bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmid shuffling and mutant isolation
Authors: Sikorski Roberts. , Keeney, Jill B , Boeke Jef D 
Published: November 2023

Abstract
Genetic analysis of mutants in Saccharomyces cerev1szae offers a unique approach to the study of biological processes. To initiate genetic studies in this organism one can mutagenize a population and screen or select for those mutants which affect the process of interest. Alternatively, one can use techniques selectively to mutagenize a single gene already known to play an important role in this process. The generation of mutant yeast strains starting from a cloned non-essential yeast gene is relatively straightforward. To remove the wild-type gene product, an essential step in analysing recessive alleles, DNA at the wild-type non-essential locus can be deleted entirely from the genome. A collection of mutant alleles can be made in vitro and introduced into the deleted host cell via episomal cloning vectors. The generation of mutant yeast strains from an essential yeast gene is a more complicated task since removal of the wild-type gene in one simple step yields an inviable genotype.
Measurement of transcription
Authors: Piper Peter W 
Published: November 2023

Abstract
This chapter discusses the experimental tricks needed to determine if a cloned yeast gene is transcriptionally active under defined physiological conditions, or if DNA constructs newly inserted into yeast cells by transformation are being efficiently transcribed in vivo. The techniques it describes rely upon the availability of a DNA probe suitable for quantification of the transcript(s) of interest by DNA-RNA hybridization. It should be read in conjunction with standard methods manuals that describe the experimental details of Northern blotting, probe preparation, blot hybridization and the mapping of transcripts on DNA (1).
DNA binding of immobilized proteins
Authors: Flytzanis Constantin N 
Published: November 2023

Abstract
The identification of proteins which have affinity for specific DNA sequences has greatly contributed to our understanding of the transcriptional control of gene expression. A plethora of transcription factors have been purified and characterized by techniques that take advantage of the specificity of recognition that such nuclear proteins exhibit towards relatively small sequences of DNA. In theory at least, having a DNA element guarantees the isolation of the protein which binds to it in vitro, and vice versa.
Cyanobacterial transformation and gene regulation
Authors: Nixon Peter , Jansson Christer 
Published: November 2023

Abstract
The cyanobacteria are a diverse group of prokaryotes that are able to carry out oxygenic photosynthesis using chlorophyll a and phycobilip troteins as their primary photosynthetic pigments. Morphologically, cyanobacteria range from simple unicellular forms to complex filamentous forms that possess several highly differentiated cell types (1). Although cyanobacteria can grow in a variety of modes, including chemoheterotrophy, their ability to perform oxygenic photosynthesis in a similar manner to higher plants, coupled with their relative ease of genetic manipulation, has led to their adoption as model systems for the study of photosynthetic processes. Indeed, unicellular cyanobacteria-like organisms are thought to be the progenitors of higher plant chloroplasts (discussed in Ref. 2). In particular, the photosynthetic electron transport chain is being intensively studied (3-5). However, other important biological problems are being studied using cyanobacteria, including nitrogen fixation, carbon fixation, light-regulated gene expression, chromatic adaptation, and cellular differentiation. In this review we describe techniques used in the genetic manipulation of cyanobacteria and the current status in our understanding of cyanobacterial gene regulation in response to changes in the environment.
Epitope mapping using libraries of random peptides displayed on phage
Authors: Dower William J , Cwirla Steven E 
Published: November 2023

Abstract
In 1985 Young et al. (1) introduced a method for cloning immunoreactive sequences, such as bacterial surface antigens, by expressing the proteins in X. plaques and identifying the clones of interest by probing with the appropriate antibodies. This method relied on the co-localization of the reactive peptide with the cloned DNA in a plaque or colony. This is a powerful technique, but it is difficult to screen more than a few million clones by this approach. Alternative methods, relying on the physical linkage of the protein and DNA, have recently become practical. These methods are known as peptide display techniques, and comprise the cloning of sequences that are expressed as peptides or proteins fused to a carrier protein and displayed on the outer surface of microorganisms. The surface peptide is immunoreactive, and the encoding DNA is carried within the microorganism. The clones of interest are isolated by affinity purification of the exposed peptides on a matrix of immobilized antibody or other binding protein. This approach, because it provides for the efficient isolation of individual microorganisms from a complex mixture, allows the screening of extraordinarily large numbers of clones.
Effect of acetyl substituents on the conformational stability and functional interactions of acetan polysaccharide
Authors: Ojinnaka C , Morris E R , Morris V J , Brownsey G J 
Published: November 2023

Abstract
Acetan is similar in structure to xanthan, and adopts a similar 51 conformation in the solid state, but has longer (pentasaccharide) sidechains, no pyruvate substituents, and an additional site of acetylation (believed to be at C(6) of the branched glucose residues). Acetan solutions show clear evidence (by optical rotation and DSC) of conformational ordering on cooling. The transition is fully reversible on heating, with no thermal hysteresis. The intrinsic viscosity of the ordered form decreases with increasing concentration of salt up to ∼10 mM KCl, yielding an estimated persistence length of ∼60 nm (in comparison with ∼50 nm for ordered xanthan). At higher salt, however, the intrinsic viscosity increases sharply, indicating extensive aggregation, which is reflected in development of xanthan-like ‘weak gel’ rheology in more concentrated solutions. Deacetylation stabilises the helix, but suppresses aggregation.
Some physico-chemical aspects of protein processing in foods
Authors: Tolstoguzov V B 
Published: November 2023

Abstract
To describe the structure formation mechanisms in foods the concept of protein conformational potential is proposed. The production of many structured foods may be regarded as the formation of intermolecular interactions throughout a processed food system using the intrarnolecular bonding potential of its proteins and polysaccharides. The term “conformational potential” describes the capacity of a protein to form the intermolecular junction zones that are required to generate the desired structural, rheological and other physico-chernical properties of a given food system. Two basic physico-chernical characteristics are mainly responsible for the protein conformational potential. These are the co-solubility of a protein with other food ingredients and the denaturation-renaturation behaviour of proteins. This new concept encourages better understanding of food protein functionality at the molecular level. To illustrate this new approach, the structure formation processes of some food systems are considered.
A comparison of the in vitro and in vivo digestibilities of retrograded starch
Authors: Botham R L , Ring S G , Noel T R , Morris V J , Englyst H N , Cummings’ J H 
Published: November 2023

Abstract
The resistance to digestion of different forms of processed starch by mammalian pancreatic a-amylase was examined in ileostomists. Chick peas and chick pea starch were processed by cooking in water at 100°c and allowed to retrograde at 4°C prior to consumption by ileostomist volunteers, the diet of the volunteers being free of other plant polysaccharides. The digestibility of the starch was assessed from analysis of the ileostomy effluent. The polysaccharide in the effluent was subjected to sugar and methylation analysis to determine the monosaccharide composition and the mode of linkage. The main resistant product from feeding the retrograded starch gel was a linear dextrin with a number average degree of polymerisation of 14. The cellular matrix modified the digestibility of the starch with both linear and branched molecules escaping digestion. From the ratio of the cell wall polysaccharides to dextrins in the effluent, it was found on average 15% of the ingested starch had escaped digestion.
Rheological investigation of polysaccharide interactions in mixed systems
Authors: doublier J L 
Published: November 2023

Abstract
The viscoelastic behaviour of polysaccharide mixtures can be investigated using oscillatory shear measurements or transient experiments and compared to that of their individual components. As examples, mixtures of a galactomannan (guar gum, locust bean gum) with another polysaccharide (xanthan gum or K-carrageenan) are described. Depending upon the polysaccharides and the composition ratio, viscoelastic behaviour changes noticeably. At the optimum of the synergistic effect, that is at a polysaccharide/galactomannan ratio of the order of 50/50, strong gels are obtained. However, their viscoelastic behaviour suggests that the molecular mechanisms underlying the properties cannot be limited to a single type of interaction. On the other hand, peculiar viscoelastic behaviour is experienced with ratios as low as 1/99, irrespective of the type of galactomannan (guar gum or locust bean gum). Despite the high content in galactomannan, the properties cannot be compared to those of macromolecular solutions such as displayed by the galactomannan alone. Typically, the behaviour is solid-like as can be seen in oscillatory shear at low frequency as well as at relatively long times in creep measurements. This means that a weak gel has been formed. The effects of temperature on the properties of xanthan/galactomannan mixtures show that those gels melt at a temperature of ∼60°C, well below the conformational transition of xanthan molecules. This clearly suggests that melting of xanthan is not required to induce melting of the mixture as usually believed. All these results are discussed on the basis of current models that have been proposed for the understanding of the mechanisms involved in synergistic interactions between polysaccharides.
The chemistry of iso-alpha-acids: an explanation of their mode of action
Authors: Simpson W J , Fernandez J L , Hughes P S , Parker D K , Price A C 
Published: November 2023

Abstract
The ability of iso-a-acids to bind metal cations is important with respect to antibacterial activity and foam. Divalent cations bind to trans-isohumulone, bringing about a change in its solubility and light absorption properties. Monovalent cations do not bind to isohumulone unless a divalent cation is present. The flavour threshold of trans-isohumulone is not markedly affected by pH indicating that both anion and undissociated molecule are flavour active.
Flocculation of brewer’s lager yeast
Authors: Aar Paul C van der , Straver Marika H , Teunissen Aloys W R H 
Published: November 2023

Abstract
Flocculation behaviour and its mechanism of brewer’s yeast (NewFlo) are studied by integrated research on biochemical, molecular genetically and physiological aspects of floe-formation during beer fermentation. Results show that besides the exposure of a protein (lectin) and its receptor (mannan), hydrophobicity of the cells plays a major role in flocculence regulation. There is a strong correlation between stop of cell division and initiation of flocculence, independent of the factor causing this division arrest.
Die Wahrnehmung des unsichtbaren Riechen und Schmecken: Moleküle als Sinnesreize
Authors: Boeckh Jürgen 
Published: November 2023

Abstract
Behavioral effects and different roles of chemical, especially olfactory sensory stimuli for nutrition, reproduction and social life in humans and their relatives. The importance of learning and valuation of odors; hedonic character, emotional and motivational effects. (2) The process of olfaction as the sensory detection and discrimination of complex chemical patterns, i.e. mixtures of certain components in certain ratios. The sensors for such stimuli in the nose, how they analyze such patterns and convey the result to the brain. (3) Olfactory centers in the brain and their modes of function.
Détection rapide des Enterobacteriaceae
Authors: Laurent F , Leitz R , Husson M O , Drocourt J L , Peladan F , Leclerc H 
Published: November 2023

Abstract
Now, in order to manage his process and the overall quality of his products, the brewer has to detect more quickly microbiological contaminants. We developed a monoclonal antibody against one special epitop of the Cunin antigene, which is common to all Enterobacteriaceae, and now, we are able to detect and count, in 3 hours, all the Enterobacteriaceae, present in a beer or a water sample. This work shows that immunology is probably one of the best ways to set up new, rapid, sensitive and specific methods to detect microbial contaminants encountered in breweries.
Assaying ion channels: design and practice
Authors: Kasai Michiki , Ide Toru , Agnew William S 
Published: November 2023

Abstract
Isolation of the molecule in chemically pure form is an important approach in the characterization of ion channels. This enables determination of molecular composition and size, and may permit functional reconstitution in artificial membranes for biochemical or electrophysiological measurements. Purification requires that the protein be solubilized before separation from other proteins associated with the membrane sample. However, unlike other enzymes, channel molecules typically lack chemical catalytic activity, and quantification in detergent solution must either be performed with a specific biochemical marker, such as a ligand, toxin, or drug that binds stoichio-metrically, or the protein must be returned to a membrane environment for measurement of ion-transporting function. Ligand binding assays constitute the single most important tool for channel and receptor quantification and purification, and the following discussion and examples are aimed at providing insights useful for designing new assay protocols. Some channels will be resistant to this approach, lacking any useful ligand, and we also describe how the progress of an ion channel purification protocol can be followed by bilayer reconstitution.
Channel cloning, mutagenesis, and expression
Authors: Whiting Paul J , Wafford Keith A , Pribilla Iris , Petri Thomas 
Published: November 2023

Abstract
The application of the techniques of molecular biology to the understanding of the structure and function of ion channels has resulted in a quantum leap in our knowledge which 15 years ago would have seemed inconceivable. The cloning of a cDNA encoding a channel protein is now considered only the first step, opening up many areas for detailed study: Computer analysis of the deduced amino acid sequence to predict putative transmembrane topology, secondary structure, and post-translational modification.
Nigral and striatal neurons
Authors: Barker Roger , Johnson Alan 
Published: November 2023

Abstract
This chapter describes simple and reliable methods for the culture of dissociated nigral and striatal neurons. We give an accurate definition of the conditions required for the survival of these cells. These data may have implications for studies on neural development as well as those concerned with neurodegeneration. In this last respect two of the commonly encountered yet major neurodegenerative diseases of the CNS are Parkinson’s disease (PD) and Huntington’s Chorea (HC), which predominantly affect the dopaminergic nigral and GAB Aergic striatal neurons respectively (1,2). This coupled to the use of these cells for intracerebral transplantation (3), has led to a large number of in vitro studies involving these neuronal populations (see Table 1 and 2). There is, however, no universally adopted technique although the methods described in this chapter are used in several laboratories and routinely produce reliable results.
Cranial sensory neurons
Authors: Davies Alun M 
Published: November 2023

Abstract
Cranial sensory neurons have many advantages for studying the different phases of neuronal development. These neurons and their progenitor cell populations are well defined and can be easily obtained for in vitro experimental studies and are accessible to experimental manipulation in ova in avian embryos from the earliest stages of their development (1,2). The peripheral target fields of several cranial sensory ganglia, such as the trigeminal ganglion, are clearly circumscribed, and this has facilitated detailed studies of the influence of the target field on various aspects of neuronal development (3-6). In contrast to the functional heterogeneity of dorsal root ganglia, cranial sensory neurons are for the most part segregated into functionally distinct populations. Perhaps as a consequence of this functional segregation, populations of cranial sensory neurons have quite distinct neurotrophic factor requirements. This has facilitated studies of the function and co-operation of different neurotrophic factors in regulating neuronal survival (7–9).
HIV infection of dendritic cells
Authors: Knight Stella C , Patterson Steven 
Published: November 2023

Abstract
Introduction
Dendritic cells (DC) are crucial for stimulation of T cells. They are derived from the bone marrow and share a common stem cell with macrophages. Granulocyte-macrophage colony stimulation factor (GM-CSF) and tumour necrosis factor alpha (TNFα) (1) promote the differentiation of CD34-positive stem cells into mature DC. Small numbers of stem cells are also present in the blood (1-2 per 105 mononuclear cells) as well as more mature DC which may constitute 0.5-2% of the cells.
Sequence analysis of virus variability based on the poymerase chain reaction (PCR)
Authors: Brown Andrew J Leigh , Simmonds Peter 
Published: November 2023

Abstract
During most stages of HIV infection, the viral population contains a large number of closely related variants that have diverged within the indvidual over the course of HIV infection. For example, env sequences of human immunodeficiency virus in lymphocytes of infected individuals may show variability of up to 10% within the same sample (1,2). Under these circumstances, sequence analysis of PCR products amplified from such samples is often unreliable due to ambiguities in the sequencing gel. While there are methods for measuring the relative frequencies of alternative nucleotides at these polymorphic sites (see section 3), this does not distinguish the linkage relationships of the variant nucleotides so it is impossible reliably to reconstruct the constituent sequences.
CD4-positive T cell responses to HIV-1 infection
Authors: Siliciano R F 
Published: November 2023

Abstract
By producing cytokines that modulate the activity of B lymphocytes, macrophages, CD8-positive T cells, and other types of cells, CD4-positive helper T cells play a central role in most immune responses, including the immune response to HIV-1. Analysis of CD4-positive T cell responses in HIV-1-infected individuals is complicated by the fact that CD4-positive cells are selectively infected by HIV-1. Following seroconversion, infected individuals experience a progressive decline in circulating levels of CD4-positive T cells (discussed in Chapter 13). In addition, a state of hyporesponsiveness of the surviving CD4-positive T cells is observed, particularly in later stages of the disease (1). Thus, in analysing the CD4-positive T cell response to HIV-1 and to opportunistic pathogens in infected individuals, the superimposed effects of HIV-l-induced immunosuppression must be considered as well. By the same token, the study of CD4-positive T cell responses in infected individuals can provide important information about the degree of immunologic impairment induced by infection. This chapter will consider some of the theoretical problems with and experimental approaches to assessing CD4-positive T cell responses in HIV-l-infected individuals. We will consider methods for measuring the overall functional integrity of the CD4-positive T cell compartment as well as methods for analysing specific CD4-positive T cell responses to HIV-1.
Ribonuclease H
Authors: Hostomska Z , Hostomsky Z 
Published: November 2023

Abstract
The ribonuclease H (RNase H) is an essential activity associated with HIV reverse transcriptase (RT). RNase H cleaves the RNA in hybrid RNA-DNA intermediates during minus-strand DNA synthesis initiated from the tRNALys, 3 primer. In the course of this ordered degradation of the genomic RNA template, the enzyme also generates a specific RNA fragment in the polypurine tract (ppt) region, which is then used as a primer for initiation of the plus-strand DNA synthesis. RNase H is also involved in the specific removal of both tRNA and ppt primers so that synthesis of the double-stranded DNA of the provirus can be completed. These well-defined functions of RNase H during reverse transcription can not be substituted by cellular enzymes. Since inhibition of any of these functions would block virus replication, RT-associated RNase H represents a valid target for antiretroviral therapy (1).
Expression of HIV proteins using recombinant baculoviruses
Authors: Jones Ian 
Published: November 2023

Abstract
Why express viral proteins in foreign systems? After all, the expression of a viral product in isolation may overlook an essential factor in the host cell environment. A variety of reasons are commonly proffered: The level of expression of any given gene product may be improved to allow antibody generation or commercial development. This is particularly true of non-structural proteins involved in control rather than virion assembly. The expressed viral product can be manipulated by mutagenesis to determine the interplay of structure and function. The function of individual viral proteins can be distinguished from those of the virion background. Experimental work with the ‘real’ virus is difficult or dangerous. These factors provide the driving force behind the sometimes difficult search for suitable expression systems for HIV genes. However, it is important from the outset to realize the limitations of what can be achieved with expression systems alone. The study of one particular gene product can only partially represent its complete role in the viral life cycle since it is the interaction of viral proteins together that results in virus replication and associated pathogenesis. Reservations aside, however, expression of a single viral product can provide much basic information on the way in which a protein functions.
Envelope expression and purification
Authors: Opstal O Van , Fabry L , Francotte M , Thiriart C , Bruck C 
Published: November 2023

Abstract
The envelope glycoproteins of human immunodeficiency viruses (HIV types 1 and 2) play a central role in the transmission of acquired immunodeficiency syndrome (AIDS) (1). The viral envelope mediates attachment of the virus to the CD4 receptor present on target cells (2-4) and the spread of virus by cellto-cell fusion (5, 6). In the infected cells, the viral envelope of HIV-1 is synthesized as a precursor glycoprotein (gp160) which is subsequently cleaved into an external surface protein gp120 and a transmembrane protein gp41, upon maturation in the Golgi (7-9). After cleavage, the two glycoproteins (held together by non-covalent interactions) are transported to the cell surface.