Practical course on analysing the diversity of microbial eukaryotes in environments 1400-ADMEE-en
This intense week-long practical course focuses on the techniques of metabarcoding the eukaryotic diversity from environmental samples using short (V4 rRNA) and long (rRNA operon) amplicons. Students will learn the pipeline from the DNA isolation step to diversity estimation and data interpretation. Students will be grouped into pairs. Over the first three days, 36 marine samples (frozen cells on filters) from a spatial transect of the coast of northern France will be processed, three by each pair of students. Short and long amplicon libraries will be prepared and sequenced in-house on Illumina MiSeq and Oxford Nanopore MinION platforms over the weekend. During the following three days, the sequence data will be bioinformatically processed to estimate diversity, which will be compared between samples and sequencing technologies.
The practical part will be accompanied by a series of lectures on the technical aspects of metabarcoding and sequencing, the diversity and ecology of microbial eukaryotes in diverse environments, and statistical approaches to data analysis.
Type of course
Course coordinators
Learning outcomes
KNOWLEDGE
1. Has the knowledge about structural, genetic, metabolic and functional diversity of eukaryotic microorganisms (K_W03)
2. Understand relations between eukaryotic microorganisms and environment, applying the hypothesis of temporal and spatial determinants of biodiversity (K_W04)
3. Is familiar with up-to-date laboratory techniques of data collection used in eukaryotic microorganisms biology (K_W12)
4. Knows the principles of planning research and performing experiments with the use of specialized methods to study microbial eukaryotes (K_W13)
ABILITIES
1. Is able to choose proper tools and techniques for solving problems of eukaryotic microbiology (K_U01)
2. Under the supervision of a scientific supervisor can plan and perform an experiment using the known methods of studying the diversity of eukaryotic microorganisms (K_U07)
3. Has the ability to prepare and deliver oral presentations in English at the B2+ level (K_U11)
SOCIAL AWARENESS
1. Understands the need to discover new species and identify known species of eukaryotic microorganisms and is able to pass this knowledge on to others (K_K01)
2. Is able to work in a team, carrying out his/her own research and co-organizing the work of the entire team (K_K04)
Assessment criteria
Project (generation of data, data analysis, presentation)
Notes
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Term 2024Z:
The course can accommodate 12 students ( 6 students from the University of Warsaw) and will be held at the research infrastructure of BIOCEV at Charles University in Prague from November 13th to 21st (7 days of classes), 2024. The course will be conducted in English and taught by lecturers from the Departments of Parasitology (Vladimír Hampl, Jiří Novák) and Zoology (Ivan Čepička, Tomáš Pánek, Seda Mirzoyan) of Charles University, Institure of Evolutionary Biology, Univerisyt of Warsaw (Anna Karnkowska, Michał Karlicki, Małgorzata Chwalińska), and Sorbonne University (Fabrice Not, Lucie Bittner). To register, please sign up in the USOS system and send an e-mail to a.karnkowska@uw.edu.pl (with the note registration for 4EU+ classes in the title). This will enable us to contact you efficiently. If the number of applicants exceeds the number of available places, preference will be given to PhD and Master students and graduates of courses in microbiology (microbiology, but also mycology, field mycology, biology of eukaryotic microorganisms) and in bioinformatics (bioinformatics, practical bioinformatics, feylogenetics and metagenomics). The final list will be announced no later than October 11, 2024. Qualified participants will receive financial support for their travel and stay in Prague. If you have any further questions, please contact the coordinator by e-mail (a.karnkowska@uw.edu.pl). |
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: