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 on System Biology in the context of modern biotechnology
Pathways, networks and systems in biology
Contribution of genomics to system biology
Properties of networks, general definitions
Physical networks and logical networks
Networks as graphs
Dynamics, stability, robustness - redundancy in networks
Interactions in networks and in biological functions: pathways, nodes
Distribution of grades in networks
The concept of “hub”
Random networks and biological networks
Examples of networks with transcription factors and DNA sequence: experimental approaches to study these networks
Examples of networks in yeast: experimental and computational approaches
Examples of networks with interactions among proteins: interactomes
Methods to identify protein-protein and protein-DNA interactions
Biological properties of hubs: conservation, robustness, duplications
Limitations in interactomes
Networks for gene regulation, protein-DNA interactions
Lactose operon in Escherichia coli
Examples in Caenorhabditis elegans, Saccharomyces cerevisiae and other organisms
TOPICS OF THE SEMINARS - The list will be soon made available
Properties of networks. Physical and logical networks, networks as graphs
Interactions within networks: links, nodes. Distribution of grades in networks. Concepts of dynamics, stability, robustness
Random networks, biological and metabolic networks
Interactions protein-DNA, protein-protein and methods for their identification. Networks of protein-DNA interactions
Gene regulation networks
Experimental approaches for the study of networks with transcription factors and DNA sequences
Interactomes and their limitations
Examples of networks from yeast and E.coli
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 woth the student.