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An oil spill is a catastrophic event that results in various toxic polycyclic aromatic hydrocarbons (PAHs) entering the environment. Polycyclic aromatic nitrogen heterocycles (PANHs) are more toxic to the environment than their parent PAHs. The high cost and paucity of available PANH standards, the lower abundance of PANHs relative to PAHs, and the difficult separation due to co-elution with PAHs have all contributed to the scarcity of related published literature on the determination of these compounds. To overcome these challenges, a new quantitative method has been successfully developed and validated for the inclusion of 113 polycyclic aromatic carbon (PAC) compounds in a single injection. The 113 compounds consist of PAHs, nitrogen heterocycles, sulfur heterocycles, and alkylated equivalents. Distinct separation of the PANHs and their alkylated counterparts (APANHs) from PAHs was achieved using a gas chromatography quadrupole time-of-flight (GC-QToF) mass spectrometer. The instrument resolved compounds by the high-resolution extraction of monoisotopic masses, allowing response correction factors (RCFs) to be determined from available PANH standards and to calculate concentrations from PAH calibration standards. The developed method was applicable to crude oil samples, generating concentrations of PANHs and relevant information on compound stability for use in oil spill forensics investigation. Development of this practical PAC method provides a powerful tool for screening toxic contaminants, assessing environmental impact, and monitoring recovery following an oil spill. [ABSTRACT FROM AUTHOR]

Antibiotic resistance is recognized as an imminent and growing global health threat. New antimicrobial drugs are urgently needed due to the decreasing effectiveness of conventional small‐molecule antibiotics. Antimicrobial peptides (AMPs), a class of host defense peptides, are emerging as promising candidates to address this need. The potential sequence space of amino acids is combinatorially vast, making it possible to extend the current arsenal of antimicrobial agents with a practically infinite number of new peptide‐based candidates. However, mining naturally occurring AMPs, whether directly by wet lab screening methods or aided by bioinformatics prediction tools, has its theoretical limit regarding the number of samples or genomic/transcriptomic resources researchers have access to. Further, manually designing novel synthetic AMPs requires prior field knowledge, restricting its throughput. In silico sequence generation methods are gaining interest as a high‐throughput solution to the problem. Here, we introduce AMPd‐Up, a recurrent neural network based tool for de novo AMP design, and demonstrate its utility over existing methods. Validation of candidates designed by AMPd‐Up through antimicrobial susceptibility testing revealed that 40 of the 58 generated sequences possessed antimicrobial activity against Escherichia coli and/or Staphylococcus aureus. These results illustrate that AMPd‐Up can be used to design novel synthetic AMPs with potent activities. [ABSTRACT FROM AUTHOR]

Objective: Environmental DNA (eDNA) detection is a transformative tool for ecological surveys which in many cases offers greater accuracy and cost-effectiveness for tracking low-density, cryptic species compared to conventional methods. For the use of targeted quantitative PCR (qPCR)-based eDNA detection, protocols typically require freshly prepared reagents for each sample, necessitating systematic evaluation of reagent stability within the functional context of eDNA standard curve preparation and environmental sample evaluation. Herein, we assessed the effects of long-term storage and freeze–thaw cycles on qPCR reagents for eDNA analysis across six assays. Results: Results demonstrate qPCR plates (containing pre-made PCR mix, primer-probe, and DNA template) remain stable at 4 °C for three days before thermocycling without fidelity loss irrespective of qPCR assay used. Primer-probe mixes remain stable for five months of − 20 °C storage with monthly freeze-thaw cycles also irrespective of qPCR assay used. Synthetic DNA stocks maintain consistency in standard curves and sensitivity for three months under the same conditions. These findings enhance our comprehension of qPCR reagent stability, facilitating streamlined eDNA workflows by minimizing repetitive reagent preparations. [ABSTRACT FROM AUTHOR]

Knowledge of the ecological mechanisms governing N2O cycling in marine sediments lags that of water columns and terrestrial soils, leaving much to be learned about how microbial community dynamics relate to variability in sediment N2O fluxes. The present study assesses these relationships across two distinct environments by focusing on the community structure and activity of N2O reducing microorganisms. The N2O sink capacity of minimally impacted Bermudian mangrove sediments was first estimated using trace‐level microsensors and profile interpretation modeling. Molecular data obtained from these sediments were then compared with those from the Northeast Subarctic Pacific (NESAP) outer continental margin, where previous measurements suggest considerable N2O effluxes. Net N2O uptake was observed for mangrove sediments under ambient and elevated dissolved inorganic nitrogen concentrations (−0.22 ± 0.15 to −0.30 ± 0.26 μmol N2O m−2 d−1), suggesting the microbial potential for N2O consumption exceeded the potential for production via combined nitrification and denitrification. Targeting of bacterial nosZI and nosII gene clusters for quantification using qPCR indicated higher abundance and expression of non‐denitrifier nosZII genes in mangrove sediments demonstrating net N2O uptake. Net N2O production in NESAP sediments was associated with higher abundance and expression of nosZI genes associated with canonical denitrifiers. These results suggest that organisms possessing atypical nosZII genes may act as important N2O scavengers in low‐nitrogen coastal sediments. Plain Language Summary: Nitrous oxide (N2O) is potent greenhouse gas that contributes to ozone depletion in the stratosphere, and atmospheric concentrations a rising as a result of human activities. The production and consumption of N2O in the environment is mediated by microorganisms, and the balance between the two processes is governed by environmental factors such as concentrations of dissolved oxygen and fixed nitrogen. However, little is known about the relationships between microbial community dynamics and rates of N2O production and consumption, especially in sediment environments. We found that minimally impacted mangrove sediments of Bermuda are net consumers of N2O, and continue to consume N2O following short term nitrogen enrichments. This N2O sink capacity was linked to higher abundances and activity levels of atypical N2O reductase genes when compared to sediments that produce N2O. These genes facilitate the consumption of N2O, and frequently occur in microbes that do not have the capacity to produce N2O via denitrification. This study provides further insight into the role of microbial community structure in regulating sediment N2O cycling, and argues for targeted conservation and restoration of coastal systems where sediment environments are in close proximity to the atmosphere. Key Points: The N2O sink capacity of minimally impacted Bermudian mangrove sediments is resilient against modest, short‐term nutrient enrichmentHigh prevalence of non‐denitrifier nosZII genes in mangrove sediments implies a crucial role as N2O scavengers in low‐nitrogen systemsNet N2O production in NESAP sediments is associated with higher expression of nosZI genes associated with canonical denitrifiers [ABSTRACT FROM AUTHOR]

Abstract Background Within chromatin, the histone variant H2A.Z plays a role in many diverse nuclear processes including transcription, preventing the spread of heterochromatin and epigenetic transcriptional memory. The molecular mechanisms of how H2A.Z mediates its effects are not entirely understood. However, it is now known that H2A.Z has two protein isoforms in vertebrates, H2A.Z-1 and H2A.Z-2, which are encoded by separate genes and differ by 3 amino acid residues. Results We report that H2A.Z-1 and H2A.Z-2 are expressed across a wide range of human tissues, they are both acetylated at lysine residues within the N-terminal region and they exhibit similar, but nonidentical, distributions within chromatin. Our results suggest that H2A.Z-2 preferentially associates with H3 trimethylated at lysine 4 compared to H2A.Z-1. The phylogenetic analysis of the promoter regions of H2A.Z-1 and H2A.Z-2 indicate that they have evolved separately during vertebrate evolution. Conclusions Our biochemical, gene expression, and phylogenetic data suggest that the H2A.Z-1 and H2A.Z-2 variants function similarly yet they may have acquired a degree of functional independence.