Bi6589 Laboratory and bioinformatic methods of plant biosystematics

Faculty of Science
Autumn 2024
Extent and Intensity
0/3/0. 3 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
In-person direct teaching
Teacher(s)
prof. RNDr. Petr Bureš, Ph.D. (seminar tutor)
Ing. Mgr. Klára Plačková (seminar tutor)
Mgr. Petra Šarhanová, Ph.D. (seminar tutor)
Ing. Jakub Šmerda, 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
Wed 9:00–11:50 D31/239
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
Course objectives
Theoretical and practical introduction to basic laboratory, molecular biological and bioinformatic methods of plant biosystematics.
Learning outcomes
The student will learn to solve questions of biosystematics and taxonomy of plants using different methodological approaches.
The student will acquire theoretical knowledge about the strategy of collecting and holding plant material, basic laboratory, molecular biological and bioinformatics methods of plant biosystematics.
Students will acquire basic practice in the molecular biological, cytometric and karyological laboratories at the same time should better understand the results and arguments presented in biological journals.
Syllabus
  • The concept of the subject is based on a model situation where there are two species from the same genus and individuals with intermediate characters between the species of interest. Using different methodological approaches, students will test whether difficult-to-classify individuals represent a manifestation of phenotypic plasticity of one/both species or whether it is a consequence of interspecies hybridization.
  • From the methodological approaches, will be presented: strategies for collecting and holding of plant material, basics of morphometrics, flow cytometry, karyological methods; students will also be introduced to the theoretical and practical basics of molecular biology (isolation and quantification of DNA, PCR, electrophoresis, sequencing). The course will also include an introduction to and work with selected statistical and bioinformatics software (R, MEGA, STRUCTURE, SplitsTree, etc.), which will enable analysis and visualization of the obtained data.
  • The all knowledge should provide enough evidence to support one of the hypotheses.
  • Students will prepare a summary paper in which they will present methodological approaches, partial analyzes and a final evaluation. Credit will be awarded based on this paper.
Literature
    required literature
  • MICHÁLKOVÁ, Ester, Jakub ŠMERDA, Klára PLAČKOVÁ, Aleš KNOLL and Petr BUREŠ. Hybridization may endanger the rare North Apennine endemic Cirsium bertolonii. Plant Systematics and Evolution. Springer, 2023, vol. 309, No 3, p. 1-21. ISSN 0378-2697. Available from: https://dx.doi.org/10.1007/s00606-023-01854-2. URL info
  • BUREŠ, Petr, Jakub ŠMERDA, Ester MICHÁLKOVÁ, Petr ŠMARDA, Aleš KNOLL and Martin VAVRINEC. Cirsium greimleri: a new species of thistle endemic to the Eastern Alps and Dinarides. Preslia. Česká botanická společnost, 2018, vol. 90, No 2, p. 105-134. ISSN 0032-7786. Available from: https://dx.doi.org/10.23855/preslia.2018.105. URL info
  • MICHÁLKOVÁ, Ester, Jakub ŠMERDA, Aleš KNOLL and Petr BUREŠ. Cirsium ×sudae: a new interspecific hybrid between rare Alpine thistles. Preslia. Česká botanická společnost, 2018, vol. 90, No 4, p. 347-365. ISSN 0032-7786. Available from: https://dx.doi.org/10.23855/preslia.2018.347. URL info
    recommended literature
  • HEYWOOD, V. H. Modern methods in plant taxonomy. 1st ed. London & New York: Academic Press, 1968, 312 pp. ISBN 68-9103. info
  • BUREŠ, Petr. Cirsium Mill. – pcháč (Cirsium Mill. – thistle). In Zdeněk Kaplan. Klíč ke květeně České republiky. Druhé, přepracované. Praha: Academia, 2019, p. 1034-1036. 11961. ISBN 978-80-200-2660-6. 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
  • BUREŠ, Petr. Cirsium Mill. - pcháč. In Klíč ke květeně České republiky. 1st ed. Praha: Academia, 2002, p. 669-671. 4928. ISBN 80-200-0836-5. 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 final report, which includes a brief introduction to the working hypotheses, description of methodological approaches, analysis of the obtained data and subsequent interpretation of the results. 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.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.
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