bluuebunny/crossref_metadata_2025 huggingface dataset:
Iron: general features of its inorganic chemistry and biochemistry
Authors: Rehder Dieter
Published: September 2023

This chapter examines iron, an exceptional transition metal that is abundant in all living organisms. Iron deficiency, dysfunctions of iron metabolism, and iron overload cause severe health problems. The biological importance of iron is linked to the ease with which it shuttles electrons between the ferric and ferrous state, and to switch readily between high- and low-spin electronic states, depending on the coordination environment. Considering this, the chapter explains the mobilization, transport, and delivery of iron. Furthermore, it tackles the biological mineralization of iron by magnetotactic bacteria and by diverse other bacterial activities. The chapter also allots sidebars to explain the concepts of coordination compounds, Mössbauer spectroscopy, as well as magnetism, and spin moment.
Oxidoreductases based on iron, manganese, and copper
Authors: Rehder Dieter
Published: September 2023

This chapter provides an overview of electron transporters employing iron, copper, and manganese, emphasizing cofactors involved in the interconversion of oxygen species. It presents some metal-based enzymes that transform and employ oxygen directly or indirectly. The chapter describes ribonucleotide reductases (RNR) that catalyse the reduction of nucleotides — the building blocks of ribonucleic acids (RNA) — to deoxyribonucleotides and thus provide the building blocks for deoxyribonucleic acids (DNA). The discussion in this chapter also covers superoxide dismutases, superoxide reductases, and peroxidases. Then it progresses to explain oxygenases that catalyse the transfer of oxo groups to a substrate, and oxidases that promote the dehydrogenation of substrates.
Oxo-transfer proteins based on molybdenum, tungsten, and vanadium
Authors: Rehder Dieter
Published: September 2023

This chapter takes a closer look at early transition metals molybdenum, tungsten, and vanadium which are involved in many catalytically conducted two-electron transfer reactions, commonly accompanied by oxygenation and deoxygenation. Nature employs these metals as active centres in enzymes in a variety of oxidation and reduction reactions. These elements are also used in industrial contexts, commonly in steel production or, in the form of their oxides, to catalyze oxidation reactions, exploiting the ease of the change in oxidation states. The chapter discusses the Molybdo- and tungsto-pyranopterins and considers an assortment of representatives of the four Mo/W-pyranopterin families: the xanthine oxidase family, sulfite oxidase family, dimethyl sulfoxide reductase family, and aldehyde: ferredoxin oxidoreductase family. In addition, the chapter tackles the vanadate-dependent haloperoxidases.
Cells and Organisms, and their Interactions with their Environment
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter examines the physical principles governing the movement of molecules, ions, and heat in biological systems, the general properties of animal cells, and their interactions with the extracellular environment. The ease with which substances can pass across a barrier is expressed by permeability constants, and the movement of ions across biological barriers is driven by electrochemical potential differences. Animal cells contain membrane-bound and non-membrane-bound organelles. Cell membranes consist of a lipid component called the lipid bilayer and a protein component. The chapter then looks at animal homeostasis, which refers to the maintenance of a relatively stable internal environment by animals using negative and positive feedback loops to control physiological systems.
Temperature regulation in endotherms
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter studies temperature regulation in endotherms. Endotherms compensate for heat loss to their environment in order to maintain their body temperature several degrees above ambient. Animals decrease their thermal conductance to minimize their rate of heat loss. This can be achieved by erecting hairs or feathers to increase the insulating layer of air, or by the operation of countercurrent heat exchangers in the extremities. The thermoneutral zone is the ambient temperature range within which an animal does not need to change its rate of heat production to regulate its temperature. The chapter then looks at how endotherms regulate their body temperature in hot conditions, cold conditions, through the seasons, and in water. Some species of endotherms exhibit regional endothermy: they generate heat and retain it in specific regions of the body. The chapter considers endothermic fishes, reptiles, and insects.
Environmental and behavioural influences on the cardiorespiratory system
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter examines the environmental and behavioural influences on the cardiorespiratory systems of animals. Changes in the demand for and supply of oxygen are met by varying components of the respiratory and circulatory systems contained within the Fick principle of convection. Feeding and digestion lead to an increase in the rate of oxygen consumption known as the specific dynamic action (SDA) or heat increment of feeding (HIF). The size and composition of the meal determines the magnitude of the increase in blood flow. Meanwhile, naturally occurring hypoxia can occur in bodies of fresh water and in some parts of the marine environment, but rarely occurs in air, except with an increase in altitude. Hibernation by mammals is a controlled process involving a reduction in metabolic rate and body temperature so that the animals can survive the cold winter months.
Hormones
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter addresses the hormonal processes in animals. There are four sub-categories of chemical communication that operate in animals, and which are recognizable by the type of cell that produces the chemical and the distance over which the chemicals exert effects. These categories include neuroendocrine secretion of neurohormones synthesized and secreted by neurosecretory cells; endocrine secretions from endocrine glands; paracrine secretions (paracrines); and autocrine secretions (autocoids). The chapter then looks at the central control processes of vertebrates: the hypothalamus, pituitary gland, and pineal gland. It also considers the vertebrate adrenal gland and thyroid gland, before studying invertebrate hormones. Insects secrete prothoracicotrophic hormone (PTTH) from brain neurons in response to cuticular stretching, which initiates a moulting cycle.
Introduction to the Clinical Immunology laboratory
Authors: Hall Angela , Scott Chris , Buckland Matthew
Published: September 2023

This chapter introduces the branch of biomedicine focused on the structure and function of the immune system. This is called immunology. The chapter acknowledges how the field is growing rapidly. The chapter explains how the diagnostics arena immunological procedures are based on numerous hematological, microbiological, biochemical, and histopathological tests. It mentions the numerous cross-over between immunology and the other pathology disciplines. In addition, the chapter points out how each immunology laboratory differs in the depth and breadth of service depending on its patients and staff expertise. It lists various immunology specialist areas ranging from immunodeficiency, autoimmunity, allergy, hypersensitivity, cellular, humoral immunity, immunochemistry, transplantation, and malignancy.
Detection of extracellular signals: the role of receptors
Authors: Hancock John T.
Published: September 2023

This chapter examines the mechanisms used by cells to perceive signals, and the immediate action taken when they do. It explains that most signals are perceived at the cell surface by a variety of protein receptors, but some signals are able to penetrate the cell and therefore must be recognized on the inside, either within the cytoplasm or in the nucleus. The chapter then explores the types of receptor, their mechanisms and actions, and how they lead to the signalling cascades inside the cell to better understand cell signalling mechanisms. The chapter also reviews the binding characteristics of receptors, as an understanding of the ability of a cell to bind to a signalling ligand will reveal the capability of a cell to respond, or not. Lastly, the chapter explicates the mechanisms of how a cell may modulate its complement of receptors. It also studies receptor sensitivity and receptor density.
Muscle
Authors: Kay Ian , Evans Gethin
Published: September 2023

This chapter provides an overview of the distinct anatomical and contractile properties of the three types of muscle in the human body: skeletal, smooth, and cardiac muscles. It highlights the interaction of actin and myosin filaments. This is central to the contraction of all types of muscle. The chapter points out that skeletal and cardiac muscle are termed ‘striated muscle’ because of the existence of sarcomeres. It also discusses the regulation of contraction of in all three muscle types, which depends on the movement of calcium into the cytosol of the cell. The chapter clarifies that in skeletal muscle, increases in cytosolic calcium are due to central nervous system activation, while in smooth muscle, increases in cytosolic calcium can be due to central nervous system activation. It explains the increases in cytosolic calcium in the cardiac muscle. These are due to the action of the conduction system of the heart.
Integrative physiology
Authors: Kay Ian , Evans Gethin
Published: September 2023

This chapter demonstrates the integrative nature of physiological systems and the effect that certain applied examples have on these systems. It reviews examples on the effects of acute and chronic aerobic exercise on the cardiovascular system, the effect of nutrition on health, and the effect of ambient temperature and pressure on physiological systems. It also talks about how acute aerobic exercise can cause an increase in cardiac output due to increases in stroke volume and heart rate and can lead to increases in mean arterial pressure due to increases in cardiac output. The chapter cites the prevalence of obesity. This has significantly increased in recent times, with numerous health consequences that are associated with this disorder. It analyszes the regulation of appetite that involves psychological and physiological interactions.
The biogenesis and nucleocytoplasmic traffic of non-coding RNAs
Authors: Elliott David , Ladomery Michael
Published: September 2023

This chapter explores non-coding RNAs (ncRNAs) that are processed during their biogenesis. It covers the processing and maturation of ribosomal RNA (rRNA), small nuclear RNA (snRNA), transfer RNA (tRNA), mitochondrial transcripts, and telomerase. It also gives an overview of the important aspects of RNA processing, including the RNA processing machinery that involves the action of other RNA molecules. The chapter reviews the main features of the biogenesis of ribosomal RNA, which is a process that is facilitated by a family of small RNA molecules known as the small nucleolar RNAs (snoRNAs). It describes the organization of rRNA processing in an important multifunctional nuclear organelle, the nucleolus.
The short non-coding RNAs and gene silencing
Authors: Elliott David , Ladomery Michael
Published: September 2023

This chapter concentrates on a group of very important RNAs with critical roles in regulating gene expression, noting that the RNA molecules involved are much shorter. It explains why short RNA molecules have been co-opted into gene expression pathways, implying that they can be hybridized very selectively to target RNA sequences and act as an efficient targeting mechanism for directing protein components to nucleic acids. It also refers to protein components that carry out catalytic reactions that include the targeted destruction of RNA and the modification of chromatin. The chapter covers important and diverse roles in cells carried out by short ncRNAs, such as the siRNAs that generally target RNA for destruction and the microRNAs that generally regulate protein translation from mRNAs. The chapter describes the siRNAs that work like an intracellular immune system with the aim of incapacitating double-stranded (ds) RNAs that have invaded the cell.
RNA biology: future perspectives
Authors: Elliott David , Ladomery Michael
Published: September 2023

This chapter considers the complexities of chromatin modifications and epigenetics, the regulation of transcription, and cotranscriptional and post-transcriptional processes. It reviews some of the topical areas of RNA biology. It begins by describing the explosion of transcriptomics data and the opportunities and challenges that this brings. It also looks at the growing prominence of non-coding RNAs (ncRNAs) and describes the use of CRISPR, an RNA-guided genome editing system that will revolutionize both basic and applied research. The chapter discusses transcriptome sequences that are derived from copying RNA sequences into cDNA using reverse transcriptase, followed by sequencing. It mentions the advent of next-generation sequencing (NGS), which is known as a key technological development.
Pre-mRNA splicing defects in development and disease
Authors: Elliott David , Ladomery Michael
Published: September 2023

This chapter considers the important contribution that RNA splicing defects make to disease, including the NOVA proteins that are important in cancer autoimmunity and splicing regulation in the nervous system. It talks about defective genes in many inherited diseases and the actual mutations within these genes that have been pinpointed by sequencing. It also elaborates how some of the mutations in the genes affect the genetic code by introducing codons for new amino acids and even stop codons that prematurely end open reading frames. The chapter describes mutations that occur in splicing signals and prevent the intron-exon structure of pre-mRNAs from being properly decoded by the spliceosome. It stresses that mutations that affect splicing signals can be particularly severe since they cause changes in the structure of mRNAs.
Stability and degradation of mRNA
Authors: Elliott David , Ladomery Michael
Published: September 2023

This chapter focuses on the stability and degradation of mRNA, highlighting other classes of RNA molecules that have regulated half-lives. It talks about regulating the stability of mRNA which provides another means of controlling gene expression. The chapter also clarifies that protein molecules can be synthesized if an mRNA is more stable. It also describes a classical way to demonstrate the stability of mRNA, which is to block transcription with the poison α-amanitin, a cyclic eight amino acid peptide found in the Amanita genus of mushrooms. The chapter covers the main issues connected with mRNA decay, which includes regulating the amount of protein produced and eliminating faulty mRNAs which could potentially produce toxic proteins. It presents special aspects of mRNA decay, such as the connection between extracellular stimuli and mRNA decay and the role of P-bodies as cytoplasmic zones of concentrated mRNA degradation.
Automation
Authors: James Tim
Published: September 2023

This chapter examines automation in clinical biochemistry. Two main types of instrument, the general chemistry analyser and the immunochemistry analyser, predominate in clinical biochemistry laboratories, but a wide range of hybrid and combination analysers are available. Key steps in an automated analytical process are often common to many instruments, although there is often significant variation in application, design, and operation. Consolidation of most of the biochemical test repertoire is now possible on a single system that comprises a set of integrated analysers. Ultimately, total laboratory automation automates three phases of laboratory testing, namely preanalytical, analytical, and postanalytical, in a continuous process. A complex automation system requires extensive monitoring and careful management to achieve consistent and optimal efficiency.
Acid–base disorders
Authors: Tierney David
Published: September 2023

This chapter assesses homeostasis of H+ions, the causes and consequences of acid-base disorders, and their laboratory investigation. The physiological control of H+ concentration is maintained by three interrelated mechanisms: buffering systems, the respiratory system, and the renal system. Intracellular and extracellular buffering systems, such as bicarbonate and haemoglobin, provide an immediate, but limited, response to pH changes. The respiratory system, which can be activated almost immediately, controls PCO2 by changing alveolar ventilation. The renal system regulates [HCO3
-] and is the slowest to respond. The physiological response to an acid-base disturbance, which limits the change in H+ concentration, is referred to as compensation. The chapter then looks at acidosis, alkalosis, and mixed acid-base disorders. Acid-base data can be interpreted in a systematic manner, from laboratory results, by examining pH status, PCO2 results, and the compensatory response by HCO3
-.
Thyroid disease
Authors: McDowell Garry
Published: September 2023

This chapter discusses thyroid disease, considering the nature and role of thyroid hormones, their regulation in the blood, and the consequences of changes in their secretion. The thyroid gland produces hormones called T4 (thyroxine) and T3 (tri-iodothyronine), which are required for normal cellular metabolism. Disorders of thyroid function can result in either excess or reduced secretion of thyroid hormones. Hyperthyroidism occurs as a result of increased release of thyroid hormones and produces the clinical features of thyrotoxicosis. It can be treated with antithyroid medication, radioiodine, or surgery to remove all or part of the thyroid gland. Meanwhile, hypothyroidism occurs as a result of deficiency of thyroid hormones and produces the clinical features of myxoedema. It can be treated by thyroid hormone replacement, usually with T4 alone. Thyroid dysfunction can be investigated by measuring the concentration of serum thyroid-stimulating hormone (TSH), free T4, and free T3.
Biochemical nutrition
Authors: Twomey Patrick , Simpson William
Published: September 2023

This chapter focuses on biochemical nutrition, looking at different types of nutrients (macronutrients, organic micronutrients, and inorganic micronutrients) and the consequences of their deficiencies and excesses. Clinically, effective nutritional care requires assessment and monitoring of nutritional status and an understanding of the effects of illness, in order to ensure appropriate provision of nutrients to patients. Prolonged nutritional imbalance leads to malnutrition. The laboratory has an important role in assessment and monitoring of specific nutrients, but results of these analyses must be interpreted appropriately, with special regard to the acute phase response (APR). Measurements are most often performed in serum or urine because of the relative analytical ease, but these measurements can only offer limited information; analyses in the laboratory rarely provide information on whole body nutrient status. The chapter then considers disordered eating patterns and nutritional intervention.
Cancer biochemistry and tumour markers
Authors: Adaway Joanne , Wieringa Gilbert
Published: September 2023

This chapter describes the role of the clinical biochemistry service in the diagnosis and monitoring of patients with cancer, the contribution of cancer-specific investigations, and the unique elements of service provision compared with those seen in nonspecialist units. Routine biochemical tests can give clues as to the presence of cancer, but further investigations are required to confirm the diagnosis. The ideal tumour marker could be used in all aspects of cancer management, from screening and diagnosis to monitoring recurrence, but unfortunately the ideal tumour marker does not exist. Nevertheless, different tumour markers have been developed and these are useful in certain types of cancer. Fields such as molecular diagnostics and pharmacogenomics are increasingly being used to improve cancer diagnosis and tailor treatment to the individual patient.
Electronic (ultraviolet–visible) absorption spectroscopy
Authors: Duckett Simon , Gilbert Bruce , Cockett Martin
Published: September 2023

This chapter outlines the principles that underlie the absorption of energy in the UV-visible region by electrons in molecules with double bonds and the associated experimental arrangements. It cites examples of organic molecules that have characteristic absorption spectra and are associated with key molecular features. It also explains how λmax is determined and related to structure and shows how the extent of absorption at a given wavelength depends upon the concentration of the sample. The chapter illustrates the effects of conjugation and the consequent use of UV-visible spectroscopy in structural and quantitative analysis. It includes examples that cover inorganic systems and those of medical and biological relevance.
X-ray diffraction and related methods
Authors: Duckett Simon , Gilbert Bruce , Cockett Martin
Published: September 2023

This chapter talks about the principles of X-ray diffraction, analysing the experimental design and the interpretation of the diffraction patterns produced by single crystals and ionic lattices. It considers information that can be obtained about molecules, including some complex examples of particular biological relevance, such as electron density maps and determination of full molecular coordinates. It also explains the main features of neutron and electron diffraction and their application to structural problems. The chapter reviews the basis of the application of diffraction techniques in solving chemical problems through the use of ions or molecules as diffraction gratings. It observes the diffraction phenomena, discussing the spacings between ions in a crystal or between the atoms in molecules.
Elimination Reactions of Haloalkanes and Related Compounds
Authors: Okusecyama Tadashi , Maskill Howard
Published: September 2023

This chapter looks at the mechanisms of elimination reactions of unimolecular elimination (E1), bimolecular elimination (E2), and E1 conjugate base or E1cB. Just as in substitution, there is some mechanistic diversity amongst elimination reactions and, because nucleophiles often also act as bases, substitution and elimination reactions of compounds RY are generally in competition with each other. The chapter covers the mechanisms of elimination reactions of RY (principally haloalkanes) to give alkenes. It also investigates the relationships between these and substitution reaction mechanisms covered in the previous chapter. Finally, the chapter shifts to elaborate on regioselectivity in elimination reactions, and competition between substitution and elimination.
Behaviour
Authors: Hosey Geoff , Melfi Vicky , Pankhurst Sheila
Published: September 2023

This chapter looks at the behaviour of animals as they respond to their environments. It specifically refers here to zoos. Ethograms are referred to as a catalogue of all kinds of behaviours seen in animals of a particular species. The chapter discusses major kinds of learning such as habituation, classical conditioning, operant conditioning, and imprinting. It highlights the importance of motivation in an animal’s behaviour and considers behavioural ecology, whichlooks into the evolution of behaviour within the context of an animal’s ecology. Additionally, the chapter talks about different sorts of mating systems such as monogamy, polygamy, and promiscuity. It compares animal behaviour in enclosures and in the wild.
Animal identification and record-keeping
Authors: Hosey Geoff , Melfi Vicky , Pankhurst Sheila
Published: September 2023

This chapter explains the identification and record-keeping of animals. It highlights the importance of keeping records such as maintaining health and welfare and aiding in conservation for captive management programmes. The chapter discusses the science behind binomial nomenclature and taxonomy. It includes a discussion on giving a temporary or permanent name to an animal such as the branding, rings, ear tags, and microchips. It looks at the degrees of intervention, invasiveness, and pain that results from these procedures. Next, the chapter shares the requirements of individual records in accordance with the Secretary of State’s Standards of Modern Zoo Practice (SSSMZP). Additionally, it notes that the International Species Information System (ISIS) has computer software formulated for zoo record-keeping.
Housing and husbandry
Authors: Hosey Geoff , Melfi Vicky , Pankhurst Sheila
Published: September 2023

This chapter looks at the accommodation and maintenance of animals in zoos. It explores the advancements in enclosure designs that cover the needs of animals, keepers, and zoo visitors. The chapter also examines the evolution of enclosure function, human-animal contact, basic housing, climate control, barriers, and safety. It explains the features of housing designed to aid husbandry. Husbandry is the process of caring for animals with routines and events. Additionally, the chapter explains the bottom-up and top-down approaches in relation to the impact of husbandry on captive animals.Next,it mentions the housing and husbandry guidelines that refer to zoo animals and that are compiled by a variety of agencies with differing degrees of comprehensiveness.
Animal welfare
Authors: Hosey Geoff , Melfi Vicky , Pankhurst Sheila
Published: September 2023

This chapter focuses on animal welfare, which is defined as the study of an animal’s quality of life. The chapter lists environment, behaviour restrictions, and adaptation to captivity as factors affecting the welfare of zoo animals. It examines the indices used to evaluate zoo animal welfare such as life-history traits, self-directed behaviours, health, and biological processes. On the topic of meeting the needs of zoo animals, the chapter considers the concept of five freedoms, which encompasses the basic needs of captive animals ranging from malnutrition, discomfort, pain, expressing natural behaviours, and distress. The chapter highlights how legislation ensures that the best practice for animal welfare is implemented.
Principles of Mendelian Inheritance
Authors: Thomas Alison
Published: September 2023

This chapter examines the principles of Mendelian genetics, which is concerned with patterns of inheritance associated with one or a few genes. Monohybrid crosses investigate the genetic basis of traits determined by a single gene. Meanwhile, dihybrid crosses consider the inheritance patterns produced by the segregation of alleles of two genes. An individual possesses two alleles for each gene, which may be similar or different. Alleles segregate into gametes during meiosis. Next, the chapter looks at the relationship between probability and Mendelian genetics. The chi-squared statistical test is used in Mendelian genetics to compare observed progeny numbers with expected ratios, because the ratios of different progeny phenotypes can be informative of underlying genetics.
The Genetics of Bacteria, Viruses, and Organelles
Authors: Thomas Alison
Published: September 2023

This chapter assesses the genetics of bacteria, viruses, and organelles. It begins by looking at the bacterial genome; most bacteria have a single circular chromosome, several million nucleotides in length. Bacteria and viruses have small haploid genomes. They are well suited to genetic studies because they have high rates of reproduction and produce large numbers of progeny. Plasmids are often present in bacterial cytoplasm. The chapter then considers how DNA can be transferred between bacterial cells by conjugation, transformation, or transduction. Viruses have DNA or RNA genomes. Bacteriophages are DNA viruses that infect bacteria, while retroviruses are RNA viruses that infect eukaryotic cells. Mitochondria and chloroplasts have their own genetic systems.
From Genotype to Phenotype I: RNA and Transcription
Authors: Thomas Alison
Published: September 2023

This chapter describes ribonucleic acid (RNA) and transcription. RNA is an intermediary in the flow of information from genotype to phenotype. In living organisms, genetic information passes from deoxyribonucleic acid (DNA) to RNA. Different types of RNA perform different roles in the information transfer from genotype to phenotype. Transcription is the process of RNA synthesis from a DNA template, and it is catalysed by RNA polymerases. Transcription involves three distinct phases: initiation, elongation, and termination. In eukaryotes, there is extensive post-transcriptional processing of the primary RNA transcript. The chapter also looks at prokaryotic transcription and the details of messenger RNA (mRNA) capping and splicing.
From Genotype to Phenotype II: RNA to Protein
Authors: Thomas Alison
Published: September 2023

This chapter explores translation, which is the mechanism by which amino acids are assembled into proteins according to information encoded in messenger RNA (mRNA). It takes place on ribosomes, which attach near the 5′ end of mRNA and move towards its 3′ end, positioning and linking amino acids according to the codons they encounter. Translation involves a number of RNA–RNA interactions: between mRNA and ribosomal RNA (rRNA), which holds the mRNA for translation; mRNA codon and transfer RNA (tRNA) anticodon; and tRNA and the rRNA of ribosomes. Translation in both prokaryotes and eukaryotes involves three main stages: initiation, elongation, and termination. The chapter then considers the post-translational modification of polypeptides.
Gene cloning essentials
Authors: Sheikh Qaiser I. , Hornby David P.
Published: September 2023

This chapter introduces gene cloning, a core part of contemporary molecular biology. Gene cloning is the insertion of a fragment of DNA into a cloning vector and the subsequent propagation of the recombinant DNA molecule in a host organism. Providing introductory principles to gene cloning, the chapter describes the common tools-vectors and enzymes-used in the process. The discussion on cloning vectors includes examinations of bacterial plasmids, yeast plasmids, yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), cosmid, bacteriophage, retroviral vectors (RNA viruses), and viral genomes. The chapter also describes the nucleases, polymerases, and ligases which are some of the enzymes used in gene cloning. Moreover, the chapter gives an overview of some of the essential processes involved in gene cloning experiments including vector and target DNA preparation, ligation, and transformation.
Polymerase chain reaction
Authors: Evison Martin
Published: September 2023

This chapter explains the polymerase chain reaction (PCR), an invaluable technique that is applied in many areas of medicine and biology, and an important tool in research about gene expression, genome analysis, and gene cloning. PCR allows the targeting and copying of almost any gene in the vast quantities needed to analyse, sequence, and visualize the DNA itself. The chapter first discusses why the discovery of PCR is central to the development of molecular biology and describes how it works by explaining three fundamental steps: denaturation, annealing, and extension or elongation. It then lays down the PCR protocol and dissects the components of the PCR reaction-the template DNA, primers, DNA polymerase enzyme, dinucleotide triphosphates (dNTPs), and other reagents. The chapter reviews the different PCR techniques such as hot-start PCR, touchdown PCR, nested PCR, RT-PCR and RACE, and quantitative PCR among others. The discussion also covers forensic DNA analysis.
Antibodies as research tools
Authors: Allsop Gavin , Colyer John
Published: September 2023

This chapter looks at how antibodies can be used as research tools to describe the behaviour of specific proteins within complex biological systems. It refreshes understanding of the antibody structure and function and explains why the antibody is an integral component of biomolecular research. The chapter tackles the manufacture of a new antibody or antibody alternative. Furthermore, it gives an overview of the three most common experimental applications of antibodies such as Western blotting, immunofluorescence microscopy, and co-immunoprecipitation. The chapter also discusses the limitations of antibody use as dictated by their intrinsic properties and describes how these limitations can be addressed to obtain reliable datasets.
Introduction to cell biology
Authors: Wang Qiuyu , Smith Chris , Davis Emma
Published: September 2023

This chapter recounts the first discovery of living cells by the Dutch linen merchant Leeuwenhoek, who observed unicellular organisms in pond water, and later blood cells, oral bacteria, and spermatozoa. It mentions the first use of the term ‘cell’ in 1665 by a curator of the Royal Society of London, who described the empty cell walls of a cork. It also considers cells as the basic structural and functional unit of all organisms, which are grouped into archaea, eucarya, and bacteria. The chapter cites the theory that life began with a group of molecules that were capable of catalyzing their self-replication. It explains that cells are largely composed of water and a variety of inorganic minerals and organic constituents.
The cytosol and cytoskeleton
Authors: Wang Qiuyu , Smith Chris , Davis Emma
Published: September 2023

This chapter explains that cytosol is a gel-like, semifluid material that surrounds the membranous organelles and particles of the cytoplasm. It describes the complex composition of the cytosol, considering it as a compartment where many metabolic reactions, protein synthesis and signal transduction pathways, and muscle contractile events occur. It also outlines the multiple functions of cytosol, such as being the site of numerous metabolism pathways and protein biosynthesis and being involved in the transport of metabolites and signal transduction. The chapter examines the cytoskeleton in the cytosol, which is a dynamic network of insoluble protein fibres that permeates the cytosol, supporting and imparting structural organization to it. It points out the essential roles cytoskeleton plays, such as actively moving macromolecules, vesicles, and organelles around the cytosol.
Golgi apparatus, the endosomal-lysosomal system, and vacuoles
Authors: Wang Qiuyu , Smith Chris , Davis Emma
Published: September 2023

This chapter deals with the Golgi apparatus, which consists of stacks of flattened membranous called dictyosomes and associated vesicles and tubules. It describes materials exported from the endoplasmic reticulum, such as lipids and proteins, that enter the cis Golgi apparatus. They are then sorted and sent to a variety of destinations from the trans face. The chapter also discusses how the Golgi apparatus chemically modifies the structures of the proteins it receives by a series of post-translational modifications. The Golgi apparatus then completes the synthesis of glycolipids. The chapter covers the functions of the endosomal-lysosomal system, which includes mediating the internalization of extracellular material, promoting the dissociation of ligands from their plasma membrane receptors, and facilitating the recycling of membrane receptors. It refers to vacuoles as large vesicles which occupy most of the cytoplasm of many eukaryotic unicellular organisms, fungi including yeasts, and mature plant cells.
Chloroplasts and photosynthesis
Authors: Wang Qiuyu , Smith Chris , Davis Emma
Published: September 2023

This chapter discusses the chloroplasts of green plants, which are surrounded by a chloroplast envelope which encloses a stroma containing a third type of membrane called the thylakoid system. The chapter explains that the chloroplast envelope consists of outer and inner membranes (OCM and ICM) that are separated by an intermembranous space. It also cites the variations in structure that occur between the chloroplasts of plants, algae, and unicellular eukaryotic photosynthetic organisms. The chapter highlights the two linked processes or sets of reactions of photosynthesis called the light-dependent and light-independent or dark reactions. It notes that light-dependent reactions occur in the thylakoid system, while the independent reactions occur in the stroma.
Cell signalling
Authors: Wang Qiuyu , Smith Chris , Davis Emma
Published: September 2023

This chapter explains that cells communicate with one another using chemical or electrical signals that activate complex signalling pathways. It describes the cells of animals and plants which communicate using extracellular messengers or ligands, noting that local communication occurs by secreting and receiving local-acting extracellular messengers, while long-distance signalling between cells uses hormones. It also outlines a variety of biological molecules that function as extracellular messengers or ligands, which include hormones, derivatives of vitamins A and D, growth factors and cytokines, eicosanoids, and neurotransmitters. The chapter explores the common features of receptors of signal molecules, such as binding a signalling molecule and receptor. It covers signal transduction pathways, which are one of the many ways organisms coordinate their activities.
Eukaryotic cell cycle, mitosis, and meiosis
Authors: Wang Qiuyu , Smith Chris , Davis Emma
Published: September 2023

This chapter describes the four phases of the eukaryotic cell cycle which occur generally as a continuous sequence, which includes the first gap (G1), synthesis (S), second gap (G2), and mitosis (M). It explains that phases G1, S, and G2 are called interphase as it is the period between successive mitotic divisions, while M is considered a major feature of the cell cycle during which chromosomes condense and move apart. It also discusses the variations on mitotic cell division, which include the variable abilities of cells to grow and divide in vivo, asymmetric cell division, differentiation, and meiosis. The chapter emphasizes the importance of precisely coordinating the different phases of the cell cycle in order to follow the correct sequence, wherein one phase is completed before the next begins. It refers to mitosis as a universal occurrence in eukaryotic organisms, suggesting that it arose at the base of the eukaryotic evolutionary stem.
Molecular Ultraviolet and Visible Spectroscopy
Authors: Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D. , Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D.
Published: September 2023

This chapter discusses the ancient Greeks, who developed their own theories on the nature of light based on the four elements: fire, air, water, and earth. It explains how the Greeks believed that light emanated from the eye in much the same way as light emanates from a candle or lamp and that color is the result of the ethereal light's interaction with the fundamental elements. The chapter also points out how the analysis of color remain a primary analytical tool, as seen in colorimetric techniques which rely on the analysis of visible color. The chapter represents a modern version of colorimetry, focusing on ultraviolet-visible (UV-vis) light as an optical instrument technique. It talks about the modern UV-vis spectrophotometer, which expanded the ability to see beyond the visible part of the electromagnetic spectrum (EMS).
Atomic Emission Spectroscopy
Authors: Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D. , Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D.
Published: September 2023

This chapter compares atomic emission spectroscopy (AES) with luminescence spectroscopy. There are fundamental differences in the techniques which involve vibronic versus purely electronic transitions. The chapter explains that AES is similar to molecular luminescence spectroscopy as the emitted light is measured from excited state analyte. It also considers AES as an atomic method that requires the sample be in the free gas state, necessitating a high-temperature atomizer that is not amenable to physical containment. The chapter points out that AES atomizers are much hotter than atomic absorption spectroscopy (AAS) as the number of atoms in the excited state is an exponential function of temperature. It outlines the atomization step in AES, which both produces atoms and causes their electronic excitation.
Raman Spectroscopy
Authors: Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D. , Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D.
Published: September 2023

This chapter cites uses of Raman spectroscopy, such as monitoring blood glucose levels without having to draw blood and determining whether a piece of art is a forgery or not. It describes Raman spectroscopy as a form of vibrational spectroscopy that plays a role in the analyst's toolbox and is very similar to infrared (IR) spectroscopy. It also recounts how Raman spectroscopy has become a useful analytical technique for the identification of organic, inorganic, and biological samples. The chapter refers to Raman-based techniques. These have elevated Raman spectroscopy to a level that challenges Fourier transform infrared (FTIR) analysis as one of the workhorse techniques of any well-equipped analytical laboratory. It mentions low-cost, handheld Raman spectrometers that are used outside the traditional laboratory in law enforcement to analyze gunpowder residue and to identify explosives and drugs.
Systematics and Diversity of Extant Amphibians
Authors: Harvey Pough F. , Andrews Robin M. , Crump Martha L. , Savitzky Alan H. , Wells Kentwood D. , Brandley Matthew C.
Published: September 2023

This chapter examines the systematics and diversity of extant amphibians. It begins by discussing several important morphological and physiological traits that characterize amphibians. Herpetologists use two different measurements of amphibian body length, and most amphibians are small in terms of both length and weight. Amphibians share numerous other traits, including ectothermy, but their life histories and skin structure are central in defining the ways these animals interact with their environments. The chapter then explores amphibian diversity on a finer scale by discussing general biological features of different families, as well as their geographic distribution and conservation status. The chapter finally looks at the systematics and phylogeny of salamanders, frogs and toads, and caecilians.
Systematics and Diversity of Extant Reptiles
Authors: Harvey Pough F. , Andrews Robin M. , Crump Martha L. , Savitzky Alan H. , Wells Kentwood D. , Brandley Matthew C.
Published: September 2023

This chapter evaluates the systematics and diversity of extant reptiles. Extant reptiles, encompassing Testudines (turtles), Rhynchocephalia (tuatara), Squamata (lizards and snakes), Crocodylia (alligators, crocodiles, and gharials), and Aves (birds), include more than 20,000 extant species and countless fossil forms. About half of these species are birds, and the other half are reptiles in the herpetological sense. The chapter describes the systematics, characteristics, distribution, and conservation status of all families of reptiles, as well as subfamilies of some diverse groups. The amniotic egg that distinguishes reptiles from amphibians opened new ecological niches that led to the evolution of different and distinctive morphologies. No longer dependent on the presence of water in order to reproduce, reptiles inhabit virtually all of Earth’s tropical, temperate, and alpine habitats. The chapter also looks at the major characteristics of reptile skin and sensory systems.
The Science of Plant Systematics
Authors: Judd Walter S. , Campbell Christopher S. , Kellogg Elizabeth A. , Stevens Peter F. , Donoghue Michael J.
Published: September 2023

This chapter considers the lineage of green plants, which is a major lineage that includes the so-called green algae and land plants. It explains that green plants share a number of features, including the presence of the photosynthetic pigments chlorophyll a and b and storage of carbohydrates in the form of starch. The chapter also examines the presence of two anterior whiplash flagella at some stage of the life cycle of green plants. The chapter also covers land plants or embryophytes, whose closest extant relatives are members of the “charophytes,” a green algal group. It traces the life histories of land plants, which involve the alternation of two morphologically distinct bodies, thick-walled spores, an embryonic stage in the life cycle, specialized structures that protect the gametes, and a cuticle.
The Human Population and Its Food Supply in the 21st Century
Authors: Chrispeels Maarten J. , Chrispeels Hanya E.
Published: September 2023

This chapter discusses the past, present, and future of the human population and its relationship to food production. In the past, the uncertainties of food production too often have led to food insecurity, and the future holds further uncertainties posed by climate change. Rapid urbanization in developing countries is changing where vegetables are grown and how they are made available to consumers. The depopulation of the land means that farming will have to become more efficient and less labour intensive. There is agreement among agricultural scientists that the way forward is to increase the productivity of farmland everywhere and to do this sustainably, reducing the impact of agriculture on the environment. The chapter then looks at how government policies play pivotal roles in global food production, as well as the importance of agricultural research and biotechnology.
Abiotic Stresses and How They Affect Crop Yield
Authors: Chrispeels Maarten J.
Published: September 2023

This chapter assesses abiotic stresses such as drought, floods, acidic soils, and soil salinity, and how they affect crop yield. Abiotic stresses cause plant cells to more highly express many genes that help the plant cope with the stress so that growth can continue, albeit at a slower rate. The formation of reactive oxygen species (ROS) is a response to many stresses. ROS damage cells but also serve as signals and cause cells to turn on stress-response genes. The chapter then considers water potential, which is the physical property of water that drives water movement from the soil through the plant and into the atmosphere. It also looks at how some common agricultural practices, other human activities, and climate change are leading to soil degradation and increased abiotic stresses.
Introduced Traits That Benefit the Consumer
Authors: Chrispeels Maarten J. , Herman Eliot M.
Published: September 2023

This chapter describes crop-plant traits that primarily benefit consumers. Functional foods can be made in several ways: by traditional plant breeding, by genetic engineering, or by the addition of ingredients as foods are being processed. The Golden Rice Project shows an example of what can be achieved scientifically to address nutritional deficiencies by plant genetic engineering, but also how difficult it can be to bring the benefits to consumers. The chapter then looks at how biofortifying crops with iron is a major goal of nutritionists. It also considers heat-stable vegetable oils, particularly soybean oil; hypoallergenic foods; and the use of genetic engineering to reduce postharvest food losses.