Syllabus
1. Introduction into Genetics The general scope of genetics, genomics and their branches. The main genetic models and their properties.
2. Applications of Genetics in Everyday Life Plant and animal breeding. Transgenic plants, animals and other organisms and their utilization in agriculture, food industry, pharmaceutics and other fields of human occupation. Genetics in medicine: biopharmaceutics, drug development, pharmacogenetics/genomics, nutrigenetics/genomics, gene therapy (possibilities, advantages and problems) and gene doping, genetic counselling (including the basic information on non-invasive and invasive methods of prenatal diagnostics, karyotype analysis and DNA diagnostics). DNA profiling and forensic genetics (including its various branches – paternity searching, criminal science; identification of victims of natural and other disasters; history/archeology/paleothology; genetic genealogy; other utilization of DNA profiles).
3. From Genotype to Phenotype 1a or What Exactly is the Gene? (the Classical Genetics – Principal Terms and Mendel Postulates) The main rules of inheritance (Johann Gregor Mendel a his postulates), their implications for phenotype expression in progeny generations. The „branching method“ and its utilization in the analysis of genotypic or phenotypic ratios. The main terms of „classical“ genetics, genetic nomenclature.
4. From Genotype to Phenotype 1b or What Exactly is the Gene? (the Classical Genetics – Expansion of Mendel Postulates and Their Limitations) The validity and limitations of Mendel postulates in specific situations: intragenic interactions (incomplete dominance, codominance); multiple allelism; lethality; genocopies, phenocopies, pleiotropy; intergenic interactions (epistasis, inhibition/suppression, complementarity, gene redundancy, polymorphic interactions, cumulative duplicity); penetrance, variable expressivity; effects of environment on phenotype expression, genetic anticipation; maternal effect.
5. From Genotype to Phenotype 2 or What Exactly is the Gene? (Chromosomal Genetics Within the Context of Heredity Rules) Chromosomal basis of the heredity. Main landmarks in the history of cytogenetics, chromosomal theory of heredity and its experimental proofs. Sex-linked, sex-limited and sex-influenced traits and their inheritance. Gene linkage and the violation of the rule of independent segregation of alleles. Uniparental and biparental non-Mendelistic inheritance associated with the existence of extranuclear DNA in eukaryotes.
6. From Genotype to Phenotype 3a or What Exactly is the Gene? (Molecular Genetics - DNA as the Genetic Material) DNA and RNA as the genetic material (the discovery of nucleic acids, their chemical composition and structure, experimental proofs of their role as the genetic material).
7. From Genotype to Phenotype 3b or What Exactly is the Gene? (Molecular Genetics – Central Dogma or How to Get from DNA to Polypeoptide) The evolving definition of the gene during the first half of the 20th century (1 gene = 1 enzyme, 1 protein, 1 polypeptide). tRNA and mRNA as mediators between DNA and polypeptide. The genetic code, how it was broken and what are its properties. The central dogma of molecular genetics and its subsequent modifications.
8. From Genotype to Phenotype 3c or What Exactly is the Gene? (Molecular Genetics – Problems with Gene Definition at the Molecular Level) Why it is not possible to unambiguously define a gene at the physical/molecular level? Gene loci and associated complications (overlapping genes, genes inside other genes, gene segments, scrambled genes, moving genes). Transcriptional definition of gene and associated complications (the main structure of gene and its regulatory regions, operons, alternative start and end sites of transcription and translation, alternative and trans splicing of transcripts, RNA editing, alternative reading frames, codon reassignment, recoding, translational bypass, less common aminoacids, trans translation, protein splicing, polyproteins, modifications of polypeptide ends, other amino acid modification, non-coding RNA).
9. From Genotype to Phenotype 4 or What Can Also Affect the Inheritance and Phenotype Expression (Epigenetics) The epigenetic inheritance (its definition, the main mechanisms and characteristics). The principal non-Mendelistic phenomenons associated with the epigenetic inheritance: X chromosome inactivation in mammals, parental imprinting, paramutation, positional effect, transcriptional and posttranscriptional gene silencing due to transgenes, environmental induction of heritable changes of gene expression, phenotypes associated with prions.
10. From Phenotype to Genotype/Gene 1a or How Is It Done (What Can Be Deduced from Hybridization: the First Steps of the Forward Genetic Analysis) The forward and the reverse genetic analysis. Random and non-random mutagenesis; genetic screening and selection. Testing of genetic hypotheses based on the hybridization results (chi-squared test). Principles and limitations of the complementation and epistatic analyses and the suppressor/enhancer analysis.
11. From Phenotype to Genotype/Gene 1b or How Is It Done (Linkage Genetic Mapping - and Some Extras) Genetic mapping based on recombination (main terms and fundamentals of the procedure, two-point and three-point tests for the determination of gene distance and order on a chromosome, linkage interference, mapping functions, linkage mapping using DNA markers, genetic polymorphisms (main types, their properties and utilization during mapping), restriction endonucleases and their utilization in genetic mapping).
12. From Phenotype to Genotype/Gene 1c or How Is It Done (Special Methods of Forward Genetic Analysis in Humans) Pedigree symbols. Main types of monogenic inheritance and their recognition from genetic pedigrees. Problems and limitations of pedigree analysis. Genetic mapping in humans based on recombination (linkage and association mapping).
13. From Phenotype to Genotype/Gene 2 or How Is It Done (Cytogenetic Analysis) The general scope of cytogenetics. Functional structures of eukaryotic mitotic (metaphasic) chromosome that are visible under microscope, morphological types of metaphasic chromosomes; karyotype, karyogram and ideogram. The main steps in the preparation of cytogenetic specimens. Homogenic and selective staining of eukaryotic chromosomes (including various types of chromosome banding). Cytogenetic nomenclature. Fluorescence in situ hybridization (its main principle, probe types, utilization for various purposes; mFISH, SKY, mBAND; GISH). Comparative genomic hybridization (CGH) and its utilization. MLPA and its utilization.
14. From Phenotype to Genotype/Gene 2 or How Is It Done (DNA Sequencing) Sample preparation before DNA sequencing (basic principles). DNA amplification (basic principles of DNA cloning and PCR, methods of DNA amplification used by the current sequencing technologies). Sequencing technologies of the 1st, 2nd and 3rd generation, their principles, advantages and limitations (Sanger/dideoxy sequencing, pyrosequencing, pH sequencing, sequencing using cyclic reverzible terminators, ligation sequencing, real-time sequencing, nanopore sequencing). Assembly and annotation of whole genome DNA sequence. Reference genomes and their main databases.
15. Genome Characteristics, Structure and Organization 1 (Genome Definition and Main Characteristics) The main data used for genome description (size; GC content; gene density, gene types and properties; repeat and regulatory sequences, ...). Sequence homology (the main types of gene homologs, gene families). Comparison of genomes among various organisms. Genome diversity within species. Genome dynamics. Pangenomes.
16. Genome Characteristics, Structure and Organization 2 (Genomes of Viruses and Related Biological Entities) Various types of viral genomes and their characterization (size; type of nucleic acid; segmented and multipartite genomes, recombination; informational content – coding and non-coding component; typical properties of viral genes and their organization...). Virophages and subviral agens (satelites and viroids) and their genetic information.
17. Genome Characteristics, Structure and Organization 3 (Genomes of Bacteria and Archaea) Characterization of bacterial and archeal genomes: size; type of nucleic acid; various components; ploidy; informational content – coding and non-coding component; typical properties of bacterial genes and their regions; gene organization within the genome; various types of repeat sequences and their potential biological roles. Structure and organization of bacterial / archaeal chromosome (DNA and pro
Annotation
The purpose of this lecture is to introduce students to the field of biology, which has tremendously grown particularly during the recent years. It enables them to relate the most important genetic discoveries of the past to present-day knowledge about cellular processes and biological diversity. The connections that link transmission genetics and molecular genetics are particularly emphasized. The basic information about methods and techniques used in classical genetics, cytogenetics, molecular genetics and genomics is given as well, together with the information about the potential of genetics in everyday life. The lecture is recommended mainly for the students of the 1st or the 2nd year of the Bachelor study programme in Biology, particularly those interested in the molecular and cellular level of genetics.
DUE TO MANY TOPICS THIS LECTURE COVERS AND MANY NEW CONCEPTS AND TERMS, STUDENTS ARE MOSTLY RECOMMENDED TO REGISTER FOR THIS LECTURE DURING THE 2ND YEAR OF THEIR BACHELOR´S STUDY.
Be aware that this lecture is in the Czech language only!