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Lecturer(s)
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Rulík Martin, doc. RNDr. Ph.D.
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Buriánková Iva, Mgr. Ph.D.
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Brablcová Lenka, Mgr. Ph.D.
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Course content
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1. Detachment of cells from environmental samples (sonication, denzity gradient centrifugation, staining by DAPI 2. Extraction of DNA using the comercial kits, gel electrophoresis 3. Pricnciples of polymerase chain reaction (PCR), and denaturing gradient gel electrophoresis (DGGE) 4. Whole-cell Fluorescence in situ hybridization (FISH), image analysis by NIS programme 5. Construction of phylogenetic trees
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Learning activities and teaching methods
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Lecture, Demonstration, Training in job and motor Skils, Laboratory Work, Work Activities
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Learning outcomes
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Laboratory exercises are aimed at improving practice in handling molecular methods used in a study of natural microbial samples. Students will be apprised of methods of DNA extraction, amplification of targeted gene by PCR, determination of quantitative proportion of different groups within microbial community by FISH method, diversity assessment by DGGE method and determination of basic overview of biology and ecology of microorganisms in environmental habitats and possible using of molecular methods for their study. Further they focus on processing of sequencing data and construction of phylogenetic trees.
At the end of a semester it is expected that student will: - know about possible using of molecular methods in microbial ecology - know how to use some molecular methods - be able to intepret results of varous studies aimed with detection of microorganisms by using molecular methods
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Prerequisites
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Elementary knowledge in microbiology and molecular and cell biology.
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Assessment methods and criteria
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Dialog, Seminar Work
Essay preparation dealing with problems in microbial ecology.
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Recommended literature
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Brown TA (2007). Klonování a analýza DNA. Univerzita Palackého v Olomouci, 389 pp.,.
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Madigan MT, Martinko JM (2006). Brock biology of microorganisms, 11th ed. (nebo pozdější vydání). Pearson Education, Inc., Upper Saddle River, NJ,.
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Oren A, Papke RT (2010). Molecular phylogeny of microorganisms. Caister Academic Press, Norfolk, UK,.
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Osborn M, Smith C (2005)(eds). Molecular microbial ecology. Taylor & Francis, New York, NY.
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Persing DH, Tenover FC, Tang YW, Nolte FS, Hayden RT, van Belkum A (eds). (2016). Molecular microbiology: Diagnostic principles and practice. Washington: DC: ASM Press.
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Rulík M, Buriánková I, Brablcová L. (2015). Vybrané kapitoly z molekulární ekologie mikroorganizmů. Olomouc.
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