bluuebunny/crossref_metadata_2025 huggingface dataset:
Anticipation and prediction
Authors: Berthoz Alain , Petit Jean-Luc , Macann Christopher
Published: November 2023

In the preceding chapter we tried to justify our feelings about the need for a new philosophy of action designed to make possible a new physiology of action. At the very centre of this new concept we place anticipation and prediction. In fact, the projective dimension, widely recognized in the neurosciences today as essential to the functioning of the brain in living organisms, depends upon the existence of a multitude of anticipatory mechanisms. But this is not enough. For, having been discovered one after the other in the course of the history of physiology, these mechanisms have to be put back together again in a coherent vision, in the absence of which they would appear as so many pragmatic solutions to particular problems.
Communicating mathematics in the late seventeenth century: The Florentine cupola
Authors: Peiffer Jeanne
Published: November 2023

The focus of this paper is on mathematical communication, on forms of exchange like correspondence, learned journals, and challenges. Towards the end of the seventeenth century, scientific information was conveyed mostly by letters, which were sometimes copied and more or less widely circulated, or even published in the new medium of learned journals. Learned journals may be defined by two aspects: miscellaneous content, which they share with letters, and periodicity of issue.
Classical Sculpture and the Culture of Collecting in Britain Since 1760
Authors: Coltman Viccy
Published: November 2023

This is a book about classical sculptures in the early modern period, centuries after the decline and fall of Rome, when they began to be excavated, restored, and collected by British visitors in Italy in the second half of the eighteenth century. Viccy Coltman contrasts the precarious and competitive culture of eighteenth-century collecting, which integrated sculpture into the domestic interior back home in Britain, with the study and publication of individual specimens by classical archaeologists like Adolf Michaelis a century later. Her study is comprehensively illustrated with over 100 photographs.
The Elaboration and Diffusion of the Text of the Monumentum Ephesenum
Authors: Rowe G D
Published: November 2023

This chapter treats three themes. The first is the elaboration of the text of the Monumentum—how it was written and by whom. The second theme is diffusion—how the text was transformed into the physical inscription. It has been universally accepted that Nero’s ad 58 edict to publish the laws for each uectigal led directly to the inscribing of the Monumentum (at an unknown date after ad 62), and the Monumentum has therefore been taken as concrete evidence for an active, reforming state. But is the link between the edict and the Monumentum secure? The third theme is the text itself—how it compares to the rest of the heterogeneous sources of Roman laws, and how its terminology and legal forms evolved over the perhaps nearly two centuries of its elaboration.
Social Organization and Conflict
Authors: Goulson Dave
Published: November 2023

With their fat and furry appearance, their slow, meandering flight amongst flowers and their docile behaviour, it is easy to dismiss bumblebees as charming but dim. Examination of a nest might confirm this opinion; it is, in appearance, a ramshackle affair compared to that of the honeybee. The pupal cells, honey pots and larvae are haphazardly arranged. Housekeeping is poor—bees often defecate in and close to the nest, and the nest is often overrun with parasites and commensals. For these reasons, and because of the difficulties involved in findings bumblebee nests, researchers were slow to investigate the bumblebee social system. Bumblebee workers were considered to be generalists, each carrying out all tasks rather than dividing up the work in the efficient way that, for example, ants or honeybees do. Similarly, although the honeybee waggle dance has been known for many years, it was erroneously assumed that bumblebees did not communicate about sources of forage (Dornhaus and Chittka 1999). However, in recent years interest in the social life of the bumblebee has undergone a renaissance. Perhaps in part because some species can now be bred in the laboratory (or the nests bought from commercial suppliers), in the past 20 years bumblebees have been used for studies of diverse topics including queen–worker conflict, caste determination, polyandry and parasite resistance, and alloethism. This work is revealing that, despite their bumbling appearance, the social life of the bumblebee is every bit as complex as that of other eusocial insects.
The Sources
Authors: Shawcross Teresa
Published: November 2023

The Chronicle of Morea contains very little explicit information regarding its sources. In this, it differs markedly from the other fourteenth-century history of Latin Greece to survive, the Istoria di Romania by Marino Sanudo Torsello, known to us in an Italian translation. Sanudo, who began composition of his Istoria between 1326 and 1328, and had substantially completed his task by 1336, not only repeatedly acknowledges his indebtedness to earlier historiography, peppering his work with assertions such as ‘as we can read in the writings of others, and principally in the Mirror of History and the Book of the Conquest of the Outremer (p.107), or ‘as I have found written at the Papal Court of Rome in a Chronicle of the Bishop of Torcello’ (p.151), but also sets out to reproduce excerpts from documents of the period (e.g. ‘as is apparent from the content of the treaty, which is as follows: We, Prince Guillaume of Achaia make known to all those who inspect the present document .. . ‘, p.117).
The Principality of Morea in Crisis: An Identity Compromised
Authors: Shawcross Teresa
Published: November 2023

In the course of the second half of the thirteenth century, the territorial integrity of the Principality of Morea was breached as a consequence of the successful pursuit by the Byzantines of a programme of re-conquest, causing relations between Latin settlers and native Greeks to come under pressure. During the same decades, the political autonomy of the Morea was compromised due to the acknowledgement of Angevin suzerainty. The claims of the ruling Villehardouin dynasty became less easy to substantiate, while the power and prestige of the aristocracy also suffered. Events appear to have reached a culmination by the 1320s. These circumstances may explain why it had become so important by the second quarter of the fourteenth century to articulate certain ideological assertions in written form. It is surely neither insignificant nor accidental that it was precisely at the time at which it faced its greatest threat that Moreot identity came to receive its most uncompromising expression. The Chronicle of Morea, as we shall see, both marked and sought to mask the dissolution of the Principality. This chapter examines the place and function of the genre of historiography in a period of political upheaval. By focusing on the perception of events by the Moreots themselves, it becomes possible to suggest a motivation for the creation of the original Chronicle. Following on from this, one can then address the issue of the elaboration of the versions in different languages. As we shall see, the textual metamorphosis of the work both reflected and sought to generate certain external realities. Of the different versions, each can be shown to occupy a particular social space, both as a product of a particular environment and as an agent at work in that environment.
Cowley’s Horatian Mice
Authors: Hopkins David
Published: November 2023

At the large foot of a fair hollow tree, Close to plow’d ground, seated commodiously, His ancient and Hereditary House, There dwelt a good substantial Country-Mouse: Frugal, and grave, and careful of the main, Yet, one, who once did nobly entertain A City-Mouse, well coated, sleek, and gay, A Mouse of high degree, which lost his way, Wantonly walking forth to take the Air, And arriv’d early, and belighted, there, For a days lodging. The good hearty Hoast, (The ancient plenty of his hall to boast) Did all the stores produce that might excite, With various tasts, the Courtiers appetite. Fitches and Beans, Peason, and Oats, and Wheat, And a large Chesnut, the delicious meat Which Jove himself, were he a Mouse, would eat. And for a Haut goust there was mixt with these The swerd of Bacon and the coat of Cheese. The precious Reliques, which at Harvest, he Had gather’d from the Reapers luxury. Freely (said he) fall on, and never spare, The bounteous Gods will for to morrow care. And thus at ease on beds of straw they lay, And to their Genius sacrific’d the day.
The English Voices of Lucretius, from Lucy Hutchinson to John Mason Good
Authors: Hopkins David
Published: November 2023

This chapter considers the ways in which writers from the mid-seventeenth to the late eighteenth century sought to give the Roman poet Lucretius an English poetic voice. Prominent attention will be paid to translations of the De Rerum Natura, in whole or part. But the chapter will also explore the ways in which specific passages from the De Rerum Natura, or the poem’s larger structures and rhetorics, were more obliquely recreated by English poets. The main focus is thus on specifically literary responses to Lucretius, rather than on the larger role of the De Rerum Natura in disseminating Epicurean ideas in England. But a distinction between ‘poetic’ and ‘philosophical’ re- sponses to Lucretius can never be absolute. English poets and critics regularly affirmed their admiration for Lucretius’ ‘poetry’, while de- ploring his ‘philosophy’. But is it possible to write convincing Lucretian poetry without displaying, or betraying, some sympathy for the Roman poet’s ideas? And can English poets, whatever their philosophical sympathies, convey anything of Lucretius’ poetic quality without being themselves poets of comparable stature?
Nature’s Laws and Man’s: Dryden’s ‘Cinyras and Myrrha’
Authors: Hopkins David
Published: November 2023

In turning from the ‘good natur’d Story’ of Baucis and Philemon from Book 8 of Ovid’s Metamorphoses to the more disturbing tale of Cinyras and Myrrha from Book 10, Dryden was engaging with an episode which he had long admired for its presentation of its heroine ‘in the violence of her passions’. The story is one of a sequence of tales narrated by Orpheus after the loss of his wife, Eurydice. Myrrha, daughter of Cinyras, King of Cyprus, is consumed with an incestuous passion for her father. So disturbed is she by her feelings that she resolves to commit suicide by hanging herself. She is discovered in the act by her nurse, who worms her secret out of her and then, after an initial expression of horror, offers to help Myrrha to consummate her desires. While Cinyras’ wife is away, officiating at the feast of Ceres, the nurse approaches him and offers him a mistress ‘of about the same age as his daughter’.
Dryden and Ovid’s ‘Wit out of Season’: ‘The Twelfth Book of Ovid his Metamorphoses’ and ‘Ceyx and Alcyone’
Authors: Hopkins David
Published: November 2023

One of the oldest and most persistent of the charges which have been levelled against the Ovid of the Metamorphoses is that the poet trivializes his depictions of pain, anxiety, and suffering by prolixity, by a callous impassivity, and by displays of tastelessly inappropriate wit. Again and again in the poem acts of violence and destruction are treated by Ovid with fanciful playfulness, and characters in the extremity of distress are made to burst into puns, epigrams, or strings of obtrusive rhetorical figures. This habit, it is alleged, reveals Ovid’s essential frigidity and frivolousness, his lack of sensitivity to human suffering, and his ‘Alexandrian’ weakness for the display of his own verbal brilliance, whatever the demands of his subject.
Neural representation of spectral and temporal information in speech
Authors: Young Eric D
Published: November 2023

Speech is the most interesting and one of the most complex sounds dealt with by the auditory system. The neural representation of speech needs to capture those features of the signal on which the brain depends in language communication. Here, we describe the representation of speech in the auditory nerve and in a few sites in the central nervous system from the perspective of the neural coding of important aspects of the signal. The representation is tonotopic – meaning that the speech signal is decomposed by frequency and different frequency components are represented in different populations of neurones.
Basic auditory processes involved in the analysis of speech sounds
Authors: Moore Brian C J
Published: November 2023

This chapter reviews basic aspects of auditory processing that play a role in the perception of speech. The frequency selectivity of the auditory system, as measured using masking experiments, is described and used to derive the internal representation of the spectrum (the excitation pattern) of speech sounds. The perception of timbre, and distinctions in quality between vowels, are related to both static and dynamic aspects of the spectra of sounds. The perception of pitch and its role in speech perception is described.
Acoustic and auditory phonetics: the adaptive design of speech sound systems
Authors: Diehl Randy L
Published: November 2023

Speech perception is remarkably robust. This chapter examines how acoustic and auditory properties of vowels and consonants help to ensure intelligibility. First, the source-filter theory of speech production is briefly described, and the relationship between vocal-tract properties and formant patterns is demonstrated for some commonly occurring vowels. Next, two accounts of the structure of preferred sound inventories, quantal theory and dispersion theory, are described and some of their limitations are noted. Finally, it is suggested that certain aspects of quantal and dispersion theories can be unified in a principled way so as to achieve reasonable predictive accuracy.
Early language acquisition: phonetic and word learning, neural substrates, and a theoretical model
Authors: Kuhl Patricia K
Published: November 2023

Infants learn language(s) with apparent ease, and behavioral and brain studies are providing valuable information about the mechanisms that underlie this capacity. Noninvasive, safe brain technologies have now been proven feasible for use with children starting at birth. The past decade has produced an explosion in neuroscience research examining young children’s processing of language at the phonetic, word, and sentence levels, and studies have begun to explore how children develop bilingual language skills.
Functional imaging of the auditory processing applied to speech sounds
Authors: Patterson Roy D , Johnsrude Ingrid S
Published: November 2023

In this paper, we describe domain-general auditory processes that we believe are prerequisite to the linguistic analysis of speech. We discuss biological evidence for these processes and how they might relate to processes that are specific to human speech and language. We begin with a brief review of (i) the anatomy of the auditory system and (ii) the essential properties of speech sounds. Section 4 describes the general auditory mechanisms that we believe are applied to all communication sounds, and how functional neuroimaging is being used to map the brain networks associated with domain-general auditory processing.
Things to think with: words and objects as material symbols
Authors: Roepstorff Andreas
Published: November 2023

This paper integrates archaeology, anthropology and functional brain imaging in an examination of the cognition of words and objects. Based on a review of recent brain imaging experiments, it is argued that in cognition and action, material symbols may be the link between internal representations and objects and words in the world. This principle is applied to the sapient paradox, the slow development of material innovation at the advent of the anatomically modern human. This translates the paradox into a long-term build-up of extended and distributed cognition supported by development in the complexity of material symbols.
Introduction
Authors: Sutherland Wilson A
Published: November 2023

In this book we are going to generalize theorems about convergence and continuity which are probably familiar to the reader in the case of sequences of real numbers and real-valued functions of one real variable.
Some concepts in topological spaces
Authors: Sutherland Wilson A
Published: November 2023

Just as in metric spaces, in topological spaces there are notions of closed sets, closure, interior, and boundary. In fact, this chapter supersedes the discussion of these concepts in metric spaces. Alternatively, one may view the latter as an introduction to this chapter. Certainly, many of the results about closed subsets in metric spaces generalize to similar results in topological spaces. It is a good idea to compare proofs; sometimes the proof in this more general context is actually simpler.
The Hausdorff condition
Authors: Sutherland Wilson A
Published: November 2023

So far in this book, we have been marching relentlessly towards generality. In this chapter we take a small step backwards, admitting that for many, though not all, purposes topological spaces are rather too general, and it is good to impose an extra condition on our spaces. To motivate this condition, let us try to generalize the idea of convergence of a sequence of real numbers to topological spaces.
Sequential compactness
Authors: Sutherland Wilson A
Published: November 2023

We recall the form of Bolzano–Weierstrass theorem stated in Chapter 4: any bounded sequence of real numbers has at least one convergent subsequence. (You may have seen an equivalent form, which says that any bounded infinite subset of real numbers has at least one limit point; the sequence version is more relevant to our purposes.) The Bolzano– Weierstrass theorem is closely related to the one-dimensional Heine Borel theorem. For example, we have proved that a continuous real-valued function on a closed bounded interval [a, b] is bounded and attains its bounds using the Heine–Borel theorem (more precisely, the special case for [a, b]); equally well this can be proved using the Bolzano–theorem— in analysis textbooks it is often proved that way, for example see Theorems 4.3.1 and 4.3.2 of Hart (2001).
Quotient spaces and surfaces
Authors: Sutherland Wilson A
Published: November 2023

It would have been logical to discuss quotient spaces immediately after subspaces and products, but it is convenient before tackling them to have available some of our compactness results. Also, quotients are sometimes found more challenging than subspaces and products, although they are close to popular expositions of topology involving Mobius bands, dough-nuts, and such geometric objects. This chapter will give a basic account of quotient spaces, and at the same time consider a few standard surfaces. There are further results about quotients on the web site.
Uniform convergence
Authors: Sutherland Wilson A
Published: November 2023

We now move towards the third of a trio of important concepts: connectedness, compactness and completeness. We shall study completeness in the context of metric spaces. An important ingredient in establishing completeness for several of our metric spaces will be uniform convergence. In this chapter, we begin the study of uniform convergence in an elementary fashion; later in the chapter we express it in terms of convergence in function spaces.
Complete metric spaces
Authors: Sutherland Wilson A
Published: November 2023

We saw in Chapter 4 how useful the completeness property of R is. From a theoretical viewpoint, completeness lets us solve equations such as x = 2 in R which have no solution in Q. Here is a practical version of the same phenomenon; we shall refer back to it a couple of times in this chapter.
History of Universities
Authors: Goddard Eric D
Published: November 2023

Volume XXIV of History of Universities contains the customary mix of learned articles, book reviews, and bibliographical information, which makes this publication such an indispensable tool for the historian of higher education. Its contributions range widely geographically, chronologically, and in subject-matter.
Mediated amperometric enzyme electrodes
Authors: Allen H , Hill O , Sanghera Gurdial S
Published: November 2023

Aim

The aim of this chapter is to outline the techniques involved, and the problems associated with, the design of redox-mediated amperometric enzyme electrodes. The practical aspects of the use of ferrocene and its derivatives as mediators for a variety of enzymes are discussed in detail with practical examples. In the final part of this chapter, the incorporation of redox proteins as mediators for amperometric enzyme electrodes is described and compared with non-biological mediators such as ferrocenes.
Immunoelectrodes
Authors: Foulds Nicola C , Frew Jane E , Green monika j.
Published: November 2023

The range of analyte concentrations encountered in clinical chemistry is extremely large-from greater than 10-3 M for species such as glucose and cholesterol to less than 10-9 M for certain drugs and hormones. It is for the detection of these low level analytes that the application of immunological techniques is essential. In these circumstances not only is there a requirement for a sensitive assay; it must also be highly specific. At such low levels of analyte even trace amounts of interferents can become significant. The rationale for attempting to combine the fields of immunology and electrochemistry in the design of analytical devices is that such systems should be sensitive due to the characteristics of the electrochemical detector whilst exhibiting the specificity inherent in the antigen -antibody interaction.
Antibody Deficiency Disorders
Authors: Kumararatne D S , Bignall A , Joyce, H J , Hazlewood M
Published: November 2023

Of the five classes of immunoglobulins, IgG, lgA, and IgM are the main components found in serum. Measurement of the serum levels of these immunoglobulins is essential for the diagnosis and monitoring of primary and secondary immunodeficiency states and lymphoid malignancies. Other indica tions for measuring serum immunoglobulin levels include: Monitoring of immunoglobulin replacement therapy. The assessment of all patients with paraproteinaemia (see Chapter 5). The monitoring of all patients on slow acting anti-rheumatic drug therapy, which occasionally produces hypogammaglobulinaemia. Elevated levels of polyclonal immunoglobulins may occur in a variety of conditions including rheumatic diseases, liver diseases and chronic infections.
Immunochemical investigations of lymphoid malignancies
Authors: Riches P
Published: November 2023

Some haematological disorders, e.g. plasma cell tumours, lymphocytic leukaemias, and lymphomas, represent abnormal proliferations of cells of the lymphoid system. Laboratory criteria (such as cell phenotyping, genetic rearrangements or analysis of secreted products) indicate that most of these are monoclonal, i.e. originate from a single clone of cells. Any monoclonal proliferation of B-cells has the potential to secrete intact or fragmented immunoglobulin molecules which characteristically migrate as an abnormal discrete band on electrophoresis of serum or urine. The immunoglobulin band seen on electrophoresis is generally termed a paraprotein or monoclonal component; this is preferred to the term ‘M band’ which is sometimes used but can be confused with lgM paraprotein.
Cellular investigations in the diagnosis of lymphoid malignancy
Authors: Campbell A C
Published: November 2023

In many cases of lymphoid malignancy the diagnosis is readily made on the basis of well-established clinical and histological criteria. However, the recognition over the past 20 years of the several pathways of lymphoid cell ontogeny, and stages of differentiation within those pathways, has led to an increasing use of immunological methods of cell characterization in the diagnosis and classification of such malignancies. The application of immunophenotyping to lymphoid cells in blood, bone marrow, or tissue biopsies sometimes offers mere confirmation of a diagnosis which is clear on the basis of other criteria. For example, the diagnosis of multiple myeloma can generally be established on the basis of paraprotein characterization in serum and urine, bone marrow cellular morphology, and radiological findings. Formal demonstration of monoclonality among the bone marrow plasmacytoid cells is not usually an essential investigation. In other groups of diseases, immunophenotyping is crucial to diagnosis, classification, prognosis, and treatment. Acute lymphoblastic leukaemias are classified according to their T- or B-cell lineage and differentiation stage; these can only be established by immunological characterization of surface or internal markers. Some poorly differentiated tumours can only be identified as lymphomas by staining of biopsy sections for T- or B-cell antigens.
Allergy
Authors: Haeney M
Published: November 2023

In Western countries, allergic diseases affect over 15% of the population but are of variable severity: thus some patients have an occasional mild reaction, some suffer life-long debilitating allergic disease while, more rarely, some react with severe or fatal anaphylactic shock. The reasons for this variability are unknown. By common usage, ‘allergy’ has come to mean a disadvantageous immune response to extrinsic antigens. With the introduction of the Gell and Coombs classification of hypersensitivity reactions, the term ‘allergy’ was restricted further, becoming almost synonymous with hypersensitivity of the immediate IgE type (Type I hypersensitivity). In this situation, antigen specific lgE, already attached to mast cell membranes, combines with antigen to trigger release of preformed mast cell mediators stored in secretory granules: these include histamine, lysosomal enzymes, and proteases, neutrophil and eosinophil chemotactic factors and heparin. Other mediators are newly generated metabolites of arachidonic acid derived via two enzyme pathways; one leads to production of prostaglandins and thromboxane, the other to leukotriene formation.
Concepts of molecular pathogenesis
Authors: Oldstone Michael B A
Published: November 2023

Pathology is the study of disease and pathogenesis is the study of the mechanism(s) by which disease occurs. In general viruses cause disease by two distinct ways. First, according to their styles of replication and viral products made or host factors induced, viruses directly damage a cell. Hence, viruses directly destroy a cell by shutting down its protein synthesis, by manufacturing products toxic to the cell or by perturbing membranes either internal (i.e. lysosomal, endosomal) or external (i.e. plasma). Disturbance of internal membranes can result in release of a stable of enzymes potentially autolytic and thus dangerous to the cell. Disturbance of the plasma membrane can lead to cell-cell fusion, formation of giant syncytia and cell lysis or improper passage of ions and fluids causing cell distortion and death. Viruses may also affect cells directly by altering a cell’s function without lysing the cell. This more subtle effect causes disease but does not cause cell lysis. According to this scenario the virus infects differentiated cells (i.e. neurons, lymphocytes, endocrine cells, etc.), and alters their synthesis of neurotransmitters, lymphokines, immunoglobulins, hormones, etc. In contrast to the other mechanisms mentioned previously whereby the end result is destruction of the infected cell, in this instance the architecture and morphology of the infected cell appears normal by light and high resolution microscopy or by assay of cell growth efficiency, total cell RNA, DNA or protein synthesis. Because less than the usual amount of the differentiated product is made, i.e. insulin, growth hormone, ablation of specific anti-viral cytotoxic T lymphocyte function and/or immunoglobulin production, homeostasis can be imbalanced and disease produced (diabetes, growth retardation, viral persistence).
Perfusion of nerve cells and separation of sodium and calcium currents
Authors: Kostyuk P G
Published: November 2023

All active responses occurring in the nerve cell are related to the opening or closing of ion channels formed in the neuronal membrane by complex polypeptide macromolecules. Ion channels produce a pathway for the flow of corresponding ions in or from the cell, driven by continuously maintained transmembrane ionic gradients.
Caged molecules activated by light
Authors: Walker Jeffery W
Published: November 2023

This chapter deals with practical aspects in the use of light activated ‘caged’ molecules in studies of cellular regulation. The term ‘caged’ was originally coined by Kaplan et al. (1) to describe the unique properties of a l(2-nitrophenyl)ethyl ester of ATP which was called caged ATP. This ATP analogue permitted a biological system to be pre-equilibrated with ATP in an inactive form. The system could then be activated by rapidly converting caged ATP to ATP using near-UV irradiation. Successful application of caged ATP to studies of ATP-requiring reactions has led to the development of compounds for investigating other biochemical processes. A summary of biological molecules that have been derivatized with similar photolabile protecting groups to render them inactive and photosensitive can be found in Table 1. The structure of one compound, caged inositol 1,4,5-trisphosphate (InsP3), and its photolysis reaction are illustrated in Scheme .
The Use of Fluorescent Indicators for Measurements of Cytosolic-Free Calcium Concentration in Cell Populations and Single Cells
Authors: Thomas Andrew P , Ville Fernando Dela
Published: November 2023

Introduction The development of fluorescent indicators of free Ca2+ ion concentration which could be loaded into cells in a non-disruptive manner initiated a revolution in studies of cellular Ca2+ homeostasis. This revolution has been led primarily by R. Y. Tsien and co-workers, who first popularized quin-2 for studies of cytosolic-free Ca2+ ([Ca2+]i) and have since contributed a series of additional Ca2+-sensitive dyes with a number of improved properties (1-5). Indicators for measurements of other ions, including Mg2+, Na+, K+, and H+ have also been developed, and new dyes continue to be introduced.
The Use of Electrodes to Study Cellular Ca2+; Metabolism
Authors: Orchard C H , Boyett M R , Fry, C H , Hunter M
Published: November 2023

1. Introduction The importance of electrodes in the study of cellular Ca2+ hardly needs emphasizing. Electrodes can be used to monitor Ca2+ flux across cell membranes and to monitor the concentration of Ca2+ both in the cell cytoplasm and in the extracellular space. Electrodes can also be used to manipulate intracellular Ca2+. Thus, electrodes have contributed a great deal to our understanding of cellular Ca2+ metabolism. The length of a chapter such as this raises two main problems. First, the equipment used in the manufacture and use of electrodes varies in detail from manufacturer to manufacturer. We have, therefore, not concentrated on the details of using one particular brand of equipment but have given such information as should enable the reader to understand, and use effectively, any brand of equipment. Second, limitation of space precludes detailed discussion. We have, therefore, cited references that give further detail for the interested reader. We would particularly recommend the books by Purves (1), Thomas (2), and Thomas (3), and one by various authors (4).
Calmodulin
Authors: Means Anthony R , Bagchi Indrani C , Vanberkum, Mark F A , Rasmussen Colin D
Published: November 2023

1. Introduction A variety of mechanisms exist to maintain intracellular Ca2+ homeostasis (1). The markable regulation of this ion has evolved in a manner so that Ca2+ serves as the only intracellular second messenger of its class. Along with cyclic AMP, Ca2+ controls a wide variety of intracellular processes. Analogous to cyclic AMP, Ca2+ most frequently executes its regulatory roles after binding with high affinity to intracellular Ca2+ binding proteins. Calmodulin is the primary example of such a receptor protein owing to its ubiquitous nature and wide ranging effects. Calmodulin utilizes a linear sequence of 12 amino acids to bind Ca2+ (2). The three-dimensional structure formed to co-ordinate Ca2+ has been called an ‘E-F hand’ or ‘calmodulin-fold’ (3). A superfamily of proteins utilizes this configuration to bind Ca2+ but calmodulin is the only member that subserves such a plethora of functions. About 30 enzymes and structural proteins have been identified that bind calmodulin with high affinity (4). The Ca2+ calmodulin complex can also regulate the intracellular concentration of other second messengers such as cyclic AMP and inositoltrisphosphate (IP3). Isoforms of adenylyl cyclase and phosphodiesterase are calmodulin-dependent and the enzyme that phosphorylates IP3 also utilizes calmodulin as a regulatory subunit. Thus it is not surprising that calmodulin is an essential protein and disruption of the single gene in yeast and fungi is lethal (5).
Phosphorothioate based double-stranded plasmid mutagenesis
Authors: Olsen David B , Eckstein Fritz
Published: November 2023

The ability to specifically modify a nucleotide sequence has facilitated many detailed studies of structure function relationships of DNA and proteins (1-3). To this end oligonucleotide-directed mutagenesis using single-stranded DNA vectors has become almost routine (see refs 4-7 and Chapters 1 to 3 in this volume). The high mutational yields using these well-established methods allow for a rather facile screening of the altered genotype. One of the limitations of MB-based procedures is that the gene of interest must be sub cloned into one of the M13 vectors described by Messing (8). Alternatively, sub cloning may be avoided if the gene is present in a phagemid vector which is a plasmid which contains an origin of replication for single stranded phage [(9); see Chapters I and 2}. However, working with these constructs sometimes requires special experience in order to obtain single stranded DNA suitable for mutagenesis.
Random chemical mutagenesis and the non-selective isolation of mutated DNA sequences in vitro
Authors: Walton Catherine , Booth R Kim , Stockley Peter G
Published: November 2023

This chapter illustrates examples of the types of problems to which random in vitro chemical mutagenesis lends itself. It outlines the most frequently used techniques of chemical mutagenesis, and describes in full experimental detail the two chemical treatments which are the simplest to apply and which generate the most nearly random distribution of mutations. The use of denaturing gradient gel electrophoresis to separate nucleic acids differing by as little as a single base-pair is also described in detail. Routine molecular biology techniques used in the construction of clones of DNA fragments and in the generation of single-stranded DNA for mutagenesis and sequencing are adequately documented elsewhere (1).
Immunogold labelling techniques
Authors: Hyatt Alex D
Published: November 2023

Over the past one to two decade the IGS method has been applied to the detection of micro-organisms, cell surface-associated and intracellular antigens. The techniques utilized in these applications include negative contrast immunoelectron microscopy (NCIEM), pre- and post-embedding TGS, freeze-fracture immunoelectron microscopy, and scanning immunoelectron microscopy (STEM). lt is beyond the scope of this chapter to discuss each IGS technique which has been utilized over the past decade, thus only the more popular IGS procedures which can be performed in routine electron microscopy laboratorie will be covered. It is therefore the aim of this chapter to present laboratory protocols for NCIEM. pre- and post-IGS of plastic sections, SIEM, and briefly the labelling of cryosections. These protocols will be based on methods which have been successfully implemented in this and other laboratories.
Freeze-fracture techniques
Authors: Kawa Seizo Fuji
Published: November 2023

Freeze-fracture techniques were developed originally to prepare cellular ultrastructures in a frozen-hydrated and living state for electron microscopy (I). The replicas made from freeze-fractured biological specimens have provided a new three-dimensional ultrastructure of cells (2). Since the elegant proof by Branton and his co-workers (3) that the freeze-fracture technique reveals the macromolecular organization of the hydrophobic interior of bilayer membranes, the technique has been extensively used in the field of biological science and has made a major contribution to our understanding of biological ultrastructure. (For nomenclature of freeze-fractured membranes, see ref. 4.)
Negative staining
Authors: Harris Robin , Horne Robert
Published: November 2023

The fundamental concept of negative staining is rather old and extremely simple, yet, as with many microscopical specimen preparation techniques, there are numerous subtleties, intricacies, and technical hazards which have to be carefully observed by the user. Gross visual examples of ‘negative staining’ are calcified fossils within dark-brown/black mud, stone and clearglass particles of varying shape surrounded by dye or ink solution, the shape of which is made visible in a ‘negative’ sense. In descriptive terms for transmission electron microscopy (TEM), salts containing heavy metal atoms, which have the property of drying from aqueous solution as an amorphous ‘glass’ rather than a crystalline layer, can surround and permeate small biological particles.
Transmission electron microscopy of vitrified biological macromolecular assemblies
Authors: Stewart Murray
Published: November 2023

There have been a number of recent reviews of the transmission electron microscopy of frozen-hydrated biological material (1-5) to which the reader is directed for a comprehensive discus ion of many aspelh of the method. This chapter provides an introduction to the methods and description of the freezing techniques and electron microscopy procedures that are employed. It first discusses the theoretical background to freezing before progressing to a description of the methods used Lo prepare thin vitrified films containing biological macromolecules.
Introduction
Authors: Vincent Julian F V
Published: November 2023

Particularly for the neophyte, it is very easy (and common!) to think that because you have obtained some numbers, then you have done some science and have gained respectability. In biomechanics it is very easy not only to do the ‘wrong’ experiment (e.g. measure shear stiffness when tensile strength is the important parameter) but to confuse a number of independent parameters and end up with data but no understanding. This is probably because the study of materials science is by no means easy. As Jim Gordon has so elegantly said (1, 2) there is a great tendency, temptation even, to dismiss the study of materials as trivial. This response is well known as the first stage in the acceptance of an idea. In reality the problems are remarkably subtle and difficult to solve, probably because so many of the parameters of materials science are intertwined and difficult to unravel.
Fracture
Authors: Vincent Julian F V
Published: November 2023

To survive, the organism must have mechanisms for resisting fracture (the initiation and propagation of cracks) in order to withstand the mechanical effects of wind, water, and gravity, to grow in such a way that bits do not fall off or split open unannounced, to resist attack from other animals, and to chew food. An organism may also cease to be able to carry the loads that it must do in order to survive, due to structural failure. This may involve fracture but also involves other forms of deformation, both elastic (i.e. recoverable) and plastic (i.e. permanent) .
The Physical Chemistry of Protein Crystallization
Authors: Mikol V , Giege R
Published: November 2023

Of all the different aspects of protein crystallization, the physics of crystal growth and its understanding have been the most neglected. Indeed, the growing of protein crystals is often believed to occur more through serendipity than as the result of a rational approach. This chapter will try to dispute this well established belief. More knowledge on the fundamentals of crystal growth should make it possible to develop easy and convenient assays for defining optimal conditions for protein crystallization. Undoubtedly, the understanding of crystallization from a physicochemical point of view has received more attention recently and crystallization is slowly emerging from its veil of mystery. Using the physicochemical concepts of small molecule crystal growth (1), this chapter will go through all the steps of crystallization: nucleation, growth, cessation of growth, and characterization of crystals. It does not deal with the preliminary X-ray structure analysis reviewed in Chapter 12. Firstly, a brief summary of the basic physical concepts underlying each step is given. This provides a simple theoretical base for the biomacromolecule crystal grower. Then the main results obtained from physical studies on each stage and practical applications are presented.
Electromyography
Authors: Gans Carl
Published: November 2023

Animals move. Much of their locomotor activity, as well as feeding, drinking, ventilation, defence, and mating involve forces and movements that commonly are generated by mmcular action. Hence, studies of the functional morphology of animal behaviours, of the biomechanics of their musculoskeletal systems and of their control characteristics commonly require information about the time and magnitude of muscular action. Electromyography is the premier technique for generating this information. (In the literature, variants of the terms electromyography and electromyogram, are commonly abbreviated as EMG and EMGs. This convenient usage is followed in the present text.)
Hydrostatic skeletons and muscular hydrostats
Authors: Kier William m.
Published: November 2023

A hydrostatic skeleton is a fluid mechanism that provides a means by which contractile elements may be antagonized (1). Hydrostatic skeletons occur in a remarkable variety of organisms with examples not only from invertebrates but also from vertebrates. A hydrostatic skeleton is typically considered to include a liquid-filled cavity surrounded by a muscular wall reinforced with connective tissue fibres. This form of hydrostatic skeleton is seen, for example, in cnidarian polyps, holothuroid echinoderms, echinoderm water vascular systems, many molluscan bodies and organs and annelid, sipunculid, ncmcrtean, and nematode worms (for reviews see refs. 1-7). Comparison of a variety of hydrostatic skeletal support systems shows that the extent and volume of the liquid-filled cavity is variable. In particular, recent work bas identified a number of hydrostatic skeletons, termed muscular hydroslah, that consist of a tightly packed three-dimensional array for muscle fibres (8, 9). Examples of muscular hydrostats include the arms and tentacles, fins, suckers and mantles of cephalopod molluscs, a variety of molluscan structures, the tongues of many mammals and lizards. and the trunk of the elephant.
Circulatory structure and mechanics
Authors: Shadwick R E
Published: November 2023

Thischapter describes techniques to investigate the structure and biomechanical characteristics of animal circulatory systems, with a focus on the viscoelastic properties of the arterial wall. These include quantification of connective tissue components, mechanical characterization of vascular ti;,sue by in vitro and in vivo methods, calculation of vascular impedance and wave velocity from vessel elasticity, and assessing in vivo pressure-flow dynamics. For further details of hacmodynamic principles and analysis the reader should consult the excellent monographs by McDonald (1), Milnor (2), and Fung (3).
Patch-clamp analysis of gap junctional currents
Authors: Veenstra R D , Brink P R
Published: November 2023

The difficulty in recording gap junction channel currents and gating activity can largely be attributed to the specialized location of this ion channel. While virtually all other ion channels are single membrane structures which permit the passage of ions between the extracellular space and the cytoplasm or between the cytoplasm and an internal organellar compartment, gap junctions link the cytoplasms of two adjacent cells. Hence, the direct measurement of junctional currents requires the ability to independently control the membrane voltage of each member of a coupled pair of cells or direct voltage-clamp recording from gap junction membranes. The two-cell voltage-clamp approach was first accomplished using two microelectrodes impaled into each cell, one for passing current and one for recording voltage (1). The two-microelectrode voltage-clamp technique is well suited for use with cells of large diameter (above 20 µ,m), while the patch-clamp technique offers the advantage of requiring only a single electrode for intracellular current injection and voltage recording from small diameter cells (below 20 µ,m) (2). The use of the double whole-cell recording (DWCR) procedure for quantitative analysis of macroscopic and single-channel gap junctional currents is now widespread and has yielded valuable new information about channel conductances and the regulation of electrical coupling in a variety of tissues (3).
Electrophysiological assessment of epithelia
Authors: Karnaky Karl J
Published: November 2023

Epithelia separate two different environments which they help create and maintain by an assortment of ion transport mechanisms. These mechanisms include the tight junction, one of the hallmarks of epithelia (1). The selective and changeable permeability of the tight junction helps confer unique signatures to the secretions and absorbates of epithelia (2). Electrophysiological techniques applied to epithelia can define actively and passively transported ions. In addition, with these techniques the researcher can reveal the rate of ion transport, the direction of net ionic movement, the identity of transporting cells in heterogeneous epithelia, and, possibly, the identity of ions passing through the paracellular pathway.
Bivariate regression
Authors: Fry John C
Published: November 2023

All biologists will use regression analysis between two variables at one time or another and all statistical packages have commands for performing bivariate or simple linear regression. Whole books have been written about regression analysis, but many are mathematically complex and impenetrable for most biologists. The easiest text I have found is by Chatterjee and Price (1). For more detail Sokal and Rohlf (2) and Rawlings (3) are also useful. These texts should be consulted by readers requiring longer or different explanations. As in Chapter 1, I will use examples analyzed with four statistical packages Minitab, SPSS/PC+ Systat, and Stat graphics. However, in this chapter almost all my sample output will be from Minitab. I will only provide sample output from the other packages when Minitab does not provide the necessary procedures. All four packages and many more besides provide excellent facilities for bivariate regression analysis.