bluuebunny/crossref_metadata_2025_split huggingface dataset:
Migrating worms
Authors: Gillespie S H 
Published: November 2023

Abstract
Toxocara canis is an ascarid parasite of canids. In the dog, ingested eggs hatch in the stomach and invade the intestinal wall where larvae are carried to the liver and are distributed to the body via the bloodstream. Lung migration occurs and larvae are coughed up and swallowed, where larvae develop into adult worms in the intestines of the dog. Eggs passed in the faeces may or may not be fertilized (Plates 3e,f and 4a). This life cycle occurs mainly in younger dogs; over the age of six months, larval development is halted at the L2 stage and larvae migrate in the tissues before becoming dormant. In pregnant bitches, larvae are activated and migrate transplacentally to infect the pups after the 42nd day of gestation. In consequence, almost all pups are infected at the time of whelping (1).
Analysis of sites phosphorylated in vivo and in vitro
Authors: Hardie D Grahame , Campbell david G , Caudwell F Barry , Haystead Timothy A J 
Published: November 2023

Abstract
There are several compelling reasons why one might wish to analyse and identify the exact site and surrounding sequence at which a particular protein is phosphorylated, either in vivo,in isolated or cultured cells, or in purified cell-free systems: (a) Identification of the protein kinase(s) responsible for phosphorylation in vivoor in intact cells. Most proteins are phosphorylated by multiple protein kinases, and one method to identify the physiologically relevant protein kinase is to compare the locations of the sites phosphorylated in intact cells with those phosphorylated by a purified protein kinase in a reconstituted cell-free system. If the sites do not match, this approach conclusively rules out the involvement of that protein kinase, while if they do match this gives strong, although not conclusive, support for the view that the protein kinase is phosphorylating the protein.
Transneuronal mapping of neural circuits with alpha herpesviruses
Authors: Strick Peter L , Card J Patrick 
Published: November 2023

Abstract
The use of alpha herpesviruses for defining functionally interconnected populations of neurones has generated considerable interest in recent years (1). Two of the most attractive aspects of using viruses for circuit definition are the fact that they pass transneuronally and replicate in synaptically linked populations of neurones. Thus, the virus is transported through a multi-synaptic pathway and the signal, (i.e. intracellular concentration of virus) progressively increases with time (Figures 1 and 2). These two attributes are clearly superior to those offered by other neuronal tracers which have been shown to pass transneuronally. Wheatgerm agglutinin horseradish peroxidase (WGA-HRP) and the C fragment of tetanus toxin (CTT) are both known to cross synapses, but they do so in such limited amounts that it is at times difficult to identify synaptic transfer with confidence. For these reasons, there has been a dramatic increase in the number of studies which have utilized herpesviruses to characterize functionally distinct populations of neurones.
Histochemistry of endogenous enzymes
Authors: Vincent S R 
Published: November 2023

Abstract
Enzyme histochemistry is the art of performing biochemical reactions on tissue sections, thereby providing the precise localization of particular enzymes. Given the cellular complexity of the nervous system, histochemical methods have played a key role in the biochemical dissection and mapping of various neurochemically distinct cell types. Enzyme histochemistry, like other histochemical techniques, is always a compromise between preserving enzyme activity and maintaining adequate histological structure. Thus aldehyde fixation is often used for two purposes, to preserve cellular morphology, and to prevent diffusion of otherwise soluble enzymes. However, it must always be borne in mind that such fixation can inhibit or destroy enzyme activity.
Serum-free media for neuronal cell culture
Authors: Butler Michael 
Published: November 2023

Abstract
The first reported work on the growth of cells in vitro was in 1907 by Harrison (1) who was able to suspend an explant of the spinal cord of a frog embryo from a microscope slide. This ‘hanging drop technique’ enabled the growth of the neuronal cells to take place within a fibrin matrix resulting from the application of a drop of lymph fluid. The observed cell growth was supported by the nutrients provided by the supernatant remaining from the clotted lymph.
Correlative electrophysiological and biochemical studies in neuronal cell lines
Authors: Dunn Philip M , Coote Paul R , Wood John N 
Published: November 2023

Abstract
Neuronal excitation is usually evoked by a chemical interaction with a specific membrane-associated receptor that results in an alteration in ion fluxes, a change in the transmembrane potential and a self-propagating wave of depolarization mediated by the activation of voltage-gated ion channels (1). The initial depolarizing event may occur through the direct action of a ligand on a receptor that has intrinsic channel activity, or indirectly through the medium of intracellular second messengers.
The molecular biology of influenza viruses and paramyxoviruses
Authors: Paterson Reay G , Lamb Robert A 
Published: November 2023

Abstract
Orthomyxoviruses and paramyxoviruses are important aetiological agents of disease in man and animals. Each year disease outbreaks caused by these viruses result in extensive morbidity and mortality. In recent years major advances have been made in our knowledge and understanding of the structure and function of orthomyxovirus and paramyxovirus genes and the proteins that they encode. In particular, the complete genome sequences of many strains of influenza A, B, and C viruses and paramyxoviruses have been obtained. The expression of cDNA copies of individual genes has led to the elucidation of coding strategies used by these viruses and has also permitted study of the synthesis and maturation of many virally-encoded proteins in the absence of other virus gene products.
Molecular analysis of immunodeficiency viruses
Authors: Schulz Thomas F , Spire Bruno 
Published: November 2023

Abstract
The rapid expansion of our knowledge of human and animal immunodeficiency viruses over the last decade would not have been possible without the availability of methods developed by molecular biologists. In this chapter we summarize some of the more commonly used molecular biological techniques employed with these viruses. As it would go beyond the remit of this chapter to list every technique that could fall under this definition, we refer the reader to some of the excellent molecular biology manuals (1, 2) for the more basic methods. The term immunodeficiency virus usually refers to animal or human lentiviruses, although a number of other viruses can also cause transient states of immunodeficiency. Table 1 contains a list of these lentiviruses. From a technical point of view, the techniques discussed in this chapter can be applied to all the viruses in this group, although some details (for example tissue culture conditions) may differ with individual viruses or virus strains. Most of the protocols in this chapter are based on our experience with the human immunodeficiency viruses HIV-1 and HIV-2.
Types of growth factor activity: detection and characterization of new growth factor activities
Authors: Mckay I A 
Published: November 2023

Abstract
This book concerns itself with peptide molecules which transmit signals between animal cells. Despite the fact that these molecules may function as growth stimulators and/or growth inhibitors and that they may modulate differentiated functions of cells, they have come to be known collectively as growth factors. Many such factors have already been described (see Appendix J), so it is the aim of this chapter to outline ways of characterizing a new factor with the emphasis on avoiding re-characterization of existing factors. Details of the individual methods involved will be covered in the following chapters or in other books of the Practical Approach series.
Induction of DNA synthesis and cell division in quiescent cells in response to small peptide growth factors
Authors: Corps Anthony N , Brown Kenneth D 
Published: November 2023

Abstract
Among the most frequently used model systems for the study of cell growth control are a number of mouse embryo-derived fibroblastic cell lines, termed 3T3 cells. The terminology reflects the original experiments designed to derive and maintain cells in a non-transformed, non-tumourigenic state, (i.e. cells which depended on the presence of serum for their growth, which did not overgrow each other, and which did not cause tumours when injected into recipient animals). It was found that passaging the cells every three days at 3 x 105cells/5 cm dish maintained the cells in optimum condition by those criteria (1).
Clonal and long-term cultures using human bone marrow
Authors: Coutinho L H , Gilleece M H , Wynter E A De , Will A , Testa N G 
Published: November 2023

Abstract
Much of our current knowledge concerning the regulation of normal haemopoiesis and its alteration in disease has resulted from advances in techniques for culturing human haemopoietic cells in vitro. The establishment of clonogenic assays for progenitor cells in semi-solid culture medium was instrumental in the identification of the haemopoietic growth factors as well as in the characterization of their biological activities. These may be better defined when serum-deprived medium and highly purified cell populations are used (see Chapter 2). In addition, these clonal assays provide quantitative and qualitative means of analysing the haemopoietic progenitor cells in a whole range of clinical settings (1-3).
Imaging gene expression in neural grafts
Authors: Sirinathsinghji D J S , Dunnett S B 
Published: November 2023

Abstract
In recent years considerable attention has been devoted to the development of techniques for the implantation of embryonic neural tissue into the adult mammalian brain as a tool for replacing damaged host tissue and repairing damaged neuronal circuits. Indeed, several studies have shown that embryonic neurones grafted into the mammalian brain can survive, grow, differentiate, and reverse many of the structural, biochemical, physiological, and behavioural deficits associated with experimental or genetic neuronal loss (1). This method thus has immense relevance to the possible treatment of human neurodegenerative disease. In addition, it is a powerful technique for the neurobiologist for the exploration of the basic cellular, receptor, and molecular mechanisms regulating the development and functional organization of specific neuronal systems within the brain.
The role of cellular transcription factors in the regulation of human immunodeficiency virus gene expression
Authors: Nabel Gary J 
Published: November 2023

Abstract
The human immunodeficiency virus (HIV) is dependent on its host cell for the synthesis and processing of viral RNA. Steady-state levels of viral RNA can be regulated by several mechanisms, including the rate of transcriptional initiation, elongation, processing, export, and packaging. Diverse regulatory mechanisms have, therefore, evolved to control viral RNA during HIV replication. These events play a critical role in the regulation of viral replication. Relative to the human genome, the genomic complexity of HIV is relatively small, &lt;0.001% in size. To regulate viral gene expression specifically, the virus has evolved its own regulatory gene products. These viral trans-activators are also dependent upon cellular factors that interact with viral proteins and cis-acting DNA and RNA regulatory elements to further modulate HIV gene expression. These mechanisms of regulation are diverse. For example, the Tat trans-activator affects the ability of a cellular transcription complex to elongate and inhibits premature termination of the HIV transcript (1, 2, Chapter 4). The Rev gene product, on the other hand, does not affect the synthesis of viral RNA but acts with cellular factors on an RNA structure after formation of the primary transcript (3, 4, Chapter 5). For these trans-activators, an intimate association has evolved between host cell factors and viral gene products. These essential trans-activators are synthesized only after viral transcription has been initiated. The regulation of the initiation of HIV transcription also plays an important role in the viral life cycle.
Cell surf ace carbohydrates: cell-type specific expression
Authors: Fukuda Minoru 
Published: November 2023

Abstract
Cell surface carbohydrates are major components of the outer surface of mammalian cells and these carbohydrates are very often characteristic of cell types. Carbohydrate structures change dramatically during mammalian development. Specific sets of carbohydrates are expressed at different stages of differentiation and in many instances these carbohydrates are recognized by specific antibodies, thus providing differentiation antigens (1-4). In mature organisms, expression of distinct carbohydrates is eventually restricted to specific cell types, providing cell-type-specific carbohydrates. Aberrations in these cell surface carbohydrates are associated with various pathological conditions, including malignant transformation.
Carbohydrate recognition in cell-cell interaction
Authors: Lowe John B 
Published: November 2023

Abstract
Mammalian cell surfaces are decorated with complex carbohydrate molecules, also known as oligosaccharides or glycoconjugates. These molecules display a remarkable degree of structural diversity, that is in turn a function of the cell type, or tissue, or particular stage of development of the cell or tissue. Observations demonstrating that cell surface oligosaccharide structure varies with the differentiation state or lineage of a cell suggest that these molecules play important roles in mediating information transfer into and out of the cell.
|Mechanisms of DNA transposition
Authors: Plasterk Ronald H A 
Published: November 2023

Abstract
All organisms studied in any detail have been found to contain transposons, discrete segments of DNA that can move within genomes. Transposons can be viewed as molecular parasites, the smallest units of selection: single (or a few) genes that move around by using all functions of the host (building blocks, energy, the replication apparatus), and that only provide the factors that are needed for the recognition of the border between themselves and their host DNA, and for the initiation of events that result in their own spread within the host genome. The only necessary explanation for their existence is that they have survived, but this does not exclude the possibility that, like many other parasites, transposons could be anywhere on the scale between parasitism and symbiosis, and thus be for their hosts either a nuisance, or an indispensable helper, or both.
| Eukaryotic transposable elements as tools to study gene structure and function
Authors: Kaiser Kim , Sentry John W , Finnegan David J 
Published: November 2023

Abstract
Eukaryotic genomes were once considered invariant. The discovery that they contain transposable elements, powerful agents of genetic change, showed this not to be the case. Transposition into coding sequence is an obvious source of variability. Transposable elements also cause chromosome rearrangement, due to a variety of mechanisms including imprecise excision and exchange between elements at different locations. Although such events normally occur in a more or less random manner, and at low frequencies, it is possible to harness transposable elements as tools for genome manipulation. This is best illustrated by the P element of Drosophila. In our discussion of P, and of similar elements from plants, we hope to indicate what might be achieved in any eukaryotic organism of interest.
Hybridization strategy
Authors: Anderson Margaret L M 
Published: November 2023

Abstract
Nucleic acid hybridization on filters has formed the basis of a range of experimental techniques that have been instrumental in developing our understanding of gene structure and function. The procedure is widely applicable having being used for many years for screening genomic and cDNA libraries, for Southern and Northern blot hybridizations, dot blot hybridizations, and hybrid selection. Techniques are constantly being refined to allow the range of applications to be extended and more recent applications have included genome mapping and sequencing (1) and the detection of mutations in diagnostic medicine (2).
Analysis of gene expression by blotting techniques
Authors: Kim Kwang-soo , Febbraio Maria , Han Tae-Hee , Wessel Thomas C , Park Dong H , Joh Tong H 
Published: November 2023

Abstract
Expression of eukaryotic genes is regulated developmentally, positionally, and temporally. In addition, the pattern of gene expression can be altered significantly by intracellular and extracellular stimuli. This regulation is achieved during transcription and processing of the mRNA product as well as during translation and post-translational modification of the resulting protein. Several major mechanisms are involved, including the limited expression of transcription and translation factors, phosphorylation, the expression of necessary co-factors, and control of RNA and protein degradation. Accurate analyses of specific mRNA transcripts and their protein products are, therefore, essential if one is to understand the mechanisms whereby individual genes are regulated.
PCR MIMICs: competitive DNA fragments for use in quantitative PCR
Authors: Siebert Paul D , Kellogg David E 
Published: November 2023

Abstract
Competitive PCR has emerged as a valuable method for determining the relative levels of mRNAs; for example, the change in mRNA expression levels or to estimate the actual number of mRNA molecules. Perhaps the greatest advantage of competitive PCR is that useful data can be obtained during either the exponential phase or plateau phase of PCR amplification
Construction of cloning and expression vectors
Authors: Hadfield Christopher 
Published: November 2023

Abstract
Numerous different types of cloning and expression vectors have been made for yeast and the majority are widely distributed amongst the international yeast research community. In the main, these are shuttle vectors that are able to propagate, and be selected for, in both yeast and Escherichia coli. This dual host capability has enabled yeast vectors to be constructed on the back of existing E. coli vectors and, in addition, has enabled recombinant derivatives to be made using efficient and powerful E. coli host-vector cloning strategies before introduction of the finished product into yeast.
High efficiency transformation with lithium acetate
Authors: Gietz R Daniel , Woods Robin A 
Published: November 2023

Abstract
The transformation of lithium acetate (LiAc) treated yeast cells with plasmid DNA was first reported in 1983 (1). The procedure was less efficient than transformation of cells converted to sphaeroplasts by treatment with Zymolyase (2, 3), but was simpler and faster. The original procedure, and subsequent improvements reported by a number of workers, involved a pre-incubation of the cells in LiAc, followed by an incubation in LiAc plus plasmid DNA, then by the addition of polyethylene glycol (PEG), and finally by exposure to a heat shock. The yields of transformants with this procedure rarely exceeded 1 × 10/µg plasmid DNA (4), compared with 2 × 105/µg for the sphaeroplast procedure (5). In 1989 it was reported that inclusion of single-stranded carrier nucleic acids (DNA or RNA) in the transformation reaction increased the efficiency of the LiAc procedure dramatically; to 1 x 10 transformants/ µg (6). Further modifications to this ‘LiAc/ssDNA/PEG’ method reduced the time required and increased the efficiency more than 20 fold (7, 8). The current version of the method, described here, is markedly simpler and has yielded up to 2.2 x 107 transformants/µg plasmid DNA.
Protein blotting using polyvinylidene fluoride membranes
Authors: Mansfield Michael A 
Published: November 2023

Abstract
Transfer of proteins from a polyacrylamide gel to a microporous membrane preserves the resolution of the electrophoretic transfer and permits further analysis using a broad array of techniques. Polyvinylidene fluoride (PVDF) was described as a protein blotting substrate in 1986 (1) and was found to be compatible with protocols defined for blotting to nitrocellulose (2). PVDF is a Teflon-type polymer composed of the basic repeating unit shown below Proteins interact with the polymer non-covalently through dipolar and hydrophobic interactions. PVDF is chemically compatible with the aqueous buffer systems used in electroblotting and immunodetection. Since PVDF is resistant to most organic solvents, however, it can withstand harsh chemical conditions in which nitrocellulose membranes dissolve or decompose. For this reason, the methods available for protein analysis on PVDF membranes are much more extensive (Table I; see (3) for review).
Transfer and blocking conditions in immunoblotting
Authors: Van Dam A 
Published: November 2023

Abstract
Every scientist who performs immunoblotting techniques wishes to resolve proteins as distinguishable bands or spots at the site where specific antigen antibody reactions occur. Additionally, no background staining should be obtained on other parts of the blot. Owing to a number of problems, distinct immunoblot patterns are not always obtained, and sometimes it is even difficult to distinguish specific staining from background reactions. These problems are, in the first place, related to the fact that the interaction between the blotting matrix and blotted antigens is not covalent, so that proteins can be lost from the matrix. Secondly, the antibody can often only react with the antigen if it is not denatured too much.
Proteins of the neuronal cytoplasmic and membrane associated cytoskeleton
Authors: Ha Yes Nandini V L , Holmes Fiona E , Roobol Anne , Carden Martin J , Baines Anthony J 
Published: November 2023

Abstract
In this chapter we present a compilation of methods that are of general use in the isolation of some components of the cytoskeleton in brain. The methods chosen illustrate the preparation of proteins that are not only of specific use in the analysis of, for example, neuronal function, but also are of use as archetypes in studies of protein assemblies relevant to a wide variety of cell types. The properties of brain microtubules and brain spectrin are taken to represent paradigms for the activities and role in structural assemblies of the corresponding proteins in non-neuronal tissue. On the other hand, the properties of neurofilaments and synapsin I are those of neurone-specific proteins. A problem with cytoskeletal proteins is that they do not possess defining enzyme activitesspectrin and neurofilament polypeptides, for example, containno known enzyme activites, and although tubulin has GTPase activity, this does not uniquely define the protein. In giving methods for purifying these proteins it is not possible to quote standard units of any activity to ensure that the protein has been correctly identified and purified. In the methods described below, we have therefore relied on describing the expected pattern of polypeptides on SDS-polyacrylamide gel electrophoresis, and have, where appropriate, given commercial sources of antibodies which can be used to test the identity of the purified proteins. In the case of tubulin and neurofilaments, their defining characteristic is their appearance in the electron microscope, and we recommend that microtubule and neurofilament