Comparative (Meta)genomic Analysis and Ecological Profiling of Human Gut-Specific Bacteriophage φB124-14

Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14). In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic analysis of both phage failed to identify any homologous sequences in 136 non-human gut metagenomic datasets searched, supporting the human gut-specific nature of this phage. Moreover, a potential geographic variation in the carriage of these and related phage was revealed by analysis of their distribution and prevalence within 151 human gut microbiomes and viromes from Europe, America and Japan. Finally, ecological profiling of φB124-14 and φB40-8, using both gene-centric alignment-driven phylogenetic analyses, as well as alignment-free gene-independent approaches was undertaken. This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored ecological landscape within the human gut microbiome

The seeds of divergence: the economy of French North America, 1688 to 1760

Generally, Canada has been ignored in the literature on the colonial origins of divergence with most of the attention going to the United States. Late nineteenth century estimates of income per capita show that Canada was relatively poorer than the United States and that within Canada, the French and Catholic population of Quebec was considerably poorer. Was this gap long standing? Some evidence has been advanced for earlier periods, but it is quite limited and not well-suited for comparison with other societies. This thesis aims to contribute both to Canadian economic history and to comparative work on inequality across nations during the early modern period. With the use of novel prices and wages from Quebec—which was then the largest settlement in Canada and under French rule—a price index, a series of real wages and a measurement of Gross Domestic Product (GDP) are constructed. They are used to shed light both on the course of economic development until the French were defeated by the British in 1760 and on standards of living in that colony relative to the mother country, France, as well as the American colonies. The work is divided into three components. The first component relates to the construction of a price index. The absence of such an index has been a thorn in the side of Canadian historians as it has limited the ability of historians to obtain real values of wages, output and living standards. This index shows that prices did not follow any trend and remained at a stable level. However, there were episodes of wide swings—mostly due to wars and the monetary experiment of playing card money. The creation of this index lays the foundation of the next component. The second component constructs a standardized real wage series in the form of welfare ratios (a consumption basket divided by nominal wage rate multiplied by length of work year) to compare Canada with France, England and Colonial America. Two measures are derived. The first relies on a “bare bones” definition of consumption with a large share of land-intensive goods. This measure indicates that Canada was poorer than England and Colonial America and not appreciably richer than France. However, this measure overestimates the relative position of Canada to the Old World because of the strong presence of land-intensive goods. A second measure is created using a “respectable” definition of consumption in which the basket includes a larger share of manufactured goods and capital-intensive goods. This second basket better reflects differences in living standards since the abundance of land in Canada (and Colonial America) made it easy to achieve bare subsistence, but the scarcity of capital and skilled labor made the consumption of luxuries and manufactured goods (clothing, lighting, imported goods) highly expensive. With this measure, the advantage of New France over France evaporates and turns slightly negative. In comparison with Britain and Colonial America, the gap widens appreciably. This element is the most important for future research. By showing a reversal because of a shift to a different type of basket, it shows that Old World and New World comparisons are very sensitive to how we measure the cost of living. Furthermore, there are no sustained improvements in living standards over the period regardless of the measure used. Gaps in living standards observed later in the nineteenth century existed as far back as the seventeenth century. In a wider American perspective that includes the Spanish colonies, Canada fares better. The third component computes a new series for Gross Domestic Product (GDP). This is to avoid problems associated with using real wages in the form of welfare ratios which assume a constant labor supply. This assumption is hard to defend in the case of Colonial Canada as there were many signs of increasing industriousness during the eighteenth and nineteenth centuries. The GDP series suggest no long-run trend in living standards (from 1688 to circa 1765). The long peace era of 1713 to 1740 was marked by modest economic growth which offset a steady decline that had started in 1688, but by 1760 (as a result of constant warfare) living standards had sunk below their 1688 levels. These developments are accompanied by observations that suggest that other indicators of living standard declined. The flat-lining of incomes is accompanied by substantial increases in the amount of time worked, rising mortality and rising infant mortality. In addition, comparisons of incomes with the American colonies confirm the results obtained with wages— Canada was considerably poorer. At the end, a long conclusion is provides an exploratory discussion of why Canada would have diverged early on. In structural terms, it is argued that the French colony was plagued by the problem of a small population which prohibited the existence of scale effects. In combination with the fact that it was dispersed throughout the territory, the small population of New France limited the scope for specialization and economies of scale. However, this problem was in part created, and in part aggravated, by institutional factors like seigneurial tenure. The colonial origins of French America’s divergence from the rest of North America are thus partly institutional

The Science of Describing: Natural History in Renaissance Europe

Out of the diverse traditions of medical humanism, classical philology, and natural philosophy, Renaissance naturalists created a new science devoted to discovering and describing plants and animals. Drawing on published natural histories, manuscript correspondence, garden plans, travelogues, watercolors, and drawings, The Science of Describing reconstructs the evolution of this discipline of description through four generations of naturalists. In the late fifteenth and early sixteenth centuries, naturalists focused on understanding ancient and medieval descriptions of the natural world, but by the mid-sixteenth century naturalists turned toward distinguishing and cataloguing new plant and animal species. To do so, they developed new techniques of observing and recording, created botanical gardens and herbaria, and exchanged correspondence and specimens within an international community. By the early seventeenth century, naturalists began the daunting task of sorting through the wealth of information they had accumulated, putting a new emphasis on taxonomy and classification. Illustrated with woodcuts, engravings, and photographs, The Science of Describing is the first broad interpretation of Renaissance natural history in more than a generation and will appeal widely to an interdisciplinary audience. TABLE OF CONTENTS List of Figures Preface and Acknowledgments Conventions 1. Introduction 2. The World of Renaissance Natural History 3. The Humanist Invention of Natural History 4. A Science of Describing 5. Common Sense, Classification, and the Catalogue of Nature 6. Conclusion: What Was Renaissance Natural History ? Notes Bibliography Index [Source: Publisher\u27s catalogue copy

Exemplarity and the use of antiquity in Erasmus

This paper explores Erasmus’s creative response to the tension between his idealization of antiquity and his Christian commitments. Because he did not distinguish ethical judgments from taste, Erasmus contradicted himself on the value of antiquity and hedged it about with many restrictions

Natureâs Bible: Insects in Seventeenth-Century European Art and Science

Artists and naturalists in seventeenth-century Europe avidly pursued the study of insects. Since entomology had not yet become a distinct discipline, these studies were pursued within the framework of natural history, miniature painting, medicine, and anatomy. In the late sixteenth century the Renaissance naturalist Ulisse Aldrovandi collected and described individual insects and their lore but showed little sustained interest in their temporal transmutations; meanwhile, the court artist Joris Hoefnagel studied the structure of insects in order to paint real and imaginary insects while giving them an emblematic interpretation. By the middle of the seventeenth century the painter Johannes Goedaert was assiduously studying insect transformations, which he saw as evidence of Godâs wondrous works. His work was critiqued and systematized by the physicians Martin Lister and Jan Swammerdam, who insisted that orderly transformation was the best sign of Godâs handiwork. These examples show how verbal descriptions and illustrations of insects easily crossed disciplinary boundaries; knowledge generated in one particular context moved into others where it was critiqued but also employed in new investigation