bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vervet monkey (Green monkey or grivet)
Authors: Kirkwood James K , Stathatos Katherine 
Published: November 2023

Abstract
The species is common and widely distributed in Africa south of the Sahara, and 21 subspecies have been recognized (Hall and Gartlan 1965; Gartlan 1969; Wolfheim 1983). It is a highly adaptable terrestrial or semi-terrestrial species (Mitchell 1979a; Rowell, 1984), found in savanna, woodland edges, rain forests, and urban parks (Bloomstrand and Maple 1987), and typically around riverine acacia trees (Rowell 1984). It does not occur in closed forests and arid areas (Gartlan 1969). It is also found on the West Indian islands of St. Kitts and Barbados to which it was introduced in the eighteenth century (Poirier 1972; Horrocks 1986). In the past, these animals were quite widely used in biomedical research (Rowell 1970). A total of 21 779 were exported to the United States between 1968 and 1973, and 11 232 were exported to the United Kingdom between 1965 and 1975 (Wolfheim 1983). They are not recorded as important biomedical research species now (Johnsen and Whitehair 1986). Zoo populations appear to be small. According to the ISIS records of 30 June 1986, there were 59 C. aethiops of various subspecies held in captivity in zoos in the United States (Bloomstrand and Maple 1987).
Rhesus macaque
Authors: Kirkwood James K , Stathatos Katherine 
Published: November 2023

Abstract
The rhesus monkey has a larger geographical distribution than almost any other primate (Smith et al. 1987). Its range extends from India and Afghanistan in the west to China and Vietnam in the east (Roonwal and Mohnot 1977). It is not listed in the IUCN red data book (IUCN 1990). In India the population is reduced but still common in the north (Southwick and Lindburg 1986). This species is widely used in biomedical research and Johnsen and Whitehair (1986) estimated that in 1984 the number of actual and potential breeding individuals at principal US research institutions was 24 934 and that the number of live births was 5582 (compared to 991 in 1973). The zoo population by comparison is small (Flesness 1986).
Stump-tailed macaque
Authors: Kirkwood James K , Stathatos Katherine 
Published: November 2023

Abstract
The range of M. arctoides extends from eastern Bangladesh eastwards through southern China and into the Malayan peninsula and Vietnam. It is declining, or has become rare in India, Thailand, and Malaysia but its status elsewhere in its range is unknown (Wolfheim 1983). It is not classified as threatened by the IUCN (1990).
NMR Resonance Assignments
Authors: Pease Joseph H B , Wemmer David E 
Published: November 2023

Abstract
3.1 Introduction
NMR (see Glossary) spectra contain information about the structure of a molecule through the chemical shift (which is sensitive to the local electronic environment), spin-spin coupling constants (which are sensitive to dihedral angles), and through relaxation [nuclear Overhauser effect (NOE)], which is sensitive to the positions of nearby spins (see Glossary for definitions of chemical shift and NOE). However, before any of this information can be put to use in determining the structure of a molecule (see Chapter 2), it must first be determined which resonances come from which spins. The process of associating specific spins in the molecule with specific resonances is called the sequence-specific assignment of resonances. For many years this was the major hurdle in interpretation of NMR data for biological molecules. However, over the past decade tremendous progress has been made through the introduction of multidimensional NMR experiments and through advances in spectrometer hardware. These improvements were combined with development of a systematic approach for analysis of the spectra, to make an efficient algorithm for obtaining assignments.
Modelling of related protein structures
Authors: Thornton Janet M , Swindells Mark B 
Published: November 2023

Abstract
4.1 Introduction
Understanding protein function requires detailed structural analysis of atomic resolution data-which can be determined by X-ray crystallography (see Chapter 1) and NMR spectroscopy (Chapter 2). However, these methods are often slow and dependent on numerous factors for their success. For example, a crystallographic determination depends on the ability to grow well-ordered crystals, whereas NMR spectroscopy is only applicable to smaller proteins of up to 200 residues. In the absence of such definitive information a structure may often be predicted by detecting similarities between the new sequence and previously solved structures. Predictions that use related proteins of known structure are usually referred to as model-building strategies, the principles of which will be discussed in this chapter.
With the rapid growth of sequence databases, model building is now the subject of numerous investigations. There are currently more than 25 000 sequences available in the OWL composite sequence database (Bleasby and Wootton 1990), many of which can be clustered into homologous families. If at least one structure within a family is available, modelling the others becomes a realistic possibility. The subsequent design of mutagenesis experiments can benefit substantially from the models produced by these procedures.
The structure of the ‘universal’ genetic code
Authors: Osawa Syozo 
Published: November 2023

Abstract
The genetic code is written as a set of all 64 possible arrangements of the four RNA nucleotides-U, C, A, and G-in the form of a triplet (codon) (see Table 1.1). Each of 61 codons is assigned to a specific amino acid; the other three are stop codons that terminate the protein synthesis and do not correspond to any amino acid. As the number of amino acids used for protein synthesis is 20, the same amino acid can be coded for by more than one codon, i.e. the code is degenerate. For example, AAA and AAG are codons for Lys; GUG, GUC, GUA, and GUG are codons for Val. Further, six codons-CGU, CGC, CGA, CGG, AGA, and AGG-are synonymous, and are translated to Arg. A box in which four codons are synonymous is called ‘family box’ or a ‘4-codon box’; there are eight family boxes. A set in which a single amino acid has two codons is called ‘2-codon set’ (see Table 1.1). Of the 13 2-codon sets, seven end with pyrimidine (Y: U or C) and six with purine (R: A or G). Codons for Arg, Leu, and Ser exist both in a family box and in a 2-codon set. There are exceptions: three codons-AUU, AUC, and AUA-are assigned to Ile (2-codon set plus 1, or family box minus 1). Met or Trp has only a single codon-AUG or UGG because codon AUA is for Ile and UGA is a stop codon. There are therefore two to six synonymous codons for a single amino acid, except for Met and Trp.
Activation and Reduction of Carbon Dioxide to Formylmethanofuran - a Unique Method of Carbon Dioxide Fixation in the Archaebacteria(archaea)
Authors: Wasserfallen Alain , Wolfe Ralph S 
Published: November 2023

Abstract
Methanogens constitute a taxonomic group of strict anaerobes characterized by their ability to generate methane from the oxidation of molecular hydrogen and the reduction of carbon dioxide or the metabolism of other simple compounds such as formate, acetate, methanol, methylamines (Jones et al. 1987). Methanogenic organisms are currently grouped into three orders (Methanobacteriales, Methanococcales, Methanomicrobiales) in what is now referred to as the domain of archaea (Woese et al. 1990). Methanogens grow in environments where the redox potential is lower than -330 mV (Smith and Hungate 1958) and have been found in nearly every anaerobic habitat. Various methanogens have been found to use the same pathway of carbon dioxide fixation (Jones et al. 1985). As shown in Fig. 10.1 the oxidation of hydrogen and reduction of carbon dioxide to methane is a thermodynamically favourable reaction. Methanogenesis from this reaction readily takes place in nature (i.e. in sediments or the rumen) where the partial pressure of hydrogen may be quite low (10-4 atm). The C1 intermediates at the formyl, formaldehyde, and methyl levels of oxidation are coenzyme bound, and are not detectable as free compounds.
How Enzymes Deal with Carbon Dioxide and Bicarbonate
Authors: O’Leary Marion H 
Published: November 2023

Abstract
Carbon dioxide is a key metabolite in living systems. Thermodynamically, it lies in a deep valley. Formation of carbon dioxide is the ultimate exothermic step in a variety of energy-producing metabolic processes. Absorption of carbon dioxide by green plants is a key endothermic step in photosynthesis.
Ecology of the birds of paradise
Authors: Frith Clifford B , Beehler Bruce M , Cooper William T , Mcguire Michael 
Published: November 2023

Abstract
A remarkable feature that defines the birds of paradise is the group’s near-obligate dependence upon the tropical dosed humid forests of Australasia, entirely east of Wallace’s Line. The dependence on humid forest is nowhere more obvious than in Australia, where one finds that continent’s four paradisaeid species restricted to small geographical enclaves of remnant rainforest. It can be safely said that the birds of paradise have evolved a close dependence on rainforest. Also, as will be discussed in this chapter, there is evidence that some Australasian rainforest trees appear to depend upon birds of paradise for important aspects of their maintenance and regeneration-seed dispersal in particular.
Linking communities and ecosystems: trophic interactions as nutrient cycling pathways
Authors: Grover James P , Loreau Michel 
Published: November 2023

Abstract
Almost the entire field of community ecology has been based on the implicit assumption that communities can be understood in terms of the populations that constitute them and their direct interactions (essentially consumption and competition). There is no doubt that this approach has been fruitful in the analysis of simple systems of few species, but one of its basic weaknesses in understanding large systems is that it ignores the constraints imposed by ecosystem functioning, such as matter and energy balances, decomposition processes and nutrient cycling. Although ecological systems are organized hierarchically (Allen and Starr 1982; O’Neill et al. 1986), so that community properties can be partly independent of general ecosystem-level constraints, the latter should affect the biological components of ecosystems and the communities they form. Significant organizing processes seem to occur from the bottom-up through vertical (trophic) interactions, which are tied to energy and nutrient flow, rather than through horizontal (competitive) interactions (Loreau 1994a). Therefore community organization has ultimately to be studied within the broader framework of ecosystem organization.
Biodiversity value and taxonomic relatedness
Authors: Williams Paul H 
Published: November 2023

Abstract
The threat of exinction hangs over not only particular species, but also entire faunas and floras. The very immensity of the variety of all life dictates that most of this richness will only ever be conserved in situ. Therefore con servationists need to know which areas contibute most to overall biodiversity. This, in tum, requires an ability to measure ‘biodiversity value’ (McNeely et al. 1990; Reid et al. 1992; Groombridge 1992; Wilson 1992).
Biodiversity conservation is not necessarily equivalent to species conservation. Species conservation, when justified as part of biodiversity conservation, appears to assume the possibility of ‘collecting the set’ of all species for protection. Under these circumstances the most threatened species are often seen as the most immediate priority (a reactive strategy), and other species are assumed to be safe for the time being. But, if it is not possible to protect everything (which is perhaps realistic at least when dealing with tropical biodiversity), and particularly if it is not possible to foresee threats or act in time for the species that were assumed safe, then a lot of resources could be invested in a few species, while elsewhere, through some unexpected change in land use, the majority might be lost. A more appropriate (proactive) strategy might be to ‘salvage the most’, because it is then that the areas with the greatest contribution to total biodiversity acquire the greatest priority. It follows that, in certain circumstances, threatened species or areas might even be seen as a poor investment, particularly if equivalent, lower risk choices for biodiversity value were available (Williams et al. 1994).
Utilising genetic information in plant conservation programmes
Authors: Ennos Richard A 
Published: November 2023

Abstract
Over the last 15 years there has been an explosion of interest in measuring genetic variation within plant species. On the one hand, a series of increasingly sophisticated methods have been applied to detect differences among individuals at the molecular level. Such variation has been dubbed ‘genetic marker variation’ (Avise 1994). In parallel with these developments, quantitative genetic analysis first developed in animal and plant breeding has been applied to natural populations to elucidate and quantify the genetic basis of phenotypic variation (Lawrence 1984). The objective of this chapter is to consider how studies of both genetic marker variation and quantitative genetic variation, when carefully interpreted, can be used to guide the development of conservation strategies for threatened plant species, and to illustrate this with reference to an ongoing conservation programme involving native pine in Scotland.
Genetic marker variation represents differences in the genetic information of plants within (or between) species. Genetic marker loci may be detected at the DNA level (RFLP, RAPD, microsatellite, minisatellite loci) (Burke et al. 1992), or by analysing the primary products (isozymes) (Hamrick 1989) or secondary products (alkaloids, monoterpenes) (Tobolski and Hanover 1971) of genes. Genetic markers may be located in any of the three genomes (nuclear, chloroplast and mitochondrial) possessed by plants. For the purposes of initial interpretation, the effects of these forms of variation are assumed to be selectively neutral, though this may not always be the case.
Developmental stability and mode of selection
Authors: Møller Anders Pape , Swaddle John P 
Published: November 2023

Abstract
Micro-evolutionary processes involve different genotypes producing phenotypes upon which selection can act. If phenotypes are non-randomly associated with fitness components, this will result in an evolutionary response to selection, provided the characters in question have an additive genetic basis, and that there are no strong negative genetic correlations preventing or delaying a response. In this chapter, we introduce the concept that the prevailing patterns of selection may affect both the phenotypes and the genotypes producing particular phenotypes. This may take place by means of genetic modifiers that control the phenotypic expression of a particular genotype, but also modify the amount of additive genetic variance being expressed phenotypically.
Adverse environmental conditions and evolution
Authors: Møller Anders Pape , Swaddle John P 
Published: November 2023

Abstract
Stress is a state well known to most readers of this book. There are numerous definitions (most people have their own), but here we adopt the definition of stress as a state caused by a factor imposing a potentially lasting injurious change to a biological system. This implies that a range of phenomena such as starvation, irradiation, and hypoxia can be considered to be stressors. Stress is a common state affecting free-living organisms, and it thereby imposes important selection pressures on individual organisms, but also affects the development of phenotypes upon which selection acts. Stress generally results from deviations from normal, local conditions to which an organism is adapted. In other words, stress can be considered to arise from suboptimal environmental conditions.
Introduction
Authors: Crozier Ross H , Pamilo Pekka 
Published: November 2023

Abstract
Social insects fascinate because of the finely coordinated organization of their societies and because of their great ecological success in many biotopes (Wilson, 1990). Studies on insect social organization have traditionally focused on understanding colonylevel phenomena. The emphases in such studies have been on understanding colony growth, the division of labour between colony members, the coordination of functions between individuals, and the communication mechanisms that make this finely tuned coordination possible (e.g. Oster and Wilson, 1978; Moritz and Southwick, 1992; Holldobler, 1995). Holldobler and Wilson (1990:29) emphasize the importance of series-parallel task processing in the enormous success of social insects (i.e. individual ants can specialize in components of social life, and do not each have to perform the entire range of tasks necessary for their colony ‘s success).
The evolution of eusociality in insects
Authors: Crozier Ross H , Pamilo Pekka 
Published: November 2023

Abstract
Hamilton (1964a,b) formalized the modern approach to the evolution of social behaviour with his notion of inclusive fitness, and also noted that the exceptionally high relatedness among sisters might lead to a predisposition of the Hymenoptera to evolve eusociality because females could benefit more by raising sisters than own daughters. A decade later Trivers and Hare (1976) combined Hamilton ‘s kin selection theory with Fisher ‘s (1930) sex ratio theory and pointed out that hymenopteran workers benefit from the high sister relatedness only if they can bias the sex ratios in favour of females. These insights give sex allocation theory the central place in considering the evolution of eusociality. In the years since Hamilton ‘s seminal papers, opinion has varied greatly over whether malehaploidy was, after all, important in the evolution of eusociality. In this chapter we follow Pamilo (1991c) and evaluate the current status of views on malehaploidy as a predisposing agent to the evolution of eusociality in the light of sex allocation theory. We apply here the inclusive fitness formulation developed in the preceding chapter. The main aims in this approach are to see whether there is a difference between diploid and male-haploid genetic systems in how readily they allow the evolution of a worker caste, and to examine how different features of insect life cycles might affect such evolution.
Flying primates: crashed, or crashed through?
Authors: Pettigrew John D 
Published: November 2023

Abstract
The flying primate hypothesis originated from the finding that megabats shared a number of advanced visual pathway characters with primates that were not found in any other mammalian order, nor in microbats. This hypothesis indicates that primates, colugos and megabats share a common ancestor with each other more recent than any shared with microbats. The hypothesis has found increasing support from other sources of evidence. Examples reviewed here include further derived brain features, both visual and non-visual, immunological studies of serum proteins with monoclonal antibodies and analysis of restriction sites and protein sequences (globins and cx-crystallin). DNA sequence data, while supporting the colugo-primate association, have been used to reject a primate-megabat connection, even though the total evidence for a colugo-megabat link is better than the generally accepted evidence for a colugo-primate link, and even though DNA sequence data and protein sequence data on the same genes give conflicting phylogenies. A resolution to this conflict is suggested by a bias in all the published DNA sequence data on bats. The shared substitutions claimed in support of bat monophyly are mostly of adenine (A) or thymine (T), in the same direction as the bias that exists in the overall base composition of DNA from metabolically-active, volant organisms. If the AT content of DNA is taken into account by using the NZ algorithm, the much-vaunted claims for bat monophyly based on DNA sequences are not supported. It is more parsimonious to assume that the AT bias responsible for the claimed association arose independently in the two lines of flying mammals.
MS/MS studies of tropane alkaloids: detection and determination of structure
Authors: Lawson* G , Ostah* N , Woolley† J G 
Published: November 2023

Abstract
Naturally occurring tropane alkaloids are a principal source of sympathomimetic amine drugs. Detection oftropane alkaloids in plant roots normally requires a lengthy extraction procedure followed by GC or GC-MS analysis (Robins et al. 1994). Alternatively, MS/MS techniques may be used as a fast analytical method for the determination of natural products (McClusky et al. 1978; Unger and Cooks 1979). This analysis, using MS/MS data from authentic compounds, means that tropane alkaloids in plant root samples can be identified without prior work-up, with consequent time saving and the use of much smaller sample sizes.
Lineage selection and transplantation of mouse ES cell-derived neural precursors
Authors: Schmandt Tanja , Glaser Tamara , Brüstle Oliver 
Published: November 2023

Abstract
Embryonic stem (ES) cells have become an indispensable experimental resource for studying cellular and molecular processes of cell differentiation under controlled conditions in vitro. Furthermore, their capacities to proliferate indefinitely and to differentiate into all somatic cell types make them a precious donor source for cell replacement strategies. The success of ES cell-based applications will critically depend on the availability of: (i) protocols for controlled in vitro differentiation; and (ii) assay systems for validating the functional performance of ES cell-derived somatic cells – the two key aspects covered in this chapter. The protocols described here are concerned specifically with mouse ES (mES) cells, which remain a paradigmatic model system for the development of novel differentiation strategies.
Lattice sums, the Madelung constant, and Paul Ewald
Authors: Templeton David H 
Published: November 2023

Abstract
Who was Paul Ewald? Several answers come to mind. Those who knew him as a person will think first of the man himself, whom they loved, respected, and admired. Then they will remember his scientific achievements or his leadership as a teacher, and editor and organizer of international crystallography. ‘The Ewald sphere’ may be the first response from many crystallographers if asked what they associate with his name. Those more familiar with his work will cite his dynamical theory of diffraction as his monument in science.
Multiple diffraction of X-rays and the phase problem
Authors: Colella R 
Published: November 2023

Abstract
In this chapter we will discuss a particular aspect of dynamical theory, namely, the use of multiple diffraction of X-rays in crystals for a solution of the phase problem. This subject, multiple Bragg scattering, a situation in which more than one set of crystallographic planes satisfy Bragg’s law simultaneously, was an area of diffraction theory in which Paul Ewald applied himself during the last years of his professional life.