1.UNIVERSITY OF UDINEMASTER COURSEIN PLANT AND ANIMAL BIOTECHNOLOGY(IN ENGLISH)

2. Master Course in Plant and Animal Biotechnology Objective Biotechnology is worldwide regarded as a strategic field for social development and progress. This view isparticularly true in a region that retains Life Science one of the avenues for development and thereforemade substantial structural investments in recent past. This process created a large and stimulatingbackground where a graduated in Plant and Animal Biotechnology finds perfect integration. This course hasthe ambitious purpose of the education of those who will have the responsibility to move up biotechnologyfrom the present pioneer status to mass production and it is therefore focused on the extreme care ofindividual student potentials in order to provide the future leadership for a yet-to-be-exploited field. This course aims to attract students wishing to apply in their professional activity the concepts andtechnologies that have characterized one of the fastest scientific advancing field in the last twenty years.The student will be the focus of the faculty activity devoted not only to concept transfer, but also todevelopment of the cultural maturity that leads to blend a critical approach together with permeability to newinformation, whose rapid accumulation is a characteristic of this field. The build up of such a complexcultural sensibility will be achieved through new and sometime non-conventional teaching approaches andthe development of practical/theoric projects by which student resources will be exploited. 3. Master Course in Plant and Animal Biotechnology Objective At graduation, the student in Plant and Animal Biotechnology not only will have acquired a large andcomprehensive knowledge of the notions relevant to specific scientific field, but he/she will also haveidentified and practiced the peculiar ways to acquire, elaborate and analyze information in this field, as wellas the ability to synthesize and expose the results of the analysis. Thanks to the topics treated and theteaching models used, the acquired professional will be recognizable in an international context, as it isnecessary for this particular field. A relevant and specific characteristic of this course will be the continuousstimulus to the abilities to project and organize: a central point in the formation of the graduate will be theunderstanding of the need to approach non-obvious context problems and to provide innovative and originalanswers. The course will include contacts with various components of international research through participation inseminars, in order to permeate the supranational dimension of the context in which the professionalgraduate will have to move. The educational objectives will be achieved through activities that includelectures, exercises and practical laboratory training. Students personal involvement will be stimulatedthrough the preparation and presentation of short reports or projects and the preparation of the thesis. Thetraining activities will be fully developed in English, placing the course in an international context. 4. Master Course in Plant and Animal BiotechnologyAdmission criteria The application and admission procedure differs for Italian university students and international students. Inorder to be eligible for admission to the Master programme, international students must have completed atleast a relevant Bachelors education with a major in biotechnology, agricultural, or veterinary science.Admission requisites will be evaluated individually; detailed information may be found in the F.A.Q. page ofthe Master programme web site (http://pab.uniud.it). The master course develops over two full academic year (four semesters) with a total of 120 ECTS (60ECTS each academic year). 5. Master Course in Plant and Animal Biotechnology First yearBiotechnology and genetics legislation (6 credits)Biotechnology in animal reproduction (8 credits)Genome analysis and bioinformatics (6 credits)Molecular nutrition of plants and animals 1(first module) (6 credits)Molecular nutrition of plants and animals 2 (second module) (6 credits)Plant-pathogen interaction (6 credits)Plant biotechnology (8 credits)Protein structure and function (6 credits)Animal physiology and welfare or Plant cell physiology and tissue culture (6 credits)Credits: degree courses are usually structured in credits (crediti formativi universitari - CFU). A university credit generally corresponds to 25 hours of global work perstudent, time for personal study included. The average workload of a full time student is conventionally fixed at 60 credits/year. 6. Master Course in Plant and Animal Biotechnology Second yearGenetic resources (6 credits)Food safety (8 credits)12 credits chosen from among the following:Principles of crop breeding (6 credits)Tree genetics and breeding (6 credits)Livestock Production 1 (6 credits)Livestock Production 2 (6 credits)Other Activities (26 credits)Training activities (2 credits)Final exam (24 credits)Credits: degree courses are usually structured in credits (crediti formativi universitari - CFU). A university credit generally corresponds to 25 hours of global work perstudent, time for personal study included. The average workload of a full time student is conventionally fixed at 60 credits/year. 7. Syllabus for classes in the Master programme in Plant and Animal BiotechnologyProgrammeBiotechnology in Animal ReproductionThe aims of the course are to provide the essential knowledge for understanding and manipulating the biology of reproduction of domestic and laboratory animals. The course will also address major biotechnology applied to animal reproduction.The estrous cycles of females and, in particular, the techniques for synchronization and superovulation of the embryos donor and recipient females will be described. During the course gametogenesis, in vivo fertilization, embryonic and fetal development will also be described.The procedures for in vivo and in vitro gametes and embryo collection, for in vitro oocyte maturation and fertilization, will be also treated in both domestic and laboratory animals. The course will deal with techniques for oocyte nuclear transfer (cloning), for obtaining transgenic animals and their possible use in animal production and biomedicine, for the embryo and sperm sexing, for the cryopreservation of gametes and embryo, the cry banking of the genetic resource, and the principal pathologies due to the application of biotechnologies of reproduction (epigenetic defects).Laboratory activity on rabbit superovulation and embryo collection and evaluation will be also organized. 8. Syllabus for classes in the Master programme in Plant and Animal Biotechnology ProgrammeGenome analysis and bioinformaticsThe course focuses on the use of Next Generation Sequencing Technologies for analyzing genome structure, diversity and function and on the bioinformatics tools required for these analyses, taking a problem-solving approach. The goal is to provide students with the basic skills required to utilize the vast amount of information which is currently being produced in plants and animals using sequencing technologies and to apply these methods to the biological problems of their interest. The course has a strong hands-on component with informatics laboratory sessions and tutorials aimed at familiarizing students with the Linux operating system, simple scripting and the different software packages used for the analysis of NGS data.The topics addressed in the course are:Introduction to eukaryotic genome structure. Next Generation Sequencing Technologies: technical specificities, pros and cons. Analytical pipelines for NGS data: from the sequencer to the scientist. Quality checking and filtering of sequences. Assembling genomes de novo. Gene prediction methods and algorithms. Aligning sequences against a reference genome: principles and softwares. Detecting single nucleotide polymorphisms. Detecting structural variants: paired end mapping and depth of coverage approaches. Estimating linkage disequilibrium and inferring haplotypes. Detecting rare variants in populations. Genotyping by sequencing methods. Gene expression analysis through RNA sequencing: detecting transcripts and estimating their abundance. SmallRNA analysis: detecting and estimating abundance of siRNA, miRNA and ta-siRNAs. Detecting epigenetic variation: analysis of DNA methylation through bisulfite sequencing; analysis of chromatin modifications through ChIP sequencing. Going from a reference genome sequence to a reference pan-genome sequence. 9. Syllabus for classes in the Master programme in Plant and Animal Biotechnology ProgrammeMolecular nutrition of plant and animals 1 (first module)The students will learn basic and applied concepts of plant nutrition; in particular mechanisms and regulatory principles of nutrient uptake and plant response to abioticstresses will be elucidated considering approaches from biochemistry and molecular biology; the role of secondary metabolites in plant adaptation to adverse conditionswill also be considered. Applied objectives are the identification of processes contributing to nutrient efficiency and stress tolerance in crop plants, and possibleimprovements by biotechnological approaches.Definition of stress. Importance of mineral nutrition. Chemistry and biochemistry of nutrients in the soil-plant system; exogenous and endogenous factors affectingnutrient availability; biochemical interactions at the soil-plant interface (the rhizosphere). Nutrient acquisition: physiological, biochemical and molecular aspects.Mechanisms for the acquisition of the main macro- and micro-nutrients. Effects of different kinds of stresses on plants; physiological, biochemical, genetic andmolecular aspects of adaptation (tolerance and resistance). Adaptive responses of plants to nutritional disorders and to adverse soil conditions (acidic soils, alkalineand calcareous soils, water stress, water logging, flooding and presence of heavy metals).Physiological role of secondary metabolites. Chemistry, biochemistry and biosynthesis of phenolic compounds, isoprenoids, alkaloids, terpenoids, lipids, S- and N-containing secondary metabolites. Production and release in the soil of metabolites involved in signal exchange between plant and soil micro-organisms.Genetic engineering of plant secondary metabolism for food and non-food application.The course will include lectures and laboratory practices on the physiological, biochemical and molecular characterization of the main mechanisms involved in mineralnutrition of plants and in their response to abiotic stress. 10. Syllabus for classes in the Master programme in Plant and Animal Biotechnology ProgrammeMolecular nutrition of plant and animals 2 (second module)- Rudiments of animal nutrition: chemical composition and analysis of feed;- Rudiments of digestion physiology and metabolism of feeds;- Energy, protein, minerals and vitamins requirements of animals;- Diet formulation;- Feeding techniques;- Useful laboratory techniques in structural and functional genomics;- Nutrigenetics;- Monogenic diseases in animals;- Nutrigenomics and pharmacogenomics;- Cellular nutrient homeostasis, proliferation and apoptosis;- Roles for nutrients in signal transduction, gene expression and proteolysis;- Nutrition and immune function;- Nutrition and stress response;- Molecular mechanisms of action of bioactive compounds in monogastrics and ruminants;- Molecular mechanisms of food allergy;- Ruminal and intestinal metagenomics;- Introduction to proteomics and metabolomics;- Bioinformatics laboratory: statistical analysis and data mining in animal nutrigenomics experiments;- Consultation of useful genetic databases in animal science. 11. Syllabus for classes in the Master programme in Plant and Animal BiotechnologyProgrammePlant biotechnologyThe course will include an introduction to theoretical aspects in Plant Biotechnology with emphasis on practical application.Overview of the main issues relating to cell culture. Direct and indirect organogenesis, somatic embryogenesis. Use of protoplasts andhaploids culture in Agricultural Biotechnology. Principles of plant transformation, techniques and applications. Dominant and co-dominant molecular markers. Analysis of electropherograms of SSR and AFLP markers. Development of molecular marker datasetswith specific software, descriptive analysis, calculation of genetic distances with different indices (Nei, Fst), PCA, construction ofdendrograms. Construction of genetic and physical maps, practical examples and applications. Molecular marker assisted selection(MAS). Cytogenetics: In Situ Hybridization. Sequencing techniques and sequence analysis: base calling, editing, contig assembly by thespecific softwares. ORF scanning, organization of a genome of higher organism. Localization of genes in genome sequences. Analysisin silico: searching for homology, comparison of gene sequences and CDS, similarity and homology between sequences. PCRamplification of plastid sequences for the barcoding of plants. RNA Interference: Principles and Applications. Gene expression analysis. 12. Syllabus for classes in the Master programme in Plant and Animal Biotechnology ProgrammePlant-pathogen interactionThe students will develop a comprehension of the molecular mechanisms underlying the interaction of fungal and bacterial pathogens with their host. They will be able to recognize the molecular signals that characterize plant diseases, the major physiological and genetic aspects of pathogenesis and virulence in the microrganisms, the different aspects of innate immunity and resistance in the plant. Within the general contexts of evolution, environmental fitness and competition among organisms, the most recent research issues with potential for disease control will be acquired.Molecular methods used in the study of plant-microorganism relationships, transposons, gene disruption, yeast two hybrids, differential display. Fungal genetics and fungal population dynamics: relevance in plant pathology. Molecular mechanisms of fungal penetration, thigmotropism, appressorium formation. Auxonic diseases and hormonal unbalance in the host: the case of olive knot. Infection, colonization and host transformation by Agrobacterium tumefaciens. Cell wall degrading enzymes. Role of polygalacturonase inhibiting proteins in plant defence. Programmed cell death and hypersensitive reaction. Avirulence and gene per gene theory. The secretion of virulence factors and the type III transport system. The harpin and the cluster hrp. Effectors. Molecular basis of recognition and defence of plants. Innate immunity and cultivar specific resistance. Phytoalexins and phytoanticipins. PR proteins and systemic acquired resistance. Molecular basis of hypovirulence in Chryphonectria parasitica.The course includes laboratory training on elicitation of hypersensitive response, induction of systemic acquired resistance and phytoalexin production. 13. Syllabus for classes in the Master programme in Plant and Animal Biotechnology ProgrammeProtein structure and functionProtein structure: definition of domain; levels of organization; protein folding and flexibility; properties of soluble and membrane- bound proteins; examples of typical protein structures.Protein sorting: cytoplasm-localized proteins; protein sorting; proteolysis.Protein characterization: purification and enzymatic analysis; purification of membrane proteins; chromatographic techniques; protein electrophoresis.Structural and conformational analysis: molecular mass determination; subunit composition; aminoacid analysis; aminoacid sequence determination; x-ray crystallography and NMR techniques; reverse genetics; structure prediction; computer-assisted protein analysis.Antibodies; structure of the antibodies; production and quality analysis of antibodies; antibody methods.Determination of protein function and prediction of structure, function, and localization: comparison between sequences; recombinant DNA techniques; site-directed mutagenesis; heterologous expression; protein engineering.Phylogenetic analysis using protein sequences: substitution matrices (PAM and BLOSUM); alignment of protein sequences; tree- building methods for protein phylogeny.Laboratory practicals: dedicated protocols are developed to show the main protein purification and protein analysis techniques. Bioinformatic paracticals are provided by guided access to biological sites and protein databases on the web. 14. Syllabus for classes in the Master programme in Plant and Animal BiotechnologyProgrammeAnimal physiology and welfareThe aim of the course is to make students acquire specific knowledge in order to provide a knowledge base of homeostasis, behavior,animal welfare in order to the study new strategy to improve well-being and a better interaction between man and animal. Basic physiology concepts of organ system Major Senses ( Sight, Hearing, Taste, Smell, and Touch) Temperature control Basic physiology concepts of homeostasis, omeoresis, allostasi, resilience. Limbic system, Emotional intelligence and cognitive intelligence The pain. Stress. 15. Syllabus for classes in the Master programme in Plant and Animal Biotechnology Programme Plant cell physiology and tissue cultureIntroduction and historical overview, importance of tissue culture system and biotechnology in modern agriculture.The metabolic regulation, the basis of metabolic control. Examples of metabolic control, the role of Ca2+ in metabolic regulation. Relations between metabolic regulation and cell compartmentation.Plant cell growth and differentiation, regulation of differentiation, totipotencyPlant growth regulators and their role in the tissue culture systemGrowth and development, overview of plants growth and development. The origins of polarity. The rate of cell elongation. Shoot and root apical meristem.Programmed cell death (PCD) paradigms in animals and plants; PCD in the life cycle of plants, the senescence.The Control of flowering. Floral evocation: internal and external cues. Cicardian rhythms: the clock within. Vernalization: promoting flowering with cold. Biochemical signalling involved in flowering.Tissue culture techniques: work in aseptic conditions; advantages of tissue culture techniques, tissue culture media and physical factors of cultivationRegeneration of plants in tissue culture system; different types of cultures: meristematic, organ, callus cultures; regeneration systems: induction of adventitious and axillary buds, induction of rooting; somatic embryogenesis; stages of plant regeneration in tissue culture system; physiological aspects of adaptation processes transfer from in vitro to in vivo conditions; cryopreservation; soma clonal variabilityProtoplast cultures, isolation of protoplast, regeneration of plants from protoplast, somatic hybridizationTissue cultures for production of secondary metabolites, bioreactors, biotransformations. 16. Syllabus for classes in the Master programme in Plant and Animal Biotechnology Programme Genetic resourcesTo provide students with knowledge about the centres of origin of the main species domesticated by the man; to provide as well students with methodological tools suitable to understand the origin of genetic diversity and to evaluate it; to show how the genetic diversity is the base of evolution and the base of the breeding as well; finally, to make students aware of the importance to conserve the genetic diversity especially in the centres of origin of the specie.Crop domestication and breeding. The emergence of agricultures in different parts of the world and their link with the centres of origin of species. The domestication syndrome: genes gained/lost during the domestication process. The domestication of new crops at the time of the great colonisations. The birth of genetics and crop breeding . Effect of domestication on genetic diversity.Population genetics. Origin of genetic diversity. Population genetic structure, the Hardy-Weinberg equilibrium and disruption mechanisms: migration, genetic drift, founder effect, bottle neck, selection. Methods of estimation of genetic diversity. Molecular taxonomy.Domestication cases study. Cereals (wheat, corn, rice), legumes (bean and soybean), potato, squash and zucchini, canola and other brassicaceae, sunflower, sugarcane and sugar beat, fruit crops (apple, peach, grape, banana), other commodities (tea, coffee, cocoa, cotton).Conservation of genetic diversity. Conservation in situ (biotopes, reserves, natural parks), conservation ex situ (base, active and core collections). Institutions with the mission of preserving the genetic diversity (FAO, IPGRI, CGIAR, Governments, local Administrations). Genetic resources and intellectual property. 17. Syllabus for classes in the Master programme in Plant and Animal Biotechnology Programme Food safetyThis course is devoted to the description of econometric and statistical tools which allow complex contexts modelling. The course structure may be described by theexpression GLM + LMM = GLM, because lessons will start treating generalized linear models (GLM) and linear mixed models (LMM), then linear generalized mixedmodels will be described (GLMM).Linear generalized models (GLM) represent a flexible generalization of linear regression as they allow the analysis of whichever response variable with distributionbelonging to the exponential family. The GLM approach represents a unified context for different statistical models, the linear model included.Linear mixed models (LMM) represent an extension of linear models which allows to describe complex data with jerarchical structures affecting the observationsindependence, through the inclusion of mixed effects inside the model formulation. Many fields of analysis, in fact, present data with jerarchical structures, longitudinaldimension or repeated measures which make observations not independent.Finally, if mixed effects have to be considered in generalized linear models formulation, the statistical econometric tools useful in this situations relate to the generalizedlinear mixed models context: GLMM.This course requires a good knowledge of base econometric methods and statistical inference, together with a good level of English language comprehension. 18. Syllabus for classes in the Master programme in Plant and Animal Biotechnology Programme Principles of crop breedingNature and objectives of plant breeding, importance of the variety factor in modern agriculture, neolithic revolution, domestication ofspecies, food availability and starvation, centres of origin o the plant species, germplasm collections, introduction of new varieties andspecies, main evolutionary schemes followed by plants, mutagenesis, interspecific hybridization, induced polyploidy, flower and flowermodifications, mating systems in plants, genetic structure in population of autogamous and allogamous species, self-incompatibilitysystems, male sterility, inheritance of quantitative traits, heritability, possible responses to selection, methods of plant breeding inautogamous, allogamous, vegetatively-propagated and apomictic plants, registration of new varieties, breeders rights, breedersexemption, farmers privilege, seed categories, natural and artificial methods of plant cloning, totipotency of the plant cell, regenerationmethods, methods of genetic transformation of plants, transgenesis in plant breeding, expression vectors, reporter genes, selectablemarkers, molecular cassettes for transgene expression in plants, elements controlling gene expression, selection of primarytransformants on the base of transgene expression levels, guidelines, rules and regulations at national and EU level for the deliberaterelease and marketing of transgenic crops. 19. Syllabus for classes in the Master programme in Plant and Animal BiotechnologyProgramme Tree genetics and breedingThe objective of this course is to illustrate the conventional methods used to select new varieties in vegetatively propagated crops with particular emphasis to fruit andtimber trees, as well as the most advanced techniques used to improve selection efficiency in wooden species. Aspects related to fruit tree breeding, including polyploidinheritance, apomixis and genetic analysis of complex loci will be presented and discussed. The course will consist of lectures, practical exercises and visits to ongoingfield trials.1. The Scope and Nature of Plant Breeding . What is Plant Breeding. Scope of the Modern Industry. Sources of Genetic Material. Germplasm Preservation.BotanicGardens, Plant Breeding Organisations, Research Bodies2. Introduction to Genetics: a review. Review of Plant Genetics Linkage and Crossing Over. DNA. Homologous Chromosomes. Plant Genetics, Mendels Principles andExperiment. Genetic Terminology. Gene Linkages. Traits inherithance3. Gamete Production, Pollination and Fertilisation in Plants: a review focused on trees. Phases of Plant Reproduction. Gamete Production. Gene Mutation: example ofcommercial cultivars produced by bud mutation. Sources of Genetic Variation: Polyploidy, Bud Sports and Chimeras. Male Sterility, self incompatibility. Effect ofEnvironment. Terminology. Use of Pollination Biology in Plant Breeding: Pollination Process, Pollination Requirements, Cross Pollination, Fertilisation, Male/FemaleRecognition, Overcoming incompatibilit, Post Fertilisation, Pollen Selection, Floral Introduction. Mitosis and Meiosi. Sexual Structures in Plants: Flowers, Fruit, Seed4. Mono Hybrid and Dihybrid Inheritance in Trees. Mono hybrid Crosses. Dihybrid Crosses. Gene Linkages. Crossing Over. Recombination. Quantitative Traits5. Practical Plant Breeding Techniques: examples in fruit and forest trees. Plant Breeding Program. Breeding Self Pollinated Crops (peach)Mass Selection. PedigreeBreeding. Bulk Population Breeding. Breeding Cross Pollinated Crops (apple, kiwifruit, grape, poplar). Single Plant Selection.Mass Selection. Progeny Selection. LineBreeding. Recurrent Selection. Backcross Breeding. Induced Polyploidy. Dormancy Factors Affecting Germination (eg. hard seeds, impermeability to water, Chemicalinhibitors, Undeveloped embryos, etc)6. Current Developments in Tree Genetics. Plant Biotechnology. Genetic Engineering. DNA Markers. Somatic Hybridisation. Micropropagation. Breeding by design.Plant Breeders Rights. Trade Marks, Patents 20. Syllabus for classes in the Master programme in Plant and Animal Biotechnology ProgrammeLivestock production 1The course has the objective to provide to students the basic knowledge in breeding of domestic animals (cattle, horses, pigs, rabbits, chicken, etc.) and fish. Duringthe course, the main techniques of traditional selection and molecular biology will be explained and discussed in detail. These principles are applicable to farm animals,companion animals, populations of rare breeds and zoo animals. The course comprises three types of teaching activities: lectures, a computer-supported practical anda practical in a modern farm. In addition, there is a laboratory practical, during which the students become acquainted with the techniques of molecular genetics. Thiscourse will also provide a foundation knowledge in the genetic-veterinary management and epidemiology of farm animals.Basic molecular laboratory methods applied to farm animals: DNA and RNA analysis. Genetic markers. Genome mapping and linkage analysis. Genomesequencing. Identification and analysis of SNPs. High-throughput marker genotyping. BACs and BAC libraries. Expressed sequence tags. DNA chips. Proteomics.BioinformaticsGenetic diseases of farm animal: Biochemical genetics. Chromosomes and chromosomal aberrations. Familiar disorders not due to single genes. Genetic control ofinhered diseaseQuantitative genetics: Relationship and inbreeding. Selection within populations. Identification and analysis of a QTL. QTL mapping and marker assisted selection.Genomic selection. Breed structure analysis. Crossing schemes 21. Syllabus for classes in the Master programme in Plant and Animal Biotechnology ProgrammeLivestock production 2The aim of the course if to present the basis of animal biodiversity for domestic animals, giving an insight ofspecies and breeds, reporting the main productive traits and their relationship with the variability of genome.Aspects concerning the conservation of animal biodiversity and breeding progress based on selection programsand molecular genetics are also presented.Biology of domestication. Origin, differentiation and ecological adaptation of animal species and breeds.Molecular basis of animal biodiversity. Linking phenotypes to variability of animal genomes. Crossbreeds,coadaptation, biodiversity and sustainable developments. Use of genomic technology for the selection andmaintenance of animal biodiversity. Description of breed traits of main species of domestic animals. Biology,behavior and productive cycles of domestic animals. The dairy and meat production systems. Training,education of animal and human-animal relationships.