Maximizing sampling efficiency to detect differences in fish community composition using environmental DNA metabarcoding in subarctic fjords

Environmental DNA (eDNA) has gained popularity as a tool for ecosystem biomonitoring and biodiversity assessment. Although much progress has been made regarding laboratory and fieldwork protocols, the issue of sampling efficiency requires further investigation, particularly in three-dimensional marine systems. This study focuses on fish community composition in marine ecosystems and aims to analyze the efficiency of sampling design given the sampling effort for distinguishing between different communities. We sampled three fjords in Northern Norway, taking samples along fjord transects and at three different depths, and amplified a fragment of the mitochondrial 12S rRNA gene of bony fishes using the MiFish primers. We evaluated the effect of (i) the number of sampling stations, (ii) samples' spatial distribution, and (iii) the data treatment approach (presence/absence versus semiquantitative) for maximizing the efficiency of eDNA metabarcoding sampling when inferring differences of fish community compositions between fjords. We found that the manner of data treatment strongly affected the minimum number of sampling stations required to detect differences among communities; because the semiquantitative approach retained some information about abundance of the underlying reads, it was the most efficient. Furthermore, we found little-to-no difference of fish communities in samples from intermediate depths when comparing vertical fish communities. Lastly, we found that the differences between fish communities at the surface were the highest across the horizontal distance and overall, samples ~30 km apart showed the highest variation in the horizontal distribution. Boosting sampling efficiency (reducing sampling effort without compromising ecological inferences) can significantly contribute to enhanced biodiversity management and efficient biomonitoring plans.publishedVersio

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Appendix B. The DNA extraction and amplified fragment length polymorphism (AFLP) protocols.

The DNA extraction and amplified fragment length polymorphism (AFLP) protocols

Appendix C. S:O ratio as a function of distance from (1) MB male and (2) the CR male cluster.

S:O ratio as a function of distance from (1) MB male and (2) the CR male cluster

Appendix E. Female Phyllospadix serrulatus spadix removal experiment.

Female Phyllospadix serrulatus spadix removal experiment

Appendix A. Location of the study areas.

Location of the study areas

Appendix D. Number of Phyllospadix serrulatus and P. scouleri seedlings found recruited to algae and seagrass, years 2006 and 2007 combined; ANOVA table for the percent cover of Phyllospadix spp. found in surveys for seedling recruitment conducted in April and May 2006 and 2007, at four sites; and ANOVA table for the percent cover of articulated coralline algae, Neorhodamela larix and Odonthalia spp., found in surveys for seedling recruitment conducted in April and May 2006 and 2007, at four...

Number of Phyllospadix serrulatus and P. scouleri seedlings found recruited to algae and seagrass, years 2006 and 2007 combined; ANOVA table for the percent cover of Phyllospadix spp. found in surveys for seedling recruitment conducted in April and May 2006 and 2007, at four sites; and ANOVA table for the percent cover of articulated coralline algae, Neorhodamela larix and Odonthalia spp., found in surveys for seedling recruitment conducted in April and May 2006 and 2007, at four sites

Appendix A. A map of the study area.

A map of the study area

Appendix A. Best fit parameters and model comparison for Case Studies 1, 2, and 3 (Tables A1 –A3); empirical histograms and best fit probability mass functions comparing the Poisson, Generalized Poisson, Negative Binomial, and Conway-Maxwell Poisson distribution fits for Case Studies 1 and 2 (Fig. A1); and point patterns from Jeltsch Fig. 7 used in Case Study 2 (Fig. A2).

Best fit parameters and model comparison for Case Studies 1, 2, and 3 (Tables A1 –A3); empirical histograms and best fit probability mass functions comparing the Poisson, Generalized Poisson, Negative Binomial, and Conway-Maxwell Poisson distribution fits for Case Studies 1 and 2 (Fig. A1); and point patterns from Jeltsch Fig. 7 used in Case Study 2 (Fig. A2)

Appendix B. Probability mass functions and R code to fit the Poisson, Negative Binomial, Generalized Poisson, and CMP distributions (and their zero-truncated versions).

Probability mass functions and R code to fit the Poisson, Negative Binomial, Generalized Poisson, and CMP distributions (and their zero-truncated versions)