bluuebunny/crossref_metadata_2025_split huggingface dataset:
Background on Caenorhabditis elegans
Authors: Hope Ian A 
Published: November 2023

Abstract
The number of researchers using Caenorhabditis elegans as a model system for biological research has grown steadily over the past three decades (see Figure 1). But interest in this species has suddenly soared in response to the success of the C. elegans genome project (1). The genome project was effectively completed in 1998, making C. elegans the first multicellular organism for which the genome has been sequenced. The genome sequence data have emphasized the considerable conservation of biological mechanisms across the animal kingdom that has become apparent through the molecular genetic characterization of biological processes. This conservation confirms the value of C. elegans as a model system, which has contributed and will continue to contribute significantly to our biological understanding of all animals including humans. C. elegans was deliberately selected as a model system (2), primarily because it possessed particularly favourable characteristics for laboratory study and also because it was assumed that similar mechanisms would direct equivalent biological processes in all animal species. This selection has now been shown to be fully justified.
Resins and anchors for solid phase organic synthesis
Authors: Winter Martin , Warrassꝉ Ralf 
Published: November 2023

Abstract
Isolation of the pure intermediates and products in a multi-step synthetic scheme is often the most time-consuming and uneconomical part in the overall process. This effort increases proportionally with the number of synthetic steps. The extent of this problem is greater when several different compounds are to be made in parallel as is the case in combinatorial chemistry. Differences in the physical and chemical properties of members of a chemical library, such as solubility, pKa values, polarity of the building blocks and intermediate products, aggravate to a great extent the standardization of a procedure or may even make it completely impracticable.
Multi-component reactions (MCRs) of isocyanides and their chemical libraries
Authors: Ugi Ivar , Dömlingꝉ Alexander 
Published: November 2023

Abstract
In principle, all chemical reactions correspond to equilibria between one or two reactants and products. In practice, however, preparative chemical reactions proceed irreversibly and, in the absence of competing reactions, extremely high yields of pure products can be obtained (1-3). If more than two (n &gt; 2) reactants are required for the synthesis of a product, usually several (at least n - 1) preparative steps must be carried out. The more preparative steps there are, the more isolation and characterization work must be achieved, and the lower the yields are after each step of the synthetic effort. In contrast with this approach, many products can also be prepared in a one-step, one-pot multi-component reaction (MCR) of three or more starting materials. MCRs are defined as a collection of subreactions taking place simultaneously and/or sequentially, each involving two reacting molecules.
Experimental techniques in fluorous synthesis: a user’s guide
Authors: Curran Dennis P , Hadidaꝉ Sabine , Studer╪ Armido , He§ Mu , Kim Sun-Young , Luo Zhiyong , Larhed* Mats , Hallberg* Anders , Linclau Bruno 
Published: November 2023

Abstract
In discovery research, the ‘reaction’ stage of a synthetic step and the ‘separation’ stage have traditionally been uncoupled. Reactions are executed and then reaction mixtures are purified by using trial and error (or, perhaps more commonly, experience) to select a suitable purification technique. Experimental techniques for combinatorial chemistry and parallel synthesis need to be simple, fast, and efficient, and these needs have precipitated the development of a number of general new approaches for making small organic molecules (1, 2) that couple reaction and separation at strategy level. The goal of strategy level separation is to plan a reaction that can be purified simply by workup (3, 4). In other words, the desired product of a reaction will partition into (or be a part of) one phase, while all the other products of the reaction will partition into another phase. The commonly used phases for organic separations are the gas phase, the water phase, the organic liquid phase, and the solid phase, and these phases can be separated by evaporation, extraction, filtration (used alone or in combination, as appropriate). A number of imaginative and effective ‘workup level’ separation techniques have recently been introduced that take advantage of these different phases (3).
Practical aspects of the experimental design for differential display of transcripts obtained from complex tissues
Authors: Medhurst Andrew D , Chambers David , Gray Julie , Davis John B , Shale Julian A , Mason Ivor , Jenner Peter , Newton Richard A 
Published: November 2023

Abstract
Differential display is a valuable technique for identifying differentially expressed m.RNAs and for cloning their cDNAs (1). Since its introduction in 1992, several technical improvements have increased the successful application of differential display (2-4). Many types of proteins (e.g. growth factors, chemokines, and proteases) have been identified using this technique, implicating their involvement in processes such as apoptosis, cell differentiation, and senescence (5). In addition, differential display constitutes a valuable tool for scientists interested in the identification of novel genes coding for proteins that may be suitable for pharmacological intervention in diseases such as cerebral ischaemia (6) and cancer (7).
Studying gene expression profiles in specialized brain regions by microSAGE
Authors: Vreugdenhil Erno , Datson Nicole 
Published: November 2023

Abstract
The human genome is thought to contain 100 000 genes of which a subset of approximately 15 000 to 20 000 genes is expressed in an individual cell. The set of genes expressed and the stoichiometry of the resulting messenger RNAs, together called a transcriptome, determine the phenotype of a cell, tissue, and whole organism. It is generally accepted that a transcriptome is largely determined by an interplay of hereditary and environmental factors. For example, in the CNS, a challenge from the environment, e.g. a learning or a traumatic experience may lead to an alteration of the transcriptome of target neurons. Thus, transcriptome analysis and subsequent transcriptome comparisons may reveal novel insights in the molecular mechanisms underlying complex processes such learning and memory formation.
Regulation of phosphoinositide-specific phospholipase C isozymes
Authors: Rhee Sue Goo , Poulin Benoit , Lee Sang Bong , Sekiya Fujio 
Published: November 2023

Abstract
The hydrolysis of a minor membrane phospholipid, phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) by a specific phospholipase C (PLC) is one of the earliest key events in the regulation of various cell functions by a number of extracellular signalling molecules (1). This reaction produces two intracellular messengers, diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (Ins(1,4,5)P3), which mediate the activation of protein kinase C (PKC) and intracellular Ca2+ release, respectively. Ins(1,4,5)P3 is further converted by the action of several distinct kinases and phosphatases to various inositol phosphates, some of which have been implicated for distinct cellular functions (see Chapter 10). PtdIns(4,5)P2 is a precursor not only for Ins(1,4,5)P3 and DAG but also for the newly emerging messenger PtdIns(3,4,5)P3 that is produced by phosphoinositide 3-kinase (2; see also Chapter 2). PtdIns(3,4,5)P3 accumulates in cells that have been activated through protein tyrosine kinase (PTK)- and G-protein-linked receptors, and has been known to modulate the activities of cellular effector molecules, such as the small GTP-binding protein Rac, the Ser/Thr protein kinase B (PKB; also known as Akt), phosphoinositide-dependent kinase (PDK; also called PKB kinase), Bruton’s tyrosine kinase (Btk), certain isoforms of PKC, and Grp-1 (a guanine nucleotide exchange factor for the small G proteins ARF) (2). PtdIns(3,4,5)P3 also appears to function as a general component of PLC-γ-dependent calcium signalling pathway (see below). PtdIns(4,5)P2 directly modulates the function of protein kinase C, phospholipase D (PLD), and phospholipase A2 (PLA2) (3–5). PtdIns(4,5)P2 regulates actin polymerization and depolymerization processes by binding to actin regulatory proteins, such as profilin, cofilin, gelsolin, α-actinin, and gCap (6; see also Chapter 5). Finally, PtdIns(4,5)P2 binds to pleckstrin homology (PH) domains and thus serves as a membrane docking site for a host of PH domain-containing proteins (7).
Selection of methods for measuring proliferation
Authors: Wieder Robert 
Published: November 2023

Abstract
In the process of defining the phenotype of a cell, one of the most frequent parameters scientists measure is the rate of proliferation. Often, the first decision that confronts us is that of choosing ‘the right assay’. The selection of an assay is critical to the outcome and depends on a variety of factors. These include the experimental conditions, the cell cycle parameters affected by the variable under investigation, and the source and state of the cells or the tissue to be assayed. To select an appropriate assay, we have to be aware of the events that constitute the cell cycle.
Cell growth and cytotoxicity assays
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. The focus is 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 adapted to other culture vessels.
Cell growth and kinetics in multicell spheroids
Authors: Durand Ralph E 
Published: November 2023

Abstract
This chapter examines cell proliferation kinetics and mechanisms of cell growth control in a complex tissue culture system: three-dimensional multicell spheroids (1). While spheroids are about to enter their fourth decade of use as an ‘in vitro tumour model’ (2), they are also very useful as a model for some normal tissues due to the co-existence of heterogeneous microenvironments that collectively influence their growth properties (3). We will, therefore, briefly characterize the system, indicate many of the novel growth perturbations that arise, and then address some of their implications vis-a-vis proliferation and quiescence.
Assessment of the role of growth factors and their receptors in cell proliferation
Authors: Bishayee Subal 
Published: November 2023

Abstract
The growth of cells in culture and, most likely , in the animal, is subject to control by various agents, such as extracellular signalling proteins (growth factors). These growth factors mediate their pleiotropic actions by binding to and activating high affinity cell surface receptors. At least five important classes of polypeptide growth factors have been identified and their interactions with cell surface receptors well characterized. These are: (a) epidermal growth factor (EGF) and EGF-like factors, a family of 6-7 kDa polypeptides that share a common receptor (EGF receptor); (b) plateletderived growth factor (PDGF), a disulfide-bonded dimeric protein (25-30 kDa) composed of two non-identical but highly homologous polypeptide chains (in different combinations); (c) insulin and insulin-like growth factors, a class of structurally related 6-7 kDa polypeptides which interact with multiple receptors; (d) transforming growth factor-13 (TGF-13; also acts as a differentiation factor), a family of 25 kDa proteins that act through multiple receptors; and (e) the interleukins and their respective receptors (reviewed in ref. 1). It is recognized that ectopic synthesis or overproduction of these growth factors can lead to an autocrine stimulation of growth and expression of the transformed phenotype (reviewed in ref. 2). In addition, aberrant expression of a growth factor receptor due to gene deletion or mutation and overexpression of a normal growth factor receptor gene can also produce transformation (3). This chapter will focus only on growth factors whose receptors display intrinsic tyrosine kinase activity.
Analysis of growth-signalling protein kinase cascades
Authors: Alessandrini Alessandro 
Published: November 2023

Abstract
One of the main questions in signal transduction is how do cells take an extracellular signal and convert it into an intracellular one. The first step that enables this process involves receptors that bind to specific extracellular signals. Most receptors have intrinsic tyrosine kinase activity or have tyrosine kinase activity associated with them. This results in a series of phosphorylation events involving endogenous Ser/Thr kinases. The final steps in a cell’s response to an extracellular signal may involve the reorganization of the cytoskeleton which may lead to motogenesis (cellular migrations) and the transcriptional activation of specific genes that may lead to mitogenesis and/or differentiation. This chapter will focus on the downstream components in signal transduction and, in particular, the MEK/ERK pathway.
Cytometric analysis of the pRB pathway
Authors: Juan Gloria , Traganos Frank , Darzynkiewicz Zbigniew 
Published: November 2023

Abstract
The term retinoblastoma protein (pRB) pathway (‘pRB pathway’) has recently been introduced to define the components and function of the cell cycle regulatory machinery directly associated with phosphorylation of the retinoblastoma susceptibility gene product (1-6). In addition to the central element, pRB, the pathway includes the cell cycle-dependent kinases which phosphorylate this protein (Cdks), activators of these kinases (several types of cyclins), their inhibitors from both the Ink and Kip families (Ckis), and the products whose activation is controlled by pRB phosphorylation, the E2F family of transcription factors (7-9). The pRB pathway serves as the master regulatory switch triggering the cell’s entrance to and progression through the S phase. In non-tumour cells, the pRB pathway responds to changes in cell environment, primarily to growth factors, hormones, and cell to cell interactions, through the respective receptors and signal transduction pathways.
Isolation and visualization of the principal compon.ents of nuclear architecture
Authors: Stein Gary S , Montecino Martin , Mcneil Sandra , Pockwinse Shirwin , Van wijnen André J , Stein Janet L , Lian Jane B 
Published: November 2023

Abstract
It is becoming increasingly evident that gene expression in vivo is functionally interrelated with nuclear architecture. The linear ordering of protein coding sequences in genes, as well as the representation of flanking and intragenic regulatory elements, only partially accounts for transcriptional responsiveness to the broad spectrum of cues from physiological signalling pathways that modulate gene expression under diverse biological circumstances. Equally important, cataloguing protein-DNA and protein-protein interactions at gene regulatory sequences is necessary but insufficient to explain the transcriptional mechanisms that are operative in intact cells and tissues. Rather, there is growing awareness that gene expression must be understood from the perspective of contributions by multiple levels of nuclear organization.
Induction of differentiation of human intestinal cells in vitro
Authors: Cross Heide S , Kallay Enikö 
Published: November 2023

Abstract
The intestinal epithelium is, in principle, a valuable tissue for the study of cell differentiation, as it is spatially organized around its proliferative units, the crypt (small intestine) or the basal section of the crypt (large intestine). The progeny of clonal undifferentiated proliferating cells express eventually at least four very different phenotypes (1), e.g. enterocytes, mucin-producing goblet cells, endocrine cells, and Paneth cells. The determinants of this phenotypic commitment are largely unknown. During the orderly upward migration of cells from crypt to villus along the crypt length in the colon, the temporal sequence of differentiative events can be well defined. However, this situation unfortunately cannot be recreated in intestinal culture systems, probably because of the absence of supportive tissues, and the inability to recapitulate this complex dynamic process with continuous cell proliferation and cell loss within a few days. Thus, in vitro studies of differentiation markers in normal intestinal cells are difficult to perform.
Proliferation and differentiation of human prostate cells
Authors: Thalhammer Therese , Cross Heide S 
Published: November 2023

Abstract
More than 200000 new cases of prostate cancer are diagnosed anually in the USA. Thus, in incidence and prevalence, prostate cancer is the most common malignancy in American men, and black men in the USA have the highest incidence of prostate cancer in the world. Some epidemiological observations in various populations suggest a vital role for steroid hormones in prostate carcinogenesis. Although androgens are clearly the most influential in this respect, others such as oestrogens, retinoids, and vitamin D compounds might also be important. With advancing age, while there is a decline in serum testosterone levels, a concomitant increase of benign prostatic hyperplasia is observed. However, the incidence of microscopic, latent prostate cancer also shows a very close correlation with increasing age and thus decreasing testosterone.
Senescence and im.mortalization of human cells
Authors: Hubbard Karen , Ozer Harvey L 
Published: November 2023

Abstract
Normal vertebrate diploid cells in culture have a finite life-span (1). The maximum number of population doublings is dependent on cell type and species. It has also been shown to vary as a function of age of the donor organism, resulting in its utilization as a model for the proliferative aspects of cellular ageing. Although cells from all species eventually cease to proliferate and become ‘senescent’, the capability to achieve infinite or continuous cell growth (i.e. became ‘immortal’) by mechanisms that overcome cellular senescence is strikingly dependent on the animal species. Rodent cells readily become ‘spontaneously’ immortal such that there are multiple established fibroblastoid cell lines; for example, mouse 3T3 cells. In marked contrast, normal chicken and human fibroblasts (HF) rarely, if ever, become immortal. The observation that many human tumours are immortal cell lines when introduced into tissue culture suggests that overcoming senescence is a stage in carcinogenesis. One experimental manilpulation that has been successful in facilitating the immortalization of HF has been through the introduction of genes from DNA tumour viruses into otherwise normal cells.
Methods to study actin assembly and dynamics in yeast
Authors: Karpova Tatiana S , Cooper John A 
Published: November 2023

Abstract
Budding yeast (Saccharomyces cerevisiae) is a good model organism for studies of the actin cytoskeleton (reviewed in rd. 1 ). Actin and many components of the yeast actin cytoskeleton are highly homologous to cytoskeletal proteins of higher eukaryotes. Another advantage of yeast is the relative simplicity of the actin cytoskeleton. For example, actin and most of the actin-binding proteins are represented by a single isoform. The genetics of yeast is well developed. The genome of yeast has been sequenced. which implifies the search for new actin-binding proteins, either by homology searches or by testing the phenotypes of mutants with targeted ORF disruption.
Video microscopy: protocols for examining the actin-based motility of Listeria, Shigella, vaccinia, and lanthanum-induced endosomes
Authors: Zeile W L , Purich D L , Southwick F S 
Published: November 2023

Abstract
Cellular locomotion takes on many forms—from macrophage tracking and capturing a bacterium during infection to platelet spreading during blood clotting to tumour cell crawling during metastasis to cells dividing during mitosis or meiosis, but the common element is exquisitely choreographed directed movement. There are literally hundreds of proteins and enzymes involved in cell motility, and many of these proteins have multiple and often redundant roles in promoting specific types of motility (e.g. lamellipodial versus filipodial extension). The challenge then for cell biologists is to unravel the protein-protein interactions and other regulatory signals that constitute each distinct mechanism of vectorial movement. To meet this challenge requires both intuition and invention in the development and systematic application of new experimental techniques. Although this chapter describes the specifics of applying video microscopy, microinjection, and immunolocalization to investigate actin-based motility of intracellular pathogens, it is also true that the strategies presented here will be of value to those interested in other forms of cell motility and studies in cell biology in general. Significantly, video microscopy, microinjection, and immunofluorescence have been used with great success in the study of signal transduction pathways, specifically the role of monomeric GTPases in cytoskeletal remodelling(1).
Metabolic alterations associated with apoptosis
Authors: Costa-Pereira Ana P , Cotter Thomas G 
Published: November 2023

Abstract
Apoptosis is an active form of cell death, induced both by endogenous and exogenous stimuli, which occurs under physiological conditions (1, 2). Morphologically, it is characterized by cellular features such as membrane blebbing, cell shrinkage, and chromatin condensation (3). Intracellular events include various types of DNA fragmentation (4), cytoskeletal alterations, and protease activation (reviewed in ref. 5).
Hidden Markov models for database similarity searches
Authors: Birney Ewan 
Published: November 2023

Abstract
Despite the huge number of genes in an organism, the protein coding genes are thought to be made from a limited number of basic protein structures. Evolution has reused these protein structures, combining them to form different proteins, and altering them in different genes to achieve different functions. The diversity of species, each with its own copies of genes made from the limited number of building blocks, means that, for a protein of interest, a number of different related proteins may be found. In this chapter, I will discuss one set of techniques which can be used to take advantage of this diversity of protein sequence. These techniques are all related to the use of profiles, which are also discussed in Chapter 5. In this chapter, the emphasis will be on the use of hidden Markov models (HMMs) for profile analysis. Some practitioners consider profiles to be a type of HMM.
Methods for discovering conserved patterns in protein sequences and structures
Authors: Jonassen Inge 
Published: November 2023

Abstract
The amount of available biomolecular data is exploding: the number of known protein sequences is increasing rapidly while the number of known structures is also increasing, though not as rapidly. A very useful observation in this situation is that common features among proteins can be used to group them into families, and then study the proteins on a family level. By a family we mean a set of proteins sharing some definite biological properties in terms of common function and/or structure, often implying that the proteins have evolved from a common ancestor, i.e. that they are homologous.