bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antisense Applications in Dictyostelium: A Lower Eukaryotic Model System
Authors: Hildebrandt Martin 
Published: November 2023

Abstract
The cellular slime mould Dictyostelium discoideum is a single-cell haploid amoeba, which, upon starvation, enters a well characterized developmental cycle. During this process, multicellular aggregates, also called pseudo plasmodia are generated, which later form a fruiting body and differentiate into a tube of non-viable stalk cells and a sorocarp of encysted spore cells. Since the many Dictyostelium proteins involved, for example, in signal transduction or cell movement are very similar to their mammalian homologucs, antisense RNA experiments in Dictyustelium are an easy and inexpensive model system to generate and study mutants lacking a protein of general interest.
Antisense Rescue
Authors: Holt Jeffrey T 
Published: November 2023

Abstract
Genetic manipulation of cells has provided a powerful approach to study gene function and the regulation of gene expression. Although genetic manipulation includes overexpression and ‘undcrexpression’ strategies, methods which inhibit gene function arc particularly important because they probe the usual function of a gene product within an appropriately expressing cell. Antibody injection (1), antisense methods (2-6). and gene targeting (7) can be used for gene inhibition; and each approach has its strengths and weaknesses.
Cell cycle control of DNA replication in Saccharomyces cerevisiae
Authors: Schwob Etienne , Nasmyth Kim 
Published: November 2023

Abstract
Living organisms grow and divide to produce genetically identical progeny. To divide continuously, a eukaryotic cell must duplicate all of its constituents including DNA, proteins, ribosomes, organelles, etc., and segregate them more or less equally to daughter cells. To perpetuate its genetic information, a cell must, how-ever, duplicate and segregate its chromosomes with high fidelity 10-6 mutation/bp and 10-5 chromosome loss/ cell division in yeast). An important question in cell biology is therefore how cells manage to replicate and segregate faithfully their chromo-somes? Furthermore, how is cell division regulated by cell growth and external conditions? This formidable task is achieved following the instructions of a programme, the cell cycle, which integrates the many biochemical events needed for chromosome duplication, transmission, and cell separation over time and space. For example, this programme ensures that DNA is replicated before sister chromatids begin to separate, or that sisters move to opposite poles.
Production of single-chain Fv monomers and multimers
Authors: FILPULA DA YID , Mcguire Jeffrey , Whitlow Marc 
Published: November 2023

Abstract
The Fv fragment (25 kDa) is a two-chain heterodimer of the antibody variable domains (VL and V8) and is regarded as the minimal structural component of an antibody required for antigen-binding activity. Fvs have been found to dis sociate into VL and V8 domains at low protein concentrations and under physiological conditions (1). This limited stability may be overcome by incor poration of a designed linker peptide to bridge isolated VL and V8 domains into a single polypeptide (2). Basic research on recombinant single-chain Fv (scFv) proteins produced from Escherichia coli has recently provided some answers to at least two basic questions about this new antibody technology.
Mapping chromatin structure in Drosophila
Authors: Swede Marci J , Wallrath Lori L , Elgin Sarah C R 
Published: November 2023

Abstract
Most of the DNA making up a eukaryotic genome is packaged into nucleosomes. Discontinuities in the nucleosome array are typically due to the binding of non-histone chromosomal proteins. These nucleosome-free regions (about 50–200 bp in length) were first identified as sites hypersensitive to digestion with DNase [ and other nucleases (reviewed in refs 1. 2). DNase I hypersensitive sites have been found 5’, 3’, and within introns of genes in organisms ranging from plants to humans (3–6). DNase I hypersensitive sites frequently map to locations of gene regulatory elements. Nucleosomes have been shown to block gene transcription when positioned over cis-acting regulatory elements in the promoter region of a variety of genes (reviewed in refs 7–10); this suggests that the formation of DNase I hypersensitive sites encompassing cis-acting elements might be a critical regulatory event providing accessibility for trans-acting regulatory factors. Consistent with this idea, the appearance of DNase I hypersensitive sites can be tissue specific and/or developmentally regulated (11–13).
Transcriptional and structural analysis of chromatin assembled in vitro
Authors: Pazin Michael J , Kadonaga James T 
Published: November 2023

Abstract
The biochemical analysis of the transcriptional properties of DNA packaged into chromatin, as it is in vivo, promises to increase our understanding of gene regulation (1–4). This chapter focuses on the assembly and transcription of chromatin by using two different extracts derived from Drosophila melanogaster embryos. We have also included techniques for the analysis of chromatin structure to verify the proper assembly of chromatin as well as to examine mechanisms of gene regulation. Hence, this chapter describes methods for the assembly of chromatin (Protocols 1-3), in vitro transcription of the reconstituted chromatin templates (Protocol 4), and analysis of chromatin structure and the binding of transcription factors to the nucleosomal templates (Protocols 5–7).
Getting started in molecular biology
Authors: Brown T A 
Published: November 2023

Abstract
In several respects molecular biology is not a user-friendly discipline. The new comer is faced with a bewildering array of techniques, some unhelpful jargon, and the impression that only the complicated experiments are worth doing. In fact, most of the apparent problems are illuso1y and a series of relatively straight forward experiments will allow any competent research worker to obtain in formation on the structure and mode of expression of a gene. This is true not only for scientists in established molecular biology laboratories but also for researchers from other areas wishing to apply DNA analysis techniques in their own projects.
Generation and identification of recombinant clones
Authors: Brown T A 
Published: November 2023

Abstract
The cells are plated on to a selective medium (or a series of media) that enables recombinant colonies (i.e. those that contain recombinant DNA molecules) to be identified. There are several different selection strategies; the appropri ate one depends on the type of vector that is being used {see also Chapter 9).
This chapter begins with methods for introducing recombinant DNA molecules into bacteria and then provides details for recombinant selection with the most important vectors. The protocols deal solely with the use of Escherichia coli as the host organism, E. coli being the host that is used for all basic gene cloning experiments.
The polymerase chain reaction
Authors: Brown T A 
Published: November 2023

Abstract
The polymerase chain reaction is a deceptively simple but remarkably versatile procedure that has applications in virtually all areas of molecular biology research. All that a PCR does is to make multiple copies of a target DNA sequence, the amplification process enabling microgram quantities of DNA to be obtained from a single starting molecule. Any segment of any DNA or RNA molecule can be amplified, provided that the sequences on either side of the targeted region are known. If genomic DNA is used as the starting material the PCR can be used in an analogous fashion to cloning, to provide a pure sample of a single gene or other DNA sequence, with the advantage that the gene is obtained after a few hours work, rather than the weeks needed to prepare and screen a genomic c. If RNA is the starting material then PCR can achieve the same objective as cDNA cloning, again much more rapidly. Only the limitation that some sequence information is needed in order to design appropriate primers for a PCR, plus the difficulty in obtaining PCR products longer than 5-10 kb long, has prevented PCR from completely replacing cloning as a means of gene isolation.
Functional analysis of DNA replication accessory proteins
Authors: Hübscher Ulrich , Mossi Romina , Ferrari Elena , Stucki Manuel , Jónsson Zophonías O 
Published: November 2023

Abstract
This chapter summarizes practical experiments that can be performed with DNA replication accessory proteins. The DNA, in preparation for DNA synthesis, has to become single-stranded to serve as a template for the replicative DNA polymerases (pols). For this a set of proteins have been identified that support the replicative and repair pols in performing processive, accurate, and rapid DNA synthesis. Furthermore these proteins prevent damage to the transient single-stranded DNA. The three best known are the proliferating cell nuclear antigen (PCNA), replication factor C (RF-C), and replication protein A (RP-A). DNA replication accessory proteins provide particular functions that are mandatory for pols. Such functions include the recruitment of particular pols when needed, the facilitation of pol binding to the primer terminus, the increase in pol processivity, the prevention of non-productive binding of the pol to single-stranded DNA, the release of the pol after DNA synthesis, and the bridging of pol interactions to other replication proteins. Thus it is not surprising that proteins carrying out such functions have been universally found in nature (reviewed in ref. 1). The eukaryotic auxiliary proteins RF-C and PCNA appear to be functional homologues of the bacteriophage T4 proteins gp44/62 and gp45, and subassemblies of the E. coli pol III holoenzyme -y-complex and β-subunit, respectively (reviewed in ref. 2).
Differenzierung von Sommer- und Wintergersten und Gerstensortenbestimmung mit der Polymerase Chain Reaction (PCR)
Authors: Schuhbeck T , Vogeser G , Geiger E 
Published: November 2023

Abstract
Many barley varieties, especially winter barleys, are of only limited suitability for brewing. This causes production problems with mixtures of varieties. Therefore batches of pure varieties, free of winter barley, are required. Distinguishing DNA by the Polymerase Chain Reaction (PCR) was investigated for the monitoring of varietal purity.
Nachweis von Fusarium graminearum und Fusarium culmorum unter Verwendung einer sektionsspezifischen Polymerase-kettenreaktion
Authors: Leiβner Christian E W , Niessen Martin L , Vogel Rudi F 
Published: November 2023

Abstract
Fusarium graminearum, F. culmorum, F. avenaceum, and Microdochium nivale are the most serious funga.l contaminants found in cereal grain. F. graminearum and F. culmorum may produce mycotoxins and have been found to be closely linked to the induction of gushing in beer. A pair of PCR primers was designed to amplify a 288 bp fragment from the DNA isolated from fusaria of the Discolor section. This PCR selectively detects F. graminearum and F. culmorum in sample material without being sensitive to other organisms present. The method described can be used in quality control in breweries and malt production.
Thermotolerant fungal glucanase in malting barley
Authors: Mannonen L , Ritala A , Nuutila A M , Kurten U , Aspegren K , Teeri T H , Aikasalo R , Kauppinen J Tammisola & V 
Published: November 2023

Abstract
Molecular breeding is becoming a useful breeding tool in improvement of plant raw material e.g. for more easy processing. The gene for fungal thermotolerant ß-glucanase was introduced into the malting barley variety Kymppi. The gene is regulated by barley e-amylase promoter and is therefore functional only during germination. First results indicate that the enzyme in transgenic seeds is active and thermotolerant. Its structure is different from the original protein but resembles the previously reported enzyme made by cultured barley cells. Further studies are currently underway. Risk assessment for cultivation of barley transformed with marker-gene was performed 1996 to give information of dispersal of transgenic pollen in field.
Evaluation de la qualité sanitaire de l’orge par le dosage de l’ergostérol
Authors: Clamagirand V , Boivin P 
Published: November 2023

Abstract
Les moisissures sont des micro-organismes infectant I’orge et pouvant entrainer des alterations qualitatives et sanitaires de celle-ci, particulterement par la syntitese de mycotoxines. Les rrtethodes couramment utilises pour estimer la contamination fongique sont le plus souvent non quantitatives et longues. L’ergosterol est un constituant spScifique des parois cellulaires des moisissures et son dosage sur orge a 6te effectu6 par HPLC-UV. Une relation entre la quantity d’ergosterol (de 3 ci 50 mg/kg) et celle de deoxynivalenol a 6te faite. Cette ntethode, tepStable et facile mettre en oeuvre, permet dtevaluer rapidement la qualite sanitaire de I’orge.
Image analysis as practical tool in barley-malt-beer chains
Authors: Laarhoven H P M van , Douma A C , Angelino S A G F 
Published: November 2023

Abstract
An automated image analysis system was evaluated for its potential in the rapid.assessment of purity and quality parameters of barley batches. The system performed purity analysis and thousand kernel weight determination successfully. For kernel size grading it was necessary to process data for each variety separately to obtain satisfactory results. Batch identification was also feasible for varietal indentity and region of growth. Elevator companies and maltsters may implement the system as a chain management tool for fast monitoring and improved control of their raw materials quality.
Hop-derived phytoestrogens in beer?
Authors: Keukeleire Denis De , Milligan Stuart R , Cooman Luc De , Heyerick Ame 
Published: November 2023

Abstract
Hops proved to be a rich source of phyto-oestrogens as established via a very sensitive and selective in vitro bioassay. Since hop-derived phyto-oestrogens may occur in beer, this could have significant health-related effects on consumers (e.g. protection against hormone-dependent cancers). The phyto-oestrogenic fraction of different hop varieties was obtained by selective solvent extraction, analysed by reversed phase gradient HPLC and identified via diode array UV and mass spectroscopic techniques. A procedure based on solid phase extraction of beer and subsequent HPLC analysis was developed to fingerprint beer phyto-oestrogens.
Expression systems
Authors: Grisshammer Reinhard , Kambach Christian , Tate Christopher G 
Published: November 2023

Abstract
The over-expression of DNA-binding proteins or their domains is essential for their purification, characterization and three-dimensional structure determination. Unfortunately, isolation of functional protein in quantities sufficient for crystallization trials or for NMR experiments is still not routine. In this chapter, we discuss two expression systems that have been used successfully to produce large amounts of soluble protein, namely Escherichia coli and the baculovirus expression system. Many proteins can be expressed in E. coli, although it is often necessary to optimize expression parameters to achieve successful production of a desired protein. Methionine-auxotroph strains allow the expression of seler10methioninyl protein which can be used for multi-wavelength anomalous diffraction techniques during structure determination. However, some proteins, such as the euka1yotic telomere binding protein, TRFI, cannot be produced in E coli for unknown reasons (T. de Lange and L. Fairall, personal communication). This protein was successfully expressed in insect cells (1), therefore, we will describe the baculovirus system in this chapter. Owing to space limitations, we will not consider yeast systems: the reader is referred to two excellent reviews containing detailed protocols (2, 3).
Gel electrophoresis and bending in cisplatin-modified linear DNA
Authors: Malinge Jean-Marc , Schwartz Annie , Leng Marc 
Published: November 2023

Abstract
Recent studies have shown that some natural DNA fragments are bent and that the bend can be deduced from the DNA electrophoretic mobility in polyacrylamide gels (1-4). Structural distortions are induced in DNA by the covalent binding of compounds such as mutagens, carcinogens or anti tumour drugs (5). The purpose of this chapter is to show the relations between electrophoretic mobility and some aspects of the structural distortions induced in linear DNA by the binding of the antitumour drug cisplatin (cis-diamminedichloroplatinum(ll)). This chapter comprises of four parts which deal, respectively, with: (i) gel electrophoresis in polyacrylamidegels; (ii) platination of oligonucleotides; (iii) ligation of the platinated oligonucleotides into multimers and their separation by gel electrophoresis;
Mapping histone positions in chromatin by protein-directed DNA crosslinking and cleavage
Authors: Travers Andrew 
Published: November 2023

Abstract
1 Introduction
The precise mapping of protein-binding sites on DNA can be facilitated by the covalent conjugation of an activatable reagent to a specific amino acid residue on the protein of interest. ln this procedure, the conjugated protein is first bound lo DNA and then the reagent is activated. Two general methods are currently used. The activated reagent can crosslink to DNA in van der Waals’ contact &lt;1nd thus sensitize the backbone to alkaline hydrolysis in the immediate vicinity of the crosslink.
Quantitative DNase I kinetics footprinting
Authors: Mollah A K M M , Brenowitz Michael 
Published: November 2023

Abstract
Nuclease protection or ‘footprinting assays’ have been extensively applied to the study of nucleoic acid-ligand interactions and nucleic acid structure. The principal virtue of foot printing is that it can precisely localize individual sites of ligand binding or tertiary contact on nucleic acid molecules. Nucleic acid molecules hundreds or thousands of nucleotides long can be analysed. By choosing any of a number of chemical or enzymatic nucleases, changes in different aspects of the nucleic acid structure Gill be visualized. Quantitative footprinting protocols can also provide individual site-specific characterization of the thermodynamics and kinetics of reactions involving nucleic acids. These protocols have&gt; been recently reviewed (1).
Molecular processing of DNA folding anoinalies in Escherichia coli
Authors: Leach David R F 
Published: November 2023

Abstract
For evolution to proceed, there must be a balance between genetic stability and rearrangement. Chromosomal arrangements that prove beneficial to an organism are expected to be maintained while retaining the potential to generate radically new organizations over an evolutionary time-scale. In order to maintain this balance, cells have evolved mechanisms to reduce the frequency of chromosomal rearrangements. An important threat to DNA stability comes from sequences that have the potential for unusual folding. Unusually folded DNAs also pose problems for DNA replication, which may be particularly critical for organisms where there is an evolutionary advantage associated with rapid cell duplication. In principle, these problems can be reduced by lowering the genomic content of foldable DNA, reducing its frequency of folding, unfolding it when it does fold, and destroying folded structures if all else fails. It should be remembered, in this context, that ‘random’ single-stranded DNA sequences will fold upon themselves, so the structures studied within non-random sequences may best be considered as extreme examples of what is possible. Studies of the effects on DNA instability of sequences with the potential to form unusual secondary structures in the bacterium Escherichia coli have revealed a number of interesting rearrangements, which may have general relevance to living cells. E. coli has also provided a simple experimental system where questions concerning the formation and processing of unusual secondary structures can be addressed in vivo. Finally, the detailed knowledge of E.coli genetics is being used to identify genes and proteins that process unusually folded DNA.
The ATM gene and stress response
Authors: Lavin Martin F , Khanna Kum Kum 
Published: November 2023

Abstract
Reactive oxygen intermediates (ROI) are generated as by-products of normal oxidative metabolism in the mitochondria and peroxisomes, and are associated with specific cell functions such as cell killing by cytotoxic T cells and natural killer (NK) cells (1, 2). While ROI can, in some cases, be utilized as part of a destructive mechanism (cell killing) there is increasing evidence that they also function as second messengers in signal transduction pathways (3, 4). Under normal conditions the potential damaging effects of the free radicals generated are neutralized by enzymes such as catalase, peroxidases, and superoxide dismutase (1). Perhaps more critical to cell survival are the damaging effects of ROI produced by exogenous agents such as ionizing radiation (5), hypoxia (6), and a variety of other compounds. ROI so produced can interact with cellular macromolecules in abstraction or addition reactions to generate additional radicals. These can either have direct effects, as in damage to DNA, or indirect effects, by initiating a cascade of reactions giving rise to membrane changes or damage (7).
Protein–protein interactions in papillomavirus replication
Authors: Mccance Dennis J 
Published: November 2023

Abstract
Certain members of the human papillomavirus genus are the etiological agents of lower genital tract cancers, in particular cervical cancer, and so an understanding of the protein-protein interactions involved in viral replication would be important if antiviral therapy were to become a reality. Viral DNA replication occurs in the upper half of stratified epithelium and this poses a problem for the virus. The viruses infect the basal epithelial cells and when these cells divide, one daughter cell moves up through the epithelium and undergoes terminal differentiation (Fig. 1A). This situation, if allowed to develop, will inhibit the ability of the virus to replicate, since differentiating cells will not contain the replicative machinery for DNA replication. Therefore papillomaviruses have acquired a strategy which involves stimulating cells into S-phase of the cell cycle where abundant replicative enzymes will be present. However, there is an important caveat to this scenario, that is, for viral DNA amplification to proceed, a certain level of keratinocyte differentiation is necessary for the switch from the early promoter to the late promoter and capsid protein production. Therefore the virus has the task of uncoupling S-phase progression from partial cell differentiation. In this chapter I will concentrate on what is known of the protein – protein interactions involved in the replication of HPV-16, but will refer to other HPV types in comparative terms or where little or nothing is known for this particular HPV type.