bluuebunny/crossref_metadata_2025_split huggingface dataset:
G proteins I: Gs and Gi
Authors: Mumby Susanne M 
Published: November 2023

Abstract
Cells respond with remarkable speed and specificity to the many environmental cues that they encounter. Signal transduction mediated by heterotrimeric G proteins is a common strategy among eukaryotes to relay extracellular information to the interior of the cell. This strategy is employed in physiological functions ranging from mating in yeast to vision in humans. External primary messengers, such as light, odorants, hormones, chemoattractants, and neurotransmitters, stimulate antennae-like receptors that activate G proteins. The activity of second-messenger-producing effectors are, in turn, modulated by the activated G proteins. A relay diagram of G-protein signalling is shown in Fig. 1. The specific examples shown, hormone-sensitive adenylyl cyclase and visual transduction (Fig. 1, lines a-c), are the most extensively studied systems, on which much of our current knowledge of G-protein-mediated signal transduction is based.
Signal transduction is initiated at the plasma membrane by G-protein-coupled receptors, characterized by amino-acid sequences predicted to form seven membrane spans (Fig. 2). Extracellular-facing aspects of the receptor bind agonist and intracellular portions thus are enabled to interact fruitfully with a cognate G protein positioned at the inner face of the plasma membrane. G proteins are composed of a, [3, and ‘Y subunits whose deduced amino-acid sequences lack clear hydrophobic stretches that would be anticipated to span the bilayer. Instead, G proteins are modified by lipids that facilitate their interaction with proteins and/ or lipids comprising the plasma membrane. Effectors, including adenylyl cyclase and ion channels, span the membrane (Fig. 2) but others do not. Light-activated cGMP phosphodiesterase (PDE), for example, is found in cytosolic and membranous fractions of retinal cells.
GTPases in protein translocation and protein elongation
Authors: Freymann Douglas M , Walter Peter 
Published: November 2023

Abstract
Each family of GTPases builds upon a structural core in distinct ways to effect the GTPase switch (1), by which the protein undergoes a transition between’active’ and ‘inactive’ states (2-4). In this chapter we describe the structure and function of two GTPase families not covered in depth elsewhere in this volume: the GTPase subunits of the signal recognition particle (SRP) and SRP receptor (SR), which mediate cotranslational protein targetting (5), and the elongation factors in protein synthesis, taking the GTPases EF-Tu and EF-G as representatives of the family (6-11). We cannot hope to do justice to the breadth of each field, but focus on orienting the reader to the role of the GTPase in the biochemistry of each system.
GTPases targetted by bacterial toxins
Authors: Aktories Klaus , Schmidt Gudula , Hofmann Fred 
Published: November 2023

Abstract
Members of the GTPase superfamily operate as molecular switches in numerous signal-transduction pathways to control such diverse cellular processes as differentiation, proliferation, and the organization of the actin cytoskeleton. These master regulators are the specific targets of a large array of bacterial protein toxins (Table 1)(1). In an extremely efficient manner, the toxins cause the covalent modification of eukaryotic GTPases, resulting in drastic changes in their biological and biochemical properties. It has been known for many years that eukaryotic GTPases are substrates for numerous distinct bacterial ADP-ribosyltransferases. Diphtheria toxin was the first example of such a bacterial toxin and was shown to elicit its biological activity by ADP-ribosylation of the GTPase elongation factor 2 (2). Other well-known ADP-ribosylating bacterial toxins are cholera toxin (3, 4) the group of heat-labile E. coli enterotoxins (5), and pertussis toxin (6), all of which ADP-ribosylate heterotrimeric G proteins of the Gs and Gi families. More recently, small GTPases belonging to the Rho and Ras subfamilies have also been shown to be targets of bacterial toxins. The group of C3-like transferases, including the prototype Clostridium botulinum exoenzyme C3 (7-9), selectively ADP-ribosylates Rho, rendering it biologically inactive, while Ras appears to be an in vivo target of the ADP-ribosyltransferase exoenzyme S from Pseudomonas aeruginosa. Small GTPases are not only substrates for bacterial ADP-ribosyltransferases, but also serve as targets for toxins that act by monoglucosylation (e.g. the large clostridial toxins) (10) or by deamidation (e.g. cytotoxic necrotizing factors) (11).
Functional genomics: approaches and methodologies
Authors: Livesey F J , Hunt Stephen P 
Published: November 2023

Abstract
Selective deployment of the genome is as important for prokaryotes with genomes of 2000 genes as it is for humans with 100000 genes. The purpose of functional genomics is to place all of the genes in the genome within a functional framework, both in the most basic terms of what the protein encoded by each gene does and also in the broadest sense of the role of each gene in the overall functioning of the cell and organism. This definition of functional genomics carries the clear implication that studies of gene function must advance on both of these levels simultaneously.
Analysis of gene expression in single cells using three prime end amplification PCR
Authors: Freeman Tom C , Dixon Alistair K , Lee Kevin , Richardson Peter J 
Published: November 2023

Abstract
Many tissues and biological systems are composed of highly heterogeneous cell populations. This makes it difficult to correlate the functional characteristics or composition of a system as a whole with the activity and molecular profile of individual cell types. In the central nervous system for example, many are attempting to dissect the biochemical basis of cell function and unravel the complex interactions that take place between neurons. In cancer, there is a great need to examine the specific changes that occur in the malignant cells in isolation of the surrounding ‘normal’ non-transformed cell population, in order to understand the progression of the disease and identify potential therapeutic targets. The ability to analyse gene expression in single or small populations of cells provides a powerful tool to identify the differences between one cell type and another, and correlate function with the presence of specific gene products. There are a number of approaches available for studying the expression of genes at the cellular level.
Proteome research: methods for protein characterization
Authors: Humphery-Smith Ian , Ward Malcolm A 
Published: November 2023

Abstract
The term proteomics was first introduced into the scientific literature in 1995 to define ‘the total protein complement of a genome’ (1) and has become an integral part of gene-expressionanalysis (2). However, proteomics did not represent a new scientific discipline, but rather one searching for an identity in the Age of Genornics. Proteomics is still largely centred upon two-dimensional (2·D) gel electrophoresis for the initial separation of complex mixtures of cellular proteins. Although this separation science has been with us for some 25years, it is only recently that the associated level of reproducibility has undergone marked improvement, while these advances have also been coupled with advances in the application of mass spectrometry to protein science. Over the last decade, mass spectrometry has become increasingly user friendly and a powerful analytical device. These tools now deliver high mass accuracy, resolution and sensitivity to a point where it is currently impurities associated with sample handling and delivery that limits the threshold of detection for this versatile analytical plat form. Mass spectrometry in the protein laboratory is now the preferred option for protein characterization and can be conducted efficiently on purified proteins present at low femtomole concentrations (3). Other approaches conducted independently to the separation sciences are starting to make their appearance and fall under the heading of second generation proteomics, which utilizes array based approaches to follow protein abundance and protein interactions (4).
Lipid modification of proteins
Authors: Hooper Nigel M , McIlhinney R A Jeffrey 
Published: November 2023

Abstract
Numerous proteins are now known to be covalently modified with one or more lipid species. Indeed, it has been estimated that between 10–50% of all pro teins within mammalian cells may be modified by lipid. Such modifications not only alter the structure of the protein but are also clearly important for the correct functioning of the individual proteins. Cytosolic proteins can be modified with myristic acid (myristoylation), on their N-terminus or by the addition of a prenyl group (farnesyl or geranylgeranyl) (prenylation), on Cys residues which often lie towards the C-terminus. In addition, both cytosolic and mem brane spanning proteins can be modified by the attachment of palmitic acid (palmitoylation) to Cys residues. It is now becoming clear that some proteins are acylated with two different lipid modifications, e.g. by myristoylation and palmitoylation or by prenylation and palmitoylation. Although integral proteins of the plasma membrane have traditionally been considered as being anchored by membrane spanning hydrophobic polypeptides, over 150 such proteins are now known to be anchored in the membrane by a glycosyl-phosphatidylinositol (GPI) moiety. This complex glycan structure is attached to the C-teminal amino acid of the mature protein and serves to tether the protein in the outer leaflet of the bilayer.
Proteolytic processing
Authors: Creemers John M W , Bailyes Elaine M , Lindberg Iris , Hutton John C 
Published: November 2023

Abstract
The eukaryotic cell incorporates a series of specialized compartments in which proteolysis proceeds in a regulated and limited manner. This processing is responsible for such diverse processes as sorting and storage of polypeptide hormones, activation of cell surface receptors, presentation to the immune system of self- and foreign antigens, internalization and dissociation of ligands from cognate receptors, and initiation of secretion via non-classical pathways. The same machinery may be exploited by pathogens as in the activation of polio viral polyproteins in the cytosol, the generation of fusigenic HIV and influenza coat glycoproteins, and for the activation of Pseudomonas and Shiga toxin complexes. The present chapter focuses principally on the secretory pathway taken by proteins which are co-translationally inserted into the lumen of the endoplasmic reticulum and which find their way to the cell surface by vesicle-mediated transport. Specifically excluded are the protein substrates and enzymes which are destined to the lysosome and only mention is made of proteolytic activity which occurs within the endosomal and antigen processing compartments. The latter omission stems in part from lack of understanding of the molecular processes involved but also because the topic is discussed in Chapter 7.
Mutation detection by single-stranded conformation polymorphism and denaturing high performance liquid chromatography
Authors: Dean Michael , Gerrard Bernard , Allikmets Rando 
Published: November 2023

Abstract
Single-stranded conformation polymorphism (SSCP) alone or in combination with heteroduplex analysis (HA) is one of the most widely used and practical manual methods for mutation detection (1). The principal advantage of this method is that it is rapid to perform and can be carried out using equipment available in most molecular biology laboratories. When properly optimized, the method is highly sensitive, and many different mutations within a DNA fragment can often be distinguished on the same gel (2,3). SSCP and HA can be performed on the same gel since, after the denaturation of the sample prior to loading, there is often the re-formation of a significant amount of double-stranded DNA which will appear in a lower position from the single-stranded products on the SSCP gel. Since heteroduplexes can often be resolved from homoduplexes, the appearance of heteroduplexes on the SSCP gel can give additional information on the presence of variants (see Chapter 6 for further discussion and complementary protocols).
Intracellular ionized calcium, magnesium, membrane potential, and pH
Authors: Rabinovitch Peter S , Junet Carl H 
Published: November 2023

Abstract
Calcium has an important role as a mediator of transmembrane signal transduction, and elevations in intracellular ionized calcium concentration ([Ca2+h) are part of the regulation of diverse cellular processes. Measurement of [Ca2+h in living cells is thus of considerable interest to investigators over a broad range of cell biology.
Eukaryotic cells in their resting state maintain an internal calcium ion con centration that is far below that of the extracellular environment, through the regulation of calcium pumps and channels within the plasma membrane and intracellular storage of insoluble calcium. Calcium influx is thought to be initiated by membrane depolarization, which opens voltage-gated channels, or by the binding of ligands to receptor-operated channels. In the latter case, the binding of agonist to its specific membrane receptor causes the activation of phospholipase C which causes the hydrolysis of a membrane phospholipid, phosphatidylinositol 4,5-bisphosphate (PIP2) to yield inositol 1,4,5-trisphosphate (IP3) and 2-diacylglycerol (DAG). IP3 or IP3 metabolites then cause the release of calcium from intracellular stores, while DAG and elevated [Ca2+h activate protein kinase C. Ca2+ and activated protein kinases then continue the cascade of diverse cellular effects. Recent studies have suggested that global intracellular Ca2+ signals arise from the summation and coordination of subcellular elementary release events termed ‘Ca2+ puffs’ (1).
An introduction to human chromosomes and their analysis
Authors: Cross I , Wolstenholme J 
Published: November 2023

Abstract
Cytogenetics is the study of genetic material at the cellular level. Within the nucleus of each cell, the genetic material (DNA), tightly coiled and conjugated with various proteins, forms a number of rod-like structures called chromosomes. In humans, each cell nucleus contains 46 chromosomes (23 pairs). One chromosome of each pair is of paternal and the other of maternal origin. Twentytwo pairs are the same in males and females and are termed autosomes. The twenty-third pair are termed the sex chromosomes and comprise two X chromosomes in females and one X and one Yin males. The chromosomes are visible as discrete, separate structures only at certain stages of cell division. In somatic cells which are dividing naturally in vivo, or that have been induced to divide in a cell culture in vitro, the mitotic cell cycle takes 12-48 h. The chromosomes become visible for a short period, known as mitosis, which lasts around 30 min in each cell cycle. For the remainder of the cycle cells are in interphase and chromosomes are despiralized and not visible, their DNA being diffuse and dispersed within the nucleus. The increasing use of ISH–the binding of labelled DNA probes to their complementary target sequences in the cellular DNA– allows some information about the chromosomal status of an individual to be obtained from the observation of interphase nuclei. However, the majority of cytogenetic investigations involve staining and observation of the chromosomes while they are in mitosis.
Molecular cytogenetic technologies
Authors: Kearney L , Hammond D W 
Published: November 2023

Abstract
The importance of cytogenelic analysis in the study of malignancy has been enhanced over the past decade by the incorporation of a range of techniques based around FISH. In the leukaemias, cytogenelic analysis provides the first step in the identification of genes involved in kukacmogrnc-sis,by identif\ring consist ent chromosomal rearrangements. HSH has ;idded to this capacity by providing a rapid and accurate method for the identification of tr;msloc;ition breakpoints and commonly deleted regions. Progress in identifying consistent rearrange ments in some solid tumours has been more laboriom. The new multicolor ka1yotyping techniques M-FISH and SKY combine the screening polenlial of cytogenetics vvith the accuracy of molecular genetics. These promise to unravel compkx katyotypes associated with many solid tumours, and to uncover new non-random rearrangements. However, these techniques still require metapbasc chromosomes, and are not applicable to all tumour lypes. The advent of CGI-I has provided access to a range of tumour types, circumvPnting rhe need for metaphase chromosomes.
In vivo mutagen-induced chromosome damage in human lymphocytes
Authors: Tawn E J , Whitehouse C A 
Published: November 2023

Abstract
TI1e study of induced chromosome changes in human lymphocytes is well estaiblished for monitoring the gcnotoxic effects of in vivo exposure to radiation and chemicals. Cytogenetic studies can be used to monitor populations for a range of environmental and occupational clastogens and mutagens (1-3) and, for radiation, can provide an estimate of individual dose (4,5). Various endpoints can be studied. These include structural chromosome aberrations, SCE and micronuclei. All require short-term cuilures of peripheral blood lymphocytes with modifications to allow lhe manifestation of the different types of genetic changes.
The role of chaperone proteins in the import and asseinbly of proteins in initochondria and chloroplasts
Authors: Voos Wolfgang , Pfanner Nikolaus 
Published: November 2023

Abstract
Mitochondria and chloroplasts are the two major organelles of eukaryotic cells that have been generated by the endosymbiotic uptake of prokaryotic cells during the early stages of eukaryote evolution (1). Both perform crucial functions mainly in the energy metabolism of the host cells. During the million of years of mutual inter-dependence with the host cell, both chloroplasts and mitochondria have lost their ability to synthesize most of their endogenous proteins. Also during this process, most of their genetic information was transferred to the nucleus. Concomitantly, mechanisms had to evolve that allow a specific transport of proteins from the cytosol to their organellar destination. Due to the endosymbiotic origin, mitochondria and chloroplasts show a special arrangement of several membranes, resulting in multiple subcompartments. Apart from the general problem of how large polypeptides are transferred across biomembranes perse, the particular organellar structure exacerbates the problem of specific preprotein targeting.
Phage display of zinc fingers and other nucleic acid-binding motifs
Authors: lsalan Mark , Choo Yen 
Published: November 2023

Abstract
DNA-binding proteins play important roles in DNA replication, recombination, restriction, modification, repair, packaging, and the control of DNA transcription into RNA. Selecting DNA-binding proteins from pools of combinatorial variants should be a valuable method for the study of these proteins, and furthermore in the design of variants with new DNA sequence-specificity or effector function. In recent years, one key step in this direction has been the selection of zinc finger motifs with predetermined DNA-binding specificity by phage display (1-11), and their use to engineer customized transcription factors for use in research and medicine (reviewed in (12) ). Although zinc finger domains are ideally suited to phage display studies, it is very likely that the lessons emerging from this work will be applicable to many other DNA- and RNA-binding motifs. To this end, the present chapter is intended to bring out these principles in addition to describing the practical aspects of creating and selecting zinc finger phage display libraries.
Introduction
Authors: Mai Sabine , Beatty Barbara G , Squire Jeremy A 
Published: November 2023

Abstract
Human chromosomes have been studied for over a century (1, 2), but not until the 1950s was it determined that the human chromosome complement was diploid and comprised of 46 chromosomes (3, 4). With the development of chromosome pre-treatment procedures and modification of DNA staining techniques in the late 1960s, the identification of each chromosome based on the definition of highly reproducible trypsin-Giemsa or fluorescent banding patterns was obtained. This landmark advance in human cytogenetics allowed researchers to rapidly address specific clinical and research questions and to make excellent progress in understanding the chromosomal basis of many genetic diseases and cancer. To this day classical cytogenetics using banding methods continues to play an important role in the identification and characterization of many different types of chromosomal abnormalities.
cDNA microarrays for fluorescent hybridization analysis of gene expression
Authors: Khan Javed , Saal Lao H , Bittner Michael L , Jiang Yuan , Gooden Gerald C , Glatfelter Arthur A , Meltzer Paul S 
Published: November 2023

Abstract
As a consequence of the human genome project (HGP) the sequence of the entire human genome will be completed by the year 2003 (1). It is estimated that the 3 billion base pairs in the human genome code for between 28000-1200000 genes (2-6).
Spite And Price
Authors: Hamilton W D 
Published: November 2023

Abstract
BY the time the paper of Chapter 4 came out in 1967 I had been living for a year in a flat in a converted mansion close to Silwood House itself. Silwood is in a belt outside London that is better described as countrified than as country, more as paddocky than ploughed, and is a belt where rambling Victorian and Edwardian houses are plentiful. Many are still homes, sometimes to well-known names. For example, John Lennon, the Beatie musician, owned the house just across the road from our Field Station, while Diana Dors, the film star, owned another just down the road. Ordinary mortals on salaries may be able to work in the area but have difficulty living there and most of the staff at Silwood either had houses many miles away or, like me, rented. My landlord at this time was Blue Star Garages Ltd, and the windows of my high-ceilinged flat looked out on their emblem reared over a filling station, one specimen of their chain. Other renting groups of graduate students were scattered through the same building and my flat was shared with Dr Yura Ulehla, a Czech plant physiologist who was then visiting the Field Station, Yura became and still is a close friend. By the time I began writing this paper I had also acquired another close friend, Christine Friess, with whom I was in love. When released at weekends from her studies in London, she usually joined us.
Friends, Romans, Groups …
Authors: Hamilton W D 
Published: November 2023

Abstract
IN 1972 for a second time I found myself asked to discuss at an international symposium the implications of kinship theory for human evolution. In this case the invitation came from Robin Fox, a social anthropologist (now at Rutgers University), and from lrven De Vore, a Harvard primatologist. The symposium was to be in Oxford in July 1973. Compared to the Smithsonian symposium it was to be as small as the other was large and slanted much more to the side of Man, less to Beast. Fox, whom I first met at the Washington conference, was at a quite different intellectual pole of his profession from such as Sir Edmund Leach, who, as mentioned in Chapter 1, had turned down my intended subsidiary study at Cambridge. Fox and I at different times had both worked at the London School of Economics. Perhaps repressed deep in the soul of that institution Hes a streak of heterodoxy that has played a part in our convergence.