The three Rs of river ecosystem resilience: Resources,recruitment, and refugia

Resilience in river ecosystems requires that organisms must persist in the face of highly dynamic hydrological and geomorphological variations. Disturbance events such as floods and droughts are postulated to shape life history traits that support resilience, but river management and conservation would benefit from greater understanding of the emergent effects in communities of river organisms. We unify current knowledge of taxonomic‐, phylogenetic‐, and trait‐based aspects of river communities that might aid the identification and quantification of resilience mechanisms. Temporal variations in river productivity, physical connectivity, and environmental heterogeneity resulting from floods and droughts are highlighted as key characteristics that promote resilience in these dynamic ecosystems. Three community‐wide mechanisms that underlie resilience are (a) partitioning (competition/facilitation) of dynamically varying resources, (b) dispersal, recolonization, and recruitment promoted by connectivity, and (c) functional redundancy in communities promoted by resource heterogeneity and refugia. Along with taxonomic and phylogenetic identity, biological traits related to feeding specialization, dispersal ability, and habitat specialization mediate organism responses to disturbance. Measures of these factors might also enable assessment of the relative contributions of different mechanisms to community resilience. Interactions between abiotic drivers and biotic aspects of resource use, dispersal, and persistence have clear implications for river conservation and management. To support these management needs, we propose a set of taxonomic, phylogenetic, and life‐history trait metrics that might be used to measure resilience mechanisms. By identifying such indicators, our proposed framework can enable targeted management strategies to adapt river ecosystems to global change.     

The COVID‐19 crisis and complexity: A soft systems approach

The COVID‐19 pandemic is a crisis with high complexity and should be understood as such by scholarship. A complexity science approach situates increasingly divergent ideological and epistemological perspectives about the crisis within the practical exigencies of containment and mitigation measures. We ask which of the seven stages of soft systems methodology contributes to deeper understandings about COVID‐19 as a policy issue, beyond the contributions of current and conventional perspectives. The discussion outlines implications for practice and places them within broader debates about tensions between scientific facts and political values.     

Mass spectrometry and the cellular surfaceome

The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.     

Modulation of enzyme activity by antibody binding to an alkaline phosphatase-epitope hybrid protein

An epitope from the HTV-1 gpl20 protein V3 loop has been insertedonto the surface of bacterial alkaline phosphatase at differentpositions in the vicinity of the enzyme active site, creatinghybrid proteins that can bind to an anti-gpl20 monoclonal antibody.One of the hybrid proteins, API1, has a 13 amino acid V3 loopsequence inserted between residues 407 and 408 of alkaline phosphatase.The enzymatic activity of this protein is modulated upon antibodybinding. API1 maintains the full activity of the wild type alkalinephosphatase but in the presence of the anti-gpl20 antibody,the enzyme activity is inhibited by 40–50%. Thus, thehybrid enzyme can be used to detect the presence of antibodyin solution. The concept of signalling proteins may have a wideapplication. Two models for the mechanism of modulation, sterichindrance and allosteric regulation, are discussed.     

Detection of trace water vapor in high-purity phosphine using cavity ring-down spectroscopy

The presence of trace water vapor in process gases such as phosphine, used for compound semiconductor epitaxial growth, can negatively affect the optical and electrical properties of the final device. Therefore, sensitive H2O measurement techniques are required to monitor precursor purity and detect unacceptable contamination levels. A commercial cavity ring-down spectrometer that monitors an H2O absorption line at a wavelength of 1392.53 nm was investigated for service in high purity PH3. Spectral parameters such as the line shape of water vapor in the presence of PH3 as well as background features due to PH3 were measured at different pressures and incorporated into the data analysis software for accurate moisture readings. Test concentrations generated with a diffusion vialbased H2O source and dilution manifold were used to verify instrument accuracy, sensitivity, linearity, and response time. H2O readings at 13.2 kPa corresponded well to added concentrations (slope=0.990+/-0.01) and were linear in the tested range (0-52.7 nmol mol-1). The analyzer was sensitive to changes in H2O concentration of 1.3 nmol mol-1 based on 3sigma of the calibration curve intercept for a weighted linear fit. Local PH3 absorption features that could not be distinguished from the H2O line were present in the purified PH3 spectra and resulted in an additional systematic uncertainty of 9.0 nmol mol-1. Equilibration to changing H2O levels at a flow rate of 80 std cm3 min-1 PH3 occurred in 10-30 minutes. The results indicate that cavity ring-down spectroscopy (CRDS) at 1392.53 nm may be useful for applications such as on-line monitoring (and dry-down) of phosphine gas delivery lines or the quality control of cylinder sources.     

Modeling prostate anatomy from multiple view TRUS images for image-guided HIFU therapy

Current planning methods for transrectal high-intensity focused ultrasound treatment of prostate cancer rely on manually defining treatment regions in 15-20 sector transrectal ultrasound (TRUS) images of the prostate. Although effective, it is desirable to reduce user interaction time by identifying functionally related anatomic structures (segmenting), then automatically laying out treatment sites using these structures as a guide. Accordingly, a method has been developed to effectively generate solid three-dimensional (3-D) models of the prostate, urethra, and rectal wall from boundary trace data. Modeling the urethra and rectal wall are straightforward, but modeling the prostate is more difficult and has received much attention in the literature. New results presented here are aimed at overcoming many of the limitations of previous approaches to modeling the prostate while using boundary traces obtained via manual tracing in as few as 5 sector and 3 linear images. The results presented here are based on a new type of surface, the Fourier ellipsoid, and the use of sector and linear TRUS images. Tissue-specific 3-D models will ultimately permit finer control of energy deposition and more selective destruction of cancerous regions while sparing critical neighboring structures.     

Occurrence,prevention and remediation of toxigenic fungi and mycotoxins in silage: a review

Ruminants are considered to be less sensitive towards mycotoxins than monogastric animals because rumen microbiota have mycotoxin‐detoxifying capacities. Therefore the effect of mycotoxins towards ruminants has been studied to a lesser extent compared with monogastric animals. Worldwide, a high proportion of the ruminant diet consists of silages made of forage crops (i.e. all parts of the crop above the stubble are harvested). In practice, silages are often contaminated with multiple mycotoxins. Exposure to a cocktail of mycotoxins can hamper animal production and have severe health consequences. In this article the different aspects associated with mycotoxin contamination of silage are reviewed ‘from seed to feed’. An overview is given on the occurrence of toxigenic fungal species and their concomitant mycotoxins in forage crops before and after ensiling. The mycotoxin load of visually non‐mouldy samples and mouldy hot spots within the same silo is also compared. Subsequently, this review delves into different problem‐solving strategies. A logical first step is prevention of mould growth and mycotoxin production in the field, during harvest and during ensiling. If prevention should fail, several remediation strategies are available. These are listed, mainly focusing on the possibilities of microbial degradation of mycotoxins in vivo in silage. © 2015 Society of Chemical Industry