bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lignin and Associated Phenolic Acids in Cell Walls
Authors: Friend John 
Published: November 2023

Abstract
Many types of phenolic compounds are found in cell wall preparations or as insoluble residues remaining after the extraction of metabolites soluble in organic solvents. This chapter describes procedures for the isolation and analysis of lignin and other phenolic compounds from plant material. Since most analytical methods for phenolic compounds are specific for phenolic hydroxy-groups, it is essential that all soluble phenolic compounds are extracted from the tissue during the preparation of the insoluble residue or cell wall fraction. Many simple phenolic compounds may not be completely extracted by nonaqueous organic solvents. Indeed, the removal of water by acetone or methanol may cause hydrogen-bonding of phenolic compounds, such as chlorogenic acid, to the insoluble residue leading to spurious results. Moreover, it is possible for phenolic compounds to be oxidized by endogenous phenolases, during the extraction procedure. The oxidation products of compounds, such as chlorogenic acid, can then chemically react with freeNH2 or -SH groups on amino acid side chains to yield complex oxidation products bound to protein. This may be cell wall protein itself, or protein which is hydrogen bonded to the cell wall during the extraction procedure.
Analysis of Components of the Plant Phosphoinositide System
Authors: Drobak Bjorn K , Roberts Keith 
Published: November 2023

Abstract
A key-role for Ca2+ as an intracellular messenger is now well established in a vast number of organisms ranging from slime-moulds to humans. Both mammalian and plant research in the Ca2+ field has, until recently, been somewhat hampered by the lack of understanding of how external signals initiate the responses mediated by the Ca2+ ion. This situation has rapidly changed with the discovery, in the early 1980s, by Berridge, Irvine, Michell, and their coworkers, that in many cell types a discrete pool of inositol-containing phospholipids constitute the missing link between extracellular signals and the modulation of intracellular Ca2+ fluxes (1-3). The pioneering work on this system (now known as the phosphoinositide signal transducing system-or the ‘PIsystem’) carried out in mammalian cells and tissues has inspired plant scientists to investigate whether a similar system is involved in the transduction of signals in plant cells. A brief outline of how this system functions is given in Section 1.1. When certain agonists (extracellular signals) arrive at the surface of the plasma membrane they bind to specific receptors. The agonist-receptor association activates phospholipase(s) C (phosphoinositidase C, PIC)-probably via interaction with one or more guanine nucleotide binding proteins (Gproteins) associated with the membrane. The primary target for PIC action is phosphatidylinositol (4,5) bisphosphate (Ptdlns (4,5) P2) a phosphorylated form of phosphatidylinositol (Ptdlns) which resides in the inner leaflet of the plasma membrane.
Metabolic Changes Following Infection of Leaves by Fungi and Viruses
Authors: Leegood Richard C , Scholes Julie D 
Published: November 2023

Abstract
Pathogenic organisms can broadly be divided into two categories, based on their mode of nutrition. Nectrotrophic pathogens, such as the damping-off fungi and soft-rot bacteria, rapidly kill and degrade the host tissue by the production of large quantities of toxins and cell-wall degrading and proteolytic enzymes. These pathogens derive the majority of their nutrients from the dead host tissue and subtle changes in the regulation of metabolism will be transient. In contrast, the biotrophs (for example viruses, rust fungi, downy and powdery mildews) are highly specialized pathogens. They require a continual supply of nutrients from the host in order to develop and reproduce. They therefore co-exist with the host for a certain period of time. This coexistence must be accompanied by regulated changes in the physiology and metabolism of the host.
Novel gene transcription in response to growth factors: gene isolation by differential plaque hybridization
Authors: Reddy P Sanjeeva , Cochran Brent H 
Published: November 2023

Abstract
Differential cDNA cloning can be used to identify differences in gene expression between any two populations of cells. This method has been used in a variety of experimental situations, but has been especially successful in allowing for the isolation of genes which are regulated by growth factors. These screens have identified genes which are regulated by PDGF (1), TPA (2), IL-2 (3), serum (4, 5), and NGF (6) to name only a few. This analysis has increased our knowledge not only about the types of genes which are regulated by different growth factors, but also helped identify entirely new gene families such as the bZIP proteins and novel cytokines (7, 8). These growth factor regulated genes are often referred to as immediate early genes, or early response genes since many of them can be induced by growth factors in the absence of new protein synthesis. For review, see Herschman, 1991 (9).
Localization of growth factor mRNA in tissue sections by in situ hybridization
Authors: Akhurst Rosemary J 
Published: November 2023

Abstract
It is becoming clear that, in vivo, the majority of growth factor bio-activities are effective locally, exerted via autocrine, paracrine, and (possibly?) intracrine mechanisms. To investigate molecular mechanisms of action it is therefore important to identify both sites of synthesis and sites of action for each growth factor. The development of in situ hybridization for detection of cellular mRNAs in tissue sections has provided a very powerful and precise tool with which to address the first of these issues. Using this technique, individual cells possessing RNA transcripts for a given gene can be unequivocally identified.
Introduction
Authors: Dyer Philip , Middleton Derek 
Published: November 2023

Abstract
This book aims to set out tried and tested protocols that will be used in a histocompatibility laboratory in support of both clinical service and research work. The techniques have been established by the chapter authors in their own laboratories but the reader is encouraged to amend and develop as necessary. The early chapters set out the serological and molecular techniques which are common in many histocompatibility laboratories. Later chapters deal with more specialized techniques which those keen to develop their range of services will find useful. The debate over the future of serological testing with the advent of molecular techniques continues but it must be remembered that the donor/recipient cross match remains of fundamental importance. The design of this book and others in the series is to facilitate use at the bench. The field of histocompatibility is rapidly moving and the chapter authors have provided their most up-to-date methods. A direct enquiry to authors will give access to further modifications.
HLA typing reagents: alloantisera and monoclonal antibodies
Authors: Middleton Derek , Boomer Julia , Heyes, Judith , Marsh Steven 
Published: November 2023

Abstract
In order to determine an individual’s HLA type two important ingredients are required. A suitable cell suspension, especially a B lymphocyte preparation when typing for class II antigens, and quality reagents containing specific antibodies against HLA antigens. The reagents are of two forms—alloantibodies produced by various sensitization procedures which are described in the first part of this chapter, and monoclonal antibodies which are described in the latter part of the chapter. Regardless of the source of alloantibodies the normal policy is to screen sera from small amounts of blood (&lt;1 ml) for suitable antibodies and then to obtain large volumes of suitable sera for use as reagents. Many laboratories screen and procure their own reagents and then exchange these with other laboratories. Other laboratories rely on obtaining their reagents from National Tissue Typing Reference Laboratories or by purchase from commercial companies.
Paternity testing
Authors: Toit Ernette Du 
Published: November 2023

Abstract
The primary objective of paternity testing is to determine whether or not a man who is falsely accused of paternity can be excluded from being the biological father of a given child. Examples of disputed parentage and methods for resolving them can be traced back to biblical days. In the Old Testament in I Kings 3 verse 16-28 Solomon made the choice of maternity. Although in Solomon’s case maternity was at issue, more commonly the question is one of paternity. The role of modern science in problems of disputed parentage began with the discovery of the ABO blood groups by Karl Landsteiner in 1900. The recognition that the inheritance of the A, B, and O blood groups followed the genetic rules observed by Gregor Mendel became the cornerstone of all that followed. Until the 1950s the only blood group systems used in paternity studies were ABO, Rh, and MN. Together they provided an exclusion of parenthood in about 50% of disputed cases.
Mapping techniques used to isolate novel major histocompatibility complex genes
Authors: Campbell R Duncan , Trowsdale, John , Dunham Ian 
Published: November 2023

Abstract
The HLA class I and class II regions each encode highly polymorphic families of cell surface glycoproteins involved in immune regulation. The class I region contains at least 17, and possibly as many as 40, highly related genes which include those encoding the classical transplantation antigens (HLA-A, -B, and -C). The class II region (HLA-D) is arranged into subregions HLA-DP, -DQ, and -DR, each containing at least one A and B pair of genes encoding the a and polypeptide chains of the class II molecule. A number of other class II related sequences (including HLA-DO, -DN, and -DM) have also been defined within the HLA-D region. The class I and class II regions are separated by the class III region which also contains genes with immune related functions such as the complement genes C2, C4, and Bf, the tumour necrosis factor (TNF) A and B genes, and the major heat shock protein HSP70 genes. In order to characterize the HLA-A to -DP region in detail, the two techniques of pulsed-field gel electrophoresis (PFGE) and chromosome walking are especially useful.
Signal transduction
Authors: Owen P J , Evans C A , Whetton A D 
Published: November 2023

Abstract
Haemopoietic growth factors and cytokines act on a range of haemopoietic stem and progenitor cells to regulate their survival, proliferation, and differentiation. They also modulate the activities of mature cells, e.g. GM-CSF can prime neutrophils to display enhanced cytotoxic activity. These factors exert their effects by binding to specific cell surface receptors, eliciting various transmembrane signalling events (1). The molecular cloning of many of these growth factors and receptors has allowed their mode of action to be studied. Some of these receptors are members of the same receptor families since they share common structural features. For example the M-CSF receptor and the SCF receptor are both members of the type II receptor/tyrosine kinase family. Similarly IL-2, IL-3, GM-CSF, G-CSF, and other cytokines share some common structural motifs in the alpha chain of their receptors (and are therefore members of the so-called cytokine receptor family). In some cases these receptors share a common (beta) subunit, (e.g. the IL-3, IL-5, and GM-CSF receptors). The IL-6 receptor has some structural similarities to the cytokine receptor family but is apparently unique in that it binds to a second membrane bound subunit (gp130) which elicits the intracellular effects of this cytokine.
Autologous bone marrow transplantation using cultured marrow cells in patients with leukaemia
Authors: Coutinho L H , Chang J , Testa N G , Dexter T M 
Published: November 2023

Abstract
Lately, autologous bone marrow transplantation has been increasingly used as a therapeutic modality in acute and chronic myeloid leukaemias for patients without a suitable HLA matched donor (1, 2). The advantages of using the patient’s own marrow are a lack of graft-versus-host disease (that is commonly seen in patients receiving allogeneic bone marrow cells), the low procedural morbidity and mortality permitting application to older patients, and the possibility of administering highly ablative and potentially more effective doses of chemoradiotherapy to larger numbers of leukaemic patients.
Quantitative autoradiography: a tool to visualize and quantify receptors, enzymes, transporters, and second messenger systems
Authors: Sharif N A , Eglen R M 
Published: November 2023

Abstract
The ditribution and relative concentration of endogenous neurochemicals and their receptors/acceptors has traditionally been determined by immunohistochemical, radioimmunological, and ligand binding techniques. Whilst ligand binding procedures conducted on tissue homogenates have permitted determination of receptor affinities for neurotransmitters and drugs, and gross receptor distribution analysis, they lack the high level of anatomical resolution and sensitivity that can be obtained using autoradiographic technique .
Non-radioactive labelling and detection of nucleic acid probes
Authors: Kessler Christoph 
Published: November 2023

Abstract
Non-radioactive indicator systems are based on the detection of various biological target molecules (analytes) by selective interaction with specific binding partners (probes). Appropriate detector systems are coupled to these probes, either directly by covalent binding or indirectly by additional specific high-affinity interaction. Most of the recently developed non-radioactive systems are based on the enzymatic, photochemical, or chemical incorporation of a reporter group (1, 2) which can be detected with high sensitivity by optical, luminescence, fluorescence, or metal-precipitating detection systems (3-5). Electrochemical detection systems using pH electrodes or sensor technology have also been described (6, 7). In addition, attempts are being made to use specific labelling and detection systems not only for the detection of different target molecule specificities, but also for the detection of a large variety of different kinds of biomolecules such as proteins or glycans (universal detection systems). The various non-radioactive systems can be classified as direct or indirect. These assays differ in the number of components and thus the number of reaction steps used for the detection reaction. Whereas direct systems are mostly used for the detection of standardized target biomolecules, the more flexible indirect systems are often applied to detect different target bio molecules of variable specificity.
Probe preparation by the polymerase chain reaction
Authors: Taylor Graham R , Noble Jayne S 
Published: November 2023

Abstract
The polymerase chain reaction (PCR) can provide an alternative to the use of nucleic acid probes in many cases, for example the detection of restriction fragment length polymorphisms (RFLPs) (1), variable number of tandem repeats (VNTRs) (2), minisatellite polymorphisms (3), and deletions (4). However, there are still many situations that require the use of hybridization probes, including pulsed-field gel electrophoresis (PFGE), in situ hybridization, simple methylation studies using methylation-sensitive restriction endonucleases, and the detection of alleles larger than 2 kbp (for example in the expansions associated with fragile X and myotonic dystrophy, refs 5, 6). In such cases, PCR can be used to generate probes from a variety of tem plates, circumventing the need to perform large-scale cultures and purifications. This chapter reviews some of the PCR-based methods for producing probes and describes protocols for the production, purification, labelling, and use of probes made by PCR.
Screening human recombinant libraries with nucleic acid probes
Authors: Fisher Gabrielle M 
Published: November 2023

Abstract
A recombinant library is a collection of nucleic acid fragments representing all or part of a genome. Libraries can be divided into two major types, genomic and complementary DNA (cDNA), based on the methodology underlying their construction. Genomic libraries are constructed from the entire genome, and, therefore, contain clones representing all genomic sequences including control elements, structural genes, intron sequences, repetitive sequences, etc. In contrast, cDNA libraries are constructed from only the expressed regions of the genome, and, therefore, reflect the sequences present in the mRNA population of the cell of origin and their relative abundance. Recombinant genomic libraries are a particularly valuable tool in the study of large and complex genomes. Genome sizes can range from less than 5 megabases (Mb) in Escherichia coli, to over 23 000 Mb in pines and other plant species, easily exceeding the 3000 Mb in the human genome (Table I). Thus, the amount of DNA in the haploid genome of different organisms does not correlate with the evolutionary complexity of the organism.
Genomic mapping and gene structure analysis
Authors: Hall Len 
Published: November 2023

Abstract
Nucleic acid hybridization with specific gene probes is an important part of many aspects of genomic mapping and gene structure analysis. Using the highly sensitive technique of Southern blotting, gene-specific probes (in the form of cloned cDNAs) can be used to obtain useful preliminary information on the size and organization of the corresponding genomic sequences, the number of gene copies, etc., thereby facilitating subsequent genomic cloning and initial clone characterization. Once genomic clones are available, further characterization will depend to some extent on the size of the gene and the reasons for studying it. Smaller genes may be sequenced in their entirety without too much effort. However, this may not be appropriate for very large genes where only the exons and regulatory regions may need to be identified and fully sequenced (probably after extensive restriction mapping of genomic clones involving Southern blotting with probes from different parts of the corresponding cDNA). In both cases, important structural features, such as the transcriptional start site and the precise location of exon/intron boundaries, will almost certainly need to be established. These can be determined with a high degree of accuracy using techniques such as primer extension analysis (for mapping transcriptional start sites) and nuclease SI mapping (for determining both transcriptional start sites and exon/intron boundaries), both of which involve the use of sequence-specific probes.
Ligation-mediated PCR
Authors: Garrity Paul A , Wold Barbara , Mueller Paul R 
Published: November 2023

Abstract
Using PCR, a DNA fragment can be exponentially amplified with two flanking primers of known sequence. However, for many applications it is desirable to amplify a DNA fragment containing only one end of known sequence or, for genomic sequencing and in vivo footprinting, a family of fragments with one end in common. In ligation-mediated PCR (LMPCR), such substrates are made suitable for PCR by the ligation of a sequence of defined length and sequence content to the undefined end. PCR is then performed using one primer specific for the gene of interest and one primer specific for the ligated sequence (1). LMPCR differs from other single-sided exponential PCR methods in that the relative lengths of the starting DNA fragments are retained with base-pair resolution in the final product, making it suitable for use in genomic sequencing and in vivo footprinting (1, 2).
Amino acid sequence analysis of blotted proteins
Authors: Cook Richard G 
Published: November 2023

Abstract
In the past 10 years, our ability to obtain amino acid sequence information on proteins and peptides has improved dramatically. The amount of protein required for sequencing has been decreased by approximately three logs from 1 nmol to 1 pmol. The major reason for this increased sensitivity has been the development of automated gas and pulsed-liquid-phase sequencers with in-line HPLC detection systems. While the chemistry utilized in sequencing remains the classic Edman degradation (with slight modifications), the protein sequencer instrumentation has been vastly improved at several levels.
Molecular evolution of plants: more genomes, fewer generalities
Authors: Wolfe Kenneth H 
Published: November 2023

Abstract
Studies on the molecular evolution of plant genes have long lagged behind those in other taxa, such as mammals, for a variety of reasons. The result has been a tendency among students of molecular evolution to assume that what is true for mammals will also be true for plants. In this review I attempt to dispel this notion by focusing on the differences between the two taxa. It is not difficult to spot the differences.
Chloroplast transformation
Authors: Hutchison Ronald S , Roffey robin A , Sayre Richard T 
Published: November 2023

Abstract
The chloroplast genomes of most higher plants and eukaryotic algae have been highly conserved throughout evolution. Chloroplast genomes from different plants are not equivalent, however. The size of the genome MAY range between 400 kb, for some algae, to 73 kb for the non-photosynthetic plant, Epifagus virginiana (1, 2; Chapter 3). However, most plants have intermediate-sized chloroplast genomes, of approximately 160 kb, which are characterized by large inverted repeats with intervening large and small single-copy regions.
Epitope mapping using synthetic peptides
Authors: Worthington Jane , Morgan Keith 
Published: November 2023

Abstract
It is of vital importance to researchers in many fields to identify the specific sequences on proteins (epitopes) that are recognized by antibodies or by T-cells. Three basic strategies for epitope identification are currently used. One approach is to use predictive algorithms to identify possible epitopes, to synthesize representative peptides, and then test them (see Chapter 2). This approach is limited by the ability of such programs to identify candidate sequences and the amino acid sequence of the protein must be known. A second approach is to make fragments of proteins by enzymatic methods or by recombinant DNA techniques (see Chapter 8) and to use these to localize an epitope to a particular region of a protein. The sequence of the whole protein need not necessarily be known at this stage and the sequence of the region containing the epitope(s) can subsequently be identified. A third strategy (epitope scanning), which again requires knowledge of the protein sequence, is to synthesize a number of small peptides (usually overlapping in sequence), each representing a small stretch of the protein, which together represent the complete amino acid sequence of the protein (or that part of it which is of interest). These small peptides are then tested by the appropriate assay system and specific epitopes identified.
Combined differential light scattering with size exclusion chromatography techniques for monitoring conformational changes in x-carrageenan
Authors: Chambers S J , Langdon M J , Williams, P A , White R J 
Published: November 2023

Abstract
Light scattering has been used for many years to characterise water soluble natural polymers. Average molecular properties have been derived from time consuming static Zimm Plot techniques using laser goniometers, while molecular weight distributions have been obtained by combining Low Angle Laser Light Scattering (LALLS) with Size Exclusion Chromatography (SEC). However, problems associated with each has limited their widespread application. Traditional static light scattering is very slow, typically taking half a day to generate a single Zimm Plot.