Lecturer(s)
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Chroňáková Alica, RNDr. Ph.D.
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Bárta Jiří, doc. Ing. Ph.D.
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Course content
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Content of lectures: 1. Introduction to aquatic microbial ecology 2. Introduction to soil microbial ecology 3. Genetic diversity, study of diversity, taxonomy based on 16S RDNA, definition of species 4. DNA/RNA approach in microbial ecology. Definition of population structure, quantity. Analyses of DNA vs. RNA. 5. DNA fingerprint methods (PCR-RFLP, ARISA, t-RFLP, DGGE/TGGE), cloning/sequenation, on-line databases 6. Principles of new sequencing methods, pyrosequencing (DNA tagging), metagenomics 7. Quantitative analyses. Principles of qPCR, relative and absolute quantification, inhibitory effects. Use of specific and nonspecific dyes and probes 8. DNA microarrays, taxonomic and functional DNA chips. 9. Detection of microorganisms with nonspecific dyes (DAPI, Picogreen) and fluorescently labeled oligonucleotide probes (FISH, CARD-FISH, FISH-MAR). Database Probase. 10. Principle of DNA-SIP, RNA-SIP, i.e. methods of studying ctive microbial populations and their functions Content of practicals: FISH, DNA, DGGE, qPCR
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Learning activities and teaching methods
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Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming), Laboratory
- Preparation for exam
- 20 hours per semester
- Preparation for credit
- 20 hours per semester
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Learning outcomes
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Objective of the curse will be to give a detailed information of new trends in soil and aquatic ecology. Lectures will unravel and discuss huge microbial diversity on our planet and introduce new molecular methods to help answers basic ecological questions.
Learn new methods of the study of microbial communities in terrestrial and aquatic ecosystems Learning methods of the laboratory cultivation of cells Genomics, single-cell gen genomics Methods of the direct cell microscopy using epifluorescent microscopy Metagenomic methods and bioinformatic tools for studying the diversity of microbial communities
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Prerequisites
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basic knowledge of genetics and molecular biology basic knowledge of work in laboratory
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Assessment methods and criteria
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Test
Mandatory subject KMB608
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Recommended literature
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de Bruijn. Handbook of Molecular Microbial Ecology, Vol. 1 + 2. 2011.
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Nannipier & Smalla. Nucleic Acids and Proteins in Soil. 2006.
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van Elsas, Jansson, Trevors. .Modern Soil Microbiology, 2. edice. 2007.
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