SubjectsSubjects(version: 945)
Course, academic year 2023/2024
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Molecular markers in systematics and plant population biology - MB120C44E
Title: Molecular markers in systematics and plant population biology
Czech title: Molekulární markery v systematice a populační biologii rostlin
Guaranteed by: Department of Botany (31-120)
Faculty: Faculty of Science
Actual: from 2022
Semester: winter
E-Credits: 3
Examination process: winter s.:
Hours per week, examination: winter s.:0/1, C [TS]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: English
Additional information: http://botany.natur.cuni.cz/dna/images/stories/pdf/protokoly-praktika/protokoly.pdf
Note: enabled for web enrollment
Guarantor: Mgr. Tomáš Fér, Ph.D.
Class: Ultrapřesný sonikátor pro štěpení DNA/RNA pro příp
Annotation -
Last update: Mgr. Michal Štefánek (04.05.2022)
The lectures/practicals are given in English if non-Czech speaking students are enrolled. A practical introduction to the methods of molecular markers in DNA lab at the Department of Botany. Students will learn methods of DNA extraction from the plant material and PCR optimization. In the second part PCR-RFLP method on chloroplast DNA is demonstrated.
Literature -
Last update: Mgr. Michal Štefánek (04.05.2022)

Weising K. et al. (2005): DNA fingerprinting in plants. Principles, methods, and applications. 2nd edition.

Caetano-Anollés G. & Gresshoff P.M. (1998): DNA markers. Protocols, applications, and overviews.

Hall B.G. (2001): Phylogenetic trees made easy.

Requirements to the exam -
Last update: Mgr. Michal Štefánek (04.05.2022)

Write out protocols from the practical part.

Syllabus -
Last update: Mgr. Michal Štefánek (04.05.2022)

* 1st day
- introduction, methods of study of DNA, differences among molecular markers
- DNA extraction from plant material (CTAB method, commercial kit) - fresh and dried material
- electrophoresis, making agarose minigels, use of DNA ladders
- working with documentation system Kodak Gel Logic 100
- determining of DNA concentration using UV spectrophotometer (Nanodrop), DNA dilution

* 2nd day
- PCR amplification, making PCR premix, methods of PCR optimization
- working with diverse termocyclers - making new PCR programs, use of gradient block for PCR optimization
- PCR method - optimization using gradient block
- electrophoresis of PCR bands and their visualization
- working with the software for gel analysis (KODAK 1D Image Analysis Software) - estimation of the lengths of PCR bands

* 3rd day (PCR-RFLP)
- PCR amplification using optimal annealing temperature
- restriction of PCR bands with restriction endonucleases

* 4th day
- dominant molecular markers and data evaluation - theory
- analysis of test gels, preparing binary data matrix
- evaluation of the data - FAMD software
- diversity calculation, PCoA, trees, networks, AMOVA - FAMD, AFLPdat, SplitsTree

* 5th day
- continue with data analysis
- Bayesian model-based approach - STRUCTURE software
- visualization of the STRUCTURE results - Structure-sum, Distruct

 
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