Expansion of Armatimonadetes through marine sediment sequencing reveals three classes with unique ecological roles

Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. With the advent of improved sampling techniques, recent scientific studies have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here we add to our understanding of understudied microbes by obtaining 77 metagenome-assembled genomes from the bacterial phylum Armatimonadetes in the Guaymas Basin, Gulf of California, and the Bohai Sea, coastal China. Seven of these MAGs are not classified at the class level. Thus, we propose to name these organisms Zipacnadia. Searches of public databases revealed that the 77 Armatimonadetes described in this study (including Zipacnadia) are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of the GB metagenomic raw reads). The Armatimonadetes described here also have unique metabolic capabilities for this phylum. They have pathways to reduce CO₂ to acetate via the Wood-Ljungdahl pathway (WLP) and generate energy through the oxidative branch of the Embden-Meyerhof-Parnas pathway using CO2 as an electron sink, maintaining the redox balance via WLP. Some of these organisms may also have an autotrophic lifestyle not previously identified in Armatimonadetes. Furthermore, these Armatimonadetes may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. The description of the Armatimonadetes identified in this study enhances our understanding of the diversity and metabolic potential of anoxic habitats worldwide.Marine Scienc

A Content Analysis of Social Media Discussions on THC-OAcetate

Novel cannabinoids require systematic research to inform policies and practices. There is a growing interest in semi-synthetic cannabinoids by consumers, manufacturers, and regulators. However, there is a scarcity of research on these substances. Online discussion forums can provide guidance for research questions when current knowledge is scarce. The current project investigates the topics and issues covered in a social media forum devoted to THC-O-acetate (THCO), a semi-synthetic cannabinoid with rapidly rising popularity. Reddit comments posted on the THCO subreddit from June 2021 through November 2021 were coded for major and minor themes by a team of five coders and a supervisor. Major themes were established and clarified through group discussions. A second round of coding confirmed major themes and identified minor themes. The analysis identified several future research topics for THC-O-acetate, including the extent of variation in product composition, the characteristics of user experiences and comparisons with other substances, whether THC-O-acetate produces psychedelic effects, concerns and adverse experiences, and user harm reduction practices. As an acetate ester, THC-O-acetate may break down when heated and release toxic ketene gas. Although several users expressed safety concerns regarding THC-O-acetate, some explicitly mentioning ketene risk, the most common administration method reported was heated inhalation

The COVID-19 emergency response assessment study: a prospective longitudinal survey of frontline doctors in the UK and Ireland

OBJECTIVES: The psychological impact of the COVID-19 pandemic on doctors is a significant concern. Due to the emergence of multiple pandemic waves, longitudinal data on the impact of COVID-19 are vital to ensure an adequate psychological care response. The primary aim was to assess the prevalence and degree of psychological distress and trauma in frontline doctors during the acceleration, peak and deceleration of the COVID-19 first wave. Personal and professional factors associated with psychological distress are also reported. DESIGN: A prospective online three-part longitudinal survey. SETTING: Acute hospitals in the UK and Ireland. PARTICIPANTS: Frontline doctors working in emergency medicine, anaesthetics and intensive care medicine during the first wave of the COVID-19 pandemic in March 2020. PRIMARY OUTCOME MEASURES: Psychological distress and trauma measured using the General Health Questionnaire-12 and the Impact of Events-Revised. RESULTS: The initial acceleration survey distributed across networks generated a sample of 5440 doctors. Peak and deceleration response rates from the original sample were 71.6% (n=3896) and 56.6% (n=3079), respectively. Prevalence of psychological distress was 44.7% (n=1334) during the acceleration, 36.9% (n=1098) at peak and 31.5% (n=918) at the deceleration phase. The prevalence of trauma was 23.7% (n=647) at peak and 17.7% (n=484) at deceleration. The prevalence of probable post-traumatic stress disorder was 12.6% (n=343) at peak and 10.1% (n=276) at deceleration. Worry of family infection due to clinical work was the factor most strongly associated with both distress (R(2)=0.06) and trauma (R(2)=0.10). CONCLUSION: Findings reflect a pattern of elevated distress at acceleration and peak, with some natural recovery. It is essential that policymakers seek to prevent future adverse effects through (a) provision of vital equipment to mitigate physical and psychological harm, (b) increased awareness and recognition of signs of psychological distress and (c) the development of clear pathways to effective psychological care. TRIAL REGISTRATION NUMBER: ISRCTN10666798

Characterizing the target selection pipeline for the Dark Energy Spectroscopic Instrument Bright Galaxy Survey

We present the steps taken to produce a reliable and complete input galaxy catalogue for the Dark Energy Spectroscopic Instrument (DESI) Bright Galaxy Survey (BGS) using the photometric Legacy Survey DR8 DECam. We analyse some of the main issues faced in the selection of targets for the DESI BGS, such as star–galaxy separation, contamination by fragmented stars and bright galaxies. Our pipeline utilizes a new way to select BGS galaxies using Gaia photometry and we implement geometrical and photometric masks that reduce the number of spurious objects. The resulting catalogue is cross-matched with the Galaxy And Mass Assembly (GAMA) survey to assess the completeness of the galaxy catalogue and the performance of the target selection. We also validate the clustering of the sources in our BGS catalogue by comparing with mock catalogues and the Sloan Digital Sky Survey (SDSS) data. Finally, the robustness of the BGS selection criteria is assessed by quantifying the dependence of the target galaxy density on imaging and other properties. The largest systematic correlation we find is a 7 per cent suppression of the target density in regions of high stellar density

Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.

The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation

Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.

The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity

The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.

Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins

Choosing a pediatric recipient for orthotopic liver transplantation

Between March 3, 1981, and June 1, 1984, 216 children were evaluated for orthotopic liver transplantation. Of the 216 patients, 117 (55%) had recelved at least one liver transplant by June 1, 1985. Fifty-five (25%) died before transplantation. The 117 patients who received transplants were grouped according to severity of disease and degree of general decompensation at the time of transplantation. The severity of a patient's medical condition with the possible exception of deep hepatic coma, did not predict outcome following orthotopic liver transplantation. Seventy variables were assessed at the time of the evaluation. Twenty-three of the 70 variables were found to have prognostic significance with regard to death from progressive liver disease before transplantation. These 23 variables were Incorporated into a multivariate model to provide a means of determining the relative risk of death among pediatric patients with end-stage liver disease. This information may allow more informed selection of candidates awaiting liver transplantation. © 1987 The C. V. Mosby Company

Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution

The crystal structure of an essential bacterial protein, YeaZ, from T. maritima identifies an interface that potentially mediates protein–protein interaction