Diffusive equilibrium in thin films provides evidence of suppression of hyporheic exchange and large-scale nitrate transformation in a groundwater-fed river

The hyporheic zone of riverbed sediments has the potential to attenuate nitrate from upwelling, polluted groundwater. However, the coarse-scale (5–10 cm) measurement of nitrogen biogeochemistry in the hyporheic zone can often mask fine-scale (<1 cm) biogeochemical patterns, especially in near-surface sediments, leading to incomplete or inaccurate representation of the capacity of the hyporheic zone to transform upwelling NO3−. In this study, we utilised diffusive equilibrium in thin-films samplers to capture high resolution (cm-scale) vertical concentration profiles of NO3−, SO42−, Fe and Mn in the upper 15 cm of armoured and permeable riverbed sediments. The goal was to test whether nitrate attenuation was occurring in a sub-reach characterised by strong vertical (upwelling) water fluxes. The vertical concentration profiles obtained from diffusive equilibrium in thin-films samplers indicate considerable cm-scale variability in NO3− (4.4 ± 2.9 mg N/L), SO42− (9.9 ± 3.1 mg/l) and dissolved Fe (1.6 ± 2.1 mg/l) and Mn (0.2 ± 0.2 mg/l). However, the overall trend suggests the absence of substantial net chemical transformations and surface-subsurface water mixing in the shallow sediments of our sub-reach under baseflow conditions. The significance of this is that upwelling NO3−-rich groundwater does not appear to be attenuated in the riverbed sediments at <15 cm depth as might occur where hyporheic exchange flows deliver organic matter to the sediments for metabolic processes. It would appear that the chemical patterns observed in the shallow sediments of our sub-reach are not controlled exclusively by redox processes and/or hyporheic exchange flows. Deeper-seated groundwater fluxes and hydro-stratigraphy may be additional important drivers of chemical patterns in the shallow sediments of our study sub-reach. Copyright © 2014 John Wiley & Sons, Ltd

Interpreting spatial patterns in redox and coupled water-nitrogen fluxes in the streambed of a gaining river reach

Water pathways through permeable riverbeds are multi-dimensional, including lateral hyporheic exchange flows as well as vertical (upwelling and downwelling) fluxes. The influence of different pathways of water on solute patterns and the supply of nitrate and other redox-sensitive chemical species in the riverbed is poorly understood but could be environmentally significant. For example, nitrate-rich upwelling water in the gaining reaches of groundwater-fed rivers has the potential to supply significant quantities of nitrate through the riverbed to surface waters, constraining opportunities to deliver the goals of the EU Water Framework Directive to achieve ‘good ecological status’. We show that patterns in porewater chemistry in the armoured river bed of a gaining reach (River Leith, Cumbria) reflect the spatial variability in different sources of water; oxic conditions being associated with preferential discharge from groundwater and reducing conditions with longitudinal and lateral fluxes of water due to water movement from riparian zones and/or hyporheic exchange flows. Our findings demonstrate the important control of both vertical and lateral water fluxes on patterns of redox-sensitive chemical species in the river bed. Furthermore, under stable, baseflow conditions (<Q90) a zone of preferential discharge, comprising 20 % of the reach by area contributes 4–9 % of the total nitrate being transported through the reach in surface water, highlighting the need to understand the spatial distribution of such preferential discharge locations at the catchment scale to establish their importance for nitrate delivery to the stream channel

Diffusive equilibrium in thin-films (DET) provides evidence of suppression of hyporheic exchange and large-scale nitrate transformation in a groundwater-fed river

The hyporheic zone of riverbed sediments has the potential to attenuate nitrate from upwelling, polluted groundwater. However, the coarse-scale (5 – 10 cm) measurement of nitrogen biogeochemistry in the hyporheic zone can often mask fine-scale (<1 cm) biogeochemical patterns, especially in near-surface sediments, leading to incomplete or inaccurate representation of the capacity of the hyporheic zone to transform upwelling NO3-. In this study, we utilised diffusive equilibrium in thin-films (DET) samplers to capture high resolution (cm-scale) vertical concentration profiles of NO3-, SO42-, Fe and Mn in the upper 15 cm of armoured and permeable riverbed sediments. The goal was to test whether nitrate attenuation was occurring in a sub-reach characterised by strong vertical (upwelling) water fluxes. The vertical concentration profiles obtained from DET samplers indicate considerable cm-scale variability in NO3- (4.4 ± 2.9 mg N/L), SO42- (9.9 ± 3.1 mg/L) and dissolved Fe (1.6 ± 2.1 mg/L) and Mn (0.2 ± 0.2 mg/L). However, the overall trend suggests the absence of substantial net chemical transformations and surface-subsurface water mixing in the shallow sediments of our sub-reach under baseflow conditions. The significance of this is that upwelling NO3--rich groundwater does not appear to be attenuated in the riverbed sediments at <15 cm depth as might occur where hyporheic exchange flows deliver organic matter to the sediments for metabolic processes. It would appear that the chemical patterns observed in the shallow sediments of our sub-reach are not controlled exclusively by redox processes and / or hyporheic exchange flows. Deeper-seated groundwater fluxes and hydro-stratigraphy may be additional important drivers of chemical patterns in the shallow sediments of our study sub-reach. This article is protected by copyright. All rights reserved

Deep roots and soil structure

In this opinion article we examine the relationship between penetrometer resistance and soil depth in the field. Assuming that root growth is inhibited at penetrometer resistances > 2.5 MPa, we conclude that in most circumstances the increases in penetrometer resistance with depth are sufficiently great to confine most deep roots to elongating in existing structural pores. We suggest that deep rooting is more likely related to the interaction between root architecture and soil structure than it is to the ability of a root to deform strong soil. Although the ability of roots to deform strong soil is an important trait, we propose it is more closely related to root exploration of surface layers than deep rooting

Image informatics strategies for deciphering neuronal network connectivity

Brain function relies on an intricate network of highly dynamic neuronal connections that rewires dramatically under the impulse of various external cues and pathological conditions. Among the neuronal structures that show morphologi- cal plasticity are neurites, synapses, dendritic spines and even nuclei. This structural remodelling is directly connected with functional changes such as intercellular com- munication and the associated calcium-bursting behaviour. In vitro cultured neu- ronal networks are valuable models for studying these morpho-functional changes. Owing to the automation and standardisation of both image acquisition and image analysis, it has become possible to extract statistically relevant readout from such networks. Here, we focus on the current state-of-the-art in image informatics that enables quantitative microscopic interrogation of neuronal networks. We describe the major correlates of neuronal connectivity and present workflows for analysing them. Finally, we provide an outlook on the challenges that remain to be addressed, and discuss how imaging algorithms can be extended beyond in vitro imaging studies

Hyperresolution information and hyperresolution ignorance in modelling the hydrology of the land surface

There is a strong drive towards hyperresolution earth system models in order to resolve finer scales of motion in the atmosphere. The problem of obtaining more realistic representation of terrestrial fluxes of heat and water, however, is not just a problem of moving to hyperresolution grid scales. It is much more a question of a lack of knowledge about the parameterisation of processes at whatever grid scale is being used for a wider modelling problem. Hyperresolution grid scales cannot alone solve the problem of this hyperresolution ignorance. This paper discusses these issues in more detail with specific reference to land surface parameterisations and flood inundation models. The importance of making local hyperresolution model predictions available for evaluation by local stakeholders is stressed. It is expected that this will be a major driving force for improving model performance in the future. Keith BEVEN, Hannah CLOKE, Florian PAPPENBERGER, Rob LAMB, Neil HUNTE

Characteristics of the Earliest Cross-Neutralizing Antibody Response to HIV-1

Recent cross-sectional analyses of HIV-1+ plasmas have indicated that broadly cross-reactive neutralizing antibody responses are developed by 10%–30% of HIV-1+ subjects. The timing of the initial development of such anti-viral responses is unknown. It is also unknown whether the emergence of these responses coincides with the appearance of antibody specificities to a single or multiple regions of the viral envelope glycoprotein (Env). Here we analyzed the cross-neutralizing antibody responses in longitudinal plasmas collected soon after and up to seven years after HIV-1 infection. We find that anti-HIV-1 cross-neutralizing antibody responses first become evident on average at 2.5 years and, in rare cases, as early as 1 year following infection. If cross-neutralizing antibody responses do not develop during the first 2–3 years of infection, they most likely will not do so subsequently. Our results indicate a potential link between the development of cross-neutralizing antibody responses and specific activation markers on T cells, and with plasma viremia levels. The earliest cross-neutralizing antibody response targets a limited number of Env regions, primarily the CD4-binding site and epitopes that are not present on monomeric Env, but on the virion-associated trimeric Env form. In contrast, the neutralizing activities of plasmas from subjects that did not develop cross-neutralizing antibody responses target epitopes on monomeric gp120 other than the CD4-BS. Our study provides information that is not only relevant to better understanding the interaction of the human immune system with HIV but may guide the development of effective immunization protocols. Since antibodies to complex epitopes that are present on the virion-associated envelope spike appear to be key components of earliest cross-neutralizing activities of HIV-1+ plasmas, then emphasis should be made to elicit similar antibodies by vaccination

Early Steps of HIV-1 Fusion Define the Sensitivity to Inhibitory Peptides That Block 6-Helix Bundle Formation

The HIV envelope (Env) glycoprotein mediates membrane fusion through sequential interactions with CD4 and coreceptors, followed by the refolding of the transmembrane gp41 subunit into the stable 6-helix bundle (6HB) conformation. Synthetic peptides derived from the gp41 C-terminal heptad repeat domain (C-peptides) potently inhibit fusion by binding to the gp41 pre-bundle intermediates and blocking their conversion into the 6HB. Our recent work revealed that HIV-1 enters cells by fusing with endosomes, but not with the plasma membrane. These studies also showed that, for the large part, gp41 pre-bundles progress toward 6HBs in endosomal compartments and are thus protected from external fusion inhibitors. Here, we examined the consequences of endocytic entry on the gp41 pre-bundle exposure and on the virus' sensitivity to C-peptides. The rates of CD4 and coreceptor binding, as well as the rate of productive receptor-mediated endocytosis, were measured by adding specific inhibitors of these steps at varied times of virus-cell incubation. Following the CD4 binding, CCR5-tropic viruses recruited a requisite number of coreceptors much faster than CXCR4-tropic viruses. The rate of subsequent uptake of ternary Env-CD4-coreceptor complexes did not correlate with the kinetics of coreceptor engagement. These measurements combined with kinetic analyses enabled the determination of the lifetime of pre-bundle intermediates on the cell surface. Overall, these lifetimes correlated with the inhibitory potency of C-peptides. On the other hand, the basal sensitivity to peptides varied considerably among diverse HIV-1 isolates and ranked similarly with their susceptibility to inactivation by soluble CD4. We conclude that both the longevity of gp41 intermediates and the extent of irreversible conformational changes in Env upon CD4 binding determine the antiviral potency of C-peptides