MCB 316: Genetics and Disease 2012 Mary A. Schuler Topics: Basic cell structure (compare and contrast bacteria, plant cells, and animal cells; internal structures including genomes) General discussions on meiosis and mitosis, reproduction in relation to the life cycles of vertebrates, budding and fission yeast, Arabidopsis, Zea mays, and Drosophila Basic Mendelian genetics (monohybrid/dihybrid crosses, inheritance patterns in model organisms with varying numbers of genes determining a trait, pedigree analysis in humans) Non-Mendelian inheritance patterns (incomplete dominance, codominance, penetrance, epistasis/gene interaction, lethals, sex-linked, multiple alleles and gene complementation) Mutation and the various affects on protein expression and phenotype (dominant vs. recessive, gain-of-function vs. loss-of-function, dominant negatives) Sex-linked inheritance patterns and disease examples (hemophilia, color-blindness, Fragile-X (introduce karyotype and PCR-based testing of disease)) Molecular basis of sex-determination in mammals and Drosophila Dosage compensation of sex-linked genes in mammals and Drosophila (Barr bodies and mosaicism) Organismal ploidy (discussion on hybrid vigor esp. in relation to plants, affects of ploidy on meiosis and fertility, tissue-specific ploidy esp. Drosophila polytene chromosomes (introduce chromosome spreads and in situ hybridizations)) Chromosome organization (centromeric structures, chromosome rearrangements, nondisjunction/aneuploidy, chromosomal fusions, phenotypic results of these events) Linkage analysis, crossing over, measuring map distances on chromosomes (examples mostly in plants, Drosophila and lastly yeast, effects of gene rearrangements on meiosis (gene loss, balancer chromosomes in Drosophila)) Localizing mutations on chromosomes (use of specific balancer stocks in Drosophila to define chromosome carrying mutation, use of deletion and duplication strains in Drosophila to sublocalize gene on chromosome, in situ hybridization techniques, use of pedigree and RFLP analysis in humans, somatic-cell hybridization technique, use of chromosome rearrangements to map Duchenne muscular dystrophy and other X-linked genes) DNA and chromatin (methods identifying DNA as genetic component in most organisms and RNA as genetic component in some viruses, DNA organization (base-pairing interactions, helical forms, methods demonstrating supercoiling), classes of chromosomal proteins, centromeres, kinetichores and telomere organization in yeast, defining genome complexity with Cot curves, in situ hybridization to localize repeats in chromosomal sequences) DNA replication (leading and lagging strand synthesis, pulse and pulse-chase methods measuring DNA and RNA synthesis, methods for sizing nucleic acids and separating cellular components (density vs. velocity gradients, differential centrifugation), origins of replication, DNA polymerases and different activities, error rates and DNA mismatch repair, unique aspects of eukaryotic replication (cyclins, nucleosomes, telomeres)) RNA synthesis and processing (various levels of gene expression from nuclear genes, types of RNA involved in synthesis of proteins including mRNA, tRNA, rRNA and snRNA, methods defining rate of RNA synthesis and half-life (pulse and pulse-chase), mechanism of RNA synthesis and types of polymerases, basal promoter structures and basal transcription factors, RNA editing of mitochondrial transcripts, nuclear pre-mRNA capping, polyadenylation, and splicing, comparison of introns between mammals and non-vertebrates, alternative splicing (vertebrate troponin T and NCAM genes, Drosophila sex determination genes)) Translation (comparison of RNA and proteins in bacterial vs. eukaryotic ribosomes, properties of the genetic code (wobble codon, relationship to nucleotide mutations) Mutations (types including silent, missense, etc., tRNA/suppressor mutation, somatic vs. germinal, isoalleles, null alleles, transitions/transversions, conditional alleles, examples of diseases associated with gene mutations (sickle cell, thalessemias, phenylketonuria, etc.), mechanisms causing natural and induced mutations (tautomeric shifts, chemicals, radiation, transposons) Transposons (characteristics using examples from bacteria, maize and Drosophila including Ac/Ds elements, P-elements, mariner elements, retrotransposons, effects of transposon mutations on genomes) Molecular genetic techniques needed for gene characterizations (restriction enzymes, plasmid vectors, phage vectors, phagemid vectors, bacterial artificial chromosomes, yeast artificial chromosomes, cDNA libraries, genomic DNA libraries, screening techniques (plaque hybridization, expression and complementation screening), Southern analysis and in situ hybridizations to define gene copy number, use of RFLP and Southern analysis to identify mutated genes, chain-termination sequencing, DNA fingerprint analysis) Methods for defining levels of gene expression (Northern Blotting analysis, RT-PCR analysis, EST and cDNA cloning, dot blotting, oligonucleotide arrays, microarrays) Gene mapping (genetic maps, cytological maps, physical maps, RFLP mapping, cloning mutant genes with no known cDNA (chromosome walking, chromosome jumping), radiation hybrid mapping, cloning, mapping of Huntington’s disease, trinucleotide repeat disorders, cystic fibrosis and sickle cell anemia disease genes, human gene therapy techniques including gene-product therapy and somatic and germline gene therapy) Creation of transgenic organisms (use of gene injection, retroviral infection and embryonic stem cells in vertebrate systems, use of T-DNA and Agrobacterium in plants, comparisons of different methods of protein production from different sources) Regulation of eukaryotic gene expression (examples of transcriptional, posttranscriptional, translational regulation, spatial and temporal regulation, factor-dependent regulation, steroid and peptide hormone regulation, enhancers and transcription factor classes) Animal development (Drosophila morphogenesis from embryo to adult, sex determination pathway, maternal vs. zygotic effect genes, dorsal-ventral axis, anteriorposterior axis, body segmentation, organ formation, comparison to colinearity in vertebrate development) Genetic basis of cancer (cell cycle regulation and checkpoint control, tumor suppressors, oncogenes, two-hit hypothesis, genetic predispositions) Special paper topics (Huntington’s disease mechanisms detected, genomics for medicine, genomics approaches to diagnosing cancer, therapeutic siRNAs, pharmaceutical production in plants)