Lecture 4 Flashcards
(17 cards)
What information does a transcriptome give?
What genes are active in time and space
What are the main techniques used in pgysical mapping?
- Restriction mapping
- STS (Sequence Tagged Site) mapping
- FISH (Fluorescence in situ Hybridisation) mapping
What is a limit to microarrays?
Limited to known sequences and are susceptible to over saturation
What information do proteomes give?
What protein coding genes are doing
What is metagenomics? Give 2 advantages
Sequencing genomic DNA from selected environmental smaples (Soil, sea water etc)
- Unbiased sampling of microbes
- Captures whole community
List 3 improvements in resolution for DNA preparation methods when physically mapping by FISH
- Centrifugal chromosome stretching (200kb-300kb res)
- FISH on interphase (25kb res but no morhology)
- Fiber-FISH on mechanically aligned DNA (10kb res)
What does RF (Recombination Frequency [at meiosis]) measure?
Genetic distance
List 3 features that genetic mapping is dependent on
- RFLPs (Restriction Fragment Length Polymorphisms)
- SSLPs (Simple Sequence Length Polymorphisms) - aka minisatellites and microsatellites (Also called VNTRs [Variable Number Tandem Repeats])
- SNPs (Single Nucleotide Polymorphisms)
Give 2 generic features of plasmids
- Common so are readily exchanged, even between distant relations
- Ones that carry essential genes are “chromosomes”
What underlies genetic mapping?
Linkage analysis
List 4 requirements for genetic variants
- Common in the genome
- Show Mendelian inheritance
- Low mutation rates
- Easily typed by molecular biological methods
List 3 ways to type DNA polymorphisms
- PCR and restriction digestion (RFLPs)
- PCR amplification and sizing (SSLP/STRs)
- Solution hybridisation (SNPs)
List 3 types of bacterial exchange and an overall consequence of such exchange
- Transformation (Plasmids)
- Transduction (Bacteriophages)
- Conjunction (Whole / segments of chromosomes
Lateral gene flow erodes the concept of species
What is an essential requirement for Hierarchical Genome Sequencing (HGS)?
Physical maps
What 3 steps are involved in radiation hybrid construction?
- X-ray irradiation; randomly broken chromosome fragments
- Fusion of cells with hamster cells; cell lines produced have 15%-35% human DNA per cell
- Cell lines can be cloned; selected to contain fragments of specific chromosome(s); called SCHs (Somatic Cell Hybrids)
List 2 uses of physical genetic maps
- Used in HGS
- Enable targeted sequencing and collaborative efforts (Human Genome)
List 3 obsticles that occur when trying to physically map with FISH
- Repetitive DNA content of probes (blocking)
- Resolution (Metaphase chromosomes approximately 1Mb)
- High labour for a low throughput
