93923 - Biological Engineering

Learning outcomes

Biological engineering encompasses engineering theories and practices applied to biological science. A basic goal of this approach is to design technology that operates in harmony with the biology of living systems. Attending this course Students will learn how to use theoretical and practical tools useful for the design and fabrication of biosynthetic parts, devices and systems. At the end of the course, Students should be able to: - design genetic circuits based on a standard modular approach, - know the general specifications of suitable cells and biomaterials and applicable tissue engineering protocols in dedicated devices (bioreactor systems); - experimentally evaluate the functionality of engineered molecular and cellular constructs; -formally describe and predict the dynamics of engineered molecular and cellular constructs by using computational modeling. -respect the regulatory framework governing experimental and clinical use thereof.

Course contents

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]

Sequencing technologies.
Mapping algorithms for NGS experiments.
Algorithms for variant calling.
Dimensionality reduction and ancestry estimates.
Analyses of RNASeq data.
Principles of Python.
Law of Mass Action.
Markov chains.
Deterministic models of gene regulatory networks.
Stochastic models of gene regulatory networks.
Stochastic simulations with the Gillespie's algorithm.

Readings/Bibliography

Slides from classes will be available.

Current literature will be circulated in class.

Teaching methods

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

Assessment methods

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 60'.

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.

Teaching tools

Mol Cell Engn Lab "Silvio Cavalcanti" #3014

Office hours

See the website of Emanuele Domenico Giordano

See the website of Simone Furini