Introduction to OMICs | Genome architecture, evolution and variation
Next generation sequencing technologies, genomics and metagenomics
Gene expression regulation, epigenetics and epigenomics
RNA structure and function, transcriptomics
Protein structure and function, modern structural biology
Proteomics
Functional biochemistry and physiology, metabolomics and fluxomics
Cell signaling, cell-cell interaction, interorgan communication, development
Single-cell OMICs, spatial multi-OMICs, functional genomics, transcriptomics and proteomics in physiology and developmental biology
OMICs in microbiology and virology, metagenomics
Gene editing tools and genetic engineering
Genetic engineering and synthetic biology |
Cell Structure and Function | General architecture of eukaryotic cell (vs prokaryotes)
Mitochondria
Mitochondria-like organelles
Apoptosis
Chloroplast
Cytoskeleton/Flagella
Nucleus/Nucleolus
Mitosis: kinetochore, chromosomes, mitotic spindle
Endomembrane system: ER, Golgi, trafficking
Integration of organelles: movement of mitochondria mitochondria along microtubules in neurons, ER/Mito contacts
Evolutionary Cell Biology |
Bioinformatics for Biologists | What is bioinformatics, typical bioinformatics problems, types of biological data, introduction to databases
Databases, database structure, most important databases of biological information and online services, NCBI, EMBL-EBI, ELIXIR infrastructure
DNA and protein sequences, sequence alignment, pairwise and multiple alignment
Position specific substitution matrices, profiles, hidden Markov models, PSI-BLAST
NCBI blast, searching sequence databases
DNA sequencing, assembly, genome assembly, contig, scaffold, next generation sequencing
Genome architecture and evolution, genome annotation, gene prediction, comparative genomics
Gene expression analysis, microarrays, RNA-Seq, ChiP-Seq, EST
Gene ontologies, signal pathways
Molecular phylogenetics
"omics" data, high throughput technologies, processing of "big data", algorithms for clustering
Structural bioinformatics: protein structure analysis - protein surface, charge, conserved residue, motifs, protein function prediction
Structural bioinformatics: prediction of 3D structure, ab initio prediction, homology modelling, protein structure databases
Molecular interaction, docking, virtual screening, drug design and discovery |
Fundamental Human Genetics | Molecular basis of genetics (DNA - structure, function, transmission of genetic information - gene to protein, methods of DNA analysis; proteins - structure)
Variation in human DNA and methods to analyse it
The origin of mutations and DNA repair mechanisms
Genes and mutations (types of mutations that affect the coding sequence and their effect on the protein)
Non-coding DNA and regulation of translation (organization of mRNA, mRNA splicing, functions of UTR's, and how mutations in these regions affect gene function in health and disease)
Non-coding DNA and regulation of transcription (gene promoter and its features, protein-DNA and protein-protein interactions involving transcription factors (TFs), identification of TF binding sites)
Higher-order organization of the human genome (DNA packaging and chromatin structure, DNA methylation, histone modifications, pathology caused by changes in chromatin structure)
Chromosomes (structure and function, methods to study chromosomes, chromosomal aberrations)
Human cells (cell cycle, cell division, cell death and communication in health and disease)
Human mitochondrial genome (organization of mtDNA and the variant mitochondrial code, origin of mitochondria and their mutual relationship with the cell, aspects of the inheritance and molecular pathology of mitochondrial disorders)
Non-coding RNA (types of ncRNA, their biogenesis, specificity and mode of action, gene expression regulation by miRNAs and lncRNAs, example(s) of diseases caused by mutations in ncRNAs or their target sequences) |
Molecular Mechanism of Disease | Introduction into research of disease mechanisms
Protein structure: crystallography and structural modelling of disease variants
CryoEM and Protein-protein interactions
NMDA Receptors in Health and Disease
Drosophila as a model for human disease
C.elegans as a model for development and cell signalling in health and disease
Primary mitochondrial disorders - from diagnostics to molecular mechanisms (biochemist's perspective)
Primary Cilia in Health and Disease
DNA repair and its impact on human health
Large Animal Models as Translational Platforms for Cell and Gene Therapy
Patient-derived 3D organoids and organ-on-chip technology in molecular oncology
Czech Centre for Phenogenomics and genetically modified mouse models of disease |
Clinical Genetics and Genomics | Congenital anomalies
Chromosomal disorders
Mendelian disorders
Inborn errors of metabolism
Neurodevelopmental syndromes
Neurodegenerative disorders
Cancer genetics
Multifactorial conditions and common disorders with hereditary factors
Reproduction & preimplantation genetics
Prenatal diagnostics
Genetic counselling
Precision medicine and gene-directed therapy
Genealogy and commercial genetic testing |
Molecular Physiology and Metabolism | Photosynthesis and plastid biology
Biotechnology and synthetic biology of photosynthetic organisms
Mitochondrial metabolism
Biology of Reactive Oxygen Species
Glycolysis and Pentose Phosphate Pathway
Lipid metabolism
Cancer metabolism and immunometabolism
Concepts of molecular integrative physiology, metabolites as signalling molecules
Aging cell, aging organism
Technologies - proteomics, metabolomics and fluxomics
Technologies - live metabolic sensors
Technologies - spatial multi-OMICs |
Epigenetics and Regulation of Gene Expression | Introduction to the basic terminology and information needed for the rest of the course (DNA methylation, histones, heterochromatin, euchromatin, DNA packaging, DNA/histone reading proteins, and their effect on the regulation of transcription). Interesting examples of epigenetic regulations from the "real life".
The structure of nucleosome, histones and histone variants, histone modifications and enzymatic complexes (writers), histone code readers, chromatin inheritance in mitosis and meiosis, examples of the effect of the chromatin structure on transcription (polycomb and trithorax).
Types and functions of short and long non-coding RNAs. Roles of ncRNAs in regulation of gene expression (heterochromatin induction, RNA-mediated DNA methylation, RNAi). Laboratory methods exploiting properties of ncRNAs (RNAi, CRISPR).
Role of epigenetic mechanisms in mammalian development (oocytes, sperm, embryos, cell differentiation), interplay between DNA methylation and histone modifications and their inheritance. Imprinting.
Role of epigenetic mechanisms in plant development and reactions to the environment, similarities between plant and mammalian epigenetics and their consequences (DNA methylation, imprinting, the effect of epigenetic mechanisms on the life cycles).
Epigenetic mechanisms contributing to dosage compensation of X-linked genes in various species (C. elegans, Drosophila, mammals).
General and specific transcription factors. Transcriptional start and end sites. Regulation of transcription initiation in prokaryotes and eukaryotes. Chromatin remodelling and nucleosome displacement in association with transcription. Gene looping.
Splicing and its role in regulation of expression. The evolution of splicing. Trans-splicing and self-splicing introns. Polyadenylation and 5' capping.
Mechanisms of RNA export from nucleus to cytoplasm and the effects on regulation of gene expression. Processes of mRNA stability regulation.
Ribosome assembly from pre-rRNA and ribosomal proteins. tRNA processing in cellular sub-compartments. Examples and functions of RNA modifications and RNA editing in regulation of translation. |
