1

Master of Science Graduate Programme in Biology

License of Ministry of science, education and sport of 16.June 2005.

DEPARTMENT OF BIOLOGY

JOSIP JURAJ STROSSMAYER UNIVERSITY OF OSIJEK

2

GENERAL INFORMATION BIOLOGY Master of Science Graduate Programme in Biology University Josip Juraj Strossmayer, Department of Biology Graduate studies in duration of two years or four semesters – Master of Science in Biology Admission requirements: completed undergraduate studies in biology and passed entrance exam On completing the graduate programme Master of biology will be able to enroll some of the postgraduate studies in the natural sciences. Masters of biology will employ in the variety of scientific institutions, industry (pharmaceutical, food, chemical, wood, etc.) and sectors that use biological knowledge such as inspection services in environmental protection. Master of biology during the study has gained knowledge and skills that will enable them to high-quality and competent expert guidance of natural parks and national parks, ponds, botanical gardens, zoos, parks in general, and biological analytical laboratories, etc. Also, they are qualified for participation in the scientific and technical teams working on research in the field of natural sciences and biomedical sciences.

3

PROGRAMME STRUCTURE

The Master of Science Graduate Programme in Biology requirements worth a total of 120 ECTS credits. This is equivalent to a duration of four semesters. The Master’s programme is divided into obligatory courses, elective courses and Master’s thesis preparation and defense. I semestar –obligatory courses C S L ECTS CODE Biochemistry 3 30 0 30 5 BM754 Animal physiology 2 30 0 15 4 BM755 Plant physiology 2 30 0 30 4 BM756 Virology 15 0 15 3 BM757 Quantitative biology 2 30 0 15 4 BM972 Marine ecology 30 15 15 4 BM759 Elective courses 90 6 300 165 15 120 30 II semestar –obligatory courses C S L ECTS CODE Plant nutrients 30 0 15 4 BM860 Basics in horticulture 15 0 15 2 BM861 Embriology and evolution of organic systems 30 0 30 4 BM862 Freshwater ekology 45 0 45 8 BM863 Molecular ecotoxicology 30 0 15 4 BM864 Scientific Research practice 1 30 2 BM865 Elective courses 90 6 300 150 0 150 30 III semestar- obligatory courses C S L ECTS CODE Ecology of Terrestrial Habitats 45 0 45 8 BM970 Imunology 15 0 15 3 BM966 Developmental biology of plants 30 0 15 3 BM967 Plant molecular ecophysiology 15 0 15 3 BM968 Animal behaviour 30 15 0 3 BM969 Scientific Research practice 2 60 2 BM971 Elective courses 90 8 300 135 15 150 30 IV semestar ECTS Acceptance of preliminars in MS theses 5 Research work 15 MS theses defence and final exam 10 30

4

Elective Courses

Course Seminar Laboratory ECTS CODE

Plant Toxicity Tests 15 0 15 2 BMZ73 Genome Evolution 15 15 0 2 BMZ79 Biochemical Mechanisms of Toxicity

15 0 15 2 BMZ74

Bird Metabolism 15 15 0 2 BMZ98 Biomolecules in Food 15 15 0 2 BMZ77 Molecular Mechanism of Oxidative Stress

15 0 15 2 BMZ75

Plant Stress Physiology 15 15 15 2 BMZ83 Enzyme Kinetics 15 0 15 2 BMZ76 Entomology 15 15 15 2 BMZ88 Underwater Biological Research 15 0 30 2 BMZ93 Plant Microtechnique and Microscopy

30 0 15 2 BMZ82

Supramolecular structures 15 15 0 2 BMZ81 Modeling of biological processes 15 15 0 2 BMZ72 Plant Cell and Tissue Culture 15 0 15 2 BMZ78 Ornithology 15 15 0 2 BMZ89 Geoinformatics in Biological Research

15 0 15 2 BMZ94

Biogeographical Inventarisation 15 0 15 2 BMZ92 Molecular Genetic 30 0 15 4 BM758 Dendrology 15 30 0 2 BMZ95 Geology and Paleontology 30 15 0 2 BMZ96 Plant Patoanatomy 15 0 15 2 BMZ80 Immunocompetence and Transplantation

15 0 15 2 BMZ84

Ecotoxicology 15 0 15 2 BMZ87 Revitalization and Protection of Aquatic Ecosystems

15 15 0 2 BMZ97

Biochemical Basis of Drug Action 15 15 0 2 BMZ99

5

OBLIGATORY COURSES

6

Biochemistry 3 (BM754) 30c + 0s + 30l ECTS 5 COURSE CONTENT: Catalytic (chymotrypsin, trypsin, elastase, cysteine, aspartyl and metalloproteases, carboanhydrase, restriction enzymes, nucleoside monophosphate kinases) and regulatory (aspartate transcarbamylase, cooperative oxygen transport by hemoglobin, isozymes, covalent modification, enzyme activation by proteolytic cleavage, blood clotting process) strategies of enzymes; membrane channels and pumps (active and passive transport, the transport of ions, second messengers, specific channels), the transmission of signals (transmembrane receptors interacting with ligands and the G-protein, inositol phosphate pathway, calcium ions as the signal source in the cytosol, diseases caused by defects in the signal transport); sensory system (detectors of smell, taste, visible light, sound and touch). Immune system (antibodies with antigen-binding and effector units, structure of immunoglobulins, binding of specific molecules using hypervariable loop, MHC complexes, suppression of the immune response to own antigens); molecular motors (members of NTPase superfamily with P-loop, myosin and actin in muscles, kinesin and dinein in microtubules, rotary motors in bacteria). LABORATORY CONTENT: Activity measurement and isoenzyme detection using electrophoresis, test for the purpose of detection lack of necessary factors for blood clotting processes, measurement of the concentration of antibodies (immunodiffusion, immunoelectrophoresis, ELISA), isolation and characterization of immunoglobulins from human blood. EXAMINATION METHODS: written and oral REQUIRED LITERATURE- basic:

Berg, J.M., Tymoczko, J.L., Stryer, L.,2012: Biochemistry ,Freeman & Comp., New York

ADDITIONAL LITERATURE:

Voet, D., Voet, J.G., 2011: Biochemistry, 4th ed. J.Wiley & Sons Inc., New York. Nelson, D.L., Cox, M.M., 2012: Lehninger Principles of Biochemistry, 6th ed., W.H. Freeman, New York Garrett, R.G., Grisham, C.M., 2010: Biochemistry, Brooks/Cole, Cengage Learning, Boston, USA Devlin, T.M. (ed.), 2010: Textbook of Biochemistry with Clinical Correlations, 7th ed., J.Wiley & Sons Inc., New York

7

Animal physiology 2 (BM755) 30c + 0s + 15l ECTS 4 COURSE CONTENT: Introduction and review of basic physiological concepts; Adaptation boundaries; Restrictive and expansive adaptation; Physical interactions between organisms and environment; Radiation, conduction, convection and evaporation; Scaling the metabolism and thermal interactions; Temperature adaptations: poikilothermy and ectothermy; Homeothermy and endothermy; Matter exchange with the environment; Osmotic exchange in aquatic and transitional animals; Water and sodium chloride exchange in terrestrial animals; Gas exchange adaptations; Energetics of locomotion; Physiological energetic balance; Environmental periodicity and physiological changes; Hibernation physiology; Diversity of feeding and digestion; Relation between morphology and physiology of alimentary system and feeding method and typeof food; Physiological problems related to herbivores; Fermentation in alimentary canal; Distribution of secondary plant components in organism and their effect on physiological processes; Exophysiology and physiology of extraterrestrial biological systems; Physiology of high and low air and water pressure; Environmental and physiological factors that regulate pheromone production. LABORATORY CONTENT: Measuring of basal metabolic rate; Influence of air pressure on fish behavior; Hibernation; Biological metabolic markers; Ecophysiological markers; Fermentation; Physiology of high pressure; Physiology of low pressure; Temperature adaptation; Adaptation on environmental dynamics; Insect pheromones and their analogues; Mammalian pheromones. Case studies. EXAMINATION METHODS: written and oral REQUIRED LITERATURE- basic: Bradshaw D., 2003: Vertebrate Ecophysiology, Cambridge University Press, Cambridge. Willmer P., Stone G., Johnston I., 2004: Environmental Physiology of Animals, Wiley-Blackwell.

ADDITIONAL LITERATURE: Paul J. R., 2001: Physiologie der Tiere, Thieme, Stuttgart. McNab B.K., 2002: The Physiological Ecology of Vertebrates, Cornell University Press, London.

8

Plant Physiology 2 (BM756) 30c + 0s + 30l ECTS 4 COURSE CONTENT: Photosynthesis (C3, C4 i CAM plants). Photosynthesis and Respiration. Heterotrophic Nutrition. Cell exchange regulation: inner cell regulation (gene and enzyme activity regulations). Intercellular regulations: plant growth regulators – auxins, gibberellins, cytokinins, ethylene and abscisic acid (chemical composition, biosynthesis, transport, physiological effects and their mechanism). Growth, differentiation and development: levels of differentiation, cause of cell differentiation, plant aging. Ecological factors regulations: the effect of light, temperature and daylight on the growth and plant development. Physiology of plant organelles and/or organs movements. LABORATORY CONTENT: Starch phosphorylase. The enzymatic degradation of the glycoside. The activity of saharase (invertase). The effect of gibberellin (GA3) on α-amylase synthesis. The effect of kinetin on leaf senescence. The effect of auxin on growth elongation of Phaseolus sp. seedlings EXAMINATION METHODS: written and oral REQUIRED LITERATURE- basic: PEVALEK-KOZLINA, B., 2003: Fiziologijabilja. Profil, Zagreb. TEIZ, L., ZEIGER, E., 2010: Plant Physiology. Sinauer Associates, Inc., Sunderland, Massachusetts. ADDITIONAL LITERATURE: BERG, J.M., TYMOCZKO, J.L., STRYER L., 2013: Biokemija, Školska knjiga, Zagreb

9

Virology (BM757) 15c + 0s + 15l ECTS 1+2 = 3 COURSE OBJECTIVES: Provide knowledge about important viral families in order to improve understanding of the diversity and importance of the viruses. Acquire basic skills and knowledge required for work in virology laboratory.

COURSE CONTENT: Viral vaccines, immunological response and interferon. Biological control of viral diseases. Evolution and ecology of viruses. Epidemiology of viral diseases. Molecular methods in detection and identification of viruses and subviral agents. Viruses of marine ecosystems. Application of viruses in gene therapy.

LABORATORY CONTENT: Laboratory diagnostics of selected viruses.

EXAMINATION METHODS: written and oral

REQUIRED LITERATURE - basic:

Presečki V (2003) Virologija, Medicinska naklada, Zagreb. All the Virology www.virology.net ADDITIONAL LITERATURE: The relevant scientific papers in virology.

10

Quantitative biology 2 (BM972) 30c + 0s + 15l

ECTS 4

COURSE CONTENT: Experimental design in laboratory conditions and in the environment. Sampling.

Monitoring. Census methods. Biodiversity Indices. Parametric statistics. Nonparametric statistics.

Multivariate methods. Cluster analysis. Interpretation of the results from statistical analyses.

Repeated measures. Monte Carly simulation. Basics of Bayesian statistics. Statistical models. Spatial

statistics. Quantification methods.

LABORATORY CONTENT: Principles of experimental design. Primary data analysis. Statistical data

analysis. Simulations. Data Quantification. Statistical and mathematical models. Applied spatial

statistics. Census methods.

EXAMINATION METHODS: written, oral and practical

REQUIRED LITERATURE – basic:

Zar, J.H., 2009. Biostatistical Analysis, Prentice Hall, (5th Edition).

Britton, F.N., 2004. Essential Mathematical Biology (2nd Edition), Springer Verlag, London.

Šošić, I., 2004: Primijenjena statistika, Školska knjiga, Zagreb.

ADDITIONAL LITERATURE:

Quinn, P.G. 2002. Experimental Design and Data Analysis for Biologists, Cambridge

University Press, Cambridge.

Sutherland, W.J., 2006, Ecological Census Techniques: A Handbook, Cambridge

University Press, Cambridge (2nd Edition).

Dalgaard, P., 2008. Introductory Statistics with R, Springer, New York (2nd Edition)

Babak S., 2012. Biostatistics with R: An Introduction to Statistics Through Biological Data, Springer,

New York.

11

Marine Ecology (BM759) 30c + 15s + 15l

ECTS 4

COURSE CONTENT: Introductory lecture –course content, literature and students obligations. Ocean

characteristics as three-dimensional environment. Primary production. Secondary production and

organic matter degradation. Epipelagic zone. Intertidal zone. Estuaries and salt swamps. Mangrove

forest. Kelp forest. Coral reefs. Deep sea organisms. Polar seas. Marine ecosystem functioning.

Fisheries and human impact on marine ecosystems. Conservation.

SEMINAR CONTENT: Microbial ecology of oceans. Biogeochemical carbon cycle in the ocean. Biogeochemical nitrogen cycle in the ocean. Ecology of hydrothermal vents. LABORATORY CONTENT: Examining effects of primary production, predator impact and influence of key-stone species with computer models. EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic:

Kaiser MJ, Attrill MJ, Jennings S, Thomas DN, et al. (2005) Marine Ecology: processes, systems, and impacts. Oxford University Press, Oxford. ADDITIONAL LITERATURE: Kirchman DL. (2000) Microbial ecology of the Oceans. Wiley, New York.

Barnes RSK, Hughes RN. (1999) Introduction to Marine Ecology, Wiley-Blackwell, New York.

12

Plant nutrients (BM860) 30c + 0s + 15l ECTS 4 COURSE CONTENT: Plant tissue analysis. Nutrient assimilation and transport in plants. Effect of soil pH on plant growth.The role and significance of mineral elements in plants. Assimilation of nitrogen, nitrates, nitrogen fixation, assimilation of amonium, sulphur, phosphate, cations. Solute transport. Carbohydrate and lipid metabolism. Secondary metabolites. Laboratory methods for plant cultivation. Symptoms of nutrient deficiency. Nutrients and eutrophication of freshwater ecosystem. LABORATORY CONTENT: Determing the presence of individual substances in plant cells and tissues (calcium, phosphate, nitrate; iron and ammonium ions; ascorbic acid; carbohydrate, inulin; and proteins). Excretion of root acids. Identifying symptoms of deficiency or excess of certain elements of plant nutrition in hydroponic growing conditions. EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic:

PEVALEK-KOZLINA, B., 2003: Fiziologija bilja. Profil, Zagreb. TAIZ, L., ZIEGER, E., 2010: Plant Physiology. Sinauer Associates, Inc., U.S.A. ADDITIONAL LITERATURE: MAATHIUS, F.J.M., 2013. Plant Mineral Nutrients. Methods and Protocol. Springer, London BENTON J.J. Jr., 2005. Hydroponics. A Practical Guide for the Soilless Grower. Second Edition. CRC Press

13

Basics in horticulture (BM861) 15c + 0s + 15l ECTS 2 COURSE CONTENT: Classification and characteristics of flower types (annual, biennia, perennials, water plants, creepers). Basics of vegetable crops growing and the most important vegetable representatives. Reproduction of vegetable and flower cultures. In vitro propagation methods. Woody plant species and park architecture. LABORATORY CONTENT: Basic methods of reproduction in plants. In vitro propagation methods. The architecture of gardens and parks. EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic:

Idžojtić M. (2009) Dendrology-leaf. Sveučilište u Zagrebu, Šumarski fakultet, Zagreb. Idžojtić M. (2013) Dendrology - flower, cone, fruit, seed. Sveučilište u Zagrebu, Šumarski fakultet, Zagreb. Parađiković N. (2009) Basic and special vegetable growing. Poljoprivredni fakultet, Osijek. Parađiković N. (1994) Greenhouses. Nova zemlja, Osijek ADDITIONAL LITERATURE: Hartmann TH, Kester DE, Davies Jr. FT, Geneve RL. (2011) Hartmann and Kester’s plant propagation: principles and practice. 8th ed. Prentice Hall, USA Pittenger DR. (2002) California Master Gardener Handbook. University of California, USA Healthy garden - organic, natural and free of chemicals (2010) Mozaik knjiga, Zagreb Scientific papers

14

Embryology and evolution of organic systems (BM862) 30c + 0s + 30l ECTS 4 COURSE CONTENT: History of embryology; structure of germinal cells and meiosis; fertilization, cleavage, types of blastulas and gastrulas; neurulation; control of embryogenesis; embryonic development of invertebrates, vertebrates and humans; embryonic origin and development of the organic systems; evolution and adaptations of invertebrate and vertebrates organic systems LABORATORY CONTENT:

Cells – characteristics, role and their importance

Processes of embryogenesis on the example of the sea urchins

Processes of embryogenesis on the example of poultry

Processes of embryogenesis on the example of frogs

Regeneration

Development extremes

Cloning

Human pregnancy and early development

EXAMINATION METHODS: seminar, written and oral REQUIRED LITERATURE – basic:

Gilbert, S.F., 2003. Developmental Biology. 7th ed. Sinauer Associates, Inc. Sadler, T.W., 2008. Langmanova medicinska embriologija. Školska knjiga, Zagreb. ADDITIONAL LITERATURE: Ruppert, E.E., Fox, R.S., Barnes, R.D., 2004. Invertebrate Zoology. A functional evolutionary approach. 7th ed. Thomson Brooks/Cole. Kardong, K.V.1994. Vertebrates: Comparative Anatomy, Function, Evolution. Brown Co., U.S.

15

Freshwater ecology (BM863) 45c + 0s + 45l ECTS 8 COURSE CONTENT: Freshwater ecosystems – typology and worldwide distribution. Water as a life medium. Water cycle. Nutrients cycle. Aquatic communities – phytoplankton, zooplankton, periphyton, benthos. Adaptation of organisms to different life conditions. Energy transfer and trophic interactions. Pollution and eutrophication of aquatic ecosystems. Climate and environmental changes. Protection and revitalization of freshwater habitats and wildlife. LABORATORY CONTENT: Field work: sampling techniques for analyses of water, sediment and biocenosis. Laboratory analyses: physico -chemical properties of water and sediment; Qualitative and quantitative analyses of biocenosis – phytoplankton; zooplankton; benthos; periphyton. Saprobiological analyse. Ecological status of freshwater habitats. Statistical analyses. EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic: Wetzel, R. G., 2001: Limnology – Lake and River Ecosystems. 3rd ed. Academic Press, San Diego, 1006 pp ADDITIONAL LITERATURE: APHA, 2001: Standard methods for examination of water and wastewater. Amer. Public Health Assoc. 20th ed. Washington, 1481 pp. Engelhart, W., 2003: Was lebt in Tümpel, Bach und Weiher? Kosmos, Stuttgart, 313 pp. Streble, H., Krauter, D., 2002: Das Leben im Wassertropfen. Kosmos, Stuttgart, 428 pp.

16

Molecular Ecotoxicology (BM864) 30c+0s+15l ECTS 4 COURSE CONTENT: Pollution and contamination; Xenobiotics; Mechanisms of xenobiotics entering in biological systems; First pass effect; Defense mechanisms; Reactions of biotransformation; First phase of xenobiotics biotransformation; Second phase of xenobiotics biotransformation; Third phase of xenobiotic biotransformation; Elimination of xenobiotics; Xenobiotic induction and inhibition; Hormonal disruptors; Xenoandrogens; Xenoestrogens; Vitelogenin; Oxidative stress as a result of physical factors and exposure to xenobiotics; Xenobiotics effects on metabolic pathways; Molecular biomarkers; p-glycoprotein and MXR; Biomarkers of exposure and effect; Xenobiotic effect on markers of metabolic activity and health condition. LABORATORY CONTENT: Xenobiotic exposure methods; In vivo test; Primary cell culture tests; Preparation of postmitochondrial and microsomal fraction; Inhibition of cholinesterase as a marker of effect of organophosphates, carbamates and detergents; Total cytochrome P450 and ethoxyresorufin-o-deethylase induction as a marker of exposure to polycyclic aromatic hydrocarbons, Glutathione concentration; Catalase and glutathione peroxidase activity as a marker of oxidative stress; Metabolic markers; Metallothionein concentration as a marker of exposure to heavy metals. EXAMINATION METHODS: written and oral

REQUIRED LITERATURE – basic:

Hoffman, D.J., Rattner, B.A., Burton, G.A., Cairns, J., 2003: Handbook of ecotoxicology, CRC Press LLC. Newman, M.C., Clements, W.H., 2008: Ecotoxicology. A comprehensive treatment, CRC Press, Taylor & Francis Group. Newman, M.C., 2009: Fundamentals of Ecotoxicology, CRC Press. ADDITIONAL LITERATURE: Mumtaz, M., 2010: Principles and practice of mixtures toxicology, WILEY-VHC. Robinson, L., Thorn, I., 2005: Toxicology and Ecotoxicology in Chemical Safety Assessment, Blackwell Publishing Ltd.

17

Scientific Research Practice 1( BM865 ) 0c + 0s + 30l ECTS 2 FIELD WORK CONTENT: Preparations for work in the field (appropriate clothing and footwear, security measures and safety, keeping a field journal). Fieldwork: exploring and mastering the methods of sampling, sample collection, conservation and labeling of samples. LABORATORY WORK CONTENT: Introduction to laboratory routines. Keeping laboratory journal. Introducing and learning about laboratory techniques. Participation in the work of the laboratory. Independent work on selected tasks.

18

Ecology of Terrestrial Habitats (BM970) 45c+0s+45l ECTS 8 COURSE CONTENT: What is terrestrial habitat and which organisms are living in it. Ecological factors which influence life of organisms in terrestrial habitat. Solar energy on Earth surface. Global atmospheric circulation. Macroclimate – parameters, their spatial and temporal variability. Water cycle. Lithology and relief as environmental factors. Topoclimate. Soil as a precondition for terrestrial habitat formation and maintenance. Pedosphere, pedogenesis, pedosystematics – basic terms. Biotic factors. Life strategies of terrestrial organisms. Matter and energy cycles in terrestrial habitat. Basic types of terrestrial habitats (biomes) and their correlation with macroclimate. Spatial distribution of biomes on Earth and their dynamics in time (global paleoecological aspect). Bioclimatic zones of Europe and Croatia. Edaphic factors and biogeocoenosis differentiation within bioclimatic zones. Spatio-temporal relation between soil and vegetation. Classification of terrestrial habitats. Overview of particular habitat types (on global, regional and local level): 1) dominant abiotic factors, 2) soil and vegetation, 3) typical organism representatives and their adaptations to habitat and interactions with habitat, 4) genesis and ecological stability, 5) anthropogenic influence. Terrestrial habitat boundaries. Environmental gradients and intermediar between terrestrial habitats and between terrestrial and marine/freshwater habitats. Anthropogenic terrestrial habitats. Levels of bioecological details in terrestrial habitat research. Overview of research themes and methods. Practical examples. LABORATORY CONTENT : Recognition of major types of terrestrial habitats on global level (biomes), recognition of terrestrial habitats in Croatia, determination of expected habitat type for set environmental factors (and vice versa), Overview of different sampling methods for particular organism groups on different habitats, qualitative and quantitative field data analysis. EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic:

Chapin, F.S. III, Matson, P., Mooney, H.A., Chapin M.C. 2002. Principles of Terrestrial Ecosystem Ecology. Springer-Verlag, New York. ADDITIONAL LITERATURE: Archibold O.W. 1995. Ecology of World Vegetation. Chapman & Hall, London, New York. Bailey, R.G. 2009. Ecosystem Geography: From Ecoregions to Sites. Springer-Verlag, New York, Dordrecht, Heidelberg, London. Ćirić, M. 1986. Pedologija, Svjetlost, Sarajevo. Gobat, J.-M., Aragno, M.,Matthey, W. 2004. The Living Soil – Fundamentals of Soil Science and Soil Biology. Science Publishers Inc., Endfield USA, Plymouth UK. Herak. M. 1990. Geologija, Školska knjiga, Zagreb. Oldeman, R.A.A. 1990. Forests: Elements of Silvology, Springer-Verlag, Berlin. Penzar I. i Penzar B. 1989. Agroklimatologija, Školska knjiga, Zagreb. Topić, J., Vukelić, J. 2009. Priručnik za određivanje kopnenih staništa u Hrvatskoj prema Direktivi o staništima EU. Državni zavod za zaštitu prirode, Zagreb.

19

Immunology (BM966) 15c+0s+15l ECTS 3 COURSE CONTENT: Properties and overview of immune response, cells and tissues of the immune system, innate immunity, antibodies and antigens, major histocompatibility complex molecules and antigen presentation, immune receptors and signal transduction, lymphocyte development, activation of T lymphocytes, effector mechanisms of cell-mediated and humoral immunity, immunological tolerance and autoimmunity, immunity to tumors, hypersensitivity disorders LABORATORY CONTENT: Immunization of experimental animals. The lymphatic system of rodents. Basic immunohistochemical methods. Isolation of ant ibodies. ELISA. Western blotting. Isolation of lymphocytes. Lymphocyte culture. Immunological reactions. Immunosuppression. EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic:

Abbas, A.K., Lichtman, A.H., Pillai, S., 2012: Cellular and Molecular Immunology, Elsevier Saunders, USA ADDITIONAL LITERATURE: Delves, P.J., Martin, S.J., Burton, D.R., Roitt, I.M., 2011: Roitt's Essential Immunology, Wiley-Blackwell, United Kingdom Janeway, A.C. (editor), 2001: Immunobiology, Garland Publishing, New York

20

Developmental Biology of Plants (BM967) 30c+0s+15l ECTS 3 COURSE CONTENT: Life cycle of seed plants and gametogenesis: microsporogenesis and megasporogenesis. Fertilisation. Embriogenesis. Postembrionic development. Germination. Cell and tissue differentiation during development of vegetative and generative organs. Molecular mechanisms of the plant growth regulators action: auxins, cytokinins, apscisic acid, jasmonic acid, brassinollides, oligosaccharides, geibberelines and ethylene. The review of methods employed in the plant development investigation: anatomical methods, molecular analysis of gene transcripts and proteins, physiological methods. LABORATORY CONTENT: During the practice students are going to study some of the chosen topics on their own and use appropriate methods in molecular biology (protein isolation, SDS electrophoresis, Western blotting, immunodetection - chemiluminescence), while other topics will be discussed and learned through the oral presentations of other students. EXAMINATION METHODS: written and oral REQUIRED LITERATURE –basic RAGHAVAN, V., 2000: Developmental Biology of Flowering Plants. Springer-Verlag, New York, Berlin, Heidelberg. PEVALEK-KOZLINA, B., 2003: Fiziologija bilja. Profil, Zagreb. BUCHANAN, B.B., GRUISSEM, W., JONES, R.L., 2006: Biochemistry and Molecular Biology of Plants. American Society of Plant Physiologists, Rockville, Maryland. LEPEDUŠ, H., CESAR, V., 2010: Osnove biljne histologije i anatomije vegetativnih organa. Sveučilište J. J. Strossmayera u osijeku, Odjel za biologiju, Osijek. ADDITIONAL LITERATURE: TAIZ, L., ZEIGER. E., 2010: Plant Physiology. 5th edition. Sinauer Associates Inc., Publishers, Sunderland, Massachusetts. BISWAL, B., KRUPINSKA, K., BISWAL, U.C., 2013: Plastid Development in Leaves during Growth and Senescence. Springer Science + Business Media Dordrecht. NOODÉN, L.D., 2004: Plant Cell Death Processes. Elsevier Academic Press, San Diego. AMBRIOVIĆ RISTOV, A., 2007: Metode u molekularnoj biologiji. Institut Ruđer Bošković, Zagreb. Additional literature will be selected from the most recent scientific publications that cover particular areas, depending on the individual interests of student.

21

Plant molecular Ecophysiology (BM968) 15c+0s+15l ECTS 4 COURSE CONTENT: The review of biotic and abiotic ecological factors; molecular mechanisms of the signal perception in plant cell and physiological response; changes of the gene expression caused by changes of temperature, light, by drought and anoxia;the effect of the airpollutants on the plant physiological status: sulfur dioxide, NOx, ozone; plant tolerance to heavy metals; molecular biology of the oxidative stress in plants; function and regulation of enzymes inHalliwell-Asada cycle; the effect of the abiotic factors (light, temperature, herbicides, heavy metals) on the organization and function of the photosynthetic apparatus. LABORATORY CONTENT: During the course students are going to study some of the topics on their own. EXAMINATION METHOD: written and oral REQUIRED LITERATURE – basic:

HELDT, H.W., 1999: Plant Biochemistry and Molecular Biology. Oxford University Press Inc., New York, Oxford. TAIZ, L., ZEIGER, E., 1998: Plant Physiology, Sinauer Associates, Inc., Publishers, Sunderland, Massachusetts. ADDITIONAL LITERATURE: ADUCCI, P., 1997: Signal Transduction in Plants. BirkhäuserVerlag, Switzerland. BASRA, A.S., 1993: Stress-Induced Gene Expression in Plants. Harwood Academic Publishers, Switzerland. SCANDALIOS, J.G., 1997: Oxidative Stress and the Molecular Biology of Antioxidant Defenses. Cold Spring Harbor Laboratory Press, New York.

22

Animal behavior (BM969) 30c+15s+0l ECTS 3 COURSE CONTENT: An introduction to animal behavior (what is behavior, the history of the study of animal behavior, proximate and ultimate causes). Mechanisms of behavior: the role of the nervous system (innate vs. learned behavior, imprinting). The motivation and organization of behavior (the internal and external mechanisms that control animal behavior). The development of behavior (natural selection, learning). Communication (living in groups, social communities, ritualization). Foraging behavior (optimal foraging theory, decision-making). Avoiding predators (primary and secondary strategy). Reproductive behavior (sexual selection, conflicts, mating systems, parental care and altruism). Human behavior. LABORATORY CONTENT: - SEMINAR CONTENT: The seminar will focus on one particular animal behavior topics/research paper and will be presented by a student. EXAMINATION METHOD: written and oral REQUIRED LITERATURE – basic:

Alcock J. 2009. Animal Behavior: An Evolutionary Approach. 9th ed, Sinauer Associates, Sunderland. Goodenough J., McGuire B., Wallace R.A. 2001. Perspectives of Animal Behavior. John Wiley and sons, Inc. New York, Brisbane, Toronto. McFarland D. 1996. Animal behaviour. Addison Wesley Longman Limited, Edinbourgh. ADDITIONAL LITERATURE: Halliday T. 1994. Animal Behavior. A Blanford book, London. Miller S., Harley J.P. 1996. Zoology. WCB Mc. Graw – Hill Companiec Inc. Boston. Wilson E.O. 2000. Sociobiology, The new synthesis. 25th ed. The President and Fellows of Harvard College.

23

Scientific Research Practice 2 (BM971) 0c + 0s + 60l ECTS 3 FIELD WORK CONTENT: Preparations for work in the field (appropriate clothing and footwear, security measures and safety, keeping a field journal). Fieldwork: exploring and mastering the methods of sampling, sample collection, conservation and labeling of samples. LABORATORY WORK CONTENT: Introduction to laboratory routines. Keeping laboratory journal. Introducing and learning about laboratory techniques. Participation in the work of the laboratory. Independent work on selected tasks.

24

ELECTIVE COURSES

25

Plant toxicity tests (BMZ73) 15c + 0s + 15l ECTS 2 COURSE CONTENT: Test types; test organisms; principles of the laboratory toxicity testing; individual display of metal and xenobiotic toxicity to algae, which in their toxicity and/or representation in industry and environment deserve special attention; source and the amount of xenobiotics in water; Duckweed test – monitoring of plant growth (fresh and dry weight, total surface of plants); photosynthetic pigments content and the amount of proteins to determine toxicity. LABORATORY CONTENT: Duckweed test; determination of metal toxicity and xenobiotics to Lemna minor and Lemna gibba (photosynthetic pigment content and inhibition of growth); statistical analysis of obtained results, evaluation and comparison to literature data. EXAMINATION METHOD: written and oral REQUIRED LITERATURE – basic:

Rai, L. C., Gaur, J.P. &Soeder, C.J., 1994: Algae and water polution. E. Schweizerbart, Stuttgart. OECD guidelines for thetestingofchemicals- Revisedproposal for a newguideline 221 Lemnasp. GrowthInhibition Test (http://www.oecd.org/dataoecd/16/51/1948054.pdf) ADDITIONAL LITERATURE: Naumann, B., Eberius, M., Appenroth, K.J., 2007: Growth rate baseddose – responserelationshipsand EC-valuesof ten heavy metalsusingtheduckweedgrowthinhibition test (ISO 20079) withLemnaminor L. clone St. Journal ofPlantPhysiology, Volume 164, Issue 12 (http://www.sciencedirect.com/science/article/pii/S0176161706003154) Landolt, E., 1986: ThefamilyofLemnaceae – a monographicstudy (Vol. 1 and 2). VeroffentlichungendesGeobotanischenInstitutesderEdig. tech. Hochschule, StiftungRübel. Zürich. http:/www.mobot.org/jwcross/duckweed/education.htm

26

Genome Evolution (BMZ79) 15c + 15s + 0l ECTS 1+1 = 2 COURSE CONTENT: Genome size in different organisms and the evolution. Number of chromosomes in eukaryotes, noncoding DNA and genome size. Genetic control of cell size. Experimentally induced changes in genome size. Natural selection and genome size. Mitochondrial DNA. Evolution of plastid DNA. B-chromosomes. Sex chromosomes. Moderated repetitive DNA. Chromosome elimination. Phylogenetic analysis SEMINAR CONTENT: Students will choose topics of their interest, prepare presentation and present them to other students. EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic:

Ryan Gregory T.R. 2007: The Evolution of the Genome. Elsevier Academic Press. Cooper G.M., Hausman R.E., 2013: The Cell: A Molecular Approach. Sinauer Associates, Inc., Sunderland, Massachusetts USA ADDITIONAL LITERATURE: Alberts B., Bray D., Lewis J., Raff M., Roberts K., Watson J.D., 2007: Molecular biology of the cell. 5th edition. Garland Publishing, Inc., New York – London. Ambriović Ristov A. et al. 2007: Metode u molekularnoj biologiji, IRB, Zagreb.

27

Biochemical Mechanisms of Toxicity (BMZ74) 15c + 0s + 15l ECTS 2 COURSE CONTENT: Basic properties of biotransforming enzymes; Biotransformation and metabolism; Stereochemical approach in xenobiotic biotransformation; First and second biotransformation phase; Nomenclature of enzymes included in biotransformation; Distribution of biotransformation enzymes in organisms; Reactions of hydrolyses; Reduction reactions; Oxidation reactions; Xenobiotics activation; P450 knockout mouse; Glucuronic acid conjugation; Sulfation reactions; Reactions of methylation; Reactions of acetylation; Conjugation with aminoacids; Conjugation with glutathione; Rhodaneses; Reaction of phosphorylation; QSAR. SEMINAR CONTENT: Within this seminar the students will study specific examples from toxicological practice. EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic:

Klaassen, D. C., 2008: Casarett & Doull's Toxicology: The Basic Science of Poisons. McGraw-Hill, New York. Timbrell J.A., 2008: Principles of Biochemical Toxicology, CRC press. ADDITIONAL LITERATURE: Stenersen J., 2004: Chemical Pesticides: Mode of Action and Toxicology, CRC press.

28

Avian metabolism (BMZ98) 15c + 15s + 0l ECTS 2 COURSE CONTENT: A survey of special metabolic demands in birds is discussed. Metabolic adaptations due to flight, water habitat, migration on long distances with no food intake and reduced oxygen supply as well as special metabolic requirements for eggs laying and hatching are included. The role of n-3 PUFA for metabolic and energetic changes is particularly discussed. Also, some aspects of avian metabolic adaptations are compared with human pathologic states like obesity and diabetes type 2, what can improve understanding of biochemical basis of their development and help in their efficient treatment SEMINAR CONTENT: - EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic:

Lewis, S. 2004: Avian Biochemistry and Molecular Biology, Cambridge University Press, Cambrige, United Kingdom. ADDITIONAL LITERATURE: Schat, K.A., Kaspers, B., Kaiser, P. 2014: Elsevier Ltd., United Kingdom.

29

Biomolecules in food (BMZ77) 15c+15s+0l ECTS 2 COURSE CONTENT: Introduction. Reaction between some food components (Carbohydrates, Lipids, Proteins, Enzymes, Vitamins, color and flavors, inorganic compounds). Biomolecular interactions; biological role of individual active molecules in foods; secondary metabolites of plants; damage caused by the action of free radicals; antioxidant properties of natural metabolites; assessment of the protective role of phytochemicals; oxidative stress and disease; the role of diet in the prevention of various diseases; the role of diet in gene expression. Polyphenols. Terpenes. Hydrococolloids. Glucosinolates. Phospholipids. Vitamins LABORATORY CONTENT: - SEMINAR CONTENT: Written report and presentation on choosen subject. EXAMINATION METHODS: oral REQUIRED LITERATURE – basic: Belitz, H.-D., W. Grosch; W., Schieberle, P. (2004) Food Chemistry. Springer-Verlag, Berlin Fennema, O.R. (1996) Food Chemistry. Marcel Dekker, Inc, New York ADDITIONAL LITERATURE: Watson, D. (1998) Natural Toxicants in Food. Sheffield Academic Press, Sheffield. Rice-Evans, C.A., Packer, L. (2003) Flavonoids in Health and Disease. Marcel Dekker, Inc, New York.

30

Molecular Mechanism of Oxidative Stress (BMZ75) 15c+0s+15l ECTS 2 COURSE CONTENT: Oxygen and reactive oxygen species. Damaging of biomolecules and cell structures in the conditions of the oxidative stress. Oxidants and cell signaling. Non-enzymatic antioxidants: ascorbic acid, glutathione, vitamin E, carotenoids, phenolics. Antioxidative enzymes: catalase, peroxidase, superoxide dismutase, glutathione reductase and monodehydroascorbate reductase. Halliwell-Asada cycle. LABORATORY CONTENT: Determination the activities of antioxidative enzymes. Determination of α-tocopherol by thin-layer chromatography. Determination of photosynthetic pigments concentration. Photosystem II efficiency measurement by the saturating pulse method. Experimental induction of the oxidative stress. EXAMINATION METHODS: written and oral REQUIRED LITERATURE- basic: BRADAMANTE, V., LACKOVIĆ, Z. (urednici), 2001: Oksidativni stres i djelotvornost antioksidansa. Medicinska naklada, Zagreb BUCHANAN, B.B., GRUISSEM, W., JONES, R.L., 2006: Biochemistry and Molecular Biology of Plants. American Society of Plant Physiologists, Rockville, Maryland. ADDITIONAL LITERATURE: SCANDALIOS, J. G., 1997: Oxidative Stress and the Molecular Biology of Antioxidant Defenses. Cold Spring Harbor Laboratory Press, New York. TAIZ, L., ZEIGER. E., 2010: Plant Physiology. 5th edition. Sinauer Associates Inc., Publishers, Sunderland, Massachusetts. INZÉ, D., VAN MONTAGU, M. (editors), 2002: Oxidative stress in Plants. Taylor & Francis, London, New York. AMBRIOVIĆ RISTOV, A., 2007: Metode u molekularnoj biologiji. Institut Ruđer Bošković, Zagreb. Additional literature will be selected from the most recent scientific publications that cover particular areas, depending on the individual interests of student.

31

Plant Stress Physiology (BMZ83) 15c+15s+15l ECTS 2 COURSE CONTENT: Abiotic stress: shortage of water and drought; temperature stress; increased salt content in soil; anoxia and hypoxia; light and UV stress; air and water pollution. Biotic stress: competition between plant species; response to predator and pathogen attack. Pollution impact on plants (heavy metals, atmospheric pollution and xenobiotics); resistance mechanisms; pollution of water and soil; chemical use in agriculture SEMINAR CONTENT: Students will individually write and present interesting topics regarding plant stress physiology LABORATORY CONTENT: During the course students will study some of the topics on their own through pratical work in laboratory EXAMINATION METHODS: written and oral REQUIRED LITERATURE- basic: Teiz, L., Zeiger, E., 2010: PlantPhysiology. SinauerAssoc. Inc., Sunderland, Massachusetts. ADDITIONAL LITERATURE: Original scientific papers AmbriovićRistov, A., 2007: Metode u molekularnoj biologiji. Institut Ruđer Bošković, Zagreb (http://www.mmb.irb.hr/) Buchanan, B., Gruissem, W., Jones, R., 2002: Biochemistry&MolecularBiologyofPlants. American SocietyofPlantPhysiologistsRockville, Maryland

32

Enzyme kinetics (BMZ76) 15c+0s+15l ECTS 2 COURSE CONTENT: Basic principles of enzyme catalysis; basic equations of enzyme kinetics; phase of the enzymatic reaction; Michealis-Menten model; determination of kinetic constants Km and Vmax; speed measurement of enzymatic reactions; influence of pH on the enzymatic catalysis; Types of inhibition of enzyme reactions; effect of inhibitors on the kinetic constanta; allosteric enzyme kinetics, stereochemistry of enzyme reactions; Kinetics of the enzyme under physiological systems; regulation of metabolic processes by kinetics of some enzymes LABORATORY CONTENT: The initial velocity of selected enzyme reactions in the presence of inhibitors will be measured and compared with uninhibited velocity. Kinetic constants of the inhibited and uninhibited enzyme will be calculated, and used to conclude about the type of inhibition, planning of enzyme assays; determining the optimum conditions for the enzymes of the physiological systems. SEMINAR CONTENT: - EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic: Nelson D. L., Cox M. M. (2013) Lehninger principles of biochemistry, W. H. Freeman & Co., 6th ed. New York Cornish-Bowden A. (2004) Fundamentals of Enzyme Kinetics, revised Edition, Portland Press, London ADDITIONAL LITERATURE: Review articles and scientific monographs

33

Entomology (BMZ88) 15c+15s+15l ECTS 2 COURSE CONTENT: Introduction to entomology. Present insects as the most important group of animals in the world. Explain the reasons: First, the immense diversity and flexibility; Secondly, the ratio of insects to man. Explain the relationship between man and insects through the fundamental determinants of specialist entomology: the transmission of diseases (medical entomology), food production (agricultural entomology), production of wood products (forest entomology), molestants (urban entomology). SEMINAR CONTENT: As part of the seminar, each student will commit to some of the topics in the field of courses that will prepare with the help of teachers and self-present. It also provides an overview video that follows the content of the program. LABORATORY CONTENT: A brief overview of morphological and anatomical characteristics of insects. Training determination insects: ordo - species, using the keys and computer programs. Sampling methods of insect, preparation and making of entomological collection. Design of entomological research. EXAMINATION METHODS: entomological collection and oral REQUIRED LITERATURE – basic: Gullan, P. J., Cranston, P.S. 2000. The insects: An outline of Entomology. Blackwell Science, USA. Service, M. 2012. Medical Entomology for Students. Fifth edition, Cambridge University Press. Mstoničkin, I., Habdija, I., Primc-Habdija, B., 1999. Beskralješnjaci: Biologija viših Avertebrata. Školska knjiga, Zagreb. ADDITIONAL LITERATURE: Peddigo, L. P. 2002. Entomology and Pest Menagment. Prentice Hall. 2. Romoser, W. S., Stoffolano, J. G., 1998. The Science of Entomology. WCB Mcgraw – Hill Companies.

34

Underwater biological research (BMZ93) 0c + 0s + 30l

ECTS 2

COURSE CONTENT: -

LABORATORY CONTENT: Sampling of bottom and sediment for the purpose of invertarisation; Water column sampling; Application of IR camera for inspection and research; Sonar usage; Making of sampling sketch and profile; Diving with autonomous diving gear.

EXAMINATION METHODS: Written and oral

REQUIRED LITERATURE- basic:

Clark A.R., 2000: Open Water Diver, SSI Croatia, Rijeka

Coyer J., Steller D., Witman J., 1990: The Underwater Catalog: A Guide to Methods in Underwater

Research, Shoals Marine Laboratory, Ithaca.

ADDITIONAL LITERATURE:

Miller C.B., 2003: Biological oceanography, Blackwell Publishing, Malden.

Medwin H., Clay C.S., 1997: Fundamentals of Acoustical Oceanography, Academic Press, New York.

Rand M.G., 1995: Fundamentals of Aquatic Toxicology, Taylor and Francis, Philadelphia – London.

35

Plant microtechnique and microscopy (BMZ82) 30c + 0s + 15l

ECTS 2 COURSE CONTENT: Introduction in plant microtechnique. Plant specimens sampling procedures. Fixation. Dehidratation. Infiltration and embedding. Microtome manipulation. Histochemical and cytochemical reactions on free hand fresh sections, sections embedded in paraffin, methacrylate or epoxy resins. Immunolocalisation. In situ hybridization of nucleic acids. Light microscopy. Different types: phase contrast microscope, differential-interference-contrast microscope, fluorescence microscope, confocal microscope. Electron microscopes: TEM and SEM (ESEM). LABORATORY CONTENT: The microscopy slide preparation: histochemical and cytochemical reactions and analysis. The application of different microscopy techniques in permanent slide analysis. EXAMINATION METHODS: written, practical and oral REQUIRED LITERATURE- basic: RUZIN, S.E., 1999: Plant Microtechnique and Microscopy. Oxford University Press, NewYork, Oxford. AMBRIOVIĆ RISTOV, A., 2007: Metode u molekularnoj biologiji. Institut Ruđer Bošković, Zagreb. ADDITIONAL LITERATURE: MALIGA, P., KLESSIG, D. F., CASHMORE, A. R., GRUISSEM, W., VARNER, J. E., 1995: Methods in Plant Molecular Biology. A Laboratory Course Manual. Cold Spring Harbor Laboratory Press, New York. O’BRIEN, T. P., MCCULLY, M. E., 1981: The Study of Plant Structure. Princples and Selected Methods. Termercarphi Pty. Ltd., Melbourne, Australia. BOWES, B.G., 1996: A Colour Atlas of Plant Structure. Manson Publishing Ltd, London. VAN DE GRAAF, K.M., RUSHFORTH, S.R., CRAWELY, J.L., 1998: A Photographic Atlas for the Botany Laboratory. 3rd edition. Morton Publishing Company, Colorado. Additional literature will be selected from the most recent scientific publications that cover particular areas, depending on the individual interests of student.

36

Supramolecular structures (BMZ81) 15c + 15s + 0l

ECTS 2

COURSE CONTENT: Lectures will be presented in the program "Chime" from a computer. The Web

materials for study will be used from the famous world Universities like Arizona, Hamburg, Virginia,

Illinois, Kenyon. These materials encompass the structural protein motifs interacting with DNA and

RNA, regulatory proteins in the gene expression, enzymes, membrane channels and pumps,

receptors, protein assemblies in photosynthesis, the key structures in immunological response,

viruses, nucleosomes and ribosomes

SEMINAR CONTENT: Seminars will be prepared and presented by students on the selected items,

according to the individual affinity

EXAMINATION METHODS: oral

REQUIRED LITERATURE- basic:

Berg, J.M., Tymoczko, J.L., Stryer, L.,2012: Biochemistry ,Freeman & Comp., New York

ADDITIONAL LITERATURE:

http://www.rcsb.org/pdb/home/home.do http://bcs.whfreeman.com/berg7 http://bcs.whfreeman.com/biochem6 www.whfreeman.com/biochem5 www.clunt.edu/BioDev/omm/exhibits.htm www.biologie.uni-hamburg.de/lehre/bza/eanfang.htm http://biology.kenyon.edu/BMB/chime.htm http://www.proteopedia.org/wiki/index.php/Main_Page http://www.ks.uiuc.edu

37

Modeling of biological processes (BMZ72) 15c + 15s + 0l ECTS 2 COURSE CONTENT: Discrete dynamical systems; Compartmental analysis and differential equations; Logistic models; Recursive functions; Stochastic processes; Interpreting stochastic data; Creating stochastic models; Model validation; A human population model; Review of matrix algebra; Eigenvalue and eigenvector analysis; Empirical models; Interpolation; The statistics of simple regression; Continuous models; Geometric analysis and non-linear equations; Continuous stochastic processes. SEMINAR CONTENT: During this seminar the students will create models on the basis of specific research examples, i.e. on real data. EXAMINATION METHODS: written and oral REQUIRED LITERATURE – basic: Mooney D., Randall S., 1999: A Course in Mathematical Modeling. ADDITIONAL LITERATURE: Bender A.E., 2000: An Introduction to Mathematical Modeling, Dover Publications, Mineola. Britton F.N., 2003: Essential Mathematical Biology, Springer Verlag, London.

38

Plant cell and tissue culture (BMZ78) 15c + 0s +15l

ECTS 2 COURSE CONTENT: Organogenesis and regeneration via in vitro plant cell, tissue and organ culture. Starting up the culture: media composition, surface sterilization of initial plant material, impact of physical factors on culture growth, explants selection, subculturing. Callus culture. Structural, physiological, biochemical and genetic aspects of organogenesis in vitro. Plant regeneration. Somatic embryogenesis. Protoplast cultures. Impact of plant cell and tissue culture on genetic engineering and breeding systems: genetically transformed plants, vegetative micropropagation. Impact in biotechnology: clone production, bioproduction of different substances. LABORATORY CONTENT: Starting up the culture: media composition, explants selection, surface sterilization of initial plant material, manipulation in sterile chamber, callus production, subculturing. In vitro regeneration. EXAMINATION METHODS: written and oral REQUIRED LITERATURE - basic: JELASKA, S., 1994: Kultura biljnih stanica i tkiva. Školska knjiga, Zagreb. AMBRIOVIĆ RISTOV, A., 2007: Metode u molekularnoj biologiji. Institut Ruđer Bošković, Zagreb. ADDITIONAL LITERATURE: EVANS, D.A., W.R. SHARP, P.V. AMMIRATO & Y. YAMADA, 1983: Handbook of plant cell culture. Volume 1: Techniques for propagation and breeding. MacMillan Publishing Co., New York – London. SHARP, W.R., D.E. EVANS, P.V. AMMIRATO & Y. YAMADA, 1984: Handbook of plant cell culture. Volume 2: Crop species. MacMillan Publishing Co., New York – London. AMMIRATO, P.V., D.E. EVANS, W.R. SHARP & Y. YAMADA, 1984: Handbook of plant cell culture. Volume 3: Crop species. MacMillan Publishing Co., New York – London. Additional literature will be selected from the most recent scientific publications that cover particular areas, depending on the individual interests of student.

39

Ornithology (BMZ89) 15c + 15s +0l ECTS 2 COURSE CONTENT: Anatomy and morphology of the birds. Behavior. Territoriality, colony, breeding, nests, incubation of the eggs, chicks, growing. Migration. Evolution. Phylogeny and classification of the birds. Endangered and protected species. Ornithology and research methods – observing, studying bird’s fauna, researching. The history of the ornithology in Croatia. Important areas for birds in Croatia. Croatian Ornithofauna. SEMINAR CONTENT: Students are obligated to write and present seminar. Seminar must content description of one taxon of the birds (with biological, ecological and zoographical characteristic, protection and IUCN status). If the taxon is endangered student have to present causes of threats and protection measures that are taken. Seminar topics may be linked to the general characteristics of birds as they fly adjustments, the evolution of birds, migration, behavior, birds etc. EXAMINATION METHODS: written and oral REQUIRED LITERATURE - basic: Hoyo J., Elliot A., Sargatal, J. 1992. Handbook of the birds of the world. Lynx editiones, Barcelona. Gill, F.B. 2007. Ornithology. Third ed. W.H. Freeman and Company, New York. Heinzel H., Fitter R., Parslow, J. 1999.Ptice Hrvatske i Europe. Hrvatsko ornitološko društvo, Zagreb. Radović D, Kralj J, Tutiš V, Radović J, Topić R 2005. Nacionalna ekološka mreža. Važna područja za ptice u Hrvatskoj. DZZP. Zagreb 84. Tutiš V, Kralj J, Čiković D, Barišić S (Ur.) 2013. Crvena knjiga ptica Hrvatske. Ministarstvo zaštite okoliša i prirode i Drţavni zavod za zaštitu prirode, Zagreb. Kralj, J., Barišić, S., Tutiš, V.,Ćirković, D.(Ur.) 2013. Atlas selidbe ptica Hrvatske.HAZU, Zavod za ornitologiju Zagreb Bibby CJ, Burgess ND, Hill DA 1992. Bird Census Techniques. London: Academic Press. ADDITIONAL LITERATURE: Podulka S.,Rohrbaugh R.W.Jr.,Bonney R. (ur.) 2004. Handbook of bird biology. Cornell Laboratory of Ornithology. New York. USA Kralj J. 1997. Ornitofauna Hrvatske tijekom posljednjih dvjesto godina. Larus 46: 8-9. Lukač G. 2007. Popis ptica Hrvatske. Natura Croatiaca, 16. Suppl. 1: 1-148. Mikuska J., Mikuška T., Romulić M. 2002: Ptice – vodič kroz biološku raznolikost Kopačkog rita. Matica hrvatska, Osijek. Hrvatska akademija znanosti i umjetnosti-Zavod za ornitologiju 2011. Prstenovanje ptica u znanosti i zaštiti prirode. Zagreb, 33 pp.

40

Geoinformatics in Biological Research (BMZ94) 15c+0s+15l ECTS 1+1=2 COURSE CONTENT: Definition and scope of geoinformatics, organization and display of spatial data, Geographic Information System (GIS), Projections and spatial transformations, Digitalization, scanning and vectorization, Georeferencing, Raster and vector GIS, Thematic layers, Attribute tables; Operations with raster and vector themes, Digital relief model and geomorphometric derivatives, spatial interpolations, spatial modelling, Physical fundamentals of remote sensing, Orthophoto, Multispectral scanners, Earth surface spectral signature, Passive and active sensors, Major satellite platforms, Spatial, temporal, spectral and thematic resolution, Subjective interpretation and delineation, Controlled and uncontrolled automatic classification, Spectral channels as a continuous estimators of biological and environmental variables, spatio-temporal series and monitoring on large area, Virtual sampling and preparation of matrix for numerical analysis, Significance of geoinformatic technologies in biological research with demonstration on practical examples, Overview of commercial and freely available geoinformatic software packages. LABORATORY CONTENT: Basic operations with vector and raster spatial data, usage of GPS devices, Autonomous making of digital thematic map, Application of basic geostatistical methods, geomorphometric analysis and data analysis obtained with remote sensing in the context of biological research. EXAMINATION METHODS: written and oral REQUIRED LITERATURE - basic: Burrough, P.A., McDonnell, R.A. 1998. Principles of geographical information systems. Barret, E.C., Curtis, L.F. 1999. Environmental Remote Sensing. Hengl, T., Reuter, H.I. 2009. Geomorphometry: Concepts, Software, Applications. Elsevier, Amsterdam, London, New York.umjetnosti, Vijeće za daljinska istraživanja i fotointerpretaciju: GEOSAT, Zagreb. ADDITIONAL LITERATURE: Bernhardsen, T. 2002. Geographic Information System, An Introduction, 3rd ed., John Willey and Sons, Toronto. Frančula, N. 2003. Digitalna kartografija. Oluić, M. 2001. Snimanje i istraživanje Zemlje iz Svemira: sateliti, senzori, primjena. Hengl, T. 2004. Geografski informacijski sustavi u inventarizaciji prirodnih resursa. Sveučilište u Osijeku, Osijek.

41

Biogeographic Inventory (BMZ92) 15c+0s+15l ECTS 2 COURSE CONTENT: Repetitorium of biogeography as a discipline which studies distribution of biodiversity in space and time. Making of biodiversity inventory lists. Qualitative (present/absent) and quantitative (population density) data. Cartographic aspect of biodiversity inventory. Location coordinates. MTB and UTM map. Field data geocoding techniques. Connection with geoinformation systems. Relation with spatial distribution of environmental factors. Direct mapping vs. mapping with numerical model. Mapping of habitat and vegetation types. Map scale and minimal mapping area. Choice of classification standard and thematic resolution. Usage of data obtained from remote sensing: expert interpretation and computer classification. Preparation of work maps and field verification. Cartographic principles (colors, symbols). Map of real, potential and climazonal vegetation. Time aspect of biogeographic data. Time series of thematic maps and biomonitoring. Merging data from different sources. Methods for spatial analysis of biogeographic data. Cartographic derivative of basic data of species, vegetation and habitat spatial distribution. LABORATORY CONTENT: Determination of exact geographic position of location. Filling field list and noting field data. Editing field data in form adequate for further analysis. Distribution mapping of different species, vegetation and habitats. Graphic editing of thematic map. Interpretation of existing cartographic content. EXAMINATION METHODS: written and oral REQUIRED LITERATURE - basic: Leveque, C., Mounolou J. C. 2003. Biodiversity. John Wiley & Sons, Ltd. Henderson P.A., 2003. Practical methods in ecology. Blackwell, UK. Topić J., Vukelić J. 2009. Priručnik za određivanje kopnenih staništa u Hrvatskoj prema direktivi o staništima EU. Državni zavod za zaštitu prirode, RH. ADDITIONAL LITERATURE: Nikolić, T., Bukovec, D., Šopf, J, Jelaska S.D. 1998. Kartiranje flore Hrvatske – mogućnosti i standardi. Nat. Croat. 7, Suppl. 1: 1-62. Bohn, U., Gollub, G., Hettwer, C. (Ur.) 2000. Map of the natural vegetation of Europe. Federal agency for nature conservation. Horvat, I. 1962. Vegetacija planina zapadne Hrvatske. Prirodoslovna istraživanja, Jugoslavenska akademija znanosti i umjetnosti, Acta Biologica 2, knjiga 30, 5-179.3. Evans, K.M. 2006. Endangered species, protecting biodiversity. Thomson Gale. Hawksworth, D.L., Bull, A.T. 2007. Plant conservation and biodiversity. Springer. Vukelić, A. Mikac, S., Baričević, D., Bakšić, D., Rosavec, R. 2008. Šumska staništa i šumske zajednice u Hrvatskoj. DZZP. Zagreb. Radović J, Čivić K, Topić R, Posavec Vukelić, V. 2009. Biološka raznolikost Hrvatske, Drugo izmijenjeno izdanje. DZZP. Zagreb. Brown, R.W., Lawrence, M.J., Pope, J. 2009. Animals – tracks, trails and signs. Bounty Books, Octopus publishing Group Ltd, London. Alegro, A. i sur. 2010. Botanički važna područja Hrvatske. Školska knjiga, Zagreb. Sutherland, W.J., 2010. Ecological Census Techniques – a handbook, Cambridge University Press, New York.

42

Molecular Genetics (BM758) 30c + 0s + 15l ECTS 2+2 = 4 COURSE CONTENT: Molecular basis of inheritance: DNA and RNA as genetic material and flow of genetic information (basic information about replication, transcription, reverse transcription and translation). Informational content of nucleic acids (primary, secondary and tertiary structure), genetic code and genes. Genome projects. Procaryotic and eukaryotic genome. Classification of genomic DNA sequences: significance and functionality of coding and non-coding sequences, classification according to copy number. "DNA identity", minisatellites and microsatellites. Genome size and C-value paradox. Significance of reorganizations in genome evolution, principles of recombination processes. Transposable elements and their role in genome evolution. DNA in eukaryotic genome: nucleosomes, chromatin and chromosomes. Genome compartments, euchromatin and heterochromatin. Centromeres and telomeres, epigenetic inheritance. Transcription in regulation and formation of a genome: RNAi mechanisms. Basic characteristics of human genome, isohore organization and comparisons with sequenced genomes of other species. Significance of structural organization of interphase nucleus in genome function. LABORATORY CONTENT: Isolation of eukaryotic genomic DNA. Restriction analysis with endonucleases, electrophoretic separation of fragmented DNA and purification of fragments of interest from agarose gels. Cloning: preparation of vector, ligation, preparation of competent cells and transformation. Selection of transformed bacterial clones on selective media, minipreps of plasmid DNA and selection of clones of interest. Southern hybridization analysis. Introduction to computer analyses of DNA sequences (restriction sites, GenBank search, alignments, basic phylogenetic analysis and similar). EXAMINATION METHODS: written and oral REQUIRED LITERATURE - basic: R.H. Tamarin (1999) Principles of genetics. 6th edition. McGraw-Hill Companies, Inc. BLACKBURN, G. M., GAIT, M. J., 1996: Nukleic acids in chemistry and biology. 2nd edition. Oxford University Press ADDITIONAL LITERATURE: ALBERTS, B., BRAY, D., LEWIS, J., RAFF, M., ROBERTS, K., WATSON, J. D., 1994: Molecular biology of the cell. 3rd edition. Garland Publishing, Inc., New York – London. LEVINE Additional literature will be also selected from most recent review articles in the field and problems of interest (e.g. Trends in Genetics, Current Opinion serials and similar)

43

Dendrology (BMZ95) 15c + 30s + 0l ECTS 2 COURSE CONTENT: Plant life-forms. The role of the woody stem in the plant life strategy. Wood anatomy - primary and secondary growth. The vascular system: morphology and evolution. Comparative anatomy and morphology of vegetative and generative organs with emphasis on evolutionary and ecological context. Ontogeny and phylogeny of tree species. Strategies of reproduction and dissemination. The position of woody species in plant evolution and systematics. Paleodendrology. Exchange of matter and energy in woody plants. Biotic and abiotic impacts on growth, development and status of woody plants. Interactions of trees and other organisms. Potential and realized ecological niche. Dendrometric parameters. Dendrochronology as retroactive monitoring of habitat conditions. Woody species as edificators of forest ecosystems. Global ecological amplitude of trees and forests. Variability of forests in space and time. SEMINAR CONTENT: Successional and degradation phases of forests. Trees in non-forest habitats. Importance of trees in the circulation of matter and energy in nature. Rare and endangered tree species. Rare and endangered forest types. Rainforests, semi-rainforests, managed forests, forest plantations. EXAMINATION METHODS: written and oral REQUIRED LITERATURE - basic:

Idžojtić M (2013) Dendrologija-cvijet, češer, plod, sjeme. Udžbenici Sveučilišta u Zagrebu, Sveučilište u Zagrebu Šumarski fakultet, Hrvatske šume d.o.o., Zagreb Idžojtić M (2009) Dendrologija-list. Udžbenici Sveučilišta u Zagrebu, Sveučilište u Zagrebu Šumarski fakultet, Hrvatske šume d.o.o., Akademija šumarskih znanosti, Zagreb Šilić Č (1990) Ukrasno drveće i grmlje. Svjetlost, Sarajevo Šilić Č (1983) Atlas drveća i grmlja. Svjetlost, Sarajevo ADDITIONAL LITERATURE: Vukelić J, Rauš Đ (1998) Šumarska fitocenologija i šumske zajednice u Hrvatskoj. Udžbenici Sveučilišta u Zagrebu, Šumarski fakultet, Zagreb Rauš Đ, Vukelić J (1995) Silvae nostrae Croatiae. Ministarstvo poljoprivrede i šumarstva Republike Hrvatske: Hrvatske šume, Zagreb Rauš Đ (1992) Šume u Hrvatskoj. Sveučilište u Zagrebu Šumarski fakultet, Hrvatske šume, Zagreb

44

Geology and paleontology (BMZ96) 30c + 15s + 0l ECTS 2 COURSE CONTENT: Introduction: definition and application of geology and paleontology; introduction to the basic terms; relationship with other sciences. Division of geology. Genesis, structure, causes and consequences of internal and external dynamics of the Earth. Review of geological periods, disposition of land, floating of continents, tectonic shifts and climate changes. Genesis, classification and dating of rocks (igneous, metamorphic, sedimentary). Paleontological taxonomy (Monera, Protozoa, Protophyta, Algae, Plantae, Sponges, Corals, Bivalves, Gastropods, Cephalopods, Polymeria, Oligomeria, Vertebrata). Evolution of the species (origin and development of life), mass extinction and recovery after the mass extinction, biodiversity. Fossils as living organisms (stromatolites, sessile invertebrates, algae) and environmental indicators. Biostratigraphy. Paleoecology. SEMINAR CONTENT: Students will learn about the different models and materials regarding the main topics of the course. Furthermore, students will choose and present one of the topics. EXAMINATION METHODS: written and oral REQUIRED LITERATURE - basic: BRIGGS, D.E.G, CROWTHER, P.R. (2003): PALEOBIOLOGY II, BLACKWELL. HERAK. M. (1990): GEOLOGIJA, ŠKOLSKA KNJIGA, ZAGREB. ADDITIONAL LITERATURE: SREMAC, J. (1999): OPĆA PALEONTOLOGIJA, SKRIPTA, PMF. MC KERROW W.S. (1981): THE ECOLOGY OF FOSSILS- AN ILUSTRATED GUIDE. MIT PRESS. MILSOM, C., RIGBY, S. (2010): FOSSILS AT A GLANCE, 2ND ED., WILEY-BLACKWELL, LONDON PLUMMER, C.C., MCGEARY, D., CARLSON, D.H. (1999): PHYSICAL GEOLOGY, 8TH ED., THE MCGRAW-HILL

COMPANIES, BOSTON. CLARKSON, E.N.K. (1998): INVERTEBRATE PALAEONTOLOGY AND EVOLUTION, 4TH ED., BLACKWELL SCIENCE LTD., LONDON.BENTON, M.J. (2000): VERTEBRATE PALAEONTOLOGY, 2ND ED., BLACKWELL SCIENCE LTD., LONDON RETALLACK, G.J. (2001): SOILS OF THE PAST: AN INTRODUCTION TO PALEOPEDOLOGY. SECOND EDITION,BLACKWELL, OXFORD, 600 P. STEWART, W.N. AND ROTHWELL, G.W. (1993): PALEOBOTANY AND THE EVOLUTION OF PLANTS, SECOND EDITION. CAMBRIDGE UNIVERSITY PRESS, CAMBRIDGE, UK.

45

Plant pathoanatomy (BMZ80) 15c + 0s + 15l ECTS 2 COURSE CONTENT: Plant anatomy. Abiotic and biotic factors as causes of pathological changes in cell structure and plant tissues. Pathological changes in cell structures (cell wall, biomembranes, cytoskeleton, ribosomes) and organelles (nucleus, mitochondria, plastids, endoplasmic reticulum, Golgi apparatus, vacuoles, peroxisomes and glyoxysomes). Pathological changes in plant tissues. LABORATORY CONTENT: Techniques in making temporary and permanent microscopic preparations. EXAMINATION METHODS: written and oral REQUIRED LITERATURE- basic: AGRIOS, G. N., 2005: Plant Pathology, Fifth edition, Academic Press, New York. TRIGIANO, R. N., WINDHAM, M. T., WINDHAM, A. S. (eds), 2006: Plant Pathology: Concepts and Laboratory Exercises, Taylor & Francis ADDITIONAL LITERATURE: BAČIĆ, T., 2003: Morfologija i anatomija bilja, Sveučilište Josipa Jurja Strossmayera u Osijeku, Pedagoški fakultet, Osijek. LEPEDUŠ, H., CESAR, V., 2010: Osnove biljne histologije i anatomije vegetativnih organa. Sveučilište Josipa Jurja Strossmayera u Osijeku, Odjel za biologiju, Osijek ŽUNA PFEIFFER, T., KRSTIN, LJ., ŠTOLFA, I., LOVAKOVIĆ, T., TIKAS, V., LEPEDUŠ, H., 2014: Praktikum iz anatomije biljaka, Sveučilište Josipa Jurja Strossmayera u Osijeku, Odjel za biologiju, Osijek

46

Protection and revitalization of aquatic ecosystems (BMZ97) 30c + 15s + 0l ECTS 2 COURSE CONTENT: Water ecosystems- structure and function. Methods for the trophic state qualification. Problems of lakes and reservoirs – types and sources of problems. Qualitative and qualitative assessment of the problem. Comprehensive water balance and mass balance. Remedial techniques – external control measures, internal control measures. Use of models. Planning for sound management of water ecosystems. SEMINAR CONTENT: Restoration methods – hypolimnetic withdrawal, precipitation of phosphorus and inactivation, sediment oxidation, sediment removal, hypolimnetic aeration, procedures to control plant biomass – harvesting, biomanipulation. Lake restoration – case studies. EXAMINATION METHODS: written and oral REQUIRED LITERATURE: Wetzel, R. G., 2001: Limnology – Lake and River Ecosystems. 3rd ed. Academic Press, San Diego, 1006 pp ADDITIONAL LITERATURE: JØRGENSEN, S.E., VOLLENWEIDER, R.A. (ur.), 1989: Guidelines of Lake Management: Vol. 1, Principles of Lake Management. International Lake Environment Committee Foundation. Shiga.