S2008 Developmental and cellular biology of plants

Přírodovědecká fakulta
jaro 2023
Rozsah
4/0/0. 4 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.
Vyučující
Tomasz Nodzynski, B.A., M.Sc., Ph.D. (přednášející)
Marta Zwiewka, B.A., M.Sc., Ph.D. (přednášející)
Garance
Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Rozvrh
Po 14:00–15:50 E26/222
Předpoklady
The course will be taught in English.
Omezení zápisu do předmětu
Předmět je otevřen studentům libovolného oboru.
Cíle předmětu
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.
Výstupy z učení
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;
Osnova
  • 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
Literatura
    doporučená literatura
  • 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 a Jiří FRIML. Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis. Molecular Plant. Oxford: Oxford University Press, 2013, roč. 6, č. 6, s. 1849-1862. ISSN 1674-2052. Dostupné z: https://dx.doi.org/10.1093/mp/sst044. info
  • ZWIEWKA, Marta, Tomasz NODZYNSKI, Stephanie ROBERT, Steffen VANNESTE a Jiří FRIML. Osmotic Stress Modulates the Balance between Exocytosis and Clathrin-Mediated Endocytosis in Arabidopsis thaliana. Molecular Plant. Cambridge (USA): Cell Press, 2015, roč. 8, č. 8, s. 1175-1187. ISSN 1674-2052. Dostupné z: https://dx.doi.org/10.1016/j.molp.2015.03.007. URL info
  • NODZYNSKI, Tomasz, Steffen VANNESTE, Marta ZWIEWKA, Markéta PERNISOVÁ, Jan HEJÁTKO a Jiří FRIML. Enquiry into the Topology of Plasma Membrane-Localized PIN Auxin Transport Components. Molecular Plant. CAMBRIDGE: Cell Press, 2016, roč. 9, č. 11, s. 1504-1519. ISSN 1674-2052. Dostupné z: https://dx.doi.org/10.1016/j.molp.2016.08.010. URL info
Výukové metody
Theory class: lectures, class discussions.
Metody hodnocení
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)
Vyučovací jazyk
Angličtina
Informace učitele
The course will be taught (lectures) on Mondays, 2 – 4 pm, room E26/222.

The schedule encompasses 12 weeks: start February 13, end 22th May last lecture (2023). The exact exam time is usually arranged with students during the course, two exams dates are given and then two dates to correct the mark if not satisfactory (during corrections difficulty of questions increases).

Location of the course will be in the building E26 (former A26), 2nd floor, room 222.

When You have taken this course consider taking, in parallel or subsequently, the complementary course S2011.
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Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Předmět je zařazen také v obdobích podzim 2011 - akreditace, jaro 2015, jaro 2016, jaro 2017, jaro 2018, jaro 2019, jaro 2020, jaro 2021, jaro 2022, jaro 2024, jaro 2025.