bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth factor-toxin chimeras and their applications
Authors: Davol Pamela A , frackelton A Raymond , calabresi paul 
Published: November 2023

Abstract
Clinically, the most successful drugs in use today are those which were designed to target specific metabolic pathways. Not surprisingly, growth factor receptors expressed on the surfaces of cells have been recognized as potentially important therapeutic targets. The specific affinity of growth factor ligands for their receptors combined with the observation that many growth factor receptors are rarely expressed at high levels on normal, non proliferating cells have made growth factor ligands attractive molecules for the delivery of toxins for the treatment of neoplastic, autoimmune, cardio vascular, and proliferative eye diseases and transplant rejection (see reviews in refs 1-3).
Drugs and inhibitors as affinity ligards
Authors: Hooper Nigel M 
Published: November 2023

Abstract
With the pharmaceutical industry ‘s search to identify ever more therapeutic agents, numerous drugs and inhibitors are being synthesized. Several of these compounds can be used as affinity ligands for the purification of a particular target protein. However, some of the earliest affinity ligands were those based on the dyes used in the textile industry, such as the synthetic polycyclic dyes Cibacron Blue and Procion Red which bind to a wide range of proteins including dehydrogenases, kinases, and other enzymes requiring adenylyl containing groups (1); the use of such dyes is described in Chapter 6. How-· ever, other proteins, e.g. albumin and interferon, bind in a less specific manner due to electrostatic and/or hydrophobic interactions with the compounds.. More recently numerous drugs and enzyme inhibitors have been used as selective affinity ligands. In some cases the interaction between the ligand and the protein has been mapped in detail, often through co-crystallization of the compound with the protein and subsequent X-ray crystallographic analysis.. However, details of how a compound interacts with a particular protein need not be known for its use as an affinity ligand.
Surface Modification of Liposomes
Authors: Torchiiin Vladimir P , Weissig Volkmar , Martin Francis J , Heath Timothy D , R.C.New Roger 
Published: November 2023

Abstract
Modification of the liposome surface is a powerful approach to control liposome properties and biological behaviour. Attachment of certain specific ligands (such as antibodies, peptides, hormones, sugars) makes liposomes targeted; attachment of contrast agents converts liposomes into efficient diagnostic tools; coating liposomes with polymers, such as poly(ethylene glycol) imparts to them an ability to circulate long without being opsonized and recognized by cells of the reticulo endothelial system, etc.
pH-sensitive liposomes
Authors: Peschka-Süss Regine , Schubert Rolf 
Published: November 2023

Abstract
In 1980, it was suggested that there might be a possible clinical application of liposomes, which are designed to release their contents in an environment such as tumour tissue with a slightly decreased pH of around 6 (1). An advanced approach of pH-sensitive liposomes is the intracellular pH-triggered release of liposome compounds from the endocytotic pathway to the cytosol.
Surface fluorescence microscopy with evanescent illumination
Authors: Axelrod D 
Published: November 2023

Abstract
The interaction of molecules with surfaces is central to numerous phenomena in biology: e.g. binding to and triggering of cells by hormones, neurotransmitters, and antigens; the deposition of proteins upon foreign surfaces leading to thrombogenesis; electron transport in the mitochondrial membrane; cell adhesion to surfaces; concentration of reactants at surfaces and consequent enhancement of their reaction rates with other surface bound molecules; the dynamical arrangement of submembrane cytoskeletal structures involved in cell shape, motility, and mechanoelastic properties; and molecular events preceding cellular secretion from intracellular granules.
Purification of macrophages
Authors: Gessani Sandra , Fantuui Laura , Puddu Patrizia , Belardelli Filippo 
Published: November 2023

Abstract
The investigation of cell populations consisting of a single cell type confers a great advantage over the complicated examination of mixed cell populations in many experimental studies. The achievement of enriched preparations of cells of the monocyte/macrophage lineage is particularly troublesome as these cells display a variety of functional and morphological phenotypes and are readily activated in response to environmental signals. Macrophage purification is further complicated when cells of this lineage represent a minority of the whole mononuclear pool (e.g. peripheral blood).
Analysis of gene expression in mononuclear phagocytes
Authors: Paulnock Donna M , Doan Joyce E S , Hamilton Thomas A 
Published: November 2023

Abstract
Specific gene expression is a hallmark of differentiated cell populations, as well as of cellular activation within specific cellular subsets. This is particularly true in the context of the mononuclear phagocyte, which has long been described on the basis of changes in cellular phenotype and function associated with activation by proinflammatory or stimulatory agents (1, 2). This chapter will provide a discussion of methods used for analysis of gene expression in the context of mononuclear phagocytes. Even in such a restricted context, however, this represents a broad and diverse subject. Furthermore, gene expression may be modulated both quantitatively and qualitatively at multiple levels, which can be broken down into transcriptional, post-transcriptional, translational, and posttranslational (subcellular localization/secretion) categories. In order to maintain reasonable scope, this chapter will be limited to considerations of experimental methodologies which address the early aspects of gene expression, i.e. transcriptional and post-transcriptional regulation.
Image warping and spatial data mapping
Authors: Baldock Richard A , Hill Bill 
Published: November 2023

Abstract
Modifying the geometry of (warping or morphing) a digital image is important for many purposes. D’Arcy Thompson (1) used coordinate transformations to model variations in form with a view to understanding the underlying processes controlling growth. More recently, warping has been required as part of the data capture or reconstruction process, i.e. to restore what is assumed to be the correct geometry. Examples are to correct for spatial distortion in the imaging process, such as perspective transformation or spherical aberration in the optics, or to convert from one coordinate frame to a rectilinear array such as in ultrasound scanning or computed tomography, or to correct for geo-metric distortions introduced in the material processing before imaging such as in microtome sections of tissue. In medical imaging complex distortion of the geometry of images may be necessary to compare images from one scanning modality to another (see Chapter 6), to compare images from the same individual over time, to average between individuals, and to compare an individual with an atlas. Morphing has also been used for special effects, particularly in film and television and for simulating morphogenesis (2). With the development of spatially organized databases, e.g. geographic information systems (GISs) or, more recently, biological databases such as the Brain Map project in the USA (3) or the Edinburgh Mouse Atlas and gene-expression database (4), it is important that data accumulated at different times, with different instruments, and in the biological situation from different individuals, are mapped onto the same standard coordinate frame.
Reconstitution of membrane proteins: the Ca2+-ATPase of sarcoplasmic reticulum
Authors: Lee Anthony G 
Published: November 2023

Abstract
1 Introduction
Biological membranes have complex structures, reflecting the wide range of functions they are required to perform: most biological membranes contain many hundreds of different species of protein and lipid. One approach to understanding this complexity is to purify individual components from the membrane and study their properties in isolation. Purification of an intrinsic membrane protein generally requires it to be first dissolved out of the membrane in some suitable detergent, so that it can then be separated from the other membrane proteins. Some membrane proteins are stable for long periods in detergent solution, but many are not; even those that are stable may show altered properties in the unusual environment of a detergent micelle. For these reasons it is better to transfer the protein, once purified, from the detergent back into a lipid bilayer; this is the process of reconstitution. Reconstitution gives the simplest membrane system that is likely to be a fair representation of the native membrane. Reconstitution can be used to define the minimum number of protein components necessary to carry out some defined function of the membrane, and to study the interactions between lipids and proteins in the membrane.
Spatial analysis of gene expression
Authors: Nonchev Stefan G , Maconochie Mark k. 
Published: November 2023

Abstract
The generation of mRNA is, in most cases, a prerequisite for gene function. Thus the study of _mRNA or transcript generation is important for understanding the potential functions of genes, and many molecular techniques have been used to analyse gene expression. Routine molecular technologies involve either the immobilization of total RNA or poly(A) + RNA on membranes followed by hybridization of DNA or RNA probes, or the use of oligonucleotide primers and reverse transcription–polymerase chain reaction (RT-PCR). However, further molecular methods are being developed, and it is likely that DNA chip and microarray technology will permit more global assays of gene expression. All the above methods are two-dimensional, since spatial information is lost by removal of the cells and tissues to provide the material for assay. It has become clear that the restriction of gene expression to discrete domains in higher eukaryotes is one important method of regulating gene function, and thus gene expression assays which are able to reflect the three dimensions of embryos, tissues and organs are likely to remain important components of genetic analyses for some time to come.
Analysing mouse chromosomal rearrangements with G-banded chromosomes
Authors: Akeson Ellen C , Davisson Muriel T 
Published: November 2023

Abstract
This section describes the preparation of metaphase chromosomes from mouse peripheral blood lymphocytes for chromosomal typing of living mice. Included is a list of mouse strains and their relative response to phyto-haemagglutinin (PHA), a list of the requirements necessary for the production of well-spread metaphase chromosomes with good morphology for banding, a Giemsa banding (G-band) method for these chromosomes, and their classification into a karyotype. The identification of mouse chromosomes is presented with a detailed process for determining aberrant chromosomes and describing the common pitfalls of misclassification. A precise description of the characteristic banding patterns (landmarks) at different stages of chromo some condensation is presented elsewhere (1). The cell-harvesting part of the procedure also can be used to prepare mitotic chromosomes directly from fetal liver or bone marrow.
Generation of transgenic mice from plasmids, BACs and YACs
Authors: Hammes Annette , Schedl Andreas 
Published: November 2023

Abstract
Transgenesis, or the stable integration of foreign DNA into a host genome, has developed into one of the most powerful techniques for analysing gene function and regulation (1). Applications of this technology are numerous and range from investigating the basic mechanisms of gene regulation to the generation of models for human diseases, which can be used for pathophysiological and therapeutic studies. The list of over-expression studies includes the use of cDNA constructs encoding transcription factors, cell surface receptors and structural proteins. In addition constructs encoding antisense RNA, to inhibit endogenous gene expression, can be used in transgenic experiments. Before describing the technical steps involved in the generation of transgenic mice, we will briefly highlight a number of important points to consider in designing a transgenic experiment. Due to space limitations this section cannot be comprehensive and the interested reader is referred to original articles where transgenic technology has been applied.
Selection of antibodies from phage libraries of immunoglobulin genes
Authors: Osbourn Jane K 
Published: November 2023

Abstract
This chapter explains the various approaches it is possible to take in the selection of phage antibodies with specific binding characteristics from large phage display libraries. The particular selection approach taken will be determined by the form and availability of the starting antigen and the desired properties of the selected antibody. One of the main benefits of the phage display approach to antibody generation is the ability to tailor the selection regime to generate antibodies with particular characteristics such as: high affinity, neutralization potency, ability to recognize specific epitopes, or to recognize specific cell types. A variety of screening regimes can also be employed to identify antibodies that can be utilized for particular applications such as: Western blot reagents, immunocytochemistry reagents, or species cross-reactivity. The phage system provides a route to the generation of antibodies to antigens that are normally inaccessible using conventional immunization techniques, for example mAbs to toxic moieties, carbohydrate-containing molecules, and anti-self antigens can easily be selected using the appropriate conditions. Methods for the generation of phage antibody libraries from immunized rodents are described elsewhere (Chapter 2) and these techniques are equally applicable to the generation of human phage antibody libraries if appropriate primers are used (1). The selec tion methods described here can be employed for immunoglobulin genes dis played in scFv, Fab, or diabody formats. The methods described provide a necessarily brief outline of the possible approaches and it should be stressed that there are no hard and fast rules for selection protocols; investigators should use as much imagination as possible in designing selection procedures which will best suit the final application of the antibody. Possible selection methods such as in vivo selection (2), selective infective phage selections (3, 4), and various deselection methods (e.g. 5) have not been discussed in detail here and reference should be made to the appropriate literature for further ideas on these approaches.
ARM complexes for in vitro display and evolution of antibody combining sites
Authors: Taussig Michael J , Groves Maria A T , Menges Margit , Liu, Hong , He Mingyue 
Published: November 2023

Abstract
Antibody VH and VL region genes are readily obtained by PCR and can be recombined at random to produce large libraries of single chain fragments (1). Such libraries may be obtained from normal or immune B lymphocytes, or con structed artificially from cloned gene fragments with synthetic H-CDR3 regions generated in vitro (2). Libraries can also be generated by mutagenesis of cloned DNA fragments encoding specific Vtt/ VL combinations and screened for mutants having improved properties of affinity or specificity.
lmmunofluorescence microscopy
Authors: Pepperkok Rainer , Girod Andreas , Simpson, Jeremy , Rietdorf Jens 
Published: November 2023

Abstract
Antibodies provide a powerful tool to localize antigens in cells or tissues by immunocytochemistry at the light or electron microscope level. The develop ment of efficient fluorescent dyes which can be coupled to antibodies for their visualization by fluorescence microscopy has pioneered a technology which is known as immunofluorescence microscopy (1PM). IFM is easy to apply to many biological and medical questions, the protocols involved are short, and the development of sophisticated imaging equipment has even made possible the acquisition of quantitative data on the 3D distribution of several antigens in the same specimen.
FACS analysis of clinical haematological samples in transplantation for cancer
Authors: Millar Barbara C 
Published: November 2023

Abstract
The systematic approach to the naming of leucocyte antigens using the cluster of differentiation (CD) designation (1) was made using monoclonal antibodies (mAbs). Direct conjugation of these antibodies or indirectly, via a two-step pro cedure, to fluorochromes permits visualization of individual cell types. The development of automated fluorescence activated cell analysis (FACS) to assess leucocytes in peripheral blood (PB) and bone marrow (BM) samples by their CD designation has provided an accurate and reproducible method, which is relatively easy, quick to perform, and permits far greater numbers of cells to be analysed than can be done using microscopy.
lmmunocytochemical staining of cells and tissues for diagnostic applications
Authors: Dodson Andrew R , Sloane John P 
Published: November 2023

Abstract
Immunocytochemistry can be defined as the in situ demonstration of cellular constituents by specific antibody-antigen reactions. It has its origins in the 1940s with the pioneering work of Coons et al. (1). Since that time many workers have developed and refined the technique, so that today it is an essential part of diagnostic pathology.
Study of protein phosphorylation in intact cells
Authors: Haystead Timothy A J 
Published: November 2023

Abstract
The phosphorylation of proteins on the amino acid residues serine, threonine and tyrosine is generally recognized as a fundamental mechanism by which the regulation of intracellular events is achieved. The process is reversible, enabling cells to respond in a dynamic way to a myriad of signals. The significance of protein phosphorylation is rapidly becoming apparent from the ongoing genome projects, with the discovery that 1–2% of the entire human genome may encode protein kinases (1). Conversely, in the case of protein tyrosine phosphatases, there may be as many genes encoding these enzymes as there are opposing tyrosine kinases. Although not as readily identified by primary structure predictions alone, there may also be numerous genes encoding regulatory subunits which control the activity of the catalytic subunits of serine/threonine phosphatases (2–5). The finding that nature has put so much evolutionary effort into controlling phosphorylation events in the cell is a testament to its importance, as well as to its complexity. The finding that many protein kinases and phosphatases are localized with their substrates in discrete subcellular compartments, and not floating in the intracellular ‘ether’ as previously thought, adds additional complexity. Methods that enable phosphorylation events to be examined directly as they happen in the intact cell in response to a particular stimulus are, therefore, highly desirable. This chapter focuses on state of the art, non-invasive, methods that enable changes in intracellular protein phosphorylation to be measured as they occur in intact cells. One of the great advantages of studying protein phosphorylation, as opposed to other regulatory mechanisms such as allosteric regulation, is that protein phosphate esters are stable at physiological pH and can survive homogenization of the cell.
Fluorescence microscopy of living vertebrate cells
Authors: Pepperkok Rainer , Shima David 
Published: November 2023

Abstract
Fluorescence microscopy of living cells has always been a powerful tool for cell biologists. Presently it is experiencing an unexpected renaissance and is on its way to having a place in almost every branch in modern biology from developmental biology to cellular biochemistry. Labelling of organelles or structures in living cells, compared with work in fixed cells, has the obvious advantage that the dynamics of the labelled structures or molecules can be studied. Also, labelling in living cells does not suffer from possible problems induced by the fixation or permeabilization of the cells as is necessary for immunofluorescence or electron microscopy.
Fluorescence microscopy in yeast
Authors: Hagan Iain M , Ayscough Kathryn R 
Published: November 2023

Abstract
The reductionist desire of the modern biologist to analyse complex problems in the genetically amenable systems which offer the fewest variables has seen yeasts come to the fore in modern cell biology as the leading model eukaryotes. Both the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe offer many advantages for the analysis of diverse aspects of cell biology. They are unicellular but also have limited options of differentiation in sexual reproduction and pseudohyphal growth. Their usual mode of growth and the tight correlation between growth and cell division have made them excellent systems for the analysis of the control of cell cycle progression. Moreover the strong classical and molecular genetics have meant that yeasts are not only a favourite of the research scientist but also appeal to the biotechnologist in their desire to produce large quantities of cloned proteins. These factors, combined with its small genome size, made budding yeast the obvious choice for a concerted effort to establish the first complete DNA sequence of a eukaryote (see Table 1 for genome website). This information in turn has heightened interest in yeast as a model system as many genes can be identified in silica and the boundaries of potential complexity of different pathways have been set. It is now known exactly how many members of a particular protein family exist in S. cerevisiae. This defines limits for modelling a particular process as the possibility that perhaps another isoform of a particular protein exists is no longer an acceptable escape clause to consolidate a flagging model.
Initial characterization of new orphan receptors
Authors: Sladek R , Giguère V 
Published: November 2023

Abstract
Nuclear receptors are transcription factors with the intrinsic ability to be regulated by changes in the intracellular levels of small lipophilic compounds. Since the molecular cloning of the glucocorticoid receptor in 1985, over 50members of the nuclear receptor superfamily have been identified (1). Most of these gene products were discovered as a result of their sequence homology with other family members: however, their sequence conservation often reveal&lt;; little about their individual function as transcription regulatory proteins. The ultimate goal for many investigators is to identify ligands for these orphan receptors: basic characterization of receptor functions including their DNA binding mode and transactivation properties provides an important first step towards realizing this goal.
Adopting orphans: finding ligands
Authors: Kersten S , Wahli w. 
Published: November 2023

Abstract
This chapter outlines the strategy for finding natural ligands for orphan nuclear receptors. The first part discusses the overall approach for identifying compounds or a class of compounds that can activatethe orphan receptor. The second part focuses on the methods that can be employed to demonstrate that the previously identified activator is indeed a bona fide ligand, meaning that the compound is able to directly bindto the orphan receptor with high affinity.