bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA editing: posttranscriptional restructuring of genetic information
Authors: Hajduk Stephen L , Sabatini robert S 
Published: November 2023

Abstract
The formation of translatable mRNAs in the mitochondrion of kinetoplastid protozoa often requires the precise addition or deletion of uridines by RNA editing. The sites of uridine insertion and deletion are specified by small guide RNAs (gRNAs) which appear to function in directing the editing reactions. The extent of RNA editing can vary from the modest four uridines inserted into the cytochrome oxidase II mRNA, to the extensive editing seen in the cytochrome oxidase III mRNA of Trypanosoma brucei, in which hundreds of uridines are added and dozens are deleted. In most cases, the precursor mRNAs and the gRNAs needed for their editing are encoded on separate mitochondrial genomes. The gRNAs are encoded by numerous minicircles while the mRNAs are encoded by the less abundant maxicircles. Thus, genetic information from separate genomes is stitched together by the process of RNA editing. In this chapter, the possible molecular basis of RNA editing will be discussed. The biochemical mechanism and the ribonucleoprotein particles (RNPs) involved in these reactions are only now being resolved. The more complex issues of biological function and evolutionary origin of editing will also be considered. We have not attempted to review the editing literature exhaustively here (that has recently been done; see Refs. 1-7) but rather present the alternative views on mechanism, origins and function of what is a truly remarkable biological phenomenon.
History and overview
Authors: Baumberg Simon 
Published: November 2023

Abstract
This chapter sets the scene for the rest of the book by describing the early development of the subject and how the main themes were established. The choice of references reflects three not easily reconcilable aims: to enable the reader to follow how the topic developed and to find a way into recent literature (in conjunction with later chapters), and to give credit to at least some of the scientists principally involved. A brief mention, with selected references, is also given of systems which do not introduce novel mechanisms but which apply to prokaryotic properties of fundamental or applied importance.
Folding proteins
Authors: Rudolph Rainer , Böhm Gerald , Lilie Hauke , Jaenicke Rainer 
Published: November 2023

Abstract
The pioneering studies by Anson, Mirsky, Pauling, Anfinsen, Baldwin, and others paved the way for protein folding to become a major topic in biochemistry (1-3). In subsequent work, theoretical and mechanistic aspects of protein folding and, in recent years, applied and biological aspects were analysed in great detail (4-6).
PCR3
Authors: Herrington C Simon , O’Leary John J 
Published: November 2023

Abstract
PCR in situ hybridization allows the detection of specific nucleic acid sequences and their distribution in the cell. It combines two powerful techniquesin situ hybridization (ISH), which allows cellular localization of DNA and RNA sequences in cells and tissues, and the polymerase chain reaction (PCR), which allows reproducible amplification of rare nucleic acid sequences. The combined technique and its variants greatly enhance the sensitivity of in situ hybridization and add morphological localization to the sensitivity of PCR. Such techniques have enormous potential for research and diagnosis but problems with reproducibility and reliability are often encountered. This book overcomes these problems by describing the key procedures in step-by-step detail and by providing the essential advice needed for success. Topics include: DNA in situ PCR and DNA PCR in situ hybridization (PCR ISH) for the detection of DNA targets in cells; reverse trancriptase in situ PCR (RT-PCR) and RT-PCR ISH for the detection of RNA targets; and PRINS (primed in situ synthesis) for chromosomal analysis in interphase nuclei and metaphase chromosome spreads. There are further chapters on fixation of tissues for PCR, selective ultraviolet radiation fractionation (SURF), application of in situ PCR to human tissues, applications and modifications of PCR-ISH, and automation of in situ amplification. PCR In Situ Hybridization is a unique and timely collection of well-tested protocols for the amplification of DNA and RNA in cells and tissues, drawing on the accumulated knowledge and experience of leading exponents of these techniques. For each topic covered, the authors provide detailed guidance on the key steps in the protocols, numerous hints and tips for success, and advice on trouble-shooting. PCR In Situ Hybridization will be invaluable to molecular biologists, pathologists, geneticists, and all those seeking to perform in situ analyses of nucleic acid molecules.
Protein detection methods
Authors: Merril Carl R , Washart Karen M 
Published: November 2023

Abstract
Advances in detection methods for proteins have paralleled the development of new separation techniques over the last three decades. Selection of the proper protein visualization procedure is as important as the separation technique employed in the analysis of proteins from complex mixtures. The ease of use, speed of detection, level of sensitivity, and integrity of the proteins following detection (i.e. to allow further processing of the proteins if necessary) are important criteria for determining the appropriate detection method. Suitable methods also need to maintain a linear and stoichiometric relationship between protein detection signal and protein concentration.
Video microscopy
Authors: Weiss Dieter G , Maile Willi , Wick Robert A , Steffen Walter 
Published: November 2023

Abstract
A new quality of microscopy, called video microscopy, emerges, if one observes the specimen, instead of with the human eye, with a video camera connected to video processing equipment working at real time. Video microscopy is, there fore, much more than just adding a camera and monitor to the microscope to share the images with a larger audience. More recently, electronic devices other than video cameras, such as high sensitivity charge coupled device (CCD) cameras and scanning light detector systems for confocal microscopy have been added to microscopes. The three fields (i) video-enhanced contrast microscopy for highest resolution work, (ii) video-intensified microscopy for low light applications, and (iii) electronic scanning microscopy for confocal microscopy and 3D imaging differ in the type of device generating the electronic image, but all three use basically the same types of analogue and digital image processors. While all these techniques are generally defined as electronic light microscopy, this chapter, video microscopy, deals with the first two techniques that involve CCD and video cameras as imaging devices. Video microscopy has produced a revolution in light microscopy of biological samples equivalent to that of the development of the immunofluorescence technique. It has once more made the traditional light microscope a powerful tool for those working on dynamic aspects of small biological systems, for example biochemists, molecular and cell biologists. It has given further resolving power to the light microscope enabling the observation of particles which bridge the size range between those normally studied by electron microscopy and those which are already well known to light microscopists as a whole, with the added advantage in that specimens can be examined alive. As well as allowing small particles to be resolved, the technique has the capacity to clean up the image, so allowing greater visibility. Also, changes of such parameters as amounts, concentrations, transport, or metabolism of specific molecules in both time and space can be quantitatively determined.
Reflection-contrast microscopy
Authors: Ploem J S , Prins F A , Velde I Cornelese-Ten 
Published: November 2023

Abstract
Fauré-Fremiet (1) used reflected light in cell biology studies half a century ago. Curtis (2) and Izzard and Lochner (3) performed the first fundamental studies of interference images of living cells on glass surfaces using reflected light microscopy. Reflection images were obtained with scanning reflecting microscopy (4, 5). Reflected-light microscopy for the study of living cells (2, 3, 6, 7) has been described as interference reflection, reflection-interference contrast, surface-contrast, and surface-:reflection interference microscopy (8). Ploem (9, 10) investigated further optical methods to improve the image contrast in reflected-light microscopy. In collaboration with Leica (11-13), an improved microscope system was developed for reflected-light microscopy. It used an aperture diaphragm with a central stop (creating an annular aperture) in the epi-illumination light path at an aperture plane conjugate with the back focal (aperture) plane of the objective (14). This was combined with epipolarization microscopy using immersion objectives equipped with a quarter lambda plate in their front lens (15). New high aperture objectives were developed for high resolution biological microscopy. This optically improved version of reflected-light microscopy was named reflection-contrast micro scopy (RCM).
Introduction of materials into living cells
Authors: Schöpke Christian , Fauquet Claude M 
Published: November 2023

Abstract
Since its inception a decade ago, particle bombardment, also known as the ‘Biolistic process’ (1), has developed into a method of considerable importance in many areas of biology (see Table 1). It has been especially successful in the genetic transformation of plants, where the presence of a cell wall poses a significant obstacle for the introduction of large molecules, including DNA. The purpose of the first part of this chapter is to illustrate the use of particle bombardment for the introduction of DNA into plant cells and the utilization of reporter genes to follow the fate of genetically transformed cells, using cassava (Manihot esculenta) as an example. The reader who is interested in more detailed information on particle gun types and on different applications of particle bombardment is referred to several recently published reviews (2-4).
Laboratory Protocols for Conditional Gene Targeting
Authors: Torres Raul M , Kühn Ralf 
Published: November 2023

Abstract
Conditional gene targeting is an emerging technique for introducing mutations into the genes of laboratory mice. This collection of protocols comes from one of the world's premier laboratories for gene targeting The Institute of Genetics in Cologne and is intended for newcomers to the field as well as more experienced researchers. Topics covered include: the Cre/loxP recombination system and gene targeting in ES cells; gene targeting strategies; Cre/loxP recombination system; Gene targeting vectors consideration and use of loxP; nonselectable modifications and removal of selection marker genes; large deletions; gene replacement; chromosomal translocations; targeted integrations; conditional gene modification; LoxP-containing transgenes; conditional gene targeting; working with ES cells; ES cell transfection overview; embryonic feeder cells; ES cells handling and use; ES cell culture and transfection; ES clone picking; identification of homologous recombinants; freezing ES clones; thawing ES clones; genomic DNA preparation; cre-mediated neomycin deletion in ES cells; generation of mice preparation; mouse breeding for ES cell injection or aggregation; injection needles and holders; blastocyst preparation/injection; embryo aggregation; blastocyst transfer;
The Xenopus oocyte expression system for the cDNA cloning and characterization of plasma membrane transport proteins
Authors: Yao* Sylvia Y M , Cassꝉ Carol E , Young* James D 
Published: November 2023

Abstract
Oocytes of Xenopus laevis, the South African clawed frog, represent a simple, but powerful system for the transient expression of heterologous proteins. These large and resilient cells have a high translational capacity and are readily microinjected with exogenous RNA or DNA. As a system for studying plasma membrane transport proteins, Xenopus oocytes are readily amenable to both radioisotope flux measurements and electrophysiological recordings. They also subject newly synthesized proteins to various forms of processing, including glycosylation and correct plasma membrane insertion. Unlike other whole-cell heterologous expression systems, Xenopus oocytes have a generally low background of endogenous transport activity, making them uniquely versatile with respect to the range of permeants and types of transporters that can be studied. The ability of Xenopus oocytes to translate foreign mRNA was first described in 1971 (1). Since then, the system has been applied with considerable success to the.study of receptors and channels and, following the landmark expressioncloning of the intestinal glucose transporter SGLTl (sodium-dependent glucose transporter 1) in 1987 (2), to transport proteins. In this chapter, we provide a laboratory guide to the Xenopus oocyte expression system for the cDNA cloning and functional and molecular characterization of plasma membrane transport proteins, illustrating some of these applications with our own studies of nucleoside transport processes in mammalian and other species. Other sources should be consulted for routine molecular biology techniques (3).
Human monoclonal antibodies to blood group antigens
Authors: Kumpel Belinda M 
Published: November 2023

Abstract
Many human alloantigens on red blood cells are not recognized by the mouse immune system, and therefore murine monoclonal antibodies to many desired blood group specificities cannot be produced using conventional murine hybrid oma technology. Among these is the Rh (rhesus) D antigen, which is the most immunogenic of the blood group alloantigens and clinically is the most import ant after the ABO blood groups. Most human monoclonal blood group antibodies have been made to the Rh D polypeptide. Monoclonal anti-D has been produced to replace or supplement plasma-derived anti-D for blood grouping (1) and for therapeutic Rh D prophylaxis for prevention of haemolytic disease of the new born (2). Also, there are more individuals with high titre anti-D than with anti bodies to other blood groups, who can donate source material. For this reason, the methods described in this chapter are those that have been used for the production of monoclonal anti-D.
Visualizing fluorescence in Drosophila–optimal detection in thick specimens
Authors: Davis Ilan 
Published: November 2023

Abstract
Drosophila has been a key model organism for studying the genetic control of development. Its success is largely due to its powerful genetics combined with the ability to visualize specific gene products in a beautiful multicellular cytology. This often involves detecting proteins and mRNA deep in whole-mount specimens such as embryos, egg chambers or imaginal discs. Such experiments can be technically challenging, since most objective lenses are designed to image sources of light located just below the coverslip. Imaging fluorescence at some distance from the coverslip creates a number of distortions which reduce the resolution and lower the signal-to-noise ratio.
Ras
Authors: Bos Johannes L 
Published: November 2023

Abstract
Ras is a molecular switch that controls the transduction of signals from cell-surface receptors to intracellular targets (Fig. la). Like all GTPases, the switch mechanism consists of activation by exchange of bound GDP for GTP, and inactivation by hydrolysis of GTP into GDP. Ras achieved notoriety in the 1980s with the discovery that 15% of all human tumours contain a point mutation in one of the three Ras genes. The resulting mutant protein is unable to hydrolyse bound GTP and therefore remains constitutively in the active conformation. As a consequence, cells experience a continuous growth-promoting signal in the absence of extracellular cues. Ras has been studied extensively and much is known about mechanisms of activation and of downstream signalling. In most cells, Ras is activated in response to a variety of extracellular signals, which stimulate tyrosine kinases either directly or indirectly. In its GTP-bound state, Ras associates with one of several effector molecules, most notably members of the Raf family, the RalGDS family, or PI3K. The biological consequences of these interactions depend greatly on the cell type and on the context of other signalling events. In addition, poorly understood parameters, such as the timing and intensity of the signal, may determine the ultimate response. Interestingly, Ras is highly conserved both in structure and function during evolution. In the yeast Saccharomyces cerevisiae, Ras is involved in nutrient response, in Schizosaccharomyces pombe Ras regulates the pheromone response in mating, and in the nematode Caenorhabditis elegans and the fruitfly Drosophila Ras is a key component of numerous developmental processes. This chapter will provide a background to Ras and present some current ideas about the molecular mechanisms of Ras signalling.
Synaptic vesicle endocytosis and recycling
Authors: Zhang Bing , Ramaswami Mani 
Published: November 2023

Abstract
‘The yang having reached its climax retreats in favor of the yin; the yin having reached its climax retreats in favor of the yang.’ -Wang Chu’ung (AD 80) on Tai Chi Tu Exocytosis and endocytosis, the yin and yang elements of the vesicle cycle, must be well balanced to ensure continuous synaptic transmission. At nerve terminals, the number of synaptic vesicles is insufficient to account for the number of quanta released during a short burst of intense nerve activity. Axonal transport of newly synthesized vesicle proteins occurs too slowly to refill the vesicle pool at the required rates. Under these circumstances, the only way to rapidly replenish synaptic vesicles is to recycle them locally through endocytosis. Thus, a major challenge is to understand how synaptic vesicles are faithfully and efficiently recovered.
Cyclin-dependent protein kinases
Authors: Gould Kathleen L 
Published: November 2023

Abstract
Cyclin-dependent protein kinases (Cdks) regulate progression through the eukaryotic cell cycle. They are also involved in the regulation of other processes such as gene expression and phosphate metabolism. Cdks are the catalytic subunits of hetero dimeric complexes and they approximate the size of a minimal protein-kinase catalytic domain (∼, 34 kDa). Alone, they lack protein kinase activity. As their name implies, By far the best understood of the Cdks are those that have important roles in cell cycle progression-Cdc2, Cdk2, and Cdk4. Cdks are activated transiently at particular stages of the cell cycle, and their activation or inactivation triggers the next events in the cycle. To ensure the coordination of these events, the activation of each Cdk is strictly regulated in a variety of ways including an elaborate cascade of protein phosphorylation events, interaction with subunits in addition to cyclins, and by regulated proteolysis of the cyclin and other subunits. Due to the wealth of knowledge concern ing Cdks and the limitations of space, it is impossible to include all pertinent information about Cdks in this chapter or to cite all the original references. Numerous recent reviews emphasize various aspects of Cdk function and regulation, and readers will be referred to these where appropriate.
Bacteriology of urine
Authors: Davies Eleri M , Lewis Deirdre A 
Published: November 2023

Abstract
The urinary tract above the level of the distal urethra is normally sterile but infection at any site within the tract is possible, from the kidney to the urethra, the commonest site of infection being the urinary bladder. In general microorganisms gain access to the urinary tract from neighbouring sites, most commonly the perianal region, resulting in ascending infection, although spread by the haematogenous route is usually responsible for infections by Salmonella spp., and Mycobacterium tuberculosis.
Antimicrobial assays
Authors: Reeves David S , Whitea Les O 
Published: November 2023

Abstract
An antibiotic was originally defined as a substance produced by a micro-organism which inhibited the growth of other micro-organisms. However many drugs loosely referred to as antibiotics are semi-synthetic derivatives of natural antibiotics (e.g. various penicillins and cephalosporins) or compounds produced solely by chemical means (e.g. sulfonamides, 4-quinolones). In addition there are true antibiotics which have useful anticancer rather than antimicrobial properties. For this reason it has become customary to refer to antimicrobial antibiotics and other antimicrobial drugs as antimicrobial agents, a term which is often reduced to antimicrobial. This terminology will be used in this chapter.
Early stages of protein folding
Authors: Roder Heinrich , ElÖve GÜlnur A , shastry m. C Ramachandra 
Published: November 2023

Abstract
Protein-folding reactions often appear deceptively simple. At equilibrium one can typically distinguish only two states, the precisely folded native state and a broad ensemble of largely featureless, unfolded conformations. Many small, globular proteins exhibit simple, first-order folding and unfolding kinetics that can be modelled as a reaction involving two states separated by a single free-energy barrier (reviewed in ref. 1). Any additional slow kinetic phases can often be attributed to heterogeneity of the unfolded state due to cis-trans isomerization of praline peptide bonds (2, 3) or to exchange of metal ligands (4-6).
Chromosome analysis and sorting by flow cytometry
Authors: Davies Derek C , Youngt Bryan D 
Published: November 2023

Abstract
Many types of cancer and genetic disease are characterized by chromosomal abnormalities. These can be detected by conventional cytogenetics, which involves photographing banded chromosomes on metaphase spreads. Although this is a widely used technique in haematology, oncology, and pre-natal diagnosis, it is a time-consuming process that relies heavily on the skill and experience of the cytogeneticist. In addition, in cancerous cells, the sometimes complex karyotypes encountered mean that such analysis is often extremely difficult. An alternative approach is to prepare a monodispersed suspension of chromosomes, stain with one or two fluorescent DNA dyes, and pass them through a flow cytometer. The intensity of the fluorescence signal from each chromosome is recorded, the values being dependent on their DNA content. In single-colour analysis, a non-base-specific dye such as ethidium bromide is used. Accumulating data from 50000 chromosomes and presenting this as a histo gram of fluorescence intensity produces a distinctive species-specific pattern of peaks. However, not all chromosomes appear as a single peak. An improvement is to use bivariate analysis that exploits the base-pair binding preferences of DNA specific dyes: usually Hoechst 33258 (which has an adenine/thymidine (AT) binding preference) in combination with chromomycin A3 (which has a guanine/cytosine (GC) binding preference). The intensity of staining with these fluorochromes is dependent not only on the DNA content but also on the base composition of each chromosome. The data accumulated can be presented as an isometric plot or, better, as a dot plot or contour map (see Figure 1). The bivariate plot resolves all the human chromosomes as separate peaks, with the exception of chromosomes 9, 10, 11, and 12.