85292 - Prokaryotic Genomes

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.

Readings/Bibliography

No specific text-books are required. The material used can be obtained on-line in the form of scientific reviews and/or specific publications in ISI journals. Alternatively, the material will be given to students as printed papers.

Teaching methods

Topics in this course will be presented using lectures, discussions and group works, practical sessions at the computer

Assessment methods

The final Course examination consists of a written test with short-answer, long-answer and multiple-choice questions. Interim course evaluation may also consist of assignments performed by students working in collaborative groups.

Teaching tools

Lectures will be given with power-point presentations. Reviews and research publications relevant to the topics of the course will be provided at the end of each lesson along with additional teaching materials. Online open sourced video’s may also be assigned to complement the lectures.

Office hours

See the website of Martina Cappelletti

See the website of Marco Rinaldo Oggioni