Master of Science Graduate University Study Programme in...

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Master of Science

Graduate University Study

Programme in Biology

License of the Ministry of Science, Education and Sports; June 16, 2005

DEPARTMENT OF BIOLOGY

JOSIP JURAJ STROSSMAYER UNIVERSITY OF OSIJEK

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GENERAL INFORMATION

BIOLOGY

Master of Science Graduate University Study Programme in Biology

Josip Juraj Strossmayer University of Osijek, Department of Biology

Graduate university studies in duration of two years or four semesters – Master of Science in

Biology

Admission requirements: completed undergraduate university study programme in biology

and entrance exam passed

On completing the graduate university study programme, a Master of biology will be able to

enrol in some of the natural sciences postgraduate studies.

The Masters of biology will employ in the variety of scientific institutions, industry

(pharmaceutical, food, chemical, wood, etc.) and sectors that require the knowledge in

biology such as inspection services in the environmental protection. The Master of biology

during their study has gained knowledge and skills that will enable them for the high-quality

and competent expert managing of the national parks, nature parks and nature reserves, ponds,

botanical gardens, zoos, parks in general, and the laboratories of analytical biology, etc. Also,

they are qualified for participation in the scientific and technical teams researching in the field

of natural sciences and biomedical sciences.

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PROGRAMME STRUCTURE

The Master of Science Graduate University Study Programme in Biology requirements

allocate a total of 120 ECTS. The duration is four semesters. The Master’s programme is

divided into obligatory courses, elective courses and Master’s thesis preparation and defence.

I semester –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 semester –obligatory courses C S L ECTS CODE

Plant Nutrients 30 0 15 4 BM860

Basics of Horticulture 15 0 15 2 BM861

Embryology and Evolution of

Organic Systems 30 0 30 4 BM862

Freshwater Ecology 45 0 45 8 BM863

Molecular Ecotoxicology 30 0 15 4 BM864

Scientific Research Practice 1 30 2 BM865


300 150 0 150 30

III semester- obligatory courses C S L ECTS CODE

Immunology 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

Ecology of Terrestrial Habitats 45 0 45 8 BM970

Scientific Research Practice 2 60 2 BM971


300 135 15 150 30

IV semester ECTS

Preliminary Acceptance of MS thesis 5

Research work 15

MS thesis defence and final exam 10

30

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Elective Courses

Course Seminar Laboratory ECTS CODE

Modelling of Biological

Processes

15 15 0 2 BMZ72

Plant Toxicity Tests 15 0 15 2 BMZ73

Biochemical Mechanisms of

Toxicity

15 0 15 2 BMZ74

Molecular Mechanism of

Oxidative Stress

15 15 2 BMZ75

Enzyme Kinetics 15 0 15 2 BMZ76

Biomolecules in Food 15 15 0 2 BMZ77

Plant Cell and Tissue Culture 15 0 15 2 BMZ78

Genome Evolution 15 15 0 2 BMZ79

Plant Pathoanatomy 15 0 15 2 BMZ80

Supramolecular Structures 15 15 0 2 BMZ81

Plant Microtechnique and

Microscopy

30 0 15 2 BMZ82

Plant Stress Physiology 15 15 15 2 BMZ83

Immunocompetence and

Transplantation

15 0 15 2 BMZ84

Ecotoxicology 15 0 15 2 BMZ87

Entomology 15 15 15 2 BMZ88

Ornithology 15 15 0 2 BMZ89

Biogeographical Inventarisation 15 0 15 2 BBZ54

Underwater Biological Research 0 30 2 BMZ93

Geoinformatics in Biological

Research

15 0 15 2 BMZ94

Molecular Genetic 30 0 15 4 BM758

Dendrology 15 30 0 2 BMZ95

Geology and palaeontology 30 15 0 2 BMZ96

Revitalization and Protection of

Aquatic Ecosystems

15 15 0 2 BMZ97

Avian Metabolism 15 15 0 2 BMZ98

Biochemical Basis

of Drug Action

15 15 0 2 BMZ99

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OBLIGATORY COURSES

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Biochemistry 3 (BM754) 30 C+0S+30L

ECTS 5

COURSE CONTENT: Catalytic (chymotrypsin, trypsin, elastase, cysteine, aspartyl and

metalloproteases, carbonic anhydrase, 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), 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 of the lack of necessary factors for blood clotting processes,

measurement of the concentration of antibodies (immunodiffusion, immunoelectrophoresis, ELISA),

isolation and characterization of immunoglobulins from the human blood.

EXAMINATION METHODS: written and oral

OBLIGATORY LITERATURE

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.

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Animal Physiology 2 (BM755) 30C+0S+15L

ECTS 4

COURSE CONTENT: Introduction and review of the 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 the aquatic and transitional animals;

water and sodium chloride exchange in the 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 the alimentary system and the feeding method and the type of food; physiological

problems related to the herbivores; fermentation in the alimentary canal; distribution of the secondary

plant components in the organism and their effect on the physiological processes; exophysiology and

physiology of the extra-terrestrial biological systems; physiology of the high and low air and water

pressure; environmental and physiological factors that regulate the pheromone production.

LABORATORY CONTENT: Measuring of the basal metabolic rate; influence of the air pressure on

the behaviour of fish; hibernation; biological metabolic markers; ecophysiological markers;

fermentation; physiology of high pressure; physiology of low pressure; temperature adaptation;

adaptation on the environmental dynamics; insect pheromones and their analogues; mammalian

pheromones. Case studies.


OBLIGATORY LITERATURE:

Bradshaw, D. (2003). Vertebrate Ecophysiology, Cambridge University Press, Cambridge.

Willmer, P., Stone, G., Johnston, I. (2004). Environmental Physiology of Animals. Wiley-Blackwell.


Paul, J. R. (2001): Physiologie der Tiere. Thieme, Stuttgart.

McNab B.K. (2002). The Physiological Ecology of Vertebrates. Cornell University Press, London.

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Plant Physiology 2 (BM756) 30C+0S+30L

ECTS 4

COURSE CONTENT: Photosynthesis (C3, C4 and 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. Regulations of the ecological factors: the effect of light, temperature and

daylight on the growth and plant development. Physiology of the 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 the growth elongation of Phaseolus sp. seedlings.



Pevalek-Kozlina, B. (2003). Fiziologija bilja. Profil, Zagreb.

Teiz, L., Zeiger, E. (2010). Plant Physiology. Sinauer Associates, Inc.,

Sunderland, Massachusetts.


Berg, J.M., Tymoczko, J.L., Strayer, L. (2013). Biokemija. Školska knjiga, Zagreb

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Virology (BM757) 15C+0S+15L

ECTS 3

COURSE OBJECTIVES: Provide knowledge about the most important viral families in order to

improve the understanding of the diversity and importance of the viruses (viri). Acquire basic skills

and knowledge required for work in virology laboratory.

COURSE CONTENT: Viral vaccines, immunological response and interferon. Biological control of

the viral diseases. Evolution and ecology of viruses. Epidemiology of viral diseases. Molecular

methods in the detection and identification of viruses and subviral agents. Viruses of the marine

ecosystems. Application of viruses in the gene therapy.

LABORATORY CONTENT: Laboratory diagnostics of the selected viruses.



Presečki, V. (2003). Virologija. Medicinska naklada, Zagreb.

All the virology at www.virology.net


The relevant scientific papers in virology.

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Quantitative Biology 2 (BM972) 30C+0S+15L

ECTS 4

COURSE CONTENT: Experimental design in the 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 the statistical

analyses. Repeated measures. Monte Carly simulation. Basics of Bayesian statistics. Statistical

models. Spatial statistics. Quantification methods.

LABORATORY CONTENT: Principles of the 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


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.


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.

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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. Fun ctioning of the marine

ecosystem. Fisheries and human impact on the marine ecosystems. Conservation.

SEMINAR CONTENT: Microbial ecology of oceans. Biogeochemical carbon cycle in the ocean.

Biogeochemical nitrogen cycle in the ocean. Ecology of the hydrothermal vents.

LABORATORY CONTENT: Examining effects of the primary production, predator impact and

influence of the key-stone species with computer models.



Kaiser, M.J., Attrill, M.J., Jennings, S., Thomas, D.N., et al. (2005). Marine Ecology: processes,

systems, and impacts. Oxford University Press, Oxford.


Kirchman, D.L. (2000). Microbial ecology of the Oceans. Wiley, New York.

Barnes, R.S.K., Hughes, R.N. (1999). Introduction to Marine Ecology. Wiley-Blackwell, New York.

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Plant Nutrients (BM860) 30C+0S+15L

ECTS 4

COURSE CONTENT: Plant tissue analysis. Nutrient assimilation and transport in plants. Effect of

the soil pH on the plant growth. The role and the significance of the mineral elements in plants.

Assimilation of the nitrogen, nitrates, nitrogen fixation, assimilation of amonium, sulphur, phosphate,

cations. Solute transport. Carbohydrate and lipid metabolism. Secondary metabolites. Laboratory

methods for the plant cultivation. Symptoms of the nutrient deficiency. Nutrients and eutrophication

of the freshwater ecosystem.

LABORATORY CONTENT: Determining the presence of individual substances in the plant cells

and tissues (calcium, phosphate, nitrate; iron and ammonium ions; ascorbic acid; carbohydrate, inulin;

and proteins). Excretion of the root acids. Identifying symptoms of the deficiency or excess of certain

elements of the plant nutrition in the hydroponic growing conditions.




Taiz, L., Zieger, E. (2010). Plant Physiology. Sinauer Associates, Inc., U.S.A.


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.

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Basics in Horticulture (BM861) 15C+0S+15L

ECTS 2

COURSE CONTENT: Classification and characteristics of the flower types (annual, biennia,

perennials, water plants, creepers). The basics of the vegetable crops growing and the most important

vegetable representatives. Reproduction of the vegetable and flower cultures. In vitro propagation

methods. Woody plant species and park architecture.

LABORATORY CONTENT: Basic methods of the reproduction in plants. In vitro propagation

methods. The architecture of the gardens and parks.



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.


Hartmann, T.H, Kester, D.E, Davies, Jr. F.T, Geneve, R.L. (2011). Hartmann and Kester’s plant

propagation: principles and practice, 8th ed. Prentice Hall, USA.

Pittenger, D.R.(2002). California Master Gardener Handbook. University of California, USA.

Healthy garden - organic, natural and free of chemicals (2010). Mozaik knjiga, Zagreb.

Scientific papers

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Embryology and Evolution of Organic Systems (BM862) 30C+0S+30L

ECTS 4

COURSE CONTENT: History of embryology; structure of the germinal cells and meiosis;

fertilization, cleavage, types of blastulas and gastrulas; neurulation; control of embryogenesis;

embryonic development of the invertebrates, vertebrates and humans; embryonic origin and

development of the organic systems; evolution and adaptations of the invertebrate’s and vertebrate’s

organic systems.

LABORATORY CONTENT:

Cells – characteristics, role and their importance

Processes of embryogenesis on the example of 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


Gilbert, S.F. (2003). Developmental Biology. 7th ed. Sinauer Associates, Inc.

Sadler, T.W. (2008). Langmanova medicinska embriologija. Školska knjiga, Zagreb.


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., USA.

http://www.amazon.co.uk/s/ref=dp_byline_sr_book_1?ie=UTF8&field-author=Kenneth+V.+Kardong&search-alias=books-uk&text=Kenneth+V.+Kardong&sort=relevancerank

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Freshwater Ecology (BM863) 45C+0S+45L

ECTS 8

COURSE CONTENT: The freshwater ecosystems – typology and worldwide distribution. Water as a

life medium. Water cycle. Nutrients cycle. The aquatic communities – phytoplankton, zooplankton,

periphyton, benthos. Adaptation of the organisms to different life conditions. Energy transfer and

trophic interactions. Pollution and eutrophication of the aquatic ecosystems. Climate and

environmental changes. Protection and revitalization of the freshwater habitats and wildlife.

LABORATORY CONTENT: Field work: sampling techniques for the analyses of water, sediment

and biocenosis. Laboratory analyses: physico -chemical properties of the water and sediment.

Qualitative and quantitative analyses of the biocenosis – phytoplankton; zooplankton; benthos;

periphyton. Saprobiological analyses. Ecological status of the freshwater habitats. Statistical analyses.



Wetzel, R. G. (2001). Limnology – Lake and River Ecosystems. 3rd ed. (selected chapters). Academic

Press, San Diego.


APHA (2001). Standard methods for examination of water and wastewater (selected chapters). Amer.

Public Health Assoc. 20th ed. Washington.

Engelhart, W. (2003). Was lebt in Tümpel, Bach und Weiher? (selected chapters). Kosmos, Stuttgart.

Streble, H., Krauter, D. (2002): Das Leben im Wassertropfen (selected chapters). Kosmos, Stuttgart.

16

Molecular Ecotoxicology (BM864) 30C+0S+15L

ECTS 4

COURSE CONTENT: Pollution and contamination; Xenobiotics; mechanisms of the xenobiotics

entering the biological systems; first pass effect; defence mechanisms; reactions of biotransformation;

first phase of the xenobiotics biotransformation; second phase of the xenobiotics biotransformation;

third phase of the xenobiotic biotransformation; elimination of the xenobiotics; xenobiotic induction

and inhibition; hormonal disruptors; xenoandrogens; xenoestrogens; vitelogenin; oxidative stress as a

result of the physical factors and the exposure to the xenobiotics; xenobiotics effects on the metabolic

pathways; molecular biomarkers; p-glycoprotein and MXR; biomarkers of the exposure and effect;

xenobiotic effect on the markers of the metabolic activity and health condition.

LABORATORY CONTENT: Xenobiotic exposure methods; the in vivo test; the primary cell culture

tests; preparation of the postmitochondrial and microsomal fraction; inhibition of the cholinesterase as

a marker of the effect of the organophosphates, carbamates and detergents; total cytochrome P450

and ethoxyresorufin-o-deethylase induction as a marker of the exposure to polycyclic aromatic

hydrocarbons, glutathione concentration; catalase and glutathione peroxidase activity as a marker of

the oxidative stress; metabolic markers; metallothionein concentration as a marker of the exposure to

the heavy metals.



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.


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.

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Scientific Research Practice 1 (BM865) 0C+0S+30L

ECTS 2

FIELD WORK CONTENT: Preparations for the field work (appropriate clothing and footwear,

security measures and safety, keeping a field journal). Fieldwork: exploring and mastering the

methods of sampling, sample collection, conservation and labelling of samples.

LABORATORY WORK CONTENT: Introduction to laboratory routines. Keeping laboratory

journal. Introducing and learning about the laboratory techniques. Participation in the laboratory

work. Independent work on the selected tasks.

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Immunology (BM966) 15C+0S+15L

ECTS 3

COURSE CONTENT: Properties and overview of the 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 the T lymphocytes, effector mechanisms of the cell-mediated and humoral

immunity, immunological tolerance and autoimmunity, immunity to tumours, hypersensitivity

disorders.

LABORATORY CONTENT: Immunization of experimental animals. The lymphatic system of the

rodents. Basic immunohistochemical methods. Isolation of the antibodies. ELISA. Western blotting.

Isolation of the lymphocytes. Lymphocyte culture. Immunological reactions. Immunosuppression.



Abbas, A.K., Lichtman, A.H., Pillai, S. (2012). Cellular and Molecular Immunology. Elsevier

Saunders, USA.


Delves, P.J., Martin, S.J., Burton, D.R., Roitt, I.M. (2011). Roitt's Essential Immunology. Wiley-

Blackwell, United Kingdom.

Janeway, A.C. (ed.) (2001). Immunobiology. Garland Publishing, New York.

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Developmental Biology of Plants (BM967) 30C+0S+15L

ECTS 3

COURSE CONTENT: Life cycle of the seed plants and gametogenesis: microsporogenesis and

megasporogenesis. Fertilisation. Embriogenesis. Postembrionic development. Germination. Cell and

tissue differentiation during the development of the 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 the methods employed in

the plant development investigation: anatomical methods, molecular analysis of the gene transcripts

and proteins, physiological methods.

LABORATORY CONTENT: During the practice students are going to study some of the selected

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 the other students.



Raghavan, V. (2000). Developmental Biology of Flowering Plants. Springer-Verlag, New York,

Berlin, Heidelberg.


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.


Taiz, L., Zeiger. E. (2010). Plant Physiology. 5th edition. Sinauer Associates Inc., Publishers,


Biswal, B., Krupinska, K., Biswal, U.C. (2013). Plastid Development in Leaves during Growth and

Senescence. Springer Science + Business Media Dordrecht.

Nooden, 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 a student.

20

Plant Molecular Ecophysiology (BM968) 15C+0S+15L

ECTS 3

COURSE CONTENT: The review of the biotic and abiotic ecological factors; molecular mechanisms

of the signal perception in the plant cell and physiological response; changes of gene expression

caused by changes of temperature, light or by drought and anoxia; the effect of the air pollutants on

the plant physiological status: sulphur dioxide, NOx, ozone; plant tolerance to heavy metals;

molecular biology of the oxidative stress in plants; function and regulation of the enzymes in

Halliwell-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 study some of the topics on their own.

EXAMINATION METHOD: written and oral


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.


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.

21

Animal Behaviour (BM969) 30C+15S+0L

ECTS 3

COURSE CONTENT: An introduction to the animal behaviour (what is behaviour, the history of the

study of animal behaviour, proximate and ultimate causes). Mechanisms of behaviour: the role of the

nervous system (innate vs. learned behaviour, imprinting). The motivation and organization of

behaviour (the internal and external mechanisms that control animal behaviour). The development of

behaviour (natural selection, learning). Communication (living in groups, social communities,

ritualization). Foraging behaviour (optimal foraging theory, decision-making). Avoiding predators

(primary and secondary strategy). Reproductive behaviour (sexual selection, conflicts, mating

systems, parental care and altruism). Human behaviour.

LABORATORY CONTENT: -

SEMINAR CONTENT: During the seminar each student focuses on one particular animal behaviour

topic/research paper and presents it to the other students.



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, Edinburgh.


Halliday, T. (1994). Animal Behaviour. A Blanford book, London.

Miller, S., Harley, J.P. (1996). Zoology. WCB McGraw-Hill Companies, Inc , Boston.

Wilson, E.O. (2000). Sociobiology, The new synthesis. 25th ed. The President and Fellows of Harvard

College.

22

Ecology of Terrestrial Habitats (BM970) 45C+0S+45L

ECTS 8

COURSE CONTENT: What is a terrestrial habitat and what organisms live there. The ecological

factors that influence life of the organisms in a terrestrial habitat. Solar energy on the Earth surface.

Global atmospheric circulation. Macroclimate – parameters, their spatial and temporal variability.

Water cycle. Lithology and relief as the environmental factors. Topoclimate. Soil as a precondition

for the terrestrial habitat formation and maintenance. Pedosphere, pedogenesis, pedosystematics –

basic terms. Biotic factors. Life strategies of the terrestrial organisms. Matter and energy cycles in a

terrestrial habitat. Basic types of the terrestrial habitats (biomes) and their correlation with the

macroclimate. Spatial distribution of the biomes on the Earth and their dynamics in time (global

paleoecological aspect). Bioclimatic zones of Europe and Croatia. Edaphic factors and

biogeocoenosis differentiation within the bioclimatic zones. Spatio-temporal relation between the soil

and vegetation. Classification of the terrestrial habitats. Overview of the particular habitat types (on

the global, regional and local level): 1) dominant abiotic factors, 2) soil and vegetation, 3) typical

organism representatives and their adaptations to the habitat and interactions with the habitat, 4)

genesis and ecological stability, 5) anthropogenic influence. Terrestrial habitat boundaries.

Environmental gradients and intermediar between the terrestrial habitats and between the terrestrial

and marine/freshwater habitats. Anthropogenic terrestrial habitats. Levels of bioecological details in

the terrestrial habitat research. Overview of the research themes and methods. Practical examples.

LABORATORY CONTENT : Recognition of the major types of the terrestrial habitats on the global

level (biomes), recognition of the terrestrial habitats in Croatia, determination of the expected habitat

type for the set environmental factors (and vice versa), Overview of the different sampling methods

for the particular organism groups in different habitats, qualitative and quantitative field data analysis.



Chapin, F.S. III, Matson, P., Mooney, H.A., Chapin M.C. (2002). Principles of Terrestrial Ecosystem

Ecology. Springer-Verlag, New York.


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., 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.

23

Scientific Research Practice 2 (BM971) 0C+0S+60L

ECTS 2

FIELD WORK CONTENT: Preparations for the field work (appropriate clothing and footwear,

security measures and safety, keeping a field journal). Fieldwork: exploring and mastering the

methods of sampling, sample collection, conservation and labelling of samples.

LABORATORY WORK CONTENT: Introduction to the laboratory routines. Keeping a laboratory

journal. Introducing and learning about the laboratory techniques. Participation in the laboratory

work. Independent work on selected tasks.

24

ELECTIVE COURSES

25

Modelling 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; a review of matrix algebra;

the 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 create models on the basis of specific

research examples, i.e. on real data.



Mooney, D., Randall, S. (1999). A Course in Mathematical Modeling. Dover Publications, Mineola


Bender, A.E. (2000). An Introduction to Mathematical Modeling. Dover Publications, Mineola.

Britton, F.N. (2003) Essential Mathematical Biology. Springer Verlag, London.

26

Plant Toxicity Tests (BMZ73) 15C+0S+15L

ECTS 2

COURSE CONTENT: Test types; test organisms; principles of the laboratory toxicity testing;

individual display of the metal and xenobiotic toxicity of the algae, which require special attention in

their toxicity and/or representation in industry and environment; the source and the amount of the

xenobiotics in the water;

Duckweed test – monitoring of the plant growth (fresh and dry weight, total surface of the plants); the

photosynthetic pigments content and the amount of proteins to determine toxicity.

LABORATORY CONTENT: Duckweed test; determination of the metal toxicity and xenobiotics to

Lemna minor and Lemna gibba (photosynthetic pigment content and inhibition of the growth);

statistical analysis of the obtained results, evaluation and comparison with the literature data.



Rai, L. C., Gaur, J.P. &Soeder, C.J. (1994). Algae and water polution. E. Schweizerbart, Stuttgart.

OECD guidelines for the testing of chemicals – Revised proposal for a new guideline 221 Lemnasp.

Growth Inhibition Test (http://www.oecd.org/dataoecd/16/51/1948054.pdf).


Naumann, B., Eberius, M., Appenroth, K.J. (2007). Growth rate based dose – response relationships

and EC-values of ten heavy metals using the duckweed growth inhibition test (ISO 20079) with

Lemnaminor L. clone St. Journal of Plant Physiology. Volume 164, Issue 12

(http://www.sciencedirect.com/science/article/pii/S0176161706003154).

Landolt, E. (1986). The family of Lemnaceae – a monographic study (Vol. 1 and 2).

Veroffentlichungen des Geobotanischen Institutes der Edig. tech. Hochschule, StiftungRübel. Zürich.

http:/www.mobot.org/jwcross/duckweed/education.htm.

27

Biochemical Mechanisms of Toxicity (BMZ74) 15C+0S+15L

ECTS 2

COURSE CONTENT: The basic properties of the biotransforming enzymes; biotransformation and

metabolism; stereochemical approach in the xenobiotic biotransformation; the first and the second

biotransformation phase; nomenclature of the enzymes included in biotransformation; distribution of

the biotransformation enzymes in the 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: During this seminar the students study the specific examples from the

toxicological practice.



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.


Stenersen, J. (2004). Chemical Pesticides: Mode of Action and Toxicology. CRC press.

28

Molecular Mechanism of Oxidative Stress (BMZ75) 15C+0S+15L

ECTS 2

COURSE CONTENT: Oxygen and reactive oxygen species. Damaging of the biomolecules and the

cell structures in the conditions of the oxidative stress. Oxidants and cell signalling. Non-enzymatic

antioxidants: ascorbic acid, glutathione, vitamin E, carotenoids, phenolics. Antioxidative enzymes:

catalase, peroxidase, superoxide dismutase, glutathione reductase and monodehydroascorbate

reductase. The Halliwell-Asada cycle.

LABORATORY CONTENT: Determination of the activities of the antioxidative enzymes.

Determination of α-tocopherol by the thin-layer chromatography. Determination of the photosynthetic

pigments concentration. Photosystem II efficiency measurement by the saturating pulse method.

Experimental induction of the oxidative stress.



Bradamante, V., Lacković, Z. (eds.) (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.


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,


Inze, D., Van Montagu, M. (eds.) (2002), Oxidative stress in Plants. Taylor & Francis, London, New

York.



areas, depending on the individual interests of students.

29

Enzyme Kinetics (BMZ76) 15C+0S+15L

ECTS 2

COURSE CONTENT: The basic principles of the enzyme catalysis; the basic equations of the

enzyme kinetics; the phase of the enzymatic reaction; the Michealis-Menten model; determination of

the kinetic constants Km and Vmax; speed measurement of the enzymatic reactions; the influence of

pH on the enzymatic catalysis; types of inhibition of the enzyme reactions; the effect of the inhibitors

on the kinetic constant; allosteric enzyme kinetics, stereochemistry of the enzyme reactions; kinetics

of the enzyme under physiological systems; regulation of the metabolic processes by the kinetics of

some enzymes.

LABORATORY CONTENT: The initial velocity of the selected enzyme reactions in the presence of

the inhibitors is measured and compared with the uninhibited velocity. The kinetic constants of the

inhibited and uninhibited enzyme will be calculated, and used to conclude about the type of the

inhibition, planning of the enzyme assays; determining the optimum conditions for the enzymes of the

physiological systems.

SEMINAR CONTENT: -



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.


Review articles and scientific monographs.

30

Biomolecules in Food (BMZ77) 15C+15S+0L

ECTS 2

COURSE CONTENT: Introduction. Reaction between some food components (carbohydrates, lipids,

proteins, enzymes, vitamins, colour and flavours, inorganic compounds). Biomolecular interactions;

biological role of the individual active molecules in foods; secondary metabolites of the plants;

damage caused by the action of free radicals; antioxidant properties of the natural metabolites;

assessment of the protective role of the phytochemicals; oxidative stress and disease; the role of the

diet in the prevention of various diseases; the role of the diet in the gene expression. Polyphenols.

Terpenes. Hydrococolloids. Glucosinolates. Phospholipids. Vitamins.

LABORATORY CONTENT: -

SEMINAR CONTENT: Written report and presentation on chosen topic.

EXAMINATION METHODS: oral


Belitz, H.D., Grosch, W., Schieberle, P. (2004). Food Chemistry. Springer-Verlag, Berlin.

Fennema, O.R. (1996). Food Chemistry. Marcel Dekker, Inc, New York


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.

31

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 the initial plant material,

impact of the physical factors on the 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 the plant cell and tissue culture

on genetic engineering and breeding systems: genetically transformed plants, vegetative

micropropagation. Impact in biotechnology: clone production, bioproduction of the different

substances.

LABORATORY CONTENT: Starting up the culture: media composition, explants selection, surface

sterilization of the initial plant material, manipulation in the sterile chamber, callus production,

subculturing. In vitro regeneration.



Jelaska, S. (1994). Kultura biljnih stanica i tkiva. Školska knjiga, Zagreb.



Evans, D.A., Sharpe, W.R., Ammirato, P.V.,Yamada, Y. (1983). Handbook of plant cell culture.

Volume 1: Techniques for propagation and breeding. MacMillan Publishing Co., New York –

London.

Sharpe, W.R., Evans, D.E.,, Ammirato, P.V., Yamada, Y. (1984). Handbook of plant cell culture.

Volume 2: Crop species. MacMillan Publishing Co., New York – London.

Ammirato, P.V., Evans, D.E., Sharpe, W.R., Yamada, Y. (1984). Handbook of plant cell culture.

Volume 3: Crop species. MacMillan Publishing Co., New York – London.



32

Genome Evolution (BMZ79) 15C+15S+0L

ECTS 2

COURSE CONTENT: Genome size in different organisms and evolution. The number of

chromosomes in eukaryotes, noncoding DNA and genome size. Genetic control of the cell size.

Experimentally induced changes in the genome size. Natural selection and genome size.

Mitochondrial DNA. Evolution of the plastid DNA. B-chromosomes. Sex chromosomes. Moderated

repetitive DNA. Chromosome elimination. Phylogenetic analysis.

SEMINAR CONTENT: Students choose topics of their interest, prepare presentations and present

them to the other students.



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.


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.

33

Plant Pathoanatomy (BMZ80) 15C+0S+15L

ECTS 2

COURSE CONTENT: Plant anatomy. Abiotic and biotic factors as causes of the pathological

changes in the cell structure and plant tissues. Pathological changes in the 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.



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.


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.

34

Supramolecular Structures (BMZ81) 15C+15S+0L

ECTS 2

COURSE CONTENT: Lectures are presented in the programme "Chime" from a computer. The Web

materials that will be used in this course are from the renowned 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 on the selected topics are prepared and presented by the students,

according to their personal preference.

EXAMINATION METHODS: oral


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


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

http://www.rcsb.org/pdb/home/home.do

http://bcs.whfreeman.com/berg7

http://bcs.whfreeman.com/biochem6

http://www.whfreeman.com/biochem5

http://www.clunt.edu/BioDev/omm/exhibits.htm

http://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/

35

Plant Microtechnique and Microscopy (BMZ82) 30C+0S+15L

ECTS 2

COURSE CONTENT: Introduction to the plant microtechnique. The plant specimens sampling

procedures. Fixation. Dehidratation. Infiltration and embedding. Microtome manipulation.

Histochemical and cytochemical reactions on the 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 the different microscopy techniques in the permanent slide

analysis.

EXAMINATION METHODS: written, practical and oral


Ruzin, S.E. (1999). Plant Microtechnique and Microscopy. Oxford University Press, NewYork,

Oxford.



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. Principles 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.



36

Plant Stress Physiology (BMZ83) 15C+15S+15L

ECTS 2

COURSE CONTENT: Abiotic stress: shortage of water and drought; temperature stress; increased

salt content in the soil; anoxia and hypoxia; light and UV stress; air and water pollution.

Biotic stress: competition between plant species; response to the predator and pathogen attack.

Pollution impact on the plants (heavy metals, atmospheric pollution and xenobiotics); resistance

mechanisms; pollution of water and soil; the use of chemicals in agriculture.

SEMINAR CONTENT: Students individually write and present some interesting topics on plant

stress physiology.

LABORATORY CONTENT: During the course students study some of the topics on their own,

through practical work in the laboratory.



Teiz, L., Zeiger, E. (2010). Plant Physiology. SinauerAssoc. Inc., Sunderland, Massachusetts.


Original scientific papers

Ambriović Ristov, 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.

37

Entomology (BMZ88) 15C+15S+15L

ECTS 2

COURSE CONTENT: Introduction to the entomology. Present insects as the most important group of

animals in the world. Explain the reasons: (a) the immense diversity and flexibility; (b) the ratio of

insects to humans. Explain the relationship between humans and insects through the fundamental

determinants of the specialized entomology: the transmission of diseases (medical entomology), food

production (agricultural entomology), production of wood products (forest entomology), molestants

(urban entomology).

SEMINAR CONTENT: Students choose some of the selected topics in this field, prepare the topic with

the help of the lecturer and present it to the other students. It also provides an overview video that follows

the content of the programme.

LABORATORY CONTENT: A brief overview of the morphological and anatomical characteristics of

insects. Training to determine insects: ordo species, using the keys and computer programmes.

Sampling methods for insects, preparation and creation of entomological collection. Design of

entomological research.

EXAMINATION METHODS: entomological collection and oral exam


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.


Peddigo, L. P. (2002). Entomology and Pest Menagment. Prentice Hall.

Romoser, W. S., Stoffolano, J. G. (1998). The Science of Entomology. WCB Mcgraw – Hill

Companies.

38

Ornithology (BMZ89) 15C+15S+0L

ECTS 2

COURSE CONTENT: Anatomy and morphology of the birds. Behaviour. Territoriality, colony,

breeding, nests, incubation of eggs, chickens, 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 have to prepare and present a seminar. Seminar has to contain a

description of one taxon of the birds (with biological, ecological and zoographical characteristic,

protection and IUCN status). If the taxon is endangered, students have to present causes of threats and

protection measures that are taken. Seminar topics may be linked to the general characteristics of birds

as the fly adjustments, the evolution of birds, migration, behaviour, etc.



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. (eds.) (2013). Crvena knjiga ptica Hrvatske. Ministarstvo

zaštite okoliša i prirode i Državni zavod za zaštitu prirode, Zagreb.

Kralj, J., Barišić, S., Tutiš, V.,Ćirković, D. (eds.) (2013). Atlas selidbe ptica Hrvatske. HAZU, Zavod

za ornitologiju Zagreb.

Bibby, C.J., Burgess, N.D., Hill, D.A. (1992). Bird Census Techniques. London: Academic Press.


Podulka, S., Rohrbaugh, R.W.Jr., Bonney, R. (eds.) (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.

Mikuška, 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.

39

Biogeographic Inventory (BBZ54) 15C+0S+15L

ECTS 2

COURSE CONTENT: Repetitorium of biogeography as a discipline which studies the distribution of

biodiversity in space and time. Creating biodiversity inventory lists. Qualitative (present/absent) and

quantitative (population density) data. Cartographic aspect of the biodiversity inventory. Location

coordinates. MTB and UTM map. The field data geocoding techniques. Connection with the

geoinformation systems. Relation with the spatial distribution of the environmental factors. Direct

mapping vs. mapping with the numerical model. Mapping of the habitat and vegetation types. Map

scale and minimal mapping area. Choice of the classification standard and the thematic resolution.

Usage of the data obtained from the remote sensing: expert interpretation and computer classification.

Preparation of the work maps and field verification. Cartographic principles (colours, symbols). Map

of the real, potential and climazonal vegetation. Time aspect of the biogeographic data. Time series of

the thematic maps and biomonitoring. Merging data from different sources. Methods for the spatial

analysis of the biogeographic data. Cartographic derivative of the basic data of the species, vegetation

and habitat spatial distribution.

LABORATORY CONTENT: Determination of the exact geographic position of the location. Filling

field list and noting field data. Editing field data in a form adequate for the further analysis.

Distribution mapping of the different species, vegetation and habitats. Graphic editing of the thematic

map. Interpretation of the existing cartographic content.



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.


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. (eds.) (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. et al. (2010). Botanički važna područja Hrvatske. Školska knjiga, Zagreb.

Sutherland, W.J. (2010). Ecological Census Techniques – a handbook, Cambridge University Press,

New York.

40

Underwater Biological Research (BMZ93) 0C+0S+30L

ECTS 2

COURSE CONTENT: -

LABORATORY CONTENT: Sampling of the bottom and sediment for the purpose of invertarisation;

water column sampling; application of the IR camera for the inspection and research; usage of the

sonar; creating sampling sketch and profile; diving with the autonomous diving gear.

EXAMINATION METHODS: Written and oral


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.


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.

41

Geoinformatics in Biological Research (BMZ94) 15C+0S+15L

ECTS 2

COURSE CONTENT: The definition and the scope of geoinformatics; organization and display of the

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 the raster and vector themes; digital relief model and

geomorphometric derivatives, spatial interpolations, spatial modelling; physical fundamentals of the

remote sensing; orthophoto; multispectral scanners; the Earth surface spectral signature; passive and

active sensors; the major satellite platforms; spatial, temporal, spectral and thematic resolution;

subjective interpretation and delineation; controlled and uncontrolled automatic classification; spectral

channels as continuous estimators of the biological and environmental variables spatio-temporal series

and monitoring on the large area; virtual sampling and preparation of the matrix for the numerical

analysis; significance of the geoinformatic technologies in the biological research with the

demonstration on the practical examples; the overview of the commercial and freely available

geoinformatic software packages.

LABORATORY CONTENT: Basic operations with the vector and raster spatial data, usage of GPS

devices; autonomous making of the thematic digital map; application of the basic geostatistical

methods, the geomorphometric analysis and the data analysis obtained with the remote sensing in the

context of the biological research.



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.


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.

42

Molecular Genetics (BM758) 30C+0S+15L

ECTS 4

COURSE CONTENT: Molecular basis of the inheritance: DNA and RNA as genetic material and the

flow of the genetic information (basic information about replication, transcription, reverse

transcription and translation). Informational content of the nucleic acids (primary, secondary and

tertiary structure), genetic code and genes. Genome projects. Procaryotic and eukaryotic genome.

Classification of the genomic DNA sequences: significance and functionality of the coding and non-

coding sequences, classification according to the copy number. "DNA identity", minisatellites and

microsatellites. The genome size and the C-value paradox. Significance of the reorganizations in

genome evolution, principles of the recombination processes. Transposable elements and their role in

the genome evolution. DNA in the eukaryotic genome: nucleosomes, chromatin and chromosomes.

Genome compartments, euchromatin and heterochromatin. Centromeres and telomeres, epigenetic

inheritance. Transcription in the regulation and formation of a genome: RNA mechanisms. The basic

characteristics of the human genome, isohore organization and comparisons with the sequenced

genomes of the other species. Significance of the structural organization of the interphase nucleus in

the genome function.

LABORATORY CONTENT: Isolation of the eukaryotic genomic DNA. Restriction analysis with

endonucleases, electrophoretic separation of the fragmented DNA and purification of the fragments of

interest from agarose gels. Cloning: preparation of the vector, ligation, preparation of the competent

cells and transformation. Selection of the transformed bacterial clones on selective media, minipreps

of the plasmid DNA and selection of the clones of interest. Southern hybridization analysis.

Introduction to the computer analyses of the DNA sequences (restriction sites, GenBank search,

alignments, basic phylogenetic analysis and similar).



Tamarin, R.H. (1999). Principles of genetics. 6th edition. McGraw-Hill Companies, Inc.

Blackburn, G. M., Gait, M. J. (1996). Nucleic acids in chemistry and biology. 2nd edition. Oxford

University Press.


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.

Additional literature will be selected from most recent review articles in the field and the 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 the vegetative and generative organs with the emphasis on

the evolutionary and ecological context. Ontogeny and phylogeny of the tree species. Strategies of the

reproduction and dissemination. The position of the woody species in the plant evolution and

systematics. Paleodendrology. Exchange of the 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 a retroactive

monitoring of the habitat conditions. Woody species as edificators of the forest ecosystems. Global

ecological amplitude of the trees and forests. Variability of the forests in space and time.

SEMINAR CONTENT: The successional and degradation phases of the 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.



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.


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 the other sciences. Division of geology. Genesis,

structure, causes and consequences of the internal and external dynamics of the Earth. Review of the

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 (the 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 learn about the different models and materials about the main topics

of this course. Furthermore, students choose and present one of the selected topics.



Briggs, D.E.G., Crowther, P.R. (2003). Paleobiology II. Blackwell.

Herak, M. (1990). Geologija. Školska knjiga, Zagreb.


Sremac, J. (1999). Opća paleontologija. Skripta, PMF.

McKerrow, W.S. (1981). The Ecology of Fossils – An Illustrated Guide. MIT Press.

Milsom, C., Rigby, S. (2010). Fossils at a Glance, 2nd edition.Wiley-Blackwell, London.

Plummer, C.C., McGreary, D. Carlson, D.H. (1999). Physical Geology. 8th edition. The McGraw-Hill

companies, Boston.

Clarkson, E.N.K. (1998). Invertebrate Palaeontology and Evolution, 4th edition. Blackwell Science

Ltd., London.

Benton, M.J. (2000). Vertebrate Palaeontology, 2nd edition. Blackwell Science Ltd., London.

Retallack, G.J. (2001). Soils of the Past. An Introduction to Paleopedology. 2nd edition. Blackwell,

Oxford.

Stewart, W.N., Rothwell, G.W. (1993). Paleobotany and the Evolution of Plants, 2nd edition.

Cambridge University Press, Cambridge, UK.

45

Protection and Revitalization of Aquatic Ecosystems (BMZ97) 15C+15S+0L

ECTS 2

COURSE CONTENT: Water ecosystems - structure and function. Methods for the trophic state

qualification. Problems of the 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 the water ecosystems.

SEMINAR CONTENT: Restoration methods – hypolimnetic withdrawal, precipitation of phosphorus

and inactivation, sediment oxidation, sediment removal, hypolimnetic aeration, the procedures to

control plant biomass – harvesting, biomanipulation. Lake restoration – case studies.



Wetzel, R. G. (2001). Limnology – Lake and River Ecosystems. 3rd ed. Academic Press, San Diego.


Jørgensen, S.E., Vollenweider, R.A. (eds.) (1989). Guidelines of Lake Management: Vol. 1, Principles

of Lake Management. International Lake Environment Committee Foundation. Shiga.

46

Avian Metabolism (BMZ98) 15C+15S+0L

ECTS 2

COURSE CONTENT: A survey of the special metabolic demands in birds. 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 the eggs laying and hatching.. The role of the n-3 PUFA for

the metabolic and energetic changes. Comparison of some aspects of avian metabolic adaptations with

human pathologic states like obesity and diabetes type 2 for better understanding of the biochemical

basis of their development and help in their efficient treatment.

SEMINAR CONTENT: -



Lewis, S. (2004). Avian Biochemistry and Molecular Biology. Cambridge University Press, Cambrige,

United Kingdom.


Schat, K.A., Kaspers, B., Kaiser, P. (2014). Elsevier Ltd., United Kingdom.

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