General Info

SUBJECT	SEMESTER	CFU	SSD	LANGUAGE
121639 - PLANT GENOMICS	-	12	-	-	Learning objectives Didactic Objectives The course aims to provide knowledge of structural and functional genomics, with a particular focus on the agricultural context, serving as a preparatory step for the future acquisition of knowledge and skills in plant production management. Additional objectives include enhancing the ability to learn and communication skills, specifically the ability to discuss topics related to genetic improvement and the genomics of agricultural species using appropriate terminology. Didactic Objectives The course aims to consolidate and expand the knowledge of the biochemical and physiological mechanisms that plants put in place to adapt to unfavorable environmental conditions and to defend themselves from pathogens. Students will acquire the ability to critically analyze and independently solve problems related to crop resilience, in the classroom, with originality, and through multidisciplinary approaches more related to genetics, molecular biology, biochemistry and plant physiology. In addition, students will develop the ability to synthesize and integrate knowledge by formulating solid judgments even on the basis of incomplete or restricted information. Such conclusions and recommendations will be communicated through the argumentation of the knowledge gained during the course and the motivations behind it, both to a specialized and nonspecialist audience, in a clear and unambiguous way. The notions and concepts acquired during the course will provide students with greater responsibility for further professional development.
PLANT GENOMES AND CHROMOSOME MANIPULATIONS LJILJANA KUZMANOVIC	First Semester	6	AGRI-06/A
GENOME SEQUENCING AND BIOTECHNOLOGICAL APPLICATION FRANCESCO SESTILI	First Semester	6	AGRI-06/A		Learning objectives Didactic Objectives The course aims to provide knowledge of structural and functional genomics, with a particular focus on the agricultural context, serving as a preparatory step for the future acquisition of knowledge and skills in plant production management. Additional objectives include enhancing the ability to learn and communication skills, specifically the ability to discuss topics related to genetic improvement and the genomics of agricultural species using appropriate terminology. Didactic Objectives The course aims to consolidate and expand the knowledge of the biochemical and physiological mechanisms that plants put in place to adapt to unfavorable environmental conditions and to defend themselves from pathogens. Students will acquire the ability to critically analyze and independently solve problems related to crop resilience, in the classroom, with originality, and through multidisciplinary approaches more related to genetics, molecular biology, biochemistry and plant physiology. In addition, students will develop the ability to synthesize and integrate knowledge by formulating solid judgments even on the basis of incomplete or restricted information. Such conclusions and recommendations will be communicated through the argumentation of the knowledge gained during the course and the motivations behind it, both to a specialized and nonspecialist audience, in a clear and unambiguous way. The notions and concepts acquired during the course will provide students with greater responsibility for further professional development. Teacher's Profile courseProgram PROGRAM The program is divided in two modules: 1) Structural Genomics, 2) Functional Genomics. 1) STRUCTURAL GENOMICS (10 hours of lesson) - Sequencing methods: 1) Second generation sequencing: ILLUMINA, Pyrosyquencing (ROCHE 454), SOLiD; 2) Third Generation Sequencing: HELICOS (Helicos Biosciences); PacBio (Pacific Biosciences); Nanopore (Oxoford Nanopore); 2) Comparison of next generation and next-netx generation sequencing methods. - Full genome sequencing strategies: hierarchical method and WHOLE GENOME SHOTGUN; - Gene Annotation; - Functional annotation; - Projects for the sequencing of whole genomes in plant species of agricultural interest. - Illustration of major databases (NCBI, EMBL, DDBJ), searches in biological databases (BLAST), sequencing software and for the design of oligonucleotides; 2) FUNCTIONAL GENOMICS - The genetic transformation of plant species. Transformation mediated by Agrobacterium or by biolistic method. Preparation of plasmid vectors. - Study of gene function: gene overexpression and knock-out (RNA antisense, RNA interference) in transgenic plants; - Preparation of constructs for the realization of cis-genic plants. - Chemical mutagenesis and TILLING; physical mutagenesis with fast ions and neutrons; insertional mutagenesis: T-DNA and transposons; - Application of mutagenesis for functional studies and breeding programs. - Site-specific modifications. Methods of "genome editing": 1) zinc-finger nucleases (ZFN), 2) transcription activator-like effector nucleases (TALENs), and 3) Clustered Regularly Interspaced Short Palindromic Repeats-associated (Cas) proteins (CRISPR / Cas) - Application of "genome editing" methods for the genetic improvement of species of agrarian interest. Laboratory exercises will focus on the following topics: 1) Search in databases of nucleotide and protein sequences. Use of bioinformatics tools to open sequence files (DNAMAN, FINCH TV, GENEIOUS). Use of the BLAST algorithm to search nucleotide or protein sequences in databases. Alignment of nucleotide and acidic amino acids through the CLUSTAL OMEGA and GENEIOUS programs. Construction of phylogenetic trees 2) Identification of SNPs on genes of interest by TILLING in durum wheat 3) Preparation of constructs for genetic transformation by cis-genic approach: Insertion of the recombinant cassette into a bacterial vector; Transformation of bacterial cells; Extraction and digestion of the recombinant plasmids with restriction enzymes 4) Use of molecular marker to select transgenic plants. examMode Power Point presentation of 2 articles related to two different lesson topics. Usually one is related to structural genomics and the other to functional genomics. During the presentation specific questions will be asked both about the articles taken in exam and the topics of the course. books Materials and power point presentations provided by the professor classRoomMode The frequence is not mandatory bibliography GENETICA un approccio molecolare. Quarta edizione Peter J. Russell Edizione italiana a cura di Carla Cicchini e Alessandra Marchetti ISBN:9788865186176 Biotecnologie e Genomica delle Piante. Rosa Rao e Antonietta Leone. Editor IDELSON-GNOCCHI. Power Point presentations and papers provided by the professor.
120023 - SAFETY IN LAB WORKING PIERLUIGI ROSSI	First Semester	2			Learning objectives Students will be able to identify potential hazards such as dangerous chemicals, biological agents, and harmful physical situations, and understand risk analysis techniques and methods to eliminate or mitigate these risks. Students will be able to recognize and evaluate chemical, biological, and physical hazards in the laboratory, plus of adopting appropriate preventive measures, such as using PPE, training workers, and creating safe operating procedures. Students will develop the ability to independently assess the likelihood and severity of potential incidents associated with identified hazards. Students will be able to effectively communicate safety practices to their colleagues and supervisors. They will also be capable of drafting and managing safety documentation and conducting training on laboratory-specific risks. Students will develop the ability to continuously update their knowledge on safety practices by following periodic reviews of safety procedures and promote a culture of safety among workers. Teacher's Profile
120498 - RESEARCH LABORATORY TRAINING ANDREA FOCHETTI	First Semester	2			Learning objectives The main learning objectives of the course is to equip students with all the necessary practical and safety skills in order to autonomously manage and execute a scientific research project, carried out mainly in biomolecular-related scientific fields. The training objectives emphasize different aspects related to correct laboratory procedures, work ethics and practical skills necessary to carry out the subsequent thesis project. The student will acquire expertise in the autonomous handling of laboratory instruments to correctly carry out scientific experiments. Planning and organization of an experimental biomolecular research project and problem-solving skills will be acquired. Furthermore, the student will master the appropriate tools necessary for the critical evaluation of scientific literature and for accurate data interpretation and analysis. Teacher's Profile courseProgram Measurement units and conversions, stoichiometry, solutions and dilutions, acid-base reactions and titrations, buffer solutions and their preparation, chemical reaction set-up and monitoring. Daily laboratory practices; Utilization of precision devices; Introduction to the use of equipment in Molecular biology and Organic Chemistry laboratories: use of high-performance liquid chromatography (HPLC) and microwave extraction systems; polymerase chain reaction (PCR) preparation and electrophoresis setup. examMode Multiple Choice Test books It is recommended to study the topics of the course using the lecturer's slides, made available on the Moodle platform. There are no specific reference texts as it is mainly a practical exam. classRoomMode Strongly recommended
119941 - ELECTIVE COURSES	First Semester	12
TWO EXAMES AMONG THE FOLLOWING:	-	-	-	-
TECHNOLOGICAL INNOVATIONS TO IMPROVE THE QUALITY OF VEGETABLE CROPS MARIATERESA CARDARELLI	First Semester	6	AGRI-02/B		Learning objectives Didactic Objectives The course aims to provide advanced knowledge and practical tools to understand, evaluate, and improve the quality of vegetable crops through the adoption of technological innovations and sustainable strategies. Students will acquire skills related to the factors influencing vegetable quality (intrinsic and extrinsic), innovative cultivation techniques (soilless systems, nutrition and irrigation management, use of sensors), and strategies to enhance the nutritional and functional value of productions (grafting, biostimulants, nutraceutical greenhouses). Particular emphasis will be placed on the integration of theoretical knowledge with applied and interpretative skills, as well as on the development of critical autonomy and communication abilities. At the end of the course, students will be able to: • Apply the acquired knowledge in real production contexts (applying knowledge and understanding); • Make independent and critical judgments regarding the use of technological innovations and crop management strategies (making judgements); • Communicate clearly and scientifically the results of their analyses and project designs (communication skills); • Independently update their knowledge and skills in relation to the evolution of technologies and cultivation practices (learning skills). Teacher's Profile courseProgram Concept and meaning of quality in vegetables: i) intrinsic properties (nutritional, organoleptic, safety) and extrinsic properties (commercial, aesthetic); ii) quality by product type: roots, leaves, fruits. Cultivation environment and production systems: greenhouse vs open field (light, temperature, humidity), soilless systems (advanced hydroponic and aeroponic systems), management of nutrition and irrigation management, growing substrates, fresh-cut produce and nitrate control, use of sensors for real-time monitoring. Strategies to improve quality: herbaceous grafting, biostimulants (types and application methods), nutraceutical greenhouses for for functional foods. Analysis of real experiences in improving vegetable quality. examMode The written test will include multiple-choice questions and open-ended questions. books Orticoltura. Principi e pratica'. Edagricole. Curatori: Pardossi, Gianquinto, Santamaria, Incrocci 'Colture fuori suolo. Idroponica e coltivazione in substrato' Edagricole. Incrocci, Malorgio, Massa. 'Biostimolanti per un'agricoltura sostenibile' Ed. Informatore Agrario. Curatori: Colla, Rouphael classRoomMode Optional
FOREST BIOTECHNOLOGY	First Semester	6	AGRI-03/B		Learning objectives The course will introduce students to the principles and experimental approaches, in continuous evolution, of plant biotechnology. The course aims to strengthen the basic knowledge on plant biotechnologies applied to forest trees (green biotechnologies, categories of biotechnological processes and products, model plants, plant tissue cultures, recombinant methods, molecular tools), offering a framework to address current scientific problems (i.e. the use of transgenic trees) and also provide a basis for specialized studies in the field of in vitro clonal propagation, genetic improvement of trees and functional genomics. In the laboratory lessons students will develop some of the techniques currently used to obtain micropropagated plants, cultures of calluses and protoplasts of forest species and to detect genetic variation. The key concepts of the course will be integrated into a series of case studies and students will improve their ability to apply them to new situations in problem solving sessions, in particular dedicated to the Mediterranean region. At the end of the course, students will have an in-depth knowledge of the basic principles of forest biotechnology and modern techniques to obtain technological products (in vitro material characterized by clonal fidelity or somaclonal variants, secondary metabolites, transgenic and cisgenic tree materials, molecular tools for the study of genetic variability). Finally, they will have acquired the ability to understand the potential of using biotech trees to increase the productivity of forest plantations even in disadvantaged environments (biotic and abiotic stresses) or to use biotech trees for the recovery of arid soils (salinity, pollution). Students will be encouraged to make use of the knowledge acquired during the course and during the laboratory exercises to apply it to specific problems such as, for example, the propagation of improved genotypes or somaclonal variants resistant to stressful biotics or abiotics or characterized by high wood productivity, as well as the conservation of threatened species or origins. Students will be able to interpret and discuss the scientific works presented in class and to identify its highlights and highlights. During the lessons, students' ability to reflect and discuss the topics covered will be stimulated, as well as the comparison of opinions to develop their communication skills. These skills will then be tested during the exam. Students will be able to expose and develop scientific topics related to the course. The active involvement of students through oral discussions in the classroom and experiences in laboratory practices will develop this skill.
120024 - PROJECT WRITING AND MANAGEMENT VALENTINA TAVERNA	Second Semester	2			Learning objectives The course aims to provide students with the skills necessary to systematically integrate European project design methodologies with Project Management techniques, both in the formulation and implementation phases of projects, with particular attention to the phases of Project Cycle Management (PCM) and the three knowledge areas of Project Management. Through the contents made available by the teacher, students will acquire the basic notions to understand the functioning of European Union funding, the related multi-year programming frameworks and the formulation of project proposals consistent with the objectives of sectoral policies. In addition to the acquisition of hard skills to apply the techniques and methodologies learned, to complete the knowledge to be acquired, a focus will be dedicated to soft skills with particular attention to the management of project stakeholders. Teacher's Profile courseProgram The course aims to guide students in acquiring the knowledge to systematically integrate Euro-project methodologies with Project Management techniques: 1. Formulation: methods for applying PM techniques from the formulation phase to better define the managerial elements of the proposal (e.g., timeline planning, risks) and efficiently manage the proposal writing phase (respecting time, cost, and quality constraints). 2. Implementation: application of PM for more effective management of funded projects, strengthening aspects such as resource management, quality, and risks not fully covered by the LFA alone. The first part of the program provides an overview of how European Union funding works and its multiannual programming frameworks (Context Knowledge: EU, Strategies, Multiannual Financial Framework). The second part of the program addresses the more operational topics of project writing and management (Project Cycle Management, Project Management, and related knowledge areas). To complete the knowledge acquisition, a focus will be dedicated to soft skills, particularly project stakeholder management. examMode Assessment consists of two main components: • Initial diagnostic test, designed to help the lecturer assess students’ prior knowledge. This test does not affect the final grade. • Final examination, divided into two parts: 1. a written test including both closed- and open-ended questions on the course contents; 2. a project proposal simulation, developed in groups (maximum four students per group), aimed at evaluating the ability to apply the acquired knowledge to practical cases. books Material provided by the teacher classRoomMode Not mandatory but suggested due to the nature of the topics bibliography Material provided by the teacher
119929 - FOOD BIOTECHNOLOGY ILARIA BENUCCI	Second Semester	6	AGRI-07/A		Learning objectives The aim of the course is to deep the student's knowledge about industrial biotechnology for food processing, by providing articulated and systematic skills on the industrial use of microorganisms and enzymes useful in different food sectors. Moreover, the course aims to provide: • the suitable ability to manage the interaction between agro-food raw materials and the related biotechnological processes, both traditional and innovative, in order to implement the quality and sustainability of the finished product; • the tools to control and to regulate the biotechnological process, defining opportunities and constraints, in order to achieve the quality characteristics sought in the food product. Students will acquire knowledge relating to the general aspects of microorganisms and enzymes; as well as to the interconnections of physio-chemical and biochemical phenomena that may occur in their application to food processes. This will allow them to address, by modern and multidisciplinary approaches, the operational tasks of managing the physio-chemical and biochemical phenomena that may occur in the application of microorganisms and enzymes to food processes. By analyzing examples of process critical issues, students will acquire the ability to interpret and understand, which will be useful to formulate judgments for the personal re-elaboration of the most suitable solutions. Students will develop the ability to discuss clearly and briefly the topics of the course, as well as argue with scientific and professional terminology the case studies addressed in the classroom and in the laboratory. Students will develop the attitude to analyze the subject matter, to study from different sources and to make the appropriate relations between the theoretical aspects of the classroom and the texts with those applied in laboratory. Teacher's Profile courseProgram - Introduction – market of food enzymes and starter cultures; EU regulations - Microbial biomasses and industrial starter cultures production - Primary and secondary metabolites - Complex products - Enzymatic catalysis - Biotechnological applications to the agri-food chains of: Bread and bakery products; Malt and beer; Still and sparkling wines; milk, cereals, legumes and dried fruit based fermented foods; Coffee; Cocoa. examMode Ongoing tests: multiple choice test; Final exam: oral discussion on different topics The determination of the final grade will take into account: the level of knowledge of the contents demonstrated (superficial, appropriate, precise and complete, complete and in-depth), the ability to apply theoretical concepts (fair, good, well-established), the ability to analyze , of synthesis and interdisciplinary connections (sufficient, good, excellent), of the capacity for critical sense and formulation of judgments (sufficient, good, excellent), of the mastery of expression (lack of exposition, simple, clear and correct, safe and correct). books - Lecture notes - Advances in Food Biotechnology, Wiley - Fundamentals of Food Biotechnology, 2nd Edition, Wiley - Food Biotechnology, Springer - Biotecnologie alimentari, Piccin mode The lessons will be both theoretical and practical and will favor the active participation so that students can acquire and apply, with advanced and specialized skills, the management of industrial use of food microorganism and enzyme and, at the same time, be able to carry out self-learning activities in the classroom and in the laboratory. Through this approach, teaching also intend to perfect the mastery of the theoretical and critical tools necessary for the analysis and interpretation of the operational specificities in different food processes. classRoomMode Optional bibliography None
119932 - CHEMISTRY OF NATURAL ORGANIC PRODUCTS ROBERTA BERNINI	Second Semester	6	CHEM-05/A		Learning objectives The course is devoted to the study of natural organic substances; in particular, secondary metabolites found in the plant world. Beginning with their respective biogenetic precursors, structural aspects, biological properties, applications, extraction techniques, purification and chemical characterization are explored. The objective of the course is to provide students with a thorough knowledge of natural organic substances, which is to be described, during the examination, with propriety of language, clarity of exposition, critical analysis and synthesis skills. Teacher's Profile courseProgram The course focuses on the study of different families of natural organic substances derived from the acetate, shikimate and mevalonate pathway. Of each of these, structural aspects, properties, biological activities and applications in agronomy, food, cosmetics, pharmaceuticals and nutraceuticals are explored. Among the classes of secondary metabolites, the phenolic substances and, among the various biological activities, the antioxidant activity are particularly explored. The techniques of extraction, purification and structural characterization of natural substances are also studied. Seminars given by colleagues from outside the University of Tuscia on topics relevant to the program are scheduled during the course. Exercises and/or teaching visits are, in addition, planned. examMode At the end of the course, students take a written exam consisting of three open-ended questions covering all topics discussed. Additionally, they deliver a PowerPoint presentation on a topic of their choice related to a molecule, a family of natural substances, or an analytical method covered in the entire program. The article or review used for the presentation is selected by the student and can be submitted to the instructor for approval before preparing the PowerPoint. Evaluation criteria include depth of knowledge, mastery of language, clarity of presentation, ability for critical analysis and synthesis, both for the written exam and the PowerPoint presentation. books Medicinal Natural Products. Paul M Dewick, John Wiley & Sons, Ltd classRoomMode Recommemded bibliography Selected scientific articles (sources: Scopus, Web of Science)
119930 - PLANT BREEDING	Second Semester	6	AGRI-06/A		Learning objectives Knowledge and understanding: the course aim to provide the student with the basic principles of crop breeding, variety registration and seed production. Applied knowledge and understanding theoretical and practical aspects of reproductive biology of higher plants are addressed including those modifications of the reproductive system that are of practical interest. Additional teaching objectives are the collection, storage and evaluation of genetic resources, the development of plant breeding schemes, the characterization, reproduction, conservative selection of plant varieties, the adoption of advanced strategies for the control of reproductive biology and the co-existence of conventional and genetically modified crops. Making judgements: the advantages and disadvantages of each presented technology are illustrated, to develop the student's critical sense. Communication skills: students are asked questions during the classes, both to keep their attention and to teach them to ask questions and give adequate answers. Being able to communicate their knowledge to competent and generic public in a clear way. Learning skills: the theoretical bases of processes underlying plant reproductive biology, plant breeding schemes and strategies to select improved varieties through conventional breeding, having developed those learning capacities that allow an autonomous study
119937 - AGRO-INDUSTRIAL PHYTOPATHOLOGICAL BIOTECHNOLOGIES SARA FRANCESCONI	Second Semester	6	AGRI-05/B		Learning objectives The course aims to consolidate and expand the knowledge of phytopathological biotechnology, deepening the new frontier techniques for an eco-sustainable control of the main agricultural phytopathologies. Students will acquire problem solving skills by approaching the subject in a multidisciplinary manner (plant pathology, physiology, molecular biology, genetics), to apply these skills in a scientific research context. Students will acquire the ability to integrate their multidisciplinary knowledge, in order to contextualize the possible social and ethical implications of phytopathological biotechnologies. This will be possible because students will be able to formulate scientific judgments/assumptions even on the basis of incomplete or limited information. Students will be able to communicate their knowledge with an appropriate scientific language, with a view to practicing speaking with specialists and non-specialists. This will be possible thanks to the exam format, which includes the presentation of a project by the student. The student will be able to study autonomously and self-managed, thanks to the fact that during the course the key notions are provided to then autonomously develop an exam project, also on the basis of the student's research inclinations. Teacher's Profile courseProgram Introduction to the course, overview of the syllabus, how the exam is conducted, assignment of case studies General concepts of plant pathology and Summary of the main phytopathogens: bacteria, phytoplasmas, fungi, oomycetes, viruses General concepts of struggle and "conventional" struggle: agronomic, genetic, legislative, with synthetic chemistry Definition of organic farming, regulation and legislation, the program of the European Green Deal and how to set up new methods of struggle Defense mechanisms of plants Mechanisms of antagonism Use of natural substances with antimicrobial action and elicitors Use of nanotechnologies: direct antimicrobial action, as carrier of active substances and nucleic acids Gene delivery for plant resistance Predictive models and phenomics Diagnostics examMode A case study will be assigned to each student, who will have to prepare a power point presentation to be exhibited during the exam date. books Teacher's slides, scientific articles recommended by the teacher mode Lectures, laboratory classRoomMode Not mandatory bibliography Teacher's slides, scientific articles recommended by the teacher
TWO EXAMES AMONG THE FOLLOWING:	-	-	-	-
DATA SCIENCE WITH -R ROBERTO MOSCETTI	First Semester	6	AGRI-04/B		Learning objectives Knowledge and understanding By the end of the course, students will grasp the core statistical principles applied to agricultural sciences, ranging from descriptive statistics to inferential methods (hypothesis testing, ANOVA, regression). They will understand the logic behind R programming, mastering the syntax required to handle complex data structures like vectors, data frames, and matrices. Furthermore, students will comprehend the theoretical and practical distinctions between supervised machine learning techniques (such as PLS, LDA, neural networks) and unsupervised ones (PCA, clustering, t-SNE), understanding exactly when and why to use them. Applying knowledge and understanding Students will be able to turn raw data into actionable insights by working independently within the R environment (RStudio, VS Code, or Positron). They will know how to write and execute scripts to import data, manage it using loops and logical conditions, and perform comprehensive statistical analyses. Specifically, they will be able to run parametric and non-parametric tests, build regression models (linear and non-linear), and implement classification and clustering algorithms. This practical skill will be directly demonstrated through the R script preparation required for the final exam. Making judgments Students will develop the critical thinking skills needed to interpret the numerical and graphical outputs generated by the software. Rather than simply running code, they will be able to assess the quality of predictive models (using metrics like RMSE or R2) and the statistical significance of their tests. A key component will be the ability to use AI assistants (LLMs) critically: students will learn to validate AI-generated code, avoiding passive “vibe coding” by identifying and fixing logical errors or hallucinations suggested by automated tools. Communication skills Students will be able to present their analysis results using appropriate technical language and high-quality data visualizations (publication-ready plots). They will be able to justify their statistical choices, such as why a non-parametric test or a specific clustering algorithm was used, both through clear comments within their exam script and by answering theoretical questions related to the first module. Learning skills The course will provide the methodology for continuous self-learning in the fast-evolving field of Data Science. Students will learn how to consult R library documentation, debug their own code, and properly use LLMs as tutors to speed up the learning of new functions or packages not covered in class, making them autonomous in tackling future analytical challenges. Teacher's Profile courseProgram Module 1 - Fundamentals (3 CFU) 1) The function of statistics in the field of agricultural sciences 2) Population, sample, variable and data 3) Qualitative (nominal, ordinal) and quantitative (discrete, continuous) variables 4) Mean, median, mode, variance, standard deviation, range and coefficient of variation 5) Asymmetry and kurtosis 6) Histograms, box plots, bar graphs and line graphs 7) Normal distribution 8) Null hypothesis and alternative hypothesis, type I and type II errors 9) t-test, z-test, ANOVA, and post-hoc tests 10) Correlation, and linear non-linear regression 11) Principal component analysis and non-linear alternatives 12) Clustering Module 2 – Applied statistics with R (3 CFU) 1) R fundamentals a) Introduction to R b) Installation and use of Integrated Development Environments (IDEs): RStudio, Positron, or VS Code c) Basic operators, variables, and vectors 2) Data structures and AI Assistant for coding a) Data structures: matrices, data frames, and lists b) Large Language Models (LLMs): how to properly use ChatGPT & Co. to boost learning, avoiding the dangerous “vibe coding” 3) Data import, manipulation, and automation a) Importing data into R from common file types (e.g., .csv, .xlsx, etc.). b) Subsetting, filtering data, and executing code using logical conditions c) Automating repetitive tasks with loops (i.e., for, and while) d) Custom functions 4) Data visualization a) Creating scatter plots, line graphs, and bar plots ready for publication b) Brief introduction to high quality plots (i.e., ggplot2) 5) Descriptive statistics and distributions a) Calculating descriptive statistics b) Normality tests c) Visualizing data distributions with histograms, boxplots, and Q-Q plots 6) Parametric and non-parametric tests a) Performing Analysis of Variance b) Post-hoc tests c) Brief overview of non-parametric alternatives 7) Linear and non-linear regression a) Building, interpreting, and visualizing simple linear models with lm() function b) Fitting non-linear models using nls() function 8) Predictive model performance a) Model performance with R2, Root Mean Squared Error (RMSE), and BIAS b) Splitting datasets into calibration (training) and prediction (testing) 9) Unsupervised learning - part 1 a) Principal Component Analysis b) Advanced techniques for complex datasets: t-SNE and UMAP 10) Unsupervised learning - part 2 a) Hierarchical clustering b) Visualizing and interpreting clustering results 11) Supervised learning - part 1 a) Multivariate regression with Partial Least Squares (PLS) b) Implementing k-fold cross-validation for building robust models 12) Supervised learning - part 2 a) Introduction to classification algorithms (e.g., Linear Discriminant Analysis, LDA; Quadratic Discriminant Analysis, QDA) b) Training neural networks examMode The final exam involves the development of a data analysis project (Project Work) based on R, to be submitted prior to the exam date, accompanied by the script used and an interpretation of the results. The oral exam will consist of a critical discussion of the submitted project, aimed at assessing proficiency in programming tools, and questions on the theoretical foundations of statistics covered during the course. books Douglas C. Montgomery - Design and Analysis of Experiments - McGraw-Hill Primary reference for Module 1. This text provides the theoretical and methodological foundations required to understand statistics applied to experimentation. It is used to deepen concepts regarding experimental design, hypothesis testing, analysis of variance (ANOVA), and regression, ensuring the necessary formal rigor before moving to computational approaches. Hadley Wickham, Mine Çetinkaya-Rundel, and Garrett Grolemund - R for Data Science (2e) - O'Reilly (available online: https://r4ds.hadley.nz/) Key resource for practical R programming in Module 2. Focused on the "tidyverse" ecosystem, this text covers essential operational skills: data import, data wrangling (cleaning and manipulation), advanced visualization, and workflow management within RStudio. Thulin, M. - Modern Statistics with R (2e) - Chapman & Hall/CRC (available online: https://www.modernstatisticswithr.com/) An advanced text bridging the gap between statistical theory and modern data science. It is used to apply the more complex statistical techniques covered in the curriculum within the R environment, including supervised and unsupervised machine learning methods (such as PCA, t-SNE, clustering, and model validation). David Harvey - Chemometrics Using R, LibreTexts (available online: https://chem.libretexts.org/Bookshelves/Analytical_Chemistry/Chemometrics_Using_R_%28Harvey%29) A specialized resource for applying R to analytical and multivariate data. This text is particularly relevant for the advanced sections of Module 2, as it bridges the gap between lab-based sciences and data modeling. It provides practical guidance on implementing chemometric tools such as Principal Component Analysis (PCA), Partial Least Squares (PLS), and clustering, which are essential for processing complex datasets like those from spectroscopy or food quality analysis. classRoomMode Attendance is strongly recommended bibliography N.A.
BIOINFORMATICS SILVIA TURCO	First Semester	6	BIOS-08/A		Learning objectives The course aims to consolidate basic knowledge regarding genomic databases and new sequencing technologies. Additionally, it will provide basic knowledge of programming languages necessary for the bioinformatics analyses addressed during the course. At the end of the course, students will be able to apply their skills to tackle and solve complex problems in the field of bioinformatics, such as the analysis and interpretation of large genomic datasets. They will also be capable of planning a genomic sequencing experiment and utilizing bioinformatics pipelines applicable in various scientific research contexts. Students will acquire the ability to integrate interdisciplinary knowledge from bioinformatics, genetics, and molecular biology to manage and solve multidimensional and complex problems. They will be able to tackle the complexity of biological data and information technologies, adapting and optimizing methodologies to address new and intricate challenges. Students will be able to communicate their chosen methodologies, results, and conclusions using technical and scientific language to both specialist and non-specialist audiences, through scientific documentation, academic articles, and oral presentations. The course will include theoretical lectures and practical exercises during which students will acquire the necessary skills for an autonomous learning in the field of bioinformatics. They will need to identify their own educational needs, address any gaps in their knowledge, and stay updated on emerging technologies and methodologies. Teacher's Profile

SUBJECT	SEMESTER	CFU	SSD	LANGUAGE
119934 - BIO-ECONOMY SIMONE SEVERINISIMONE SEVERINISIMONE SEVERINISIMONE SEVERINI	First Semester	6	AGR/01		Learning objectives The course aims to provide students with theoretical and operational knowledge about the bioeconomy. Specifically, the course aims to provide the ability to use and analyze economic and political information and data, to understand the logic and the present and future scenarios of the bioeconomy, with reference to the agri-food sector. The theoretical knowledge will be consolidated by practical exercises on case studies and by the reading, understanding and critical analysis, based on the knowledge gradually acquired, of scientific literature of particular relevance for the aims of the course, both suggested by the teacher and found independently by the students. At the end of the course, students should have acquired critical and judgment skills, as well as being able to find, critically analyze and use economic and political information and data regarding the present and future scenarios of the bioeconomy, with reference to the agri-food sector. During the numerous opportunities for discussion with the teacher and colleagues in the classroom, students will refine their skills in communicating and transmitting what they have learned, using appropriate economic terminology, also in order to acquire full knowledge and mastery of the topics covered in the program. Students will acquire the necessary autonomy to delve deeper, in particular, into the economic aspects addressed and will be able to independently analyze, from an economic perspective, economic and political information and data. Teacher's Profile courseProgram Topics: Bioeconomy concepts Principles of Industrial Organization Food industry and food value chains Risk and vulnerability of Food Value Chains Economics of Innovation. Teacher's Profile courseProgram Topics: Bioeconomy concepts Principles of Industrial Organization Food industry and food value chains Risk and vulnerability of Food Value Chains Economics of Innovation. Teacher's Profile courseProgram Topics: Bioeconomy concepts Principles of Industrial Organization Food industry and food value chains Risk and vulnerability of Food Value Chains Economics of Innovation. Teacher's Profile courseProgram Topics: Bioeconomy concepts Principles of Industrial Organization Food industry and food value chains Risk and vulnerability of Food Value Chains Economics of Innovation.
119935 - PLANT GENOMICS AND STRESS RESPONSES	-	12	-	-	Learning objectives The course aims to provide knowledge of structural and functional genomics, with a particular focus on the agricultural context, serving as a preparatory step for the future acquisition of knowledge and skills in plant production management. Additional objectives include enhancing the ability to learn and communication skills, specifically the ability to discuss topics related to genetic improvement and the genomics of agricultural species using appropriate terminology.
GENOME SEQUENCING AND BIOTECHNOLOGICAL APPLICATION FRANCESCO SESTILI	Second Semester	6	AGR/07		Learning objectives The course aims to provide knowledge of structural and functional genomics, with a particular focus on the agricultural context, serving as a preparatory step for the future acquisition of knowledge and skills in plant production management. Additional objectives include enhancing the ability to learn and communication skills, specifically the ability to discuss topics related to genetic improvement and the genomics of agricultural species using appropriate terminology. Teacher's Profile courseProgram PROGRAM The program is divided in two modules: 1) Structural Genomics, 2) Functional Genomics. 1) STRUCTURAL GENOMICS (10 hours of lesson) - Sequencing methods: 1) Second generation sequencing: ILLUMINA, Pyrosyquencing (ROCHE 454), SOLiD; 2) Third Generation Sequencing: HELICOS (Helicos Biosciences); PacBio (Pacific Biosciences); Nanopore (Oxoford Nanopore); 2) Comparison of next generation and next-netx generation sequencing methods. - Full genome sequencing strategies: hierarchical method and WHOLE GENOME SHOTGUN; - Gene Annotation; - Functional annotation; - Projects for the sequencing of whole genomes in plant species of agricultural interest. - Illustration of major databases (NCBI, EMBL, DDBJ), searches in biological databases (BLAST), sequencing software and for the design of oligonucleotides; 2) FUNCTIONAL GENOMICS - The genetic transformation of plant species. Transformation mediated by Agrobacterium or by biolistic method. Preparation of plasmid vectors. - Study of gene function: gene overexpression and knock-out (RNA antisense, RNA interference) in transgenic plants; - Preparation of constructs for the realization of cis-genic plants. - Chemical mutagenesis and TILLING; physical mutagenesis with fast ions and neutrons; insertional mutagenesis: T-DNA and transposons; - Application of mutagenesis for functional studies and breeding programs. - Site-specific modifications. Methods of "genome editing": 1) zinc-finger nucleases (ZFN), 2) transcription activator-like effector nucleases (TALENs), and 3) Clustered Regularly Interspaced Short Palindromic Repeats-associated (Cas) proteins (CRISPR / Cas) - Application of "genome editing" methods for the genetic improvement of species of agrarian interest. Laboratory exercises will focus on the following topics: 1) Search in databases of nucleotide and protein sequences. Use of bioinformatics tools to open sequence files (DNAMAN, FINCH TV, GENEIOUS). Use of the BLAST algorithm to search nucleotide or protein sequences in databases. Alignment of nucleotide and acidic amino acids through the CLUSTAL OMEGA and GENEIOUS programs. Construction of phylogenetic trees 2) Identification of SNPs on genes of interest by TILLING in durum wheat 3) Preparation of constructs for genetic transformation by cis-genic approach: Insertion of the recombinant cassette into a bacterial vector; Transformation of bacterial cells; Extraction and digestion of the recombinant plasmids with restriction enzymes 4) Use of molecular marker to select transgenic plants examMode Power Point presentation of 2 articles related to two different lesson topics. Usually one is related to structural genomics and the other to functional genomics. During the presentation specific questions will be asked both about the articles taken in exam and the topics of the course. books Materials and power point presentations provided by the professor mode Lectures (18 hours), case study presentations (18 hours), and laboratory exercises (18 hours). classRoomMode the frequence is not mandatory bibliography GENETICA un approccio molecolare. Quarta edizione Peter J. Russell Edizione italiana a cura di Carla Cicchini e Alessandra Marchetti ISBN:9788865186176 Biotecnologie e Genomica delle Piante. Rosa Rao e Antonietta Leone. Editor IDELSON-GNOCCHI. Power Point presentations and papers provided by the professor. Teacher's Profile courseProgram PROGRAM The program is divided in two modules: 1) Structural Genomics, 2) Functional Genomics. 1) STRUCTURAL GENOMICS (10 hours of lesson) - Sequencing methods: 1) Second generation sequencing: ILLUMINA, Pyrosyquencing (ROCHE 454), SOLiD; 2) Third Generation Sequencing: HELICOS (Helicos Biosciences); PacBio (Pacific Biosciences); Nanopore (Oxoford Nanopore); 2) Comparison of next generation and next-netx generation sequencing methods. - Full genome sequencing strategies: hierarchical method and WHOLE GENOME SHOTGUN; - Gene Annotation; - Functional annotation; - Projects for the sequencing of whole genomes in plant species of agricultural interest. - Illustration of major databases (NCBI, EMBL, DDBJ), searches in biological databases (BLAST), sequencing software and for the design of oligonucleotides; 2) FUNCTIONAL GENOMICS - The genetic transformation of plant species. Transformation mediated by Agrobacterium or by biolistic method. Preparation of plasmid vectors. - Study of gene function: gene overexpression and knock-out (RNA antisense, RNA interference) in transgenic plants; - Preparation of constructs for the realization of cis-genic plants. - Chemical mutagenesis and TILLING; physical mutagenesis with fast ions and neutrons; insertional mutagenesis: T-DNA and transposons; - Application of mutagenesis for functional studies and breeding programs. - Site-specific modifications. Methods of "genome editing": 1) zinc-finger nucleases (ZFN), 2) transcription activator-like effector nucleases (TALENs), and 3) Clustered Regularly Interspaced Short Palindromic Repeats-associated (Cas) proteins (CRISPR / Cas) - Application of "genome editing" methods for the genetic improvement of species of agrarian interest. Laboratory exercises will focus on the following topics: 1) Search in databases of nucleotide and protein sequences. Use of bioinformatics tools to open sequence files (DNAMAN, FINCH TV, GENEIOUS). Use of the BLAST algorithm to search nucleotide or protein sequences in databases. Alignment of nucleotide and acidic amino acids through the CLUSTAL OMEGA and GENEIOUS programs. Construction of phylogenetic trees 2) Identification of SNPs on genes of interest by TILLING in durum wheat 3) Preparation of constructs for genetic transformation by cis-genic approach: Insertion of the recombinant cassette into a bacterial vector; Transformation of bacterial cells; Extraction and digestion of the recombinant plasmids with restriction enzymes 4) Use of molecular marker to select transgenic plants examMode Power Point presentation of 2 articles related to two different lesson topics. Usually one is related to structural genomics and the other to functional genomics. During the presentation specific questions will be asked both about the articles taken in exam and the topics of the course. books Materials and power point presentations provided by the professor mode Lectures (18 hours), case study presentations (18 hours), and laboratory exercises (18 hours). classRoomMode the frequence is not mandatory bibliography GENETICA un approccio molecolare. Quarta edizione Peter J. Russell Edizione italiana a cura di Carla Cicchini e Alessandra Marchetti ISBN:9788865186176 Biotecnologie e Genomica delle Piante. Rosa Rao e Antonietta Leone. Editor IDELSON-GNOCCHI. Power Point presentations and papers provided by the professor.
ENGINEERING CROP RESPONSE TO STRESSES DANIEL VALENTIN SAVATIN	Second Semester	6	BIO/04		Learning objectives Module I - Genome sequencing and biotechnological Applications The course aims to provide knowledge of structural and functional genomics, with a particular focus on the agricultural context, serving as a preparatory step for the future acquisition of knowledge and skills in plant production management. Additional objectives include enhancing the ability to learn and communication skills, specifically the ability to discuss topics related to genetic improvement and the genomics of agricultural species using appropriate terminology. Module II - Engineering crop response to stresses The course aims to consolidate and expand the knowledge of the biochemical and physiological mechanisms that plants put in place to adapt to unfavorable environmental conditions and to defend themselves from pathogens. Students will acquire the ability to critically analyze and independently solve problems related to crop resilience, in the classroom, with originality, and through multidisciplinary approaches more related to genetics, molecular biology, biochemistry and plant physiology. In addition, students will develop the ability to synthesize and integrate knowledge by formulating solid judgments even on the basis of incomplete or restricted information. Such conclusions and recommendations will be communicated through the argumentation of the knowledge gained during the course and the motivations behind it, both to a specialized and nonspecialist audience, in a clear and unambiguous way. The notions and concepts acquired during the course will provide students with greater responsibility for further professional development. Teacher's Profile courseProgram Plant response to biotic and abiotic stresses Abiotic stresses: drought; salinity; flooding; high and low temperature; oxidative stress; mineral toxicity (es: Al3+). Biotechnological strategies for engineering plants with resistance to drought: discussion of scientific papers. Biotic stresses: Plant defence mechanisms against pathogens; constitutive and induced defenses. Systemic acquired resistance (SAR). Plant immunity. Pathogen perception and signal transduction. Biotechnological strategies for engineering plants with resistance to pathogens (discussion of scientific papers): Plant or exogenous genes with antimicrobial activity or contrasting virulence factors; plant or pathogen genes inducing or reinforcing plant immunity. Transgenic commercial crops resistant to virus and insects. Genetically modified crops: ethical and social issues with particular reference to transgenic crop resistant to pathognes; possible biotechnological approaches to overcome critics. Case study: corn MON810. Environmental changes and crop diseases. Plant transformation: Agrobacterium, reporter genes; constitutive, tissue-specific, inducible and synthetic promoters. examMode Power Point presentation of 2 articles related to two different lesson topics. Usually one is related to biotic stresses and the other to abiotic stresses. During the presentation specific questions will be asked both about the articles taken in exam and the topics of the course. books -Buchanan, Gruissem, Jones: Biochimica e Biologia molecolare delle piante. Zanichelli -Altman A. Paul, Hasegawa M. (Editors) Plant Biotechnology and Agriculture: Prospects for the 21st Century. Academic Press Elsevier -Chrispeels M.J. e Sadava D. E. Genetica, Biotecnologie e Agricoltura Sostenibile, 2005. (traduzione italiana a cura di Sala F. et al.). Casa Editrice Idelson-Gnocchi. Teaching material supplied by the professor including slides of classes and scientific papers mode The course is delivered in mixed mode classRoomMode In presence. bibliography -Buchanan, Gruissem, Jones: Biochimica e Biologia molecolare delle piante. Zanichelli -Altman A. Paul, Hasegawa M. (Editors) Plant Biotechnology and Agriculture: Prospects for the 21st Century. Academic Press Elsevier -Chrispeels M.J. e Sadava D. E. Genetica, Biotecnologie e Agricoltura Sostenibile, 2005. (traduzione italiana a cura di Sala F. et al.). Casa Editrice Idelson-Gnocchi. Teaching material supplied by the professor including slides of classes and scientific papers
119936 - WOODY FRUIT CROP BIOTECHNOLOGY	First Semester	6	AGR/03		Learning objectives Student will acquire knowledge on molecular physiology and applied biology (genetics and epigenetics) related to the vegetative and productive behavior of fruit tree species, on their adaptation to different environmental conditions and cultural practices. Students will also learn knowledge on the evolution of the synthesis and accumulation pathways of metabolites in fruits, usable in genetic improvement for obtaining functional foods, using innovative technologies. The knowledge acquired and the experience carried out attending the lectures and the lab exercises will enable students to penetrate the topics, through analysis, and by using critical methodology to understand the problems and to put forward hypotheses for overcoming them, as well as to formulate innovative application hypotheses, with originality and with multidisciplinary approaches (genetics, molecular biology, biochemistry, plant physiology, ecophysiology and cultivation of tree plants), in applied tree plant biology. The understanding of the issues, their framing in biological and agronomical processes, and the generation of hypotheses for biotechnological applications will strengthen the student's ability to synthesize and integrate knowledge and enable him/her to generate judgements anchored in reality and advance hypotheses to acquire new information with scientific rigor. The set of experiences conducted will enable the student to expose his knowledge, reflections and conjectures to a wide audience, enriched by extensive knowledge of cultivation, scientific literature and methodologies, and with the necessary robustness due to a solid training that will enable him to generate original conclusions. The student will thus be able to address a specialized audience and clearly disseminate knowledge to a broad public. Attending classroom lectures, exercises and study visits, the student will acquire the tools for in-depth independent knowledge and independent thinking.
119942 - INTERNSHIP	First Semester	6
119933 - QUALITY OF PLANT-BASED FOODS STEFANIA MASCI	Second Semester	6	AGR/07		Learning objectives After acquiring basic knowledge about the constitution of plant varieties, the methodologies and issues related to the control and traceability of raw materials of plant origin are further explored, with particular focus on wheat Acquisition of research methods and development of critical thinking regarding issues related to the quality of plant-based raw materials and their traceability. The knowledge acquired during the course and the experience in critically reading scientific articles will provide students with critical skills, not only regarding technical and scientific aspects but also the ethical and social issues related to the topics covered. Both during classes and exams, great importance is placed on the ability to adequately communicate the topics covered, requiring different approaches depending on the type of audience. Lectures, study visits, and practical exercises are designed to provide students with all the elements needed for independent study. Teacher's Profile courseProgram The course is organized with a preliminary part during which various crops are illustrated in terms of the relative qualitative aspects, with greater in-depth analysis of wheat, the problems relating to traceability , along with the biochemical and molecular techniques whose knowledge is necessary for the understanding of the specific topics that will be addressed in the second part. Specifically, this preliminary part of the program includes: • Definition of crop quality and description of the main qualitative characteristics • Possibility of genetic intervention to improve quality characteristics • Legislation in regard to traceability and tracking in supply chains, certification and labeling, individual and collective marks, certification of quality • Definition of food fraud • Analytical methods: proteomics, standards and quantitative PCR (RT-PCR), chromatography, ELISA test, molecular markers, including DNA barcoding In the second part specific problems related to plant-based products are presented. Stable subjects are wheat-based products and genetically modified plants. According to the time necessary to carry out exhaustively these two major issues, other issues are treated, on the basis of the preferences expressed by the students, such as, for example, vegetable oils and wine traceability. Concerning wheat-based products, bread and pasta, with the relevant legal definitions and the processes that lead to their realization are illustrated. A few typical breads are also described and case studies in which biochemical and molecular techniques are used for their traceability are presented. Part of the course is devoted to adverse reactions to wheat (in particular allergies, celiac disease and non-celiac wheat sensitivity). With regard to genetically modified plants, the substantial equivalence issue is developed, along with legislation issues. The main methods of traceability and risk assessment, are discussed by presenting specific case studies. All case studies are presented in order to stimulate the students critical skills. Every case study is presented by giving particular importance to the aim of the work, the procedure to be followed to achieve the proposed objective, the critical discussion of the results. The practical classes provided are: • SDS-PAGE of pasta products to control the varietal composition declared on the label, through the comparison of the electrophoretic profiles obtained by extracting proteins from pasta products, with that from the declared wheat varieties • SDS sedimentation test for the prediction of dough technological properties. Two durum and two bread wheats with opposing technological properties are usually compared in order to highlight differences • SE-HPLC for the prediction of dough technological properties. Two durum and two bread wheats with opposing technological properties are usually compared in order to highlight differences • ELISA test on pasta for celiac people to control the effective absence of gluten using polyclonal antibodies against gluten proteins examMode A PowerPoint presentation related to a topic chosen by the student, but agreed with the lecturer, is normally required, followed by two questions on the program. A crop or a product of plant origin, or a topic present in the programme, is chosen, on the basis of which the lecturer assigns 2 specific papers, at least one of which is a review (also chosen by the student himself, subject to the lecturer's approval) on which the student relies to elaborate his/her oral presentation, which must last no less than 15 minutes and no more than 20. A score between 18 and 30 is given to the presentation and to each of the answers to the two questions on the general part, taking into account the student's level of content knowledge, ability to analyze, synthesize and make interdisciplinary connections, critical thinking and clarity of exposition. The final mark corresponds to the average of the individual marks and it is necessary to have a sufficiency in each question. It is advisable to contact the lecturer at least one month before the exam call books The teacher makes the slides and the bibliographic materials available mode Lessons are carried out in classroom, while the practical classes are held in the dedicated classroom. In this latter case, if the number of students is greater than 25, the exercitations are carried out in turns. Some practical classes (specifically the SE-HPLC and the ELISA test) are carried out in groups of 4-5 students in the teacher's lab. Normally a study visit is carried out at a milling plant or at the cereal technology laboratories of CREA (Rome) classRoomMode The lessons are carried out in classroom, while the practical classes are held in the dedicated classroom . In this latter case, if the number of students is greater than 25, the exercitations are carried out in turns. Some practical classes (specifically the SE-HPLC and the ELISA test) are carried out in groups of 4-5 students in the teacher's lab. Normally a study visit is carried out at a milling plant or at the cereal technology laboratories of CREA (Rome) bibliography The teacher makes the slides and the bibliographic materials available
119943 - THESIS	Second Semester	24

SUBJECT	SEMESTER	CFU	SSD
121642 - QUALITY PLANT-BASED FOODS	First Semester	6	AGRI-06/A
121645 - PLANT GENOMICS AND METAGENOMICS	First Semester	6	AGRI-06/A
121644 - FOOD ANALYSES AND BIOSEPARATION METHODS	First Semester	6	AGRI-06/A
121643 - PROCESSING BIOTECHNOLOGIES IN FOOD INDUSTRIES	First Semester	6	AGRI-06/A
119765 - ELECTIVE COURSE	First Semester	6
119939 - BIOINFORMATICS	Second Semester	6	BIOS-08/A	Learning objectives The course aims to consolidate basic knowledge regarding genomic databases and new sequencing technologies. Additionally, it will provide basic knowledge of programming languages necessary for the bioinformatics analyses addressed during the course. At the end of the course, students will be able to apply their skills to tackle and solve complex problems in the field of bioinformatics, such as the analysis and interpretation of large genomic datasets. They will also be capable of planning a genomic sequencing experiment and utilizing bioinformatics pipelines applicable in various scientific research contexts. Students will acquire the ability to integrate interdisciplinary knowledge from bioinformatics, genetics, and molecular biology to manage and solve multidimensional and complex problems. They will be able to tackle the complexity of biological data and information technologies, adapting and optimizing methodologies to address new and intricate challenges. Students will be able to communicate their chosen methodologies, results, and conclusions using technical and scientific language to both specialist and non-specialist audiences, through scientific documentation, academic articles, and oral presentations. The course will include theoretical lectures and practical exercises during which students will acquire the necessary skills for an autonomous learning in the field of bioinformatics. They will need to identify their own educational needs, address any gaps in their knowledge, and stay updated on emerging technologies and methodologies.
119937 - AGRO-INDUSTRIAL PHYTOPATHOLOGICAL BIOTECHNOLOGIES	Second Semester	6	AGRI-05/B	Learning objectives The course aims to consolidate and expand the knowledge of phytopathological biotechnology, deepening the new frontier techniques for an eco-sustainable control of the main agricultural phytopathologies. Students will acquire problem solving skills by approaching the subject in a multidisciplinary manner (plant pathology, physiology, molecular biology, genetics), to apply these skills in a scientific research context. Students will acquire the ability to integrate their multidisciplinary knowledge, in order to contextualize the possible social and ethical implications of phytopathological biotechnologies. This will be possible because students will be able to formulate scientific judgments/assumptions even on the basis of incomplete or limited information. Students will be able to communicate their knowledge with an appropriate scientific language, with a view to practicing speaking with specialists and non-specialists. This will be possible thanks to the exam format, which includes the presentation of a project by the student. The student will be able to study autonomously and self-managed, thanks to the fact that during the course the key notions are provided to then autonomously develop an exam project, also on the basis of the student's research inclinations.
119932 - CHEMISTRY OF NATURAL ORGANIC PRODUCTS	Second Semester	6	CHEM-05/A	Learning objectives The course is devoted to the study of natural organic substances; in particular, secondary metabolites found in the plant world. Beginning with their respective biogenetic precursors, structural aspects, biological properties, applications, extraction techniques, purification and chemical characterization are explored. The objective of the course is to provide students with a thorough knowledge of natural organic substances, which is to be described, during the examination, with propriety of language, clarity of exposition, critical analysis and synthesis skills.
119929 - FOOD BIOTECHNOLOGY	Second Semester	6	AGRI-07/A	Learning objectives The aim of the course is to deep the student's knowledge about industrial biotechnology for food processing, by providing articulated and systematic skills on the industrial use of microorganisms and enzymes useful in different food sectors. Moreover, the course aims to provide: • the suitable ability to manage the interaction between agro-food raw materials and the related biotechnological processes, both traditional and innovative, in order to implement the quality and sustainability of the finished product; • the tools to control and to regulate the biotechnological process, defining opportunities and constraints, in order to achieve the quality characteristics sought in the food product. Students will acquire knowledge relating to the general aspects of microorganisms and enzymes; as well as to the interconnections of physio-chemical and biochemical phenomena that may occur in their application to food processes. This will allow them to address, by modern and multidisciplinary approaches, the operational tasks of managing the physio-chemical and biochemical phenomena that may occur in the application of microorganisms and enzymes to food processes. By analyzing examples of process critical issues, students will acquire the ability to interpret and understand, which will be useful to formulate judgments for the personal re-elaboration of the most suitable solutions. Students will develop the ability to discuss clearly and briefly the topics of the course, as well as argue with scientific and professional terminology the case studies addressed in the classroom and in the laboratory. Students will develop the attitude to analyze the subject matter, to study from different sources and to make the appropriate relations between the theoretical aspects of the classroom and the texts with those applied in laboratory.
120981 - TECHNOLOGICAL INNOVATIONS TO IMPROVE THE QUALITY OF VEGETABLE CROPS	Second Semester	6	AGRI-02/B	Learning objectives Didactic Objectives The course aims to provide advanced knowledge and practical tools to understand, evaluate, and improve the quality of vegetable crops through the adoption of technological innovations and sustainable strategies. Students will acquire skills related to the factors influencing vegetable quality (intrinsic and extrinsic), innovative cultivation techniques (soilless systems, nutrition and irrigation management, use of sensors), and strategies to enhance the nutritional and functional value of productions (grafting, biostimulants, nutraceutical greenhouses). Particular emphasis will be placed on the integration of theoretical knowledge with applied and interpretative skills, as well as on the development of critical autonomy and communication abilities. At the end of the course, students will be able to: • Apply the acquired knowledge in real production contexts (applying knowledge and understanding); • Make independent and critical judgments regarding the use of technological innovations and crop management strategies (making judgements); • Communicate clearly and scientifically the results of their analyses and project designs (communication skills); • Independently update their knowledge and skills in relation to the evolution of technologies and cultivation practices (learning skills).
120024 - PROJECT WRITING AND MANAGEMENT	Second Semester	2		Learning objectives The course aims to provide students with the skills necessary to systematically integrate European project design methodologies with Project Management techniques, both in the formulation and implementation phases of projects, with particular attention to the phases of Project Cycle Management (PCM) and the three knowledge areas of Project Management. Through the contents made available by the teacher, students will acquire the basic notions to understand the functioning of European Union funding, the related multi-year programming frameworks and the formulation of project proposals consistent with the objectives of sectoral policies. In addition to the acquisition of hard skills to apply the techniques and methodologies learned, to complete the knowledge to be acquired, a focus will be dedicated to soft skills with particular attention to the management of project stakeholders.

Learning objectives

Didactic Objectives
The course aims to provide advanced knowledge and practical tools to understand, evaluate, and improve the quality of vegetable crops through the adoption of technological innovations and sustainable strategies. Students will acquire skills related to the factors influencing vegetable quality (intrinsic and extrinsic), innovative cultivation techniques (soilless systems, nutrition and irrigation management, use of sensors), and strategies to enhance the nutritional and functional value of productions (grafting, biostimulants, nutraceutical greenhouses). Particular emphasis will be placed on the integration of theoretical knowledge with applied and interpretative skills, as well as on the development of critical autonomy and communication abilities.
At the end of the course, students will be able to:
• Apply the acquired knowledge in real production contexts (applying knowledge and understanding);
• Make independent and critical judgments regarding the use of technological innovations and crop management strategies (making judgements);
• Communicate clearly and scientifically the results of their analyses and project designs (communication skills);
• Independently update their knowledge and skills in relation to the evolution of technologies and cultivation practices (learning skills).

Teacher's Profile

courseProgram

Concept and meaning of quality in vegetables: i) intrinsic properties (nutritional, organoleptic, safety) and extrinsic properties (commercial, aesthetic); ii) quality by product type: roots, leaves, fruits.
Cultivation environment and production systems: greenhouse vs open field (light, temperature, humidity), soilless systems (advanced hydroponic and aeroponic systems), management of nutrition and irrigation management, growing substrates, fresh-cut produce and nitrate control, use of sensors for real-time monitoring.
Strategies to improve quality: herbaceous grafting, biostimulants (types and application methods), nutraceutical greenhouses for for functional foods.
Analysis of real experiences in improving vegetable quality.

examMode

The written test will include multiple-choice questions and open-ended questions.

books

Orticoltura. Principi e pratica'. Edagricole. Curatori: Pardossi, Gianquinto, Santamaria, Incrocci
'Colture fuori suolo. Idroponica e coltivazione in substrato' Edagricole. Incrocci, Malorgio, Massa.
'Biostimolanti per un'agricoltura sostenibile' Ed. Informatore Agrario. Curatori: Colla, Rouphael

classRoomMode

Optional

Learning objectives

The course will introduce students to the principles and experimental approaches, in continuous evolution, of plant biotechnology. The course aims to strengthen the basic
knowledge on plant biotechnologies applied to forest trees (green biotechnologies, categories of biotechnological processes and products, model plants, plant tissue cultures,
recombinant methods, molecular tools), offering a framework to address current scientific problems (i.e. the use of transgenic trees) and also provide a basis for specialized studies in the field of in vitro clonal propagation, genetic improvement of trees and functional genomics. In the laboratory lessons students will develop some of the techniques currently used to obtain micropropagated plants, cultures of calluses and protoplasts of forest species and to detect genetic variation. The key concepts of the course will be integrated into a series of case studies and students will improve their ability to apply them to new situations in problem solving sessions, in particular dedicated to the Mediterranean region. At the end of the course, students will have an in-depth knowledge of the basic principles of forest biotechnology and modern techniques to obtain technological products (in vitro material characterized by clonal fidelity or somaclonal variants, secondary metabolites, transgenic and cisgenic tree materials, molecular tools for the study of genetic variability). Finally, they will have acquired the ability to understand the potential of using biotech trees to increase the productivity of forest plantations even in disadvantaged environments (biotic and abiotic stresses) or to use biotech trees for the recovery of arid soils (salinity, pollution).
Students will be encouraged to make use of the knowledge acquired during the course and during the laboratory exercises to apply it to specific problems such as, for example, the propagation of improved genotypes or somaclonal variants resistant to stressful biotics or abiotics or characterized by high wood productivity, as well as the conservation of threatened species or origins. Students will be able to interpret and discuss the scientific works presented in class and to identify its highlights and highlights.
During the lessons, students' ability to reflect and discuss the topics covered will be stimulated, as well as the comparison of opinions to develop their communication skills.
These skills will then be tested during the exam. Students will be able to expose and develop scientific topics related to the course. The active involvement of students through oral discussions in the classroom and experiences in laboratory practices will develop this skill.

Learning objectives

Knowledge and understanding
By the end of the course, students will grasp the core statistical principles applied to agricultural sciences, ranging from descriptive statistics to inferential methods (hypothesis testing, ANOVA, regression). They will understand the logic behind R programming, mastering the syntax required to handle complex data structures like vectors, data frames, and matrices. Furthermore, students will comprehend the theoretical and practical distinctions between supervised machine learning techniques (such as PLS, LDA, neural networks) and unsupervised ones (PCA, clustering, t-SNE), understanding exactly when and why to use them.

Applying knowledge and understanding
Students will be able to turn raw data into actionable insights by working independently within the R environment (RStudio, VS Code, or Positron). They will know how to write and execute scripts to import data, manage it using loops and logical conditions, and perform comprehensive statistical analyses. Specifically, they will be able to run parametric and non-parametric tests, build regression models (linear and non-linear), and implement classification and clustering algorithms. This practical skill will be directly demonstrated through the R script preparation required for the final exam.

Making judgments
Students will develop the critical thinking skills needed to interpret the numerical and graphical outputs generated by the software. Rather than simply running code, they will be able to assess the quality of predictive models (using metrics like RMSE or R2) and the statistical significance of their tests. A key component will be the ability to use AI assistants (LLMs) critically: students will learn to validate AI-generated code, avoiding passive “vibe coding” by identifying and fixing logical errors or hallucinations suggested by automated tools.

Communication skills
Students will be able to present their analysis results using appropriate technical language and high-quality data visualizations (publication-ready plots). They will be able to justify their statistical choices, such as why a non-parametric test or a specific clustering algorithm was used, both through clear comments within their exam script and by answering theoretical questions related to the first module.

Learning skills
The course will provide the methodology for continuous self-learning in the fast-evolving field of Data Science. Students will learn how to consult R library documentation, debug their own code, and properly use LLMs as tutors to speed up the learning of new functions or packages not covered in class, making them autonomous in tackling future analytical challenges.

Teacher's Profile

courseProgram

Module 1 - Fundamentals (3 CFU)
1) The function of statistics in the field of agricultural sciences
2) Population, sample, variable and data
3) Qualitative (nominal, ordinal) and quantitative (discrete, continuous) variables
4) Mean, median, mode, variance, standard deviation, range and coefficient of variation
5) Asymmetry and kurtosis
6) Histograms, box plots, bar graphs and line graphs
7) Normal distribution
8) Null hypothesis and alternative hypothesis, type I and type II errors
9) t-test, z-test, ANOVA, and post-hoc tests
10) Correlation, and linear non-linear regression
11) Principal component analysis and non-linear alternatives
12) Clustering

Module 2 – Applied statistics with R (3 CFU)
1) R fundamentals
a) Introduction to R
b) Installation and use of Integrated Development Environments (IDEs): RStudio, Positron, or VS Code
c) Basic operators, variables, and vectors

2) Data structures and AI Assistant for coding
a) Data structures: matrices, data frames, and lists
b) Large Language Models (LLMs): how to properly use ChatGPT & Co. to boost learning, avoiding the dangerous “vibe coding”

3) Data import, manipulation, and automation
a) Importing data into R from common file types (e.g., .csv, .xlsx, etc.).
b) Subsetting, filtering data, and executing code using logical conditions
c) Automating repetitive tasks with loops (i.e., for, and while)
d) Custom functions

4) Data visualization
a) Creating scatter plots, line graphs, and bar plots ready for publication
b) Brief introduction to high quality plots (i.e., ggplot2)

5) Descriptive statistics and distributions
a) Calculating descriptive statistics
b) Normality tests
c) Visualizing data distributions with histograms, boxplots, and Q-Q plots

6) Parametric and non-parametric tests
a) Performing Analysis of Variance
b) Post-hoc tests
c) Brief overview of non-parametric alternatives

7) Linear and non-linear regression
a) Building, interpreting, and visualizing simple linear models with lm() function
b) Fitting non-linear models using nls() function

8) Predictive model performance
a) Model performance with R2, Root Mean Squared Error (RMSE), and BIAS
b) Splitting datasets into calibration (training) and prediction (testing)

9) Unsupervised learning - part 1
a) Principal Component Analysis
b) Advanced techniques for complex datasets: t-SNE and UMAP

10) Unsupervised learning - part 2
a) Hierarchical clustering
b) Visualizing and interpreting clustering results

11) Supervised learning - part 1
a) Multivariate regression with Partial Least Squares (PLS)
b) Implementing k-fold cross-validation for building robust models

12) Supervised learning - part 2
a) Introduction to classification algorithms (e.g., Linear Discriminant Analysis, LDA; Quadratic Discriminant Analysis, QDA)
b) Training neural networks

examMode

The final exam involves the development of a data analysis project (Project Work) based on R, to be submitted prior to the exam date, accompanied by the script used and an interpretation of the results. The oral exam will consist of a critical discussion of the submitted project, aimed at assessing proficiency in programming tools, and questions on the theoretical foundations of statistics covered during the course.

books

Douglas C. Montgomery - Design and Analysis of Experiments - McGraw-Hill
Primary reference for Module 1. This text provides the theoretical and methodological foundations required to understand statistics applied to experimentation. It is used to deepen concepts regarding experimental design, hypothesis testing, analysis of variance (ANOVA), and regression, ensuring the necessary formal rigor before moving to computational approaches.

Hadley Wickham, Mine Çetinkaya-Rundel, and Garrett Grolemund - R for Data Science (2e) - O'Reilly (available online: https://r4ds.hadley.nz/)
Key resource for practical R programming in Module 2. Focused on the "tidyverse" ecosystem, this text covers essential operational skills: data import, data wrangling (cleaning and manipulation), advanced visualization, and workflow management within RStudio.

Thulin, M. - Modern Statistics with R (2e) - Chapman & Hall/CRC (available online: https://www.modernstatisticswithr.com/)
An advanced text bridging the gap between statistical theory and modern data science. It is used to apply the more complex statistical techniques covered in the curriculum within the R environment, including supervised and unsupervised machine learning methods (such as PCA, t-SNE, clustering, and model validation).

David Harvey - Chemometrics Using R, LibreTexts (available online: https://chem.libretexts.org/Bookshelves/Analytical_Chemistry/Chemometrics_Using_R_%28Harvey%29)
A specialized resource for applying R to analytical and multivariate data. This text is particularly relevant for the advanced sections of Module 2, as it bridges the gap between lab-based sciences and data modeling. It provides practical guidance on implementing chemometric tools such as Principal Component Analysis (PCA), Partial Least Squares (PLS), and clustering, which are essential for processing complex datasets like those from spectroscopy or food quality analysis.

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Learning objectives

The course aims to consolidate basic knowledge regarding genomic databases and new sequencing technologies. Additionally, it will provide basic knowledge of programming languages necessary for the bioinformatics analyses addressed during the course. At the end of the course, students will be able to apply their skills to tackle and solve complex problems in the field of bioinformatics, such as the analysis and interpretation of large genomic datasets. They will also be capable of planning a genomic sequencing experiment and utilizing bioinformatics pipelines applicable in various scientific research contexts. Students will acquire the ability to integrate interdisciplinary knowledge from bioinformatics, genetics, and molecular biology to manage and solve multidimensional and complex problems. They will be able to tackle the complexity of biological data and information technologies, adapting and optimizing methodologies to address new and intricate challenges. Students will be able to communicate their chosen methodologies, results, and conclusions using technical and scientific language to both specialist and non-specialist audiences, through scientific documentation, academic articles, and oral presentations. The course will include theoretical lectures and practical exercises during which students will acquire the necessary skills for an autonomous learning in the field of bioinformatics. They will need to identify their own educational needs, address any gaps in their knowledge, and stay updated on emerging technologies and methodologies.

Teacher's Profile

CHOICE GROUPS	YEAR/SEMESTER	CFU	SSD	LANGUAGE
TWO EXAMES AMONG THE FOLLOWING:	-	12	-	-
120981 - TECHNOLOGICAL INNOVATIONS TO IMPROVE THE QUALITY OF VEGETABLE CROPS MARIATERESA CARDARELLI	First Year / First Semester	6	AGRI-02/B
119938 - FOREST BIOTECHNOLOGY	First Year / First Semester	6	AGRI-03/B
121641 - DATA SCIENCE WITH -R ROBERTO MOSCETTI	First Year / Second Semester	6	AGRI-04/B
119939 - BIOINFORMATICS SILVIA TURCO	First Year / Second Semester	6	BIOS-08/A

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