bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular assays for Rev
Authors: Malim M H 
Published: November 2023

Abstract
The human immunodeficiency virus type-1 (HIV-1) Rev trans-activator is a nuclear phosphoprotein absolutely essential for virus replication. It is expressed from fully spliced (∼ 2 kb) viral mRNAs and is required for the expression of viral proteins, e.g. Gag, Pol, and Env, from the unspliced ( ∼ 9 kb) and singly spliced (∼ 4 kb) mRNAs. The cis-acting target for Rev, the Rev response element (RRE), is an elaborate RNA stem and loop structure that is located within the env gene and is therefore present in all 9 kb and 4 kb transcripts. Although Rev has been the focus of considerable research effort in recent years, its precise mechanism of action still remains elusive; specifically, models invoking the inhibition of splicing, the activation of nucleocytoplasmic RNA transport, the stabilization of RNA, and the induction of translation in the cytoplasm have all been proposed (reviewed in refs 1 and 2).
Vpu
Authors: Cohen E A , Gottlinger H G 
Published: November 2023

Abstract
The vpu gene in the central region of the HIV-1 genome partially overlaps the env reading frame and is predicted to encode a protein of 81 amino acids with a hydrophobic N-terminus and a hydrophilic C-terminus. Vpu is unique to HIV-1 and is absent from HIV-2 and SIV (1). Biochemical studies have shown that Vpu is a phosphorylated type I integral membrane protein and is capable of forming homo-oligomers (2, 3). Immunofluorescence and immune electron microscopy studies have demonstrated that Vpu is concentrated in the Golgi apparatus and in endosomal vesicles (4, 5). Vpu can also be localized to the cell membrane, but does not accumulate there, suggesting that it may be recycled between different cellular compartments (5). Vpu is not incorporated into the virion.
Generation of HLA-specific human monoclonal antibodies
Authors: Pistillo Maria Pia , Ferrara Giovanni Battista 
Published: November 2023

Abstract
HLA class I and class II antigens encoded in the major histocompatibility complex (MHC) are polymorphic membrane glycoproteins whose function is to bind immunogenic peptides inside the cell and transport them to the cell surface, where they can be presented to specific T cells. The interaction between T cell receptor, HLA molecules, and the presented peptides is essential for self and non-self discrimination and for the generation of immune responses. The earliest approaches used to define the polymorphism of HLA molecules were essentially serological based on the use of conventional (polyclonal) antisera derived from polytransfused patients, multiparous women, skin graft recipients, or from planned immunization of healthy volunteers (1-3). Such sera frequently reacted not only with cells carrying the immunizing HLA molecule, but also with cells carrying antigens controlled by other HLA alleles at the same locus. This finding was mainly due to the antibody complexity for the presence of several antibody populations that recognized different epitopes of the HLA molecule and (or) the same epitope with different affinities.
Assembly of MHC molecules: requirements of glycosylation, oxidized glutathione, and peptides
Authors: Ribaudo Randall K 
Published: November 2023

Abstract
The ordered assembly of multisubunit proteins such as MHC molecules from their component chains is a fundamental process in the generation of functional complexes such as receptors, signalling complexes, and presentation molecules. Typically, these processes involve not only the constituent chains which make up the mature complex, but also rely on the action of chaperones, and other accessory proteins. Assembly of the two chains of class I MHC molecules occurs in the endoplasmic reticulum and is dependent on the simultaneous presence of the polymorphic heavy chain, and the nonpolymorphic light chain, 132-microglobulin. Careful pulse chase analysis has demonstrated that the two chains rapidly associate in the endoplasmic reticulum (1), and remain there associated with the molecular chaperone calnexin until they acquire an appropriate peptide (2-5). At this point the trimeric complex can exit the ER and traverse the golgi to the cell surface. From the time of initial translocation of the independent chains to the ER to their final appearance on the cell surface, domains fold, disulfide bonds form, carbohydrate residues are added, and peptide is acquired.
Derivation and analysis of MHC transgenic mice
Authors: Sponaas Anne-Marit , Mellor Andrew 
Published: November 2023

Abstract
Transgenesis is the term given to the process whereby cloned DNA is introduced into the germline of a host organism so that it becomes stably integrated into host chromosomes and is inherited from one generation to another. Procedures making transgenesis possible in mice were worked out in the early 1980s. Immunologists have been particularly active in exploiting the potential of this new genetic approach for studying immunological phenomena.
Deuterated vitamin E: measurement in tissues and body fluids
Authors: Burton Graham W , Daroszewska Malgorzata 
Published: November 2023

Abstract
Vitamin E, being the major (≥90%) lipid-soluble, chain-breaking antioxidant in mammalian tissues and body fluids (1–3), is important for the in vivo protection of lipid membrane and lipoprotein structures against free radical lipid peroxidation. The most abundant forms of vitamin E in foodstuffs are n- and γ-tocopherols (α-T and γ-T; Figure 1). α-T, the most biologically active form of vitamin E, is not only the most efficient radical-trapping scavenger (i.e. chain-breaking antioxidant) among the tocopherols but also one of the best in the entire class of simple phenolic antioxidants (4, 5).
Measurement of antioxidant gene expression
Authors: Bingle Colin D 
Published: November 2023

Abstract
As the reader will have already seen in the rest of this volume, the measurement of levels of antioxidant proteins using a variety of functional assays can yield valuable information to the researcher. To gain a better understanding of the processes regulating levels of antioxidant proteins within a particular experimental system it is becoming clear that studies aimed at investigating regulation at the genetic level are increasingly important. The present chapter details a number of basic protocols which should allow the researcher new to molecular biology to begin to study the steady-state levels of antioxidant gene expression. Such protocols have been used for example to study developmental regulation of antioxidant proteins (1) and their induction by hyperoxia (2), ozone (3), and inflammatory mediators (4). These protocols are by no means exhaustive and in depth discussion of the methods and theory of RNA analysis are given in references 5 and 6. Measurement of steady-state RNA levels also opens the way to further studies of the transcriptional status of antioxidant genes using techniques which allow direct analysis of the genes of interest.
Quality assurance in immunodiagnostics
Authors: Bullock David g. , mackenzie finlay 
Published: November 2023

Abstract
The primary function of immunodiagnostic investigations, as with any healthcare laboratory investigation, is to provide the clinician with analytical data obtained from examination of specimens submitted from patients and to assist in interpreting these results, in order to assist in diagnosis and control of therapy for the individual patient, for research or for public health purposes. Quality assurance is a global term to describe those means of ensuring that the results being issued from a laboratory are dependable and sufficiently accurate and precise to allow decisions to be taken with confidence, i.e. that the service is fit for the purpose. If such confidence is lacking, additional costs will accrue, not only in terms of inappropriate resource utilization through repeat testing etc., but also suffering of individual patients and, in some cases, the entire community. QA measures are not a luxury or optional extra, but must be an integral part of the investigational process in providing an appro priate and effective clinical service.
Introduction
Authors: Smith Deborah F , Parsons Marilyn 
Published: November 2023

Abstract
The eukaryotic parasites are a diverse group of organisms that range from some of the most ancient single-celled species (e.g. Giardia lamblia) to the cytologically complex metazoan helminths. Despite this extreme diversity in body form, all endoparasites share the common features of living within and exploiting a host organism. This exploitation has resulted in the evolution of some remarkable adaptations at the biochemical level: many parasites have dispensed with whole metabolic pathways, while developing novel strategies for the evasion of host defences. In addition, complex mechanisms have evolved to facilitate transmission of parasites to new hosts. Typically, parasites take advantage of the relationships between two species to facilitate transmission: for example, the mosquito takes a bloodmeal from a malarious individual and thereby becomes infected with the parasite. Transmission is not passive, but rather involves parasite development. Therefore most parasites undergo complex, multiphasic life cycles that can involve extracellular and intracellular stages and, for unicellular parasites, maintenance as actively dividing populations or as dormant, non-dividing cysts.
Protein recognition of specific DNA and RNA binding sites
Authors: Stockley Peter G 
Published: November 2023

Abstract
Facetiously, it has been said that there are only two substantive problems in biology. These are: one, to understand how protein molecules recognize and interact with nucleic acids, and, two, to understand the consequences thereof! This is obviously a massive over-simplification, although it does contain a grain of truth. This chapter will address the first of these problems whilst the remainder of this book will deal with aspects of the second. Nucleic acid recognition will be illustrated by reference to specific examples drawn from the regulation of prokaryotic gene expression. This will necessarily not be a comprehensive review given the wealth of knowledge now available in this area. Some discussion of eukaryotic examples will be introduced for comparison purposes. In some cases, the examples chosen to illustrate particular features of nucleic acid recognition are also the topics of separate chapters elsewhere in this book, and in those cases the reader should follow the cross-referencing instructions to obtain more detailed discussions of the biology of the systems being discussed.
Repressors and activators
Authors: Busby Stephen J W 
Published: November 2023

Abstract
The study of adaptive responses in bacteria led to the discovery of a panoply of gene regulatory proteins (1). These are mostly DNA-binding proteins and their role is to modulate promoter activity, thereby coupling the expression of specific genes to changes in the environment. Gene regulatory proteins are ubiquitous: they are essential for all processes of adaptation and differentiation in all living cells. At first sight this is a very complex topic, made incomprehensible by the sheer number of different factors and different modes of operation. The aim of this chapter is to tackle the central question of how gene regulatory proteins function, and to describe a small number of key examples from the microbial repertoire, that reveal principles applicable to most systems.
Post-transcriptional control
Authors: Gu Zhiping , Lovett Pauls. 
Published: November 2023

Abstract
The regulation of gene expression can potentially occur at several stages in the stepwise transfer of information from a gene to its protein product. While transcription initiation appears to be pivotal in the control of expression of many genes, modern methodologies for gene and RNA manipulation have identified various forms of post-transcriptional control in bacteria and eukaryotes. Post-transcriptional control formally refers to all regulation that occurs after transcription. However, this chapter will focus on forms of control that specifically affect translation.
Integration of control devices. II. Sporulation and antibiotic production
Authors: Yudkin Michael D , Chater Keith F 
Published: November 2023

Abstract
An earlier chapter described the specialized characteristics that E. coli cells adopt during stationary phase, and the complex regulation that establishes this differentiated state. In equivalent situations, some other bacteria of diverse taxonomic groups show more obvious physiological and morphological differentiation, to give rise to antibiotic production and to resting cells called spores that are somewhat (or in some cases very much) tougher and longer-lived than stationary phase E. coli cells.
Genetically engineered antibodies
Authors: Owens Raymond J 
Published: November 2023

Abstract
Monoclonal antibody technology has produced immunoglobulins with specificities to a wide range of clinically relevant antigens, including tumourassociated markers, viral coat proteins, and lymphocyte cell surface glycoproteins. However, the use of rodent antibodies in human diagnosis or therapy poses a number of problems. Foremost amongst these is the immunogenic nature of the immunoglobulins (1). This in turn limits the use of repeated doses of antibody essential for chronic treatment. The availability of human monoclonal antibodies would greatly reduce this problem but such antibodies are generally restricted in their range of specificities. Further, human hybridomas are often unstable and/or poor producers preventing the production of large amounts of the human immunoglobulin.
Enzyme amplification systems in ELISA
Authors: Self Colin H , Bates David L , Cook David B 
Published: November 2023

Abstract
Enzyme amplification was devised to allow the development of highly sensitive and rapid immunoassays (1).Enzyme labels were amongst the earliest alternative labels to radioisotopes introduced to immunoassay. With the limited specific activity of radioisotopes, it had been realized that, theoretically, enzymes had a much more sensitive detection capability because of their capacity for continuous catalysis of transformation of substrate to deliver some form of signal; for example colour, fluorescence, or electric current. The original concept of enzyme amplification was developed in response to the fact that, in routinely used tests, enzyme labels were not able to generate sufficient signal to compete with the then much more widely employed radioactive labels. Increasing substrate incubation times to days rather than minutes or hours simply served to increase background signals. Enzyme labels capable of much greater powers of signal generation were required to enable the development of not only more sensitive, but faster immunoassays. The major advantage of employing a sensitive enzyme measurement even in a competitive method with its inherently limited sensitivity (2), was seen to be the ability to deliver a very rapid assay system (3).
Enzyme immunoassays for detection of cell surface molecules, single cell products, and proliferation
Authors: Pearce N W , Sedgwick J D 
Published: November 2023

Abstract
For more than 25 years, immunoenzymatic techniques have been applied extensively to the localization of antigens and antibodies in tissue sections as well as to the quantitation of immunoglobulins (lg) and specific antibodies present in body fluids or in cell culture supernatants. The enzyme-linked immunosorbent assay (ELISA) is a sensitive, rapid, and versatile assay system for the quantitation of antigens and antibodies and is now used extensively for the measurement of soluble molecules. However aside from an early report by Avrameas and Guilbert in 1971 (1) on the application of immuno-enzymatic technology to the analysis of cell surface molecules on isolated lymphoid cells, it is only in the past 15 years that the principles have routinely been applied to the analysis of the varied immunological and biochemical properties of cells in suspension. It is these latter procedures that will be the subject of this chapter.
Antibody affinity measurements
Authors: Saunal Hélène , Karlsson, Robert , Regenmortel March. V Van 
Published: November 2023

Abstract
In order to assess the biological activity of antibody (Ab) molecules, it is necessary to measure the strength of their interaction with the antigen (Ag) in terms of the equilibrium constant KA (1). This constant corresponds to the inverse of the Ab concentration which is needed to obtain 50% of complexed species. Since formation and dissociation of complexes continuously occur the equilibrium state is dynamic. The rates of association and dissociation are of considerable interest since they give information on the way the equilibrium is reached. Changes in reaction rate and affinity can be used to probe structure-activity correlations in one of the reactants (2–4) and to select appropriate reagents for the immunodetection of biological substances.
Analysis of soluble adhesion molecules
Authors: Laan M G Bouma,M P , Dentener, M A , Buurman W A 
Published: November 2023

Abstract
Adhesion of leucocytes to endothelial cells, and their subsequent transendothelial migration into target tissues are crucial events in the development of an inflammatory reponse. This leucocyte-endothelial interaction is mediated by specific adhesion molecules, expressed on the endothelial cell surface, that recognize and bind to their specific ligands on leucocytes. During the last decade, a number of endothelial adhesion molecules have been identified, including E-selectin, intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1), which mediate the successive steps of the adhesion process (1). Expression of these adhesion molecules can be induced by a wide range of inflammatory mediators, thereby tightly controlling leucocyte recruitment during inflammatory responses. Also, adhesion molecules are believed to play an important role in the invasive and metastatic cellular processes in the development of cancer (2).
Developtnental regulation of imprinting by DNA methylation
Authors: Chaillet J Richard 
Published: November 2023

Abstract
Genomic imprinting is an unusual and fascinating form of gene regulation in which the two alleles of a gene are distinguished by their parental origin (1-3). Besides potential genotypic (sequence) differences, the two parental alleles of most mammalian genes are indistinguishable in the somatic tissue of the organism. The difference between these non-imprinted genes and the extraordinary imprinted ones originates in characteristic epigenetic marks (imprints) placed on parental alleles. The imprints are established in the germlines of the parents, are transmitted to the embryo following fertilization, and henceforth distinguish the parental alleles of an imprinted locus. One discernible manifestation of this phenomenon is a difference in expression between the maternal and paternal alleles. This role of genomic imprinting in governing the level of allelic activity is an absolute requirement for normal mammalian embryogenesis (2, 4). Fundamental disturbances in the imprinting process, which preclude the 'balanced' inheritance of differentially marked maternal and paternal alleles, frequently result in abnormal embryonic development (5-11). The consequences of many such deviations from biparental (biallelic) inheritance have emphasized the profound importance of the process and have encouraged attempts to understand its molecular mechanism.
Intracellular transport of secretory proteins within intact transient heterokaryons and homokaryons
Authors: Valtersson Conny , Mizuno Masahiro , Dutton, Anne H , Singer S J 
Published: November 2023

Abstract
The overall intracellular pathway taken by secretory proteins inside eukaryotic cells, from their synthesis to their exteriorization, was laid out some time ago (Palade 1975). Initially, proteins to be secreted are synthesized on ribosomes that become attached to the cytoplasmic surfaces of the membranes of the endoplasmic reticulum (ER), and as the proteins are translated they are translocated across the membrane into the lumen of the ER. Following this, the secretory protein (suitably modified) is transferred from the ER to the cis-faces of the Golgi apparatus (GA). After passage through successive Golgi saccules and the trans-Golgi network, the secretory protein is deposited in granules which ultimately fuse with the plasma membrane to release the protein to the exterior of the cell.
PCR in situ hybridization (PCR ISH)
Authors: O’leary John J 
Published: November 2023

Abstract
A major limitation of solution-phase PCR is the inability to visualize and localize amplified product within cellular and tissue specimens. In situ hybridization (ISH) does permit localization of specific nucleic acid sequences at the individual cell level. In conventional non-isotopic in situ detection systems, most protocols do not detect single-copy genes, except for those incorporating elaborate sandwich detection techniques (1).
Reverse transcriptase in situ PCR for RNA detection
Authors: Embleton M Jim 
Published: November 2023

Abstract
Most published applications of in situ PCR for amplification of specific nucleic acid sequences in cells or tissues have been for the detection of genes or viruses which are present in low copy numbers or in a minority of the cell population. Detection may be either indirect, for example by hybridizing a labelled oligonucleotide probe to the amplified DNA, or direct, where the product is amplified with labelled oligonucleotide primers. A variety of labels for oligonucleotides have been used in different situations, including fluorescent dyes for direct microscopic visualization (1,2), and ligands such as biotin or digoxigenin (3-5), which can be used for visualization by other means involving enzyme-substrate systems or binding of labelled antibodies. An application of in situ PCR which so far has been less well exploited is the production of cDNA for cloning. For most cloning applications amplification from nucleic acid templates extracted from cells or tissues is perfectly adequate, and is technically easier to achieve than in situ PCR. However, there are some situations in which it is desirable to co-amplify two separate gene sequences within the same cell, and to maintain them in some form of spatial or physical linkage. The options for this are to carry out PCR on single cells isolated from each other (e.g. in single wells of a microtitre plate), or intracellular PCR on a population of cells. Where the target genes comprise a very large heterogeneous pool, it is impractical to establish huge numbers of single-cell PCRs. A method was therefore devised to perform the PCR in situ on a population of fixed and permeabilized cells which maintained their integrity throughout the process, and to arrange for the amplified sequences to be linked physically within the cells so that they could be recovered in the combinations originally expressed by the cells (1). The specific purpose of this technique was the rescue and linkage of immunoglobulin variable region (V) genes from a population of B lymphocytes containing a multitude of different rearranged immunoglobulin genes, in order to prepare libraries encoding recombinant antibody fragments representative of the original repertoire.