bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Protein Folding by Protein Engineering
Authors: Matouschek Andreas , Serrano Luis , Fersht Alan R 
Published: November 2023

Abstract
Denatured proteins can in many cases refold to the native structure. It is generally accepted that the folding has to progress along a specific pathway (1), although Harrison and Durbin (2) have argued that folding could follow many different parallel pathways (jigsaw puzzle model). Several different models of protein folding have been proposed. The framework model (3) suggests that the earliest steps are the formation of native secondary structure elements, while an alternative model proposes that folding begins with a rapid hydrophobic collapse (4-7). A somewhat different view is reflected in the micro-domain folding models (8-10) which propose that small structural subdomains of the protein assume their native structure early during folding. These initiation sites either grow directly by extension or by diffusion and collision with other subdomains. If there are several initiation sites it is easily imaginable that many different, parallel, folding pathways exist. The molten globule hypothesis of protein folding (11, 12) suggests that a 'molten globule' intermediate occurs late on the folding pathway of all proteins. This intermediate is compact and has native-like secondary structure but fluctuating tertiary interactions. Its conversion into the native state is the rate-determining step of protein folding.
Preparation of synthetic oligodeoxynucleotide probes
Authors: Brown Tom , Grzybowski John 
Published: November 2023

Abstract
Detection of oligonucleotide probes can be achieved after the addition of non-radioactive reporter groups, thereby precluding the hazardous, expensive, and time-consuming introduction of radiolabels such as3H,32P,35S, and 1251. In general, high sensitivity detection can be achieved via the attachment of a hapten to the oligonucleotide. A primary antibody which binds to the hapten is added and then a secondary antibody-enzyme conjugate, specific for the primary antibody, is introduced. Typically, visualization is achieved by the addition of a substrate which reacts with the enzyme to produce a colour reaction (Figure IA). A more direct variation on this technique in volves the use of a primary antibody with a suitable enzyme already attached (Figure JB). The attachment of multiple labels or haptens has facilitated the visualization of oligonucleotide probes in quantities previously obtainable only by radiolabelling (1, 2).
Protein blotting using semi-dry electrophoretic transfer equipment
Authors: Jacobson Gunilla 
Published: November 2023

Abstract
Electrophoretic transfer of proteins from polyacrylamide gels to an immobilizing matrix is a widely used technique (1). When a protein is bound to a membrane it is more accessible to specific detection methods than in the gel and the separated bands are not broadened by diffusion. The technique has found wide application in detection, identification, and characterization of proteins and protein-protein interactions (2, 3). These applications are given in the remaining chapters of this text. In semi-dry electrophoretic transfer a stack of wetted filter papers surrounding the gel and the blotting membrane is used as a buffer reservoir, instead of a tank as in conventional electrophoretic transfer (4, 5).
Sample preparation for protein electrophoresis and transfer
Authors: Lee Vaughan H , Dunbar Bonnie S 
Published: November 2023

Abstract
A critical yet often overlooked step in the process of analysing proteins by electrophoresis and transfer is the method used for solubilization. We have found for many protein samples that the method of sample preparation is the most important consideration for optimal results with protein blotting after one-dimensional or two-dimensional polyacrylamide gel electrophoresis (PAGE). The best method for solubilization of a protein sample is dependent on the type of protein sample and the physicochemical nature of the individual proteins to be analysed. There is no one method that will give optimal solubilization and/or resolution of all proteins.
Strategy for purification of organelles from parasites: protein blotting as one of the initial steps
Authors: Sammons David W 
Published: November 2023

Abstract
Purification of organelles is essential for studies of the cell biology of eukaryotic cells and their parasites, and is essential for the complete understanding of the host/parasite membrane organizational and spatial interrelationships. Organelle-specific antigens or structures can be manipulated to assist in the isolation and purification of organelles; however, it is sometimes technically difficult to achieve unless consideration is made of all separation alternatives. Available principles of separation are size, density, charge, immunoaffinity, paramagnetic, and combinations of these in the presence of various buffers and detergents.
Bioluminescence-enhanced detection systems in protein blotting
Authors: Erich Geiger Reinhard 
Published: November 2023

Abstract
Bioluminescence is a natural phenomenon found in many lower forms of life (1-3). Naturally occurring bioluminescent systems differ with regard to the structure and function of enzymes and cofactors as well as in the mechanism of the light-emitting reactions (4, 5). Because of its high sensitivity, firefly (Photinus pyralis) bioluminescence has been used for many years for the sensitive determination of ATP (6). More recently, further highly sensitive bioluminescent and chemiluminescent methods have become available for many different analytes (7-10). Recently, bioluminescent detection of nucleic acid hybridization and protein blotting have been reported (11, 12). A new type of enzyme substrate based on luciferin derivatives, which are highly sensitive for the corresponding enzymes in the test detection systems, are described. These new substrates (13, 14) can be used for unmodified enzymes and for enzyme conjugates, applied in enzymatic activity test systems, in reporter gene tests (15), in enzyme immunoassays (16), in protein blot analysis (17, 18), and ion nucleic acid hybridization tests (12, 19).
Phagemids and other hybrid vectors
Authors: Alting-mees Michelle a. , Vaillancourt Peter , Short Jay M 
Published: November 2023

Abstract
In the past, gene analysis was dependent on subcloning DNA fragments between specialized vector systems. The most common step was subcloning from a plasmid or lambda cloning vector into the filamentous bacteriophage M13 for production of a single-stranded DNA template, which could then be used for sequencing by the Sanger chain termination method (1). Once the sequencing analysis was completed, the DNA fragment was subcloned into another specialized vector, such as a promoter vector designed for efficient in vitro transcription, or an expression vector for protein production.
Extrachromosomal cloning vectors of Saccharomyces cerevisiae
Authors: Sikorski Roberts S 
Published: November 2023

Abstract
The baker’s yeast Saccharomyces cerevisiae has become the experimental organ ism of choice for a diverse group of investigators. Sophisticated genetic techniques can be used to examine such fundamental cellular processes as cell cycle control, protein processing, gene expression, or receptor signalling. The transfer and expression of heterologous genes in yeast has provided evidence that many of these processes share mechanisms conserved throughout evolution.
Photosynthesis research: aspects and perspectives
Authors: Herrmann Reinhold g. 
Published: November 2023

Abstract
Biological photosynthesis, that is, the conversion of solar energy into high-energy chemical metabolites (ATP, NADPH, and carbohydrates), is globally the most fundamental biochemical process. It provides energy, organic matter, and oxygen for nearly all biotic processes, and it is the only renewable energy source of our planet. Life in its present form depends on it. The conversion of solar to chemical energy, which in oxygenic photosynthesis is accompanied by the evolution of molecular oxygen, is catalysed by thylakoid membranes that are found in prokaryotic cells and in the photosynthetic organelles (chloro-, rhodo-, phaeoplasts, etc.) of eukaryotic cells. Because of the capability of that energy conversion, thylakoid membranes occupy a unique position among biomembranes. Additional aspects of photosynthetic energy metabolism appeared with the advent of, and the concomitant division of labour in, multicellular eukaryotes. The tissues of the complex cellular societies of thallophytes, bryophytes, and vascular plants, each assigned a limited range of functions essential to the healthy operation of the community, are involved in fundamental biological processes intimately related to photosynthesis, such as carbohydrate transport, or carbohydrate and lipid storage. Various photosynthetic specialists appeared at this level. Many of these advanced processes operate with distinct plastid variants, e.g. bundle sheath chloroplasts, amyloplasts, or elaioplasts.
Immunization with peptide—carrier complexes: traditional and multiple-antigen peptide systems
Authors: Tam James P 
Published: November 2023

Abstract
Among various strategies for immunization, the strategy of using synthetic peptides is perhaps the most appealing, both in conceptual simplicity and in practical convenience (1-10). It is a minimalist approach that uses a peptide segment with one or a few of the desired epitopes of a protein or whole organism, both of which are many times larger than the peptide. By keeping only the essential epitope(s) and eliminating all other, unwanted, portions of the protein or organism, a synthetic peptide immunogen provides, in theory, the desired selectivity. Advances in solid-phase synthesis have made the preparation of peptides a routine task in most laboratories. In addition, access to synthetic peptides has been made easy by the proliferation of core facilities in universities and of commercial laboratories specialized for the preparation of peptides to order. Thus, the use of synthetic peptides has become a well accepted method for the preparation of site-specific antibodies for various biochemical and functional studies.
Non-isotopic detection of nucleic
acids on membranes
Authors: Hughes J R , Evans M F , Levy E R 
Published: November 2023

Abstract
Membrane-based methods of DNA and RNA analysis have traditionally relied on the use of radiolabelled probes. Whilst they offer a robust and sensitive system there are associated problems involving the instability of the isotope, the requirement for designated laboratory areas and equipment for the handling of the isotope, and the specialist removal of waste. These problems have led to the development of a number of non-isotopic techniques for the analysis of nucleic acids that are sensitive enough to detect unique copy sequences within genomic digests. Non-isotopic alternatives are classified into two categories (indirect and direct) depending on the method of labelling the probe. The majority of systems available for filter assays involve indirect detection of a labelled probe in several stages (Figure 1):a. Label the sequence b. Hybridize the sequence to membrane-bound nucleic acid. c. Detect nucleic acid: probe hybrids via the specific binding of a nonradioactive reporter system.
Agar from Namibian Gracilaria spp
Authors: Gidley Michael J , Hedges Nicholas D , Hoffmann Rainer A , Dawes Christopher P 
Published: November 2023

Abstract
Agar has a long history of use as a food ingredient in East Asia (1), but has traditionally found application only in niche markets in Western foods. However, with increasing emphasis on food ingredients with both high functionality and a history of traditional use, it is envisaged that the global utilisation of agar as a food ingredient will increase in the future (2,3). This will require a greater understanding of the nature of agar polymers extracted from various potential algal sources, and improved knowledge of the relationship between molecular structure and functional properties.
Shapes and sizes of food polysaccharides by sedimentation analysis-recent developments
Authors: Harding Stephen E 
Published: November 2023

Abstract
Knowledge of the fundamental behaviour of food polysaccharides on a “microscopic” scale (in terms of their sizes. shapes, molecular weight distribution and interaction parameters) in dilute and concentrated solution form - both by themselves and in mixtures - is important for the proper understanding of their behaviour in food products on a “macroscopic” scale (such as gelling, thickening ability and phase separation). This information can help us choose the “right” polysaccharide with the “right” properties for a particular product.
Performance characteristics of some synthetic emulsifiers
Authors: El-Shattory Y , Aly Saadia M , Megahed M G 
Published: November 2023

Abstract
Many of our foods are emulsions. The commonly recognized ones are milk, butter, mayonnaise, salad dressings, gravies, and ice cream. Some of the other easily recognized emulsions and foods in which emulsions are an important step in production are beverages, cakes, candy, frostings, marshmallow, condiment preparations, shortening, margarine, pickles, flavoring oils, yeasts and eggs (1).
Shear hardening of gellan gum gels
Authors: Tsiami A , Morris V J , Brownsey G J 
Published: November 2023

Abstract
Gellan gum is a bacterial polysaccharide that is marketed as a broad spectrum gelling agent. It has received food approval in Japan, limited FDA approval for food use in the USA and approval is being sought for food application in the UK and EC. Preliminary rheological studies of aqueous gellan gels at low ionic strength showed consistent elastic properties, these becoming increasingly variable with increase in ionic strength. Stress relaxation experiments were chosen to examine the mechanical behaviour of the gels and provide a possible explanation of these effects. At low ionic strength, the gels approximate to elastic gels whereas at high ionic strength the increased stress relaxation behaviour resembles that shown by colloidal-like systems. However, unlike colloidal systems, when the gels were subjected to successive applications of stress, the magnitude of the stress relaxation decreased and the relaxation modulus increased, indicative of a shear hardening phenomenon. Interpretation in terms of a heterogeneous nature of the gels has implications for such textural properties as flavour release.
Recent advances in the rheological characterisation of gelatin gels
Authors: Ross-Murphy S 
Published: November 2023

Abstract
In the last few years significant progress has been made in the study of gelatin gels and gelation. Indeed the previously accepted view, wherein initial renaturation of the collagen-like triple helix was followed by substantial aggregation to a “fringed micelle” structure, has been shown not to be consistent with the measured cross-sectional radius of gyration, nor with the increase in optical rotation and modulus on a log time axis. These results are reviewed; they suggest that gelatin gels involve a rubber-like network. Rheological data are consistent with this view. Results presented below for the concentration dependence of gel modulus agree well with an ideal branched chain model, with no independent parameters. In separately deducing these parameters we have exploited data from a number of other (non-rheological) experiments carried out by other workers.
Tailor-made pectins for specific influencing of the sensory rheological properties of preserves, jams, jellies, marmalades and other jellified products
Authors: Kratz Evamarie 
Published: November 2023

Abstract
The increasing quality demand on jams, jellies and marmalades is not limited on gel strength but also includes consistency, texture and syneresis behaviour. The optimum consistency for the consumer may vary from country to country and product to product. In some countries the consumer may prefer very firm, brittle gels for some products, in other countries an especially soft and spreadable gel texture (Swiss Consistency) is requested. In general an extra jam is required to show a firmer consistency than a fruit dessert or a fruit spread.
Biotechnology for the improvement of malting barley
Authors: Mannonen Leena , Kurten Ulrika , Ritala Anneli , Salmenkallio-Marttila Marjatta , Hannus Rütta , Aspegren Kristian , Teeri Teemu , Kauppinen Veli 
Published: November 2023

Abstract
A method for the transformation of barley has been developed. The first application of this method for the genetic improvement of malting barley quality is the transfer of a gene coding for thermostable B-glucanase that enhances modification of the malt and helps towards a trouble-free brewing process. In the first phase research has been focused on barley cell culture technology and on development of the gene transfer methods.
Resorufin-labelled casein as a substrate for protease activity in beer
Authors: Mochaba F , Torline P A , Axcell B 
Published: November 2023

Abstract
A simple and sensitive assay for yeast proteolytic activity has been developed using resorufin-labelled casein as a substrate. Pitching yeast propagated in a brewery produced high levels of extra-cellular protease activity in the wort at all stages throughout fermentation. On the other hand, yeast propagated under “ideal” laboratory conditions showed only minimal extra-cellular protease activity during laboratory 2 1 fermentation. Although yeast excretes a certain amount of proteolytic activity even during active periods of growth, higher levels are secreted when cell growth declines or on death. The assay can be used as a measure of yeast suitability for pitching.
The application of membranes for new approaches to brewery operations
Authors: Bühler T M , Burrell K , Eggars H U , Reed R J R 
Published: November 2023

Abstract
Crossflow filtration of beer through low cost ceramic membranes is economically attractive. Frequent and rapid cleaning maintains satisfactory flux. A pore size of 0.5 µm gives a bright, near-sterile product without any loss of beer components. A pore size of 1.3 µmis suited to bottoms filtration. Crossflow filtration of wort from mash using membranes is achieved using two stages: coarse separation followed by polishing, enabling reduced plant size and cost. Hydrophobic PTFE membranes can be used to remove excess dissolved co from beer. co fluxes as high as 6.2 kg/m 1.h have been achieved.
Assembly, post-translational processing, and subcellular localization of ion channels
Authors: Millar Neil S , Moss Stephen J , Green William N 
Published: November 2023

Abstract
Most ion channels are complex, multi-subunit transmembrane proteins (1-3). Aconsequence of this structural complexity is that the correct functional expression of ion channels requires a diverse series of post-translational events including covalent modifications and subunit oligomerization. After protein synthesis and translocation into the endoplasmic reticulum (ER) membrane, newly-synthesized transmembrane polypeptides may undergo a variety of post-translational modifications (such as proteolytic cleavage, phosphorylation, glycosylation, fatty acylation, and disulphide bond formation). Individual polypeptides must also fold correctly into their native conformation and, in many cases, multiple polypeptide subunits must be accurately assembled into multi-subunit ion-channel complexes. Finally, the modified and assembled ion channels must be delivered to their appropriate subcellular location. Clearly, these subunit folding and oligomerization events must be carried out with great accuracy if ion channels are to perform their appropriate physiological function. How the processing, assembly, and subcellular localization of ion channels is achieved with sufficient accuracy is clearly of great interest and significance and has been the subject of a great deal of recent research.
Astrocytes
Authors: Marriott Derek R , Hirst Warren D , Ljungberg M Cecilia 
Published: November 2023

Abstract
The close anatomical association between astrocytes and neurons has long been suggestive of some functional interplay between these cells. However, the structural complexity of the CNS has often precluded definitive studies of astrocytes in vivo. As a consequence the elucidation of their functional properties has relied, almost entirely, on tissue culture techniques. Cultured astro cytes are easily accessible to experimental manipulation and can now be routinely prepared with greater than 95% homogeneity.
Microglia: the tissue macrophage of the CNS
Authors: Woodroofe M Nicola , Cuzner M Louise 
Published: November 2023

Abstract
Microglia are distinct from neurons and macroglia and are of probable mesodermal origin. Monocytes/macrophages infiltrate the central nervous system (CNS) during development and in the adult animal take on the ramified morphology of resting microglia, no longer expressing the full complement of macrophage markers (1). Microglia are present in all brain areas but are not uniformly distributed, being enriched in grey matter (2). In the mouse brain the proportion varies from 5% in the cortex to 12% in the substantia nigra. The morphology of microglia in vivo varies according to their location and microenvironmental factors and ranges from compact amoeboid cells to ramified, branched cells, with considerable variation in the length and complexity of branching of the processes. Their plasticity is emphasized by their rapid morphological changes in response to mechanical or pathological insults.
Virological and molecular genetic techniques for studies of established HIV isolates
Authors: Peden Keith W C , Martin Malcolm A 
Published: November 2023

Abstract
In this chapter we describe the methods commonly used for the preparation of HIV stocks from cell culture systems, their propagation in tissue culture, assays to measure virus production, and the quantification of virus infectivity. In addition, we shall discuss approaches used for the isolation and construction of infectious molecular clones of HIV, and the manipulation of these clones to introduce mutations. We do not intend that this will be an exhaustive survey of the methods used, and the ones included obviously reflect the bias and experience of the authors.
Vectors based on HIV
Authors: Richardson J H , Lever A M L 
Published: November 2023

Abstract
Retroviral vectors based on murine and avian retroviruses are widely used as an efficient method of gene transfer into mitotic cells (1). They have the advantages of: stable, single copy gene insertion into a host cell chromosome minimal toxicity and cytopathicity targeted gene transfer into cells bearing the appropriate viral receptor suitability for use in vivo Recently, retroviral vector technology has been taken into clinical use with Moloney murine leukaemia virus (M-MuLV) vectors being used as the mode of gene delivery in the first trials of human gene therapy. Vectors derived from HIV-1 have been developed not only as a vehicle for foreign gene transfer but also as a tool to study genomic RNA encapsidation (2), virus replication (3), and cell entry (4, 5). Specific advantages of a vector system based on HIV include:
Quantitative assays for virus neutralization
Authors: Mckeating Jane 
Published: November 2023

Abstract
Introduction
Neutralizing antibodies provide one of the main host defences against viral infection. They are associated with protective immunity resulting from successful vaccination against numerous viruses, including vaccinia, poliomyelitis, measles, rubella, adeno, and rabies. However, the mechanisms by which antibodies neutralize viral infection are generally not well understood. The block to infection may occur at the level of viral-receptor interaction or at one of many events leading to viral fusion and entry (1).