bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular interactions in herpes simplex virus DNA replication
Authors: Stow Nigel D 
Published: November 2023

Abstract
The family Herpesviridae comprises a diverse and interesting group of viruses characterized by their distinctive virion morphology and the possession of large linear double-stranded DNA genomes which range in size from approximately 120-250 kb (for review see refs 1, 2). Many vertebrate species are natural hosts to herpesviruses including fish, amphibians, reptiles, birds, marsupials, and mammals, and eight viruses that infect man have been identified. The family has historically been sub-divided into the Alpha-, Beta-, and Gammaherpesvirinae subfamilies on the basis of bio-logical properties; a classification largely (but not completely) supported by our rapidly advancing understanding of the genetic relationships amongst these viruses based upon DNA sequencing studies. The prototype and most extensively studied herpesvirus is herpes simplex virus type 1 (HSV-1), a human pathogen belonging to the Alphaherpesvirinae which is most frequently responsible for cold-sore lesions around the lips and mouth. In common with most other herpesviruses, HSV-1 is able to enter a latent state in its natural host. The latent viral genomes reside in a quiescent form within neuronal cells of the sensory ganglia but a variety of stimuli can trigger sporadic reactivation of viral replication giving rise to the recurrent symptoms of disease.
Analysis of DNA virus proteins involved in neoplastic transformation
Authors: Hall Kersten T , Zajdel Maria E Blair , Blair G Eric 
Published: November 2023

Abstract
The small DNA tumours viruses, simian virus 40 (SV40), polyoma viruses, human adenoviruses (e.g. Ad2, Ad5, and Ad12), and human papillomaviruses (e.g. HPV16 and HPV18) encode at least one oncogene product responsible for transformation of cells in culture and formation of tumours in animals. These oncogene products modulate signal transduction and other cellular pathways to abrogate normal cell cycle control mechanisms, and this results in rapid cell proliferation. To achieve this, virus oncogene products frequently interact with cellular proteins such as pRb, p53, or c-Src. Here we give a broad overview of the properties of the major transforming proteins encoded by the small DNA tumour viruses, and their cellular targets. A more detailed treatment of these topics is given in articles in Fanning (1). In addition, a number of reviews give thorough background information on the topics of transforming proteins of human adenoviruses (2-5), SV40 (6), polyoma viruses (7), and human papillomaviruses (8, 9). A good general source book for information on oncogenes, including those of DNA viruses, is Hesketh (10).
Reverse genetics
Authors: Barstead Robert J 
Published: November 2023

Abstract
The nematode Caenorhabditis elegans has about 19000 genes. Approximately 2000 of these have been identified in forward genetic screens for animals with mutant phenotypes. The generation and analysis of such mutants has been the key to the success of the C. elegans model because the in vivo function of a gene can be inferred from its mutant phenotype. In principle, it is possible to identify mutations in the remaining 17000 genes using various forward genetic screens. In practice, however, it is unlikely that forward genetics will lead to such an end in the foreseeable future. Further, now that nearly all the sequence of C. elegans is known, many genetics projects run in reverse: where a gene is identified first through its sequence and then mutations are recovered that inactivate or alter its function. Several imperatives have driven the effort to develop strategies for the targeted inactivation of genes in C. elegans. One might expect that such strategies would include recombination mediated gene replacement, where a wild type copy of a gene is replaced with a mutant copy. Regrettably, recombination mediated gene replacement, though effective in many other systems, has not worked with C. elegans. However, this chapter will describe four strategies that have worked. First, I will describe a method for the epigenetic inactivation of genes using double stranded RNA from the target locus. Following this I will describe three strategies to generate germline mutations at specific target loci. Each of the latter involves a mutagenesis step followed by the selective identification of animals carrying mutations at the target locus.
One-bead one-compound combinatorial library method
Authors: Liu Gang , Lam Kit S 
Published: November 2023

Abstract
The ‘one-bead one-compound’ combinatorial library was prepared by a ‘split synthesis’ method (1-3, see also Chapter 1) such that each solid phase bead displays only one chemical entity although there are approximately 1013 copies of the same compound on a 100 μm bead. This bead-supported library is then assayed for a specific biological activity using on-bead binding (1), or functional assays (4). Alternatively, the compound on each bead is released from the solid support via a cleavable linker for subsequent solution phase assays (5). In either solid phase or solution phase assays, the positive beads are then identified, physically isolated, and subjected to structural determination. If the compound on the bead is a peptide, each individual positive bead is inserted into a cartridge of an automatic protein sequencer for sequence analysis. Alternatively, the peptide or non-peptide compound on each bead is released chemically or photochemically and the releasate is analysed by mass spectrometry. If the structure of the compound cannot be easily determined by mass spectrometry, one can use chemical encoding (6-8) or radiofrequency tagging (9, Chapter 4) strategies.
Combinatorial library synthesis using polymer-supported catalysts
Authors: Kobayashi Shu 
Published: November 2023

Abstract
Combinatorial synthesis (Chapters 1-7), a synthetic strategy which leads to large numbers of structurally distinct molecules, in association with high-throughput screening techniques is making a significant impact not only on the field of drug discovery (1, 2) but also on the development materials sciences and catalysis (Chapters 14, 16).Owing to the availability of a myriad of high-yielding and highly selective reactions, complex and structurally diverse natural and synthetic compounds can be prepared by traditional organic synthesis strategies. However, these reactions do not necessarily provide useful methods for the synthesis of large chemical libraries where each member must be obtained in high yield and selectivity. Thus, we are facing the challenge of developing new reliable synthetic methodologies to prepare these libraries, just as new methodologies for natural product synthesis were required forty years ago (3).
Combinatorial approaches to chiral catalyst discovery
Authors: Snapper Marc L , Hoveyda Amir H 
Published: November 2023

Abstract
In most combinatorial approaches to drug discovery, lead compounds are generally identified from large, structurally diverse libraries (1). Preliminary findings are then often optimized through the subsequent design and examination of more limited libraries that focus and expand on the initial results. In a similar manner, this layered approach to drug discovery and optimization can be adapted to catalyst development (Scheme 1, see also Chapters 14 and 15). In the first phase, a wide range of catalyst candidates can be screened to select specific complexes that effect a reaction of interest. Once a catalyst has been identified that demonstrates the desired reactivity, efforts can then tum toward optimizing the conditions and system to yield the desired selectivity. This two-tiered development strategy can offer distinct advantages in the discovery and identification of catalysts for asymmetric reactions. If the catalyst discovery and optimization protocols are sufficiently rapid and reliable, there is no prerequisite for finding general solutions to catalytic reactions; each reaction can enjoy a catalyst that is designed specifically for the substrate and transformation of interest.
The use of RT-PCR differential display in single-celled organisms and plant tissues
Authors: Nuccio Michael L , Hsieh, Tzung-Fu , Thomas Terry L 
Published: November 2023

Abstract
Differential display of eukaryotic mRNA is a fast and powerful PCR-based technique developed to compare relative variation in gene expression between RNA populations (1, 2). This technique provides a way to monitor differentially expressed genes across various tissues, developmental stages, or physiological states by systematically amplifying cDNA derived from mRNA populations and displaying them on a polyacrylamide gel. The bands that are identified as potential targets of interest can subsequently be isolated, reamplified, and cloned for further verification. Differential display is flexible in two ways. First, it is unnecessary to begin experiments with a poly(A) enriched RNA fraction; they can be performed with as little as 1 µ,g of total RNA per sample. Secondly, many comparisons between samples can be made using various primer combinations in the assay.
Use of suppression subtractive hybridization strategy to identify differential gene expression in brain ischaemic tolerance
Authors: Wang Xinkang , Feuerstein Giora Z 
Published: November 2023

Abstract
Differential gene expression has important functional implications in normal cell growth, differentiation, and in pathophysiological conditions. Ischaemic pre-conditioning (PC) is a phenomenon produced by a short duration of ischae mia that results in a subsequent resistance to severe ischaemic tissue injury (i.e. ischaemic tolerance). This phenomenon has been described in heart and brain (1-3). To identify genes that are specifically regulated in PC, we applied a tech nique using a PCR-based cDNA subtractive strategy termedsuppression subtractive hybridization(SSH) (4).
Construction and applications of gene microarrays on nylon membranes
Authors: Mooney Jeffrey L , Kayne Paul S , O‘brien Shawn P , Debouck Christine M 
Published: November 2023

Abstract
The rapid advancement of expressed sequence tag (EST) and genomic sequencing has been paralleled by the need to develop methodologies for the functional characterization of newly identified genes. Since the expression pattern of a gene provides direct or indirect information about its function, a number of new approaches have been developed to determine the normal tissue distribution of large numbers of genes and/or to identify genes that are differentially expressed between two or more given tissues or cell types. Some of these methods are designed for thede novaisolation of genes expressed at different levels in compared tissues or cell types, e.g. differential display (DD) (1), and related methods such as RNA fingerprinting by arbitrary primer PCR (RAP-PCR) (2), also representation difference analysis (RDA) (3), and suppressive subtractive hybridization (SSH) (4). The other methods exploit high-throughput sequencing and sequence databases either to estimate transcript abundance, e.g. EST numerical analysis (5) and serial analysis of gene expression (SAGE) (6), or to construct DNA microarrays of thousands of gene sequences derived from the databases, e.g. oligonucleotide arrays (7) or gene fragment arrays (8). Individual laboratories need to balance the pros and cons of each technique, including labourintensiveness and the need for expensive equipment, and decide which of these methodologies is best suited to study their particular biological problem.
Enzymes involved in the synthesis of PtdIns(4,5)P2 and their regulation: PtdIns kinases and PtdInsP kinases
Authors: Tolias Kimberley F , Carpenter Christopher L 
Published: November 2023

Abstract
Phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) is a glycerol-phospholipid found predominantly in the inner leaflet of eukaryotic plasma membranes (Fig. 1). Although it constitutes less than 0.05% of total cellular phospholipids, PtdIns(4,5)P2 plays a critical role in intracellular signalling. PtdIns(4,5)P2 is best known for its ability to serve as a precursor for the second messengers inositol 1,4,5-trisphosphate (Ins(1,4,5)P3) and diacylglycerol (DAG). Ins(1,4,5)P3 and DAG are generated from the hydrolysis of PtdIns(4,5)P2 by phospholipases C (PLCs) following agonist stimulation (1, 2). Production of Ins(1,4,5)P3 triggers a transient rise in intracellular calcium (Ca2+), while the generation of DAG activates protein kinase C (PKC) family members.
Regulation of chloride channel conductance by Ins(3,4,5,6)P4; a phosphoinositide-initiated signalling pathway that acts downstream of Ins(1,4,5)P3
Authors: Ho Melisa W Y , Carew Mark A , Yang Xiaonian , Shears Stephen B 
Published: November 2023

Abstract
The Ins(1,4,5)P3-mediated mobilization of cellular Ca2+stores is a well-known consequence of stimulus-dependent PtdIns(4,5)P2turnover (1). Thus, reviews on the actions and metabolism of Ins(1,4,5)P3, together with reviews on the Ca2+channels that are gated by Ins(1,4,5)P3, often feature prominently in multichapter publications that are devoted to ‘phosphoinositide’ biology. However, much less attention has typically been given to a receptor-dependent metabolic event that occurs downstream of Ins(1,4,5)P3, namely, the Ins(1,3,4)P3-regulated Ins(3,4,5,6)P41-kinase/ Ins(1,3,4,5,6)P51-phosphatase metabolic cycle (Fig. 1). The interconversion of Ins(1,3,4,5,6)P5with Ins(3,4,5,6)P4is significant because Ins(3,4,5,6)P4is a cellular signal that inhibits the ionic conductance through Ca2+-activated Cl–channels in the plasma membrane (2). These ion channels contribute to the regulation of salt and fluid secretion, and may also participate in osmoregulation, pH balance, and control of smooth muscle excitability (3–6). Thus, Ins(3,4,5,6)P4may regulate several important physiological processes. The inclusion of a review of this topic in a volume devoted to phosphoinositides provides a timely opportunity to draw more attention to this signalling process.
Gene expression analysis via cDNA microarrays of laser capture microdissected cells from fixed tissue
Authors: Salunga Ranelle c , Guo Hongqing 
Published: November 2023

Abstract
The enormous number of DNA and mRNA sequences available to researchers, coupled with cDNA microarray technology, now allows for gene expression to be studied on a massive scale. Using microarrays, thousands of genes from organisms such as S. cerevisiae (1, 2) and A. thaliana (3), as well as those from mammalian species (4), have been analysed. However, most methods that have been described to date have relied on acquiring microgram quantities of messenger RNA or poly(A) RNA from pure populations of cells, in order to synthesize cDNA probes (1-6).
Expression data and the bioinformatics challenges
Authors: Heller Michael J , Tu Eugene , Holmsen Anita 
Published: November 2023

Abstract
First, and foremost, although every gene is present on its respective chromosome in every cell of an organism, it is not necessarily being transcribed into an active gene product. In fact, the current assumption is that many of the genes are silent or expressed at very low levels in certain cell types. In other words, the number of instances of many genes’ mRNA is, presumably zero. So, although we might know exactly what function a gene might code for-its capability or use value-in practice, it might have no utility at all in a particular cell under certain conditions.
Threading methods for protein structure prediction
Authors: Jones David , Hadley Caroline 
Published: November 2023

Abstract
As the attempts to sequence entire genomes increases the number of protein sequences by a factor of two each year, the gap between sequence and structural information stored in public databases is growing rapidly. In stark contrast to sequencing techniques, experimental methods for structure determination are time-consuming, and limited in their application, and therefore will not be able to keep pace with the flood of newly characterized gene products. The develop ment of practical methods for predicting protein structure from sequence is therefore of considerable importance in the field of biology.
Protein family-based methods for homology detection and analysis
Authors: Henikoff Steven , Henikoff Jorja 
Published: November 2023

Abstract
Most methods for homology detection have traditionally relied upon pairwise comparisons of protein sequences, and in recent years, several improvements in pairwise methods have been introduced (see Chapter 8). But, with sequence data becoming available at an accelerating rate, there is an increasing opportunity to use multiple related sequences for improved homology detection. Even when functional information is lacking for known members of a protein family, these members can be aligned and the alignments used in searches. Protein multiple alignments have been shown to improve performance of secondary structure prediction methods by identifying constraints on positions (1, 2), and so it seems reasonable to expect that improvements will be likewise obtained by using multiple alignments for homology detection and analysis. In this chapter were view some of the numerous methods that are aimed at achievement of this goal.
Epithelial stem cell identification, isolation and culture
Authors: Hudson David 
Published: November 2023

Abstract
This chapter will discuss the ways in which the identification and characterization of stem cells from various epithelial tissues can be approached. Specific protocols are given for techniques that have been shown to be effective in studies involving one of the best-characterized epithelial stem cell models, epidermal keratinocytes. First, methods involved in the separation of an epithelial cell type from other cells will be examined, followed by ways in which the proliferative capacity of such a cell type can be assessed. Secondly, methods used for the maintenance of primary stem cells in culture and ways of characterizing stern cells using immunocytochernistry will be described. Details of Basic Cell Culture have been described in another edition of The Practical Approach series (1).
High performance liquid chromatographic assays
Authors: Syed Shabih E H 
Published: November 2023

Abstract
Liquid chromatography is a separation process in which a mixture is separated into its individual components followed by their detection with a suitable monitor. Optimization of the resolution of the separated components, as well as speed of separation, has been a major interest of many researchers for a very long time. It is well known that the above parameters are directly affected by the size and nature of stationary-phase particles. In conventional liquid chromatography, where gravity was usually used to pull the solvent or mobile phase through a column packed with a stationary phase, a lower limit on the size of particles was eventually reached beyond which flow under gravity completely diminished.
Electrochemical assays: the pH-stat
Authors: Brocklehurst Keith 
Published: November 2023

Abstract
pH-stat assays are used to monitor the progress of chemical reactions in which protons are liberated or taken up. This is achieved by measuring the quantity of base or acid that needs to be added at various times to keep the pH essentially constant. The technique was developed in 1923 by Knaffle-Lenz (1) in connection with his work on esterases. It has since been applied widely in many biochemical systems (see ref. 2 for early examples and refs. 3 – 5 for more recent examples). In a more general sense, ‘stat’ techniques are used to monitor an even greater variety of reactions in which a chemical species that is either generated or consumed can be detected by using electrodes. Reactions involving metal ions can be monitored by using ion-selective electrodes and reactions involving redox changes by using platinum electrodes.
Plant cell biology
Authors: Ceriotti Aldo , Vitale Alessandro , Paris Nadine , Frigerio Lorenzo , Neuhaus Jean-Marc , Hillmer Stefan , Robinson David G 
Published: November 2023

Abstract
The ability to express heterologous proteins in plant cells, and to study the subcellular localization of heterologous and endogenous polypeptides is central to many studies in the field of plant cell biology. Heterologous expression and metabolic labelling are, together, two powerful tools to study intracellular transport and protein-protein interactions. However, it is often the combination of biochemical and immunohistochemical approaches that gives the more comprehensive view of what is really happening within the cell. Accordingly, the first part of this chapter will present a protocol for transient expression in tobacco protoplasts, while two other sections will be devoted to immuno labelling for confocal microscopy observation and immunogold electron micro scopy, respectively.
Protein purification
Authors: Slade Susan E , Dalton Howard 
Published: November 2023

Abstract
This chapter outlines the main features and requirements for the successful purification of a target protein from either its native or recombinant host. For each of the commonly used separation techniques an experimental protocol is described. The aim of purification is to obtain pure target protein in a structurally or functionally active form from a crude lysate. In many cases, pure protein is required only so its gene can be isolated using amino acid sequence information, in which case only a small quantity of protein may be required. Therefore, it is important to establish the purity and quantity of protein required from the procedure before embarking on any purification method. Often this decision is determined by the availability of raw material and the concentration of target protein within the host cell or culture supernatant. The increasing use of mass spectrometry to determine molecular mass, subunit composition, amino acid sequence, and establish the nature of protein-ligand interactions, requires a high level of target protein purity
Biophysical methods in structural cell biology
Authors: Agbandje-McKenna Mavis , Edison Arthur S , McKenna Robert 
Published: November 2023

Abstract
Over the past several decades biophysical methods have become essentials tools for studying biology at the molecular level, and have become an inter disciplinary subject with interplay into biology, chemistry, and physics. It has also become very apparent that the instrumentation and methods used are key components for elucidating structure and function at the molecular level. Biological processes are governed by numerous intricate arrays of macro molecular interactions. The role of the structure biologist is to visualize these interactions in three dimensions. This is essential for a full understanding of these interactions, as ‘seeing is believing’, and provides a means whereby strategies can be devised to ‘correct’ interactions that go wrong or ‘prevent’ undesirable interactions caused by diseases.
Sterilization
Authors: Roberts Peter L 
Published: November 2023

Abstract
Effective sterilization techniques are essential prerequisites for practising the art of cell culture. Cell cultures provide an ideal environment for the growth of micro-organisms including viruses, and it is only by excluding such agents that cells can be successfully cultured and meaningful experimentation can be carried out. In this chapter the various methods used for sterilization will be reviewed including some theoretical background but concentrating on practical aspects of their use. In addition to cellular micro-organisms, the unique problems posed by viruses and prions will be considered. For further general background information see refs. 1–3.