Declines in Puget Sound sediment-dwelling communities and a new focus on climate, nutrient, and other ecosystem stressors

The Washington State Department of Ecology has been collecting data on Puget Sound sediment-dwelling (benthic) invertebrates since 1989, as part of the Marine Sediment Monitoring Program. Benthic organisms serve key functions, including processing and storage of organic material and cycling of nutrients needed by other components of the ecosystem. Benthic invertebrates are an integral part of the marine food web and biogeochemical processes that support salmon, orcas, and humans and are a key component of the Puget Sound ecosystem. We are finding significant declines in the overall condition of benthic communities, with 44% of the study area adversely affected. Many of the adversely affected benthic communities were found in terminal inlets and bays. Throughout Puget Sound, an increase of pollution/hypoxia-tolerant species and a decrease in sensitive species has occurred over time. Deterioration of benthic communities does not correspond well with changes in individual chemical contaminants measured or laboratory tests of sediment toxicity. The spatial distribution of benthic communities is in part defined by the changing physical and oceanographic habitat. Changes in the abundance and composition of the benthic invertebrate community over time may indicate responses of the ecosystem to climatic stressors and large-scale ecological shifts such as changing hydrological, nutrient, oxygen, or acidic conditions

Quantification of Pharmaceuticals, Personal Care Products, and Perfluoroalkyl Substances in Elliott Bay sediments (Seattle, Washington)

Pharmaceuticals and Personal Care Products (PPCPs) and Perfluoroalkyl Substances (PFASs) are identified as Chemicals of Emerging Concern (CECs) in Puget Sound due to their potential to cause adverse toxicological, biological, and ecological effects when introduced into the environment. Characterization of sources, transport patterns, and the fate of CECs in the environment has been prioritized as part of the Puget Sound Ecosystem Monitoring Program toxics monitoring strategy. These chemicals have been detected in ground water, rivers, and streams in the Pacific Northwest and in influent, effluent, and biosolids from Puget Sound municipal wastewater treatment plants over the past decade. They were also detected in sediments from ten long-term monitoring stations located throughout Puget Sound and thirty stations in Bellingham Bay in 2010. We report here on CECs detected in sediments from Elliot Bay, collected in 2013 at thirty stations selected using a random stratified design. Sediments were tested for the presence of 119 PPCPs and 13 PFASs. Analyses were conducted by AXYS Analytical Services Ltd., Sidney, BC, Canada, using AXYS Method MLA-075. This method uses liquid chromatography with tandem mass spectrometry (LC/MS/MS). Acid and base fractions were extracted, followed by five instrumental analyses in positive and negative electrospray ionization (ESI) modes. Results of these analyses are summarized and presented graphically to indicate the concentration and distribution of PPCPs and PFASs in Elliott Bay sediments, with comparisons made to concentrations measured in Bellingham Bay sediments

Biological mechanisms of aging predict age-related disease co-occurrence in patients

Genetic, environmental, and pharmacological interventions into the aging process can confer resistance to multiple age-related diseases in laboratory animals, including rhesus monkeys. These findings imply that individual mechanisms of aging might contribute to the co-occurrence of age-related diseases in humans and could be targeted to prevent these conditions simultaneously. To address this question, we text mined 917,645 literature abstracts followed by manual curation and found strong, non-random associations between age-related diseases and aging mechanisms in humans, confirmed by gene set enrichment analysis of GWAS data. Integration of these associations with clinical data from 3.01 million patients showed that age-related diseases associated with each of five aging mechanisms were more likely than chance to be present together in patients. Genetic evidence revealed that innate and adaptive immunity, the intrinsic apoptotic signaling pathway and activity of the ERK1/2 pathway were associated with multiple aging mechanisms and diverse age-related diseases. Mechanisms of aging hence contribute both together and individually to age-related disease co-occurrence in humans and could potentially be targeted accordingly to prevent multimorbidity

Muscle satellite cells adopt divergent fates: a mechanism for self-renewal?

Growth, repair, and regeneration of adult skeletal muscle depends on the persistence of satellite cells: muscle stem cells resident beneath the basal lamina that surrounds each myofiber. However, how the satellite cell compartment is maintained is unclear. Here, we use cultured myofibers to model muscle regeneration and show that satellite cells adopt divergent fates. Quiescent satellite cells are synchronously activated to coexpress the transcription factors Pax7 and MyoD. Most then proliferate, down-regulate Pax7, and differentiate. In contrast, other proliferating cells maintain Pax7 but lose MyoD and withdraw from immediate differentiation. These cells are typically located in clusters, together with Pax7-ve progeny destined for differentiation. Some of the Pax7+ve/MyoD-ve cells then leave the cell cycle, thus regaining the quiescent satellite cell phenotype. Significantly, noncycling cells contained within a cluster can be stimulated to proliferate again. These observations suggest that satellite cells either differentiate or switch from terminal myogenesis to maintain the satellite cell pool

Spatial distribution of benthic macroinvertebrate biomass in Puget Sound: establishing a baseline

Since 1989, Ecology’s Marine Sediment Monitoring Program has collected data to assess the condition of Puget Sound’s sediment-dwelling invertebrate communities (benthos). These long-term data reveal declines in benthos abundance and taxa richness in parts of Puget Sound that do not appear to be correlated with concentrations of chemical contaminants in the sediment. In 2016, a biomass and size classification component was added to the suite of benthic community indices analyzed, as part of a large-scale program redesign intended to shed more light on alternate causes of declining benthos, such as climate change and nutrient enrichment. Benthic invertebrate biomass not only influences rates of nutrient cycling in the sediment (as organisms feed and bioturbate), but also relates to the contribution of planktonic larvae to the marine food web. Biomass estimates can provide valuable information on size structure within benthic communities not captured by abundance data alone, and may help us understand the effects of various stressors on the size and development of individual organisms. This poster will present a spatial distribution of benthic invertebrate biomass from the 2016 Long-term Monitoring Program, which will serve as a baseline for future monitoring efforts and allow for the examination of relationships between biological communities and the physical processes that govern them

Characterizing changes in Puget Sound benthic infaunal invertebrate assemblages: A functional approach

Puget Sound benthic infaunal invertebrate assemblages (benthos) have been sampled and characterized for eight regions and six urban bays as part of the Puget Sound Ecosystem Monitoring Program (PSEMP) since 1997. A suite of structural abundance and diversity indices, and an overarching Benthic Index, have been applied to the benthos data to illustrate and interpret community condition both spatially and temporally throughout the Sound. In general, community composition varies between locations, and significant declines in condition have been observed for most of the resampled study areas. Relational analyses conducted on baseline data collected from 1997-1999 showed correspondence between community structure, station depth, and the related variables of sediment particle size and percent total organic carbon; however, no clear relationship was seen between community structure and levels of toxic contaminants in the sediments. To better understand the mechanisms driving community composition and its changes over time, feeding guild and functional role classifications have been assigned to 1,589 benthic taxa and applied to all benthos data. All benthos data collected from 1997-2012 have been reexamined to recharacterize the regional and urban bay benthic assemblages on a functional, rather than structural level. Relationships are examined between these functional measures of benthic assemblages and their associated suite of physical and chemical sediment measurements. Results will be discussed, along with a discussion of other environmental measures which may affect benthos community composition, including water column parameters, phytoplankton shifts, nutrient conditions, and chemicals of concern not currently measured by the PSEMP

Lessons from long time-series of benthic invertebrate communities in the southern Salish Sea, and an expansion of parameters to assess nutrient loading and climate change pressures

Changes in habitat and benthic invertebrates indicate responses of the ecosystem to stressors. Since 1989, the Washington State Department of Ecology has monitored sediments and benthic invertebrate communities annually at ten sentinel stations. This is a unique and important dataset, providing yearly insights into benthic community structure and abundance cycles of individual species. Except where events destabilized the habitats and communities, the sediments at these ten long-term stations, and the invertebrate communities inhabiting them, have largely remained stable over time, though with some drift and cycles in species composition and abundance. A few of these long-term stations, however, have experienced profound change. Little to no relationship has been found between the sediment contaminants measured at these ten stations and the benthic communities. The lack of correlation likely relates to factors such as low contaminant levels, and cleanups and source control of point-source pollution. Annual changes at these stations will be discussed and placed in context with patterns seen at larger geographic scales. To date, benthos monitoring has included only count and species-level identification of organisms collected in sediment grabs. This numeric information, combined with functional feeding guild grouping, has provided insight into patterns of resource-use by the benthos. The sediment program is expanding its focus and adding new parameters, to assess the response of the benthos to pressures associated with nutrient loading and climate change. With this new emphasis, biomass measurements and other ecological function information (such as bioturbation rates, temperature sensitivity, tolerance to hypoxic conditions, etc.) will be explored to better understand benthic invertebrate community changes in response to current or future nutrient loading and climate change pressures in Puget Sound

UKRN Institutional tasks implied by the UK Open Research Data Concordat

This UKRN working paper outlines the tasks that are either explicitly or implicitly proposed for research institutions by the UK Open Research Data Concordat (2016). It also reflects on how those tasks are relevant to the recommendations from the 2018 report issued by the UK Government from the Open Research Data Task Force. The aim of this paper is to describe more clearly what UK research institutions might be expected to do to support open research data, which may be a helpful basis for sector-wide discussion on both those expectations and how they are being met. The tasks are grouped under the headings of organisational support, infrastructure, recognition, restrictions on open data, costs, and strategy

‘Playing’ with Evidence: combining creative co-design methods with realist evidence synthesis

Breaking the cycle of declining physical function and physical activity can improve health and independence for people with long-term conditions. Services within primary care are well placed to empower individuals and communities to achieve this. However, the best approach is uncertain, and must consider needs of people with long-term conditions and complexities of service delivery. This study aimed to understand how to reduce decline in physical function and physical activity in people with long-term conditions. We used realist methods integrated with co-design to provide an explanatory account of what works (or does not), for whom and in what circumstances, to generate ideas about service innovation, and provide recommendations for primary care. A key aspect was tracking evidence from different sources, presenting it creatively by converting it into physical games, enabling stakeholders to ‘play with’ and make-sense of it, to inform co-design work, enabling them to draw upon their own experiences and a wider understanding. In this article, we focus on the game activities, adding to the co-design games’ literature and suggest that this expands participants’ knowledge base beyond their experiences, empowering them to contribute more to the process and creating a strong link between the realist and co-design methods

Data-driven identification of ageing-related diseases from electronic health records.

Reducing the burden of late-life morbidity requires an understanding of the mechanisms of ageing-related diseases (ARDs), defined as diseases that accumulate with increasing age. This has been hampered by the lack of formal criteria to identify ARDs. Here, we present a framework to identify ARDs using two complementary methods consisting of unsupervised machine learning and actuarial techniques, which we applied to electronic health records (EHRs) from 3,009,048 individuals in England using primary care data from the Clinical Practice Research Datalink (CPRD) linked to the Hospital Episode Statistics admitted patient care dataset between 1 April 2010 and 31 March 2015 (mean age 49.7 years (s.d. 18.6), 51% female, 70% white ethnicity). We grouped 278 high-burden diseases into nine main clusters according to their patterns of disease onset, using a hierarchical agglomerative clustering algorithm. Four of these clusters, encompassing 207 diseases spanning diverse organ systems and clinical specialties, had rates of disease onset that clearly increased with chronological age. However, the ages of onset for these four clusters were strikingly different, with median age of onset 82 years (IQR 82-83) for Cluster 1, 77 years (IQR 75-77) for Cluster 2, 69 years (IQR 66-71) for Cluster 3 and 57 years (IQR 54-59) for Cluster 4. Fitting to ageing-related actuarial models confirmed that the vast majority of these 207 diseases had a high probability of being ageing-related. Cardiovascular diseases and cancers were highly represented, while benign neoplastic, skin and psychiatric conditions were largely absent from the four ageing-related clusters. Our framework identifies and clusters ARDs and can form the basis for fundamental and translational research into ageing pathways