The negative relief of larger floodplains

AbstractLarge floodplains have multiple and complex negative relief assemblages in which depressions fall below local or general floodplain surfaces at a variety of scales. The generation and dynamics of negative relief along major alluvial corridors are described and compared. Such depressions are significant for the storage and passage of surface waters, the creation of a range of riparian, wetland, lacustrine and flowing-water habitats, and the long-term accumulation of organic materials.Working on trunk channel remnants, drowned valleys and subsidence basins, fluvial processes modify floodplain negative relief through differential erosion and sedimentation. Effectively this takes place in three genetic zones: rheic, transitional and perirheic. We show that transitional zones marginal to active channels significantly diversify form complexes, and we demonstrate the diachronous nature of zonal processes and the complex nature and pace of depression modification and infilling. Four less well-understood sets of coupled phenomena are assessed: (i) floodplains associated with discontinuous river banks, (ii) the scales and types of scroll bar generation, (iii) factors underlying the contrasts between meander and braidplain surface relief, and (iv) the generation and function of large floodplain wetlands and lakes.The survival likelihood of surface negative relief relates to geomorphological connectivity; this is described for each of the rheic, transitional and perirheic zones. The implications for contemporary aquatic system management are discussed. A key to understanding and managing negative relief on large river floodplains, and their associated ecologies and sedimentation, is to quantify both sedimentological and hydrological river-floodplain connectivity

Morphology and spacing of river meander scrolls

Many of the world’s alluvial rivers are characterised by single or multiple channels that are often sinuous and that migrate to produce a mosaicked floodplain landscape of truncated scroll (or point) bars. Surprisingly little is known about the morphology and geometry of scroll bars despite increasing interest from hydrocarbon geoscientists working with ancient large meandering river deposits. This paper uses remote sensing imagery, LiDAR data-sets of meandering scroll bar topography, and global coverage elevation data to quantify scroll bar geometry, anatomy, relief, and spacing. The analysis focuses on preserved scroll bars in the Mississippi River (USA) floodplain but also compares attributes to 19 rivers of different scale and depositional environments from around the world. Analysis of 10 large scroll bars (median area = 25 km2) on the Mississippi shows that the point bar deposits can be categorised into three different geomorphological units of increasing scale: individual19 ‘scrolls’, ‘depositional packages’, and ‘point bar complexes’. Scroll heights and curvatures are greatest near the modern channel and at the terminating boundaries of different depositional packages, confirming the importance of the formative main channel on subsequent scroll bar relief and shape Fourier analysis shows a periodic variation in signal (scroll bar height) with an average period (spacing) of 167 m (range 150-190 m) for the Mississippi point bars. For other rivers, a strong relationship exists between the period of scroll bars and the adjacent primary channel width for a range of rivers from 55 to 2042 m wide. On average, scroll spacing is ̴50% of the main channel width. The strength of this correlation over nearly two orders of magnitude of channel size indicates a scale independence of scroll bar spacing and suggests a strong link between channel migration and scroll bar construction with apparent regularities despite different flow regimes. This investigation of meandering river dynamics and floodplain patterns shows that it is possible to develop a suite of metrics that describe scroll bar morphology and geometry that can be valuable to geoscientists predicting the heterogeneity of subsurface meandering deposits

The role of discharge variability in determining alluvial stratigraphy

We illustrate the potential for using physics-based modeling to link alluvial stratigraphy to large river morphology and dynamics. Model simulations, validated using ground penetrating radar data from the Río Paraná, Argentina, demonstrate a strong relationship between bar-scale set thickness and channel depth, which applies across a wide range of river patterns and bar types. We show that hydrologic regime, indexed by discharge variability and flood duration, exerts a first-order influence on morphodynamics and hence bar set thickness, and that planform morphology alone may be a misleading variable for interpreting deposits. Indeed, our results illustrate that rivers evolving under contrasting hydrologic regimes may have very similar morphology, yet be characterized by marked differences in stratigraphy. This realization represents an important limitation on the application of established theory that links river topography to alluvial deposits, and highlights the need to obtain field evidence of discharge variability when developing paleoenvironmental reconstructions. Model simulations demonstrate the potential for deriving such evidence using metrics of paleocurrent variance

Interaction between the NS4B amphipathic helix, AH2, and charged lipid headgroups alters membrane morphology and AH2 oligomeric state — Implications for the Hepatitis C virus life cycle

AbstractThe non-structural protein 4B (NS4B) from Hepatitis C virus (HCV) plays a pivotal role in the remodelling of the host cell's membranes, required for the formation of the viral replication complex where genome synthesis occurs. NS4B is an integral membrane protein that possesses a number of domains vital for viral replication. Structural and biophysical studies have revealed that one of these, the second amphipathic N-terminal helix (AH2), plays a key role in these remodelling events. However, there is still limited understanding of the mechanism through which AH2 promotes these changes. Here we report on solid-state NMR and molecular dynamics studies that demonstrate that AH2 promotes the clustering of negatively charged lipids within the bilayer, a process that reduces the strain within the bilayer facilitating the remodelling of the lipid bilayer. Furthermore, the presence of negatively charged lipids within the bilayer appears to promote the disassociation of AH2 oligomers, highlighting a potential role for lipid recruitment in regulating NS protein interactions

Influence of Dunes on Channel‐Scale Flow and Sediment Transport in a Sand Bed Braided River

This is the final version. Available on open access from the American Geophysical Union via the DOI in this recordData availability: Project data is stored in, and available from, the UK Centre for Ecology & Hydrology (http://eidc.ceh.ac.uk).Current understanding of the role that dunes play in controlling bar and channel-scale processes and river morphodynamics is incomplete. We present results from a combined numerical modeling and field monitoring study that isolates the impact of dunes on depth-averaged and near-bed flow structure, with implications for morphodynamic modeling. Numerical simulations were conducted using the three-dimensional Computational Fluid Dynamics code OpenFOAM to quantify the time-averaged flow structure within a 400 m x 100 m channel using DEMs for which: (i) dunes and bars were present within the model; and (ii) only bar43 scale topographic features were resolved (dunes were removed). Comparison of these two simulations shows that dunes enhance lateral flows and reduce velocities over bar tops by as much as 30%. Dunes influence the direction of modeled sediment transport at spatial scales larger than individual bedforms due to their effect on topographic steering of the near-bed flow structure. We show that dunes can amplify, dampen or even reverse the deflection of sediment down lateral bar slopes, and this is closely associated with 3D and obliquely orientated dunes. Sediment transport patterns calculated using theory implemented in depth-averaged morphodynamic models suggests that gravitational deflection of sediment is still controlled by bar-scale topography, even in the presence of dunes. However, improved parameterizations of flow and sediment transport in depth-averaged morphodynamic models are needed that account for the effects of both dune- and bar- scale morphology on near-bed flow and sediment transport.Natural Environment Research Council (NERC

Quantification of bedform dynamics and bedload sediment flux in sandy braided rivers from airborne and satellite imagery

Images from specially‐commissioned aeroplane sorties (manned aerial vehicle, MAV), repeat unmanned aerial vehicle (UAV) surveys, and Planet CubeSat satellites are used to quantify dune and bar dynamics in the sandy braided South Saskatchewan River, Canada. Structure‐from‐Motion (SfM) techniques and application of a depth‐brightness model are used to produce a series of Digital Surface Models (DSMs) at low and near‐bankfull flows. A number of technical and image processing challenges are described that arise from the application of SfM in dry and submerged environments. A model for best practice is presented and analysis suggests a depth‐brightness model approach can represent the different scales of bedforms present in sandy braided rivers with low‐turbidity and shallow (< 2 m deep) water. The aerial imagery is used to quantify the spatial distribution of unit bar and dune migration rate in an 18 km reach and three ~1 km long reaches respectively. Dune and unit bar migration rates are highly variable in response to local variations in planform morphology. Sediment transport rates for dunes and unit bars, obtained by integrating migration rates (from UAV) with the volume of sediment moved (from DSMs using MAV imagery) show near‐equivalence in sediment flux. Hence, reach‐based sediment transport rate estimates can be derived from unit bar data alone. Moreover, it is shown that reasonable estimates of sediment transport rate can be made using just unit bar migration rates as measured from 2D imagery, including from satellite images, so long as informed assumptions are made regarding average bar shape and height. With recent availability of frequent, repeat satellite imagery, and the ease of undertaking repeat MAV and UAV surveys, for the first time, it may be possible to provide global estimates of bedload sediment flux for large or inaccessible low‐turbidity rivers that currently have sparse information on bedload sediment transport rates

Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes

Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous management. This management strategy consists of two conventional and three conservation systems, all receiving annual poultry litter. High throughput sequencing of the 16S ribosomal RNA was carried out on samples of cattle manure, poultry litter, soil, and runoff collected from each manureshed. In addition, four representative ARGs (intl1, sul1, ermB, and blactx-m-32) were quantified from manures, soil, and runoff using quantitative PCR. Results revealed that conventional practice increased soil ARGs, and microbial diversity compared to conservation systems. Further, ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. After 15-years of conservation practices, relationships existed between heavy metals and ARGs. In the soil, Cu, Fe and Mn were positively linked to intl1, sul1, and ermB, but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, and physicochemical parameters. Overall, this study provides system-level linkages of microbial communities, ARGs, and physicochemical conditions based on long-term conservation practices at the soil-water-animal nexus

Quality of hospital care for sick newborns and severely malnourished children in Kenya: A two-year descriptive study in 8 hospitals

BACKGROUND: Given the high mortality associated with neonatal illnesses and severe malnutrition and the development of packages of interventions that provide similar challenges for service delivery mechanisms we set out to explore how well such services are provided in Kenya. METHODS: As a sub-component of a larger study we evaluated care during surveys conducted in 8 rural district hospitals using convenience samples of case records. After baseline hospitals received either a full multifaceted intervention (intervention hospitals) or a partial intervention (control hospitals) aimed largely at improving inpatient paediatric care for malaria, pneumonia and diarrhea/dehydration. Additional data were collected to: i) examine the availability of routine information at baseline and their value for morbidity, mortality and quality of care reporting, and ii) compare the care received against national guidelines disseminated to all hospitals. RESULTS: Clinical documentation for neonatal and malnutrition admissions was often very poor at baseline with case records often entirely missing. Introducing a standard newborn admission record (NAR) form was associated with an increase in median assessment (IQR) score to 25/28 (22-27) from 2/28 (1-4) at baseline. Inadequate and incorrect prescribing of penicillin and gentamicin were common at baseline. For newborns considerable improvements in prescribing in the post baseline period were seen for penicillin but potentially serious errors persisted when prescribing gentamicin, particularly to low-birth weight newborns in the first week of life. Prescribing essential feeds appeared almost universally inadequate at baseline and showed limited improvement after guideline dissemination. CONCLUSION: Routine records are inadequate to assess newborn care and thus for monitoring newborn survival interventions. Quality of documented inpatient care for neonates and severely malnourished children is poor with limited improvement after the dissemination of clinical practice guidelines. Further research evaluating approaches to improving care for these vulnerable groups is urgently needed. We also suggest pre-service training curricula should be better aligned to help improve newborn survival particularly

Action spectroscopy of the isolated red Kaede fluorescent protein chromophore

Incorporation of fluorescent proteins into biochemical systems has revolutionized the field of bioimaging. In a bottom-up approach, understanding the photophysics of fluorescent proteins requires detailed investigations of the light-absorbing chromophore, which can be achieved by studying the chromophore in isolation. This paper reports a photodissociation action spectroscopy study on the deprotonated anion of the red Kaede fluorescent protein chromophore, demonstrating that at least three isomers–assigned to deprotomers–are generated in the gas phase. Deprotomer-selected action spectra are recorded over the S1 ← S0 band using an instrument with differential mobility spectrometry coupled with photodissociation spectroscopy. The spectrum for the principal phenoxide deprotomer spans the 480–660 nm range with a maximum response at ≈610 nm. The imidazolate deprotomer has a blue-shifted action spectrum with a maximum response at ≈545 nm. The action spectra are consistent with excited state coupled-cluster calculations of excitation wavelengths for the deprotomers. A third gas-phase species with a distinct action spectrum is tentatively assigned to an imidazole tautomer of the principal phenoxide deprotomer. This study highlights the need for isomer-selective methods when studying the photophysics of biochromophores possessing several deprotonation sites

A Multifaceted Intervention to Implement Guidelines and Improve Admission Paediatric Care in Kenyan District Hospitals: A Cluster Randomised Trial

Philip Ayieko and colleagues report the outcomes of a cluster-randomized trial carried out in eight Kenyan district hospitals evaluating the effects of a complex intervention involving improved training and supervision for clinicians. They found a higher performance of hospitals assigned to the complex intervention on a variety of process of care measures, as compared to those receiving the control intervention