Plant Molecular Eciphysiology

obligatory courses

The aim of the course is to introduce of students to the problems of molecular mechanisms of plant adaptation to variable environment and methods used. The subjects is realized in form of lectures (30 h) and exercices (60 h). Students realize projects with the use of methods used in molecular biology including bioinformatics.

Classroom

Plant molecular ecophysiology: subject, practical aspects, basic methods; conservation of biological material: theoretical background and methods; Genetically Modified Organisms: theoretical background, law regulations, methods of identification; high-throughput methods for transcriptome profiling; theoretical background, use in plant physiology, statistics and basic tools of bioinformatics.

Full description:

1. Abiotic and biotic stress. Molecular mechanisms of plant response to stress. Methods of plant stress response analysis. Methods of gene expression analysis.

2. The role of Programmed Cell Death (PCD) in plants. PCD and necrosis. Ultrastructural and molecular methods of PCD analysis in plants.

3. Genetically Modified Organisms: production, application, importance. Law regulations of GMO use in Poland and EU. Methods of GMO identification: RT PCR, qRT PCR, ELISA.

4. High-throughput methods for transcriptome profiling: transcriptome sequencing and microarrays. Microarray platforms. Use of microarrays in molecular plant ecophysiology. Microarray experiment: design, performance, data analysis. Microarray data deposition.

Laboratory:

1. Gene expression change in response to abiotic stress.

RNA isolation from maize leaf treated with low temperature. RNA purifying. RNA quality control. Analysis of expression of selected genes (PAL, peroxidases) with) with the use of semiqualitative PCR, estimation of activity of PAL and peroxidases in maize leaves.

2. Identification of PCD in plants.

DNA isolation from maize kernels at different developmental stages. DNA electrophoresis.

3. Identification of GMO .

DNA isolation from transgenic soybean (40-3-2, Roundup Ready ) and wild type with CTAB method. Identification of CaMV 35S promotor by PCR. DNA electroophoresis. Fast identification of GMO with ELISA tests.

4. The use of microarrays for transcriptome profiling in stress treated plants

Presentation of procedure on the example pf microarrays dedicated for maize

Computer lab. Normalization, statistics and analysis of microarray data.

Lab manual (do pobrania ze strony: http://www.biol.uw.edu.pl/ibebr/dydaktyka)

Bioinformatyka. Baxevanis A.D., Ouellette B.F.F. (red). PWN, Warszawa, 2005.

Prasad M.N.V. Plant Ecophysiology. J. Wiley & Sons, New York.Turner P.C., 1996. McLennan A.G., Bates A.D., White M.R.H. Biologia Molekularna. PWN, Warszawa, 2007.

Nobel, P. S. Physicochemical and Environmental Plant Physiology. Elsevier Academic Press, 2005.

KNOWLEDGE

1. Student knows and understands biochemical and molecular background of plant reactions to environmental changes. (K_W09 BI1)

2. Student understands organism-environment interactions, using hypotheses on the temporal and spatial determinants of plant reactions to abiotic stressors. (K_W14 BI1)

3. Student is acquainted with terms used in plant molecular ecophysiology, as well as with scientific literature and state of the art in this area. (K_W13 BI1)

SKILLS

1. Student can choose and apply research techniques used in plant molecular ecophysiology, depending on environmental context of the experiment. (K_U01 BI1)

2. Students can, with the help of a supervisor, plan and carry out an experiment using already known research techniques. They can propose methods for a given type of experiment and assess both suitability and limitations of those methods, depending on the material studied. (K_U06 BI1, K_U07 BI1)

3. Student is able to work in a team, realizing advanced research projects in plant molecular ecophysiology, preparing multimedial or written presentations. (K_U07 BI1, K_U08 BI1)

SOCIAL COMPETENCES

1. Student demonstrates the ability to work in a team and is able to organize workspace for themselves and other members of the team. (K_K07 BI1)

2. Student can recognize, what the ethics and fairness during the research and result interpretation mean for the society. (K_K03 BI1)

3. Student demonstrates responsibility for assessing the risks arising from the use of research techniques and the creation of ergonomic and safe working conditions. (K_K05 BI1)

Laboratory evaluation criteria: short reports of obtained results

Lectures – multimedial presentation of obtained results or final report

no