Content (Syllabus outline)

Key characteristics of bacterial genomes/operones. Regulation of transcription in bacteria (RNA polymerase, activators, repressors, small RNAs, characteristic promoters, DNA modifications).

Genetic switches used in synthetic biology.

Classification of bacteriophages acording to their morphology, their key characteristics and genetic material (shared gene and synteny analysis, average nucleotide identity-ANI).

Bacteriophages in the environment and in our body. Role of bacteriophages in bacteria evolution (transduction, gene-transfer agents, defective phages). Bacteriophage evolution and ecology. Molecular/bioinformatic approaches fo

bacteriophage identification.

Selected molecular mehanisms of: (i) phage entry into the bacterium, (ii) phage take-over/modulation of the processes in bacterium, (iii) amplification of the bacteriophage genome, (iv) assembly of phage capsid and the virion, (v) release of the bacteriophages from the bacterium. 

Bacterial defence against bacteriophages: (i) phage entry prevention (vesicle formation, masking of surface receptors; (ii) mutations in receptor, modulation of receptor gene  expression); (iii) prevention of phage DNA injection; (iv) prokaryotic argonaute proteins, (v) abortive infection; (vi) phage capsid assembly interferance; (vii) by establishing dormancy during bacteriophage infection.

Bacteriophage-based tools and their applications. Applications of the CRISPR-Cas system. Engineering of bacteriophages for the aplications in diagnostics.

Specific mechanisms of bacteriophage gene regulation. Communication between bacteriophages, the use of bacterial quarm sensing signal molecules by bacteriophages.

Bacteriophage-eukaryotic host interactions.  Bacteriophage modulation of human immune response. Phage entry into eukaryotic cells. Role of bacteriophages on the human microbiome dynamics.

Characterization of bacteriophage bacteria interactions. Effect of bacteria on bacteriophage multiplication. Multiplication of bacteriophages on laboratory and industrial scale, modeling of multiplication.

Isolation of bacteriophages with different separation techniques.

Phage therapy. Phage display. Phages as DNA vaccines and vaciine carriers. Bacterial biosensor devices for pathogenic bacteria. Use of bacteriophages in food science as biopreservatives. Biocontrol of plant pathogens and the use of phages for disinfection of surfaces. Bacteriophage nanocages as vehicles for gene delivery into mammalian cells.

Practicals:

Annotation of a bacteriophage genome within a bacterium, bioinformatic analysis and bacteriophage identification. Screen for the phage-borne proteins with biotechnological potential.

Analysis of a bacteriophage lysogenic/lytic switch. Establishment of a lysogenic strain. Study of communication of bacteriophages within one bacterium.

Bacteriophage multiplication: determination of multiplication parameters (adsorption constant, latent period, burst size).

Prerequisites

Enrolment in the MSc program.