Content of Lectures: -sructure of viruses: capsid, envelope, genome, viral proteins, multipartite and multiparticle viruses, control elements - What viruses are and what they are not: defective viruses, subviral elements (defective interfering RNAs, satellite RNAs, viroids), helper viruses, virophages, giant viruses - Virus classification: Baltimore vs. evolutionary taxonomy, classification of the selected famous viruses - "Life" strategies of viruses: different ways of viral replication, transcription and translation - Not everything is in the code: splicing, alternative splicing and RNA editing in viruses - How cells defend themselves: viral infection receptors, defense of cell and organism, animal immunity - How not to be seen: viral countermeasures against cellular defenses (analysis of specific viral "countermeasures" for the phenomena discussed in the previous lecture) - How viruses evolve: mutation, recombination, host change, endogenous viruses - How viruses spread: physical spread, vectors of animal and plant viruses, multiplication of viruses in vectors, basic epidemiological concepts - Research of viruses at the molecular level: methods of detection of viruses and viral molecules, analysis of genetic information, NGS, computer programs - From the life of the virus: a more detailed analysis of selected viruses and their life cycle (HIV, SARS-CoV-2, Poliovirus, CaMV) Content of Tutorials: Computer analyses/modeling of the phenomena discussed in the lectures - on the genomes/protein sequences of selected viruses. For the last seminar (or two - depends on the number of students), the students will give short presentations about the selected virus. - structure of the viral genome: identification of genes and ORFs, 2D structure of RNA/DNA and important elements of the viral genome (5'UTR, 3'UTR, IRES, TE, ITR) - structure of viral proteins: search for antigenic epitopes, functional domains, transmembrane domains, 3D protein models (PyMOL) - classification of viruses and their relationships: species demarcation criteria, genome alignment, phylogenetic analyzes of genes and protein sequences, GenBank database (NCBI) - relatedness of distant groups of viruses: analysis of protein sequences of viral polymerases ? 4 types of polymerases, alignment of the members of selected groups, functional domains, similarities within the group, similarities between groups - viral "life" strategies on the genome sequences: read-through proteins, ribosomal frameshifting, polyproteins - identification of cleavage sites - other important parts of viral genomes: palindromes, repeats and inverted repeats in viral genomes, polyA-signals, splicing sites and alternative splicing - evolution of viruses: analysis of mutations, synonymous vs. non-synonymous mutations, mutation hot-spots, indel mutations
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