bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mathematical description of neuronal firing patterns
Authors: Hindmarsh J L , Rose R M 
Published: November 2023

Abstract
The purpose of this chapter is to explain in a simple and direct manner how to build and develop mathematical models of the behaviour of the membrane potential of a neurone. We do this by presenting models of increasing sophistication. In Section 2, a model due to FitzHugh is used to illustrate the main ideas. This is followed in Section 3 by a series of models, each an elaboration of the previous one. The models of these two sections are qualitative in nature and independent of the precise details of the various ionic currents present in the cell.
Almost all the ideas we introduce below are represented graphically. The necessary graphs can be easily reproduced using a microcomputer, and the reader is strongly encouraged to do so. Some notes on the BASIC programs that have been used to produce Figures 6a and 6b are to be found in the appendix to this chapter.
Electrophysiological techniques for studying the quantitative pharmacology of the isolated spinal cord
Authors: Wallis D I 
Published: November 2023

Abstract
The spinal cord from the neonate mammal provides a useful in vitro preparation for investigating the physiology and pharmacology of motoneurones and the pathways that converge onto them. This chapter gives examples of isolated spinal cord preparations from the neonate rat and illustrates the types of experiment that can be conducted.
Generating mosaics by site-specific recombination
Authors: Golic Kent G 
Published: November 2023

Abstract
Does the developmental fate assumed by a cell depend on signals that it received from its neighbouring cells? This is the fundamental question addressed by the study of cellular interaction during development. If cell-cell communication can be implicated in the specification of cell fates then a series of further questions can be asked. Which cells are talking and which are listening? What molecules are involved and how do they work? When are these molecules needed? In organisms in which there are mutations available that alter cell fate these questions can be fruitfully investigated by the analysis of mosaics. There are molecular techniques available that can tell when and where a gene is expressed; genetic mosaics can be used to determine which part of this expression pattern is functionally significant (see also Dudley and Poethig, this volume).
Cell transplantation
Authors: Prokop Andreas , Technau Gerhard M 
Published: November 2023

Abstract
Cell transplantation is a powerful tool for studying cellular interactions during development. It allows the behaviour of cells of known origin in various kinds of environments to be studied. Thus, cell transplantation has been used in both vertebrates and invertebrates to address several types of questions. For example, isotopic and isochronic transplantations of cells have been used to study the developmental potential of cells (1-9). Heterotopic transplantations allow one to test for the regional determination of cells and their ability to communicate with the surrounding tissue (1, 10-12). Heterochronic transplantations allow one to test for the reversibility of the determination of the transplanted cells or for the time period in which particular cellular communication processes are active (13, 14). Using heterogenetic transplantations (transplantation of mutant or transformed cells into wild-type hosts or vice versa) it is possible to test for the interrelations between genetic functions and for the autonomy or nonautonomy of phenotypes (15, 16). Interspecific transplantations of cells have been used to study the functional compatibility of mechanisms that involve intercellular communication (17, 18).
Using the two-hybrid system to detect protein-protein interactions
Authors: Bartel Paull , Chien Cheng-Ting , Sternglanz Rolf , Fields Stanley 
Published: November 2023

Abstract
Protein-protein interactions are essential in almost all biological processes, including replication, transcription, secretion, signal transduction, and metabolism. Thus a central question in the study of any protein is to determine what other proteins are in contact with it. The answer, in the case of oncogene-encoded proteins for example, has provided enormous insights into the problems of cell cycle control and differentiation. It is, therefore, clear that intense research efforts will continue to focus on identifying proteins that interact with some protein of interest, referred to here as the target protein. Current approaches to detect interacting proteins include traditional methods such as co-immunoprecipitation, crosslinking, and copurification through gradients or chromatographic columns (see Midgley and Lane, Chapter 6 of this volume). These biochemical methods have the major disadvantage that interacting proteins are generally known only as bands of a particular relative mobility on a polyacrylamide gel. To progress from these bands to cloned genes is often a difficult undertaking, involving such methods as the initial purification of sufficient protein for amino acid sequencing or antibody production, followed by additional work to screen a library for the corresponding.
A brief history of the cell cycle
Authors: Reed Steven I , Hutchison christopher J , macneill stuart 
Published: November 2023

Abstract
A particular feature of research into the eukaryotic cell cycle is the diverse range of experimental organisms in use in laboratories around the world, ranging from unicellular yeasts, filamentous fungi (Aspergillus),marine invertebrates (e.g. clams and starfish), and flies, to vertebrates such as Xenopus,mice, and humans. In this chapter we briefly review the history of the eukaryotic cell cycle in terms of the organisms and experimental approaches used, and show how diverse species have contributed, and will continue to contribute, to our current understanding of the workings of the cell cycle.
Controlling entry into tnitosis in fission yeast
Authors: Macneill Stuart a. , Fantes peter a. 
Published: November 2023

Abstract
Universal control over entry into mitosis
As described in Chapter 1 the timing of entry into mitosis in eukaryotic cells is determined by the timing of activation of a protein complex (called MPF) containing one molecule of a cyclin-dependent kinase (cdc2) and one of cyclin B. The genes encoding the cdc2 and cyclin B (cdc13) proteins in the fission yeast Schizo-saccharomyces pombewere identified genetically as being required for entry into mitosis long before their biochemical function was known or even guessed at. Similarly, two key regulators of cdc2 function, the cdc25 tyrosine phosphatase and the weel protein kinase, were first identified and characterized genetically in fission yeast. At present, many other elements implicated in the mitotic control network are known only in this organism. Here we review recent advances in understanding the biochemical basis of the regulatory network that controls entry into mitosis in S. pombe,in identifying new elements involved in this regulatory network, and in understanding how entry into mitosis is integrated with other cell cycle events. We begin with a brief introduction to the biology of the fission yeast cell cycle.
RNA-catalysed RNA processi•ng
Authors: Jacquier Alain 
Published: November 2023

Abstract
RNA processing reactions, as most chemical reactions occurring in living cells, are greatly accelerated by enzymatic catalysis. Proteins were, for a long time, the only class of molecules known to support enzymatic activity. The discovery, a decade ago, that several RNA processing events could be catalysed by RNA molecules (1, 2) thus revolutionized our views in several areas of biology and, most particularly of course, in the RNA processing field. These catalytic RNA molecules have been called ‘ribozymcs’.
Simple tips for photomicrography of embryos
Authors: Stern Claudio d. 
Published: November 2023

Abstract
Illustrating the results of experiments both appropriately and attractively is an important aspect of embryological (as of other) research. Here we give some guidelines that should help to decide how to photograph embryos and improve the resulting photomicrographs, concentrating on some common errors. Good microscopy is as important as the camera techniques themselves and we will start by quickly reviewing some of the basic techniques, giving their advantages and disadvantages for some common applications. At the end of this chapter we will give some advice on how to visualize and photograph embryos after specific techniques.
Chick Limb Buds
Authors: Tickle Cheryll 
Published: November 2023

Abstract
Since the pioneering work of Harrison, Zwilling, Saunders, and others, the limb has become one of the classical model systems in which to study cell interactions in development. A considerable body of work in the last few decades has established the basic principles of limb development and regeneration. Amphibians are often used for studying limb regeneration, while the chick limb has been the main source of information about limb development. Experiments on chick limb buds have led to the identification of regions such as the apical ectodermal ridge (AER), zone of polarizing activity (ZPA) and progress zone as key players (for reviews see refs. 1-6). Recently, molecular approaches have started to be combined successfully with more classical experiments (e.g. ref. 7), and localized misexpression of genes achieved through the use of retroviral vectors (8) (see Chapter 20).
Nuclear Transplantation
Authors: Gurdon John B 
Published: November 2023

Abstract
Nuclear transplantation is a procedure by which the nuclear material of a fertilized egg is replaced by that of another cell. The purpose of this procedure is twofold. The primary purpose, and that for which the technique was devised, is to ask whether the genetic material in a somatic cell is functionally equivalent to that of the zygote nucleus. If a somatic nucleus can replace the zygote nucleus in an egg by supporting normal development, this shows that there has been no loss or permanent inactivation of genes in the course of development leading to the formation of the somatic cell in question. Once this result has been achieved, a related question is how the nucleus of a specialized cell can be switched back to an embryonic state so as to express all genes required for normal development. The second and more recent purpose of nuclear transplantation is to create substantial numbers of genetically identical individuals from the nuclei of one embryo. This second aim has possible practical value in propagating animals with a valuable genetic constitution.
Laser Ablation of Cells
Authors: Eisen Judith , Warga Rachel M , Edgar, Lois G , Wood William B 
Published: November 2023

Abstract
In principle, almost any cell that can be visualized with Nomarski DIC optics can be ablated by laser-irradiation. But such optical clarity is a property of the embryos of only a few animal species, such as the nematode, Caenorhabditis elegans, some other invertebrates (sea urchin, annelids, etc.), and fish embryos. In this chapter, we give some basic methods for laser ablation of individual cells in fish and nematode embryos, but the methods are broadly applicable to embryos of other species where cells can be resolved sufficiently clearly in the intact embryo by interference optics.
Introduction of Genes Using Retroviral Vectors
Authors: Price Jack 
Published: November 2023

Abstract
Retroviruses are naturally evolved agents of gene transfer. Because they work under normal physiological conditions, they can be used to introduce genes into cells in vivo. Potentially, therefore, they can introduce genes into embryos over a wide range of developmental stages. The principal developmental study to which they have been applied is cell lineage, where the transferred gene is non-functional; a more recent application is the use of retroviruses as a localized agent of transgenesis.
|Site-specific recombinases and their interactions with DNA
Authors: Johnson Reid C 
Published: November 2023

Abstract
Site-specific recombination reactions are associated with a wide range of biological processes, especially where generation of genetic diversity is a principal goal. For example, regulatory mechanisms involving site-specific inversion reactions have enabled bacteria to evade host immunity systems by regulating the expression of multiple surface proteins (1). Viruses have evolved highly regulated site-specific recombination systems to integrate into, and excise from, host chromosomes (2). These reactions also play important roles in the partitioning of chromosomes (3, 4) and in the selective activation of genes during terminal differentiation in at least two different prokaryotic systems (5, 6). In eukaryotes, site-specific recombination reactions are responsible for mediating assembly of immunoglobulin and T-cell receptor gene fragments, though progress on the biochemical characterizations of these reactions has been slow (7). The FLP system in yeast, however, has been extensively studied (8) and will be discussed below.
|The HMG-box domain
Authors: Bianchi Marco E 
Published: November 2023

Abstract
The HMG-box is a new kind of eukaryotic protein domain involved in DNA binding. It has been discovered in a number of chromatin proteins, general transcription factors, and transcriptional regulators which control tissue differentiation and sex determination. The most unusual feature of HMG-boxes is that they recognise and/ or produce primarily conformational features in DNA, even if some members of this family can also bind sequence-specifically to particular sites on linear DNA. The diverse set of HMG-box-containing proteins (which we will call ‘HMG-box proteins’ from now on) appear to be involved in a broad spectrum of DNA transactions, ranging from transcription to DNA packaging in chromatin. Such versatility is uncommon and suggests that the ability of HMG-boxes to manipulate DNA can be used in similar ways in highly different functional contexts.
Measurement of mitochondrial protonmotive force
Authors: Brand Martin D 
Published: November 2023

Abstract
Protonmotive force is the central intermediate in bioenergetics. Mitochondria normally produce it by pumping protons from the mitochondrial matrix across the inner membrane during electron transport. Protonmotive force drives the synthesis of ATP by the ATP synthase as well as several other important bioenergetic reactions such as ion transport, transhydrogenation, and proton leak-mediated heat production.
Identification, functional assessment, and quantitation of receptors and membrane regulatory proteins whose ligands are C3 and C4
Authors: Nickells Michael W , Atkinson John P 
Published: November 2023

Abstract
Activation of the complement system leads to the deposition of C3b and C4b on the surface of activators. C3b and C4b in turn are ligands for complement receptor type 1, CR1 (Table 1) which is primarily expressed on peripheral blood cells and mediates the binding of the activators to these cells. C3b and C4b may then be cleaved specifically by the serum serine protease, factor I. This reaction occurs only in the presence of a cofactor protein such as CR1 or factor H (see Figure 1). The resulting proteolytic fragments of C3b and C4b are now poorly recognized by CR1 but serve as ligands for additional complement receptors, namely CR2, CR3, and CR4. These receptors are expressed on B lymphocytes or phagocytic cells.
Southern blotting of cytokine genes
Authors: Diaz M O , Mckeithan T W 
Published: November 2023

Abstract
Southern blot analysis of genomic sequences (1) is one of the basic tools of molecular genetics. This technique is principally used to determine the physical organization of particular DNA sequences for which a probe is available. Its power of resolution has recently been extended up into the megabase (106 base-pair) level by the technique of pulsed field gel electrophoresis (2). In many cases, the organization of large gene families, and the distance between particular cytokine genes have been determined using this technique.
Polymerase chain reaction to quantitate cytokine Mrna
Authors: Platzer Cornelia , Blankenstein Thomas 
Published: November 2023

Abstract
Cytokines display their function preferentially at local sites, occurring transiently and in low concentrations. For more effective intervention in pathophysiologic processes mediated by cytokines it is important to study their complex cross-regulatory network in vivo. Therefore, it is necessary to quantify cytokines in local sites of expression. Detection of the protein is hampered by usually low production of cytokines, by their short half-life in vivo and by the lack of specificity of certain antibodies for intracellular estimation. Consequently, analysis of mRNA has been widely used as substitute for studying variations in local cytokine levels. However, conventional methods of mRNA analysis such as ‘Northern’ and ‘dot blot’ hybridization, and nuclease protection mapping are not sensitive enough to detect mRNA in samples limited by low cell number or low copy-number per cell. Moreover, these methods permit only crude quantification. Thus, polymerase chain reaction (PCR) strategies have been developed that allow quantification of cytokine mRNA at a very sensitive level. Various quantitative RT-PCR procedures have been reported, most relying on the use of external standards and comparing products generated in separate reactions. However, because of the exponential nature of the PCR reaction small variations in the amplification efficiency may result in considerable changes of product yields. In addition, the amount of product can reach plateaux during later stages of the reaction due to consumption of PCR compounds or generation of inhibitors. These problems can be overcome by the use of internal controls in competitive PCR as has been employed by several groups (1–6).
Two-dimensional gel electrophoresis for purification, sequencing, and identification of cytokine-induced proteins in normal and malignant cells
Authors: Smith Diana M , Tran Huu M , Epstein Lois B 
Published: November 2023

Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D PAGE) permits high resolution and purification of individual proteins from complex mixtures of proteins. Proteins are separated first according to their charge, employing isoelectric focusing (IEF), and then in the second dimension, according to their molecular mass. 2D PAGE is unequalled in its ability to simultaneously resolve hundreds of proteins from cellular extracts and at the same time provide data on their isoelectric point (pl), molecular mass (Mr), electrophoretic pattern, and relative abundance (1–3). Thus, a large amount of global information concerning the regulatory effects of cytokines on the expression of multiple individual proteins can be obtained in one experiment. 2D PAGE, computer-based analysis of gels and the more recent advances in protein microsequencing technologies, coupled with the capability of searching protein databases for homologous proteins, permits investigators working in the field of cytokine research to answer basic and complex questions about the actions of these important regulatory molecules. For example, it is possible:
Antiviral activity of cytokines
Authors: Lewis John A 
Published: November 2023

Abstract
A variety of biological materials exhibit the ability to induce an antiviral state in cells. To date the best known antiviral agents are the interferons (IFNs), a family of proteins and glycoproteins which are synthesized by virus infected cells or by cells treated with various chemicals and are capable of inhibiting cell-growth as well as inhibiting virus replication and modulating immune responses. Certain other cytokines have been reported to show antiviral properties (1, 2) but in general these effects have not been investigated in depth and the mechanisms underlying such responses are not understood. Assays for specific cytokines are usually of two kinds: bioassays which measure the potency of a preparation are generally based on some specific response of cells to the agent of interest while enzyme-linked immuno-absorbent assay (ELISA) procedures offer a simple and usually sensitive means of measuring the mass of the substance. This chapter describes general procedures for assaying antiviral responses based on our experience with IFNs. Further procedures are described in Chapter 21 and a companion volume (3). These methods can be readily adapted for other cytokines with suspected or demonstrated antiviral activity.
The generation and quantitation of cell-mediated cytotoxicity
Authors: Grimm Elizabeth , Loudon William 
Published: November 2023

Abstract
Cell-mediated cytoxicity (CMC) is defined as the process by which a cell of the immune system directly kills another cell. CMC is composed of a specific series of events occurring between an effector cell (lymphocyte or monocyte) and a susceptible target cell which ultimately results in the delivery of a ‘lethal hit’ by the effector to the target cell. An obligate event in CMC, which distinguishes it from other modes of immunologically mediated target cell killing (e.g. complement-mediated cytolysis) is intimate cell membrane contract between the effector and the target, referred to as conjugate formation. This brief chapter will be restricted solely to the description of lymphocyte mediated CMC systems. Many excellent reviews cover the complicated processes which encompass effector cell-mediated recognition, conjugate formation, triggering, and delivery of the lethal hit ultimately resulting in the death of the specific target (1, 2).
Cytokine regulation of endothelial cells
Authors: Allavena P , Dejana E , Bussolino F , Vecchi A , Ani A Mantov 
Published: November 2023

Abstract
Endothelial cells (EC) have long been considered a ‘passive’ lining of blood vessels, endowed with negative properties, the most important one being that of representing a non-thrombogenic substrate for blood. As such, EC were viewed to participate in tissue reactions essentially as targets for injurious agents. The possibility of isolating and culturing EC from various tissues gave the tools for studying their complex reactions to a variety of activating stimuli. EC have, in this way, emerged as active participants in many physiological and pathological processes. It is now evident that haemostasis, inflammatory reactions, and immunity involve close interactions between immunocompetent cells and vascular endothelium. In particular, the ontogeny and function of white blood cells require an intimate relationship with vascular EC. Cytokines are mediators of these complex bidirectional interactions between leukocytes and vascular elements (for review see 1, 2).
Biological assays for haemopoietic growth factors
Authors: Testa N G , Heyworth C M , Lord B I , Wynter E A De 
Published: November 2023

Abstract
The aim of this chapter is to summarize in vitro standard assays used to investigate the myeloid growth factors interleukin-3 (IL-3), granulocyte-macrophage colony-stimulating factor (GM-CSF), granulocyte colonystimulating factor (G-CSF), macrophage colony-stimulating factor (M-CSF), and erythropoietin (Epo). Such methods are illustrated by experimental protocols using murine cells, and with selected examples using human bonemarrow cells.