S2008 Developmental and cellular biology of plants

Faculty of Science
Spring 2020
Extent and Intensity
4/0/0. 4 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
Tomasz Nodzynski, B.A., M.Sc., Ph.D. (lecturer)
Marta Zwiewka, B.A., M.Sc., Ph.D. (lecturer)
Guaranteed by
Mgr. Jiří Friml, Dr. rer. nat.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 14:00–15:50 E26/222
Prerequisites
The course will be taught in English.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
The objective of this course is to familiarize the students with plant research (more specific point below).
Give a brief historical overview how plant research has contributed to the development of science at large.
Familiarize the students with methods of genetics, molecular and developmental biology as well as cell biology used in plant research.
Introduce the role of AUXIN hormone in plant development.
Discuss the cellular and molecular mechanisms facilitating auxin function (signalling and transport).
Highlight the role of other plant hormones.
Learning outcomes
Student will be able to:
- Use the laws of genetic trait segregation (Mendel laws) and interpret the results of genetic crosses;
- Apply basic molecular biology techniques to design genetic constructs used for elucidation of gene function or utilized to alter the function of a gene or protein produced by the gene;
- Apply principles of Forward and reverse Genetics strategies in the identification of gene function;
- Apply basic biochemical techniques to link the protein to the gene and understand the gene function;
- Apply basic cell biology techniques to link the protein to the gene and understand gene function;
- Utilize the knowledge of plant hormonal signaling to modify aspects of plant development;
Syllabus
  • A. Current approaches and methods of experimental plant molecular genetics and, developmental biology as well as cell biology.
  • 1. Segregation by Mendel law
  • 2. Classification and morphology of plants
  • 3. Anatomy and Physiology of roots
  • 4. Biochemical approaches, heterologous systems.
  • 5. Cell biology, cell structure
  • 6. Genetics: From a phenotype to the gene
  • 7. Plant Model systems
  • 8. How to get your favourite gene
  • a. Candidate gene approach
  • b. From the protein back to the gene
  • c. Functional complementation
  • d. Expression pattern: Enhancer and Gene trap, Differential expression (subtractive hybridization, microarray)
  • e. Forward genetics (The worse the better) Mutagenesis (EMS, T-DNA, transposon, activator tagging), Ups and downs of genetic screening, Gene identification and verification, Suppressor screens
  • f. QTL
  • 3. Towards a gene function
  • a. Reverse genetics (indexed mutant libraries, TILLING)
  • b. Ectopic expression
  • c. Chimeras and mosaics
  • d. Site directed mutagenesis, swaps
  • e. Phenotype analysis - from the eye to molecular markers
  • 4. Expression and localization
  • a. Quick and dirty - Northern and Western blots, RT-PCR
  • b. Reporter genes (transcriptional and translational fusions, applications)
  • c. mRNA in situ hybridization
  • d. Protein in situ localisation
  • 5. Friends and neighbors
  • a. Yeast-two-hybrid
  • b. Split ubiquitin
  • c. Genetic interactions
  • d. Upstream and downstream
  • 6. Special methods and tools
  • a. DR5 auxin response reporter
  • b. Laser ablations and laser capture
  • c. Transient transfection
  • d. Heterologous systems
  • e. Microscopy: Light and fluorescence: epifluorescence , confocal
  • B. Auxin 1. The components
  • a. Receptors
  • b. Signaling
  • Discovery of auxins. Towards the players: biochemistry, genetics (AXRs), molecular biology (AUX/IAAs and ARFs), integrative model.
  • c. Auxin transport - PINing down the players
  • Physiology, Chemiosmostic model, molecular components (PINs, AUXs) - expression, localization, function.
  • Subcelullar trafficking and cell polarity
  • Cycling of the auxin transport components, auxin transport inhibitors and their effects, relevance of cycling for auxin transport, endocytosis in plants, polar targeting.
  • Isolation of gnom mutant, GNOM protein - biochemical function and role in development. Connection to the auxin transport. GNOM and endosome recycling.
  • 2. Role of Auxin in Plant Development
  • a. From production to action
  • b. Tropism
  • c. Organogenesis
  • C. Highlighting other plant hormones
  • Cytokinin
  • Ethylene
  • Strigolactones
Literature
    recommended literature
  • Genetic screens and Forward Genetics : (Page and Grossniklaus, 2002); PIN mediated auxin transport: (Petrášek et al., 2006); Subcellular trafficking: (Dhonukshe et al., 2007; Nodzyński et al., 2012; Zwiewka and Friml, 2012);
  • NODZYNSKI, Tomasz, Mugurel I FERARU, Sibylle HIRSCH, Riet DE RYCKE, Claudiu NICULAES, Wout BOERJAN, Jelle VAN LEENE, Geert DE JAEGER, Steffen VANNESTE and Jiří FRIML. Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis. Molecular Plant. Oxford: Oxford University Press, 2013, vol. 6, No 6, p. 1849-1862. ISSN 1674-2052. Available from: https://dx.doi.org/10.1093/mp/sst044. info
  • ZWIEWKA, Marta, Tomasz NODZYNSKI, Stephanie ROBERT, Steffen VANNESTE and Jiří FRIML. Osmotic Stress Modulates the Balance between Exocytosis and Clathrin-Mediated Endocytosis in Arabidopsis thaliana. Molecular Plant. Cambridge (USA): Cell Press, 2015, vol. 8, No 8, p. 1175-1187. ISSN 1674-2052. Available from: https://dx.doi.org/10.1016/j.molp.2015.03.007. URL info
  • NODZYNSKI, Tomasz, Steffen VANNESTE, Marta ZWIEWKA, Markéta PERNISOVÁ, Jan HEJÁTKO and Jiří FRIML. Enquiry into the Topology of Plasma Membrane-Localized PIN Auxin Transport Components. Molecular Plant. CAMBRIDGE: Cell Press, 2016, vol. 9, No 11, p. 1504-1519. ISSN 1674-2052. Available from: https://dx.doi.org/10.1016/j.molp.2016.08.010. URL info
Teaching methods
Theory class: lectures, class discussions.
Assessment methods
Assessment methods:

Assessment will be based on the interaction with students during the course (Questions, Discussions). Student activity will be recorded and will have an influence in the calculation of the final mark.

Final oral exam will consist of multiple questions concerning the subject matter of the course. The answers on the questions will be scored and summarized in as final performance percentage; bonus % for activity during the course will be added.

There are 2 modes of course completion:

a) Colloquium – the evaluation will be represented as pass (Z- above 50,1 % of correct answers) or fail (N) grade/result. 1 additional credit will be awarded for finalising the course with the colloquium (3 points in total for this completion variant).

b) Exam – it will commence in the same fashion as colloquium, but the final result will be graded (from F = worst grade to A = best grade). 2 additional credit(s) will be awarded for finalising the course with an exam (4 points in total for this completion variant).

Scoring system (% of correct answers):
F-(0,0-50,0)
E-(50,1-60,0)
D-(60,1-70,0)
C-(70,1-80,0)
B-(80,1-90,0)
A-(90,1-100,0)
Language of instruction
English
Further comments (probably available only in Czech)
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2011 - acreditation, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.
  • Enrolment Statistics (Spring 2020, recent)
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