Course: Environmental DNA

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Course title Environmental DNA
Course code KBE/053
Organizational form of instruction Lecture
Level of course Master
Year of study not specified
Frequency of the course In academic years starting with an odd year (e.g. 2017/2018), in the winter semester.
Semester Winter
Number of ECTS credits 2
Language of instruction Czech
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)
  • Choma Michal, RNDr. Ph.D.
  • Blabolil Petr, RNDr. Ph.D.
Course content
Content of lectures - introduction to DNA (chemical properties of macromolecules, molecular-biological background, overview of available methods) - eDNA obtaining (sources of eDNA, sampling, extraction) - DNA pre-processing (PCR, primers) - qPCR, dPCR, gene expression - sequencing - overview of all generations, NGS emphasised, fingerprinting techniques (PCR-RFLP, ARISA, t-RFLP, DGGE/TGGE) - amplicon studies, metagenomics, metatranscriptomics, metaproteomics - bioinformatics - basic workflows and tools, their principles, databases, data interpretation - use of eDNA in terrestrial ecosystems, plants, mixed samples - use of eDNA in aquatic ecosystems, animals, diet analysis

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming), Work with text (with textbook, with book), Work with multi-media resources (texts, internet, IT technologies), Case studies
Learning outcomes
The aim is to introduce students to basics and principles of studying environmental DNA and subsequent use in science and practice. The understanding of principles, methods and workflow is emphasised.
The course is framed as an introduction to theme. It is anticipated, that after absolving, student will be able to understand methods of eDNA study, know the workflows, assumptions, pros and cons of particular methods in order to understand and critically evaluate their outputs.
Prerequisites
Suitable particularly for students of Environmental Management, Biology and Bioinformatics. Basic knowledge of genetics at high school level is anticipated.

Assessment methods and criteria
Combined exam

Prior to exam, student is expected to present a critical analysis of a chosen published eDNA study, ideally related to his/her aim or thesis field. Adequacy of methods used by authors is to be discussed and the student should consider possible alternatives and discuss if their potential use could improve the quality of the presented study.
Recommended literature
  • Taberlet, Pierre; Bonin, Aurélie,; Zinger, Lucie,; Coissac, Eric. Environmental DNA : for biodiversity research and monitoring. First edition. Oxford : Oxford University Press, 2018. ISBN 978-0-19-876728-2.


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): Environmental Management (1) Category: Ecology and environmental protection - Recommended year of study:-, Recommended semester: Winter