Phylodynamic Patterns in Pathogen Ecology and Evolution.

The rapid evolution of viral pathogens requires us to consider epidemiological, ecological and evolutionary processes as coupled together and occurring at the same timescale. Rotavirus and influenza account for high levels of morbidity and mortality worldwide and are two important examples of such dynamics. In this work, I investigate the different evolutionary and ecological processes that shape the antigenic structure and phylogenetic characteristics of these two viruses. In the first part of my work, I use a theoretical model of influenza A/H3N2 to identify the relative importance of antigenic novelty, competition between lineages, and changes in the susceptibility of the host population to circulating strains in determining the evolutionary and epidemiological trajectory of the virus. I develop this model further to correspond with patterns of immunity and infection observed in rotavirus, and investigate how reassortment, the swapping of gene segments between viruses, influences the formation and replacement of rotavirus genotypes through immune mediated processes. In the second part of my work, I use a tool (SeasMig), which I developed, to infer alternative stochastically generated migration and mutation events along phylogenetic trees in a Bayesian manner. Using SeasMig, I first show how the seasonality of A/H3N2 influenza incidence corresponds to rates of immigration and emigration of the virus. Subsequently, I tease out the different evolutionary and ecological processes, which drive changes in the US rotavirus population following onset of routine vaccination. My work has implications for identifying likely evolutionary mechanisms, which may lead to reduced vaccine efficacy, and for vaccine strain selection.PhDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113494/1/dzinder_1.pd

Common myths about electrosurgery

The electrosurgery device market is lucrative and highly competitive. Several device manufacturers exist, and many creative techniques are used to differentiate products. Some device manufacturers make claims in marketing campaigns that are difficult to reconcile with the laws of physics or basic physiology. The variety of claims may be confusing to surgeons desiring to purchase new electrosurgical products. Understanding a few basic principles of electrosurgery physics can allow a surgeon to be a more informed consumer of electrosurgical products. This article discusses the basic physics of electrosurgery and then addresses several common misconceptions about electrosurgery and electrosurgical device

Shrinking Suburbs in a Time of Crisis

The Routledge Companion to the Suburbs provides one of the most comprehensive examinations available to date of the suburbs around the world. International in scope and interdisciplinary in nature, this volume will serve as the definitive reference for scholars and students of the suburbs. This volume brings together the leading scholars of the suburbs researching in different parts of the world to better understand how and why suburbs and their communities grow, decline, and regenerate. The volume sets out four goals: 1) to provide a synthesis and critical appraisal of the historical and current state of understanding about the development of suburbs in the world; 2) to provide a forum for a comprehensive examination into the conceptual, theoretical, spatial, and empirical discontents of suburbanization; 3) to engage in a scholarly conversation about the transformation of suburbs that is interdisciplinary in nature and bridges the divide between the Global North and the Global South; and 4) to reflect on the implications of the socioeconomic, cultural, and political transformations of the suburbs for policymakers and planners. The Routledge Companion to the Suburbs is composed of original, scholarly contributions from the leading scholars of the study of how and why suburbs grow, decline, and transform. Special attention is paid to the global nature of suburbanization and its regional variations, with a focus on comparative analysis of suburbs through regions across the world in the Global North and the Global South. Articulated in a common voice, the volume is integrated by the very nature of the concept of a suburb as the unit of analysis, offering multidisciplinary perspectives from the fields of economics, geography, planning, political science, sociology, and urban studies.https://scholarworks.wm.edu/asbookchapters/1069/thumbnail.jp

Für mehr Zirkularität - Flächenbedarfe der Bauschuttaufbereitung als Grundlage zur Kreislaufführung mineralischer Bau- und Abbruchmaterialien

Der Einsatz hochqualitativer, mineralischer Sekundärrohstoffe spielt im sächsischen Bausektor eine untergeordnete Rolle. Fehlende Informationen und Planungen über geeignete Flächen zur Errichtung von Bauschuttaufbereitungsanlagen zur Herstellung von Sekundärmaterialien hemmen den Ausbau der Aufbereitungskapazitäten. Das vorgestellte Flächenbedarfsabschätzungs-Tool soll dem entgegenwirken. Es ermöglicht anhand identifizierter Kriterien die Suche nach geeigneten Flächen sowie das Ranking potenzieller Standorte und damit den Abgleich von Flächenbedarf und -angebot auf Basis frei verfügbarer Geodaten. Erste Ergebnisse der Analysen zeigen, dass die Flächennachfrage größer ist als das Flächenangebot. Perspektivisch muss diese Flächennachfrage im Zuge der strategischen Flächennutzungs- und Regionalplanung berücksichtigt werden, wenn die Kapazitäten der Bauschuttaufbereitung erhöht werden sollen. Das Flächenbedarfsabschätzungs-Tool soll den Planungsträgern zur eigenständigen Nutzung übergeben werden und so Planungsprozesse unterstützen

Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline

Background: Influenza A/H3N2 has been circulating in humans since 1968, causing considerable morbidity and mortality. Although H3N2 incidence is highly seasonal, how such seasonality contributes to global phylogeographic migration dynamics has not yet been established. Results: Incorporating seasonally varying migration rates improves the modeling of migration. In our global model, windows of increased immigration map to the seasonal timing of epidemic spread, while windows of increased emigration map to epidemic decline. Seasonal patterns also correlate with the probability that local lineages go extinct and fail to contribute to long term viral evolution, as measured through the trunk of the phylogeny. However, the fraction of the trunk in each community was found to be better determined by its overall human population size Conclusions: Seasonal migration and rapid turnover within regions is sustained by the invasion of 'fertile epidemic grounds' at the end of older epidemics. Thus, the current emphasis on connectivity, including air-travel, should be complemented with a better understanding of the conditions and timing required for successful establishment.Models which account for migration seasonality will improve our understanding of the seasonal drivers of influenza,enhance epidemiological predictions, and ameliorate vaccine updating by identifying strains that not only escape immunity but also have the seasonal opportunity to establish and spread. Further work is also needed on additional conditions that contribute to the persistence and long term evolution of influenza within the human population,such as spatial heterogeneity with respect to climate and seasonalityComment: in BMC Evolutionary Biology 2014, 1

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the ‘pink berry’ consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and 34S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0–500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ34S-sulfide decreased from 6‰ to −31‰ from the exterior to interior of the berry. These values correspond to sulfate–sulfide isotopic fractionations (15–53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the ‘pink berry’ consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and 34S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0–500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ34S-sulfide decreased from 6‰ to −31‰ from the exterior to interior of the berry. These values correspond to sulfate–sulfide isotopic fractionations (15–53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria

Non Coding RNAs and Viruses in the Framework of the Phylogeny of the Genes, Epigenesis and Heredity

The origin of genes is one of the most enigmatic events in the origin of life. It has been suggested that noncoding (nc) RNA was probably a precursor in the formation of the first polypeptide, and also at the origin of the first manifestation of life and genes. ncRNAs are also becoming central for understanding gene expression and silencing. Indeed, before the discovery of ncRNAs, proteins were viewed as the major molecules in the regulation of gene expression and gene silencing; however, recent findings suggest that ncRNA also plays an important role in gene expression. Reverse transcription of RNA viruses and their integration into the genome of eukaryotes and also their relationship with the ncRNA suggest that their origin is basal in genome evolution, and also probably constitute the first mechanism of gene regulation. I am to review the different roles of ncRNAs in the framework of gene evolution, as well as the importance of ncRNAs and viruses in the epigenesis and in the non-Mendelian model of heredity and evolution

Pathways and bioenergetics of anaerobic carbon monoxide fermentation

Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the potential of converting CO-rich gas, such as synthesis gas, into bio-based products. Three main types of fermentative CO metabolism can be distinguished: hydrogenogenesis, methanogenesis, and acetogenesis, generating hydrogen, methane and acetate, respectively. Here, we review the current knowledge on these three variants of microbial CO metabolism with an emphasis on the potential enzymatic routes and bio-energetics involved.The authors involved were financially supported by an ERC grant (project 323009) and the Gravitation grant (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science Foundation (NWO)