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Chapter

Cover An Introduction to Molecular Evolution and Phylogenetics

Genome  

Accident and design

This chapter evaluates genomes. Genome size varies dramatically between species. Much of the variation is due to repeated sequences, rather than differences in number of different genes. Whole genome duplications can provide the raw material for establishing new lineages. On a finer scale, shorter repeat sequences are prone to accidents in replication that increase or decrease the number of copies. Because of this high rate of change, short repeats are likely to vary in number between individuals. Other repeat sequences play a more active role in their own duplication, containing regulatory signals and genes that cause them to be copied and inserted throughout the genome. Transposable elements not only fill the genome with copies of themselves, they also remodel their host's genome. The changes caused by these 'jumping genes' have profound effects on genome structure and evolution.

Chapter

Cover An Introduction to Molecular Ecology

Genomes  

This chapter focuses on genomes. The genome is recognized to be the complete set of an organism's DNA. The chapter discusses the history of the first genome sequences. It gives an overview of notable genomes and their date of publication. The chapter highlights the Human Genome Project in line with competing sequencing strategies for eukaryotic genomes and comparative genomics. It notes that whole genome shotgun (WGS) and next generation sequencing (NGS) are used to sequence genomes. Genome reassembly is the major challenge of sequencing a large eukaryotic genome. In addition, the chapter explains microbiomes being used in metabarcoding and metagenomics approaches. It also explores genome annotation.

Chapter

Cover The Evolution of Life

The Dynamic Genome  

This chapter studies the genome itself, which is the source of all the hereditary information underlying the adaptation of organisms to their environment. The evolution of the genome is naturally one of the most pressing issues in evolutionary biology. Why are many genomes much larger than they need to be? How does the gain and loss of genes contribute to evolution? How do new genes come into being? Molecular genetics is beginning to provide answers to fundamental questions like these, and the answers have turned out to depend on the Darwinian rules that govern genome dynamics. The chapter then considers how evolving genomes diverge, how genes are modified at different rates, how eukaryotic genomes have evolved novel features, and how genetic elements may evolve cooperation or conflict.

Chapter

Cover Evolution

The Evolution of Genes and Genomes  

This chapter tackles the evolution and origin of genes and genomes. New genes are an important source of evolutionary novelty and adaptation, which can either originate through eukaryotes, retrotransposition from mRNA to DNA, or horizontal gene transfer (HGT). The chapter considers how genome size and genome coding vary dramatically among species by referencing viruses, prokaryotes, animals, and plants. It also looks into the neutral theory of molecular evolution and the evolution of protein-coding genes by changes to their sequences and their expression. The chpater notes that whole genome duplication is responsible for the large differences in gene number among closely related groups of organisms.

Chapter

Cover Medical Microbiology

Bacterial pathogenesis  

Lynn G. Dover

This chapter focuses on bacterial pathogenesis. Most of the bacteria that colonize our bodies do so without causing us any harm. However, some bacteria are inherently more damaging than others. Their degree of pathogenicity is described in the term ‘virulence’, which can be quantified by establishing experimental metrics such as median lethal dose and median time to death. Virulence and pathogenicity are dependent upon the composition of the bacterial genome; pathogen genomes encode many virulence factors which operate in a concerted fashion to express pathogenicity. The chapter then describes the characteristics of pathogenic bacteria that allow them to adhere to epithelial surfaces (adhesins), evade the immune system (evasins and impedins), invade tissues (invasins), and damage underlying tissues (toxins). It looks at toxinogenesis and considers pan-genomes, mobile genetic elements, and the acquisition virulence factors.

Chapter

Cover Biological Science

Information  

Genes and Genomes

This chapter looks at genes and genomes, and references the chemical structures of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). It notes the two-stage process of protein synthesis, which are transcription and translation. DNA replication is extremely accurate. However, damaged DNA can be repaired by the use of direct repair and excision repair mechanisms. However, it should be noted that the repairs are error-prone and may lead to cancer. The chapter mentions that DNA replication is semi-conservative, so each strand acts as a template for the polymerization of complementary nucleotides. The chapter also looks into genome organization and packaging in prokaryotic and eukaryotic cells.

Chapter

Cover Biological Science

Information  

Genes and Genomes

This chapter looks at genes and genomes, and references the chemical structures of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). It notes the two-stage process of protein synthesis, which are transcription and translation. DNA replication is extremely accurate. However, damaged DNA can be repaired by the use of direct repair and excision repair mechanisms. However, it should be noted that the repairs are error-prone and may lead to cancer. The chapter mentions that DNA replication is semi-conservative, so each strand acts as a template for the polymerization of complementary nucleotides. The chapter also looks into genome organization and packaging in prokaryotic and eukaryotic cells.

Chapter

Cover Introduction to Bioinformatics

The panorama of life  

This chapter discusses the basic sizes, contents, and organizing principles of simple and complex genomes. A single gene coding for a particular protein corresponds to a sequence of nucleotides. In cells, genes may appear on either strand of DNA. Bacterial protein-coding genes are continuous regions of DNA, while in eukaryotes, the nucleotide sequences that encode amino acid sequences of proteins are organized in a more complex manner. The chapter then looks at proteomics and transcriptomics. It considers how the genomes of prokaryotes and eukaryotes differ systematically, before exploring the variety of transcribed RNA molecules encoded in the human genome. The chapter then highlights the power of DNA sequences in studying human history, including inference of human migration patterns, and as records of plant and animal domestication. It also assesses the power of comparative genomics to identify features responsible for differences between species.

Chapter

Cover Molecular Biology

Genomics and genetic variation  

This chapter focuses on genomics and genetic variation. The field of genomics studies both the similarities and differences between the genomes of living organisms. The chapter therefore has two key themes: the evolutionary conservation of genomes on the one hand and the variation that leads to differences between individuals and species on the other. Selection and genetic drift work on genetic variation to shape natural populations. Evolutionary differences between species involve changes in size of genomes, the structure of genomes, and the number of genes, as well as the sequence of genes. The chapter then considers human genomics. Our rapidly expanding knowledge of the sequence and haplotype structure of the human genome allows us to trace our history, as well as to identify genes associated with many different traits and important diseases, but also carries with it the responsibility to use the information wisely.

Book

Cover Genomics

Lia Chappell, Sarah J Lindsay, Phil Jones, Julian Parkhill, Jonathan Roberts, Nancy Holroyd, Michal Szpak, and Francesca Gale

Genomics starts with a look at rare diseases from a genomics perspective. It then moves on to consider cancer genomics. There follows a chapter about genomes and ethics. Pathogen genomics is also examined in detail. There is also a chapter on parasite genomics. Human evolution is considered next. Finally, reading and writing genomes is looked into.

Chapter

Cover Genomics

Pathogen Genomics  

This chapter evaluates pathogen genomics. As scientists developed sequencing tools at the end of the 1970s, virus genomes were the first to be tackled, because of their small size. Viruses, and then bacteria, formed the test bed for developments that went on to enable the sequencing of human genomes, but they are also of interest, and of value, in themselves. A pathogen genome tells us a lot about how pathogens grow and interact with their environment. The genome also tells us how the pathogens avoid both our immune systems and the weapons we have developed to overcome them, such as vaccines and antibiotics. Beyond this fundamental information, a genome is also a written record of the evolutionary history of the pathogen. The chapter then looks at metagenomics and how genomics is being used by academics and companies to develop new vaccines and antibiotics in a directed way.

Chapter

Cover Concepts in Bioinformatics and Genomics

Genomics  

This chapter displays genomics analysis with an emphasis on next-generation sequencing (NGS), and annotation of bacterial genomes. It uncovers the underlying principles of dideoxy sequencing and selected next-generation sequencing technologies. The chapter also examines the theory of polymerase chain reaction (PCR) and the general categories of DNA that constitute the human genome (the genomic landscape). The chapter then shifts to investigate how DNA fingerprinting is performed and the degree of synteny shared between genomes. It reviews the whole genome shotgun strategy approach to genome sequencing, then examines how gene prediction software programs predict and annotate genes in genomes. Finally, the chapter describes the haplotype, the HapMap Project, and the significance of the HapMap project. It then looks into the benefits and concerns of having knowledge of personal genome data.

Chapter

Cover Introduction to Genomics

Comparative Genomics  

This chapter analyses the three major divisions of living things (archaea, bacteria, and eukaryotes) based on the sequences of 16S rRNA genes. It notes the prevalence of historical gene transfer among prokaryotes. Historical gene transfer is not consistent with the hierarchical Linnaean classification scheme. The chapter discusses the general distribution of genome sizes and gene numbers while determining the characteristics of different types of genome organization in viruses, prokaryotes, and eukaryotes. The chapter notes the impact of gene duplication on genome evolution and considers the mechanism of genome change at the levels of individual bases, genes, chromosome segments, and whole genomes. It differentiates homologue, orthologue, and paralogue as well. The chapter also expounds on the human genome and the idea of a model organism in the study of human diseases.

Book

Cover Genetics

Philip Meneely, Rachel Dawes Hoang, Rachel Dawes Hoang, Iruka N. Okeke, and Katherine Heston

Genetics begins with an evaluation of evolution, genomes, and genes. It looks at the Central Dogma of molecular biology. Other topics covered include genome structure, organization, and variation; descent and modification; single-gene traits; mendelian genetics; x-linked genes; sex chromosomes; and the inheritance of multiple genes. The book also looks at genes in chromosomes, genetic maps, human genetic mapping, exchange, evolution, and transcription. Finally, there are chapters on networks of gene regulation, genetic analysis of cellular processes, genetics of population, and metagenomes.

Chapter

Cover Genetics

Human Genetic Mapping, Genome-wide Association Studies, and Complex Traits  

This chapter brings together fundamental concepts of genetics and genomes on complex traits and genome-wide association studies, which focus primarily on human traits and diseases. It explores genome-wide association studies in order to build upon the basic principles that identify contributing genes and causative mutations. It provides an approach that shows how genome-wide associations integrate genomic variation, complex phenotypes, and evolutionary history. The chapter mentions the Human Genome Project, which made it possible to identify hundreds of individual genes that affect disease phenotypes. It focuses on human genetic diseases and provides an analysis of the human genome, which allowed a much deeper understanding of many aspects of the overall biology of Homo sapiens.

Chapter

Cover Biochemistry and Molecular Biology

Cells and viruses  

This chapter offers a broad survey of the structures and properties of cells and viruses, providing a biological background for the more detailed mechanisms of cell biology, biochemistry, and molecular biology. It explains that cells are the units of living systems, wherein each cell is surrounded by a lipid membrane and has a DNA genome. The two main classes of cellular organism are prokaryotes and eukaryotes, including archaea that are a third class of organism that can live in unusual environments. The chapter examines the large numbers of ribosomes in both prokaryotic and eukaryotic cells, which are large complex structures of RNA and proteins found in the cytosol. The cytoplasm of eukaryotic cells can be defined as the content of the cell excluding the nucleus, while the cytosol refers to the soluble constituents of the cytoplasm from which membrane-bounded organelles have been removed.

Book

Cover An Introduction to Molecular Evolution and Phylogenetics
An Introduction to Molecular Evolution and Phylogenetics first talks the reader through the story of DNA. It then delves into more detail describing DNA as the immortal germline. The text then considers mutation, and also looks at replication, the genome, genes, selection, and drift. The text goes on to consider species and the origin of species. It also describes the role of alignment, phylogeny, and hypotheses. Finally, it looks at rates in terms of tempo and mode and dates in terms of time.

Chapter

Cover Introduction to Genomics

Introduction and Background  

This chapter introduces genomics by identifying genomes, genes, their roles, scope, history, and organization. It aims to recognize the contributions to any individual’s phenotype from their genome sequence, life history, and epigenetic factors. It explains major genome projects and the current library of genome information, which include high-throughput sequencing, de novo sequencing, resequencing, and exome sequencing. It also relates genes and minds to the study of neurogenomics. The chapter furthermore introduces proteomics and the mechanism of protein evolution in relation to natural selection. It argues that modern genomics merged biological data, computer science, and statistics in an effort to archive high amounts of data.

Chapter

Cover Introduction to Genomics

The Human Genome Project: Achievements and Applications  

This chapter discusses the Human Genome Project, including its history and links to various organizations. The chapter acknowledges that technological advancement has turned genome sequencing into a high-throughput data-generation engine and anticipates that pharmacogenomics, or personalized medicine, will continue to grow. It explains that identifying the genetic substrate underlying diseases can become crucial in clinical treatment as gene editing using CRISPR/Cas technology could be used to repair defective genes of human embryos. The chapter considers how humans differ from other species and from one another, and looks into DNA and the application of genomics in the context of personal identification and parental determination. The chapter also mentions the ethical, legal, and social issues linked to genomics and the Human Genome Project.

Chapter

Cover Human Virology

Arenaviruses: Lassa and haemorrhagic fevers  

This chapter discusses the family of arenaviruses. These cause widespread haemorrhagic fevers in tropical countries, especially in Africa and South America. There is an animal reservoir and periodically the viruses jump the species barrier to infect humans, often agricultural workers. The chapter considers arenaviruses as unusual negative-stranded RNA viruses with two ambisense single-stranded RNA segments, L(ong) and S(hort), meaning that protein-coding open reading frames are present in both directions 5’ to 3’ and 3’ to 5’ of the virus RNA segments. The genome segments have complementary termini and can form pan-handle structures by base pairing. The chapter looks at S RNA, which encodes for the virus glycoprotein in the 5’ to 3’ direction and the nucleoprotein on the opposite strand in a 3’ to 5’ direction.