Life goes on: Spatial heterogeneity promotes biodiversity in an urbanized coastal marine ecosystem.

Both human populations and marine biodiversity are concentrated along coastlines, with growing conservation interest in how these ecosystems can survive intense anthropogenic impacts. Tropical urban centres provide valuable research opportunities because these megacities are often adjacent to mega-diverse coral reef systems. The Pearl River Delta is a prime exemplar, as it encompasses one of the most densely populated and impacted regions in the world and is located just northwest of the Coral Triangle. However, the spatial and taxonomic complexity of this biodiversity, most of which is small, cryptic in habitat and poorly known, make comparative analyses challenging. We deployed standardized settlement structures at seven sites differing in the intensity of human impacts and used COI metabarcoding to characterize benthic biodiversity, with a focus on metazoans. We found a total of 7184 OTUs, with an average of 665 OTUs per sampling unit; these numbers exceed those observed in many previous studies using comparable methods, despite the location of our study in an urbanized environment. Beta diversity was also high, with 52% of the OTUs found at just one site. As expected, we found that the sites close to point sources of pollution had substantially lower diversity (44% less) relative to sites bathed in less polluted oceanic waters. However, the polluted sites contributed substantially to the total animal diversity of the region, with 25% of all OTUs occurring only within polluted sites. Further analysis of Arthropoda, Annelida and Mollusca showed that phylogenetic clustering within a site was common, suggesting that environmental filtering reduced biodiversity to a subset of lineages present within the region, a pattern that was most pronounced in polluted sites and for the Arthropoda. The water quality gradients surrounding the PRD highlight the unique role of in situ studies for understanding the impacts of complex urbanization pressures on biodiversity.

Decline of a distinct coral reef holobiont community under ocean acidification.

BACKGROUND: Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome. RESULTS: We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation. CONCLUSIONS: We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract.

Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study.

BACKGROUND: Congenital heart disease (CHD) is the most common major congenital anomaly and causes significant morbidity and mortality. Epidemiologic evidence supports a role of genetics in the development of CHD. Genetic diagnoses can inform prognosis and clinical management. However, genetic testing is not standardized among individuals with CHD. We sought to develop a list of validated CHD genes using established methods and to evaluate the process of returning genetic results to research participants in a large genomic study. METHODS: Two-hundred ninety-five candidate CHD genes were evaluated using a ClinGen framework. Sequence and copy number variants involving genes in the CHD gene list were analyzed in Pediatric Cardiac Genomics Consortium participants. Pathogenic/likely pathogenic results were confirmed on a new sample in a clinical laboratory improvement amendments-certified laboratory and disclosed to eligible participants. Adult probands and parents of probands who received results were asked to complete a post-disclosure survey. RESULTS: A total of 99 genes had a strong or definitive clinical validity classification. Diagnostic yields for copy number variants and exome sequencing were 1.8% and 3.8%, respectively. Thirty-one probands completed clinical laboratory improvement amendments-confirmation and received results. Participants who completed postdisclosure surveys reported high personal utility and no decision regret after receiving genetic results. CONCLUSIONS: The application of ClinGen criteria to CHD candidate genes yielded a list that can be used to interpret clinical genetic testing for CHD. Applying this gene list to one of the largest research cohorts of CHD participants provides a lower bound for the yield of genetic testing in CHD.

The Biomedical Research Hub: a federated platform for patient research data.

OBJECTIVE: The objective was to develop and operate a cloud-based federated system for managing, analyzing, and sharing patient data for research purposes, while allowing each resource sharing patient data to operate their component based upon their own governance rules. The federated system is called the Biomedical Research Hub (BRH). MATERIALS AND METHODS: The BRH is a cloud-based federated system built over a core set of software services called framework services. BRH framework services include authentication and authorization, services for generating and assessing findable, accessible, interoperable, and reusable (FAIR) data, and services for importing and exporting bulk clinical data. The BRH includes data resources providing data operated by different entities and workspaces that can access and analyze data from one or more of the data resources in the BRH. RESULTS: The BRH contains multiple data commons that in aggregate provide access to over 6 PB of research data from over 400 000 research participants. DISCUSSION AND CONCLUSION: With the growing acceptance of using public cloud computing platforms for biomedical research, and the growing use of opaque persistent digital identifiers for datasets, data objects, and other entities, there is now a foundation for systems that federate data from multiple independently operated data resources that expose FAIR application programming interfaces, each using a separate data model. Applications can be built that access data from one or more of the data resources.

The founding charter of the Omic Biodiversity Observation Network (Omic BON).

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

Effects of low pH on the coral reef cryptic invertebrate communities near CO2 vents in Papua New Guinea.

Small cryptic invertebrates (the cryptofauna) are extremely abundant, ecologically important, and species rich on coral reefs. Ongoing ocean acidification is likely to have both direct effects on the biology of these organisms, as well as indirect effects through cascading impacts on their habitats and trophic relationships. Naturally acidified habitats have been important model systems for studying these complex interactions because entire communities that are adapted to these environmental conditions can be analyzed. However, few studies have examined the cryptofauna because they are difficult to census quantitatively in topographically complex habitats and are challenging to identify. We addressed these challenges by using Autonomous Reef Monitoring Structures (ARMS) for sampling reef-dwelling invertebrates >2 mm in size and by using DNA barcoding for taxonomic identifications. The study took place in Papua New Guinea at two reef localities, each with three sites at varying distances from carbon dioxide seeps, thereby sampling across a natural gradient in acidification. We observed sharp overall declines in both the abundance (34-56%) and diversity (42-45%) of organisms in ARMS under the lowest pH conditions sampled (7.64-7.75). However, the overall abundance of gastropods increased slightly in lower pH conditions, and crustacean and gastropod families exhibited varying patterns. There was also variability in response between the two localities, despite their close proximity, as one control pH site displayed unusually low diversity and abundances for all invertebrate groups. The data illustrate the complexity of responses of the reef fauna to pH conditions, and the role of additional factors that influence the diversity and abundance of cryptic reef invertebrates.

Identification of Inhibitors of Fungal Fatty Acid Biosynthesis.

Fungal fatty acid (FA) synthase and desaturase enzymes are essential for the growth and virulence of human fungal pathogens. These enzymes are structurally distinct from their mammalian counterparts, making them attractive targets for antifungal development. However, there has been little progress in identifying chemotypes that target fungal FA biosynthesis. To accomplish this, we applied a whole-cell-based method known as Target Abundance-based FItness Screening using Candida albicans. Strains with varying levels of FA synthase or desaturase expression were grown in competition to screen a custom small-molecule library. Hit compounds were defined as preferentially inhibiting the growth of the low target-expressing strains. Dose-response experiments confirmed that 16 hits (11 with an acyl hydrazide core) differentially inhibited the growth of strains with an altered desaturase expression, indicating a specific chemical-target interaction. Exogenous unsaturated FAs restored C. albicans growth in the presence of inhibitory concentrations of the most potent acyl hydrazides, further supporting the primary mechanism being inhibition of FA desaturase. A systematic analysis of the structure-activity relationship confirmed the acyl hydrazide core as essential for inhibitory activity. This collection demonstrated broad-spectrum activity against Candida auris and mucormycetes and retained the activity against azole-resistant candida isolates. Finally, a preliminary analysis of toxicity to mammalian cells identified potential lead compounds with desirable selectivities. Collectively, these results establish a scaffold that targets fungal FA biosynthesis with a potential for development into novel therapeutics.

Are indigenous territories effective natural climate solutions? A neotropical analysis using matching methods and geographic discontinuity designs.

Indigenous Territories (ITs) with less centralized forest governance than Protected Areas (PAs) may represent cost-effective natural climate solutions to meet the Paris agreement. However, the literature has been limited to examining the effect of ITs on deforestation, despite the influence of anthropogenic degradation. Thus, little is known about the temporal and spatial effect of allocating ITs on carbon stocks dynamics that account for losses from deforestation and degradation. Using Amazon Basin countries and Panama, this study aims to estimate the temporal and spatial effects of ITs and PAs on carbon stocks. To estimate the temporal effects, we use annual carbon density maps, matching analysis, and linear mixed models. Furthermore, we explore the spatial heterogeneity of these estimates through geographic discontinuity designs, allowing us to assess the spatial effect of ITs and PAs boundaries on carbon stocks. The temporal effects highlight that allocating ITs preserves carbon stocks and buffer losses as well as allocating PAs in Panama and Amazon Basin countries. The geographic discontinuity designs reveal that ITs' boundaries secure more extensive carbon stocks than their surroundings, and this difference tends to increase towards the least accessible areas, suggesting that indigenous land use in neotropical forests may have a temporarily and spatially stable impact on carbon stocks. Our findings imply that ITs in neotropical forests support Nationally Determined Contributions (NDCs) under the Paris Agreement. Thus, Indigenous peoples must become recipients of countries' results-based payments.

Rural Telehealth Use during the COVID-19 Pandemic: How Long-term Infrastructure Commitment May Support Rural Health Care Systems Resilience.

Amid concerns of inadequate medical supplies and staffing anticipated from a surge in COVID-19 cases, many health care systems across the United States (U.S.) began shutting down non-essential patient services in March 2020. These sudden shifts bring up questions about the long-term effects of COVID-19 on already fragile rural health care systems and the ability of rural populations, including farmers and farm workers, to meet their health care needs. To provide alternative and safe access to health care, the Federal government relaxed telehealth regulations, which effectively removed some of the largest regulatory barriers that had limited the adoption of telehealth in the U.S. In this commentary, we draw on the example of the Marshfield Clinic Health System (MCHS), a large rural health care system in Wisconsin and provide an early assessment of how it adjusted its telehealth services during the early months of COVID-19. While the long-term effects of the pandemic on rural health care systems will not be known for some time, the example of MCHS points to the importance of on-going and sustained investments to support the resilience of health care systems and their ability to weather crises. With early evidence that MCHS patients and practitioners are interested in continuing to use telehealth post-COVID-19, we conclude our commentary by offering three recommendations to remove hurdles and improve quality of telehealth care.

Hybrid pixel direct detector for electron energy loss spectroscopy.

We characterize a hybrid pixel direct detector and demonstrate its suitability for electron energy loss spectroscopy (EELS). The detector has a large dynamic range, narrow point spread function, detective quantum efficiency ≥ 0.8 even without single electron arrival discrimination, and it is resilient to radiation damage. It is capable of detecting ~5 × 106 electrons/pixel/second, allowing it to accommodate up to 0.8 pA per pixel and hence >100 pA EELS zero-loss peak (ZLP) without saturation, if the ZLP is spread over >125 pixels (in the non-dispersion direction). At the same time, it can reliably detect isolated single electrons in the high loss region of the spectrum. The detector uses a selectable threshold to exclude low energy events, and this results in essentially zero dark current and readout noise. Its maximum frame readout rate at 16-bit digitization is 2250 full frames per second, allowing for fast spectrum imaging. We show applications including EELS of boron nitride in which an unsaturated zero loss peak is recorded at the same time as inner shell loss edges, elemental mapping of an STO/BTO/LMSO multilayer, and efficient parallel acquisition of angle-resolved EEL spectra (S(q, ω)) of boron nitride.

Uptake, translocation, and metabolism of glyphosate, glufosinate, and dicamba mixtures in Echinochloa crus-galli and Amaranthus palmeri.

BACKGROUND: Echinochloa crus-galli (L.) Beauv. and Amaranthus palmeri S. Wats are two common and problematic weeds prevalent across the Midsouth of the USA. Herbicide absorption, translocation, and metabolism were investigated as potential sources of herbicide antagonism on A. palmeri and E. crus-galli using 14 C-labeled herbicides. Three 14 C-labeled herbicides, glyphosate, glufosinate, and dicamba, were utilized individually in separate experiments. RESULTS: Uptake of 14 C-glyphosate in E. crus-galli was 15% of the total applied radioactivity for glyphosate/glufosinate (897 + 595 g a.i./a.e. ha-1 ) compared to 25% for glyphosate alone. Similarly, uptake of 14 C-glyphosate in A. palmeri reduced by 10% when applied with glufosinate. Applying glyphosate/dicamba (897/560 g a.e. ha-1 ) reduced 14 C-glyphosate uptake in both species. In the 14 C-glufosinate experiment, both species absorbed less 14 C-glufosinate when mixed with glyphosate compared to glufosinate alone. No metabolic degradation of glyphosate was observed in either species. E. crus-galli metabolized dicamba 23 times faster than A. palmeri. When glufosinate was applied with dicamba, metabolic degradation of 14 C-dicamba was limited in both species. For example, 99.9% of the applied radioactivity was recovered in A. palmeri as the parent compound when 14 C-glufosinate dicamba was applied with glufosinate, compared to 95.7% for dicamba alone. CONCLUSION: These findings demonstrate absorption, translocation, or metabolism of dicamba, glufosinate, and glyphosate can be affected by mixing with another herbicide. As mixing two herbicides is often a critical component of resistance management, careful investigation into the performance of these mixtures in the field is needed. © 2020 Society of Chemical Industry.

The role of forest conversion, degradation, and disturbance in the carbon dynamics of Amazon indigenous territories and protected areas.

Maintaining the abundance of carbon stored aboveground in Amazon forests is central to any comprehensive climate stabilization strategy. Growing evidence points to indigenous peoples and local communities (IPLCs) as buffers against large-scale carbon emissions across a nine-nation network of indigenous territories (ITs) and protected natural areas (PNAs). Previous studies have demonstrated a link between indigenous land management and avoided deforestation, yet few have accounted for forest degradation and natural disturbances-processes that occur without forest clearing but are increasingly important drivers of biomass loss. Here we provide a comprehensive accounting of aboveground carbon dynamics inside and outside Amazon protected lands. Using published data on changes in aboveground carbon density and forest cover, we track gains and losses in carbon density from forest conversion and degradation/disturbance. We find that ITs and PNAs stored more than one-half (58%; 41,991 MtC) of the region's carbon in 2016 but were responsible for just 10% (-130 MtC) of the net change (-1,290 MtC). Nevertheless, nearly one-half billion tons of carbon were lost from both ITs and PNAs (-434 MtC and -423 MtC, respectively), with degradation/disturbance accounting for >75% of the losses in 7 countries. With deforestation increasing, and degradation/disturbance a neglected but significant source of region-wide emissions (47%), our results suggest that sustained support for IPLC stewardship of Amazon forests is critical. IPLCs provide a global environmental service that merits increased political protection and financial support, particularly if Amazon Basin countries are to achieve their commitments under the Paris Climate Agreement.

Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium.

Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.

Magnetic elastomers for stretchable inductors.

In this work, silicone loaded with magnetic particles is investigated for creating a composite with higher permeability while still maintaining stretchability. Magnetic and mechanical properties are first characterized for composites based on both spherical and platelet particle geometries. The first magnetic-core stretchable inductors are then demonstrated using the resulting ferroelastomer. Solenoid inductors based on liquid metal galinstan are then demonstrated around a ferroelastomeric core and shown to survive uniaxial strains up to 100%. Soft elastomers loaded with magnetic particles were found to increase the core permeability and inductance density of stretchable inductors by nearly 200%.

The founding charter of the Genomic Observatories Network.

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

A decadal view of biodiversity informatics: challenges and priorities.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

Controlled exposure study of air pollution and T-wave alternans in volunteers without cardiovascular disease.

BACKGROUND: Epidemiological studies have assessed T-wave alternans (TWA) as a possible mechanism of cardiac arrhythmias related to air pollution in high-risk subjects and have reported associations with increased TWA magnitude. OBJECTIVE: In this controlled human exposure study, we assessed the impact of exposure to concentrated ambient particulate matter (CAP) and ozone (O3) on T-wave alternans in resting volunteers without preexisting cardiovascular disease. METHODS: Seventeen participants without preexisting cardiovascular disease were randomized to filtered air (FA), CAP (150 µg/m3), O3 (120 ppb), or combined CAP + O3 exposures for 2 hr. Continuous electrocardiograms (ECGs) were recorded at rest and T-wave alternans (TWA) was computed by modified moving average analysis with QRS alignment for the artifact-free intervals of 20 beats along the V2 and V5 leads. Exposure-induced changes in the highest TWA magnitude (TWAMax) were estimated for the first and last 5 min of each exposure (TWAMax_Early and TWAMax_Late respectively). ΔTWAMax (Late-Early) were compared among exposure groups using analysis of variance. RESULTS: Mean ± SD values for ΔTWAMax were -2.1 ± 0.4, -2.7 ± 1.1, -1.9 ± 1.5, and -1.2 ± 1.5 in FA, CAP, O3, and CAP + O3 exposure groups, respectively. No significant differences were observed between pollutant exposures and FA. CONCLUSION: In our study of 17 volunteers who had no preexisting cardiovascular disease, we did not observe significant changes in T-wave alternans after 2-hr exposures to CAP, O3, or combined CAP + O3. This finding, however, does not preclude the possibility of pollution-related effects on TWA at elevated heart rates, such as during exercise, or the possibility of delayed responses.

A call for an international network of genomic observatories (GOs).

We are entering a new era in genomics-that of large-scale, place-based, highly contextualized genomic research. Here we review this emerging paradigm shift and suggest that sites of utmost scientific importance be expanded into 'Genomic Observatories' (GOs). Investment in GOs should focus on the digital characterization of whole ecosystems, from all-taxa biotic inventories to time-series 'omics studies. The foundational layer of biodiversity-genetic variation-would thus be mainstreamed into Earth Observation systems enabling predictive modelling of biodiversity dynamics and resultant impacts on ecosystem services.