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Advanced Genetic Analysis Finding Meaning in a Genome

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ISBN-10: 1405103361

ISBN-13: 9781405103367

Edition: 2003

Authors: R. Scott Hawley, Michelle Y. Walker

List price: $115.50
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Providing the how and why of the essential tools needed for genetic analysis, this text provides an easy guide through difficult genetic concepts and techniques. Text boxes highlight key questions and timely examples.
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Book details

List price: $115.50
Copyright year: 2003
Publisher: John Wiley & Sons, Incorporated
Publication date: 1/31/2003
Binding: Paperback
Pages: 256
Size: 7.25" wide x 9.50" long x 0.50" tall
Weight: 1.342
Language: English

Types of mutations
Muller's classification of mutants
Modern mutant terminology
DNA-level terminology
Dominance and recessivity
Dominance and recessivity at the level of the cell
Difficulties in applying the terms "dominant" and "recessive" to sex-linked mutants
The genetic utility of dominant and recessive mutants
Gallery of model organisms
Our favorite organism: Drosophila melanogaster
Our second favorite organism: Saccharomyces cerevisiae
Our third favorite organism: Caenorhabditis elegans
Our new favorite organism: zebrafish
Phage lambda
Phage T4
Arabidopsis thaliana
Mus musculus (the mouse)
Mutant hunts
Why look for new mutants?
Reason 1: To identify genes required for a specific biological process
Reason 2: To isolate more mutations in a specific gene of interest
Reason 3: To obtain mutations tools for structure-function analysis
Reason 4: To isolate mutations in a gene so far identified only by molecular approaches
Mutagenesis and mutational mechanisms
Method 1: Ionizing radiation (usually X-rays and gamma-rays)
Method 2: Chemical mutagens
Method 3: Transposons as mutagens
Method 4: Targeted gene disruption (a variant on transposon mutagenesis)
What phenotype should you screen (or select) for?
Actually getting started
Your starting material
Pilot screens
Keeping too many, keeping too few
How many mutants is enough?
A screen for embryonic lethal mutations in Drosophila
The balancer chromosome
A screen for sex-linked lethal mutations in Drosophila
Making phenocopies by RNAi and co-suppression
Reviews of mutant isolation schemes and techniques in various organisms
The complementation test
The essence of the complementation test
Rules for using the complementation test
How might the complementation test lie to you?
Second-site non-complementation (SSNC) (non-allelic non-complementation)
Type 1 SSNC (poisonous interactions): the interaction is allele-specific at both loci
Type 2 SSNC (sequestration): the interaction is allele-specific at one locus
Type 3 SSNC (combined haplo-insufficiency): the interaction is allele-independent at both loci
Summary of SSNC
An extension of second-site non-complementation: dominant enhancers
A successful screen for dominant enhancers
A more rigorous definition of the complementation test
An example of using the complementation test in yeast
Transformation rescue is a variant of the complementation test
One method for determining whether or not a dominant mutation is an allele of a given gene, or how to make dominants into recessives by pseudo-reversion
Pairing-dependent complementation: transvection
Synthetic lethality and genetic buffering
A basic definition of genetic suppression
Intragenic suppression (pseudo-reversion)
Intragenic revertants can mediate translational suppression
Intragenic suppression as a result of compensatory mutants
Extragenic suppression
Transcriptional suppression
Suppression at the level of gene expression
Suppression of transposon insertion mutants by altering the control of mRNA processing
Suppression of nonsense mutants by messenger stabilization in C. elegans
Translational suppression
Simplicity: tRNA suppressors in E. coli
The numerical and functional redundancy of tRNA genes allowing suppressor mutations to be viable
Suppression of a frameshift mutation using a mutant tRNA gene
Suppressing a nonsense codon using unaltered tRNAs
Suppression by post-translational modification
Extragenic suppression as a result of protein-protein interaction
Searching for suppressors that act by protein-protein interaction in eukaryotes
Extragenic suppression as a result of "lock-and-key" conformational suppression
Suppression without physical interaction
Bypass suppression
"Push me, pull you" bypass selection by counterbalancing of opposite activities
Extra-copy suppression as a form of bypass suppression
Suppression of dominant mutations
Designing your own screen for suppressor mutations
Summary and a warning
Intragenic suppression of antimorphic mutations that produce a poisonous protein
Bypass suppression of a telomere defect in the yeast S. pombe
Determining when and where genes function
Epistasis: ordering gene function in pathways
Ordering gene function in a biosynthetic pathway
The use of epistasis in non-biosynthetic pathways: determining if two genes act in the same or different pathways
The real value of epistasis analysis is in the dissection of regulatory hierarchies
How might an epistasis experiment mislead you?
Mosaic analysis: where does a given gene act?
Tissure transplantation studies
Loss of the unstable ring X chromosome
Mitotic recombination
Genetically controllable mitotic recombination: the FLP-FRT system
Genetic fine-structure analysis
Intragenic mapping (then)
The first efforts towards finding structure within a gene
The unit of recombination and mutation is the base pair
Intragenic mapping (now)
Intragenic complementation meets intragenic recombination: the basis of fine-structure analysis
The formal analysis of intragenic complementation
An example of fine-structure analysis for a eukaryotic gene encoding a multifunctional protein
A genetic and functional dissection of the HIS4 gene in yeast
Fine-structure analysis of genes with complex regulatory elements in eukaryotes
Genetic and functional dissection of the cut gene in Drosophila
Pairing-dependent intragenic complementation
Genetic and functional dissection of the yellow gene in Drosophila
The influence of the zeste gene on pairing-dependent complementation at the white locus in Drosophila
Genetic and functional dissection of BX-C in Drosophila
Genetic and functional dissection of the rudimentary gene in Drosophila
Meiotic recombination
An introduction to meiosis
A cytological description of meiosis
A more detailed description of meiotic prophase
Crossingover and chiasmata: recombination involves the physical interchange of genetic material and ensures homolog separation
The classical analysis of recombination
Measuring the frequency of recombination
The curious relationship between the frequency of recombination and chiasma frequency (and why it matters)
Map lengths and recombination frequency
Determining the fraction of bivalents with zero, one, two, or more exchanges (tetrad analysis)
Statistical estimation of recombination frequencies (LOD scores)
The actual distribution of exchange events
Practicalities of mapping
The mechanism of recombination
Gene conversion
Previous models
The currently accepted mechanism of recombination: the DSBR model
The molecular biology of synapsis
Do specific chromosomal sites mediate pairing?
Crossingover in compound X chromosomes
Does any sister chromatid exchange occur during meiosis?
Using tetrad analysis to determine linkage
Mapping centromeres in fungi with unordered tetrads
Meiotic chromosome segregation
Types and consequences of failed segregation
The origin of spontaneous nondisjunction
The centromere
The isolation and analysis of the S. cerevisiae centromere
The isolation and analysis of the Drosophila centromere
Segregational mechanisms
How chiasmata ensure segregation
Achiasmate segregation
Identifying genes that encode centromere-binding proteins in yeast
The concept of the epigenetic centromere in Drosophila and humans
Achiasmate heterologous segregation in Drosophila females
Partial author index
Subject index