bluuebunny/crossref_metadata_2025 huggingface dataset:
Matrices, multiplication tables and representations
Authors: J.S Ogden
Published: September 2023

This chapter begins with a description of single symmetry operations in terms of simple matrices. This is followed with illustrations of sequential symmetry operations. The chapter analyses the concept of a symmetry group through a consideration of multiplication tables, including an introduction to representations and basis functions. It also shows the group multiplication table and explains how simple mathematical functions can act as bases for the irreducible representations in the point groups C2V and D2. The chapter discusses matrices as arrays of either numbers or variables that come in various shapes and sizes. It describes the four basic shapes of matrices: column matrix, row matrix, square matrix, and rectangular matrix.
Electromagnetic waves and photons
Authors: Cox P. A.
Published: September 2023

This chapter discusses electromagnetic waves and photons. It begins by reviewing some basic ideas on the properties of waves, introducing the wave properties of radiation. There are several reasons for starting with a discussion of electromagnetic radiation. Historically, it was in this area that the quantum theory first developed. The applications of the light-quantum hypothesis, as it was first called, also provide key pieces of evidence for the quantization of energy in atoms and molecules. The chapter then looks at the evidence for the wave nature of light and of X-rays, before putting these two forms of radiation into the context of electromagnetic radiation in general. It also considers Albert Einstein's analysis of the photoelectric effect. Finally, the chapter assesses the statistical nature of photons.
The hydrogen atom
Authors: Cox P. A.
Published: September 2023

This chapter focuses on the hydrogen atom, which is the most important chemical application of the quantum theory. The hydrogen atom was Erwin Schrödinger's immediate goal when he developed his equation, and the solution obtained in 1926 persuaded him and indeed most interested physicists that his theory was successful. Indeed, the solutions of Schrödinger's equation — known as atomic orbitals — form the basis of our understanding, not only of atomic structure, but also of chemical bonding in molecules and solids. The chapter begins by considering the Rutherford–Bohr atom. It then looks at hydrogenic ions. The solutions described in the chapter are 'exact', in the mathematical sense that they can be obtained from the Schrödinger's equation without approximation. However, they are not quite 'correct', because this equation does not truly describe a real hydrogen atom.
Hydroformylation and related reactions
Authors: Whyman Robin
Published: September 2023

This chapter focuses on hydroformylation, or the OXO (oxonation) reaction, which is used to describe the addition of CO and H2O to the C=C bond of an olefin or other unsaturated compounds. It talks about the synthesis of fatty alcohols from terminal olefins such as hept-l-ene. It also analyzes linear alcohols prepared by hydroformylation of mixtures of C12 olefins obtained by the controlled oligomerization of propylene, used in the synthesis of biodegradable detergents. The chapter deals with the bulk of productions via hydroformylation which involves relatively simple olefins. This is applied to a great variety of substituted olefins, both simple and complex. It illustrates several variations of olefin hydroformylation processes that have been commercialized.
Band theory
Authors: Mingos D.M.P.
Published: September 2023

This chapter examines band theory, which extends the molecular orbital theory ideas which were developed for simple molecules to infinite solids. It is particularly useful for discussing the electrical conductivity and magnetic properties of compounds where the interactions between the individual components, be they atoms or molecules, are significant. The chapter then briefly reviews the basic concepts underlying a molecular orbital analysis of the bonding in a simple diatomic molecule derived from second row atoms. As the two atoms of the diatomic molecule which are initially a long distance apart are brought together, molecular orbitals which are delocalized over the whole molecule are generated by the overlap of symmetry-matching atomic orbitals. The chapter then looks at metallic radii and densities, doped semiconductors, graphite, photoconductivity, and transition metal oxides.
Magnetic phenomena to multiple metal-metal bonds
Authors: Mingos D.M.P.
Published: September 2023

This chapter begins by describing magnetic phenomena. It explains that the magnetic properties, diamagnetism and paramagnetism, of an individual complex can be related to those observed for a solid sample containing many billions of molecules. However, there are other compounds where the electron spins on any particular molecule are influenced by those on neighbouring molecules; hence, the observed magnetic behaviour is a collective phenomenon. The chapter notes that if the ordering occurs in such a way that the electron spins on the metals all orientate preferentially in a parallel fashion, ferromagnetism results. If the electron spins on the metals preferentially align in an anti-parallel fashion, anti-ferromagnetism results. Then, the chapter considers multiple metal–metal bonds, the formation of which requires the effective overlap between the d orbitals of the metal atoms.
Polyhedral skeletal electron pair theory
Authors: Mingos D.M.P.
Published: September 2023

This chapter explores the polyhedral skeletal electron pair theory (PSEPT), which relates the three-dimensional structures of polyhedral molecules to the total number of valence electrons. It represents an analogue of the valence shell electron pair (VSEPR) theory for three-dimensional cage molecules. The simplest three-dimensional cage structures have each vertex connected to three other vertices. The chapter then illustrates some typical three-connected polyhedral skeletal geometries. Such molecules may be described using conventional two-centre two-electron bonding schemes based on the effective atomic number rule. The chapter also looks at transitional metal polyhedral molecules and electron-rich clusters..
Tolman cone angle
Authors: Mingos D.M.P.
Published: September 2023

This chapter discusses the Tolman cone angle. It explains that the properties of ligands are determined not only by their electronic properties but also their steric requirements; the Tolman cone angle concept represents then an attempt to put these steric effects on a more quantitative basis. For complexes of organophosphine ligands, the space occupied by the ligand is estimated on the basis of the imaginary cone which radiates from the metal and just touches the Van der Waals surfaces of the hydrogen atoms on the surface of the ligand. The chapter notes that the methodology may be extended to other commonly used ligands and the substituents in a phosphine ligand do not define a perfect cone. Then, it clarifies that the Tolman angle depends on the relative orientations of the rings or alkyl groups and therefore may vary from complex to complex.
Resonance spectroscopy
Authors: Brisdon Alan K.
Published: September 2023

This chapter examines resonance spectroscopy. Nuclear magnetic resonance (NMR) spectroscopy is probably the single most widely used and important physical technique available to the modern practical chemist. This is because of its wide applicability, its relative ease of use, and the amount of chemical and structural information that can be obtained from its use. The technique is frequently associated only with proton and carbon nuclei but there are many other elements to which it can potentially be applied. The chapter then looks at nuclear quadrupole resonance (NQR) spectroscopy. In NMR experiments, an external field is applied to cause a splitting of the normally degenerate nuclear spin states, but this is not necessary in NQR experiments because when there is an asymmetric charge distribution within the molecule, a molecular electric field gradient is generated. The chapter also considers electron spin resonance (ESR) spectroscopy.
Stereochemistry of reactions
Authors: Procter Garry
Published: September 2023

This chapter discusses the stereochemistry of reactions. A reaction involves the making and breaking of bonds, and this comes about by the interaction of one species with another, such as addition of a nucleophile to a carbonyl group. Bond formation occurs by the interaction of electrons and orbitals of both components. When two such components interact, in principle all the electrons and orbitals in each will interact to some extent. The two most important types of orbitals in analysing reactions in organic chemistry are σ bonds, π bonds, and their respective antibonding orbitals. The chapter then considers C–C σ bonding and antibonding orbitals. It also looks at orbital interactions and reactions, as well as the stereoelectronics of some common reactions.
Additions to C–C double
Authors: Procter Garry
Published: September 2023

This chapter focuses on additions to C–C double bonds. There are two particularly important types of additions to C–C double bonds. The reaction can be concerted, in which a new bond is formed to each end of the double bond more or less simultaneously. At the other extreme, the two bond forming events are effectively independent of each other, except that for mechanistic reasons one must precede the other. The chapter considers some of the more important types of additions, including hydroboration, Diels–Alder cycloaddition, electrophilic addition, and conjugate addition. An important general type of electrophilic addition which is useful in stereoselective organic synthesis involves cyclization. There are two possible modes of cyclization: endo and exo ring closures. The chapter also looks at cyclopropanation.
The effect of surface structure on reactivity
Authors: Bowker Michael
Published: September 2023

This chapter discusses the effect of the surface structure on reactivity. Since the nature of the surface involved in heterogeneous catalysis is crucial to performance, it is important to consider the structure as a starting point for the discussion of catalytic properties. Generally speaking, surfaces with lower coordination surface atoms have the highest surface free energy, the highest reactivity for adsorption, and the strongest binding for the adsorbate (high adsorption heat). Because the surface is a region of high energy, thermodynamics dictates that there will be a tendency to minimise this energy. In nature, this occurs in several ways, including surface relaxation, surface reconstruction, sintering, and adsorption. The chapter then considers the surface structure of catalysts, as well as the structure dependence and independence of catalytic reactions. The best evidence for the influence of structure on a reaction comes from studies using model catalysts, namely single crystals.
Introduction
Authors: Winterton R. H. S.
Published: September 2023

This introductory chapter briefly discusses some background context on the subject of heat transfer. It begins with a quick overview of the basic heat transfer mechanisms: conduction, convection, and radiation, additionally splitting the topic of convection into two areas: natural and forced convection. Additionally, the chapter delves into the symbols used for the various quantities later in the work. Next, the closely related subject of thermodynamics is briefly explored, as are other topics that will assist in providing a better understanding of heat transfer, such as the behaviour of the boundary layer. Finally, this chapter notes some omissions conducted throughout the rest of the title for the sake of brevity.
Heat exchange between black surfaces
Authors: Jones H. R. N.
Published: September 2023

This chapter deals with the radiation exchange between black surfaces, in which case the only radiation leaving a given surface is thermal emission. It assumes that the medium between the surfaces neither emits nor absorbs radiation as all incident radiation on a black surface is absorbed and none is reflected. It also includes radiative transfer problems that involve surfaces that are built around a consideration of the radiative fluxes incident and leave a given surface. The chapter discusses the general approach of analysing a configuration of terms of transfer between various pairs of surfaces, which forms the basis of all radiation calculations. It highlights the calculation of the rate of heat transfer if the geometry, view factor, and temperatures of the two surfaces are known.
The molecular orbital approach and polyatomic molecules
Authors: Winter Mark J.
Published: September 2023

This chapter addresses the molecular orbital approach and polyatomic molecules. The molecular orbital approach involves the identification of groups of orbitals whose symmetries allow overlap to form molecular orbitals. Molecular orbitals may be bonding, antibonding, or non-bonding relative to their component atomic orbitals. Molecular orbitals may hold one or two electrons. Moreover, molecular orbitals may link 1 to n atoms in a molecule, where n is the number of atoms in the molecule. Molecular orbital analysis and Lewis structures may lead to lone pairs but the nature of these lone pairs may differ. The chapter then looks at triatomic molecules EX2 and tetraatomic molecules EX3.
Metal classification and electron counting
Authors: Mark J. Winter
Published: September 2023

This chapter sets out some basics of metal complex classification and electron counting which allow us to keep track of electrons. It describes the oxidation state of the metal as one of the earliest forms of classification of metals complexes. It also points out that the oxidation number is not a physical property as implied by the term ‘oxidation state’, but it is a number derived by applying a set of rules when removing the ligands in a thought experiment. The chapter talks about metal electronic configurations in the gas phase. These differ from those for the metal when complexed. It explains that the oxidation number is the charge remaining on the central metal atom when all the ligands are removed in their closed shell configuration.
Further reading
Authors: Mark J. Winter
Published: September 2023

Further reading
X-Ray Crystallography
Authors: Clegg William
Published: September 2023

X-Ray Crystallography gives an account of the technique, emphasising its wide-ranging practical application to engineering and the physical and biological sciences. The first chapter looks at the fundamentals of X-ray crystallography. Chapter 2 looks at X-ray crystallography in practice. The third chapter contains a number of case studies, while the final chapter looks at other related topics.
Introduction
Authors: Hore P.J
Published: September 2023

This introductory chapter provides an overview of nuclear magnetic resonance (NMR). Molecules are inconveniently small and difficult to observe directly. To learn about their structures, motions, reactions, and interactions we need microscopic spies able to relay information on their molecular hosts without significantly perturbing them. The spies that form the subject of this book are atomic nuclei, and the attribute that makes them successful at espionage is their magnetism. The chapter then looks at spin angular momentum and nuclear magnetism. In a magnetic field, the energy levels are split apart by an amount proportional to the size of the nuclear magnetic moment and the strength of the field. NMR spectroscopy uses electromagnetic radiation to cause transitions between the energy levels.
Chemical exchange
Authors: Hore P.J
Published: September 2023

This chapter evaluates the theory of chemical exchange, which is straightforward compared to the complex computations required to obtain chemical shifts and J-couplings. Chemical exchange effects in nuclear magnetic resonance (NMR) arise from dynamic chemical and conformational equilibria. The chapter studies the cases of symmetrical two-site exchange and unsymmetrical two-site exchange. NMR lines are broadened by slow exchange. Meanwhile, differences in the NMR frequencies of exchanging spins (δν) can be averaged by fast exchange. The magnitude of δν relative to the exchange rate constant(s) determines whether the exchange is 'slow' or 'fast'. Ultimately, chemical exchange effects give information on the rates and mechanisms of chemical reactions, molecular rearrangements, and internal motions.
Phase cycling and pulsed field gradients
Authors: Hore P. J. , Jones J. A. , Wimperis S.
Published: September 2023

Introduction

We have already encountered the concept of phase cycling: NMR experiments can be repeated several times with different pulse phases and the resulting signals added and subtracted in such a way as to cancel any unwanted contributions. For example, a two-step cycle...
Quantum mechanics
Authors: Hore P. J. , Jones J. A. , Wimperis S.
Published: September 2023

Introduction

In Part B of this book we turn to a rigorous quantum mechanical description of NMR experiments. We explain what product operators really are, justify the way they have been used to understand the operation of NMR pulse sequences, and derive many...
Density matrices
Authors: Hore P. J. , Jones J. A. , Wimperis S.
Published: September 2023

Introduction

The introduction of operator exponentials provides a huge simplification in describing the evolution of NMR spin states, but the solution is still given as a vector of coefficients, which has to be further interpreted to obtain information about the observable NMR signal. In this...
Combinatorial and parallel synthesis
Authors: Patrick Graham L.
Published: September 2023

This chapter explains combinatorial and parallel synthesis, which became have becomean established tools in drug discovery and drug development. It notesThe chapter considers the role of combinatorial and parallel synthesis being used in medicinal chemistry projects. Additionally,It introduces solid phase techniques, which are used to carry out reactions where the starting material is linked to a solid support such as a resin bead. The chapter then looks intodiscusses parallel synthesis, wherein a reaction is carried out in a series of wells such that each well contains a single product. It refers to the mixtures of compounds deliberately produced in each reaction vessel as combinatorial synthesisNext, the chapter introduces combinatorial synthesis, a method in which mixtures of compounds are deliberately produced in each reaction vessel to allow chemists to produce a vast number of novel structures in little time. Moreover, the chapter explores the structure determination of active compounds while referencing tagging, photolithography, and dynamic combinatorial synthesis.
Synthesis of natural products and their analogues
Authors: Patrick Graham L.
Published: September 2023

This chapter notes the synthesis of natural products and their analogues. It recognises recognizes the difficulty of synthesising synthesizing natural compounds, which is related to four key reasons: due to variousthe number and variety of functional groups present in them, the presence of multicyclic or unusual ring systems, the number of asymmetric centres, and the number and variety of substituents. Moreover,While functional groups are vital to synthesis, as their presence in the final product poses a problems. The chapter also discusses different ways to obtain clinically important natural products: such as extraction from a natural sources, harvesting, semi-synthetic methods, and full synthesis. It explores the role of cell cultures and genetic engineering in this context by referencing considering the modification of microbial cells and normal host cells. Additionally, it the chapter explains the how analogues of natural products may be obtained via methods such as biosynthesis, fermentation, synthesis from the natural product itself, fragmenting, synthesis from biosynthetic intermediates, genetically modified cells, and genetically modified enzymes.
Scientific Data Analysis
Authors: Currell Graham
Published: September 2023

Scientific Data Analysis consists of two parts. Part I covers how to understand the statistics in scientific data analysis. It looks at statistical concepts, regression analysis, hypothesis testing, and comparing data. Part II looks at analysing experimental data. Within this part, the topics of project data analysis, single response variables, related variables, frequency data, and multiple variables are examined.
Regression analysis
Authors: Currell Graham
Published: September 2023

This chapter discusses regression analysis. It begins with the familiar process of drawing a best-fit straight line through a set of experimental data points on an x–y graph, and then derives the statistics in a format that links into the more advanced analyses developed throughout the rest of the book. The chapter concentrates on the practical application of linear regression in science, including the derivation of uncertainties and its use for nonlinear data. It uses linearization techniques to convert nonlinear data to a straight-line relationship for further analysis. Finally, the technique of a least squares fit is used as a link into the development of iteration as a method for 'solving' complex mathematical problems.
Related variables
Authors: Currell Graham
Published: September 2023

This chapter assesses the techniques used to analyse the effect that one or more factors may have on a single response variable. The data can be described as univariate and may be either interval or ordinal data. The chapter begins by presenting analyses relevant to single samples of replicate data (e.g. the Wilcoxon test), before looking at two data samples, which is essentially a special case of a one factor analysis with just two levels. It then considers investigations that test, or measure, the effect of just one factor, but with more than two levels (e.g. one-way ANOVA, the Kruskal–Wallis test, and repeated measures). Finally, the chapter develops investigations of more than one factor together with possible interactions. The general linear model is used as a flexible approach for conducting ANOVA calculations, and the effect of a covariate term is addressed through the ANCOVA (analysis of covariance).
Prologue
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

The prologue introduces the principles that unify biology, using Nobel Laureate Paul Nurse’s Five Great Ideas of Biology as a starting point. The links between these ideas and the ways in which they are connected are discussed and the concept of model organisms is introduced as a way to understand these interactions in a way that can apply to all living things.
X-linked Genes and Sex Chromosomes
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter discusses the presence or absence of sex chromosomes that determines the sex of the individual. It explains that sex is defined by having two different sex chromosomes or being heterogametic, such as human males that are XY. It also looks at the consequences for the inheritance of genes on the X chromosome, wherein different patterns of inheritance are observed for X-linked traits in males and females. The chapter reviews the non-disjunction of the sex chromosomes or the failure to segregate normally during meiosis that results in individuals with unusual numbers of X or Y chromosomes, illuminating some of the different modes of sex determination in some species. It defines sexual dimorphism, wherein different species exhibit physical differences between the sexes in anatomy, physiology, coloration, and behaviour.
Translation: From Nucleic Acids to Amino Acids
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter reviews RNA transcripts made from the DNA sequence of a gene which are translated into the amino acid sequence of polypeptides. It explains that the process of translation is highly similar in all living organisms and arose only once with relatively small modifications during evolution. It also highlights genome-based analysis of transcription that has led to the realization that the genomes of nearly all organisms are pervasively transcribed. The chapter reviews the Central Dogma that originally did not include non-coding RNA but posits that the functional molecules in the cell are polypeptides and that a gene encodes the capacity to make a polypeptide. It details the process of translating information from the string of nucleotides in nucleic acids into the string of amino acids in polypeptides.
Networks of Gene Regulation
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter cites operons in bacteria as an example of gene regulatory networks, and it discusses transcriptional regulatory networks in eukaryotic organisms using recent information from many genome annotation projects, such as ENCODE. It explains that every gene has its own transcription pattern and changes in that pattern can have significant effects on phenotypes and morphological variation. It also points out that individual patterns of gene transcription must be coordinated so that the organism is transcribing all of the correct genes at the correct times and places. The chapter moves beyond the regulation of the expression of an individual gene to the orchestrated regulation of many genes. It highlights the processes by which gene expression is coordinated that are different in bacteria and eukaryotes but have some similar principles.
The Genetics of Populations
Authors: Meneely Philip , Hoang Rachel Dawes , Hoang Rachel Dawes , Okeke Iruka N. , Heston Katherine
Published: September 2023

This chapter delves into population genetics with a human focus and explores the assumptions of the Hardy—Weinberg equilibrium model. It reviews the many different types of evolutionary change which can operate in order to shape the genetic structure of a population and the imprints these leave at the level of the genome. It also features long-term studies of bacterial populations presented as a method to explore evolution experimentally. The chapter describes how transmission of alleles and genotypes within a population can be assessed, even when the individual matings cannot be monitored. It defines non-random mating as the main process that affects genotype frequencies without affecting allele frequencies directly, which can result in population stratification.
The Origin of Variation
Authors: Bell Graham
Published: September 2023

This chapter focuses on the origin of variation. In every generation, mutation and recombination produce genetic variation; some variants reproduce faster than others and therefore increase in frequency. Variation and selection recur in every generation. There are therefore two theories of evolution: the first is that it is directed by variation, and the second that it is directed by selection. The inevitability of mutation implies the continuous operation of selection. Moreover, the rate of mutation will limit the extent to which adaptation can be improved by selection. The chapter then looks at how genes are often transferred from distant relatives in bacteria. Horizontal transfer, or lateral transfer, represents a sort of macromutation that provides a lineage with a new gene without the need for a gradual process of mutation and selection. The chapter also considers how new genes arise by modification and recombination.
The Origin of Species
Authors: Bell Graham
Published: September 2023

This chapter assesses how lineages that acquire new genes evolve into new species. Lineages always tend to change because they adapt to new conditions of growth or evolve different ways of mating. In time, they may become sufficiently different from their ancestor to be recognized as a distinct species. The chapter then looks at how diversification is the natural tendency of lineages; how populations that are permanently separated may diverge through drift or selection; and how divergent selection leads to more or less strongly marked varieties. It also considers how species are recognized when ecologically distinctive forms become sexually isolated; how rapid speciation gives rise to swarms of sister species; and how diversity is the dynamic equilibrium between the origin and extinction of species.
The Origin of Innovation
Authors: Bell Graham
Published: September 2023

This chapter addresses the origin of innovation. Implementing innovations evolve when new ecological opportunities arise. From time to time, new conditions of life become available. If no extant group is well-adapted to these conditions, selection will favour the evolution of a new range of specialized types. Meanwhile, potentiating innovations evolve through fundamental genomic changes. From time to time, new genes, combinations of genes, and consortia of genes evolve that can form the basis of innovations that permit new kinds of organism to evolve. Ultimately, three kinds of genetic processes might contribute to the evolution of an innovation: modification, duplication, and fusion. The chapter then considers how new structures evolve from old structures, and how duplication provides an opportunity for functional divergence. It also looks at how the fusion of dissimilar cells has led to new kinds of eukaryotes.
Evolving Bodies
Authors: Bell Graham
Published: September 2023

This chapter begins by exploring how multicellularity and differentiation give rise to complex individuals. Of all the major transitions that have punctuated the history of life, the appearance of complex multicellular organisms is perhaps the most striking. After 2000 My of bacteria with very simple organization, a new kind of organism evolved, powered by mitochondria and capable of forming complex bodies. Once the ancient bacterial limits had been surpassed—probably only once—many new ways of life become possible. Multicellular organisms, moreover, have features such as differentiation and death that are the consequences of new evolutionary processes. The chapter then looks at how major clades have distinctive body plans, and how the evolution of tetrapod body plans is based on a group of multiply duplicated genes. It also considers how the life history of an individual is its schedule of survival and reproduction.
Experimental Evolution
Authors: Bell Graham
Published: September 2023

This chapter reviews experimental evolution. Many of the evolutionary processes extend over long periods of time—long, that is, on human timescales of a few decades. With the resource of a laboratory, we can follow the evolution of large populations over thousands of generations in a few months. Such experiments can be used to probe evolutionary mechanisms in deep time. They have shifted evolutionary biology from a comparative science that interprets patterns of variation into an experimental science capable of documenting the smallest details of how evolution occurs. The chapter then outlines the two basic ways of setting up a microcosm: through batch culture or continuous culture. It also considers how deleterious mutation is balanced by purifying selection, and how beneficial mutation drives directional selection.
Viral replication and genetics
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter argues that viruses are at a major disadvantage in the task of reproducing themselves compared with higher forms of life. The latter all multiply by some form of fission, which ensures that the daughter cells start their existence with a full complement of genetic information, along with the enzymes necessary to replicate and catalyse the synthesis of new proteins. A virus, on the other hand, depends on the machinery of a cell. It enters the cell with nothing but its own genome, a molecule of nucleic acid that may encode for only twenty or so genes compared with 30,000 genes for a mammalian cell. The chapter explains that viruses rely heavily on the host cell for the materials they need for reproduction involving many cellular proteins and cell pathways. It shows why the replication of viruses is more complicated in some respects than that of other micro-organisms.
Hepatitis E
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter deals with hepatitis E, which is the sole member of the genus Hepevirus. Higher hygiene levels in developed countries have encouraged the relative demise of this virus that is now more common in less developed countries alongside hepatitis A. Nevertheless, the virus still causes 20 million infections per year with 3 million acute illnesses. The chapter discusses the recent detection of the virus in pooled plasma products and suggests that infection in Europe is probably more frequent than previously considered as around one quarter of the UK population have antibody to the virus. The HEV was originally classified in the Caliciviridae family. But the HEV gene order is not identical to caliciviruses, and the HEV genes that can be compared are more closely related to rubella virus. The chapter mentions that HEV was reclassified as the only member of the genus Hepevirus in the new family Hepeviridae.
Coronaviruses (including SARS CoV and MERS CoV)
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter discusses coronaviruses. These infect humans, birds, and other animals. The first two human strains identified infect the respiratory tract and are normally confined to the ciliary epithelium of the trachea, nasal mucosa, and alveolar cells of the lungs. The chapter points out that the typical symptom of the coronavirus is the common cold, and the first isolates were obtained in the UK from volunteers at the Medical Research Council (MRC) Common Cold Research Unit, Salisbury. Coronaviruses have the largest known genomes of any RNA virus and a helical nucleocapsid more commonly possessed by negative-strand RNA viruses, including two other coronaviruses which caused the Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). The chapter explores the family Coronaviridae and sub family Coronavirinae that belong to an order of viruses named Nidovirales and contain three genera, Alpha-, Beta-, and Deltacoronavirus.
Filoviruses: zoonotic Marburg and Ebola
Authors: Oxford John , Kellam Paul , Collier Leslie
Published: September 2023

This chapter analyses filoviruses, most of which have been isolated or characterized in the last four decades. They cause haemorrhagic fevers in tropical countries and their common property is their existence in an animal reservoir in which they persist quietly until disturbed by human intrusion. The chapter mentions that the filoviruses are sometimes known as exotic viruses as some are named after the town or area where an outbreak was first investigated, such as the filovirus ‘Marburg’ that was named after the town in Germany where seven people died after infection. In the Marburg outbreak, the common link between the infected people was the handling of monkeys or monkey tissue, which had been imported from Africa to provide kidney tissue for preparing a poliomyelitis vaccine. The chapter distinguishes the Marburg virus from the Ebola virus by the size of their genomes and their different protein composition.
Introduction
Authors: Lesk Arthur M.
Published: September 2023

This introductory chapter provides an overview of proteins, which are a family of biological macromolecules that provide a variety of three-dimensional structures exquisitely shaped for their many different individual functions. They include structural proteins, enzymes, antibodies, regulatory proteins, sensors, transporters and pumps, and transducers. The common features of the chemical structures of proteins make possible a common synthetic mechanism: ribosomes assemble the great variety of proteins under the direction of different messenger RNA (mRNA) sequences. Both the DNA sequences of genes and the amino acid sequences of proteins are one-dimensional. The chapter asks: how then do proteins achieve their three-dimensional biologically active states? The three-dimensional structures of proteins are inherent in their amino acid sequences. It is the combination of a common synthetic machinery — the gene sequence dictating the amino acid sequence — with spontaneous folding to the native three-dimensional structure, that underlies the mechanism of molecular evolution.
Protein folding and design
Authors: Lesk Arthur M.
Published: September 2023

This chapter describes the mechanism of protein folding. The relationship between amino acid sequence and protein structure, demonstrated by spontaneous folding and reversible denaturation, establishes a logical connection between the one-dimensional world of genetic information in DNA and the three-dimensional world of biological structure. The study of the process of protein folding addresses the question of how a polypeptide sequence gets from the denatured to the native state. The chapter then discusses the basic principles of thermodynamics and kinetics, and their application to protein folding. It also examines chevron plots, looking at the effect of denaturants on rates of folding and unfolding. Moreover, the chapter considers the relationships among several general concepts that have emerged from investigations of protein folding. These include the molten globule and the folding funnel. Finally, the chapter studies the GroEL–GroES system, as well as protein engineering.
Proteomics and systems biology
Authors: Lesk Arthur M.
Published: September 2023

This chapter studies systems biology and proteomics. Systems biology tries to synthesize proteomic, genomic, and other data into an integrated picture of the structure, dynamics, logistics, and, ultimately, the logic of living things. The chapter begins by looking at the methods for separation and analysis of proteins, including several techniques based on polyacrylamide gel electrophoresis (PAGE). It then considers the experimental techniques and results of measurements of protein expression patterns, including mass spectrometry and microarrays, and RNA sequencing (RNAseq). The chapter also explores the developments in metagenomics and metaproteomics: the applications of methods from the laboratory to natural ecosystems. Finally, it examines protein complexes, gene regulation, and the adaptability of the yeast regulatory network.
Molecular ecology: roots and branches
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter looks into molecular ecology. First, it introduces ecology as the scientific study of organisms' distribution and abundance before defining molecular ecology as the application of molecular genetic methods. The aim is to address ecological questions. The chapter explains the theory of evolution by natural selection which has been used as a vital framework in modern biology. It considers neutral theory and notes random genetic drift. Both of these discoveries increased the understanding of evolution. They look into the levels of polymorphism found in nature. The chapter illustrates the history and progress of molecular ecology and cites its links to technology, species identification, and genetic markers. It mentions how ecological genomics is exploring the workings of genetics in wild populations exposed to environmental variation.
Next generation sequencing
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter evaluates the concept behind next generation sequencing (NGS). It highlights how NGS is largely responsible for the emergence of new research fields like ecological genomics and population genomics. The chapter then enumerates the history of the first, second, and third generation sequencing before narrating the technological advancements of NGS. It lists various NGS platforms such as 454 pyrosequencing, HiSeqX Ten, and Sequencing by Oligonucleotide Ligation and Detection (SOLiD). The chapter explores deep and targeted sequencing as well. Next, the chapter looks at transcriptomics and epigenomics. It explores the possibility of NGS as a panacea for molecular ecology.
Neutral and adaptive molecular variation
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter looks into mutation in terms of neutral and adaptive molecular variations. It clarifies how genetic variation is dependent on the population as immigration and emigration could change allele frequencies. The chapter looks into the theory behind molecular evolution and the McDonald-Kreitman test. The latter is used as a statistical measure of neutrality versus selection using DNA sequences. Heterozygosity-fitness correlations are used for studying the impact of inbreeding in natural populations. The chapter notes allozymes and nuclear DNA markers as neutral markers which are regarded as not completely neutral. Additionally, the chapter explores genomics as the study of adaptive variation.
Genomics
Authors: Rowe Graham , Sweet Michael , Beebee Trevor J. C.
Published: September 2023

This chapter looks at genomics as the methodologies and processes used to sequence, assemble, and study the structure and function of genomes. It looks at comparative genomics. Specifically, it considers the genomes of red algae, lions, tigers, and snow leopards, aiming to reveal complex hybrid origins of root knot nematodes (RKN). Next, the chapter explores gene architecture and gene expression. The chapter also looks at the link between population genomics and population genetics. In addition, it explores the concept of genome sequencing, comparative biology, evolutionary genomics, phylogenomics, proteomics, metabolomics, epigenomics, transcriptomic approaches, and conservation biology. The chapter recognizes the technological advances improving genome editing by referencing CRISPR.
The display of numbers
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter begins by defining the term ‘variable’, which refers to the thing or quantity that can have a varying amount or number or size. Chemistry uses many variables, including amount, mass, rate, energy emitted or absorbed, voltage, current, area, and volume, which are usually represented by a symbol of some kind. Variables are defined in terms of units and numbers. The chapter then explains the process of writing algebraic phrases with standard factors and using scientific notation, significant figures, and decimal places. Sometimes the amount of a variable is so large or so very small that it is better to use a shorthand notation called factors. A standard factor is sometimes called a prefix. Scientific notation is a different form of shorthand to the standard factors but fulfils the same function.
Algebra I
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter discusses mathematical symbols. Mathematical symbols are all operators. In mathematics, the instructions giving us the result we want are contained within the operator which describes an action performed on numbers or other elements. The operator may be regarded as a function, map, or transformation, in the sense that it ‘maps’ elements from one set to elements from another set. Simple operators tell us what operation to perform. Ultimately, an operator must operate on something, which is known as the argument. The chapter then looks at the Delta operator, which tells us to subtract the initial value of the argument from its final value, the Sigma operator, which tells us to add up a series of terms, and the Pi operator, which is a shorthand symbol that tells us to multiply together a series of terms. It also considers other operators encountered in chemistry.
Algebra II
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter examines the correct order to perform a series of operations. When a calculation involves more than one operator, the resultant value depends on the order in which we employ the various operators. Only if we perform the operations in the correct order will the answer be correct. The BODMAS scheme is the simplest way to remember the correct order in which to perform a calculation comprising several operations. The letters in BODMAS stand for Brackets, Of, Division, Multiplication, Addition, and Subtraction. Brackets have the highest priority because we regard everything inside a bracket as separate and self-contained. Meanwhile, the word ‘of’ points toward more complicated operators such as powers and roots.
Algebra III
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter details the process of simplifying equations. Collecting together similar terms is one of the easiest ways of simplifying an equation. ‘Similar terms’ means algebraic portions that have the same form or content. We collect terms together because the process simplifies otherwise complicated expressions. Indeed, collecting terms saves time and allows us to simplify our mathematics. ‘Collecting terms’ is a form of factorizing. Another powerful way of simplifying equations is through cancelling. When we cancel, we look for similar terms on the top and bottom of a fraction. The terms will not cancel completely if one is a multiple of the other. In such cases, cancelling will leave a factor.
Integration II
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter begins by assessing the process of separating the variables. After separating the variables, we generate two constants of integration, one of either sides of the equation. The two constants of integration on the two sides of the equation will differ and we sometimes need to distinguish between these constants. After integration, we often rearrange the equation. The chapter then looks at the process of integrating with limits, which is an alternative way of removing a constant of integration. We employ the concept of limits if we know the upper and lower value of the principal variable which determine the range over which the integral will be calculated. Finally, the chapter considers the process of integration involving partial differentials.
Integration IV
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter begins by describing the process of integrating areas. There are many methods to determine the area beneath the curve of a function, including weighing, counting, and rectangles. However, integration affords the most accurate method of determining an area. Integrating a function is more complicated if a line or curve dips below the x-axis because it creates two separate, distinct areas. The chapter then looks at the process of integrating volumes. Just as it is possible to determine an area of a two-dimensional surface, so we can determine a three-dimensional volume by rotating a function about an axis. We rotate a function about the x-axis by integrating a function of x with respect to x. This procedure generates a volume called a solid of revolution. Finally, the chapter considers multiple integration.
Graphs II
Authors: Monk Paul , Munro Lindsey J.
Published: September 2023

This chapter examines the algebraic equation of a straight-line graph, which can be written as y = m x ＋ c. The gradient of the map is m, while c is the intercept of the graph on the y-axis. A line is straight when, if drawn in Cartesian coordinates, the gradient is constant and does not change. We may need to reduce the equation if the equation has a form, n × y = m x ＋ c, by dividing throughout by n. The chapter then looks at the process of satisfying the equation of a line, as well as the process of determining the full equation of a straight line and the trend line of a graph with scatter.