Protists are ubiquitous components of terrestrial and aquatic environments, as well as animal and human microbiomes. Despite this, little is known about protists in urban environments. The ~7400-mile ...sewer system of New York City (NYC) collects human waste from ~8 million human inhabitants as well as from animals, street runoff, and groundwater, providing an ideal system to study these microbes. We used 18S rRNA amplicon sequencing and shotgun metagenomic sequencing to profile raw sewage microbial communities. Raw sewage samples were collected over a 12-month period from 14 treatment plants of the five NYC boroughs, and compared with samples from other environments including soil, stormwater, and sediment. Sewage contained a diverse protist community dominated by free-living clades, and communities were highly differentiated across environments. Seasonal differences in protist composition were observed; however, network analysis and functional profiling demonstrated that sewage communities were robust and functionally consistent. Protists typically associated with human and animal guts or feces were frequently detected. Abundance of these parasites varied significantly both spatially and temporally, suggesting that spikes could reflect trends in the source population. This underscores sewage as a valuable model system for monitoring patterns in urban microbes and provides a baseline protist metagenome of NYC.
Abstract
This article is focused on problematic distinctions of difference among animals in the lineage of great apes. It combines several theoretical perspectives on evolutionary relationships, ...technological innovation, the development of body parts as tools, and a semiotic interpretation of what André Leroi‐Gourhan called technicity. Foundational questions in social theory are developed using biosemiotics, particularly as concerns a materialist understanding of religion and the magical aspects of cultural representation. This, it is argued, provides a framework for theorizing social history in terms of real ecological relations, embodied meaning, and the transference of meaning onto objects. Understood semiotically, the material history of Hominidae, encompassing animals with different kinds of motility, dexterity, and techno‐semiotic orientations towards the world, is inclusive and relational rather than exclusively anthropocentric, as is the case for social theory based on the artifice of language and articulations of belief, creativity, and cultural distinction that are thought to be distinctive of the genus
Homo
.
Abstrait
Biosémiotique et histoire des hominidés : technicité, animaux et limites de l'exceptionnalisme humain
Résumé
Le présent article est consacré à des critères de distinction problématiques entre les espèces de la lignée des grands singes. Il combine plusieurs approches théoriques des relations évolutionnaires, de l'innovation technologique, du développement de parties du corps pour servir d'outils, avec une interprétation sémiotique de ce qu'André Leroi‐Gourhan appelait la technicité. Des questions fondamentales de théorie sociale sont développées à l'aide de la biosémiotique, notamment la compréhension matérialiste de la religion et les aspects magiques de la représentation culturelle. L'auteur avance que l'on dispose ainsi d'un cadre pour théoriser l'histoire sociale en termes de relations écologiques réelles, de signification incarnée et de transfert de la signification dans des objets. Sous l’éclairage de la sémiotique, l'histoire matérielle des hominidés, qui incluent des espèces diverses par leurs modes de motricité, leur dextérité et leur orientation techno‐sémiotiques vers le monde, est inclusive et relationnelle, et non exclusivement anthropocentrique comme l'est la théorie sociale basée sur l'artifice du langage et les articulations de croyance, de créativité et de distinction culturelle dans lesquelles on voit une caractéristique distinctive du genre
Homo
.
Many of the world's major cities are located in coastal zones, resulting in urban and industrial impacts on adjacent marine ecosystems. These pressures, which include pollutants, sewage, runoff and ...debris, temperature increases, hardened shorelines/structures, and light and acoustic pollution, have resulted in new evolutionary landscapes for coastal marine organisms. Marine environmental changes influenced by urbanization may create new selective regimes or may influence neutral evolution via impacts on gene flow or partitioning of genetic diversity across seascapes. While some urban selective pressures, such as hardened surfaces, are similar to those experienced by terrestrial species, others, such as oxidative stress, are specific to aquatic environments. Moreover, spatial and temporal scales of evolutionary responses may differ in the ocean due to the spatial extent of selective pressures and greater capacity for dispersal/gene flow. Here, we present a conceptual framework and synthesis of current research on evolutionary responses of marine organisms to urban pressures. We review urban impacts on genetic diversity and gene flow and examine evidence that marine species are adapting, or are predicted to adapt, to urbanization over rapid evolutionary time frames. Our findings indicate that in the majority of studies, urban stressors are correlated with reduced genetic diversity. Genetic structure is often increased in urbanized settings, but artificial structures can also act as stepping stones for some hard‐surface specialists, promoting range expansion. Most evidence for rapid adaptation to urban stressors comes from studies of heritable tolerance to pollutants in a relatively small number of species; however, the majority of marine ecotoxicology studies do not test directly for heritability. Finally, we highlight current gaps in our understanding of evolutionary processes in marine urban environments and present a framework for future research to address these gaps.
Medical systems function in specific cultural contexts. It is common to speak of the medicine of China, Japan, India, and other nation-states. Yet almost all formalized medical systems claim ...universal applicability and, thus, are ready to cross the cultural boundaries that contain them. There is a critical tension, in theory and practice, in the ways regional medical systems are conceptualized as "nationalistic" or inherently transnational. This volume is concerned with questions and problems created by the friction between nationalism and transnationalism at a time when globalization has greatly complicated the notion of cultural, political, and economic boundedness. Offering a range of perspectives, the contributors address questions such as: How do states concern themselves with the modernization of "traditional" medicine? How does the global hegemony of science enable the nationalist articulation of alternative medicine? How do global discourses of science and "new age" spirituality facilitate the transnationalization of "Asian" medicine? As more and more Asian medical practices cross boundaries into Western culture through the popularity of yoga and herbalism, and as Western medicine finds its way east, these systems of meaning become inextricably interrelated. These essays consider the larger implications of transmissions between cultures.
Salt marshes play an important role in the global nutrient cycle. The sediments in these systems harbor diverse and complex bacterial communities possessing metabolic capacities that provide ...ecosystem services such as nutrient cycling and removal. On the East Coast of the USA, salt marshes have been experiencing degradation due to anthropogenic stressors. Salt marsh islands within Jamaica Bay, New York City (USA), are surrounded by a large highly urbanized watershed and have declined in area. Restoration efforts have been enacted to reduce further loss, but little is known about how microbial communities develop following restoration activities, or how processes such as nitrogen cycling are impacted. Sediment samples were collected at two sampling depths from five salt marsh islands to characterize the bacterial communities found in marsh sediment including a post-restoration chronosequence of 3–12 years. We used 16s rRNA amplicon sequencing to define alpha and beta diversity, taxonomic composition, and predicted metabolic profile of each sediment sample. We found significant differences in alpha diversity between sampling depths, and significant differences in beta diversity, taxonomic composition, and predicted metabolic capacity among the five sampling locations. The youngest restored site and the degraded natural sampling site exhibited the most distinct communities among the five sites. Our findings suggest that while the salt marsh islands are located in close proximity to each other, they harbor distinct bacterial communities that can be correlated with post-restoration age, marsh health, and other environmental factors such as availability of organic carbon.
Importance
Salt marshes play a critical role in the global nutrient cycle due to sediment bacteria and their metabolic capacities. Many East Coast salt marshes have experienced significant degradation over recent decades, thought largely to be due to anthropogenic stressors such as nitrogen loading, urban development, and sea-level rise. Salt marsh islands in Jamaica Bay (Queens/Brooklyn NY) are exposed to high water column nitrogen due to wastewater effluent. Several receding marsh islands have been subjected to restoration efforts to mitigate this loss. Little is known about the effect marsh restoration has on bacterial communities, their metabolic capacity, or how they develop post-restoration. Here, we describe the bacterial communities found in marsh islands including a post-restoration chronosequence of 3–12 years and one degraded marsh island that remains unrestored. We found distinct communities at marsh sites, despite their geographic proximity. Differences in diversity and community composition were consistent with changes in organic carbon availability that occur during marsh development, and may result in differences in ecosystem function among sites.
Service systems produce all services of significance and scope, yet the concept of a service system is not well articulated in the service literature. This paper presents three interrelated ...frameworks as a first attempt to define the fundamentals of service systems. These frameworks identify basic building blocks and organize important attributes and change processes that apply across all service systems. Although relevant regardless of whether a service system uses information technology, the frameworks are also potentially useful in visualizing the realities of moving toward automated service architectures. This paper uses two examples, one largely manual and one highly automated, to illustrate the potential usefulness of the three frameworks, which can be applied together to describe, analyze, and study how service systems are created, how they operate, and how they evolve through a combination of planned and unplanned change. PUBLICATION ABSTRACT
Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of ...particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Premise of the Study
Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes that drive their diversification and genetic differentiation. ...Distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, although asexual and sexual reproductive structures are observable, the lack of information about recombination rates makes inferences about reproductive strategies difficult. We investigated the population genomics of Cetradonia linearis, a federally endangered lichen in the southern Appalachians of eastern North America, to test the relative contributions of environmental and geographic distance in shaping genetic structure, and to characterize the mating system and genome‐wide recombination.
Methods
Whole‐genome shotgun sequencing was conducted to generate data for 32 individuals of C. linearis. A reference genome was assembled, and reads from all samples were aligned to generate a set of single‐nucleotide polymorphisms for further analyses.
Key Results
We found evidence for low rates of recombination and for isolation by distance, but not for isolation by environment. The species is putatively unisexual, given that only one mating‐type locus was found. Hindcast species distribution models and the distribution of genetic diversity support C. linearis having a larger range during the Last Glacial Maximum in the southern portion of its current extent.
Conclusions
Our findings contribute to the understanding of factors that shape genetic diversity in C. linearis and in fungi more broadly. Because all populations are highly genetically differentiated, the extirpation of any population would mean the loss of unique genetic diversity; therefore, our results support the continued conservation of this species.
Climatic and geomorphological changes during the Quaternary period impacted global patterns of speciation and diversification across a wide range of taxa, but few studies have examined these effects ...on African riverine fishes. The lower Congo River is an excellent natural laboratory for understanding complex speciation and population diversification processes as it is hydrologically extremely dynamic and recognized as a continental hotspot of diversity harboring many narrowly endemic species. A previous study using genome-wide SNP data highlighted the importance of dynamic hydrological regimes to the diversification and speciation in lower Congo River cichlids. However, historical climate and hydrological changes (e.g., reduced river discharge during extended dry periods) have likely also influenced ichthyofaunal diversification processes in this system. The lower Congo River offers a unique opportunity to study climate-driven changes in river discharge, given the massive volume of water from the entire Congo basin flowing through this short stretch of the river. Here, we, for the first time, investigate the impacts of paleoclimatic factors on ichthyofaunal diversification in this system by inferring divergence times and modeling patterns of gene flow in four endemic lamprologine cichlids, including the blind cichlid, Lamprologus lethops. Our results suggest that Quaternary climate changes associated with river discharge fluctuations may have impacted the diversification of species along the system. Our study, using reduced representation sequencing (2RADseq), indicates that the lower Congo River lamprologines emerged during the Early-Middle Pleistocene transition, characterized as one of the earth's major climatic transformation periods. Modeling results suggest that gene flow across populations and between species was not constant but occurred in temporally constrained pulses. We show that these results correlate with glacial-interglacial fluctuations. The current hyper-diverse fish assemblages of the lower Congo River riverscape likely reflect the synergistic effects of multiple drivers fueling complex evolutionary processes through time.
Efficacy and Effectiveness of Antidepressants Pigott, H. Edmund; Leventhal, Allan M.; Alter, Gregory S. ...
Psychotherapy and psychosomatics,
01/2010, Letnik:
79, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Background: This paper examines the current status of research on the efficacy and effectiveness of antidepressants. Methods: This paper reviews four meta-analyses of efficacy trials submitted to ...America’s Food and Drug Administration (FDA) and analyzes STAR*D (Sequenced Treatment Alternatives to Relieve Depression), the largest antidepressant effectiveness trial ever conducted. Results: Meta-analyses of FDA trials suggest that antidepressants are only marginally efficacious compared to placebos and document profound publication bias that inflates their apparent efficacy. These meta-analyses also document a second form of bias in which researchers fail to report the negative results for the pre-specified primary outcome measure submitted to the FDA, while highlighting in published studies positive results from a secondary or even a new measure as though it was their primary measure of interest. The STAR*D analysis found that the effectiveness of antidepressant therapies was probably even lower than the modest one reported by the study authors with an apparent progressively increasing dropout rate across each study phase. Conclusions: The reviewed findings argue for a reappraisal of the current recommended standard of care of depression.
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