Content (Syllabus outline)

Introduction to microbial genomics and proteomics and presentation of key principles and terminology. Review of current and emerging DNA sequencing technologies and areas of their application: genome sequencing, RNAseq, ChIP-seq. Errors that often occur during sequencing. Annealing of sequences: OLC, de Bruijn graphs, comparison of annealing programs. Status of genome projects: from draft to completion and applicability of individual stages. Properties of microbial genomes: length, GC content and the reasons for it. GC skew and its applicability to determine the origin of replication. Using statistics of oligonucleotide words in genomes to identify relationships, for identification of specific genome parts, which were transferred via the lateral gene transfer, or acquired through metagenomic sequencing. Finding genes in DNA by different methods: Markov chains, hidden Markov models. Examples: GeneMark, GeneMarkS, Glimmer, Prodigal. Core and pangenom of microbial species and genera. Reconstruction of phylogenetics by comparing the core genome and its value in epidemiology. Genomic islands and their importance in the evolution of genomes. New genes: duplication against lateral transfer. The tree of life or the network of life? Ubiquitous exchange of genes from the beginning of life onwards. Genome change in pathogens, parasites and symbionts. What can genomic analyzes of gene and spacer regions reveal about the translation initiation and translation strength in bacterial species.

Protein separation and identification. Low and high performance methods for identification of amino acid sequence of the proteins studied. Quantification of studied proteins by gel electrophoresis and other methods. Bio-informatic analysis of protein sequences. Structural proteomics and determination of protein structures in three-dimensional space. Protein interactions at different levels (molecular, cellular) and protein modification. Cellular proteomics as a scientific branch, which enables localization of proteins and protein interactions in a cellular space. Using the proteomic approach in microbial physiology, ecology and ecotoxicology.

Prerequisites

The condition to enter the course is enrolment into the 1st or 2nd year of the level two of Microbiology. For students from other study courses of natural sciences knowledge of basic principles in Microbial genetics and Molecular biology is required, equivalent to the knowledge of microbiology  students acquired at these courses at the level I. study of microbiology.

A condition to enter the final exam is a passed colloquium and seminar.