Discovery of the widespread site-specific single-stranded nuclease family Ssn.

Site-specific endonucleases that exclusively cut single-stranded DNA have hitherto never been described and constitute a barrier to the development of ssDNA-based technologies. We identify and characterize one such family, from the GIY-YIG superfamily, of widely distributed site-specific single-stranded nucleases (Ssn) exhibiting unique ssDNA cleavage properties. By first comprehensively studying the Ssn homolog from Neisseria meningitidis, we demonstrate that it interacts specifically with a sequence (called NTS) present in hundreds of copies and surrounding important genes in pathogenic Neisseria.

Evolutionary insights into the emergence of virulent spirochetes.

Pathogenic are spirochete bacteria which cause leptospirosis, a re-emerging zoonotic disease of global importance. Here, we use a recently described lineage of environmental-adapted leptospires, which are evolutionarily the closest relatives of the highly virulent species, to explore the key phenotypic traits and genetic determinants of virulence. Through a comprehensive approach integrating phylogenomic comparisons with and phenotyping studies, we show that the evolution towards pathogenicity is associated with both a decrease of the ability to survive in the environment and the acquisition of strategies that enable successful host colonization.

The microbiological outcomes of culture-negative blood specimens using 16S rRNA broad-range PCR sequencing: a retrospective study in a Canadian province from 2018 to 2022.

Unlabelled: Broad-range 16S rRNA PCR and sequencing of 1,183 blood specimens from 853 unique patients yielded an interpretable sequence and bacterial identification in 29%, 16S rRNA amplification with uninterpretable sequences in 53%, and no amplification in 18%. This study highlights the potential utility of this technique in identifying fastidious gram-negative and anaerobic bacteria but the frequent recovery of environmental and contaminant organisms argues for its judicious use.

Importance: The existing literature focuses on its performance compared to blood cultures in patients with sepsis, leaving a gap in the literature regarding other blood specimens in suspected infectious syndrome across the severity spectrum.

An imputed ancestral reference genome for the complex better captures structural genomic diversity for reference-based alignment workflows.

Reference-based alignment of short-reads is a widely used technique in genomic analysis of the complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas both of which are based on a lineage 4 sequence. As such, these reference sequences do not capture all of the structural variation known to be present in the ancestor of the MTBC.

Copper management strategies in obligate bacterial symbionts: balancing cost and benefit.

Bacteria employ diverse mechanisms to manage toxic copper in their environments, and these evolutionary strategies can be divided into two main categories: accumulation and rationalization of metabolic pathways. The strategies employed depend on the bacteria's lifestyle and environmental context, optimizing the metabolic cost-benefit ratio. Environmental and opportunistically pathogenic bacteria often possess an extensive range of copper regulation systems in order to respond to variations in copper concentrations and environmental conditions, investing in diversity and/or redundancy as a safeguard against uncertainty.

Monkeypox in Montréal: Epidemiology, Phylogenomics, and Public Health Response to a Large North American Outbreak.

Background: Monkeypox, a viral zoonotic disease, is causing a global outbreak outside of endemic areas.

Objective: To characterize the outbreak of monkeypox in Montréal, the first large outbreak in North America.

Design: Epidemiologic and laboratory surveillance data and a phylogenomic analysis were used to describe and place the outbreak in a global context.

Laboratory Features of Trichinellosis and Eosinophilia Threshold for Testing, Nunavik, Quebec, Canada, 2009-2019.

Prolonged eosinophilia is characteristic of trichinellosis. To determine the optimal eosinophil threshold for reflex Trichinella testing, we examined all 43 cases in Nunavik, Quebec, Canada, during 2009-2019. Using receiver operating characteristic analysis, we determined that eosinophil counts >0.

Monkeypox Virus Infection in Humans across 16 Countries - April-June 2022.

Background: Before April 2022, monkeypox virus infection in humans was seldom reported outside African regions where it is endemic. Currently, cases are occurring worldwide. Transmission, risk factors, clinical presentation, and outcomes of infection are poorly defined.

Remdesivir for the treatment of patients in hospital with COVID-19 in Canada: a randomized controlled trial.

Background: The role of remdesivir in the treatment of patients in hospital with COVID-19 remains ill defined in a global context. The World Health Organization Solidarity randomized controlled trial (RCT) evaluated remdesivir in patients across many countries, with Canada enrolling patients using an expanded data collection format in the Canadian Treatments for COVID-19 (CATCO) trial. We report on the Canadian findings, with additional demographics, characteristics and clinical outcomes, to explore the potential for differential effects across different health care systems.

Specificity of SARS-CoV-2 Antibody Detection Assays against S and N Proteins among Pre-COVID-19 Sera from Patients with Protozoan and Helminth Parasitic Infections.

We aimed to assess the specificity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody detection assays among people with tissue-borne parasitic infections. We tested three SARS-CoV-2 antibody-detection assays (cPass SARS-CoV-2 neutralization antibody detection kit [cPass], Abbott SARS-CoV-2 IgG assay [Abbott Architect], and Standard Q COVID-19 IgM/IgG combo rapid diagnostic test [SD RDT IgM/SD RDT IgG]) among 559 pre-COVID-19 seropositive sera for several parasitic infections. The specificity of assays was 95 to 98% overall.

Remdesivir and systemic corticosteroids for the treatment of COVID-19: A Bayesian re-analysis.

Background: The global death toll from coronavirus disease 2019 (COVID-19) has exceeded 2 million, and treatments to decrease mortality are needed urgently.

Objectives: To examine the probabilities of a clinically meaningful reduction in mortality for remdesivir and systemic corticosteroids.

Design, Setting And Participants: This was a probabilistic re-analysis of clinical trial data for corticosteroids and remdesivir in the treatment of hospitalized patients with COVID-19 using a Bayesian random effects meta-analytic approach.

Wildlife population trends in protected areas predicted by national socio-economic metrics and body size.

Ensuring that protected areas (PAs) maintain the biodiversity within their boundaries is fundamental in achieving global conservation goals. Despite this objective, wildlife abundance changes in PAs are patchily documented and poorly understood. Here, we use linear mixed effect models to explore correlates of population change in 1,902 populations of birds and mammals from 447 PAs globally.

Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters.

Likelihood-based methods are commonplace in phylogenetic systematics. Although much effort has been directed toward likelihood-based models for molecular data, comparatively less work has addressed models for discrete morphological character (DMC) data. Among-character rate variation (ACRV) may confound phylogenetic analysis, but there have been few analyses of the magnitude and distribution of rate heterogeneity among DMCs.

Ossification sequence heterochrony among amphibians.

Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia.

Assessing the phylogenetic utility of sequence heterochrony: evolution of avian ossification sequences as a case study.

The evolution of developmental sequences, or sequence heterochrony, is an emerging field of study that addresses the temporal interplay between evolution and development. Some phylogenetic signal has been found in developmental sequence data, but sampling has generally been limited to small numbers of taxa and few developmental events. Here we present the largest ossification sequence dataset to date.

Methods for the analysis of developmental sequence data.

Heterochrony, evolutionary changes in developmental timing, can be studied either by examining changes in growth or changes in the sequence of developmental events. Developmental sequence data has the potential to address many important questions in the field of developmental evolution, but methodological challenges remain due to the biological and logical dependence of events in a ranked sequence. In the past 10 years, the study of sequence heterochrony has undergone a rebirth, with the creation of several new methods for the analysis of this type of data.

Ossification sequence of the common tern (Sterna hirundo) and its implications for the interrelationships of the Lari (Aves, Charadriiformes).

The hypotheses of relationships within Lari (gulls) are highly unstable, and depend on whether morphological or molecular data are examined. Developmental sequence data are thought to contain phylogenetic information, but have never been applied to the problem of avian systematics. In this article, we describe the ossification sequence of the Common Tern (Sterna hirundo), and compare the pattern observed to published descriptions of other Charadriiformes, specifically the Great Skua (Stercorariidae) and various species of gulls (Laridae).

Estimating evolution of temporal sequence changes: a practical approach to inferring ancestral developmental sequences and sequence heterochrony.

Developmental biology often yields data in a temporal context. Temporal data in phylogenetic systematics has important uses in the field of evolutionary developmental biology and, in general, comparative biology. The evolution of temporal sequences, specifically developmental sequences, has proven difficult to examine due to the highly variable temporal progression of development.

Evolution of budding yeast prion-determinant sequences across diverse fungi.

Prions are transmissible self-replicating alternative states of proteins. Four prions ([PSI+], [URE3], [RNQ+] and [NU+]) can be inherited cytoplasmically in Saccharomyces cerevisiae laboratory strains. In the case of [PSI+], there is increasing evidence that prion formation may engender mechanisms to uncover hidden genetic variation.