bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population and ecological genetics
Authors: Brookfield J F Y 
Published: November 2023

Abstract
Drosophila melanogaster is a cosmopolitan species that lives as a human commensal. The family Drosophilidae belongs to the Dipteran Sub-Order Cyclorrhapha and is thought to be primitively saprophytic, living on fermenting substrates. However, immense variety now exists in the food sources exploited by different species. Of 3020 species in the 61 genera of the family, 1677 are in the genus Drosophila, a result that must partially reflect incomplete sampling of the others (1). The taxonomic richness of the group potentially allows the comparison of D. melanogaster genes with those of other species at many different levels of evolutionary divergence. The phylogenetic relationships of species of Drosophila are imperfectly known, but a number of subgenera, species groups, species subgroups, and species complexes are recognized between the generic and specific ranks. The melanogaster species group, including also D. simulans, D. mauritiana, D. sechellia, D. yakuba, D. teissieri, D. erecta, and D. arena has a phylogeny that has been well established through study of the polytene chromosomes and DNA sequence divergence. These species are important in some tests for selection outlined below. The species group originated in Africa, and the first bifurcation, separating the ancestor of D. arena and D. erecta from that of the others, occurred between 15 and 20 million years ago.
Methods to map origins of replication in eukaryotes
Authors: Gerbi Susan A , Bielinsky Anja K , Liang Chun , Lunyak Victoria V , Urnov Fyodor D 
Published: November 2023

Abstract
According to the replicon model of Jacob, Brenner, and Cuzin (1), initiation of DNA replication is achieved via the binding of a trans-acting protein (the initiator) to a cis-acting sequence (the replicator). The initiator recruits the replication machinery to the replicator, and DNA synthesis ensues. Studies in prokaryotes, fungi, and viruses of metazoans have provided ample experimental support for this hypothesis, and in such model systems as E. coli, S. cerevisiae, and SV40, a considerable amount of experimental data exist about the nature of replicators and the initiator protein(s) (see refs 2-4 for recent reviews). A useful and interesting property of replicators in these organisms is that they retain function when placed on an episome. The autonomously replicating sequence (ARS) assay that exploits this property allowed researchers to use the power of ‘reverse genetics’ to identify and study the replicators in these systems (for example, ref. 5). Unfortunately, the ARS assay has not been as useful for studying replicators in metazoa, where the efficiency of episome replication seems more related to the length rather than the sequence of the insert (6-8). There are additional complexities: sequences as much as 50 kb away from the origin can influence its activity (9), and proper chromatin organization of the DNA is important for replication initiation (10).
The use of Xenopus laevis interphase egg extracts to study genomic DNA replication
Authors: Walter Johannes , Newport John 
Published: November 2023

Abstract
Cell-free extracts derived from the eggs of Xenopus laevis are a powerful experimental system to study genomic DNA replication in higher eukaryotes (1-3). DNA templates (either plasmid DNA or Xenopus sperm chromatin) added to these extracts are packaged into nuclei and then replicated under normal cell cycle control. This process occurs rapidly and efficiently and can be extensively manipulated in order to elucidate underlying biochemical mechanisms.
Viral in vitro replication systems
Authors: Bullock Peter A 
Published: November 2023

Abstract
It is possible to study the duplication of DNA using a number of in vitro replication systems, including those employing prokaryotic (1) as well as eukaryotic replication factors (2). In many instances, the eukaryotic replication factors were identified by fractionation of cellular extracts that support the in vitro replication of viral DNA (3-5 for reviews). Prominent among the in vitro viral DNA replication systems are those that support adenovirus, papillomavirus, and papovavirus DNA replication. Additional systems for studying viral DNA replication (e.g. herpesvirus, poxvirus, and parvovirus) have been described (2).
Analysis of DNA replication complexes by DNA probing
Authors: Borowiec James A , Gillette Thomas G , Smelkova Natalia V , Iftode Cristina 
Published: November 2023

Abstract
This chapter describes techniques used to characterize complexes formed in solution between replication proteins and DNA. Although general DNA probing or ‘footprinting’ techniques used to probe standard protein:DNA complexes are provided, special emphasis will be placed on those methods most useful to investigators studying the interaction of DNA replication proteins with DNA replication substrates. Thus, the reader will find a variety of DNA probing techniques that can reveal the presence and location of distorted DNA within complexes. We discuss chemical and enzymatic probes useful for examining the disposition of single-stranded DNA (ssDNA) often found in replication intermediates. We also describe the use of interference assays which allow the determination of DNA contacts important for protein binding, and for the characterization of transient complexes formed between replication proteins and DNA.
Microtubule dynamics, molecular motors, and chromosome behavior
Authors: Vernos Isabelle , Karsenti Eric 
Published: November 2023

Abstract
Perhaps because of its aesthetically pleasing and exquisite geometrical shape, the mitotic spindle has fascinated researchers for more than a hundred years. In 1896, Wilson (see ref. 1) had already described accurately the shape of the spindle and the principal phases of mitosis. He described how two centrosomes moved around the nucleus, how fibers grew between the migrating centrosomes and how chromosomes eventually aligned on the 'equatorial plate' of the mitotic spindle. It was already clear that chromosome segregation took place on the fibers of the spindle during anaphase, providing the two daughter cells with equivalent chromosome numbers.
Monitoring of trichothecene producing Fusarium species in brewing cereals using a group specific Polymerase Chain Reaction
Authors: Niessen M L , Vogel R F 
Published: November 2023

Abstract
A pair of PCR primers (Tox5-1 and Tox5-2) was designed and a PCR set up and optimized. With the primer pair used a 658 bp fragment was amplified from DNA isolated from Fusarium species described as producers of trichothecene mycotoxins. Non-trichothecene producers, cereals, and bacteria gave no signal in the assay. Trichothecene producers were detected in samples of contaminated malts. Results showed that the method developed is group specific for the detection of all Fusarium species capable of producing trichothecenes. The method may be used for quality monitoring in the brewing and malting industry.
Enzymes from barley which solubilize β -glucan
Authors: Bamforth C W , Moore J , McKillop D , Williamson G , Kroon P A 
Published: November 2023

Abstract
ß-Glucan solubilase releases ß-glucan and probably pentosans from cell walls making them more accessible to endo-B-glucanases and pentosanases respectively. An improved assay for measuring solubilase activity has been developed. Solubilase is present in raw barley and is relatively heat stable. Four fractions of solubilase activity have been located. Two of the fractions contain feruloyl esterase. Ester linkages involving ferulic acid, probably with the arabinoxylan component of the cell walls, may be disrupted by solubilase.
Proanthocyanidin-free malting barley - a solution of the beer haze problem
Authors: Jende-Strid B 
Published: November 2023

Abstract
Technical stabilization of beer is not necessary if proanthocyanidin-free malt is used for brewing. At Carlsberg a breeding programme for development of proanthocyanidin-free malting barley varieties has resulted in a commercial malting barley variety “Caminant” with a yield performance and a malting quality which is comparable to other malting barley varieties on the market. Production scale maltings and brewing trials with Caminant show, that it is possible to produce malts and beers which live up to the breweries’ specifications. New improved proanthocyanidin-free malting barley varieties are under way. Breweries can avoid the expenses of technical beer stabilization by use of good proanthocyanidin-free malting barley.
Application industrielle de I’ensemencement de ferment au cours du maltage pour 1’amélioration de la qualité sanitaire et biophysique du malt
Authors: Boivin Patrick , Malanda M’Baka 
Published: November 2023

Abstract
Geotrichum, a yeast naturally present in malting, has been used industrially in malting with the aim of controlling the development of the microflora and improving the biophysical and microbiological quality of malt.
Lactic acid starter cultures for prevention of the formation of Fusarium mycotoxins during malting
Authors: Laitila A , Tapani K -M , Haikara A 
Published: November 2023

Abstract
Contamination of barley by mycotoxigenic and active gushing inducing fusaria are of concern to maltsters and brewers. The ability of lactic acid bacteria to restrict the growth of Fusarium graminearum and F. culmorum species was studied in vitro and in laboratory scale maltings. Five from 15 lactic acid bacteria tested notably retarded the growth of Fusarium fungi. Addition of the most active lactobacilli into the steeping diminished the amount of Fusarium contamination and formation of deoxynivalenol and zearalenone during malting when naturally infested barley was used. Formation of mycotoxins during malting was also studied with artificially contaminated barley.
Caractérisation rapide des différentes étapes du maltage par spectroscopie moyen infrarouge en réflexion totale atténuée
Authors: Allosio Nathalie , Robert Paul , Bertrand Dominique , Boivin Patrick 
Published: November 2023

Abstract
To produce a malt of good quality, it is necessary to have a rapid method to control the malting process. However, very few rapid physical techniques are available to maltsters to characterise their products. The feasibility of attenuated total reflectance, a method allowing rapid analysis of wet products with strong absorption such as green malt, has been tested. The application of principal component analysis to spectra scanned in the mid infrared with this method, shows that it is possible to classify samples according to their malting step.
Influence de la composition en hétérocycles azotés de malts spéciaux sur le profil aromatique de la bière
Authors: Herent Marie-France , Vanthoumhout Cedric , Collin Laurence Gijs & Sonia 
Published: November 2023

Abstract
Les malts caramels sont utilisés dans la production de btères spSciales auxquelles ils confèrent une coloration et un ardme caractéristiques. Ce dernier est essentiellement apporté par des heterocycles azotés tels que lés dérives pyrazines et thiazoles.
Possibilities to use Agrobacterium tumefaciens as a gene transfer vector in hop
Authors: Gurriaràn M J , Benftez J L , López M A , Ordàs R J , Tamés R S 
Published: November 2023

Abstract
A. tumefaciens promises to be a suitable vector to obtain transgenic hop plants. Slices from organogenic callus were cocultivated with the bacteria. Growth and vir gene induction by in vitro extracts and exudates were studied. The bacteria grew in in vitro extracts, and vir D expression was not induced by exudates. This agrees with the fact that transient gene expression was only observed in those slices cocultivated in the presence of Nicotiana bentamiana leaf discs. The situation could be overcome by addition of supplement vir gene inducers, opening the way to get hop plants tolerant to herbicides or pests.
A new mashing-in system that reduces oxygen uptake
Authors: Yamaguchi lchiro , Ueda Tsutomu , Ujihara Shigeru , Yamada Minoru , Fukushima Shuji 
Published: November 2023

Abstract
In order to improve beer flavour stability, a new mashing-in system that reduces oxygen uptake was introduced into a brewery. This system entails purging ingredients with carbon dioxide, then feeding them from the bottom of vessels. In addition, deaerated water was also used for brewing liquor. Compared with the conventional system, the new system decreased the trans-2-nonenal content of packaged beer while taste test results also indicated that the new system results in less oxidation. In relative terms, feeding ingredients from the bottom was more effective in reducing oxygen uptake than deaerating the brewing liquor.
Studies on the survival of amylose-lipid complexes under mashing conditions
Authors: Wilhelmson A , Vainikka M , Home S 
Published: November 2023

Abstract
The aim of this study was to clarify whether the amylose-lipid complexes remain unhydrolyzed under mashing conditions. As amylose-lipid complexes are difficult to analyze from a complicated matrix such as spent grains, the hydrolysis of these complexes was studied by incubating pure barley starch in malt enzyme extracts with varying enzyme activities. After the incubation, most of the starch lipids were found in the insoluble precipitate. The hydrolysis of amylose-lipid complexes during incubation was strongly influenced by the amylolytic activity of the malt extract. At lower enzyme activities the complexed amylose was more slowly hydrolysed than the free amylose.
Weiterentwicklung der thermischen Brildenverdichtung
Authors: Fohr Markus , Meyer-Pittroff Roland 
Published: November 2023

Abstract
Die thermische Briidenverdichtung mit einem Dampfstrahlverdichter hat sich als Alternative zur mechanischen Briidenverdichtung bei der Wiirzekochung etabliert. Es besteht jedoch noch Entwicklungsbedarf hinsichtlich des Einsatzes regelbarer Dampfstrahlverdichter und, wie auch bei anderen Wurzekochsystemen,
Einfluß einer Vekuumverdampfung vor der Würzekülung auf Bierqualität und Geschmacksstabilität
Authors: Lustig Stefan , Kunst Thomas , Hill Peter 
Published: November 2023

Abstract
During the hot stand of wort in the whirlpool, various compounds are formed by thermally mediated reaction mechanisms, and are only partially removed in the steam. Since these compounds lead to unwanted aromas in finished beer and are known to impair taste stability, enhanced removal by vacuum evaporation from the whirlpool was investigated. A successful plant-scale trial achieved separation of hot trub at reduced pressure of 0.5 bar. The influence of this procedure on the quality of the wort and beer, as well as the taste stability of beer, was investigated.
Utilisation d’1802 pour évaluer l’impact du phénomène d’oxydation durant le brassage et le stockage de la bière
Authors: Collini S , Noel S , Bonte S , Metais N , Bodart E , Peladan F , Dupire S 
Published: November 2023

Abstract
To understand the oxygen incidence in bottled beer, 1802 has been injected in the headspace just before ageing. Although very potent for sulfite, polyphenol and isohumulone degradations, bottled oxygen has been found not to be incorporated in the flavouring fraction, indicating that cardboard aroma is not issued from lipid oxidation. The impact of oxygen during mashing has been evidenced on the final beer. A comparison of trans-2-nonenal contents of worts produced in presence of nitrogen, 1602 or 1802 clearly indicates that three synthesis pathways and two degradation mechanisms modulate the alcenal concentration in the unboiled wort. The nonenal potential measurement after wort filtration appears to be a good indicator in predicting subsequent beer ageing.
Identification of foam-stabilizing proteins under conditions of normal beer dispense and their biochemical and physico-chemical properties
Authors: Douma A C , Mocking-Bode H C M , Kooijman M , Stolzenbach E , Orsel R , Bekkers A C A P A , Angelino S A G F 
Published: November 2023

Abstract
To investigate which proteins are relevant for foam stabilization, the protein composition of beer and ageing beer foam was compared. During foam ageing, a strong accumulation of a relatively hydrophobic 8-18 kD protein group was observed. Protein Z, the most abundant beer protein, showed favourable physico-chemical characteristics for foam stabilization. The 8-18 kD protein group was able to enhance the beneficial visco-elastic properties of protein films composed of protein Z. Methods to quantify the level and ratio of 8-18 kD and 40 kD protein may enable the determination of foam protein quality in beer as well as during malting and brewing.
DNA wrapping in Escherichia coli RNA polymerase open promoter complexes revealed by scanning force microscopy
Authors: Rivetti Claudio 
Published: November 2023

Abstract
Transcription is the first step in the expression of the genetic information encoded in DNA In Escherichia coli, this process is carried out by RNAP, a single enzyme that can exist in two forms: the core enzyme, with a subunit composition α2 β β Mr 380 000, is responsible for the actual RNA synthesis and the holoenzyme, which possesses an additional er subunit that enables RNAP to recognize promoters and to initiate transcription. In prokaryotes, the majority of the promoters are recognized by the 70 kDa IT o factor. IT70-RNAP binds to the promot’r to form a close promoter complex (CPC) which spontaneously isomeriz’S through various int’rm’diatcs into an open promoter complex (OPC) containing an unwound DNA section (for review see refs. 1 and 2). Upon addition of nucleoside triphosphat’s RNAP b’gins RNA synthesis. u factor is released, and the core enzyme moves in a highly processiv’ manner along the DNA until a t’rminator is reached (3, 4). During transcription, RNAP translocates on the DNA, unwinding the DNA ahead and rewinding it in its wake, thereby maintaining the transcription bubble with no net free energy cost.
Laser UV-laser photoreactivity of nucleoprotein complexes in vitro
Authors: Buckle Malcolm , Place Christophe , Pemberton lain K 
Published: November 2023

Abstract
In order to define a kinetically competent nucleoprotein complex, a complete description of all the contacts and conformational changes characterizing both its formation and subsequent function is required. Chemical, physical and biological probes are all used to generate this information. Such probes must, however, report a specific structure that is both structurally unique and also singular with respect to time. The two overall stringent requirements for such probes are that they are first non-perturbing and second, highly specific (1), In this chapter we describe the use of high-energy photons to excite and study nucleoprotein interactions in vitro. The use of a similar system in vivo is described in Chapter 15.
Analysis of DNA-protein interactions by time-resolved fluorescence spectroscopy
Authors: Thompson E H Z , Millar D P 
Published: November 2023

Abstract
In addition to its uses as a probe of macromolecular structure and dynamics, fluorescence spectroscopy is emerging as a powerful tool for studies of DNA protein interactions. Particular advantages of fluorescence-based measurements include: the ability lo observe interactions under conditions of thermodynamic equilibrium; their sensitivity, allowing investigations at concentrations approaching the Kd values of many DNA-protein interactions; the ability to monitor complexation events in solution, accommodating a widC’ variety of conditions: and, most of all. the short time-scale of the emission process. Since the emission of a photon occurs on the same time-scale as a number of dynamic processes including solvent relaxation, intersystem crossing, charge transfer, and quenching-it is highly sensitive to the characteristics of the local environment.
Site-specific protein-DNA photocrosslinking
Authors: Kim Tae-Kyung , Lagrange Thierry , Reinberg Danny 
Published: November 2023

Abstract
Transcription and replication involve multiprotein-DNA complexes with molecular weight masses in excess of 400 kDa (1-5). Understanding transcription and replication will require understanding the arrangement of proteins relative to DNA in these complexes. High-resolution structures of components of the complexes have been determined (1-5). However, the intact, fully assembled, complexes are too large for high-resolution structure-determination by current methods. Therefore, efforts to define the arrangement of proteins relative to DNA within the intact complxes must rely heavily on biochemical methods.
Transcription-coupled and global genoine repair in yeast and huinans
Authors: Tijsterman Marcel , Verhage Richard A , Brouwer Jaap 
Published: November 2023

Abstract
Nucleotide excision repair (NER) is able to remove a wide variety of DNA lesions from the genome. Incision of the damaged strand on both sides of the lesion is followed by resynthesis of excised DNA using the non-damaged strand as a template. The role of the proteins involved in this cut-and-paste mechanism is studied biochemically, and these studies have recently culminated in the reconstitution of eukaryotic NER in vitro using repair components purified from both yeast and human cells (see Chapter 5 for a detailed discussion on the proteins involved). Whereas these in vitro assays allowed the identification of a minimal set of proteins (here referred to as core-NER proteins) required to perform the reaction on naked DNA, analysis of repair in vivo indicated that additional proteins are necessary for the efficient removal of damage from genomic DNA. These factors are believed to be involved in the first step of the NER pathway: the recognition of different types of DNA damage in a genome that is continuously undergoing various cellular processes (e.g. transcription, replication, recombination) and which, in addition, is folded into chromatin with different levels of complexity.
Interaction of DNA virus proteins with host cytokines
Authors: Lalani Alshad S , Nash Piers , Seet Bruce T , Robichaud Janine , Mcfadden Grant 
Published: November 2023

Abstract
It has become evident that large DNA viruses have adapted a variety of strategies to modulate the host immune response to virus infection. Recently, a variety of DNA virus-encoded gene products have been identified with activities targeted towards modulating the cytokine networks of the inflammatory response of their host. Members of the poxvirus family were the first DNA viruses shown to encode secreted versions of cellular cytokine receptors, and currently a dozen virus proteins that interact with cytokines have been identified in both the poxvirus and herpesvirus families (Table 1) (1, 2). Viral cytokine receptor mimics (also known as ‘viroceptors’) are soluble or membrane-bound proteins that may share significant homology to the ligandbinding domains of cellular cytokine receptors, and function by sequestering cytokine ligands from interacting with their cognate cellular receptors.
Chemotherapy of DNA virus infections
Authors: Cane Patricia A , Pillay Deenan 
Published: November 2023

Abstract
In recent years there have been considerable advances in the development of effective antiviral drugs. Much of this progress has been driven by the need to combat human immunodeficiency virus (HIV) infection, but there are currently nearly thirty antiviral agents in clinical development or licensed for use in humans against DNA viruses. These are listed, together with their principal activities, in Table 1. In theory, any of the stages of the replication cycle of a virus (attachment, penetration, uncoating, replication, maturation, and release) are potential targets for antiviral drugs, but in the case of DNA viruses most of the effective drugs act by inhibiting DNA replication. Such drugs are mainly either nucleoside analogues such as acyclovir, ganciclovir, and lamivudine, or phosphate analogues such as foscarnet.