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Last update: Mgr. Alexandr Sember, Ph.D. (31.08.2022)
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Last update: RNDr. Irena Lichá, CSc. (29.05.2018)
Literature Powerpoint presentations as well as references to original articles and books/book chapters will be provided to particular topics. |
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Last update: Mgr. Alexandr Sember, Ph.D. (31.08.2022)
The lectures will be held in person, every Monday from 14:50 in the orange auditorium B312 on V7. The exam is written, a test is composed of ten questions which adhere exclusively to the topics presented Contact email: alexandr.sember@natur.cuni.cz |
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Last update: RNDr. Irena Lichá, CSc. (29.05.2018)
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 |