SYNTHETIC AND SISTEMS BIOLOGY

Synthetic and systems biology propose an interdisciplinary research approach to the mechanisms underlying the living world, using modelling approaches and simulation experiments, for an integrated understanding and a holistic view of the functioning of biological systems.

In particular, Synthetic and systems biology integrate and use knowledge and methodologies from different disciplines, such as chemistry, physics, biology, cell & molecular biology, microbiology, mathematics and computer science, and apply them in an integrated way to the study of the living world and its molecular and cellular processes.

The educational objective of the course is to introduce the student to these issues and provide the general principles of synthetic and systems biology, as well as a series of basic methodological tools from various disciplines for a deeper and integrated understanding (Systems biology) of mechanisms that control biological processes in order to redesign and produce (Synthetic biology) biological systems (eg. DNA or RNA-based genetic circuits) already present in nature or to design and manufacture biological components and systems that do not yet exist, for biotechnological applications in biomedical or other field.

Synthetic and systems biology can be considered, in fact, the new generation of genetic engineering, seen with an integrated approach in which the cell is a "chemical-biological factory". We will use examples close to Biomedical and Pharmaceutical Technologies and Biotechnologies and provide the tools to understand the literature of the sector.

The course is organized in frontal lectures. Flipped Classroom teaching approaches will be used, starting from original articles and reviews.

Students are expected to attend Seminars & Webinars on specific topics, under the supervision of the teacher

Some previous knowledge of mathematics, general biology, cellular & molecular biology and genetics is highly advisable, as well a suitable level of English to read references and attend seminars & webinars in the language. On request, books and reviews will be indicated to those students that need support on specific introductory subjects.

Should teaching be carried out in mixed mode or remotely, it may be necessary to introduce changes with respect to previous statements, in line with the programme planned and outlined in the syllabus. Learning assessment may also be carried out on line, should the conditions require it.

Introduction to Synthesis and Systems Biology. Definition, origin and nature of complexity in biology.

Cellular, molecular and genetic circuits; synthetic genetic oscillators, and genetic switches; elements of genetic logic

Molecular computations in vitro and in cells: DNA computers and biocomputing
Synthesis of gene expression regulatory circuits. Synthesis of orthogonal cellular forms (transcription, translation, signaling, metabolic pathways).
In vitro molecular evolution and molecular repertoires. Molecular and protein interferences: ex. siRNA and intracellular antibodies

The genetic code: foundations, origins and evolution. Engineering of the genetic code: expand the genetic code. In vivo incorporation of non-natural nucleotides into nucleic acids. In vivo incorporation of non-natural amino acids into proteins.
Synthetic biology of nucleic acids and their replication. XNA, synthetic nucleic acids
Minimum genomes and the "minimum cell". To the artificial cell?

Metabolic engineering. Models and methods of modeling in biology. The model organisms. Mammalian Cell Classifiers. Synthetic biology in innovative diagnostics and therapy.

Methods and methodologies in Synthesis and Systems Biology: high-throughput technologies; bioinformatics, data bases and specific software

Optogenetics: light as an orthogonal signal. Optogenic transcription control. Optogenic control of functional activity: examples.

Ethical aspects

There are no official textbook. All the material will be available trough the platform Studium (studium.unict.it), ancd will be given by the teacher, including original articles, reviews on specific topics and the slides used during the lessons.

It is useful to use for specifci topics, the following textbook (use last edition available, please)

Alberts et al., Molecular Biology of the Cell, Garland

Milo & Phillips, Cell biology by the Numbers, Garland

Biologia Sintetica, a cura di Silvio Cavalcanti, Patron editore

Alon, An Introduction to System Biology, Chapman & Hall/CRC

Baldwin et al, Synthetic Biology. A Primer, Revised Edition, Imperial College Press

Blossey, Computational Biology . Chapman & Hall/CRC

Klipp et al, SystemsBiology 2nd Ed, Wiley-VCH

Kuldell et al, BioBuilder. Synthetic Biology in the lab, O'Reilly

Lipp et al, Systems Biology in Practice, Wiley-VCH

Nesbeth, Synthetic Biology, CRC Press

Pevsner, Bioinformatics and Functional genomics 2nd ed., Wiley-Blackwell