bluuebunny/crossref_metadata_2025_split huggingface dataset:
lymphocyte and ADCC responses
Authors: Gotch Frances , Broliden Kristina 
Published: November 2023

Abstract
Infection with HIV-1 (or HIV-2 or SIV) induces initial and long-lasting high levels of MHC class I restricted CD8-positive cytotoxic T lymphocytes (CTL) which interact through their specific T cell receptors (TCRs) with processed viral fragments (peptides) presented on the surface of infected cells in association with an MHC molecule (1). Infected cells are thus destroyed. CTL have been demonstrated against most of the HIV-1 gene products including gag, pol env, nef, and vif (2). CTL have mostly been studied using peripheral blood lymphocytes (PBL), but they have also been isolated from infected organs such as lungs (3), lymph nodes (4), and the central nervous system (CNS) (5). There appears to be a progressive decline in HIV-specific CTL activity which parallels the development of HIV-related disease (4). The measurement and identification of the activity, specificity, and frequency of HIV-specific CTL, and their variation with time, may indicate their relative importance in modulating HIV infection. Identification of CTL epitopes is also essential for subunit vaccine design.
Reverse transcriptase
Authors: Beard W A , Wilson S H 
Published: November 2023

Abstract
The reverse transcriptase (RT) of human immunodeficiency virus type-1 (HIV-1) converts the single-stranded (+) viral RNA genome into double¬ stranded proviral DNA prior to its integration into the host genomic DNA. The HIV-1 RT has therefore been the target for anti-viral drug design (1). The cloning of the RT in biologically active form has made large quantities of enzyme available for biophysical and kinetic studies. In vivo, the heterodimeric form (p66/p51) of RT is believed to be the result of carboxy-terminal proteolytic cleavage of one subunit of the homodimer (p66/p66) (2). Crystal structures of RT complexed with DNA (3) and a non-nucleoside inhibitor (4) have recently been published. In addition, pre-steady state kinetic studies are now available (5- 7). This detailed structural and kinetic information is pro¬ viding the prerequisite information for rational drug design of specific and potent inhibitors.
Transient assay for Nef-induced down-regulation of CD4 antigen expression on the cell surface
Authors: Skowronski J , Mariani R 
Published: November 2023

Abstract
The nef genes of the human and simian immunodeficiency viruses encode closely related proteins of 25 kDa to 27 kDa which are expressed in the cytoplasm of virally-infected cells. Nef is essential for SIV pathogenesis in the rhesus monkey model of human AIDS (1) but does not appear to be required for viral growth in vitro. As a result, nef genes of many commonly studied viral isolates are truncated prematurely, or contain loss-of-function alleles. Recent observations from several laboratories indicate that a large fraction of nef alleles derived from either laboratory HIV and SIV isolates, or cloned directly from peripheral blood leucocytes of HIV-infected patients, are able to decrease CD4 antigen expression on the cell surface. This effect of nef on CD4 expression is neither species-, nor cell type-specific. CD4 downregulation has been documented in both human and murine CD4-positive T cells, and in non-lymphoid cells expressing endogenous, or transfected, CD4 genes (2-6). The CD4 antigen is required both for the normal development and function of helper T cells, and to mediate immunodeficiency virus infection (7). Thus, the interaction of nef with CD4 is likely to have profound, yet mostly unexplored, consequences for the HIV-I-infected CD4-positive T cell.
Cyclic nucleotides: measurement and function
Authors: Butt Elke , Walter Ulrich 
Published: November 2023

Abstract
The activation of human platelets is inhibited by a variety of agents which exert their effects through distinct mechanisms. Examples include inhibitors of thromboxane A2 generation (e.g. aspirin), inhibitors of thrombin (e.g. hirudin), scavengers of ADP (e.g. apyrase), and physiological and pharmacological cyclic nucleotide-elevating agents (1,2). Vascular endothelial cells, under basal conditions and in response to numerous vasoactive agents, synthesize and release prostacyclin (PGI2) and endothelium-derived relaxing factor, nitric oxide (EDRF; or NO), two of the most important physiological platelet inhibitors. PGI2 and EDRF/NO increase the intracellular messenger molecules cAMP and cGMP, respectively, in human platelets and other target cells. The inhibition of platelet activation caused by PGI2 and EDRF/NO is mediated by cAMP- and cGMP-dependent protein kinases (cAMP-PK, cGMP-PK), respectively. As shown in Table 1, human platelets contain par ticularly high concentrations of cAMP-PK and cGMP-PK (3). The type III cGMP-inhibited phosphodiesterase (cGI-PDE) is an additional important target for cGMP. Elevation of cAMP mediated by cGMP inhibition of the cGI-PDE contributes to the well known synergism between cGMP- and cAMP-elevating platelet inhibitors (4). In human platelets, established cAMP-PK substrates include the small molecular weight G protein rap lB, the subunit of glycoprotein lb (GPib ), the focal adhesion protein VASP, caldesmon, myosin light chain kinase (MLCK), cGI-PDE, and actin-binding protein (ABP) (2). Only the focal adhesion protein VASP is an established substrate for cGMP-PK in platelets although other substrates, perhaps also rap lB and GPib , may exist. The physiological effects of cyclic nucleotide-elevating platelet inhibitors are terminated by cyclic nucleotide-degrading phosphodiesterases (PDEs) and by protein phosphatases which dephosphorylate the cAMP-PK and cGMP-PK substrates. In human platelets, the major PDEs responsible for cAMP or cGMP hydrolysis are type III cGI-PDE and type V cGMP binding, cGMP-specific PDE (cGB-PDE), respectively (4,5).
Isolation and functional properties of antigen presenting cells
Authors: Stockinger Brigitta 
Published: November 2023

Abstract
T cell recognition of antigen depends crucially on degradation of protein and binding of protein fragments to MHC molecules which ‘present’ these fragments to T cells. The term ‘antigen presentation’ is used to summarize the complex events of antigen internalization, processing of antigen into peptide fragments, peptide transport, and MHC/peptide interaction until the final appearance of peptide/MHC complexes on the surface of antigen presenting cells. Two separate pathways exist using largely non-overlapping sources of antigen and distinct intracellular compartments for binding to different MHC molecules. Most biosynthesized, intracellular antigens are degraded in the cytosol and peptides are translocated into the endoplasmic reticulum (ER), where they bind to MHC class I molecules and after transport to the cell surface are recognized by class I restricted cytotoxic T cells. The MHC class II presentation pathway does not make use of peptides in the ER since the peptide binding site of MHC class II is blocked by the invariant chain. Instead MHC class II molecules are re-routed to endosomal compartments where the invariant chain is degraded, so that peptides from exogenous proteins that have been internalized by antigen presenting cells (APCs) or from endogenous sources of protein that can enter these compartments bind to invariant chain-free MHC class II for recognition by class II restricted T cells.
The 20S proteasome and antigen presentation
Authors: Seelig Angela , M.-Kloetzel Peter 
Published: November 2023

Abstract
The 20S protesome is the major cytosolic proteinase complex of eukaryotic cells. This 700 kDa multisubunit enzyme complex is involved in ubiquitin independent proteolysis and is also central to the ATP/ubiquitin-dependent intracellular protein degradation pathway where it represents the proteolytic core of the ‘26S’ proteinase complex (1, 2). Thus, proteasomes are involved in the turnover or activation of transcription factors (3, 4), in cell cycle control (5), and the generation of antigenic peptides which are presented at the cell surface by MHC class I molecules (for review see refs 6 and 7).
Methods for studying the role of the major histocompatibility complex in NK cell cytotoxicity
Authors: Pena J , Solana R , Borrego, F , Rolstad B 
Published: November 2023

Abstract
Our knowledge about how T cells recognize foreign cells has been increased through studies of the interactions between the T cell receptors (TCR) and antigenic peptides presented by class I or class II molecules. The role of the MHC is now equally challenging in NK cell research, as it has been shown that NK cells can recognize certain MHC class I specificities. The receptors that NK cells utilize to recognize class I antigens have recently been identified, and named KiR (killer inhibitory receptors). An attractive idea supported by experimental data is the ‘missing self’ hypothesis (1, 2) which envisages NK cells as a surveillance mechanism against cells showing reduced or aberrant expression of certain MHC class I molecules regarded as ‘self’ by the immune system (for reviews see refs. 3 and 4).
Superoxide dismutase
Authors: Goldstein Sara , Czapski Gidon 
Published: November 2023

Abstract
The superoxide anion radical (02) is considered to be a highly toxic entity in many biological systems (1–4). It is formed in normal metabolism as well as through the action of many drugs, poisons, and radiation (1–4). It is also involved in radiation damage, DNA damage, phagocytosis, ageing, cancer, etc. Superoxide dismutases (SODs) are metalloenzymes that catalyse very efficiently the dismutation of superoxide ions into oxygen and hydrogen peroxide. It has been widely recognized that these enzymes, which are present in almost all living organisms, provide a defence system that is essential for their survival under aerobic conditions. The deleterious role of superoxide during ischaemia (5), which occurs in organ transplantation and many surgical interventions and during heart and brain events, suggests that SOD may have a potential clinical use. This led many investigators to search for SOD mimics, a search which arose because human SODs have short metabolic half-lifes (&lt;10 min), and do not penetrate into the cells.
Protein translocation into the endoplasmic reticulum
Authors: Romisch Karin , Corsi Ann 
Published: November 2023

Abstract
In eukaryotic cells all non-organellar protein synthesis starts on free ribosomes in the cytoplasm (1). Nascent chains destined for the secretory pathway are marked as such by an N-terminal signal peptide (2, 3). The signal peptide is recognized and bound by a ribonudeoprotein complex, the signal recognition particle (SRP), as soon as it emerges from the ribosome (4). Binding of SRP to the signal peptide retards or stops translation (5) and allows for targeting of the SRP-nascent chain-ribosome complex to the endoplasmic reticulum {ER) membrane (6). Interaction of SRP with its receptor in the ER membrane subsequently leads to its dissociation from the nascent chain (5, 7). Translation resumes and the secretory protein is translocated into the ER where its signal peptide is cleaved, and glycosylation, folding, and oligomerization take place (8-11). In the past two decades a large body of work has focused on the elucidation of the first step of the secretory pathway, translocation into the ER. The results allow us to draw a detailed picture of the components involved and their respective functions.
Biogenesis of constitutive secretory vesicles, secretory granules, and synaptic vesicles-£acts and concepts
Authors: ohashi Masato , bauerfeind, rudolf , Huttner wieland b. 
Published: November 2023

Abstract
Vesicle-mediated secretion from animal cells utilizes three types of secretory vesicles (1, 2) (Fig. 1). The first type is the constitutive secretory vesicle (CSV), which is thought to be common to all eukaryotic cells and which mediates the continuous secretion of newly synthesized proteins. The second type is the secretory granule, in neurones also referred to as the large dense core vesicle, which occurs only in cells capable of regulated protein secretion and which mediates the stimulus-dependent release of stored proteins and biogenic amines. The third type is the synaptic vesicle of neurones, which mediates the release of neurotransmitters but lacks secretory proteins, and its counterpart in certain endocrine cells, the synaptic-like microvesicle (SLMV). In this chapter, we will summarize current knowledge, and describe concepts concerning the molecular machinery involved in the biogenesis of these vesicles, its regulation, and the protein sorting processes that occur in the course of vesicle formation.
Time-resolved fluorescence immunoassay
Authors: Barnard Geoff 
Published: November 2023

Abstract
Today, immunoassay methodology is applied in many branches and disciplines of scientific investigation. The procedures are essentially of two types, competitive and non-competitive, and historically these have been typified by radioimmunoassay (RIA) and immunoradiometric assay (IRMA), respectively (see Chapter 1). In recent years, however, there has been the widespread adoption of procedures using alternative detection systems that avoid the use of radioisotopes (e.g. enzymes, luminescent compounds etc.). In particular, over the last 10 years, it has become well established that time resolved fluorescence immunoassay (FIA) can offer unique advantages over most other non-radioisotopic procedures (1).
The RAS/RAF/ERK signal transduction pathway
Authors: Macdonald Susan G , McCormick Frank 
Published: November 2023

Abstract
The importance of RAS proteins in human cancer was established in 1982, when the first human oncogene was recognized to be a mutant version of a normal H-RAS allele (1). These early observations prompted exhaustive efforts to identify effectors of RAS proteins, and so to understand their precise molecular function. These efforts have led to the conclusion that a major effector pathway for RAS proteins is the MAP kinase cascade (2--4; and Fig. 1). Recently, the existence of other effector pathways has been inferred, and will be discussed below. Here we summarize biochemical and biological properties of the mammalian RAS--RAF-MEK-MAP kinase signal transduction pathway and discuss questions about the pathway that remain to be answered.
Toxoplasma as a model genetic system
Authors: Sibley L David , Howe Dank , Wan kiew-lian , Khan shahid , Aslett martin a. , Ajioka James W 
Published: November 2023

Abstract
Several important biological attributes make Toxoplasma well suited for genetic studies. First, the parasite is easily maintained in the laboratory, having the ability to grow productively in virtually any vertebrate cell line. Second, it is possible to produce mutants and to propagate clones indefinitely. Phenotypic analysis of mutants is aided by the fact that replicative stages are haploid. Third, it is possible to conduct classical genetic studies and rudimentary genetic and physical linkage maps are available. Finally, molecular genetic studies are supported by DNA transformation using a variety of selectable markers. These properties make Toxoplasma unique among the world of parasites where biological and technological limitations have generally limited application of genetics.
Biogenesis of specialized organelles: glycosotnes and hydrogenosotnes
Authors: Sommer Jurg M , Bradley Peter J , Wang c. C , Johnson Patricia J 
Published: November 2023

Abstract
Compartmentalization of cellular functions into organelles is a characteristic of all eukaryotic cells. The development of highly specialized intracellular organelles in response to unusual host environments is most strikingly demonstrated by two structures found in certain parasitic protozoa: the glycosomes of trypanosomatids and the hydrogenosomes of trichomonads. These unique organelles represent a major cellular difference between host and parasite and have thus been studied extensively as possible targets for chemotherapeutic agents. Both of these organelles participate in the production of ATP, although in very different ways. The glycosome increases the rate of glycolysis by at least an order of magnitude, while the hydrogenosome participates in substrate-level phosphorylation, converting pyruvate to acetate, CO2, and molecular hydrogen in the process. The evolutionary origin of these organelles has been a matter of much speculation in the past, but recent molecular studies of their biogenesis have confirmed that the glycosomes are derived from an ancestral microbody related to the peroxisome, while the hydrogenosomes of trichmonads may share a common progenitor organelle with mitochondria.
Promoters, sigma factors, and variant RNA polymerases
Authors: Helmann John D 
Published: November 2023

Abstract
Transcription, the copying of genetic information from its DNA repository into functional RNA molecules, is catalyzed by RNA polymerase (RNAP). In this chapter we review the structure and function of bacterial RNAP, discuss the DNA determinants of promoter strength, and consider several examples of alterations to RNAP which regulate gene expression.
Switch systems
Authors: Saunders J R 
Published: November 2023

Abstract
Bacteria of many species are frequently observed to exhibit profound phenotypic changes, typically affecting colonial appearance or behavior. Most often, such changes are evident in pathogenic bacteria, where genetic switches modulate expression of a variety of virulence determinants (1). Such variation is the result of a diverse range of genetic mechanisms that are manifested in what are somewhat imprecisely grouped together as either phase variation or antigenic variation. Phase variation results from quantitative changes in gene expression that may range from what are, in essence, simple on-off genetic switches, through to modulation of the volume of expression of functional gene product at either the transcriptional or translational level. In contrast, antigenic variation is evident as qualitative changes in the nature of one or more surface components. In the main, such variations are detected by sequence changes involving more complicated switches that lead to the expression of an antigenically altered protein. Antigenically variable components have been studied largely because of their importance in bacterial virulence. However, equivalent changes in surface-exposed components of non-pathogenic bacteria almost certainly occur and may have particular selective advantages in their particular environments. Moreover, qualitative changes in a variable gene product could take place without necessarily having effects on the immunological properties of the variable component concerned.
Enzyme-linked immunoassays
Authors: Kemeny D M 
Published: November 2023

Abstract
Enzyme-linked immunoassays are in widespread use in all areas of biological science today. Their popularity stems from their ease of use and safety. In this chapter I will review the current status of ELISA including assay format, reagent choice, assay optimization, and quantification. Other variations on the method such as the ELISA plaque assay, signal amplification systems, and affinity measurement will be addressed by other authors in these volumes. My comments will be restricted to assays set-up and developed in the user’s own laboratory and to plastic microtitre plate-based assays (which apply equally to plastic tubes or pins) as these are the most widely used. However readers should be aware of their limitations and alternatives which have been reviewed extensively elsewhere (1,2).
Photoluminescence immunoassays
Authors: Hemmilä I A 
Published: November 2023

Abstract
In biospecific assay technologies the detection of a label is most often based on measurement of emitted light. The emission can originate, for example, from radiation (radioimmunoassays, radioluminescence, RIA, IRMA), from a fluorescent compound (fluoroimmunoassays, FIA, IFMA), or the fluorescent end-product of an enzymatic reaction (fluorometric EIAs, ELFIA), from a luminogenic label (luminoimmunoassay, LIA), or luminogenic substrate after enzymatic triggering (enzyme-linked chemiluminescence immunoassay, ECLIA), from a phosphorescent compound (phosphoro-immunoassay), or from photoluminescent lanthanide chelate (time-resolved fluoroimmuno-assay). In the case of lanthanides the emission emanates directly from the long life-time excited ionic state of the metal and is today classified with the generic term luminescence (the term fluorescence being defined as emission emanating from excited singlet level of TI-electrons and hence is restricted to aromatic hydrocarbons). In immunoassays the lanthanide emission is measured with a fluorometer using time resolution. These assays are generally named fluoroimmunoassays, or more specifically time-resolved fluoroimmunoassays, and to avoid confusion, never luminoimmunoassays.
Ligand blotting
Authors: Soutar Anne K , Wade David P 
Published: November 2023

Abstract
Ligand blotting is a method of detecting or identifying proteins on the basis of their specific biological function. It is similar to immunoblotting (Western blotting; see Chapter 1) in that cell proteins are solubilized, fractionated by polyacrylamide gel electrophoresis (PAGE), and transferred electrophoretically (blotted) to a nitrocellulose or similar membrane. However, specific proteins can then be identified on the membrane by their ability to bind a particular ligand, rather than with a specific antibody as in immunoblotting. The ligand can be another protein or peptide, a nucleic acid or, indeed, any molecule that binds with high affinity and for which a detection system is available. So far, the method has been particularly useful for studies on membrane proteins, such as cell surface receptors, which can be difficult to assay in cell extracts.
Prokaryotic in vivo expression systems
Authors: Appelbaum Edward R , Shatzman Allan R 
Published: November 2023

Abstract
Bacterial expression systems are commonly used for production of heterologous gene products of both eukaryotic and prokaryotic origin. This chapter will discuss strategies and provide protocols for the expression of heterologous proteins in Escherichia coli, which is the bacterial system that is most widely and routinely used for this purpose. While many specialized vectors are available for gene expression in other Gram-negative and Gram-positive bacteria, such systems are usually employed for the genetic analysis and manipulation of specific organisms, rather than for high level expression of proteins to be purified and used for research. The emphasis of this chapter is on protocols that are suitable for producing proteins in the laboratory for research purposes. There are additional considerations in the selection of systems for large scale production (i.e. hundreds of litres or more of culture) and for production of proteins for clinical investigation or commercial use. In this chapter we briefly review some of the major factors to consider in selecting an E. coli expression strategy and provide protocols that have been successful in our laboratories in a variety of expression applications. Additional details and extensive literature citations are available in several recent reviews (1-6).
Genotnic imprinting in the mouse: possible final analysis
Authors: Cattanach B M , Beechey C V 
Published: November 2023

Abstract
The concept of a marking or imprinting of genes/ chromosomes in the germline such that maternal and paternal copies behave differently in the zygote has its routes in the Sciara and coccid insect work of Crouse (1), and Brown and Nelson-Rees (2), and has since been adopted to cover a number of seemingly related but diverse phenomena in various plant and animal species (3, 4).