bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and characterization of DNA helicases
Authors: Bean Daniel W , Matson Steven W 
Published: November 2023

Abstract
DNA helicases catalyse disruption of the hydrogen bonds between the two strands of duplex DNA to generate single-stranded DNA (ssDNA) products (1, 2). This reaction is generally referred to as an unwinding reaction. The ssDNA product(s) of the unwinding reaction is then available for use as a template for DNA replication or repair, or as a substrate in recombination. Enzymes that catalyse the unwinding of duplex RNA, RNA secondary structure, and DNA:RNA hybrids have also been described (3-7). These enzymes have important roles in mRNA biogenesis, transcription, and translation. Thus, helicase catalysed unwinding is not confined to the unwinding of duplex DNA. In fact, there are examples of enzymes that catalyse the un winding of more than one of these substrates (8-10). The well characterized T-antigen, for example, unwinds both duplex DNA and RNA:DNA hybrids (9). Presumably these substrate preferences are related to the biological function of the protein, although these relationships are not always immediately obvious. None the less, it is clear that all transactions involving either DNA or RNA require the (transient) existence of a single-stranded intermediate, and thus helicases play key roles in all aspects of nucleic acid metabolism (11).
Analysis of telomere replication activities: telomerase and telomere binding proteins
Authors: Harrington Lea A 
Published: November 2023

Abstract
This chapter outlines the types of assays currently available for the analysis of two major classes of proteins important for telomere replication: telomerase, and telomere binding proteins. Since many of the other activities important for telomere replication, including DNA polymerases and helicases, are not necessarily telomere-specific, they will not be discussed here. There have been many recent advances in the detection of telomerase activities in vitro. The finding that telomerase activity is detected in a wide variety of human cancers, and is present at very low levels or undetectable in many normal, somatic tissues, has considerably raised interest in the study of telomerase activity regulation (reviewed in ref. 1). In addition, the recent identification and cloning of telomere binding proteins and telomerase components from several organisms has opened the way for a detailed biochemical examination of telomerase structure and function in many organisms (reviewed in refs 2-4).
Mitotic changes in the nuclear envelope
Authors: Miller Brian R , Forbes Douglass J 
Published: November 2023

Abstract
In higher eukaryotes, the disassembly of the nuclear envelope is one of the most dramatic events to occur at mitosis. The nuclear envelope consists first and foremost of a double membrane system surrounding the chromosomes. Lying under the inner nuclear membrane is a filamentous network composed of the nuclear lamins and associated proteins. At multiple places in the envelope, the inner and outer nuclear membranes fuse at the nuclear pore complexes. Nuclear pores are large, multi­ protein structures responsible for the signal-mediated transport of molecules into and out of the nucleus (Fig. 1). The lamina, pores, and the membrane system itself are all disassembled at the beginning of mitosis and reassembled during telophase.
Inheritance of the cytoplasm during cell division
Authors: Shima David T , Warren Graham 
Published: November 2023

Abstract
The inheritance process for nuclear DNA consists of a biogenesis phase (replication) and a partitioning phase (mitosis/meiosis). The inheritance of the cytoplasm also has biogenesis and partitioning phases, in which cytoplasmic components must double in unit mass, then be appropriately divided between nascent daughter cells during cytokinesis, respectively. The need to inherit cytoplasmic constituents such as mitochondria and chloroplasts is obvious since their self-contained DNA is absolutely required for proper organelle and cellular function and therefore must be transmitted to progeny through each cell division (1). Similarly, the endoplasmic reticulum (ER), the major site of synthesis for membrane lipids and proteins, must be derived from pre-existing membranes since there is no apparent mechanism to assembly these cellular membranes de novo (2).
Einsatz eines Separators zur Kühltrubentfernung
Authors: Eils Hans-Georg , Jünemann Andreas 
Published: November 2023

Abstract
A separator for the removal of cold trial was tested in a full scale trial. The flow was 700 hl/h and the system was designed to replace the presently used process of cold !rub removal with sedimentation tanks. A 50 % reduction of cold trub was aimed for. To achieve this target the construction of the separator had to be optimised and trials with different parameters had to be carried out. In selecting the proper conditions the target could be met. The beer quality with the new system was the same as with cold !rub removal by means of sedimentation. Flavour stability was positively influenced by cold trub removal with the separator. Preliminary results of experiences in a new word cooling plant will be reported.
The in vivo 31P-NMR analysis of brewing yeast and its practical application to brewing
Authors: Furukubo Susumu , Matsumoto Takehiro , Yomo Hideko , Fukui Nobuyuki , Ashikari Toshihiko , Kakimi Yoshi 
Published: November 2023

Abstract
We have established a procedure to measure the state of intracellular phosphor-containing substances of a brewing yeast by the 31P-NMR analysis. Cytoplasmic pH value of intact cells can be precisely determined from the state of intracellular inorganic phosphate. Fermentation performance tests revealed that the yeasts with higher cytoplasmic pH value had grown and assimilated amino acids with higher degree. Cytoplasmic pH value was proved to be a good index to assess yeast vitality for the subsequent fermentation. By applying this method to the practical brewing, various conditions of yeast handling and fermentation process could be optimized.
Bitterness by HPLC, a practical solution for routine QA use in breweries
Authors: Cope R , Hegarty P K , White F H 
Published: November 2023

Abstract
HPLC of iso-a-acids has been possible for at least two decades but routine adoption of the technology has been slow because of the complexity of the technique. A practical solution to this problem is described which involves the automated use of commercially available Solid Phase Extraction Disc technology. This robotic HPLC method has been routinely adopted in seven Bass laboratories. Inter collaborative test results show significantly improved repeatability and reproducibility over the Brenner method, which is currently internationally accepted for bitterness measurement in beers. HPLC results also suggest that Brenner results do not accurately reflect the iso-a-acid content of many beers.
Planungsgrundsätze und Betriebserfahrungen beim Brauereineubau
Authors: Eβlinger H M 
Published: November 2023

Abstract
In the planning of the new brewery of Freiberger Brauhaus AG particular emphasis was laid on quality and economy. In addition to meeting completion date and cost targets, the requirements included a modular expandable brewery with the shortest pipe runs and highly automated operation. The investments in environmental protection and energy economy combined with technological advance and minimal depreciation were particularly stressed. Currently there are 10 staff in general areas, 9 in the workshop, 12 in production and 24 in paclaging who produce over 650,000 hi beer per annum, requiring 35 kWh primary energy, 9 kWh electricity and 3.5 hi water per hi of beer produced.
Practical aspects of fluorescence resonance energy transfer (FRET) and its applications in nucleic acid biochemistry
Authors: Stuhmeier Frank , Clegg Robert M 
Published: November 2023

Abstract
Fluorescence spectroscopic methods can be used to detect substance (which contain fluorescent chromophores) at very low concentratiom and are especially useful for studying biomolecular structures and their dynamics in solution (see (l-3) for introductions into fluorescence spectroscopy). FRET, which is a non-radiative exchange of excitation energy between two chromophores, is strongly dependent on the distance between the tv.ro chromophores. If two such molecules are attached to a single biopolymer at different and well-defined positions, l-’Rl.:I can be used to estimate the distance between the two chromophores, and these data can be used to study structural aspects of the macromolecule. The distances that can be estimated arc in the range of0.5 to= 10 nm, which are in the same range as many distances in macromolecules. Because well-defined biopolymers can be synthesized and labelled at defined sites, FRET has become an important tool for structural studies io biophysics.
Determination of DNA-ligand interactions by fluorescence correlation spectroscopy
Authors: Langowski J , Tewes M 
Published: November 2023

Abstract
The quantitative characterization of protein-DNA interactions is of fundamental importance for our understanding of the mechanism of transcription regulation. A number of methods are applied to measure the thermodynamics and kinetics of such interactions, but many of those commonly used, such as gel shift, nitrocellulose filter binding, or surface plasmon r’sonance arc restricted to systems that are bound to or confined within some kind of matrix.
Nucleotide incorporation by DNA dependent RNA and DNA polymerases
Authors: Sclavi Bianca , Roux Pascal , Bue Henri 
Published: November 2023

Abstract
The steady-state analysis of the’ incorporation of nucleotide substrates by nucleic acid polymerases has be’en a subject of intensive research for many years. It has provided interesting re’ Wards in its specific field, for example a heller understanding of the faithfi.11 or the incorrect incorporation of nucleotides into zin elongating template by a specific enzyme. It has also proved to be of great use for a more indirect purpose, namely the understanding of how, in a time-resolved manner, nucleic acid polymerases interact with their cognate templates as the copying process is initiated or proceeds at steady state. This topic the subject of this chapter. Such assays were initially used in a rather crude. analytical manner. For example run-off transcription experiments were inserted into purification protocols to assess the degree of purity of a preparation of RNA polymerase or the extent of activation generated by a given factor. We describe here how more quantitative assays, performed with purified enzymes and templates, provide significant information on the interactions occurring between the two partners. Such assays arc essential prerequisites for the establishment of a plausible kinetic scheme which will in turn be challenged by the specific molecular methods developed in other chapters of this volume.
and elongation phases.
Authors: Temiakov Dmitry , Karasavas Pamela E , McAllister William T 
Published: November 2023

Abstract
Although the DNA-dependent RNA polymerase (RNAP) encoded by bacteriophage T7 consists of a single subunit, this enzyme is able to carry out all of the steps in the transcription cycle as the more complex multi subunit RNAPs. Its relatively simple structure, together with the availability of structural data, makes the phage RNAP an attractive model for studies of transcription at the molecular kvd (for review, see refa. 1 and 2).
Analysing the substructure of mammalian nuclei, in vitro
Authors: Jackson Dean A 
Published: November 2023

Abstract
If we are to understand the importance and complexities of interactions within the nucleus, as they exist in vivo, it is vital to develop approaches that allow us to access nuclear contents in vitro in such a way that the multiple layers of their organization can be analysed. This can only be worthwhile, however, if every effort is made to maintain and protect the organization as it exists inside the cell. Chapters 6 and 7 have shown how these goals can be pursued whilst using FISH and immunofluorescence to study chromosome structure in whole cells and tissues. There are particular additional problems in studying complex underlying nuclear structures using classical biochemical approaches. This chapter details the principal methods through which attempts have been made to study nuclear substructures that are important for both nuclear structure and function.
Macromolecular interactions in hepatitis B virus replication and particle assembly
Authors: Nassal Michael 
Published: November 2023

Abstract
Hepatitis B virus (HBV) is the causative agent of acute and chronic hepatitis B in humans. Chronic infection in particular poses a serious problem to public health. According to the World Health Organization (WHO), about 5% of the world population are HBV carriers, with a greatly increased risk for developing liver cirrhosis and, eventually, primary liver cell carcinoma. It is estimated that more than one million deaths per year are due to liver disease associated with chronic HBV infection. While an effective prophylactic vaccination based on a recombinant virus envelope protein is available, there is as yet no generally effective therapy (1, 2). The only currently approved treatment is the high-dose systemic administration of interferon-a but virus elimination is achieved in less than one-third of the patients. Hence the search for novel targets to combat chronic HBV infection continues to be one driving force for efforts to understand in detail the molecular mechanisms underlying the viral infectious cycle.
Epstein–Barr virus proteins involved in cell immortalization
Authors: Rowe Martin , Eike Floettmann J 
Published: November 2023

Abstract
The discovery in 1964 of herpesvirus particles in tumour cell lines derived from patients with Burkitt’s lymphoma (1) was a crucial observation that subsequently led to the so-called Epstein-Barr virus (EBY) being the first virus to be implicated in the pathogenesis of a human cancer. This gammaherpesvirus has since been associated with several other malignant diseases, including nasopharyngeal carcinoma, B cell lymphomas in immunosuppressed patients, certain T cell lymphomas, and Hodgkin’s disease (2). Absolute proof of the involvement of EBY in these malignancies was hampered by the unexpected finding that EBY was in fact a ubiquitous virus, being carried as a persistent and largely asymptomatic infection by more than 95% of adults in all populations world-wide (2). However, in support of its potential oncogenic properties, EBY was found to be a powerful transforming agent for normal resting human B lymphocytes in vitro, resulting in the regular outgrowth of EBY-immortalized lymphoblastoid cell lines (LCL) (3). Viral gene expression in LCL is restricted to about nine of the approximately 100 genes encoded by EBY and, since LCL are largely non-permissive for virus production, the EBY genes expressed in LCL were defined as latent genes. Six of the latent genes encode the nuclear antigens, EBNA-1,- 2, -3A,-3B, -3C., and -LP, while three encode the latent membrane proteins, LMP-1, -2A, and -2B; the most abundantly expressed latent transcripts in LCL are non-polyadenylated RNA, the EBERs, that do not encode proteins.
Interactions between viral and cellular proteins during DNA virus replication
Authors: Botting Catherine H , Hay ronald T 
Published: November 2023

Abstract
Initiation of viral DNA synthesis is preceded by assembly of a pre initiation complex at the viral origin of DNA replication. This nucleoprotein complex is composed of interacting viral and cellular proteins, which together recognize the viral origin of DNA replication and impart great specificity to the process. The initiation event is then triggered, and the pre-initiation complex dissociates as elongation proceeds. Thus the protein-protein and protein-DNA interactions involved are dynamic, with association and dissociation being induced by conformational changes, which may be triggered by one or more binding changes distal to the interaction under study. The methods described below have been used to study protein-protein and protein-DNA interactions in adenovirus DNA replication. It is therefore of value to describe briefly this replication system, to give context to the methods.
Synthesis and screening of positional scanning synthetic combinatorial libraries
Authors: Pinilla Clemencia , Appel Jon R , Blondelle Sylvie E , Dooley Colette T , Eichler Jutta , Nefzi Adel , Ostresh John M , Martinꝉ Roland , Wilson Darcy B , Houghten Richard A 
Published: November 2023

Abstract
Combinatorial library synthesis and screening methods, which enable the rapid identification of highly active compounds, have revolutionized basic research and drug discovery. A number of different combinatorial approaches based on the principles of solid phase synthesis have been used to generate enormous molecular diversities, including peptides, peptidomimetics, and small organic molecules. The advantage of the various combinatorial approaches compared to traditional drug synthesis and screening methods is the very large number of compounds that can be simultaneously synthesized and rapidly screened in biological assays.
Analytical methods in combinatorial chemistry
Authors: Yan Bing , Chu╪ Yen-ho , Shapiroꝉ Michael , Richmond§ Ramsay , Chinꝉ Jefferson , Liuꝉ Lina , Yuꝉ Lina 
Published: November 2023

Abstract
This chapter describes an array of techniques successfully applied to the optimization of solid phase organic synthesis (SPOS) (1, 2), quality control (QC) of combinatorial libraries, and in the selection of active lead compounds. Since low quality of the final library is largely attributable to poorly developed chemistry at the optimization stage, investing more time and effort in reaction optimization is crucial in combinatorial synthesis. QC data gives confidence on both the molecular diversity generated and the subsequent screening results. While the screening of pure compounds is a well-developed routine operation, the screening of compound mixtures is more difficult and this will be covered at the end of this chapter. Various analytical techniques are described below in the order encountered in a combinatorial synthesis process.
An introduction to differential display and related techniques
Authors: Robertson Harold A , Lesliet Ronald A 
Published: November 2023

Abstract
It is worth acknowledging, as there is no way around it, that differential display has been, and remains, a controversial technique. Any technique that engenders articles with the word ‘dismay ‘ in the title (1) must be controversial! More than a thousand articles, however, have now been published describing results achieved with the use of the differential display technique and hundreds of genes have been ‘discovered ‘. This book has been written with the firm belief that much of the scepticism that differential display has engendered is based upon a frequent poor understanding of the technique and the premature publication of many studies. Such studies have often been undertaken by groups who were early to recognize the power of this technique in biological applications but who had not yet achieved the necessary technical expertise to apply the technique successfully. Thus, in the heady days after the introduction of the technique by Liang and Pardee in 1992 (2), many biologists with divergent areas of expertise (neurobiology, psychology, plant sciences, pharmacology) rushed into applying the technique in their particular systems without, perhaps, a sufficiently solid background in modern molecular biology. This was a testi monial to the apparent simplicity of the technique and to the potential breadth of biological systems to which the technique might be applied.
A modified approach for the efficient display of 3 ‘ end restriction fragments of cDNAs
Authors: Subrahmanyamt Y V B K , Yamaga Shigeru , Newburger Peter E , Weissman Sherman M 
Published: November 2023

Abstract
One of the remarkable developments in science in the last few years has been the progressive improvement in technology and paradigms for obtaining the sequence of very large amounts of genomic DNA. In parallel with this develop ment, sequences identifying specific mRNAs have accumulated from random sequencing of segments of cDNA clones as well as from genomic sequences. The development of approaches for rapidly and economically screening the expression patterns ofmRNAs in different tissues or cell types and as a function of different physiological or pharmacological perturbations promises to generate bodies of data of the same order of magnitude and biological significance as the sequences themselves.
Cloning of differentially expressed brain cDNAs
Authors: Denovan-Wright Eileen M , Gilby Krista L , Howlett Susan E , Robertson Harold A 
Published: November 2023

Abstract
The ability of cells to alter gene expression in response to stimuli or during development and ageing underlies the plasticity of the central nervous system. Although there are multiple levels of control of gene expression, induction or repression of specific genes is an important first step in the regulation of the function of the CNS. Therefore, molecular screening and selection techniques based on comparing mRNA populations can reveal important differences in gene expression between and among brain tissues.
Differential display is a PCR-based screening method (for an overview see 1) that is especially useful to study changes in steady-state levels of mRNA in heterogeneous tissue such as brain for several reasons (1). First, this screening technique can be used to identify novel brain mRNAs or previously described mRNAs whose relative expression levels are altered as a result of a physiological change, a disorder, a disease state, or the administration of pharmacological agents. Secondly, it is possible to simultaneously compare multiple tissues, treatments, and time points (up to 60 comparisons per experiment and primer set) using small amounts of tissue from a number of individual animals for the original isolation of RNA. These features distinguish differential display from methods that require prior information about specific gene expression and from methods that are used to screen or select cDNAs from only two states. Moreover, differential display can be easily established in any laboratory that has basic molecular biology equipment and supplies.
Pleckstrin homology domains: phosphoinositide-regulated membrane tethers
Authors: Lemmon Mark A , Ferguson Kathryn M 
Published: November 2023

Abstract
Pleckstrin homology (PH) domains are small β-sandwich protein modules of approximately 120 amino acids that were first noted as a twice-repeated pattern in pleckstrin, the major protein kinase C substrate in platelets (1). In simultaneous communications to Nature(2) and Cell(3) in 1993, it was pointed out that a variety of proteins involved in cellular signalling also contain PH domains. Subsequent reports extended the number of putative PH domains to more than 100 (4, 5), and this number continues to grow. Confirmed or putative PH domains have been found in the following classes of intracellular protein (Fig. 1):