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The plasmid-encoded quinolone resistance gene qnrS1 was recently found to be commonly associated with ciprofloxacin resistance in Nigeria. We mapped the qnrS1 gene from an Escherichia coli isolate obtained in Nigeria to a 43.5 Kb IncX2 plasmid. The plasmid, pEBG1, was sufficient to confer ciprofloxacin non-susceptibility, as well as tetracycline and trimethoprim resistance, on E. coli K-12. Deletion analysis confirmed that qnrS1 accounted for all the ciprofloxacin non-suceptibility conferred by pEBG1 and tetracycline and trimethoprim resistance could be attributed to tetAR and dfrA14 genes respectively. While it contained a complete IncX conjugation system, pEBG1 was not self-transmissible likely due to an IS3 element inserted between the pilX5 and pilX6 genes. The plasmid was however efficiently mobilizable. pEBG1 was most similar to another qnrS1-bearing IncX2 plasmid from Nigeria, but both plasmids acquired qnrS1 independently and differ in their content of other resistance genes. Screening qnrS1-positive isolates from other individuals in Nigeria revealed that they carried neither pEBG1 nor pNGX2-QnrS1 but that IncX plasmids were prevalent. This study demonstrates that the IncX backbone is a flexible platform that has contributed to qnrS1 dissemination in Nigeria.

The plasmid-encoded quinolone resistance gene qnrS1 was recently found to be commonly associated with ciprofloxacin resistance in Nigeria. We mapped the qnrS1 gene from an Escherichia coli isolate obtained in Nigeria to a 43.5 Kb IncX2 plasmid. The plasmid, pEBG1, was sufficient to confer ciprofloxacin non-susceptibility, as well as tetracycline and trimethoprim resistance, on E. coli K-12. Deletion analysis confirmed that qnrS1 accounted for all the ciprofloxacin non-suceptibility conferred by pEBG1 and tetracycline and trimethoprim resistance could be attributed to tetAR and dfrA14 genes respectively. While it contained a complete IncX conjugation system, pEBG1 was not self-transmissible likely due to an IS3 element inserted between the pilX5 and pilX6 genes. The plasmid was however efficiently mobilizable. pEBG1 was most similar to another qnrS1-bearing IncX2 plasmid from Nigeria, but both plasmids acquired qnrS1 independently and differ in their content of other resistance genes. Screening qnrS1-positive isolates from other individuals in Nigeria revealed that they carried neither pEBG1 nor pNGX2-QnrS1 but that IncX plasmids were prevalent. This study demonstrates that the IncX backbone is a flexible platform that has contributed to qnrS1 dissemination in Nigeria.

As urban growth expands and natural environments fragment, it is essential to understand the ecological roles fulfilled by urban green spaces. To evaluate how urban green spaces function as wildlife habitat, we estimated mammal diversity and metacommunity dynamics in city parks, cemeteries, golf courses, and natural areas throughout the greater Chicago, Illinois, USA region. We found similar α-diversity (with the exception of city parks), but remarkably dissimilar communities in different urban green spaces. Additionally, the type of urban green space greatly influenced species colonization and persistence rates. For example, coyotes (Canis latrans) had the highest, but white-tailed deer (Odocoileus virginianus) the lowest probability of persistence in golf courses compared to other green space types. Further, most species had a difficult time colonizing city parks even when sites were seemingly available. Our results indicate that urban green spaces contribute different, but collectively important, habitats for maintaining and conserving biodiversity in cities.

Research on urban wildlife can help promote coexistence and guide future interactions between humans and wildlife in developed regions, but most such investigations are limited to short-term, single-species studies, typically conducted within a single city. This restricted focus prevents scientists from recognizing global patterns and first principles regarding urban wildlife behavior and ecology. To overcome these limitations, we have designed a pioneering research network, the Urban Wildlife Information Network (UWIN), whereby partners collaborate across several cities to systematically collect data to populate long-term datasets on multiple species in urban areas. Data collected via UWIN support analyses that will enable us to build basic theory related to urban wildlife ecology. An analysis of mammals in seven metropolitan regions suggests that common species are similar across cities, but relative rates of occupancy differ markedly. We ultimately view UWIN as an applied tool that can be used to connect the public to urban nature at a continental scale, and provide information critical to urban planners and landscape architects. Our network therefore has the potential to advance knowledge and to improve the ability to plan and manage cities to support biodiversity.

Time is a fundamental component of ecological processes. How animal behavior changes over time has been explored through well-known ecological theories like niche partitioning and predator–prey dynamics. Yet, changes in animal behavior within the shorter 24-hr light–dark cycle have largely gone unstudied. Understanding if an animal can adjust their temporal activity to mitigate or adapt to environmental change has become a recent topic of discussion and is important for effective wildlife management and conservation. While spatial habitat is a fundamental consideration in wildlife management and conservation, temporal habitat is often ignored. We formulated a temporal resource selection model to quantify the diel behavior of 8 mammal species across 10 US cities. We found high variability in diel activity patterns within and among species and species-specific correlations between diel activity and human population density, impervious land cover, available greenspace, vegetation cover, and mean daily temperature. We also found that some species may modulate temporal behaviors to manage both natural and anthropogenic risks. Our results highlight the complexity with which temporal activity patterns interact with local environmental characteristics, and suggest that urban mammals may use time along the 24-hr cycle to reduce risk, adapt, and therefore persist, and in some cases thrive, in human-dominated ecosystems.

Biomass burning (BB) is a primary source of atmospheric chemistry reactants, aerosols, and greenhouse gases. Smoke plumes have air quality impacts local to the fire itself and regionally via long distance transport. Open burning of agriculture fields in Southeast Asia leads to frequent seasonal occurrences of regional BB-induced smoke haze and long-range transport of BB particles via the northeast monsoon. The Airborne and Satellite Investigation of Asian Air Quality (ASIA-AQ) campaign visited several areas including the Philippines, South Korea, Thailand, and Taiwan during a time of agricultural burning. This campaign consisted of airborne measurements on the NASA DC-8 aircraft aimed to validate observations from South Korea's Geostationary Environment Monitoring Spectrometer (GEMS) and to address local air quality challenges. We developed a method that used a combination of BB markers to identify ASIA-AQ DC-8 data influenced by BB and flag them for further analysis. Specifically, we used rolling slope enhancement ratios of CO/CO2 and CH4/CO along with mixing ratios of CH3CN, HCN, and CO, and particle scattering coefficient measurements. The flag was triggered when a combination of these variables exceeded a flight specific threshold. We found varying levels of BB-influence in the areas studied, with data flagged for BB being < 1 % for the Philippines and Korea, and < 2 % for Taiwan, but 19 % for Thailand. Our method for flagging ASIA-AQ BB-affected data can be used to focus additional analyses of the ASIA-AQ campaign such as pairing with back trajectories, satellite hotspot products, and microphysical aerosol characteristics.

Cloud droplet chemical composition is a key observable property that can aid understanding of how aerosols and clouds interact. As part of the Clouds, Aerosols and Monsoon Processes – Philippines Experiment (CAMP2Ex), three case studies were analyzed involving collocated airborne sampling of relevant clear and cloudy air masses associated with maritime warm convection. Two of the cases represented a polluted marine background, with signatures of transported East Asian regional pollution, aged over water for several days, while the third case comprised a major smoke transport event from Kalimantan fires. Sea salt was a dominant component of cloud droplet composition, in spite of fine particulate enhancement from regional anthropogenic sources. Furthermore, the proportion of sea salt was enhanced relative to sulfate in rainwater and may indicate both a propensity for sea salt to aid warm rain production and an increased collection efficiency of large sea salt particles by rain in subsaturated environments. Amongst cases, as precipitation became more significant, so too did the variability in the sea salt to (non-sea salt) sulfate ratio. Across cases, nitrate and ammonium were fractionally greater in cloud water than fine-mode aerosol particles; however, a strong covariability in cloud water nitrate and sea salt was suggestive of prior uptake of nitrate on large salt particles. A mass-based closure analysis of non-sea salt sulfate compared the cloud water air-equivalent mass concentration to the concentration of aerosol particles serving as cloud condensation nuclei for droplet activation. While sulfate found in cloud was generally constrained by the sub-cloud aerosol concentration, there was significant intra-cloud variability that was attributed to entrainment – causing evaporation of sulfate-containing droplets –and losses due to precipitation. In addition, precipitation tended to promote mesoscale variability in the sub-cloud aerosol through a combination of removal, convective downdrafts, and dynamically driven convergence. Physical mechanisms exerted such strong control over the cloud water compositional budget that it was not possible to isolate any signature of chemical production/loss using in-cloud observations. The cloud-free environment surrounding the non-precipitating smoke case indicated sulfate enhancement compared to convective mixing quantified by a stable gas tracer; however, this was not observed in the cloud water (either through use of ratios or the mass closure), perhaps implying that the warm convective cloud timescale was too short for chemical production to be a leading-order budgetary term and because precursors had already been predominantly exhausted. Closure of other species was truncated by incomplete characterization of coarse aerosol (e.g., it was found that only 10 %–50% of sea salt mass found in cloud was captured during clear-air sampling) and unmeasured gasphase abundances affecting closure of semi-volatile aerosol species (e.g., ammonium, nitrate and organic) and soluble volatile organic compound contributions to total organic carbon in cloud water.

Understanding how biodiversity responds to urbanization is challenging, due in part to the single-city focus of most urban ecological research. Here, we delineate continent-scale patterns in urban species assemblages by leveraging data from a multi-city camera trap survey and quantify how differences in greenspace availability and average housing density among 10 North American cities relate to the distribution of eight widespread North American mammals. To do so, we deployed camera traps at 569 sites across these ten cities between 18 June and 14 August. Most data came from 2017, though some cities contributed 2016 or 2018 data if it was available. We found that the magnitude and direction of most species’ responses to urbanization within a city were associated with landscape-scale differences among cities. For example, eastern gray squirrel (Sciurus carolinensis), fox squirrel (Sciurus niger), and red fox (Vulpes vulpes) responses to urbanization changed from negative to positive once the proportion of green space within a city was >∼20%. Likewise, raccoon (Procyon lotor) and Virginia opossum (Didelphis virginiana) responses to urbanization changed from positive to negative once the average housing density of a city exceeded about 700 housing units/km². We also found that local species richness within cities consistently declined with urbanization in only the more densely developed cities (>∼700 housing units/km²). Given our results, it may therefore be possible to design cities to better support biodiversity and reduce the negative influence of urbanization on wildlife by, for example, increasing the amount of green space within a city. Additionally, it may be most important for densely populated cities to find innovative solutions to bolster wildlife resilience because they were the most likely to observe diversity losses of common urban species.

The NASA North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) ship and aircraft field campaign deployed to the western subarctic Atlantic between the years 2015 and 2018. One of the primary goals of NAAMES is to improve the understanding of aerosol–cloud interaction (ACI) over the Atlantic Ocean under different seasonal regimes. ACIs currently represent the largest source of uncertainty in global climate models. During three NAAMES field campaigns (NAAMES-1 in November 2015, NAAMES-2 in May 2016, and NAAMES-3 in September 2017), multiple 10 h science flights were conducted using the NASA C-130 aircraft to measure marine boundary layer aerosol and cloud properties. The standard flight pattern includes vertical spirals where the C-130 transitioned from high altitude to low altitude (and vice versa), collecting in situ measurements of aerosols, trace gases, clouds, and meteorological parameters as a function of altitude. We examine the data collected from 37 spirals during the three NAAMES field campaigns, and we present a comprehensive characterization of the vertical profiles of aerosol properties under different synoptic conditions and aerosol regimes. The vertical distribution of submicron aerosol particles exhibited strong seasonal variation, as well as elevated intra-seasonal variability depending on emission sources and aerosol processes in the atmospheric column. Pristine marine conditions and new particle formation were prevalent in the wintertime (NAAMES-1) due to low biogenic emissions from the surface ocean and reduced continental influence. Higher concentrations of submicron aerosol particles were observed in the spring (NAAMES-2) due to strong phytoplankton activity and the arrival of long-range-transported continental plumes in the free troposphere with subsequent entrainment into the marine boundary layer. Biomass burning from boreal wildfires was the main source of aerosol particles in the region during the late summer (NAAMES-3) in both the marine boundary layer and free troposphere.

The ongoing Antibody Mediated Prevention (AMP) trials will uncover whether passive infusion of the broadly neutralizing antibody (bNAb) VRC01 can protect against HIV acquisition. Previous statistical simulations indicate these trials may be partially protective. In that case, it will be crucial to identify the mechanism of breakthrough infections. To that end, we developed a mathematical modeling framework to simulate the AMP trials and infer the breakthrough mechanisms using measurable trial outcomes. This framework combines viral dynamics with antibody pharmacokinetics and pharmacodynamics, and will be generally applicable to forthcoming bNAb prevention trials. We fit our model to human viral load data (RV217). Then, we incorporated VRC01 neutralization using serum pharmacokinetics (HVTN 104) and in vitro pharmacodynamics (LANL CATNAP database). We systematically explored trial outcomes by reducing in vivo potency and varying the distribution of sensitivity to VRC01 in circulating strains. We found trial outcomes could be used in a clinical trial regression model (CTRM) to reveal whether partially protective trials were caused by large fractions of VRC01-resistant (IC50>50 μg/mL) circulating strains or rather a global reduction in VRC01 potency against all strains. The former mechanism suggests the need to enhance neutralizing antibody breadth; the latter suggests the need to enhance VRC01 delivery and/or in vivo binding. We will apply the clinical trial regression model to data from the completed trials to help optimize future approaches for passive delivery of anti-HIV neutralizing antibodies.