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• 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 λ 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‐β 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