has been developed and showed that it is able to explain the regulatory roles of particular isozymes in cyanobacteria. The goal is to apply the same method on Escherichia coli, i.e., to integrate metabolic, transcriptomic and other omics data in order to study the role of isozymes within Escherichia coli. The IIP intern will contribute to the research of this lab.
Numerical and experimental assessment of flow pattern in algal bioreactors and/or fish tanks - This project aims to explore the possibility of water flow simulation for the fish tanks/macroalgae movements. This project is motivated by the understanding of the water flow in fish tanks is critical problem for the growing sector of intensive aquaculture. E.g., the feed distribution and self-cleaning of the tanks is directly influencing the fish growth conditions. The researchers are looking for the possibility to predict fish tank flow without the realization of expensive experiments to improve their experimental design. The development of the water flow simulation is therefore up to date problem in aquaculture.The macroalgae are used as new feeding supplement for the fish cultivation to optimize aquaculture fish feeding. The optimal cultivation of the macroalgae is still open problem where the factors of water flow play important role in the algae growth optimization. Understanding of the influence of the flow to the algae growth is of high importance. The IIP intern will contribute to the research for this project during the following processes: First, numerical part of the project resides in numerical simulations of fluid flow within either (i) macroalgal bioreactor, or (ii) fish tank. Using a CFD (computational fluid dynamics) code, e.g., COMSOL Multiphysics, the effect of design parameters and operating conditions on tank hydrodynamics will be analyzed.
Second, experimental part is proposed to both calibrate the numerical model (identify CFD model parameters and material constants) and validate its use. In order to measure the flow velocity field and the macroalgae motion either a classical method based on ADV (Acoustic Doppler velocimetry) or/and their recently developed innovative methods will be employed.
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.