Integrated Molecular Evolution by Rogers, Scott Orland -- Read -- Imperial Library of Trantor

Index

Cover Half Title Title Page Copyright Page Table of Contents Preface Acknowledgments Author SECTION I Life and Evolution

Chapter 1 Definitions of Life

Introduction RNA and Life Defining Life Imagining Cellular and Molecular Dimensions Key Points Additional Readings

Chapter 2 Earth and Evolution

Introduction What Is Evolution? Earth History A Short History of the Study of Evolution Earth History as One Year Key Points Additional Readings

SECTION II Biomolecules

Chapter 3 DNA, RNA, and Proteins

Introduction Nucleic Acids Translation Amino Acids and Polypeptides Lipids Carbohydrates Key Points Additional Readings

Chapter 4 The Central Dogma and Beyond

Introduction Ribosomal RNA Transfer RNA (tRNA) Messenger RNA Other Small Noncoding RNA Beyond the Central Dogma Key Points Additional Readings

Chapter 5 Ribosomes and Ribosomal RNA

Introduction Ribosomes as Ribozymes Origin of the Ribosome Translation How Many rDNA Copies Are Needed? Mechanisms for Increasing rRNA Gene Copy Number Complexity of Ribosomes Key Points Additional Readings

Chapter 6 Structure of the Genetic Code

Introduction Evolution of the Genetic Code Why a Triplet Codon? The First Genetic Code Life before Translation Key Points Additional Readings

Chapter 7 DNA Replication

Introduction Fidelity of Replication Variations of Replication Topology during Replication Replication of Chromosomes Key Points Additional Readings

Chapter 8 DNA Segregation

Introduction Variations on DNA Segregation in Bacteria and Archaea Mitosis Variations in Mitosis and the Cell Cycle Variations in Chromosome Number Changes in DNA Amount through the Cell Cycle Meiosis Sexual Reproduction Key Points Additional Readings

SECTION III Genetics

Chapter 9 Mendelian and Non-Mendelian Characters

Introduction Alleles The Basics of Mendelian Inheritance Codominance, Incomplete Dominance, Overdominance, and Underdominance Epistasis Quantitative Trait Loci Recombination and Linkage Non-Mendelian Traits Key Points Additional Readings

Chapter 10 Population Genetics

Introduction Hardy–Weinberg Equilibrium Population Size Life Histories Modes of Reproduction Key Points Additional Readings

Chapter 11 Alleles through Time

Introduction Natural Selection Levels of Selection Random Genetic Drift Mating and Dispersal Gene Flow Other Factors Affecting Allelic Proportions Key Points Additional Readings

Chapter 12 Changes to DNA

Introduction Classes of Mutations Causes of Mutations Mutation during Replication DNA Repair Genetic Recombination Key Points Additional Readings

Chapter 13 Infectious Changes to DNA: Viruses, Plasmids, Transposons, and Introns

Introduction Integration into Chromosomes Viruses Introns Transposable Elements Plasmids Key Points Additional Readings

SECTION IV Multicellularity

Chapter 14 Multigene Families

Introduction Ribosomal RNA Gene Family Globin Gene Family Bacterial Flagella Gene Family Laccase Gene Family Histone Gene Family Orthologs and Paralogs Polyploidization and Multigene Family Evolution Key Points Additional Readings

Chapter 15 Horizontal Gene Transfer

Introduction Plasmids Viruses Symbionts and Organelles Parasites and Pathogens Origin of Gram-Negative Bacteria Signs of HGT Introns Key Points Additional Readings

Chapter 16 Development: Part I—Cooperation among Cells

Introduction Quorum Sensing Development in Animals Nematode Development Homeotic Genes and Proteins Arthropod Development Development in Vertebrates Hierarchy and Evolution of Homeotic Genes Key Points Additional Readings

Chapter 17 Development: Part II—Plants

Introduction Plant Morphology Development in Plants Gene Expression during Development Formation of Leaves and Floral Organs Plants versus Animals Key Points Additional Readings

Chapter 18 Cancer

Introduction Progression of Cancer Genes Involved in Cancer Types of Cancer Causes of Mutations in Carcinogenesis

Point Mutations Recombination Amplification Viruses DNA Viruses

Hormones Key Points Additional Readings

SECTION V Molecular Biology and Bioinformatic Methods

Chapter 19 Extraction and Quantification of Biological Molecules

Introduction Extraction of Nucleic Acids Using CTAB Purification of Organellar DNA Extraction of RNA Quantification of Nucleic Acids Agarose Gel Electrophoresis Extraction of Proteins Quantification of Proteins Polyacrylamide Gel Electrophoresis Key Points Additional Readings

Chapter 20 Recombinant DNA and Characterization of Biological Molecules

Introduction Polymerase Chain Reaction Recombinant DNA Methods Southern Hybridization Determination of Gene Copy Number Microscopy Protein Analysis Key Points Additional Readings

Chapter 21 Sequencing and Alignment Methods

Introduction Development of DNA Sequencing Methods High-Throughput Technologies Next-Generation Sequencing Protein Sequencing Sequence Homology Searches Aligning Sequences Key Points Additional Readings

Chapter 22 Omics: Part I

Introduction Genomics Transcriptomics Metagenomics/Metatranscriptomics Microbiomics Key Points Additional Readings

Chapter 23 Omics: Part II

Introduction Proteomics Structural Genomics RNAomics Epigenomics Metabolomics Functional Genomics Key Points Additional Readings

Chapter 24 Species Concepts and Phylogenetics

Introduction What Is a Species? Classification of Life Reconstruction of Evolutionary History Phylogenetics Tree Terminology Choosing a Genomic Region for Phylogentics Other Considerations When Performing Phylogenetic Analyses Models of Mutation Analyzing Aligned Sequences Unweighted Pair Group Method with Arithmetic Mean Neighbor Joining Maximum Parsimony Maximum Likelihood Bayesian Phylogenetic Analysis Bootstrapping Vertical versus Horizontal Evolutionary Events Key Points Additional Readings

Chapter 25 Phylogenetic Networks and Reticulate Evolution

Introduction Phylogenetic Analyses of Reticulate Events Advantages of Phylogenetic Networks Horizontal Gene Transfers Species Hybridization Recombination Transposition Reassortment Examples of Reticulate Evolution Events Key Points Additional Readings

Chapter 26 Phylogenomics and Comparative Genomics

Introduction Improvements in Sequencing and Phylogenomics What to Compare Single-Nucleotide Polymorphisms Microsatellites and Minisatellites How to Compare Testing for Selection Incongruent Trees Comparative Genomics Synteny Key Points Additional Readings

SECTION VI Genomes

Chapter 27 RNA Viruses

Introduction C-Value Paradox Genomes and Genomics RNA Virus Genomes Human Immunodeficiency Virus Influenza A Virus Ebola Virus Key Points Additional Readings

Chapter 28 DNA Viruses

Introduction Bacteriophage ϕX174 Bacteriophage Lambda (λ) Bacteriophage T4 Mimivirus Key Points Additional Readings

Chapter 29 Bacteria and Archaea

Introduction Escherichia coli Photosynthetic Bacteria Aquifex Euryarchaeota Crenarchaeota Key Points Additional Readings

Chapter 30 Mutualists and Pathogens

Introduction Termite Gut Microbes Smallest Bacterial Genome Coresident Symbionts Animal Parasite Genome Mixing and Sorting Key Points Additional Readings

Chapter 31 Endosymbionts and Organelles

Introduction Intracellular Endosymbionts Mitochondria How Many Genes Make a Functional Mitochondrion? Chloroplasts How Many Genes Make a Functional Chloroplast? Differential Development and Function Chimeric Pathways Endosymbioses Leading to Other Organelles Key Points Additional Readings

Chapter 32 Protein Trafficking

Introduction Signal Peptides in Bacteria Signal Peptide Systems in Eukarya Protein Trafficking in Mitochondria Protein Trafficking in Chloroplasts Evolution of Protein Trafficking Systems Key Points Additional Readings

Chapter 33 Eukaryotic Genomes

Introduction Origin of the Nucleus and Mitochondrion Multicellularity Chromalveolata Opisthokonta

Saccharomyces cerevisiae Caenorhabditis elegans Drosophila melanogaster

Archaeplastida

Arabidopsis thaliana Oryza sativa

Key Points Additional Readings

Chapter 34 Human Genome

Introduction The Human Genome Medical Genetics Single-Nucleotide Polymorphisms Forensics Human Migration Key Points Additional Readings

Index

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