bluuebunny/crossref_metadata_2025 huggingface dataset:
Conservation Prioritization Using Metapopulation Models
Authors: Nicholson Emily , Ovaskainen Otso
Published: November 2023

While nominally aiming to maximize species persistence, most methods for conservation planning use surrogates such as area, amount of habitat, or population size, rather than explicit measures of viability such as extinction risk (Chapter 2; Cabeza and Moilanen 2001, 2003). The difficulty lies in relating the landscape pattern, such as the area of habitat or its spatial configuration, to a biological benefit, such as species viability, with a sound basis in ecological theory. One of the principal ways of considering the effects of spatial configuration of habitat is to model the underlying spatial population processes. In highly fragmented landscapes consisting of networks of habitat fragments, this can be done within the metapopulation framework, which is based on the processes of the local extinction and colonization of patches of habitat. While some local populations may go extinct, the habitat patches can be repopulated by migrants originating from neighbouring patches, thus ensuring the persistence of the metapopulation as a whole (Hanski 1994; Verboom et al. 2001). In the metapopulation context, population viability becomes a function of the ecology of the species and the amount, quality, and spatial configuration of habitat.
Marxan and Relatives: Software for Spatial Conservation Prioritization
Authors: Ball Ian R , Possingham Hugh P , Watts Matthew E
Published: November 2023

The original intent of Marxan and its predecessors was to solve a version of the minimum set reserve design problem (Cocks and Baird 1989; Chapter 3). In this problem, conservation targets are set for a number of biodiversity features (e.g. three populations of each species), and Marxan selects planning units that represent these targets for a minimum total cost, while allowing for more or less emphasis on spatially clustering the selected planning units. Marxan is now used to solve a range of spatial prioritization problems beyond the selection of reserves. The Marxan software is freely available and interacts with a variety of geographical information system (GIS) tools. It designs clumped reserve systems that make sense to a policy maker or planner.
The ConsNet Software Platform for Systematic Conservation Planning
Authors: Sarkar Sahotra , Fuller Trevon , Aggarwal Anshu , Moffett Alexander , Kelley Christopher D
Published: November 2023

Central to systematic conservation planning is the use of software planning tools for decision support (Sarkar et al. 2006; Margules and Sarkar 2007), the most important of which are being reviewed in this book. Contemporary planning practices require tools that are accessible over the Internet and integrated with Geographical Information Systems (GIS) such as ArcGIS®. Availability, as well as computational efficiency (speed), are important when these tools are used for real-time negotiations involving stakeholders. Integration with GIS, especially for visualization, is important if the tools serve as decision support systems for formulating plans under alternative scenarios of habitat change. The ConsNet Portal is a Web-based resource for conservation planning. It includes an online interactive course (the ConsNet Primer) and the ability to run two software packages (ResNet and MultCSync) over the Web. These packages form part of the ConsNet Software Platform which consists of a suite of software packages for decision support during the identification of nominal conservation area networks (CANs). These packages enable the selection of CANs, analysis of the performance of biodiversity surrogates, establishment of connectivity between selected areas, and multi-criteria analysis (MCA) for incorporating socio-political criteria into network design.
From Theory to Practice: Designing and Situating Spatial Prioritization Approaches to Better Implement Conservation Action
Authors: Knight Andrew T , Cowling Richard M , Possingham Hugh P , Wilson Kerrie A
Published: November 2023

Ever since nations and states have embarked on programmes to establish systems of protected areas, there have been a variety of methods applied to prioritize localities for nature conservation – that is, facilitate decision-making as to which places are best suited to integration into a network of protected areas. Scoring approaches were traditionally applied for ranking areas for acquisition throughout the 1970s and 1980s (Chapters 1 and 3; see Smith and Theberge 1986 for review). Subsequently, the advent of the first area selection algorithm in the early 1980s that explicitly applied the concept of complementarity (Kirkpatrick 1983) triggered a rapid advance in development of spatial prioritization techniques for conservation (Pressey 2002). A diverse range of tools is now available for identifying areas important for ensuring the persistence of nature, including C-Plan (Chapter 16), ResNet (Chapter 17), Marxan and CLUZ (Chapter 14), and Zonation (Chapter 15). Techniques have evolved beyond simply representing natural features to including species distribution models (Chapters 6 and 7), metapopulation (Chapter 8) and climate change modelling (Chapter 13), population viability analysis (Chapter 9), and explicitly accounting for uncertainty (Chapter 11) and economic costs (see Naidoo et al. 2006 for review). Our technical understanding of data issues is comprehensive (Knight et al. 2006b). This focus on testing ecological data and techniques to quantifiably establish their limitations has elevated spatial prioritization analyses to a mainstay of the conservation science literature. Through the theoretical development and testing of spatial prioritization techniques, we have devised not only these tools, but also key conservation planning concepts and theories (Chapter 2), encouraged the articulation of conservation problems, facilitated the identification of key data gaps, and provided transparent and repeatable techniques for the identification of priority areas and actions.
From Empedocles to Wittgenstein
Authors: Kenny Anthony
Published: November 2023

From Empedocles to Wittgenstein is a collection of fifteen historical essays in philosophy, written by Sir Anthony Kenny in the early years of the 21st century. In the main they are concerned with four of the great philosophers whom he most esteems, namely Plato, Aristotle, Aquinas, and Wittgenstein. The author is not only one of the most respected historians of philosophy, and possibly the widest-ranging, but also one of the most successful at writing on the subject for a broad readership. In this volume he presents scholarly explorations of some themes which caught his interest as he worked on his acclaimed four-volume New History of Western Philosophy.
Does Socrates Claim To Know That He Knows Nothing?
Authors: Fine Gail
Published: November 2023

1 Or so we are told. I do not know when this claim was first attributed to Socrates. One early source often thought to do so is Cicero, Acad 1. 16: ‘nihil se scire dicat nisi id ipsum’. Cf. 1. 44–5: ‘itaque Arcesilas negabat esse quicquam quod sciri posset, ne illud quidem ipsum quod Socrates sibi reliquisset, ut nihil scire se sciret’. (Notice that the only cognitive terms Cicero uses are forms of scire.) Cf. 2. 74. For this reading of what Cicero says, see J. Annas, ‘Plato the Skeptic’, in P. Vander Waerdt (ed.), The Socratic Movement (Ithaca, NY, 1994), 309–40 at 310. For a recent challenge to this reading, see M. F. Burnyeat, ‘Antipater and Self-Refutation’, inB. Inwood and J. Mansfeld (eds.), Assent and Argument (Leiden, 1997), 277–310 at 290–300; see further n. 5 below.
Excavating Dissoi Logoi
Authors: Bailey D T J
Published: November 2023

I begin with a necessary apology for the extreme obscurity of the text I shall discuss. The Dissoi Logoi, whose fourth chapter is the subject of this paper, is perhaps unique among texts in the history of philosophy for its murkiness. It is an anonymously authored philosophical work appearing to argue, among other things, for the sameness and then the difference of properties such as good and bad, just and unjust, true and false. Almost every aspect of it likely to interest scholars is monstrously undetermined.
Neurologie
Authors: Scull Andrew
Published: November 2023

As he began to lose his wits for the first time in 1788, George III announced to all who would listen that “I’m nervous, I’m not ill, but I’m nervous; if you would know what is the matter with me, I am nervous.”Sadly for him, the court and his physicians did not agree. Mad they called him, and soon he was being bled, blistered, starved, vomited, and purged, tied to his chair, menaced, placed in a strait waistcoat, whipped, and cut off from all contact with the outside world. Modern historians have broadly embraced the idea that his hallucinations, delusions, and delirious ravings were in all probability the side effects of an inherited metabolic disorder, porphyria, a disease that, appropriately enough, turned his urine purple. And certainly the king was far too disturbed ever to have been considered merely hysterical. But his embrace of the language of nervousness mirrored that of his subjects, among whom disordered nerves were now themaladie à la mode.
Realist-Expressivism and Conventional Implicature
Authors: Copp David
Published: November 2023

Anna says that capital punishment is morally wrong, yet whenever she hears that a criminal is about to be executed, she seems indifferent. There is never any indication that she disapproves of capital punishment, other than the fact that she says it is wrong. When we challenge her, she continues to insist that capital punishment is wrong, but she agrees that she has no negative attitude toward it. She denies that she disapproves of it. Something appears to be amiss. Her assertion seems to be at odds with the indifference that she displays and avows. Perhaps she does not really believe that capital punishment is wrong. Perhaps she does not know her own mind, or perhaps she is being insincere. Or perhaps she does not have a thorough understanding of what she is saying, in saying capital punishment is wrong.
Reasons as Evidence
Authors: Kearns Stephen , Star Daniel
Published: November 2023

Normative reasons are strange beasts. On the one hand, we are all intimately familiar with them. We couldn’t live for long without the guidance they continually offer us when we are trying to work out what to believe and what to do. At the same time, they seem to resist being analyzed in other terms. We can say that they “count in favor of ...” (acts, beliefs, intentions, desires, emotions, etc.), and some have thought that this rather uninformative characterization is pretty much all we will ever be able to come up with when attempting to answer the question, what are reasons? (Scanlon 1998: 17; Parfit 2007).
Constitutivism and the Inescapability of Agency
Authors: Ferrero Luca
Published: November 2023

The norms of rationality and morality have special authority; they are categorically binding. They bind agents regardless of their contingent motives, preferences, and intentions. By contrast, the norms of particular games, institutions, and practices are only conditionally binding. They have normative force only for agents who have a good enough reason to participate in them. A statement that one ought to move the knight along the diagonals, for instance, expresses an ought-according-to-the-norms-of-chess. But the oughts of rationality and morality are not qualified with the clause ‘-according-to-the-norms-of-rationality/morality’; they rather tell us, as Stephen Darwall writes, ‘what we ought to do simpliciter, sans phrase.’
Paratragedy in Plato’s Gorgias
Authors: Trivigno Franco v.
Published: November 2023

Recent scholarship on Plato̓s Gorgias has focused on three distinct axes of interpretation: first, the intractability of Callicles as an interlocutor and the limits of Socratic dialectic; second, the function and meaning of the eschatological myth with which the dialogue ends;3 and third, the dialogue̓s relationship to tragedy and, in particular, to Euripides̓ Antiope, which is quoted and referenced at length.
Treatment of small cell lung cancer
Authors: Falk Stephen , Williams Chris
Published: November 2023

Small cell lung cancer can grow and spread aggressively. Chemotherapy is the major treatment for small cell lung cancer. Radiotherapy is given to the lungs of patients with disease confined within the chest. Radiotherapy is given to the brain when there is a good response to chemo-therapy. In contrast to other types of lung cancer where surgery is the mainstay of treatment, chemotherapy and radiotherapy are the major treatments used. This is because small cell lung cancer can grow and spread rapidly. Less than 1% of patients receive surgery, usually as part of investigation of a small nodule within the lung where it is removed to make a diagnosis. For these patients surgery should always be followed by chemotherapy. The prognosis is that about half of this unusual group of patients will survive.
Treatment of the symptoms and complications of lung cancer
Authors: Falk Stephen , Williams Chris
Published: November 2023

Many patients will have symptoms from their lung cancer when they first see their doctor, or will likely develop symptoms later if the tumour is not controlled. This section outlines some of the problems that can arise and discusses how they are treated, although it is important to remember that many patients will develop only a few of these symptoms. Of course, the best treatment for any symptom is to get rid of the underlying cause—the cancer. However, even if this is not possible for some patients, there are many ways in which symptoms can be reduced to improve quality of life.
What is myotonic dystrophy?
Authors: Harper Peter S
Published: November 2023

Most people who start to read this book will know little or nothing about myotonic dystrophy. They may have just been diagnosed as having it, or they may have learned that someone in their family is affected, but they will have only a hazy idea as to what the implications are for themselves. If this applies to you, this chapter is a good starting point. If you already have a fair amount of information, you can move on to the later chapters.
Advances in research
Authors: Harper Peter S
Published: November 2023

Myotonic dystrophy is one of the most complex disorders known to medicine. There is a great deal of research currently being undertaken into myotonic dystrophy. It took 10 years of very painstaking research before the myotonic dystrophy gene was finally pinned down and isolated in early 1992. Research on how the gene changes in myotonic dystrophy actually cause the muscle damage and other problems is now progressing very rapidly.
Management and treatment now
Authors: Harper Peter S
Published: November 2023

Although there are no treatments specific to myotonic dystrophy, there is a lot that can be done in the management and treatment of particular aspects of myotonic dystrophy that can greatly help you. Each case of myotonic dystrophy is different, and different patients will need different approaches according to how severe particular problems are and their age. The information in this chapter can be used if you are meeting doctors or professionals to discuss management.
The future — towards effective prevention and cure for myotonic dystrophy
Authors: Harper Peter S
Published: November 2023

There is no proven medical treatment that influences the rate at which myotonic dystrophy deteriorates or which can prevent its onset in those carrying the genetic change. There is a great deal of research that is ongoing into myotonic dystrophy. Now that the genes responsible for myotonic dystrophy have been identified, the focus of new research is on finding effective treatment.
Introduction
Authors: Wright Michael , Hamzah Ednin , Phungrassami Temsak , Bausa-Claudio Agnes
Published: November 2023

Southeast (SE) Asia is divided into two sub-regions. Mainland Southeast Asia comprises countries such as Cambodia, Laos, Myanmar, Thailand, and Vietnam. Maritime Southeast Asia encompasses the island states of Brunei, Indonesia, the Philippines, Singapore, and Timor Leste. Malaysia, with two states on the island of Borneo and the others on the Malay Peninsula, straddles the two (Fig. 1.1).
Epistemic Humility, Arguments from Evil, and Moral Skepticism
Authors: Howard-Snyder Daniel
Published: November 2023

The conclusion is frequently more nuanced: “it is very likely that there is no such reason’’ or “more likely than not” or “more likely than it otherwise would be”. Some critics reject the premise: we do see how some reason would justify God. These are the theodicists. Others accept the premise but reject the conclusion: the evidence or non-evidential warrant for God’s existence is much better than the evidence for no justifying reason.
Evaluating Religion
Authors: Kapitan Tomis
Published: November 2023

Controversies about religion, the value of religious practices, the grounds for religious beliefs, or the benefits and dangers of religious institutions, are probably as old as religion itself. The disagreements are usually vivid and longstanding; apart from politics, few sectors of human civilization can rival religion in division, acrimony, and bloodshed. Criteria for rationally assessing these debates are desirable, therefore, and to provide them is the object of this chapter. But little headway can be made on this matter without first circumscribing the topic. Just what is “religion”? What makes something “religious”? How extensively can these concepts be applied? Without answers to such questions, we cannot be sure how broad a sweep is made by a given critique or defense of religious phenomena.
Ockhamism and Molinism—Foreknowledge and Prophecy
Authors: Warfield Ted A
Published: November 2023

On earlier occasions I have argued for the compatibility of human freedom with divine foreknowledge and defended that argument from criticisms. On those occasions I provided and defended only my positive argument for my compatibilist position. I did not reply to standard arguments for the incompatibility of human freedom and divine foreknowledge. Nor did I say anything substantive about the “Ockhamist” approach to the foreknowledge issue thatI favor.
Radioisotope Detection Using X-Ray Film
Authors: Laskey Ron A
Published: November 2023

During the last two decades gel electrophonsis has steadily replaced other methods for analytical fractionation of macromolecules. This chapter describes and discusses methods of detecting radioisotopes within flat samples such as acrylamide or agarosc gels, nitrocellulose t1ltcrs, thin layer chromatography plates and paper chromatograms. For all of these samples X-ray film provides a convenient non-destructive means of isotope detection which combines high sensitivity with high resolution.
Strategy and Tactics in Receptor Binding Studies
Authors: Hulme E C , Birdsall N J m.
Published: November 2023

The questions answerable by receptor-binding studies fall into two major categories: Firstly, there are fundamental questions which one may ask about: the molecular pharmacology of receptors, the mechanism of ligand binding, and the nature and mechanism of receptor-effector in1eractions. Secondly, there are applied questions which concern the cell biology and anatomical distribution of receptors, particularly: their concentrations in different tissues, their distribution on different eel! types, their ontogenetic development, and how their synthesis, membrane insertion, coupling, degradation. and re cycling are regulated in a given cell! type.
Peptide mapping and the generation and isolation of sequenceable peptides from receptors
Authors: Wheatley M
Published: November 2023

As increasing numbers of receptors are purified to homogeneity, research interests are aimed at elucidating structural information about the receptor proteins themselves. This encompasses obtaining general sequence information often used for constructing the probes required for cloning the receptors, and in addition investigating the location within the molecule of functionally important amino-acid residues or moieties. A popular approach to this is site-directed mutagen ésis of a residue or region of interest, followed by expression of the protein and its characterization. By virtue of its indirect approach, it is sometimes difficult to relate any observed change in function with a given mutation. A complementary and synergistic approach is to chemically modify the pure receptor directly, and then analyse the protein by peptide-mapping studies and protein-sequencing techniques. The aim of this chapter is to provide the information necessary for peptide mapping receptors utilizing the low-technology, and therefore relatively cheap, high-resolution system of sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Furthermore, information will be presented pertinent to the preparation and purification of receptor-derived peptides suitable for sequencing. It is not within the scope of this chapter to describe the actual sequencing procedure itself. When appropriate, examples from our research on muscarinic acetylcholine receptors (mAChRs) will be presented.
IL-2 as a short-range physiological mediator
Authors: Mitchison N A
Published: November 2023

It is now generally accepted that the immune system neither could nor does operate as a perfect gas, in which cells, antigens, and cytokines move at random. On the contrary, movement is under tight constraint, mainly as a result of adhesion between cells. Adhesions, plus the polarized secretion to which they give rise, control the site of action of cytokines, and make these molecules function largely as ultra-short range signal transmitters. In this respect cytokines differ profoundly from classical hormones in their systemic activity, although the boundary is blurred by agents such as the pituitary releasing hormones which act more or less locally. A comparison with neurotransmitters would be more apt, and the promiscuity of these molecules echoes the promiscuity found among the cytokines of the immune system. Consideration of neurosecretion should remind immunologists that long-range and short-range transmitters probably evolve from one another, and that the arrangement of cytokines as it occurs in man should be regarded as a snapshot rather than a stable picture. Furthermore, some of the molecules that transmit information between cells may have started their evolution inside cells; purinergic transmission may be a case in point.
Importance of steroidogenesis in specific hormone action
Authors: Funder John W
Published: November 2023

Six classes of hormonal steroids are currently recognized in mammalian systems – mineralocorticoids, glucocorticoids, androgens, oestrogens, progestins, and vitamin D. This classification was made historically on effector grounds – growth of a cock’s comb for androgens, hepatic glycogen deposition for glucocorticoids– long before anything was known of receptors or the subcellular mechanism of steroid action. In invertebrates, ecdysones are clearly an additional class of physiological steroid hormone, and in a variety of species both endocrine and paracrine (neurosteroid) roles are currently being explored for a number of steroids (e.g. dehydroepiandrosterone, pregnenolone). What remains true, however, is that of the hundreds of different steroids in various body compartments a (patho)physiological role as a signal is assigned to fewer than a dozen, with the rest being considered as precursors, biosynthetic intermediates, or degradation products.
Nuclear hormone receptors as transcriptional activators
Authors: Gronemeyer Hinrich
Published: November 2023

Multicellular organisms have established sophisticated techniques of information transfer between cells and body compartments. The information that is transmitted can be highly complex and can result in the alteration of gene programmes involved in cellular differentiation, proliferation, or reproduction. Despite the complexity of these events, the inducing signals can be relatively simple molecules, such as small peptides or cholesterol derivatives. Apparently, the need for a high speed of information transfer means that the signals must be small, highly diffusable molecules. However, only limited structural information can be stored in the chemical structures of, for example, steroids, thyroids, or retinoids, and therefore the interpretation of the signal is of major importance and requires a highly specialized system that specifies the appropriate gene programmes. This interpretation can be based on signal-specific nuclear receptors that are expressed in target cells – those cells that are genetically determined to respond to the signal. Understanding the molecular mechanisms by which the information stored in the signal is converted into gene programming is one of the exciting areas of molecular biology.
Repression of transcription by nuclear receptors
Authors: Drouin Jacques
Published: November 2023

We now have a fairly detailed understanding of the mechanisms by which nuclear receptors recognize their target genes and activate transcription (Chapters 3 and 5). Much less can be said about the ways in which these receptors repress transcription of other target genes. At the onset, it is interesting to note that early studies of the action of steroids on their target tissues indicated, for example, that glucocorticoids decrease the level of about the same number of liver proteins as they stimulate. In all likelihood, many of these changes will be ascribed to transcriptional regulation.
Mammalian Cell-Cycle Analysis
Authors: Darzynkiewicz Zbigniew
Published: November 2023

A plethora of methods designed to probe the cell cycle of mammalian cells has been developed in the past several decades. The scope of this chapter makes it impossible to fully describe them. Therefore, the essential features of the most useful techniques are presented. Outlines of particular protocols, virtues, drawbacks, and applications of the methods, and practical notes regarding critical steps, are given. To master these techniques, the reader is encouraged to consult the articles which describe them more extensively, and which arc referenced throughout the text. The aim of this chapter, therefore, is to introduce diverse techniques, which may be of help in selecting the most appropriate approach for a particular task.
Cell-Cycle Analysis Using The Filamentous Fungus Aspergillus Nidulans
Authors: Oakley B R , Osmani S A
Published: November 2023

The filamentous fungus Aspergillus nidulans has proved to be an excellent experimental system for the identification, isolation, and analysis of genes that are essential lo cell-cycle progression and regulation. Studies in A. nidulans have led to the discovery of several key elements of cell-cycle progression and regulation that were not first identified in other experimental systems (1). It is a homothallic ascomycetous fungus that has both a sexual and an asexual life cycle (Figure 1). The classical genetics and molecular genetics of A. nidulans have been previously described (2) and are, in many respects, as advanced as the yeast systems. his the purpose of this chapter to describe some of the techniques that can be utilized to study the cell cycle in A. nidulans.
Analysis Of Dna Replication Origins And Directions By Two-Dimensional Gel Electrophoresis
Authors: Huberman Joel A
Published: November 2023

Prior lo 1987 when the 2D gel electrophoretic ‘replicon mapping’ techniques were inlroduced (1, 2), no generally applicable method was available for the identification or characterization of cukaryotic DNA replication origins. Consequently, it was uncertain whether or not specific origins existed. Thanks to new results obtained with the 2D gel techniques (and, more recently, with additional origin mapping methods, refs 3-5), a great deal of information about eukaryotic origins is now available. Several recent reviews discuss the biological importance of these new results (6--9).
Preparation of DNA for use as probes
Authors: Byrnes Lucy , Enenkel Barbara , Gannon Frank , Smith Terry
Published: November 2023

The primary goal of this chapter is to describe the preparation of DNA for use as probes. The preparation of RNA probes and oligonucleotide probes are covered in Chapters 7 and 5, respectively. Preparative methods to obtain a specific DNA fragment from either a plasmid or phage which contains it are initially described. The generation of mixed DNA probes corresponding to the messenger RNAs present in a cell is the next general topic covered in this chapter. Finally the chapter describes the preparation of adequate target material for DNA hybridization and detection using probes.
Homogenization of tissues and cells
Authors: Graham John M
Published: November 2023

Many investigations into the structure and function of cells and tissues require, at some stage, the isolation of a particular membrane or subcellular organelle. The successful isolation and fractionation of subcellular membranes from any source, from animal cells, plant cells, or microbial organisms depends critically on the ability to disrupt the cell in such a way that the subcellular particle of interest can be isolated in high yield and as free from contaminating structures as possible. Moreover, the isolated biological particle should retain as much of its normal structural and functional integrity as possible and be in a form which is amenable to the analytical techniques to be used subsequently.
Isolation and characterization of peroxisomes
Authors: Völkl A , Baumgart, E , Fahimi H D
Published: November 2023

Peroxisomes (PO) are organelles ubiquitously distributed to most pro- and eukaryotic cells (1, 2). Depending on the cell type and the sets of enzymes which they contain, synonymous designations such as glyoxisomes or glycosomes are used with ‘microbodies’ as the all-embracing term. Mostly, PO are spherical or spheroidal particles with a diameter between 0.2–1.0 µm. In some tissues, however (3–6), they may be irregularly shaped.
PFGE in the study of a bacterial pathogen (Haemophilus Influenzae)
Authors: Hood D W
Published: November 2023

Bacterial chromosomes are relatively small and much simpler to analyse than the larger, more complex, genomes of higher eukaryotic organisms. Pulsed field gel electrophoresis (PFGE) is capable of resolving DNA molecules up to ten million nucleotides in length which should enable one to view the complete genome of most bacteria as a single electrophoretic band. Restriction endonuclease digestion of bacterial genomic DNA and resolution of the resulting fragments by PFGE has facilitated the construction of physical maps of bacterial chromosomes. Since the first bacterial chromosomal restriction map was determined for Escherichia coli (1) these have now been obtained for an ever-increasing number of bacterial species. They are proving to be extremely useful in studying many aspects of the genome and genetic and molecular studies on chromosome organization and function can now be carried out directly on intact chromosomes. In particular, for the subject of this chapter, genomic maps have enhanced our investigation of the genetic organization of pathogenicity determinants in the bacterium Haemophilus influenzae. These studies will serve to illustrate various aspects and uses of pulsed field gel electrophoresis relevant to the analysis of bacterial chromosomes.
Measurement of inositol phosphate turnover in intact cells and cell-free systems
Authors: Shears Stephen B
Published: November 2023

The question as to whether a particular stimulus activates PLC activity in intact cells can be answered by demonstrating either that levels of the inositol lipid substrates decrease (see Chapter 1), or that there are increases in the levels of Ins(l,4,5) P  3 (see below and Chapter 8) and/or 1,2-diacylglycerol. However, more detailed knowledge of the rate of PLC activity will not be obtained from these specific assays alone. For example, one of the consequences of receptor occupation is a stimulation of inositol lipid resynthesis to ensure a compensatory supply of substrate to ensure continuing PLC activity (3).
Mass assay of inositol and its use to assay inositol polyphosphates
Authors: Balla Tamas
Published: November 2023

Myo-inositol was discovered in 1850 as a component of muscle tissue, but its importance was not recognized until about 100 years later when deprivation of dietary inositol in various animals was shown to cause disorders including alopecia and lipodystrophy in liver and intestinal epithelial cells (see ref. 1 for review). These changes could be reversed by administration of inositol and increased in severity when the intestinal flora was destroyed, since inositol is probably produced by intestinal microorganisms. Furthermore, several mammalian cell lines have been found to require inositol to sustain growth (2), although some cells can grow without added inositol because they can synthesize sufficient amounts to support their needs (3).
Preparation of RNA:protein complexes for X-ray crystallography and NMR
Authors: Price Stephen R , Oubridge Chris , Varani Gabriele , Nagai Kiyoshi
Published: November 2023

Understanding the molecular mechanism of RNA recognition by protein requires knowledge of the three-dimensional structure of RNA:protein complexes through application of X-ray crystallographic and NMR spectroscopic techniques. To date, much of our knowledge of this recognition is derived from studies of complexes of tRNA and aminoacyl-tRNA synthctases (Gin, Asp, Ser. and Lys) (1-4) or elongation factors (5).
Proteolysis Of Native Proteins As A Structural Probe
Authors: Hubbard Simon , Beynon Robert J
Published: November 2023

A common use of proteinases in vitro is the degradation of proteins to limit peptide mixtures in which all susceptible bonds have been cleaved (Chapter 8). To facilitate this process, the substrate would usually be first denatured, by heat, urea, guanidinium hydrochloride, by precipitation with trichloroacetic acid or similar treatments. As a result of the destruction of the higher-order structure in the substrate, all susceptible (i.e. in accordance with the primary cleavage specificity) bonds will be attacked rapidly and with rates that, compared with native state digestions, are approximately similar and influenced only by local changes in subsite occupancy; in this way, the peptide mixture limit is rapidly generated. The need for the prior denaturation step implicitly assumes that retention of native structure will slow or modify the proteolytic attack, and this is indeed the case. The role of three-dimensional structure of a protein substrate in modification of extent and rapidity of proteolysis is incompletely understood, but a recurrent observation is that proteolysis is more limited, both in the extent and in the rate of hydrolysis. This restriction of proteolytic attack on native proteins also underpins most proteolytic interactions of physiological relevance, and thus, the study of limited proteolysis is also relevant to processes in vivo.
Electron microscopy of viruses
Authors: Gelderblom H R , Biel S
Published: November 2023

Though occasionally considered as laborious, old-fashioned, and unnecessary, the detection and identification of viruses and other agents by electron microscopy (EM) can make an important contribution to many basic and applied biomedical routine procedures. In some fields, for example, vaccine production, EM even forms an integral part of the production controls (Table 1). While the majority of direct and indirect virus detection techniques (e.g. ELISA, PCR) are highly sensitive, but also highly specific for just one individual species or family of agents, EM works differently. Based on its undirected approach and its high resolution, EM is able to detect routinely and characterize morphologically all structures greater than 15 nm in diameter, which fortunately coincides with the size of the smallest viruses (1).
In vitro replication of RNA viruses
Authors: Banerjee R , go M , Izumi R , Datta U , Dasgupta A
Published: November 2023

RNA viruses are very diverse and utilize many distinct strategies for replicating their genomes. The genome organization of these viruses vary widely, thus the translation and replication strategies employed must also be varied. However, despite all the complexities of RNA viruses and their differing replication strategies, there are many similarities at the molecular level (1). Some of the common in vitro techniques employed to study these RNA replication strategies as well as methodologies to study in vitro RNA-protein interactions will be discussed in this chapter.
Interaction of standard mechanism, canonical protein inhibitors with serine proteinases
Authors: Laskowski Michael
Published: November 2023

Proteinases have a cradle-to-grave relationship with proteins. They assist in the birth of the proteins by removing the initiating methionine (Met) residues. They further aid in delivering them to an appropriate destination by removing the signal peptides. At death, they convert both exogenous proteins (food digestion) and endogenous proteins (protein turnover) to amino acids, which are then utilized for new protein synthesis. However, the most striking is the interaction of proteins with proteinases in their adult life. Protein processing turns numerous activities on or off. These activities in turn are responsible for a large range of biological phenomena such as blood clotting, clot dissolution, protein hormone action, emergence of the silk moth from cocoons, penetration of outer layers of ova by sperm, differentiation, cell death, and apoptosis (1). Along with so many important functions there are also many dangers associated with proteolysis. It must be rigidly controlled in time and place in order to be effective. Clotting from head to toe from a cut or digesting one’s own pancreas rather than that of one’s victim would be just a few untoward examples of uncontrolled proteolysis.
Keeping and raising zebrafish
Authors: Brand Michael , Granato Michael , Nüsslein-Volhard Christiane
Published: November 2023

Over the past decade, the zebrafish has become an important model organism for biological research. In recent years, more than 1800 zebrafish mutants have been identified, providing a rich resource for the study of embryonic development in vertebrates. An increasing number of laboratories are now starting to use this unique collection of zebrafish mutants for their research. Raising and maintaining zebrafish is more demanding than keeping stocks of invertebrates, but less so than keeping stocks of mammals. This chapter is aimed at giving a background on how to raise mutant and laboratory wild-type stocks and how to maintain them in good breeding conditions. We describe aquarium systems and water conditions as well as procedures to raise and breed zebrafish. While this chapter is aimed primarily at investigators entering the zebrafish field, the recipes and protocols may also provide useful information for experienced zebrafish researchers. The major demands to aquaria systems are posed by the problem of keeping the water in good condition. If the water is not constantly kept clean, the fish will suffer from the toxicity of their own excretions and derivatives thereof. The simplest way to keep the water clean is to keep fish at very low densities and to replace the water at regular intervals. A more elaborate method is to equip the aquaria with biological filters through which the water is circulated and purified. The filters contain material with a large surface area on which bacteria can grow, which degrade toxic ammonium to less toxic nitrates. In larger systems, water from several (often more than 1000) tanks may be recycled through one large common filter (recirculating systems).
Mapping and cloning
Authors: Geisler Robert
Published: November 2023

In order to identify zebrafish genes affected by mutations, both mutations and candidate genes are commonly placed on genome maps (Figure 1). Two types of maps are relevant for this approach: genetic maps, in which the probability of meiotic recombination between markers is used to determine their distance and construct the map; and radiation hybrid maps, in which breakage induced by radiation takes the place of recombination. Mutations can be placed only on genetic maps. This type of map is produced by scoring a large number of polymorphic markers on a panel of F2 fish from a reference cross. Two markers are close to each other if they give a similar pattern of alleles across the panel. Mutations are placed on the map indirectly, by scoring previously mapped markers on a panel of mutant.
RNA editing by cytidine deamination in mammals
Authors: Driscoll Donna M , Innerarity Thomas L
Published: November 2023

The editing of apolipoprotein B (apoB) mRNA was the first example of RNA editing discovered in mammals. The C→U conversion at nucleotide 6666 by a site-specific cytidine deaminase converts a glutamine codon (CAA) to an in-frame stop codon (UAA). apoB is an attractive system for the investigation of RNA editing and processing because the reaction, which can be studied in vitro, involves the modification of a single nucleotide. The past decade has seen tremendous progress in our understanding of the mechanism of apoB mRNA editing. This chapter will focus on the cis-acting sequences that maintain the specificity of editing, the trans-acting factors that mediate this reaction, and the biology of apoB mRNA editing in normal physiology and in transgenic animal models. We hope to provide a historical perspective as well as a discussion of recent developments and controversies in the field.
Bibliographic databases
Authors: Trawick Barton W , McEntyre Johanna R
Published: November 2023

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA. Use of the literature is fundamental to the pursuit of all knowledge. Through searching and reading, we learn what our peers are doing, develop a broader perspective on our field of interest, get: ideas, and confirm our discoveries During the course of twentieth century science, ‘the literature’ has become an expanding knowledge base that represents the collective archive of the work carried out by the international scholarly community. Recent technological advances make an increasing proportion of the literature available electronically (see Figure 1). This chapter offers an introductory guide for molecular biologists to stable bibliographic resources that are available over the Internet.
Internet tools for cell and developmental biologists
Authors: Vize Peter D
Published: November 2023

The type of data generated by cell and developmental biologists is often not well suited to presentation in printed media. How can one depict a migrating cell, vesicular cycling, or embryo gastrulation with a small number of still photographs or data tables? Such dynamic processes are better suited to illustration by active means, and the Internet is an effective system for transmitting information in such forms. Dynamic data forms are not the only ones well served by the Internet-three dimensional networks are also more simple to store, visualize, and maintain using database technology. An example of 3D data sets that are well suited to Internet storage and distribution are cross-talking signal transduction pathways, where simple hyperlinks allow users to jump from pathway to pathway in multiple dimensions. This chapter discusses both general principles and specific techniques of using the Internet for the exploration of cell and developmental biology.
Virtual reality for biologists
Authors: Amon Tomaz
Published: November 2023

As the name implies, the Virtual Reality Modelling Language (VRML) is a computer language for describing three-dimensional structural models or ‘worlds’. Much like HTML, it can be written with an ordinary text editor, then viewed with appropriate visualization software; this is the approach we use in this chapter to introduce the concepts.
Association Between State Paid Family and Medical Leave and Breastfeeding, Depression, and Postpartum Visits
Authors: Perry Madeline F. , Bui Lilian , Yee Lynn M. , Feinglass Joe
Published: November 2023

OBJECTIVE:

To evaluate the association of state paid family and medical leave policies with the likelihood of breastfeeding, postpartum depression symptoms, and attendance of the postpartum visit.

METHODS:

This was a cross-sectional study that used 2016–2019 data from PRAMS (Pregnancy Risk Assessment Monitoring System) for 43 states and Washington, DC. We describe the association of state paid family and medical leave generosity with rates of breastfeeding, postpartum depression symptoms, and attendance of the postpartum visit. Logistic and Poisson regression models tested the significance of state paid family and medical leave coverage generosity after controlling for individual respondent sociodemographic characteristics, with sensitivity analyses for respondents with deliveries covered by Medicaid insurance.

RESULTS:

Of the 143,131 respondents, representative of an estimated 7,426,725 population, 26.2% lived in eight states and DC with the most generous paid family and medical leave, 20.5% lived in nine states with some paid family and medical leave, and 53.3% lived in 26 states with little or no paid family and medical leave. Overall, 54.8% reported breastfeeding at 6 months or at time of the survey, ranging from 59.5% in the most generous paid family and medical leave states to 51.0% in states with the least paid family and medical leave coverage. Postpartum depression symptoms varied from 11.7% in the most generous states to 13.3% in the least generous states (both P<.001). State differences in postpartum visit attendance rates (90.9% overall) did not differ significantly. After adjusting for respondent characteristics, compared with states with the least paid family and medical leave, breastfeeding was 9% more likely (adjusted incidence rate ratio [aIRR] 1.09, 95% CI, 1.07–1.11) in states with the strongest paid family and medical leave coverage and 32% more likely (aIRR 1.32, 95% CI, 1.25–1.39) in analyses limited to respondents with deliveries covered by Medicaid insurance. A more generous state paid family and medical leave policy was significantly associated with a lower likelihood of postpartum depression symptoms compared with states with the least paid family and medical leave (adjusted odds ratio 0.85, 95% CI, 0.76–0.94) and a modest but significant increase in postpartum visit attendance (aIRR 1.03, 95% CI, 1.01–1.04) among respondents with deliveries covered by Medicaid insurance.

CONCLUSION:

Respondents from states with strong paid family and medical leave had a greater likelihood of breastfeeding and had lower odds of postpartum depression symptoms, with stronger associations among respondents with deliveries covered by Medicaid insurance. Despite major potential health benefits of paid family and medical leave, the United States remains one of the few countries without federally mandated paid parental leave.