Modeling managed aquifer recharge processes in a highly heterogeneous, semi-confined aquifer system

Widespread groundwater overdraft in alluvial aquifer systems like the Central Valley (CV) in California, USA, has increased interest in managed aquifer recharge (MAR). Like most clastic sedimentary basins, recharge to the productive semi-confined CV aquifer system remains a challenge due to the presence of nearly ubiquitous, multiple confining units (silt and clay) that limit recharge pathways. Previous studies suggest the presence of interconnected networks of coarse-texture sand and gravel deposits that bypass regional confining units over a small fraction of the CV near the American and Cosumnes rivers. Here, variably saturated infiltration and recharge processes were simulated across a domain that includes high-resolution representation of the heterogeneous alluvial geologic architecture in this area. Results show that recharge potential is highly dependent on subsurface geologic architecture, with a nearly 2 order-of-magnitude range of recharge across the domain. Where interconnected coarse-texture recharge pathways occur, results show that these features can (1) accommodate rapid, high-volume MAR and (2) propagate widespread and rapid pressure responses over multi-kilometer distances in the semi-confined aquifer system. For all MAR simulations, results show that the majority of MAR is accommodated by filling unsaturated-zone (UZ) pore volume. Results also show that coarse-texture UZ facies (where present) accommodate the majority of MAR volume during early time, but fine-texture facies ultimately accommodate the majority of the total MAR volume, even for coarse-dominated sites. These findings highlight the large variability of MAR potential across the landscape and demonstrate the importance of fine-texture facies for accommodating MAR in alluvial aquifer systems

Domestic well vulnerability to drought duration and unsustainable groundwater management in California's Central Valley

Millions of Californians access drinking water via domestic wells, which are vulnerable to drought and unsustainable groundwater management. Groundwater overdraft and the possibility of longer drought duration under climate change threatens domestic well reliability, yet we lack tools to assess the impact of such events. Here, we leverage 943 469 well completion reports and 20 years of groundwater elevation data to develop a spatially-explicit domestic well failure model covering California's Central Valley. Our model successfully reproduces the spatial distribution of observed domestic well failures during the severe 2012-2016 drought (n = 2027). Next, the impact of longer drought duration (5-8 years) on domestic well failure is evaluated, indicating that if the 2012-2016 drought would have continued into a 6 to 8 year long drought, a total of 4037-5460 to 6538-8056 wells would fail. The same drought duration scenarios with an intervening wet winter in 2017 lead to an average of 498 and 738 fewer well failures. Additionally, we map vulnerable wells at high failure risk and find that they align with clusters of predicted well failures. Lastly, we evaluate how the timing and implementation of different projected groundwater management regimes impact groundwater levels and thus domestic well failure. When historic overdraft persists until 2040, domestic well failures range from 5966 to 10 466 (depending on the historic period considered). When sustainability is achieved progressively between 2020 and 2040, well failures range from 3677 to 6943, and from 1516 to 2513 when groundwater is not allowed to decline after 2020

Bayesian hydrograph separation in a minimally gauged alpine volcanic watershed in central Chile

This study examines the question of how much information one can extract from a tracer-based hydrograph separation in a remote and minimally gaged alpine catchment in Chile. We combine PCA-based endmember mixing analysis to identify the sources of flow contribution to the Diguillín River with a hierarchical Bayesian mixing model to integrate spatial and temporal variability in endmember concentration and quantify the source contributions to streamflow over time. The PCA-analysis shows that precipitation isotopes do not vary by elevation (e.g. snow and rainfall had identical signatures) but vary significantly by season, and that a third endmember is necessary to bound streamflow variability at the basin outlet, which was not captured by our field sampling. One of the main advantages of Bayesian methods is the quasi-machine learning capabilities, where we treated the third endmember as a parameter from which the mixing model could both estimate proportional contributions as well as posterior estimates for the tracer concentrations. The two tracer, three endmember hydrograph separation revealed groundwater to be the largest and precipitation (rain and snow) to be the smallest contributor, on average, to streamflow with the third unknown endmember contributing around 40% of streamflow during the Winter wet season. We hypothesize that interflow is occurring as the third endmember in the Alto Diguillín subwatershed, based on inferred tracer values and the presence of alluvium atop impermeable bedrock along certain reaches. More work is necessary to observe and sample these flowpaths, which was not possible during this study. The results of this work have implications for water resource management, since groundwater sustains the majority of streamflow in the Diguillín, and climate change will impact the timing and quantity of baseflow and interflow. Overall, we demonstrate the utility of combining PCA with Bayesian statistical modeling and inference to extract maximum information from a limited field dataset in a remote alpine catchment. The findings of this work can guide future water management in the Diguillín, but also provide clear questions for future research

Hydrogeological response to climate change in alpine hillslopes

Climate change threatens water resources in snowmelt-dependent regions by altering the fraction of snow and rain and spurring an earlier snowmelt season. The bulk of hydrological research has focused on forecasting response in streamflow volumes and timing to a shrinking snowpack; however, the degree to which subsurface storage offsets the loss of snow storage in various alpine geologic settings, i.e. the hydrogeologic buffering capacity, is still largely unknown. We address this research need by assessing the affects of climate change on storage and runoff generation for two distinct hydrogeologic settings present in alpine systems: a low storage granitic and a greater storage volcanic hillslope. We use a physically based integrated hydrologic model fully coupled to a land surface model to run a base scenario and then three progressive warming scenarios, and account for the shifts in each component of the water budget. For hillslopes with greater water retention, the larger storage volcanic hillslope buffered streamflow volumes and timing, but at the cost of greater reductions in groundwater storage relative to the low storage granite hillslope. We found that the results were highly sensitive to the unsaturated zone retention parameters, which in the case of alpine systems can be a mix of matrix or fracture flow. The presence of fractures and thus less retention in the unsaturated zone significantly decreased the reduction in recharge and runoff for the volcanic hillslope in climate warming scenarios. This approach highlights the importance of incorporating physically based subsurface flow in to alpine hydrology models, and our findings provide ways forward to arrive at a conceptual model that is both consistent with geology and hydrologic principles. Copyright © 2016 John Wiley & Sons, Ltd

Crumbs 3b promotes tight junctions in an ezrin-dependent manner in mammalian cells

AMT-L is supported by the School of Biology, University of St Andrews. AMT-L, PAR and FJGM were funded by the Anonymous Trust, University of St Andrews. PAR is supported by the Melville Trust for the Care and Cure of Cancer. The mass spectrometry work was supported by the Wellcome Trust [grant number 094476/Z/10/Z], which funded the purchase of the TripleTOF 5600 mass spectrometer at the BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews. The clinical study was supported by the Department of Pathology, Albert Einstein College of Medicine/ Montefiore Medical Center.Crumbs3 (CRB3) is a component of epithelial junctions that has been implicated in apical-basal polarity, apical identity, apical stability, cell adhesion and cell growth. CRB3 undergoes alternative splicing to yield two variants: CRB3a and CRB3b. Here, we describe novel data demonstrating that as with previous studies on CRB3a, CRB3b also promotes the formation of tight junctions. However, significantly we demonstrate that the 4.1-ezrin-radixin-moesin (FERM) binding motif (FBM) of CRB3b is required for CRB3b functionality and that ezrin binds to the FBM of CRB3b. Furthermore, we show that ezrin contributes to CRB3b functionality and the correct distribution of tight junction proteins. We demonstrate that both CRB3 isoforms are required for the production of functionally mature tight junctions and also the localization of ezrin to the plasma membrane. Finally, we demonstrate that reduced CRB3b expression in head and neck squamous cell carcinoma (HNSCC) correlates with cytoplasmic ezrin, a biomarker for aggressive disease, and show evidence that whilst CRB3a expression has no effect, low CRB3b and high cytoplasmic ezrin expression combined may be prognostic for HNSCC.PostprintPeer reviewe

Are rapid diagnostic tests more accurate in diagnosis of plasmodium falciparum malaria compared to microscopy at rural health centres?

<p>Abstract</p> <p>Background</p> <p>Prompt, accurate diagnosis and treatment with artemisinin combination therapy remains vital to current malaria control. Blood film microscopy the current standard test for diagnosis of malaria has several limitations that necessitate field evaluation of alternative diagnostic methods especially in low income countries of sub-Saharan Africa where malaria is endemic.</p> <p>Methods</p> <p>The accuracy of axillary temperature, health centre (HC) microscopy, expert microscopy and a HRP2-based rapid diagnostic test (Paracheck) was compared in predicting malaria infection using polymerase chain reaction (PCR) as the gold standard. Three hundred patients with a clinical suspicion of malaria based on fever and or history of fever from a low and high transmission setting in Uganda were consecutively enrolled and provided blood samples for all tests. Accuracy of each test was calculated overall with 95% confidence interval and then adjusted for age-groups and level of transmission intensity using a stratified analysis. The endpoints were: sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). This study is registered with Clinicaltrials.gov, NCT00565071.</p> <p>Results</p> <p>Of the 300 patients, 88(29.3%) had fever, 56(18.7%) were positive by HC microscopy, 47(15.7%) by expert microscopy, 110(36.7%) by Paracheck and 89(29.7%) by PCR. The overall sensitivity >90% was only shown by Paracheck 91.0% [95%CI: 83.1-96.0]. The sensitivity of expert microscopy was 46%, similar to HC microscopy. The superior sensitivity of Paracheck compared to microscopy was maintained when data was stratified for transmission intensity and age. The overall specificity rates were: Paracheck 86.3% [95%CI: 80.9-90.6], HC microscopy 93.4% [95%CI: 89.1-96.3] and expert microscopy 97.2% [95%CI: 93.9-98.9]. The NPV >90% was shown by Paracheck 95.8% [95%CI: 91.9-98.2]. The overall PPV was <88% for all methods.</p> <p>Conclusion</p> <p>The HRP2-based RDT has shown superior sensitivity compared to microscopy in diagnosis of malaria and may be more suitable for screening of malaria infection.</p

Climate Change and the Potential Spreading of Marine Mucilage and Microbial Pathogens in the Mediterranean Sea

Background: Marine snow (small amorphous aggregates with colloidal properties) is present in all oceans of the world. Surface water warming and the consequent increase of water column stability can favour the coalescence of marine snow into marine mucilage, large marine aggregates representing an ephemeral and extreme habitat. Marine mucilage characterize aquatic systems with altered environmental conditions. Methodology/Principal Findings: We investigated, by means of molecular techniques, viruses and prokaryotes within the mucilage and in surrounding seawater to examine the potential of mucilage to host new microbial diversity and/or spread marine diseases. We found that marine mucilage contained a large and unexpectedly exclusive microbial biodiversity and hosted pathogenic species that were absent in surrounding seawater. We also investigated the relationship between climate change and the frequency of mucilage in the Mediterranean Sea over the last 200 years and found that the number of mucilage outbreaks increased almost exponentially in the last 20 years. The increasing frequency of mucilage outbreaks is closely associated with the temperature anomalies. Conclusions/Significance: We conclude that the spreading of mucilage in the Mediterranean Sea is linked to climate-driven sea surface warming. The mucilage can act as a controlling factor of microbial diversity across wide oceanic regions and could have the potential to act as a carrier of specific microorganisms, thereby increasing the spread of pathogenic bacteria

Predicting the Electron Requirement for Carbon Fixation in Seas and Oceans

Marine phytoplankton account for about 50% of all global net primary productivity (NPP). Active fluorometry, mainly Fast Repetition Rate fluorometry (FRRf), has been advocated as means of providing high resolution estimates of NPP. However, not measuring CO2-fixation directly, FRRf instead provides photosynthetic quantum efficiency estimates from which electron transfer rates (ETR) and ultimately CO2-fixation rates can be derived. Consequently, conversions of ETRs to CO2-fixation requires knowledge of the electron requirement for carbon fixation (Φe,C, ETR/CO2 uptake rate) and its dependence on environmental gradients. Such knowledge is critical for large scale implementation of active fluorescence to better characterise CO2-uptake. Here we examine the variability of experimentally determined Φe,C values in relation to key environmental variables with the aim of developing new working algorithms for the calculation of Φe,C from environmental variables. Coincident FRRf and 14C-uptake and environmental data from 14 studies covering 12 marine regions were analysed via a meta-analytical, non-parametric, multivariate approach. Combining all studies, Φe,C varied between 1.15 and 54.2 mol e- (mol C)-1 with a mean of 10.9±6.91 mol e- mol C)-1. Although variability of Φe,C was related to environmental gradients at global scales, region-specific analyses provided far improved predictive capability. However, use of regional Φe,C algorithms requires objective means of defining regions of interest, which remains challenging. Considering individual studies and specific small-scale regions, temperature, nutrient and light availability were correlated with Φe,C albeit to varying degrees and depending on the study/region and the composition of the extant phytoplankton community. At the level of large biogeographic regions and distinct water masses, Φe,C was related to nutrient availability, chlorophyll, as well as temperature and/or salinity in most regions, while light availability was also important in Baltic Sea and shelf waters. The novel Φe,C algorithms provide a major step forward for widespread fluorometry-based NPP estimates and highlight the need for further studying the natural variability of Φe,C to verify and develop algorithms with improved accuracy. © 2013 Lawrenz et al

Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for “challenging” microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4–13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations