bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly of Multi-Subunit Structures
Authors: Price Nicholas C 
Published: November 2023

Abstract
Many proteins associate specifically to generate a range of novel structures and functions. These include enzymes and proteins involved in key cellular control mechanisms. The process of subunit association in these relatively simple systems also represents a model for understanding the assembly of more complex biological structures such as large multi-enzyme complexes, ribosomes, and viruses. X-ray crystallography has provided a great deal of detailed information concerning the nature of the interactions between the subunits in the native state of multi-subunit proteins, but can give only limited insight into the mechanisms of association. Several fundamental questions are posed by such assembly processes.
Use of speciality phosphoramidites in PCR
Authors: Mclean Michael J 
Published: November 2023

Abstract
In the decade or so since the introduction of automated oligonucleotide synthesizers, the ability to use these machines for the incorporation of unnatural residues into nucleic acids has led to the chemical synthesis of a wide variety of phosphoramidite derivatives. When included in an oligomer synthesis, these entities provide a source of site-specific, stable modifications of the backbone, thus enabling a rigorous determination of their biochemical effects.
Chemical methods for 5’ non- isotopic labelling of PCR probes and primers
Authors: Andrus Alex 
Published: November 2023

Abstract
Synthetic oligonucleotides are now accessible to most laboratories conducting molecular biology experiments. The decreases in preparation time, costs, and the expertise required have enabled the annual production and use of several million oligonucleotides (1). PCR undoubtedly consumes more of these sequences than any other application. Many PCR experiments require the covalent attachment (labelling, tagging, conjugation) of small molecules to perform ancillary functions, in addition to base-specific annealing to complementary nucleic acid and 3’ chain extension by polymerase. The labels (reporter groups) conduct or facilitate detection, quantification, isolation, sizing, and location of the amplified sequence. Covalent attachment of molecules, such as fluorescent dyes, biotin, and proteins, can be made at virtually any site on the oligonucleotide, including the 5’- and 3’-termini, through the sugars and bases, and by internucleotide phosphate modification (2). The sequence- and base-specific hybridization properties must be preserved, as well as the chain extension capacity for PCR primers. The methods described in this chapter will focus only on examples of specific, chemical 5’-labelling of oligonucleotides, for use as PCR primers and probes of PCR products (3). Post-synthesis protocols such as cleavage/deprotection, analysis, purification, and 5’-labelling operations are described. Enzymatic labelling methods conducted before, during, or after PCR have been reviewed elsewhere (4).
Solid phase PCR
Authors: Stamm Stefan , Brosius Jurgen 
Published: November 2023

Abstract
The method of solid-anchored PCR uses specific oligonucleotides coupled to a solid phase as primers for cDNA synthesis (1) and results in cDNA that is covalently linked to the solid phase. Typical solid phase matrices are agarose (1), acrylamide (1), magnetic (2-4), or latex beads (5). A solid phase with cDNA attached, generated using oligo(dT) as a primer, contains sequence information similar to a cDNA library, that is, it represents a ‘solid phase library’ (1, 3, 4). The cDNA that is attached to the solid phase can be used directly as a template for PCR reactions or can be modified enzymatically prior to the PCR reaction. Oligonucleotides that are attached to a solid phase can also serve for affinity purification of RNA (2). RNA isolated in this way can be directly reverse transcribed, using the primer that is coupled to the solid phase. Subsequent PCR reactions can employ this primer with or without additional internal primers. Since the cDNA is coupled to a solid phase, changing buffer conditions or primer composition is conveniently achieved by washing the solid phase and resuspending it in a different PCR reaction mixture. The general principle of solid anchored PCR is shown in Figure 1.
Solid phase sequencing of PCR products
Authors: Wahlberg Johan , Hultman Thomas , Uhlén Mathias 
Published: November 2023

Abstract
Solid phase methods have proven to be extremely useful for the separation and synthesis of biomolecules. The advantages of solid phase approaches are a combination of good yields and reproducible results. Furthermore, the facilitated separation of the solid phase from the reaction solution allows routine methods suitable for automation to be designed. This chapter describes protocols for the use of magnetic beads in combination with the biotinstreptavidin system for solid phase DNA sequencing of PCR products. The use of a solid support for the preparation of sequencing templates enables efficient production of single-stranded DNA with simultaneous removal of PCR buffers, dNTPs, and PCR primers. The immobilization of the PCR product also makes it possible to avoid competition of the sequencing primer with the complementary strand of the template obtained when using the double-stranded DNA fragments directly.
cDNA cloning by RT-PCR
Authors: Edwards Jean Baptiste Dumas Milne , Ravassard Philippe , Icard-Liepkalns Christine , Mallet Jacques 
Published: November 2023

Abstract
The methods available for the characterization of mRNAs have progressed enormously since the mid 1970s. This includes the isolation of RNAs, cloning and bacterial amplification of specific mRNAs, Northern blotting studies, in situ hybridization, and nuclease protection assays that allow the description of mRNA metabolism in cells.
Measurement of mRNA stability
Authors: Brown Alistair J P 
Published: November 2023

Abstract
The level of an mRNA in the cell is determined both by its rate of synthesis and by its rate of decay. Since mRNA half-lives range from about 1 min to over 1 h in the yeast, Saccharomyces cerevisiae (1–4), differential rates of mRNA decay have a fundamental influence upon the overall pattern of protein synthesis in this model eukaryote. However, the structural features which determine the stability of an mRNA in yeast and the mechanisms by which they mediate their effects remain largely obscure. Multiple parameters influence the stability of an mRNA. They include the 3′ poly(A) tail, the 5′-cap, mRNA translation, and various structural determinants that lie within an mRNA (5–10). Also, many of these parameters are inter-related. For example, the inactivation of the poly(A)-binding protein leads to a decrease in mRNA translation (11), and some mRNA destabilizing elements are known to depend upon translation for their function (6). An increasing number of groups are demonstrating how significant contributions can be made to the field by combining molecular, genetic, and biochemical approaches with careful RNA analysis (1–11).
Virus-like particles: Ty retrotransposons
Authors: Kingsman Alan J , Adams Sally E , Burns Nigel R , Martin-Rendon Encarna , Marfany Gemma , Hurd Douglas W , Kingsman Andsusan M 
Published: November 2023

Abstract
The Saccharomyces cerevisiae genome contains a number of movable genetic elements known as retrotransposons. In moving from one genomic location to another they use an RNA intermediate and a reverse transcriptase reaction that is reminiscent of stages in the mammalian and avian retrovirus life cycles (1, 2). Like retroviruses, the yeast retrotransposons package their RNA intermediate into particles. These are known as virus-like particles (VLPs). The particles of one of the yeast elements, Tyl, is the subject of this chapter. They have been used to produce fusion proteins, authentic proteins, and novel vaccines. In addition, they are used to study fundamental aspects of retrotransposon biology.
The Kl killer toxin: molecular and genetic applications to secretion and cell surface assembly
Authors: Brown Jeffrey L , Roemer Terry , Lussier Marc , Sdicu, Anne-Marie , Bussey Howard 
Published: November 2023

Abstract
The killer phenomenon is widespread among yeasts, having been demonstrated in at least eight genera (1). The best characterized is the Kl killer system of Saccharomyces cerevisiae (2-5). Kl killer strains are immune to the toxin they produce, and secrete a small pore-forming toxin that kills sensitive strains. Kl killer strains maintain a double-stranded RNA (dsRNA) viral genome of two distinct species: M1, a medium-sized dsRNA (1.8 kb) encoding the killer toxin and immunity precursors, and L-A, a larger dsRNA (4.6 kb) required for the replication and maintenance of M1. These two dsRNAs are packaged separately with a common capsid protein (encoded by L-A) to form virus-like particles that are transmitted cytoplasmically during vegetative growth and conjugation (6).
Introduction and basic set-up for protein transfer
Authors: Dunbar Bonnie S 
Published: November 2023

Abstract
Since the first studies on the electrophoretic transfer of proteins from acrylamide or other gels to paper or membrane ‘matrices’, there have been numerous modifications to the types of equipment used for these purposes. Detailed studies have also been carried out which include the development of methods for sample preparation and the electrophoretic separation of complex protein samples and for the transfer techniques and renaturation of molecules. The modifications of methods for specific techniques illustrate the need for an in-depth understanding of the basic principles of protein transfer techniques.
Detection and characterization of glycoprotein carbohydrate chains after electrophoretic separation
Authors: Irimura Tatsuro , Kawashima Hiroto 
Published: November 2023

Abstract
Lectins and carbohydrate-specific antibodies are often used for the detection of carbohydrate chains after electrophoretic separation of glycoproteins. Lectin blotting and antibody blotting can be applied before or after electrophoretic transfer of the glycoproteins to nitrocellulose membranes (1). The structural information from these blotting experiments is based on the carbohydrate binding specificity of the immunochemical agents applied. The information can be substantiated by partial modification of the glycoprotein carbohydrate chains prior to the reaction with immunochemical agents (2). To further elucidate the carbohydrate structures of electrophoretically separated glycoproteins, a simple method for the release of oligosaccharides from glycoproteins has also been developed (3). In this method, glycoproteins are electroblotted onto Immobilon transfer membranes. A small piece of the membrane with a glycoprotein band is cut out, dried in a desiccator and subjected to gas-phase hydrazinolysis. The released oligosaccharides, after re-N-acetylation, can be characterized by lectin affinity chromatography, gel permiation chromatography, and other means of oligosaccharide analysis.
Plasmid replication and maintenance
Authors: Nordstrom Kurt 
Published: November 2023

Abstract
All the essential genetic information in bacteria is located in one double stranded, circular DNA molecule, the chromosome. In addition, it is the rule, rather than the exception, that bacteria contain other DNA molecules, plasmids, that live in harmony with their hosts. These are separate entities, replicate autonomously, and control their own replication. They are present in defined copy numbers (average number of molecules per cell) during exponential growth of their hosts. The copy number is determined by genes present on the plasmids but is also affected by the host and by growth conditions (1). In this chapter, replication of plasmids as well as the control of replication will be discussed, with particular emphasis on plasmids that replicate in Escherichia coli.
Nuclear genes involved in chloroplast gene expression
Authors: Rochaix Jean-David 
Published: November 2023

Abstract
Chloroplast biogenesis depends on the concerted action of two distinct genetic systems located in the nucleus and in the plastids. While the informational content of chloroplasts is well known from the complete sequences of several plastid genomes (1,2,3,4; Chapter 3), the role of nuclear genes involved in this process is less understood and appears to be rather complex. A large number, most likely over 1000 nuclear genes, are involved in chloroplast biogenesis. Many of these genes encode components of the photosynthetic apparatus and of the chloroplast genetic and protein synthesizing systems. Others encode polypeptides from the stroma and from the plastid envelope, and several participate in various chloroplast metabolic processes.
Transgenic plants with special emphasis on photosynthetic carbon metabolism
Authors: Riesmeier JÖrg W , Rossmann Jens , Müller-röber Bernd , Willmitzer Lothar 
Published: November 2023

Abstract
Carbon metabolism in photosynthetically active cells of higher plants is of central importance for the allocation of carbohydrates formed to tissues that are dependent on the supply of carbon and energy. Carbohydrates are needed either to fuel housekeeping functions or for the formation of storage pools. Many control mechanisms influence carbohydrate formation and partitioning into different pools. Photosynthetic carbon metabolism will therefore be discussed with respect to the main pathways occurring in photosynthetically active tissues and the regulation of these pathways.
Non-isotopic detection of RNA in situ
Authors: Howard Pringle James 
Published: November 2023

Abstract
The synthesis of RNA plays a crucial role in the molecular biology of the cell and is, therefore, an important process to study. Although RNA can provide a source of genetic information in the genome of RNA viruses, its main role in the cell is to aid the transfer of genetic information from genomic DNA to functional proteins during gene expression. The process is regulated at each step in the pathway from DNA to RNA to protein (1). This includes the control of transcription of heterogeneous nuclear RNA (hnRNA), hnRNA processing to produce mature mRNA via the spliceosomes, mRNA transportation to the cytoplasm, and mRNA translation into proteins. The majority of cellular RNAs including tRNAs, rRNAs, and small nuclear RNAs (snRNA) have catalytic functions in this process (2, 3).
Combination of non-radioactivein situ hybridization andimmunocytochemistry
Authors: Mullink H , Vos W , Jiwa N M , Horstman A , Rieger E , Meijer C J L M 
Published: November 2023

Abstract
i&gt;In situ hybridization is a powerful tool for the detection and localization of nucleic acid sequences in cells and tissue sections. In this way, the presence of specific DNA fragments as well as (messenger) RNA products can be demonstrated with preservation of morphology (1-3). As morphology may be impaired during in situ hybridization, additional information regarding the cells involved may be required, depending on the scientific or diagnostic problem being studied. Since a particular cellular phenotype is characterized by the presence of specific proteins or antigens, immunocytochemical staining is required to reveal it. This phenotype can be studied by careful comparison of adjacent tissue sections stained by in situ hybridization and immunocytochemistry respectively. However, a more accurate and easier method is to analyse both simultaneously in one single, double-stained section. Moreover, only this approach allows the study of individual cells.
PCR analysis of RNA
Authors: Yokozaki Hiroshi , Tahara Eiichi 
Published: November 2023

Abstract
The polymerase chain reaction (PCR) has become an invaluable technique for amplifying small amounts of DNA for a wide range of molecular biological analyses. First strand cDNA, which is the product of reverse transcription of messenger RNA, can also serve as a template for PCR, such that gene expression can be analysed from only trace amounts of mRNA. It can be applied not only to the molecular cloning of genes, but also to RNA blot analysis (1), nuclease protection assay (2), and mRNA phenotyping (3) for the study of low copy number transcripts. The enzyme reverse transcriptase (RT) synthesizes first strand cDNA using mRNA as template. By combining this reaction with subsequent polymerase chain reaction (PCR) amplification, low abundance mRNA species can be analysed in cells or tissue specimens. In this section, conventional protocols for the extraction of total RNA, the RT reaction, and for PCR after the RT reaction are given.
Protein-stabilized water-in-oil-in-water emulsions
Authors: Dickinson Eric , Evison Jane , Owusu Richard K , Williams Andrea 
Published: November 2023

Abstract
Multiple water-in-oil-in-water (W/0/WJ emulsions are inherently less stable than ordinary oil-in-water (0/W) emulsions. In addition to the usual processes of creaming, flocculation and coalescence of the outer (oil) droplets, there is-with a multiple emulsion-the possibility of destabilization due to swelling and coalescence of the inner droplets, leading to rupture of the duplex film between inner and outer aqueous phases. These tendencies are exacerbated by the presence of both hydrophilic and hydrophobic emulsifiers which may migrate between inner and outer oil-water interfaces with consequent detrimental effects for emulsion stability. The use of a two-stage process to make a W/0/W emulsion that is stable to creaming requires extremely vigorous emulsification conditions during the second stage in order to produce droplets no bigger than a few micrometres in diameter. These vigorous conditions have the undesirable potential for disrupting the primary water-in-oil (W/0) emulsion droplets, thereby reducing the yield of multiple emulsion.
Xanthan polytetramer: conformational stability as a barrier to synergistic interaction
Authors: Foster T J , Morris E R 
Published: November 2023

Abstract
The genetically-engineered polytetramer variant of xanthan, in which the terminal mannose residues of each sidechain are absent, shows a thermoreversible conformational transition in solution (as monitored by DSC, CD and optical rotation). As found for xanthan, there is no detectable thermal hysteresis on cooling, and lffm decreases linearly with In I (where Tm is the transition midpoint temperature and I is ionic strength), but the Tm values for polytetramer are substantially higher. Native polytetramer shows normal solution rheology, but develops some xanthan-like ‘weak-gel’ properties after heating and cooling through the temperature-range of the conformational transition. We suggest that the polymer, as biosynthesised, is fully ordered along each chain, but renatures with shorter ordered sequences that promote network formation. Polytetramer shows no evidence of synergistic association with locust bean gum or konjac glucomannan, in contrast to xanthan and (particularly) de-acetylated xanthan, which gave massive viscous interactions even in very dilute solution. The difference is attributed to the enthalpic stability of the polytetramer helix (Afl “‘ 8.5 J/g, in comparison with -4.0 J/g for xanthan) preventing conformational rearrangement into heterotypic junctions. Non-acetylated polytetramer (also geneticallyengineered) gave a similar high value of AfI and again showed no evidence of synergistic interaction. As found for xanthan, the absence of acetate groups lowers Tm, indicating that they contribute to the stability of the ordered structure.
Barley germination and mass spectrometry
Authors: Angelino S A G F , Tas A C , Vos G F La , Mocking H C M 
Published: November 2023

Abstract
During barley germination in malting, various changes take place which affect the composition and internal structural features of the kernel. These changes can be monitored using a sophisticated mass spectrometric technique coupled with data analysis for interpretation of the extensive mass data sets obtained.
Comparaison de divers supports d’immobilisation cellulaire
Authors: Ruhaut L , Barbeau J Y , Shingleton M , Marc I 
Published: November 2023

Abstract
To build a continuous fermentation process, we have studied, in three steps, a large selection of potential yeast carriers. This study contained: a cell immobilization capacity evaluation in agitated process a mercury porosimetric characterisation a comparative wort fermentation on various material beds.
Beer flavor stability improvement and correlations to carbonyl profile
Authors: Bright David R , Patino Hugo , Schroedl David T , Nyarady Stefan A 
Published: November 2023

Abstract
Improvement of the flavour stability of packaged beer is a goal of many brewers. As part of this objective, knowledge of changes in the carbonyl profile of packaged beer during warm storage was targeted as an important step toward understanding the mechanisms of flavour staling. Using a new GC analytical method developed specifically to reduce artifact formation and shorten analysis time, 92 aldehydes, ketones, esters, alcohols and unknown compounds of several test and control beers were monitored during warm storage. Significant differences in carbonyl concentrations were observed between different beers and between different storage temperatures.
The specific role and interaction of yeast enzymatic systems in the removal of flavour-potent wort carbonyls during fermentation
Authors: Debourg A , Laurent M , Dupire S , Masschelein C A 
Published: November 2023

Abstract
In this work, we have studied the in vivo removal of wort carbonyl compounds by brewing yeast strains transformed with different genes encoding enzymes involved in aldehyde degradation. Moreover, using mutant strains and yeast cell-free extracts in the presence of specific substrates and inhibitors, we have investigated the role of different enzymatic activities on the reduction of wort carbonyl compounds. Results indicated an important heterogeneity in the enzymatic carbonyl compounds reduction systems. Nevertheless, it is the first time that these activities as well as the cofactor requirements are well characterized in yeast.
Application of machine vision methods to in-line measurement of yeast (and other particulate matter) in beer
Authors: Forrest I S , Grant I J 
Published: November 2023

Abstract
A knowledge of the concentration and size of particulate material in wort and beer is important at various stages in brewing. In particular, since yeast concentration is critical for beer quality and flavour during fermentation, filtration and cask conditioning, a measure of its concentration is essential. This paper describes the application of machine vision methods in the development of a general purpose, non-contacting, and non-intrusive instrument. The system determines the concentration and size distribution of yeast and other particulate matter from 2 to 100 microns. Examples are presented of the application of the instrument to in-line measurements during the brewing process.
The use of lux gene technology for rapid detection of spoilage bacteria
Authors: Davies Anne M , Hammond John R M , Lindhardt Charlotte 
Published: November 2023

Abstract
Most bacteria do not produce light, but can be induced to do so by infection with a bacteriophage containing the Lux genes coding for bacterial bioluminescence. The modified bacteriophage used in these studies is able to infect Obesumbacterium proteus. While initial light emission requires a certain threshold cell density, cells infected during logarithmic growth emit light in proportion to cell number. Sensitivity of the test is influenced by strain, age and metabolic condition of target cells,5 assay medium and presence of yeast cells. The test is able to detect 4 x 10 cells per ml of original sample, within a working day.