bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linker scanning mutagenesis
Authors: Luckow Bruno , Schütz Günther 
Published: November 2023

Abstract
Techniques for in vitro mutagenesis of DNA play a major role in molecular biology. They are powerful tools in dissecting the relationship between structure and function of a given gene. A typical analysis of gene function proceeds in several steps with an increasing degree of resolution. Deletion mutations are usually analysed first; once a functionally important region has been delimited by deletion mapping, this site can be characterized in more detail by linker scanning mutagenesis and by single point mutations introduced by methods described elsewhere in this book. In linker scanning (LS) mutations a short segment of the DNA of interest is replaced by a new synthetic sequence without inserting or deleting base-pairs, thereby introducing a cluster of point mutations at the replacement site. Generation of a series of mutations in which the replacement site is systematically moved, allows scanning of the DNA of interest to identify regions which are critical for the activity of a gene product or in regulating gene expression. LS mutations give a relatively high degree of resolution, while the number of mutations required to perform a systematic analysis of a region of interest is reduced, compared to single base substitutions. In contrast to deletions, LS mutations do not alter the original distances between different DNA sequences. This makes the unequivocal interpretation of experimental results much easier.
Design of Crystallization Experiments And Protocols
Authors: Carter C W 
Published: November 2023

Abstract
Despite the fact that most pure proteins should be expected to crystallize readily under some set of conditiom, that ‘winning combination’ of solution conditions may be rather hard to find a priori. Often, there is little apparent connection between the degree to which proper protocols are observed and the degree to which satisfactory results are obtained. For this reason one should assume the worst at the outset for any new macromolecule or intermolecular complex, and try to identify potentially important factors by setting up efficient screening trials. The best all-round experiments for this purpose are factorial designs used by several generations of industrial chemists (1-3). Factorial experiments have been applied explicitly to the problem of protein crystallization (4-11). They serve not only to screen conditions, but also to provide information simultaneously about the effects of a number of different possible ‘factors’. Factorial experiments are the statistician’s answer to the ‘needle-in-the-haystack’ problem in any of its many guise . The less one knows about the behaviour of a system, the harder it will be to find an optimum combination, and the more important it is to think carefully about the experiments to use in order to characterize it. This reasoning is especially relevant to the crystallization of a new macro molecule.
Crystallization of Membrane Proteins
Authors: Relss-Husson F 
Published: November 2023

Abstract
Crytallization of integral membrane proteins is one of the most recent developments in protein crystal growth: in 1980, for the first time, two membrane proteins were successfully crystallized, bacteriorhodopsin (1) and porin (2). Since then, a number of membrane proteins (about 20) yielded three-dimensional crystals. In a few cases, the quality of the crystals was sufficient for X-ray diffraction studies. The first atomic structure of a membrane protein, a photosynthetic bacterial reaction centre, was described in 1985 (3), followed by closely-related structures of reaction centres from other bacterial pecies (4-6). The structure of porin was recently determined (7). Crystallization of membrane proteins is now a very actively growing field, and has been discussed in several reviews (8, 9).
Soaking of Crystals
Authors: Stura E A , Chen P 
Published: November 2023

Abstract
Once crystals of a macromolecule are obtained there are many circumstances where it is necessary to change the environment in which the macromolecule is bathed. By changing the environment of the cry tab it is possible to bind inhibitors, activators, substrate , products, and heavy atoms to the macro molecule, which may have sufficient freedom to undergo some conformational changes in response to these effectors. In fact, macromolecular crystals typically have a high solvent content which ranges from 27-95% (I, 2). Part of this solvent (typically 10%) is tightly associated with the protein matrix as ‘bound solvent’ (3), which occupies well-defined positions in refined crystal structures and can be considered to be a hydration shell around the protein. This shell consists of both water molecules and other ions present In the solution. The remaining solvent is free to diffuse within the macromolecular reticulum and can be replaced.
Shape and scaling
Authors: Swartz Sharon M , Biewener Andrew A 
Published: November 2023

Abstract
Size influences virtually every facet of an organism’s biology, including its biomechanical function. Changes in body size occur during growth (ontogeny), as well as during evolution and may range from tenfold to 100-fold during the growth of an individual to as much as one-thousand-fold to one-million-fold (depending on the breadth of taxa considered) during the evolution of a lineage. Frequently, such large differences in body size require that the shapes of structural components of the organism change to maintain their functional integrity. Analysis of the shape of biological structures, therefore, provides an important empirical approach for identifying and interpreting mechanical constraints underlying the form and function of skeletal support systems. Before discussing practical aspects of methodology in the analysis of shape, we discuss both conceptual and statistical issues related to scaling analyses of shape.
Force platform and kinematic analysis
Authors: Btewener Andrew a. , Full rorert j. 
Published: November 2023

Abstract
Animals exert forces to move objects in their environment and to move themselves from place to place. Body segment motion, in turn, produces inertial forces that must also be countered by the muscles controlling motion at related joints. Kinetics involves the study of the forces acting on rigid bodies. Kinematics is the study of the motions produced by those forces. Linking the two analyses together, provides a powerful non-invasive approach for studying the hiomechanics of animal locomotion, and motor activity in general. For instance, measurements of the forces applied externally to an animal’s body (such as ground reaction forces exerted on an animal’s limbs when it runs), coupled with kinematic and anatomical data of the limb, allows an analysis of the internal forces that limb muscles must produce to counter externally applied forces. The data obtained from such studies are fundamental to our understanding of how the design of muscu\oske\ctal structures is related to the physical demands placed upon them during various functional activities of the animal in question. In addition, kinematic analysis alone can provide estimates of the inertial loads associated with body segment motion that must be controlled by musdes. Such analyses are particularly important in relation to studies of nervous system control of motor function.
Mechanical work in terrestrial locomotion
Authors: Blickiian R , Full Robert J 
Published: November 2023

Abstract
The amount of metabolic energy required to travel a given distance by an animal using legged, terrestrial locomotion exceeds the costs of swimming by a factor of more than eight and of flying by more than a factor of four (I). Since terrestrial locomotion is expensive, it is reasonable to assume that the relatively high metabolic power input should generate a considerable, and therefore easily measurable, amount of mechanical power output. Surprisingly, a simple and direct link between metabolic and mechanical power during terrestrial locomotion has proved to be elusive (2). Fortunately, the challenge of investigating the link has been rewarding because these studies have and will continue to increase our knowledge of musculoskeletal function for all modes of locomotion.
Assays of cell adhesion
Authors: Hoffman S 
Published: November 2023

Abstract
Classic embryological studies suggested that cell adhesion along with cell migration, cell proliferation, cell death, and differentiation are the primary cellular processes of development. Later studies demonstrated that cells pre pared from embryonic tissues would reaggregate in a relatively tissue-specific manner, but little was known about the molecular mechanisms involved. The study of cell adhesion became a prominent topic in modern cell biological research in the 1970s and 1980s with the identification of specific adhesion molecules. It then became possible to study and compare the functions, distributions, and structures of these molecules (1-5).
The Xenopus oocyte cell-cell channel assay for functional analysis of gap junction proteins
Authors: Dahl Gerhard 
Published: November 2023

Abstract
The paired Xenopus oocyte expression system was originally designed as a functional assay to identify mRNAs involved in the formation of intercellular channels, the functional units of the gap junction (4). Subsequently, the paired oocyte assay was used to demonstrate that the expression of a single exogenous gene, rat connexin32, could induce intercellular communication (3). Thus, a functional criterion for the identity of a gap junction or cell-cell channel-forming protein was established. More recently, a number of genes encoding proteins highly related to connexin32 have been cloned (1). This proliferation of potential gap junction proteins has increased the utility of functional expression systems designed to examine cell-cell channels.
Compartmented culture analysis of nerve growth
Authors: Campenot Robert B 
Published: November 2023

Abstract
The compartmented culture was initially designed as a model system to study the formation and maintenance of neuronal projections. In compartmented cultures, axons (neurites) originating from neurones plated in a proximal compartment grow across a silicone grease barrier and enter into a separate fluid environment within a distal compartment, analogous to axons from neuronal cell bodies in one location in the nervous system projecting their axons through nerves or tracts to targets in another location (Figure 1). The first experimental use of the system was to show that axons of sympathetic neurones will enter into and grow within a distal compartment only if it is supplied with nerve growth factor (NGF) (1). Among the important principles established by this work is that NGF promotes growth of the neurite at its site of application to the neurite and not elsewhere, which is exactly what would be expected of a factor whose function is to direct nerve growth to or within a target location. Thus, NGF locally produced in vivo within the target tissue (and by Schwann cells and fibroblasts in the nerve after injury) would be expected to locally promote nerve growth (and regeneration). Work with compartmented cultures indicates that the immediate mechanisms by which NGF promotes growth are localized to the site of growth and do not involve the cell body or gene expression.
Crossed and hierarchical analysis of variance
Authors: Iles Terence c. 
Published: November 2023

Abstract
This chapter describes the analysis of experiments where measurements are made of the response to several factors, extending the one-way ANOVA where just one factor is investigated. Experiments where the response is measured at all combinations of levels of several factors are called factorial experiments. The value of such experiments is in the opportunity of assessing the interrelationships or interactions between factors; it is possible that the response to one factor may differ according to the levels of a second factor. Also, a single well-designed factorial experiment is usually more efficient than a series of single-factor experiments. Texts that describe details of the analysis of variance of factorial experiments for non-mathematicians are Winer (1) and Sokar and Rolf (2). Further information, though in a more mathematical style, can be found in Miller (3) and Milliken and Johnson (4).
Atlas Protein Interact V 1 C
Authors: Singh Juswinder , Thornton Janet M 
Published: November 2023

Abstract
Amino acid side-chain packing arrangements are of major concern to any scientist interested in modelling protein interactions, including protein engineers, drug designers, molecular modellers, and crystallographers. Despite their important role in protein structure and function, no guide yet exists which describes and analyses the different packing geometries.
These two volumes provide a unique and comprehensive reference to the 400 possible types of amino acid side-chain interactions observed in proteins of known three-dimensional structure. Each type of interaction has been substantially analysed to provide valuable data relating to its favourability and stability. The data is presented both statistically as histograms and in the form of stereo plots, providing an invaluable source of information on the nature of the forces which hold proteins together.
Cellular Interactions in Development
Authors: Hartley David A 
Published: November 2023

Abstract
As progress in cell developmental biology carries on at a breakneck speed, new techniques constantly arise to plug the gaps left by traditional strategies. Cellular Interactions in Development provides detailed discussion and protocols of some of these new techniques, which allow the manipulation of developing organisms such as Drosophila or plants, when and where cells interact with each other to influence their development. The book looks at the really exciting innovations of the identification and functional test of molecules which control these cellular behaviours. The book also describes a number of new ways of hunting for these important proteins involved in cellular communication. A fully comprehensive manual which will prove indispensable to researchers in the fields of cell, developmental, and molecular biology.
Clonal analysis in plants
Authors: Dudley Mark , Poethig R Scott 
Published: November 2023

Abstract
Little is known about the nature of cell-cell interactions in plants as many of the most useful methods for studying this problem are difficult, if not impossible, to employ in plants. One of the most significant technical problems is the tendency of plant cells and tissues to dedifferentiate in new environments. As a result, methods that are routinely used to examine cellular interactions in many other systems, such as tissue grafts, cell mixing experiments, or microsurgical manipulations, are not generally useful for studying cellular interactions in plants (although they have been used to study interactions between tissues or organs). In order to study the cellular interactions that regulate cellular and multicellular patterns of cellular differentiation, these interactions must be studied in situ, with a minimum of experimental manipula tion. The ability to juxtapose cells with different developmental potentials in genetic mosaics is one of the few methods by which this can be achieved in plants.
Cloning cell surface molecules by transient expression in mammalian cells
Authors: Simmons David L 
Published: November 2023

Abstract
Since the mid 1980s, there has been a rapid increase in our knowledge about the specific cell surface molecules mediating cell-cell interactions and adhesion events. This has been largely due to the success of molecular cloning techniques, allowing the isolation of functional cDNA clones, encoding these glycoproteins.
There are a number of approaches that can be adopted for cloning cDNAs but one technique in particular, developed by Aruffo and Seed in 1987 (1-3), has been central to this enterprise. It is based on the transient expression of cDNA libraries in mammalian cells and the rescue of specific cDNA clones by antibody capture and panning. The efficacy of this procedure has transformed the field of clone isolation to such an extent that once a suitable antibody or ligand or cell line has been identified which recognizes a cell surface molecule, molecular cloning the cDNA encoding it is now an essentially trivial process.
Purifying and assaying mesoderm-inducing factors from vertebrate embryos
Authors: Smith Jim c. 
Published: November 2023

Abstract
The first cell-cell interaction in amphibian development is mesoderm induction, when a signal from the vegetal hemisphere of the embryo induces overlying equatorial cells to form mesoderm rather than ectoderm (see Figure 1). The last five years have seen a great increase in our understanding of mesoderm induction, largely due to the discovery of several ‘mesoderm-inducing factors’-molecules which induce prospective ectodermal tissue of the amphibian embryo to differentiate as a variety of mesodermal cell types such as muscle, notochord, mesenchyme, and mesothelium. Most of these inducing factors are members of the transforming growth factor type (TGF ) or fibroblast growth factor (FGF) families (1), and one of the most potent, activin, has been shown to induce expression of mesoderm-specific genes, or of mesodermal cell behaviour, in mouse (2), bird (3), and fish (4), as well as amphibian embryos. This indicates that mesoderm induction occurs in all vertebrates and the process is thus of considerable interest and importance.
S phase and its regulation
Authors: blow J Julian 
Published: November 2023

Abstract
During S phase of the eukaryotic cell cycle, chromosomal DNA is replicated precisely once as a prelude to its segregation to the daughter cells at mitosis. Replication is achieved by between 103 and 105 pairs of replication forks initiating at sites scattered throughout the genome, the number varying with the size of the genome and the length of S phase. These initiation events must be carefully regulated in at least three different ways. First, since most cells do not arrest in the G2 phase of the cycle, it is important that entry into S phase only occurs in cells that are legitimately committed to undergoing the complete cell division cycle. Second, it is important that initiation is coordinated with other cell cycle events so that the ploidy of the cell is maintained by the alternation of S and M phases. Third, it is important to regulate initiation events within each S phase, so that all the chromosomal DNA is completely replicated but no DNA is replicated more than once.
Nematode embryos
Authors: Edgar Lois G , Wood William B 
Published: November 2023

Abstract
The free-living soil nematode Caenorhabditis elegans has many advantages for investigation of development and physiology in a simple animal. Its three- day life cycle, simple growth requirements, hermaphroditic mode of development, and indefinite survival at liquid nitrogen temperature are superbly suited to genetic analysis. Moreover, its transparency throughout the life cycle, small size, simple anatomy, and invariant cell lineage have made possible detailed descriptions of normal and mutant development at the level of individual cells (reviewed in ref. 1). This chapter describes methods for handling and cultivating this nematode and for collecting and studying its embryos.
Embryos and larvae of invertebrate deuterostomes
Authors: Holland Nicholas d. , Holland Linda Z 
Published: November 2023

Abstract
The recent information explosion on pattern-determining genes has reawakened interest in the nature of segmentation, the universality of developmental mechanisms, the phylogenetic relations between animal phyla, and the origin of the vertebrates in particular. Much insight can be expected to come from developmental studies of invertebrate deuterostomes: a group which includes the closest relatives of the vertebrates. All invertebrate deuterostomes are marine, and they comprise (discounting the enigmatic arrow worms) echinoderms, hemichordates, tunicate chordates, and acraniate chordates.
Avian embryos
Authors: Stern Claudio d. 
Published: November 2023

Abstract
The avian embryo offers a very accessible system in which molecular studies can be combined with ‘classical’ embryology. Transplantation, cell labelling, immunocytochemistry, and chemical treatments can be combined with in situ hybridization and Northern analysis to study changes in gene expression after experimental manipulations. Moreover, with new techniques for producing transgenic birds now becoming available, the developmental effects of targeted mutations can be studied in cellular as well as molecular detail.
Transplantation in Avian Embryos
Authors: Stern Claudio D 
Published: November 2023

Abstract
This chapter briefly introduces two techniques for microsurgery. In the first, embryos are operated whilst in modified New culture (Chapter 6, Protocol 3). This is suitable for operations on embryos of up to 1 day’s incubation, and embryos can be cultured for up to 36 h. As an example, an operation in which the anterior tip of the primitive streak (Hensen’s node, the organizer of the amniote embryo) is grafted into an ectopic site in a host embryo is described (see ref. 1). The second technique is for operations in ovo, through a window in the shell, suitable for embryos of 1-3 days’ incubation. The example given is that of a graft of segmental plate (see ref. 2). With some care and a few precautions, embryos operated in this way can be grown to hatching. Older embryos can be operated as described in Chapter 13. A histochemical method for revealing the quail nucleolar marker in chimaeras is also given (adapted from ref. 3).
Immunocytochemistry of embryonic material
Authors: Stern Claudio d. 
Published: November 2023

Abstract
The localization and characterization of protein and carbohydrate molecules in embryos is an essential part of any study on the molecular bases of developmental processes. Methods for immunocytochemistry and for the characterization of antigens are in wide use and well established, and have been reviewed extensively elsewhere (1, 2). Embryonic material, particularly at early stages of development, presents special problems. First of all, it is sometimes difficult to find the correct compromise between antigen preservation, sensitivity of the method of localization, and good structural preservation. Second, when characterizing the antigen(s), it is sometimes difficult to obtain sufficiently large amounts of antigen for detection by conventional immunoblots (Western blots). The following small set of protocols work particularly well for the localization of embryonic antigens in tissue sections at the light microscope level and in whole mounts. A simple, reliable, and sensitive method for the characterization of antigens from small amounts of embryonic material is also included.
Oligosaccharides
Authors: Kennedy John F , Pagliuca Giampiero 
Published: November 2023

Abstract
Oligosaccharides are traditionally defined as polymers of monosaccharides containing from two to ten residues. However, since the naturally occurring polysaccharides rarely contain less than 25-30 residues, it is possible to consider the range of polymers having between two and about 20-25 residues as oligosaccharides, particularly when considering the analytical methods involved. As oligosaccharides fall into the classification between mono saccharides and polysaccharides it is not surprising that the methods used for oligosaccharide analysis are extensions of those used for either mono saccharide or polysaccharide analysis. This chapter uses a slightly different format to that of Chapter 1 in order to give the maximum information, within the limitations of available space, on the modifications which have to be made in adapting the methods described in detail for the analysis of mono saccharides and polysaccharides. Rather than repeat descriptions of practical details etc. this chapter concentrates on the types of methods which can be applied and their relative merits and shortcomings.