Faculty Publications (BioMed Central & Faculty of Science)

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Articles from BioMed Central by University of Victoria, Faculty of Science authors. Also other journal articles by UVic Faculty of Science authors.

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    Paleolimnological study of Elk Lake: 150-500 years of inferred water quality developments
    (University of Victoria, 2002) Groeneveld, Roel
    Elk Lake is a relatively small (246 ha) and shallow (>18m) lake situated on Vancouver Island (BC, Canada). It turned into a eutrophic system over the last 50 years, most likely due to anthropogenic disturbances of its watershed. Because the state of the ecosystem before settlement of the area is not known, the present situation cannot be compared to the original condition of the lake. This hampers present day water quality management because there is no reference value against which current ecological information and scenarios for the lake’s future can be compared. Paleolimnological methods and techniques can enable researchers to retrieve historic data from sediment cores. This approach can be very useful for identifying the important developments in the state of the water quality of the Elk Lake ecosystem over the past 150 years, and for linking these to historic records on natural and anthropogenic disturbances that occurred in the watershed. In this project, the sediment cores were retrieved form the lake using a modified gravity corer. 210Pb-dating of sediment subsamples was done using alpha spectrometry. Concentrations of nutrients, heavy metals and other elements were determined, and for each subsample the relative abundance of the present diatom species (or genera) was assessed as well. Furthermore, water quality data on Elk Lake for the past decades was retrieved from government databases. Readily visible are the doubling and tripling of heavy metal concentrations in the lakes sediment between the first and second half of the 19th century. Sediment accumulation rates show a sharp increase from 1950 onward. The stable C:N ratio indicates that sources of organic matter present in the water column hardly changed over the past 400 years. Of the present diatoms, Aulacoseira was the most dominant genus over the past centuries. During the last decades, eutrophic genera like Stephanodiscus became increasingly abundant. This is in line with public observations that the water quality of Elk Lake has been deteriorating since the mid 1980s. The integration of the results of all analyses made it possible to identify three important events or developments affecting the lake’s condition: the 16th century megadrought; the settlement of the Greater Victoria area, and the intensified land use after World War II. Against expectations, the construction of both the Victoria Waterworks and the Patricia Bay Highway were not extractable from the results. Advanced statistical analyses may be necessary to retrieve more information from the collected data set. In that aspect, the diatom data should be verified before this set of data is reused in other (follow-up) projects. After verification, this subset can be used for detailed inferences of water quality developments in Elk Lake.
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    Inferring benthic megafaunal sediment reworking activity in relation to bottom water oxygen in Barkley Canyon, NE Pacific from video and acoustic imaging analysis
    (Deep Sea Research Part I: Oceanographic Research Papers, 2024) Ciraolo, Alessia C.; Snelgrove, Paul V. R.; Schillinger, Douglas; De Leo, Fabio
    Sediment reworking activity influences benthic functioning expressed as nutrient fluxes and carbon cycling. Multiple studies have addressed sediment reworking based on observations from individual instrument types (e.g., video camera, side-scan sonar, multibeam), but none have considered reworking based on two or more complementary instruments. We therefore analyzed deep-sea megafaunal and reworked sediment traces by combining and comparing observations from non-invasive instruments, an underwater video camera and a rotary sonar, as part of the node of Ocean Networks Canada's NEPTUNE cabled observatory, located at 396 m depth in Barkley Canyon Upper Slope, NE Pacific Ocean. Specifically, we examined sediment traces and benthic megafaunal communities during two different sampling periods (May and September 2013) and at two different spatial scales of analysis. The camera images (∼0.5 m2) documented significantly lower megafaunal density during the period of reduced oxygen concentrations (May). Although we did not observe significant differences in sediment trace diversity and density between the two study periods, we were interested in how the relief traces generated by unidentified gastropods (likely the family Solariellidae) influenced sediment mixing. Relief traces showed higher density in low oxygen (May, 1.87 count m−2) than in high oxygen (September, 1.17 count m−2) conditions. Sonar images (∼1268 m2), which lacked sufficient resolution to allow identification of benthic organisms, documented distributions of biological pits (regions of low backscatter), a significantly greater proportion of bioturbated seafloor area, and increased in pit size with increased oxygen levels. Pits dominated sonar images at this location and persisted through the two study periods. Most sonar field of view subsections showed a significant increase in circularity of pit shapes, likely explained by increased reworked sediment with increasing oxygen concentration. We conclude that, except for relief burrows, higher reworked sediment area coincided with the highest oxygen concentration, which aligns with previously established reduced metabolic activity by benthos adapted to oxygen minimum zones. Furthermore, we emphasize the complementarity of the two imaging techniques (video and sonar) in understanding deep-sea benthic ecosystem dynamics, as well as the importance of considering multiple spatial scales when investigating proxies of bioturbation activity.
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    Models and data used to predict the abundance and distribution of Ixodes scapularis (blacklegged tick) in North America: A scoping review
    (The Lancet Regional Health - Americas, 2024) Sharma, Yogita; Laison, Elda K. E.; Philippsen, Tanya; Ma, Junling; Kong, Jude; Ghaemi, Sajjad; Liu, Juxin; Hu, François; Nasri, Bouchra
    Tick-borne diseases (TBD) remain prevalent worldwide, and risk assessment of tick habitat suitability is crucial to prevent or reduce their burden. This scoping review provides a comprehensive survey of models and data used to predict distribution and abundance in North America. We identified 4661 relevant primary research articles published in English between January 1st, 2012, and July 18th, 2022, and selected 41 articles following full-text review. Models used data-driven and mechanistic modelling frameworks informed by diverse tick, hydroclimatic, and ecological variables. Predictions captured tick abundance (n = 14, 34.1%), distribution (n = 22, 53.6%) and both (n = 5, 12.1%). All studies used tick data, and many incorporated both hydroclimatic and ecological variables. Minimal host- and human-specific data were utilized. Biases related to data collection, protocols, and tick data quality affect completeness and representativeness of prediction models. Further research and collaboration are needed to improve prediction accuracy and develop effective strategies to reduce TBD.
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    Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada
    (Ecological Indicators, 2024) Acharya-Patel, Neha; Groenwold, Emma; Lemay, Matthew A.; Clemente-Carvalho, Rute; Morien, Evan; Dudas, Sarah; Rubidge, Emily; Yang, Cecilia Lingyu; Coombe, Lauren; Warren, René L.; Frid, Alejandro; Birol, Inanc; Helbing, Caren C.
    The rocky reefs of British Columbia’s (BC) coast are a productive ecosystem, home to 38 rockfish species (Genus: Sebastes) that are culturally and economically important. Quantitatively assessing rockfish populations is vital to support conservation and stock assessment needs. Self-contained underwater breathing apparatus (SCUBA) diving surveys are a commonly used monitoring method in BC. However, this resource-intensive approach is challenging, particularly for cryptic or deeper species. Herein, we compared environmental DNA (eDNA) detection methods with SCUBA diving surveys to capture overall rockfish biodiversity. We employed two eDNA methods: 1) a targeted quantitative real-time polymerase chain reaction (qPCR) approach to monitor species of particular importance to First Nations collaborators and decision makers, and 2) a metabarcoding approach for assessing community composition using the previously published MiSebastes assay. Both approaches are confounded by the little DNA sequence divergence among species and high sequence variation within species. Overcoming these challenges using a whole mitochondrial approach with the mtGrasp and unikseq pipelines, we generated highly useful eDNA tools. We found that eDNA methods were highly comparable to dive surveys, as both methods indicated a similar ecological reality, including species detections and distributions. Though there are certain species that cannot be distinguished by the MiSebastes assay, eDNA metabarcoding still detected more rockfish species overall. Both eDNA methods show potential for use alongside conventional methods for scalable incorporation into community-based monitoring programs.
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    Weakly nonlinear analysis of a two-species non-local advection-diffusion system
    (Nonlinear Analysis: Real World Applications, 2024) Giunta, Valeria; Hillen, Thomas; Lewis, Mark A.; Potts, Jonathan R.
    Nonlocal interactions are ubiquitous in nature and play a central role in many biological systems. In this paper, we perform a bifurcation analysis of a widely-applicable advection–diffusion model with nonlocal advection terms describing the species movements generated by inter-species interactions. We use linear analysis to assess the stability of the constant steady state, then weakly nonlinear analysis to recover the shape and stability of non-homogeneous solutions. Since the system arises from a conservation law, the resulting amplitude equations consist of a Ginzburg–Landau equation coupled with an equation for the zero mode. In particular, this means that supercritical branches from the Ginzburg–Landau equation need not be stable. Indeed, we find that, depending on the parameters, bifurcations can be subcritical (always unstable), stable supercritical, or unstable supercritical. We show numerically that, when small amplitude patterns are unstable, the system exhibits large amplitude patterns and hysteresis, even in supercritical regimes. Finally, we construct bifurcation diagrams by combining our analysis with a previous study of the minimizers of the associated energy functional. Through this approach we reveal parameter regions in which stable small amplitude patterns coexist with strongly modulated solutions.
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    Therapeutic drug monitoring of clozapine in human serum by high-throughput paper spray mass spectrometry
    (Journal of Mass Spectrometry and Advances in the Clinical Lab, 2024) Saatchi, A.; Zarkovic, T. M.; Borden, S. A.; Palaty, J.; Gill, Chris
    Introduction: Monitoring the atypical antipsychotic drug clozapine is crucial to ensure patient safety. This article showcases a high-throughput analytical method for measuring clozapine and its primary metabolite norclozapine (N-desmethylclozapine) in serum using paper spray mass spectrometry (PS-MS). Objectives: This study aimed to assess the viability of a PS-MS method for the rapid measurement of clozapine and norclozapine in human serum samples as an alternative to liquid chromatography mass spectrometry (LC-MS). Methods: Serum samples were processed by protein precipitation followed by deposition of the supernatant containing labelled internal standards onto paper spray substrates mounted in cartridges. Analytes were then analyzed using a triple quadrupole mass spectrometer equipped with a commercial paper spray ionization source. The results obtained from the patient samples were compared to those from a validated LC-MS assay. Results: PS-MS calibrations for clozapine and norclozapine were linear (R2 > 0.99) over five days. Between-run precision was below 8 %, and within-run precision did not exceed 10 %. When compared to a validated LC-MS method, the mean bias for 39 patient samples was −9% for clozapine and −1% for norclozapine, with no outliers. Mass spectrometry ion ratio comparisons indicated no interference for patient samples above the lower limit of quantification. There was less than 7 % change in the measured concentrations of both analytes over five days for samples dried on paper substrates. Notably, virtually no maintenance of the MS source was required during this study. Conclusion: This study illustrates the potential of PS-MS for serum drug monitoring in the clinical laboratory.
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    Loss of Dna2 fidelity results in decreased Exo1-mediated resection at DNA double-strand breaks
    (Journal of Biological Chemistry, 2024) Mojumdar, Aditya; Granger, Courtney; Lunke, Martine; Cobb, Jennifer A.
    A DNA double-strand break (DSB) is one of the most dangerous types of DNA damage that is repaired largely by homologous recombination or nonhomologous end-joining (NHEJ). The interplay of repair factors at the break directs which pathway is used, and a subset of these factors also function in more mutagenic alternative (alt) repair pathways. Resection is a key event in repair pathway choice and extensive resection, which is a hallmark of homologous recombination, and it is mediated by two nucleases, Exo1 and Dna2. We observed differences in resection and repair outcomes in cells harboring nuclease-dead dna2-1 compared with dna2Δ pif1-m2 that could be attributed to the level of Exo1 recovered at DSBs. Cells harboring dna2-1 showed reduced Exo1 localization, increased NHEJ, and a greater resection defect compared with cells where DNA2 was deleted. Both the resection defect and the increased rate of NHEJ in dna2-1 mutants were reversed upon deletion of KU70 or ectopic expression of Exo1. By contrast, when DNA2 was deleted, Exo1 and Ku70 recovery levels did not change; however, Nej1 increased as did the frequency of alt-end joining/microhomology-mediated end-joining repair. Our findings demonstrate that decreased Exo1 at DSBs contributed to the resection defect in cells expressing inactive Dna2 and highlight the complexity of understanding how functionally redundant factors are regulated in vivo to promote genome stability.
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    Mass spectrometry imaging methods for visualizing tumor heterogeneity
    (Current Opinion in Biotechnology, 2024) Duncan, Kyle; Pětrošová, Helena; Lum, Julian; Goodlett, David Robinson
    Profiling spatial distributions of lipids, metabolites, and proteins in tumors can reveal unique cellular microenvironments and provide molecular evidence for cancer cell dysfunction and proliferation. Mass spectrometry imaging (MSI) is a label-free technique that can be used to map biomolecules in tumors in situ. Here, we discuss current progress in applying MSI to uncover molecular heterogeneity in tumors. First, the analytical strategies to profile small molecules and proteins are outlined, and current methods for multimodal imaging to maximize biological information are highlighted. Second, we present and summarize biological insights obtained by MSI of tumor tissue. Finally, we discuss important considerations for designing MSI experiments and several current analytical challenges.
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    Otolith mineralogy affects otolith shape asymmetry: A comparison of hatchery and natural origin Coho salmon (Oncorhynchus kisutch)
    (Journal of Fish Biology, 2023) Quindazzi, Micah; Gaffney, Leigh P.; Polard, Emma; Bohlender, Nick; Duguid, Will; Juanes, Francis
    Many aspects of natural and hatchery origin salmonid genetics, physiology, behaviour, anatomy and life histories have been compared due to the concerns about what effects domestication and hatchery rearing conditions have on fitness. Genetic and environmental stressors associated with hatchery rearing could cause greater developmental instability (DI), and therefore a higher degree of fluctuating asymmetry (FA) in various bilaterally paired characters, such as otoliths. Nonetheless, to appropriately infer the effects of DI on otolith asymmetry, otolith mineralogy must be accounted for. Vateritic otoliths differ substantially from aragonitic otoliths in terms of mass and shape and can artificially inflate any measurement of FA if not properly accounted for. In this study, measurements of otolith asymmetry between hatchery and natural origin Coho salmon Oncorhynchus kisutch from three different river systems were compared to assess the overall differences in asymmetry when the calcium carbonate polymorph accounted for 59.3% of otoliths from hatchery origin O. kisutch was vateritic compared to 11.7% of otoliths from natural origin O. kisutch. Otolith mineralogy, rather than origin, was the most significant factor influencing the differences in asymmetry for each shape metric. When only aragonitic otoliths were compared, there was no difference in absolute asymmetry between hatchery and natural origin O. kisutch. The authors recommend other researchers to assess otolith mineralogy when conducting studies regarding otolith morphometrics and otolith FA.
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    Dynamics of juvenile salmon and forage fishes in nearshore kelp forests
    (Aquatic Conservation: Marine and Freshwater Ecosystems, 2023) Shaffer, Anne; Gross, Justin; Black, Morgan; Kalagher, Amelia; Juanes, Francis
    1. North-east Pacific juvenile salmon and forage fishes, including the endangered salmon species Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), chum (Oncorhynchus keta), and pink (Oncorhynchus gorbuscha), and the forage fishes species of Pacific herring (Clupea pallasi), surf smelt (Hypomesus pretiosus), and sand lance (Ammodytes hexapterus), utilize kelp environments. Many details of the kelp forest ecosystem function for these fishes are lacking. 2. Kelp forests, salmon, and forage fishes are declining precipitously as the global climate shifts and developments along coastal shorelines expand. It is therefore essential to understand kelp forest function for these species. 3. Analysis of 7 years of snorkelling survey videos indicates that both forage fishes and salmon use kelp forests throughout the outmigration season, and that their interactions occur in small and large groups, primarily along the outer edge of kelp beds. Over the course of outmigration, juvenile Chinook and coho salmon encounter sand lance first, followed by smelt and herring. The majority of interactions are intermingling, in which a subset proceed to predation, primarily on herring. 4. It is important to develop and implement specific fishery and habitat conservation measures to preserve and restore these functions. Long-term research has shown that intact, conserved nearshore habitats function better ecologically than restored habitats, and individual kelp forests can function differently for forage fishes and salmon. Therefore, conservation plans should be developed to conserve wild kelp forests which are documented to provide ecosystem function for salmon and forage fishes, by protecting them from various development impacts, including dredging, filling, and water-quality decline. 5. Coastal restoration is often only successful when ecosystem-limiting factors that result in a loss of habitat are resolved. Kelp forest restoration, therefore, should be prioritized for regions of known high historical kelp forest importance, with restoration actions focused on correcting the limiting factors that caused loss and/or degradation.
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    Herbivory through the lens of ecological processes across Pacific coral reefs
    (Ecosphere, 2023) Kindinger, Tye; Adam, Thomas C.; Baum, Julia K.; Dimoff, Sean A.; Hoey, Andrew S.; Williams, Ivor D.
    Coral reefs are in global decline primarily due to climate change. Herbivory is often viewed as key to maintaining coral-dominated reefs, and herbivore management is gaining traction as a possible strategy for promoting reef resilience. The functional impact of herbivorous fishes has typically been inferred from total biomass, but robust estimates of ecological processes are needed to better inform management targets. Here, we provide a framework to calculate rates of herbivory across Pacific reefs. We synthesized available observations of foraging metrics in relation to fish body size and found considerable variation, even among closely related species. We then applied these allometric functions to survey data and calculated rates of herbivory for acanthurids and scarines, which make up the vast majority of herbivorous fish biomass in the Pacific. Estimated rates of algal consumption, area scraped, and bioerosion varied across islands, with noticeable differences that may align with the relative influence of human population density among underlying herbivore functional groups. We found no evidence of compensatory relationships among herbivore processes whereby decreasing rates in one type of herbivory is offset by increasing rates in another. We observed nonlinear, positive relationships between fish biomass and rates of herbivory. Yet, for a given biomass, the corresponding rates of herbivory varied among regions, and we observed instances where islands with the greatest biomass did not also have the highest rates of herbivory. Islands with the largest size classes of herbivores did not consistently exhibit greater rates of herbivory, and we did not find a clear, consistent pattern between the number of fish species and corresponding rates of herbivore processes. Cropping Acanthurus spp. provided the greatest proportion of algal consumption at every island, yet no single species accounted for the majority of this process, whereas we identified parrotfish species that provided >75% of scraping or bioerosion at certain islands. Our results emphasize the importance of considering the species and size composition of herbivore assemblages when estimating processes, rather than relying on total biomass alone. Lastly, we highlight gaps in foraging observations and additional work needed to further broaden our ability to quantify the ecological processes of herbivores.
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    Toward automated infrared spectral analysis in community drug checking
    (Drug Testing and Analysis, 2023) Gozdzialski, Lea; Hutchison, Abby; Wallace, Bruce; Gill, Chris; Hore, Dennis
    The body of knowledge surrounding infrared spectral analysis of drug mixtures continues to grow alongside the physical expansion of drug checking services. Technicians trained in the analysis of spectroscopic data are essential for reasons that go beyond the accuracy of the analytical results. Significant barriers faced by people who use drugs in engaging with drug checking services include the speed and accuracy of the results, and the availability and accessibility of the service. These barriers can be overcome by the automation of interpretations. A random forest model for the detection of two compounds, MDA and fluorofentanyl, was trained and optimized with drug samples acquired at a community drug checking site. This resulted in a 79% true positive and 100% true negative rate for MDA, and 61% true positive and 97% true negative rate for fluorofentanyl. The trained models were applied to selected drug samples to demonstrate a proposed workflow for interpreting and validating model predictions. The detection of MDA was demonstrated on three mixtures: (1) MDMA and MDA, (2) MDA and dimethylsulfone, and (3) fentanyl, etizolam, and benzocaine. The classification of fluorofentanyl was applied to a drug mixture containing fentanyl, fluorofentanyl, 4-anilino-N-phenethylpiperidine, caffeine, and mannitol. Feature importance was calculated using shapely additive explanations to better explain the model predictions and k-nearest neighbors was used for visual comparison to labelled training data. This is a step toward building appropriate trust in computer-assisted interpretations in order to promote their use in a harm reduction context.
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    Generation mechanism and prediction of an observed extreme rogue wave
    (Scientific Reports, 2022) Gemmrich, Johannes; Cicon, Leah
    Rogue waves are individual ocean surface waves with crest height [Formula: see text] or trough-to-crest height H that are large compared to the significant wave height [Formula: see text] of the underlying sea state: [Formula: see text] or [Formula: see text]. The physics of rogue wave generation and the potential of predicting the rogue wave risk are open questions. Only a few rogue waves in high sea states have been observed directly, but they can pose a danger to marine operations, onshore and offshore structures, and beachgoers. Here we report on a 17.6m high rogue wave in coastal waters with [Formula: see text] and [Formula: see text] which are likely the largest normalized heights ever recorded. Simulations of random superposition of Stokes waves in intermediate water depth show good agreement with the observation. Non-linear wave modulational instability, a well known cause for rogue waves in laboratory settings, did not contribute significantly to the rogue wave generation. A parameter obtained from a routine spectral wave forecast provides a practical risk prediction for rogue waves. These results confirm that probabilistic prediction of oceanic rogue waves based on random superposition of steep waves are possible and should replace predictions based on modulational instability.
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    Holocene fire regimes, fire-related plant functional types,and climate in southcoastal British Columbia forests
    (Ecosphere, 2023) Giuliano, Camille; Lacourse, Terri
    Paleoecological records of past fire events and forest composition provide long-term ecological context for modern changes in fire regimes and forest dynamics. Here, we use pollen and contiguous macroscopic charcoal analyses of lake sediments from Pender Island, British Columbia, Canada to reconstruct changes in fire regimes over the last 10,000 years and investigate how these interact with changes in climate and forest composition with a focus on fire-related plant functional types. The relatively warm and dry early Holocene was characterized by high charcoal accumulation rates, fire episodes of moderate severity, and a mean fire return interval of 100 ± 27 years. Forests at the time were open-canopy Pseudotsuga menziesii forests with abundant fire endurer taxa (e.g., Pteridium aquilinum) that have a competitive advantage in regimes of frequent fire. Fire continued to occur every ~100 years, on average, during the establishment of Quercus garryana savanna communities; however, a decrease in charcoal peak magnitudes suggests the fire regime shifted to one characterized by smaller and/or lower intensity surface fires. As temperature and moisture deficits decreased in the mid- and late Holocene (i.e., after ~6000 calendar years before present), mean fire return intervals lengthened to 176 ± 54 years and increased variability in charcoal peak magnitudes suggests a mixed fire regime of low-moderate-intensity fires combined with infrequent crown or stand-replacing fires. Relatively stable and moderate climate, longer fire return intervals, and mixed-severity fires allowed P. menziesii (a fire resister) to dominate closed-canopy forests and for fire avoiders to gradually become more common forest constituents. Millennial-scale climate change has acted as the dominant driver of changes in both fire regimes and forest composition over the last 10,000 years; however, changes in fire-related plant functional types highlight the important role that interactions between vegetation and fire play in long-term fire regimes and forest dynamics.
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    Infaunal community responses to ancient clam gardens
    (ICES Journal of Marine Science, 2019) Cox, Kieran; Gerwing, Travis; Macdonald, Tara; Hessing-Lewis, Margot; Millard-Martin, Ben; Command, Rylan J.; Juanes, Francis; Dudas, Sarah E.
    Aquatic ecosystems have been managed for millennia. Indigenous communities in North America pioneered numerous marine resource management strategies to ensure food security and support thriving economies, which have been active throughout the Northwest Coast of North America for over 14 000 years. Developed to increase shellfish productivity, clam gardens have been active for millennia. The diverse infaunal communities within these ecosystems can act as indicators of habitat alterations and provide an opportunity to study ecological community responses to seascapes shaped by millennia-old resource management structures. To determine how community structure differs between clam gardens and unmodified areas, we assessed infaunal diversity and density between intertidal mudflats, sandflats, and clam gardens. Differences in community composition were found among site types, with certain taxa, including culturally important species increasing within clam gardens. Per cent similarity analyses indicated that infaunal communities were more dissimilar among, than within site types. Furthermore, regression trees indicated that increases in diversity and density were closely correlated with the amount of shell and gravel within each habitat, which are associated with clam garden function and management practices. Species-specific and environmental responses to clam gardens indicate that human modifications in nearshore habitats created novel and distinct types of soft sediment communities.
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    Monotonicity and positivity analyses for two discrete fractional-order operator types with exponential and Mittag–Leffler kernels
    (Journal of King Saud University - Science, 2023) Mohammed, Pshtiwan Othman; Srivastava, Hari M.; Baleanu, Dumitru; Al-Sarairah, Eman; Sahoo, Soubhagya Kumar; Chorfi, Nejmeddine
    The discrete analysed fractional operator technique was employed to demonstrate positive findings concerning the Atangana-Baleanu and discrete Caputo-Fabrizo fractional operators. Our tests utilized discrete fractional operators with orders between 1<φ<2, as well as between 1<φ<32. We employed the initial values of Mittag–Leffler functions and applied the principle of mathematical induction to ensure the positivity of the discrete fractional operators at each time step. As a result, we observed a significant impact of the positivity of these operators on ∇Q(τ) within Np0+1 according to the Riemann–Liouville interpretation. Furthermore, we established a correlation between the discrete fractional operators based on the Liouville-Caputo and Riemann–Liouville definitions. In addition, we emphasized the positivity of ∇Q(τ) in the Liouville-Caputo sense by utilizing this relationship. Two examples are presented to validate the results.
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    The pseudoarc is a co-existentially closed continuum
    (Topology and Its Applications, 2016) Eagle, Christopher J.; Goldbring, Isaac; Vignati, Alessandro
    Answering a question of P. Bankston, we show that the pseudoarc is a co-existentially closed continuum. We also show thatC (X), for X a nondegenerate continuum, can never have quantifier elimination, answering a question of the first and third named authors and Farah and Kirchberg.
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    Molecular basis for differential activation of p101 and p84 complexes of PI3Kγ by Ras and GPCRs
    (Cell Reports, 2023) Rathinaswamy, Manoj K.; Jenkins, Meredith L.; Duewell, Benjamin R.; Zhang, Xuxiao; Harris, Noah J.; Evans, John T.; Stariha, Jordan T. B.; Dalwadi, Udit; Fleming, Kaelin D.; Ranga-Prasad, Harish; Yip, Calvin K.; Williams, Roger L.; Hansen, Scott D.; Burke, John
    Class IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells and can form two distinct complexes (p110γ-p84 and p110γ-p101), which are differentially activated by G protein-coupled receptors (GPCRs) and Ras. Using a combination of X-ray crystallography, hydrogen deuterium exchange mass spectrometry (HDX-MS), electron microscopy, molecular modeling, single-molecule imaging, and activity assays, we identify molecular differences between p110γ-p84 and p110γ-p101 that explain their differential membrane recruitment and activation by Ras and GPCRs. The p110γ-p84 complex is dynamic compared with p110γ-p101. While p110γ-p101 is robustly recruited by Gβγ subunits, p110γ-p84 is weakly recruited to membranes by Gβγ subunits alone and requires recruitment by Ras to allow for Gβγ activation. We mapped two distinct Gβγ interfaces on p101 and the p110γ helical domain, with differences in the C-terminal domain of p84 and p101 conferring sensitivity of p110γ-p101 to Gβγ activation. Overall, our work provides key insight into the molecular basis for how PI3Kγ complexes are activated.
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    Bycatch-threatened seabirds disproportionally contribute to community trait composition across the world
    (Global Ecology and Conservation, 2024) Richards, Cerren; Cooke, Rob; Bowler, Diana E.; Boerder, Kristina; Bates, Amanda
    Human pressures in the ocean are restructuring biological communities, driving non-random extinctions, and disrupting marine ecosystem functioning. In particular, fisheries bycatch, the incidental mortality of non-target species, is a major threat to seabirds worldwide. Direct bycatch data are often scarce. Instead, leveraging trait-based analyses with fine-scale fisheries data could answer fundamental questions about spatial patterns of bycatch-threatened species and facilitate targeted conservation strategies. Here, we combine a dataset of species' traits and distribution ranges for 361 seabird and sea duck species with spatially resolved fishing effort data for gillnet, longline, trawl, and purse seine gears. First, we quantify geographic patterns of seabird community traits. Second, we describe how community traits could shift under local extinction scenarios in areas where bycatch-threatened seabirds spatially overlap with fishing activities. These objectives allow us to highlight the collective contribution of species currently threatened from bycatch to ecosystem functioning. We reveal distinct spatial variation in the community weighted mean of five seabird traits (body mass, generation length, clutch size, diet guild, and foraging guild) are evident. Moreover, our results show that fisheries bycatch is selectively removing a distinct suite of traits from the community within particular oceanic regions. Specifically, fisheries bycatch is threatening species with larger body masses, slower reproductive speeds (smaller clutch sizes and longer generation lengths), and specialised diet and foraging guilds. The spatial non-uniformity of the community trait shifts suggests that within specific marine regions, communities have limited redundancy and therefore may have less insurance to buffer against declines in ecosystem functioning. Our extinction scenario warns that seabirds currently threatened from fisheries bycatch substantially contribute to community functional composition. Management actions that incorporate species’ traits and fine-scale fisheries datasets as tools for marine spatial planning will add an important dimension when evaluating the success of conservation initiatives.
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    Seasonal and regional variability of model-based zooplankton biomass in the Salish Sea and evaluation against observations
    (Progress in Oceanography, 2023) Suchy, Karyn D.; Olson, Elise; Allen, Susan E.; Galbraith, Moira; Herrman, BethElLee; Keister, Julie E.; Perry, R. Ian; Sastri, Akash R.; Young, Kelly
    We used a three-dimensional coupled biophysical model to examine zooplankton dynamics in the Salish Sea, NE Pacific. First, we evaluated the two zooplankton classes of the SalishSeaCast model using a transboundary zooplankton dataset comprised of observation data from the Canadian and United States waters of the Salish Sea from 2015 to 2019. Model zooplankton classes correspond to micro- and meso-zooplankton whose biomass is tightly coupled to phytoplankton through modelled food web dynamics (Z1) and mesozooplankton with life cycle-based seasonal grazing impacts (Z2). Overall, the model effectively captured seasonal patterns in observed biomass, although with slightly higher biomass estimates for both Z1 and Z2 (Bias = 0.10 and 0.08 g C m−2, respectively). Model fit varied regionally, with a weaker model fit being observed in nearshore regions. In addition, an autumn peak in Z2 was observed in the model, but not in the observations, suggesting some seasonal variations in model fit. Following the model evaluation, we used the model to determine seasonal and regional patterns of zooplankton grazing. Seasonally, the main peak in modelled zooplankton biomass increased in April or May in most of the regions defined within the Salish Sea and was driven by grazing on diatoms. Regionally, depth-integrated zooplankton biomass was consistently highest in areas adjacent to regions of strong tidal mixing. In addition, model-based zooplankton grazing was highest in the tidally mixed regions where phytoplankton biomass was high due to advection into the region despite low primary productivity. Our model-based results provide an opportunity to examine bottom-up food web processes at spatio-temporal scales not achievable with in situ sampling and help to elucidate key drivers of lower trophic level dynamics within the Salish Sea.
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