A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities

AbstractSeafloor massive sulfide (SMS) mining will likely occur at hydrothermal systems in the near future. Alongside their mineral wealth, SMS deposits also have considerable biological value. Active SMS deposits host endemic hydrothermal vent communities, whilst inactive deposits support communities of deep water corals and other suspension feeders. Mining activities are expected to remove all large organisms and suitable habitat in the immediate area, making vent endemic organisms particularly at risk from habitat loss and localised extinction. As part of environmental management strategies designed to mitigate the effects of mining, areas of seabed need to be protected to preserve biodiversity that is lost at the mine site and to preserve communities that support connectivity among populations of vent animals in the surrounding region. These “set-aside” areas need to be biologically similar to the mine site and be suitably connected, mostly by transport of larvae, to neighbouring sites to ensure exchange of genetic material among remaining populations. Establishing suitable set-asides can be a formidable task for environmental managers, however the application of genetic approaches can aid set-aside identification, suitability assessment and monitoring. There are many genetic tools available, including analysis of mitochondrial DNA (mtDNA) sequences (e.g. COI or other suitable mtDNA genes) and appropriate nuclear DNA markers (e.g. microsatellites, single nucleotide polymorphisms), environmental DNA (eDNA) techniques and microbial metagenomics. When used in concert with traditional biological survey techniques, these tools can help to identify species, assess the genetic connectivity among populations and assess the diversity of communities. How these techniques can be applied to set-aside decision making is discussed and recommendations are made for the genetic characteristics of set-aside sites. A checklist for environmental regulators forms a guide to aid decision making on the suitability of set-aside design and assessment using genetic tools. This non-technical primer document represents the views of participants in the VentBase 2014 workshop

Sustained methane emissions from China after 2012 despite declining coal production and rice-cultivated area

China’s anthropogenic methane emissions are the largest of any country in the world. A recent study using atmospheric observations suggested that recent policies aimed at reducing emissions of methane due to coal production in China after 2010 had been largely ineffective. Here, based on a longer observational record and an updated modelling approach, we find a statistically significant positive linear trend (0.36 ± 0.04 ( $\pm1\sigma$ ) Tg CH _4 yr ^−2 ) in China’s methane emissions for 2010–2017. This trend was slowing down at a statistically significant rate of -0.1 ± 0.04 Tg CH _4 yr ^−3 . We find that this decrease in growth rate can in part be attributed to a decline in China’s coal production. However, coal mine methane emissions have not declined as rapidly as production, implying that there may be substantial fugitive emissions from abandoned coal mines that have previously been overlooked. We also find that emissions over rice-growing and aquaculture-farming regions show a positive trend (0.13 ± 0.05 Tg CH _4 yr ^−2 for 2010–2017) despite reports of shrinking rice paddy areas, implying potentially significant emissions from new aquaculture activities, which are thought to be primarily located on converted rice paddies

Sustained methane emissions from China after 2012 despite declining coal production and rice-cultivated area

China's anthropogenic methane emissions are the largest of any country in the world. A recent study using atmospheric observations suggested that recent policies aimed at reducing emissions of methane due to coal production in China after 2010 had been largely ineffective. Here, based on a longer observational record and an updated modelling approach, we find a statistically significant positive linear trend (0.36 &plusmn; 0.04 () Tg CH4 yr&minus;2) in China's methane emissions for 2010&ndash;2017. This trend was slowing down at a statistically significant rate of -0.1 &plusmn; 0.04 Tg CH4 yr&minus;3. We find that this decrease in growth rate can in part be attributed to a decline in China's coal production. However, coal mine methane emissions have not declined as rapidly as production, implying that there may be substantial fugitive emissions from abandoned coal mines that have previously been overlooked. We also find that emissions over rice-growing and aquaculture-farming regions show a positive trend (0.13 &plusmn; 0.05 Tg CH4 yr&minus;2 for 2010&ndash;2017) despite reports of shrinking rice paddy areas, implying potentially significant emissions from new aquaculture activities, which are thought to be primarily located on converted rice paddies. &nbsp;</p

Air Pollution, Urgent Asthma Medical Visits and the Modifying Effect of Neighborhood Asthma Prevalence

Background: Social and environmental stressors, may modify associations between environmental pollutants and asthma symptoms. We examined if neighborhood asthma prevalence (higher: HAPN vs. lower: LAPN), a surrogate for underlying risk factors for asthma, modified the relationship between pollutants and urgent asthma visits. Methods: Through zip code, home addresses were linked to New York City Community Air Survey’s land use regression model for street-level, annual average nitrogen dioxide (NO2), particulate matter (PM2.5), elemental carbon (EC); summer average ozone (O3); winter average sulfur dioxide (SO2) concentrations. Poisson regression models were fit to estimate the association (prevalence ratio, PR) between pollutant exposures and seeking urgent asthma care. Results: All pollutants, except O3 were higher in HAPN than LAPN (P0.05). Conclusions: Relationships between modeled street-level pollutants and urgent asthma were stronger in LAPN compared to HAPN. Social stressors that may be more prevalent in HAPN than LAPN, could play a greater role in asthma exacerbations in HAPN versus pollutant exposure alone

sFDvent: A global trait database for deep‐sea hydrothermal‐vent fauna

Motivation: Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite grow‐ ing interest in a trait‐based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single re‐ pository for species traits for deep‐sea chemosynthesis‐based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global‐scale trait database for deep‐sea hydrothermal‐vent fauna – sFD‐ vent (sDiv‐funded trait database for the Functional Diversity of vents). We formed a funded working group to select traits appropriate to: (a) capture the performance of vent species and their influence on ecosystem processes, and (b) compare trait‐based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal‐vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we characterise the sFDvent da‐ tabase, describe our approach, and evaluate its scope. Finally, we compare the sFD‐ vent database to similar databases from shallow‐marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross‐ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique DOI. Main types of variable contained: Six hundred and forty‐six vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided. Spatial location and grain: Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid‐ocean ridges and 6 back‐arc spreading centres. Time period and grain: sFDvent includes information on deep‐sea vent species, and associated taxonomic updates, since they were first discovered in 1977. Time is not recorded. The database will be updated every 5 years. Major taxa and level of measurement: Deep‐sea hydrothermal‐vent fauna with spe‐ cies‐level identification present or in progress. Software format: .csv and MS Excel (.xlsx).This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p&lt;0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p&lt;0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p&lt;0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP &gt;5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Constraining the progenitors of short gamma-ray bursts

So far the progenitors of short γ-ray bursts (SGRBs) have proved elusive. Their presence within both old and young environments and their bias against starforming regions provide tantalising evidence of a neutron star binary or neutron star - black hole merger origin. Within this thesis we study an array of characteristics of the population of SGRBs focussing in particular on their host environments and afterglow properties in the optical and X-ray bands. In particular we consider a set of SGRBs with no detectable host galaxy to deep limits and no clear host in the field from probabilistic arguments. These GRBs either represent a population at high redshift or with high offsets from low redshift hosts. Comparing the offsets of these GRBs from their potential hosts with random positions on the sky we find they are somewhat closer than expected, suggesting these GRBs are more likely to have been kicked from relatively local hosts. We also consider the issue of classification, given suggestions that the often used two second duration divide for SGRBs may produce a sample with a high contamination from collapsar objects or potentially a suggested third class of intermediate objects. We look at a sample of optically-detected SGRBs below the nominal two second divide and go on to consider properties of a larger sample of GRBs comparing varying duration bins. From constructed optical lightcurves and SEDs, we constrain the presence of extinction, jet breaks, supernovae and kilonovae. Though there is a suggestion that such a sample would be 40% contaminated from collapsar objects we find, from supernova constraints combined with duration and spectral hardness fits from Bromberg et al. (2013) that only 22% of objects in our sample could have been collapsars. The optical constraints placed on a kilonova (an r-process transient associated with neutron star mergers), suggest this transient is fainter than has sometimes been predicted but is consistent when considering additional opacities from the rprocess material which could cause strong reddening to the infra-red. Finally, we do not find evidence for a distinct class of intermediate GRBs, though there are likely additional progenitors which create GRB-like objects. At the intermediate duration we do find two unusual individual events not typical of LGRBs: GRBs 100816A and 060505. We find that GRB100816A is most likely a mis-classified SGRB, from its position within its host and the constraint on any associated supernova