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Abstract The cultivation of seafood now outpaces extraction from wild populations. This novel state in the history of human-marine ecosystem interactions highlights the importance of identifying cultivation practices that balance production and conservation. Here, we test the hypothesis that two shellfish cultivation practices, one that spans decades and the other millennia, bolsters habitat complexity, which increases epifaunal (surface) invertebrate diversity. To do so, we conducted multiple surveys of 24 First Nations clam gardens, shellfish aquaculture farms, and non-walled or unmodified beaches along the west coast of Canada. We show that habitat alterations specific to each cultivation practice restructure epifaunal communities at several ecological and spatial scales. Distinct communities within clam gardens and shellfish farms are a function of habitat complexity at 25–50 and 50–100 cm resolutions and changes in the amount of gravel, bivalve shells, and seaweeds. Our findings highlight how resource cultivation can contribute to achieving sustainable human-ecosystem interactions.

Microvascular integrity is disrupted following spinal cord injury (SCI) by both primary and secondary insults. Changes to neuronal structures are well documented, but little is known about how the capillaries change and recover following injury. Spatiotemporal morphological information is required to explore potential treatments targeting the microvasculature post-SCI to improve functional recovery. Sprague-Dawley rats were given a T10 moderate/severe (200 kDyn) contusion injury and were perfuse-fixed at days 2, 5, 15, and 45 post-injury. Unbiased stereology following immunohistochemistry in four areas (ventral and dorsal grey and white matter) across seven spinal segments (n = 4 for each group) was used to calculate microvessel density, surface area, and areal density. In intact sham spinal cords, average microvessel density across the thoracic spinal cord was: ventral grey matter: 571 ± 45 mm−2, dorsal grey matter: 484 ± 33 mm−2, ventral white matter: 90 ± 8 mm−2, dorsal white matter: 88 ± 7 mm−2. Post-SCI, acute microvascular disruption was evident, particularly at the injury epicentre, and spreading three spinal segments rostrally and caudally. Damage was most severe in grey matter at the injury epicentre (T10) and T11. Reductions in all morphological parameters (95–99% at day 2 post-SCI) implied vessel regression and/or collapse acutely. Transmission electron microscopy (TEM) revealed disturbed aspects of neurovascular unit fine structure at day 2 post-SCI (n = 2 per group) at T10 and T11. TEM demonstrated a more diffuse and disrupted basement membrane and wider intercellular clefts at day 2, suggesting a more permeable blood spinal cord barrier and microvessel remodelling. Some evidence of angiogenesis was seen during recovery from days 2 to 45, indicated by increased vessel density, surface area, and areal density at day 45. These novel results show that the spinal cord microvasculature is highly adaptive following SCI, even at chronic stages and up to three spinal segments from the injury epicentre. Multiple measures of gross and fine capillary structure from acute to chronic time points provide insight into microvascular remodelling post-SCI. We have identified key vascular treatment targets, namely stabilising damaged capillaries and replacing destroyed vessels, which may be used to improve functional outcomes following SCI in the future.

Abstract Macroscale studies of aquatic ecosystems are needed to address many contemporary broad‐scale problems related to global change, particularly to inform national‐scale environmental policies. In this data paper, we fill two important gaps in data availability for lakes at the scale of the conterminous U.S., the lack of: (1) high‐resolution geographic representations of lakes and their watersheds and (2) an open data platform to connect disparate U.S. national‐scale lake datasets. We describe the LAGOS‐US LOCUS v1.0 data module that includes a detailed User Guide, which is part of the LAGOS‐US extensible research‐ready open data platform. This platform can be used to study the 479,950 lakes and reservoirs larger than or equal to 1 ha across the entire conterminous U.S. at multiple scales of space and time. The LOCUS module includes spatially‐explicit information on lakes and their watersheds, including location information, physical characteristics, and identifiers of other important national‐scale datasets.

The relationships between clam gardens and human settlement throughout the millennia reflects the inseparable links among human demographics, marine management systems, and the social-ecological contexts in which they are embedded. However, it can be difficult to assign causation between the initiation and development of eco-cultural innovations like clam gardens and the proliferation of human societies due to the temporal uncertainties associated with both. Here, we bring together data on the shape of the local relative sea level curve, clam garden wall elevation as determined by GIS and drone imagery, radiocarbon dates of clam garden walls, and ecological and archaeological field observations, to assign proxy ages for the clam garden walls of different tidal heights in Kanish and Waiatt Bay on northern Quadra Island, British Columbia, Canada. These data, combined with our mapping and dating of settlement sites, demonstrate a temporal relationship between clam garden building effort and the densification of human settlements. In Kanish Bay, where we have high resolution data, clam gardens begin to be constructed in significant numbers at least 3,800 years ago; this corresponds to a time of increased establishment of large human settlements. The corresponding increase in settlements and clam gardens reflects both the need to increase sustainable food production and the larger number of people who could sustain the ecological and social foundations of the production system. The correlation between number and area of clam gardens and the number of new, large settlements continues until ∼2000 years ago. After this time, existing settlements increase in size, but no additional large settlements were established. New clam gardens continue to be built but in seemingly lower numbers. This shift in settlements and clam gardens suggest that a threshold in social-ecological carrying capacity may have been reached in this land- and seascape. In the last few centuries, there is a dramatic decline in the number of clam gardens and evidence of human settlement, corresponding to social and ecological changes associated with European colonization. Taken together, these data demonstrate the strong linkages among Indigenous peoples, their lands and seas, and resilient food systems over the millennia.

The need to diversify science includes increasing both the diversity of science practitioners and the voices included in decision-making processes. Indigenous communities have been sought out to provide Indigenous knowledge to mainstream science research programs. As working across the mainstream science and community boundary is increasingly codified into the future of natural sciences, models for equitable collaboration and roles within project structures are needed. The goal of this project is to present a framework for collaboration between mainstream science and Indigenous communities. Specifically, we are addressing an under-recognized role central to partnership, a boundary spanner, who acts as the fulcrum facilitating collaboration. To better understand the role of boundary spanners in collaborative projects, we engaged six boundary spanners who participated in semi-structured interviews and workshops. Emergent common experiences and perspectives of how boundary spanners can be supported and their role in collaborative projects were defined and articulated. The boundary spanners identified 10 characteristics that contribute to equitable partnership between mainstream science and Indigenous communities. From the perspective of the boundary spanners, they detailed how collaborative projects can be structured to increase long-term partnerships and community support of research projects. Equitable collaboration between Indigenous communities and mainstream science is frequently only achieved when individuals at the interface of the mainstream science and Indigenous community have a high level of cultural competency. Equally important is the support provided to the boundary spanners and early engagement of partner Indigenous communities. Through the use of story and metaphor, we highlight the voices of boundary spanners and how their contributions can best be used.

The Atlantic salmon (Salmo salar) is an economically important fish, both in aquaculture and in the wild. In vertebrates, macrophages are some of the first cell types to respond to pathogen infection and disease. While macrophage biology has been characterized in mammals, less is known in fish. Our previous work identified changes in the morphology, phagocytic ability, and miRNA profile of Atlantic salmon adherent head kidney leukocytes (HKLs) from predominantly “monocyte-like” at Day 1 of in vitro culture to predominantly “macrophage-like” at Day 5 of culture. Therefore, to further characterize these two cell populations, we examined the mRNA transcriptome profile in Day 1 and Day 5 HKLs using a 44K oligonucleotide microarray. Large changes in the transcriptome were revealed, including changes in the expression of macrophage and immune-related transcripts (e.g. csf1r, arg1, tnfa, mx2), lipid-related transcripts (e.g. fasn, dhcr7, fabp6), and transcription factors involved in macrophage differentiation and function (e.g. klf2, klf9, irf7, irf8, stat1). The in silico target prediction analysis of differentially expressed genes (DEGs) using miRNAs known to change expression in Day 5 HKLs, followed by gene pathway enrichment analysis, supported that these miRNAs may be involved in macrophage maturation by targeting specific DEGs. Elucidating how immune cells, such as macrophages, develop and function is a key step in understanding the Atlantic salmon immune system. Overall, the results indicate that, without the addition of exogenous factors, the adherent HKL cell population differentiates in vitro to become macrophage-like.

Responsible mine closure and repurposing are key to contributing to sustainable development by ensuring successful environmental rehabilitation and reducing socioeconomic risks. However, mine closure has primarily focused on remediation and rehabilitation of mined lands with limited consideration of stakeholder perspectives and the broader social, economic, and cultural impacts of closure. In this paper, we use stakeholder input to evaluate and compare three different repurposing alternatives for the tailings dam area of a mine in the state of Colorado, USA, which is expected to close in the next twenty years. By using multi-attribute utility theory (MAUT), we determine which alternative better reflects stakeholder preferences and results in the most economically, environmentally, and socially sustainable outcome. Our results show that although stakeholder groups have different ideas about what constitutes sustainable development in the context of mine closure and repurposing, it is possible to identify to what extent different scenarios can address these perspectives. We argue that integrating stakeholder views into mine closure design and repurposing can lead to more responsible and sustainable mine closure that is unique to a particular setting and stakeholder needs, and we provide a methodology that mining companies may use to understand stakeholder priorities and preferences.

Despite calls to action, writing pedagogy in the English classroom remains outdated, and caustic partisanship among theorists may be to blame. The author proposes a "principled approach" to the teaching of writing, combining the best elements of verified instructional methods to generate six components ensuring student growth.

Cell-derived extracellular vesicles (EVs) participate in cell-cell communication via transfer of molecular cargo including genetic material like miRNAs. In mammals, it has previously been established that EV-mediated transfer of miRNAs can alter the development or function of immune cells, such as macrophages. Our previous research revealed that Atlantic salmon head kidney leukocytes (HKLs) change their morphology, phagocytic ability and miRNA profile from primarily “monocyte-like” at Day 1 to primarily “macrophage-like” at Day 5 of culture. Therefore, we aimed to characterize the miRNA cargo packaged in EVs released from these two cell populations. We successfully isolated EVs from Atlantic salmon HKL culture supernatants using the established Vn96 peptide-based pull-down. Isolation was validated using transmission electron microscopy, nanoparticle tracking analysis, and Western blotting. RNA-sequencing identified 19 differentially enriched (DE) miRNAs packaged in Day 1 versus Day 5 EVs. Several of the highly abundant miRNAs, including those that were DE (e.g. ssa-miR-146a, ssa-miR-155 and ssa-miR-731), were previously identified as DE in HKLs and are associated with macrophage differentiation and immune response in other species. Interestingly, the abundance relative of the miRNAs in EVs, including the most abundant miRNA (ssa-miR-125b), was different than the miRNA abundance in HKLs, indicating selective packaging of miRNAs in EVs. Further study of the miRNA cargo in EVs derived from fish immune cells will be an important next step in identifying EV biomarkers useful for evaluating immune cell function, fish health, or response to disease.

Abstract Background Following injury to the central nervous system, increased microglia, secretion of pro- and anti-inflammatory cytokines, and altered blood-brain barrier permeability, a hallmark of degeneration, are observed at and immediately adjacent to the injury site. However, few studies investigate how regions remote from the primary injury could also suffer from inflammation and secondary degeneration. Methods Adult female Piebald-Viral-Glaxo (PVG) rats underwent partial transection of the right optic nerve, with normal, age-matched, unoperated animals as controls. Perfusion-fixed brains and right optic nerves were harvested for immunohistochemical assessment of inflammatory markers and blood-brain barrier integrity; fresh-frozen brains were used for multiplex cytokine analysis. Results Immediately ventral to the optic nerve injury, immunointensity of both the pro-inflammatory biomarker inducible nitric oxide synthase (iNOS) and the anti-inflammatory biomarker arginase-1 (Arg1) increased at 7 days post-injury, with colocalization of iNOS and Arg1 immunoreactivity within individual cells. CD11b+ and CD45+ cells were increased 7 days post-injury, with altered BBB permeability still evident at this time. In the lower and middle optic tract and superior colliculus, IBA1+ resident microglia were first increased at 3 days; ED1+ and CD11b+ cells were first increased in the middle and upper tract and superior colliculus 7 days post-injury. Increased fibrinogen immunoreactivity indicative of altered BBB permeability was first observed in the contralateral upper tract at 3 days and middle tract at 7 days post-injury. Multiplex cytokine analysis of brain homogenates indicated significant increases in the pro-inflammatory cytokines, IL-2 and TNFα, and anti-inflammatory cytokine IL-10 1 day post-injury, decreasing to control levels at 3 days for TNFα and 7 days for IL-2. IL-10 was significantly elevated at 1 and 7 days post-injury with a dip at 3 days post-injury. Conclusions Partial injury to the optic nerve induces a complex remote inflammatory response, characterized by rapidly increased pro- and anti-inflammatory cytokines in brain homogenates, increased numbers of IBA1+ cells throughout the visual pathways, and increased CD11b+ and ED1+ inflammatory cells, particularly towards the synaptic terminals. BBB permeability can increase prior to inflammatory cell infiltration, dependent on the brain region.

Engineers and applied scientists form the backbone of the mining and petroleum industries, yet rarely figure in social science accounts of natural resource extraction. This article begins to fill that gap by ethnographically exploring how community conflicts have prompted engineers and applied scientists working in these industries to reconsider the relationship between the surface and subsurface dimensions of their work. To make social concerns on the surface matter to how drilling and extraction would happen, they tried to make these two domains legible to one another. Using mapping and modeling, they created new techniques for making “social” concerns visible and actionable by field operators, even as they expressed reservations about unduly flattening the inherent complexity of human thought, action, and emotion in the process. While these practices opened space for other engineers and applied scientists to incorporate the concerns of nearby residents into their plans and practices, they also raised questions about the appropriateness of commensuration, or the process of translation through which things and values are made comparable.

Abstract Background Due to the limited availability and high cost of fish oil in the face of increasing aquaculture production, there is a need to reduce usage of fish oil in aquafeeds without compromising farm fish health. Therefore, the present study was conducted to determine if different levels of vegetable and fish oils can alter antiviral responses of salmon macrophage-like cells (MLCs). Atlantic salmon (Salmo salar) were fed diets containing 7.4% (FO7) or 5.1% (FO5) fish oil. These diets were designed to be relatively low in EPA + DHA (i.e. FO7: 1.41% and FO5: 1%), but near the requirement level, and resulting in comparable growth. Vegetable oil (i.e. rapeseed oil) was used to balance fish oil in experimental diets. After a 16-week feeding trial, MLCs isolated from fish in these dietary groups were stimulated by a viral mimic (dsRNA: pIC) for 6 h (qPCR assay) and 24 h (microarray and qPCR assays). Results The fatty acid composition of head kidney leukocytes varied between the two dietary groups (e.g. higher 20:5n-3 in the FO7 group). Following microarray assays using a 44K salmonid platform, Rank Products (RP) analysis showed 14 and 54 differentially expressed probes (DEP) (PFP

Abstract Background Following partial injury to the central nervous system, cells beyond the initial injury site undergo secondary degeneration, exacerbating loss of neurons, compact myelin and function. Changes in Ca2+ flux are associated with metabolic and structural changes, but it is not yet clear how flux through specific ion channels contributes to the various pathologies. Here, partial optic nerve transection in adult female rats was used to model secondary degeneration. Treatment with combinations of three ion channel inhibitors was used as a tool to investigate which elements of oxidative and structural damage related to long term functional outcomes. The inhibitors employed were the voltage gated Ca2+ channel inhibitor Lomerizine (Lom), the Ca2+ permeable AMPA receptor inhibitor YM872 and the P2X7 receptor inhibitor oxATP. Results Following partial optic nerve transection, hyper-phosphorylation of Tau and acetylated tubulin immunoreactivity were increased, and Nogo-A immunoreactivity was decreased, indicating that axonal changes occurred acutely. All combinations of ion channel inhibitors reduced hyper-phosphorylation of Tau and increased Nogo-A immunoreactivity at day 3 after injury. However, only Lom/oxATP or all three inhibitors in combination significantly reduced acetylated tubulin immunoreactivity. Most combinations of ion channel inhibitors were effective in restoring the lengths of the paranode and the paranodal gap, indicative of the length of the node of Ranvier, following injury. However, only all three inhibitors in combination restored to normal Ankyrin G length at the node of Ranvier. Similarly, HNE immunoreactivity and loss of oligodendrocyte precursor cells were only limited by treatment with all three ion channel inhibitors in combination. Conclusions Data indicate that inhibiting any of a range of ion channels preserves certain elements of axon and node structure and limits some oxidative damage following injury, whereas ionic flux through all three channels must be inhibited to prevent lipid peroxidation and preserve Ankyrin G distribution and OPCs.

The immune system is composed of two subsystems—the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates—the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.

Ancient systems of mariculture were foundations of social-ecological systems of many coastal Indigenous Peoples. However, since such systems either do not leave tangible remains in the archaeological record, and/or are hard to date, we know little about their development and use. Clam gardens, traditional mariculture features located within the intertidal zone along the Northwest Coast of North America, are composed of a rock wall positioned at the low tide mark and a flattened terrace on the landward side of the wall. Because these features are largely composed of rock and sediment, and have complex formation histories, they can be difficult to age. On northern Quadra Island, British Columbia, we identify three variations in clam garden form, constructed in different geomorphological settings, each of which require different sampling approaches to obtain ages on construction and ongoing use. To age the clam gardens, we consider radiocarbon dating of invertebrates that inhabit beach deposits (both pre- and post-garden construction), and the relationship of the gardens and clam samples to the local sea level history and taphonomic processes. Within our study area, we find clam gardens have been in use for 3500 years, likely corresponding to other social and ecological changes of the time. These data allow us to formulate guidelines on samples most suitable to constrain the age of initial and on-going wall construction and use of clam gardens, which can be extrapolated to dating other ancient mariculture features in other regions. Such dating programs are the foundation for understanding the long-term development of traditional marine management practices and how they are situated in broader social-ecological systems.

Before using nanoparticles for therapeutic applications, it is necessary to comprehensively investigate nanoparticle effects, both in vitro and in vivo. In the associated research article [1] we generate multimodal polymeric nanoparticles functionalized with an antibody, that are designed to deliver an anti-oxidant to astrocytes. Here we provide additional data demonstrating the effects of the nanoparticle preparations on an indicator of oxidative stress in an immortalized Müller cell line in vitro. We provide data demonstrating the use of nanoscale secondary ion mass spectroscopy (NanoSIMS) to identify specific ions in bulk dried NP. NanoSIMS is also used to visualize 40Ca microdomains in the z dimension of optic nerve that has been subjected to a partial optic nerve transection. The associated article [1] describes the use of NanoSIMS to quantify 40Ca microdomains in optic nerve from animals treated with various nanoparticle preparations and provides further interpretation and discussion of the findings.

Red blood cell (RBC) alloimmunization represents a significant immunological challenge for some patients. While a variety of immune constituents likely contribute to the initiation and orchestration of alloantibodies to RBC antigens, identification of key immune factors that initiate alloantibody formation may aid in the development of a therapeutic modality to minimize or prevent this process. To define the immune factors that may be important in driving alloimmunization to an RBC antigen, we determined the specific immune compartment and distinct cells that may initially engage transfused RBCs and facilitate subsequent alloimmunization. Our findings demonstrate that the splenic compartment is essential for formation of anti-KEL antibodies following KEL RBC transfusion. Within the spleen, transfused KEL RBCs are found within the marginal sinus, where they appear to specifically co-localize with marginal zone (MZ) B cells. Consistent with this, removal of MZ B cells completely prevented alloantibody formation following KEL RBC transfusion. While MZ B cells can mediate a variety of key downstream immune pathways, depletion of follicular B cells or CD4 T cells failed to similarly impact the anti-KEL antibody response, suggesting that MZ B cells may play a key role in the development of anti-KEL IgM and IgG following KEL RBC transfusion. These findings highlight a key contributor to KEL RBC-induced antibody formation, wherein MZ B cells facilitate antibody formation following RBC transfusion.

Impaired or suboptimal fetal growth is associated with an increased risk of perinatal morbidity and mortality. By utilizing readily available clinical data on the relative size of the fetus at multiple points in pregnancy, including delivery, future epidemiological research can improve our understanding of the impacts of maternal, fetal, and environmental factors on fetal growth at different windows during pregnancy. This study presents mean and standard deviation ultrasound measurements from a clinically representative US population that can be utilized for creating Z-scores to this end. Between 2006 and 2012, 18, 904 non-anomalous pregnancies that received prenatal care, first and second trimester ultrasound evaluations, and ultimately delivered singleton newborns at Brigham and Women's hospital in Boston were used to create the standard population. To illustrate the utility of this standard, we created Z-scores for ultrasound and delivery measurements for a cohort study population and examined associations with factors known to be associated with fetal growth. In addition to cross-sectional regression models, we created linear mixed models and generalized additive mixed models to illustrate how these scores can be utilized longitudinally and for the identification of windows of susceptibility. After adjustment for a priori confounders, maternal BMI was positively associated with increased fetal size beginning in the second trimester in cross-sectional models. Female infants and maternal smoking were associated with consistently reduced fetal size in the longitudinal models. Maternal age had a non-significant association with increased size in the first trimester that was attenuated as gestation progressed. As the growth measurements examined here are widely available in contemporary obstetrical practice, these data may be abstracted from medical records by investigators and standardized with the population means presented here. This will enable easy extension of clinical data to epidemiologic studies investigating novel maternal, fetal, and environmental factors that may impact fetal growth.