bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteriology of the respiratory tract
Authors: O’Hara Steve , Lowes J Andrew , Smith Grace 
Published: November 2023

Abstract
The isolation and detection of potential pathogens of the respiratory tract in disease is often complicated by the presence of commensal flora in the upper tract. Unless specialized specimen collection techniques are used most respiratory tract specimens sent to a diagnostic laboratory are contaminated with commensal flora. Reporting of all isolates present with their antibiotic sensitivities is inappropriate and may be misleading. Microscopy and cultural findings must be interpreted taking into account the quality of the specimen, the expected commensal flora of a given site through which the specimen was collected, the relative amounts of potential pathogens, and the clinical history of the patient including antimicrobial treatment.
Bacteriology of superficial and deep tissue infection
Authors: Baker Nicola , Bushella Ann , Hawkey Peter M 
Published: November 2023

Abstract
The range and variety of clinical samples seen and microbes grown from these infections is enormous. The approach will be to outline general methods, concentrating on the major pathogens, and then to examine specific techniques appropriate to different sites of infection, with cross-reference to other chapters. To get the most useful results from these samples it is important to know the site (anatomical) and nature (primacy/secondary, acute/chronic) of the infection. If the sample is of high priority (pus, tissue, and some fluids) then the laboratories must liaise with the clinicians, and expend maximum effo1t to obtain a micro biological diagnosis. If the sample is of lower priority (most ‘wound swabs’ fall into this category) then the laboratory may legitimately process the sample in a routine manner. The samples that deserve extra effort are not always immediately apparent, and it is part of the role of the clinical microbiologist to pick them out. Finally, intelligent and informed interpretation of culture results and appropriate clinical liaison will make all the difference as far as the clinician (and patient) is concerned, between useful and useless laboratory reports.
Bacteriology of intestinal disease
Authors: Pedler Stephen , Graham Clive 
Published: November 2023

Abstract
There is a formidable list of bacteria which are known or suspected to cause gastrointestinal infection in human beings. This list is not unchanging; organ isms are sometimes added to it, while the status of other organisms varies with the passage of time. In the first edition of this book, for example, examination for enteropathogenic E. coli was recommended for an specimens from children aged three years or under, while current practice in many laboratories is not to examine specimens for these organisms routinely. Conversely, the criteria for examining specimens for Verocytotoxic E. coli have been expanded so that many more specimens are now routinely examined for this organism. Since the first edition antibiotic treatment has been increasingly recognized as useful in certain gastrointestinal (GI) infections, and with that the problem of antibiotic resistance in pathogenic bacteria has increased in importance.
Laboratory investigation of health care-associated infection
Authors: Hawkey Peter M , Kerr Kevin G 
Published: November 2023

Abstract
Whilst most hospital microbiology laboratories are very busy processing the large numbers of specimens detailed in the previous chapters, they will also be required periodically to investigate and direct the control of episodes of cross-infection. Although this chapter will concentrate on hospital-acquired infection (nosocomial infection), it is increasingly recognized that the infections previously regarded as typically nosocomial in origin, such as those caused by methicillin-resistant Staphylococcus aureus, may emerge, and be transmitted, in the community. Indeed the UK Department of Health Report Getting ahead of the curve (1) suggests that terms such as nosocomial infection are misleading and that ‘health care-associated’ infection is a more appropriate term.
Epidemiological methods in the investigation of acute bacterial infections
Authors: Palmer Stephen R 
Published: November 2023

Abstract
Epidemiology is the study of the occurrence and causes of disease in populations. In contrast to the clinical situation when an individual patient is the focus of concern, the epidemiological approach relates the disease in the individual to the occurrence or risk of disease in others within the relevant population. This means taking into account not only the microbiological, but all personal. environmental. and social factors which influence the occurrence and presentation of the disease. A well-defined methodology exists (1). which demands specialized skills, but every clinical microbiologist will need to be familiar with certain basic concepts and methods (2) and to take an epidemiological perspective from time to time. Examples include the investigation of sources and modes of transmission in outbreaks, applying public health measures to the control of outbreaks. preventing the spread of sporadic cases of certain infections (such as diphtheria, typhoid, meningococcal meningitis), and devising preventive strategies, for instance for nosocomial legionnaires’ disease.
Case study 3: Folding of influenza haemagglutinin in the living cell
Authors: Ellgaard Lars , Helenius Ari 
Published: November 2023

Abstract
Almost all the available information on protein folding has been obtained by analysing the refolding of denatured proteins in vitro in the presence or absence of added molecular chaperones. As described elsewhere in this book, studies using this approach are providing an ever more detailed picture of the biophysical principles underlying assisted and non-assisted folding of polypeptide chains.
Functions of carbohydrates revealed by transgenic technology
Authors: Stanley Pamela 
Published: November 2023

Abstract
Mammalian glycans are assembled as covalent attachments to protein or lipid by the sequential action of glycosyltransferases and processing glycosidases (see Chapter 1). The addition or removal of each sugar is a precise reaction catalyzed by an enzyme specific for the sugar and the linkage configuration. Therefore it is possible to block glycan synthesis, or to add an extraneous sugar to preformed glycan units, by, respectively, the inactivation or the induction of a glycosylation enzyme. This has been termed glycosylation engineering and has been used to define the functions of particular sugar residues or sugar determinants associated with glycoconjugates. Initially, this approach was implemented using somatic cell genetics. Both loss-of-function and gain-of-function glycosylation mutants have been isolated from cultured cells (1-4) and used in glycosylation engineering (5). Once glycosyltransferase genes were cloned, gain-of-function transfectants could be created to identify functions for sugars (6) and antisense constructs could be used to eliminate a glycosylating activity (7, 8). In the last few years these approaches have been applied to the mouse in order to study the consequences of overexpressing, misexpressing or eliminating a glycosylation enzyme in a complex mammalian organism. Mutant mice provide experimental models for known human diseases. They also may identify new bases for disease, as well as new steps in the synthesis and catabolism of mammalian glycans. This chapter will discuss the properties of transgenic and knockout mice with altered glycosylation, identify difficulties of interpretation at the mechanistic level, and discuss future directions and methods for obtaining mouse glycosylation mutants.
Roles of sphingolipids and glycosphingolipids in biological membranes
Authors: Hirabayashi Yoshio , Ichikawa Shinichi 
Published: November 2023

Abstract
In 1884, Thudichum showed that the sphingolipids, galactosylceramide and sphingomyelin, were the major lipid components of human brain. Since then, the chemical structures of these lipids have been extensively studied and many different species of sphingolipid have been identified. In mammalian cells, there are two major classes of sphingolipid: glycosphingolipids (GSLs) and sphingomyelin, both of which contain hydrophobic ceramide. GSLs, in which oligosaccharides are the hydrophilic component, are generally minor components of cell membranes in animals and plants, while sphingomyelin, in which phosphocholine is the hydrophilic component, is more abundant in membranes. The ceramide portion of these sphingolipids is embedded in the outer leaflet of the plasma membrane and the sugar moiety or phosphocholine group projects into the extracellular space. A characteristic feature of GSLs is their structural diversity, in both the ceramide and the oligosaccharide chain. GSLs with sugar chains containing sialic acid are termed gangliosides.
Viral transformation of lymphocytes
Authors: Meinl Edgar , Fickenscher Helmut 
Published: November 2023

Abstract
The main limitations of molecular and biochemical studies of human T lymphocytes are twofold. First, the phenotype of T-lymphoblastic tumour cell lines like Jurkat (1) is significantly altered in comparison to primary cells with respect to signal transduction (2) and gene regulation. Second, primary T-cell cultures are inevitably limited in their lifespan. It is often laborious and frequently impossible to grow primary T lymphocytes to large numbers, and it requires considerable effort to amplify antigen-specific T cells (as described in Chapter 10). The use of irradiated feeder cells may cause difficulties in the interpretation of results derived from T cells expanded in this way. Immortalization of human T cells should be the ideal way to solve such problems. T-cell transformation should ideally lead to permanent growth independent of restimulation procedures, whilst conserving the essential features of the primary, parental T cells. Various approaches for immortalizing human T cells have been tried. The technique of T-cell fusion hybridomas is successful for rodent cells, but is much more difficult to achieve with human T cells where it is hampered by the genomic instability of the clones (as discussed in Chapter 4).
Murine T-cell culture
Authors: Mills Kingston h. G 
Published: November 2023

Abstract
The development of techniques for propagating and cloning T cells has had a dramatic impact on the field of immunology. Indeed, the study of cellular immunology, and many aspects of molecular immunology, are now almost totally dependent on cell-culture techniques. T cells cultured from blood, spleen, lymph nodes, or other lymphoid organs have been successfully used to establish that CD4+ and CD8+ T-cell responses recognize antigen in association with major histocompatibility complex (MHC) class I or class II gene products (1, 2) and that functionally distinct T-cell subtypes can be discriminated on the basis of cytokine secretion (3). The ability to clone antigen-specific T cells has also allowed the definitive identification and functional analysis of distinct T-cell subpopulations, and has provided the ideal tools for studies on the mechanisms of antigen processing, presentation, and T-cell receptor interaction with peptide-MHC complexes. Furthermore, the study of T-cell subtypes in vitro has provided valuable information for manipulating the induction and function of these cells in vivo, and this has important implications for future developments in immunotherapy and vaccines (4).
Quality assurance in the clinical laboratory
Authors: Gratama Jan W , Barnettt David 
Published: November 2023

Abstract
Each clinical diagnostic laboratory must have a strategy to assure the quality of its products. The focus in this chapter is on flow cytometric immunophenotyping assays; cases in point are:
for quantitative assays:
(a) enumeration of lymphocyte subsets, and
(b) enumeration of CD34+ haematopoietic progenitor cells (HPC); and for qualitative assays:
(c) leukaemia/lymphoma immunophenotyping, and
(d) screening for the HLA-B27 antigen. Quality assurance strategy includes:
Analysis of cell proliferation using the bromodeoxyuridine/Hoechst ethidium bromide method
Authors: Ormerod Michael G , Poott Martin 
Published: November 2023

Abstract
The fluorescence of bis-benzimidazole dyes (Hoechst 33258 and Hoechst 33342) bound to DNA is quenched by the thymidine analogue, 5-bromodeoxyuridine (BrdUrd). Consequently, continuous labelling with BrdUrd and subsequent staining of DNA with Hoechst 33258 allows the discrimination of chromatids accord ing to the number ofreplications they underwent during the observation period. The potential of this technique for analysing the progression of cells through their cycle has been established in several laboratories (see, for example, refs 1 and 2 and references therein). Cell-cycle kinetics are analysed using continuous BrdUrd labelling and bivariate Hoechst 33258/ethidium bromide (EB) flow cytometry. By the quenching of fluorescence from the Hoechst dye, cells are separated according to how many phases of DNA replication they have traversed, whereas the fluorescence of the non-quenched EB resolves the cell cycle into the G1, S, and G2 compartment. In this chapter, we refer to Hoechst/EB but propidium iodide (PI) can also be used in place of EB. Both dyes have been used to prepare the data shown in the figures.
Genetic analysis of ascomycete fungi
Authors: Harris Steven D 
Published: November 2023

Abstract
Filamentous fungi, in particular Aspergillus nidulans and Neurospora crassa, have historically played an important, yet under-appreciated, role as model eukaryotic organisms (1, 2). In this context, the primary attribute of these fungi is the ease with which they can be manipulated using both classical and molecular genetic techniques. Because they are haploid, the generation and analysis of mutants is a relatively straightforward process in A. nidulans and N. crassa. A variety of approaches can be used to generate mutations; ranging from traditional chemical mutagenesis to more recent transformation-based strategies. Similarly, an unlimited array of screening protocols can be used to select the desired mutant. Once obtained, a mutant must be subject to rigorous characterization to determine if the relevant phenotype is caused by one or more mutations, and if the mutation is recessive or dominant. The protocols employed to answer these questions in the filamentous fungi have remained essentially unchanged over the past forty years. The purpose of this review is to summarize the approaches used for genetic analysis in the ascomycete fungi, with particular emphasis on A. nidulans, N. crassa, and the plant pathogen Magnaporthe grisea. The first section will cover strategies used to identify and isolate mutants, whereas the second section will summarize the protocols employed for the analysis of a mutant.
Meiotic studies in humans
Authors: Hulten M A , Barlow A L , Tease C 
Published: November 2023

Abstract
The investigation of meiotic chromosomes presents a special technical challenge. First, the material is difficult to obtain for ethical and practical reasons. Second, meiotic chromosomes undergo a highly complex pattern of behaviour and it is essential to have a clear understanding of this process before undertaking analysis of scarce human material.
Investigation of meiosis may be undertaken either for basic research purposes or as an aid to a clinical diagnosis. Study of germ cell chromosome behaviour is of particular relevance to reproductive medicine. Errors in the cell division and maturation processes that generate human eggs and spermatozoa often result in impaired fertility. Through analysis of germ cells, it may be possible to determine the underlying causes of infertility and to obtain information of considerable value to subsequent counselling of patients. The increasing use and importance of in vitro fertilization and intracytoplasmic sperm injection as approaches to overcome infertility enhance the desirability of data from meiotic cells.
Basic techniques for the preparation and analysis of chromosomes from bone marrow and leukaemic blood
Authors: Czepulkowski B 
Published: November 2023

Abstract
This chapter is the first of five covering all aspects of the cytogenetic study of the leukacmias and related disorders. It serves to provide basic and general infom1ation on the culture, staining and analysis of the tissues normally used for such studies, namely bone marrow and peripheral blood. Protocols for the use of other sample types such as lymph node and solid tumour tissue, and further techniques specific to particular disease types are provided in subsequent chapters.
Cytogenetics in acute lymphoblastic leukaemia
Authors: Czepulkowski B , Gibbons B 
Published: November 2023

Abstract
In the past, cytogrnctic analysis of ALL has been lmnpcrcd by the difficulty in obtaining good quality chromo omes for c1.naly i . Poor spreading, fuzzy chromosomes and indistinct bands me, mt that only about 50% of cases analysed were found to have an abnormal clone, or because of metc1phases that could not be analysed, a number of case were cla,sified as failures. Improvements in cytogcnetic techniques have increased the success rate and abnormality rates observed in ALL. and also given an insight into the importance of cytogenetic abnorm. ilities in the pathophysiology c1nd prognosis of haemato logical malignancies, including ALL ,\bnormalities were detected in only about halt of all ALL patients in initial banding studies (1) but now most centres report chromosomal abnormalities in 60-85% of ALL cases (2-6). In cases with a normal katyotype or in failed cases, interphase FISII provides an additional technique by which chromosome abnormalities of prognostic importance can be identified. Such cases are now routinely screened with panels of probe to detect cases of high hyperdiploidy.
Chaperones in signal transduction
Authors: Smith David F 
Published: November 2023

Abstract
Hsp90, typically the most abundant chaperone in the cytoplasmic compartment of cells, has gained a reputation for its functional interactions with a wide variety of signalling proteins (for recent reviews see 1, 2–:4). Examples include the steroid receptors and several transcription factors unrelated to steroid receptors, a variety of tyrosine and serine/ threonine kinases, and other regulatory enzymes such as telomerase (5) and nitric oxide synthase (6–:8). In vitro refolding assays with model substrates have shown that Hsp90 on its own has the general ability to stabilize proteins in a folding competent state (9–:11), but there is limited evidence to support a major role for Hsp90 in general nascent chain folding. Still, unstable or alternative folding appears to be a common feature among the signalling proteins that are native targets for Hsp90. Another striking feature of native Hsp90 complexes is the in-variable presence of some combination of partner co-chaperones that bind Hsp90.
Molecular chaperone systems in the endoplasmic reticulum
Authors: Pelletier Marc F , Bergeron John J M , Thomas David Y 
Published: November 2023

Abstract
The endoplasmic reticulum (ER) is an organelle defined microscopically as a network of saccular and tubular membranes in continuity with the nuclear envelope. This definition can be further refined into a distinction between the rough endoplasmic reticulum to which ribosomes are attached, and the smooth endoplasmic reticulum which consists of a network of ribosome-free tubules and is the site of exit of secretory cargo vesicles. The ER can also be defined functionally as the site of lipid metabolism, carbohydrate metabolism, drug detoxification, and the entry point for proteins into the secretory pathway. Proteins that are secreted from cells, and proteins which are destined for cellular membranes, are synthesized on the ribosomes of the rough endoplasmic reticulum and translocated into the lumen of the ER, where they are glycosylated, become folded, disulfide bonds are formed, and some multiprotein complexes are assembled. Before proteins are transported out of the ER they are subjected to a ‘quality control’ process which assesses their state of folding and then, if they are correctly folded, allows them to exit the ER by packaging into transport vesicles. Proteins that are not folded correctly can have several fates. They are usually retained in the ER for further cycles of the quality control process or they are retrotranslocated out of the ER and degraded in the cytosol by the proteasomal system, or they can accumulate in the ER as aggregates.
The function of chaperones and proteases in protein quality control and intracellular protein degradation
Authors: Maurizi Michael R 
Published: November 2023

Abstract
During the last few years we have witnessed a major revolution in our understanding of the importance and the mechanism of intracellular protein degradation. We have come to appreciate that highly selective protein degradation occurs in all organisms and is a component of many essential regulatory pathways. We have also learned that protein degradation plays an important part in maintaining protein quality control within the cell. Most excitingly, we now have a grasp of the basic mechanism of ATP-dependent protein degradation and have begun to develop an understanding of how cells protect their proteins from inadvertent destruction while assuring that appropriate proteins are efficiently targeted for degradation. Studies of the structure and mechanism of the ATP-dependent proteases responsible for the majority of intracellular protein degradation have revealed unanticipated parallels between the proteolytic machinery of cells and the molecular chaperone systems responsible for the folding of cellular proteins and the assembly or disassembly of macromolecular complexes. This progress has led to a unified model of protein degradation and protein quality control, in which protein surveillance and structural remodelling mediated by chaperone systems and the chaperone components of ATPdependent proteases serve as the keystone.
Patterning the Xenopus Embryo
Authors: Smith J C , White R 
Published: November 2023

Abstract
The problem we wish to address concerns the mechanism by which the vertebrate early gastrula forms from the fertilized egg, with the right genes activated in the right places and with cells poised to undergo the movements of gastrulation. We will concentrate on the amphibian embryo, where the detailed molecular events of early embryogenesis are probably better understood than in any other vertebrate. This understanding is due to what might be regarded as the ‘traditional’ advantages of the amphibian embryo: its large size, the ease of grafting, the ability to culture cells in a simple salt solution, and the ease with which molecules can be overexpressed by RNA or DNA injection. These advantages have recently been supplemented by the introduction of transgenesis in Xenopus (by Amaya and Kroll (1, 2)), allowing, in principle, genes to be expressed in virtually any tissue of interest.