Informace o předmětu

S2008 Developmental and cellular biology of plants

Rozsah

4/0/0. 4 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.
Vyučováno kontaktně

Vyučující

Tomasz Nodzynski, B.A., M.Sc., Ph.D. (přednášející)
Mgr. Vendula Pukyšová, 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

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

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 19, end 14th May last lecture (2024). 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.

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá blokově.

S2008 Developmental and cellular biology of plants

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)
Mgr. Vendula Pukyšová, 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 19. 2. až Ne 26. 5. 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

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 19, end 14th May last lecture (2024). 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.

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

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.

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

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, 2.22 or on-line in this time, pre-recorded lectures and then consultation on MS-Teams or directly lectures on MS-Teams (preferred).

The schedule encompasses 12 weeks: start February 21, end 16th May last lecture (2022). 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 2.22.

When You have taken this course consider taking, in parallel or subsequently, the complementary course S2011.

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

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 1. 3. až Pá 14. 5. Po 14:00–15:50 online_BCH2

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, 2.22 or on-line in this time, pre-recorded lectures and then consultation on MS-Teams or directly lectures on MS-Teams (preferred).

The schedule encompasses 12 weeks: start March 1, end 17th May last lecture (2021). 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 2.22.

When You have taken this course consider taking, in parallel or subsequently, the complementary course S2011.

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

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 14:00 to 16:00 from 17/2 to 11/5.

Location of the course will be in the building A26, 2nd floor, room 2.22.

When You have taken this course consider taking, in parallel or subsequently, the complementary course S2011.

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

Rozsah

2/0/0. 2 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)
Sibu Simon, 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 18. 2. až Pá 17. 5. 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 14:00 to 16:00 from 18/2 to 13/5.

Location of the course will be in the building A26, 2nd floor, room 2.22.

When You have taken this course consider taking, in parallel or subsequently, the complementary course S2011.

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

Rozsah

2/0/0. 2 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)
Sibu Simon, 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 14:00 to 16:00 from 19/2 to 14/5.

Location of the course will be in the building A26, 2nd floor, room 2.22.

When You have taken this course consider taking, in parallel or subsequently, the complementary course S2011.

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

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)
Helene Robert Boisivon, Ph.D. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Kontaktní osoba: Tomasz Nodzynski, B.A., M.Sc., Ph.D.
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Rozvrh

Po 20. 2. až Po 22. 5. St 9:00–11:50 E26/222

Předpoklady

The course will be taught in English.

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• A. Current approaches and methods of experimental plant genetics
• 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 favorite 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
• B. Auxin 1. The components
• a. Receptors
• b. Signaling
• Discovery of auxins. Towards the players: biochemistry (ABP1), 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. d.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. Development
• a. From production to action
• b. Tropism
• Physiology, genetics, molecular and cell biology of gravitropism: Integration of approaches for understanding of the single process.
• c. Root meristem
• Arabidopsis meristem pattern, intercellular signals: quiescent centre, stem cells, auxin as the positional signal, radial patterning - SHR/SCR.
• d. 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.
• e. 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.
• C. Cytokinin - Complexity of plant hormone signaling
• Biosynthesis, degradation, perception, signal transduction (Histidine kinase two component system), isolation and verification of the receptors and downstream components, Function in plant development.
• D.Ethylene - A success of forward genetics
• Genetic dissection of ethylene signaling, molecular characterization and arrangement of the pathway, Histidine kinase two component system
• E. The complexity pf hormone crosstalk

Výukové metody

Theory class: lectures, class discussions.

Metody hodnocení

Oral examination. Assessment will be based on the interaction with students during the course (Questions, Discussions). Final oral exam will consist in questions related to each parts of the course. To pass the exam, the student will have to answer at least one question from each part of the course.

Vyučovací jazyk

Angličtina

Informace učitele

The course will be taught by lectures on Wednesdays 9am to 12am from 22/2 to 7/5. Location of the course will be in building A26.

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)
Helene Robert Boisivon, Ph.D. (přednášející)
Tomasz Nodzynski, B.A., M.Sc., Ph.D. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Kontaktní osoba: Helene Robert Boisivon, Ph.D.
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Rozvrh

Po 25. 4. až Pá 29. 4. každý pracovní den 9:00–15:50 E26/222

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Výukové metody

Theory class: lectures, class discussions.

Metody hodnocení

Oral examination. Assessment will be based on the interaction with students during the course (Questions, Discussions). Final oral exam will consist in questions related to each parts of the course. To pass the exam, the student will have to answer at least one question from each part of the course.

Vyučovací jazyk

Angličtina

Informace učitele

The course will be taught within one week (whole day: 9am to ±4 pm). The course will be taught 25th to 29th of April. Location of the course will be in building A26.

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (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 13. 4. 9:00–15:50 E26/222, Út 14. 4. 9:00–15:50 E26/222, St 15. 4. 9:00–15:50 E26/222, Čt 16. 4. 9:00–15:50 E26/222

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Informace učitele

This year (2015), following dates: 20. - 23.4. od 9 - 17 hodin., 3.NP. mistnost 329 24.4. od 9 - 17 hodin, 2.NP. mistnost 222

Další komentáře

Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2024 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2023 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2022 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2021 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2020 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2019 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2018 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2017 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2016 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2015 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Předmět se v období podzim 2014 nevypisuje.

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

S2008 Developmental and cellular biology of plants

Údaje z období podzim 2011 - akreditace se nezveřejňují

Rozsah

2/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.

Vyučující

Mgr. Jiří Friml, Dr. rer. nat. (přednášející)

Garance

Mgr. Jiří Friml, Dr. rer. nat.
Ústav biochemie – Chemická sekce – Přírodovědecká fakulta

Omezení zápisu do předmětu

Předmět je otevřen studentům libovolného oboru.

Osnova

• 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.

Vyučovací jazyk

Angličtina

Další komentáře

Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.

• Statistika zápisu (nejnovější)