Learning outcomes of the course unit
The objective of the course is to provide to students the general principles of System Biology, elucidating them with examples taken from Biotechnology, and providing instruments to understand the literature in the field.
Some previous knowledge of mathematics, general biology, molecular biology and genetics is highly advisable, as well a suitable level of English to read references in the language.
Course contents summary
System Biology is the systematic and quantitative investigation of cell functions, cells and organisms, spanning the link between molecular biology and physiology. It is based on knowledge of molecular, chemical and physical processes underlying these functions, integrated with a modellinstic mathematical approach. System Biology stems from the new methods for experimental analysis, based on the sequencing of whole genomes and on high-throughput analytical methodologies (genomics, transcriptomics). System Biology sees the cell as a "chemical factory" in which substances from outside are processed to provide energy and materials, in sophisticated processes performed by specialised molecules encoded by the DNA.
Introduction to System Biology in the context of modern biotechnology
The graphs theory
The topology of a network (grade, distance, diameter, clustering coefficient, betweenness)
Network interaction and biological functions
Models of network (random, scale-free, hierarchical)
Modules, motives and hierarchical network
The concept of “hub”
Identification of interactions between transcription factors and their binding sites (ChIP)
Examples of networks with transcription factors and DNA sequence: experimental approaches to study these networks
Yeast one-hybrid, two-hybrid and three-hybrid; reverse two-hybrid
Examples of networks with interactions among proteins: interactomes and their limitations
Methods to identify protein-protein and protein-DNA interactions
Origin of robustness: redundancy of nodes, presence of alternative routes
A robust systems: cancer
Network of gene regulation: an example: from C. elegans and TGF-β
Network of synthetic letality: progress towards a gene interaction network: example in S.cerevisiae
Systems biology and mathematical modelling: how to build a model, stoichiometrical models, metabolical models or kinetic models. Example; Systems biology approach to study the biogenesis of arginine in E.coli.
SOME OF THE TOPICS DISCUSSED DURING THE SEMINARS:
Properties of networks.
Network regulation based on miRNA
Gene regulation networks Experimental approaches for the study of networks with transcription factors and DNA sequences
Marine food chains
System biology versus synthetic biology
Circadian rhythms and systems biology
The material for studying the topics is provided by the teacher and is available as booklet. It will be based on papers from the international literature and on slides shown during the lectures.
The course is organised with frontal lectures and discussion of cases from the literature, based on original papers. In depth discussion on specific topics is presented as seminars.
Assessment methods and criteria
Student will be assessed by an oral examination, based on a personal study performed by the student on a topic previously agreed with the teacher. During the slide presentation the lecturer verifies the communication skills, the knowledge acquired and the application of knowledge. Judgement autonomy is verified in the discussion with the student.