bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitroassembly of steroid receptor-Hsp90 complexes
Authors: Smitii D F 
Published: November 2023

Abstract
Receptors for the steroid hormones—oestrogens, androgens. progesterone, glucocorticoids, and mineralocorticoids-typically exist in heteromeric complexes prior to binding hormone (for a recent. comprehensive review s&lt;:C ref. 1 ). After hormone binding or certain non-hormonal signals. the receptor monomer dissociates from complexes and undergoes a series of biochemical changes that lead to its activation as a transcription factor. In early studies of steroid receptors, the un activated receptor was commonly observed to migrate as an 8--10S complex by density gradient centrifugation while the activated receptor migrated at 4-5S, the approximate i/e of a receptor monomer or dimer.
The functioning of molecular switches in three dimensions
Authors: Wittinghofer Alfred 
Published: November 2023

Abstract
Two major groups of GTP-binding proteins have been identified. The first is rather small and includes FtsZ and tubulin, both of which polymerize to form fibre-like structures. The second is a major class and consists of many families or superfamilies sharing common sequence motifs and a common core structure. These are referred to as GTP-binding proteins or GTPases and they act as regulatory molecules in all eukaryotic cells (1). The common core structure is relatively well conserved within but not necessarily between families. The major families are described in the first eight chapters of this book and include the protein biosynthesis factors such as elongation factors Tu (EF-Tu) and G (EF-G) and their mammalian homologues EF-la and EF-2, the superfamily of Ras-related proteins, the a subunits of heterotrimeric G proteins, the signal recognition particle and its receptor together with the bacterial counterparts Ffh and FtsY, and the dynamin/Mx type of proteins (2, 3). In addition to these two groups there are a few GTP-specific metabolic enzymes, such as adenylosuccinate synthetase or PEP-carboxykinase, but these have no sequence conservation either between each other or to the proteins mentioned above, and will not be considered here any further. Although the protein biosynthesis factors were the first GTP-binding proteins to be discovered and many ground-breaking biochemical and structural studies have been carried out on these, this chapter will focus primarily on small GTP-binding proteins and G proteins since these are more closely related to each other and their biology in eukaryotic cells has been studied intensively in recent years. Structural aspects of GTP-binding proteins have been dealt with in earlier reviews (4, 5).
Toxins that affect neurotransmitter release
Authors: O’kane Cahir J , Schiavo Giampietro , Sweeney Sean T 
Published: November 2023

Abstract
As a perceptive observer once remarked, given enough genetic variation, evolution can select for machine-gun resistance in dogs. Less surreally, one outcome of evolutionary arms races between predators and prey has been the evolution of toxins that can immobilize their victims effectively and in small amounts, by interfering with synaptic transmission. A happier outcome is that some of these toxins have greatly aided our understanding of the roles of several key synaptic proteins that function in neurotransmitter release.
Dissecting the molecular mechanisms of neurotransmitter release in Drosophila
Authors: Pennetta Giuseppa , Wu mark N , Bellen Hugo J 
Published: November 2023

Abstract
Most intercellular communication in nervous systems relies on the release of neurotransmitters at chemical synapses. A detailed understanding of the presynaptic mechanisms underlying neurotransmitter release may not only provide basic insights into regulated secretion, but may also help us in the design of therapeutic agents to modulate this process. It has become apparent in the past five years that the vast majority of the proteins implicated in neurotransmitter release are extremely well conserved in the animal kingdom. Hence, model systems amenable to sophisticated genetic analyses such as C. elegans and Drosophila, are playing an important role in improving our understanding of the function of these proteins in vertebrates.
Representational difference analysis of cDNA
Authors: Hubank M , Schatz D G 
Published: November 2023

Abstract
Accurate analysis of gene expression has become achievable in recent years thanks to the development of a variety of sophisticated techniques (1). In this chapter we describe the polymerase chain reaction (PCR)-based subtractive hybridization technique of cDNA representational difference analysis (cDNA RDA). cDNA RDA can be used to identify genes whose expression differs between two or more populations, and unlike gene array approaches. requires only basic laboratory equipment. cDNA RDA is a flexible, relatively inexpensive, and highly effective technique in which target cDNA fragments are sequentially enriched by favourable hybridization kinetics and subsequently amplified by PCR. The positive selection of differences and removal of common genes targets identifi cation to only those genes which differ between populations, resulting in great sensitivity, and allowing application of the technique to very low amounts of starting material, including fluorescence-activated cell sorter (FACS) purified populations of cells.
Bacteriology of normally sterile body fluids
Authors: Murphy Olive , Freeman Roger 
Published: November 2023

Abstract
The detection of micro-organisms in a normally sterile body fluid has important diagnostic, therapeutic, and prognostic implications. Whilst culture of the infecting bacteria will allow identification and antibiotic sensitivity testing to be carried out, these infections are often serious and a rapid diagnosis is required to ensure correct chemotherapy. Various strategies have been adopted to accelerate the diagnosis with the development of rapid culture and non culture techniques. The recovery of a bacterium from these specimens should always be considered significant until proven othe1wise. Organisms should be identified to species level; not an arduous task as most infections are caused by a single species. This chapter describes current methods for the examination of the various categories of normally sterile body fluids and interpretation of these data.
Protein folding monitored by mass spectrometry
Authors: Robinson Carol V 
Published: November 2023

Abstract
Mass spectrometry (1) is one of the more recent techniques to be applied to protein folding (2, 3). Much of the excitement surrounding its application derives from its ability to distinguish populations of folding intermediates. To obtain information that will distinguish protein molecules containing different amounts of secondary structure during a folding reaction, it is necessary to introduce a label. The pulse-labelling approach, developed for use in conjunction with NMR, described in Chapter 3, is ideally suited since the mass of protons and deuterons differ. Measuring the mass of the protein therefore reveals different amounts of protons and deuterons, on the basis of which partially folded states can readily be identified, since they contain numbers of deuterons intermediate between the numbers present in the unfolded and fully folded states. The challenge for mass spectrometry is to maintain the secondary struc ture during the ionization of the protein so that the label in solution is retained in the gas phase. Elcctrospray ionization (ESI-MS) is the method of choice since it produces multiply charged gas-phase ions by solvent evaporation from protein molecules in solution, with little perturbation of the secondary structure.
Assembly of multi-subunit structures
Authors: Seckler Robert 
Published: November 2023

Abstract
Many cellular proteins are oligomers of identical or different polypeptides, and in most cases, the biological activity of such proteins depends strictly on their quaternary structure. Modifying the assembly of such homo-oligomeric or hetero-oligomeric proteins could be a very specific and efficient way of drug targeting (1-3). This would be greatly facilitated by knowledge about the structural basis of subunit interface stability and of oligomer assembly mechanisms. The Protein Data Bank of three-dimensional structures now contains more than 2000 entries of oligomeric proteins and a number of very large multisubunit structures have been determined in recent years (Table 1). The folding and assembly pathways of many oligomeric proteins have been characterized over the past three decades (4-6) and equilibrium dissociation and unfolding transitions have been analysed for a number of dimeric and a very few higher-number oligomeric proteins (7, 8).
Cellular functions of molecular chaperones
Authors: Leroux Michel R , Hartl F Ulrich 
Published: November 2023

Abstract
Proteins are faced with the potential problems of aggregation and denaturation throughout their existence. First, they are synthesized on ribosomes as unfolded polypeptide chains that must reach their stably folded conformations, either as monomers or oligorneric species, or else be eliminated on the basis that they cannot serve useful purposes in the cell. This is no easy task, given that the aggregation-prone nascent polypeptide chain cannot fold to its native state until the complete protein (or individual protein domain) is freed from the ribosome. Secondly, the cellular environment is densely populated with macromolecules that increase the risk that the nascent polypeptide will become entangled with other cellular components and aggregate rather than fold. After their biogenesis, proteins must fulfil their cellular functions in limited time spans, within an environment that is highly regulated but may undergo fluctuations in temperature and chemical composition (due to exposure to external agents or to disease, for example). Such cellular insults can cause irreversible damage to proteins and consequently shorten their life span. Whether due to impaired function or to the time for natural turnover, the culminating point of a protein’s life is invariably to be unfolded and minced back to basic constituents by the cellular proteolytic degradation machinery.
Protein glycosylation
Authors: Ashford David A , Platt Fran 
Published: November 2023

Abstract
The most common co- and post-translational modification of eukaryotic proteins is the covalent attachment of oligosaccharides. The vast majority of cell surface and secreted proteins are glycosylated, as are the envelope proteins of many viruses. It is now clear that the presence of glycans on glycoproteins affects both the structural and functional properties of the protein, such as protein folding and conformation, stability to denaturation, solubility, and resistance to proteolysis as well as key biological properties such as receptor binding, modulation of enzyme activity, and cellular recognition events (1-5). This chapter is intended as a guide to the analysis of the glycosylation of proteins and to techniques for the manipulation of protein glycosylation. A previous title in the Practical Approach series (6) and other recent books and articles (7-10) have covered glycobiology, glycosylation, and carbohydrate analysis more extensively and they (and the references they contain) can provide more detail for readers who wish to know more.
Cell surface 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 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 (1-6). 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.
Diseases-with deficiencies in asparagine-linked glycosylation
Authors: Schachter Harry 
Published: November 2023

Abstract
The study of human disease, particularly of congenital disease, has traditionally provided a rich source of insight into biochemical pathways and their functions. The field of glycobiology has long been plagued by many unanswered questions concerning the biological functions of protein glycosylation. As described in other chapters of this book, a series of discoveries over the past 25-30 years has provided some answers. Human disease has contributed greatly to this enlightenment (1, 2). Table 1 lists six autosomal recessive diseases in which a defect in the synthesis of Asn-linked glycans (N-glycans) has been clearly demonstrated. Since at least 0.5-1% of the transcribed human genome is devoted to the production of proteins involved in the synthesis, degradation and function of glycoconjugates (3), many other such congenital diseases may exist. This chapter will focus on three of these diseases which have proved beyond any doubt that N-glycans are essential for normal human development, carbohydrate-deficient glycoprotein syndromes types I and II (or congenital disorders of glycosylation, CDG I and CDG II, as they are now called) in section A of the chapter and hereditary erythroblastic multinuclearity with a positive acidified serum lysis test (HEMPAS, congenital dyserythropoietic anemia type II) in section B of the chapter.
DNA pooling methods for association mapping of complex disease loci
Authors: Barcellos Lisa F , Germer Soren , Klitz William 
Published: November 2023

Abstract
The rapid development and application of highly informative microsatellite markers throughout the human genome has greatly facilitated the identification of disease loci in hundreds of rare Mendelian disorders. Utilization of large multigenerational pedigrees with multiple affected individuals is a proven strategy for isolating chromosomal regions containing disease genes using microsatellite markers and traditional lod score linkage analysis. Linkage studies are often followed by association studies to further define the candidate region and to identify the putative disease gene. Linkage disequilibrium, the basis of marker associations, is typically found within a distance of 500 kb, about 0.5 (cM), although, in general, this distance may vary considerably according to population history, across different regions of the genome, and with marker type (1–4). Disease genes mapped to date, however, have shown linkage disequilibrium with markers sufficiently close to the disease gene to guide discovery of the disease locus. Examples of these successes include cystic fibrosis, Huntington disease, Wilson disease, Batten disease, Friedreich ataxia, myotonic dystrophy, torsion dystonia, hereditary haemochromatosis, diastrophic dysplasia, adult onset polycystic kidney disease, familial breast cancer, and many others.
Preparation of lymphocytes and identification of lymphocyte subpopulations
Authors: Plebanski Magdalena 
Published: November 2023

Abstract
This chapter provides the common methods used to isolate lymphocytes and accessory cells from humans and animals (see Section 2), handle them after recovery (see Sections 3 and 4) and, if necessary, sub fractionate them (see Sections 5 and 6). It provides general advice as to which methods may be best used for the particular objectives of your experiment, and cross-references to methods throughout the book. It is common when using a new method to follow it precisely. But what if your house is on fire while you are in the middle of purifying a lymphocyte subpopulation? Should you risk leaving your precious cells on the bench? To help avoid some dilemmas, in addition to standard methods, this chapter aims to provide a measure of the adaptability of different experimental procedures.
Immunohistochemistry of lymphoid organs
Authors: Biddolph Simon c. , Gatter kevin c. 
Published: November 2023

Abstract
Immunohistochemistry is a technique for localizing and identifying cellular or tissue components (antigens) by means of an antigen-antibody interaction, the site of the interaction being identified by the application of an appropriate labelling system. This technique plays an important part in diagnostic cellular pathology and biomedical research, and this chapter describes in detail the preparation of lymphoid cells and tissues for immunohistochemistry. It outlines the most frequently used labelling systems, and gives full details of the systems we find most useful in our laboratory. The distribution of different lymphocyte subpopulations in lymphoid tissue is also described.
Human CD4 culture
Authors: Gorak-stolinska P , Wallace d. , Kemeny a. Noble d. M 
Published: November 2023

Abstract
Advances in technologies to isolate, grow, and clone CD4 T cells of chosen specificities have facilitated our understanding of the generation of T-cell receptor diversity and the role of the MHC class I and class II gene products in antigen presentation (1-3). Antigen-specific T-cell lines have been used in the immunotherapy of cancer (4) and in the study of the immunopathology of chronic viral infections (5). Using T-cell clones, the rules governing the T-cell recognition of proteins and synthetic peptides are now being understood, thereby facilitating the production of synthetic vaccines that elicit either class Ior class II-restricted T-cell immunity (6).
Analysis of DNA-general methods
Authors: Ormerod M G 
Published: November 2023

Abstract
The measurement of DNA was one of the first and is still one of the most wide spread applications of flow cytometcy. Malignant cells are frequently aneuploid and there have been many studies of the possible prognostic significance of ploidy in human tumours. The content of DNA also gives information about the cell cycle, so that this measurement can be of value in cell biology. In particular, it can yield useful information about the action of cytotoxic drugs. The measurement of DNA may also be combined with estimation of an antigen, so that the expression of a particular protein through the cell cycle may be measured or, in a cell mixture, the ploidy or cell cycle of a particular class of cell estimated (see Chapter 5, Section 11, and Chapter 9).
All the established methods use dyes which bind specifically and stoichio metrically to nucleic acids and whose fluorescence is enhanced on binding. The properties of the more important of these compounds are described in Chapter.
Genome analysis in flamentous fungi
Authors: Farman Mark L 
Published: November 2023

Abstract
Fungal genome analysis is an extremely broad topic in the sense that the isolation of most fungal genes cloned to date was made possible by using techniques to analyse and manipulate the fungal genome. In this chapter I have focused on methods for genetic and physical mapping of chromosomes and large chromosomal fragments, as might be applied in the analysis of chromosome structure and for map-based cloning of genes. The first sections outline approaches and methods for mapping chromosomes and analysing intact chromosomal DNAs, while the later sections cover the construction and screening of bacterial artificial chromosome (BAC) libraries as a means of isolating and propagating large chromosome fragments for more detailed analyses. Many of the protocols provided are useful not only in chromosome walking studies but can also be applied or adapted for other uses, including isolation of genes from libraries.
Cell biology of the duplication cycle in fungi
Authors: Momany Michelle 
Published: November 2023

Abstract
Filamentous fungi undergo an ordered series of events during growth and division. These events include mitosis, periods of isotropic and polar growth, cytoskeletal rearrangements, and partitioning of cytoplasmic contents via septa (1). Because the cells within a hypha do not physically separate from one another these events are known as a ‘duplication cycle’ rather than a cell cycle.
Chromosome staining and banding techniques
Authors: Benn P A , Tantravahi U 
Published: November 2023

Abstract
Diagnostic cytogenetic laboratories routinely base their results on the analysis of banded chromosome preparations with band resolution levels of 400-650 bands per haploid chromosome set. Most laboratories use Giemsa banding as their primary technique and subsequently apply a variety of other staining methods or FISH to further characterize abnormal or unusual findings. In this chapter we review the chromosome staining methods available.
In many instances, FISH can complement or provide an efficient and appropriate alternative to the staining methods described. For example, the centromeric regions and telomeres can be readily distinguished by chromosome staining. However, FISH can also detect these regions and the use of a chromosome-specific centromere or subtelomere FISH probe is the preferred approach when there is a particular candidate chromosome under consideration as the source of an abnormality. The reader should refer to Chapter 6 for additional information on currently available FISH probes. Staining and banding is usually quicker and cheaper but lacks the specificity of Fish.
In situ hybridization
Authors: Leitch A R , Lim K Y 
Published: November 2023

Abstract
Gall and Pardue (1969) and John et al. (1969) were the first to localize nucleic acids directly to biological material (1, 2). They used radioactively labelled RNA to detect ribosomal DNA (rDNA) in cytological preparations. Since then, and particularly since the early 1990s, the uses of the method have exploded, so much so that it is now commonplace to find the method being used in both molecular and cell biology experiments. Indeed in situ hybridization, which can be used to localize DNA or RNA directly to biological material, should now be considered as routine as Southern or Northern hybridization. For further advice beyond this chapter and relating to the localization of DNA in situ, readers are welcome to contact either Dr Leitch or Dr Lim and for RNA in situ, either Dr Webb or Dr McFadden.
Introduction to phage biology and phage display
Authors: Russel Marjorie , Lowman Henry B , Clackson Tim 
Published: November 2023

Abstract
Display of peptides and proteins on filamentous phage-phage display-is an in vitro selection technique that enables polypeptides with desired properties to be extracted from a large collection of variants. A gene of interest is fused to that of a phage coat protein, resulting in phage particles that display the encoded protein and contain its gene, providing a direct link between phenotype and genotype. This allows phage libraries to be subjected to a selection step (e.g. affinity chromatography), and recovered clones to be identified by sequencing and re-grown for further rounds of selection. Since the initial description of the approach by Smith (1), it has become established as a powerful method for identifying polypeptides with novel properties, and altering the properties of existing ones (for reviews, see 2-5).