Proceedings of the 23rd annual Central Plains irrigation conference

Presented at Proceedings of the 23rd annual Central Plains irrigation conference held in Burlington, Colorado on February 22-23, 2011.Includes bibliographical references.Irrigation water management practices could greatly benefit from using soil moisture sensors that accurately measure soil water content or potential. Therefore, an assessment on soil moisture sensor reading accuracy is important. In this study, a performance evaluation of selected sensor calibration was performed considering factory- laboratory- and field-based calibrations. The selected sensors included: the Digitized Time Domain Transmissometry (TDT, Acclima, Inc., Meridian, ID) which is a volumetric soil water content sensor, and a resistance-based soil water potential sensor (Watermark 200, Irrometer Company, Inc., Riverside, CA). Measured soil water content/potential values, on a sandy clay loam soil, were compared with corresponding values derived from gravimetric samples. Under laboratory and field conditions, the factory-based calibrations for the TDT sensor accurately measured volumetric soil water content. Therefore, the use of the TDT sensor for irrigation water management seems very promising. Laboratory tests indicated that a linear calibration for the TDT sensor and a logarithmic calibration for the watermark sensor improved the factory calibration. In the case of the watermark, a longer set of field data is needed to properly establish its accuracy and reliability

Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this record.CRISPR (clustered regularly interspaced short palindromic repeats) loci and their associated (cas) genes encode an adaptive immune system that protects prokaryotes from viral1 and plasmid2 invaders. Following viral (phage) infection, a small fraction of the prokaryotic cells are able to integrate a small sequence of the invader's genome into the CRISPR array1. These sequences, known as spacers, are transcribed and processed into small CRISPR RNA guides3-5 that associate with Cas nucleases to specify a viral target for destruction6-9. Although CRISPR-cas loci are widely distributed throughout microbial genomes and often display hallmarks of horizontal gene transfer10-12, the drivers of CRISPR dissemination remain unclear. Here, we show that spacers can recombine with phage target sequences to mediate a form of specialized transduction of CRISPR elements. Phage targets in phage 85, ΦNM1, ΦNM4 and Φ12 can recombine with spacers in either chromosomal or plasmid-borne CRISPR loci in Staphylococcus, leading to either the transfer of CRISPR-adjacent genes or the propagation of acquired immunity to other bacteria in the population, respectively. Our data demonstrate that spacer sequences not only specify the targets of Cas nucleases but also can promote horizontal gene transfer.Natural Environment Research Council (NERC)Biotechnology & Biological Sciences Research Council (BBSRC)Rita Allen Scholars ProgramNational Institutes of Health (NIH

The DYMECS project: a statistical approach for the evaluation of convective storms in high-resolution NWP models

A new frontier in weather forecasting is emerging by operational forecast models now being run at convection-permitting resolutions at many national weather services. However, this is not a panacea; significant systematic errors remain in the character of convective storms and rainfall distributions. The DYMECS project (Dynamical and Microphysical Evolution of Convective Storms) is taking a fundamentally new approach to evaluate and improve such models: rather than relying on a limited number of cases, which may not be representative, we have gathered a large database of 3D storm structures on 40 convective days using the Chilbolton radar in southern England. We have related these structures to storm life-cycles derived by tracking features in the rainfall from the UK radar network, and compared them statistically to storm structures in the Met Office model, which we ran at horizontal grid length between 1.5 km and 100 m, including simulations with different subgrid mixing length. We also evaluated the scale and intensity of convective updrafts using a new radar technique. We find that the horizontal size of simulated convective storms and the updrafts within them is much too large at 1.5-km resolution, such that the convective mass flux of individual updrafts can be too large by an order of magnitude. The scale of precipitation cores and updrafts decreases steadily with decreasing grid lengths, as does the typical storm lifetime. The 200-m grid-length simulation with standard mixing length performs best over all diagnostics, although a greater mixing length improves the representation of deep convective storms

Updraft Width Modulates Ambient Atmospheric Controls on Convective Cloud Depth

The depth of convective clouds affects vertical transport of atmospheric constituents, influencing downstream weather and climate. Atmospheric controls on the maximum depth reached by moist convection are investigated with radar‐tracked convective cells tagged with sounding‐derived atmospheric parameters from a field campaign in central Argentina. Regression analyses show that narrow (16‐km diameter) cell depths respond to disparate factors, where cell areas are defined using composite reflectivity signatures. Undiluted lifted parcel indices including convective available potential energy (CAPE) and level of neutral buoyancy (LNB) are top predictors of wide cell maximum depth while mid‐tropospheric relative humidity is the top predictor of narrow cell maximum depth. Because narrow cells are more numerous than wide cells, the overall outcome of the full cell population does not strongly correlate with CAPE and LNB conditions. Tracked cells and atmospheric conditions in a simulation with 3‐km grid spacing covering the field campaign produce similar results to those observed. Narrow cells that are relatively deep have a cooler and moister mid‐troposphere with weaker free tropospheric subsidence, while relatively deep wide cells have much warmer and moister lower tropospheric conditions. These atmospheric differences are present 1 hr before cell initiation at both a fixed observing site and variable cell initiation locations. Simulated narrow cell maximum equivalent potential temperature decreases with height at a rate similar to the ambient vertical gradient, causing these cells to fall short of their LNB and supporting the view that entrainment‐driven dilution is a dominant control on their depth

Regulation of microRNA biogenesis and turnover by animals and their viruses

Item does not contain fulltextMicroRNAs (miRNAs) are a ubiquitous component of gene regulatory networks that modulate the precise amounts of proteins expressed in a cell. Despite their small size, miRNA genes contain various recognition elements that enable specificity in when, where and to what extent they are expressed. The importance of precise control of miRNA expression is underscored by functional studies in model organisms and by the association between miRNA mis-expression and disease. In the last decade, identification of the pathways by which miRNAs are produced, matured and turned-over has revealed many aspects of their biogenesis that are subject to regulation. Studies in viral systems have revealed a range of mechanisms by which viruses target these pathways through viral proteins or non-coding RNAs in order to regulate cellular gene expression. In parallel, a field of study has evolved around the activation and suppression of antiviral RNA interference (RNAi) by viruses. Virus encoded suppressors of RNAi can impact miRNA biogenesis in cases where miRNA and small interfering RNA pathways converge. Here we review the literature on the mechanisms by which miRNA biogenesis and turnover are regulated in animals and the diverse strategies that viruses use to subvert or inhibit these processes

Opinion: A critical evaluation of the evidence for aerosol invigoration of deep convection

Deep convective updraft invigoration via indirect effects of increased aerosol number concentration on cloud microphysics is frequently cited as a driver of correlations between aerosol and deep convection properties. Here, we critically evaluate the theoretical, modeling, and observational evidence for warm- and cold-phase invigoration pathways. Though warm-phase invigoration is plausible and theoretically supported via lowering of the supersaturation with increased cloud droplet concentration in polluted conditions, the significance of this effect depends on substantial supersaturation changes in real-world convective clouds that have not been observed. Much of the theoretical support for cold-phase invigoration depends on unrealistic assumptions of instantaneous freezing and unloading of condensate in growing, isolated updrafts. When applying more realistic assumptions, impacts on buoyancy from enhanced latent heating via fusion in polluted conditions are largely canceled by greater condensate loading. Many foundational observational studies supporting invigoration have several fundamental methodological flaws that render their findings incorrect or highly questionable. Thus, much of the evidence for invigoration has come from numerical modeling, but different models and setups have produced a vast range of results. Furthermore, modeled aerosol impacts on deep convection are rarely tested for robustness, and microphysical biases relative to observations persist, rendering many results unreliable for application to the real world. Without clear theoretical, modeling, or observational support, and given that enervation rather than invigoration may occur for some deep convective regimes and environments, it is entirely possible that the overall impact of cold-phase invigoration is negligible. Substantial mesoscale variability of dominant thermodynamic controls on convective updraft strength coupled with substantial updraft and aerosol variability in any given event are poorly quantified by observations and present further challenges to isolating aerosol effects. Observational isolation and quantification of convective invigoration by aerosols is also complicated by limitations of available cloud condensation nuclei and updraft speed proxies, aerosol correlations with meteorological conditions, and cloud impacts on aerosols. Furthermore, many cloud processes, such as entrainment and condensate fallout, modulate updraft strength and aerosol–cloud interactions, varying with cloud life cycle and organization, but these processes remain poorly characterized. Considering these challenges, recommendations for future observational and modeling research related to aerosol invigoration of deep convection are provided.</p

Droplet collection efficiencies inferred from satellite retrievals constrain effective radiative forcing of aerosol–cloud interactions

Process-oriented observational constraints for the anthropogenic effective radiative forcing due to aerosol–cloud interactions (ERFaci) are highly desirable because the uncertainty associated with ERFaci poses a significant challenge to climate prediction. The contoured frequency by optical depth diagram (CFODD) analysis supports the evaluation of model representation of cloud liquid-to-rain conversion processes because the slope of a CFODD, generated from joint MODerate Resolution Imaging Spectroradiometer (MODIS)-CloudSat cloud retrievals, provides an estimate of cloud droplet collection efficiency in single-layer warm liquid clouds. Here, we present an updated CFODD analysis as an observational constraint on the ERFaci due to warm rain processes and apply it to the U.S. Department of Energy's Energy Exascale Earth System Model version 2 (E3SMv2). A series of sensitivity experiments shows that E3SMv2 droplet collection efficiencies and ERFaci are highly sensitive to autoconversion, i.e., the rate of mass transfer from cloud liquid to rain, yielding a strong correlation between the CFODD slope and the shortwave component of ERFaci (ERFaciSW; Pearson's R=-0.91). E3SMv2's CFODD slope (0.20 ± 0.04) is in agreement with observations (0.20 ± 0.03). The strong sensitivity of ERFaciSW to the CFODD slope provides a useful constraint on highly uncertain warm rain processes, whereby ERFaciSW, constrained by MODIS-CloudSat, is estimated by calculating the intercept of the linear association between the ERFaciSW and the CFODD slopes, using the MODIS-CloudSat CFODD slope as a reference.</p

Ultrasound and x-ray imageable poloxamer-based hydrogel for loco-regional therapy delivery in the liver

Intratumoral injections have the potential for enhanced cancer treatment efficacy while reducing costs and systemic exposure. However, intratumoral drug injections can result in substantial off-target leakage and are invisible under standard imaging modalities like ultrasound (US) and x-ray. A thermosensitive poloxamer-based gel for drug delivery was developed that is visible using x-ray imaging (computed tomography (CT), cone beam CT, fluoroscopy), as well as using US by means of integrating perfluorobutane-filled microbubbles (MBs). MBs content was optimized using tissue mimicking phantoms and ex vivo bovine livers. Gel formulations less than 1% MBs provided gel depositions that were clearly identifiable on US and distinguishable from tissue background and with minimal acoustic artifacts. The cross-sectional areas of gel depositions obtained with US and CT imaging were similar in studies using ex vivo bovine liver and postmortem in situ swine liver. The gel formulation enhanced multimodal image-guided navigation, enabling fusion of ultrasound and x-ray/CT imaging, which may enhance targeting, definition of spatial delivery, and overlap of tumor and gel. Although speculative, such a paradigm for intratumoral drug delivery might streamline clinical workflows, reduce radiation exposure by reliance on US, and boost the precision and accuracy of drug delivery targeting during procedures. Imageable gels may also provide enhanced temporal and spatial control of intratumoral conformal drug delivery