Molecular methods in plant pathology (146071)

Students gain knowledge about molecular techniques indispensable in detection of important groups of plant pathogens and in analysing their diversity. They acquire knowledge about the functioning of phytopathological laboratories and skills necessary for organizing the work in molecular laboratory. Competence in working in accordance with the diagnostic laboratory protocols as well as in obtaining, preparation and using of reagents, accessories and laboratory equipment is gained through the work in molecular phytopathological laboratory.

• Lectures
  (both oral and e-learning)
• Auditory Exercises
  theoretical preparations for practical work in diagnostics
• Laboratory practice/exercises
  practical work in laboratory for molecular diagnostics.
• Practicum
  practical team work in order to prepare reagents for diagnostics
• Seminars
  reading of contemporary scientific articles from the field of molecular methods (based on the expressed student interest), critical thinking, commenting and writing on the topic together with presentation of gained knowledge.

Teachers' obligations

All teaching materials are prepared and organized by the teachers. All lectures are available in Moodle system as well as tools for bidirectional communication students-teachers. On the same platform there are all information related to the course as well as calendar of major events in the module.

Students' obligations

Attending lectures, exercises and seminars is mandatory but students participate in learning through the system for e-learning, too. Students with more abscences from classes than allowed by official regulations lose possibility for exam accession. The same is for the attendance at exercises and seminar sessions.

1. Introduction to modul content. Laboratory equipment in molecular biology L, Lab - Introducton to modul content. Introductory presentation of molecular laboratory equipment and accessories with usage instructions and safety precautions. Details on equipment needed for polymerase chain reaction (PCR) protocols realization and visualisation of their results (thermocycler, electrophoretic appliances, UV-transiluminator, gel documentation systems). Preparation of equipment, accessories and reagents for molecular analysis (weighing, calculating of required concentrations, dilutions preparation, suspending of primers and other concentrates).
2. Introduction to modul content. Laboratory equipment in molecular biology L, Lab - Introducton to modul content. Introductory presentation of molecular laboratory equipment and accessories with usage instructions and safety precautions. Details on equipment needed for polymerase chain reaction (PCR) protocols realization and visualisation of their results (thermocycler, electrophoretic appliances, UV-transiluminator, gel documentation systems). Preparation of equipment, accessories and reagents for molecular analysis (weighing, calculating of required concentrations, dilutions preparation, suspending of primers and other concentrates).
3. Basic molecular techniques in plant pathology L, E, Pe-L - General molecular methods in plant pathology - intoduction. Basics of serological diagnostical IF protocol (immunofluorescence). PCR method. Specificity of different PCR protocols. Electrophoretic techniques used in analysis off different biological macromolecules (nucleic acids, etc.). Methods of molecular hybridization based on using of different types of molecules.
4. Basic molecular techniques in plant pathology L, E, Pe-L - General molecular methods in plant pathology - intoduction. Basics of serological diagnostical IF protocol (immunofluorescence). PCR method. Specificity of different PCR protocols. Electrophoretic techniques used in analysis off different biological macromolecules (nucleic acids, etc.). Methods of molecular hybridization based on using of different types of molecules.
5. Basic molecular techniques in plant pathology L, E, Pe-L - General molecular methods in plant pathology - intoduction. Basics of serological diagnostical IF protocol (immunofluorescence). PCR method. Specificity of different PCR protocols. Electrophoretic techniques used in analysis off different biological macromolecules (nucleic acids, etc.). Methods of molecular hybridization based on using of different types of molecules.
6. Methods for DNA and RNA isolation L - Protocols for nucleic acids isolation.
7. Methods for DNA and RNA isolation. PCR reaction. L+Lab - Protocols for nucleic acids isolation. Preparations for implementing procedure of polymerase chain reaction (PCR). Implementation of diagnostic protocol of polymerase chain reaction (PCR) in viral plant pathogen diagnostics.
8. PCR reaction Lab - Preparations for implementing procedure of polymerase chain reaction (PCR). Implementation of diagnostic protocol of polymerase chain reaction (PCR) in viral plant pathogen diagnostics.
9. Electrophoretic analysis of nucleic acids Lab - Implementation of „submarine“ horizontal electrophoresis of plant pathogen's nucleic acids in agarose gel.
10. Applications of molecular methods in diagnostics of most important plant pathogens L, E - Implementing diagnostic protocol of PCR in bacterial plant pathogen. Molecular diagnostics of bacterium Erwinia amylovora based on amplification of DNA fragments.
11. Advantages of molecular methods in plant pathogens diagnostics L - Comparation of general and advanced molecular diagnostic techniques vis-a-vis classical diagnostic techniques in plant pathology. Analysis of advantages and suitability of molecular diagnostic methods vis-à-vis classical techniques in terms of real obstacles that appear during implementation of molecular protocols (rapidity, precision, simultaneous analysing of large number of samples, storage/analysis of large set of results (data) obtained).
12. Advantages of molecular methods in plant pathogens diagnostics L - Comparation of general and advanced molecular diagnostic techniques vis-a-vis classical diagnostic techniques in plant pathology. Analysis of advantages and suitability of molecular diagnostic methods vis-à-vis classical techniques in terms of real obstacles that appear during implementation of molecular protocols (rapidity, precision, simultaneous analysing of large number of samples, storage/analysis of large set of results (data) obtained).
13. Seminar S, Pe-L - Selection of topics (current topics related to mol. methods in plant pathology) that will be elaborated by students and on which they will prepare presentation using the recent literature (topics elected will be mainly based on the expressed student interest). Presentations of seminar topics that have been revised by the lecturer. Group discussion.
14. Seminar S, Pe-L - Selection of topics (current topics related to mol. methods in plant pathology) that will be elaborated by students and on which they will prepare presentation using the recent literature (topics elected will be mainly based on the expressed student interest). Presentations of seminar topics that have been revised by the lecturer. Group discussion.
15. Seminar S, Pe-L - Selection of topics (current topics related to mol. methods in plant pathology) that will be elaborated by students and on which they will prepare presentation using the recent literature (topics elected will be mainly based on the expressed student interest). Presentations of seminar topics that have been revised by the lecturer. Group discussion.

1. Lectures in the form of multimedia presentations (available for students on Merlin e-platform)
2. Klement Z, Rudolph K, Sands DC (1990) Methods in Phytobacteriology. Akadémiai Kiadó, Nyomd Vàllalat, Budapest. (selected chapters)
3. Khan, A.J., Dijkstra, J. (2006). Handbook of Plant Virology. New York, London, Oxford: Food Products Press. (selected chapters)
4. Agrios, G.N., (2005). Plant Pathology . -5th ed., Elsevier Academic Press. (selected chapters)

1. Dimmock N, Easton A, Leppard K (2007) Introduction to modern virology, Wiley-Blackwell. (selected chapters)
2. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (2002) Short protocols in molecular biology: A Compendium of methods from current protocols in molecular biology. Wiley. (selected chapters)
3. Paterson RRM, Bridge PD (1994) Biochemical techniques for filamentous fungi, CAB International. (selected chapters)
4. Juretić N (2002): Osnove biljne virologije, Sveučilište u Zagrebu i Školska knjiga, Zagreb.

• Toolbox molecular biology, University of Wageningen, Netherlands
• Applied Molecular Microbiology, University of Wageningen, Netherlands
• Phytopathological diagnosis and biotechnology, University of Bari, Italy