bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction
Authors: Singh Juswinder , Thornton Janet M 
Published: November 2023

Abstract
All things are made of atoms, and everything that living things do can be understood in terms of the jigglings and wigglings of atoms
Richard P. Feynman
The structure, function, and stability of a protein is dependent upon the interactions between its amino acid groups. Although proteins are simple polymers, they adopt complex three-dimensional folds, which are a consequence, in part, of the packing geometries adopted by the protein side chains. Since these twenty groups differ in their size, shape, and chemistry they vary in their packing arrangements with each other. Determining the types of packing geometry adopted by these pairs is crucial to understanding the nature of the forces which stabilize protein structures.
Nuclear organization of pre¬ mRNA splicing factors and substrates
Authors: huang Sui , Spector david l. 
Published: November 2023

Abstract
Pre-mRNA transcripts must be processed and transported to the cytoplasm where the mature mRNAs are translated into proteins. For most RNA polymerase II tran-scripts, this processing includes addition of a 7-methyl-guanosine cap structure at the 5’ end of the nascent RNA transcripts; hnRNP assembly; removal of non-coding intron regions and ligation of exons; 3’ end cleavage and polyadenylation; and the ex¬ change of hnRNP proteins for mRNP proteins. Splicing occurs in a multicomponent complex termed a spliceosome. Many of the detailed biochemical steps involved in the prc-mRNA splicing reaction have been extensively studied in vitro and are well understood (for reviews sec Chapters 3-8). However, the integration of the splicing reaction with other related cellular functions, such as transcription and RNA trans-port, is best studied in intact cells. The cellular approach to understanding the organization of nuclear function has lagged somewhat behind the in vitro approach. However, during the past few years, major inroads have been made toward our understanding of where in the nucleus pre-mRNA splicing occurs and how the organization of both splicing factors and substrates are interrelated to the transcrip¬ tional activity of the cell. In this chapter, the nuclear organization of both snRNP and non-snRNP RNA processing factors, as well as pre-mRNA substrates, arc examined. In addition, their organization throughout the cell cycle, and the relationship of their nuclear distribution to the transcriptional activity of the cell, are discussed.
Studying cell movements in vivo by time-lapse video microscopy
Authors: Thorogood Peter v. , Amanze dee 
Published: November 2023

Abstract
Cell movement plays an important role during embryonic development (1). Much of what is presently known about cell movement is based on the behaviour of cultured cells. Despite refinements of culture conditions, however, extrapolation from events in vitro to behaviour in the embryo is difficult. Direct observation of living cells in vivo, when this can be done, is clearly preferable. Naturally transparent tissues such as the cornea (2), nematode embryos (3) (Chapter 2) and teleost fish embryos (4) (Chapters 4 and 9) (Figure /) lend themselves particularly well to in vivo analyses of cell movement. Techniques such as Nomarski DIC (Chapter 8), confocal scanning microscopy, and the labelling of living cells with fluorescent dyes coupled with fluorescence microscopy (Chapter 9), have begun to give us a much better appreciation of how cells normally behave in vivo.
Culture of Avian Neural Crest Cells
Authors: Dupin Elisabeth , Arin Nicole M Le Dou 
Published: November 2023

Abstract
As the unique source of very diverse cell types in the adult (such as peripheral glial and neuronal cells, mesenchymal cells, melanocytes, and endocrine cells), the neural crest (NC) of the vertebrate embryo has been the subject of considerable research effort aimed at elucidating several basic embryological problems related to cell commitment and differentiation, and to the segregation of cell lineages during morphogenesis. Although NC derivatives and migration pathways of crest cells have been mapped with great precision in birds, much remains to be known about the mechanisms underlying cell determination and phenotypic diversification in NC development. Attempts to understand the molecular basis of these fundamental processes have led many laboratories to undertake in vitro experiments where the differentiation of defined populations of NC cells can be analysed in controlled environmental conditions.
DNA-protein interaction at high resolution
Authors: Luisi Ben 
Published: November 2023

Abstract
Forty years on since the elucidation of a fiber-diffraction model for double-stranded DNA, structural scrutiny of the molecule continues to provide insights into key biological processes. Over the course of the last decade, and, in particular, during the last few years, there has been an explosive growth in high resolution structure determinations of DNA, DNA-binding proteins, and their complexes. These studies have provided a wealth of detailed stereochemical information, revealing how the DNA molecule´s sequence is read and how its structure is manipulated. Surprisingly, the mechanical properties of DNA have been implicated in these recognition processes, and this realization has revitalized an interest in the structure of the molecule itself. Herein, some of the principal lessons about DNA structure and mechanics, and their bearing on protein-DNA interactions, will be described.
|Enzymes that supercoil DNA
Authors: Wang James C 
Published: November 2023

Abstract
Supercoiled DNA has been known for three decades. It became clear in the sixties that a double-stranded DNA ring with intact strands could be viewed as two multiply intertwined and topologically linked single-stranded rings (1, 2). The degree of topological linkage of the complementary strands in such a ring is specified by a quantity Lk termed the linking number. For discussions in this chapter, Lk for a DNA ring is defined as the minimal number of times one strand must be passed through a transient break in the other in order to unlink the two complementary strands in a right-handed, double-stranded DNA ring (see ref. 3 for alternative definitions of Lk).
|Recognition of DNA damage and repair
Authors: Sancar Aziz 
Published: November 2023

Abstract
DNA is a highly reactive molecule. In particular, the bases and the phosphodiester bond are modified at a genetically unacceptable rate by common cellular metabolites (1). External agents ranging from ultraviolet and ionizing radiation to polycyclic aromatic hydrocarbons and methylating agents add to the cellular burden of maintaining genetic integrity. In addition, mismatches and 1-3 nucleotide loops are produced during replication and recombination reactions. Although mismatches, strictly speaking, are not considered as DNA damage, physiologically they have some of the same consequences and biochemically they are processed by similar mechanisms (2) as DNA lesions. Both non-physiological DNA modifications and base mismatches occur with such a high frequency that these structures might be considered among the most common targets for high-specificity DNA binding proteins which do not rely on DNA sequence.
|Structure-recognition by DNA junction resolving enzymes
Authors: LILLEY David M J 
Published: November 2023

Abstract
The junction resolving enzymes are a widespread class of nucleases that are characterised by a selectivity for branched DNA. Their role lies in recombination and repair events, in the recognition and manipulation of branched DNA intermediates of various kinds. In general, such enzymes exhibit relatively little specificity for base sequence, but exquisite selectivity for DNA structure. This involves recognition of DNA structure on a relatively large scale, and understanding the mechanism of this aspect of molecular recognition provides a fascinating challenge.
Making nucleic acid probes
Authors: Alphey Luke , Parry Huw D 
Published: November 2023

Abstract
The ability to make specific labelled nucleic acid probes has been central to the rapid expansion of molecular biology. The methods are part of the basic repertoire of a molecular biology laboratory. Rather than attempting to detail all of the methods historically used to label nucleic acids, we describe easy, rapid, and reproducible protocols for routine work. In the following chapter we will describe a set of frequently used hybridization protocols that utilize probes labelled as we detail here.
Screening ‘A expression libraries with antibody and protein probes
Authors: Margolis Benjamin , Young Richard A 
Published: November 2023

Abstract
The λgtll vector-host system and related gene expression systems permit the isolation of specific recombinant DNA sequences by virtue of the antigenicity or activity of the expressed gene product. The expressed protein, or domain of the protein, can be detected by using antibodies or through binding to a specific substrate such as a DNA fragment or a polypeptide. The design of the λgtll,, λZAP, and λEXlox systems have been described in detail elsewhere (1-4). We describe here features of the recombinant DNA libraries and the antibody and the protein probes that are important for successful screening. We also describe our favourite screening protocols using antibody and protein probes.
Expression of foreign proteins in E. coli using plasmid vectors and purification of specific polyclonal antibodies
Authors: Williams Jim A , Langeland James A , Thalley Bruce S , Skeath, James B , Carroll Sean B 
Published: November 2023

Abstract
For several decades antibodies have been used to identify, localize, quantitate, and analyse proteins. Before the advent of gene cloning, only natural sources were available for the isolation of proteins to which antibodies were raised. Low protein yields and impurities often compromised the quality and quantity of antibodies that could be produced. In addition, the vast majority of proteins that play critical roles in regulating cellular processes were completely unknown. As powerful genetic approaches have been devised to isolate the genes involved in a vast array of biological processes in diverse organisms, most proteins are now first identified at the gene level. The analysis of the structure, expression, regulation, and function of proteins identified in this manner usually requires the production of specific antibodies that can be used to detect the protein in different cells, tissues, organisms, and other biological samples.
The baculovirus expression system
Authors: Gunvanti Patel , Jones Nicholas C 
Published: November 2023

Abstract
Detailed biochemical and structural analysis of proteins encoded by cloned mammalian genes requires efficient expression systems for their high level expression and purification. Although very many proteins have been successfully over-produced in bacteria, there are certain inherent disadvantages which often makes this approach unsuitable. Foreign proteins over-expressed in bacteria often accumulate as insoluble occlusion bodies which require harsh denaturing agents to purify the recombinant protein. In addition, proteins produced in bacteria are not post-translationally modified. Since in many cases protein modification is crucial to activity, their over-production and purification from bacteria will be of limited use in functional studies. This chapter describes the helper-independent baculovirus expression system which offers a convenient and efficient method of over-producing posttranslationally modified proteins in a eukaryotic cell and may therefore be the method of choice under many circumstances. This system takes advantage of unique features in the life cycle of baculoviruses, including the production of two classes of viral progeny, and the presence of the strong polyhedrin promoter which is non-essential both for viral replication and the production of infectious extracellular virus. We describe the key features of this expression system including the latest modifications which will facilitate the isolation of recombinant baculoviruses expressing foreign proteins. Descriptions of general DNA manipulations, protein analysis, tissue culture procedures, and handling of baculoviruses can be found in other laboratory manuals (1-5).
High efficiency gene transfer into mammalian cells
Authors: Chisholm Vanessa 
Published: November 2023

Abstract
Over the past decade, recombinant or hcterologous gene expression in mammalian cells has emerged as an essential tool for studying multiple aspects of cukaryotic biology. The development of highly efficient vector based gene transfcction methods has provided researchers with almost un limited possibilities for the use of engineered protein products derived from mammalian cell culture. What has become apparent is that highly individual ized scientific questions can be routinely addressed using a relatively distinct battery of these types of expression protocols. The choice of technique and how it can be effectively used depends primarily on the specific requirements of the experiment. An extensive series of expression vector designs have been developed. Some arc more suited to introducing and analysing gene products transiently while others are better for the stable and continued expression of heterologous DNA in cells. Vectors have been constructed to exploit certain cell types. Likewise, transfection methodscan becategorized into those more effect ive for short-term expression analysis and those more suited to select stably expressing cell lines. The identification of recombinant products has evolved from time-consuming radioactive assays to more straightforwardimmunoassays and luminescent techniques. What may appear to be a most formidable field of players to choose from is best approached by becoming familiar with the basic characteristics essential for the efficient transfer and subsequent expression of genes in mammalian cells. In general terms these include:
Construction and characterization of vaccinia virus recombinants
Authors: Mackett Mike 
Published: November 2023

Abstract
The use of cowpox to vaccinate against smallpox was popularized by Jenner at the end of the 18th century and ultimately led to the eradication of smallpox. Although cowpox was used as a vaccine for a short period, the closely related poxvirus vaccinia has been in use for this purpose since the 1850s. Cowpox and vaccinia virus have played an important role in the history of human medicine since they represent the first widely used human vaccine and the only vaccine whose use has resulted in the eradication of a human disease. Surprisingly, interest in poxviruscs in general, and in vaccinia virus in particular, increased substantially after the disappearance of smallpox. This interest has arisen largely from the development of vaccinia virus as an expression vector with the potential use of vaccinia virus recombinants as live vaccines against pathogens other than the smallpox virus.
Chromosome-specific gridded cosmid libraries: construction, handling, and use in parallel and integrated mapping
Authors: Nizetic Dean , Lehrach Hans 
Published: November 2023

Abstract
The analysis of the information in human genomic DNA is based on the cloning and molecular characterization of the genes together with the genetic analysis of the phenotypes a-;sociated with the genetic loci under study. Libraries of cloned genomic DNA serve as essential intermediates to relate the information from the genetic analysis of phenotypic variation to the molecular analysis of the genes (I). Such libraries, can be either constructed in a yeast or bacterial vector-host system. The yeast system. using yeast artificial chromosomes (YACs) (2) as vectors, is well suited for rapid coverage of long genomic regions and entire chromosomes (3) (see also Chapter 4). This offers easier integration of the data with the genetic and physical maps of the genomic DNA, for example in the comparison of the maps of cloned DNA to long-range restriction maps of genomic DNA constructed using restriction endonucleases that cut at infrequent intervals. The yeast system is however not the best choice for the application of methods to identify transcribed regions (genes), to analyse the transcription unit and exon-intron organization, and to obtain the sequence of the genes. The longer the YAC clones arc, the more frequently they suffer from deletions, rearrangements, co-cloning, and chimerism, which makes the establishment of a highresolution map difficult. Moreover, irrespective of the YAC length, the isolation of pure YAC DNA from the genomic DNA of the host is difficult to achieve in most cases (sec Chapter 4 for a discussion of these problems). The bacterial (E. coli)-based vector systems (phage, cosmid, Pl, F-) (4-6) are much more suitable for the characterization of transcribed sequences (7-10), to study the molecular organization of the genes (11), and to provide material for DNA sequencing. The isolation of the cloned DNA in a pure state, free from the DNA of the host, is much more straightforward. Cosmid libraries are probably the simplest to use. They can be constructed with very high efficiency, allowing libraries to be made from limited amounts of DNA, and have been in use for longer than the Pl, PAC, and other new bacterial vector systems.
Amplification of DNA microdissected from mitotic and polytene chromosomes
Authors: Saunders Robert D C 
Published: November 2023

Abstract
Techniques permitting access to defined chromosomal regions are invaluable for the analysis of complex genomes. Microcloning is one such technique, which is particularly powerful when applied to dipteran polytene chromosomes. Microcloning was first described by Scalenghe et al. (1), who microdissected approximately JOO kb from the white region of the Drosophila melanogaster X chromosome, and recovered DNA fragments cloned in a phage lambda insertion vector, essentially by conventional cloning methods in miniature. Despite the obvious technical problems in transferring this technique to the study of mitotic chromosomes, microcloning has been applied to the analysis of specific chromosome regions of a variety of organisms.
Long-range restriction mapping
Authors: Bickmore Wendy 
Published: November 2023

Abstract
Mapping large and complex genomes relies on techniques that permit the analysis and manipulation of long stretches of DNA, hundreds to thousands of kilobases in length. This has been achieved largely through the developments of pulsed field gel electrophoresis (PFGE)-allowing the resolution of large DNA fragments, and yeast artificial chromosome vectors (YACs) for cloning large DNA fragments. Being able to resolve very large fragments of DNA also necessitates being able to restrict DNA into suitably long length . This can be accomplished with restriction enzymes with large, and therefore rare recognition sequences. In vertebrates, large restriction fragments can also be generated using restriction enzymes with CpG dinucleotides in their recognition sequences (this also applies to plant DNAs and includes enzymes with CpXpGs in their recognition sites). The principle cleavage sites for CpG recognizing enzymes in vertebrate genomic DNA, as well as providing convenient landmarks for the construction of long-range restriction maps, also mark out the position of many of the genes-critically important in organism where only a few per cent of the DNA has a coding capacity. This chapter aims to demonstrate how to create and interpret long-range restriction maps. primarily, of mammalian genomes.
Studies of cellular energetics using 31P Nmr
Authors: Brindle Kevin M , Fulton Alexandra M , Simon-peter Williams 
Published: November 2023

Abstract
Nuclear magnetic resonance (NMR) has become an established technique for the non-invasive study of metabolism in systems ranging from microbial cells to the human brain. It is a tremendously versatile technique in terms of the nuclei that can be monitored and thus the type of problems that can be addressed. For example flux of material in a metabolic pathway can be monitored by feeding the system a C-labelled substrate and then monitoring the subsequent isotope redistribution using C NMR (1). Ion fluxes and gradients can be monitored using Na and K NMR or by using Rb NMR in studies where Rb+ is used as a replacement for K+ (2). The intracellular concentrations of cations such as Ca2+ and Mg2+ can be monitored using 19F NMR in tissues which have been loaded with fluorine labelled chelating agents which bind these ions (3).H NMR can be used to monitor the levels of a variety of cellular metabolites and, in imaging studies, to determine the spatial distribution of water and hence the structure of the system under study. Although all these nuclei can be used to a greater or lesser extent to study cellular bioenergetics we will restrict our discussion here to the nucleus which has made the greatest contribution in this area, the naturally abundant isotope of phosphorus, P.
Physical mapping: YACs, BACs, cosmids, and nucleotide sequences
Authors: Bancroft Ian 
Published: November 2023

Abstract
The most detailed description of a genome is its nucleotide sequence, which represents a complete genetic blueprint. Within a short time of writing, the complete nucleotide sequence of the genome of Arabidopsis will have been determined and will become a key resource for plant scientists studying processes in Arabidopsis and many other plants. We discuss the systematic approaches that have been used to generate Arabidopsis nucleotide sequences and the opportunities that the sequence data offer for mapping.
Web-based bioinformatic tools for Arabidopsis researchers
Authors: Rhee Seung Y , Flanders David J 
Published: November 2023

Abstract
The introduction briefly defines the term ‘bioinformatics’ and describes sources of bio-informatic data. The body of the chapter is divided into four sections, followed by a short glossary: (a) How to get connected to the Internet and how to use Web browsers. (b) A flowchart describing an experimental scenario that uses bio-informatic tools.
Determination of the cell proliferative fraction in human tumours
Authors: Silvestrini Rosella , Daidone Maria Grazia , Costa Aurora 
Published: November 2023

Abstract
During the last two decades, increasing effort has been made to obtain as much information as possible on the cell proliferative fraction of individual clinical tumours in order to increase the knowledge on tumour biology and to provide clinicians with data on consecutive series of patients. As a consequence, an impressive number of reports has supported the relevance of cell kinetics as a tool to investigate growth pattern, biological heterogeneity and clinical progression of human tumours (1-4).