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Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2021-03-08 We show that Ce13d DNAzymes can use non-electrostatic interactions to assist RNA cleavage by making simple Phosphorothioate (PS) modifications at the cleavage junction. In this case, Iodine can replace the role of a metal cofactor, acting directly on the scissile phosphate group. This finding has broadened the scope of DNAzyme catalysis. This DNAzyme was further engineered for fluorescence-based I2 detection with a detection limit of 4.7 nM. In addition, Oxidation of I− with Fe3+ produced I2 in situ, allowing detection of Fe3+ down to 78 nM. https://creativecommons.org/licenses/by/4.0/
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Data for: Comparative valuation of potential and realized ecosystem services in Southern Ontario, Canada
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2021-04-16 Because realized ecosystem services are directly consumed by people and clearly illustrate the link between ecosystem services and human well-being, the aim of this project was to distinguish potential and realized ecosystem services in Southern Ontario's landscape. The initial dataset used for this project was the Southern Ontario Land Resource Information System (SOLRIS) land use updated to 2016 for ecoregions 6E and 7E. Our analysis of these data yields a total potential value of the bundled ecosystem services of $19 billion per year for Southern Ontario. To estimate the value of the realized (or used) ecosystem services, the potential values are scaled by the corresponding relative use indices. The resulting value of the realized ecosystem services is $9.7 billion per year, that is, about 50% of the value of the potential ecosystem services. https://creativecommons.org/licenses/by/4.0/
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Anthropogenic Phosphorus Mass Balance in Ontario Counties and Watersheds
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2021-12-31 Parameters from the Net Anthropogenic Phosphorus Inputs model (NAPI) estimated on a county scale: annual crop uptake of phosphorus, annual net input from livestock (i.e. manure), annual phosphorus from milkhouse runoff, annual phosphorus applied as fertilizer, annual phosphorus inputs from domestic detergent use, and annual human phosphorus consumption in kg. Values were compiled from the Agricultural Census and the Population Census from Statistics Canada for each census year which occurred every five years beginning in 1961, values in between were linearly interpolated. Phosphorus content values for detergent, livestock, crops, and human consumption were compiled from literature (see individual spreadsheets for more information). ID is the Standard Geographic Code that represents the county, standardized to 2011. The region represents the agricultural region the county is in: South (1), West (2), Central (3), East (4), North (5). The raw data were downloaded from the publicly available census available at: http://odesi2.scholarsportal.info/webview/ in the Agriculture tab. Suppressed data were estimating using residual hectares unaccounted for in the region totals and historical trends. All data were standardized to the census subdivision distribution in 2011, i.e. any divisions that were amalgamated into other divisions were accounted for. This data set was produced to support the objectives of two projects. These are: 1) Legacies of Agricultural Pollutants (LEAP) funded by Natural Sciences and Engineering Research Council of Canada and other international partners. 2) "Lake Futures: Enhancing Adaptive Capacity and Resilience of Lakes and Their Watersheds". Lake Futures is a Pillar 3 project under the Global Water Futures Program funded by Canada First Research Excellence Fund. https://creativecommons.org/licenses/by/4.0/
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Meteorological and hydrological data from the Alder Creek Watershed, Grand River Basin, Ontario.
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2019-09-20 The Alder Creek field observatory was instrumented by the Southern Ontario Water Consortium as the middle member of three watersheds with different degrees of urbanization. Field data were collected via the deployment of electronic instruments and manual measurements in the Alder Creek watershed to answer questions related to water management at the watershed scale. Field sites were chosen based on: 1) an attempt to distribute measurement locations spatially throughout the watershed, 2) permissions obtained from local residents, businesses, and stakeholders (e.g., the Regional Municipality of Waterloo) for installations, and 3) interest in monitoring local processes such as depression focused recharge. Cellular network telemetry was used to regularly transmit remote field data to a computer at the University of Waterloo. This was part of a “smart” watershed design whereby field data could be reviewed by technicians to make decisions regarding field monitoring and equipment maintenance. Data collection schedules could also be adjusted remotely. This datasets will be also used to support the research objectives of the Global Water Futures Program https://creativecommons.org/publicdomain/zero/1.0/
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Effects of Freeze-Thaw Cycling on Methanogenic Hydrocarbon Degradation: Experimental and Numerical Simulation Results
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2023-10-01 Experimental results and numerical simulation results for study investigating the effects of freeze-thaw cycling on methanogenic hydrocarbon degradation. Experiment was a soil batch incubation experiment. Experimental results include: porewater chemistry data (e.g., dissolved organic carbon, toluene, dissolved inorganic carbon, acetate concentrations), headspace gas concentration data, and headspace gas isotope composition data. https://creativecommons.org/licenses/by/4.0/
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Simultaneous Detection of L-Lactate and D-Glucose Using DNA Aptamers in Human Blood Serum
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2023-03-09 L-lactate is a key metabolite indicative of physiological states, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need other substrates. In this work, DNA aptamers for L-lactate were obtained using a library-immobilization selection method and the highest affinity aptamer reached a Kd of 0.43 mM as determined using isothermal titration calorimetry. The aptamers showed up to 50-fold selectivity for L-lactate over D-lactate and had little responses to other closely related analogs such as pyruvate and 3-hydroxybutyrate. A fluorescent biosensor based on the strand displacement method showed a limit of detection of 0.55 mM L-lactate, and the sensor worked in 90% serum. Simultaneous detection of L-lactate and D-glucose in the same solution was achieved. This work has broadened the scope of aptamers to simple metabolites and provided a useful probe for continuous and multiplexed monitoring. https://creativecommons.org/publicdomain/zero/1.0/
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Reactive Silicon Data in Hamilton Harbour, Lake Ontario
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2019-04-03 This project investigated nutrient silicon cycling in Hamilton Harbour, Lake Ontario. A field sampling program was undertaken to collect water, suspended sediment, and bottom sediment samples from Hamilton Harbour, which were then analysed for dissolved and particulate reactive silicon. Sediment cores were also used in sediment core incubation experiments to determine the flux of silicon from sediments to the water column. This data was collated into a reactive silicon mass balance model to determine silicon inputs, outputs and internal cycling processes within Hamilton Harbour. https://creativecommons.org/publicdomain/zero/1.0/
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Relationship between soil CO2 fluxes and soil moisture: Anaerobic sources explain fluxes at high water content
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2023-11-17 This dataset contains carbon dioxide (CO2) and methane (CH4) gas fluxes, porewater chemistry and solid phase chemistry results of soil incubation experiments where headspace oxygen conditions (oxic versus anoxic) and soil moisture content were adjusted to evaluate the effects of soil moisture and oxygen availability on soil carbon cycling. https://creativecommons.org/licenses/by/4.0/
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Oxidation of Fe(II) by Flavins under Anoxic Conditions
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2021-02-16 This project aims to understand the redox reaction between Fe(II) and flavins. Our study demonstrated that aqueous Fe(II) can be oxidized by the oxidized form of riboflavin and flavin mononucleotide at pH 7–9. Both the rates and extents of oxidation increased with increasing concentration of oxidized flavins and increasing solution pH. Our data are from experiments, which mainly consist of the chemical variables, were collected in the Ecohydrology lab at the University of Waterloo using the batch reaction system. All the experiments were conducted in 125 mL serum bottles at 22±1 ℃ in an anaerobic glovebox (95% N2 and 5% H2). The bottles contained Teflon-coated magnetic stir bars and were wrapped in aluminum foil to exclude light. Prior to an experiment, a solution containing 20 mM buffer and 10 mM NaCl was purged with N2 (99.998%) for at least 2 h to remove O2, then transferred to the anaerobic glovebox. Aqueous Fe2+ and uncomplexed RBF and FMN concentrations were analyzed by using a Flexstation Multimode Microplate Reader. The total concentrations of RBF and FMN were determined at 450 nm on a UV-vis spectrometer kept in the anaerobic glovebox Additional details on the project are available in Environmental Science and Technology publication titled "Oxidation of Fe(II) by flavins under anoxic conditions" (doi: 10.1021/acs.est.0c02916) https://creativecommons.org/licenses/by/4.0/
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Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2021-03-12 A DNA library with glycyl–histidine-functionalized tertiary amine moiety modification at the cleavage junction was used for in vitro selection of Zn2+-dependent DNAzyme. Four DNAzymes were isolated and each of these DNAzymes displays different cooperative binding of metal ions. An interesting relationship between the number of metal ions involved in DNAzyme catalysis and selectivity was established, and this study showed that it could be a useful way to develop highly specific metal sensors. https://creativecommons.org/licenses/by/4.0/
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Probing Metal-Dependent Phosphate Binding for the Catalysis of the 17E DNAzyme
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2022-06-10 The RNA-cleaving 17E DNAzyme exhibits different levels of cleavage activity in the presence of various divalent metal ions, with Pb2+ giving the fastest cleavage. In this study, the metal–phosphate interaction is probed to understand the trend of activity with different metal ions. For the first-row transition metals, the lowest activity shown by Ni2+ correlates with the inhibition by the inorganic phosphate and its water ligand exchange rate, suggesting inner-sphere metal coordination. Cleavage activity with the two stereoisomers of the phosphorothioate-modified substrates, Rp and Sp, indicated that Mg2+, Mn2+, Fe2+, and Co2+ had the highest Sp:Rp activity ratio of >900. Comparatively, the activity was much less affected using the thiophilic metals, including Pb2+, suggesting inner-sphere coordination. The pH–rate profiles showed that Pb2+ was different than the rest of the metal ions in having a smaller slope and a similar fitted apparent pKa and the pKa of metal-bound water. Combining previous reports and our current results, we propose that Pb2+ most likely plays the role of a general acid while the other metal ions are Lewis acid catalysts interacting with the scissile phosphate. https://creativecommons.org/publicdomain/zero/1.0/
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Transport and retention of phosphorus in Lake St. Clair (Huron - Erie Corridor)
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2022-04-27 The main aim of this research is to understand the within-lake dynamics, transport, and retention of nutrients, particularly total and soluble reactive phosphorous, in Lake St. Clair. This data set will support the project titled "Lake Futures: Enhancing Adaptive Capacity and Resilience of Lakes and Their Watersheds". Lake Futures is a Pillar 3 project under the Global Water Futures Program funded by Canada First Research Excellence Fund. https://creativecommons.org/licenses/by/4.0/
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Removal and Degradation of Microplastics Using the Magnetic and Nanozyme Activities of Bare Iron Oxide Nanoaggregates
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2022-12-31 Removal and degradation of microplastics are often carried out separately. In this work, hydrophilic bare Fe3O4 nanoaggregates allowed efficient removal of the most common microplastics including high-density polyethylene, polypropylene, polyvinyl chloride, polystyrene, and polyethylene terephthalate. Full extraction was achieved using Fe3O4 at 1% of the mass of microplastics. Hydrogen bonding is the main force for the adsorption of Fe3O4. Unlike the more commonly used hydrophobically modified Fe3O4 nanoparticles, the bare Fe3O4 benefitted from the peroxidase-like activity of its exposed surface, enabling further catalytic degradation of microplastics with nearly 100% efficiency and easy recovery of the Fe3O4. https://creativecommons.org/publicdomain/zero/1.0/
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Arsenic Oxidation by Flavin-Derived Reactive Species under Oxic and Anoxic Conditions
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2020-02-29 The objective of this research is to see how the redox and pH conditions impact the oxidation of arsenic (As) in the presence of reduced and oxidized riboflavin species. Batch experiments using simple dark-brown glass reactors were conducted under anoxic (glovebox filled with 97-98% nitrogen and 2-3% hydrogen gases) and oxic (purified air introduced to the reactors through tubes) conditions and a range of pre-designed solution pH from 5.2 to 9.0. Variables collected in this research include the concentrations of arsenate (As(V)), arsenite (As(III)), total riboflavin, oxidized riboflavin and hydrogen peroxide (H2O2), all as a function of time. As(V) and As(III) concentrations in solution samples collected at different time points from 1 to 55 min were determined by hydrogen-generation atomic fluorescence spectrometry (HG-AFS, PS Analytical) with a detection limit of 0.5 μg/L. To measure As concentrations below this limit, anodic stripping voltammetry was performed using a 797 VA Computrace equipped with the TRACE Gold sensor (Metrohm, Application Bulletin 416/3). The total riboflavin concentrations were determined by measuring the fluorescence signal at the excitation/emission wavelength of 450/520 nm with a Flexstation-3 Multimode Reader (Molecular Devices) equipped with black/clear bottom 96-well microplates. The concentrations of oxidized riboflavin were measured by UV-vis spectrophotometry, with absorbance measured on a Flexstation-3 Multimode Reader (Molecular Devices). The detection limit of total riboflavin and oxidized riboflavin is 16 nmol/L. The concentrations of H2O2 were measured following the protocol of the commercial Fluorimetric Hydrogen Peroxide Assay Kit (Sigma-Aldrich). The fluorescence was measured at the excitation/emission wavelength of 540/590 nm, with a detection limit of 0.01 μmol/L. Additional details on the experimental setup for data collection can be found in the Supporting Information at https://doi.org/10.1021/acs.est.9b03188. The data in this research were collected in the Ecohydrology Research Group laboratories at the University of Waterloo. Funding for this work was provided by the Canada Excellence Research Chair in Ecohydrology, https://creativecommons.org/publicdomain/zero/1.0/
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Selection of Aptamers for Sensing Caffeine and Discrimination of Its Three Single Demethylated Analogues
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2022-06-10 With the growing consumption of caffeine-containing beverages, detection of caffeine has become an important biomedical, bioanalytical, and environmental topic. Four high-quality aptamers for caffeine were isolated and were carefully characterized. A structure-switching fluorescent sensor was designed showing a detection limit of 1.2 μM caffeine, which reflected the labeled caffeine concentration within 6.1% difference for eight commercial beverages. In 20% human serum, a detection limit of 4.0 μM caffeine was achieved. In addition, these four fluorescent aptamer sensors can form a sensing array, caffeine and the three analogues were well separated from nine other closely related molecules. https://creativecommons.org/publicdomain/zero/1.0/
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Modeling multi-year phosphorus dynamics in a bioretention cell: phosphorus partitioning, accumulation, and export
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2023-07-01 Abstract: Nutrient phosphorus (P) export from urban areas via stormwater runoff contributes to eutrophication of downstream aquatic ecosystems. Bioretention cells are a Low Impact Development (LID) technology promoted as a green solution to attenuate urban peak flow discharge, as well as the export of excess nutrients and other contaminants. Despite their rapidly growing implementation worldwide, a predictive understanding of the efficiency of bioretention cells in reducing P runoff remains limited. Here, we present a reaction-transport model data and codes that was used to simulate the fate and transport of P in a bioretention cell facility in the greater Toronto metropolitan area. The model incorporates a representation of the biogeochemical reaction network that controls P cycling within the cell. We used the model as a diagnostic tool to determine the relative importance of processes immobilizing P in the bioretention cell. The model predictions were compared to multi-year observational data on 1) the outflow loads of total P (TP) and soluble reactive P (SRP) during the 2012-2017 period, 2) TP depth profiles collected at 4 time points during the 2012-2019 period, and 3) sequential chemical P extractions performed on core samples from the filter media layer obtained in 2019. According to the modeling results, groundwater recharge was principally responsible for decreasing the surface water discharge from the bioretention cell (63% runoff reduction). From 2012 to 2017, the cumulative outflow export loads of TP and SRP only accounted for 1% and 2% of the corresponding inflow loads, respectively. Accumulation in the filter media layer was the predominant mechanism responsible for the reduction in P outflow loading (57% retention of TP inflow load) followed by plant uptake (21% TP retention). Of the P retained within the filter media layer, 48% occurred in stable, 41% in potentially mobilizable, and 11% in easily mobilizable forms. There were no signs that the P retention capacity of the bioretention cell would approach saturation in the near future. The design of this bioretention facility seems therefore especially efficient at controlling urban P runoff. This Dataset includes the model scripts and modelled results dataset for Elm Drive bio retention cell. https://creativecommons.org/licenses/by/4.0/
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Predicted 21st Century Non-growing Season Net Ecosystem Exchanges of CO2 from the Mer Bleue Bog: Support Vector Regression Model Outputs for RCP2.6, RCP4.5 and RCP8.5
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2021-05-10 In this study, we determine key environmental variables affecting non-growing season net ecosystem exchanges of CO2 (NGS-NEE) from a temperate peatland (Mer Bleue Bog; Ottawa, Canada) and predict future NGS-NEE under three climate scenarios (RCP2.6, RCP4.5, and RCP8.5) using a variable selection methodology, global sensitivity analysis, and data-driven model. Future NGS-NEE predictions, model training parameters, and global sensitivity analysis results are provided. https://creativecommons.org/licenses/by/4.0/
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Bedload sediment transport and morphologic data in semi-alluvial rivers conditioned by urbanization and stormwater management
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2019-08-13 Watershed urbanization and stormwater management (SWM) alter the hydrologic and geomorphologic processes of rivers. This purpose of this study is to characterize the bedload sediment transport regime of semi-alluvial gravel-bed rivers, and how it is affected by watershed urbanization and common SWM strategies. Data was collected from three rivers in the Greater Toronto Area of Southern Ontario: Ganatsekaigon Creek (City of Pickering), Wilket Creek (City of Toronto), and Morningside Creek (City of Toronto). The grain size distribution at each site was calculated using a Wolman Pebble count with a 200-stone sample size. Bedload transport was monitored over three years using Radio Frequency Identification (RFID) tracer stones, and periodic topographic surveys were conducted. A total of 300 tracers in 3 size classes were seeded in each site in August 2015. Tracer positions were recorded after each major rainfall event during the active field season each year, resulting in a total of 10, 12, and 13 recoveries in Ganatsekaigon Creek , Wilket Creek, and Morningside Creek, respectively. With each recovery, the travel distance of each tracer since its last known position is calculated. Detailed topographic surveys of the channel bed were conducted in the summers of 2016 and 2018 using a total station. Surveys were used to create DEM of Difference (DOD) at each site after a Triangular Irregular Network interpolation. https://creativecommons.org/publicdomain/zero/1.0/
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The Effects of Temperature and Soil Moisture on CO2 and CH4 Flux
Federated Research Data Repository / dépôt fédéré de données de recherche
— 2022-11-01 This dataset contains results from laboratory soil incubations with peat samples of different depth intervals retrieved at seven Canadian peatland locations. CO2 release fluxes (and CH4 fluxes for some samples) from peat samples were measured using Li-8100 and Li-8150 system under variable moisture levels across a temperature sequence ranging from -10 to 35 °C in an environmental chamber. The resulting CO2 production rates were fitted to equations describing the observed moisture and temperature trends. https://creativecommons.org/publicdomain/zero/1.0/

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