bluuebunny/crossref_metadata_2025 huggingface dataset:
External defences: entry and exit
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter concentrates on the effective barrier against invasion by most pathogens. It begins with discussing the skin and the secretions of its various glands. The chapter then proceeds to track the terminal parts of the respiratory tract and its importance. It also explains the first difficulty encountered by microbes on their way to the intestine. Like the air we breathe, food and water are inevitably contaminated with microbes, although proper cooking and water filtering can substantially reduce this contamination. The chapter then details some episodes of bacterial infection in the bladder (cystitis), specifically in the urogenital tract. Next, the chapter analyzes a number of diseases which can be caught by a baby from the mother. It also elaborates on the main escape routes used by pathogens and the importance of vectors to both the entry and exit of pathogens.
Innate immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter opens with a discussion on pattern-recognition by the innate immune system. It points out that one of the key roles of the innate immune system is to distinguish between self and non-self, and where possible between self and pathogen. The chapter then argues that the recognition is mediated by the interaction of two sets of complementary molecules: pathogen-associated molecular patterns (PAMPs) and pattern-recognition receptors (PRRs). The chapter also assesses the intracellular responses triggered by pathogen or damage recognition. It also describes and displays some examples of humoral innate immune mechanism and mediators of innate immunity. Finally, the chapter uncovers the three cells of innate immunity: phagocytic cells, dendritic cells, and mast-cells. It then explains the purpose of acute inflammation and the cellular interactions between the adaptive and innate immunity systems.
Immunodeficiency III: secondary immunodeficiency and AIDS
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter concentrates on the defects in secondary immunodeficiencies and its principal causes. It emphasizes that secondary immunodeficiency results from some influence external to the immune system-infection, malnutrition, etc-ranging from the slightly increased risk of infection following surgery to the severe and progressive immune failure of HIV/AIDS. Since most adult immunodeficiency falls into this category, the chapter discusses both innate and adaptive immunity. The chapter also elaborates on other infection which has an effect on the immune system as well as the immunosuppression caused by the other infections. Next, the chapter considers other causes of immunodeficiency, then analyzes the infections in immunodeficient patients.
Ectoparasites and immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter explores how skin parasites can be vectors for many major pathogens. It follows how vector-derived substances, largely in saliva, can influence the subsequent host response to the pathogen once transmitted, an interesting example of synergy between three different species which may contribute to the stability of their relationship. The chapter begins with a discussion on leishmaniasis and the sandfly. It then examines ticks, the vectors for several viral, bacterial, and Rickettsial diseases. The chapter also examines the intense reactions of mosquitoes and malaria, then explains the nature of tsetse flies and simulium (blackfly). Finally, the chapter discusses peeks at the effect of vector bites and saliva on the disease. It also studies mites, allergy, and resistance.
Waves
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Harmonic waves 19

Brief illustration 3.1: Resultant waves 20

The electromagnetic field 20

Brief illustration 3.2: Wavenumbers 20

Checklist of concepts 21

Checklist of equations 22

Why do you need to know this material?

Several important investigative techniques in physical chemistry,...
The emergence of quantum theory
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The quantization of energy 33

Black-body radiation 34

Brief illustration 4.1: Wien's displacement law 34

Example 4.1: Using the Planck distribution 35

Spectroscopy 36

Brief illustration 4.2: The Bohr frequency condition 37

Wave-particle duality 37

The photoelectric effect 37...
Hydrogenic atoms
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The structure of hydrogenic atoms 150

The separation of variables 151

Brief illustration 17.1: The angular part of the hydrogenic wavefunction 153

The radial solutions 153

The atomic orbitals and their energies 155

The atomic orbitals 155

Brief illustration...
Homonuclear diatomic molecules
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Electron configurations 216

σ Orbitals and π orbitals 216

Brief illustration 24.1: Ground-state configurations 218

The overlap integral 218

Brief illustration 24.2: Overlap integrals 219

Period 2 diatomic molecules 219

Brief illustration 24.3: Bond order 220

Example 24.1: Judging the...
Heteronuclear diatomic molecules
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Polar bonds 225

The molecular orbital formulation 225

Brief illustration 25.1: Heteronuclear diatomic molecules 1 225

Electronegativity 225

Brief illustration 25.2 Electronegativity 226

The variation principle 226

The procedure 227

Brief illustration 25.3: Heteronuclear diatomic molecules 2 228
Polyatomic molecules
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The Hückel approximation 232

An introduction to the method 232

Brief illustration 26.1: Ethene 232

The matrix formulation of the method 232

Example 26.1: Finding molecular orbitals by matrix diagonalization 233

Applications 234

Butadiene and π-electron binding...
Ab initio methods
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Configuration interaction 251

Brief illustration 29.1: Configuration interaction 252

Example 29.1: Finding the energy lowering due to CI 252

Many-body perturbation theory 253

Example 29.2: Setting up Møller–Plesset perturbation theory 254

Checklist of concepts 254

Checklist of equations 255

Why do...
Crystal structure
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Periodic crystal lattices 330

Brief illustration 37.1: Bravais lattices 333

The identification of lattice planes 333

The Miller indices 333

Brief illustration 37.2: Miller indices 334

The separation of planes 334

Example 37.1: Using the Miller indices 334

X-ray...
Electrical, optical, and magnetic properties of solids
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Electrical properties 353

Conductors 354

Brief illustration 39.1: The Fermi–Dirac distribution at T=0 355

Insulators and semiconductors 355

Brief illustration 39.2: The effect of doping on semiconductivity 356

Optical properties 356

Brief illustration 39.3: Optical properties of a semiconductor...
Molecular rotation
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Moments of inertia 388

Example 41.1 Calculating the moment of inertia of a molecule of inertia of a molecule 390

The rotational energy levels 391

Spherical rotors 391

Brief illustration 41.1: Spherical rotors 392

Symmetric rotors 392

Example 41.2: Calculating...
The canonical ensemble
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The concept of ensemble 524

Dominating configurations 525

Brief illustration 54.1: The canonical distribution 525

Fluctuations from the most probable distribution 526

Brief illustration 54.2: The role of the density of states 526

The mean energy of a system...
Thermochemistry
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Calorimetry 560

Conventional calorimetry 561

Brief illustration 57.1: The calorimeter constant 561

Example 57.1: Calculating a change in enthalpy 562

Differential scanning calorimetry 562

Standard enthalpy changes 563

Enthalpies of physical change 563

Brief illustration 57.2: Forward and reverse...
The Second Law
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The recognition of spontaneous change 595

Brief illustration 59.1: Spontaneous changes 595

Brief illustration 59.2: The Kelvin statement 596

The direction of spontaneous change 596

Brief illustration 59.3: The molecular basis of spontaneous change 597

Entropy 597

Brief illustration 59.4: The...
The statistical entropy
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The statistical definition of entropy 599

The Boltzmann formula 600

Brief illustration 60.1: The Boltzmann formula 600

The connection with the thermodynamic entropy 600

Brief illustration 60.2: The change in entropy 601

The entropy in terms of the partition function...
The thermodynamic entropy
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The entropy as a state function 608

The Carnot cycle 609

Brief illustration 61.1: The Carnot cycle 610

The independence of working substance 610

Brief illustration 61.2: Thermal efficiency 611

Generalization to any cycle 611

The thermodynamic temperature...
Phase diagrams: one-component systems
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The phase rule 658

Brief illustration 67.1: Constituents and components 658

The Ehrenfest classification 659

Brief illustration 67.2: The Ehrenfest classification 660

One-component systems 660

Phase characteristics 660

Brief illustration 67.3: Triple points 661

Three typical phase diagrams...
The response of equilibria to the conditions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The response of equilibria to pressure 728

Brief illustration 75.1: The effect of compression 729

The response of equilibria to temperature 730

The van ’t Hoff equation 730

Example 75.1: Measuring a reaction enthalpy 731

The value of K...
Diffusion
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The thermodynamic view 782

Brief illustration 81.1: The thermodynamic force 783

Brief illustration 81.2: The thermodynamic force and the drift speed 784

The diffusion equation 784

Simple diffusion 784

Brief illustration 81.3: The diffusion equation 785

Diffusion with convection...
Collision theory
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Collision rates in gases 837

Brief illustration 87.1: Collision density 837

The energy requirement 838

Brief illustration 87.2: The rate constant 839

The steric requirement 840

Brief illustration 87.3: The steric factor 840

Example 87.1: Estimating a steric factor 841

Checklist...
Adsorption and desorption
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Adsorption isotherms 922

The Langmuir isotherm 922

Using the Langmuir isotherm 923

The isosteric enthalpy of adsorption 924

Measuring the isosteric enthalpy of adsorption 925

The BET isotherm 925

Using the BET isotherm 927...
Analytical centrifugation
Authors: Campbell Iain D.
Published: September 2023

Introduction

Hand-driven centrifuges were used in the middle ages to separate milk products. Today, a variety of preparative centrifuges, ranging from small desktop to large scale devices, are in routine use in almost all molecular biology laboratories. We focus here on the analytical ultracentrifuge (AUC),...
Ultraviolet/visible spectroscopy
Authors: Campbell Iain D.
Published: September 2023

Introduction

Absorption in the UV (~200–400 nm) and visible (~400–750 nm) ranges arises from electronic transitions between energy states in a chromophore (Gr: “color bringer”). This absorption can give rise to color, vision, and the conversion of sunlight into energy by plants. Color...
Computational biology
Authors: Campbell Iain D.
Published: September 2023

Introduction

Computational biology is the application of computational methods to all levels of exploration; molecules to ecosystems. This is huge area of research that can be subdivided in various ways. The computer is, of course, also an indispensible tool in every branch of biophysics discussed...
Biological molecules
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to remind readers about some of the molecules of life, their nomenclature and some of their properties.

Nucleic acids are made from linear chains of nucleotides (Figure T1A). Phosphate groups bridge the 3’and 5’positions of...
How Does the Immune System Destroy?
Authors: Cunningham Anne C.
Published: September 2023

This chapter examines how the immune system destroys pathogens. The immune system has to recognize and destroy a diverse range of infectious agents which can infect any part of the body, including parasites, helminths, yeasts, bacteria, and viruses. The innate effector mechanisms to destroy extracellular pathogens include phagocytosis and complement fixation, while the innate effector mechanisms to destroy/expel helminths include eosinophils/goblet cell hyperplasia. In order to kill intracellular pathogens or tumour cells, the immune system must destroy the affected body cells. The innate effector mechanisms to destroy intracellular pathogens include Natural Killer (NK) cells. The adaptive immune system uses similar effector mechanisms but introduces strategies to make them specific. For extracellular pathogens, antibody-coated pathogens are destroyed by phagocytosis; while helminths are destroyed by specific IgE and eosinophils. For intracellular pathogens, NK cells can destroy antibody-coated cells (antibody-dependent cellular cytotoxicity (ADCC)) and cytotoxic T lymphocytes (CTL) can destroy infected/transformed body cells.
The Role of the Immune System in Health and Disease
Authors: Cunningham Anne C.
Published: September 2023

This chapter focuses on the role of the immune system in health and disease. A well-functioning immune system should be in balance—it should recognize and destroy those things that cause harm (infectious agents, tumours) but ignore those things which are harmless. However, some individuals have gene defects in immune response genes. These are rare but can help in understanding how the immune system works. Immunodeficient patients are more susceptible to infections, do not necessarily respond to vaccines, and may be more at risk of developing tumours. Immunodeficiency can also lead to autoimmunity—when the immune system attacks the body. Meanwhile, ‘hypersensitivities’ are inflammatory immune responses mediated by adaptive immune responses (i.e. lymphocytes). Transplant rejection is also affected by adaptive immune responses. In contrast, established tumours are anti-inflammatory environments. Immunotherapy aims at inducing adaptive immune responses specific to the tumour.
Genome stability and gene expression
Authors: Cox Lynne S. , Harris David A. , Pears Catherine J.
Published: September 2023

This chapter assesses genome stability and gene expression. Genetic information is stored in DNA in the order of nitrogenous bases. Information in DNA must be accurately copied, ready to be passed to the next cell generation. DNA replication is the accurate and precise copying of DNA template by DNA polymerase. To access the information encoded in DNA, a relatively short-lived copy of the genetic information is made by transcription into RNA. The three-letter nucleotide code of messenger RNA is then translated into the amino acids of protein. Any errors in the bases of DNA must be corrected by specific DNA repair processes for the integrity of the genetic code to be maintained. DNA regions can be cut and rejoined differently to alter genome sequence by DNA recombination. The chapter then considers DNA exchange in bacteria.
Muscle Physiology
Authors: MacDougall Duncan , Sale Digby
Published: September 2023

This chapter focuses on muscle physiology. It considers how muscles are controlled by the nervous system and how the nervous system and muscles work together to produce what are commonly called strength and power performance. It also demonstrates the ability of muscles to generate force and power and the ability of the nervous system to activate the muscles appropriately for a given task in which performance depended. The chapter describes the composition of muscles of cells called muscle-fibers, which range in thickness from about 50-100 μm and in length from a few to several millimeteres. It refers to myofibrils that make up about 85% of the contents of a muscle-fiber, while the remaining 15% are largely composed of sarcoplasmic reticulum (SR), mitochondria, glycogen granules, and fat droplets.
Reference materials and standards
Authors: Evans E. Hywel , Foulkes Mike E.
Published: September 2023

This chapter analyses the different types of reference materials and reviews the importance of traceability in analytical chemistry. It discusses the selection of an appropriate reference material for use in a variety of scenarios in analytical chemistry. It also describes reference materials in detail, including the definition and uses of reference materials that are set out in a series of publications by the International Organization for Standardization (ISO). The chapter explains that a reference material is any substance that has been characterized for a particular chemical or physical property which can be quantitative or qualitative. It demonstrates how reference materials can be used for instrument calibration or method validation.
Introduction to anatomy and embryology
Authors: Murray Joanne , Locke Ian
Published: September 2023

This chapter begins by examining anatomy and physiology. Anatomy defines the spatial/structural relationships between the various components and organ systems of the body. Meanwhile, physiology is the study of the function of the body and the systems within it. Fine anatomy is the detailed, microscopical structure of individual organs or tissues. The chapter then describes the gross features of the human body and differentiates between fine and gross anatomy. The human body is composed of 11 major organ systems; each of these systems is composed of various cell and tissue types. The chapter also looks at fertilization and implantation, before considering foetal development. Finally, it studies the continued development of the ageing human through childhood, adolescence, adulthood, and into old age.
Cells of the cardiovascular and lymphatic systems
Authors: Blann Andrew
Published: September 2023

This chapter outlines the cells and organs of the cardiovascular and lymphatic systems, and looks at how together they form the circulation. Almost all of the cells that make up the vessels and organs are endothelial cells, smooth muscle cells, heart muscle cells (cardiomyocytes), macrophages, and fibroblasts. In various combinations they make up vessels (arteries, veins, capillaries, and lymphatics) and the organs of the heart, thymus, spleen, and lymph nodes. The chapter then examines the different types of disease that affect the cells, vessels, and organs of the cardiovascular and lymphatic systems. These include atherosclerosis (involving arteries), venous thromboembolism or VTE (involving veins), and tumour-associated lymphadenopathy (affecting lymph nodes).
Cells of the endocrine system
Authors: Brincat Judy
Published: September 2023

This chapter discusses the cells of the endocrine system, which are scattered throughout the body. They occur either within an epithelial surface such as the endocrine cells of the respiratory tract and alimentary canal, or within the stroma of another organ such as the C- or parafollicular cells of the thyroid, or the cells comprising the islets of Langerhans situated among the glands of the exocrine tissue of the pancreas. Endocrine cells also aggregate to form discrete organs or endocrine glands such as the adrenal glands, parathyroids, thyroid, pituitary, and pineal gland. The functions of the endocrine system are essential for maintaining homeostasis and the coordination of body growth and development, and are similar to those of the nervous system. Both systems communicate information to peripheral cells and organs, and because their functions are interrelated they are often referred to as the neuroendocrine system.
Skin and breast
Authors: Orchard Guy
Published: September 2023

This chapter examines the main cell types that compose the skin, which represents the largest organ of the human body. The skin has homeostatic and regulatory functions that protect and regulate the body systems. It also has a sensory perceptive role. It is the largest sensory organ of the human body and has receptors for touch, pain, pressure, and temperature. The structures responsible for this role are called corpuscles. Finally, the skin also has a metabolic role. The subcutaneous fat provides the body with triglycerides for energy, if required; in addition, the epidermal cells synthesize vitamin D (previtamin D3), which is primarily important in bone structure. The chapter also considers breast tissue, which is a specialized form of apocrine glands.
Characterisation Methods in Inorganic Chemistry
Authors: Weller Mark T. , Young Nigel A.
Published: September 2023

Characterisation Methods in Inorganic Chemistry uses a technique-based, problem-solving approach to show how analytical methods are used to characterize the structures and properties of inorganic compounds. Chapters include an examination of fundamental aspects of characterization methods in inorganic chemistry and diffraction methods and crystallography. Other topics include nuclear magnetic resonance, vibrational spectroscopy, electronic absorption and emission spectroscopy, and X-ray and photoelectron spectroscopy. The text also covers mass spectroscopy, chemical and thermal analysis techniques, magnetism, electron paramagnetic resonance spectroscopy, and Mössbauer spectroscopy. Finally, the book considers example problems to illustrate the characterization of inorganic compounds using a combination of the techniques discussed in previous chapters.
Bioinorganic Chemistry
Authors: Rehder Dieter
Published: September 2023

Bioinorganic Chemistry starts with an introduction. The text then moves on to look at bio-elements in the periodic table, the alkaline and alkaline earth metals. The next chapter looks at iron. Chapter 5 is about oxygen transport and the respiratory chain. There follow chapters on oxidoreductases based on iron, manganese, and copper; oxo-transfer proteins based on molybdenum, tungsten, and vanadium; the sulfur cycle; and nitrogenase and nitrogen cycle enzymes. The text then moves on to examine the methane cycle and nickel enzymes, photosynthesis, the biochemistry of zinc, metal- and -metalloid-carbon bonds, and inorganics in medicine.
Oxygen transport and the respiratory chain
Authors: Rehder Dieter
Published: September 2023

This chapter focuses on oxygen, which became the main atmospheric constituent about 2.4 billion years ago and paved the way for evolutionary processes. The discussion covers the uptake, storage, transport, and reduction of oxygen by iron and copper proteins. The chapter explains oxygen transport by haemoglobin and myoglobin, as well as by haemerythrin and haemocyanin. Then it looks at the respiratory chain which is in the mitochondria of the cells of eukaryotes. It illustrates the electron and proton shuttle in the mitochondrial respiratory chain, discussing the processes taking place in four membrane-bound, interlinked protein complexes. The chapter likewise tackles iron-sulfur proteins and iron porphyrins.
The sulfur cycle
Authors: Rehder Dieter
Published: September 2023

This chapter addresses both geochemical and biogenic sulfur cycling, including their tight interconnections. It presents the cycling of sulfur between the atmosphere and the marine hydrosphere. The cycling involves redox processes and both biogenic and abiotic methylation and demethylation of sulfur. Two of the key compounds are dimethylsulfoniopropionate and its metabolite dimethyl sulfide. The chapter also provides an overview of key inorganic and organic sulfur compounds that are life-sustaining and/or play a substantial role in sulfur cycling. Then it looks at the biogenic metabolism of sulfur, discussing several of the key steps in the biogenic conversion of inorganic sulfur compounds into organic sulfur species relevant for catabolic processes.
Nitrogenase and nitrogen cycle enzymes
Authors: Rehder Dieter
Published: September 2023

This chapter focuses on the enzymes involved in the nitrogen cycle. One of its focal points is nitrogen fixation, or nature's way of converting nitrogen gas reductively to ammonium ions for direct use in life processes. Biological nitrogen fixation is the natural counterpart of industrial nitrogen fixation by the Haber–Bosch process. The chapter also addresses the procedural methodology by which nature cycles nitrogen between ammonia (with nitrogen in its lowest oxidation state), nitrogen gas, and nitrate (with nitrogen in its highest oxidation state), highlighting that the understanding of the versatility and differentiation by which this biochemical processing of nitrogen occurs has been a vital issue in bioinorganic chemistry in the past decades, and will be of prime interest also in the coming years. The chapter tackles nitrogenase models and model reactions and explains nitrification and denitrification. Lastly, it takes a closer look at nitric oxide.
The methane cycle and nickel enzymes
Authors: Rehder Dieter
Published: September 2023

This chapter discusses methane, which plays a key role in the global carbon cycle. The discussion acknowledges that methane is an increasingly important energy source in industrial production, in heating households, and powering alternative fuel cars but is also increasingly contributing to the greenhouse effect. The chapter explains biogenic and non-biogenic methane production. It describes serpentinization, a geochemical process involved in the abiotic formation of methane. The chapter also explains methanogenesis — the conversion of inorganic and organic carbon compounds to methane. Then it tackles the reverse of methanogenesis: the oxidative conversion of methane to carbon species in higher oxidation states. The chapter also provides some insights into some nickel-containing enzymes such as hydrogenases, CO-dehydrogenase and acetyl-coenzyme-A synthetase, urease, and superoxide dismutase.
Animal Physiology
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

Animal Physiology is composed of five parts. Part One looks at animals and their environment. It considers diversity and cells, organisms, and interactions. Part Two looks at water and salts including kidneys, excretion, water balance of land animals, and body fluid regulation. The text then goes on to examine issues related to temperature. It asks: how is temperature regulated? Part Four considers oxygen and respiration. The last part of the book is about coordination and integration. It looks at topics such as hormones, reproduction, muscles, animal movement, and integration of the respiratory and circulatory systems.
Energy Metabolism: Generating Energy from Food
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter discusses energy metabolism in animals. It focuses on how animals meet their bodies' demands for energy and on the common processes involved in the flow of energy. This process starts with the acquisition of food and sees the transfer of energy from food to molecules of adenosine triphosphate (ATP), the common currency for energy transfer and utilization in animal cells. Metabolism can be broadly subdivided into catabolism and anabolism. Most animals extract the bulk of their energy from the oxidation of carbohydrates and fats in the presence of molecular oxygen—a process called aerobic respiration. Oxidation of carbohydrates in the absence of oxygen can also provide energy through anaerobic respiration. The chapter then looks at the diverse feeding strategies that animals adopt.
Respiratory systems
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter highlights respiratory systems of animals. Gas exchange occurs across the general body surface, gills, lungs or tracheoles. There are four basic types of gas-exchanger: infinite pool exchangers, countercurrent exchangers, ventilated pool gas-exchangers, and cross-current exchangers. Some species of animals that live in water but have access to air may use lungs in addition to their skin and/or gills for gas-exchange. Animals that can breathe both water and air are known as bimodal breathers. The chapter then looks at the tracheal system of insects. The gas-exchange systems of insects, millipedes and centipedes do not rely to any great extent on a circulatory system to transport the respiratory gases between the environment and the metabolizing cells. The respiratory gases are transported through air-filled tubes called tracheae, which divide into smaller branches and eventually give rise to the tracheoles, where gas-exchange occurs.
Transport in respiratory systems and acid–base balance
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter reviews the transport of the respiratory gases in the respiratory systems of animals. Two major respiratory pigments are found in the blood: the copper-based haemocyanin and the iron-based haemoglobin. The maximum concentration of oxygen in the blood when the blood pigment is fully saturated is the oxygen-carrying capacity. Meanwhile, carbon dioxide is carried mostly as bicarbonate ions in the plasma of vertebrates, some as carbamino compounds, after it combines with amino acid residues on respiratory pigments, and a small amount is in solution. The chapter then looks at the acid–base balance of animals, before considering the transport of metabolic substrates in the blood to the metabolizing cells.
Cardiovascular systems
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter discusses the cardiovascular systems of animals. Most invertebrates have an open circulatory system, although decapod crustaceans and some species of non-cephalopod molluscs have an incompletely closed system. Vertebrates have a closed circulatory system: all blood vessels are lined with endothelium. In water-breathing invertebrates, the ventricle propels the blood around the body and then through the gills for gas-exchange. The chapter then looks at the structure and function of blood vessels. In vertebrates, blood vessels consist of three layers: tunica intima, tunica media, and tunica externa. The rate of flow of a fluid through a long straight rigid tube is described by Poiseuille's equation. The major factor affecting the resistance to blood flow is the radius of a blood vessel.
Neurons, nerves and nervous systems
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter evaluates the nervous systems in animals. All animals except Placozoa and Porifera (sponges) have a well-defined nervous system, which is the main means of communication between the animal and the outside world. Animals with bilateral symmetry have a central and a peripheral nervous system. The central nervous system (CNS) in invertebrates is organized in ganglia close to sensory structures, while the CNS in vertebrates consists of the brain and the spinal cord. The chapter then looks at the ionic basis of electrical activity in neurons, before considering how neurons communicate with each other. Signal transmission between neurons takes place at synapses, which are of two types: electrical synapses and chemical synapses.
Control of sodium, water and calcium balance
Authors: Butler Patrick J. , Brown J. Anne , Stephenson D. George , Speakman John R.
Published: September 2023

This chapter explores the control of sodium, water, and calcium balance in animals. The renin–angiotensin system is the main regulator of aldosterone secretion; aldosterone is the main salt-conserving hormone of tetrapods. Aldosterone stimulates salt absorption from the distal nephron and fluids in various non-renal tissues: amphibian urinary bladder, coprodeum and colon of birds, and sweat glands of mammals. Regulation of salt secretion by the salt glands of marine birds and reptiles is mainly via the actions of neuropeptides released from nerve fibre endings that innervate the secretory epithelia and blood vessels of the glands. The chapter then looks at diuretic and antidiuretic hormones, as well as hypercalcaemic and hypocalcaemic hormones.
Clinical Immunology
Authors: Hall Angela , Scott Chris , Buckland Matthew
Published: September 2023

Clinical Immunology introduces the topic with an assessment of the clinical immunology laboratory. It then looks at immunoglobulins. The subject of allergies is examined next. The text contains a chapter that tackles autoimmune rheumatological disease and another chapter looks at autoimmune kidney disease. The text moves on to examine organ-specific autoimmunity. Other autoimmune diseases considered include autoimmune skin disease and autoimmune liver disease. The book also discusses neuroimmunology, flow cytometry, and primary immunodeficiency. Finally, the human immunodeficiency virus (HIV) is discussed. The book ends with a look at histocompatibility and immunogenetics.
Allergy
Authors: Hall Angela , Scott Chris , Buckland Matthew
Published: September 2023

This chapter explains the exaggerated response to common environmental substances which we know as allergies. It acknowledges the increasing incidence of allergy disease. The chapter refers to allergy as a type I hypersensitivity reaction then recognizes IgE antibodies' two-stage reaction: induction/sensitization and reactive phases. It notes how component resolved diagnostics (CRD) can define disease eliciting components and help develop avoidance advice. Moreover, the chapter indicates allergen-specific IgG antibody testing, which helps in the diagnosis of respiratory conditions caused by chronic exposure to inhaled allergens. It clarifies how allergy diagnosis is based on clinical assessment supplemented by laboratory investigations. In addition, the chapter clarifies that quality assurance can be problematic due to no reference standards available for allergen preparation.
Organ-specific autoimmunity
Authors: Hall Angela , Scott Chris , Buckland Matthew
Published: September 2023

This chapter focuses on organ-specific autoimmune diseases. It shows that these are more common among women than men. The chapter notes how the presence of an autoimmune disease increases the risk of developing other autoimmune diseases due to the overlap seen in organ-specific autoimmune diseases. Disease markets, also known as characteristic antibodies, are often found among them. The chapter explains the main laboratory tools for detecting auto-antibodies such as indirect immunofluorescence and enzyme-linked immunosorbent assay (ELISA). It clarifies how most autoimmune diseases' environmental triggers are mostly unknown with the exemption of coeliac disease since its trigger is gluten. The chapter explains the treatment being directed at replacing lost factors or modifying the immune response.
An introduction to cellular signalling
Authors: Hancock John T.
Published: September 2023

This chapter opens with an introduction to one of the most important aspects of modern biochemistry and cell biology: cell signalling. It explores various aspects of cell signalling and the main principles and components behind the signalling mechanisms. The chapter argues that cell signalling is not only important for understanding the functioning of a normal cell but is also of vital importance for understanding the growth and activity of an aberrant cell or a cell combating adverse conditions. The chapter also examines what makes a good signal. It then investigates the different ways in which cells signal to each other and defines cell-to-cell signalling. Lastly, the chapter turns to the discovery of oncogenes, genes that cause the uncontrolled growth of cells that may lead to cancerous growths, and the discovery of cytokines, which held great hopes for a cure for a variety of diseases.
Reactive oxygen species, reactive nitrogen species and redox signalling
Authors: Hancock John T.
Published: September 2023

This chapter explains our current understanding of how reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated and perceived, and how they propagate their messages. It argues that the main components involved here include those used in phosphorylation and cyclic nucleotides. The chapter also explains that ROS and RNS are in control of a host of cellular functions. It emphasizes that ROS and RNS are now known to be important as signals in many biological systems, including prokaryotes, animals, and plants. Lastly, the chapter considers redox signalling and molecular mechanisms of hydrogen peroxide signalling.
Insulin and the signal transduction cascades it invokes
Authors: Hancock John T.
Published: September 2023

This chapter uses insulin signalling as an example of biological systems. As the chapter discusses, once insulin has been produced, transported, and perceived, a surprisingly diverse signalling transduction mechanism may be used to bring about the final alteration of cellular function. The chapter also highlights the importance of signalling to normal cellular function, as well as its contribution to the wellbeing of an organism. The chapter also investigates how insulin leads to a complex web of intracellular signalling that involves many components. It then explores how insulin may lead to modulation of many facets of metabolism, often through an influence on nuclear events. Lastly, the chapter reviews the dephosphorylation of various proteins involved in insulin signalling.
Perception of the environment
Authors: Hancock John T.
Published: September 2023

This chapter focuses on the molecular signalling of the mammalian eye. It emphasizes that all cells must be able to perceive elements of their environment, whether that includes the presence of compounds from other parts of the same organism or cues from outside. By discussing a complex signalling mechanism, the chapter illustrates how components described in earlier sections may come together to form coherent signalling pathways. It also elaborates on other systems used by organisms to perceive their environment to highlight the importance and diversity of such systems and to show that most draw on a repertoire of components. Next, the chapter considers the presence of chemicals and the response to mechanical forces, which are relevant to animals and plants.
Cardiovascular physiology
Authors: Kay Ian , Evans Gethin
Published: September 2023

This chapter focuses on the cardiovascular system. This provides cells with oxygen and nutrients and transports metabolic waste products away from cells. The chapter talks about the heart and the extensive system of vessels known as the circulatory system. It explains that the heart acts as a pump while the circulatory system acts as a transport system for blood. The chapter highlights the normal functioning of the cardiovascular system which is essential in order to maintain an appropriate cellular environment for all cells in the human body. It emphasizes that the heart can be thought of as a pump that ejects blood into the pulmonary and systemic circulations.
The respiratory system
Authors: Kay Ian , Evans Gethin
Published: September 2023

This chapter details the principal role of the respiratory system, which is to provide an exchange of gases between the body and the environment. It outlines the functions of the respiratory system, such as its contribution to the maintenance of plasma pH and the production of sound. It also explains how the respiratory system ensures that adequate amounts of oxygen are delivered to tissues and carbon dioxide is efficiently removed when exchanging gases in a variety of environmental challenges. The chapter talks about the paired lungs that sit inside the thorax, which are formed from a series of bifurcations of a single trachea. It details how air enters the lung by a suction pump, wherein inspiration results in an increase in volume and a decrease in pressure inside the lungs.
RNA can form versatile structures
Authors: Elliott David , Ladomery Michael
Published: September 2023

This chapter discusses some of the biological functions of RNA structures, including their use as thermosensors in pathogenic bacteria and RNA structures that strongly bind target molecules. It outlines three hierarchical levels of structural organization used by RNA molecules: primary structure, secondary structure, and tertiary structure. The primary structure is the linear sequence of nucleotides in a nucleic acid or nucleotide sequence and the secondary structure is composed of helices that form through base pairing. The tertiary structure is the highest level of organization, in which RNA molecules with secondary structure fold up into very compact and highly organized structures. The chapter explains that DNA molecules are found in long double helices which extend along their full lengths, while RNA molecules form shorter double helices between single-stranded regions.
Catalytic RNAs
Authors: Elliott David , Ladomery Michael
Published: September 2023

This chapter looks at how RNA molecules catalyse chemical reactions, a domain which was previously thought to be reserved only for proteins. It clarifies that RNA has a more limited set of functional groups for building catalysts, which are confined to just four different nucleotides: A, C, G, and U. It also highlights the ability of RNA molecules to form structures which also enables the assembly of RNA active sites. The chapter outlines the important function of metal ions in ribozymes, which includes helping RNA structures form and balance the strong negative charge in ribozyme active sites that result from high densities of RNA strands. It also mentions that the purine and pyrimidine bases of RNA have NH groups that can potentially act as hydrogen donors or acceptors in acid-base catalysis.
Co-transcriptional pre-mRNA processing
Authors: Elliott David , Ladomery Michael
Published: September 2023

This chapter discusses the pre-mRNA processing events that occur co-transcriptionally. It covers the synthesis of the 7-methyl guanosine 5? cap, pre-mRNA splicing, and the formation of the 3? end of an mRNA by cleavage and polyadenylation. It also considers the connections that exist between chromatin structure and pre-mRNA processing, including the special case of metazoan histone mRNA 3? end formation. The chapter reviews the essential elements of the process of transcription, structure, and function of the RNA polymerases. It explores the process of transcription that is required to appreciate the links between transcription and pre-mRNA processing events, as well asthe connection between transcription and post-transcriptional processes that is illustrated by the properties of the C-terminal domain (CTD) of RNA polymerase II.
Kidney disease
Authors: Lamb Edmund
Published: September 2023

This chapter describes the basic anatomy and functions of the kidneys as a foundation to understanding their pathophysiology and the rationale underlying the diagnostic and management strategies involved in kidney disease. The kidneys perform a central role in the maintenance of homeostasis, affected by filtration, followed by differential reabsorption and secretion of solutes and water as the ultrafiltrate passes through the nephron. Kidney disease may be either acute or chronic. Acute kidney injury is associated with rapidly occurring metabolic derangement and carries a high mortality, while chronic kidney disease may occur as the result of a variety of specific kidney diseases. The chapter also looks at end-stage renal disease. The general approach to kidney disease detection involves urinalysis, assessment of glomerular filtration rate (GFR), and detection or measurement of proteinuria using reagent strip devices.
Liver function tests
Authors: Sherwood Roy
Published: September 2023

This chapter describes the liver and its functions in health and then considers its major diseases of interest in clinical practice. It also looks at liver function tests, particularly their use in investigation of disease, together with their advantages and limitations. The liver has many metabolic functions, being involved in carbohydrate, fat, steroid, and protein synthesis; storage of essential vitamins and metals; and the detoxification of endogenous and exogenous substances. Liver function tests are requested to aid in diagnosis, to determine prognosis, and to monitor response to treatment. A typical panel of LFTs includes the aminotransferases AST (aspartate aminotransferase) and ALT (alanine aminotransferases) to detect hepatocyte damage; bilirubin to assess conjugation and detect biliary obstruction; alkaline phosphatase (ALP) and gamma-glutamyl transferase (GGT) to identify cholestasis; and albumin and international normalized ratio (INR) to measure synthetic function.
Gastrointestinal disorders and malabsorption
Authors: McDowell Garry , Brydon Gordon
Published: September 2023

This chapter assesses gastrointestinal biochemistry and physiology, the optimization of the gut for digestion and absorption, and how diagnostic tests have evolved to investigate the breakdown of gut homeostasis. Disease within the gut can result in breakdown of normal homeostasis leading to inefficient digestion and absorption of nutrient with inappropriate loss of fluid and minerals. Laboratory tests of gastrointestinal function have been designed to measure gastric, exocrine pancreatic, jejunal, and ileal function, which are the main sites of digestion, absorption, and conservation. The chapter then looks at gastric tests, pancreatic exocrine function tests, and faecal calprotectin. It also considers gastrointestinal tract diseases, including lactose intolerance. Bacterial colonization of the small bowel is usually secondary to stasis and can result in lipid maldigestion through bile acid deconjugation. Meanwhile, coeliac disease is a major cause of jejunal dysfunction.
Inherited metabolic disorders and newborn screening
Authors: Preece Mary Anne
Published: September 2023

This chapter explores inherited metabolic disorders and newborn screening. Inherited metabolic disorders can be inherited by autosomal recessive, autosomal dominant, or X-linked modes of inheritance. They arise due to a defective enzyme causing deficiency of a product, accumulation of a substrate, or product from a minor pathway. Inherited metabolic disorders include those affecting amino acids, the urea cycle, organic acids, fatty acids, carbohydrates, glycogen storage, lysosomal storage, and peroxisomes. Defects of enzymes in the haem biosynthetic pathway cause a group of disorders called the porphyrias. Antenatal diagnosis is used to detect IMDs prior to birth by measuring enzyme activity or DNA analysis. Ultimately, a nationwide screening programme is available for detection of certain IMDs, for example phenylketonuria and congenital hypothyroidism.