93923 - BIOLOGICAL ENGINEERING

Conoscenze e abilità da conseguire

L’ingegneria biologica ricomprende teorie e pratiche ingegneristiche applicabili alle scienze biologiche con lo scopo di progettare tecnologia biomimetica e bioibrida. Frequentando questo corso lo Studente impara a utilizzare strumenti teorici e pratici per la progettazione e la fabbricazione di parti, dispositivi e sistemi biosintetici, e per l’analisi di dati sperimentali a livello molecolare e cellulare. In particolare, al termine del percorso formativo lo Studente: -ha imparato a progettare circuiti genetici con un approccio modulare standard, -conosce le specifiche generali di cellule e biomateriali appropriati per sviluppare protocolli di ingegneria dei tessuti biologici in sistemi bioreattori dedicati, -sa valutare sperimentalmente la funzionalità di costrutti molecolari e/o tessutali ingegnerizzati, -sa come descrivere e predire formalmente le dinamiche di comportamento di costrutti molecolari e/o tessutali ingegnerizzati mediante simulazione numerica, -è informato sul rispetto del quadro normativo che regola l’uso sperimentale e clinico di quanto sopra, -conosce le tecniche bioinformatiche per analizzare esperimenti di sequenziamento nucleotidico.

Contenuti

SYNTHETIC BIOLOGY & TISSUE ENGINEERING [MODULE 1]

Unconventional applications for nucleic acids, e.g. a) DNA nanodevices; b) DNA computing; c) autonomous molecular computers for logical control of gene expression.
What is synthetic biology?
The international Genetically Engineered Machine competition.
The Registry: a promoter and a terminator for transcription, a ribosome binding site (RBS) for translation.
Small regulatory RNAs.
The lab room and the equipment.
Safety is priority: Biological safety and disposal.
E. coli DNA: Chromosomes, plasmids and copy number.
Chemical solutions and agar plates.
BioBrick™ standard assembly and agarose gel electrophoretic analysis.
Preparation and transformation of E. coli cells.
Fluorimetry, fluorescence microscopy or flow cytometry to measure a fluorescent reporter?
The lac operon.
Rational design of modular circuits for gene transcription: a test of the bottom-up approach.
A synthetic post-transcriptional controller to explore the modular design of gene circuits.

Stem cells in tissue engineering (TE).
TE scaffolds: chemical, physical and biological properties of natural and synthetic biomaterials of interest for the aim; scaffold fabrication methods; bioactive substance delivery; cell/biomaterial interactions (biocompatibility e differentiation assessment).
TE bioreactor systems: cell culture in bioreactors for TE; examples/applications.

BIG DATA MANAGEMENT & MATHEMATICAL MODELING [MODULE 2]

Technologies for DNA sequencing
Mapping algorithms for second and third generation sequencing experiments
Bioinformatic pipelins for for variant calling
Analyses of RNA sequencing experiments
Description of chemical reactions by mathematical models based on the law of mass action
Modelling of the synthetic circuits by Markov chains
Deterministic models of gene regulatory networks
Stochastic models of gene regulatory networks
Stochastic simulations of synthetic circuits with the Gillespie's algorithm

Testi/Bibliografia

Slides from classes will be available.

Current literature will be circulated in class.

Metodi didattici

Traditional lectures in class, and practical activity in the lab for small students' groups attendance.

Modalità di verifica e valutazione dell'apprendimento

The exam will be a written test (multiple choice questions, open questions and calculations), intended to restitute contents presented in class. The task must be completed in a maximum of 90'.

An organic vision of the topics addressed in class, the presence of a critical sense, the possession of clarity and expressive precision and specific language will be evaluated with marks of excellence.

Having studied but uncritically expressing the contents, communicating them in a non-specialist form will lead to proportionally less remunerative scores.

You do not pass the exam in case of learning gaps.

Strumenti a supporto della didattica

Mol Cell Engn Lab "Silvio Cavalcanti" #3014

Orario di ricevimento

Consulta il sito web di Emanuele Domenico Giordano

Consulta il sito web di Simone Furini