Syllabus
Syllabus
1) Current views on the chromatin structure and its topology in the nucleus - topologically associated domains (TADs), lamin associated domains (LADs), chromosome territories, functional significance
2) Fluorescence in situ hybridization – the principles and the protocol overview - direct and indirect labeling of FISH probes and probe detection (advantages and limitations) - principles of probe labeling (nick translation, random priming, DOP PCR, primed in situ labelling (PRINS) etc.) - effect of formamide on DNA denaturation, the role of other chemical agens in the basic FISH protocol - the resolution of FISH-based techniques, stringency
3) Current markers and methods of molecular cytogenetics - tandemly-repeated sequences, satellite DNA (satDNA), Cot DNA, microsatellites, transposable elements (TEs), telomeres and interstitial telomeric sites (ITSs), multigene families (histone genes, snDNA, rDNA) and their bearing to karyotype analysis - mechanisms and models describing evolutionary dynamics of tandem repeats (concerted evolution, birth-and-death evolution, impact of gene conversion and unequal crossing-over along with recent insights into mechanisms of these phenomena) - detailed physical mapping of adjacent or co-localized markers (fibre-FISH) - mapping of single-copy regions – tyramide signal amplification FISH (TSA FISH), BAC (bacterial artificial chromosome) FISH - oligo-paint FISH - whole chromosome painting probes (WCP) and their intra- and interspecific (Zoo-FISH) application - FISH with probes derived from whole genomic DNA- genomic in situ hybridization (GISH) and comparative genomic hybridization (CGH) - utilization of next generation sequencing (NGS), available genomic data and particular databases for generation of new cytogenetic markers - examples of integrated approach combining cytogenetic methods with data of other (phylogenetic, taxonomic, ecological, evolutional, genomic) approaches
4) Application of molecular cytogenetics in analyses of specialized chromosomes - methods suitable for deciphering the emergence and evolution of sex/neo-sex chromosomes and B chromosomes, with emphasis on specific cases (Rumex, Drosophila, Orthoptera, Lepidoptera, spiders, fishes, frogs, reptiles, marsupials) - unusual and extreme cases of sex chromosome differentiation - methods suitable for unmasking master sex determining genes (or other sex-linked genetic content) including state-of-the-art sequencing and bioinformatic tools - turnover of sex chromosomes and its high rate in cold-blooded vertebrates
5) Contribution of molecular cytogenetics to research of polyploidy, hybridization, asexual/unisexual reproduction and genome elimination - applications and resolution power for resolving between auto- vs. allopolyploidy scenario in recent and older evolutionary events; evolutionary dynamics of post-polyploid genome restructuring, re-diploidization - homoploid vs. allopolyploid hybrids, unique case of recurrent hybridization in sturgeons - gynogenesis, hybridogenesis (with special emphasis on fishes and amphibians - Ambystoma, Cobitis, Pelophylax) - genome elimination in frogs, fishes and nematods and associated battery of suitable methods for its investigation
6) Molecular cytogenetics and karyotype evolution - mechanisms of karyotype evolution (chromosome rearrangements and their impact on reproductive isolation, karyotype orthoselection, meiotic/centromeric drive) - trends of karyotype evolution in particular taxonomic groups (with emphasis on typical as well as outstanding examples) - centromere repositioning - microchromosomes - polymorphisms, karyomorphs, chromosome races, cryptic species - hybrid zones, introgression - karyotype stasis - unique patterns of karyotype evolution in polyploids and taxa with holocentric chromosomes - mapping of conserved synteny and its bearing to reconstruction of ancestral karyotypes - chromothripsis as a potential driving force behind karyotype evolution
Annotation
The semestral course extends and complements the classical cytogenetic set of lectures - Cytogenetics (MB140P05). The scope is mainly directed towards latest developments in the field, with an emphasis on methodological advancements and integrated arrangements with other science disciplines.
The scope will be continuously slightly modified depending on student´s suggestions and demands. The course is suitable for students of master's degree and higher, however, students of bachelor's degree programs, preferably in the third grade, are also wellcome.
For easy understanding of the lectures´ content I recommend to attend (concurrently or in previous years) also the following subjects: Cytogenetics (MB140P05) and Genetics (MB140P17), as well as some of the basic molecular biology lectures (MB140P71, MB140P20 or MB140P41), eventually other subjects with genetic or evolutionary content.