bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycolipids
Authors: Morrison I M 
Published: November 2023

Abstract
Glycolipid is the general term applied to a wide range of compounds. The most important and complex are of biological origin, being distributed throughout animal, plant, and microbial cells, but some synthetic examples have industrial applications. Along with glycoproteins, they form the class of glycoconjugates. The carbohydrate, or ‘glyco-components are oligo saccharide chains which are frequently branched. They can also carry covalently-bound, non-carbohydrate substituents such as acetate or sulfate groups. It is the precise carbohydrate structure which confers the biological specificity to a particular glycolipid.
Techniques for transformation of E. coli
Authors: Hanahan Douglas , Jessee Joel , Bloom Fredric R 
Published: November 2023

Abstract
The transfer of plasmid DNA into E. coli, so-called ‘plasmid transformation’, is a cornerstone of modern molecular biology. The original observation that calcium ions induced a state of competence, whereby E. coli cells would take up DNA and establish it in the cell (1, 2), set the foundation for a number of techniques for inducing competence toward plasmid transformation. One class of techniques is founded on this original observation that Ca2+ and other divalent and multivalent cations can induce competence. More recently, an alternative technique, electroporation, involving application of a transient high voltage electrical field to a mixture of E. coli cells and plasmid DNA, has proved to be remarkably efficient. Electroshock transformation techniques currently produce the highest efficiencies of any known methodology. In this chapter we present a spectrum of techniques that together produce reliable transformations at differing efficiencies, and for distinctive purposes. These range from low efficiency colony transformations, which can be performed in a few minutes without advance preparation of competent cells, to electro shock transformations whereby high complexity plasmid libraries can be produced with minimal amounts of starting material. We also describe methods for properly storing E. coli strains that will be used for preparation of competent cells, as well as methods for producing frozen competent cells, and discuss other parameters which are important for reliable production of competent cells. This chapter is adapted from a more comprehensive presentation on methods for and genetic factors influencing plasmid transformation of E. coli and other bacteria (3).
The utilization of cloned DNAs to study gene organization and expression
Authors: Parry Huw D , Alphey Luke 
Published: November 2023

Abstract
In this chapter we present a collection of techniques for the analysis of gene expression. The methods described are those most commonly employed in studies of eukaryotic gene regulation. They utilize cloned genes as the sub jects of study and as a means of generating nucleic acid probes. Southern hybridization is a powerful technique for providing a physical map of a gene on the chromosome. Information on the number of copies of the gene in the genome and the degree of similarity of the gene under study to other known homologues may also be obtained. Similarly, northern blotting provides in formation on the size and abundance of specific mRNA molecules in preparations of poly(A) +RNA.A range of techniques are available to determine the 5’ and 3’ termini of an RNA molecule and the positions of any splice sites within them. RNase and Sl mapping provide both qualitative and quantitative information about messenger RNA (mRNA) structure. Many eukaryotic genes are regulated at the transcriptional level. Sequencing of a promoter region often reveals elements having homology to known transcription factor binding sites. The gel retardation and foot printing methods provide useful information on the binding of specific transcription factors to the promoter regions of genes. Once sequence-specific DNA binding proteins have been identified they may be isolated by DNA affinity chromatography (1). Purified proteins may then be used for in vitro transcription studies to build up a complete understanding of the molecular interactions driving gene expression.
DNA sequencing
Authors: Alphey Luke 
Published: November 2023

Abstract
There are two principal methods for determining the sequence of DNA. These are based either on specific chemical degradation of a DNA molecule labelled at one end (the Maxam and Gilbert method) or on the enzymatic synthesis of labelled DNA, using dideoxynucleotides to terminate the elongating strand (the Sanger dideoxy method). Although there are specific applications which require the Maxam and Gilbert method, the vast majority of DNA sequence is today determined by use of the dideoxy chain termination method.
Use of vectors based on gene amplification for the expression of cloned genes in mammalian cells
Authors: Bebbington Christopher 
Published: November 2023

Abstract
The ability of cloned genes to function when introduced into mammalian tissue culture cells has proved to be invaluable in studies of gene expression. It also provides a means of obtaining, in large quantities, proteins which are otherwise scarce or which arc the completely novel products of gene manipu lation. The great advantage in obtaining human or other mammalian proteins from mammalian cells is that they are generally correctly folded, and arc more frequently appropriately modified and completely functional than when expressed in microbial or insect cells. Secretion of proteins containing signal peptides may also be more efficient in mammalian cells than insect cells.
Retroviral vectors
Authors: Brown Anthony M C , Dougherty Joseph P 
Published: November 2023

Abstract
“The exploitation of retroviruses as genetic vectors provides an important and versatile method of introducing and expressing cloned genes in eukaryotic cells, both in culture and in vivo. Several features of retroviruses favour their choice for this purpose, as an alternative to DNA-mediated gene transfer methods or other viral vector systems. First, the relatively small genomes of retroviruses can be easily manipulated to introduce foreign genes in such a way that any resulting defects in viral replication can he complemented in trans. Secondly, the viruses can be grown to high titres in cell culture. Most importantly, the efficiency of infection of susceptible cells is extremely high. Together with high titres of virus, this can permit infection of almost 100% of the target cells in a homogeneous culture. After infection, retroviral DNA becomes stably integrated in the host cell genome in a precisely defined manner such that virtually all of the infected cells can express the genes carried by the virus. Moreover, retroviruses contain powerful transcriptional enhancer elcmcnls that allow high levels of expression in a wide range of cell types.
Genetic manipulation of embryonic stem cells
Authors: Mohn Amy , Koller Beverly H 
Published: November 2023

Abstract
Embryonic stem (ES) cells are pluripotent stem cell lines established from mouse embryos cultured in vi1ro to the early post-implantation stage of development (1, 2). ES cell lines are established by transferring blastocysts to tissue culture plates seeded with a feeder layer consisting of either primary embryonic fibroblasts or cells of an established embryonic fibroblast line. Under these conditions, the embryo continues to grow, hatching from the zona pellucida and attaching to the feeder layer. As the trophectoderm cells spread out, the cells of the inner cell mass, which would normally give rise to the embryo proper, are exposed to the feeder layer. In many cases, the cells of the inner cell mass begin to proliferate upon contact with the feeder layer, forming: a small dump of cells, which can be picked away from the trophectoderm cells and expanded. After several weeks of growth in culture, these cells often reach a point where they can be propagated using established tissue culture techniques (3). With proper tissue culture conditions, an ES cell line established by this technique can be maintained in a pluripotent, undifferentiated, and euploid state. This maintenance of pluripotency is critical to the applications of ES cells in biological research.
Genomic and expression analysis of transgenic animals
Authors: Waller Sarah Jane , Funkhouser Judith Mcniff , Chooi Kum-Fai , Murphy David 
Published: November 2023

Abstract
Analysis of transgene expression is a cardinal part of any transgenic study. Transgenic pups born from microinjected eggs need to be identified (section 2), and then bred to produce a line (see Chapter 6, section 8.2). Expression of the transgene in the transgenic animals can then be analysed at the RNA (section 3) and protein (section 4) levels. It is very important to examine for transgene expression in as many tissues as possible, including those in which one does not expect to find its expression. Most transgenic animals that express their transgenes do so in a manner that is appropriate to the regulatory elements present. However, a number of transgenes are expressed ectopically, due either to influences of the adjacent cellular DNA or to unforeseen interactions between cA-acting elements in fusion genes. Such ectopic expression may produce unexpected and inappropriate results, including ill health, which should be taken into account when interpreting the results of the study. A thorough post-mortem examination is therefore also recommended for all animals expressing new transgenes (section 5).
Cloning into yeast artificial chromosomes
Authors: Anand Rak Esh 
Published: November 2023

Abstract
The analysis of large and complex genomes requires both mapping and cloning of DNA. Until a few years ago the largest fragment of DNA that could be cloned was - 40 kb in length using a cosmid vector (see Chapters I and 2). The development of yeast artificial chromosome (YAC) cloning vectors has greatly extended this cloning range. Following the description of the YAC vector system (1) the size of DNA fragment that could be maintained as a YAC has increased by almost one order of magnitude. This has greatly facilitated the study of complex genomes and has been instrumental in the efforts to construct the first generation physical map of the entire human genome (2). titre plates provides a valuable long-term resource which can be simultaneously accessed by several researchers. Consequently, it is important to plan carefully before embarking on this exercise that requires substantial time and resource. This chapter will mainly concentrate on the construction of a YAC library. For completeness, determination of the average YAC size within the library and a PCR-based library screening method have also been included.
Control and regulation in bioenergetics
Authors: Brown Guy C 
Published: November 2023

Abstract
Control and regulation have traditionally been studied in a non-quantitative way, in order to determine where and how metabolic rates and levels are changed. The analysis of ‘control’ is concerned with where within a system the rates of pathways or levels of intermediates can be changed, i.e. which enzymes or transporters limit the system rates or levels. The analysis of ‘regulation’ is concerned with how a physiological change in rate or level is brought about. A variety of quantitative approaches are now available to help estimate the extent to which different metabolic components control rates and levels, and the extents to which different mechanisms are involved in producing a response to some effector or physiological change. These quantitative approaches have in turn changed our concepts of control and regulation, and how we should talk about them. Bioenergetics has had a traditional emphasis on quantitative analysis, and thus these approaches have rapidly been applied to a variety of bioenergetic systems, including bacteria, mitochondria, chloroplasts, and proteoliposomes.
Patch-clamping of mitochondrial membranes and of proteoliposomes
Authors: Ballarin Cristina , Catta Sorgato M 
Published: November 2023

Abstract
The electrophysiological analysis of mitochondrial membranes developed in recent years has shown the presence of several high conductance ion channels (1). The physiological roles played by these channels are not yet clearly established. However, the continuous increase of information and the contributions of different expertise render the topic an exciting focus of interest.
The complement system: an introduction
Authors: Sim Robert B , Dodds Alister W 
Published: November 2023

Abstract
The complement system is a very important component of immune defence against infection. It is part of the innate (non-adaptive) immune system, and can respond to challenges by microorganisms before an adaptive immune response has developed. Hereditary deficiencies of complement proteins are rare, but individuals who lack part of the complement system are generally at increased risk of recurrent infection. Complement promotes and regulates the phagocytosis or lysis of foreign cells, particles, or macromolecules and host tissue breakdown products. The human complement system is composed of more than 30 proteins, both soluble (in blood plasma and other body fluids) and membrane bound (on blood cells and other tissues), which interact with each other when the system is activated by various stimuli. The properties of the proteins are summarized in Tables 1-3. The cell-surface proteins act either as receptors for fragments of soluble complement proteins, or as regulatory proteins, which control the activities of soluble complement proteins, and protect the cells on which they are situated from attack by complement.
Immunochemical methods for the detection of complement components and complement activation
Authors: Svehag Sven-Erik , Graham R , Leslie Q 
Published: November 2023

Abstract
Complement activation plays an important role in the inflammatory response and in the pathogenesis of many infectious diseases. Simple assays such as radial immunodiffusion and nephelometry are available for measuring concentrations of native complement components in biological fluids. These assays have focused on C4, C3, and factor B as participants in different phases of the complement cascade reaction. However, since hypercatabolism and increased synthesis of complement components such as C3 and factor B may occur concurrently, the information related to in vivo complement activation which may be obtained from measurements of native complement components is limited. In addition, measurements of native complement components may be affected by the presence of activation products in the sample if not properly collected and stored. On the other hand, direct measurement of generated activation products by newer techniques can provide a reliable indication of ongoing complement activation. Such measurements may be used to monitor disease activity and the effect of therapeutic treatment. They do not, however, provide information about the functional state of the complement system. When such information is desirable, functional tests, such as haemolytic assays (see Chapter 2) or assays measuring the opsonic capability (1) of the system, should be used.
C1-inhibitor deficiency and angio-oedema
Authors: Jackson John 
Published: November 2023

Abstract
Tissue swelling or oedema may occur for a variety of reasons. Most frequently, it occurs as a normal response to tissue damage and is a direct consequence of an increase in the vascular permeability that accompanies all inflammatory processes. Because this form of oedema evolves from enhanced blood vessel permeability, it is referred to as angio-oedema. Angio-oedema is an essential component of the inflammatory response, as it allows access to damaged tissues by migrating cells such as those of the immune system. These cells are the vectors of the early critical response to tissue damage and they orchestrate the initiation of tissue repair.
Formation and regulation of the membrane attack complex
Authors: Morgan B Paul , Van Den Berg Carmen W 
Published: November 2023

Abstract
Complement was originally discovered more than a century ago because of its haemolytic and bacteriolytic activities, both consequences of the poreforming capacity of the membrane attack complex (MAC). Following cleavage of CS by the convertase of either activation pathway, the five terminal components of complement (C5b through to C9) become tightly associated in the hetero-oligomeric MAC which inserts deeply into the membrane bilayer and forms a transmembrane pore. Control of MAC lysis is provided by a battery of fluid-phase and membrane protective factors and by active defence mechanisms.
Complement and immune complexes
Authors: späth Peter J , Schifferli Jürg A 
Published: November 2023

Abstract
The antibodies generated by B lymphocytes are found in various body compartments. A large fraction is secreted directly into the gastrointestinal and respiratory tracts where they play an important role in preventing cell-surface binding and invasion of microorganisms. High antibody concentrations are also found in the extravascular space, particularly in plasma. These antibodies react with their specific antigens, whether the antigens are exogenous (e.g. bacteria, viruses, proteins, carbohydrates) or of self-origin. The formation of immune complexes (IC) with soluble or fixed antigens (cell membranes or basement membranes) is often followed by the activation of the complement cascade. Whereas locally high antibody density is essential for complement activation by IgG, only one IgM molecule may be sufficient to fix and activate Cl, the first component of complement. Twenty years ago, it became possible for the first time to measure IC and fragments of complement proteins in plasma. This led to the hope that the monitoring of these parameters would permit definition of therapeutic strategies.
Non-human complement
Authors: Nonaka Masaru 
Published: November 2023

Abstract
Early phylogenetic studies of the complement system detected a ‘complementlike’ haemolytic activity in most vertebrate species tested, as well as in some invertebrate species (1). As will be discussed below, however, functional assay of complement haemolytic activity is problematic, and recent molecular studies have not yet been successful in identifying a genuine complement component or its gene in invertebrates. In contrast, the presence of the complement system has been established at the molecular level, that is, complement proteins and/or cDNA clones have been identified which show primary structure homology with human counterparts, from all major classes of vertebrates, including the most primitive extant vertebrates, jawless fish.
Preservation and handling of stock centre clones
Authors: Scholl Randy , Davis Keith , Ware Doreen 
Published: November 2023

Abstract
The responsibility for preservation and distribution of DNA clones for molecular genetic research and the genome project in Arabidopsis is shared by two centres, the Arabidopsis Biological Resource Centre (ABRC), Ohio State University, which was established in September 1991, and the European Community DNA Stock Centre at the Max-Planck Institute in Kñln, Germany. In addition to DNA resources, the ABRC shares responsibility for seed stock preservation and distribution and dissemination of information for the Arabidopsis community. Hence the DNA laboratory is integrated with the centre’s other services, allowing these complementary efforts to be fully co-ordinated. While preservation of biological resources including DNA is a primary function of the stock centres, they also strive to serve the rapidly changing needs of plant molecular biology research. This review will address the practical problems associated with all aspects of the ABRC DNA operation. Protocols utilized for clone characterization, preservation, and dissemination will be featured. Other topics which will be discussed are the philosophy of DNA centre operation, organization of information relating to DNA stocks, and the future of DNA centre operations.
Genetic mapping using recombinant inbred lines
Authors: Lister Clare , Anderson Mary , Dean Caroline 
Published: November 2023

Abstract
New markers can be positioned on a genetic or molecular map by comparison of the segregation of parental alleles in a population containing recombinant chromosomes, with the segregation data of other markers in the same population. Marker order is determined by identifying which markers (e.g. i-vii) co-segregate in a number of recombinant chromosomes (schematically illustrated in Figure 1). The fewer the recombination events that separate two markers the closer together they map on a chromosome. If one recombination event separates two markers in 100 chromosomes, then the two markers are considered to map 1 centimorgan (cM) apart.
Assays for human B cell responses to cytokines
Authors: Callaro Robin E , Kotowicz Karolena T , Smith Susan H 
Published: November 2023

Abstract
B lymphocyte responses are determined by complex interactions between antigen, cell-surface ligands, and soluble growth and differentiation factors (cytokines) binding to specific receptors on the cell surface. To date, at least 17 of more than 40 recombinant cytokines are known to stimulate B cell activation, proliferation and/or differentiation (Table 1). Many of these cytokines are derived from T cells and are involved in T cell-B cell collaboration, but some are made by B cells, monocytes, and a variety of non-lymphoid cells such as endothelial cells and fibroblasts.
T cells and cytokines
Authors: Cohen S B A , Clayton J , Londei M , Feldmann M 
Published: November 2023

Abstract
The functions of T cells and cytokines are intimately interlinked. It was not until T cell growth factors were defined and subsequently purified, and the cDNA encoding it cloned as ‘interleukin 2’ (1), that abundant non-malignant T cells could be cultured. The isolation of this and other T cell growth factors, now included in the broader category of cytokines, has permitted the development of long-term T cell-lines and clones. T cells can be isolated from normal healthy individuals or patients with disease, according to their antigen specificity and/or phenotype, and then perpetuated in long-term culture by cytokine stimulation. IL-2 is the major T cell cytokine used but certain subsets of T cells will proliferate in response to other cytokines, some independent of IL-2. For example IL-3 will stimulate most α β T cell receptor expressing CD4™cos−Tcells to proliferate, in man and mouse (2, 3).
Assays of cell growth and cytotoxicity
Authors: Skehan Philip 
Published: November 2023

Abstract
This chapter describes non-radioactive assays commonly used to measure changes in cell growth and cytotoxicity induced in a cell population by treatment with agents such as drugs, hormones, nutrients, and irradiation. It focuses specifically on mammalian cell cultures, but the methods can be used with a wide variety of cells, tissues, and microorganisms. Because of the ease and speed with which large numbers of samples can be processed by optical plate readers, most of the protocols which follow are designed specifically for 96-well plates, but are easily adaptable to other culture vessels.