bluuebunny/crossref_metadata_2025 huggingface dataset:
Combinatorial Chemistry and High Throughput Screening
Authors: Rostron Chris
Published: September 2023

This chapter explores combinatorial chemistry and high throughput screening. During the 1980s, a rapid increase in molecular biology techniques had resulted in the development of rapid, efficient drug testing systems, known as high throughput screening (HTS). These techniques were able to provide accurate results on extremely small quantities (μg) of test substances. However, in order to be used economically, HTS requires rapid production of very large numbers of test substances which could not be met by traditional synthesis. Combinatorial chemistry was developed to provide new test molecules in sufficient numbers to meet this need. The chapter investigates solid phase synthesis, solution phase synthesis, and polymer-assisted solution phase synthesis. It also considers chemical tagging, deconvolution, purification, combinatorial libraries, and chemogenomics.
Biotechnology and Biopharmaceuticals
Authors: Rostron Chris
Published: September 2023

This chapter studies biotechnology and biopharmaceuticals. The rapid developments in biotechnology over the last 30 years have not only impacted on the biological assays of potential drug molecules but also have changed the nature of drug design and development. Whereas small molecules dominated the search for new drugs for many years and have been the focus of previous chapters, biopharmaceuticals now tend to dominate the search for and design of potential new drugs. These biopharmaceuticals are being produced by recombinant DNA (rDNA) technology. It should be remembered that rDNA largely gives rises to molecules that are protein in nature with all the difficulties associated with the production, delivery and use of such molecules as drugs. The chapter explains that the protein molecules currently used or being investigated as drugs include hormones, cytokines, and antibodies. In addition, advances in genomics has led to the development of gene therapy and antisense therapy, involving recombinant genes and oligonucleotides respectively as therapeutic agents.
Drug Metabolism
Authors: Rostron Chris
Published: September 2023

This chapter highlights one of the significant aspects of the pharmacokinetic phase of drug action, i.e. those factors which control the journey of a drug from initial delivery to its site of action. Drug metabolism can be defined as the chemical alteration of a drug by a biological system, with the principal objective of eliminating the drug from that system. As most drugs are molecules which are foreign to the body, they are subjected to these metabolic processes. A significant factor controlling the concentration of a drug reaching its site of action will be how much of it will be metabolized before it reaches its site of action. The design of a new drug, therefore, demands an understanding of the metabolic processes for that drug and, equally importantly, the biological activity of any products of that metabolism. The chapter then considers oxidation, reduction, hydrolysis, and phase II metabolism.
The hydrosphere
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter introduces the hydrosphere, emphasizing the critical importance of water and its unique properties. It discusses the distribution of water throughout the Earth, the physical and chemical properties of water, and the methods of expressing concentration of solutes in water. It highlights that water is one of the essentials that support all forms of plant and animal life, noting that the quality of the environment is defined by the quality of water. The chapter points out that unsafe drinking water, turbid lakes and rivers, or ponds green with algae are obvious signs of a degraded water environment. Water covers 73% of the Earth's surface, almost three times as much as the continents, but it is also a crucial component of the atmosphere and the terrestrial environment.
Distribution of species in aquatic systems
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter deals with the distribution of species in aquatic systems, including how to calculate and diagrammatically represent their distribution based on empirically determined constants. It illustrates the methodology for generating a single variable species distribution diagram and introduces two variable species distribution diagrams that are relevant to natural aquatic environments. It also covers redox chemistry in water and the concept of electron activity before introducing pE/pH diagrams, with a detailed example of the sulfur system. The chapter notes that the species distribution or speciation for an element or compound depends on the nature of the chemical and the particular environmental conditions in which it is found. It elaborates on the calculation or prediction of the forms that will be present in aquatic ecosystems, assuming that one has access to the appropriate analytical data and the required thermodynamic constants.
The chemistry of solid wastes
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter discusses the chemistry of solid wastes. It looks at how best to make use of them in creative ways that cause little adverse impact on the natural environment. It looks at the various types of bulk solid wastes and their potential to be useful resources, as well as at the chemical issues related to managing wastes from mining and metal production. It outlines the uses of organic wastes, especially as compost and as an energy source, and the processes that can be used to manage mixed urban wastes and the related environmental considerations. The chapter mentions bulk solid wastes, which are produced as a by-product of the normal and fundamental activities of living. These include food scraps, ash from fires, and excreta from humans and animals. It refers to the circular economy, which turns goods at the end of their service life into resources for others.
Introduction to Genomics
Authors: Lesk Arthur M.
Published: September 2023

Introduction to Genomics provides insight into many topics in the field of genomics, including the similarities and differences between organisms, how different organisms evolved, and how our understanding of genomics may inform human health and well-being in the future. After a general introduction, the book looks at the human genome project before turning its attention to mapping, sequencing, annotation, and databases. It also looks at evolution and genomic change. The text examines the following topics in more detail: the genomes of prokaryotes and viruses, the genomes of eukaryotes, and comparative genomics. It looks at the impact of genomics on human health and disease and the relationship between genomics and anthropology. Finally transcriptomics, proteomics, metabolomics, and systems biology are considered.
Evolution and Genomic Change
Authors: Lesk Arthur M.
Published: September 2023

This chapter focuses on the coordination of changes in genotype and phenotype during evolution. It considers evolution to be an exploration that leads to discovery and change. It expounds on the principles of biological classification and the grammar of biological nomenclature, citing the biological taxonomy used for identifying different life forms. It differentiates between similarity and homology as well. It shows the measurements of similarities between gene or protein sequences amongst different species. The chapter explains the construction and calculation of phylogenetic trees, which are diagrams showing ancestordescendant relationships. The chapter includes a description of the general idea of pattern recognition and introduces tools used in an effort to recognize similarities among sequences. It lists types of pattern matching, which is a basic tool of bioinformatics, such as dot plot and the BLOSUM62 matrix.
The cell membrane and membrane proteins
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter talks about biological membranes that have a lipid bilayer structure made up of a variety of different lipids held together by noncovalent bonds. It shows that lipids are arranged with their hydrophobic tails pointing to the middle of the bilayer and their hydrophilic sections to the outside. Lipid bilayers are two-dimensional fluids that can self-seal. They permit endocytosis, a process by which cells take in material, and enable cells to eject molecules in a reverse process called exocytosis. The chapter mentions fatty acid components and shows how these may be saturated or unsaturated in a cis configuration, which are essential for maintaining the bilayer in a fluid condition. Trans unsaturated fatty acids resemble saturated fatty acids in that they are straight chain, not kinked.
Energy release from fat
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter shows the way that energy is released from fat involving the oxidation of fatty acids released from triacylglycerols. These are first converted into fatty acyl-Coenzyme As (CoAs). Then the acyl groups are transported into the mitochondria. The chapter emphasizes that fatty acyl-CoA cannot enter the mitochondrion, but an enzyme of the outer membrane transfers it to carnitine and a transport system transfers the acylcarnitine into the matrix where another enzyme transfers the acyl group back to CoA. In the matrix, the fatty acyl-CoA is converted into acetyl-CoA by a process called β-oxidation in which carbon atoms are released two at a time in the form of acetyl-CoA. The chapter describes the fatty acid chain of acyl-CoAs, which is dehydrogenated by a series of enzymes that produce β-ketoacyl-CoAs. Acetyl units are split off by the enzyme ketoacyl-CoA thiolase, which attaches each to CoASH and releases acetyl-CoA.
Protein synthesis and controlled protein breakdown
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter defines protein synthesis as the joining together of amino acids in the correct sequence to form a polypeptide chain. This involves three phases: initiation, chain elongation, and termination. The chapter analyzes messenger RNA (mRNA) and shows that it encodes the amino acid sequence of the protein in the form of triplets of bases known as codons. Of the 64 codons, AUG is the initiator or start codon, encoding methionine, and three codons are stop codons and the genetic code is degenerate as most amino acids are encoded by more than one codon. The chapter outlines the sequence of codons in an mRNA molecule. This is translated by cytosolic ribosomes. Ribosomes have a large and a small subunit, each containing RNA and many proteins.
Manipulating DNA and genes
Authors: Papachristodoulou Despo , Snape Alison , Elliott William H. , Elliott Daphne C.
Published: September 2023

This chapter looks at the technology of DNA manipulation. This has become the most powerful approach to many biological and medical problems. It shows how DNA manipulation permits the isolation of genes, the determination of their nucleotide sequences, the detection of abnormal genes, and the production of human and other proteins in unlimited amounts in hosts such as yeast and bacteria. DNA can be cut with precision at known sequences using a battery of restriction enzymes. The chapter describes DNA sequences which can be identified by hybridization with probes obtained by isolation or synthesis. Recombinant DNA molecules, in which different pieces of DNA are joined together, can be produced in a number of ways.
Periodic trends
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter discusses trends in the physical and chemical properties of the elements. It emphasizes that understanding periodicity—the regular manner in which the physical and chemical properties of the elements vary with atomic numbers–is vital in the chemistry of the elements and their compounds. The chapter takes a closer look at valence electron configurations, atomic parameters, occurrence, metallic character, and oxidation states. In examining the periodic characteristics of compounds, the chapter also discusses the presence of unpaired electrons, coordination numbers, bond enthalpy trends, and binary compounds. Lastly, it tackles the wider aspects of periodicity and the anomalous nature of the first member of each group.
The Group 2 elements
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter tackles Group 2 elements. This group includes beryllium, magnesium, calcium, strontium, barium, and radium. The latter four are known as alkaline earth metals, but the term is often applied to the whole of Group 2. The chapter describes the occurrence and extraction, and uses and compounds, of these elements, including the anomalous properties of beryllium. It also provides information about the elements' simple compounds, complexes, and organometallic compounds. The chapter also draws comparisons with the elements of Group 1 and explains how the insolubility of some of the calcium compounds leads to the existence of many inorganic minerals that provide raw materials for the infrastructure of our built environment and provide the building blocks from which many rigid biological structures are formed.
The Group 16 elements
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter discusses the essential features of the chemistry of the Group 16 elements: oxygen, sulfur, selenium, tellurium, polonium, and livermorium. All of these are nonmetals, apart from polonium, the heaviest member of the group. The chapter observes the rich variation in the structures of the compounds they form. It highlights that oxygen differs significantly from the other members of the group: it is the most electronegative element in Group 16 and is the only gas. Then it looks at hydrides, halides, and metal oxides. The chapter also looks at metal sulfides, selenides, tellurides, and polonides. Next, it tackles compounds formed between oxygen and its congeners in Group 16.
Homogenate Sample Analysis
Authors: Presneau Nadège , Hye Abdul , Ashton Nicholas
Published: September 2023

This chapter presents a molecular analysis of nucleic acids and proteins from homogenate samples and introduces the various technologies used for analysing nucleic acids. The chapter also discusses the principles and key technical considerations of polymerase chain reaction (PCR)-based technologies and techniques for exploring DNA and RNA. It expounds on the significance of protein modification. Additionally, the chapter discusses the major proteomic techniques, namely Western blotting, two-dimensional gel electrophoresis (2-DGE), enzyme-linked immunosorbent assay (ELISA). It also outlines the principles of mass spectrometry and discusses the methodological options for the investigation of post-translational modifications as well as the possible ways to quantify nucleic acids and proteins using these methods. The chapter also shares examples of technological applications in the context of molecular diagnosis and understanding disease processes.
Statistical Thermodynamics
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

Statistical Thermodynamics starts by looking at the Boltzmann law. It then turns to sum over states and applications of the molecular partition function. It then considers the molecule and the mole. Chapters also look at distinguishable and indistinguishable particles, two-level systems, and thermodynamic functions. Chapters then examine the ideal monatomic gas and the ideal diatomic gas. The text also looks at ortho and para spin states. Towards the end, it looks at heat capacity and Third Law entropy.
The ideal diatomic gas: internal degrees of freedom
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter explains the ideal diatomic gas in terms of internal degrees of freedom. It cites polyatomic species storing energy through translational motion, rotational motion, vibrational motion, and electronic excitation. The chapter discusses the separability of energy modes and shows that this allows for the calculation of a molecule's total energy. Additionally, the outcome of weak coupling assumptions will allow the formulation of the molecular partition function. This occurs separately for each energy mode as well. The chapter discusses factorizing translational energy modes and internal energy modes. Moreover, it notes that translational modes of motion can be applied to molecules carrying more than one atom in the same way in which they are applied to monatomic species.
Alcohols, Phenols, Ethers, Organic Halogen Compounds, and Amines
Authors: Rostron Chris
Published: September 2023

This chapter considers a number of functional groups, such as oxygen in the air and oxygen as a component of water. It is also found in many molecules. Functional groups are made, changed, and destroyed in chemical reactions. The chapter highlights oxygen's value as a component of functional groups that stems from its high electronegativity, which means that it strongly attracts electrons. The chapter describes the hydroxyl group as the most biologically significant functional group as it is one of the most widely occurring in nature, being present in carbohydrates, proteins, and nucleic acids. The properties of carbohydrates, for example, are essentially a combination of hydroxyl chemistry and the chemistry of aldehydes and ketones.
How Do We Define Life?
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter focuses on the definition of life. It explains how life is represented by a set of five functional qualities: metabolism, membranes, defence, replication and continuity, and variation and selection. Variation and selection are the basis of evolution and have resulted in the diversity of life on Earth. The five functional qualities compromise an integrated system while existing in many different scales. The chapter focuses on the characteristics of the qualities of life, which include the replication and transmission of characteristics to subsequent generations and the acquisition, storage, manipulation, and transmission of energy derived from the Sun.
Rates of Change
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter looks into range of change and considers how graphs indicate the rate from the slope or gradient in a variety of biological scenarios. It defines rate as the ratio of two quantities that usually have different units. Quantifying life changes helps biologists to make comparisons and identify underlying mechanisms of life. For example, exponential growth can be used to model phenomena, such as the replication of DNA or the spread of a disease. The logistic growth model is used to describe growth when resources are limiting growth and population size. The chapter considers the rates involving exponential decay.
Microbial Diversity
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter explores the notion of microbial diversity. In response to the huge number of living organisms across the planet, the idea of creating taxonomies was developed for the biological classification and grouping together of organisms that share properties. The chapter tackles the main ways of gathering information to determine the classification of an organism: classification taxonomy and molecular taxonomy. The habitats of soil, freshwater, and seawater showcase the incredible diversity of microbial life. The chapter also considers how technologies like sequencing and metagenomics unveiled the expanse of unculturable microbes. It provides an overview of the diversity of bacteria, Archaea, fungi, and protists by detailing their characteristics and features.
Communication and Control 1
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter covers the processes of signalling in the nervous system and the endocrine system. Cells respond to environmental changes and communicate to coordinate processes, such as growth, differentiation, metabolism, and even cell death. Thus, signalling within the body involves communication between neurons. The chapter also looks at the conduction of an action which has the potential to align the length of a neuron's axon. Signal transmission between neurons occurs most commonly through the release of a chemical neurotransmitter at the synaptic terminal. The chapter then notes the four main types of receptors of cellular signalling: ionotropic and metabotropic receptors, kinase-linked receptors, and steroid receptors.
Communication and Control 3
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter discusses communication and control within organ systems. Organs and tissues work together as groups to facilitate varying physiological processes necessary for life. The organ systems work together in concert to achieve specific goals and maintain homeostasis. Homeostasis occurs in many forms, such as the regulation of body temperature, blood pressure, blood volume, acid-base balance, and glucose concentration. The chapter then details how the autonomic nervous system and endocrine system control the activity of different organ systems. It cites the hypothalamus as the major control and integration centre for both systems and provides a functional link between the two.
Immune System
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter discusses the components and purpose of the immune system. The immune system is designed to recognize and destroy anything dangerous to the body, which includes pathogens and tumour cells. In the absence of a functional immune system, people quickly become sick and die if they do not have the intervention of modern medicine. The chapter explores the differences between innate immunity and adaptive immunity and the subsequent immunodeficiencies that happen when diseases affect the development and function of lymphocytes. It acknowledges vaccination as one of the major medical achievements that can provide lifelong immunity against a range of infectious diseases.
Designing Experiments
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter highlights the importance of good experimental design, which involves deciding what subjects to measure and how to measure them. Good experimental design helps ensure the work complies with three key tenets of good science: reliable, valid, and reproducible. The most important goals of experimental design are to reduce noise and to improve accuracy. The chapter considers varying solutions to the issues of noise and bias, which include control and randomization. It then looks at the notion of using pseudoreplication for examining the independence of data within and between samples in an effort to choose valid analyses, while also considering the implications for the interpretation of non-representative samples and reverse causation.
Respiratory System
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter explores the anatomy and function of the respiratory system. Respiration can be divided into cellular respiration, which produces adenosine triphosphate (ATP) from the breakdown of nutrients, and external respiration, wherein gaseous exchange takes place with the air in the lungs to take in oxygen and breathe out carbon dioxide. Ventilation of the lungs involves work to stretch the lungs themselves and overcome the resistance of movement through the airways. The chapter acknowledges how the prevention of lung ventilation can result in brain damage and death. It cites how feedback systems monitor the oxygen and carbon dioxide levels and control the rate and depth of ventilation.
Resolution, accurate mass, and sensitivity
Authors: McCullagh James , Oldham Neil
Published: September 2023

This chapter explains resolving power, resolution, accurate mass, and sensitivity, and shows how these properties can be used for analytical purposes. It highlights the key properties of a mass spectrometer, which include the limit to which an instrument can separate ions of different m/z value and the error limit within which an instrument can measure an ion's m/z value relative to its theoretical value. It also refers to the relationship between the ion current measured by the mass spectrometer and the concentration of the sample analyte. The chapter clarifies that analyzers with high resolving power are also of significant advantage in measuring large molecules, such as peptides and proteins. It talks about how mass spectrometry (MS) is used to denote a degree of accuracy that allows determination of the elemental composition of an ion.
Separation techniques and quantification
Authors: McCullagh James , Oldham Neil
Published: September 2023

This chapter addresses the basic principles of analyte separation in the context of mass spectrometry (MS), which include separations that occur inside the mass spectrometer before the mass analyzer and those that take place prior to ionization using interfaced techniques. It discusses how combined separation and detection systems are connected, and how the analysis is combined to provide additional chemical and quantitative information. It also focuses on chromatographic techniques and its direct relevance to MS performance. The chapter outlines the principles of quantitative analysis which use chromatography coupled to MS. It highlights the advantages and disadvantages of different types of chromatographic calibration.
Atoms: the foundations of life
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter discusses atoms and their components, looking at protons, electrons, and neutrons. It begins by defining chemical elements, and studies the periodic table, which displays all the known chemical elements in order of ascending atomic number. Periodicity is the gradual change in chemical property from element to element as one moves across a period, and the similarity of chemical and physical properties exhibited by elements within the same group. The chapter then explores atomic composition and structure, distinguishing between the Bohr model and the quantum mechanical model of atomic structure. The chapter discusses ions, which are atoms that have either gained or lost one or more electrons, and the ionization energy, which describes the amount of energy required to remove an electron from an atom. It also explains how isotopes are atoms of the same element that contain different numbers of neutrons. Finally, the chapter considers the electronic configuration of atoms, valence shells and valence electrons, and electron excitation.
Isomerism: generating chemical variety
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter explores the concept of isomerism—the joining together of identical groups of atoms to form different molecules. Structural isomers are molecules that have the same chemical composition but whose atoms are joined together in different ways. Stereoisomers possess the same atoms, which exhibit the same connectivities. However, stereoisomers exhibit different configurations. Stereoisomers fall into two groups: cis–trans isomers, and enantiomers. Cis–trans isomers are stereoisomers that possess groups of atoms locked in specific configurations, while enantiomers are non-superimposable mirror images of one another. Cis–trans isomerism is most common in molecules that possess one or more double bonds. The chapter describes the nomenclature used to differentiate isomers, including E/Z nomenclature and the use of Fischer projections. The chapter then looks at chirality in biological systems and why it is important, before considering the chemistry of isomers.
Chemical reactions, oxidation, and reduction: bringing molecules to life
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter discusses chemical reactions, asking what it is that distinguishes different chemical reactions, and what it is that unifies all reactions. A chemical reaction is a chemical change occurring within one compound, or an interaction between two or more starting compounds, to form one or more end compounds. It involves the redistribution of valence electrons as existing chemical bonds are broken, and new chemical bonds are formed. Bonds cleave in a heterolytic manner when the electrons that represent the bond redistribute unequally, with two electrons going to the atom at one end of the bond but none to the other atom. Conversely, bonds cleave in a homolytic manner when the electrons that represent the bond redistribute equally, with one electron going to the atom at one end of the bond, and one to the other atom. The chapter introduces the concepts of nucleophiles and electrophiles, and the process of nucleophilic attack. It also considers the processes of oxidation and reduction and their importance in biological systems, and discusses how standard reduction potentials can be used to determine the relative strength of a reducing agent.
Energy: what makes reactions go?
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter explores the nature of energy, looking at how energy transfer drives the biochemical processes on which organisms depend for life. Energy is the capacity something has to do work, and is transferred between a system and its surroundings in the form of work and heat. The chapter introduces the concepts of enthalpy and entropy, and explains how the energy change associated with a chemical reaction is called the enthalpy change of reaction. Meanwhile, entropy is a measure of the energetic disorder of a system. The chapter also considers spontaneous reactions and what determines their spontaneity, and introduces the concept of Gibbs free energy.
Working with different information sources
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter explores how to get the most from texts, journals, and the internet, and how to evaluate the academic value of a variety of sources. These activities require different approaches to reading because there are very different goals associated with them. The chapter reviews: the types of publication available and how they might be used; using internet sources; referencing and bibliographies; different reading goals and how to approach them; and finally, note-making strategies. The chapter ends by setting out an approach to critically review a research paper. This is an exercise that a student will almost certainly have to undertake at some point during their studies.
Creating academic posters
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter explains the purpose of academic posters and suggests seven key steps for creating them effectively. Poster presentations are a common academic format and are a regular feature at academic conferences. Though conferences are unlikely for the undergraduate, the poster format is sometimes used as a form of assessment for undergraduate courses. Designing academic posters can be a difficult and time-consuming task. As such, the chapter discusses the purpose of posters and the key steps involved in creating them, to make designing and producing quality academic posters become an achievable goal. Designing posters is a particularly useful skill for studies beyond undergraduate level.
Organic Stereochemistry
Authors: Robinson Michael J.T.
Published: September 2023

Organic Stereochemistry starts by introducing the many common stereochemical terms used throughout the book. The second chapter is an account of the structures of simple unstrained organic molecules followed by examples of strained molecules. The third chapter deals with conformational analysis of acyclic and carbocyclic molecules, ending with a short exposition of molecular mechanics. The fourth chapter is about stereoisomerism in molecules and compounds. A full description of enantiomerism and diastereomerism is followed by an explanation of the nomenclature for absolute and relative configurations of molecules and for topism. A short chapter that follows then describes racemates, their resolution, and methods for determining enantiomeric purity. The book concludes with a survey of stereoselective and stereospecific reactions, including the use of chiral catalysts and auxiliaries, rules for predicting stereoselectivity, and double asymmetric synthesis.
Racemates and resolution
Authors: Robinson Michael J.T.
Published: September 2023

This chapter extends the concept of stereoisomerism to groups of molecules, e.g., in crystals, or a molecule surrounded by a solvent or adsorbed on a surface. It argues that these are essential in some methods for resolving racemic compounds, i.e., separating mixtures of enantiomeric compounds. The chapter also discusses the scalar properties in terms of interatomic distances and energies. It notes that these are independent of the absolute configuration of a chiral molecule that is either isolated or in an achiral environment. The chapter then jumps to investigate how enantiomeric chiral molecules interact with other chiral molecules. It introduces a mixture of enantiomeric compounds called
racemates
, then presents the properties of racemates. Ultimately, the chapter explores the crystal structures of racemates, resolution through diastereomeric derivatives, and the resolution using chiral chromatographic stationary phases.
Elements and periodicity
Authors: Winter Mark J. , Andrew John E.
Published: September 2023

This chapter discusses the elements and the periodic table. Matter is made up from very small particles called atoms. To date, 109 different atom types are known and named, and each type is referred to as an element. The chapter begins by describing the atomic structure. An atom consists of a positively charged nucleus surrounded by negatively charged electrons. While all atoms of one element possess the same number of protons, the nuclei of atoms of any one element may contain different numbers of neutrons. Conceptually, one of the simplest models of atomic structure is the Bohr model. The chapter then focuses on the periodic table, which was originally constructed as a way to organize the chemical elements into groups of elements with related chemical properties, before explaining periodicity. One of the clearest classifications for the elements is into metals and non-metals.
Structural bioinformatics and drug discovery
Authors: Lesk Arthur M.
Published: September 2023

This chapter focuses on structural bioinformatics and drug discovery. Understanding protein structures in detail is essential for determining their functions and mechanisms of action, and for clinical and pharmacological applications. The chapter begins by looking at the concept of protein folding: the process by which the one-dimensional amino acid sequence encoded by a gene takes up a definite and biologically active three-dimensional conformation. It then considers the hydrophobic effect and its implications for the structures and energetics of folded proteins. The chapter also outlines the classification of protein folding patterns, as presented by the Structural Classification of Proteins (SCOP) database and website. Finally, the chapter presents some basic approaches to the prediction of protein structure from amino acid sequence, and the Critical Assessment of Structure Prediction (CASP) programs.
Introduction to systems biology
Authors: Lesk Arthur M.
Published: September 2023

This chapter describes systems biology. The key idea of systems biology is integration. Indeed, an initial goal of systems biology is to identify the active networks in cells, organisms, and ecosystems, and to understand the properties of their components and the interactions among them. The integrated activities of components of cells depend on networks of interactions. The chapter then looks at the general features of graphs, and the representation of networks by graphs. It considers which kinds of biological interaction patterns can profitably be thought of as networks. The chapter also identifies the distinction between static and dynamic properties of networks, before assessing the concepts of entropy and complexity and how to apply them to biological data. Finally, it outlines the properties of the Burrows-Wheeler transform and its applications.
Partial differentiation
Authors: Sivia D.S. , Rhodes J.L. , Rawlings S.G.
Published: September 2023

This chapter explores partial differentiation. It focuses principally on the case where a parameter z is a function of just two variables, x and y: z = f(x, y). We can visualize such a situation by thinking of z as representing a height, with x and y being the two-dimensional coordinates of a point on the (flat) ground. While a realistic rendering of the topographical scene requires artistic ability, a more practical means of displaying the salient information is to draw a contour map; these are found in geographical atlases, where hills and valleys are depicted by a series of lines which join together regions of equal altitude. The chapter then looks at second and higher derivatives, increments and chain rules, the Taylor series, maxima and minima, and constrained optimization.
Growth, post-embryonic development, and regeneration
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter looks into growth, post-embryonic development, and regeneration after the patterning of the embryo. It highlights the importance of controlling growth and size in terms of development and cell proliferation. The chapter discusses the process of cell proliferation during embryonic development. It notes the key role of the metamorphosis of insects and vertebrate amphibians in line with post-embryonic development. Additionally, the chapter explores how adults could regenerate body parts by using amphibians, insects, and zebrafish as model organisms. It includes examines the process of senescence, which is caused by damage to cells that accumulates over time, and clarifies while clarifying that ageing is also under genetic control.
Tests of relationship: correlation
Authors: Hawkins Dawn
Published: September 2023

This chapter highlights tests of relationship for two interdependent variables, particularly the parametric Pearson correlation test and the nonparametric Spearman correlation test. Correlation is about investigating the covariation between variables, and not the variation of a dependent variable in relation to an independent variable. Both the Pearson’s test and the Spearman’s test are used to look for a correlational relationship between two variables. In both cases, we would be testing for a linear relationship. The chapter offers guidance on what sample sizes to use when planning to collect data for use in these tests, demonstrates how to perform each test by hand and with SPSS using real data sets, and illustrates how to identify and report the key results of both tests.
Introducing the generalized linear model: general linear model
Authors: Hawkins Dawn
Published: September 2023

This chapter reviews the generalized linear model (GLZM), which is an extremely useful and increasingly popular framework approach to analysing data. Since it relies on making assumptions about the distribution of data, it is parametric. In particular, the chapter looks at the general linear model (GLM), a sub-framework of the generalized linear model which uses the normal distribution. GLM can be used to conduct analyses that parallel all the most commonly used parametric null hypothesis significance tests (NHST), such as t-tests, Anova, and linear regression. In other words, GLM can be used to test for differences between two or more samples and for relationships between two samples. GLM can also be used to do both at the same time, and it can handle more than two explanatory variables. The chapter then outlines the multiple model approach to analysis before introducing alternatives to a GLM within the GLZM framework.
Genomes, chromosomes, and epigenetics
Authors: Meneely Philip
Published: September 2023

The genetic information for the biological processes that a species carries out is contained within the DNA sequence of its genome. The DNA sequences of many genomes having been completed, the next steps in genomic analysis involve annotation of the sequence, that is, identifying the functional elements within that sequence. These functional elements include such sequenced based information as transcripts, splice variants, and binding sites for proteins. While most of the attention in molecular genetics has been focused on the genes and their DNA sequences, the DNA in eukaryotic cells is packaged as chromatin fibers into chromosomes. Changes in chromosome structure are important in regulating transcription, recombination, replication, and many other biological processes but, because these important changes occur locally and dynamically, they have only recently been studied on a genome-wide scale. Thus, in addition to the DNA sequence itself, the functional elements to be annotated include structural modifications in chromatin. These modifications result in heritable changes in the gene function without corresponding changes in the DNA sequence; and they are known as epigenetic changes. Epigenetics has a long history in genetic analysis; with contemporary experimental tools, we are beginning to understand the common molecular basis for some epigenetic phenomena.
Reverse genetics
Authors: Meneely Philip
Published: September 2023

This chapter focuses on reverse genetics in which the start point is the DNA sequence of a cloned gene, and the mutant phenotype—and hence biological function of the gene—is inferred from that sequence. The chapter starts with an exploration of the reverse genetic analysis carried out on budding yeast and mice. It explores two approaches to reverse genetics: gene disruption and gene replacements. It includes a discussion of the Cre-lox system as an example of gene replacement achieved by site-specific recombination.
Epistasis and genetic pathways
Authors: Meneely Philip
Published: September 2023

This chapter explains epistasis, whereby the phenotype of one gene masks the phenotype of a different gene, and describes how it can be exploited to construct the logical pathway of the gene interactions that underlie a biological process. It notes that every biological process is the outcome of genes or gene products working together in pathways and networks, which may be linear or branched, and may involve many genes or few genes. The chapter discusses how gene interactions in negative, positive, and parallel pathways are inferred by using double mutants.
Information in biomedical science
Authors: Blann Andrew D.
Published: September 2023

This chapter looks at the variety of different types of information in the biomedical sciences, the bases of different types of data, and key features of qualitative information. It covers the fundamentals of quantitative information, the mean, standard deviation, the median and interquartile range, the numerical basis of the reference range, and scaling methods that permit the quantitative analysis of qualitative information. The chapter provides a broad overview of the issues surrounding information handling and statistical analysis as applied to biomedical science. It explores the different ways in which information can be described and analysed, including the issues that relate to best practice when it is being handled.
Major Challenges and New Opportunities in Cancer
Authors: Divan Aysha , Royds Janice A.
Published: September 2023

This chapter highlights the major challenges and new opportunities in the study and research of cancer. Despite the advances in the development of more targeted therapies and of new treatment modalities, a number of areas continue to challenge the successful treatment of cancer. These include metastatic tumour spread and resistance to therapy. Nevertheless, the cancer genomics revolution, combined with the development of new technologies such as single-cell analysis, has also created substantial opportunities, leading to the identification and use of biomarkers in the clinical management of cancer and enabling the monitoring of disease resistance. These in turn are facilitating the use of more personalized treatment regimes based on the molecular profile of the patient's tumour, including precision cancer medicine and cancer gene therapy. The chapter also looks at new directions in cancer immunotherapy.
Energy
Authors: Behrens Paul
Published: September 2023

This chapter focuses on the energy system, to investigate the ways in which energy is currently used in the food system and how this use may develop in the future. It outlines the physical nature of energy and power and describes the different sources of energy. The discussion highlights that food production uses around 15–20% of the total energy produced for human needs. The discussion covers two critical issues in energy use: the improved availability of energy in poorer countries and the implementation of low-carbon technologies in all countries. Furthermore, it explains the zero-carbon energy system. The chapter also explores how food systems can be decarbonized. Finally, it looks at the role agricultural systems could play in the energy transition itself.
Consumption
Authors: Bríd Walsh , Daniela Vicherat-Mattar , Ehrhardt David
Published: September 2023

This chapter focuses on the promotion of sustainable food consumption, which promotes the consumer use of goods and services to meet needs, while minimizing the use of natural resource stocks, pollutants, and contaminants, and reducing waste and emissions throughout the entire product life cycle. The chapter highlights that the food choices of consumers are influenced by a range of determinants, such as social and cultural influences (for example, heritage attachments, status, and fashion), cost and price, and the attitude-behaviour gap. The chapter also tackles the strategies to enhance sustainable food consumption including pricing, labelling, nudging, green advertising, and system-wide reforms.
Defending against the invaders
Authors: Fullick William
Published: September 2023

This chapter evaluates the defences that make up the human immune system, which are crucial to our ability to fight off infectious diseases. The innate immune system has a variety of defences to prevent pathogens from infiltrating the body. Macrophages such as mast cells, dendritic cells, basophils, and eosinophils aid in recognizing pathogens and chemically signalling to other aspects of the immune system, such as phagocytes, T-cells, and B-cells. The T-cell and B-cell pathways are known as the adaptive immune response, as they are capable of adapting to new pathogens. They also 'remember' antigens, through the use of T and B memory cells, allowing the body to quickly respond to any pathogens that it has encountered before. The chapter then looks at autoimmune disorders, which are caused when the immune system fails to recognize other cells within the body and attacks them in the same way that it attacks pathogens.