bluuebunny/crossref_metadata_2025_split huggingface dataset:
ER-Golgi membrane traffic and protein targeting
Authors: Machamer Carolyne. 
Published: November 2023

Abstract
In eukaryotic cells, the vast majority of proteins destined for secretion or insertion at the plasma membrane follow a common pathway through the cell (1). They are synthesized on ribosomes bound to the endoplasmic reticulum (ER) membrane, cotranslationally translocated completely or partially into the ER lumen (see Chapter 4), and then transported via multiple budding and fusion steps through the Golgi complex to the cell surface. Many co- and post-translational modifications occur to newly synthesized proteins as they move through this exocytic pathway. In the ER, polypeptides must be folded properly: formation of disulfide bonds, core glycosylation, and oligomerization contribute to this process. In the Golgi complex, oligosaccharides are processed and proteolytic processing can occur. The enzymes involved in these modifications are resident proteins of the ER or Golgi complex, and must be retained in the appropriate compartment in the face of substantial membrane flow.
Mass spectrometric detectors
Authors: Chapman John R 
Published: November 2023

Abstract
Mass spectrometry (MS) is one of the most powerful physical methods available for identifying analytes in terms of their molecular mass (Mr) and for elucidating their molecular structures. Furthermore, MS possesses a unique attribute compared to other spectroscopies, namely its high sensitivity, so that it provides one of the few methods that is entirely suitable for the identification, structural elucidation, and for the quantitative measurement of even trace amounts of the various analytes present in a mixture. Generally, however, and certainly for complex mixtures, by combining MS with a chromatographic technique the molecular identity of each of the separated components of a mixture may be more readily ascertained. Historically, the first combination of MS with a separation technique was that achieved with gas chromatography, namely GC-MS, but as will become evident from the present chapter, during the last decade this desirable practice has been extended to HPLC to give the hyphenated technique usually designated as LC-MS.
Ion-exchange chromatography of proteins and peptides
Authors: Henry Michael P 
Published: November 2023

Abstract
The phenomena that occur during protein HPIEC are no different from those seen in the earliest forms of ion-exchange chromatography of these biopolymers. The first ion exchangers were particulate, large diameter (&gt; 50 micron), porous, soft gels derived from polystyrene, polysaccharides, and polyacrylates. Modern high-performance media are microparticulate in nature and are derived from silica, hydroxylated polyethers, polystyrenes, and crosslinked. non porous polyacrylates. The buffers and pH ranges employed in HPIEC are the same as those used in soft-gel chromatography.
On the other hand, the physical ruggedness of modern ion-exchange packing materials has changed certain aspects of the methodology of this technique. For example, since chromatography is so rapid there is less need for low temperatures and the stability they bring. Columns may be used many times (several hundred) before discarding.
Principles of immunodiagnostic tests and their development; with specific use of radioisotopes as tracers
Authors: Edwards Raymond , Blincko Stuart , Howes Iain 
Published: November 2023

Abstract
Immunodiagnostic tests, or immunoassays used for diagnostics, have been used extensively in many scientific disciplines and in many different ways. Such tests encompass any analytical method which use antibodies as reagents, the results from which assist a diagnostic interpretation. The most obvious use has been found in clinical applications, but, the term can be applied equally to other areas of investigation, e.g. food spoilage agents, environmental pollution and illicit drug use. Thus in a wider sense, it would be applied to the assessment of any intrinsic factor associated with a state or condition to be ascertained.
Growth factor receptors in cell transformation
Authors: Heldin Carl-Henrik , Rönnstrand Lars 
Published: November 2023

Abstract
The growth of cells is regulated by polypeptide factors that stimulate or inhibit proliferation. More than 50 such growth regulatory factors are known (Chapter 2). They exert their effects on cells by binding to specific receptors at the cell surface. For factors that stimulate cell proliferation, activation of protein tyrosine kinases appears to be a common and maybe obligatory event. Several growth factors bind to receptors with intrinsic tyrosine kinase domains which are activated after ligand binding. Other growth factors bind receptors which after ligand binding form complexes that contain intracellular tyrosine kinases.
Oncogenic transcription factors: FOS, JUN, MYC, MYB, and ETS
Authors: Baker Suzanne J , Curran Tom 
Published: November 2023

Abstract
Many oncogenes encode important components of the cellular machinery that are responsible for the translation of growth and differentiation signals in response to a diverse array of extra- and intracellular stimuli. Included in this broad range of oncogenic molecules are growth factor receptors (see Chapters 2 and 3), cytoplasmic signalling molecules (Chapters 4 and 5), and nuclear transcription factors. Transcription factors are critical components of signal transduction pathways that can transmit a regulatory signal to altered patterns of gene expression. It is not surprising that the disruption of normal regulation of such important control points can contribute to tumorigenesis. This chapter will focus on several transcription factors originally discovered as transforming genes carried by retroviruses (for a historical review see ref. 1). The intention is to provide a generalized view of the mode of action and regulation of these genes and their relationship to cellular growth and differentiation rather than a comprehensive review of the extensive literature.
Mammalian cell cycle control
Authors: Pines Jonathon 
Published: November 2023

Abstract
A proliferating cell must co-ordinate DNA replication and chromosomal separation to ensure that the genome is replicated completely, and that a single copy is correctly inherited by each daughter cell. The cell cycle is the coordinated series of events that achieves these aims. Our current understanding of the basic mechanism underlying the cell cycle is that many of the key events are initiated by a family of conserved serine/threonine protein kinases, the cyclin-dependent kinases (CDKs), that are activated by the cyclin family of proteins.
The retinoblastoma gene product and its relatives
Authors: La Thangue Nicholas B 
Published: November 2023

Abstract
An overwhelming body of cancer research supports the idea that the integration of growth-promoting and growth-restraining pathways maintains the fidelity of the cell cycle (see Chapter 7). During the genesis of tumour cells, such pathways become aberrantly regulated, culminating in an absence of cell cycle control and uncontrolled proliferation. A key player in negative regulation of the cell cycle is the retinoblastoma tumour suppressor gene product (pRB), historically identified through studies on the rare recessive paediatric eye tumour, retinoblastoma, where predispositior, to the hereditary form of the disease correlates with a loss of heterozygosity at chromosome 13q14 (1, 2). These studies, together with the recessive nature of the disease, suggests that inactivation of the RB gene is important in the generation of retinoblastoma, and implied a negative role for pRB in regulating proliferation. Subsequent molecular characterization of the RB gene indicated that the locus is invariably mutated in both hereditary and sporadic retinoblastoma as well as in a variety of other types of tumour (2, 3).
Integration of control devices. I. Pathogenicity
Authors: Dorman Charles J 
Published: November 2023

Abstract
One of the driving forces behind microbiological research has been the desire to understand how and why some bacteria cause disease in humans, in animals, or in plants. The employment of molecular genetic and cell biological techniques has led to the identification of factors which make key contributions to the ability of bacteria to be pathogenic. These may be classified as dedicated virulence factors (for example, toxins) which one might expect to find exclusively in pathogenic bacteria and, accessory virulence factors (for example, nutrient uptake systems) which might be equally important in the commensal and the pathogenic situation (1).
Antibodies packaged in eggs
Authors: Jensenius Jens Christian , Koch Claus 
Published: November 2023

Abstract
Like mammals, chickens make antibodies in response to challenge with antigen. Numerous publications have described the humoral antibody response in chickens to various antigens given by different routes and with different adjuvants (reviewed in refs 1 and 2). It is well established that chickens possess at least three immunoglobulin isotypes: a high molecular weight IgM type immunoglobulin, and two 7—8S immunoglobulins, an IgG type constituting the major plasma immunoglobulin, and an IgA type in external secretions, e.g. in the gall bladder and oviduct (3). The term ‘IgY’ is often used for the chicken IgG type immunoglobulin. This nomenclature was suggested by Leslie and Clem (4) to reflect some unusual features of chicken IgG heavy chains. Later data, especially recent results from molecular cloning, have shown that IgY has a fourth constant heavy chain domain, which shows homology to the hinge region of mammalian IgG (5,6). These data also suggest that avian IgY may be related to a common ancestor for mammalian IgG and IgE. However, we find that the available information justifies the use of ‘IgG’ to denote the chicken 7S immunoglobulin and we shall do so throughout this text.
Immunofluorescence and immunoenzyme histochemistry
Authors: Brandtzaeg P , Halstensen T S , Huitfeldt, H S , Alnes K N V 
Published: November 2023

Abstract
In 1941 Albert Coons and co-workers for the first time labelled the immunoglobulin (lg) fraction of an antiserum with fluorescein to visualize the corresponding antigen in tissue sections by fluorescence microscopy (1,2). A new morphological discipline, based on probing for structural or functional markers, was thereby founded. The term immunohistochemistry should preferably be reserved for immunological probing in tissue sections, while immunocytochemistry usually refers to cell smears, cytospin preparations, and monolayer cultures. For simplicity, immunohistochemistry will be used as a general methodological term in this chapter.
Flow cytofluorimetry
Authors: Damgaard G , Nielsen, C H , Leslie R G Q 
Published: November 2023

Abstract
The employment of flow cytofluorimetry (FC) in both qualitative and quantitative investigations of cell phenotype and activity has increased explosively in recent years. The strength of the technique lies in the fact that detailed information is acquired on individual cells passing through the detector system: information which, upon acquisition of data from a predetermined number of cells, can be processed to provide a statistical profile for the cell population, or populations, of interest. Thus FC differs fundamentally from the traditional radiometric approach, which only provides information on the cell population as a whole. In addition, the technique has largely supplanted fluorescence microscopy in the study of single cell suspensions, because it is able to provide quantitative data on much greater numbers of cells very rapidly.
Assays for Complement Receptors
Authors: Bartók István , Walport Mark J 
Published: November 2023

Abstract
The complement system is a group of about a dozen cell surface molecules and 20 glycoproteins present in the plasma of vertebrates. The first complement-mediated activity to be described was destruction of bacteria by fresh serum. This lytic activity of serum was composed of a heat stable component, antibody, and heat labile ‘complementary’ proteins. Complement has a complex series of effector activities which fall into three broad categories. The first category of effector activities follow the binding of the major complement opsonins, C3b and C4b and their catabolic products, to three types of complement receptor, complement receptors types 1, 2, and 3 (CRl, CR2, and CR3) located on a wide variety of cell types. The consequences of ligation of these receptors include phagocytosis of opsonized particles, activation of leucocytes and the transport of immune complexes. The interactions of complement with these three receptors forms the major focus of this chapter. The second category of effector activities of complement is the activation of inflammatory mechanisms by the interaction of the anaphylatoxins, C5a and C3a, with specific receptors present on leucocytes. The third category of effector activities results from the insertion of the membrane attack complex of complement into cell membranes. The consequences of this are lysis, particularly of bacteria and non-nucleated cells, and cellular activation by sublytic doses of membrane attack complex.
Identifying proteins for proteome studies: a two-dimensional gel electrophoresis approach
Authors: Sanchez Jean-Charles , Wilkiks Marc R , Appel Ron D , Williams Keith L , Hochstrasser Denis F 
Published: November 2023

Abstract
In the study of biological systems, it is known that genetic analysis alone cannot always predict any particular phenotype. This is because gene expression and protein post-translational modification arc modified by a complex interaction of genes, cellular events. and the environment. This phenomena, known as epigenesis, also encompasses the redundancy of gene and cellular networks that can often accomplish similar tasks and adapt themselves to reach identical end-point’&gt;. For the researcher, genetic analysis of biological systems is therefore not necessarily reliable for the accurate prediction of phenotype or disease in many cases (1).
Ligand binding
Authors: Levitzki Alexander 
Published: November 2023

Abstract
Receptors arc the focus of a number of different research disciplines. Hormones. neurotransmitters. drugs, antibodies, and lections exert their bio chemical effects through an initial interaction with specific receptors. Even lysosomal enzymes reach their target. the lysosome, through a receptor mediated pathway. The binding of the ligand to its specific receptor triggers a cascade or biochemical reaction that eventually leads to the final physiological response.
Affinity labelling
Authors: Colman Roberta F 
Published: November 2023

Abstract
An important approach to identifying amino acid residues within the hiding sites of enzymes is to exploit the specificity of the enzyme for a natural subs1ratc or regulatory ligand to limit chemical modification to the immediate vicinity of that site. In this approach. termed affinity labeling. a reagent is designed that is structurally similar to the normal ligand of the enzyme. but which also features a functional group capable of reacting covalently with many different amino acids. The expectation is that the affinity label will initially form a reversible enzyme-reagent complex analogous to the cyma-ligand complex and, once bound at the specific site, will react irreversibly with an amino acid residue within that site. The application o[ this technique can result in tagging of a particular binding site of a purified protein or in the labelling of one protein within a complex mixture of proteins. Affinity labeling can he used to localize a given site within a protein of knave amino acid sequence and thus to evaluate experimentally a site that was predicted on the basis of an amino acid sequence motif. It allows comparisons to be made between the substrate sites of the cyma in solution and those site localized within the crystalline form by X-ray diffraction. It can be used to test whether a compound bound irreversibly at a substrate site influences the enzyme conformation, subunit interaction, or the reactivity of other ligand site-,. Affinity labels with appropriate chromogenic or fluorescent substituents can be used to introduce spectral probes into specific sites on enzymes to report on the environment. on conformational changes, or on distances between functional sites. Affinity labelling can also provide the knowledge base to make rational choices of target amino acids for its directed mutagenesis. The general principles of affinity labelling have been summari1.ed in books and review articles (1-3).
Protein expression in mammalian cells
Authors: Otter-Nilsson Marlies , Nilsson Tommy 
Published: November 2023

Abstract
Protein expression has become a major tool to analyse intracellular processes, both in vitro and in vivo. The choice of expression system depends entirely on the purpose of the study. For some cases, transient transfection is the most obvious choice because of its relatively short time investment. In other cases, homogeneous populations and large quantities of cells may be required, which involves making cell lines stably expressing the desired protein. It may also be advantageous to express proteins under inducible promotors; this is particularly true if the protein exerts pathological effects on the cell. There are several inducible systems available but none, so far, is easy and straight-forward. Expression through virus infection is also possible. Here, large quantities of cells can be infected at the same time and the protein assayed for shortly after infection. The drawback, however, with this method is the need for special precautions when making and handling virus stocks and likely side-effects exerted by the virus on the cellular machinery upon infection. Protein expression can also be achieved directly via microinjection of plasmid DNA directly into the nucleus of the host cell. This allows for protein expression in single cells which may be desirable when performing video microscopy. Thus the choices of expression systems are multiple and one should carefully consider the range of these available before investing time and other resources in the experiments themselves. It is the goal of this chapter to describe the various expression systems so as to make this choice easier.
Expression in Xenopus oocytes and cell-free extracts
Authors: Matthews Glenn M 
Published: November 2023

Abstract
Adult female Xenopus laevis carry approximately 40000 oocytes at various stages of development. During growth, oocytes accumulate cellular components which carry the developing embryo through many cell cycles. Although much of the content of the fully grown oocyte consists of yolk proteins absorbed from the maternal circulation, there is also a large reserve of translational components required for the high level of protein synthesis which occurs during the period immediately after fertilization. The oocyte also contains a store of each of the three RNA polymerases sufficient to support zygotic transcription up to the 30000 cell stage (1).
Cell-free coupled transcription–translation systems from Escherichia coli
Authors: Kramer Gisela , Kudlicki, Wieslaw , Hardesty Boyd 
Published: November 2023

Abstract
Development of a bacterial cell-free coupled transcription-translation system in which a specific polypeptide was synthesized and could be identified was pioneered by Zubay (1). E. coli genomic DNA or bacteriophage DNA was used as the template for protein expression. Zubay (1) also pointed out that E. coli extracts are unsuitable for translation of isolated mRNA because of their rapid degradation. This statement still holds true despite the development of RNase-deficient E.coli strains.
Imprinting at the mouse and human IGF2R loci
Authors: Neumann Bjorn , Wutz Anton , Smrzka Oskar W , Barlow Denise P , Lyle Robert 
Published: November 2023

Abstract
The mammalian insulin-like growth factor 2 receptor (IGF2R), also known as the cation-independent mannose-6-phosphate receptor (MPR300), is a multifunctional protein, primarily involved in lysosomal transport (1, 2). This transmembrane receptor, hereafter called IGF2R, binds insulin-like growth factor 2 (IGF2) and numerous ligands tagged with mannose-6-phosphate to target them to the lysosomes. Thus, lysosomal targeting mediated through the IGF2R functions as a pathway for the transport of lysosomal enzymes and, in the case of IGF2, as a clearance mechanism (3-5). IGF2R binds other secreted growth factors, such as proliferin (6), and is probably required for the activation of transforming growth factor 13 (TGF-13) (7). The involvement of IGF2R in embryonic growth control (5) and the observed loss of heterozygosity at the IGF2R locus in both hepatocellular carcinomas (8, 9) and breast tumours (10) suggests that IGF2R may function as a tumour supressor gene.
Starch gel electrophoresis of allozymes
Authors: May Bernie 
Published: November 2023

Abstract
Thirty years ago a novel, relatively simplistic methodology revolutionized our ability to study evolution (starch gel electrophoresis of allozymic proteins). Lewontin and Hubby (1) and Harris (2) illustrated convincingly how allozyme electrophoresis permitted a wealth of Mendelian data on populations to be gathered in a relatively short period of time. The availability of these data has revolutionized many fields of evolutionary biology, including systematics, Sociobiology, genomic organization, and population genetics. Prior to the appearance of allozyme electrophoresis only morphological and behavioural mutants were available to study single gene variation. This new technique brought the electrophoretic separation of proteins together with the specificity of histochemical detection of the protein products of single loci (3). Now dozens of simple Mendelian markers are available in most organisms. The utter simplicity of this methodology has permitted thousands of scientists to use this technique in their research.
Cleavage of mismatched bases using chemical reagents
Authors: Giannelli Francesco , Green, Peter M , Ramus Susan J 
Published: November 2023

Abstract
Chemical cleavage of mismatch (CCM) was developed in 1988 as a method for screening cloned pieces of DNA for single base mismatches (1), but in combination with PCR was very soon used for the direct analysis of genomic DNA (2) and, later, for the analysis of mRNA (3). This technique detects mismatches in hybrid DNA. Heteroduplexes are formed by adding labelled normal DNA usually to an excess of unlabelled patient DNA. The heteroduplexes are reacted with either hydroxylamine which recognizes mismatched C bases or osmium tetroxide which recognizes mismatched T bases. Any mismatched or unmatched C or T bases are modified by the respective chemicals so that the modified strand can be cleaved with piperidine at the site of the mismatch. The products are analysed by electrophoresis on a denaturing polyacrylamide gel and the size of the fast running cleavage bands indicates the site of the mismatch. All manipulations involving the chemicals must be performed in a fume-hood.