Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets.

Background: Culture-independent diagnostic tests are gaining popularity as tools for detecting pathogens in food. Shotgun sequencing holds substantial promise for food testing as it provides abundant information on microbial communities, but the challenge is in analyzing large and complex sequencing datasets with a high degree of both sensitivity and specificity. Falsely classifying sequencing reads as originating from pathogens can lead to unnecessary food recalls or production shutdowns, while low sensitivity resulting in false negatives could lead to preventable illness.

High-throughput transcriptomics toxicity assessment of eleven data-poor bisphenol A alternatives.

Bisphenol A (BPA), a widely used chemical in the production of plastics and epoxy resins, has garnered significant attention due to its association with adverse health effects, particularly its endocrine-disrupting properties. Regulatory measures aimed at reducing human exposure to BPA have led to a proliferation of alternative chemicals used in various consumer and industrial products. While these alternatives serve to reduce BPA exposure, concerns have arisen regarding their safety and potential toxicity as regrettable substitutes.

Systematic reanalysis of copy number losses of uncertain clinical significance.

Background: Reanalysis of exome/genome data improves diagnostic yield. However, the value of reanalysis of clinical array comparative genomic hybridisation (aCGH) data has never been investigated. Case-by-case reanalysis can be challenging in busy diagnostic laboratories.

Draft genomes of meropenem-resistant from the cloacae of turtles in Lake Opinicon, Canada.

We report the draft genome sequences of seven meropenem-resistant bacterial isolates from the cloacae of painted and musk turtles at Lake Opinicon, Canada. This study improves our understanding of the spread of meropenem-resistant bacteria in the wild.

Interstitial lung disease in children with Rubinstein-Taybi syndrome.

Introduction: Rubinstein-Taybi syndrome (RSTS) is a rare genetic syndrome caused primarily by a mutation in the CREBBP gene found on chromosome 16. Patients with RSTS are at greater risk for a variety of medical problems, including upper airway obstruction and aspiration. Childhood interstitial lung disease (ILD) thus far has not been definitively linked to RSTS.

A Gut Feeling: Abdominal Symptoms as an Initial Presentation of EVALI.

Electronic cigarette or vaping product use-associated lung injury (EVALI) is a disease process that has become prevalent in the United States. The Centers for Disease Control and Prevention reported there have been almost 2700 cases of this condition in the United States as of January 14, 2020, with >50% of these patients aged ≤24. We present a 13-year-old boy with a history of functional abdominal pain who presented with recurrent episodes of nausea, emesis, periodic fevers, and severe episodic abdominal pain after a 12-month history of significant electronic cigarette use.

Genome analysis provides insights into microaerobic toluene-degradation pathway of Zoogloea oleivorans Buc.

Zoogloea oleivorans, capable of using toluene as a sole source of carbon and energy, was earlier found to be an active degrader under microaerobic conditions in aquifer samples. To uncover the genetic background of the ability of microaerobic toluene degradation in Z. oleivorans, the whole-genome sequence of the type strain Buc was revealed.

Nitric Oxide Dismutase () Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers.

Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via NO to N, NO is proposed to be directly disproportionated into N and O in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers.

Danger in the vapor? ECMO for adolescents with status asthmaticus after vaping.

Electronic nicotine delivery systems (ENDS) use is on the rise in the adolescent and young adult populations, especially in the wake of sweet flavored ENDS solutions and youth-targeted marketing. While the extent of effect of ENDS use and aerosolized flavorings on airway epithelium is not known, there remains significant concern that use of ENDS adversely affects airway epithelial function, particularly in populations with asthma. In this case series, we review two cases of adolescents with history of recent and past ENDS use and asthma who required veno-venous extracorporeal membrane oxygenation (VV-ECMO) for status asthmaticus in the year 2018.

Transcriptome-Stable Isotope Probing Provides Targeted Functional and Taxonomic Insights Into Microaerobic Pollutant-Degrading Aquifer Microbiota.

While most studies using RNA-stable isotope probing (SIP) to date have focused on ribosomal RNA, the detection of C-labeled mRNA has rarely been demonstrated. This approach could alleviate some of the major caveats of current non-target environmental "omics." Here, we demonstrate the feasibility of total RNA-SIP in an experiment where hydrocarbon-degrading microbes from a BTEX-contaminated aquifer were studied in microcosms with C-labeled toluene under microoxic conditions.

Elucidating carbon sources driving microbial metabolism during oil sands reclamation.

Microbial communities play key roles in remediation and reclamation of contaminated environments via biogeochemical cycling of organic and inorganic components. Understanding the trends in in situ microbial community abundance, metabolism and carbon sources is therefore a crucial component of effective site management. The focus of this study was to use radiocarbon analysis to elucidate the carbon sources driving microbial metabolism within the first pilot wetland reclamation project in the Alberta oil sands region where the observation of HS had indicated the occurrence of microbial sulphate reduction.

Unexpected Diversity and High Abundance of Putative Nitric Oxide Dismutase (Nod) Genes in Contaminated Aquifers and Wastewater Treatment Systems.

Unlabelled: It has recently been suggested that oxygenic dismutation of NO into N and O may occur in the anaerobic methanotrophic "Candidatus Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment.

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes.

Stable isotope probing of RNA has enthused researchers right from its first introduction in 2002. The concept of a labelling-based detection of process-targeted microbes independent of cellular replication or growth has allowed for a much more direct handle on functionally relevant microbiota than by labelling of other biomarkers. This has led to a widespread application of the technology, and breakthroughs in our understanding of carbon flow in natural microbiomes, autotrophic and heterotrophic physiologies, microbial food webs, host-microbe interactions and environmental biotechnology.