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Abstract In the 465,000 km2 Canadian Prairies ecozone, robust hydrological input data for hydraulic model applications are uncommon because of the sparse monitoring network and the intermittently connected stream network. New hydrological datasets can offer a valuable advancement for making water management decisions and designing infrastructure in this water stressed region. The Prairie Hydrology Design and Analysis Product (PHyDAP) was created to address existing limitations, and provides a comprehensive regional dataset for use in hydraulic modelling applications. PHyDAP is a collection of outputs from a physically based hydrological modelling framework, run for periods ranging from 38 to 150 years, according to three climate forcing datasets. The dataset includes vertical and lateral fluxes (rainfall, snowmelt, upland runoff, and open water evaporation) and basin streamflow, at hourly or 3-hourly intervals for the >4000 small basins of approximately 100 km2 that span the region. This contribution describes the motivation for this work and methodology used to derive the data product, summarizes the data and its accessibility, and provides an overview of potential use cases.

Abstract Functional analysis of high throughput experiments using pathway analysis is now ubiquitous. Though powerful, these methods often produce thousands of redundant results owing to knowledgebase redundancies upstream. This scale of results hinders extensive exploration by biologists and can lead to investigator biases due to previous knowledge and expectations. To address this issue, we present vissE, a flexible network-based analysis and visualisation tool that organises information into semantic categories and provides various visualisation modules to characterise them with respect to the underlying data, thus providing a comprehensive view of the biological system. We demonstrate vissE’s versatility by applying it to three different technologies: bulk, single-cell and spatial transcriptomics. Applying vissE to a factor analysis of a breast cancer spatial transcriptomic data, we identified stromal phenotypes that support tumour dissemination. Its adaptability allows vissE to enhance all existing gene-set enrichment and pathway analysis workflows, empowering biologists during molecular discovery.

In many regions, a tradeoff exists between draining wetlands to support the expansion of agricultural land, and conserving wetlands to maintain their valuable ecosystem services. Decisions about wetland drainage are often made without identifying the impacts on the services these systems provide. We address this gap through a novel assessment of impacts on ecosystem services via wetland drainage in the Canadian prairie landscape. Draining pothole wetlands has large impacts, but sensitivity varies among the indicators considered. Loss of water storage increased the magnitude of median annual flows, but absolute increases with drainage were higher for larger, less frequent events. Total phosphorus exports increased in concert with streamflow. Our analysis suggested disproportionate riparian habitat losses with the first 30% of wetland area drained. Dabbling ducks and wetland-associated bird abundances respond strongly to the loss of small wetland ponds; abundances were predicted to decrease by half with the loss of only 20%–40% of wetland area. This approach to evaluating changes to key wetland ecosystem services in a large region where wetland drainage is ongoing can be used with an economic valuation of the drainage impacts, which should be weighed against the benefits associated with agricultural expansion.

Shallow ponds can provide ideal conditions for production of greenhouse gases (GHGs) carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), and thus are important to include in global and regional GHG budgets. The Canadian Prairie Pothole Region contains millions of shallow natural ponds, and we investigated GHG dynamics in 145 ponds across the region. Ponds were consistently supersaturated with CH4, often supersaturated with CO2 (57% occurrence), and often undersaturated with N2O (65% occurrence). Spring measurements showed higher N2O saturation (p = 0.0037) than summer, while summer had higher CH4 (p

Wetland drainage has been pervasive in the North American Prairie Pothole Region. There is strong evidence that this drainage increases the hydrological connectivity of previously isolated wetlands and, in turn, runoff response to snowmelt and rainfall. It can be hard to disentangle the role of climate from the influence of wetland drainage in observed records. In this study, a basin-classification-based virtual modelling approach is described that can isolate these effects on runoff regimes. The basin class which was examined, entitled Pothole Till, extends throughout much of Canada's portion of the Prairie Pothole Region. Three knowledge gaps were addressed. First, it was determined that the spatial pattern in which wetlands are drained has little influence on how much the runoff regime was altered. Second, no threshold could be identified below which wetland drainage has no effect on the runoff regime, with drainage thresholds as low as 10 % in the area being evaluated. Third, wetter regions were less sensitive to drainage as they tend to be better hydrologically connected, even in the absence of drainage. Low flows were the least affected by drainage. Conversely, during extremely wet years, runoff depths could double as the result of complete wetland removal. Simulated median annual runoff depths were the most responsive, potentially tripling under typical conditions with high degrees of wetland drainage. As storage capacity is removed from the landscape through wetland drainage, the size of the storage deficit of median years begins to decrease and to converge on those of the extreme wet years. Model simulations of flood frequency suggest that, because of these changes in antecedent conditions, precipitation that once could generate a median event with wetland drainage can generate what would have been a maximum event without wetland drainage. The advantage of the basin-classification-based virtual modelling approach employed here is that it simulated a long period that included a wide variety of precipitation and antecedent storage conditions across a diversity of wetland complexes. This has allowed seemingly disparate results of past research to be put into context and finds that conflicting results are often only because of differences in spatial scale and temporal scope of investigation. A conceptual framework is provided that shows, in general, how annual runoff in different climatic and drainage situations will likely respond to wetland drainage in the Prairie Pothole Region.

Abstract Background Malignant pleural effusions (MPEs) are a common complication of advanced cancers, particularly those adjacent to the pleura, such as lung and breast cancer. The pathophysiology of MPE formation remains poorly understood, and although MPEs are routinely used for the diagnosis of breast cancer patients, their composition and biology are poorly understood. It is difficult to distinguish invading malignant cells from resident mesothelial cells and to identify the directionality of interactions between these populations in the pleura. There is a need to characterize the phenotypic diversity of breast cancer cell populations in the pleural microenvironment, and investigate how this varies across patients. Methods Here, we used single‐cell RNA‐sequencing to study the heterogeneity of 10 MPEs from seven metastatic breast cancer patients, including three Miltenyi‐enriched samples using a negative selection approach. This dataset of almost 65 000 cells was analysed using integrative approaches to compare heterogeneous cell populations and phenotypes. Results We identified substantial inter‐patient heterogeneity in the composition of cell types (including malignant, mesothelial and immune cell populations), in expression of subtype‐specific gene signatures and in copy number aberration patterns, that captured variability across breast cancer cell populations. Within individual MPEs, we distinguished mesothelial cell populations from malignant cells using key markers, the presence of breast cancer subtype expression patterns and copy number aberration patterns. We also identified pleural mesothelial cells expressing a cancer‐associated fibroblast‐like transcriptomic program that may support cancer growth. Conclusions Our dataset presents the first unbiased assessment of breast cancer‐associated MPEs at a single cell resolution, providing the community with a valuable resource for the study of MPEs. Our work highlights the molecular and cellular diversity captured in MPEs and motivates the potential use of these clinically relevant biopsies in the development of targeted therapeutics for patients with advanced breast cancer.

Abstract Exotic species are often vilified as “bad” without consideration of the potential they have for contributing to ecological functions in degraded ecosystems. The red-eared slider turtle (RES) has been disparaged as one of the worst invasive species. Based on this review, we suggest that RES contribute some ecosystem functions in urban wetlands comparable to those provided by the native turtles they sometimes dominate or replace. While we do not advocate for releases outside their native range, or into natural environments, in this review, we examine the case for the RES to be considered potentially beneficial in heavily human-altered and degraded ecosystems where native turtles struggle or fail to persist. After reviewing the ecosystem functions RESs are known to provide, we conclude that in many modified environments the RES is a partial ecological analog to native turtles and removing them may obviate the ecological benefits they provide. We also suggest research avenues to better understand the role of RESs in heavily modified wetlands.

Significant challenges from changes in climate and land use face sustainable water use in the Canadian Prairies ecozone. The region has experienced significant warming since the mid-20th century, and continued warming of an additional 2 ∘C by 2050 is expected. This paper aims to enhance understanding of climate controls on Prairie basin hydrology through numerical model experiments. It approaches this by developing a basin-classification-based virtual modelling framework for a portion of the Prairie region and applying the modelling framework to investigate the hydrological sensitivity of one Prairie basin class (High Elevation Grasslands) to changes in climate. High Elevation Grasslands dominate much of central and southern Alberta and parts of south-western Saskatchewan, with outliers in eastern Saskatchewan and western Manitoba. The experiments revealed that High Elevation Grassland snowpacks are highly sensitive to changes in climate but that this varies geographically. Spring maximum snow water equivalent in grasslands decreases 8 % ∘C−1 of warming. Climate scenario simulations indicated that a 2 ∘C increase in temperature requires at least an increase of 20 % in mean annual precipitation for there to be enough additional snowfall to compensate for enhanced melt losses. The sensitivity in runoff is less linear and varies substantially across the study domain: simulations using 6 ∘C of warming, and a 30 % increase in mean annual precipitation yields simulated decreases in annual runoff of 40 % in climates of the western Prairie but 55 % increases in climates of eastern portions. These results can be used to identify those areas of the region that are most sensitive to climate change and highlight focus areas for monitoring and adaptation. The results also demonstrate how a basin classification-based virtual modelling framework can be applied to evaluate regional-scale impacts of climate change with relatively high spatial resolution in a robust, effective and efficient manner.

Cell-free protein synthesis (CFPS) reactions have grown in popularity with particular interest in applications such as gene construct prototyping, biosensor technologies and the production of proteins with novel chemistry. Work has frequently focussed on optimising CFPS protocols for improving protein yield, reducing cost, or developing streamlined production protocols. Here we describe a statistical Design of Experiments analysis of 20 components of a popular CFPS reaction buffer. We simultaneously identify factors and factor interactions that impact on protein yield, rate of reaction, lag time and reaction longevity. This systematic experimental approach enables the creation of a statistical model capturing multiple behaviours of CFPS reactions in response to components and their interactions. We show that a novel reaction buffer outperforms the reference reaction by 400% and importantly reduces failures in CFPS across batches of cell lysates, strains of E. coli, and in the synthesis of different proteins. Detailed and quantitative understanding of how reaction components affect kinetic responses and robustness is imperative for future deployment of cell-free technologies.

Synthetic polymer nano-objects with well-defined hierarchical structures are important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Here the authors demonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers.