SubjectsSubjects(version: 901)
Course, academic year 2022/2023
  
Advances in molecular cytogenetics - MB140P10
Title: Pokroky v molekulární cytogenetice
Czech title: Pokroky v molekulární cytogenetice
Guaranteed by: Department of Genetics and Microbiology (31-140)
Faculty: Faculty of Science
Actual: from 2020
Semester: winter
E-Credits: 3
Examination process: winter s.:written
Hours per week, examination: winter s.:2/0 Ex [hours/week]
Capacity: unlimited
Min. number of students: 5
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Level: specialized
Note: enabled for web enrollment
Guarantor: Mgr. Alexandr Sember, Ph.D.
Teacher(s): Mgr. Alexandr Sember, Ph.D.
Opinion survey results   Examination dates   Schedule   
Annotation -
Last update: Mgr. Alexandr Sember, Ph.D. (21.09.2021)
!THIS SEMESTER (FALL 2021) THE COURSE WILL BE LECTURED IN ENGLISH!

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.
Literature -
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.

Requirements to the exam -
Last update: Mgr. Alexandr Sember, Ph.D. (21.09.2021)

THIS FALL (2021) THE COURSE WILL BE LECTURED IN ENGLISH!!! 

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
during the class. The answers should be written as complete sentences. Maximum number of points is 50. A
student has a possibility to ehnance the number of points by preparing an essay and/or by answering few
competition qestions asked randomly two-times per semester. The test is classified as follows: from 42
points = 1; from 33 points = 2; from 25 points = 3. Emphasis is placed on the logical context. An entire
lecture time is reserved to write the test.

Contact email: alexandr.sember@natur.cuni.cz

Syllabus -
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

 
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