PřF:C8535 Developmental and cellular bio - Course Information

C8535 Developmental and cellular biology of plants

Extent and Intensity

2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

Mgr. Jiří Friml, Dr. rer. nat. (lecturer), prof. RNDr. Jiří Fajkus, CSc. (deputy)
Tomasz Nodzynski, B.A., M.Sc., Ph.D. (lecturer)
Marta Zwiewka, B.A., M.Sc., Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jiří Fajkus, CSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science

Prerequisites (in Czech)

Předpokladem pro porozumění předmětu je absolvování základů molekulární biologie a genetiky nebo biochemie.

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

• Genomics and Proteomics (programme PřF, N-BCH)
• Molecular Biology and Genetics (programme PřF, N-EXB)

Course objectives

This is a course of plant developmental genetics for advanced students. The newest findings of plant hormone signal transduction and molecular mechanisms of basic developmental processes will be approached from the perspective of developmental genetics, molecular and cell biology. The main focus is on the use of a model organism Arabidopsis thaliana. Course aims mainly to gain insight into the practical use of current experimental approaches and methods for study of molecular mechanisms of plant development.
The main objectives of the course are:
To gain an overview about the main methods plant experimental biology including their advantages and limitations;
Use of these approaches will be demonstrated on the selected problems from developmental and cell biology;
Successful participants will be able to choose the most suitable experimental strategy for their scientific projects.

Syllabus

• A. Current approaches and methods of experimental plant genetics
• 1. Historical development of experimental methodology Arabidopsis thaliana as the model organism - advantages, limitations.
• 2. How to get your favorite gene
• a. Monte Carlo 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
• f. Biochemical approaches, heterologous systems.
• 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. Transient transfection
• c. Heterologous systems
• d. Laser ablations and laser capture
• B. From the signal to the gene
• 1.Ethylene - A success of forward genetics
• Genetic dissection of ethylene signaling, molecular characterization and arrangement of the pathway, Histidine kinase two component system.
• 2. Cytokinin - Complexity of plant hormone signaling
• Biosynthesis, degradation, perception, signal transduction, isolation and verification of the receptors and downstream components. Lessons from protoplasts.
• 3. Auxin - Highly desired, ever elusive
• Discovery of auxins. Towards the players: biochemistry (ABP1), genetics (AXRs), molecular biology (AUX/IAAs and ARFs), integrative model.
• 4. Auxin transport - PINing down the players
• Physiology, Chemiosmostic model, molecular components (PINs, AUXs) - expression, localization, function.
• C. From the process to the mechanism
• 1. Embryogenesis - apical-basal axis formation
• Pattern formation during embryogenesis, Arabidopsis mutants, gene identities, implication of auxin, auxin distribution and transport, PIN expression, polarities, roles, model.
• 2. Root meristem - down to the stem cells
• Arabidopsis meristem pattern, intercellular signals: quiescent centre, stem cells, auxin as the positional signal, radial patterning - SHR/SCR.
• 3. Organogenesis - so different and so similar
• Overview of different organogenesis processes, shoot derived organs, root-derived organs, correlations between local auxin gradients, transport and organ formation.
• 4. Unifying principles - gradients of morphogens and growth axis
• D. Into the cell
• 1. 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.
• 2. Lessons from GNOM
• Isolation of gnom mutant, GNOM protein - biochemical function and role in development. Connection to the auxin transport. GNOM and endosome recycling.
• 3. Root gravitropism - integration of approaches
• Physiology, genetics, molecular and cell biology of gravitropism: Integration of approaches for understanding of the single process.

Literature

• VIETEN, Anne, Michael SAUER, Philip B BREWER and Jiří FRIML. Molecular and cellular aspects of auxin-transport-mediated development. TRENDS IN PLANT SCIENCE. 2007, vol. 12, No 4, p. 160-168. ISSN 1360-1385. info
• FRIML, J., P. BENFEY, E. BENKOVÁ, M. BENNET, T. BERLETH, N. GELDNER, M. GREBE, M. HEISLER, J. HEJÁTKO, G. JURGENS, T. LAUX, K. LINDSEY, W. LUKOWITZ, C. LUSCHNIG, R. OFFRINGA, B. SCHERES, R. SWARUP, R. TORRES-RUIZ, D. WEIJERS and E. ZAŽÍMALOVÁ. Apical-basal polarity: why plant cells dont standon their heads. Trends Plant Sci. 2006, vol. 11, No 1, p. 12-14. ISSN 1360-1385. info
• SAUER, Michael, Jozef BALLA, Christian LUSCHNIG, Marie WIŠNIEWSKA, Vilém REINÖHL, Jiří FRIML and Eva BENKOVÁ. Canalization of auxin flow by Aux/IAA-ARF-dependent feed-back regulation of PIN polarity. Genes & Development. Spojené státy americké: Cold Spring Harbor Laboratory Press, 2006, vol. 20, No 20, p. 2902-2911. ISSN 0890-9369. info
• ABAS, L., R. BENJAMINS, N. MALENICA, T. PACIOREK, J. WISNIEWSKA, J.C. MOULINIER-ANZOLA, T. SIEBERER, J. FRIML and C. LUSCHNIG. Intracellular trafficking and proteolysis of the auxin efflux facilitator PIN2 in Arabidopsis is proteasomedependent and involved in root gravitropism. Nature Cell Biology. 2006, vol. 2006, No 8, p. 249-256, 7 pp. ISSN 1465-7392. info
• PETRÁŠEK, J., J. MRAVEC, R. BOUCHARD, J. BLAKESLEE, M. ABAS, D. SEIFERTOVÁ, J. WISNIEWSKA, Z. TADELE, M. ČOVANOVÁ, P. DHONUKSHE, P. SKŮPA, E. BENKOVÁ, L. PERRY, P. KŘEČEK, O.R. LEE, G. FINK, M. GEISLER, A. MURPHY, C. LUSCHNIG, E. ZAŽÍMALOVÁ and J. FRIML. PIN proteins perform a rate-limiting function in cellular auxin efflux. Science. 2006, vol. 2006, Apr 6, p. advanced on line, 8 pp. ISSN 0036-8075. info
• DUBOVÁ, Jaroslava, Jan HEJÁTKO and Jiří FRIML. Reproduction of Plants. In Encyclopedia of Molecular Cell Biology and Molecular Medicine. 2nd ed. Weinheim: Wiley-VCH Verlag GmbH & Co, KGaA, 2005, p. 249-295. Vol. 12. ISBN 3-527-30649-8. info

Teaching methods

lectures

Assessment methods

Lectures in a one week block, completed by the colloquium. A condition for successful closure is the active participation at the lectures and at the informal discussion at the end of the course. The discussion will recapitulate selected more difficult topics from the course.

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
The course is taught: in blocks.

• Enrolment Statistics (Spring 2013, recent)
  
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