bluuebunny/crossref_metadata_2025 huggingface dataset:
From genetics to genomes
Authors: Lesk Arthur M.
Published: September 2023

This chapter provides a background on genetics and genomes, and the development of DNA sequencing by biochemist Frederick Sanger. It begins by outlining some of the important landmarks in the history of genomics, from the classical work of Charles Darwin and Gregor Mendel, through Thomas Hunt Morgan and Alfred Sturtevant, to the discovery of the double-helical structure of DNA and the development of the human genome project. The chapter then distinguishes different types of maps: genetic linkage maps, chromosome banding patterns, restriction maps, and DNA sequences. It also looks at the basic computational problems of pattern matching. DNA sequence data can be used for personal identification, including the verification of family relationships, and crime investigation. Finally, the chapter considers the ethical, legal, and social problems associated with DNA sequence databases.
Control of organization and organization of control
Authors: Lesk Arthur M.
Published: September 2023

This chapter studies more general control mechanisms, including gene expression. Life is a dynamic process, requiring robust control mechanisms. The chapter then looks at the goals of transcriptomics and proteomics—the measurement of amounts and distributions of RNAs and proteins within a cell or organism. Two major techniques for exploring the transcriptome are microarrays and RNA sequencing (RNAseq). DNA microarrays, or DNA chips, are devices for checking a sample simultaneously for the presence of many sequences. The chapter also considers the importance of protein–protein interaction networks, the methods available for generating them, and some of the databases that collect and present them. It details the structures and some of the building blocks of regulatory networks.
Fundamentals
Authors: Iggo Jonathan A. , Luzyanin Konstantin V.
Published: September 2023

This chapter provides an overview of nuclear magnetic resonance (NMR) spectroscopy, which is commonly first encountered in organic chemistry, and attention is focused on the NMR spectroscopy of a single element, hydrogen. There are, however, many other elements that have isotopes with nuclear spin; if these elements are taken into account, NMR becomes perhaps the most important spectroscopic technique today for the characterization of inorganic compounds in solution and is of growing importance in the solid state. In solution, spin ½ nuclei give well-resolved, sharp resonances for each NMR active site in the molecule, while in the solid state, cross-polarization results in an increase in sensitivity and magic angle spinning results in an increase in resolution. The rules for interpreting NMR spectra depend only on the nuclear spins present. The chapter then presents some basic theory of NMR and a formalism for the prediction of NMR spectra in solution.
Structure determination
Authors: Iggo Jonathan A. , Luzyanin Konstantin V.
Published: September 2023

This chapter discusses the interpretation of NMR spectra to deduce the structure of the compound. When analysing an NMR spectrum, we should consider the groups of spins present, not individual spins. It is important to look for symmetrical patterns to identify the chemical shifts (the number of chemically different groups of spins of the nuclide/element observed) present in the molecule. We should then use the coupling pattern/multiplicity and coupling constants to identify the neighbouring groups and number of spins in each neighbouring group responsible for each coupling pattern. Coupling may be homonuclear—the coupling partner is of the same nuclide, so its resonance appears in the same spectrum —or heteronuclear—the coupling partner is of a different nuclide, so its resonance appears in 'the other' NMR spectrum. The rules for interpreting homo- and heteronuclear couplings are the same.
Experimental methods: pulses, the vector model, and relaxation
Authors: Iggo Jonathan A. , Luzyanin Konstantin V.
Published: September 2023

This chapter examines how an NMR spectrum is recorded and how we can tailor the spectroscopic experiment to maximize the information we are interested in. It begins by looking at how the NMR signal is created, and NMR spectra acquired. Traditionally, this was done using the continuous wave method; modern spectrometers use the pulse Fourier transform method. Meanwhile, the vector model provides a simple means to visualize the effect of an excitation pulse on the NMR magnetization and the evolution of the magnetization vector in the rotating frame and can be used to understand simple pulse sequences. Relaxation is an important consideration when using excitation pulses and sample averaging, since we must allow the system to return to equilibrium before starting the excitation sequence again. Relaxation can also provide valuable structural information and dynamic information about a sample that is not accessible through analysis of the chemical shifts and couplings.
Dynamic NMR spectroscopy
Authors: Iggo Jonathan A. , Luzyanin Konstantin V.
Published: September 2023

This chapter focuses on dynamic NMR spectroscopy. Intra- and intermolecular dynamic processes affect the appearance of NMR spectra. When the dynamic process is slow, separate resonances are observed for each site. When the process is fast, a resonance at the weighted average chemical shift is seen. Exchange not only affects the chemical shift but also the couplings seen. If the dynamic process is intermolecular exchange, decoupling is observed due to the breaking of the bonds between the exchanging groups. If the process is intramolecular a weighted average coupling constant is seen to all the neighbouring spins involved. Dynamic processes can be studied by both variable temperature spectroscopy and by EXSY NMR, allowing the intimate mechanism of the dynamic process to be determined.
The solid state
Authors: Iggo Jonathan A. , Luzyanin Konstantin V.
Published: September 2023

This chapter studies the solid state. Although NMR spectroscopy in solution continues to be the most widely used magnetic resonance spectroscopic technique, NMR in the solid state is rapidly growing in importance. In addition to the problems of low sensitivity and low natural abundance for many important nuclides encountered in solution, NMR in the solid state faces additional challenges due to interactions such as dipolar coupling, chemical shift anisotropy, and quadrupolar interactions that are averaged out in solution by molecular tumbling but remain in the solid state due to the restricted mobility of the molecules/ions. Cross-polarization can be used to improve the signal to noise in spectra by allowing more scans to be acquired for signal averaging in the same amount of time. Analysis of CP build-up rates also provides information about things such as internuclear distances and molecular motions.
Basic algebra and arithmetic
Authors: Sivia D.S. , Rhodes J.L. , Rawlings S.G.
Published: September 2023

This chapter provides an overview of basic algebra and arithmetic. To avoid ambiguities, the text introduces an order ranking the priorities of the various basic arithmetical operations has been agreed; this convention , which can be remembered by the acronym BODMAS. According to BODMAS, things occurring inside a bracket must be evaluated first; the next most important operation is 'orders', as in powers and roots; then, it is division or multiplication, as they appear left-to-right;, and lastly addition or subtraction. The chapter also then looks at powers, roots, and logarithms; quadratic equations; simultaneous equations; the binomial expansion; arithmetic and geometric progressions; and partial fractions. The situations in which partial fractions arise involve the ratios of two polynomials, where the denominator can be written as the product of simpler components.
Trigonometry
Authors: Sivia D.S. , Rhodes J.L. , Rawlings S.G.
Published: September 2023

This chapter examines trigonometry. It starts with a discussion of angles and circular measure. An angle is a measure of rotation or turn, and it is usually specified in degrees. The chapter notes that, despite our familiarity with degrees, a circular measure that is often more useful in a mathematical context is a radian. Unless degrees are mentioned explicitly, it is best to assume that all angles are implicitly given in radians. The chapter then looks at sines, cosines, and tangents; Pythagorean identities; compound angles; factor formulae; inverse trigonometric functions; and the sine and cosine rules. The sine and cosine formulae relate the lengths of the sides of a general triangle to its angles.
Data analysis
Authors: Sivia D.S. , Rhodes J.L. , Rawlings S.G.
Published: September 2023

This chapter focuses on data analysis. One of the things that sets science apart from other systems of trying to make sense of the world is the use of empirical evidence. A scientific theory must therefore be able to make predictions that can be compared with observations. Since the amount of data obtained in an experiment is limited, and subject to noise in the measurement process and uncertainty in the parameters required for their analysis, the conclusions reached have to be couched in conditional terms with an appropriate statement about their reliability. The chapter then looks at the basic rules of drawing inferences, common probability distributions, parameter estimation, propagation of errors, and model comparison.
Principles of Development
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

Principles of Development starts off by presenting some background history and basic concepts. The next chapterIt then looks at is about the Ddrosophila life cycle and the development of the body plan. Other topics covered include vertebrate life cycles, experimental techniques and human development, and the vertebrate body plan for Xenopus and zebrafish and the chick and mouse. Other chapters look at the development of nematodes and sea urchins, morphogenesis, cell differentiation and stem cells, and germ cells, fertilization and sex. The text then goes on to look at organogenesis, the development of the nervous system, and the growth, post-embryonic development, and regeneration. Finally, the text looks at plant life cycle and development, evolution, and development.
History and basic concepts
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter focuses on delivering a conceptual framework for the study of development. It discusses the history of developmental biology by referencing Aristotle raising the issue over epigenesis and preformation. Then, the chapter looks into cell theory changing the initial concept behind embryonic development and heredity. It notes the major processes involved in development: pattern formation, morphogenesis, cell differentiation, and growth. The developmental potential of cells becomes more limited as the development continues. Additionally, the chapter highlights how development is a central element in evolution after exploring the changes in embryonic development. It adds how the information for embryonic development is found within the fertilized egg called the diploid zygote.
Development of the Drosophila body plan
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter looks into the development of the fruit fly, Drosophila melanogaster, in order to get a greater understanding of the morphological complexity of animals. It highlights how other animals’ developmental genes have been identified thanks to their homology with Drosophila melanogaster’s genes. The chapter discusses the development and life cycle of Drosophila melanogaster. It also looks into the process of oogenesis, fertilization, segmentation, and gastrulation in terms of cell and zygote development. In addition, the chapter notes the specification of segment identity such as with Hox genes. It also includes how segment and compartment boundaries are involved in patterning and the polarizing of segments of an organism.
Vertebrate development III: chick and mouse—completing the body plan
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter explores some features of vertebrate development involved in completing the body plan, using the chick and the mouse as model organisms. It focuses on the development of the spinal cord, somites, antero-posterior axis of the body, neural crest cells, and left-right asymmetry in the body. The chapter acknowledges the striking differences seen between birds, mammals, and amphibians, in terms of early development. It notes the significance of nourishment in relation to the early development of the chick and mouse. Moreover, the chapter mentions the similarities in how germ layers are specific and patterned among all vertebrates despite the different topologies of embryos.
Development of nematodes and sea urchins
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter looks into the body plan development of invertebrates for nematodes and sea urchins. It notes the general plan of animal development: cleavage leads to a blastula, which then undergoes gastrulation with the emergence of a body plan. The chapter also cites the differences between regulative development and mosaic development. Nematodes are said to undergo mosaic development, while sea urchins undergo regulative development. Next, the chapter explains how specification on a cell-by-cell basis often utilize asymmetric cell division and the unequal distribution of cytoplasmic factors. It highlights the significance of cytoplasmic localization, cell lineage, and local intercellular interactions in terms of specifying the fate of a cell.
Morphogenesis: change in form in the early embryo
Authors: Wolpert Lewis , Tickle Cheryll , Arias Alfonso Martinez , Lawrence Peter , Locke James
Published: September 2023

This chapter discusses morphogenesis. This involves the dramatic change of embryos amidst their early development during gastrulation. It notes how gastrulation involves extensive rearrangements, and directed movement of cells from one location to another. Additionally, the chapter lists the key properties of cells involved in the generation of the animal embryonic form: cell adhesiveness, cell shape, and cell migration. It highlights cell migration as a major feature of animal morphogenesis. The chapter includes epithelia and mesenchyme as the two main types of cellular organization in embryos. It also explains particular patterns of cell division, cell packing, and cell polarization that result in the formation of a hollow, spherical blastula, or blastocyst.
Describing a single sample
Authors: Hawkins Dawn
Published: September 2023

This chapter discusses how to conduct analyses to describe a single sample of data. We can do this by producing summary numbers, names, tables, or pictures (otherwise known as graphs, charts, or figures). The chapter begins by explaining when and how to calculate descriptive statistics for the central tendency (mean, median, and mode) and variability (range, interquartile range, standard deviation, and variance) of a sample. Descriptive statistics are numbers or names used to summarize the information in a sample. The chapter then considers the attributes, types, and importance of frequency distribution tables and graphs. It also introduces pie charts, boxplots, and error bars before demonstrating how to use Statistical Package for the Social Sciences (SPSS) to produce descriptive statistics and graphs of a single sample.
Tests of relationship: regression
Authors: Hawkins Dawn
Published: September 2023

This chapter covers tests of relationship for a dependent/independent variable pair, focusing on parametric bivariate linear regression. Bivariate regression analysis involves a null hypothesis significance test which assesses whether the line is sloped, as compared to horizontal. A horizontal line means that there is no relationship, whereas a sloping line means that when the independent variable changes, so does the dependent variable. The chapter then offers guidance on what sample sizes to use when planning to collect data for use in bivariate linear regression, demonstrates how to perform the test by hand and with SPSS using real data sets, and illustrates how to identify and report the key results of bivariate linear regression. It also differentiates between model I and model II regression.
The basis for genetic analysis
Authors: Meneely Philip
Published: September 2023

This chapter introduces genetics and looks at the history of genes. It considers properties of genes, such as inheritance, allelism, linkage, and mutation. Gregor Mendel correctly identified that genes are inherited as cellular elements. He noted also that diploid organisms have two copies of each gene. The chapter shows how various gene components were identified since Mendel's discovery, including how Thomas Hunt Morgan found that genes are affixed on chromosomes at varying positions. The chapter describes how most genomes are transcribed and numerous genes encode RNA as their final product. The chapter considers why scientists are unable to name every gene that is discovered, and explains how genetic analysis uses the properties of genes as an approach to solve or dissect a complex biological problem.
Pathology of Cancer
Authors: Divan Aysha , Royds Janice A.
Published: September 2023

This chapter discusses the pathology of cancer. Tumours are behaviourally classified as benign or malignant based on characteristics identified by the physician, pathologist, or radiologist. In addition to benign or malignant, a further important classification that determines treatment and prognosis is the morphological classification. This is based on the type of malignant cell and its degree of differentiation. There are various stages in diagnosis of solid tumours, starting with gross examination and then imaging, and finally histology. Meanwhile, cancer screening involves looking for cancer before a person has any symptoms, with the aim of catching cancer at an early stage when it is easier to treat. Douglas Hanahan and Robert Weinberg first coined the term 'hallmarks of cancer' in 2000 to describe the essential biological processes necessary for tumour formation. These hallmarks are generalized features that are considered fundamental to cancer cell biology.
Molecular Epidemiology
Authors: Divan Aysha , Royds Janice A.
Published: September 2023

This chapter examines the influence of genetics, environmental factors, and lifestyle behaviours on the risk of cancer developing. It begins by describing global cancer trends, including incidence, mortality, geographical variations, and gender variations. Cancers can be familial (inherited) or sporadic. In inherited cancers, the disease causing mutation is carried in the germline and so is present in all cells of the body at birth. This does not cause cancer on its own and additional somatic mutations are still required for cancer to develop. However, only about 5–10 per cent of all cancers result directly from gene defects inherited from a parent. The rest occur through mutations acquired in somatic cells, and are sporadic. These mutations can arise due to exposure to certain environmental factors, lifestyle behaviours, and some infectious agents as well as spontaneous mutations arising, for example through errors in DNA replication.
Key Players and Pathways in Cancer
Authors: Divan Aysha , Royds Janice A.
Published: September 2023

This chapter introduces signalling pathways and their relationship to cancer. The signalling pathways that are perturbed during tumour initiation and progression underpin the hallmarks of cancer. In general, tumour cells exhibit elevated cell proliferation, repressed cell death, and decreased differentiation relative to normal cells. Altered signalling in tumours was at first considered to involve linear pathways, but it is now recognized that a network view, with essential cross-talk between signalling hubs, is entailed. Thus, cancer-associated genes form key nodes or hubs in a complex of signalling pathways. Some oncogene/tumour suppressor 'products', none more so than p53, satisfy the criteria of being important nodes and are critical for our understanding of carcinogenesis. The chapter then considers telomeres, non-coding RNAs, changes in the cell's metabolism, and tumour immunity.
Cancer Treatment and Clinical Management
Authors: Divan Aysha , Royds Janice A.
Published: September 2023

This chapter presents an overview of cancer prognosis and current treatments such as surgery, radiotherapy, and chemotherapy. It begins by looking at cancer prevention. Predicting the expected outcome for patients diagnosed with cancer is a critical step in their management; however, prognostication has remained somewhat subjective, leading to suboptimal clinical outcomes. The chapter then considers immunotherapy, which aims to treat cancer by generating or enhancing an immune response against the tumour. Immunotherapy differs from other methods of cancer treatment in that it does not target the tumour cell directly but instead targets the immune system. Principally, three strategies are utilized: immune checkpoint blockade, adoptive T cell transfer, and cancer vaccines. The chapter also describes how clinical trials of new candidate drugs are currently undertaken.
Introduction
Authors: Bosker Thijs , Behrens Paul , Ehrhardt David
Published: September 2023

This chapter provides significant contexts on how the human population grew dramatically after two major evolutions: the Agricultural Revolution and the Industrial Revolution. It highlights that population growth among humans has required resources to be diverted from natural systems to human societies, including food, water, and energy. The chapter also explains the Holocene, a period of relative stability in the Earth's climate which enabled population growth. Furthermore, it discusses the Anthropocene, a new geological epoch associated with the global and pervasive impacts of human activities on the environment. The chapter also discusses how ecological footprints are calculated and introduces the concepts of biocapacity, resource stocks, and resource flows. Then it tackles the key environmental and societal challenges related to food production. Lastly, it looks at the role of governance in overcoming sustainability challenges.
Food Systems
Authors: Oosterveer Peter , Brons Anke
Published: September 2023

This chapter looks at how food systems are organized in a globalized economy. The chapter also differentiates between mainstream food systems, which aim for economic efficiency and rely on the intensive use of technology, including machinery, chemical fertilizers, and pesticides, and alternative food systems, which prioritize quality over efficiency in the food supply chain, and usually pay specific attention to certain aspects in the food chain, such as organic production processes, ethics of production, and the relationships between producer and consumer. Next, the chapter defines what sustainable food systems look like and identifies ways to measure food system sustainability. Finally, the chapter explores methods for enhancing the sustainability of food systems such as building on what works and reforming food governance.
The bacterial origins of photosynthesis
Authors: Murphy Denis , Cardona Tanai
Published: September 2023

This chapter provides a detailed investigation of where, when, and how photosynthesis originated and then evolved in non-eukaryotic organisms. It looks at some of the best accepted geological evidence for the earliest photosynthesis that comes from marine sedimentary deposits in rocks from the Buck Reef Chert in South Africa dated to 3.4 Ga. It also talks about rocks found in the Isua Greenstone Belt in Greenland, dating back from about 3.8 Ga, which harbour geochemical signatures consistent with photosynthesis. The chapter highlights the possibility that anoxygenic photosynthesis had already evolved well before 3 Ga, at a time when the Earth was still a highly anaerobic planet. It covers the two key evolutionary innovations required for the evolution of photosynthesis: first is the evolution of the reaction centre (RC) proteins, and second is a requirement for the evolution of biosynthetic pathways of chlorophylls and related pigments.
Endosymbiosis: How eukaryotes acquired photosynthesis
Authors: Murphy Denis , Cardona Tanai
Published: September 2023

This chapter looks at how an oxygenic cyanobacterial cell is taken up by a scavenging heterotrophic eukaryotic cell. It reviews evidence that a very rare and unique event led to the combination of a cyanobacterial cell with a much larger heterotrophic eukaryotic cell to form the first eukaryotes capable of oxygenic photosynthesis. It also discusses how primary endosymbiosis started the beginning of the evolution of photosynthetic algae and plants, both terrestrial and aquatic. The chapter investigates the reduction of cyanobacterial endosymbiont from a free-living organism to an organelle. It details how plastids evolved in algae and plants, sometimes acquiring new non-photosynthetic functions related to storage, reproduction, or defence.
Blood cultures
Authors: Law Derek
Published: September 2023

This chapter focuses on blood cultures, which are extremely important clinical samples that are requested by clinicians when the signs and symptoms suggest the possibility of bacteraemia or septicaemia. Because of the importance of obtaining rapid results with blood cultures, this is one area of microbiology where automation is commonplace. The chapter then explores the different blood culture methods, outlining the procedures for sample taking, transport, and processing. A blood culture involves taking a sample of blood from a patient and inoculating the blood into a blood culture bottle; the bottle is then transported to the laboratory for incubation. The chapter explains the different procedures for dealing with negative and positive bottles. It also looks at bacterial pathogens, false-positive results, and specialized testing for endocarditis.
Investigation of wound, tissue, and genital samples
Authors: Davies Steve , Tovey Mark
Published: September 2023

This chapter addresses the investigation of wound, tissue, and genital samples. The skin and mucosa form an extremely effective physical barrier to the outside environment as part of the host’s immune defence system. If this integrity is breached, entry of bacteria can occur, which could potentially lead to infection. The majority of organisms associated with skin, mucosal, and soft tissue infections are commensals; these may act as opportunistic pathogens once this defence has been overcome. This may occur in a number of ways: as a result of surgery or other medical intervention, trauma, burns, inflammation, or due to an underlying medical condition. Genital infections can also be a result of opportunism as well as sexual transmission. Wound, genital, eye, ear, nose, and throat swabs are some of the most commonly received samples in the clinical laboratory. The chapter then describes the laboratory investigation of these and other specimens.
Populations, Patchiness, and Movement
Authors: Gilbert Francis , Gilbert Hilary
Published: September 2023

This chapter describes how population sizes change. Understanding the dynamics of populations involves studying the key demographic processes of birth, death, immigration, and emigration. Much of twentieth-century population ecology concentrated on explaining population dynamics of closed populations, using the effects of density on births and deaths, while ignoring movement. The equilibrium theory of island biogeography changed this focus onto the study of movement as a key determinant of species richness. This focus was then transferred into the idea of the metapopulation, a set of extinction-prone populations on patches kept going by the movement of individuals. Natural landscapes consist of many patches of suitable habitat in a sea of unsuitable habitat. Movement across such landscapes is an important element in the population dynamics of many organisms.
Why are study and communication skills important?
Authors: Overton Tina , Johnson Stuart , Scott Jon
Published: September 2023

This chapter explores the key study and communication skills that are needed by chemistry students beyond school level. It stresses that good study and communication skills are vital to doing well at university, as they enable students to study efficiently and effectively and perform to the best of their ability in their chosen area of chemistry. But the benefits of having strong study and communication skills are by no means limited to one’s university education. The chapter highlights that appropriate experience and the ability to articulate strengths clearly and convincingly to potential employers—that is, someone’s employability—can help a student to succeed in their working life beyond university. It elaborates the importance of using opportunities to assess what needs to be done to become more employable.
f-Block Chemistry
Authors: Aspinall Helen C.
Published: September 2023

f-Block Chemistry starts off by discussing the fundamentals of this topic. It then moves on to consider electronic structure, magnetism, and spectroscopy. The next topic of discussion is binary compounds. There are two chapters on coordination chemistry and organometallic chemistry. The text then looks at applications of the topics discussed thus far. Finally, the text examines extraction and purification of lanthanoids and actinoids.
The red blood cell in health and disease
Authors: Blann Andrew , Holtom Pam
Published: September 2023

This chapter illustrates the structure and function of the red cell and how it is adapted for its purpose of carrying oxygen. It considers the morphology of the cell and interrelationships between size, shape, and colour. The chapter highlights key aspects of the cell biology and molecular genetics of erythropoiesis and of haemoglobin generation. It discusses how the red cell operates in health and in disease, noting that the principal disease associated with the red blood cell is anaemia. The chapter lists the different types of haemoglobin and explains the relationship between their structure and function. It clarifies the importance of red blood cell enzymes and metabolic intermediates, including the aetiology and consequences of polycythaemia vera and erythrocytosis.
Normal haemostasis
Authors: Moore Gary
Published: September 2023

This chapter outlines the processes that cause blood to clot in a controlled manner and presents an overview of the interplay between the various components. It explains the importance of effective haemostasis and the interplay between its elements. It lists the major components of haemostatic mechanisms. It also describes the mechanisms of primary and secondary haemostasis and fibrinolysis. The chapter details the crucial functions of the mechanisms of haemostasis, such as maintaining the blood contained within the vasculature in a fluid state and removing the blood clot upon completion of wound healing. It elaborates how haemostatic mechanisms maintain the fluidity of circulating blood and are essentially anticoagulant in nature.
Basic Principles of Plant Disease
Authors: Beales Paul
Published: September 2023

This chapter explains that all plants get sick, whether they are wild or cultivated. It talks about how some plants suffer only mildly with no visible symptoms, while others succumb to more notable conditions such as leaf spots, leaf streaks and mosaics, stem cankers, swellings, scabs, and galls. The chapter looks at plant diseases that have been described since we have been able to record history. Early writings, including the Bible, mention famines and social depravity caused by rusts, mildews, and smuts. This chapter discusses how plant diseases affect the economy, environment, and social well-being of a country. It reviews records that show the number of plant diseases that have entered and established viable populations in countries around the world. These are increasing at an alarming rate..
Plant Pathogens: Bacteria
Authors: Elphinstone John
Published: September 2023

This chapter examines bacterial plant diseases which affect a wide range of crops, ornamentals, and environmentally important plants and trees. It first reviews descriptions of bacterial plant diseases by the early pioneers in plant bacteriology, wherein many different genera of bacteria which damage plants were reported. It also highlights the enormous global impact of bacterial plant diseases in both social and financial terms. The chapter outlines types of economic losses that range from minor blemishes, such as spots, areas of dead tissue, or yellowing on leaves or fruit, to more serious rots, wilts, blights, and diebacks, which can spread through and devastate entire crops or areas of natural vegetation. It elaborates on how minor symptoms of bacterial plant diseases can still be economically significant if the loss in quality affects marketability, such as in the cases of high-value ornamental plants or food crops.
Viruses and Virus-like Pathogens of Plants
Authors: Fox Adrian
Published: September 2023

This chapter highlights plant viruses which have evolved alongside their plant hosts over millions of years, emphasizing the breadth of their diversity. This diversity is potentially as great as the diversity of the plant species they infect. It describes viruses as incredibly small obligate parasites that cannot survive and reproduce outside of the cells of their plant hosts. It also clarifies how the challenges caused by the small size of plant viruses are being addressed with the advent of advanced genomic sequencing techniques. The chapter reviews how diagnostic technologies revolutionize the understanding of the diversity and role of viruses in the wider environment. It talks about virus infections and states that these are not normally fatal to their host but can still cause a range of symptoms that can result in produce not being sold due to internal and external blemishes.
Biological Controls and Integrated Crop Management
Authors: Little Julian
Published: September 2023

This chapter looks at bees and hoverflies searching for nectar and aphids tapping into the sugar-rich sap, which are considered part of the natural interdependence of living things. It reviews the growing interest in the use of biological control methods, which use living organisms or the products of living organisms to control plant pathogens and reduce the impact of plant diseases on crops. It also examines agricultural systems that have the potential to manage plant diseases, such as Chalara ash dieback and Dutch elm diseasex, in natural ecosystems. The chapter explains how the use of biological control attempts to deal with the plant pathogens or vectors of disease without destroying the ecological balance. It highlights the use of biocontrols and biostimulants as the two main approaches to biological control.
Polyatomic molecules
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter demonstrates how to predict shapes of polyatomic molecules and how to explain the bonding within them, including how the three bonding theories can be extended from diatomic to polyatomic molecules. The Lewis model, valence bond theory, and molecular orbital theory are looked at in turn, as each provides a different insight into structure and bonding. The chapter discusses the formal charges on the atoms in a molecule or ion, which are used to predict which of several possible structures a compound is likely to adopt. It describes bonding in a compound by predicting the hybridization of the central atoms and how the hybrid orbitals interact with the orbitals on other atoms. It also shows how to use resonance forms in describing the bonding in compounds that contain bonds that appear to be different in the Lewis structure but are found to be the same experimentally.
Solids
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter looks closely at covalent, metallic, and ionic bonding in solid state structures, which is important as the properties of solid state materials depend on their structures and bonding. Some of the characteristic/properties of molecular solids, covalent network structures, metals, and ionic solids are summarized. The chapter describes the differences between cubic close packing (ccp) and hexagonal close packing (hcp). It demonstrates how to predict the limiting radius ratio for different geometries and how to use the radius ratio rule to predict the structures of ionic compounds. It also outlines how to calculate packing efficiencies and densities, lattice enthalpies using Born–Haber cycle compounds, and lattice energies using the Born–Landé equation and the Kapustinskii equation.
Gases
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter traces the interest of chemists in gases, noting that, in historical terms, the study of gases involved some of the earliest and most important scientific measurements and helped to develop many ideas of atomic theory and stoichiometry. In more modern terms, many reactions that are important in the chemical industry involve reactions between gases. The chapter describes the experimental evidence for the relation between n, p, V, and T in the ideal gas equation and the assumptions underlying the kinetic theory of gases. It talks about the Maxwell–Boltzmann distribution of molecular speeds and its dependence on the temperature and the molar mass of the gas and elaborates what is meant by effusion and application of Graham's law. It also highlights the role of models in explaining the behaviour of chemical systems and the difference between an empirical approach and a theoretical approach.
Phase equilibrium and solutions
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter introduces some of the ideas and concepts that govern phase behaviour and looks at the factors that determine why compounds exist in a particular phase under a particular set of conditions. What governs the transitions between phases and some properties of mixtures and solutions are also covered. The chapter illustrates how to state and use the Clapeyron equation to describe the effect of pressure on melting temperatures and the Clausius–Clapeyron equation to describe the effect of pressure on vaporization and sublimation temperatures. It explains what is meant by colligative properties and how to apply the idea to osmotic pressure. It also interprets single-component phase diagrams, including their main features.
d-Block chemistry
Authors: Burrows Andrew , Holman John , Lancaster Simon , Overton Tina , Parsons Andrew , Pilling Gwen , Price Gareth
Published: September 2023

This chapter describes the d-block elements, which are all metals and are among the most useful of all the elements. Nowadays, many of the d-block metals are used in construction materials and nine of the elements are essential for life, and compounds of the d-block elements are used as catalysts, pigments, and medicines. The chapter looks at the trends in atomic radii, ionic radii, and ionization energies across the first row of the d block. It explains why the second and third row elements in a d-block triad have similar chemistries but are rather different from the first row element. It discusses the valence electronic configuration for any d-block ion and the general trend in the most stable oxidation states of the first row d-block elements, including its origin.
Fundamental processes
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter covers a widely used approach in thermodynamics — breaking down the process of interest into a series of simpler steps. The enthalpy change associated with the overall process is then equal to the sum of the changes for the individual steps. Commonly occurring steps include phase transitions, ionization and electron gain, and bond dissociation and formation. Phase transitions include freezing, melting, vaporizing, and their analogues in membranes. Ionization is the process of losing one or more electrons and electron gain is the opposite. Bond dissociation and bond formation are fundamental steps in many chemical reactions, and are essential components in the analysis of the overall enthalpy change accompanying a biochemically significant reaction. To describe these processes quantitatively, the chapter discusses the necessity of specifying the conditions, such as the pressure and temperature, under which they take place.
Water in transition
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter examines water in transition. It explains that water (like any other substance) tends to make a transition to the phase with lowest molar Gibbs energy. As the chapter reveals, the freezing, melting, evaporating, and condensing of water are phase changes that have a profound effect on the environments in which life is found. The thermodynamic analysis of these phase changes opens up a route to understanding many other properties and some of the roles of water in cells. To that end, the chapter begins by examining the variation of Gibbs energy with pressure. Afterward, the variation of Gibbs energy with temperature is discussed.
Water at equilibrium in solution
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter shows that, at equilibrium, the chemical potential of water is the same on each side of a water-permeable membrane. It begins by showing that, apart from lowering the vapour pressure of water, a non-volatile solute has three main effects: it raises the boiling point of a solution, it lowers the freezing point, and it gives rise to an osmotic pressure. These properties, which are called ‘colligative properties’, are independent of the identity of the solute, provided the solution is ideal. Next, to understand why cells neither collapse nor burst easily, the chapter explores the thermodynamics of transfer of water through membranes and specifically the phenomenon of osmosis. Finally, the chapter discusses the thermodynamic properties of water in terms of the water potential.
Enzyme inhibition
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter discusses enzyme inhibition. A major aspect of the regulation of enzyme activity and therefore of the balance of reaction rates in organisms is the possibility that a compound can inhibit the enzyme's action. The modulation of the activity of enzymes with effector molecules is essential for the coordination of the huge number of reactions that occur in cells. Thus, this chapter shows how to set up the rate laws for a variety of different models of inhibition. In many cases inhibition is a part of an organism's biochemical strategy, but it could result from external influences, such as the application of a drug or a poison.
Many-electron atoms
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter focuses on many-electron atoms. The atomic orbitals developed for hydrogenic atoms are used to describe the electronic structure of many-electron atoms by using the building-up principle, a set of rules for predicting the order in which electrons occupy the available energy states, allowing for the repulsion between electrons and the Pauli exclusion principle. The building-up principle accounts for the structure of the periodic table and the variation through it of atomic radii, ionization energies, and electron affinities. One application of this material is to the discussion of an important inorganic contributor to life: zinc. The chapter also looks into the orbital approximation and the role of electron repulsion.
Photoactivation and its consequences
Authors: Atkins Peter , Ratcliffe George , Wormald Mark , Paula Julio de
Published: September 2023

This chapter discusses photoactivation and its consequences. Processes in photobiology typically involve a competition between chemical reaction and the decay of excitation energy. Molecules that have been excited electronically can either react or lose their excitation energy in other ways, including fluorescence. The chapter shows how the kinetics of the processes that can follow photo-excitation can be explored by setting up rate equations like those used in chemical kinetics, and the influence of specifically introduced quenching molecules can be explored quantitatively. With these processes understood, they can be applied to the central issues of photobiology, including vision, photosynthesis, and the damage to DNA that may result from exposure to sunlight.
Health and safety
Authors: Glencross Hedley , Taylor Alison
Published: September 2023

This chapter examines the legal requirements and regulations governing occupational health and safety, including the methods used to assess and control risks. It focuses on the risks and controls particular to biomedical science laboratories. The Health and Safety at Work Act (HASAWA) and the Management of Health and Safety at Work Regulations form the legal framework that ensures the safety of everyone in the workplace. Risk assessment is the primary tool prescribed in legislation to ensure high standards of health and safety. Risk assessments identify hazards and those who are potentially in danger; they evaluate the risks associated with those hazards and suggest how the risks can be reduced to acceptable levels. Ultimately, ensuring a high standard of health and safety in the workplace is desirable because the overt costs associated with incidents and injuries are considerable.
Electrochemistry
Authors: Robinson Peter
Published: September 2023

This chapter assesses electrochemistry, which is the study of the chemical changes produced by electrical currents and also the production of electrical currents by chemical reactions. All electrochemical techniques involve the use of two electrodes and the measurement of the potential difference between them (potentiometry) or the current that flows between them (voltammetry). Potentiometry involves the generation of a spontaneous potential that is measured against that produced by a reference electrode as a potential difference. In voltammetric techniques, electrochemical reactions are not spontaneous, but are forced to occur by an imposed external voltage. The chapter then outlines the likely uses of electrode devices within a clinical laboratory and describes their fundamental principles of operation. It also looks at biosensors, which are widely used in the analysis of glucose concentrations for the diagnosis and management of diabetes.
Centrifugation
Authors: Wang Qiuyu , Ahmed Nessar , Smith Chris
Published: September 2023

This chapter explores centrifugation, which is the mechanical process of separating mixtures by applying centrifugal forces. It is one of the most widely used techniques in biochemistry, molecular and cellular biology, and in the biomedical sciences. The chapter begins by explaining the basics of centrifugation theory. Centrifugation is a separation technique conducted in an instrument called a centrifuge. A centrifuge holds a spinning rotor containing samples in tubes that are rotated around a central axis by a motor. This spinning of the rotor generates a centrifugal force that separates the components in the mixture on the bases of differences in size and/or density. The major centrifugation techniques used are differential and density gradient centrifugation. When using centrifuges, all appropriate safety considerations must be observed.