Biochemical, Biomolecular, and Chemical Approaches for Manipulating Biological Systems
A.Y. 2024/2025
Learning objectives
The course aims to provide an in-depth understanding of the biochemical and genetic aspects of prokaryotic and eukaryotic cells, as well as cell culture and genome editing techniques; the biochemical and genetic aspects of model organisms used in research and cellular and molecular techniques for gene manipulation and regulation of gene expression, applicable to models of disease. Additionally, the course aims to provide knowledge related to the structure, function, and analysis of biological and synthetic macromolecules, such as oligonucleotides and analogues, as well as the cellular processes in which they are involved and their applications in modulating gene expression. Furthermore, it delves into the techniques of designing, synthesizing and modifying oligonucleotides and oligonucleotide analogues for their use in the manipulation of biological systems.
Expected learning outcomes
Upon completion of the course, students are expected to master their knowledge in biochemistry, genetics, and cell biology and the main methodologies used in molecular and cellular biotechnology, also applicable at designing therapies. Students should also be able to identify techniques and technologies for the design and generation of synthetic oligonucleotides to manipulate biological systems, aiming to develop advanced therapies. Furthermore, students should have skills related to the application of cell and animal models for the study of communicable and noncommunicable diseases and should be able to critically evaluate experimental design and validation approaches aimed at manipulating biological systems in physiological and pathological settings.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
Course syllabus
The course consists of 56 hours of lectures, divided into three sections.
Chemical Approaches (16 hours). This section focuses on studying synthetic biological macromolecules to manipulate/study biological systems. Topics covered will include:
· Oligonucleotides, structure and function (duplex, triplex, quadruplex,...)
· Synthesis and bioconjugation methods
· Structural characterization of oligonucleotides
· Oligonucleotide analogues (PNA)
· Use of oligonucleotide analogues in the design of antisense, aptamers, antagomiR
· Aptamers - SELEX
· Semisynthetic proteins - synthetic methods and applications in chemical biology/therapeutics
Biochemical Approaches (16 hours). This section will focus on biochemical aspects related to the main approaches aimed at manipulating living systems. Topics covered will include:
· Gene editing systems (e.g., CRISPR/Cas9 and Adenine Base Editing)
· Nucleic acids in the manipulation of living systems (mRNA, miRNA, antisense oligonucleotides)
· Manipulations of biological systems through epigenome modifications
· Methods for evaluating the expression of manipulated genes.
Examples of applications of these approaches from scientific literature will be provided.
Biomolecular and Cellular Approaches (24 hours). This section is dedicated to the study of cellular models and their manipulation. Topics covered will include:
· Cell cultures: primary and immortalized. Differences, culture techniques, applications.
· Principles in using and obtaining stem cells and induced pluripotent stem cells (iPSC) and methods for the differentiation into cell models of interest.
· From 2D cell cultures to 3D cultures (e.g., organoids).
· Techniques and examples of co-culture in the study of cell-cell communication (organ-on-chip, microfluidic devices).
· Role of the extracellular matrix in cell cultures.
· Nucleic acid transfer techniques in cellular models and methodologies for phenotype evaluation
The theoretical aspects discussed during the course will be integrated with application examples based on recent scientific research articles in the fields of cancer, neurodegenerative and neuromuscular diseases, cardiometabolic diseases, and other relevant diseases
Chemical Approaches (16 hours). This section focuses on studying synthetic biological macromolecules to manipulate/study biological systems. Topics covered will include:
· Oligonucleotides, structure and function (duplex, triplex, quadruplex,...)
· Synthesis and bioconjugation methods
· Structural characterization of oligonucleotides
· Oligonucleotide analogues (PNA)
· Use of oligonucleotide analogues in the design of antisense, aptamers, antagomiR
· Aptamers - SELEX
· Semisynthetic proteins - synthetic methods and applications in chemical biology/therapeutics
Biochemical Approaches (16 hours). This section will focus on biochemical aspects related to the main approaches aimed at manipulating living systems. Topics covered will include:
· Gene editing systems (e.g., CRISPR/Cas9 and Adenine Base Editing)
· Nucleic acids in the manipulation of living systems (mRNA, miRNA, antisense oligonucleotides)
· Manipulations of biological systems through epigenome modifications
· Methods for evaluating the expression of manipulated genes.
Examples of applications of these approaches from scientific literature will be provided.
Biomolecular and Cellular Approaches (24 hours). This section is dedicated to the study of cellular models and their manipulation. Topics covered will include:
· Cell cultures: primary and immortalized. Differences, culture techniques, applications.
· Principles in using and obtaining stem cells and induced pluripotent stem cells (iPSC) and methods for the differentiation into cell models of interest.
· From 2D cell cultures to 3D cultures (e.g., organoids).
· Techniques and examples of co-culture in the study of cell-cell communication (organ-on-chip, microfluidic devices).
· Role of the extracellular matrix in cell cultures.
· Nucleic acid transfer techniques in cellular models and methodologies for phenotype evaluation
The theoretical aspects discussed during the course will be integrated with application examples based on recent scientific research articles in the fields of cancer, neurodegenerative and neuromuscular diseases, cardiometabolic diseases, and other relevant diseases
Prerequisites for admission
Good knowledge of Molecular and Cellular Biology, Biochemistry, and Chemistry
Teaching methods
Lectures with the aid of PowerPoint presentations. Presentations will be provided to students through the "teaching materials" page on the myAriel platform. Attendance to lessons is strongly recommended to better grasp the connections between the subjects of various lectures. During classes teachers often interact with students and ask questions to stimulate the discussion and deeper understanding of concepts and topics.
Information about the organization of the lessons and any other information about teaching will be available on the teaching site myAriel: it is therefore recommended to consult it regularly
Information about the organization of the lessons and any other information about teaching will be available on the teaching site myAriel: it is therefore recommended to consult it regularly
Teaching Resources
Bibliography and other learning materials:
· pdf of the slides posted on the web sites of each teacher (myAriel)
· Culture of Animal Cells, R. Ian Freshney Wiley https://onlinelibrary.wiley.com/doi/book/10.1002/9780470649367
· Molecular Biology of The Cell, Alberts J et al https://www.ncbi.nlm.nih.gov/books/NBK21054
· Lewin's Genes XII, Jocelyn E. Krebs, Elliott S. Goldstein, Stephen T. Kilpatrick; Jones & Bartlett Learning press
https://www.jblearning.com/science-technology/biological-physical-science/molecular-cellular-biology/productdetails/9781284104493
· Principi di Biochimica di Lehninger, D.L. Nelson e M.M Cox; Zanichelli
· Scientific articles provided and available on the myAriel portal
· pdf of the slides posted on the web sites of each teacher (myAriel)
· Culture of Animal Cells, R. Ian Freshney Wiley https://onlinelibrary.wiley.com/doi/book/10.1002/9780470649367
· Molecular Biology of The Cell, Alberts J et al https://www.ncbi.nlm.nih.gov/books/NBK21054
· Lewin's Genes XII, Jocelyn E. Krebs, Elliott S. Goldstein, Stephen T. Kilpatrick; Jones & Bartlett Learning press
https://www.jblearning.com/science-technology/biological-physical-science/molecular-cellular-biology/productdetails/9781284104493
· Principi di Biochimica di Lehninger, D.L. Nelson e M.M Cox; Zanichelli
· Scientific articles provided and available on the myAriel portal
Assessment methods and Criteria
The exam consists of a single oral test. Students must demonstrate that they have acquired knowledge of the main methodologies and techniques to investigate cellular processes of interest in diseases and to design therapies. Students must be able to apply the gained knowledge to experimental design, including methodologies to assess the effects of biological system manipulation and solve technical and experimental issues
BIO/10 - BIOCHEMISTRY - University credits: 2
BIO/13 - EXPERIMENTAL BIOLOGY - University credits: 3
CHIM/06 - ORGANIC CHEMISTRY - University credits: 2
BIO/13 - EXPERIMENTAL BIOLOGY - University credits: 3
CHIM/06 - ORGANIC CHEMISTRY - University credits: 2
Lessons: 56 hours
Professor(s)
Reception:
Ask for appointment
Dipartimento di Scienze Farmacologiche e Biomolecolari, via Balzaretti 9
Reception:
Monday 2 p.m. - 4 p.m.
DiSFeB - via Balzaretti 9