1. Basics of bioinformatics

• Definition
• Database sources
• Basic analytical tools - search for similar sequences, identification of open reading frames, search for consensus sequences, construction of gene maps

2. Biological macromolecules - structure and function

• Nucleic acids and nucleotids
• Proteins and aminoacids
• Polysacharides and their subunits

3. Basic processes and functions of genetic material

• Replication
• Transscription and post-transcriptional editing, reverse transcription
• Translation and genetic code
• Mutations and DNA repair

4. Structure of chromosomes and chromatin

• Prokaryotic and eukaryotic chromosome, its topology and composition
• Chromatin and nucleosome as its basic subunit
• Basic functional elements of eukaryotic chromosomes - centromeres, telomeres and replication origins non-histone chromatin proteins

5. Basic structural features of the organization of genomes of individual organisms, including humans

• Coding and non-coding DNA - structural genes, RNA genes (rRNA, pre-miRNA and shRNA), transposons, gene distribution
• Comparison of genomes of different types of organisms
• Gene catalogues
• Organellar genomes

6. Epigenetics and epigenomics

• Definition of epigenetics
• Epigenetic processes and their molecular mechanisms (examples)
• Epigenetic mechanisms of gene expression regulation
• Genetic and epigenetic regulation of ontogeny

7. Gene

• Mendel's concept, Mendel's principles of heredity
• Other possible definitions of a gene/concept of a gene, in terms of its function and material nature
• Basic structure of prokaryotic and eukaryotic genes

8. Identification of genes

• Ab initio
• Experimental

9. Reverse genetics

• targeted mutagenesis and genome editing. Preparation, Identification and analysis of sequence-specific mutants
• Methods of identifying the exact location of advertising or editing
• Confirmation of a causal link between phenotype and mutation

10. Direct genetics

• Use of insertional mutant libraries in direct genetics procedures
• Searching libraries of insertional mutants according to different criteria, phenotypic profiling
• Identification of the mutated locus

11. Chemical genetics and its applications

12. Regulation of gene expression

13. Mechanism of gene silencing by RNA interference and its application in practice

• positive and negative regulation of gene expression, induction and repression
• Regulation of gene expression in prokaryotes and viruses, examples
• Regulation of gene expression in eukaryotes

14. Gene expression analysis

• Quantitative - qRT PCR, chips, RNASeq - NGS transcriptional profiling
• Qualitative - transcriptional fusion, translational fusion, tissue- and cell-specific analysis - transcriptional maps, in vivo RNA localization analysis
• In silico - electronic databases and searching in them

15. Sequencing and its use in genomics

• Genome/transcriptome complexity reduction methods for sequence analysis - renaturation and exonucleases, methylation filtering, chromosome sorting, targeted rRNA/rDNA depletion, panels
• The principle of Sanger sequencing
• Principles of the main current NGS and third-generation sequencing methods - Solexa/Illumina, Ion Torrent, Oxford Nanopore, PacBio

16. Genomics of cellular communications

• Methods of localization of molecules in vivo - proteins, RNA, RNA localization codes
• Intracellular protein transport and its functional significance - protein sorting and its signals, nuclear transport, mitochondrial transport
• Advanced confocal microscopy techniques in the study of intracellular localization of proteins - FRAP, photoactivatable fluorescent proteins, FLIM, FCS

17. Basics of systematic biology

• Concept
• Mechanisms of reciprocal gene regulation
• Gene regulatory networks - positive and negative self-regulatory loops and their functional significance

18. Systems biology tools

• Gene Ontology Analysis
• Mathematical modelling of gene regulatory networks

19. Practical applications of functional genomics

• Individualized medicine - multigene disease conditioning, use of gene clustering
• Molecular diagnostics and gene therapy
• Regenerative medicine
• Biotechnology - importance and safety of GMOs

1. Introduction to proteomics

• Peptide, protein, proteoform, proteome, proteotype, genome-transcriptome-proteome-metabolome relationship
• Biogenic origin of proteins and peptides, amino acids and their properties, primary, secondary, tertiary and quaternary structure, types of proteins - structural, functional, post-translational modifications - basic types and their importance
• Enzymes as biocatalysts, enzyme stability, active site - cofactors, coenzymes, prosthetic groups, enzyme kinetics - enzyme reaction rate, activity, Michaelis-Menten equation, determination of KM and maximum rate, enzyme regulation - activation, inhibition
• Evolution of proteins and protein complexes, mutations (synonymous and non-synonymous), duplication, divergence, selection pressures; domain rearrangements, neofunctionalization

2. Methods in proteomics

• Preparation of protein samples - basic procedures of protein isolation, fractionation of modified peptides/proteins
• Recombinant proteins - expression system (bacterial, yeast, insect cells with baculoviruses), basic procedures of isolation and purification of recombinant proteins, use of affinity anchors and their removal
• Separation and fractionation of proteins/peptides - chromatographic methods (RPLC, IMAC, MOAC, SEC, HILIC, HIC), electromigration methods (electrophoresis, isoelectric focusing), multidimensional separation of complex mixtures, importance of separation in proteomics
• Characterization of proteins - immunoassay, mass spectrometry (principle; ionization techniques; mass analysis, ion detection; combined techniques; tandem mass spectrometry; qualitative, quantitative and structural analysis), methods for determining the molecular weight of proteins

3. Expression/differential proteomics

• Protein expression and its regulation - gene level, splicing, post-translational silencing, etc.
• Expression proteomics approaches - isolation, separation, proteome/proteotype characterization
• Qualitative analysis - protein identification, its methods and procedures (mass spectrometry, database searching, de novo sequencing, immunoassay, Edman sequencing)
• Protein quantification - methods and procedures (principle of relative and absolute quantification, isotope mass labelled and label-free MS approach, immunoblot (western blot))

4. Structural proteomics

• Protein structure - domains, folding
• Relationship of structure, properties and function of proteins - transport, immunochemistry, cytoskeleton, receptors
• Structural analysis approaches - methods and their applications (CD, X-ray crystallography...)
• Modelling - structural model and its refinement

5. Funkční proteomika

• Proteinové interakce – domény, typy interakcí (protein-protein, protein-DNA, protein-ligand), interaktom, komplexom, význam proteinových interakcí
• Vliv PTM na proteinové interakce – proteinové domény rozeznávající PTM
• Metody analýzy protein-proteinových interakcí in vivo – koimunoprecipitace, kvasinkový dvouhybridní test (Y2H), koimunoprecipitace, tandemová afinitní purifikace (TAP-Tag), bimolekulární fluorescenční komplementace (BiFC), analýza zprostředkované membránové vazby (MeRA)
• Charakterizace proteinových komplexů – metody izolace a analýzy proteinových komplexů

6. Proteomická bioinformatika

• Proteomické databáze a nástroje – typy, obsažené informace
• Využití bioinformatických databází v proteomice

7. Proteomické aplikace

• Možnosti využití proteomiky v základním a aplikovaném výzkumu (studium mechanizmů buněčných procesů, struktura proteinů, klinické aplikace, identifikace bakterií atp.)
• Základní experimentální přístupy pro řešení výše uvedených aplikací