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Lecturer(s)
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Dolinová Iva, Mgr. Ph.D.
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Svobodová Lucie, Ing. Ph.D.
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Course content
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Lectures: 1. Cell - characterization and features. Difference between prokaryotic and eukaryotic cell. Cell organization and regulation. Intercellular communication. Basic methods and tools for study of cell processes. 2. Cell genetics. Differences between prokaryotes and eukaryotes during cell division. Mutations. Regulation of gene expression: up-regulation and down-regulation. DNA analysis using real-time PCR. 3. Genome sequencing. Next generation sequencing. Metagenomics, metatranscriptomics, and metabolomics. 4. Fluorescence and optical microscopy. Characterization of cells using image analysis. 5. Electron microscopy and scanning probe microscopy. Principles of TEM, SEM, STM, AFM and its usage in cellular and other biological structures. 6. Structure of organic compounds, their identification and quantification: electrophoresis, chromatography and mass spectrometry. 7. Modeling of biological systems. Comparison of methods and algorithms for modeling and simulation experiments with models representing different biological systems. Seminars and practicals: 1. Modeling of intracellular processes. Simulation of cell behavior in different environments using Matlab software. 2. DNA analysis using real-time PCR. Interpretation of obtained data. 3. Next Generation Sequencing - introduction of PGM Ion Torrent. Data purification process. Discussion about evaluation and interpretation of data. 4. Image analysis of micrographs obtained by optical and fluorescence microscopy. 5. Analysis of blood cells using optical microscopy followed by AFM. Analysis of biological systems using AFM. 6. Gas chromatography and mass spectrometry. Examples of techniques for sample preparation before analysis. 7. Characterization of cell culture using respirometry and data analysis.
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Learning activities and teaching methods
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Monological explanation (lecture, presentation,briefing), Self-study (text study, reading, problematic tasks, practical tasks, experiments, research, written assignments), Laboratory work
- Preparation for credit
- 16 hours per semester
- Class attendance
- 28 hours per semester
- Semestral paper
- 15 hours per semester
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Learning outcomes
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Methods and tools for studying of biological systems on cellular and sub-cellular level. Students acquire knowledge on current analysis methods: genome sequencing, real-time qPCR, optical and fluorescence microscopy, atomic force microscopy, scanning electron microscopy, mass spectrometry, chromatography and respirometry. Introduction to modeling of cell behavior. Students will learn the principles of the analysis and methods within facilities available at TUL.
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Prerequisites
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Course is a continuing of bachelor degree program Biomedicine technique: Modeling and simulation of physiological processes, Introduction to systems and signals.
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Assessment methods and criteria
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Combined examination
Active presence on seminars/practicals, laboratory protocols. Written examination.
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Recommended literature
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Ivanov A.R., Lazarev A.V.. Sample preparation in biological mass spectrometry. Springer 2011.
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MICHAEL J. a kol. Biological Electron Microscopy Theory, Techniques, and Troubleshooting. Boston: Springer, 2013. ISBN 978-1461348566.
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POTŮČEK, Jiří. Metodologie modelování biologických systémů. Praha: České vysoké učení technické, 2009. ISBN 978-80-01-04412-4.
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