The goal of the course is to teach the students fundamental theoretical and practical aspects of analytical cytometry. The course covers multiple areas of methods in microscopy with special focus on flurescence and its application in confocal microscopy, morphometric measurements and their applications in cytology, determination of vital parameters and live cell imaging, basic methods for sample preparation etc.
1. R.D. Goldman a kol.: Live Cell Imaging – A Laboratory Manual, Cold Spring Harbour Laboratory Press, 2010
2. J.B. Pawley a kol.: Handbook of Biological Confocal Microscopy, Springer, 2006
3. D. Anselmetti a kol.: Single Cell Analysis, Wiley-Blackwell, 2009
4. A. Hibbs a kol.: Confocal Microscopy for Biologists, Kluwer Academic/Plenum Publishers, 2004
1.) Fundamentals of fluorescent methods, principles of fluorescence. 2.) Principles of confocal microscopy 3.) Principles of flow cytometry. 4.) Cell sorting. 5.) Analyses on living cells – principles, hardware requirements. 6.) Methods for vital parameters. 7.) Analyses, imaging methods with regard to lipids, cytoskeleton dynamics or cell division. 8.) Fluorescent dyes and their applications in analytical cytometry. 9.) Staining of nucleic acids, lipids, proteins, cytosceleton stainings, visualization of cell organelles. 10.) Vital stainings. 11.) Membrane transport. 12.) Reactive oxygen and nitrogen species (ROS, NOS). 13.) Mitochodrial membrane potential, pH etc.
The goal of the course is to teach the students fundamental theoretical and practical aspects of analytical cytometry. The course covers multiple areas of methods in microscopy with special focus on flurescence and its application in confocal microscopy, morphometric measurements and their applications in cytology, determination of vital parameters and live cell imaging, basic methods for sample preparation etc.
Attendance of practicals (at least 90%), final examination
Application of bacteria in industrial processes and for biochemicals production. Ethanol production - beer, wine, acetic acid and acetone production, production of antibiotics. Bioreactors, application of zeasts in industrial processes. Application of recombinant DNA techniques in industry. Lactic acid bacteria and its application in food industry – production of cheese and youghurt, probiotics. Microbiology in food quality control. Application of microorganisms in environment protection – microbiologgy of wastewater treatment, bioremediation, biofuels, microbiology of biogas plants.
Application of bacteria in industrial processes, biochemicals production. Application of recombinant DNA techniques in industry. Lactic acid bacteria and its application in food industry. Microbiology in food quality control. Application of microorganisms in environment protection – wastewater treatment, bioremediation, biofuels, microbiology of biogas plants.
Evaluation of practicals: 30%
Final evaluation:
Oral examination - 70%
The students will acquire in-depth knowledge on the important role of microoganisms in different fields like food (production of beer, wine, milk products, probiotics), chemical and pharmaceutical industry (production of vitamins, hormones, amino acids, enzymes, comodity chemicals), vaccines and their production, wastewater treatment, as well as microbial bioremediation, biofuels and biomining.
Cvrčková F. Úvod do praktické bioinformatiky. Česko: Academia, 2006. 148 s. ISBN 80-200-1360-1.
Brown, T. A. Genomes 3. 3rd ed. New York : Garland Science Publishing. 2007. 713 p. ISBN 0-8153-4138-5
Nei M, Kuma, S. Molecular Evolution and Phylogenetics. Oxford University Press. 2000. 333 p. ISBN 978-0195135855
Lemey P, Salemi M, Vandamme A-M. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing / Edition 2. Cambridge University Press. 2009. 750 p. ISBN 978-0521730716
Manuals for used software and online tools
Introduction to bioinformatics - definition and content of the subject, brief history, overview of basic tools for biological data processing.
Biological and biomedical databases I. - search and acquisition data - PubMed, GenBank, SwissProt.
Biological and biomedical databases II. - search and acquisition data - PDB, KEGG, OMIM, REBASE.
Sequence analysis - input/output data formats, analysis of biopolymer sequences with a focus on nucleic acids - analysis of chromatograms, assembly of sequences, use of MEGA tools, Unipro UGENE tools, CAP3 server, data publication in the GenBank database.
Pairwise sequence comparisons - local comparisons, use of blastn, blastp, blastx tools in the analysis of nucleic acid and protein sequences, setting of parameters, biological significance of obtained results.
Analysis of protein sequences - identification of protein motifs and domains, use of CDD and PFAM database.
Searching for open reading frames in nucleic acid sequences - use of various tools (ORFfinder, NEBcutter).
Restriction analysis - use of various tools for searching suitable enzymes for restriction analysis (REBASE, NEBcutter).
Design and verification of primers for PCR analysis - properties of primers, use of various tools (Primer3, Primer-BLAST).
Phylogenetic analysis - comparison of multiple sequences using Clustal, MUSCLE tools, analysis of evolutionary and phylogenetic relatedness of organisms - creation and analysis of phylogenetic trees, use of various construction methods, biological significance of obtained results
Sequencing of the new generation I. - brief overview of massive parallel sequencing methods, output formats of obtained data, use of Unix operating systems in data processing.
Next generation sequencing II. - whole-genome sequencing, de novo sequencing, mapping to the reference sequence.
Next generation sequencing III. - metagenomic analysis of environmental samples
Molecular identification of organisms - global sequence comparisons (EZ Taxon, UNITE database, BOLD system).
attendance at lectures and practicals (at least 80%), continuous evaluation of the performance of tasks, final examination
Introduction to Bionformatics, free accessible biological and biomedical databases, free available bioinformatics tools. Analysis of biopolymers - nucleic acids and proteins. Pairwise sequence comparisons, multiple sequence comparisons, analysis of evolutionary and phylogenetic relatedness of biopolymers, creation and analysis of phylogenetic trees, molecular identification of organisms.
The students will acquire basic knowledge of biological databases, acquisition and analysis of sequencing data, biological approaches in phylogenetic analysis, construction and interpretation of phylogenetic trees and methods for molecular identification of organisms
Farrar W.B.: Cancer Stem Cells. Cambridge University Press, 2010
Majumder S.: Stem Cells and Cancer. Springer Science+Business Media, LLC 2009
Scatena R., Mordente A., Giardina B.: Advances in Cancer Stem Cell Biology. Springer Science+Business Media, LLC 2012
Simmons A.: Hematology. A Combined Theoretical & Technical Approach, W.B. Saunders Company, Philadelphia, 1989
Yu J.S.: Cancer Stem Cells. Methods and protocols. Humana Press, a part of Springer Science+Business Media, LLC 2009
Relevantné vedecké práce z uvedenej problematiky publikované v odborných časopisoch a dostupné v medzinárodných databázach (https://www.ncbi.nlm.nih.gov/pubmed/; https://www.scopus.com/search/form.uri?display=basic; https://www.sciencedirect.com/), napr. Zakrzewski a kol., Stem cells: past, present, and future. Stem Cell Research & Therapy (2019), 10:68: https://doi.org/10.1186/s13287-019-1165-5
Batlle – Clevers, Cancer stem cells revisited. Nature medicine (2017), 23 (10): doi:10.1038/nm.4409
Tweedel, The Adaptability of Somatic Stem Cells: A Review. Journal of Stem Cells and Regenerative Medicine (2017), 13(1)
Ferraro – Lo Celso. Adult stem cells and their niches. Adv Exp Med Biol. (2010), 695: 155–168. doi:10.1007/978-1-4419-7037-4_11
1.Stem cell, the features of stem cells
2. Pluripotent/multipotent hematopoietic stem cell
3. The investigation methods of stem cells, the models of functional organization of population of hematopoietic stem cells, differentiation antigens
4. Myeloid hematopoietic stem cell
5. Megakaryocyte–erythroid progenitor cells
6. Common lymphoid progenitors
7. Microenvironment of stem cells, homing and mobilization of hematopoietic stem cells
8. Plasticity of stem cells and factors regulating self-renewal, proliferation and differentiation
9. Cytokines, hematopoietic growth factors and interleukins in hematopoiesis
10. Clinical use of cytokines and hematopoietic stem cells
11. Embryonic and induced pluripotent stem cells and their potential in regenerative medicine
12. Adult stem cells and their potential in regenerative medicine
13. Cancer stem-like cells.
1. Stem cell, the features of stem cells;
2. Pluripotent/multipotent hematopoietic stem cells;
3. The investigation methods of stem cells, the models of functional organization of population of hematopoietic stem cells, differentiation antigens;
4. Myeloid hematopoietic stem cell;
5. Megakaryocyte–erythroid progenitor cells;
6. Common lymphoid progenitor;
7. Microenvironment of stem cells, homing and mobilization of hematopoietic stem cells;
8. Plasticity of stem cells and factors regulating self-renewal, proliferation and differentiation;
9. Cytokines, hematopoietic growth factors and interleukins in hematopoiesis;
10. Clinical use of cytokines and hematopoietic stem cells;
11. Embryonic and induced pluripotent stem cells and their potential in regenerative medicine;
12. Adult stem cells and their potential in regenerative medicine;
13. Cancer stem-like cells.
The aim of the course is to ground students with basic knowledge about biology of hematopoietic stem cells and about the embryonic, adult and cancer stem cells. The purpose of the course is to acquaint student with regulation of self-renewal, proliferation, differentiation and plasticity of stem cells, as well as the humoral factors involved in these processes. Moreover, the microenvironment of stem cells and clinical use of cytokines and hematopoietic stem cells will be discussed during the course, together with the induced pluripotent stem cells and potential usage of stem cells in regenerative medicine.
Form of teaching: Lecture, exercises.
Redommended scope of teaching (in lessons):
weekly: 1+2, per study period: 14+28.
Study method: full-time.
Number of ECTS credits: 4
Zar, J.H. 1996. Biostatistical analysis. 3rd ed. Prentice Hall.
Legendre, P. & L. Legendre. 1998. Numerical Ecology, 2nd English ed. Elsevier.
Borcard, D., Gillet, F. & P. Legendre. 2018. Numerical Ecology with R.
Oral exam, completion of exercises, elaboration of a semester assignment
Slovak, English
Lectures:
1. Biometric data and their graphical presentation, univariate statistics data
2. Normalization and standardization of data
3. Exploratory data analysis
4. Basics of Univariate Statistics, Part 1
5. Basics of Univariate Statistics, 2nd time
6. Biometric data and graphical presentation, data of multivariate statistics
7. Binary, quantitative and semi-quantitative data in biometrics
8. Multivariate clustering analyses
9. Ordinal analyses of multivariate data, methods of hypothesis formation
10. Ordinal analyses of multivariate data, methods testing hypotheses
11. Introduction to biometric data processing in the context of spatial diversity
12. Selected topics of biometric processing of digital image data
13. Introduction to Chemometric Data Processing
14. Biometrics and biodiversity
Exercises:
Implementation of the lectured topics on sample datasets. Past, R environment.
Data Normalization and Standardization, Logarithmic and Box-Cox Transform, Histogram, Biplot, 3D Plot, Radar Fence, Bar-Box-Pie-Jitter-Violin Graph, Summary Statistics, Normality and Homoscedasticity Tests, t Test, F Test, Mann-Whitney Test, Kolmogorov-Smirnov Test, One-Factor and Two-Factor ANOVA, Correlation Table, Heatmap, ANCOVA, pivot table, clustering analyses, K-means clustering, principal component analysis, canonical correspondence analysis, non-metric multidimensional scaling, linear discriminant analysis, redundancy analysis, MANOVA, one-factor and two-factor PERMANOVA, linear regression, Mantel's test, autocorrelation analysis, Thin-plate splines, elliptic fourier analysis, allometric analysis, alpha and beta diversity indicators
The course is focused on practical processing of biometric data. It should provide students with knowledge of basic tools for processing their own measurements in the processing of final theses.
To gain theoretical and practical knowledge on plant tissue culture in vitro.
Abdin M.Z., Kiran U., Kamaluddin M., Ali A. (eds.): Plant Biotechnology: Principles and Applications. 2017, Springer Nature Singapore Pte Ltd., Singapore
Chawla H.S.: Introduction to Plant Biotechnology. 2009, third edition, Science Publisher, Enfield, USA
Periodicals and Internet sources
active participation at the practicals, protocols
Active participation at the practicals, protocols, oral examination
1. Definition of biotechnology. History of biotechnology.
2. History of plant biotechnology.
3. Aseptic techniques.
4. Nutrition media and culture conditions.
5. Micropropagation. Tissue and organ cultures.
6. Callus. Cell suspension culture.
7. Protoplasts. Somatic hybridization.
8. Somatic embryogenesis. Organogenesis.
9. Somaclonal variation.
10. Secondary metabolites production. Bioreactors. Biotransformation. Immobilization.
11. Plant secondary metabolism. Elicitors. Elicitation.
12. Genetic transformation. Direct and indirect methods.
13. Agrobacterium-mediated transformation. The genes carried by Ti and Ri plasmids.
14. Selection markers. Reporter genes.
15. Germplasm storage. Gene banks. Slow growth method.
16. Cryopreservation.
17. Metabolic engineering. The role of tissue and organ specific plant promoters.
18. Genetic engineering. Plants resistant to biotic and abiotic stresses.
19. Molecular farming. Plant-based edible vaccines. Plastome engineering.
20. RNA silencing. The application of microRNAs in plant biotechnology.
Definition and history of plant biotechnology. Aseptic techniques, culture conditions. Micropropagation, types of plant explant cultures used in biotechnology. Somatic hybridization and embryogenesis, direct and indirect organogenesis. Somaclonal varation. Secondary metabolites production, bioreactors, biotransformation, immobilization and elicitation. Genetic transformation, direct and indirect methods of transformation. Types of vectors, promotors, selection markers and reporter genes used in plant transformation. Germplasm storage, gene banks. Cryopreservation and slow growth method. Genetically modified organisms - metabolic engineering, genetic engineering, plants resistant to biotic and abiotic stresses, molecular farming, the role of tissue and organ specific plant promoters, plastome engineering, plant-based edible vaccines. RNA silencing, the application of microRNAs in plant biotechnology.
To gain theoretical and practical knowledge on plant tissue culture in vitro.
Oral examination.
To gain knowledge and experience in genetic processes at the cell level using the newest scientific findings in cytogenetics. To get acquainted in detail with the results resulting from human genome mapping.
Alberts, B., Heald, R., Hopkin, K., Johnson, A., Morgan, D., Roberts, K., & Walter, P. (2022). Essential Cell Biology (6. vydanie). W. W. Norton & Company. ISBN: 978-1-324-03343-1
Liehr, T. (2021). Cytogenomics. Elsevier, Academic Press. ISBN: 978-0-12-823579-9
Snustad, P.D., Simmons, M.J.: Principles of Genetics. John Wiley and Sons, 5th edition 2009, 871 pp.
Periodicals
Internet sources
The protocols and worksheets will be evaluated in case of the practical activities or distance learning. The e-learning course UBEV/Cytogenetika a karylógia is available in Moodle.
written tests, written examination;
Practicals: The protocols and worksheets from the practical activities or distance learning are required. The e-learning course UBEV/Cytogenetika a karylógia is available in Moodle.
1. Introduction to the Study of the Subject – From Cytogenetics to Cytogenomics
Historical Context and Current Research Focus, Main Areas of Cytogenetic Research – Molecular Cytogenetics, Molecular Genetics and Genomics, Epigenetics and Epigenomics, Nucleomics. (1h)
2. Methods in Cytogenetic Research. Basic Cytogenetic Methods (Karyotyping, Chromosome Banding), Flow Cytometry, PCR-Based Methods, Hybridization Techniques, Spectral Karyotyping. (1h)
3. Nuclear Architecture. Functional Aspects of Chromatin Structure and Organization. Interphase Nucleus. (2h)
4. Regulation of Chromatin Structure. Epigenetic Modifications, Chromatin Structure. Changes in Methylation Status and Human Diseases. (2h)
5. Genome and Cell Division – Changes in Chromatin Organization During the Cell Cycle – Mitosis, Meiosis. (2h)
6. Cell Cycle Disorders Leading to Chromosomal Aberrations. (1h)
7. The Human Genome from a Cytogenetic Perspective. Key Insights. Repetitive Sequences in the Human Genome and Their Origins. Major Groups of Transposons in the Human Genome. (2h)
8. Cytogenetics in Biomedical Research and Practice. Numerical Chromosome Abnormalities and Their Consequences. Cancer Cytogenetics. (1h)
Organisation of eukaryotic genome. Nuclear skeleton. Nucleolus, nucleolar skeleton. Chromatin structure and changes of chromatin. Levels of DNA organisation in cell nucleus. Chromosomes. Cell cycle. Genetic regulation of a cell cycle. Molecular cytology. Basic characteristics of the Human genom project - what we can learn from it?
To gain knowledge and experience on genetic processes at the cell level using the newest scientific findings of cytogenetics. To get acquainted in detail with the results and significance of human genome mapping (HUGO project).
written examination
1. BUZKOVÁ, K. 2006. Fitness jóga. Praha: Grada. 167 s.
2. ČECHOVSKÁ, I., MILEROVÁ, H., NOVOTNÁ, V. Aqua-fitness. Praha: Grada. 136 s.
3. EVANS, M ., HUDSON, J., TUCKER, P. 2001. Umění harmonie: meditace, jóga, tai-či, strečink. 192 s.
4. JARKOVSKÁ, H., JARKOVSKÁ, M. 2005. Posilováni s vlastním tělem 417 krát jinak. Praha: Grada. 209 s.
5. KOVAŘÍKOVÁ, K. 2017. Aerobik a fitness. Karolium, 130 s.
Completion: passed
Condition for successful course completion:
- active participation in line with the study rule of procedure and course guidelines
- effective performance of all tasks- aerobics, water exercise, yoga, Pilates and others
Slovak language
Brief outline of the course:
1. Basic aerobics – low impact aerobics, high impact aerobics, basic steps and cuing
2. Basics of aqua fitness
3. Basics of Pilates
4. Health exercises
5. Bodyweight exercises
6. Swimming
7. Relaxing yoga exercises
8. Power yoga
9. Yoga relaxation
10. Final assessment
Students can engage in different sport activities offered by the sea resort – swimming, rafting, volleyball, football, table tennis, tennis and other water sports in particular.
Content standard:
The student demonstrates relevant knowledge and skills in the field, which content is defined in the course syllabus and recommended literature.
Performance standard:
Upon completion of the course students are able to meet the performance standard and:
- perform basic aerobics steps and basics of health exercises,
- conduct verbal and non-verbal communication with clients during exercise,
- organise and manage the process of physical recreation in leisure time
To provide the students with a knowledge of basic biological principles of carcinogenesis.
L. Pecorino: Molecular Biology of Cancer. Mechanisms, Targets, and Therapeutics. Fifth Edition, Oxford University Press, 2021
Robert A. Meyers: Cancer, From Mechanisms to Therapeutic Approaches, Wiley-VCH Verlag GmbH & Co. KGaA, 2007, ISBN 978-3-527-31768-4
Robert G. McKinnell et al.: The Biological Basis of Cancers, Second Edition, Cambridge University Press, 2006, ISBN 13: 978-0-521-84458-1
Vincent T. DeVita, Jr, et al.: Cancer Principles & Practice of Oncology, 3rd Edition, Wolters Kluwer/Lippincott Williams & Wilkins, 2012, ISBN 13: 978-1-4511-1639-7
John D. Schuetz and Toshihisa Ishikawa: Adcances in Cancer Research ABC Transporters and Cancer, Elsevier/Academic Press 2015, ISBN 978-0-12-801251-2
Roberto Scatena et al.: Advances in Cancer Stem Cell Biology, Springer, 2012, ISBN 978-1-4614-0808-6, DOI 10.1007/978-1-4614-0809-3
KBMB/MB1a, KBMB/MKB1a
Oral examination
Tumor development. Tumor growth and metastatic potential. Cell cycle regulation and pathogenesis of cancer. Apoptosis in tumor growth and metastasis. Oncogenes and cancer. Tumor suppressor genes. Metastasis suppressor genes. Angiogenesis in cancer. Cell surface glycoproteins and their receptors. Proteinases and their inhibitors in cancer invasion. Radio-, chemo- and immunotherapy.
To provide the students with a knowledge of basic biological principles of carcinogenesis.
Oral examination
Mentioned in the approved thesis assignment.
The diploma thesis is the result of the student's own creative work. It must not show elements of academic fraud and have to meet the criteria of proper research practice defined in Rector's Decision no. 21/2021, which establishes the rules for assessing plagiarism at the Pavol Jozef Šafárik Univesity in Košice and its components. The fulfillment of the criteria is verified mainly in the training process and in the process of defending the thesis. Failure to comply with them is grounds for initiation of disciplinary proceedings.
The student carries out his activities under the guidance of the supervisor. The result of the student's work should be the fulfillment of the objectives stated in the approved thesis assignment.
With the diploma thesis, the student demonstrates mastery of the extended theory and professional terminology of the field of study, the acquisition of knowledge, skills and competences in accordance with the declared profile of the graduate of the study program, as well as the ability to apply them in an original way when solving the selected problem of the field of study. The student will demonstrate the ability of independent professional work from a content, formal and ethical point of view. Further details of the diploma thesis are determined by Directive no. 1 /2011 on the basic requirements of the final theses and the Study Regulations of the UPJŠ in Košice for 1st, 2nd and combined 1st and 2nd degrees.
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Mayr, E.: Co je evoluce. Aktuální pohled na evoluční biologii. Academia Praha, 2009.
Flegr, J.: Evoluční biologie. Academia Praha 2005
Kejnovský, E., Hobza, R.: Evoluční genomika. (http://www.evolucnigenomika.cz/Skripta/Evolucni%20genomika%20skripta%202008.pdf) 2009
Futuyma, D.J.: Evolution. Sinauer Associates, Sunderland, 2005.
Briggs D., Walters S. M.: Proměnlivost a evoluce rostlin. Univerzita Palackého, Olomouc, 2001.
Dobzhansky T. et al.: Evolution. San Francisco 1977.
E.J.Larson : Evolúcia. Neobyčajná história jednej vedeckej teórie. Slovart, 2006.
.
In the written exam, the student must demonstrate, in addition to knowledge in the field of evolutionary biology, knowledge of analytical and synthetic thinking when solving the answers to problem-formulated questions, while using knowledge from the entire bachelor's and master's studies of his field.
1. Introduction to evolutionary biology. Historical development of ideas about the evolution of life. Evidence of the theory of evolution.
2. The origin and evolution of the first forms of life on Earth.
3. Theory of natural selection.
4. Molecular evolution I: Evolutionary processes at the gene level. Molecular evolution.
5. Molecular evolution II: Evolutionary processes at the level of species and populations.
6. Molecular evolution III: Evolution of genetic systems.
7. Reproductive strategies of plants, sexuality, asexuality and evolution.
8. Macroevolution and microevolution. Types of speciation. Evolutionary trends of green plants.
9. Extinction - a sad but natural part of evolution.
10. Overview of animal evolution.
11. Origin and development of man I.
12. Origin and development of man II.
Graduates of the course will gain an overview of evolutionary theories in the past and today, and based on the most modern scientific knowledge about macro- and microevolutionary processes in living nature at various levels of investigation and knowledge, they should be able to analytically solve scientific, but also philosophical questions in the field of evolutionary theory. He is able to argue and critically evaluate different views on evolution and apply his knowledge in different types of work tasks not only in an academic environment, but also in practice, e.g. in agriculture, ecology, environmental protection and the like.
.
The aim of lectures is to explain the effects of environmental factors and mechanisms of adaptations in animals and humans.
1. Piantadosi C.A. Biology of Human Survival: Life and Death in Extreme Environments. Oxford Press 2003.
2. Wilmer P and co.: Environmental Physiology of Animals. Blackwell Publishing Inc., 2004
3. Chown SL, Nicolson SW: Insect Physiological Ecology. Oxford University Press 2004
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Elaboration of semestral thesis.
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1. Definition of the subject. External environment characteristics. Environmental factors, classification, time factor. Reaction, adaptation, deformation. Classification of adaptations. Stress reaction, general adaptation syndrome.
2. Pathological reaction, pathological state, disease. General characteristics of disease – pain, fever, inflammation.
3. Ageing, theories, physiological changes in ageing. Death of organism. Adaptations to food intake changes and food composition. Food intake regulation.
4. Caloric restriction, starving, increased caloric intake, obesity. Time factor in food intake.
5. Thermoregulation, heat and cold adaptations. Hibernation, diapause.
6. Altitude and hyperbaric adaptations. Osmoregulation.
7. The effects of hypergravity and microgravity, physiological changes during space flight. Sound, ultrasound, infrasound effects.
8. Electromagnetic fields. Effects of electric current. Infrared, visible, ultraviolet radiation and their significance for organisms. Microwaves. Laser.
9. Ionising radiation, classification, sources. The effects of ionising radiation.
10. Xenobiotics, biotransformation. Air, water, and soil pollutants.
11. Drug abuse, mechanism of drug action. The effects of opioids and CNS depressants – sedatives, hypnotics, and alcohol.
12. The effects of CNS stimulants – amphetamines, cocaine, methylxanthines, nicotin. The effects of hallucinogens and solvents.
13. Carcinogenesis, chemical, physical, and biological carcinogens. Oncogenes, tumour suppressor genes. Prevention of carcinogenesis. Prions.
To understand the basic mechanisms of adaptations to environmental factors in animals and humans.
written exam
1. BERTRAND, Jean-Claude, et al. (ed.). Environmental microbiology: fundamentals and applications. Dordrecht: Springer, 2015.
2. MITCHELL, Ralph; GU, Ji-Dong (ed.). Environmental microbiology. John Wiley & Sons, 2010.
3. HUDECOVÁ, D.: Mikrobiológia 1. Bratislava: STU, 2002.
4. SCHMIDT, Tom. Topics in ecological and environmental microbiology. Elsevier, 2012.
5. SIGEE, David. Freshwater microbiology: biodiversity and dynamic interactions of microorganisms in the aquatic environment. John Wiley & Sons, 2005.
6. VAN ELSAS, Jan Dirk, et al. Modern soil microbiology. CRC press, 2006.
Attendance of practicals (at least 90%), final oral examination
Evolution and biodiversity of microorganisms, methods for studying microorganisms, biofilms and microbial mats. Microorganisms in environment, microbiology of soil and water, microorganisms in extreme environments. The influence of abiotic factors on microorganisms. Biogeochemical cycles and the role of microorganisms: the carbon, hydrogen, oxygen, nitrogen, sulphur, phsphorus and iron cycle. Interactions between microorganisms and other organisms - interactions in the digestive tract normal and pathological microflora of humans and other animals. Interactions between microorganisms and plants - mycorhiza.
Evolution and biodiversity of microorganisms, microorganisms in environment, the influence of abiotic factors on microorganisms, biogeochemical cycles, interactions between microorganisms and other organisms
Evaluation of practicals: 30%
Final evaluation: Oral examination - 70%
To provide students data on participation of microorganisms in biosphere processes, characteristics of most frequently occuring microbial communities and interactions ofmicroorganisms with other organisms.
To provide the students with the basic facts on normal development of animals.
Langman, J.: Medical Embryology. Williams & Wilkins, Baltimore, London, 1981
Moore, K. L., Persaud, T. V. N.: Before we are born. W.B. Saunders Company Philadelphia, 1993
Oral examination.
If necessary, subject may be realized in distant form of study.
1. History of embryology.
2. Asexual and sexual reproduction. Gametogenesis. Conversion of germ cells into female and male gametes, sexual hormones.
3 .Fertilization.
4. Development of the embryo. Cleavage of the zygote. The main concepts of embryonic
development of amphioxus: Blastulation, gastrulation, germ layers formation, throughout organogenesis.
5. Cleavage, blastulation, gastrulation and notogenese of the amphibians.
6. Cleavage, blastulation, gastrulation and notogenese of the reptiles.
7. Cleavage, blastulation, gastrulation and notogenese of the aves.
8. Cleavage, blastulation, gastrulation and notogenese of the mammals. Development of the foetal membranes. Implantation. Placentation in mammals.
9. Organogenesis. Muscular and skeletal systems.
10. Digestive system.
11. Cardiovascular system Respiratory system.
12. Urinary system. Male and female reproductive systems.
13. Nervous system. Eye and ear.
To provide the students with the basic facts on normal development of animals.
Seminar paper. Oral examination.
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Erdelská O., Švubová R., Mártonfiová L., Lux A. (2017): Embryológia krytosemenných rastlín. Veda, Bratislava
Richards, A. J. (1997): Plant Breeding Systems. Chapman & Hall, London
1. Participation at the practices - work with permanent slides, work with living material, outline of the studied phenomena and their description
2. Passing the examination
1. Embryology as science
2 Breeding strategies
3. Female gametophyte
4. Male gametophyte
5. Pollination, progamogenetic phase of fertilization processes
6. Fertilization, gamogenetic and postgamogenetic phase, incompatibilities
7. Embryo, general characeters and development
8. Embryo of monocotyledones and dicotyledones
9. Endosperm
10. Apomixis
11. Seed, germination of seeds
12. Embryology of gymnosperms
Student knows basic breeding strategies and reproduction ways of angiosperms. He/she is informed about micro- and megagametogenesis from archesporal cell up to mature gametophyte. He/she knows the origin of new organism and the processes leading to it. He/she is familiar with phenomena connected with embryo development and its relations to other parts of seeds. He/she is informed on apomixis. He/she knows the way from seed to photosyntethising plant of new generation. He/she obtains information on origin and development of the embryo of gymnosperms.
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To teach the students to know and to be aware of the importance of the behavioural aspect in biological sciences
Franck, D.: Verhaltensbiologie. Einfuhrung in die Ethologie. Georg Thieme-Verlag, 1993
Manning, A., Dawkins, M. S.: An introduction to animal behaviour. Cambridge University Press, 1992
DRICKMER, L.C., VESSEY, S.H., MEIKLE, D. Animal Behavior: mechanisms, ecology, evolution. 4th ed. Dubuque : Wm. C. Brown Publishers, 1996.
Internet
UBEV/PMZ1
Thematical presentations
Fulfilled conditions for the exercises
Successfully completed oral exam
History and development of ethology. Ethological methods. The innate forms of behaviour. The simplest forms of learning – conditioning and instrumental learning. Higher form of learning. Social behaviour. Sexual behaviour. Play behaviour. Biological rhythms. Orientation in space and animal migrations. Communication systems of animals. Emotions. Aggression in animal and human behaviour. Abnormal forms of behaviour
To teach the students to know and to be aware of the importance of the behavioural aspect in biological sciences
Oral examination.
J. Pevsner: Bioinformatics and Functional Genomics, 3rd Edition, ISBN: 978-1-118-58178-0
Internet sources
Full-time form of practical teaching: active participation in practicals, practical courses protocols, written exam. In case of distance learning: active participation in practicals (the online method) using the MOODLE course UBEV/FG/14 Funkčná genomika, practical courses protocols, written exam.
English
• Introduction to functional genomics, Biological databases and other resources for functional genome analysis, A real-case applications of the functional genomics
• Genome and functional genomics: sequenced model organisms, conceptual and methodological input of genome sequencing, structural vs. functional genome annotation
• Genome-wide reverse genetics: techniques to create collections of genome-wide mutants and their use in functional genomics
• Transcriptomics: methods to obtain transcriptome data, in silico processing of transcriptomic data, differential expression
• Proteomics: methods to obtain proteome data, quantitative vs. qualitative proteomics, data analysis, data mining
• Metabolomics: methods to obtain metabolomic data, quantitative vs. qualitative metabolomics, data analysis, data mining
* Interactomics - protein networks, methods in interactome and signalome studies, data analysis, practical use of the acquired knowledge on interactome and signalome
exam
Functional genomics attempts to answer questions about the function of DNA at the levels of genes, RNA transcripts, and proteins. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional “gene-by-gene” approach. The outcome of this course will be understanding of the approaches and methods used in functional genomics and their application in research as well as in practice.
BILASOVÁ, V. – ANDREANSKÝ, E.: Epistemológia a metodológia vedy. Prešov: FF PU 2007.
FAJKUS, B.: Filosofie a metodologie vědy. Praha: Academia 2005.
BEDNÁRIKOVÁ, M. Úvod do metodológie vied. Trnavská univerzita: Trnava 2013.
DÉMUTH, A. Filozofické aspekty dejín vedy. Trnavská univerzita: Trnava 2013.
FEYERABEND, P.: Proti metodě. Prel. J. Fiala. Praha: Aurora 2001.
KUHN, T. S.: Štruktúra vedeckých revolúcií. Prel. Ľ. Valentová. Bratislava 1982.
Attendance: A student may have one unexcused absence in seminar at the most. Absence in more than one seminar must be reasoned and substituted by consultations. Conditions of continuous and final control: during the semester a student is continuously checked and assessed according to his/her activity. To be awarded the credits, a student must pass a test from knowledge obtained in the lectures and seminars. Results of the test will make up the final grade.
Slovak
• Falsificationism and critical realism by K. R. Popper.
• Development and critique of the Popper’s concept.
• Understanding the science development in the work by T. S. Kuhn.
• Methodology of scientific research programmes of I. Lakatos.
• Methodological anarchism of P. Feyerabend.
• W.V.O. Quine – the issue of relation between theory and empiricism.
The course is aimed at getting familiar with the basic issues of methodology and philosophy of science. Significant part will be devoted to presenting the main concepts of the philosophy of science in the 20th century and this aim will be achieved by reading the source and interpretive texts.
Taiz L., Zeiger E., Plant physiology. Fifth edition. Sinauer ass., Sunderland 2010
Taiz L, Zeiger E, ed. 2018 Plant physiology and development, 6th editon, Oxford
1. Attending lectures is mandatory, participation in practicals is also mandatory
2. Handing over the developed protocols from practicals constitutes 20% of the grade
3. Preparation of a written test consisting of 70 questions (min. 60%)
1. Growth and morphogenesis: growth phases and kinetics; cell wall, differentiation.
2. Photoreceptors of red and blue light.
3. Hormones: metabolism and transport; mechanism and physiological effects;
4. Auxins, gibberellins,
5. Cytokinins, abscisic acid, ethylene
6. Brassinosteroids, jasmonic acid and strigolactone.
7. Polarity. Apical dominance. Regeneration and transplantation.
8. Biological rhythms, molecular clock mechanism
9. Dormancy. Germination.
10. Flowering induction: expression, determination, photoperiodism
11. Development of floral organs.
12. Aging and programmed cell death.
13. Orientation in space: phototropism, gravitropism and nastic movements.
To learn about basic methods and approaches in physiology of plant growth and development.
The student will learn the basic concepts related to plant development and deepen the basic knowledge about the regulation of individual processes. They will get acquainted with signal transmission in plants and the influence of various factors (light, phytohormones, ...) on the growth and development of plants at various levels.
During the exercises, the student should master the basic preparation of growth media, work with a microscope and evaluate the results obtained.
To provide students with a basics of human genetics, with the role of genetic factors in pathologic processes, with the inheritance, diagnostics and treatment of genetic disorders.
Friedman JM, Dill FJ, Hayden MR, McGillivray BC (1996): Genetics 2/e. Williams & Wilkins, Baltimore, Maryland, USA
Lewis R.: Human Genetics: Concepts and Applications, 9th Edition. McGraw-Hill, New York, 2010
Passarge E.: Genetics, 3rd Edition, Thieme, 2007
Full-time form of experimental and practical teaching: active participation in practicals, written and oral exam. In case of distance learning: active participation in practicals (the online method) using the MOODLE course UBEV/Human Genetics, written exam.
slovak and english
The genetic basics of physiological variability and pathological traits of individuals; human population genetics; immunological variability; the patterns of inheritance and pedigree problem solving; the basic methods used in human genetics - genealogy, linkage analysis and the gene mapping, cytogenetic analysis and karyotyping, the DNA diagnosis of pathological traits; the treatment of genetic disorders.
To provide students with a basics of human genetics, with the role of genetic factors in pathologic processes, with the inheritance, diagnostics and treatment of genetic disorders.
Acquire knowledge about genetic interactions in population. Describe the theoretical and historical ground of population genetics. Identify, characterize and compare fundamental mechanisms (mutation, selection, migration, genetic drift). Interactions leading to intra- and interpopulation variability in population structure. Genetic diversity analysis.
HALLIBURTON. R. (2004): Introduction to Population Genetics. Pearson Prentice Hall.
HARTL, D. L. and CLARK, A. G. (2007): Principles of Population Genetics. 4th ed. Sinauer.
RELICHOVÁ, J. (2001): Genetika populací. Masarykova univerzita Brno.
Hedrick, P.W.: Genetics of Populations. Jones and Bartlett Publishers 2000.
Full-time form of teaching: active participation in practicals, written and oral exam. In case of distance learning: active participation in practicals (the online method), practical courses protocols, written exam using the tests prepared in the MOODLE course UBEV/GEP/12 Genetika populácií.
Factors affecting populations. Genetic variability in populations. Polymorphism, heterozygosity. Fundamental models in population genetics. Hardy-Weinberg theorem for 2, 3 and n alleles. Special cases of random mating (Bruce’s genotype ratios, Sex-linked genes). Population genetics and mutations. Assortative mating, calculation and interpretation of inbreeding coefficient. Genetic drift, fixation/elimination of alleles in small populations. One-way, two-way migration. Natural selection in haploid and diploid populations. Populations of plants, animals and human. Darwin’s evolution theory, molecular evolution.
Factors affecting populations. Genetic variability in populations. Polymorphism, heterozygosity. Fundamental models in population genetics. Hardy-Weinberg theorem for 2, 3 and n alleles. Special cases of random mating (Bruce’s genotype ratios, Sex-linked genes). Population genetics and mutations. Assortative mating, calculation and interpretation of inbreeding coefficient. Genetic drift, fixation/elimination of alleles in small populations. One-way, two-way migration. Natural selection in haploid and diploid populations. Populations of plants, animals and human. Darwin’s evolution theory, molecular evolution.
Acquire knowledge about genetic interactions in population. Describe the theoretical and historical ground of population genetics. Identify, characterize and compare fundamental mechanisms (mutation, selection, migration, genetic drift). Interactions leading to intra- and interpopulation variability in population structure. Genetic diversity analysis.
Exam.
BROWN, Terence A. Gene cloning and DNA analysis: an introduction. Wiley-blackwell, 2020.
DALE, Jeremy W.; VON SCHANTZ, Malcolm; PLANT, Nicholas. From Genes to Genomes: Concepts and Applications of DNA Technology. John Wiley & Sons, 2011.
HOWE, Christopher. Gene cloning and manipulation. Cambridge University Press, 2007.
Independent elaboration of a presentation on a topic related to the subject. Completion of exercises. Oral examination
English
Cloning and expression of genes in yeast and animal cells. In vitro amplification techniques for DNA and RNA molecules. In vitro mutagenesis. Biotechnology and genetic engineering. Preparation of biologically active substances and recombinant vaccines.
Obtaining the knowledge on cloning and gene expression in various host systems, their use in biotechnological and biological research. Acquisition of knowledge about more complex and latest genetic methods and procedures and their use in solving specific biological problems.
The practical course will focus on basic techniques and skills in immunology laboratories in order to have technical foundation to suggest experimental analysis of some immunological questions.
Study materials provided by teacher.
UBEV/IMU1/03
activity at the lessons, protocols from practical work,
activity at the lessons, protocols from practical work,
oral examination
Special immunology practicals cover common immunological techniques as well as techniques relevant to the research projects at the department. The main aim is to understand the host immune response to infection. Practicals also include a study of the histophysiology of animal immune organs. The students will learn to perform immunological experiments, including critical evaluation of the results.
The practical course will focus on basic techniques and skills in immunology laboratories in order to have technical foundation to suggest experimental analysis of some immunological questions.
oral examination
This course introduces the students to the basic concepts of immunology as well as highlights the role and importance of immunology in various human diseases. The aim of Immunology lessons is the presentation of the organization and function of the immune system, as well as the comprehension of complex molecular and cellular interactions during the induction of immune responses.
Janeway Ch. A., Travers P., Walport M., Schlomchik M.: Immunobiology. Garland Science, 2004
Murphy, K. (2012): Jeneway’s Immunobiology. 8th ed. Garland Science
Delves, P.J. et al. (2011): Roitt’s essential immunology 12th ed Wiley-Blackwell
UBEV/MB1a, UCHV/BCH1a
no
Recognition.
Oral examination.
Basic immunology: Lymphatic System Anatomy, The Innate Immune System, The Induced Responses of Innate Immunity, The Adaptive Immune Response, Antigens and Antibodies, Antigen Recognition by B-cell and T-cell Receptors, Antigen Presentation to T-lymphocytes, Complement, Clinical immunology: Allergy and other Hypersensitivities, Autoimmunity and Transplantation, Tumor Immunology, Disorders of The Immune System.
This course introduces the students to the basic concepts of immunology as well as highlights the role and importance of immunology in various human diseases. The aim of Immunology lessons is the presentation of the organization and function of the immune system, as well as the comprehension of complex molecular and cellular interactions during the induction of immune responses.
Oral examination.
1. JUNGER, J. et al. Turistika a športy v prírode. Prešov: Fakulta humanitných a prírodných vied PU v Prešove. 2002. 267s. ISBN 80-8068-097-3.
2. PAVLÍČEK, J. Člověk v drsné přírodě. 3. vyd. Praha: Práh. 2002. ISBN 8072520598.
3. WISEMAN, J. SAS: příručka jak přežít. Praha: Svojtka & Co. 2004. 566s. ISBN
8072372807.
Completion: passed
Condition for successful course completion:
- active participation in line with the study rule of procedure and course guidelines,
- effective performance of all the tasks defined in the course syllabus
Slovak language
Brief outline of the course:
1. Principles of conduct and safety in the movement in unfamiliar natural environment
2. Preparation and guidance of a hike tour
3. Objective and subjective danger in the mountains
4. Principles of hygiene and prevention of damage to health in extreme conditions
5. Fire building
6. Movement in the unfamiliar terrain, orientation and navigation
7. Shelters
8. Food preparation and water filtering
9. Rappelling, Tyrolian traverse
10. Transport of an injured person, first aid
Content standard:
The student demonstrates relevant knowledge and skills in the field, which content is defined in the course syllabus and recommended literature.
Performance standard:
Upon completion of the course students are able to meet the performance standard and should:
- acquire knowledge about safe stay and movement in natural environment,
- obtain theoretical knowledge and practical skills to solve extraordinary and demanding situations connected with survival and minimization of damage to health,
- be able to resist and face situations related to overcoming barriers and obstacles in natural environment,
- be able implement the acquired knowledge as an instructor during summer sport camps for children and youth within recreational sport.
History of microbiological diagnostics. Laboratory practice. Methods of laboratory diagnostics of microorganisms. Phenotypic methods of species identification of microorganisms. Molecular-biological methods of identification of microorganisms. Methods of species identification in microbial communities. Applications of microbiological-diagnostic methods in practice. Virulence factors of microorganisms and their interaction with immune mechanisms. Clinically important representatives of bacterial, viral, fungal and parasitic diseases of animals and humans.
Students will gain an overview of classical and modern diagnostic microbiological methods routinely used in microbiological laboratories. Through hands-on practical classes, the students will acquire important laboratory skills that will promote theory-practice integration.
1. JUNGER, J. et al. Turistika a športy v prírode. Prešov: FHPV PU v Prešove. 2002. ISBN 8080680973.
Internetové zdroje:
1. STEJSKAL, T. Vodná turistika. Prešov: PU v Prešove. 1999.
Dostupné na: https://ulozto.sk/tamhle/UkyxQ2lYF8qh/name/Nahrane-7-5-2021-v-14-46-39#!ZGDjBGR2AQtkAzVkAzLkLJWuLwWxZ2ukBRLjnGqSomICMmOyZN==
Completion: passed
Condition for successful course completion:
- active participation in line with the study rule of procedure and course guidelines
- effective performance of all tasks: carrying a canoe, entering and exiting a canoe, righting a canoe, paddling
Slovak language
Brief outline of the course:
1. Assessment of difficulty of waterways
2. Safety rules for rafting
3. Setting up a crew
4. Practical skills training using an empty canoe
5. Canoe lifting and carrying
6. Putting the canoe in the water without a shore contact
7. Getting in the canoe
8. Exiting the canoe
9. Taking the canoe out of the water
10. Steering
a) The pry stroke (on fast waterways)
b) The draw stroke
11. Capsizing
12. Commands
Content standard:
The student demonstrates relevant knowledge and skills in the field, which content is defined in the course syllabus and recommended literature.
Performance standard:
Upon completion of the course students are able to meet the performance standard and:
- implement the acquired knowledge in different situations and practice,
- implement basic skills to manipulate a canoe on a waterway,
- determine the right spot for camping,
- prepare a suitable material and equipment for camping.
To provide the students with knowledge about the principal metabolic processes in living cells.
1. Murray, R. K., Grammer, D. K., Mayes, P. A., Rodwell, V.W.: Harper‘s Biochemistry. Prentice-Hall, Appleton & Lange, 1993
2. Vasudevan D.M. and co.: Textbook of Biochemistry for Medical Students. Jaypee Brothers Medical Publishers 2011
UCHV/BCH2a, UBEV/FZ1/03
.
Oral examination.
Carbohydrates – significance and role in animal organisms. Inborn errors of carbohydrate and lipid metabolism in humans. Lipid metabolism. Role of the liver and adipose tissue in lipid metabolism. Plasma lipoproteins – metabolism and disorders. Cholesterol and atherosclerosis. Protein metabolism and its inborn errors. Water and solute metabolism. Physiology and regulatory mechanisms of water-base balance in animal organisms. Metabolic regulation. Topochemistry of metabolic processes
To provide the students with knowledge about the principal metabolic processes in living cells.
Oral examination, performed preferably in full-time form, if necessary in distance form.
The aim of the subject is to teach students, how to process biological material for analyses using light, fluorescent and electron microscope and to acquaint them with microscopic techniques, which are most commonly used in the biological research.
Gage et al.: Whole animal perfusion fixation for rodents, 2012, Journal of Visualized Experiments, 65:e3564, 1-9
Paddock W.: Principles and Practices of Laser Scanning Confocal Microscopy, 2000, Molecular Biotechnology, 16, 127-149
Griffiths and Lucocq: Antibodies for immunolabelling by light and electron microscopy: not for the faint hearted, 2014, Histochem Cell Biol, 142:347-360
A. Kaech: An Introduction to Electron Microscopy Instrumentation, Imaging and Preparation, Centre for Microscopy and Image Analysis, University of Zurich, 2013
M. Držík a kol.: Moderná mikroskopia a digitálne spracovanie obrazu, FMFI UK, Bratislava, 2008
J. Polónyi, P. Mráz: Metódy elektrónovej mikroskopie živočíšnych tkanív. Veda Bratislava,
1988M.
Bobák, J. Horák: Elektrónová mikroskopia. Učebné texty, PF UK Bratislava, 1981
active presence at lectures and exercises
1. Visible light and its properties. Lenses, objectives.
2. History of microscopy, principles of visualization of biological samples using brightfield microscope.
3. Special types of light microscopes.
4. Isolation of biological material, fixation, dehydration, embedding and staining of samples for light microscopy.
5. Types of microtomes used in histology laboratories and their operation.
6. Principles of fluorescence, fluorescent molecules and fluorescent methods for analysis of biological samples.
7. Principles of immunolabelling of biological samples for brightfield and fluorescent microscopy.
8. Analysis of biological samples using epifluorescent and confocal microscope.
9. Processing and contrasting of biological samples for transmission and scanning electron microscopy.
10. Methods of immunolabelling of biological samples using colloidal gold nanoparticles and principles of autoradiography.
11. Construction and operation of electron microscope, types of electron microscopes used in biological research.
12. Special types of electron microscopes.
13. Photography of samples and analysis of resulting image.
The aim of the subject is to teach students, how to process biological material for analyses using light, fluorescent and electron microscope and to acquaint them with microscopic techniques, which are most commonly used in the biological research.
Final evaluation: Final evaluation will be realized during the last week of winter semester in the form of discussion. Students are required to prove their knowledge on the topics discussed during the lectures and exercises.
To provide the students with an information on importance of the use of models in genetic research, to acquire knowledge on basic genetic models and results achieved by the models in genetic research.
Snustad, P.D., Simmons, M.J.: Genetika. Nakladatelství Masarykovy univerzity, Brno, 2009, 871 pp., 2017, 864 pp.
Periodicals in the field of genetics,
Internet sources
ÚBEV/GE1/03
protocols
protocols,
preparation of a project: Model organism for my diploma thesis,
oral examination
Basic properties of model organisms used in genetics. Viral models in genetics (Tobacco mosaic virus, Lambda phage, PhiX174 phage, corona viruses). Prokaryotic model systems (Escherichia coli, Diplococcus pneumoniae, Agrobacterium tumefaciens and A. rhizogenes). Another prokaryotic models (Bacillus subtilis, Caulobacter crescentus, Mycoplasma genitalium, Synechocystis sp.), model systems of simple eukaryotic organisms (Saccharomyces cerevisiae, Neurospora crassa, Aspergillus nidulans, Dictiostelium discoideum). Animal model systems (Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, Mus musculus). Another animal models (Xenopus laevis, Ambystoma mexicanum, Chrysemys picta, Anolis carolinensis, Fugu rubripes, Gallus gallus, Heterocephalus glaber). Plant model organisms (Pisum sativum, Arabidopsis thaliana, Nicotiana tabacum, Zea mays, Selaginella moellendorffii, Brachypodium distachyon, Lotus japonicus, Populus trichocarpa). Genetic databases. Model organisms and their importance in the study of fundamentals of human genetic disorders.
To provide the students with genetic models of prokaryotic and eukaryotic organisms used in genetic research.
oral examination
Masarovičová E., Repčák M. et al. Fyziológia rastlín. 2. dopl. vydanie. Vyd. UK Bratislava 2008;
Taiz L.et al. Plant Physiology and Development. Sixth editon. Sinauer ass.,Sunderland 2014;
Repčák M. et al. Návody na cvičenia z fyziológie rastlín. 4. preprac. vyd. UPJŠ
Košice 2014
Bhatla S.C., Lal M.A. Plant Physiology, development and metabolism. Springer Nature Singapore Pte Ltd. 2018
1. Active participation in laboratory practicals. Reasoned absence can be justified by the teacher for a maximum of 4 hours (one two-hour course) without the need for replacement. In the case of a longer justified absence, the teacher will determine an alternative form of mastering the missed teaching.
2. Before the practicals, students have to study the main theses of the task that will be realized. Students will receive an exact schedule of tasks according to individual lessons at the beginning of the semester.
3. Students make a written record of the practicals. Students will evaluate the resultsfrom and draw a conclusion. The form in which this activity will be checked is determined by the teacher at the beginning of the semester. After this check the task is considered validly completed.
4. Whole pacticals are considered to be finally completed upon valid completion of all tasks. The exception is the justified non-participation (point 1). Completion of practicals is obligatory before the exam.
5. The exam of the subject takes place orally. Students ask two questions and have a max. 30 minutes to prepare.
Any changes or modifications to the conditions for completing the course due to the COVID19 pandemic, or other serious reasons, are continuously published on the electronic bulletin board of the course.
The subject significantly deepens knowledge from the bachelor's degree. The student should gain an overview of the basic biochemical processes in plants. Emphasis is placed on understanding the principles of their functioning and their significance for plants. Acquaintance of students with basic biochemical research methods of plant metabolism within the practical part. The result of education is also the ability to process and express own results.
S.F. Gilbert, M.J.F. Barresi: Developmental Biology, 11th edition, Sinauer Associates, Inc., 2016
written examination (pass three tests)
Molecular and regulatory basis of ontogenesis:
1) Totipotency of zygote and genomic equivalence as general pre-requisite for ontogenetic development. Cell adhesion and migration, positional information, developmental signals and morfogens. 2) Induction, determination and differentiation. Selective gene expression, combinatory control of gene expression, lateral inhibition. 3) Mechanisms of epigenetic memory. DNA methylation, genomic imprinting, X-chromosome inactivation. Morphogenesis (asymmetry and polarity of cells, reorganization of cytoskeleton, embryonic folding and flexion). 4) Genes controllig development (selector genes, regulators and super-regulators, homeotic genes). Programmed cell death (apoptosis autophagy). 5) 1st test.
Ontogenetic development of drosophila:
6) Oogenesis. Specification and polarization of oocyte, determination of oocyte axes. Fertilization, cleavage and early embryogenesis. 7) Early embryo polarization and determination of embryo axes. Specification of body segments, segmentation genes. 8) Gastrulation (germ layers formation, neurulation). Morphogenesis and cell rearrangements. Development of some organs and organ systems. Pupation and metamorphosis. 9) 2nd test.
Ontogenetic development of mammals:
10) Fertilization. Cleavage and early embryogenesis (blastulation, gastrulation, neurulation). 11) Early embryo polarization and determination of embryo axes. Induction of primitive streak and germ layers formation. Specification and development of CNS. Somitogenesis, myogenesis. 12) Development of some organs and organ systems. 13) 3rd test.
Acquiring of basic knowledge about molecular and regulatory mechanisms of ontogenetic development of multicellular organisms (animal and plant organisms).
.
Briggs D., Walters S. M.: Proměnlivost a evoluce rostlin. – CUP, UP Olomouc 2001.
Mártonfi P.: Systematika cievnatých rastlín. 4. vydanie - Vydavateľstvo UPJŠ, Košice, 2013.
Marhold K., Suda J.: Statistické zpracování mnohorozměrných dat v taxonomii (Fenetické metody). – Karolinum, UK Praha 2002.
Turland et al. (Eds.):International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017 Regnum Vegetabile - Koeltz Scientific Books, 2018. https://www.iaptglobal.org/icn
Stuessy T. F.: Plant Taxonomy. - 2n Ed. New York 2009.
Judd W. S., Campbell Ch. S., Kellogg E. A. & Stevens P. F., Donoghue M. J.: Plant Systematics. A Phylogenetic Approach, 4th edition. – Sinauer Associates, Sunderland, 2016.
Simpson M. G.: Plant Systematics. – Elsevier, Amsterdam etc., 3. ed., 2019.
.
1. Lectures on the subject are not compulsory, but are highly recommended, exercises are compulsory.
2. Students must master the basic methods of collecting botanical samples in the field for various types of analysis, work with plant material in the karyological and palynological laboratory and in the flow cytometry laboratory, learn the basic principles of molecular taxonomy, be able to understand articles using phenetic and cladistic methods, he orients himself in the basic principles of botanical nomenclature.
3. An oral exam is part of the completion of the subject.
1. Taxonomy of plants. The importance of classification and the problems associated with it. Information sources and taxonomic data. Morphology and anatomy, embryology, palynology, cytology, karyology, ecology, phytogeography.
2. Determination of taxonomic relationships.
3. Approaches to biological classification. Examples of past and present plant systems. The "Angiosperm Phylogeny Group IV" system.
4. Variability of plants and its study. Early works on plant variability. Multivariate data in taxonomy - phenetic data analysis.
5. The size of the plant genome and approaches to its study. Flow cytometry. Angiosperm genome size evolution.
6. Parallel and convergent evolution. Examples: parasitism, insectivory and C4-metabolism.
7. Basic principles of cladistics.
8. Cladistic studies - revealing the branches of evolution.
9. Principles of molecular systematics of plants.
10. Basics of botanical nomenclature. International code of nomenclature of algae, fungi and plants.
11. Taxonomic publications and examples of taxonomic studies I. Examples from the genus Viola.
12. Taxonomic publications and examples of taxonomic studies II. Examples from the genus Onosma.
Exercises (they take place in blocks):
1. Introduction to plant taxonomy exercises. Herbarium documents and their meaning.
2. Fieldwork in botany, collection of samples, processing of plant material, practical demonstrations.
3.- 4. Palynological methods. Collection and preparation of samples, observation of preparations and their evaluation.
5.- 6. Karyological methods in plant taxonomy. Sampling, preparation of specimens, observation and evaluation of specimens.
7.- 8. Phenetic data analysis – examples and demonstrations of plant material processing, multivariate data analysis, clustering and ordination methods.
9.- 10. Use of flow cytometry in plant taxonomy. Determination of the degree of ploidy and the size of the plant genome. Determination of reproductive method of plants - FCSS (flow cytometric seed screen).
11.-12. Molecular systematics of plants. Parsimony analysis of DNA sequences, phenetic analysis of AFLP DNA fragments - examples and demonstrations.
13. Basics of botanical nomenclature. International code of nomenclature of algae, fungi and plants. Practical tasks.
The subject of plant taxonomy is a basic subject for understanding modern systematics of plants and its importance for the study of various taxonomic groups, the student is oriented in the used methods of taxonomic work and their evaluation, is able to create taxonomic hypotheses and design a way of verifying these hypotheses. He is able to use the knowledge in basic botanical research, but also to apply it to solving problems in plant breeding, in agricultural practice, in the evaluation of plant biota in plant protection and biodiversity preservation.
.
BENCE, M. et al. 2005. Plávanie. Banská Bystrica: FHV UMB. 198s. ISBN 80-8083-140-8.
[online] Dostupné na: https://www.ff.umb.sk/app/cmsFile.php?disposition=a&ID=571
BUZKOVÁ, K. 2006. Fitness jóga, harmonické cvičení těla I duše. Praha: Grada. ISBN 8024715252.
JARKOVSKÁ, H, JARKOVSKÁ, M. 2005. Posilování s vlastním tělem 417 krát jinak. Praha: Grada. ISBN 9788024757308.
KAČÁNI, L. 2002. Futbal:Tréning hrou. Bratislava: Peter Mačura – PEEM. 278s. ISBN
8089197027.
KRESTA, J. 2009. Futsal.Praha: Grada Publishing, a.s. 112s. ISBN 9788024725345.
LAWRENCE, G. 2019. Power jóga nejen pro sportovce. Brno: CPress. ISBN 9788026427902.
SNER, Wolfgang. 2004. Posilování ve fitness. České Budějovice: Kopp. ISBN 8072322141.
STACKEOVÁ, D. 2014. Fitness programy z pohledu kinantropologie. Praha: Galén. ISBN 9788074921155.
VOMÁČKO, S. BOŠTÍKOVÁ, S. 2003. Lezení na umělých stěnách. Praha: Grada. 129s. ISBN
8024721743.
Min. 80% of active participation in classes.
Slovak language
Brief outline of the course:
The Institute of physical education and sport at the Pavol Jozef Šafárik University offers 20 sports activities aerobics; aikido, basketball, badminton, body-balance, body form, bouldering, floorball, yoga, power yoga, pilates, swimming, fitness, indoor football, SM system, step aerobics, table tennis, chess, volleyball, tabata, cycling.
Additionally, the Institute of physical education and sport at the Pavol Jozef Šafárik University offers winter courses (ski course, survival) and summer courses (aerobics by the sea, rafting on the Tisza River) with an attractive programme, sports competitions with national and international participation.
Sports activities in all their forms prepare university students for their professional and personal life. They have a great impact on physical fitness and performance. Specialization in sports activities enables students to strengthen their relationship towards the selected sport in which they also improve.
BENCE, M. et al. 2005. Plávanie. Banská Bystrica: FHV UMB. 198s. ISBN 80-8083-140-8.
[online] Dostupné na: https://www.ff.umb.sk/app/cmsFile.php?disposition=a&ID=571
BUZKOVÁ, K. 2006. Fitness jóga, harmonické cvičení těla I duše. Praha: Grada. ISBN 8024715252.
JARKOVSKÁ, H, JARKOVSKÁ, M. 2005. Posilování s vlastním tělem 417 krát jinak. Praha: Grada. ISBN 9788024757308.
KAČÁNI, L. 2002. Futbal:Tréning hrou. Bratislava: Peter Mačura – PEEM. 278s. ISBN
8089197027.
KRESTA, J. 2009. Futsal.Praha: Grada Publishing, a.s. 112s. ISBN 9788024725345.
LAWRENCE, G. 2019. Power jóga nejen pro sportovce. Brno: CPress. ISBN 9788026427902.
SNER, Wolfgang. 2004. Posilování ve fitness. České Budějovice: Kopp. ISBN 8072322141.
STACKEOVÁ, D. 2014. Fitness programy z pohledu kinantropologie. Praha: Galén. ISBN 9788074921155.
VOMÁČKO, S. BOŠTÍKOVÁ, S. 2003. Lezení na umělých stěnách. Praha: Grada. 129s. ISBN
8024721743.
active participation in classes - min. 80%.
Slovak language
Brief outline of the course:
The Institute of physical education and sport at the Pavol Jozef Šafárik University offers 20 sports activities aerobics; aikido, basketball, badminton, body-balance, body form, bouldering, floorball, yoga, power yoga, pilates, swimming, fitness, indoor football, SM system, step aerobics, table tennis, chess, volleyball, tabata, cycling.
Additionally, the Institute of physical education and sport at the Pavol Jozef Šafárik University offers winter courses (ski course, survival) and summer courses (aerobics by the sea, rafting on the Tisza River) with an attractive programme, sports competitions with national and international participation.
Sports activities in all their forms prepare university students for their professional and personal life. They have a great impact on physical fitness and performance. Specialization in sports activities enables students to strengthen their relationship towards the selected sport in which they also improve.
BENCE, M. et al. 2005. Plávanie. Banská Bystrica: FHV UMB. 198s. ISBN 80-8083-140-8.
[online] Dostupné na: https://www.ff.umb.sk/app/cmsFile.php?disposition=a&ID=571
BUZKOVÁ, K. 2006. Fitness jóga, harmonické cvičení těla I duše. Praha: Grada. ISBN 8024715252.
JARKOVSKÁ, H, JARKOVSKÁ, M. 2005. Posilování s vlastním tělem 417 krát jinak. Praha: Grada. ISBN 9788024757308.
KAČÁNI, L. 2002. Futbal:Tréning hrou. Bratislava: Peter Mačura – PEEM. 278s. ISBN
8089197027.
KRESTA, J. 2009. Futsal.Praha: Grada Publishing, a.s. 112s. ISBN 9788024725345.
LAWRENCE, G. 2019. Power jóga nejen pro sportovce. Brno: CPress. ISBN 9788026427902.
SNER, Wolfgang. 2004. Posilování ve fitness. České Budějovice: Kopp. ISBN 8072322141.
STACKEOVÁ, D. 2014. Fitness programy z pohledu kinantropologie. Praha: Galén. ISBN 9788074921155.
VOMÁČKO, S. BOŠTÍKOVÁ, S. 2003. Lezení na umělých stěnách. Praha: Grada. 129s. ISBN
8024721743.
min. 80% of active participation in classes
Slovak language
Brief outline of the course:
The Institute of physical education and sport at the Pavol Jozef Šafárik University offers 20 sports activities aerobics; aikido, basketball, badminton, body-balance, body form, bouldering, floorball, yoga, power yoga, pilates, swimming, fitness, indoor football, SM system, step aerobics, table tennis, chess, volleyball, tabata, cycling.
Additionally, the Institute of physical education and sport at the Pavol Jozef Šafárik University offers winter courses (ski course, survival) and summer courses (aerobics by the sea, rafting on the Tisza River) with an attractive programme, sports competitions with national and international participation.
Sports activities in all their forms prepare university students for their professional and personal life. They have a great impact on physical fitness and performance. Specialization in sports activities enables students to strengthen their relationship towards the selected sport in which they also improve.
BENCE, M. et al. 2005. Plávanie. Banská Bystrica: FHV UMB. 198s. ISBN 80-8083-140-8.
[online] Dostupné na: https://www.ff.umb.sk/app/cmsFile.php?disposition=a&ID=571
BUZKOVÁ, K. 2006. Fitness jóga, harmonické cvičení těla I duše. Praha: Grada. ISBN 8024715252.
JARKOVSKÁ, H, JARKOVSKÁ, M. 2005. Posilování s vlastním tělem 417 krát jinak. Praha: Grada. ISBN 9788024757308.
KAČÁNI, L. 2002. Futbal:Tréning hrou. Bratislava: Peter Mačura – PEEM. 278s. ISBN
8089197027.
KRESTA, J. 2009. Futsal.Praha: Grada Publishing, a.s. 112s. ISBN 9788024725345.
LAWRENCE, G. 2019. Power jóga nejen pro sportovce. Brno: CPress. ISBN 9788026427902.
SNER, Wolfgang. 2004. Posilování ve fitness. České Budějovice: Kopp. ISBN 8072322141.
STACKEOVÁ, D. 2014. Fitness programy z pohledu kinantropologie. Praha: Galén. ISBN 9788074921155.
VOMÁČKO, S. BOŠTÍKOVÁ, S. 2003. Lezení na umělých stěnách. Praha: Grada. 129s. ISBN
8024721743.
min. 80% of active participation in classes
Slovak language
Brief outline of the course:
The Institute of physical education and sport at the Pavol Jozef Šafárik University offers 20 sports activities aerobics; aikido, basketball, badminton, body-balance, body form, bouldering, floorball, yoga, power yoga, pilates, swimming, fitness, indoor football, SM system, step aerobics, table tennis, chess, volleyball, tabata, cycling.
Additionally, the Institute of physical education and sport at the Pavol Jozef Šafárik University offers winter courses (ski course, survival) and summer courses (aerobics by the sea, rafting on the Tisza River) with an attractive programme, sports competitions with national and international participation.
Sports activities in all their forms prepare university students for their professional and personal life. They have a great impact on physical fitness and performance. Specialization in sports activities enables students to strengthen their relationship towards the selected sport in which they also improve.
The goal is to teach the students on II. stage some theoretical and practical aspects of flow cytometry. The course will cover theoretical bases of fluorescence, its detection, multiparametric analyses and practical applications in clinical diagnosis and scientific research.
1. H.M. Shapiro: Practical Flow Cytometry, WILEY-LISS, 2003. (ISBN:0-471-41125-6)
2. A.L. Givan: Flow Cytomtery: First principles, WILEY-LISS, 2001, (ISBN 0-471-22394-8)
3. J. Dolezel a kol.: Flow Cytometry with Plant Cells, Willey-VCH, 2007, (ISBN: 978-3-527-31487-4)
1.) Conditions for completing the course, completing training in health and safety regulations. 2.) Fluorescence, types of fluorescent devices, flow cytometer. 3.) Principle of flow cytometry, data presentation, gating strategy. 4.) Particles size in flow cytometry, flow cytometry in cell biology, zoology and microbiology. 5.) Cell sorting. 6.) Cell cycle analysis. 7.) Detection of phosphatidylserine translocation and viability. 8.) Compensation, spectraviewer. 9.) Analysis of mitochondrial membrane potential and activation of caspases. 10.) Detection of stem cells. 11.) Immunophenotyping. 12.) Flow cytometry in botany. 13.) DNA content and genome size. Data evaluation strategies, FlowJo software.
The goal is to teach the students on II. stage some theoretical and practical aspects of flow cytometry. The course will cover theoretical bases of fluorescence, its detection, multiparametric analyses and practical applications in clinical diagnosis and scientific research.
To provide the students with the principles of preparation and application of techniques of recombinant DNA.
Old, R.W., Primrose, S. B.: Principles of Genetic Manipulation. An Introduction to Genetic Engineering. Blackwell Scientific Publication, London, 1992
S.B. Primrose and R.M. Twyman: Principles of gene manipulation and genomics. 7th Edition, 2006. ISBN 140513544
Fitzgerald-Hayes, M and Reichsman, F: DNA and Biotechnology. Academic Press, 2009. Third edition. ISBN 9780080916354
T.A.Brown: Gene Cloning and DNA Analysis: An Introduction. Wiley-Blackwell, 2016. 7th edition. ISBN: 978-1-119-07254-6
Active participation in seminars - elaboration of assignments and protocols for practical exercises completed by continuous assessment (30% of the total assessment), written examinations of the content of lectures (60% of the total assessment), oral exam (10% of the total assessment).
Overview of the basic structure and functioning of biomolecules (proteins, nucleic acids), basic concepts and chemical principles applied to biological systems (water as a solvent, buffers, pH), general laboratory techniques (buffer preparation, centrifugation, dialysis, lyophilization).
Enzymes used in gene manipulation (nucleases, restriction endonucleases, lysozyme, proteinases, etc.). Cell lysis methods. Principles of individual isolation units and tasks of individual components, isolation of genomic DNA, methods of plasmid isolation, isolation of DNA from different cell types, isolation and specifics of work with RNA molecules. Electrophoretic techniques (agarose and polyacrylamide, resolution, sensitivity, voltage, color, visualization, different types of electrophoresis. Spectroscopic analysis of biomolecules (general principles, overview of methods and their principle, UV-Vis spectroscopy, MALDI-TOF). and analysis of biomolecules by chromatography.Production of proteins and their purification and characterization (preparation of cell extracts, protein stabilization, precipitation, selection of purification technique by tags) Hybridization methods (Southern, Northern, Western).
To provide the students with the principles of preparation and application of techniques of recombinant DNA.
Oral examination.
Lectures: This course is focused on basic concepts of morphology, molecular biology, genetics, genomics, evolution and taxonomy of viruses. Students will receive information about bacteriophages, viruses infecting bacteria as well as viruses causing major human and animal diseases (oncogenic viruses, herpes, coronaviruses, HIV) as well as viruses infecting plant cells and prions. Attantion is also devoted to the pathogenesis and epidemiology of viral infections and laboratory diagnosis of viral infections.
Laboratory classess are designed to master the basic methodological procedures for the identification and enumeration of bacteriophages, as well as the basic procedures used for the detection of viruses infecting eukaryotic cells.
SYLABUS:
• Introduction to the issue and terminology
• Virus morphology
• Life cycle and genetics of viruses
• Life cycle and genetics of viruses II
• Classification and taxonomy of viruses
• Bacteriophages - bacterial viruses
• Viruses causing major human and animal diseases
• Satellites, viroids, prions, viruses infecting plant cells
• Prevention and treatment of viral infections
• Pathogenesis and epidemiology of viral diseases
• Laboratory diagnosis of viral infections
• Evolution of viruses
Virology course will provide in-depth knowledge and understanding the biology, genetics and genomics of viruses.You will become familiar with professional terminology in the field of virology, understand the specifics of the biology of viruses, their multiplication, spreading and how they cause diseases. Through hands-on practical classes, the student will acquire the fundamental skills regarding the characterization and enumeration of bacteriophages.
To provide students the latest knowledge in the field of molecular microbiology of prokaryotic microorganisms and their viruses
Elaboration and presentation of pre-assigned topics. Active participation in discussions on lecture topics. Final evaluation in the form of a discussion on a randomly selected topic from the syllabus.
1. Diversity of prokaryotic microorganisms, "black matter" in molecular microbiology 2. Energy metabolism of prokaryotic cell - redox tower, lithotrophy principle, anoxygenic photophosphorylation 3. Peculiarities of gene expression regulation in prokaryotic cells, sporulation regulation in Bacillus spp. 4. Molecular mechanisms of adaptation of prokaryotic cells to extreme environments 5. Biology of restriction-modification systems and coevolution of bacteriophages and RMS 6. Genetics, genetic organization of bacteriophages, modular structure of bacteriophage genomes, CRISPR / Cas systems 7. Bacterial plasmids, their evolution, diversity, modular structure, incompatibility systems, copy number control. 8. Mechanisms of spreading antibiotic resistance in a non-clinical environment
Students will expand and consolidate their knowledge on basic molecular microbiological processes in prokaryotic organisms, while gaining the latest knowledge in selected areas of molecular biology and genetics of prokaryotic cells. Within the course, they will also practice skills in working with scientific literature and methods of synthesis and processing of obtained information, as well as their presentation to the professional community.
The main goal of the subject is to get knowledge on the basic reasons of recent distribution of the animals on the Earth, zoogeographic regionalization of the Earth´s surface and human influence on the faunal distribution in the history.
Buchar, J., 1983: Zoogeografie. SPN Praha
Darlington, P.J., 1998: Zoogeography: The geographical distribution of animals. Krieger, USA
Lomolino M.V., Brown J.H., Riddle B. R., 2005: Biogeography. Sinauer Associates, 1-845
Plesník, P., Zatkalík, F., 1996: Biogeografia. Vysokoškolské skriptá, PríFUK Bratislava
ÚBEV/ZO1/03
ÚBEV/VEK1/03
ÚBEV/ZOO1/03
active participation in seminars
preparation of the oral presentation to the selected topic
semestral written test
Active participation in seminars.
Preparation of oral presentation to a selected topic.
Completion of two semestral written examinations.
Oral examination.
This course will review our current understanding of the patterns of animal distribution and the processes that influence distributions of species and their attributes. Zoogeography will integrate information on the historical and current ecology, genetics, and physiology of animals and their interaction with environmental processes (continental drift, climate) in regulating geographic distributions. The course will emphasize descriptive and analytical approaches useful in hypothesis testing in zoogeography and will illustrate applied aspects of zoogeography (e.g. refuge design in conservation).
The main goal of the subject is to get knowledge on the basic reasons of recent distribution of the animals on the Earth, zoogeographic regionalization of the Earth´s surface and human influence on the faunal distribution in the history.
oral examination