Degree Course: Biologia sperimentale e bioinformatica Syllabus for A.Y. 2022/2023  

The course aims to provide basic concepts of programming in Python and R languages, as well as an introduction to the Linux environment, in which these languages can be used to develop programs for the analysis and management of huge amounts of biological data.
The ability to work in a Linux environment and to develop programs in Python and R is considered, in the scientific community, an indispensable set of knowledge for:
• supporting study and research in the field of biomedical sciences;
• dealing with and manage the analysis of huge amounts of biological data from current "High throughput" experimental platforms;
• acquiring the tools for modeling biological big data.
• acquiring HPC (High-Performance-Computing) computing skills for the analysis of biological problems that cannot be solved on standard computing resources.


EXPECTED LEARNING RESULTS:

KNOWLEDGE AND UNDERSTANDING. At the end of the training activity, the student will be able to apply their knowledge to design and develop pipelines for the analysis of biological big data in Python or R running in a linux computing environment both on a single server node and on a multi-node cluster (HPC) .

ABILITY TO APPLY KNOWLEDGE AND UNDERSTANDING. The knowledge acquired by the students will be useful to be able to analyze and manipulate biological big data in order to understand and model the molecular mechanisms contained in the data.

AUTONOMY OF JUDGMENT.
Students must be able to critically interpret the results obtained through the development and execution of the programs discussed in class, as well as choose the most suitable programming language to pursue a specific goal.

COMMUNICATION SKILLS. Students must have the ability to transmit the knowledge acquired in a clear and understandable way, for example by associating each developed program with a pseudo-code, and must demonstrate the ability to present programs to external users through detailed documentation.

LEARNING ABILITY. Students must be able to describe the fundamental topics of Programming, in oral form. This ability will be developed through active involvement through oral discussions in the classroom and exercises carried out in the computer room on specific topics related to the course.

The course provides the theoretical bases of proteomics, interatomics and matabolomics as relevant scientific disciplines able to provide useful structural and dynamic information about the proteoma and metaboloma. The course will introduce students to the principles and the experimental approaches, and the learning objectives will be achieved by presenting students with the state of innovation in the specific field with a substantial presence in the laboratories. Particular attention will be given to the study of mass spectrometry techniques for the identification of proteins, metabolites and alterations of protein expression, thus enabling them to shed light on the biological complexity of a tissue in order to differentiate / identify a pathological state from the physiological one.
LEARNING OUTCOMES
1) Knowledge and understanding. The student will develop the knowledge of the principles of proteomics and metabolomics. Indispensable for experimental analysis and interpretation of results in biochemical and molecular biological disciplines.
2) Applying knowledge and understanding. The student will also be introduced to the knowledge of the major classes of small biological molecules and metabolites and will learn the basic metabolic pathways through which these molecules are degraded and synthesized. He will be familiar with the main separation methods (2Dgel, HPLC), will use high performance instrumentation (such as MALDI TOF / TOF, ESI-TRAP, ORBITRAP MS) for the identification of proteins and metabolites and will deal with bioinformatic tools for data visualization and interpretation.
3) Making judgments. Students will be able to independently carry out observations and experiments in the field of Proteomics or metabolomics. They will also have critical thinking and evaluation skills to rationalize them in an interpretative model.
4) Communicative skills. Students will be able to work in groups and communicate clearly their knowledge
or the results of their research.
5) Learning skills. Students will need to learn autonomously by using advanced texts in Italian and English. English texts will be provided during the year. Students will also be able to perform bibliographic research even at advanced level, selecting relevant topics of proteomics and metabolomics.

The course of CELLULAR BIOCHEMISTRY (MODULE A) AND BIOMOLECULAR TECHNIQUES (MODULE B) intends to provide students with (i) theoretical knowledge in the field of cellular biochemistry, deepening the mechanisms that regulate the cell cycle in eukaryotes, (ii) theoretical and practical knowledge in protein engineering, and iii) theoretical and practical knowledge of the major molecular biology and biochemical techniques applied to the study of genes, genomes, proteins and proteomes. Experimental approaches will be discussed, making use also of bioinformatics, to address complex biological questions in biochemistry and molecular biology.
In detail, for MODULE A:
The course intends to go into two themes of considerable scientific interest:
1) deepening the biochemical and molecular mechanisms of cell cycle control in eukaryotes with particular emphasis on the experimental approaches used for its elucidation;
2) protein engineering elements that allow the design in silico recombinant proteins by using bioinformatics tools and finally the expression and purification of recombinant proteins using both prokaryotic and eukaryotic organisms. This last part of the course includes practical laboratory related to the cloning of a eukaryotic gene and its expression in bacteria.
For MODULE B:
Specifically, it is intended to provide students with specific skills for the manipulation and analysis of nucleic acids and proteins (mutagenesis and genome editing techniques, differential proteomic), for the analysis of gene expression levels (qPCR, microarrays, differential transcriptomic) and gene expression regulation (study of epigenetic modifications and protein-DNA interactions), for the study of transduction signal pathways by protein-protein interaction analysis. The advances in the field of the sequencing of whole genomes and the application of biomolecular techniques in diagnostic field will be also discussed. Bioinformatics tools will be used for in silico prediction of interaction between biomolecules, or as complementary for the use of the discussed techniques (for input or output analysis). Finally, laboratory practical experiences will be organized to acquire techniques for studying nucleic acids and proteins.

b) EXPECTED LEARNING OUTCOMES
1) Knowledge and understanding
At the end of the course the students will:
MODULE A: To have in-depth knowledge of the biochemical and molecular basics of cell cycle control in eukaryotes. They will also learn the main techniques for the in silico design and expression of recombinant proteins in heterologous systems. In general, they will have developed the ability to understand the pivotal experimental approaches for acquiring knowledge.
MODULE B: To know the basic techniques used in the field of fundamental and applied research. They will have an in-depth knowledge of molecular and advanced techniques and the related bioinformatics tools to support them; they will know the importance of statistical validation of the results of an experiment and of the controls that make an experiment scientifically reliable.
2) Applying knowledge and understanding
At the end of the course the students will:
MODULE A: Be encouraged to use the knowledge acquired for their application to specific problems, such as the design of new, more potent and / or more selective proteins for their use in various fields of interest (biomedical, agri-food, etc.). They will be able to put into practice the acquired knowledge to perform the planned experiments during the practical experience.
MODULE B: Be able to use the acquired knowledge to evaluate and interpret the results of an experiment, identify its strengths and weaknesses and optimize it by evaluating the possible impact of variations in key experimental parameters; orient themselves among the main qualitative and quantitative methods to select the most suitable ones for studying the biological problem of interest; perform the experiments carried out during the practical part of the course.
3) Making judgements
MODULE A and MODULE B: Students will be able to interpret and discuss the scientific papers presented during the course and be able to design and express new proteins with different characteristics. Students will have to acquire the ability to understand and critically discuss the experimental results obtained in the laboratory and use them as a starting point for planning subsequent experiments.
4) Comunication skills
MODULE A: During the lessons students will be stimulated to discuss and compare different point of views in order to develop their communicative abilities that will be verified during the preliminary and final examinations at the end of training activities.
MODULE B: Students should have the ability to convey the acquired knowledge in a clear and comprehensible manner, even to people who are not in the field, and must demonstrate the ability to present information also with schemes and formulas.
5) Learning skills
MODULE A and MODULE B: Students will have to be able to describe scientific topics related to the course. This skill will be developed through the active involvement of students during class discussions and practical experiences during the hours dedicated to the experimental laboratory.

The course of CELLULAR BIOCHEMISTRY (MODULE A) AND BIOMOLECULAR TECHNIQUES (MODULE B) aims to provide students with (i) theoretical knowledge in the field of cellular biochemistry, deepening the mechanisms regulating the cell cycle in eukaryotes, (ii) theoretical and practical knowledge in protein engineering, and iii) theoretical and practical knowledge of the major molecular biology and biochemical techniques applied to the study of genes, genomes, proteins and proteomes. Experimental approaches will be discussed, making use also of bioinformatics, to address complex biological questions in biochemistry and molecular biology.
In detail, for MODULE A:
The course aims to deepen knowledge of two topics of considerable scientific interest:
1) deepening the biochemical and molecular mechanisms of cell cycle control in eukaryotes with particular emphasis on the experimental approaches used for its elucidation;
2) protein engineering elements that allow the design of recombinant proteins by using bioinformatics tools and also the expression and purification of recombinant proteins using both prokaryotic and eukaryotic organisms. This last part of the course includes a practical laboratory related to the cloning of a eukaryotic gene and its expression in bacteria.

b) EXPECTED LEARNING OUTCOMES

1) Knowledge and understanding
At the end of the course the students will:
MODULE A: To have in-depth knowledge of the biochemical and molecular basics of cell cycle control in eukaryotes. They will also learn the main techniques for the in silico design and expression of recombinant proteins in heterologous systems. In general, they will have developed the ability to understand the pivotal experimental approaches for acquiring knowledge.

2) Applying knowledge and understanding
At the end of the course the students will:
MODULE A: Be encouraged to use the knowledge acquired for their application to specific problems, such as the design of new, more potent and/or more selective proteins for their use in various fields of interest (biomedical, agri-food, etc.). They will be able to put into practice the acquired knowledge to perform the planned experiments during the practical experience.

3) Making judgments
MODULE A: Students will be able to interpret and discuss the scientific papers presented during the course and be able to design and express new proteins with different characteristics. Students will have to acquire the ability to understand and critically discuss the experimental results obtained in the laboratory and use them as a starting point for planning subsequent experiments.

4) Communication skills
MODULE A: During the lessons, students will be stimulated to discuss and compare different points of view in order to develop their communicative abilities which will be verified during the preliminary and final examinations at the end of training activities.

5) Learning skills
MODULE A: Students should be able to describe scientific topics related to the course. This skill will be developed through the active involvement of students during class discussions and practical experiences during the hours dedicated to the experimental laboratory.

The course of CELLULAR BIOCHEMISTRY (MODULE A) AND BIOMOLECULAR TECHNIQUES (MODULE B) intends to provide students with (i) theoretical knowledge in the field of cellular biochemistry, deepening the mechanisms that regulate the cell cycle in eukaryotes, (ii) theoretical and practical knowledge in protein engineering, and iii) theoretical and practical knowledge of the major molecular biology and biochemical techniques applied to the study of genes, genomes, proteins and proteomes. Experimental approaches will be discussed, making use also of bioinformatics, to address complex biological questions in biochemistry and molecular biology.
In detail, for MODULE B:
Specifically, it is intended to provide students with specific skills for the manipulation and analysis of nucleic acids and proteins (mutagenesis and genome editing techniques, differential proteomic), for the analysis of gene expression levels (qPCR, microarrays, differential transcriptomic) and gene expression regulation (study of epigenetic modifications and protein-DNA interactions), for the study of transduction signal pathways by protein-protein interaction analysis. The advances in the field of the sequencing of whole genomes and the application of biomolecular techniques in diagnostic field will be also discussed. Bioinformatics tools will be used for in silico prediction of interaction between biomolecules, or as complementary for the use of the discussed techniques (for input or output analysis). Finally, laboratory practical experiences will be organized to acquire techniques for studying nucleic acids and proteins.

b) EXPECTED LEARNING OUTCOMES:
1) Knowledge and understanding
MODULE B:To know the basic techniques used in the field of fundamental and applied research. They will have an in-depth knowledge of molecular and advanced techniques and the related bioinformatics tools to support them; they will know the importance of statistical validation of the results of an experiment and of the controls that make an experiment scientifically reliable.
2) Applying knowledge and understanding
MODULE B:At the end of the course the students will be able to use the acquired knowledge to evaluate and interpret the results of an experiment, identify its strengths and weaknesses and optimize it by evaluating the possible impact of variations in key experimental parameters; orient themselves among the main qualitative and quantitative methods to select the most suitable ones for studying the biological problem of interest; perform the experiments carried out during the practical part of the course.
3) Making judgements
MODULE B: Students will be able to interpret and discuss the scientific papers presented during the course and be able to design and express new proteins with different characteristics. Students will have to acquire the ability to understand and critically discuss the experimental results obtained in the laboratory and use them as a starting point for planning subsequent experiments.
4) Comunication skills
MODULE B: Students should have the ability to convey the acquired knowledge in a clear and comprehensible manner, even to people who are not in the field, and must demonstrate the ability to present information also with schemes and formulas.
5) Learning skills
MODULE B: Students will have to be able to describe scientific topics related to the course. This skill will be developed through the active involvement of students during class discussions and practical experiences during the hours dedicated to the experimental laboratory.

The English language course aims to familiarize students with the techniques of writing in the English languagewhich differs from writing in Italian. Thsi course also allows students to produce documents and/or short essays which are relevant for their course of study.
The course therefore focuses on two of the four language skills - writing and reading - without forgetting listening and speaking.
To achieve these objectives, classes are exclusively taught in English. It is for this reason that the grammatical basis of the language and its phonological aspects are not neglected but analyzed whenever the need arises.
The final goal is the achievement of level B2 of the Common European Framework of Reference (CEFR), adopted by the Council of Europe by means of which the student:
* Can understand the main ideas of complex text on both concrete and abstract topics, including technical discussions in his / her field of specialization.
* Can interact with a certain fluency and spontaneity that make natural interaction with native speakers possible without effort for the interlocutor.
* Can produce clear and detailed text on a wide range of topics and explain a point of view on a topic providing the pros and cons of the various options.
These objectives are achieved by developing and consolidating the four language skills but above all applying the linguistic knowledge that is gradually being acquired.
Particular attention is paid to the text and context; text analyzes are carried out to identify the specific and pertinent vocabulary, the register to be used and the method of outlining and writing an essay.
Texts of various topics are submitted to students but the main focus is on on scientific topics, crucial to their course of study; also audio will be distributed to develop the ability of oral comprehension; moreover, at each lesson, students must prepare and present some topics of interest in Power Point version.

The course aims to train students in various sectors of Bioinformatics, with particular attention to the knowledge of innovative tools used to support research in the biological field.
In detail, the training objectives concern:
1) Basic knowledge of biological databases
2) Query of biological databases in a programmatic way (examples of programmatic query of the various NCBI databases, https://www.ncbi.nlm.nih.gov/guide/all/, through the use of API- application programming interface).
3) Pairwise alignment algorithms of nucleotide and amino acid sequences;
4) Substitution matrices;
5) Heuristic algorithms for local alignment of sequences against sequence databases.
6) Multiple sequence alignment algorithms
7) Methods for the construction of phylogenetic trees
8) Database search methods through multiple sequence alignments
9) 9) Algorithms for the prediction of RNA structure
10) Algorithms for the prediction of secondary structure of proteins
11) Methods for the comparison between protein structures
12) Classical algorithms for the prediction of protein folding
13) Algorithms based on machine learning for the prediction of protein folding


KNOWLEDGE AND UNDERSTANDING.
Students must show that they have learned bioinformatics topics included in the course, namely: acquisition of the basic principles of bioinformatics; how biological databases are designed, managed and populated; how sequence similarity searches and alignments of single or multiple sequences are performed; how evolutionary analysis of sequence data is performed through multiple alignments and construction of phylogenetic trees; how secondary and tertiary protein structure predictions are made.


ABILITY TO APPLY KNOWLEDGE AND UNDERSTANDING. Students should have an understanding of the computational approaches discussed in class and be able to apply them to specific biological problems.

AUTONOMY OF JUDGMENT. Students must be able to critically interpret the results obtained through the bioinformatics tools discussed in class, as well as choose the most suitable ones to reach a specific goal.

COMMUNICATION SKILLS. Students must have the ability to transmit the knowledge acquired in a clear and understandable way, even to non-competent people, and must demonstrate the ability to present the acquired information.

LEARNING ABILITY. Students should be able to describe the various topics of Bioinformatics, in oral form. This ability will be developed through active involvement in oral discussions in the classroom and exercises carried out in the computer room on specific topics related to the course.

The teaching is aimed at providing students with a solid and integrated culture in experimental biology and in the various sectors of applied biology and the achievement of equally solid and complete skills in the use of analytical methodologies and advanced methods for the study and understanding of mechanisms molecular of biological processes and for their application in the industrial, health, ecological-evolutionary and biotechnological fields.
LEARNING OUTCOMES
• Knowledge and understanding: The student will have to demonstrate knowledge of the theoretical and methodological elements of experimental and applied biology, with particular regard to the molecular, biotechnological and biochemical aspects of biological processes, to the knowledge of the interactions between molecules, biomolecules and cells, in normal or altered conditions.
• Applying knowledge and understanding: The student will have acquired theoretical and methodological skills that will allow him to apply the correct investigation strategies to solve specific problems in the field of experimental and applied biology. In particular, he / she must be able to interpret and process scientific data derived from the study of scientific articles and databases that use the methodological approaches of experimental and applied biology, also using bioinformatics tools.
• Making judgments: Acquisition of independent judgment in reference to the evaluation and interpretation of experimental data reported in scientific articles.
• Communication skills: Acquisition of expression skills with appropriate scientific terminology. Acquisition of adequate skills and tools for communication for what concerns the processing and the presentation of data.
• Learning skills: Acquisition of adequate skills for the deepening of further skills and knowledge for what concerns the consultation of bibliographic material for continuous updating

The use of molecular and bioinformatic tools has significantly contributed to our understanding of ecological and evolutionary processes underlying the genesis of biodiversity and the fundamental principles of modern conservation biology. The course aims to provide the student with a thorough understanding of these tools and the main ecological and evolutionary issues that can be addressed through their application. The course will also investigate the molecular mechanisms underlying the adaptation of organisms to environmental changes, both current and past, the molecular methods for monitoring the different hierarchical levels of biodiversity, and elements of molecular demography.

EXPECTED LEARNING OUTCOMES

1) Knowledge and understanding. Students who complete this course will be able to solve ecological and evolutionary problems using molecular ecology tools. In general, they will develop the ability to understand the application of the tools of molecular ecology proper for understanding the main eco-evolutionary processes that shape diversity in natural populations.

2) Applying knowledge and understanding. Students who complete this course will be able to apply the knowledge obtained using experimental and bioinformatics tools typical of molecular ecology for solving problems in the ecological and evolutionary fields. In particular, this knowledge will be applied in conservation biology and in invasion biology.

3) Making judgements. Students who complete this course will be able to apply critical reading of scientific literature to formulate informative hypotheses of experimental data.

4) Communication skills. Students will be stimulated to discuss and compare opinions during the course to develop their communication skills. At the end of the course, students will have the ability to communicate the knowledge acquired clearly and understandably.

5) Learning skills. At the end of the course, students will be able to formulate solid scientific questions based on evidence and develop experimental paths by gradually integrating scientific literature and acquired technical knowledge.

The main educational objective of the Chemistry of Natural Organic Substances course consists in providing the student with general concepts, specific knowledge, and adequate examples to be able to classify natural organic substances on the basis of their chemical structure, to know their biosynthetic origin and the corresponding biological properties, analyzing the most important classes of organic compounds of natural origin produced in the course of secondary metabolism by the animal and plant cells. The training objective will also be achieved thanks to the description and use of examples relating to the application of computational chemistry and bioinformatic techniques in order to predict structure-activity relationships and identify the main pharmacophores present in the molecule. Thanks to this information, the student will be able to recognize the biosynthetic origin and the structural family to which a natural organic substance belongs, and to place it in a general context relating to its possible cellular functions and its possible applications in the pharmaceutical, nutraceutical field. and cosmetic. Knowledge will also be provided to understand the main and most recent applications of natural organic substances in the bio-nanotechnology sector, with particular reference to the science of renewable and biodegradable materials, the production of bioplastics and bio-inks, and the design and development of biocatalysts. and biosensors for synthetic, clinical and environmental uses. The student will thus be in possession of critical tools to associate the presence of certain structural characteristics in the molecule with the mechanism of action exerted by the substance at the molecular level, highlighting the relationships between structure and activity, so as to be able to predict, in a critical sense, the possible biological activities associated with a specific molecular architecture.

LEARNING OUTCOMES
• Knowledge and understanding: Knowledge of the structural reasons that allow the classification of a natural organic substance. Knowledge of the main biological activities associated with the different families of natural organic substances also in the light of computational and bioinformatic analyses. Knowledge of the biosynthesis pathways of secondary metabolites in animal and plant cells. Knowledge of the relationships between chemical structure and biological activity. Knowledge of the application of natural organic substances in biotechnology.
• Applying knowledge and understanding: In addition to the knowledge acquired through the study of the chemistry of natural organic substances, students will be able to deepen the concepts acquired through the guided reading of scientific publications and the use of dedicated software for the classification of organic substances based on their chemical structure, thus linking the topics covered in the course to experimental research.
• Making judgments: At the end of the course the student will have acquired the necessary training for a complete autonomy of judgment regarding the possibility of using a certain natural organic substance for the development of a service, a process, or a product in the pharmaceutical, nutraceutical, cosmoceutical, cosmetic, materials science and bio-nanotechnology fields.
• Communication skills: students will be continuously and constantly invited to actively participate in the lesson in order to deepen the subject and to collect proposals for possible solutions in the case of complex scenarios. In this activity, students will be asked to confront each other in order to support their ideas also by making use of bioinformatic tools, such as software dedicated to the 3D representation and nomenclature of chemical structures. The teaching tool is aimed at increasing communication skills and the ability to know how to work and discuss in a group, all aimed at consolidating the concepts acquired.
• Learning skills: The learning skills of the students will be assessed during the course by discussing the contents of scientific publications that will allow them to follow the state of art, highlighting the ability of restitution and of problem solving of the student.

The course, which provides an intermediate level of knowledge of the English language, is aimed at strengthening the main language structures to B2 level of the CEFR.