bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time series analysis
Authors: Dunstan F D J 
Published: November 2023

Abstract
In many biological and medical situations a variable is observed sequentially over a period of time. The resulting set of observations, ordered with respect to time, is called a time series. For example, if the temperature in a certain place is measured at noon on each day for a year, the resulting set of values is a time series of length 365 (provided the year is not a leap year). Similarly, if the acidity level of a lake is measured monthly for five years, a time series of length 60 results. While, in many branches of statistics, when a set of observations is made they are assumed to be independent for subsequent analysis, one of the key features of a time series is that the observations are almost invariably dependent. The analysis of the series acknowledges this dependency in modelling the series and, in some applications, exploits this dependency to forecast future values. In the past, time series analysis has been developed largely in the areas of economics and engineering, but recently there has been a growing realization that it is a subject with important applications in biology and medicine and there is increasing interest in its use in these fields.
Electrophysiology of Xenopus oocytes: an expression system in molecular neurobiology*
Authors: Fraser S P , Moon C , Djamgoz M B A 
Published: November 2023

Abstract
Oocytes are unfertilized egg cells which can reach more than 1 mm diameter at later stages of development in lower vertebrates and thereby enable intracellular recording with multiple electrodes to be performed with ease (1). Furthermore, all the biochemical steps, from translation of messenger ribonucleic acid (mRNA) to insertion of protein into the plasma membrane, which normally occur rapidly upon fertilization, may also be induced by injection of ‘foreign’ mRNAs (2, 3). If the resulting protein is capable of generating an electrophysiological signal, as in the case of neurotransmitter/ hormone receptors, ion channels, and pumps, then electrophysiological recording can be used to assay the induced characteristic. Oocytes of the clawed frog Xenopus laevis in particular have been found to be highly efficient in this respect. They have become indispensible in studies aiming al elucidation of the molecular basis of function in proteins, especially those of the nervous system. The aim of this chapter is to give an account of the electrophysiology of Xenopus oocytes with an emphasis on practical aspects. An earlier account of this topic (‘Functional expression in the Xenopus oocyte of mRNAs for receptors and ion channels’) was given in 1987 by Barnard and Bilbe in Neurochemistry: A Practical Approach.
Iontophoresis in the mammalian central nervous system
Authors: Roberts M H T , Gould T 
Published: November 2023

Abstract
The microiontophoretic application of drugs onto neurones of the central nervous system can be one of the more seriously misused of pharmacological techniques. It remains, however, almost the only way of applying relatively few molecules rapidly into the vicinity of central synapses. The technique gets closer to mimicking synaptically released neurotransmitter than any other, but its limitations must be thoroughly understood or very misleading data will emerge. This chapter will outline the strengths of the technique, as well as the methodological constraints, and will give practical examples of how it may sensibly be used. It will also discuss common mistakes which should be avoided.
The cdc2 kinase: structure, activation, and its role at tnitosis in vertebrate cells
Authors: Basi Gabriele , Draetta Guilio 
Published: November 2023

Abstract
In the current view of eukaryotic cell cycle control, the existence of factors which positively regulate the progression through different phases of the cell cycle is assumed. In the last few years much progress has been made towards the molecular characterization of a factor which promotes entry into mitosis called MPF (M-phase promoting factor). The first evidence for the existence of such a factor dates back to studies in the slime mould Physarum polycephalum(1). P. polycephalumis a plasmodial organism (myxomycete) in which nuclear division is naturally synchronous, and therefore it is particularly suitable for studying the regulatory mechanisms controlling entry into mitosis. Experiments in which plasmodia at different stages of the cell cycle were fused, revealed the existence of a positive regulator of mitotic initiation, the levels of which fluctuated during the cell cycle, reaching a peak just prior tomitosis. The results also indicated that protein synthesis was required for the appearance of the mitotic factor and suggested that a translocation of this factor from the cytoplasm to the nucleus occurred shortly before the qnset of mitosis. More than twenty years after this initial observation, MPF was characterized and it was confirmed that the view proposed for the regulation of mitosis in P. polycephalumis essentially correct for all eukaryotes.
Capping, methylation, and 3’-end formation of pre-Mrna
Authors: Wahle Elmar , Keller Walter 
Published: November 2023

Abstract
This chapter deals with three covalent modifications of mRNA precursors that do not change the RNA’s coding sequence: capping of the 5’ end; cleavage at the 3’ end followed, in nearly all cases, by the addition of a poly(A) tail; and methylation of internal bases. Both terminal modifications-cap and poly(A) tail-arc thought to be involved in the same set of reactions, splicing, RNA transport, translation initiation, and RNA stabilization or regulation of mRNA decay. Interestingly, there are indications of a direct or indirect interaction between 5’ end and 3’ end (1, 2). The function of internal methylations is unknown.
Trans-splicing
Authors: Nilsen Timothy w. 
Published: November 2023

Abstract
Intermolecular (trans-) splicing is by definition an RNA-processing reaction which precisely joins exons from separately transcribed RNAs. As discussed elsewhere in this volume, there are four types of cis-splicing reactions: excision of group I introns (in many cases by autocatalysis) (see Chapter 1); excision of group II introns (in some cases by autocatalysis) (see Chapter 1); snRNP-mediated splicing of nuclear pre-mRNAs (see Chapters 4-7); and enzymatic removal of introns from pre-tRNAs (reviewed in 1, 2).
mRNA editing
Authors: simpson Larry , Thiemann otavio h. 
Published: November 2023

Abstract
RNA editing is a term that was coined by Benne et al. (1) to describe the apparently post-transcriptional insertion of four Us at three sites in the coding region of the cytochrome oxidase subunit II (COII) mRNA in two kinetoplastid species, Crithidia fasciculata and Trypanosoma brucei. This modification overcame a -1 frameshift in the COII gene that had been shown to be evolutionarily conserved in these two species and also in Leishmania tarentolae (2). As additional examples of RNA sequence modifications were reported in a variety of organisms (2-10), RNA editing’ came to be defined in a broad sense as any process that results in the production of an RNA molecule which differs in nucleotide sequence in coding regions from the DNA template, with the exception of classical ds-splicing (11). However, even this definition was rendered obsolete by the discovery of specific sequence changes in rRNAs and tRNAs in several organisms, in one case involving the insertion of cytidine residues (12, 13) and in some cases the substitution of uridine for cytidine (14) or guanosine for adenosine residues (15). In this review we will only discuss the trypanosome type of RNA editing, which has been termed insertion-deletion editing by Bass (16), to distinguish it from the substitution editing found in other cells.
Fate maps and cell lineage analysis
Authors: Altaba Ariel Ruiz i , Warga, Rachel m. , Stern Claudio D 
Published: November 2023

Abstract
Knowledge about the fates of cells during development is of fundamental importance to our understanding of developmental mechanisms (1). In organisms like the nematode Caenorhabditis elegans, cell number is sufficiently reduced and the embryo is small and transparent enough to make lineage analysis by direct observation of cell divisions relatively straightforward. However, in systems where cell number is greater, special techniques have to be introduced to follow cell fates.
Microinjection Into Drosophila Embryos
Authors: Ingham Philip , Forbes Zan Dy 
Published: November 2023

Abstract
Microinjection of Drosophila embryos is relatively easy to perform and has several important applications. The most common of these is injection of DNA for the production of transgenic flies; the same general approach can be used for injection of RNA, oligonucleotides, metabolites, lineage tracers, cytoplasm, and antibodies, and for transplantion of nuclei or cells between embryos.
Cloning Genes Using the Polymerase Chain Reaction
Authors: Holland Peter W H 
Published: November 2023

Abstract
The polymerase chain reaction (PCR) is an in vitro method for amplifying regions of DNA, utilizing information based on nucleotide sequences flanking the region of interest (1-3). PCR is used in the study of DNA sequence variation, genomic organization or gene expression (the latter using cDNA as a template, reverse transcribed from RNA; Chapter 24). PCR can also be used to amplify DNA from previously uncharacterized genes, if predictions can be made regarding the sequence of part of the gene(s).
Monosaccharides
Authors: Chaplin M F 
Published: November 2023

Abstract
Monosaccharides exhibit a great variety of structural types with vastly different chemical and physical properties. In contrast to the several methods available for the extensive analysis of the other major class of biological molecules, the amino acids, there is no single method which is suitable for the quantitative or qualitative analysis of all monosaccharides. The method of choice will depend on a number of factors including the accuracy required and resources available. There are two techniques available for the quantitative analysis of mixtures of monosaccharides, high performance liquid chromatography (HPLC) and gas-liquid chromatography (GLC). If only a qualitative analysis is needed, either paper chromatography (PC) or thin-layer chromatography (TLC) may be used. Single monosaccharides may be identified by means of mass spectrometry (MS), infra-red spectroscopy (IR), or proton or carbon-13 nuclear magnetic resonance (1H-NMR, 13C-NMR), and quantified by use of specific colorimetric or enzymatic assays.
Neutral polysaccharides
Authors: Pazur John H 
Published: November 2023

Abstract
Polysaccharides are polymers of monosaccharide units joined together by glycosidic bonds which are formed by the elimination of the elements of water between the hemiacetal hydroxyl group of one residue and a primary or secondary hydroxyl group of an adjacent residue (1). Polysaccharides may consist of a small or a large number of residues and in structure may be linear, branched, or occasionally cyclic polymers. These polymers may be homopoly saccharides composed of a single type of residue or may be heteropoly saccharides composed of two or more different types of residues. Originally polysaccharides were named to reflect biological sources or properties of the polymer and many such names have remained in common usage. At the present time, it is the recommendation of the Joint Commission on Biochemical Nomenclature that polysaccharide nomenclature follow the general principles established for organic nomenclature (2). Glycan is the name recommended for a polysaccharide by the Commission.
Glycoproteins
Authors: Montreuil Jean , Bouquelet Stephane , Debray Henri , Lemoine Jerome , Michalski Jean-Claude , Spik Enevieve , Strecker Gerard 
Published: November 2023

Abstract
Glycoproteins (for recent reviews, see refs 1--4), which together with glycolipids constitute the class of glycoconjugates, result from the covalent association of carbohydrate moieties (glycans) with proteins. Glycosylation of proteins represents one of the most important post-translational events because of the universality of the phenomenon. Most proteins are glycosylated, the glycoproteins being widely distributed in animals, plants, micro organisms, and viruses. In addition, the development of recombinant proteins of therapeutic interest represents a formidable challenge since the structure of recombinant glycoproteins must conform with that of the natural ones (5). It has been established that glycans perform important biological roles including.
|DNA bending by sequence and proteins
Authors: Travers Andrew A 
Published: November 2023

Abstract
A fundamental problem confronting any living organism is how to package an immense length of DNA in an organised manner into a small volume. One solution is to compact the DNA by the tight bending of the duplex in the form of a superhelix which can itself then be folded into a more compact structure. Because the DNA double helix possesses axial stiffness, the bending necessary for this packaging is normally mediated by proteins which may themselves then promote further assembly into higher-order nucleoprotein structures. However, in addition to this primary structural role, DNA bending is also an essential component in the formation of the nucleoprotein complexes required for site-specific recombination and for the initiation of transcription and DNA replication.
Oxygen, proton and phosphate fluxes, and stoichiometries
Authors: Hinkle Peter C 
Published: November 2023

Abstract
The measurement of coupling ratios should never be considered a routine undertaking, for history shows that practically every example went through several stages of eliminating systematic errors before the current relative consensus was reached. For example, traditionally the P/O ratio of mitochondria with succinate was thought to ‘approach’ 2.0, but currently it is considered to be 1.5 (1). This is partly due to the fact that measurements of oxygen and protons are rather prone to error. Errors may also result from the frame of mind of the experimenter. Since ratios are dimensionless and reflect the mechanism of the coupling process they are hard to view with objective detachment. I will not review the sad history of errors in ratio determinations, which have happened to most workers in the field, including myself, but will describe examples of what seem to be the most reliable methods currently used to measure coupling ratios and some of the sources of error which should be avoided.
Membrane permeability and transport
Authors: Voegele Ralf T , Marshall Emmalee V , Wood Janet M 
Published: November 2023

Abstract
The limited permeability of biological membranes to large and/or hydrophilic solutes allows cells to modulate their own composition and to base their energy metabolism on transmembrane electrochemical potential gradients. Our current understanding of those phenomena, which were first placed within a comprehensive theoretical framework by Peter Mitchell (1), is based on measurements of membrane structure, of membrane permeability, and of transmembrane solute fluxes mediated by enzymes denoted as transporters. Photosynthetic and respiratory electron transport chains and ion-motive adenosine triphosphatases (ATPases) mediate creation of the membrane potential (Δψ), formation of transmembrane electrochemical potential gradients (Δμ1), and coupling of those gradients to the synthesis and hydrolysis of ATP. The membrane potential, solute gradients, ATP, and phosphoenolpyruvate (PEP) serve as the energy supplies powering many other transport reactions. Methodologies for the estimation of Δψ and of the protonmotive force (ΔμH+) are described in Chapter 3 of this volume. This chapter describes methodologies for the measurement of passive and transporter-mediated transmembrane solute fluxes. It does not describe methods specifically designed for the study of membrane channels. Detailed descriptions of theories, procedures for the preparation of cells, organelles, and membrane vesicles, and of methods for transport measurements can be found in other books in the Practical approach series and in the Methods in enzymology series of books.
Reconstitution of bioenergetic proteins and the uses of proteoliposomes
Authors: Wrlgglesworth john M 
Published: November 2023

Abstract
A variety of membrane proteins are involved in bioenergetic processes such as ATP synthesis, ATP hydrolysis coupled to ion and metabolite translocation, and redox reactions coupled to proton and sodium ion pumping. A study of their mechanism of action is often aided by purification and reconstitution into artificial bilayer systems, the most widely used of which is the liposome (1, 2). The advantage of reconstituted systems is that vectorial reactions of the protein can be recreated under defined conditions. The disadvantages are largely methodological. Problems can arise in the choice of reconstitution method, the lipid composition of the bilayer for optimum activity, and the yield and homogeneity of the final preparation. In addition, the properties of the vesicles themselves can impose constraints on the function of the protein. For example, the small vesicle size produced by some methods of preparation means that the electrogenic movement of just a few charged molecules can generate a significant membrane potential.
Quantitative biological assays for individual cytokines
Authors: Wadhwa Meenu , Bird Christopher , Page Lisa , Mire-Sluis Anthony , Thorpe Robin 
Published: November 2023

Abstract
Bioassays for IL-α and β commonly utilize the ability of this cytokine to induce IL-2 production by T cell-lines such as EL4.6.1 and LBRM 33, or in primary cultures of thymocytes (LAF assay). Alternatively, IL-1 can be assayed by measuring its ability to stimulate the proliferation of lines such as the subclone DlOS of the murine T-helper cell line D10.64.1 (8). A subclone, NOB-1, of the murine thymoma line EL4.6.l provides a simple and sensitive bioassay for IL-1 (see Figure 1). This line produces IL-2 in response to both human and murine IL-1, which is measured using the CTLL-2 cell-line based assay (see Section 2.1).
Identification and localization of cytokeratins
Authors: Mackenzie Ian C , Gao Zhirong 
Published: November 2023

Abstract
The patterns of polarization, stratification, and maturation that characterize epithelial differentiation in vivo are usually lost when epithelial cells are grown on plastic substrates using standard cell culture methods. However, epithelia cultured on organic matrices containing mesenchymal cells often redevelop regionally specific patterns of growth and structure, and such culture techniques thus provide unique opportunities for the in vitro investigation of many aspects of epithelial differentiation and function. The demonstrable effects of mesenchyme on epithelial differentiation in organotypic cultures illustrate the importance of tissue interactions in the maintenance of normal epithelial structure. Organotypic cultures provide valuable systems for the study of the actions and molecular nature of these mesenchymal influences.
Xenobiotic metabolism in epithelial cell cultures
Authors: Guillouzo Andre , Chesne Christophe 
Published: November 2023

Abstract
Individuals are exposed to a variety of xenobiotics which are present in their environment (i.e. air, water, etc.), are administered (i.e. medicines), or are ingested (i.e. beverages and foods). Many of these compounds are lipophilic and must be converted to more hydrophilic metabolites in order to be eliminated. Most, if not all epithelial cells, contain some capacity to metabolize foreign compounds, however hepatocytes contain the most diverse and active xenobiotic metabolizing system. This explains why the hepatic enzyme profile has been the most extensively analysed and why it is critical to determine hepatic biotransformation of new compounds that could reach the systemic circulation. To gain this information, in vitro liver models and particularly cultured liver cells are increasingly used.
A model of the blood—testis barrier for studying testicular toxicity
Authors: Steinberger Anna , Jakubowiak Andrzej 
Published: November 2023

Abstract
Although diverse classes of chemicals have been found to produce spermatogenic damage in experimental animals, their primary target site(s) and/or mechanisms of action are, in most cases, not known (1). Certain compounds, e.g. diester phthalates, need to be metabolized to monoesters in the liver or gut before they can exert a toxic effect on the testis (2). A toxicant may affect the male gametes indirectly by interfering with the production of androgens by Leydig cells, or with various functions of Sertoli cells, e.g. metabolism, vectorial secretion, and the formation of specialized tight junctions. As Sertoli cells are frequently affected by exposure to testicular toxicants, they have been most widely utilized in studies of testicular toxicity in vitro.
Chromatin replication and assembly
Authors: Sogo José M , Laskey Ronald A 
Published: November 2023

Abstract
Chromosome replication is one of the most complex problems facing the cell. Not only must it produce exactly two accurate copies of the parental DNA, but it must copy patterns of chromosomal proteins. In this chapter we start by introducing the mechanism of eukaryotic DNA replication and some of the proteins involved. Next we consider eukaryotic origins of replication focusing on the contrast between the well-defined simple replication origins of lower eukaryotes or viruses and the paradoxically complex origins of metazoan cells. We then discuss how old nucleosomes are distributed and new nucleosomes assembled at replication forks. Finally we consider the termination of replication and the problems posed when two adjacent replication forks meet.
Initiation of expression: remodelling genes
Authors: Hager Gordon , Smith Catharine , Svaren, John , Hörz Wolfram 
Published: November 2023

Abstract
The periodic nucleosomal organization of DNA in eukaryotic cells has been appreciated for more than twenty years (1). However, despite the ubiquity of nucleosomes, the exact role which nucleosome structure plays in transcriptional regulation has been, and remains, a subject of vigorous debate. The omnipresent nature of nucleosome structure itself, which was initially an advantage in chromatin studies, has made it difficult to target studies in vivo to this problem.
Epigenetic regulation in Drosophila: a conspiracy of silence
Authors: Eissenberg Joel C , Elgin Sarah C R , Paro Renato 
Published: November 2023

Abstract
Understanding the mechanisms of epigenetic regulation, by which cell-specific gene silencing is established and stably maintained, is a major unresolved challenge. Gene expression in eukaryotes relies upon the accessibility of the DNA template to RNA polymerase and a variety of accessory proteins. It is clear that the accessibility of regulatory elements can be controlled by the chromatin structure at a given locus: in spite of the availability in a given cell of all of the requisite DNA-binding proteins, a gene can remain silent, and this silenced state can be propagated faithfully through mitosis. This might be accomplished by alternative modes of packaging DNA into a nucleosome array, but almost certainly involves other types of packaging as well.