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Course codeCourseTeacher(s)
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In-depth disciplinary, thematic or curricular courses
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Theoretical and Practical Bioinformatics Approaches in Animal and Food ScienceP. Stevanato
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Prerequisites:Basic knowledge on molecular biology
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Target skills and knowledge:This class is to enable students with an understanding of concepts in the theory and practical of next generation sequencing and analysis of bioinformatics data. At the end of the course, the student is expected to have a good knowledge of various genome sequencing technologies and platforms and related data analysis of the genome, transcriptome, and microbiome.
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Course contents:1. Sequence analysis - Understanding a DNA sequence, basic concepts of sequence similarity, identity and homology, database searching: BLAST, FASTA and other sequence analysis tools to assign homology. Primer designing, PCR and Sanger sequence analysis. 2. Transcriptome analysis - Concepts in RNA-seq data analysis: data pre-processing and data-processing steps: mapping algorithms such as BWA and Bowtie2; differential gene expression analysis using RNA-seq data, statistical methods, relative merits of various platforms. Primer design for downstream validation. Measuring gene, lncRNA, siRNA from RNA-seq data. 3. Microbiome Analysis - 16s rRNA data analysis, clustering/phylogenetic tree based of alignment, clustering based on composition. Annotation based on databases, principal component analysis and other clustering tools. 4. SNP analysis - Resequencing of target genes or whole genomes, Gene prediction algorithms, identification of variants – SNPs/SNVs. Concepts behind genome wide association studies. Introduction to various applications.
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Assessment plan:Surveys and online written tests
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Planned learning activities and teaching methods:Lectures and videos explaining the theoretical concepts and practical online exercises on data analysis
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Additional notes about suggested reading:Teaching material in the form of videos will be shared with students
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Textbooks (and optional supplementary readings):Referenced scientific papers
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Food TechnologyA. Lante
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Prerequisites:None
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Target skills and knowledge:
The course is aimed at familiarizing students with new trends in food science and technology, highlighting how the basic concept of quality has been changed by the strides taken by science and technology.
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Course contents:Food quality attributes. Current challenges. Mild Technologies for Improving Food Quality.
Food Industry case studies.
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Assessment plan:The final exam will consist in a written text
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Planned learning activities and teaching methods:
The course will consist of theoretical classes and a practical session.
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Additional notes about suggested reading:All the material of the course will be provided online in the Moodle platform
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Textbooks (and optional supplementary readings):
Selected scientific papers
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Food Microbiota & Human microbiomeC. Nadai
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Prerequisites:Basic knowledge of microbiology
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Target skills and knowledge:The course is aimed at familiarizing students with the composition of microbial populations living in foods and their main positive or negative activities. The concept of human microbiome will be also discussed, along with the description of the principal microbial categories and their main effects on human metabolism
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Course contents:Composition of microbial populations of main fermented foods
Composition of the human microbiome
Main functions of the human microbiome.
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Assessment plan:The final exam will consist in a written text
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Planned learning activities and teaching methods:The course will consist of theoretical classes and a practical session devoted to the knowledge of main bioinformatic tools for the study of microbiomes
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Additional notes about suggested reading:All the material of the course will be provided online in the Moodle platform
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Textbooks (and optional supplementary readings):Selected scientific papers
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Nutrigenomics in livestock sectorD. Giannuzzi
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Prerequisites:Basic knowledge of molecular biology (genome structure, control mechanisms of transcription and transduction)
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Target skills and knowledge:The goal of the course is to provide the students with an understanding the meaning of nutrigenomic and nutrigenetic terms and their contextualization in livestock production, together with their applicability as a new exciting reseaarch field.
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Course contents:The course will cover the following aspects: Mechanisms of nutrient-genome interaction; Effect of bioactive chemicals in foods and supplements on animal metabolism and role on gene expression; Innovative, functional and nutraceutical feeds; Disease prevention and treatment using nutrition; Role of epigenetics in the differences of individual response to diet; Role of the microbiome in influencing gene expression; Overview of research and applications of nutrigenomics in the different domestic species.
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Assessment plan:Written examinations designed to test the knowledge acquired during the course
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Planned learning activities and teaching methods:Each topic/group of topics will consist of teoretical classes
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Additional notes about suggested reading:The material used for the course will be made available to students through the Moodle platform some days before the beginning of the lessons
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Textbooks (and optional supplementary readings):none
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Animal welfare assessment and risk managementF. Gottardo
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Prerequisites:Basic knowledge on farm animal rearing systems
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Target skills and knowledge:At the end of the course, the student should be familiar with the emerging issues relating to the welfare of farm animals during the breeding, transport and slaughter stages. Developments in positive welfare indicators and new animal-based welfare indicators should also be known.
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Course contents:The course is developed in 4 lessons with final group work:
1) An introduction aimed at providing a brief summary of the evolution of the topic of animal welfare.
2) Identification of emerging issues in animal welfare during the breeding and rearing phase
3) Identification of emerging animal welfare issues during the transport phase of the process
4) Identifying emerging welfare issues during slaughter.
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Assessment plan:Working in groups to collaborate on analysing a specific problem that will be presented and discussed with peers.
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Planned learning activities and teaching methods:Lectures and discussion with the PHD students on the updats of the "Animal Welfare Science"
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Additional notes about suggested reading:document produced by the EFSA Panel on Animal Health and Welfare (AHAW) EFSA
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Textbooks (and optional supplementary readings):PPT presentation as well as suggested readings will be provided to the students on Moodle platform
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Animal-based Vs. Plant-based foodsM. De Marchi, G. Niero
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Prerequisites:None
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Target skills and knowledge:The course is aimed at comparing the intrinsic quality traits and sustainability of animal-derived food products (i.e., milk and meat) with their plant-based substitutes.
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Course contents:Chemical composition of milk and milk substitutes: fat, proteins, minerals, carbohydrates, and vitamins profiles; relevance of milk and milk substitutes in human nutrition and health. Chemical composition of meat and meat substitute: fat, proteins, minerals, carbohydrates, and vitamins profiles; traces of antibiotics and pollutants; relevance of meat and meat substitutes in human nutrition and health. Sustainability issues: pros and cons about sustainability of animal-derived food products and their plant-based substitutes. Writing a survey to pitch for public perception and consumer awareness on the topic of “Plant-based food: an alternative to animal-derived food?”.
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Assessment plan:Short report about public perception and consumer awareness on the topic of “Plant-based food: an alternative to animal-derived food?”. The report will be based on the results of a public survey, which will be prepared during the course.
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Planned learning activities and teaching methods:Lectures for introducing theoretical concepts; interactive lectures to prepare the survey.
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Additional notes about suggested reading:The material (i.e., slides, papers, book chapters, videos and multimedia files) will be made available to students through Moodle platform.
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Textbooks (and optional supplementary readings):None
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Integrated assessment of sustainability in livestock systemM. Berton, F. Bordignon, M. Schiavon
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Prerequisites:None
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Target skills and knowledge:At the end of the course, students will have acquired knowledge on the different facets of sustainability in livestock systems, methods and tools for their evaluation and management.
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Course contents:The course consists of a theorical part introducing students to the sustanibility concept and its application on livestock systems, and of a teorical-practical part that allows students to acquire knowledge and skills on how to evaluate and manage sustainability in livestock farming systems, also with case studies and active-learning activities. The course will be divided into the following modules: 1. What is sustainability and which descriptors are useful to frame a livestock system 2. Relationship between animal production and natural environment and environmental matrices (water, soil, atmosphere) 3. How to measure emissions in the farm 4. Evaluating sustainability: Life Cycle Assessment and beyond 5. Sustainable livestock systems: ruminants (Berton); 6. Sustainable livestock systems: monogastrics and fish.
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Assessment plan:Class exercises assigned and supervised by the teachers.
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Planned learning activities and teaching methods:Lectures and group-working activities on specific case studies
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Additional notes about suggested reading:The material (i.e., slides, papers, book chapters, videos and multimedia files) will be made available to students through Moodle platform.
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Textbooks (and optional supplementary readings):None
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Investment decisions under uncertainty (IDUU)C. D'Alpaos & M. Moretto (TBC)
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Prerequisites:
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Target skills and knowledge:Upon completion of the course students will have acquired a critical understanding of basics principles of capital budgeting and investment decisions under uncertainty and will be able to determine the real-options value for simple capital investment projects.
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Course contents:The course reviews current techniques of capital budgeting and details an approach based on the pricing of Real Options which provides a means of quantifying the elements of managerial flexibility in the face of unexpected changes in markets. More specifically: Investment Decisions and Capital Budgeting; Risk, Return and the Opportunity Cost of Capital; Risk and Capital Budgeting: the Capital Asset Pricing Model; Uncertainty and Consumer/Investor Behavior; The Contingent Claim Analysis (CCA); Real Options Theory; Examples (e.g., Managerial Flexibility, Weather Derivatives, Scale Production, Land Use).
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Assessment plan:Paper discussion, Final test at the end of the course. Grading is based on class participation and interaction (20%), group work (40%) final test (40%).
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Planned learning activities and teaching methods:
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Additional notes about suggested reading:
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Textbooks (and optional supplementary readings):a) Brealey, Myers, Allen (2019): Principles of Corporate Finance, McGraw-Hill, International Edition
b) Ross, Jordan (2018): Fundamentals of Corporate Finance, McGraw-Hill, International Edition c) Lambrecht (2017): Real Options in Finance, Journal of Banking and Finance, 81, pp. 166-171
d) Schneider, Imai: Valuing Investments in Digital Business Transformation: A Real Options Approach
e) Dixit, Pindyck (1994), Investment under Uncertainty, Princeton University Press
f) Trigeorgis L. (1996): Real Options: Managerial Flexibility and Strategy in Resource Allocation, MIT Press
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Biostatistics and Clinical epidemiologyL. Desquilbet
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Prerequisites:
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Target skills and knowledge:
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Course contents:The course is dedicated to basics in biostatistics and study design for causal inference. In detail the course is focused on train student to understand the results obtained from usual statistical tests, to critically read statistics presented in tables, to avoid miss-interpretation of the p-values, to appreciate the a priori statistical power of the study, to interpret the results from univariate survival analyses (Kaplan-Meier curves), to interpret the results from univariate and multivariate regression models and to identify the presence of confounding bias and to discuss the impact of such bias.
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Assessment plan:
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Planned learning activities and teaching methods:This MasterClass is organized in 3 days, dedicated to basics in biostatistics and study design for causal inference. Lectures are during the mornings and practicals during the afternoons. Practicals will be based on results presented in published papers. The examples will be drawn from veterinary medicine, but can easily be extended to clinical research in human medicine.
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Additional notes about suggested reading:
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Textbooks (and optional supplementary readings):
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Experimental design in Crop Science: principlesL. Marini
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Prerequisites:none
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Target skills and knowledge:
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Course contents:This course provides students with an opportunity to enhance their understanding of the principles and processes of experimental design in agricultural sciences. The course will provide students with a foundation in critical thinking, experimental design and data analysis that will be applicable to independent research projects. Students will also explore the practical requirements and limitations of scientific research. This practical activity will be mostly developed in groups of 3-4 PhD students and a final plenary session will be useful to discuss their experimental designs.
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Assessment plan:
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Planned learning activities and teaching methods:Class exercises assigned and supervised by the teachers.
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Additional notes about suggested reading:
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Textbooks (and optional supplementary readings):
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Experimental design in Crop Science: from lab to fieldL. Marini
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Prerequisites:none
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Target skills and knowledge:
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Course contents:The course covers fundamental principles and procedures of experimental designs in in many disciplines related to Crop Science PhD School. Emphasis will be on proper experimental designs when the researchers and PhD students are dealing with single or multiple factors, appropriate use of balanced and unbalanced designs, proper consideration of years and locations, the proper use of research data to determine association among variables versus the predictive value of variables, and problems associated with field experiments versus those associated with controlled environments such as greenhouses, growth chambers, and biotechnological and molecular genetics labs.
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Assessment plan:
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Planned learning activities and teaching methods:Class exercises assigned and supervised by the teachers.
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Additional notes about suggested reading: