Prokaryotic Genomes (Genomics Degree Programme) - M. Cappelletti + M. Oggioni

Learning outcomes

By the end of the module the student has knowledge of the main approaches for genomic data analysis and annotation in prokaryotes, with an emphasis on the use of next generation sequencing for the functional and structural analysis of genomes. In particular the student is able to: understand the structure of genetic variability and its phenotypic effects, browse prokaryotic genomes, apply methods for genomic data analysis, and correctly interpret and plan genomic studies in bacteria.

Course contents

The Prokaryotic Genomes course (Module1+Module2) will focus on the following topics:

• Introduction to Prokaryotes: the prokaryotic cell, size, shape and arrangement of bacterial cells, structures internal and external to the cell wall, microbial growth
• Diversity of Prokaryotic World: bacterial and archeal taxonomy and phylogeny, the tree of life, molecular chronometers and phylogenetic tree, ecological niches, diversity based on nutrition, metabolism and physiology
• Genome sequencing: Genome sequencing technologies, Genome Reconstruction/assembly, Genome Annotation
• Prokaryotic genomes and plasticity: genome structure and partitioning, bacterial plasmids and transposable elements, Genomic Islands, core genomes VS accessory genomes, bacterial conjugation, transduction and transformation
• Comparative genomics of Prokaryotes and Microbial Genome Databases
• Mutagenesis as a Genomic Tool for Studying Gene Function: types of mutation, Transposon Mutagenesis and Targeted Mutagenesis
• Functional Genomics: Transcriptomics (RNA-seq and Microarray), Proteomics, Metabolomics, etc.

Full course website

Systems and Synthetic Microbiology (Genomics Degree Programme) - M. Cappelletti

Learning outcomes

By the end of the course, the student has knowledge on the integrative approaches and strategies to study a microorganism as a complex system and to discover and model its properties in the context of synthetic biology, gene regulation, and microbial genome engineering across multiple scales. In particular, the course provides the student with systems and synthetic biology understanding of microorganisms and microbial ecosystems with industrial and environmental interest for biotechnological applications.

Course contents

Introduction to the basic concepts in the field of systems and synthetic microbiology; genome-wide engineering approaches and targeted genome editing methods for synthetic microbiology purposes; the idea of networks and their representation as graphs; the structure, dynamics, and evolution of metabolic networks; the building of biological parts and their function on the microbial systems level; the synthetic biology as a tool to build biological systems; synthetic biology tools for microbial genetic and metabolic engineering (e.g. BioBrick, pSEVA); genetic and metabolic circuits in microbial systems; design, construction and expression of synthetic pathways in microorganisms; synthetic and minimal genomes; systemic disciplines applied to microbial biotechnology (several case studies will be the subject of students analysis)

Course full website

Microbial Biotechnologies (Molecular and industrial biotechnology Degree Programme) - S. Fedi

Learning outcomes

At the end of the course the student will have the basic knowledge on a few topics of industrial and environmental biotechnologies. In particular the student will know the molecular and metabolic features of those microorganisms used for i) biodegradtion of contaminants, ii) production of alternative energy sources as biogas, iii) enzyme production, and iv) development of commercial products with a high social impact.

Course contents

• Course organization along with details on the assessment methods. Introduction to the various topics.
• Microbial degradation of linear and branched hydrocarbons. Degradation of aromatics. Dehalogenation of haloaromatics. Genetic regulation of the catabolic pathways for the organic contaminants degradation. Catabolic pathways' evolution.
• Microorganism used in agriculture. Production of insecticides of microbial origin. Microbial production of antibiotics.
• Biotransformation of inorganics and their potential use in nanotechnologies
• Bacterial interaction with bacterial cells. Mechanism of oxidation/reduction of inorganics to be used for bacterial growth. Nanowires: generalities and applications.
• Bacterial cells and generation of biogas and electricity
• Interaction of bacterial cells with anodes and cathodes for the production of electricity (MFC) and/or valuable commercial chemicals. Bacterial production of biogas: generalities and microroganisms used for CH4 and H2 production in anerobiosis and phototrophy.

Laboratory

The student will acquire:

1) basic methods for the isolation and characterization of environmental samples with specific physiological features.

2) a few molecular methods to characterize complex microbial communities aiming to search for specific functional genes involved in biotech applications