PřF:Bi6589 Plant biosystematics methods - Course Information

Bi6589 Laboratory and bioinformatic methods of plant biosystematics

Extent and Intensity

0/3/0. 3 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Petr Bureš, Ph.D. (seminar tutor)
Mgr. Petr Šmarda, Ph.D. (seminar tutor)
Ing. Jakub Šmerda, Ph.D. (seminar tutor)
Mgr. František Zedek, Ph.D. (seminar tutor)

Guaranteed by

prof. RNDr. Petr Bureš, Ph.D.
Department of Botany and Zoology – Biology Section – Faculty of Science
Contact Person: Ing. Jakub Šmerda, Ph.D.
Supplier department: Department of Botany and Zoology – Biology Section – Faculty of Science

Timetable

Mon 9:00–11:50 D36/225

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• Plant Biosystematics (programme PřF, N-BOT)
• Ecological and Evolutionary Biology (programme PřF, B-EKB)

Course objectives

Theoretical and practical introduction to basic laboratory, molecular biological and bioinformatic methods of plant biosystematics.

Learning outcomes

Students will acquire the theoretical knowledge of basic laboratory, molecular biological and bioinformatic methods of plant biosystematics.
Students will acquire basic practice in the molecular biological, cytometric and karyological laboratories.
Students will be able to process raw sequence data or data from fragmentation analyzes and to choose and use a suitable bioinformatics tool to analyze them (e.g. to construct phylogeny, to perform selection analysis or analysis of genetic diversity of species and populations).

Syllabus

• 1) Introductory lesson
  - Syllabus, training of students for work in the laboratory
  2) Isolation of nucleic acids
  - Basic principles of DNA / RNA isolation; CTAB isolation, isolation using a commercial kit
  - Practical exercises
  3) PCR
  - Principle of the polymerase chain reaction (PCR) method and its modifications
  - Practical exercises
  4) Electrophoresis
  - Principles, variants, evaluation of electrophoretic gels
  - Practical exercises
  5) Flow cytometry
  - Principles of flow cytometry and its application in determining the genome size, AT/GC base ratio in the genome, degree of ploidy, endopolyploidy and the reproductive system (sexual vs. apomixis)
  - Practical exercises
  6) Stomata and karyology
  - Nucleotypic effect
  - Methods of cell size measurement (stomata)
  - Counting of chromosomes
  - Practical exercises
  7) Basics of working with sequences
  - Principles of sequencing techniques: Sanger sequencing, New Generation Sequencing (NGS)
  - Sequence databases (GenBank, Blast), sequence file formats
  - Fundamentals of work with sequences in the MEGA program (coding and non-coding sequences, nucleotide and amino acid sequences, translation, genetic code)
  - Practical exercises
  8) Sequence Alignment
  - Basic principles of alignment methods
  - Alignment of nucleotides, amino acids, codons
  - Aligning software and web interfaces (MEGA, PRANK, GUIDANCE, BAli-Phy)
  - Practical exercises
  9) Construction of phylogenetic trees, analysis of selection modes
  - Principles of the main methods (Neighbor-joining, maximum parsimony, maximum likelihood, Bayesian methods)
  - Dating phylogenetic trees using fossils
  - Analysis of selection modes acting on coding genes
  - Practical exercises
  10) Molecular markers for population analysis
  - Types of molecular markers; dominant x codominant markers
  - Example studies
  - Working with fragmentation analysis data
  - Software
  - Binary matrix creation
  11) Fundamentals of Population Analysis I
  - PCoA, tree methods
  - Genetic diversity x divergence
  - Spatial structure of populations (AMOVA, spatial autocorrelation)
  12) Fundamentals of Population Analysis II
  - Work in STRUCTURE software, data interpretation
  13) METACENTRUM
  - Utilization of METACENTRUM computational capacities in cases of large data files and computational time-consuming tasks. Scripts for selected software
  - turning in semestral works/protocols
  

Literature

recommended literature
• HEYWOOD, V. H. Modern methods in plant taxonomy. 1st ed. London & New York: Academic Press, 1968, 312 pp. ISBN 68-9103. info
• ŠMARDA, Jan, Jiří DOŠKAŘ, Roman PANTŮČEK, Vladislava RŮŽIČKOVÁ and Jana KOPTÍKOVÁ. Metody molekulární biologie (Methods of molecular biology). 2. dotisk 1. vydání. Brno: Masarykova univerzita, 2010, 194 pp. ISBN 978-80-210-3841-7. info
• SILVERTOWN, Jonathan and Deborah CHARLESWORTH. Introduction to plant population biology. 4th ed. Oxford: Blackwell Science, 2001, viii, 347. ISBN 0-632-04991-X. info

Teaching methods

Teaching takes the form of theoretical lectures and practical exercises. Practical methods are explored by students in the laboratory and by working with selected software. Students will regularly prepare homeworks, the fulfillment of which is a prerequisite for entering the next lesson, as homework often involves preparing the data needed for the next lesson.

Assessment methods

To get the credit for the course, students have to elaborate two protocols from processing of raw data (e.g., from sequences to a dated phylogenetic tree or from rough AFLP data to the genetic structure of the population visualized in the STRUCTURE program) and interpret these analyzes. To pass the course attendance is required in classes. Two absences are possible. However, in the case absences, the obligation to prepare a homework for the next lesson remains.

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.

• Enrolment Statistics (Autumn 2020, recent)
  
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