Bi8930 Developmental and cellular biology of plants

Faculty of Science
Spring 2011
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Mgr. Jiří Friml, Dr. rer. nat. (lecturer), prof. RNDr. Jiří Fajkus, CSc. (deputy)
Guaranteed by
prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology - Biology Section - Faculty of Science
Contact Person: prof. RNDr. Jiří Fajkus, CSc.
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
there are 9 fields of study the course is directly associated with, display
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.
  • 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.
  • MRAVEC, Jozef, Petr SKŮPA, Aurélien BAILLY, Klára HOYEROVÁ, Pavel KŘEČEK, Agnieszka BIELACH, Jan PETRÁŠEK, Jing ZHANG, Vassilena GAYKOVA, York-Dieter STIERHOF, Petre I. DOBREV, Kateřina SCHWARZEROVÁ, Jakub ROLČÍK, Daniela SEIFERTOVÁ, Christian LUSCHNIG, Eva BENKOVÁ, Eva ZAŽÍMALOVÁ, Markus GEISLER and Jiří FRIML. ) Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter. Nature. Lodon, UK: Nature Publishing Group, 2009, Neuveden, No 459, p. 1136-1140. ISSN 0028-0836. info
  • PETRÁŠEK, Jan and Jiří FRIML. Auxin transport routes in plant development. Development. Cambridge: Company of Biologists, 2009, Neuvedeno, No 136, p. 2675-2688. ISSN 0950-1991. info
  • RŮŽIČKA, Kamil, Mária ŠIMÁŠKOVÁ, Jerome DUCLERCQ, Jan PETRÁSEK, Eva ZAŽÍMALOVÁ, Sibu SIMON, Jiří FRIML, Marc C. E VAN MONTAGU and Eva BENKOVÁ. Cytokinin regulates root meristem activity via modulation of the polar auxin transport. Proceedings of the National Academy of Sciences of the United States of America. 2009, vol. 106, No 11, p. 4284–4289. ISSN 0027-8424. info
  • RŮŽIČKA, Kamil, Karin LJUNG, Steffen VANNESTE, Radka PODHORSKÁ, Tom BEECKMAN, Jiří FRIML and Eva BENKOVÁ. Ethylene regulates root growth through effects on auxin biosynthesis and transport-dependent auxin distribution. PLANT CELL. 2007, vol. 19, No 7, p. 2197-2212. ISSN 1040-4651. info
  • 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
  • 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
Teaching methods
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 from the course.
Language of instruction
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
The course is taught: in blocks.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Autumn 2002, Autumn 2003, Autumn 2004, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, spring 2012 - acreditation.
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