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Morris, D.

Publications and source records attributed to Morris, D..

At least 19 recordsLinked to original sources

DroneMegaDetector, A Generalised Model For Detecting Large Mammals In Aerial Imagery

Large-scale drone surveys can generate imagery across substantial geographic areas, but automated analysis remains challenging because animal appearance, target density, imaging conditions and target scale can vary considerably between surveys. We present a general-purpose RF-DETR Medium object detector developed for large-scale aerial drone imagery and evaluate its ability to generalise across taxa, environments and survey conditions. Unlike specialist counting systems that primarily return point detections, the proposed detector produces explicit bounding boxes, providing a spatial representation that can support counting as well as downstream detection, classification and tracking workflows. We evaluated the detector on an internal held-out test set and independent external datasets spanning cattle, birds, caribou and hippopotamuses, together with imagery acquired under substantially different survey conditions. On the comparative Cattle dataset, RF-DETR matched OWL across the reported point-localisation and counting metrics, while on Caribou it achieved almost identical point-based detection performance and similar aggregate counting error. Performance varied across the broader external benchmark, with reduced transfer to unseen avian imagery and differences between models across datasets. At high altitude on SAVMAP, all evaluated approaches experienced substantial performance degradation, demonstrating a shared limitation associated with small target scale. Overall, the results show that a general-purpose detector trained on heterogeneous drone imagery can provide competitive localisation and counting performance across diverse datasets while retaining explicit bounding-box outputs. The trained model weights and inference code are provided online to support reproducible large-scale aerial wildlife monitoring and further development of drone-based computer-vision workflows.

ecology↗

Single-time-point shotgun metagenomics of four Irish Integrated Constructed Wetlands reveals microbial dynamics in wastewater treatment.

Over the past 20 years, the Integrated Constructed Wetland (ICW) concept has been applied in Ireland for wastewater treatment, offering a nature-based solution for reducing pollutants and antimicrobial resistance genes (ARGs) in effluents and receiving environments. However, wastewater microbial communities remain inadequately characterized and their dynamics across treatment largely unexplored. Here, we present a culture-independent investigation of four Irish ICWs, aiming to advance our understanding of microbial dynamics in wastewater treatment. Shotgun metagenomic sequencing was conducted on influent and effluent samples collected in biological triplicates from four ICWs treating agricultural, companion animal, industrial, and municipal wastewater, alongside eight positive and ten negative controls for filtering and sequencing. End-to-end metagenomic analysis was performed with SqueezeMeta. Taxonomic placement of high-quality metagenome-assembled-genomes (HQ-MAGs) was confirmed with GTDB-Tk. Decontamination and statistical analyses were conducted in R. Coassembled contigs were screened for ARGs, virulence- and plasmid-associated sequences. Results revealed statistically significant shifts in taxonomic and functional profiles across treatment. Effluent populations exhibited generally higher richness than corresponding influents, yet were more similar to one another across locations. Multi-log-scale increases were observed in the relative abundance of environmental genera (Legionella, Methylotenera, Thiothrix), alongside reductions in common faecal/human indicators (Bacteroides, Lactococcus, Prevotella), and up to 80% ARGs removal. Collectively, our findings provide insights into ICW efficacy, showing that they can drive marked shifts in wastewater microbiome and ARG reduction. Our culture-independent approach retrieved 34 HQ-MAGs, including 19 potentially novel taxa, uncovering previously uncharacterized microbial diversity that is potentially unique to the Irish environment and warrants further investigation.

microbiology↗

Life without cytoplasm: sperm sustain protein production utilizing cytoplasmic droplets and mitochondria as translational apparatuses

Sperm present a unique paradox: heavily compacted chromatin silences transcription, and loss of cytoplasm during spermiation eliminates the conventional translational apparatus, yet sperm require [~]10 days of protein-demanding epididymal maturation to acquire motility and fertilization competence. How sperm produce the necessary proteins has remained enigmatic. Here, we show that mammalian sperm sustain protein synthesis through a biphasic translational program. In testicular sperm, a residual cytoplasmic droplet retains the full complement of translational machinery, including ribosomes and intact tRNAs, and supports nascent protein synthesis. As sperm enter the epididymis, this droplet is progressively fragmented, and protein synthesis shifts to the midpiece, where mitochondrial translation machinery becomes active. Proteomic and functional analyses indicate that both systems contribute to sperm maturation. Inhibiting cytoplasmic translation in testicular sperm or mitochondrial translation in epididymal sperm abolishes motility. These findings reveal how cytoplasm-free sperm overcome transcriptional silence to complete maturation and support male fertility. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/744062v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@e4285forg.highwire.dtl.DTLVardef@11685d7org.highwire.dtl.DTLVardef@1ad1913org.highwire.dtl.DTLVardef@1495d6a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Exposure route drives SARS-CoV-2 infection patterns in non-human primates

Public health policy and clinical interventions against infectious diseases rely on understanding the factors that govern the initiation and progression of infections inside hosts. Animal infection experiments are essential tools to study these complex, multi-scale processes under controlled conditions, and they have shown that the dose and route of exposure can influence within-host disease dynamics. However, observed differences are difficult to quantify and to disentangle from confounding factors because small sample sizes limit the statistical power and scientific scope of individual studies. Here, by compiling and analyzing the largest published database of non-human primate challenge experiments (107 studies; 721 animals; 22,183 observations), we quantify how exposure conditions and demographic factors shape within-host SARS-CoV-2 infection kinetics in the respiratory and gastrointestinal tracts. We show that exposure route has stronger effects on kinetics than dose, age, sex, or species, with directly exposed tissues exhibiting distinct spatiotemporal kinetics from non-exposed tissues. We estimate 50% infectious doses for different tissues and show that they vary greatly (from <101.2 up to >107.4 pfu) depending on the exposure route. We find that dose effects on kinetics are also route-and tissue-specific, primarily influencing nasally-inoculated animals. Our results suggest that exposure route drives infection kinetics more strongly than dose in a critical model system for translational medicine, and they demonstrate the untapped potential for meta-analysis to extract additional insights from costly animal experiments.

microbiology↗

STING activation reshapes the tumor microenvironment leading to tumor regression in osteosarcoma

Osteosarcomas are characterized by a high degree of aneuploidy, chromothripsis and micronuclei, yet these tumors typically have an immunosuppressive, macrophage-rich, T-cell depleted tumor microenvironment. cGAS-STING dysregulation is a possible mechanism by which immune activation in response to tumor genomic instability could be repressed. We identified almost universal repression of cGAS or STING in human osteosarcomas. However, a STING-activation gene signature was predictive of survival in osteosarcoma patients suggesting potential for activation of this pathway in the osteosarcoma tumor microenvironment. Indeed, in immunocompetent osteosarcoma models, systemic STING agonism led to complete regression and induced lasting immunologic memory. Host STING activation is sufficient to promote this anti-tumor immunity even in the absence of tumor STING. These results nominate the cGAS-STING pathway as an important therapeutic target in osteosarcoma, a disease in which no new curative therapies have been developed in the last 40 years. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/684275v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@15b1e5corg.highwire.dtl.DTLVardef@12650aaorg.highwire.dtl.DTLVardef@79ef71org.highwire.dtl.DTLVardef@15704c9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Quantifying ecosystem degradation via energetic deficits

Ecosystem degradation is accelerating, threatening biodiversity and human economies. Quantifying this degradation relative to a reference baseline remains a key challenge. Yet, this quantification is essential to provide the necessary resources to regenerate ecosystems. We address this challenge by studying the energetics of population dynamics, where energy inputs such as sunlight and rainfall are transformed into other forms of energy embodied as biomass. This approach provides a unifying framework to quantify degradation across diverse ecosystems via the energetic ecodeficit: the extra energy supply the degraded ecosystem would require to regenerate to a reference state. This energetic deficit can then be translated into a monetary ecodeficit, representing the economic cost of regeneration, considering the local cost of embodied energy. Our analysis reveals nonlinear relationships between biomass loss and energetic ecodeficit, including points of no return beyond which restoration becomes economically infeasible. We showcase our methodology using the current mammal deficits across the African savanna, finding that the monetary ecodefict is about 100 times larger than current estimates. Our work demonstrates how integrating energetic principles into conservation planning can transform ecosystem valuation globally, linking ecosystems and economies sustainably.

ecology↗

High Enzyme Promiscuity in Lignin Degradation Mechanisms in Rhodopseudomonas palustris CGA009

Lignin is a universal waste product of the agricultural industry and is currently seen as a potential feedstock for more sustainable manufacturing. While it is the second most abundant biopolymer in the world, most of it is currently burned as it is a very recalcitrant material. Many recent studies, however, have demonstrated the viability of biocatalysis to improve the value of this feedstock and convert it into more useful chemicals, such as polyhydroxybutyrate, and clean fuels like hydrogen and n-butanol. Rhodopseudomonas palustris is a gram-negative bacterium which demonstrates a plethora of desirable metabolic capabilities, including aromatic catabolism useful for lignin degradation. This study uses a multi-omics approach, including the first usage of CRISPRi in R. palustris, to investigate the lignin consumption mechanisms of R. palustris, the essentiality of redox homeostasis to lignin consumption, elucidate a potential lignin catabolic superpathway, and enable more economically viable sustainable lignin valorization processes.

bioengineering↗

Heterologous expression of critical pathway genes leads to complex pattern of increased yield of bioplastic precursors in Paraburkholderia sacchari ITP 101

Recent research endeavors have turned to sustainably generating useful chemicals from biological platforms. However, conventional model organisms, such as Escherichia coli and Saccharomyces cerevisiae, face limitations, particularly in terms of substrate range and yield for certain metabolites. In this study, we share our work toward the development of the non-model bacterium, Paraburkholderia sacchari (hereafter P. sacchari), as a microbial factory for the production of polyhydroxyalkanoates (PHAs), which are precursors for biodegradable plastic. The particular PHAs of interest produced by P. sacchari include poly(3-hydroxybutyrate) (PHB) and the co-polymer produced by the combination of PHB and 3-hydroxyvalerate (3HV) called poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). P. sacchari produces PHB from mixtures of hexose and pentose sugars commonly found in lignocellulosic biomass, however PHBV requires co-feeding with propionate. Both plastic precursors have industrial interest, so both PHB and 3HV were chosen as production targets. Due to studies in other bacteria demonstrating PHB yield can be improved by overexpressing genes for critical pathway enzymes, we hypothesized there is a bottleneck in the production pathway leading to PHB in P. sacchari as well. To explore this, heterologous genes coding for the three critical enzymes were taken from Cupriavidus necator H16 (hereafter C. necator) and inserted via plasmid; phaA and bktb (homologous genes for {beta}-ketothiolase), phaB (acetyl-CoA reductase), and phaC (PHA polymerase). PHB production increased following overexpression of phaB, indicating acetoacetyl-CoA as the limiting enzyme. In fact, overexpression of phaB with the synthetic Anderson promoter, BBa_J23 104, increased titer by 162% over wildtype. On the other hand, strategies to improve 3HV had mixed results. Heterologous overexpression of propionyl-CoA transferase (pct from C. necator), which converts propionate into propionyl-CoA-the starting substrate for the 3HVproduction, showed a 145% increase in 3HV. Yet, internal sourcing of propionyl-CoA from succinyl-CoA following introduction of the sleeping beauty mutase (sbm) operon from E. coli showed no 3HV production. To this end, Max/Min Driving Force (MDF) thermodynamic analysis of critical PHBV pathways revealed two major limitations of 3HV production: 1) internal sourcing is not thermodynamically favorable; and 2) recycling of propionyl-CoA through the methyl citrate cycle (MCC) is more favorable than 3HV formation. Overall, we have shown promising progress and suggest future directions toward an industrially useful strain of P. sacchari for PHB and PHBV production. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/624694v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1942ebaorg.highwire.dtl.DTLVardef@187ec83org.highwire.dtl.DTLVardef@b8b439org.highwire.dtl.DTLVardef@4015d6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsParaburkholderia sacchari has interest as a bioproduction platform for PHAs from complex feedstocks. Removal of PHA pathway bottleneck increases PHB yield by 162%. Improved conversion of fed-in propionate increases 3HV yield by 145%. Internal sourcing of propionyl-CoA does not successfully yield 3HV. Thermodynamic analysis provides insight into difficult conversion of propionyl-CoA to 3HV.

bioengineering↗

Soil communities following clearcut and salvage harvest have different early successional dynamics compared with post-wildfire patterns

Understanding the impacts of harvest and subsequent silviculture practices at stand scales on the below-ground biota, and their associated nutrient cycling processes, is needed to more fully evaluate the sustainable management of boreal forest systems. While stand replacing wildfire is the primary natural disturbance mechanism in jack pine-dominated boreal forest systems; clearcut harvest also results in stand renewal so is sometimes used in silvicultural systems to emulate natural disturbance and renewal processes. In this study, we simultaneously assessed the successional trajectories of three major taxa of the below ground soil community, bacteria, fungi, and arthropods using DNA metabarcoding. The objectives of this study were to use a chronosequence framework to: 1) assess whether the soil communities following clearcut harvest and wildfire converge along a successional gradient, 2) assess when the soil community recovers following clearcut harvest to the pre-disturbance, mature, wildfire reference condition, and 3) assess the effects of cumulative disturbance on soil community succession (i.e., wildfire followed by salvage harvesting of fire-killed trees). We found that richness (alpha diversity) did not illustrate any clear patterns of convergence and could, therefore, underestimate recovery times, especially for soil arthropods. Comparisons of the underlying community composition (beta diversity) proved to be more informative. In this case, we found that different soil taxa following clearcut harvest recovered on different timelines compared with succession following stand-replacing wildfire. In general, bacteria appear to be the first to converge to post-wildfire conditions followed by arthropods, however, fungi did not converge within the time frame of the chronosequence. This suggests that more extended periods are required to achieve complete recovery of the soil fungal community to the pre-disturbance condition. The cumulative disturbance associated with salvage harvest appeared to have a greater (compounded) effect on soil communities when compared with wildfire or clearcut harvest. This work showcases the performance of a scalable method for monitoring a diverse arrange of soil biota using DNA metabarcoding. In future work, tracking fungal and arthropod soil communities may provide more insights into the longer-term effects of current forest management practices and provide guidance when comparing alternative approaches. Open Research StatementSequences have been deposited to the NCBI SRA under the GRDI-Ecobiomics project accession PRJNA565010 for the BioSample accessions SAMN26926703 - SAMN26926795 used in this study. The MetaWorks v1.9.3 multi-marker metabarcode bioinformatic pipeline is available from https://github.com/terrimporter/MetaWorks. The ITS classifier based on the ITS UNITE+INSD full dataset v8.2 and trained to work with the RDP Classifier (https://github.com/terrimporter/UNITE_ITSClassifier). The COI classifier v4 is available from https://github.com/terrimporter/CO1Classifier. The code used to produce figures, including infile and metadata files, will be available on https://github.com/terrimporter/Chronosequence_HarvestType.

ecology↗

Environmental stability of HPAIV H5N1 in raw milk, wastewater and on surfaces

H5N1 influenza outbreaks in dairy cows necessitate studying potential transmission routes among livestock and to humans. We measured the stability of infectious H5N1 influenza virus in raw milk, wastewater, and on contaminated surfaces. We found relatively slow decay in milk, indicating that contaminated milk and fomites pose plausible transmission risks.

microbiology↗

The Rapidly Evolving X-linked miR-506 Family Finetunes Spermatogenesis to Enhance Sperm Competition

Despite rapid evolution across eutherian mammals, the X-linked miR-506 family miRNAs are located in a region flanked by two highly conserved protein-coding genes (Slitrk2 and Fmr1) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linked miR-506 family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernable defects, but simultaneous ablation of five clusters containing nineteen members of the miR-506 family led to reduced male fertility in mice. Despite normal sperm counts, motility and morphology, the KO sperm were less competitive than wild-type sperm when subjected to a polyandrous mating scheme. Transcriptomic and bioinformatic analyses revealed that these X-linked miR-506 family miRNAs, in addition to targeting a set of conserved genes, have more targets that are critical for spermatogenesis and embryonic development during evolution. Our data suggest that the miR-506 family miRNAs function to enhance sperm competitiveness and reproductive fitness of the male by finetuning gene expression during spermatogenesis. Significance StatementThe X-linked miR-506 family has rapidly evolved in mammals, but their physiological significance remains elusive. Given their abundant and preferential expression in the testis and sperm, these X-linked miRNAs likely play a functional role in spermatogenesis and/or early embryonic development. However, the deletion of either individual miRNA genes or all of the five miRNA clusters encoding 38 mature miRNAs did not cause major fertility defects in mice. When these mutant males were subjected to conditions resembling polyandrous mating, the mutant sperm were much less competitive than the wild-type sperm, rendering the mutant males "functionally sub-fertile". Our data suggest that the miR-506 family of miRNAs regulates sperm competition and the reproductive fitness of the male.

developmental biology↗

Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station.

Klebsiella species, including Klebsiella pneumoniae, Klebsiella aerogenes, and Klebsiella quasipneumoniae, are opportunistic pathogens that are known to cause infections in humans. Hypervirulent Klebsiella pneumoniae (hvKP) is a subgroup of K. pneumoniae that has gained attention due to its global dissemination and its ability to cause invasive infections in community settings amongst immunocompetent individuals as well as its increasing levels of antibiotic resistance. Our study reports the first complete genotypic analysis including mobile genetic elements (MGEs) of Klebsiella isolates from the International Space Station (ISS). The genomes of K. pneumoniae, K. aerogenes, and K. quasipneumoniae provided valuable insights into their antimicrobial resistance, virulence, thermotolerance, disinfectant resistance, and MGEs. All isolates belonged to emerging lineages with pathogenic potential, with K. quasipneumoniae ST138 presenting spatial and temporal persistence aboard the ISS, possibly due to its genotypic profile encoding for numerous resistance genes to disinfectants and heavy metals. We also report on the isolation of a yersiniabactin encoding K. pneumoniae, belonging to the emerging high-risk ST101 clone, aboard the ISS. Potential dissemination of hvKp strains on ISS could pose a putative risk to the immunocompromised crew. The presence of MGEs containing virulent loci could facilitate horizontal gene transfer to other benign microorganisms on the ISS, potentially increasing their virulence. In addition, genetic divergence from their respective lineages for some Klebsiella genomes was predicted and hypothesized to be due to the unique spaceflight environmental pressures. These findings highlight the importance of monitoring problematic microbial communities in space to understand their surviving abilities and potential impact on human health. ImportanceThe International Space Station (ISS) is a unique hermetically sealed environment that poses environmental pressures not encountered on Earth, including microgravity and radiation While the adaptability of bacteria during spaceflight is not fully understood, recent research has suggested that it may be species and even clone specific. Given the spaceflight-induced suppression of the human immune system, it is essential to understand the genomics of potential human pathogens in spaceflight. Such understanding could provide valuable insights into species and lineages of medical astromicrobiological importance. Here, we used hybrid assembly approaches and comparative genomics to provide the first comprehensive genomic characterisation of 10 Klebsiella isolates retrieved from the ISS. Our findings revealed that K. quasipneumoniae ST138 exhibits spatial and temporal persistence aboard the ISS, with evidence of genomic divergence from the ST138 lineage on Earth. Additionally, we characterized plasmids from Klebsiella species of ISS origin, which encoded disinfectant and thermoresistance genes suggesting that these might aid adaptability. Furthermore, we identified an MGE containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high risk" ST101 clone. Our work provides valuable insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the behaviour of potential pathogenic bacteria in space.

microbiology↗

ATP is a major determinant of phototrophic bacterial longevity in growth arrest.

How bacteria transition into growth arrest as part of stationary phase has been well-studied, but our knowledge of features that help cells to stay alive in the following days and weeks is incomplete. Most studies have used heterotrophic bacteria that are growth-arrested by depletion of substrates used for both biosynthesis and energy generation, making is difficult to disentangle the effects of the two. In contrast, when grown anaerobically in light, the phototrophic bacterium Rhodopseudomonas palustris generates ATP from light via cyclic photophosphorylation and builds biomolecules from organic substrates such as acetate. As such, energy generation and carbon utilization are independent from one another. Here we compared the physiological and molecular responses of R. palustris to growth arrest caused by carbon source depletion in light (energy-replete) and dark (energy-depleted) conditions. Both sets of cells remained viable for six to ten days, at which point dark-incubated cells lost viability whereas light-incubated cells remained fully viable for 60 days. Dark-incubated cells were depleted in intracellular ATP prior to losing viability, suggesting that ATP depletion is a cause of cell death. Dark-incubated cells also shut down measurable protein synthesis, whereas light-incubated cells continued to synthesize proteins at low levels. Cells incubated in both conditions continued to transcribe genes. We suggest that R. palustris may completely shut down protein synthesis in dark, energy-depleted, conditions as a strategy to survive the nighttime hours of day/night cycles it experiences in nature, where there is a predictable source of energy in the form of sunlight during days. IMPORTANCEThe molecular and physiological basis of bacterial longevity in growth arrest is important to investigate for several reasons. Such investigations could improve treatment of chronic infections, advance use of non-growing bacteria as biocatalysts to make high yields of value-added products, and improve estimates of microbial activities in natural habitats, where cells are often growing slowly or not at all. Here we compared survival of the phototrophic bacterium Rhodopseudomonas palustris under conditions where it generates ATP (incubation in light) and where it does not generate ATP (incubation in dark) to directly assess effects of energy depletion on long-term viability. We found that ATP is important for long-term survival over weeks. However, R. palustris survives 12h periods of ATP depletion without loss of viability, apparently in anticipation of sunrise and restoration of its ability to generate ATP. Our work suggests that cells respond to ATP depletion by shutting down protein synthesis.

microbiology↗

Comparative aerosol and surface stability of SARS-CoV-2 Variants of Concern

SARS-CoV-2 is transmitted principally via air; contact and fomite transmission may also occur. Variants-of-concern (VOCs) are more transmissible than ancestral SARS-CoV-2. We find that early VOCs show greater aerosol and surface stability than the early WA1 strain, but Delta and Omicron do not. Stability changes do not explain increased transmissibility.

microbiology↗

All boreal forest successional stages needed to maintain the full suite of soil biodiversity following natural wildfire in jack pine-dominated forest ecosites

Wildfire is a natural disturbance in boreal forest systems that has been predicted to increase in frequency, intensity, and extent due to climate change. Most studies tend to assess the recovery of one component of the community at a time but here we use DNA metabarcoding to simultaneously monitor soil bacteria, fungi, and arthropods along an 85-year chronosequence following wildfire in jack pine-dominated ecosites. We describe soil successional and community assembly processes to better inform sustainable forest management practices. Soil taxa showed different recovery trajectories following wildfire. Bacteria shared a large core community across stand development stages (~ 95-97% of their unique sequences) and appeared to recover relatively quickly by crown closure. By comparison fungi and arthropods shared smaller core communities (64-77% and 68-69%, respectively) and each stage appeared to support unique biodiversity. We show the importance of maintaining a mosaic ecosystem that represents each stand development stage to maintain the full suite of biodiversity in soils following wildfire, especially for fungi and arthropods. These results will provide a useful baseline for comparison when assessing the effects of human disturbance such as harvest or for assessing the effects of more frequent wildfire events due to climate change.

ecology↗

First reported detection of the mobile colistin resistance genes, mcr-8 and mcr-9, in the Irish environment

The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eight mcr positive Enterobacterales (one mcr-8 and seven mcr-9) were recovered from six samples (freshwater (n=2), healthcare facility wastewater (n=2), wastewater treatment plant influent (n=1) and integrated constructed wetland influent (piggery farm waste) (n=1)). While the mcr-8 positive K. pneumoniae displayed resistance to colistin, all seven mcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 {+/-} 4.1 (10-61), including the carbapenemases, blaOXA-48 (n=2) and blaNDM-1 (n=1), which were harboured by three of the isolates. The mcr genes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs of mcr genes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.

microbiology↗

A role for myeloid miR-155 in regulating hypoxia induced seizures in neonatal C57BL/J6 mice

Hypoxic ischaemic injury (HIE) in the neonatal brain has significant consequences on neurodevelopment and increases the occurrence of neurological deficits in infants. HIE is also a leading cause of neonatal seizures. Therapeutic options for the treatment of HIE are very limited. Hypoxia-ischemia directly damages brain tissue in a primary-wave of injury which activates a cascade of events triggering local and systemic inflammatory responses, driven by the innate immune system, which contribute to a significant secondary-wave of injury taking place as early as 6 hours post-hypoxia-ischaemia. Levels of the well documented inflammatory microRNA, miR-155 are elevated in rodent seizure and epilepsy models. Here, we assessed the impact of, miR-155 deletion in myeloid cells, on regulating inflammation and seizure severity in a preclinical model of neonatal hypoxia-induced seizures (Hypoxia-Sz). Wildtype miR-155 (miR-155+/+LysMCre) mice were compared to a mouse line in which miR-155 was deleted in myeloid cells (miR-155fl/fl LysMCre). We demonstrate significant upregulation of miR-155 target genes, brain-derived neurotrophic factor (bdnf), arginase-2 (arg-2), ship-1 and socs-1 in miR-155fl/fl LysMCre mice compared to controls at various time points following Hypoxia-Sz. Conversely, we report decreased mRNA levels of pro-inflammatory cytokines IL-1{beta} and IL-6 and lower protein levels of IL-1{beta} in miR-155fl/fl LysMCre mice as compared to WTs. Myeloid miR-155 deletion significantly reduced behavioural seizure severity score, reduced electrographically (EEG) measured seizure frequency and seizure burden as compared to mice to wildtypes, suggesting miR-155 regulation of seizure occurrence in this model. Behavioural tests for motor functions at 5 weeks post Hypoxia-Sz demonstrated differences between genotypes. Excitingly this work highlights that inhibition of miR-155, specifically in myeloid cells, may hold therapeutic benefit for both seizures and comorbidities associated with hypoxic brain injury.

neuroscience↗

Fungal community dynamics and carbon mineralization in coarse woody debris across decay stage, tree species, and stand development stage in northern boreal forests

Fungi are primary agents of coarse woody debris (CWD) decay in forests, playing an essential role in nutrient cycling and carbon storage. Characterizing fungal communities within CWD will promote further understanding of the fungal controls on CWD decomposition. We compared fungal community assemblages using alpha and beta diversity metrics, carbon mineralization, and physical and chemical properties of CWD across 3 tree species (trembling aspen [Populus tremuloides], black spruce [Picea mariana], and jack pine [Pinus banksiana]), 5 decay classes, and 2 stand development stages, differing in time-since-stand replacing disturbance (i.e., young/self-thinning and mature/steady-state) in Ontarios boreal forest region. In total, we sampled 180 individual CWD logs from 6 independent stands, with 3 replicates per each species x decay class combination at each site. We found that fungal community structure significantly differed across tree species, decay stage, and stand age. Higher proportions of white rot fungi were found in trembling aspen CWD, whereas higher proportions of brown rot fungi were found in black spruce and jack pine CWD. Proportions of specialized wood decay fungi increased with decay stage and were higher in CWD located in mature forest stands. Fungal diversity was highest in decay class 4 CWD. We found that Mn and K concentrations, total carbon, C/N ratio, carbon mineralization (mg CO2 g dry CWD-1 d-1), and moisture content were important predictors of fungal composition across CWD species and/or decay stage, though how CWD chemistry influences fungal species composition (and vice versa) is unknown. Carbon mineralization was highest in trembling aspen CWD and increased with decay stage, perhaps facilitated by increased N concentrations. This study suggests that forest management guidelines that consider both deadwood quantity and quality will support a broader range of fungal species and communities through post-disturbance stand development, thereby conserving biodiversity over the longer-term in our managed forest systems.

ecology↗