L 1-8 Flashcards
what are common model organisms
- yeast
- C. elegans
- drosophila melanogaster
- arabidopsis thaliana
- mouse
- human
why is yeast a good model organism
- have a haploid and diploid stages of life
- can introduce DNA into yeast to create mutants
why is c. elegans a good model organism
- can add DNA via microinjections
- can reduce gene function via RNAi
why is drosophila melanogaster a goood model organism
- transposable elements
- amenable to mutagenesis and chromosomal rearrangements such as deletions and inversions
why is arabidopsis thaliana a good model organism
- 6 week lifecycle
- amenable to mutagenesis
- transformation via plasmids
why is mus musculus a good model organism
- great similarities in gene content and genome organisation with humans
- physiology and developement similarity to humans
- amenable to genetic manipulation: mutagenesis, transgenics, knockouts, knockin, conditional alterations of gene activity
why are humans good model organisms
- haplotype analysis
- pedigree analysis and positional cloning
- large scale genomic projects
what are the mendelian phenotypes
- Variation in singe gene causes phenotype change
- Pathological change = monogenic disease
- Expected inheritance pattern
- Dominant and recessive alleles
- Autosomal and sex linked
what is phenylketonuria (PKU)
- autosomal recessive
- error of metabilsm
- profound conginitive defects
- deficiency of phenylalanine hydroxylase
- deficiency blocks tyrosine production
what are the problems confounding pedigree analysis in humans
- small family size
- participation in molecular analysis
- uncertain/misreported paternity
- phentype/genotype variations (mild disease, multipple seperate diseases, pleiotropy)
what are the reasons for genotype/phenotype vatiations
- penetrance
- expressivity
what is penetrance
the probabaility that a disease will appear in an individual when a disease allele is present
- 100% penetrence = 100% diseased
- 25% penetrence = 25% penetrence
what is expressivity
difference in severity and symptoms of a disease
what is pleiotropy
- one gene has many functions
- may be required for different reasons in different tissues
- loss of function causes phenotype affecting multiple systems
- different mutations may affect function in specific tissues or a subset of functions
what is nail-patella syndrome (NPS) and what is it an example of
- pleiotropy
- nail abnormalities, patella absent or poorly developed, glaucoma, kidney disease
- LMX1B mutation
- multi-tissue expression
- the gene has roles in each of these different tissues during developement and this is why different parts of the body are affected
maternal effect
- genotype and phenotype mismatch
- phenotype depends on gene expression/actvity early in devopement
- embryonic gene expression/function provided by mother prior to zygotic expression
- mothers genotype dictates offspring phenotype rather than offsprings own genotype
what is an allelic series
- different mutations in the same gene have different phenotypes
-each allele affects protein function in a different manner
what is an example of an allelic disease
fibroblast growth factor receptor mutations
what is a fibroblast growth factor receptor
- family creates paracrine factors acting in developement
- responsible for:
- introducing specific cells to become mesoderm
- production of blood vessels
- limb outgrowth
- growth and differentiation of numerous cell types
explain the allelic series of fibroblast growth factor receptors mutations
-receptor proteins contain multiple domains, many isforms (growth, differentiation, growth arrest, motility)
- disruption of different parts of the amino acid and protein changes disease type
- thanataphoric dysplasia
- muenke syndrome
- achondroplasia
- crouzondermoskeletal syndrome
- hypochondroplasia
- thanataphoric dysplasia
- SADDAN
what is genetic heterogeneity
- different mutations cause same phenotype
- mutations in same gene (allelic heterogeneity)
- mutations in different genes - locus heterogeneity
what are some examples of genetic heterogeneity
Disease examples:
- Cystic Fibrosis – many mutations in CFTR cause same phenotype (allelic)
- Retinitis Pigmentosa – many different genes cause RP when
mutated (locus)
- multiple epiphyseal dypslatia (locus)
- pseudochondroplasia
what is multiple epiphyseal dypslatia
- short stature and early onset osteoarthritis
- locus heterogeneity
- the reason is due to protein protein interaction network involved in the cartilage structure
what is pseudoachondroplasia
- more servere than multiple epephyseal dysplasia
- mutations generate structurally abnormal COMP protein
- COMP protein expressed in chondrocytes and tendons - generates defects in those tissues
what are allelic series and locus heterogeneity simplified
Allelic series - one gene - several disorders
locus heterogeneity - several genes - one disorder
what is a linkage map
- based on recombination during meiosis
- during meiosis, recombination of furthar apart markers/sequences is more than those closer together
- not always related to phsical distance some recombination hot/ cold spots
what is pre-genome analysis
- identify genetic markers whose genotype correlates with presence of disease/phenotype
- mandelian inheritance (diseased genotype the same in all patients)
- genotype in this region is not shared with healthy individuals
what is post genome linkage analysis
- human polymorphic markers with known location
- (SNP) single nucleotide polymorphisms
- assess markers over region of chromosome
- combination of alleles presnt on same chromosome homolog = haplotype
- shared haplotype indicate potential similarities in phenotype
- large scale analysis of haplotype, provides genome differeing between populations
- haplotype block in linkage diequilibrium - recombination events between close markers are rare
-can analyse just a few SNPs to determine haplotype
can ask if haplotype is associated with disease
what is exome sequencing
- Applicable to human disease
- Applicable to identify phenotypes in other organisms
- Many genome sequences available – not just common models
- Capture and isolation of all exons from genome
- Direct sequencing of coding regions
- Identify variations (mutations?)
what is next generation sequencing
- sequencing of many DNA molecules in parellel
- uses PCR amplification and coloured labells
what are the major modifications of next generation sequencing
- dont need gene specific primers
- parallel sequencing of pool samples
- rapid data generation of large datasets
- short read (50bp-450bp)
-alignment ot genome needed
what are the exome sequence limitations
- only samples known coding regions (1% of genome)
- doesnt identify chromosomal stractural alterations, only sequence alterations
- many variations in each individual
- false positives and negatives due to PCR amplification
what are polygenic phenotypes
- many phenotypes affected by multiple different genes, each making a small contribution to phenotype
- linkage hard to identify
- each allele has different degree of influence over phenotype
environmental behavioural influence
give examples of phylogenic diseases
- hypertension
- alcoholism
- psychiatric disease
what is the difference between heterogeneity and polygenic disease
what is the difference between heterogeneity and polygenic disease
- locus heterogeneity, many genes cause same disease through individual mutations (eacch has mandelian inheritance pattern
- polygenic disease, multiple genes cause disease through combined action of alleles
what is a genome wide assiciation study
- use SNP markers to generate haplotype for all genomic regions
- identify common haplotype from affected pools and unaffected pools
- assess genes in region for links to phenotype
what are the advantages of GWAS
- compare large groups, identify regions contributing to small amount of variation of phenotype
-useful for common diseases with polygenic basis
what are the advantages of GWAS
- compare large groups, identify regions contributing to small amount of variation of phenotype
-useful for common diseases with polygenic basisa
what are the disadvantages of GWAS
- need large nunmber of individuals in each group
- associated regions often contain on genes or unlikely candidates
- association to causation difficult to demonstrate (need functional experiments to validate)
what are the principles of independent assortment
- traits are inherited independent of each other
-if traits analysed individually each shows 3:1 inheritance - concluded 2 dominant 2 recessive - ratio of offspring from a two-trait cross 9:3:3:1
what were the contradictions found in mendels observations
- plant height
- seed diemeter
what did francis galton discover
- studied seed size in pea plants
- saw no clear phenotype of large vs small, however did have a variation of 1-2%
- observed offspring with no clear hertible impact
conflict between mendelian genetics and biometrics
- mendelieans, variation in discrete characters drives evolution, new mutants have large effects
- biometricians, evolution is natural selection acting on continously distributed characters
what is the modern theory of inheritence
- some phenotypes controlled by one gene
- many alleles (based changes can be observed for each gene
- some phenotypes controlled by many genes and interactions
what is a quantitative trait
- phenotypes are not one or two choices but rather, vary along a range of values
- controlled by interactions between genes and environment
what is an example of a quantitative trait
hypercholesterolemia
what is a quantitative trait loci
genetic regions that influence phenotypic variation of a complex trait, often through genetic interactions with each other and the environment.
what causes pigmentation differences
- melanosomes, cellular compartments that store melanin
- eumelanin - black/brown
- pheomelanin - red/yellow
what is the evolutionary function of melanin
protection against UV radiation, reduces synthesis of vitamin D
how to do QTL identification in mice
- identify phenotype of interest
- test inbred strains for phenotype
- determine genetic region that contributes to phenotype (major effect)
- evaluate genes in region as candidates
what were the conclusions of the alcoholic study
- stxbp1 is likely to be gene that causes ethanol preference QTL on mouse chromosome 2
- further studies into role of protein structure change are needed to determine molecular basis of phenotype
what is transgenic rescue
add wild type allel to mutant and see phenotype disappear
what is a knock in
generate same sequence change in wild type mice and induce same phenotype
what is epigenetics
- conrad waddington (1905-1975) “the branch of biology which studies the causal interactions between genes and their products, which bring the phenotype into being”
- epigenetics regerto the study of heritable changes that occur without a modificaiton in DNA sequence of the genes
what are the four types of epigenetic mechanisms
- DNA methylation
- histone modification
- nucleosome remodelling
-non-coding RNA-methylation
what is DNA methylation
- serves as a signal to how that DNA should be packed within the nucleus whether or not it should be present or easy for transcription
- blocks transcription of methylated gene
- imprint can differ depending on parental chromosome
opposite to acetylation
what diseases are due to imprinting
- Prader-Willi syndrome
- Angelman syndrome
what is Prader-Willi syndrome
- failure to thrive, short stature, impared conitive developement , respiratory distress, excessive eating and obesity
- micro deletions of chromosome 15
- imprinting center on chromosome 15, stop and increase transcription
what is Angelmans syndrome
- developmental delay, hyperactivity, impaired cognitive developement, seizures
- microdeletions of chromosome 15
- imprinting center on chromosome 15, stop and increase transcription
how does the imprint marking change
- During fertilisation there is an epigenetic reprogramming cycle
- Adult have differentiated cells
- The adult forms germ cells that are not imprinted
- After fertilisation a new marking of the imprints occurs
how is imprinting established
- Differentiated gametes must undergo widespread epigenetic reprogramming upon fertilisation
- After the mammalian 8 cell stage the zygotic genome is activated
- Two cell lineages form in mammalian embryo - inner cell mass and trophectoderm
- The inner cell mass is what gives rise to the embryo itself
- The trophectoderm gives rise to the placenta
- ICM further forms into epiblast (EPI) and primitive endoderm
Genes have different degree of methylation in inner cell mass and trophectoderm
how does cloning work
- take adult cell
- remove nucleus
- transfer to oocyte with nucleus removed
- implant into mother
what is the common dyndrome associated with cloning
large offspring syndrome, due to adult imprinting
what are the symptoms of large offspring syndrome
- respiratory distress
- up to 2-fold increase in birth weight
- skeletal defects
- immunological defects
- placental defects
what are the causes of large offspring syndrome
- improper placental developement due to imprinting defect in epigenetic markers
- abnormal gene expression in developement
- imprinted genes especially effected
- genes required for pluripotency affected
- gene expression changes, some genes not expressed
is epigenetics the cause of clone abnormalities
- methylation defects at imprinted locus in cloned cattle with large offspring syndrome showed: large loss of methylation
- cloned female and male animals used in natural matings have pups that show no defects like LOS
- offspring have same genotype but different epigenetic imprint
in what organisms does imprinting occur
mammals and plants
how are histone proteins modified
lysine residues can be acetylated (causeing packing)
what is the barker hypothesis
he believed nutrient restriction caused increased mortality rates and cardiovascular disease from 1910 to 1970 due to epigenetics
what is a thriftly phenotype
nutrient conditions during pregnancy have effect on health in adult life
how does a thrifty phenotype occor
- programming (persisting changes in phsiology and metabolism causes histone modification
- experience adequate nutrition after birth, modified physiology cannot compensate and causes obesity and cardiovascular disease
