A modified anthrax toxin-based enzyme-linked immunospot assay reveals robust T cell responses in symptomatic and asymptomatic Ebola virus exposed individuals

Background Ebola virus (EBOV) caused more than 11,000 deaths during the 2013–2016 epidemic in West Africa without approved vaccines or immunotherapeutics. Despite its high lethality in some individuals, EBOV infection can produce little to no symptoms in others. A better understanding of the immune responses in individuals who experienced minimally symptomatic and asymptomatic infection could aid the development of more effective vaccines and antivirals against EBOV and related filoviruses. Methodology/Principle findings Between August and November 2017, blood samples were collected from 19 study participants in Lagos, Nigeria, including 3 Ebola virus disease (EVD) survivors, 10 individuals with documented close contact with symptomatic EVD patients, and 6 control healthcare workers for a cross-sectional serosurvey and T cell analysis. The Lagos samples, as well as archived serum collected from healthy individuals living in surrounding areas of the 1976 Democratic Republic of Congo (DRC) epidemic, were tested for EBOV IgG using commercial enzyme-linked immunosorbent assays (ELISAs) and Western blots. We detected antibodies in 3 out of 3 Lagos survivors and identified 2 seropositive individuals not known to have ever been infected. Of the DRC samples tested, we detected antibodies in 9 out of 71 (12.7%). To characterize the T cell responses in the Lagos samples, we developed an anthrax toxin-based enzyme-linked immunospot (ELISPOT) assay. The seropositive asymptomatic individuals had T cell responses against EBOV nucleoprotein, matrix protein, and glycoprotein 1 that were stronger in magnitude compared to the survivors. Conclusion/Significance Our data provide further evidence of EBOV exposure in individuals without EVD-like illness and, for the first time, demonstrate that these individuals have T cell responses that are stronger in magnitude compared to severe cases. These findings suggest that T cell immunity may protect against severe EVD, which has important implications for vaccine development

Stable-isotope techniques to investigate sources of plant water

Stable isotopologues of water (mainly 1H216O, HD16O and 1H218O) have been used for decades as tracers of the Earth's water cycle. In this chapter, we briefly describe the theoretical background and state-of-the-art techniques of the use of water stable isotopes to investigate the sources of plant water. We aim to provide the basic understanding of stable isotope fractionation within the Earth's critical zone that is relevant for studies of plant water sources. We then present a practical guide of their most common applications in field studies and the most common and up-to-date laboratory procedures. We finally introduce the existing statistical approaches for estimating the relative contributions of water sources to plant transpiration. By acknowledging the advantages and limitations of each approach, we aim to provide an overview of the current techniques to researchers in the fields of plant ecophysiology, ecohydrology and forest ecology, so that they can make informed decisions when designing their experiments

Dynamic, structured heterogeneity of water isotopes inside hillslopes

Use of the stable isotopes of water (δD, δ18O) to determine vegetative water sources, runoff paths, and residence times generally assumes that, other than shallow evaporative enrichment, the isotopic composition of precipitation is conserved as it travels through the subsurface to the stream channel. Here we follow rainfall through a thick (up to 25m) vadose zone of soil, saprolite, and weathered bedrock mostly composed of argillite, and underlying a steep (32°) forested hillslope. We discover a persistent structured heterogeneity of water isotopes inside the hillslope. Summer dry season causes evaporative enrichment of the soil, but not in the saprolite and weathered bedrock. In winter, the mobile water, generated by successive rainstorms with widely varying isotopic composition, mixes in the vadose zone, elevating soil and rock moisture content, and eventually recharging the groundwater with isotopically invariant water similar to the seasonally averaged rainfall. Yet throughout the winter the less mobile winter soil and rock moisture remains relatively light, and water extracted from the interior of argillite lies well to the left of the local meteoric water line. This persistently light composition of soil and rock moisture and the deviation from average meteoric values suggest that subsurface fractionation, or the inheritance of paleo-meteoric rock moisture associated with rock uplift may lead to large enduring isotopic differences between high and low mobility water. These differences suggest that the use of water isotopes as tracers must consider the possibility of subsurface isotopic evolution and the influence of exchange with more tightly held water

Species differences in the seasonality of evergreen tree transpiration in a Mediterranean climate: Analysis of multiyear, half-hourly sap flow observations

In Mediterranean climates, the season of water availability (winter) is out of phase with the season of light availability and atmospheric moisture demand (summer). We investigate the seasonality of evergreen tree transpiration in a Mediterranean climate, using observations from a small (4000 m2), forested, steep (32) hillslope, in the northern California Coast Range. We analyze 3 years of half-hourly measurements from 39 sap flow sensors in 26 trees, six depth profiles of soil moisture measured by TDR, and spatially distributed measurements of micrometeorology from five locations. The sap flow measurements show that two common evergreen tree species have different seasons of peak transpiration. Douglas-firs (Pseudotsuga menziesii) maintain significant transpiration through the winter rainy season and transpire maximally in the spring, followed by a sharp decline in transpiration in the summer dry season. Pacific madrones (Arbutus menziesii), and to a lesser extent other broadleaf evergreen species (Quercus wislizeni, Notholithocarpus densiflorus, Umbellularia californica), in contrast, transpire maximally in the summer dry season. The seasonal patterns are quantified using principal component analysis. Markov chain Monte Carlo estimation of response to environmental variables shows that the difference in transpiration seasonality arises from different sensitivities to atmospheric evaporative demand and root-zone moisture. The different sensitivities to atmospheric evaporative demand also create species differences in transpiration variability at synoptic time scales. Using the sap flow measurements and a regional forest inventory, a bottom-up regional transpiration estimate is constructed. The estimate suggests that sensitivity of Douglas-fir transpiration to water stress suppresses dry season evapotranspiration at the regional scale. Key Points Three year, half-hourly record of sap flow, micrometeorology, and soil moisture PCA shows offset in peak transpiration season between needleleaf and broadleaf species Douglas-fir water stress response could reduce dry season transpiration at large scale © 2014. American Geophysical Union. All Rights Reserved

Species differences in the seasonality of evergreen tree transpiration in a Mediterranean climate: Analysis of multiyear, half-hourly sap flow observations

In Mediterranean climates, the season of water availability (winter) is out of phase with the season of light availability and atmospheric moisture demand (summer). We investigate the seasonality of evergreen tree transpiration in a Mediterranean climate, using observations from a small (4000 m2), forested, steep (32) hillslope, in the northern California Coast Range. We analyze 3 years of half-hourly measurements from 39 sap flow sensors in 26 trees, six depth profiles of soil moisture measured by TDR, and spatially distributed measurements of micrometeorology from five locations. The sap flow measurements show that two common evergreen tree species have different seasons of peak transpiration. Douglas-firs (Pseudotsuga menziesii) maintain significant transpiration through the winter rainy season and transpire maximally in the spring, followed by a sharp decline in transpiration in the summer dry season. Pacific madrones (Arbutus menziesii), and to a lesser extent other broadleaf evergreen species (Quercus wislizeni, Notholithocarpus densiflorus, Umbellularia californica), in contrast, transpire maximally in the summer dry season. The seasonal patterns are quantified using principal component analysis. Markov chain Monte Carlo estimation of response to environmental variables shows that the difference in transpiration seasonality arises from different sensitivities to atmospheric evaporative demand and root-zone moisture. The different sensitivities to atmospheric evaporative demand also create species differences in transpiration variability at synoptic time scales. Using the sap flow measurements and a regional forest inventory, a bottom-up regional transpiration estimate is constructed. The estimate suggests that sensitivity of Douglas-fir transpiration to water stress suppresses dry season evapotranspiration at the regional scale. Key Points Three year, half-hourly record of sap flow, micrometeorology, and soil moisture PCA shows offset in peak transpiration season between needleleaf and broadleaf species Douglas-fir water stress response could reduce dry season transpiration at large scale © 2014. American Geophysical Union. All Rights Reserved

Vegetation induced changes in the stable isotope composition of near surface humidity

Obtaining the d-excess parameter from oxygen and hydrogen stable isotope composition of meteoric waters has the potential power to reconstruct changes in atmospheric water pools (e,g. sources, origins and overall balance) and the climatic conditions that prevail during surface evaporation. Recently, plant and ecosystem scientists turned their attention using d-excess information to inform questions at these scales. Here, we use the d-excess parameter to evaluate the influence of forest canopies on atmospheric humidity within a mixed evergreen forest in coastal California. We found that during the day, when transpiration was at a maximum, the d-excess of atmospheric water vapour exceeded model predictions for the background atmosphere into which the ecosystem evapotranspiration mixes. At night when transpiration was minor, the d-excess of atmospheric water vapour was on average less than model predictions for an ocean derived water vapour source. The observed diurnal fluctuations around the d-excess of the modelled background water vapour provided a strong evidence that during the day as the land surface warms and the boundary layer grows plants alter the isotope composition of atmospheric humidity via non-steady state isotope effects. In contrast, at night equilibrium isotope effects dominate as the atmosphere stabilizes. These day and nighttime fluctuations around the d-excess of ocean derived water vapour highlight the importance of plant transpiration for the isotope hydrology of near surface humidity and subsequently for the isotope composition of condensate like dew, an important water input to this ecosystem. © 2013 John Wiley & Sons, Ltd

Slope‐Aspect Induced Climate Differences Influence How Water Is Exchanged Between the Land and Atmosphere

Cross-slope climate differences in the midlatitudes are ecologically important, and impact vegetation-mediated water balance between the earth surface and the atmosphere. We made high-resolution in situ observations of air temperature, relative humidity, soil moisture, insolation, and sap velocity observations on 14 Pacific madrone trees (Arbutus menziesii) spanning adjacent north and south slopes at the University of California's Angelo Coast Range Reserve. To understand the cross-slope response of sap velocity, a proxy for transpiration, to microclimate, we modeled the sap velocity on each slope using a transpiration model driven by ambient environment and parameterized with a Markov Chain Monte Carlo parameter estimation process. The results show that trees on opposing slopes do not follow a shared pattern of physiological response to transpiration drivers. This means that the observed sap velocity differences are not due entirely to observed microclimate differences, but also due to population-level physiological differences, which indicates acclimation to inhabited microclimate. While our present data set and analytical tools do not identify mechanisms of acclimation, we speculate that differing proportions of sun-adapted and shade-adapted leaves, differences in stomatal regulation, and cross-slope root zone moisture differences could explain some of the observed and modeled differences

High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020

ABSTRACT Acinetobacter baumannii causes difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria. This study aimed to characterize the diversity and genetic mechanisms of carbapenem resistance among A. baumannii strains isolated from hospitals in southwestern Nigeria. We sequenced the genomes of all A. baumannii isolates submitted to Nigeria’s antimicrobial resistance surveillance reference laboratory between 2016 and 2020 on an Illumina platform and performed in silico genomic characterization. Selected strains were sequenced using the Oxford Nanopore technology to characterize the genetic context of carbapenem resistance genes. The 86 A. baumannii isolates were phylogenetically diverse and belonged to 35 distinct Oxford sequence types (oxfSTs), 16 of which were novel, and 28 Institut Pasteur STs (pasSTs). Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. The majority (n = 54) of the isolates were carbapenem resistant, particularly the IC7 (pasST25; 100%) and IC9 (pasST85; >91.7%) strains. blaOXA-23 (34.9%) and blaNDM-1 (27.9%) were the most common carbapenem resistance genes detected. All blaOXA-23 genes were carried on Tn2006 or Tn2006-like transposons. Our findings suggest that a 10-kb Tn125 composite transposon is the primary means of blaNDM-1 dissemination. Our findings highlight an increase in blaNDM-1 prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverse A. baumannii lineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings. IMPORTANCE Acinetobacter baumannii bacteria are increasingly clinically relevant due to their propensity to harbor genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterized the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings

Serology results, 1976 Democratic Republic of Congo.

<p>Serology results, 1976 Democratic Republic of Congo.</p