bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of in situ PCR techniques to human tissues
Authors: Bagasra Omar , Bobroski Lisa E , Amjad Muhammed , Pomerantz, Roger J , Hansen John 
Published: November 2023

Abstract
Since we first reported our findings regarding in situ amplification of the HIV-1 gag gene in an HIV-1-infected cell line in March 1990 (1), there has been an explosion of research in the area of in situ polymerase chain reaction (in situ PCR). There are over 300 publications describing various forms of in situ gene amplifications (reviewed in 2,3,13) , identifying various infectious agents, tumour marker genes, cytokines, growth factors and their receptors, and other genetic elements of interest, in peer-reviewed journals (1–25). The solution-based PCR method for amplifying defined gene sequences has proved a valuable tool not only for basic researchers but also for clinical scientists. Using even a minute amount of DNA or RNA and choosing a thermostable enzyme from a large variety of sources, the gene of interest can be amplified and then analysed and/or sequenced. Thus genes or segments of gene sequences present only in a small sample of cells or a small fraction of mixed cellular populations can be examined. However, one of the major drawbacks of solution-based PCR is that it does not allow the association of amplified signals of a specific gene segment with the histological cell type(s) (13,14). For example, it would be advantageous to determine what types of cells in the peripheral blood carry aberrant genes in a leukaemia patient and what percentage of leukaemia cells is present after various forms of anti tumour therapy.
Applications and modifications of PCR in situ hybridization
Authors: Patterson Bruce K 
Published: November 2023

Abstract
The localization of genes in specific cells and tissues has been instrumental in many disciplines for defining disease pathogenesis. This pursuit has united scientists studying such diverse topics as oncogene expression, viral infections, and plant pathology. In its earliest incarnation, molecular biologists met with pathologists to use large subgenomic probes to detect genes in situ. This process relied on the intrinsic amplification of genes during transcription into mRNA to accumulate enough target to be detected.
Mitochondrial DNA isolation, separation, and detection of fragments
Authors: White P Scott , Tatum Owatha L , Tegelstrom Hakan , Densmore III Llewellyn D 
Published: November 2023

Abstract
The 'revolution' that began in the 1980s with the application of mitochondrial DNA (mtDNA) analyses to address questions of molecular evolutionary and population biology has now largely become the paradigm for such work (1). Studies ranging in scope from purely systematic problems to identification and recognition of species to documentation of genetic changes in populations that have occurred over a very short period of time, are based on both indirect or direct estimates of nucleic acid variation. While progress continues to be made in analysing coding regions of nuclear DNA, the sequences retained in organellar genomes are still the most widely studied by evolutionary biologists. Restriction site or fragment analyses of mtDNA and direct sequencing of specific regions of the mitochondrial genome following amplification by the polymerase chain reaction (PCR) are currently the methods of choice for the majority of population level studies. The reasons for the increasingly wide spread application of mtDNA markers in studies of animal populations are many; however, there are also a few noteworthy drawbacks (reviewed in ref. 1). Figure 1 shows the typical vertebrate gene order of mtDNA, with birds having a single rearrangement involving ND 6 (a subunit of NAD dehydrogenase) and tRNAGlu not found in other vertebrates examined to date. Other minor rearrangements have been reported, and gene order can provide important synapomorphies (shared derived characters) for deciphering some relationships.
Silane-modified surfaces for biomaterial immobilization
Authors: Shriver-lake Lisa C 
Published: November 2023

Abstract
Biosensors, affinity chromatography, and many bio analytical methods require a high density of functional molecules, low non-specific protein adsorption, long-term stability, and durability (1). Proteins, including antibodies and enzymes, and cells have been immobilized onto solid supports for these and other applications over the last 30 years. In the biosensor arena, optical transduction methods are increasingly employed. With this increase, solid supports such as fused silica and quartz are appropriate substrates for immobilization. Non-specific protein adsorption to these substrates has been a major problem.
Antibodies as immobilization reagents
Authors: Egodage Kamal L , Wilson George S 
Published: November 2023

Abstract
Immobilized antibodies have been used extensively as reagents for the isolation of chemical and biological molecules where there are no naturally occurring ligands. Due to high specificity of the antibodies, the immobilization of specific antigens on different matrices in the required orientation and in high concentration, for use in analytical and biological applications, is possible. The ability to elicit an immune response to a hapten by conjugation to a carrier molecule extends the applicability of antibodies as immobilizing ligands to small molecules. Although polyclonal antibodies have been used as capture matrices, the advent of monoclonal antibody technology has extended and enhanced the use of this approach. Antibodies covalently immobilized to different solid matrices have been used for extraction of biomolecules in plasma (1–3), and for purification of enzymes (4—8), and receptors (9–11). They have also been used as reagents in purification, concentration, and analysis of environmental samples (12, 13). Immobilized antibodies have also been used to prepare immunoreactors for flow injection imrnunoassays (14-16) and to prepare enzyme reactors (17–19).
Bioanalytical applications of self-assembled monolayers
Authors: Liedberg Bo , Cooper Jonathan M 
Published: November 2023

Abstract
The ‘self-assembly’ of thin molecular films of biological or chemical moieties onto surfaces is a process which is of enormous interest in diverse areas of technology, due to the apparent simplicity by which a solid support can be modified or functionalized. Consequently, there has been a tremendous growth in the interest shown in the use of these systems during recent years, with a recognition of their importance in the development of novel surface coatings. It is now dear that, when the deposition procedure is carefully controlled, it is possible to ‘spontaneously’ deposit a single layer of particular species (or, indeed, a mixed monolayer of different species) on a surface, giving rise to the use of the term ‘self-assembled monolayer’ or SAM. Although it is the purpose of this chapter to describe the application of SAMs to bioanalytical methodologies, it should also be acknowledged that the uses of these techniques are numerous and now impinge on many areas of modern materials science. For example, ultrathin SAMs, with predefined compositions have now been used in order to obtain a deeper understanding of interfacial phenomena like adhesion, lubrication, wetting, nucleation, and crystal growth (1, 2).
Protein adsorption: friend or foe?
Authors: Johnston Erika , Ratner Buddy D 
Published: November 2023

Abstract
The phenomenon of protein adsorption is widely observed in nature and in technology. For example, consider marine fouling, contact lenses, food processing equipment, cell growth surfaces, and biosensors. Also, the biocompatibility of medical implants may be driven by the surface adsorbed layer of proteins. When a biological solution comes in contact with a clean surface, proteins and other surface active molecules diffuse rapidly from the bulk liquid and become reversibly or irreversibly adsorbed to the surface (1). Although the compositional mixture, conformation, and binding strength of the adsorbed proteins may vary with time, the conditioning layer is persistent and will mediate all future interactions between the surface and components in the surrounding liquid. The effects attributable to conditioning layers can be separated into two types: those directly associated with the conditioning layer itself (changes in permeability, lubricity, texture, etc.) and those due to cells (e.g. macrophages, platelets, bacteria) that are activated or attracted by the adsorbed material.
Micropatterning cell adhesiveness
Authors: Clark Peter 
Published: November 2023

Abstract
The ability to micro pattern adhesiveness for cells has been exploited by a number of research groups to provide model surfaces for investigating cell behaviour, and for devising technologies in cell and tissue engineering (1–11). These techniques have been developed to make surfaces which provide differentially adhesive cues for cultured cells, i.e. areas which are permissive for cell adhesion and locomotion, with adjacent non-permissive areas. The techniques were developed using a variety of approaches, but have in common the use of, at least at some stages, the micro fabrication technologies of the electronics industries. Though a brief description of the facilities required will be given, it is not within the scope of this chapter to deal with the details of the methods for standard micro fabrication, or for micro-mask formation, which today usually involves computerized ‘writing’, e.g. electron-beam writing of electron-sensitive resists. It will be assumed that anyone embarking on adhesion micro patterning will have access to masks and to micro fabrication facilities, and the protocols will reflect this. The electronics and physics departments of many universities have such facilities. Similarly, it will be assumed that experience of general cell culture and access to the appropriate facilities is available; only general background and non-standard cell culture methods will be detailed.
Sol-gel matrices for protein entrapment
Authors: Dave Bakul C , Dunn Bruce , Valentine Joan S , Zink Jeffrey I 
Published: November 2023

Abstract
Traditional inorganic glasses are not generally considered to be a suitable host matrix for immobilization of biological molecules. Consequently, stabilization of proteins and enzymes within inorganic silica glasses is very unusual (1). This breakthrough in immobilization methods has been made possible by the sol-gel method of synthesizing inorganic solids (2). The sol-gel approach is a solution-based synthesis technique for making inorganic materials at low temperature. The main advantage of the sol-gel method is that inorganic oxide glasses are synthesized by hydrolysis of simple alkoxo precursors (3). In the case of silica-based systems, the hydrolysed precursors then condense together to form a predominantly SiO2 glass framework. In this way, SiO2-based silica glass can be conveniently fabricated using Si(OR)4 precursors at room temperature without the extreme temperatures required for conventional glass melting methods. Sol-gel-derived silica glasses are highly porous structures containing an interstitial solvent phase. A high molecular weight dopant molecule added to the initial reaction mixture becomes trapped in the interconnected porous network as the final SiO2 glass structure forms (4). In addition, since the pore diameters are much less than the wavelength of light, the sol-gel glasses are optically transparent. This enables one to monitor spectroscopically the nature of events associated with encapsulation and reactivity of the dopant molecules (5).
Immobilization of ‘smart’ polymer-protein conjugates
Authors: Stayton Patrick S , Hoffman Allan S 
Published: November 2023

Abstract
The remarkable molecular recognition capabilities of proteins provide the basis for many important clinical, industrial, and laboratory applications. Key existing technologies include separations, hiosensors, bio transformations, diagnostics, and targeted drug delivery. The central event in protein-mediated recognition processes is typically a protein:ligand binding step, which is characterized by a combination of high specificity and affinity, and in the case of enzymes by a high affinity for the reaction coordinate transition state. While these molecular recognition capabilities have proven extremely useful, many practical problems limit the utility of proteins because nature has not optimized them for the device environment.
Fluorophore-labelled saccharide electrophoresis for the analysis of glycoproteins
Authors: Jackson Peter 
Published: November 2023

Abstract
It has become apparent that the carbohydrate m01etles of glycoproteins (glycones) have important and varied functions (1-3) and this knowledge has stimulated considerable advances in methods for their purification and analysis. However these procedures are not routine. Current analytical strategies usually involve the release of the free saccharide (glycan) from the glycoprotein or glycopeptide followed by chromatographic isolation and structural determination using a variety of techniques including compositional analysis, chemical and enzymatic degradation, lectin binding, mass spectrometry, and nuclear magnetic resonance (4-10).
Designing new agonists/antagonists of growth factor receptors-the rational design of a superantagonist of the IL-6 receptor
Authors: Ciliberto G , Lahm A , Paonessa G , Savino R , Toniatti C 
Published: November 2023

Abstract
Growth factors and cytokines assemble multisubunit receptor complexes stabilized by a variety of protein:protein interactions (1), each of which plays a distinctive role in signalling and activating biological responses. Identifying functional epitopes on the cytokine surface thus opens up possibilities for engineering variants with predefined properties for potential use as therapeutic agents. We have applied this concept to the rational design of receptor antagonists of human interleukin-6 (IL-6).
A chimeric approach for studying receptor binding domains in EGF-like molecules
Authors: Van Zoelen E J J , Lenferink A E G , Vugt M J H Van , Van de Poll M L M 
Published: November 2023

Abstract
The use of chimeric proteins has gained increasing popularity in studies on the structure-function relationship of biologically active peptides. Using recombinant DNA technology, proteins can readily be made in which specific domains have been exchanged for corresponding domains from other proteins. The use of chimeras obtained by such a domain-exchange approach has been shown to be particularly fruitful when comparing the biological properties of two structurally related proteins. It is essential that the two proteins of inter est have different biological activities, and that a direct assay is available to distinguish these activities. That is the reason why this approach has been used particularly for proteins with specific binding or signalling activity, including polypeptide growth factors, growth factor receptors, and nuclear transcription factors.
Defining growth factor function through tissue-specific expression of dominant-negative receptor mutants
Authors: Werner Sabine 
Published: November 2023

Abstract
Elucidating the function of growth factors and their receptors during development and in the adult organism is one of the most challenging tasks in growth factor biology. A few years ago, only descriptive expression data were available which suggested multiple roles of growth factors in development. However, the development of transgenic mouse technologies has provided new insights into the function of growth factors and their receptors in vivo. These technologies allow gain-of-function experiments (over-expression of ligands or receptors) as well as loss-of-function experiments (gene knock-outs by homologous recombination in embryonic stem cells). Knock-out studies have shed light on the function of many growth factors in embryonic development. While these studies can reveal the earliest essential function of a particular growth factor or its receptor, the specific role of these genes at later stages of development may be obscured due to the early embryonic lethality. In addition, the loss of one member of a gene family may be compensated for by overlapping expression of another, related gene (1). Such a compensation could be particularly important for growth factors which are members of a large family of related ligands, e.g. the fibroblast growth factors (FGFs) and the epidermal growth factor (EGF) receptor ligands. This hypothesis is supported by the very ‘mild’ phenotypes of FGF-5, FGF-7, and transforming growth factor-a (TGFa) knock-out mice (2-5). These animals reveal only a defect in the hair, although FGF-5, FGF-7, and TGFa are widely expressed in the embryo and-in the case ofFGF-7 and TGFa-also in the adult animal (6-8).
Practice and benefits of microcolumn HPLC
Authors: Yang Frank J 
Published: November 2023

Abstract
The application of microcolumn HPLC have grown significantly in recent years, especially since the current trends in HPLC are to employ continuously smaller diameter columns in order to reduce solvent consumption, to enhance sample detection, to allow a direct interface with mass spectrometers, and to facilitate sample limited applications and hyphenated techniques. Microcolumn HPLC is the HPLC of choice for the most modern HPLC bench-top MS applications, being used for several ionization techniques including particle beam (1-3), continuous flow FAB (4-9), EI/CI (10-13), and electrospray and nanospray interfaces (14-20). The major driving force behind the rapid growth of microcolumn HPLC in the past few years has been the commercialization of bench-top low cost mass spectrometers with electrospray and nanospray interfaces. At reduced flow rates, a few µ1/min and down to sub-µl/min, maximum sensitivity and baseline stability can be achieved. Thus, it can be expected that microcolumn HPLC-MS will become even more popular than capillary GCMS in the near future as the ability to connect microcolumn HPLC directly to the mass spectrometer will be propitiated by the development of low cost, easy to use, high sensitivity, and high reliability mass spectrometer, and supported by the low flow rates used in microcolumn HPLC.
Detection devices
Authors: Scott Raymond P W 
Published: November 2023

Abstract
In chromatography, the detection device is as essential to a successful analysis as the distribution system that produces the separation, and over the years there has been a continuous synergistic development between these two essential components of the chromatograph. As the columns and thin-layer plates have become more efficient, the solute bands have become reduced in size, and the solute concentrations smaller. These changes have educed the development of detectors, with higher sensitivities, and smaller sensor volumes. The improved detectors, in turn, have evoked improvements in column technology which have produced higher separating efficiencies. It is clear that the design of the detecting device is critical in high resolution chromatography.
Lectins as affinity probes
Authors: Sheldon Philip S 
Published: November 2023

Abstract
In 1888, Hermann Stillmark described the agglutination of erythrocytes by an extract from castor beans. Soon after this initial observation, the proteins which we now know as lectins, began to be used as tools in biomolecular research (1). Paul Ehrlich carried out pioneering studies in immunology using plant agglutinins and toxins as model antigens. Concanavalin A (Con A) from jack beans was the first lectin to be purified and crystallized. The observations that Con A precipitated glycogen and that sucrose inhibited haemagglutination led to the proposal that haemagglutination was a consequence of interactions between Con A and carbohydrate on the cell surface. As it emerged that haemagglutination was species- and blood type-specific, the term lectin became used to refer to plant agglutinins which were blood group-specific.
Strategies and methods for purification of Ca2+ -binding proteins
Authors: Fitzpatrick Sandra L , Waisman Da Yid M 
Published: November 2023

Abstract
Caz+ has been demonstrated to be the key second messenger in a variety of stimulus-response systems. These Caz+ regulated processes include muscle contraction, secretory events such as exocytosis, cell cycle regulation, cellular differentiation, and gene transcription. The Ca2+-binding proteins play a fundamental role in the Ca2+ signalling pathway: they transduce changes in intracellular Ca2+ into cellular activation. For example, Ca2+-dependent modulatory proteins such as calmodulin or annexin II tetramer undergo conformational changes in response to increases in intracellular Ca2+. The interaction of the Ca2+ -binding protein with Caz+ results in the generation of a conformational change in the protein and when in this active conformation these proteins can bind to and affect a variety of intracellular proteins or enzymes. Alternatively, Ca2+ -binding proteins directly participate in cellular signal transduction by containing in the structure of the Ca2+ -binding protein both Ca2+-binding domains and catalytic domains. For example, certain isozymes of protein kinase C contain Ca2+/phospholipid-binding domains and a catalytic domain.
Cationic Liposomes in Gene Delivery
Authors: Sullivan Sean , Gong Yan , Hughes Jeffrey 
Published: November 2023

Abstract
Gene therapy provides a new paradigm for the treatment of human diseases. Although gene therapy trials have been initiated worldwide for greater than two decades, little has been achieved clinically in curing diseases. A major hurdle is the lack of efficient delivery systems for in vitro and in vivo studies. An ideal system should have the following characteristics: be targetable, biodegradable, nontoxic, and stable for storage. Gene delivery systems are generally categorized into viral and plasmid-based vectors. Plasmid-based systems are also extremely useful for in vitro studies and will be the focus of the chapter.
lsothermic Titration Calorimetry (ITC)
Authors: Lasch J 
Published: November 2023

Abstract
This chapter covers a technique which measures the heats associated with the binding of surfactants to liposomes. It starts with the technique and sample handling and proceeds to the estimation of critical surfactant parameters. The estimation of these parameters is outlined in three main sections comprising the CMC, surfactant partitioning into lipid membranes, and liposome solubilization. Surfactants-induced transitions of lipid bilayers take place in a four-stage process (1). Surfactants added to liposomes are incorporated into the lipid membranes up to a critical (saturating) surfactant/lipid ratio, Rsat· Increasing the ratio above Rsat, the lipid bilayers are progressively destroyed and mixed vesicles start to coexist with mixed micelles. When the total content of surfactant in the aggregates reaches R501, all membranes are dissolved leaving only mixed micelles and the solubilization is complete. The micellar intermediate structures are cylindrical mixed micelles (CMM), lipid-rich spherical or ellipsoidal mixed micelles (SMM or EMM), and finally lipid-poor mixed micelles (1) (Figure 1).
Detection of sequence variation using primer extension
Authors: Syvänen A -C 
Published: November 2023

Abstract
Most of the currently used methods for detecting single nucleotide polymorphisms or point mutations are based on amplification of the target DNA by the PCR technique or another amplification method, which allows sensitive and specific analysis of the target DNA sequence by a variety of methods. Previously known sequence variants are distinguished in the amplified fragments by hybridization with sequence-specific oligonucleotide (SSO) probes (see chapter 7) or with the aid of nucleic acid modifying enzymes, such as restriction enzymes, DNA ligases, or DNA polymerases (see chapters 8 and 9).