Course: Methods in Microbial Molecular Ecology

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Course title Methods in Microbial Molecular Ecology
Course code KBE/261
Organizational form of instruction Lecture + Lesson
Level of course Doctoral
Year of study not specified
Frequency of the course In each academic year, in the summer semester.
Semester Summer
Number of ECTS credits 6
Language of instruction English
Status of course Compulsory-optional
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Lecturer(s)
  • Bárta Jiří, doc. Ing. Ph.D.
Course content
Content of lectures: 1. Specifity of DNA/RNA isolation from soil and water ecosystems 2. PCR amplification of spec. regions DNA of Bacteria and Archaea 3. Online databases (RDP, GenBank, SILVA) 4. DGGE/TGGE - fingerprinting of microbial communities 5. qPCR -quantitative PCR (absolute quantification of selected genes) 6. EEA - extracellular enzyme activities - connection with decomposition of organic matter Content of practicals 1. DNA/RNA isolation from soil and water ecosystems 2. PCR amplification of spec. regions DNA of Bacteria and Archaea 3. DGGE - fingerprinting of microbial communities 4. qPCR -quantitative PCR (absolute quantification of selected genes) 5. EEA - measuring of extracellular enzyme using MUP-substratets

Learning activities and teaching methods
Monologic (reading, lecture, briefing)
  • Preparation for classes - 20 hours per semester
  • Semestral paper - 20 hours per semester
  • Preparation for exam - 20 hours per semester
Learning outcomes
Objective of the curse is to introduce advanced molecular methods which help to study the huge quantity and diversity of microbial word in different environments
basic knowledge of bioinformatic tools in microbial community analyses
Prerequisites
knowledge of basic genetics and molecular biology

Assessment methods and criteria
unspecified
basic genetic and molecular biology courses biology of microorganisms
Recommended literature
  • Brock: Biology of Microorganisms 12. nebo 13. vydání (Madigan, Martinko, Dunlap, Clark).
  • Modern Soil Microbiology, 2. Edice (van Elsas, Jansson, Trevors).
  • R studio.
  • Arthur Lesk. Introduction to Bioinformatics. ISBN 0199651566.


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Hydrobiology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Ecosystem Biology (1) Category: Ecology and environmental protection - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Ecosystem Biology (1) Category: Ecology and environmental protection - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Hydrobiology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Ecosystem Biology (1) Category: Ecology and environmental protection - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Hydrobiology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer