General Info

SUBJECT	SEMESTER	CFU	SSD	LANGUAGE
119928 - PLANT GENOMES AND CHROMOSOME MANIPULATIONS LJILJANA KUZMANOVIC	First Semester	6	AGR/07		Learning objectives This course aims to provide the tools to acquire the cultural, theoretical and experimental bases in the field of genomics, also aimed at the application of genome manipulations for the improvement of plant species of agricultural importance. The course will give particular emphasis to acquisition of knowledge in the following areas: 1. how genomes are organized at a structural and functional level; 2. how knowledge from model species can be transferred to species of agricultural interest (e.g. rice, wheat); 3. how knowledge can be used to manipulate genomes for beneficial purposes (genomics-assisted breeding). Through the contents and methods of carrying out the program, also including the analysis of scientific articles, students will acquire and be able to process complex and multidisciplinary information and identify possible breeding strategies assisted by plant genomics. Communication skills will be stimulated through periodic interactive teacher-student summaries and in the final assessment phase (exam), normally based on a presentation concerning a course topic, chosen by the student. Through the information provided and the teaching methodology, the student will be able to gain familiarity with the scientific method and its application to genomics and related disciplines, to be able to proceed with in-depth and specialized studies with an advanced level of autonomy. Teacher's Profile courseProgram 1. Genome size and organisation: - Comparing prokaryotic and eukaryotic genomes: the C-value paradox described through examples of various Angiosperm plants; - Forces influencing genome size and expansion-contraction mechanisms (unequal crossing-over; illegitimate recombination). 2. Types, abundance and organization of genic and non-genic sequences in the eukaryotic chromosome: 2.1. Non-gene sequences - Telomeric, centromeric and intercalary highly repeated sequences; micro- and mini-satellites; - Transposable elements (TE) in Eukaryotes: comparison with prokaryotic IS elements; classes of TE and relative mode of transposition di ET and abundance in various Eukaryotic genomes: DNA- and RNA-TE or retroelements; effect of TE on size and structure of Eukaryotic genomes; amplification of TE through intra- and inter-element unequal crossing-over; 2.2. Eukaryotic genes: - Fine structure and structural variability (e.g. intron abundance and size) among taxa; exon re-shuffling and development of novel genes; - Gene families and super-families: gene duplication and divergence (neo- and sub-functionalization); examples of the histone gene family, of resistance gene families in plants and of the human globin super-family. 3. Genome compartmentalization: mosaic organization (isochores) of the human genome and of plant genomes; “gene-rich” and “gene-poor” regions; TE as main components of inter-genic spaces; comparison between genetic and physical maps: “hot” and “cold” spots of recombination and their correlation with gene density and transcription. 4. Comparative genomics: - Intergenomic and interspecific micro- and macro-synteny and colinearity; the “circle diagram” of grass genomes; levels of conservation: homoeologous chromosomes and orthologous genes; - Chromosome rearrangements and disruption of synteny and colinearity: evidence from comparative mapping and comparative sequencing. 5. Evolution and adaptive mechanisms of plant genomes, with particular focus on polyploidy; rapid genome changes following the polyploidisation event: maintenance and elimination of duplicated genes/sequences: examples from natural and neo-synthesized Triticum polyploids; gene silencing. 6. Epigenetics and epigenomics: modifications of chromatin structure (chromatin remodelling) mediated by DNA methylation, histone methylation/acetylation, RNA molecules; epigenetic changes associated with polyploidization. 7. Plant genome manipulations aimed at practical applications - Targets of manipulations for breeding purposes: utilisation of genetic variability outside the “target” species - From the creation of amphidiploids to single chromosome addition and substitution lines to targeted interspecific transfer of chromosome segments (chromosome engineering) in agriculturally relevant plant species: strategies and case studies, with particular focus on Triticeae species (wheat and related species), Solanum spp., Medicago spp., Lolium-Festuca complex. examMode A PowerPoint presentation is usually proposed on a topic chosen by the student from those covered in the course. Of the chosen topic, the teacher provides 1-3 (typically 2) scientific articles, one of which generally consists of a "review", while the other deals with a specific aspect of the same topic. During the presentation, the teacher normally asks some in-depth questions, also related to other aspects of the program. The mark given takes into account the level of knowledge of the contents, the ability to analyze, summarize and connect, even interdisciplinary, the ability to sense critically and the clarity of the exhibition. books - Teaching material (e.g. lesson slides) and scientific articles provided by the teacher and available on the institutional website; - Additional scientific articles on students' request, both for the preparation of the exam test and for the deepening of aspects of specific, individual interest; Selected chapters from: - Grotewold E, Chappell J, Kellogg E.A. - Plant Genes, Genomes and Genetics, 2015- John Wiley & Sons, DOI:10.1002/9781118539385 - Plant genome diversity - vol. 1 & 2 - Springer, 2012 - Goldberg et al. - From genes to genomes - McGraw-Hill (2021-) - Russell PJ - iGenetics: A Molecular Approach: Pearson New International Edition (English Edition, 2013-) classRoomMode Attendance is not mandatory, but encouraged, above all to stimulate discussion, both on what the teacher has exposed and on the scientific articles taken as reference and proposed by the teacher bibliography In addition to references indicated within the "Textbooks" section, students will be allowed to access a Google Drive folder containing a collection of scientific papers on the main subjects discussed during the teaching course
119929 - FOOD BIOTECHNOLOGY ILARIA BENUCCI	First Semester	6	AGR/15		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
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 courseProgram The course will focus on hazard identification and safety procedures that are necessary for working in laboratories. Starting from detailed reports of major laboratory accidents, classes will engage students in investigating dangers and latent risks keeping in mind that such working contexts may involve unique hazardous scenarios. To do so, specific risks and accident modes will be covered while an extensive coverage of those tools that allow dynamic safety assessments will be provided. More specifically, the following aspects related to lab working will be covered: - Terms and definitions regarding safety aspects, accident examples; - Chemical hazards; - Biological hazards (agents and pathogens); - Physical hazards (ergonomics, radiations, noise); - Safety hazards (electricity, fire, explosions); - System-related factors that affect lab working and that generate particualr pyschological responses from workers; - The human factor and the effectiveness-thoroughness trade-off in lab working; - The “cultures” of safety in work organisations and safety management systems; - Risk analysis and safety assessment - countermeasures, personal protective equipment requirements and emergency procedures. examMode Written examination consisting of two questions: one mandatory question from the lecturer, one chosen by the candidate from two options proposed by the test. 15-20 lines is the expected length for each answer. Pass/fail are the only available results for the test. books Provided by the lecturer mode Lessons will be provided in class, plus available via zoom links and recorded on Unitus Moodle. classRoomMode In-person classes, lessons recorded for academic year 2023/2024 are available bibliography Leveson, N.G. - System Safety Engineering: Back to the Future (2002) - Massachusetts Institute of Technology Leveson, N.G. - Engineering a Safer World - Systems Thinking Applied to Safety (2011) - MIT Press Cambridge, MA
TWO EXAMES AMONG THE FOLLOWING:	-	-	-	-
AGRO-INDUSTRIAL PHYTOPATHOLOGICAL BIOTECHNOLOGIES SARA FRANCESCONI	First Semester	6	AGR/12		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
FOREST BIOTECHNOLOGY ELENA KUZMINSKY	First Semester	6	AGR/05		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. Teacher's Profile courseProgram The class and lab. activities lectures will be focused on the following groups of topics/abilities. - General introduction to plant biotechnology: history, global significance of modern plant biotechnology, biotech trees; - Model plants for tree species: the need of a model plant for tree species; - Vegetative propagation and tissue culture (tree cloning, micropropagation, cryopreservation, callus culture, haploid plants, protoplast isolation, production of secondary metabolites); - General introduction to the genetically modified trees; Methods of genetic transformation of forest trees (Agrobacterium, biolistic, and electroporation) - Applications of recombinant DNA technology for the improvement of forest trees - General introduction to the Omics sciences (genomics, proteomics and metabolomics) - Sequencing of tree species (history and main methodologies), Next generation sequencing - Molecular markers history, molecular markers currently used in plant biotechnology - Marker Assisted Selection examMode Oral exam on the course program to verify the ability to know and link the contents of the course. The exam consists of an oral exam. We would like to remind students that, in order to take the exam, they must register for the exam session in question at the “Portale dello studente”. The exam is the same for both attending students and non-attenders. The exam takes place according to the University Teaching Regulations. The exam is scored out of a maximum of 30 points (minimum mark 18/30), which will go into the calculation of your grade point average, and evaluates your: 1. knowledge of course contents (superficial, appropriate, accurate and complete, complete and in-depth), 2. ability to integrate and critically discuss course contents (sufficient, good, very good), 3. skill in planning a monitoring activity starting from a case study (sufficient, good, very good), 4. level of clarity in exposition (lack of exposure, simple, clear and correct, safe and correct). books 1. Plant Cell Culture, essential methods (2010). Edited by M.R. Davey and P. Anthony. Wiley-Blackwell. 2. Tree biotechnology (2014). Edited by K. G. Ramawat, J. M. Mérillon, M. R. Ahuja. CRC Press. 3. Plant Biotechnology and Agriculture: Prospects for the 21st Century (2012). Edited by Altman A and Hasegawa PM. Accademic Press. 4. Plants, genes, and Crop Biotechnology (2003). Edited by M.J. Chrispeels & D.E. Sadava. Jones and Bartlett publishers. Non-attending students are encouraged to contact the teacher for information about the program, teaching materials, and how to evaluate the benefit. mode Classroom lecture sessions with PowerPoint presentations with figures and process diagrams for a total of 38 hours. In addition, there are 10 hours of teaching labs in which the students will hold micropropation, callus culture and regeneration process, protoplast isolation and use; moreover, the students will apply DNA extraction, PCR technique with relative electrophoretic run and evaluation of the amplicons classRoomMode Strongly recommended, especially for lab practices, but not mandatory. bibliography See textbooks. Teacher's Profile courseProgram The class and lab. activities lectures will be focused on the following groups of topics/abilities. - General introduction to plant biotechnology: history, global significance of modern plant biotechnology, biotech trees; - Model plants for tree species: the need of a model plant for tree species; - Vegetative propagation and tissue culture (tree cloning, micropropagation, cryopreservation, callus culture, haploid plants, protoplast isolation, production of secondary metabolites); - General introduction to the genetically modified trees; Methods of genetic transformation of forest trees (Agrobacterium, biolistic, and electroporation) - Applications of recombinant DNA technology for the improvement of forest trees - General introduction to the Omics sciences (genomics, proteomics and metabolomics) - Sequencing of tree species (history and main methodologies), Next generation sequencing - Molecular markers history, molecular markers currently used in plant biotechnology - Marker Assisted Selection examMode Oral exam on the course program to verify the ability to know and link the contents of the course. The exam consists of an oral exam. We would like to remind students that, in order to take the exam, they must register for the exam session in question at the “Portale dello studente”. The exam is the same for both attending students and non-attenders. The exam takes place according to the University Teaching Regulations. The exam is scored out of a maximum of 30 points (minimum mark 18/30), which will go into the calculation of your grade point average, and evaluates your: 1. knowledge of course contents (superficial, appropriate, accurate and complete, complete and in-depth), 2. ability to integrate and critically discuss course contents (sufficient, good, very good), 3. skill in planning a monitoring activity starting from a case study (sufficient, good, very good), 4. level of clarity in exposition (lack of exposure, simple, clear and correct, safe and correct). books 1. Plant Cell Culture, essential methods (2010). Edited by M.R. Davey and P. Anthony. Wiley-Blackwell. 2. Tree biotechnology (2014). Edited by K. G. Ramawat, J. M. Mérillon, M. R. Ahuja. CRC Press. 3. Plant Biotechnology and Agriculture: Prospects for the 21st Century (2012). Edited by Altman A and Hasegawa PM. Accademic Press. 4. Plants, genes, and Crop Biotechnology (2003). Edited by M.J. Chrispeels & D.E. Sadava. Jones and Bartlett publishers. Non-attending students are encouraged to contact the teacher for information about the program, teaching materials, and how to evaluate the benefit. mode Classroom lecture sessions with PowerPoint presentations with figures and process diagrams for a total of 38 hours. In addition, there are 10 hours of teaching labs in which the students will hold micropropation, callus culture and regeneration process, protoplast isolation and use; moreover, the students will apply DNA extraction, PCR technique with relative electrophoretic run and evaluation of the amplicons classRoomMode Strongly recommended, especially for lab practices, but not mandatory. bibliography See textbooks.
NEW EXTRA CURRICULAR GROUP	-	-	-	-
NANOTECHNOLOGY IN CROP PROTECTION	First Semester	3	AGR/12
	First Semester	3	AGR/12
119930 - PLANT BREEDING ANDREA MAZZUCATO	Second Semester	6	AGR/07		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 Teacher's Profile courseProgram - Introduction, history and aim of plant breeding, concept of ideotype. - Biology of plant reproduction: floral morphology, macro and microsporogenesis, macro and microgametogenesis, pollination, progamic phase, fertilization, embryogenesis, seed and fruit development. Molecular biology of flowering induction and flower development, genes controlling inflorescence, flower and floral organs identity, ABC(DE) model. Mode of reproduction (sexual reproduction, vegetative propagation, apomixis), sex determination (hermaphroditism, monoecism, dioecism), mating system (autogamy and allogamy), experimental characterization of plant reproductive system and of outcrossing rate. Male sterility (genetic, cytoplasmic and genetic-cytoplasmic, functional and conditional). Self-incompatibility (sporophytic and gametophytic). Apomixis, cytoembryological bases, genetic control, breeding of obligate and facultative apomictic species, perspectives of transferring apomixis to sexual species. Fruit set and development, parthenocarpy, biotechnological approaches to control fruit set. Fruit ripening, mutants affected in ripening and in pigment accumulation. - Sources of genetic variability: gene pool concept, germplasm collection and storage, seed banks, germplasm evaluation, variability induced by mutagenesis, somaclonal variation. - Intra and interspecific cross, sexual interspecific barriers, biotechnologies to facilitate interspecific crossing, in vitro fertilization and embryo rescue. - Theory of selection: principles of theory of selection for monogenic and polygenic characters, penetrance and expressivity. - Genetic population structure in autogamous, allogamous, vegetatively propagated and apomictic species. - Breeding schemes for autogamous species: selection in existing populations: mass selection and pure line selection. Selection in segregating populations: pedigree, bulk and single seed descent methods, double haploids. Backcross method to transfer a dominant and a recessive allele, linkage drag, principles of marker assisted selection, multiline varieties, F1 hybrids in autogamous species. - Breeding schemes for allogamous species: mass selection, recurrent selection, synthetic varieties, F1 hybrids in allogamous species, use of male sterility in hybrid production schemes. - Principles of genetics of seed production: evaluation of new varieties, subscription to the Register of Varieties, maintenance selection and seed production, isolation, generations of seed multiplication. Legislation related to seed production and marketing. Biotechnologies for the protection of plant varieties (molecular markers for distinctiveness), estimation of genic flux and gene flux containment in conventional and genetically modified varieties. Seminars: students will be invited to attend one or two seminars focussing on technical and/or scientific aspects related to topics of the course. Practical activities: practical activity will be dedicated to the knowledge of genetic variability in a crop species, to the examination of mutants involved in reproductive biology, to technicalities to carry out controlled crosses and to a visit to a company or experimental station involved in breeding and/or seed production of crop species. examMode The candidate should demonstrate the acquisition of knowledge in the field of plant breeding. The judgment and the final grade will take into account the knowledge and concepts acquired, the ability to analyze problems, to connect interdisciplinary knowledge, mastery and clarity of expression and exposure: The exam will be oral. The exam will generally consist on the discussion of three topics, of which one to be chosen by the candidate, that cover the three areas of the program, biology of crop plant reproduction, schemes and methods of plant breeding, seed production and legislation. books Barcaccia G. e Falcinelli M., Genetica e genomica, vol. II, 2005, Miglioramento genetico, Liguori. Lorenzetti F. et al., Miglioramento genetico delle piante agrarie, 2018, Edagricole. Ciriciofolo E. e Benincasa, Sementi: Biologia, produzione e tecnologia, 2018 Edagricole. Material from the lecturer through the portal. mode The course is organized in 5 CFUs of teaching in classroom plus 1 CFU of practical activity in didactic laboratories, didactic-experimental farm and/or visits in private companies or farms. classRoomMode Attending the course is not compulsory, but strongly recommended bibliography Additional materials related to several topics of the program will be indicated by the lecturer during classes and will be then available on Moodle.
119931 - PLANT BIOTECHNOLOGY AND PHARMACEUTICAL PRODUCTS MARCELLO DONINI	Second Semester	6	BIO/15		Learning objectives The course aims to provide in-depth cultural knowledge and understanding skills at both theoretical and experimental level on the design, production and application of recombinant molecules with high added value in the pharmaceutical field. Particular importance is given to promoting independent judgment, understanding and communication skills through the presentation and examination of different traditional biological systems for the production of biological drugs. The knowledge acquired during the course will allow students to develop the ability to synthesize and integrate information by formulating solid judgments, through the in-depth analysis of sources that could also be initially partial and incomplete. Students will develop the ability to communicate on issues related to pharmaceutical biotechnology with academic partners, with operators of the private sector and with non-specialist figures. Students will be able to learn and find the correct sources for an independent and autonomous study Teacher's Profile
119932 - CHEMISTRY OF NATURAL ORGANIC PRODUCTS ROBERTA BERNINI	Second Semester	6	CHIM/06		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)
120024 - PROJECT WRITING AND MANAGEMENT MASSIMO ROMANELLI	Second Semester	2			Learning objectives The course aims to teach basic principles about project writing and presentation techniques. Students will acquire knowledge on grant writing and principles, as well as on poster and oral presentation structure and preparation. During the course students will acquire skills on understanding research topics, writing a grand proposal autonomously, preparing posters and oral presentations. At the end of the course, students should be able to lead the reader into the topic and scope of the research proposal, describe the theoretical or practical research problem intended to address, state the specific question(s) to answer, explain how the project idea will solve or alleviate the problem or the social need as well as, to explain how the idea, if successful, will result in breakthrough innovation. Teacher's Profile courseProgram The course aims to provide the basic elements of project writing and management and the main EU funding programmes concerning: Orienting among the opportunities offered by EU funding under direct, indirect or shared management; The design phase involving analysis of the call and work programme; definition of objectives, partnership, impact; work programme; state of the art; budget and resources; project evaluation. The management and scientific implementation phase of the project (meeting deliverables, reports, etc.); The financial reporting phase (periodic and final financial reports; European and national rules) Marie Skłodowska-Curie Actions (MSCA), the opportunities and positions for participation in European research projects for young Early Stage Researchers (ESR) and the EURAXESS portal will be described. examMode Multiple-choice and free-choice test with practical exercise in project writing and budgeting books No textbooks are adopted for the course but the teaching material quoted in the presentations uploaded on moodle and downloadable on EU institutional platforms are considered open source reference resources. mode Running on the basis of PPT presentations and with the aid of PC navigation available in the Geoinformatics classroom classRoomMode The attendance is not mandatory bibliography https://commission.europa.eu/funding-tenders_en ec.europa.eu/info/funding-tenders/opportunities/portal/screen/home PM2 www.pm2alliance.eu
TWO EXAMES AMONG THE FOLLOWING:	-	-	-	-
BIOINFORMATICS SILVIA TURCO	First Semester	6	BIO/11		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 courseProgram Course program: • Bioinformatics introduction and application examples. • Molecular biology pills: Prokaryotes and Eukaryotes, genome size, DNA and chromatin structure, the RNA world, the central dogma, RNA interference, epigenetics. • Databases: history, sequences and structures, primary, secondary, composite. NCBI, GenBank, Pubmed. • Literature Tools: Mendeley, Scholar, Scopus. • Local and global alignment: BLAST Vs Emboss needle. EBI tools. • First generation sequencing technologies: Maxam-Gilbert Vs Sanger sequencing. Automated Sanger • Next generation sequencing technologies: Roche 454, Ion Torrent, Illumina, Solid. • Third generation sequencing technologies PacBio, Nanopore. • Terminology and definitions: Coverage, Paired-end sequencing, Alignment, Phred score, FASTA format, FASTQ file, SAM and BAM, VCF file, GFF file, Barcoding, Trimming, FastQC, Quality check, Assembly. • Unix-Bash basic command lines. • De novo assembly, Reference-based assembly, Genome annotation. examMode The exam is oral, with general question regarding the arguments in the program. The student will be evaluated for his/her critical thinking, knowledge acquisition and participation during the practical lectures. books All the necessary course material will be provided during the course and will be available on Moodle. mode The course is organized in frontal theoretical lessons and practical lessons. classRoomMode Attendance is not mandatory but highly recommended. bibliography 1) The Third Revolution in Sequencing Technology, Erwin L. van Dijk, , * Yan Jaszczyszyn, Delphine Naquin and Claude Thermes. Trends in Genetics, September 2018, Vol. 34, No. 9 © 2018 Elsevier Ltd. https://doi.org/10.1016/j.tig.2018.05.008 2) Kchouk M, Gibrat JF, Elloumi M (2017) Generations of Sequencing Technologies: From First to Next Generation. Biol Med (Aligarh) 9:395. doi:10.4172/0974-8369.1000395 3) Overview of Next-Generation Sequencing Technologies. Barton E. Slatko, Andrew F. Gardner and Frederick M. Ausubel. Current Protocols in Molecular Biology e59, April 2018. doi: 10.1002/cpmb.59 4) Konrad Paszkiewicz, Modern approaches to sequencing, University of Exeter.
ADVANCED TISSUE CULTURE CRISTIAN SILVESTRI	First Semester	6	AGR/03		Learning objectives Knowledge and understanding: Students will acquire advanced knowledge of plant tissue culture techniques, the use of PGRs, micropropagation, somatic embryogenesis, organogenesis, genetic transformation and genome editing (CRISPR/Cas and VIGS), virosis, thermotherapy, and cryotherapy. Applying knowledge and understanding: Students will apply advanced techniques to solve problems in plant tissue culture, improve protocols and in vitro culture techniques, including those aimed at plant breeding. Making judgment: Students will develop the ability to evaluate the effectiveness of techniques and protocols used, solve specific problems, and adapt techniques to different plant species. Communication skills: Students will improve their communication skills to present their research results clearly and efficiently. Learning skills: The course encourages continuous learning, preparing students to constantly update themselves on new techniques and discoveries in the field of plant tissue culture and genetic transformation, also through the use of common search engines (Scopus, WoS, Google Scholar). Teacher's Profile courseProgram Advanced Techniques of Plant Tissue Culture, Manipulation of growth regulators for specific outcomes, novel hormones, less frequently used growth regulators and small molecules peptides, troubleshooting common issues in tissue culture, Advanced Applications of Micropropagation (Photoautotrophic culture, liquid culture and bioreactors). Micropropagation of economically important plant species Somatic Embryogenesis and Organogenesis and genetic transformation techniques: Challenges and strategies for improving efficiency, recalcitrance. Protocols for CRISPR/Cas and VIGS. Principle and application of trans-grafting. Plants for Health: From Secondary Metabolites to Molecular Farming. Advanced Techniques for Genetic Stability and Virus Elimination techniques in tissue culture (Thermotherapy and Cryotherapy). Integration of omics data for improving tissue culture protocols. Regulatory frameworks for genetically modified organisms. examMode Assessment will be based on exams, laboratory reports and presentations books Students will have access to a selection of scientific articles and study materials provided by the instructor during the course mode The course will include lectures, laboratory sessions, seminars, and discussions. Practical demonstrations and case studies will be used to reinforce theoretical concepts. classRoomMode The attendance of the course is not mandatory. However, it is strongly recommended bibliography Plant Tissue Culture, Development, and Biotechnology Edited ByRobert N. Trigiano, Dennis J. Gray
120498 - RESEARCH LABORATORY TRAINING ANDREA FOCHETTIFABRIZIO OLIVIERI	Second 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 Teacher's Profile

SUBJECT	SEMESTER	CFU	SSD	LANGUAGE
119934 - BIO-ECONOMY DAVIDE DELL'UNTO	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 1. Importance of the Bio-Economy for the national economy, with particular reference to the agri-food sector. 2. Introduction of some concluded and ongoing research: consumer choices (healthy foods), producer choices (use of chemical inputs, gas emissions greenhouse, investments in digital technologies in agriculture). 3. Introduction to economic theory: a. Definitions, circular flow diagram, production possibilities frontier and opportunity cost. b. Market supply and demand functions and their determinants. c. Market equilibrium. d. Effects on the market of the application of economic policy instruments. e. Consumer theory: total utility, marginal utility, indifference curves and optimal choices. f. Producer theory: entrepreneur's profit, analysis of the individual components (product price, quantity produced). g. Production function with a variable production factor. h. Production function with 2 variable factors: isoquant and isocost functions, and optimal choices. i. Type of costs in the short and long run and cost geometry in the short run. j. Market in perfect competition: characteristics, consequences, different profit situations (positive, zero, negative), entry and exit from the market. 4. Technological innovation, value and protection of intellectual property. 5. Theory on Cost-Benefit Analysis. Classroom exercise on the application of cost-benefit analysis to a traditional genetic improvement program and to one based on Assisted Evolution Technologies (AET). 6. Classification and evaluation criteria of capital at the service of the agri-food company. 7. The economic balance of the agri-food company: structure and contents of the balance sheet and the income statement. 8. Community strategies and policies: Bio-Economy strategies, Green Deal, Farm to Fork. 9. Illustration of the case studies for the exam and the methods for drafting the written report and the oral presentation. examMode Written mid-term test and final exam with multiple-choice questions. books Teaching materials indicated and provided by the teacher. mode The lessons will be held in mixed mode: in person and connected via Zoom Meetings. classRoomMode Attendance at classes is not mandatory, but highly recommended. bibliography None.
119935 - PLANT GENOMICS AND STRESS RESPONSES	-	12	-	-	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.
MODULE II FRANCESCO SESTILI	Second Semester	6	AGR/07		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 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.
MODULE II DANIEL VALENTIN SAVATIN	Second Semester	6	BIO/04		Learning 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 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 ROSARIO MULEO	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. Teacher's Profile courseProgram Lectures will be supported by powerpoint presentations of the issues and will be available to students. In addition, novelty articles, which are published during the teaching period, will be distributed and discussed with the aims to advance the knowledge on the topics of the teaching subjects. Gene network regulation of development and production: branching and tree vigour, changing phase, alternate fruit bearing, flower induction, fruit development and maturation, postharvest fruit regulation. The genetic network that controls plant interaction with biotic and environmental factors: a) photoreceptors and regulation of shadow avoidance response, phase changing, photoperiodic rhythmic responses; b) temperature receptors system and adaptive responses to high and low temperatures, vernalization and flower development and fruiting; c) flooding and adaptive response; d) water and minerals sensors and regulating plant nutrition and metabolite compounds; e) communication between plants (and scion-rootstock) and plant with other organisms; e) plant gene regulation host/parasite-predators: the case of Erwinia amylovora (Fire blight, Pseudomonas spp; Venturia, etc.). Plant organs: fruit and leaf as bio-factory of structural and secondary metabolites. Genetic and epigenetics regulation of secondary metabolites synthesis and catabolism: apple and grape mutants cases. Use of bioinformatics for the detection and isolation of functional allelic genes (and orthologs), small RNAs and methylation status of regulatory sequences playing an important role into relevant biological processes. Overview of isolation, cloning, sequencing of functional genes and/or functional sequences; generation of constructs to apply in improvement biotechnology programmes. Gene transfer in woody plants. Innovative techniques for studying gene expression and epigenetics. Molecular tools as markers for assisted selection and genetic improvement. Main biotechnological improvement fruit crop plants, examples. The experiences of transgenes in fruit tree species and new system to reduce juvenility and applying of Cisgenome and Editing genome. The relevant plant and productive traits that require biotechnology and genetic improvement among the main fruit tree species. Laboratory exercises will take place in the Laboratory of Molecular eco-physiology of woody plants and tissue culture ( rooms 232-234) and 2CFU (16 hrs) will be dedicated. Practice exercises will be by conducted in the laboratory to complete the acquisition of the technologies: On fruit crops plants, it will run on: nucleic acid extraction, purification and quantitative and qualitative assessment; phylogenetic analysis of the extra- and intra-species diversity applying molecular markers (AFLP, SSR, EST, etc.). Particular attention will be paid to the HRM and ARMS techniques for the analysis of SNPs markers and methylation status (developed in the laboratory), semi-quantitative and quantitative allelic expression analysis; epigenetic analysis of cloned plants for the verification of the genetic identity with random and dedicate procedures (M-SAP, EpiHRMAssay, etc). Finally, bioinformatic tools will be also used to tanscriptome and genome analyses, and biological function analysis. examMode The final valuation will consider knowledge and concepts acquired, ability to analyze problems, connect interdisciplinary knowledge, make hypotheses and judgments, and mastery and clarity of expression and exposition. The candidate will be asked five questions spanning the entire program, each of which is scored from 0 to 10. The final grade is the average of the five individual marks. In critical situations, such as a high number in the reservation of candidates, or peculiarities of one or more candidates, the examination may be conducted in written form with five open-ended questions, graded as for the oral. Candidates will be given one and a half hours to answer. In addition, at the request of individual students, it is still possible to take the examination in written or oral form, regardless of what is reported in the official roll call. At the candidate's request, a PowerPoint presentation exploring a topic chosen by the student but agreed upon with the lecturer may be displayed, followed by three questions on the syllabus. The presentation will be given a score from 0 to 10 and each of the answers to the three questions. The lecturer was deemed appropriate, in order to increase the clarity of the exposition may ask questions. The final grade will be formulated considering the level of content knowledge, ability to analyze, synthesize and make interdisciplinary connections, critical thinking and clarity of exposition. The final grade corresponds to the average of the individual grades. books Biodiversity, Chapman & Hall, London, 1988 G. Valle, M. Helmer Citterich, M. Attimonelli, G. Pesole., Introduzione alla Bioinformatica, Zanichelli, 2003 LITZ R.E., BIOTECHNOLOGY OF FRUIT AND NUT CROPS., CABI PUBLISHING, 2004 Articoli e materiale didattico forniti direttamente dal docente mode The course features up to 60% of the hours in the classroom, and the remaining 40% administered as field laboratory activities, visits in farms. The course will be taught in Italian, with slides and supplementary material in Italian and English. Although the frequency is not obligatory, the frequency of laboratory activities and exercises is strongly recommended, and which cannot be less than 70% of the scheduled hours. Observations on development of the fruit tree plant will be carried out, and laboratory activities on gene expression of important networks of plant development and plant production, epigenetic analysis with EpyHRMAssay technology, secondary metabolism analysis and bioinformatic analysis genomic, transcriptomic. Metabolic measurements and other parameters of fruit quality will be carried out in the fruits of some cultivated species. Metabolites measurements and other fruit quality parameters will be measured in some fruit crops. Lectures will be supported by powerpoint presentations containing mindmaps, comments on graphs and photograph, illustration of cell function and biotechnology tools and procedure of the issues and will be available to students to promote further discussion and forum. Additionally, novelty articles published recently and/or during the teaching period will be distributed and discussed with the aims to advance the knowledge on the topics of the teaching subjects. Therefore, students will be called to the debate to increase understanding and hypothesize possible solutions. classRoomMode The course features up to 60% of the hours in the classroom, and the remaining 40% administered as field laboratory activities, visits in farms.- bibliography Biodiversity, Chapman & Hall, London, 1988 G. Valle, M. Helmer Citterich, M. Attimonelli, G. Pesole., Introduzione alla Bioinformatica, Zanichelli, 2003 LITZ R.E., BIOTECHNOLOGY OF FRUIT AND NUT CROPS., CABI PUBLISHING, 2004 Articoli e materiale didattico forniti direttamente dal docente
119942 - INTERNSHIP	First Semester	6
119941 - ELECTIVE COURSES	First Semester	12
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 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 or 3 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

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

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.

Teacher's Profile

courseProgram

The class and lab. activities lectures will be focused on the following groups of topics/abilities.
- General introduction to plant biotechnology: history, global significance of modern plant biotechnology, biotech trees;
- Model plants for tree species: the need of a model plant for tree species;
- Vegetative propagation and tissue culture (tree cloning, micropropagation, cryopreservation, callus culture, haploid plants, protoplast isolation, production of secondary metabolites);
- General introduction to the genetically modified trees; Methods of genetic transformation of forest trees (Agrobacterium, biolistic, and electroporation)
- Applications of recombinant DNA technology for the improvement of forest trees
- General introduction to the Omics sciences (genomics, proteomics and metabolomics)
- Sequencing of tree species (history and main methodologies), Next generation sequencing
- Molecular markers history, molecular markers currently used in plant biotechnology
- Marker Assisted Selection

examMode

Oral exam on the course program to verify the ability to know and link the contents of the course.
The exam consists of an oral exam. We would like to remind students that, in order to take the exam, they must register for the exam session in question at the “Portale dello studente”. The exam is the same for both attending students and non-attenders.
The exam takes place according to the University Teaching Regulations. The exam is scored out of a maximum of 30 points (minimum mark 18/30), which will go into the calculation of your grade point average, and evaluates your:
1. knowledge of course contents (superficial, appropriate, accurate and complete, complete and in-depth),
2. ability to integrate and critically discuss course contents (sufficient, good, very good),
3. skill in planning a monitoring activity starting from a case study (sufficient, good, very good),
4. level of clarity in exposition (lack of exposure, simple, clear and correct, safe and correct).

books

1. Plant Cell Culture, essential methods (2010). Edited by M.R. Davey and P. Anthony. Wiley-Blackwell.
2. Tree biotechnology (2014). Edited by K. G. Ramawat, J. M. Mérillon, M. R. Ahuja. CRC Press.
3. Plant Biotechnology and Agriculture: Prospects for the 21st Century (2012). Edited by Altman A and Hasegawa PM. Accademic Press.
4. Plants, genes, and Crop Biotechnology (2003). Edited by M.J. Chrispeels & D.E. Sadava. Jones and Bartlett publishers.
Non-attending students are encouraged to contact the teacher for information about the program, teaching materials, and how to evaluate the benefit.

mode

Classroom lecture sessions with PowerPoint presentations with figures and process diagrams for a total of 38 hours. In addition, there are 10 hours of teaching labs in which the students will hold micropropation, callus culture and regeneration process, protoplast isolation and use; moreover, the students will apply DNA extraction, PCR technique with relative electrophoretic run and evaluation of the amplicons

classRoomMode

Strongly recommended, especially for lab practices, but not mandatory.

bibliography

See textbooks.

Teacher's Profile

courseProgram

examMode

books

mode

classRoomMode

Strongly recommended, especially for lab practices, but not mandatory.

bibliography

See textbooks.

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

courseProgram

Course program:
• Bioinformatics introduction and application examples.
• Molecular biology pills: Prokaryotes and Eukaryotes, genome size, DNA and chromatin structure, the RNA world, the central dogma, RNA interference, epigenetics.
• Databases: history, sequences and structures, primary, secondary, composite. NCBI, GenBank, Pubmed.
• Literature Tools: Mendeley, Scholar, Scopus.
• Local and global alignment: BLAST Vs Emboss needle. EBI tools.
• First generation sequencing technologies: Maxam-Gilbert Vs Sanger sequencing. Automated Sanger
• Next generation sequencing technologies: Roche 454, Ion Torrent, Illumina, Solid.
• Third generation sequencing technologies PacBio, Nanopore.
• Terminology and definitions: Coverage, Paired-end sequencing, Alignment, Phred score, FASTA format, FASTQ file, SAM and BAM, VCF file, GFF file,
Barcoding, Trimming, FastQC, Quality check, Assembly.
• Unix-Bash basic command lines.
• De novo assembly, Reference-based assembly, Genome annotation.

examMode

The exam is oral, with general question regarding the arguments in the program. The student will be evaluated for his/her critical thinking, knowledge acquisition and participation during the practical lectures.

books

All the necessary course material will be provided during the course and will be available on Moodle.

mode

The course is organized in frontal theoretical lessons and practical lessons.

classRoomMode

Attendance is not mandatory but highly recommended.

bibliography

1) The Third Revolution in Sequencing Technology, Erwin L. van Dijk, , * Yan Jaszczyszyn, Delphine Naquin and Claude Thermes. Trends in Genetics, September 2018, Vol. 34, No. 9 © 2018 Elsevier Ltd. https://doi.org/10.1016/j.tig.2018.05.008
2) Kchouk M, Gibrat JF, Elloumi M (2017) Generations of Sequencing Technologies: From First to Next Generation. Biol Med (Aligarh) 9:395. doi:10.4172/0974-8369.1000395
3) Overview of Next-Generation Sequencing Technologies. Barton E. Slatko, Andrew F. Gardner and Frederick M. Ausubel. Current Protocols in Molecular Biology e59, April 2018. doi: 10.1002/cpmb.59
4) Konrad Paszkiewicz, Modern approaches to sequencing, University of Exeter.

Learning objectives

Knowledge and understanding: Students will acquire advanced knowledge of plant tissue culture techniques, the use of PGRs, micropropagation, somatic embryogenesis,
organogenesis, genetic transformation and genome editing (CRISPR/Cas and VIGS), virosis, thermotherapy, and cryotherapy. Applying knowledge and understanding: Students will apply advanced techniques to solve problems in plant tissue culture, improve protocols and in vitro culture techniques, including those aimed at plant breeding.
Making judgment: Students will develop the ability to evaluate the effectiveness of techniques and protocols used, solve specific problems, and adapt techniques to different
plant species. Communication skills: Students will improve their communication skills to present their research results clearly and efficiently. Learning skills: The course encourages continuous learning, preparing students to constantly update themselves on new techniques and discoveries in the field of plant tissue culture and genetic transformation, also through the use of common search engines (Scopus, WoS, Google Scholar).

Teacher's Profile

courseProgram

Advanced Techniques of Plant Tissue Culture, Manipulation of growth regulators for specific outcomes, novel hormones, less frequently used growth regulators and small molecules peptides, troubleshooting common issues in tissue culture, Advanced Applications of Micropropagation (Photoautotrophic culture, liquid culture and bioreactors). Micropropagation of economically important plant species Somatic Embryogenesis and Organogenesis and genetic transformation techniques: Challenges and strategies for improving efficiency, recalcitrance. Protocols for CRISPR/Cas and VIGS. Principle and application of trans-grafting. Plants for Health: From Secondary Metabolites to Molecular Farming. Advanced Techniques for Genetic Stability and Virus Elimination techniques in tissue culture (Thermotherapy and Cryotherapy). Integration of omics data for improving tissue culture protocols. Regulatory frameworks for genetically modified organisms.

examMode

Assessment will be based on exams, laboratory reports and presentations

books

Students will have access to a selection of scientific articles and study materials provided by the instructor during the course

mode

The course will include lectures, laboratory sessions, seminars, and discussions. Practical demonstrations and case studies will be used to reinforce theoretical concepts.

classRoomMode

The attendance of the course is not mandatory. However, it is strongly recommended

bibliography

Plant Tissue Culture, Development, and Biotechnology
Edited ByRobert N. Trigiano, Dennis J. Gray

CHOICE GROUPS	YEAR/SEMESTER	CFU	SSD	LANGUAGE
TWO EXAMES AMONG THE FOLLOWING:	-	12	-	-
119937 - AGRO-INDUSTRIAL PHYTOPATHOLOGICAL BIOTECHNOLOGIES SARA FRANCESCONI	First Year / First Semester	6	AGR/12
119938 - FOREST BIOTECHNOLOGY ELENA KUZMINSKY	First Year / First Semester	6	AGR/05
119939 - BIOINFORMATICS SILVIA TURCO	First Year / Second Semester	6	BIO/11
119940 - ADVANCED TISSUE CULTURE CRISTIAN SILVESTRI	First Year / Second Semester	6	AGR/03
NEW EXTRA CURRICULAR GROUP	-		-	-
119340 - NANOTECHNOLOGY IN CROP PROTECTION	First Year / First Semester	3	AGR/12
118339 -	First Year / First Semester	3	AGR/12

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