Introduction to Genetic Analysis 12th Edition

Introduction to Genetic Analysis 12th Edition:

About this Book
Cover Page
Half Title Page
About the Authors
Title Page
Copyright Page
Contents in Brief
Contents
The Evolution of a Classic
Problem-Solving Skills for Success
Powerful Pedagogy
Acknowledgments
Chapter 1: The Genetics Revolution
1.1 The Birth of Genetics
Gregor Mendel—A monk in the garden
Mendel rediscovered
The central dogma of molecular biology
1.2 After Cracking the Code
Model organisms
Tools for genetic analysis
1.3 Genetics Today
From classical genetics to medical genomics
Investigating mutation and disease risk
When rice gets its feet a little too wet
Recent evolution in humans
The complex genetics of color blindness
Summary
Key Terms
Problems
Part 1: Core Principles in Transmission Genetics
Chapter 2: Single-Gene Inheritance
2.1 Single-Gene Inheritance Patterns
Mendel’s pioneering experiments
Mendel’s law of equal segregation
2.2 Genes and Chromosomes
Single-gene inheritance in diploids
Single-gene inheritance in haploids
2.3 The Molecular Basis of Mendelian Inheritance Patterns
Structural differences between alleles at the molecular level
Molecular aspects of gene transmission
Alleles at the molecular level
2.4 Some Genes Discovered by Observing Segregation Ratios
A gene active in the development of flower color
A gene for wing development
A gene for hyphal branching
Predicting progeny proportions or parental genotypes by applying the principles of single-gene inheritance
2.5 Sex-Linked Single-Gene Inheritance Patterns
Sex chromosomes
Sex-linked patterns of inheritance
X-linked inheritance
2.6 Human Pedigree Analysis
Autosomal recessive disorders
Autosomal dominant disorders
Autosomal polymorphisms
X-linked recessive disorders
X-linked dominant disorders
Y-linked inheritance
Calculating risks in pedigree analysis
Summary
Key Terms
Solved Problems
Problems
Appendix 2-1 Stages of Mitosis
Appendix 2-2 Stages of Meiosis
Chapter 3: Independent Assortment of Genes
3.1 Mendel’s Law of Independent Assortment
3.2 Working with Independent Assortment
Predicting progeny ratios
Using the chi-square test on monohybrid and dihybrid ratios
Synthesizing pure lines
Hybrid vigor
3.3 The Chromosomal Basis of Independent Assortment
Independent assortment in diploid organisms
Independent assortment in haploid organisms
Recombination
3.4 Polygenic Inheritance
3.5 Organelle Genes: Inheritance Independent of The Nucleus
Patterns of inheritance in organelles
Cytoplasmic segregation
Cytoplasmic mutations in humans
mtDNA in evolutionary studies
Summary
Key Terms
Solved Problems
Problems
Chapter 4: Mapping Eukaryote Chromosomes by Recombination
4.1 Diagnostics Of Linkage
Using recombinant frequency to recognize linkage
How crossovers produce recombinants for linked genes
Linkage symbolism and terminology
Evidence that crossing over is a breakage-and-rejoining process
Evidence that crossing over takes place at the four-chromatid stage
Multiple crossovers can include two or more than two chromatids
4.2 Mapping By Recombinant Frequency
Map units
Three-point testcross
Deducing gene order by inspection
Interference
Using ratios as diagnostics
4.3 Mapping with Molecular Markers
4.4 Using the Chi-Square Test to Infer Linkage
4.5 The Molecular Mechanism of Crossing Over
4.6 Using Recombination-Based Maps in Conjunction with Physical Maps
Summary
Key Terms
Solved Problems
Problems
Chapter 5: Gene Interaction
5.1 Interactions Between the Alleles of a Single Gene: Variations on Dominance
Complete dominance and recessiveness
Incomplete dominance
Codominance
Recessive lethal alleles
Penetrance and expressivity
5.2 Interaction of Genes in Pathways
Biosynthetic pathways in Neurospora
Gene interaction in other types of pathways
5.3 Inferring Gene Interactions
Sorting mutants using the complementation test
Analyzing double mutants of random mutations
Summary
Key Terms
Solved Problems
Problems
Chapter 6: The Genetics of Bacteria and Their Viruses
6.1 Working with Microorganisms
6.2 Bacterial Conjugation
Discovery of conjugation
Discovery of the fertility factor
Strains
Linear transmission of the genes from a fixed point
Inferring integration sites of and chromosome circularity
Mapping of bacterial chromosomes
Broad-scale chromosome mapping by using time of entry
Fine-scale chromosome mapping by using recombinant frequency
F plasmids that carry genomic fragments
Plasmids
6.3 Bacterial Transformation
The nature of transformation
Chromosome mapping using transformation
6.4 Bacteriophage Genetics
Infection of bacteria by phages
Mapping phage chromosomes by using phage crosses
6.5 Transduction
Discovery of transduction
Generalized transduction
Specialized transduction
Behavior of the prophage
Insertion
Mechanism of specialized transduction
6.6 Physical Maps and Linkage MAPS Compared
Summary
Key Terms
Solved Problems
Problems
Part 2: Core Principles in Molecular and Developmental Genetics
Chapter 7: DNA: Structure and Replication
7.1 DNA is the Genetic Material
The discovery of bacterial transformation: The Griffith experiment
Evidence DNA that is the genetic material in bacteria: The Avery, MacLeod, and McCarty experiments
Evidence DNA that is the genetic material in phage: The Hershey–Chase experiment
7.2 DNA Structure
DNA Structure before Watson and Crick
The building blocks of
Chargaff’s rules of base composition
Diffraction analysis of : Rosalind Franklin
The DNA double helix structure: Watson and Crick
7.3 DNA Replication is Semiconservative
Evidence that DNA replication is semiconservative: The Meselson–Stahl experiment
Evidence for a replication fork: The Cairns experiment
7.4 Replication in Bacteria
Unwinding the DNA double helix
Assembling the replisome: replication initiation
DNA Polymerases catalyze chain elongation
DNA Replication is semidiscontinuous
DNA Replication is accurate and rapid
7.5 DNA Replication in Eukaryotes
Eukaryotic origins of replication
DNA Replication and the yeast cell cycle
Replication origins in higher eukaryotes
Telomeres and telomerase: Replication termination
Summary
Key Terms
Problems
Chapter 8: RNA: Transcription, Processing, and Decay
8.1 RNA Structure
RNA is the information-carrying intermediate between DNA and proteins
Consequences of the distinct chemical properties of RNA
Classes of RNA
8.2 Transcription and Decay of mRNA in Bacteria
Overview: DNA as transcription template
Stages of transcription
Transcription initiation in bacteria
Transcription elongation in bacteria
Transcription termination in bacteria
mRNA decay in bacteria
8.3 Transcription in Eukaryotes
Transcription initiation in eukaryotes
RNA polymerase I promoters and GTFs
RNA polymerase II promoters and GTFs
RNA polymerase III promoters and GTFs
RNA polymerase II transcription elongation
Transcription termination in eukaryotes
8.4 Processing of mRNA in Eukaryotes
Capping
Polyadenylation
The discovery of splicing
The splicing mechanism
snRNAs in the spliceosome may carry out the catalytic steps of splicing
Alternative splicing can expand the proteome
RNA editing
RNA nucleotide modification
RNA export from the nucleus
8.5 Decay of mRNA in Eukaryotes
mRNA decay mechanisms
The discovery of RNA interference (RNAi)
siRNA-mediated RNA decay and transcriptional silencing
RNAi protects the genome from foreign DNA
Summary
Key Terms
Problems
Chapter 9: Proteins and Their Synthesis
9.1 Protein Structure
9.2 The Genetic Code
A degenerate three-letter genetic code specifies the 20 amino acids
The genetic code is nonoverlapping and continuous
Cracking the code
Stop codons
Degeneracy of the genetic code limits the effects of point mutations
9.3 tRNAs and Ribosomes
tRNAs are adaptors
Wobble base pairing allows tRNAs to recognize more than one codon
Ribosome structure and function
9.4 Translation
Translation initiation
Translation elongation
Translation termination
Nonsense suppressor mutations
9.5 Translational and Post-Translational Regulation
Protein folding
Post-translational modification of amino acid side chains
Phosphorylation
Ubiquitination
Protein targeting
Summary
Key Terms
Solved Problems
Problems
Chapter 10: Gene Isolation and Manipulation
10.1 Detecting and Quantifying DNA, RNA, and Protein
Detecting and quantifying molecules by Southern, Northern, and Western blot analysis
Detecting and amplifying DNA by the polymerase chain reaction
10.2 Generating Recombinant DNA
DNA cloning
DNA libraries
Identifying a clone of interest from a genomic or cDNA library
Genomic and cDNA clones are used in different ways
Cloning by PCR
10.3 Sequencing DNA
10.4 Engineering Genomes
Genetic engineering in Saccharomyces cerevisiae
Genetic engineering in plants
Genetic engineering in animals
CRISPR-Cas9 genome engineering
Summary
Key Terms
Solved Problems
Problems
Chapter 11: Regulation of Gene Expression in Bacteria and Their Viruses
11.1 Gene Regulation
The Basics of Bacterial Transcriptional Regulation: Genetic Switches
A First Look at the Lac Regulatory Circuit
11.2 Discovery of the Lac System: Negative Regulation
Genes Controlled Together
Genetic Evidence for the Operator and Repressor
Genetic Evidence for Allostery
Genetic Analysis of the Lac Promoter
Molecular Characterization of the Lac Repressor and the Lac Operator
11.3 Catabolite Repression of the Lac Operon: Positive Regulation
The Basics of Lac Catabolite Repression: Choosing the Best Sugar to Metabolize
The Structures of Target DNA Sites
A Summary of the Lac Operon
11.4 Dual Positive and Negative Regulation: The Arabinose Operon
11.5 Metabolic Pathways and Additional Levels of Regulation: Attenuation
11.6 Bacteriophage life Cycles: More Regulators, Complex Operons
Regulation of the Bacteriophage ? life Cycle
Molecular Anatomy of the Genetic Switch
Sequence-Specific Binding of Regulatory Proteins to DNA
11.7 Alternative Sigma Factors Regulate Large Sets of Genes
Summary
Key Terms
Solved Problems
Problems
Chapter 12 Regulation of Transcription in Eukaryotes
12.1 Transcription Factors Regulate Transcription
Transcription factors bind distal and proximal enhancers
Transcription factors: lessons from the yeast GAL system
Gal4 binds enhancers called upstream activation sequences
Gal4 domains function independently of one another
Regulation of Gal4
Combinatorial control of transcription: lessons from yeast mating type
12.2 Chromatin Structure
Histones
Nucleosomes
Chromatin folding
12.3 Chromatin Regulates Transcription
Histone modification: a type of chromatin modification
The histone code hypothesis
DNA modification: another type of chromatin modification
Chromatin remodeling
Connecting chromatin structure to transcription: lessons from the interferon-? gene
12.4 Chromatin in Epigenetic Regulation
Cellular memory
Position-effect variegation
Genomic imprinting
X-chromosome inactivation
Summary
Key Terms
Problems
Chapter 13: The Genetic Control of Development
13.1 The Genetic Approach to Development
13.2 The Genetic Toolkit for Drosophila Development
Classification of genes by developmental function
Homeotic genes and segmental identity
Organization and expression of Hox genes
The homeobox
Clusters of Hox genes control development in most animals
13.3 Defining the Entire Toolkit
The anteroposterior axis
Expression of toolkit genes
13.4 Spatial Regulation of Gene Expression in Development
Maternal gradients and gene activation
Drawing stripes: Integration of gap-protein inputs
Making segments different: integration of inputs
13.5 Post-Transcriptional Regulation of Gene Expression in Development
RNA splicing and sex determination in Drosophila
Regulation of mRNA translation and cell lineage in C. elegans
Translational control in the early embryo
miRNA control of developmental timing in C. elegans and other species
13.6 From Flies to Fingers, Feathers, and Floor Plates: The Many Roles of Individual Toolkit Genes
13.7 Development and Disease
Polydactyly
Holoprosencephaly
Cancer as a developmental disease
Summary
Key Terms
Solved Problems
Problems
Chapter 14: Genomes and Genomics
14.1 The Genomics Revolution
14.2 Obtaining the Sequence of a Genome
Turning sequence reads into an assembled sequence
Whole-genome sequencing
Traditional WGS sequencing
Next-generation WGS sequencing
Whole-genome-sequence assembly
14.3 Bioinformatics: Meaning from Genomic Sequence
The nature of the information content of DNA
Deducing the protein-encoding genes from genomic sequence
14.4 The Structure of the Human Genome
Noncoding functional elements in the genome
14.5 The Comparative Genomics of Humans with other Species
Phylogenetic inference
Of mice and humans
Comparative genomics of chimpanzees and humans
14.6 Comparative Genomics and Human Medicine
The evolutionary history of human disease genes
The exome and personalized genomics
Comparative genomics of nonpathogenic and pathogenic E. coli
14.7 Functional Genomics and Reverse Genetics
“ ’Omics”
Reverse genetics
Summary
Key Terms
Solved Problems
Problems
Part 3: Core Principles in Mutation, Variation, and Evolution
Chapter 15: DNA Damage, Repair, and Mutation
15.1 Molecular Consequences of Point Mutations
The types of point mutations
The molecular consequences of a point mutation in an open reading frame
The molecular consequences of a point mutation in a noncoding region
15.2 Molecular Basis of Spontaneous Mutations
Evidence for spontaneous mutations: The Luria and Delbrück fluctuation test
Mechanisms of spontaneous mutations
15.3 Molecular Basis of Induced Mutations
Mechanisms of induced mutagenesis
Identifying mutagens in the environment: The Ames test
15.4 DNA Repair Mechanisms
Direct repair of damaged DNA
Base excision repair
Nucleotide excision repair
Mismatch repair
Translesion synthesis
Repair of double-strand breaks
Summary
Key Terms
Problems
Chapter 16: The Dynamic Genome: Transposable Elements
16.1 Discovery of Transposable Elements in Maize
McClintock’s experiments: the Ds element
Ac (Activator) and Ds (Dissociation) today
Transposable elements: Only in maize?
16.2 Transposable Elements in Bacteria
Evidence for transposable elements in bacteria
Simple and composite transposons
Mechanism of transposition
16.3 Transposable Elements in Eukaryotes
Class 1: retrotransposons
Class 2: DNA transposons
Utility of DNA transposons as tools for genetic research
16.4 The Dynamic Genome: More Transposable Elements Than Ever Imagined
Large genomes are largely transposable elements
Transposable elements in the human genome
Plants: LTR-retrotransposons thrive in large genomes
Safe havens
16.5 Regulation of Transposable Element Movement by the Host
RNAi silencing of transposable elements
Genome surveillance
Summary
Key Terms
Solved Problems
Problems
Chapter 17: Large-Scale Chromosomal Changes
17.1 Changes in Chromosome Number
Aberrant euploidy
Aneuploidy
The concept of gene balance
17.2 Changes in Chromosome Structure
Deletions
Duplications
Inversions
Reciprocal translocations
Robertsonian translocations
Applications of inversions and translocations
17.3 Phenotypic Consequences of Chromosomal Changes
Chromosome rearrangements and evolution
Chromosome rearrangements and cancer
Overall incidence of human chromosome mutations
Summary
Key Terms
Solved Problems
Problems
Chapter 18: Population Genetics
18.1 Detecting Genetic Variation
Single nucleotide polymorphisms (SNPs)
Microsatellites
Haplotypes
Other sources and forms of variation
18.2 The Gene-Pool Concept and the Hardy–Weinberg Law
18.3 Mating Systems
Assortative mating
Isolation by distance
Inbreeding
The inbreeding coefficient
Population size and inbreeding
18.4 Genetic Variation and its Measurement
18.5 The Modulation of Genetic Variation
New alleles enter the population: mutation and migration
Recombination and linkage disequilibrium
Genetic drift and population size
Selection
Forms of selection
Balance between mutation and drift
Balance between mutation and selection
18.6 Biological and Social Applications
Conservation genetics
Calculating disease risks
DNA forensics
Summary
Key Terms
Solved Problems
Problems
Chapter 19: The Inheritance of Complex Traits
19.1 Measuring Quantitative Variation
Types of traits and inheritance
The mean
The variance
The normal distribution
19.2 A Simple Genetic Model for Quantitative Traits
Genetic and environmental deviations
Genetic and environmental variances
Correlation between variables
19.3 Broad-Sense Heritability: Nature Versus Nurture
Measuring heritability in humans using twin studies
19.4 Narrow-Sense Heritability: Predicting Phenotypes
Gene action and the transmission of genetic variation
The additive and dominance effects
A model with additivity and dominance
Narrow-sense heritability
Predicting offspring phenotypes
Selection on complex traits
19.5 Mapping QTL in Populations With Known Pedigrees
The basic method for QTL mapping
From QTL to gene
19.6 Association Mapping in Random-Mating Populations
The basic method for GWAS
GWA, genes, disease, and heritability
Summary
Key Terms
Solved Problems
Problems
Chapter 20: Evolution of Genes, Traits, and Species
20.1 Evolution by Natural Selection
20.2 Natural Selection in Action: An Exemplary Case
The Selective Advantage of HbS
The Molecular Origins of HbS
20.3 Molecular Evolution
The Development of the Neutral Theory of Evolution
The Rate of Neutral Substitutions
The Signature of Purifying Selection on DNA Sequences
The Signature of Positive Selection on DNA Sequences
20.4 Evolution of Genes and Genomes
Expanding Gene Number
The Fate of Duplicated Genes
The Fate of Duplicated Genomes
20.5 Evolution of Traits
Adaptive Changes in a Pigment-Regulating Protein
Gene Inactivation
Regulatory-Sequence Evolution
Loss of Characters Through Regulatory-Sequence Evolution
Regulatory Evolution in Humans
20.6 Evolution of Species
Species Concepts
Mechanisms of Reproductive Isolation
Genetics of Reproductive Isolation
Summary
Key Terms
Problems
A Brief Guide to Model Organisms
Escherichia Coli
Saccharomyces Cerevisiae
Neurospora Crassa
Arabidopsis Thaliana
Caenorhabditis Elegans
Drosophila Melanogaster
Mus Musculus
Beyond Model Organisms
Appendix A: Genetic Nomenclature
Appendix B: Bioinformatic Resources for Genetics and Genomics
Glossary
Answers to Selected Problems
Notes
Index
Back Cover

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