Biotechnology and Genomic for Industry and Environment

Educational objectives

Biotechnological research plays a major role in responding to the environmental and development challenges facing living being today. Genetic engineering and the consequent possibility of Gene Therapy in a targeted and specific way represent one of the most exciting and promising advances in science.
The teaching of Genetic Engineering and Gene Therapy aims to give the student a knowledge of the main techniques of Molecular Biology and recombinant DNA applied to the resolution of real scientific problems. The knowledge and skills acquired in this teaching, also through the performance of experiments and practical exercises, will constitute a reference framework for the study of biotechnological applications and for the analysis of their impact on human health.

Specific skills
The students who have passed the exam will be able to know and to understand (acquired knowledge)

- the problems concerning the molecular resolution of a scientific problem;
- the mechanisms of regulation of gene expression and the technological methods available to intervene on it;
- the influence of the new sequencing technologies for the extended description and for the study of the dynamics of the transcriptomes;
- the complex interactions between biological macromolecules.

The students who have passed the exam will be able to (acquired expertise):
- use the specific terminology;
- perform DNA isolation and manipulation experiments
- construct cloning and expression vectors;
- interpret DNA and RNA sequencing data;
- apply the nucleic acid modification methodologies in eukaryotic cells.

Educational objectives

At the end of the course the student will be able to describe:

-the techniques used for the characterization of nanomaterials, using specific examples to illustrate them
- the main techniques for the bio production of nanomaterials
- the most recent advances in nanobiotechnology for the safety of human health and the environment

Specific objectives
1. Knowledge and understanding - The student will acquire the essential concepts, experimental approaches and techniques used in nanobiotechnology in the biomedical, agri-food and environmental fields, using specific examples.
2. Ability to apply knowledge and understanding - The student will acquire the ability to interpret and discuss current research in nanobiotechnology in the biomedical, agri-food and environmental fields
3. Critical and judgment skills - The student will learn to design experiments in the field of nanobiotechnology and to critically evaluate their results and ethical implications
4. Ability to communicate what has been learned – The student will learn to discuss and present experimental data
5. Ability to continue studying autonomously throughout life - The student will acquire not only the scientific foundations, but also the methodologies and specific vocabulary of the sector. This knowledge will allow the student to continue their studies independently, even after the end of the course and the passing of the exam.

Educational objectives

These classes aim to build a deep knowledge on the molecular mechanisms in plant development.The student will get in touch with cutting edge techniques to study gene expression regulation in plants. Students will gain knowledge on genetic networks, mathematical and growth models deriving from Arabidopsis. The described molecular mechanisms will be analysed also in an Evo-Devo fashion. During the classes Journal Clubs on freshly published papers will be held.
Program
1. Basic principles of developmental biology
2. Differences and similarities in organ development between animals and plants
3. Pattern formation
4. Generation of morphogen gradients (inter- and intracellular communication, polar auxin transport, similarities with retinoic acid, generation of morphogen sensors)
5. Stem cell niches
6. Clonal analysis and transactivation systems (CRE/LOX, UAS/GAL4, LHGR/OP)
7. Molecular mechanisms determining the formation and maintenance of stem cells (PLT transcription factors, WOX homeobox genes)
8. The WUS/CLV and SHR/SCR systems in stem cell niche homeostasis
9. Molecular mechanisms regulating asymmetric cell divisions (Cyclins, Retinoblastoma, etc.) and mathematical models describing bistable circuit formation
10. Use of confocal microscopy, light sheet microscopy, and vertical microscopes to study organ growth
11. Evolution of the stem cell niche and its regulatory molecular mechanisms from algae to angiosperms
12. Molecular mechanisms underlying cellular differentiation (hormones, lncRNAs, morphogen minima generation, etc.)
13. The role of the DREAM complex and retinoblastoma in cellular differentiation
14. Differences and similarities in cell cycle regulation between animals and plants
15. Involvement of telomeres in maintaining stem cell activity in plants
16. The role of microRNAs in plant development and techniques for their study (LNA, MIMICRY, STTDM-MIMICRY, microRNA sensors)
17. Evolution of microRNAs: similarities and differences between animals and plants
18. MicroRNAs in robust and plastic organ development (role of miR165 and miR160 in homeotic transformations)
19. Genetic and molecular improvement of plants for adaptation to extreme conditions
20. Use of morphogenetic factors to enhance the generation of transgenic plants
21. Species-specific molecular mechanisms driving morphological diversity and their industrial applications
22. Evolution of cis-regulatory elements in plants
23. Continuous and discontinuous developmental models
24. Generation of computational models predicting morphogen activity
25. Post-translational protein modifications and their role in organ development (fucosylation, glycosylation, etc.)

Educational objectives

Knowledge of theoretical, methodological and experimental tools to understand, treat and plan in vivo experiments using the animal model systems for biotechnological research.
Analysis and evolution of genomes of C.elegans and Mus musculus, description of genetic systems of high throughput mutagenesis and transgenesis. Forward and reverse genetics approaches: site-directed mutagenesis, RNA inteference and their applications.
Study of technologies based on DNA microarrays, Next Generation Sequencing (NGS) and qRT-PCR to analyze gene expression profiles and interaction between nucleic acids and chromatin proteins. Experimental strategies for Epigenome analysis and methods to analyze the expression patterns of proteins by using specific
antibodies or in vivo "protein trap" with GFP.
The course will illustrate the potential of animal model systems (transgenic or knockout) in the biomedical, translational and environmental research.

Educational objectives

This course aims to illustrate the characteristics of different model organisms and their use in industrial platforms, also analyzing the various improvement strategies. The course aims to identify and evaluate the appropriate choice of the model organism based on the type of biotechnological application addressed, depending on the different industrial sectors (eg food, pharmaceutical and chemical). The course includes lectures and laboratory sessions, dedicated to learning the ability to cultivate and manipulate some of the model systems treated.

Specific objectives

A)Knowledge and understanding
- Knowledge of the main organisms used in industrial platforms
- Knowledge and understanding of the main production processes based on the different cellular systems
- Knowledge and understanding of improvement strategies for obtaining products on an industrial level

B) Applying knowledge and understanding
- be able to use specific terminology
- to identify the right procedures to solve the basic questions of the use of different model systems
-practicing the strategies for the improvement of the model organisms studied
-be able to cultivate and handle the different model systems treated during the course

C) Making judgements
- acquire critical judgment skills, through the study of model systems and their use in various industrial platforms
- learning by questioning

D) Communication skills
-be able to communicate what has been learned during the oral exam

E) Learning skills
- learning the specific terminology
- be able to make the logical connections between the topics covered
- be able to identify the most relevant topics

Educational objectives

General skills

The course aims to provide advanced knowledge on the methodological approaches used for the improvement of plant and algae crops, aimed at the development of new varieties or strains to be used for the sustainable production of biofuels and value-added products for the industry, for sustainable crop protection against stresses and biomonitoring.

Specific skills

A) Knowledge and understanding

To acquire detailed knowledge of:

- types and use of waste plant biomasses of agroforestry origin and dedicated crops for the production of biofuels and other products of industrial interest;
- traits of crops that affect the efficiency of use of the biomass derived from them, with particular attention to the composition of the cell wall;
- advanced methodologies for the study of the plant cell wall;
- conventional and advanced methods of genetic improvement of plant crops;
- characteristics and methods of analysis of nuclear and plastid genomes of plants and microalgae;
- methods of transferring genetic information from model species to species of agro-industrial interest;
- methods of integrating genomics, transcriptomics and metabolomics data for the identification of genes that influence the exploitation of plant biomass and algal and the response to biotic and abiotic environmental stresses.
- biological characteristics and cultivation methods of microalgae;
- approaches used to identify algae strains with characteristics useful for industry and the environment;
- applications of microalgae for the production of biodiesel and products for industrial use;
- methods of genetic improvement of microalgae (mutagenesis and selection, genetic transformation and genome editing);
- sustainable strategies for the defense of plants against abiotic and biotic stresses;
- biomonitoring of pollution through biosensors;

B) Applying knowledge and understanding

- design of experiments aimed at developing new plant varieties or microalgal strains with improved characteristics for their industrial and environmental exploitation;
- design of a genetic screening in microalgae and outline of the main ways of identifying mutations;
- understand and critically discuss the different approaches used to improve the efficiency of use of plant biomass through genetic and biotechnological methods.

C) Making judgements

- Critical judgment skills, through the study of reviews and scientific articles on key aspects of the field and in-depth discussions
- Ability to evaluate the correctness and scientific rigor in the topics related to the topics covered by the course.

D) Communication skills

- Acquisition of adequate skills and useful tools for communication in Italian and in foreign languages (English), using graphic and formal languages, with regard to the scientific language.

E) Learning skills

- ability to interpret and deepen knowledge;
- ability to use cognitive tools for continuous updating of knowledge;
- ability to compare for the consolidation and improvement of knowledge.

Educational objectives

At the end of the course the student will be able to describe:

- understand agricultural genetics and the differences with animal genetics, using specific examples to illustrate them
- the main discoveries in the sector and methods of genetic improvement
- the biotechnological methodologies applied to the selection of plants and the various methods of genetic improvement applied to the various species of agricultural and non-agricultural interest

Specific objectives:
1. Knowledge and understanding - The student will acquire the essential concepts, experimental approaches and techniques used in breeding, using specific examples.
2. Ability to apply knowledge and understanding - The student will acquire the ability to set up a genetic improvement program by applying all the most modern conventional and non-conventional techniques
3. Critical and judgment skills - The student will learn to determine which breeding scheme is the most suitable based on the characteristics of the genome of the plant of interest
4. Ability to communicate what has been learned – The student will learn to discuss and present experimental data
5. Ability to continue studying autonomously throughout life - The student will acquire not only the scientific foundations, but also the methodologies and specific vocabulary of the sector. This knowledge will allow the student to continue their studies independently, even after the end of the course and the passing of the exam.

Educational objectives

General objectives:
At the end of the course the student will be able to describe:

the techniques used in plant pathological biotechnology, using specific examples to illustrate them
the main discoveries in the sector, including recent ones
the most recent advances in biotechnology or the use of biotech approaches to prevent or limit diseases and damages (both quantitative and qualitative) caused by them in plants and their products

Specific objectives:
Knowledge and understanding - The student will acquire the essential concepts, experimental approaches and techniques used in plant pathological biotechnology to deal with plant diseases caused by viroids, viruses and microorganisms also in the light of ongoing climate change, using specific examples.
Ability to apply knowledge and understanding - The student will acquire the ability to interpret and discuss current research in plant pathological biotechnology
Critical and judgment skills - The student will learn to design experiments in the field of phytopathological biotechnology and to critically evaluate the results and legal implications
Ability to communicate what has been learned – The student will learn to discuss and present experimental data
Ability to continue studying autonomously throughout life - The student will acquire not only the scientific foundations, but also the methodologies and specific vocabulary of the sector. This knowledge will allow the student to continue their studies independently, even after the end of the course and the passing of the exam.

Educational objectives

General Skills
Provide students with knowledge regarding the use of sensory devices in environmental and food industry contexts for monitoring industrial processes, authenticity, quality, and food safety.

Specific Skills
a) Knowledge and understanding skills
-Knowledge and understanding of various types of sensory devices and the different analytical techniques applied;
-Knowledge and understanding of the biochemical and technological basics for their use;
-Knowledge and understanding of methods for sensor development;

b) Ability to apply knowledge and understanding
-Ability to use specific terminology;
-Ability to identify the targets to be identified through the sensors and the use of suitable receptors for the analysis to be performed;
-Ability to recognize the best analytical techniques to use for the development of a specific sensor;

c) Autonomy of judgment
-Acquiring critical judgment skills on the use of these analytical devices based on the different analytical techniques learned;
-Learning to ask questions for the elaboration and deepening of the knowledge acquired;

d) Communication skills
Ability to communicate what has been learned during the oral examination;

e) Learning ability
-Learning specific terminology
-Logical connection of acquired knowledge
-Identifying the most relevant themes of the topics covered.

Educational objectives

Understanding and engaging with the complexity of sustainable food production systems require training in different disciplines (primary production, ingredient and food processing, logistics, consumer science and food policy) and a strategic approach that can address this complexity at the system level. This food system study enables students to apply the principles of a systemic approach to food production systems with a focus on environmental, economic, and social sustainability. The course analyses production systems at both ends of the spectrum: highly productive systems with relatively high inputs and emissions to the environment, and low productive systems with low input use and depletion of soil fertility.

General objectives:
After completing this course students will be able to:

Use a systemic approach in the context of food production systems;
Understand evaluation methods used to assess the environmental impact of food production systems in different agro-ecological and socio-economic contexts and at different levels (e.g. farm, regional and global);
Understand present and future strong and weak points of different food production systems in terms of economic, social and environmental sustainability.

Specific objectives
Overview of the complexity of food production systems
Key knowledge on systems thinking approach
Analysis and comparison of the performance of food production systems and the environmental issues
The assessment of environmental sustainability using key indicators
Assess the complexity and diversity of food production systems;
Understand the principles of system analysis and how it can be applied in the context of food production systems;

Educational objectives

The course aims to provide students with advanced theoretical and practical knowledge in the field of microbial biotechnologies applied to the food industry, with particular emphasis on innovation, sustainability, and the valorization of agri-food supply chains.

Students will acquire:
- Advanced skills in the use of traditional and innovative biotechnologies for the production and quality improvement of fermented foods in the following sectors: dairy; enology (wine, beer, sparkling wines); leavened bakery products; fermented vegetables; fermented meats; and functional foods with high nutritional and health value.
- The ability to develop and manage biotechnological processes for the valorization of surplus and by-products from agri-food supply chains, aimed at creating new sustainable and innovative food products, reducing waste, and promoting a circular economy.
- Practical and operational expertise in biotechnology laboratories, through experimental activities focused on the use of selected starter cultures and the design, management, and control of fermentation processes at both laboratory and pilot scale.

Educational objectives

Educational Goals

The teaching of Biomaterials aims to provide fundamental knowledge and basic principles for the study of materials, both polymeric and non-polymeric, of natural and synthetic origin, highlighting the correlations between chemical structure and properties and the most current problems in the study and technological application. The main objective of the course is to provide the tools to understand the relationship between structure and activity of the main classes of biomaterials, in particular deepening the study of the main chemical-physical characteristics, of the polymerization reactions, of the characterization techniques, together with the aspects related to the preparation, study and applications of biomaterials through nanostructuring approaches.
Lectures are developed starting from the classification of the various types of biomaterials, the concepts of biocompatibility and biodegradability, the description of the general characteristics of polymeric materials, the polymerization methods up to the analysis of the various classes of polymers of natural origin, their extraction , purification and chemical-physical characterization. In particular, the main biopolymer classes from renewable sources will be examined for applications in industrial biotechnologies: polysaccharides, proteins and polyesters.
The knowledge acquired in this teaching constitutes a framework of reference for subsequent competences, understood in their broadest meaning.

Students who have passed the exam will be able to know and understand (acquired knowledge)
- the nature of polymeric biomaterials and their main structural characteristics.
- the main methods of polymerization, by polycondensation and polyaddition, with examples taken from both synthetic and natural polymers derived from them.
- the main characterization techniques for defining the structure of macromolecules.
- the most recent literature developments in the field of nanostructured biopolymer formation.
- aspects related to the study of the main and current applications of amorphous and nanostructured biopolymer materials.

Students who have passed the exam will be able to (skills and skills acquired):
- critically interpret the structure of technological biopolymers, interpreting their reactivity and potential applications
- understand the connection with the other cultural areas of the CdS, in particular the aspects of analytical chemistry, inorganic chemistry, organic chemistry and physical chemistry.
- develop the ability to communicate what has been learned, through oral examination tests.
- ability to develop independent study through the indication of accessible sources of updating.

Educational objectives

General objectives
The course aims to introduce the student to the topic of interactions between the eukaryotic genome and the environment. These interactions are carried out by a multiplicity of molecular mechanisms that allow the organism to respond to environmental stimuli that go, as a whole, under the name of Epigenetics. The student will acquire knowledge regarding:
- the various ways in which the eukaryotic genome becomes dynamic to respond to environmental stimuli, thus modulating the levels of gene expression;
- the main modifications of DNA and chromatin that are involved in this regulation;
- involvement in the epigenetic mechanisms of non-coding RNA;
- the main methods of study of epigenetic mechanisms at the level of the single gene and at the genomic level (epigenomics);
- specific examples through which the notion of "environment" is detailed (intra- and extra-cellular microenvironment, external environment, behavioral influences).

Specific Objectives

Knowledge and understanding.
The student will acquire the essential concepts and methodologies used for the study of epigenetics and epigenomics. It will also have the opportunity to explore the many different areas in which epigenetic regulation comes into play in the life of all eukaryotic organisms (metabolism, external environment, behavior).

Ability to apply knowledge and understanding.
Being the course mainly theoretical, the student will acquire the ability to understand and interpret the results of research related to the field of epigenetics and epigenomics.

Critical and judgmental skills.
The student will acquire the ability to critically evaluate and discuss application aspects, deepening technical articles in the international scientific literature.

Ability to communicate what has been learned.
The students, in the classroom, will be encouraged to present, in front of their colleagues, a short presentation in powerpoint format concerning an experimental work proposed by the teacher.

Ability to continue the study independently in the course of life.
The course will provide the scientific and technical knowledge (theoretical level) that constitute a detailed reference framework to be able to independently tackle an experimental learning path within a research laboratory.

Educational objectives

To acquire: 1) fundamental concepts of NMR spectroscopy and of the statistical models for the metabolomics; 2) methodologies to characterize the metabolic phenotypes and to evaluate the effects of biotic, a-biotic and genetic perturbations on different biological systems.

Educational objectives

The rapid and continuous sequencing of the genomes of microorganisms has opened interesting perspectives in the study of Microbiology and has allowed us to understand globally the various and relevant role played by microorganisms in interactions with their hosts (animal and plant) and/or with the environment. The Course on Molecular Microbiology and Microbial Genomics aims to provide students with the knowledge necessary to understand the structural and functional organization of prokaryotic genomes. In particular, the course aims to integrate in a logical path the knowledge related to the study of prokaryotic genomes (Bacteria and Archea), starting from the minimal genomes up to the analysis of multipartite genomes highlighting the main strategies adopted by prokaryotic cells to respond in an efficient and rapid way to the continuous changes in environmental parameters.

Specific skills

A) Knowledge and understanding: After completing the course students will be able to know and understand:
- Evolution of prokaryotic genome;
- Molecular strategies used for genomic and metagenomics analysis;
- Role of CRISPR-CAS loci in Bacteria and Archea and in potential application in genome editing;
- Novel antibacterial strategies;
- Principles and potential application of synthetic biology
- Epigenetic regulation in Bacteria

B) Applying knowledge and understanding
- Understand at molecular level the evolution of microrganims and the potentiality of the genomic approach;
- Contribute to solving problems in the medical or environmental field arising from interactions between microorganisms and host or environment

C) Making judgments
- Being able to integrate the knowledge acquired on the microbial genomes to the development of innovative antibacterial therapies in order to be able to formulate a rigorous opinion on major ethical and social issues such as vaccinations or genomic editing ;

D) Communication skills
- Being able to communicate with a scientific and rigorous language the potentiality of the new technologies based on products of microbial origin both in the development of new vaccines and in the manipulation of eukaryotic cells;

E) Learning skills
-Being able to critically study at a genomic and functional level the microbiota and their interactions with the host and the environment.
- Create logical connections between the knowledge acquired in bacterial and eukaryotic models

Educational objectives

The aim of the course is to provide the basic knowledge of Pharmacogenomics from a cellular point of view and to investigate the molecular mechanisms that underlie the responses to drugs and therapies. Personalized medicine has become famous and it is applied for the choice of the right therapy for diseases. The examples provided highlight the developments obtained by this discipline and all its biotechnological applications.
Specific training objectives are: in the introductory part: learn the fundamental concepts concerning the metabolism of molecules of pharmaceutical interest and of xenobiotic compounds. Understanding how the genetic variability of individuals influences the response to drugs, from the point of view of cellular-molecular mechanisms. Subsequently, the biotechnological aspects are presented in the fields of synthetic biology, production and research of biological drugs, the study of bacterial genomes for the discovery of new vaccines and the study of host-bacterium interaction. It is also presented the concepts of Biosafety and Biosecurity.

Students will be able to know and understand:

• the basic knowledge of pharmacogenomics and pharmacogenetics.
• The study of the human genome.
• how the human genome affects the adverse drug response.
• Cellular mechanisms of response to anticancer drugs.
• Biotechnology in the field of medical oncology.
• the study of bacterial and viral genomes for the discovery of new vaccines.
• Synthetic biology methodologies: synthetic genomes and molecule production.

Students who take the exam will be able to:

• critically analyze biotechnologies in the medical field.
• Interpreting the cellular response to anticancer drugs in a general way based on genetic variability.
• Interpret and evaluate the importance of bacterial and viral genomic sequences for biotechnology applications.
• Identify new technologies that will reduce the use of animal models in clinical trials.
• Evaluate the importance of biosafety and biosecurity.

Educational objectives

Competenze specifiche

A) Conoscenza e comprensione

Acquisire una conoscenza dettagliata di:
storia delle idee ecologiche
etica
etica dell’ambiente
concetto di natura
concetto di sostenibilità
principio di precauzione
diritti di cittadinanza
diritti delle generazioni future

B) Applicazione di conoscenza e comprensione
comprendere e discutere criticamente testi specifici sui vari argomenti

C) Esprimere giudizi
Capacità di giudizio critico, attraverso lo studio di recensioni e articoli scientifici su aspetti chiave del campo e discussioni approfondite.

D) Abilità comunicative
Acquisizione di competenze adeguate e strumenti utili per la comunicazione in italiano e nelle lingue straniere (inglese), attraverso l'uso di linguaggi specialistici

E) Capacità di apprendimento
Capacità di interpretare e approfondire la conoscenza;
Capacità di utilizzare strumenti cognitivi per l'aggiornamento continuo della conoscenza;
Capacità di confrontare per il consolidamento e il miglioramento della conoscenza.

Educational objectives

Understanding and engaging with the complexity of sustainable food production systems require training in different disciplines (primary production, ingredient and food processing, logistics, consumer science and food policy) and a strategic approach that can address this complexity at the system level. This food system study enables students to apply the principles of a systemic approach to food production systems with a focus on environmental, economic, and social sustainability. The course analyses production systems at both ends of the spectrum: highly productive systems with relatively high inputs and emissions to the environment, and low productive systems with low input use and depletion of soil fertility.

General objectives:
After completing this course students will be able to:

Use a systemic approach in the context of food production systems;
Understand evaluation methods used to assess the environmental impact of food production systems in different agro-ecological and socio-economic contexts and at different levels (e.g. farm, regional and global);
Understand present and future strong and weak points of different food production systems in terms of economic, social and environmental sustainability.

Specific objectives
Overview of the complexity of food production systems
Key knowledge on systems thinking approach
Analysis and comparison of the performance of food production systems and the environmental issues
The assessment of environmental sustainability using key indicators
Assess the complexity and diversity of food production systems;
Understand the principles of system analysis and how it can be applied in the context of food production systems;