Functional attributes of epilithic diatoms for palaeoenvironmental interpretations in South-West Greenland lakes

Benthic diatoms are commonly used for palaeoenvironmental reconstruction in Arctic regions, but interpretation of their ecology remains challenging. We studied epilithic diatom assemblages from the shallow margins of 19 lakes from three areas (coast-inland-ice sheet margin) along a climate gradient in Kangerlussuaq, West Greenland during two periods; shortly after ice-off (spring) and in the middle of the growth season (summer). We aimed to understand the distribution of Arctic epilithic diatoms in relation to water chemistry gradients during the two seasons, to investigate their incorporation into lake sediments and to assess their applicability as palaeoenvironmental indicators. Diatoms were correlated with nutrients in the spring and alkalinity/major ions in the summer, when nutrients were depleted; approximately half of the variance explained was independent of spatial factors. When categorised by functional attributes, diatom seasonal succession differed among regions with the most obvious changes in inland lakes where summer temperatures are warmer, organic nutrient processing is prevalent and silicate is limiting. These conditions led to small, motile and adnate diatoms being abundant in inland lakes during the summer (Nitzschia spp., Encyonopsis microcephala), as these functional attributes are suited to living within complex mats of non-siliceous microbial biofilms. Seasonal succession in silica-rich lakes at the coast was less pronounced and assemblages included Tabellaria flocculosa (indicating more acidic conditions) and Hannaea arcus (indicating input from inflowing rivers). The nitrogen-fixing diatom Epithemia sorex increased from the coast to the ice sheet, negatively correlating with a gradient of reactive nitrogen. The presence of this diatom in Holocene sediment records alongside cyanobacterial carotenoids during arid periods of low nitrogen delivery, suggests that it is a useful indicator of nitrogen limitation. Nitzschia species appear to be associated with high concentrations of organic carbon and heterotrophy, but their poor representation in West Greenland lake sediments due to taphonomic processes limits their palaeoenvironmental application in this region. Proportions of epilithic taxa in lake sediment records of coastal lakes increased during some wetter periods of the Holocene, suggesting that snowpack-derived nutrient delivery may offer diatom taxa living at lake margins a competitive advantage over planktonic diatoms during the “moating” ice melt period. Thus, further research investigating linkages between epilithic diatoms, snowpack and nutrient delivery in seasonally frozen lakes is recommended as these taxa live on the ‘front-line’ during the spring and may be especially sensitive to changes in snowmelt conditions

A landscape perspective of Holocene organic carbon cycling in coastal SW Greenland lake-catchments

Arctic organic carbon (OC) stores are substantial and have accumulated over millennia as a function of changes in climate and terrestrial vegetation. Arctic lakes are also important components of the regional C-cycle as they are sites of OC production and CO2emissions but also store large amounts of OC in their sediments. This sediment OC pool is a mixture derived from terrestrial and aquatic sources, and sediment cores can therefore provide a long-term record of the changing interactions between lakes and their catchments in terms of nutrient and C transfer. Sediment carbon isotope composition (δ13C), C/N ratio and organic C accumulation rates (C AR) of14C-dated cores covering the last ∼10,000 years from six lakes close to Sisimiut (SW Greenland) are used to determine the extent to which OC dynamics reflect climate relative to lake or catchment characteristics. Sediment δ13C ranges from −19 to −32‰ across all lakes, while C/N ratios are 20 (mean = 12), values that indicate a high proportion of the organic matter is from autochthonous production but with a variable terrestrial component. Temporal trends in δ13C are variable among lakes, with neighbouring lakes showing contrasting profiles, indicative of site-specific OC processing. The response of an individual lake reflects its morphometry (which influences benthic primary production), the catchment:lake ratio, and catchment relief, lakes with steeper catchments sequester more carbon. The multi-site, landscape approach used here highlights the complex response of individual lakes to climate and catchment disturbance, but broad generalisations are possible. Regional Neoglacial cooling (from ∼5000 cal yr BP) influenced the lateral transfer of terrestrial OC to lakes, with three lakes showing clear increases in OC accumulation rate. The lakes likely switched from being autotrophic (i.e. net ecosystem production > ecosystem respiration) in the early Holocene to being heterotrophic after 5000 cal yr BP as terrestrial OC transfer increased

The Arctic in the twenty-first century: changing biogeochemical linkages across a paraglacial landscape of Greenland

The Kangerlussuaq area of southwest Greenland encompasses diverse ecological, geomorphic, and climate gradients that function over a range of spatial and temporal scales. Ecosystems range from the microbial communities on the ice sheet and moisture-stressed terrestrial vegetation (and their associated herbivores) to freshwater and oligosaline lakes. These ecosystems are linked by a dynamic glacio-fluvial-aeolian geomorphic system that transports water, geological material, organic carbon and nutrients from the glacier surface to adjacent terrestrial and aquatic systems. This paraglacial system is now subject to substantial change because of rapid regional warming since 2000. Here, we describe changes in the eco- and geomorphic systems at a range of timescales and explore rapid future change in the links that integrate these systems. We highlight the importance of cross-system subsidies at the landscape scale and, importantly, how these might change in the near future as the Arctic is expected to continue to warm

Quantifying neutralising antibody responses against SARS-CoV-2 in dried blood spots (DBS) and paired sera

The ongoing SARS-CoV-2 pandemic was initially managed by non-pharmaceutical interventions such as diagnostic testing, isolation of positive cases, physical distancing and lockdowns. The advent of vaccines has provided crucial protection against SARS-CoV-2. Neutralising antibody (nAb) responses are a key correlate of protection, and therefore measuring nAb responses is essential for monitoring vaccine efficacy. Fingerstick dried blood spots (DBS) are ideal for use in large-scale sero-surveillance because they are inexpensive, offer the option of self-collection and can be transported and stored at ambient temperatures. Such advantages also make DBS appealing to use in resource-limited settings and in potential future pandemics. In this study, nAb responses in sera, venous blood and fingerstick blood stored on filter paper were measured. Samples were collected from SARS-CoV-2 acutely infected individuals, SARS-CoV-2 convalescent individuals and SARS-CoV-2 vaccinated individuals. Good agreement was observed between the nAb responses measured in eluted DBS and paired sera. Stability of nAb responses was also observed in sera stored on filter paper at room temperature for 28 days. Overall, this study provides support for the use of filter paper as a viable sample collection method to study nAb responses.</p

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Procalcitonin Is Not a Reliable Biomarker of Bacterial Coinfection in People With Coronavirus Disease 2019 Undergoing Microbiological Investigation at the Time of Hospital Admission

Abstract Admission procalcitonin measurements and microbiology results were available for 1040 hospitalized adults with coronavirus disease 2019 (from 48 902 included in the International Severe Acute Respiratory and Emerging Infections Consortium World Health Organization Clinical Characterisation Protocol UK study). Although procalcitonin was higher in bacterial coinfection, this was neither clinically significant (median [IQR], 0.33 [0.11–1.70] ng/mL vs 0.24 [0.10–0.90] ng/mL) nor diagnostically useful (area under the receiver operating characteristic curve, 0.56 [95% confidence interval, .51–.60]).</jats:p

Implementation of corticosteroids in treating COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK:prospective observational cohort study

BACKGROUND: Dexamethasone was the first intervention proven to reduce mortality in patients with COVID-19 being treated in hospital. We aimed to evaluate the adoption of corticosteroids in the treatment of COVID-19 in the UK after the RECOVERY trial publication on June 16, 2020, and to identify discrepancies in care. METHODS: We did an audit of clinical implementation of corticosteroids in a prospective, observational, cohort study in 237 UK acute care hospitals between March 16, 2020, and April 14, 2021, restricted to patients aged 18 years or older with proven or high likelihood of COVID-19, who received supplementary oxygen. The primary outcome was administration of dexamethasone, prednisolone, hydrocortisone, or methylprednisolone. This study is registered with ISRCTN, ISRCTN66726260. FINDINGS: Between June 17, 2020, and April 14, 2021, 47 795 (75·2%) of 63 525 of patients on supplementary oxygen received corticosteroids, higher among patients requiring critical care than in those who received ward care (11 185 [86·6%] of 12 909 vs 36 415 [72·4%] of 50 278). Patients 50 years or older were significantly less likely to receive corticosteroids than those younger than 50 years (adjusted odds ratio 0·79 [95% CI 0·70–0·89], p=0·0001, for 70–79 years; 0·52 [0·46–0·58], p80 years), independent of patient demographics and illness severity. 84 (54·2%) of 155 pregnant women received corticosteroids. Rates of corticosteroid administration increased from 27·5% in the week before June 16, 2020, to 75–80% in January, 2021. INTERPRETATION: Implementation of corticosteroids into clinical practice in the UK for patients with COVID-19 has been successful, but not universal. Patients older than 70 years, independent of illness severity, chronic neurological disease, and dementia, were less likely to receive corticosteroids than those who were younger, as were pregnant women. This could reflect appropriate clinical decision making, but the possibility of inequitable access to life-saving care should be considered. FUNDING: UK National Institute for Health Research and UK Medical Research Council

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data