Molecular biology of plants

biological sciences

intermediate

BI1_W03, BI1_W04, BI1_W05

Basics of molecular biology and genetics at the level of the third year of Biology or related studies.

The aim of the course is to discuss the molecular mechanisms underlying the most important developmental processes in plants, i.e. genomics, proteomics, and metabolomics. Exercises have the character of computer classes and introduce into bioinformatics and population genetics of plant organisms based on DNA and protein analyses.

The lecture content includes 1. Basics of plant genomics - the main molecular techniques used in the analysis of plant genetic variability, including: PCR-based genetic markers, sequencing, and analysis of gene expression in DNA microarrays. 2. Molecular regulation of the cell cycle - a reminder of the role of DNA, RNA, proteins, fatty acids, polysaccharides in the plant life cycle. 3. Regulation of the plant development process - transport of metabolites, hormone biosynthesis, cell signalling, senescence and cell death. 4. Analysis of genes encoding basic enzymes and building blocks of plant cells - signalling molecules and protein receptors. 5. Basics of plant population genetics - analysis of DNA polymorphism and proteins of related species, phylogenesis, Hardy-Weinberg equilibrium law in plant populations. 6. Proteomics and protein homology analysis. 7. Plant genetic engineering - application of transgenic plants (GMOs) in agriculture, industry and pharmacy. 8. Molecular basis of plant genome editing. 9. Ethical problems related to modern plant biotechnology. 10. Metabolomics - detection of basic secondary metabolites in plants. 11. Plant-environment interactions, including the molecular basis of plant defence reactions to biotic (pathogen attack) and abiotic (physical or chemical stress) factors. 12. Genetic structure and gene flow in forest tree populations. 13. Palnt alergens. 14. Basics of forensic botany based on molecular analysis of the genome.

Exercises rely on computer analysis of the sequence, function, and structure of proteins. Students calculate algorithms for alignment and comparison of amino acid and nucleotide sequences, construct phylogenetic trees and learn methods for calculating the frequency, heterozygosity, and inbreeding of plant populations, and also perform PCoA and phylogenetic analysis of the studied species.

Compulsory literature:

1. Biochemistry & Molecular Biology of Plants. Ed. B.B. Buchanan, W. Gruissem, and R.L. Jones. Wiley Blackwell, American Society of Plant Biologists, 2018.

2. Agrobiotechnology. Ed. K. Kowalczyk. Ed. University of Life Sciences in Lublin, Lublin 2013

3. Molecular biotechnology: genetic modifications, advances, problems. J. Buchowicz. PWN, 2nd edition, 2009.

4. Plant biotechnology. Ed. S. Malepszy. PWN, Warsaw 2009.

5. Easy phylogenetic trees. User guide. B.G. Ball, WUW, 2008.

6. GMO in the light of the latest research. Ed. K. Niemirowicz-Szczytt. SGGW, Warsaw 2012.

7. Basics of population genetics. Ed. D.L. Hartl, A.G. Clark. WUW, Warsaw, 2009.

8. Proteomics and metabolomics. Ed. A. Kraj, A. Drabik, J. Silberring, WUW, Warsaw 2010.

Supplementary literature:

9. Molecular biology. Short lectures. P.C. Turner, A.G. McLennan, A.D. Bates, M.R.H. White. PWN SA, Warsaw, 2012.

10. Genetics. Short lectures. P.C. Winter, G.I. Hickey, H.L Fletcher. PWN Warsaw, 2004.

11. Molecular markers, natural history and evolution. J.C. Avise. WUW, Warsaw, 2008.

12. Basics of biotechnology. C. Ratledge, B. Kristiansen. PWN, Warsaw 2011.

13. Current scientific publications proposed by the lecturer.

Subject effects in terms of knowledge:

Objective effect 1: The graduate knows and understands all the main problems in the field of various biological branches as well as in the field of mathematics and chemistry, separate for the correct and correct operation of the phenomena occurring in the plant cell at the molecular level, i.e. DNA, RNA and proteins, and knows their connections with other disciplines, such as biochemistry and genetics

Learning outcome 2: The graduate knows and understands the basic categories of concepts and terminology in the subject dealing with the molecular biology of plants, and also has knowledge of the development of this science and applies to many research methods, including analyzing for detecting differences in the detection of DNA, RNA and proteins

Learning outcome 3: The graduate knows and understands the basic techniques and research tools, such as PCR analysis, electrophoretic separation and sequencing, the approach in the molecular biology of the plant and in the field of calculations and statistics at a level that allows them to be used for the analysis of genetic polymorphism at the level of genomics and proteomics plants.

Objective effects in terms of skills:

Learning outcome 4: The graduate is able to access the source based on the Internet database in the field of biochemistry, genetics and proteomics, understands the literature in the field of plant molecular biology in Polish; read and understand scientific texts in English

Objective effect 5: The graduate is able to plan and organize research work as well as interact and act in a group, including various roles in it, as well as perform the research tasks assigned to him.

Social outcomes:

Outcome 6: The graduate is ready to critically assess his knowledge, received content and additional knowledge in solving cognitive and other problems in the field of plant molecular biology

Subject learning outcomes assigned to lectures (1-3)

Subject learning outcomes assigned to exercises (4-6)

Lecture grade:

Average grade from two partial tests, covering material from lectures.

Test exam consisting of multiple-choice and "true/false" questions.

The condition for admission to the final exam is passing the exercises.

Final rating:

94 - 100% very good (5.0)

88 - 93% good plus (4.5)

80 - 87% good (4)

70 - 79% sufficient plus (3.5)

60 - 69% sufficient (3)

below 59.9% unsatisfactory (2)

For active attendance at the lectures, it is possible to raise the final grade to a higher one if the percentage value obtained for the average of grades or points is, respectively: 58-59% (for grade 3); 67-69% (3.5 rating); 77-79% (per grade 4); 86-87% (4.5 grade) and 92-93% (5 grade).

Exercise grade:

The grade for exercises consists of the average of two grades: the average grade based on the partial grades received during the semester from tests and activity in classes, and the grade from the final colloquium. The classes are passed if the student: (i) actively participated in at least 85% of the classes; (ii) worked during the classes in a way that allowed positive assessment of social skills and competences obtained during the classes (described in the syllabus as subject learning outcomes 4-6).

Scope of colloquium grades:

94 - 100% very good (5.0)

88 - 93% good plus (4.5)

80 - 87% good (4)

70 - 79% sufficient plus (3.5)

60 - 69% sufficient (3)

below 59.9% unsatisfactory (2)

For active participation in classes, it is possible to raise the final grade to a higher one, as in the case of the lecture grade.

Knowledge:

grade 2 (fail): The graduate knows and does not understand the most important problems, terminology and concepts in the field of molecular biology, biochemistry and genetics, concerning the basic phenomena and processes occurring in a plant cell at the level of DNA, RNA and proteins; does not know and understand basic research techniques and tools, such as PCR analysis, electrophoretic separation and sequencing, nor in the field of computer science and statistics at a level that allows them to be used for genetic polymorphism analyzes at the level of plant genomics and proteomics

grade 3 (sufficient): A graduate at the basic level knows and understands the most important problems, terminology and concepts in the field of molecular biology, biochemistry and genetics, concerning the basic phenomena and processes occurring in a plant cell at the level of DNA, RNA and proteins; knows the basic research techniques and tools, such as PCR analysis, electrophoretic separation and sequencing, as well as tools in computer science and statistics at a level that allows them to be used for genetic polymorphism analyzes at the level of plant genomics and proteomics

grade 4 (good): The graduate knows and understands the most important problems, terminology and concepts in the field of molecular biology, biochemistry and genetics at a good level, concerning the basic phenomena and processes occurring in a plant cell at the level of DNA, RNA and proteins; knows the basic research techniques and tools, such as PCR analysis, electrophoretic separation and sequencing, as well as computer science and statistics tools at a level that allows them to be used for genetic polymorphism analyzes at the level of plant genomics and proteomics

5 (very good): The graduate knows and understands the most important problems, terminology and concepts in the field of molecular biology, biochemistry and genetics at a very good level, concerning the basic phenomena and processes occurring in a plant cell at the level of DNA, RNA and proteins; knows very well the basic techniques and research tools, such as PCR analysis, electrophoretic separation and sequencing, as well as computer science and statistics tools at a level that allows them to be used for genetic polymorphism analyzes at the level of plant genomics and proteomics

Skills:

grade 2 (fail): The graduate is not able to properly select sources based on online databases in the field of biochemistry, genetics and proteomics, understands literature in the field of plant molecular biology in Polish at all and does not read scientific texts in Polish with understanding English; cannot plan and organize individual work or cooperate and work in a group, assuming different roles in it, and is unable to perform research tasks commissioned by the teacher

grade 3 (sufficient): The graduate at the basic level is able to properly select sources based on online databases in the field of biochemistry, genetics and proteomics, at the basic level understands literature in the field of plant molecular biology in Polish and reads scientific texts with understanding in English; at a basic level, is able to plan and organize individual work as well as cooperate and work in a group, assuming various roles in it, as well as perform research tasks commissioned by the teacher

for the grade 4 (good): A graduate at a good level is able to properly select sources based on online databases in the field of biochemistry, genetics and proteomics, has a good understanding of literature in the field of plant molecular biology in Polish and reads scientific texts in English with understanding ; is able to plan and organize individual work well, as well as cooperate and work in a group, assuming various roles in it, and also performs well the research tasks commissioned by the teacher

for the grade 5 (very good): The graduate is able to properly select sources based on online databases in the field of biochemistry, genetics and proteomics at a very good level, understands the literature in the field of plant molecular biology in Polish very well and reads scientific texts with understanding in English; is able to plan and organize individual work very well, as well as cooperate and work in a group, assuming various roles in it, and also performs research tasks commissioned by the teacher very well.

Competences:

grade 2 (fail): The graduate is not at all ready to critically assess his knowledge, perceived content and does not recognize the importance of knowledge in solving cognitive and practical problems in the field of plant molecular biology

for the grade 3 (superior): A graduate at the basic level is ready to critically assess his knowledge, perceived content and sufficiently recognizes the importance of knowledge in solving cognitive and practical problems in the field of plant molecular biology

not relevant