bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications of chromosomal in situ hybridization
Authors: Levy Nicolas , Mattei Marie-GeneviÈve 
Published: November 2023

Abstract
In situ hybridization (ISH) is a technique which allows one to detect the sequences complementary to a given nucleic acid molecule in metaphase or interphase chromosomes, and in tissue specimens. This chapter will describe the applications of ISH to metaphase and interphase chromosomes. The application of ISH to tissues, to monitor the expression of specific genes, is covered in Chapter 8. The principle of ISH is simple, and is based on the complementarity of the two strands of the DNA molecule. The probe, a DNA or RNA sequence, is labelled with a radioisotope or chemical reporter group, and denatured. Target DNA, i.e. metaphase or interphase chromosomal DNA, is also denatured so as to be accessible to the probe. Complementary sequences in the probe and target are then allowed to hybridize. Depending on the type of probe used, the hybridized sites are then detected either by autoradiography or by using an immunofluorescence procedure.
Analysis of gene expression by PCR: a quantitative approach
Authors: Striker Liliane J , Peten Emmanuel P , Striker Gary E 
Published: November 2023

Abstract
The introduction of PCR has added a new degree of sensitivity and specificity in the study of gene expression in tissues or cells (1). It is now possible to obtain accurate and sensitive measures of gene expression in small samples of tissue, or in a few cells in vitro, using a variation of PCR which allows quantification in the attomolar range. This represents a considerable increase in sensitivity over other analytical methods such as Northern blot analysis or nuclease protection assays. In addition, it is possible to assay gene expression by PCR in tissue samples, without resorting to extraction of the mRNA.
Optimizing PCR
Authors: Kjijo K K , Ruano G 
Published: November 2023

Abstract
Although this entire volume is intended to provide explicit, practical guidelines and protocols for PCR in its myriad manifestations, we wish to start with a series of perspectives on various aspects of the several processes that are collectively called the polymerase chain reaction. No individual protocol will be optimal for all PCR reactions, nor will any single, simple set of variables to be optimized necessarily produce a functioning protocol for a specific case. Therefore, in order to optimize PCR, the researcher must have a mental picture of the underlying processes and be able to grasp how the various aspects of a protocol affect the chemical reactions. The relevance of most of the underlying physico-chemical principles can be understood mechanistically to allow a researcher to optimize a PCR reaction for a specific application. In this chapter, we present some of these principles and our perspective on the process without resorting to precise physico-chemical characterizations and quantification. If such a detailed treatment is required, it can be found in Ruano et al. (1).
Fingerprinting of DNA and RNA using arbitrarily primed PCR
Authors: Welsh John , Perucho Manuel , Peinado Miguel , Ralph David , Mcclelland Michael 
Published: November 2023

Abstract
Arbitrarily primed PCR is a modification of PCR that provides an informationrich fingerprint of genomic DNA. This method is based on the selective amplification of genomic sequences that, by chance, are flanked by adequate matches to an arbitrarily chosen primer. If two template genomic DNA sequences are different, their arbitrarily primed PCR products display different banding patterns. Such differences can be exploited in ways largely analogous to the uses of restriction fragment length polymorphisms, including genetic mapping, taxonomy, phylogenetics, and the detection of mutations.
Measurement of neurotransmitters and their associa.ted second messengers in vivo
Authors: Cadogan A K , Marsden C A 
Published: November 2023

Abstract
Measurement of neurotransmitters in vivo Neurotransmitter release has been measured in vivo over the last decades using a variety of techniques. Among the many innovations that have appeared are the cortical cup which was introduced in 1953 (1) and the push-pull cannula introduced in 1961 (2). One of the main drawbacks with the above methods was that they involved an open system in which the brain came into direct contact with the perfusion fluid. One method which overcame this problem was the introduction of brain microdialysis (also known as intracerebral dialysis, intracranial dialysis, and transstriatal/cortical dialysis). An alternative approach is the use of in vivo voltammetric electrodes which can also be successfully applied to brain slices forming an alternative to con ventional superfusion methods. The preparation and application of voltam metric electrodes have recently been reviewed in another book in this series (3). Microdialysis is in principle the only technique which can collect virtually any substance from remote brain regions with a limited amount of tissue trauma. Described as early as 1966 by Bito and colleagues (4), this method has been refined and undergone several technical improvements (5-7) to rapidly become a popular bioanalytical sampling tool in brain research. The major advantage of the in vivo microdialysis method is that it can be used in the freely-moving animal allowing one to make correlations between changes in extracellular neurotransmitter levels and behaviour.
Virulence plasmids
Authors: Tolmasky Marcelo E , Actis Luis A , Crosa Jorge H 
Published: November 2023

Abstract
The term plasmid was originally used by Lederberg (1) to describe all extra chromosomal hereditary determinants. Currently, the term is restricted to autonomously replicating extrachromosomal DNA. Their sizes range from 1 kb to more than 200 kb (2), and even larger plasmids were detected in Rhizobium (3). Although they replicate autonomously, plasmids rely on host encoded factors for their replication. Plasmids are not essential for the survival of bacteria, but they may nevertheless encode a wide variety of genetic determinants which permit their bacterial hosts to survive better in an adverse environment or to compete better with other micro-organisms occupying the same ecological niche. The medical importance of plasmids that encode for antibiotic resistance, as well as specific virulence traits has been well documented. In this chapter we describe techniques used in our laboratory for studying plasmid-encoded virulence factors such as the iron-uptake systems encoded by pJM1 in Vibrio anguillarum (4), and by pColV-K30 in Escherichia coli (5), as well as antibiotic resistance coded for by plasmids isolated from pathogenic Klebsiella pneumoniae strains (6).
Plasmids in Agrobacterium tumefaciens and Rhodococcus fascians
Authors: Desomer Jan , Marc Rolf Deblaere , Montagu Van 
Published: November 2023

Abstract
In this chapter, we would like to provide an overview of the main techniques used in our laboratory to identify, isolate, and analyse plasmids (and the functions they encode) in plant-tumourigenic bacteria from the Gram negative genus Agrobacteriumand from the Gram-positive genus Rhodococcus. Although these bacteria are evolutionary far apart, in both cases phytopatho genicity is determined by large conjugative plasmids, and similar genes have been detected on plasmids from both groups of bacteria (1). The plasmid based recombinant DNA technology developed for Agrobacterium can also be applied to other bacteria that interact with plants, such as the nitrogen fixing rhizobacteria (2).
Structure and replication of chloroplast DNA
Authors: Sugiura Masahiro 
Published: November 2023

Abstract
The demonstration of a unique DNA species in chloroplasts over 30 years ago (e.g. Ref. 1) has led to studies of the structure of chloroplast DNA (ctDNA). These studies were accelerated by development of techniques such as gene cloning and DNA sequencing in the mid-1970s. The first physical map of ctDNA was constructed for maize in 1976 (2). Within 10 years the entire sequences of ctDNAs were determined for tobacco, liverwort, and then rice (3-5). Sequences for defined regions of many other ctDNAs were also completed. These sequencing efforts have revealed an enormous amount of information about the chloroplast genome (6, 7). The genes and their organization in ctDNA were thought to be well conserved through land plant evolution (8). Each ctDNA was shown to contain nearly 100 different genes which could be classified into two main classes: genes involved in transcription and translation and those related to photosynthesis (9). Recent structural analysis of ctDNAs from a variety of other land plants and algae has modified previous understanding. Chloroplast genomes among the plant kingdom are much more diversified in gene content and gene organization than we thought. A non-photosynthetic parasitic flowering plant has been shown to contain a grossly reduced plastid genome that has lost both photosynthetic and chlororespiratory genes (10). Black pine, a gymnosperm, lacks all chlororespiratory genes (T. Wakasugi et al., in preparation).
Transcriptional and post-transcriptional gene regulation in plastids
Authors: Abrahamson Susan , Gruissem Wilhelm 
Published: November 2023

Abstract
Plastids perform several essential functions in plant cells, from photosynthetic carbon fixation to amino acid biosynthesis and fatty acid production. Since the discovery almost 40 years ago that plastids contain DNA, much of the molecular research in chloroplasts has focused on the structure and organization of the plastid genome structure and the expression of its approximately 150 genes (Chapter 3). This chapter will discuss our current understanding of the mechanisms that control gene expression in this unique organelle, and many aspects will focus on the photosynthetic chloroplast as an example. We will begin with a brief introduction to the biology of plastids and a historical overview of the study of plastid transcription. We will then discuss the components of the transcription machinery, the role transcription has in plastid gene expression, and the different types of contrgls that operate at the post-transcriptional level in the regulation of plastid gene expression during plant development.
Characterisation of industrial high methoxyl pectins
Authors: Kravtchenk T P , Voragen A G J , Pilnik W 
Published: November 2023

Abstract
Pectic substances are extracted industrially and are widely used in the food industry, mainly as a gelling agent. Food technologists are therefore primarily interested in their physical behaviour. Together with rheological measurements, the fine structure of extracted pectins has been intensively investigated during the last decades. These studies clearly showed that the strength of pectin gels is affected by numerous structural features such as molecular size and degree of methoxylation. However, the complexity of industrial pectin samples has prevented the attainment of the ultimate stage that would be the prediction of the physical behaviour from the chemical analysis.
Short chain fatty acids and metabolic effects in humans
Authors: Bornet F R J , Alamowitch C , Slama G 
Published: November 2023

Abstract
Short chain fatty acids are the major end products of dietary fiber degradation by anaerobic bacteria in the large bowel. The principal short chain fatty acids are acetate, propionate and butyrate. They are rapidly absorbed, stimulate salt and water absorption and provide an energy source for the colonic epithelium. Butyrate is mostly utilized as an energetic substrate by the colonocytes. It has been suggested that short chain fatty acids could contribute to the lipidemic and glycemic effects of fiber. In isolated hepatocytes, acetate inhibits glycolysis and stimulates gluconeogenesis while propionate has the opposite effects. Propionate inhibits cholesterol synthesis in vitro. They are very few studies in healthy humans. The acute intake of acetate does not seem to affect metabolism in man. No mention is made of its influence in case of chronic intake. The studies reveal the propionate tendency to reduce glycemia in fasting subjects and to enhance their sensitivity to insulin. The real part played by the short chain fatty acids in the glucose metabolism causes controversy and further investigations into their chronic intake in man are required.
Physical influences on the growth of food-poisoning bacteria in emulsion systems
Authors: Brocklehurst Tim F , Coleman Heather P , Gunning Paul A , Parker Maryl. , Robins Margaret M 
Published: November 2023

Abstract
In order to emulate the growth of food-poisoning bacteria in foods of a given chemical composition, microbiologists have traditionally used homogeneous culture media modified to have a similar chemical environment to the food in question. Hitherto, much less attention has been given to the influence of the physical structure of a food on the growth of bacteria. Experiments have shown that the microstructure of such colloidal systems can inhibit the growth of bacteria. Growth rates and microscopic observations of the growth of food-borne pathogenic bacteria in oil-in-water emulsions are reported and discussed with reference to physical characteristics of the emulsions.
European Brewery Convention
Authors: Narzillß L 
Published: November 2023

Abstract
Europe's illustrious Brewery Convention--held every two years--draws together brewers from around the world to exchange ideas on all aspects of the science and technology related to their craft. The papers presented here reflect this wealth of research and knowledge. They cover all stages of the brewing process, form raw materials and fermentation techniques to quality control and new innovations like low-alcohol beer. Each paper is presented in the original language with accompanying summaries in English, French, and German. The volume provides a valuable, state-of-the-art reference for all those involved in the brewing industry and fermentation biotechnology.
The economics and utilisation of brewing materials in the 1990’s
Authors: Brookes Peter A 
Published: November 2023

Abstract
Considerable improvement in the quality and efficient use of brewing materials has occurred over the past 40 years. Development work has been driven by the desire to more fully understand the mechanisms involved in the interactions taking place in malting, mashing, wort boiling and fermentation. The market place in the early 1990’s, however, is affected by recession, environmental concerns and a changing pattern of demand for alcoholic drinks. An analysis will be made of the most effective way of using cereals, sugar and hop resins to produce beer of the highest quality. The brewer who uses these materials with greatest efficiency will prosper.
The regulation of starch granule size in endosperm of developing barley grains
Authors: Tillett Ian J L , Bryce James H 
Published: November 2023

Abstract
A significant proportion of small “B-type” starch granules from barley is not degraded during malting and mashing. Our aim is to understand starch granule synthesis so that carbohydrate can be redirected to the large degradable “A-type” granules. Following digestion to remove cell walls and proteins from individual endosperms, the size and number of starch granules, and the wave pattern of their growth during grain development were determined using Image Analysis. SDS-PAGE and Western blotting with antibodies to starch synthases showed that enzymes of starch synthesis were specifically associated with both types of starch granules.
A simple and rapid test for gushing tendency in brewing materials
Authors: Vaag Pia , Riis Preben , Knudsen Anne-Dorte , Pedersen Stig , Meiling Ella 
Published: November 2023

Abstract
Gushing in beer may be caused by microbial components present in the brewing materials. Tests for gushing tendency are indispensable, but often laborious and time-consuming. A simple and rapid test has been developed, based on extraction of gushing factors from brewing materials, addition of the extract to bottles of non-gushing finished beer, followed by the gushing test. The test can be completed within four days and is more sensitive and more reproducible than a twelve-day mini-brew test used at present. Moreover, the extraction test can be used for determination of gushing tendency in adjuncts as well as in malt.
Lactic starter cultures in malting-a novel solution to gushing problems
Authors: Haikara A , Uljas H , Suurnäkki A 
Published: November 2023

Abstract
Lactic acid bacteria were tested as starter cultures during malting as natural preservatives for restricting the growth of Fusarium moulds in order to prevent gushing. Addition of Lactobacillus plantarum and Pediococcus pentosaceus cultures during malting diminished Fusarium and bacterial contamination of barley and malt due to the antimicrobial substances produced by these lactobacilli.
Yeast flocculation: biochemical characterization of yeast cell wall components
Authors: Garsoux G , Haubursin H , Bilbault S , Dufour J P 
Published: November 2023

Abstract
Comparison of flocculating and non-flocculating cells was performed with one brewery yeast strain. Cells cultivated at 10°C exhibited floes during the late exponential phase. However, cells grown at 28°C did never flocculate. The growth temperature did not inhibit cell-cell interactions but probably induced or repressed the synthesis of a cell wall component involved in flocculation. Surface analysis (hydrophobicity, electrostatic charge, chemical composition) and biochemical characterization of cell wall mannoproteins were carried out to identify the origin of this differential behaviour
HIV infection of macrophages
Authors: Collin Matthew , Montaner Luis J , Georges Herbin , Gordon Saimon 
Published: November 2023

Abstract
The susceptibility of mononuclear phagocytes to infection by HIV has long been recognized. The principal aims of recent research have been first, to describe the frequency and distribution of infected macrophages (m&lt;|&gt;) in the body and of the viruses that infect them and secondly, to understand the replicative cycle of HIV in m&lt;J&gt;, and document the effects of HIV on m&lt;|&gt; function. The first area relies heavily upon histological studies and primary isolation of viruses, whereas the second, which is the main focus of this chapter, depends largely on infecting cells in vitro with established isolates of HIV. We describe the isolation of monocytes and their maturation in vitro, followed by methods to prepare and titrate the infectivity of m&lt;|)-tropic HIV. The final section deals with general considerations for HIV experiments with m&lt;j&gt;.
Detection of viral DNA by the polymerase chain reaction (PCR)
Authors: Krogstad Paul , Zack Jerome A 
Published: November 2023

Abstract
The polymerase chain reaction (PCR) has revolutionized the study of human retroviruses. Numerous methods have been employed to detect and analyse products resulting from amplification of retroviral DNA. These have included ethidium bromide staining of electrophoretically separated products, and hybridization of radiolabelled or chemiluminescent probes to dot blot DNA samples or Southern blot transfers (1). We and our collaborators have developed and employed a PCR method in which one of the oligonucleotide PCR primers is radiolabelled, allowing direct detection of electrophoretically separated products. We have used this method to quantitatively analyse DNA samples from experiments in which cells are infected in vitro, and for analysis of brain tissue, peripheral blood cells, and other tissues infected in vivo by human immunodeficiency virus type 1 (HIV-1) and human T cell leukaemia virus types I (HTLV-I) and II (HTLV-II) (2–5). In the sections that follow, we describe preparation of DNA samples and their analysis, using this PCR method.
Identification, isolation, and characterization of platelet glycoproteins mediating platelet adhesion
Authors: Mcgregor John L , Gayet Odile , Mercier Nathalie , Mcgregor Lilian , Chignier Elza 
Published: November 2023

Abstract
Platelets play a vital role in haemostasis by the formation of a plug or thrombus at a site of vessel wall injury. The function of these anucleated cells is largely dependent on the presence of a number of glycoproteins. Moreover, adhesion and aggregation of platelets to disrupted atheroma plaque, leading in some cases to vessel occlusion, is also mediated by glycoproteins. The importance of glycoproteins in platelet functions has led to extensive work, using various techniques, to identify structural/functional sites on these glycoproteins implicated in interacting with various ligands. The aim of this chapter is to describe a number of techniques used in studying glycoproteins involved in platelet adhesion to extracellular matrix proteins or to leucocytes.
Methods for measuring agonist-induced phospholipid metabolism in intact human platelets
Authors: Holub Bruce J , Watson Steve P 
Published: November 2023

Abstract
Stimulation of platelets by agonists causes marked alterations in phospholipid metabolism (1,2). The activation of phospholipase C results in the degradation of phosphoinositides, noteably phosphatidylinositol 4,5-bisphosphate (PI 4,5-P2), resulting in the production of the second messengers diacylglycerol (DG) and inositol 1,4,5-trisphosphate (Ins l,4,5-P3) (3,4). DG is further metabolized to phosphatidic acid (PA) via DG kinase. In addition to PI 4,5-P2 hydrolysis via phospholipase C with agonist stimulation, phosphatidylinositol (PI) is sequentially phosphorylated upon receptor occupancy to phosphatidylinositol 4-phosphate (PI 4-P) and PI 4,5-P2 via PI and PI 4-P kinase activities, respectively (5). Recently, novel phosphorylated phosphoinositide compounds, namely phosphatidylinositol 3,4-bisphosphate (PI 3,4-P2) and phosphatidylinositol 3,4,5-trisphosphate (PI 3,4,5-P3), have been identified in stimulated platelets (5). The activation of phospholipase A2 following agonist stimulation of platelets cleaves platelet membrane phospholipids, including PI, phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS), at the sn-2 position producing the corresponding 1-acyl lysophospholipids and releasing predominately arachidonic acid (AA, 20 : 4n-6) (1,6). AA is further metabolized via cyclo-oxygenase to thromboxane A2 (TxA2), a potent potentiator of platelet activation (6).
lmmunocytochemical and electron microscopic studies of platelets
Authors: Israels Sara J , Gerrard Jon M 
Published: November 2023

Abstract
Although platelets were one of the first types of cells to be studied using the electron microscope, a clear understanding of normal platelet architecture using electron microscopy had to await improved techniques for the isolation, preservation, and fixation of these cells. Similarly, an understanding of the changes in blood platelet fine structure during clotting required improvements in preparative techniques. The preservation and fixation of certain platelet subcellular structures, notably dense granules and contractile filaments, have presented particular challenges. In this chapter, we describe basic fixation procedures for platelet transmission electron microscopy, and for immunofluorescent and immunoelectron microscopic studies, while providing a brief overview of some other aspects of platelet electron microscopic studies.
Glutathione
Authors: Anderson Marye. 
Published: November 2023

Abstract
Glutathione (GSH; v-γ-glutamyl-L-cysteinylglycine) is present in most mam malian cells. It is usually the most abundant cellular thiol (up to 10 mM); cysteine is usually present in lower levels (about 10% of GSH). GSH is an antioxidant, and it participates in many biological phenomena. It is involved in the transport of certain amino acids, it is a coenzyme for various enzymes, and it protects against oxygen radicals and toxic compounds (1–6).