Biology subjects

Davies, K.

Publications and source records attributed to Davies, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Order Matters: Ambient RNA correction confounds doublet detection in single-cell RNA sequencing

A common technical artifact in droplet-based single-cell RNA sequencing (scRNA-seq) is the capture of two cells in the same droplet, termed doublets. Doublets may present as hybrid cell types, and their removal is a critical step during quality control. Another form of contamination is ambient RNA, which originates from free floating RNA released from other cells in suspension, likely during cell death. As with doublets, ambient RNA results in unexpected gene expression patterns. Most suggested analysis pipelines include ambient RNA correction before doublet detection however no formal investigation into how doublet detection is affected by ambient RNA correction has been conducted. Here, we evaluate the impact of ambient RNA correction on the performance of doublet detection using novel engineered and multiplexed datasets. We apply three of the most widely-used methods for removing ambient RNA (decontX, soupX, CellBender), in conjunction with up to six doublet detection methods (scDblFinder, scds, bcds, cxds, scrublet, DoubletDetection). We find that doublet detection tools perform best when done prior to ambient RNA correction, with the exception of CellBender. Performing ambient RNA correction first, particularly for decontX, leads to an increased proportion of doublet droplets retained in the dataset compared with calling doublets on uncorrected data. We show that both decontX and soupX partially mask doublet signal by removing proportionally more ambient RNA from doublets that remain undetected after ambient RNA correction. Our results show that the performance of doublet detection is significantly impacted by the use of ambient RNA correction tools. We suggest a new workflow that implements doublet detection prior to ambient RNA correction unless using CellBender.

bioinformatics↗

bioRxiv2026

First detected incursions of avian influenza H5N1 clade 2.3.4.4b into mainland Australia from the Southern Ocean

High pathogenicity avian influenza H5N1 clade 2.3.4.4b has caused a panzootic of devastating impact to poultry and wildlife globally. The Australian continent and broader Oceania until recently remained the last major region without confirmed detections. Here we report the first H5N1 clade 2.3.4.4b detections from two live seabirds - a brown skua and a southern giant petrel - found on the south coast of Western Australia in June 2026. Virus genome sequencing showed that both viruses were most closely related to H5N1 viruses detected recently on sub-Antarctic islands in the Southern Indian Ocean. In time-calibrated phylogeographic analyses, both viruses sampled in Western Australia clustered with viruses from Heard Island, a sub-Antarctic external territory of Australia. Ancestral location reconstruction also identified Heard Island as the most probable source location, although unsampled intermediate locations cannot be excluded. The two Western Australian detections were estimated to be independent incursions from Heard Island, rather than local transmission on mainland Australia. There was no evidence of reassortment with endemic avian influenza viruses in Australia, and both virus sequences retained key avian-like genetic markers and lacked known substitutions for reduced antiviral susceptibility. These detections revealed a Southern Ocean pathway of recurrent H5N1 incursions into Australia, highlighting the risk of potential establishment on the mainland and the need for heightened surveillance and rapid, nationally-coordinated, virus genomic characterisation.

microbiology↗

bioRxiv2026

Functional divergence of the NSs protein defines interferon antagonism and viral fitness across Bhanja virus lineages.

Bhanja virus (BHAV) is a tick-borne bandavirus (Family Phenuiviridae) with a broad geographic distribution and documented neuroinvasive capacity, yet its molecular biology remains poorly understood. Within the genus Bandavirus, the non-structural protein NSs functions as the primary antagonist of innate immune responses, although mechanistic details for BHAV remain unknown. We established a reverse genetics platform for BHAV by combining virion RNA sequencing with terminal untranslated region mapping, enabling generation of recombinant viruses and systematic investigation of viral determinants. Using this system, we characterized recombinant BHAV replication in mammalian and arthropod cell lines and demonstrated that interferon competence is a critical determinant of viral replication in mammalian cells. Notably, we observed substantial amino acid divergence within the NSs protein across geographically distinct BHAV isolates, despite higher conservation of other viral proteins. To investigate the functional significance of this variation, we generated recombinant viruses expressing heterologous NSs proteins from African and European isolates. Viruses expressing NSs from ibAr2709 or R1819 isolates exhibited enhanced capacity to suppress interferon-beta induction compared to the prototype IG690 strain, correlating with increased viral protein accumulation in interferon-competent cells. Mechanistic studies revealed that BHAV NSs proteins inhibit interferon induction upstream of IRF3, with ibAr2709 and R1819 NSs showing selective inhibition of TBK1 phosphorylation. However, unlike highly pathogenic bandaviruses such as severe fever with thrombocytopenia syndrome virus (SFTSV), BHAV NSs proteins exhibit comparatively weak antagonism of downstream interferon signalling. In vivo studies using interferon alpha/beta receptor-deficient mice demonstrated that NSs sequence variation influences viral replication in splenic tissue without substantially altering disease phenotype. Together, these findings establish BHAV reverse genetics tools for future investigation and reveal how naturally-occurring NSs divergence modulates innate immune antagonism and viral fitness while maintaining an overall attenuated disease phenotype. Author SummaryBhanja virus is a tick-borne virus distributed across Asia, Africa, and Europe that causes neurological disease, yet little is known about how it replicates or evades immunity. We developed the laboratory tools to create recombinant Bhanja viruses and investigate viral functions. We discovered that the virus replicates efficiently in cells lacking interferon responses but is severely restricted in normal immune-competent cells, revealing interferon as a major barrier to viral growth. We observed that Bhanja virus isolates from distinct geographic regions have different versions of a viral protein called NSs that suppresses interferon responses. Isolates from Africa and Europe were better at blocking interferon production than the original Asian strain, correlating with increased viral growth in immune-competent cells. However, unlike related viruses that cause more serious disease such as SFTSV, BHAV NSs proteins only partially antagonise interferon. While this weak antagonism likely contributes to the attenuated phenotype observed in our experimental systems, the natural pathogenesis of Bhanja virus in human hosts and tick vectors remains to be determined. This study provides tools for examining Bhanja virus biology and demonstrates that small viral differences in viral sequence can meaningfully influence evasion of innate immunity and viral fitness without triggering severe disease.

microbiology↗

bioRxiv2026

Single-cell CRISPR activation screens in primary B cells discover gene regulatory mechanisms for hundreds of autoimmune risk loci.

Genome-wide association studies (GWAS) have discovered thousands of genetic variants linked to autoimmune disease, and yet the molecular pathways underlying autoimmunity have remained elusive. A key challenge is that >90% of identified GWAS risk loci are in non-coding genomic regions making it difficult to predict their relevance to disease. Here, we have curated fine-mapped non-coding risk variants from over 30 different autoimmune traits including common conditions such as systemic lupus erythematosus (SLE), Crohns disease, and multiple sclerosis, and reveal shared genetic signatures between diverse autoimmune diseases. We subsequently performed a high-throughput single-cell multi-omic CRISPR activation screen targeting 763 autoimmune risk loci in primary human B cells (a highly relevant cell type to autoimmune diseases) and discover 524 cis-regulatory target gene effects for 378 risk loci, with many risk loci regulating multiple gene targets. This Single Cell Analysis of Non-coding Distal Autoimmune Loci (SCANDAL) provides a powerful experimental resource linking non-coding risk loci to many disease-relevant genes, including lowly-expressed cytokines and transcription factors for which perturbation effects can be difficult to quantify with other CRISPR-based strategies. We reveal how increased transcriptional activity at one non-coding risk locus can drive transcription at other risk loci within the same regulatory landscape that may be relevant to understand genetic pleiotropy of autoimmune diseases. Finally, we quantified allele-specific effects on target gene expression with massive parallel reporter assays and prime editing to discover a gain-of-function variant associated with SLE that controls expression of the transcription factor REL/cREL which subsequently binds dozens of risk loci and target genes associated with different autoimmune diseases. Our study provides a valuable resource linking non-coding risk loci with their cis-regulatory target genes and advances our understanding of the shared genetic networks and mechanisms involved in autoimmunity.

genomics↗

bioRxiv2026

DUCK-Net: Automated deep learning segmentation of Ductular Reaction in murine liver injury captures multicellular niche dynamics from H&E morphology

Ductular Reactions (DRs) are dynamic and complex multicellular responses that occur as a result of various hepatic injuries. Precise identification and quantification of the extent of DRs is a cornerstone of pre-clinical modelling of liver disease, with links to inflammation, fibrosis, regeneration, and disease severity. Here, we apply a deep learning model, Deep Understanding Convolutional Kernel or DUCK-Net, to the automated detection and segmentation of DRs in whole-slide histopathological images of murine models of liver damage. Following annotation of a training dataset by a specialist liver histopathologist, we demonstrate accelerated performance and accurate detection, achieving a mean Dice coefficient (model-expert segmentation overlap) of 85.4% and a specificity of 98%, indicating minimal false positives. Evaluation of model validity and utility was achieved with a histological time course of cholestatic injury and recovery using 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine diet (DDC) in mice. When assessed against a multiple linear regression model incorporating core epithelial and stromal components of the DR as quantified using IHC, DUCK-Net predicted the spatiotemporal response to injury and repair/resolution with a coefficient of determination (R2) of 0.88. Moreover, DUCK-Net kinetics strongly correlated with published spatial transcriptomic (Stereo-seq) analysis of the DDC model, demonstrating that H&E-based segmentation captures molecular DR dynamics comparable to, or exceeding that of individual IHC markers without the need for immunostaining. DUCK-Net provides a novel and accessible platform for rapid, accurate histological quantification of liver injury reflective of the matrix-rich, multicellular regenerative niche observed in DRs.

cell biology↗

bioRxiv2025

SFTSV NSs protein is a novel tick antiviral RNAi response suppressor

Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne phenuivirus causing high mortality in humans. While the non-structural protein NSs is dispensable for replication in interferon-deficient mammalian cells, we demonstrate for the first time that NSs is essential for viral replication in tick cells. SFTSV infection triggers canonical Dicer-2-mediated antiviral RNA interference (RNAi) in tick cells, producing virus-derived small interfering RNAs (siRNAs) that target viral transcripts for degradation. We show that NSs functions as a viral suppressor of RNAi by selectively engaging and depleting single-stranded RNAs derived from 22-nucleotide siRNAs, likely limiting their incorporation into RNA-induced silencing complexes (RISC). Complementation with a heterologous RNAi suppressor (p19 protein) partially rescues replication of NSs-deficient virus, validating the RNAi suppressive function of NSs. These findings reveal that successful tick-borne viral replication requires host-specific immune evasion strategies and establish NSs-mediated RNAi suppression as essential for SFTSV persistence in arthropod vectors. Significance StatementThis study reveals a critical requirement for SFTSV infection that differs between hosts. While the viral NSs protein is dispensable in interferon deficient mammalian cells, it is essential for replication in tick cells, the natural vectors of the virus. We show that NSs functions as a viral RNA silencing suppressor by associating with virus derived small RNAs and limiting their availability to the tick antiviral RNA interference machinery. This provides mechanistic insight into how tick-borne viruses evade arthropod immune defences through engagement of functional siRNAs rather than broad inhibition of RNA interference pathways. Together, these findings demonstrate that SFTSV employs distinct immune evasion strategies in different hosts and identify NSs as a key determinant of vector cell infection.

microbiology↗

bioRxiv2025

Epithelial state-transitions permit inflammation-induced tumorigenesis.

Chronic inflammation across tissues is associated with an increased risk of developing cancer1-3. While potentially oncogenic somatic mutations have been demonstrated to persist and expand in healthy organs4-6, what triggers a subset of cells harbouring deleterious mutations to transition into a neoplasm or an aggressive adenoma with poor prognosis7,8 is not well-understood. Unlike normal, healthy cells, benign cells harbouring mutations perceive inflammation in chronic disease differently, potentiating the progression from physiological inflammation to tumorigenesis9. Here, we reveal that a subset of epithelial cells with mutations are poised to transition from pre-neoplastic state to early neoplasm, through rewiring of epithelial IL-1{beta} responses and inflammatory macrophage recruitment. We characterise this process by leveraging a mouse model of biliary tract cancer (cholangiocarcinoma), in which deleterious mutations are introduced to tumour suppressor genes in common cancer pathways (Trp53 and Pten), and by quantifying differences in cell states and corresponding gene expression dependencies in the absence or presence of liver inflammation. Critically, we find that targeting the epithelial-derived signals of tissue-wide inflammation (namely COX2) is insufficient to limit tumorigenesis; rather, targeting the reactivation of oncogene-induced developmental signals, such as NOTCH, prevents this pre-neoplastic to neoplastic transition, demonstrating that oncofoetal switching is a pharmacologically-tractable target in patients with a high risk of developing cancers on the background of inflammation.

cancer biology↗

bioRxiv2025

Tissue scarring provides a biomechanical framework to promote mammalian bile duct regeneration through the activation of integrin-SRC/FAK signalling.

Following chronic injury, the adult mammalian bile duct regenerates by forming new branches, essentially replumbing the ductular system to overcome blockages and breaks. To regenerate effectively, biliary epithelial cells (BECs) receive a range of pro-mitogenic signals from myofibroblasts, which concurrently deposit a collagen-rich scar around the duct as it regrows. Despite epithelial regeneration and scarring occurring side-by-side, whether the deposition of scar tissue regulates ductular regeneration per se remains unclear. By inducing ductular fibrosis and regeneration in vivo, we show that the formation of collagen-I-rich scars around regenerating ducts changes the local biomechanical properties of these tissues, promoting the growth of ducts. Critically, this changing structural landscape is perceived by a spatially restricted population of biliary epithelial cells which forms a "leading-tip" of integrin-2-high cells. This leading-tip undergoes partial-EMT-type reprogramming, allowing it to become migratory and coordinate ductular regeneration. We show that this process is directly driven through an integrin-2-SRC/FAK signalling axis; thereby connecting epithelial regeneration directly to the changing fibrotic environment in chronic ductular disease. HighlightsO_LIChronic liver disease results in the formation of stiff, collagen scars around ducts. C_LIO_LINew ducts acquire high levels of integrin-2 which is spatially localised to a "leading-tip", which loses epithelial features. C_LIO_LIIntegrin-2{beta}1-SRC/FAK signalling regulates ductular migration by linking changes in the bio-structural composition of the liver with ductular cells. C_LI

cell biology↗

bioRxiv2025

Antibody responses against bacterial glycans affinity mature and diversify in germinal centers.

Anti-carbohydrate antibodies (Abs) play crucial roles in pathogen control, but their generation remains poorly understood. By studying responses to Streptococcus pyogenes in humans, we reveal that the glycan-targeted response shifts from IgM towards IgG and IgA memory with age and antigen exposure across blood, spleen, and tonsils. Both natural colonization and controlled human infection with S. pyogenes increased class-switched B cells, with evidence of within-clone switching. Glycan-specific B cells readily participated in germinal center (GC) responses and showed robust somatic hypermutation despite a molecular signature consistent with receiving reduced T cell help. We conclude that mucosal pathogen encounters elicit glycan responses that class-switch, evolve and diversify through the GC. These findings reveal how age and infection history can influence the quality, quantity, and isotype use of glycan-specific B cells, with implications for the design and schedule of glycan-containing vaccines.

immunology↗

bioRxiv2024

NKG2A-mediated immune modulation of natural killer cells by Staphylococcus aureus

Natural killer (NK) cells are specialized lymphocytes that help protect against viruses and cancer. However, in the context of bacterial infections, NK cells can be harmful, rather than protective. Such immune pathogenesis by NK cells has been linked to the over-production of pro-inflammatory cytokines like interferon-{gamma} (IFN-{gamma}). In this context, IFN-{gamma}-deficient mice display increased survival rates in response to Staphylococcus aureus (S. aureus), which causes life-threatening, invasive systemic infections with high mortality rates in humans. However, little is known about how NK cells respond to S. aureus in humans. In this study, we found that the peripheral blood of patients with bloodstream S. aureus infection was enriched for NKG2A+ NK cells with greater cytokine producing capacity, compared to those hospitalized with Escherichia coli bloodstream infections. As a possible mechanistic cause, superantigens from S. aureus promoted the expansion of CD57- NKG2A+ NK cells which produced IFN-{gamma} through an IL-12-independent mechanism and exhibited reduced levels of CD16 compared to unstimulated NK cells. These data suggest that S. aureus bloodstream infection in humans promotes a phenotypic shift towards NKG2A+ NK cells with greater IFN-{gamma} producing capacity, providing a plausible way to promote inflammation-driven disease pathogenesis. AUTHOR SUMMARYNatural Killer (NK) cells are specialized immune cells that provide crucial defence against viruses but can also respond to bacterial infections, especially in humans. During bloodstream infection by Staphylococcus aureus, a Gram-positive bacterial pathogen that causes life-threatening infections in humans, NK cells may actually be harmful, rather than protective, to the host. However, very little is known about the NK cell response to invasive Staphylococcus aureus infections in humans. Here, we show that human patients with bloodstream Staphylococcus aureus, but not Escherichia coli, infections have an increased frequency of NK cells with increased pro-inflammatory capacity. Furthermore, we show that toxins produced by Staphylococcus aureus, which help the bacteria evade the protective effects of T cells the immune system ("superantigens"), promoted the expansion of these pro-inflammatory NK cells, providing a possible mechanistic cause for their increased presence in patients with bloodstream Staphylococcus aureus infections. Collectively, these results suggest that Staphylococcus aureus infection triggers phenotypic and functional changes in NK cells that provide a plausible way to promote inflammation-driven disease pathogenesis

immunology↗

bioRxiv2024

Detecting the bodys reproductive hormonal brake against tissue overgrowth: micrin/SgII-70

A new humoral factor has been detected, within a project aiming to disclose the bodys reproductive hormonal brake against tissue overgrowth, micrin ( my-crin). It is hypothesized that micrin braking, gonadal and hypothalamic, is lifted at puberty and wanes with age, bringing on prostatic enlargement and cancers. Factor purification has involved fractionation of ovine and bovine ovarian follicular fluid and blood plasma and serum, with evaluation via rat bioassays in vivo and in vitro. Analysis averse, the molecular effector provided a chemical conundrum. Evidence from mass spectrometry (MS) has been problematic, with spectra from MALDI-TOF, the only productive MS modality, confused by a target polypeptide exhibiting artefacts during processing, storage and MALDI set-up in terms of C-terminal truncation and water losses, together with N-terminal grand fragmentations and dimerizations (factor fragments doubled up). Evidence from chemical sequencing of amino acid (aa) residues was likewise baffling, but consistent with a spiralised depolymerisation within the Edman reaction chamber of a unitary polypeptide. Data decryption has overcome molecular intractability, supported by the results of tryptic digestion and epitope mapping using immunohistochemistry (IHC). The detected inhibitory factor is sleuthed to relate to secretogranin II (SgII), the neurosecretory prohormone, in the form of a secreted acidic 70-aa polypeptide derivative called here SgII-70 ( sig two seventy). The product of peptide splicing, micrin/SgII-70 is potentially an amphipathic molecular ampersand (&), with ends entwined (via salt bridging), the knotty totality compromising Edman and MALDI analyses and molecular modelling whilst conferring protease and heat resistance. The two ends of the factor are conceptualised as binding at the same time to a dimeric cellular receptor, to stoichiometric effect, providing fewer smaller cells within a counting mechanism of tissue-mass regulation. Hexapeptide mimetics simulating both ends of the hormone together have been demonstrated in different species and settings, in the cause of antiorganotrophism (tissue reduction) and reproductive modulation. Therapeutic exploitation beckons for mimetics of the bodys hormonal brake, micrin/SgII-70, in tissue overgrowth conditions such as endometriosis, PCOS, BPH and cancer, and in infertility.

immunology↗

bioRxiv2024

Uukuniemi virus infection causes a pervasive remodelling of the RNA-binding proteome in tick cell cultures

Cellular RNA-binding proteins (RBPs) are pivotal for the viral lifecycle, mediating key host-virus interactions that promote or repress virus infection. While these interactions have been largely studied in the vertebrate host, no comprehensive analyses of protein-RNA interactions occurring in cells of arbovirus vectors, in particular ticks, have been performed to date. Here we systematically identified the responses of the RNA-binding proteome (RBPome) to infection with a prototype bunyavirus (Uukuniemi virus; UUKV) in tick cells and discovered changes in RNA-binding activity for 283 proteins. In an orthogonal approach, we analysed the composition of the viral ribonucleoprotein by immunoprecipitation of UUKV nucleocapsid protein (N) in infected cells. We found many tick RBPs that are regulated by UUKV infection and associate with viral nucleocapsid protein complexes. We confirmed experimentally that these RBPs impact UUKV infection. This includes the tick homolog of topoisomerase 3B (TOP3B), a protein able to manipulate the topology of RNA, which showed an effect on viral particle production. Our data thus reveals the first protein-RNA interaction map for infected tick cells. Research highlightsO_LIUUKV RNAs interact with nearly three hundred tick cell RBPs. C_LIO_LIDemonstrated an enrichment of N protein interactors within the upregulated RIC data suggesting a direct involvement in viral RNA metabolism and translation. C_LIO_LIDeveloped a robust methodology to silence gene expression in tick cell cultures. C_LIO_LIThe TOP3B complex facilitates efficient packaging of UUKV virions. C_LI

microbiology↗

bioRxiv2023

An ovine model for investigation of the microenvironment of the male mammary gland

The specific biology of the male breast remains relatively unexplored in spite of the increasing global prevalence of male breast cancer. Delineation of the microenvironment of the male breast is restricted by the low availability of human samples and a lack of characterisation of appropriate animal models. Unlike the mouse, the male ovine gland persists postnatally. We suggest that the male ovine mammary gland constitutes a promising adjunctive model for the male human breast. In this study we evaluate the male ovine mammary gland microenvironment, comparing intact and neutered males. Assessment of the glandular histo-anatomy highlights the resemblance of the male gland to that of the neonatal female sheep and confirms the presence of rudimentary terminal duct lobular units. Irrespective of neutered status, cell proliferation in epithelial and stromal compartments is low in males, and cell proliferation in epithelial cells and in the intralobular stroma is significantly lower than in pubertal female sheep. Between 42% and 72% of the luminal mammary epithelial cells in the male gland express the androgen receptor, and expression is significantly reduced by neutering. Luminal epithelial cells within the intact and neutered male gland also express oestrogen receptor alpha, but minimal progesterone receptor expression is observed. The distrubution of mammary leukocytes within the ducts and stroma is similar in the female mammary gland of sheep and other species. Both macrophages and T lymphocytes are intercalated in the epithelial bilayer and are more abundant in the intralobular stroma than the interlobular stroma, suggesting that they may have a protective immunological function within the vestigial glandular tissue of the male sheep. Mast cells are also observed within the stroma. These cells cluster nearer the glandular tissue and are frequently located adjacent to blood vessels. The abundance of mast cells is significantly higher in intact males compared to neutered males, suggesting that hormone signalling may impact mast cell recruitment. In this study, we demonstrate the utility of the male ovine mammary gland as a model for furthering our knowledge of postnatal male mammary biology.

pathology↗

bioRxiv2023

The most remarkable migrants - systematic analysis of the Western European insect flyway at a Pyrenean mountain pass

In 1950 David and Elizabeth Lack chanced upon a huge migration of insects and birds flying through the Pyrenean Pass of Bujaruelo, later describing the spectacle as combining both grandeur with novelty. The intervening years have seen many changes to land use and climate, posing the question as to the current status of this migratory phenomenon, while a lack of quantitative data has prevented insights into the ecological impact of this mass insect migration and into the factors affecting it. To address this, we revisited the site in autumn over a 4-year period and systematically monitored diurnal insect species and numbers. We document an annual mean of 17.1 million day-flying insects from 5 orders moving south, with mass migration events associated with warmer temperatures, the presence of a headwind, sunlight, low windspeed, and low rainfall. Diptera dominated the migratory assemblage and annual numbers varied by more than fourfold with larger annual migration flows associated with higher autumn temperatures in Northwest Europe. Finally, using observed environmental thresholds for migration, we estimate an annual bioflow of at least 14.6 billion day-flying insects migrating south over the whole Pyrenean Mountain range, highlighting the importance of this route for seasonal insect migrants.

zoology↗

bioRxiv2022

Extensions of mean-field approximations for environmentally-transmitted pathogen networks

Many pathogens spread via environmental transmission, without requiring host- to-host direct contact. While models for environmental transmission exist, many are simply constructed intuitively with structures analogous to standard models for direct transmission. As model insights are generally sensitive to the underlying model assumptions, it is important that we are able understand the details and consequences of these assumptions. We construct a simple network model for an environmentally-transmitted pathogen and rigorously derive systems of ordinary differential equations (ODEs) based on different assumptions. We explore two key assumptions, namely homogeneity and independence, and demonstrate that relaxing these assumptions can lead to more accurate ODE approximations. We compare these ODE models to a stochastic implementation of the network model over a variety of parameters and network structures, demonstrating that with fewer restrictive assumptions we are able to achieve higher accuracy in our approximations and highlighting more precisely the errors produced by each assumption. We show that less restrictive assumptions lead to more complicated systems of ODEs and the potential for unstable solutions. Due to the rigour of our derivation, we are able to identify the reason behind these errors and propose potential resolutions.

microbiology↗

bioRxiv2021

Ecological constraints on highly evolvable olfactory receptor genes and morphology

While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. Phyllostomid bats, an ecologically diverse clade that evolved plant-visiting from an insectivorous ancestor, suggest the evolution of novel food detection mechanisms is a key innovation: phyllostomids behaviorally rely strongly on olfaction, while echolocation is supplemental. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration is coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants -- a potential ecological constraint on sensory evolution. Significance StatementThe evolutionary relationship between genes and morphology is complex to decipher, and macroevolutionary trends are often measured independently; this is especially challenging to quantify in unstable genomic regions or hypervariable traits. Odorant cues are detected by proteins encoded by the largest and fasted-evolving gene family in the mammalian genome and expressed in epithelia distributed on elaborate bony structures in the nose, posing a challenge to quantification. Yet, the direct interaction of the olfactory system with environmental signals strongly suggest that selection shapes its immense diversity. In neotropical bats, where reliance on plant-visiting evolved from an insectivorous ancestor, we discovered clear dietary differences amongst species, but only after considering morphological and molecular data simultaneously, emphasizing the power of a coupled analysis.

evolutionary biology↗

bioRxiv2020

Effective in-vitro inactivation of SARS-CoV-2 by commercially available mouthwashes

Infectious SARS-CoV-2 can be recovered from the oral cavities and saliva of COVID-19 patients with potential implications for disease transmission. Reducing viral load in patient saliva using antiviral mouthwashes may therefore have a role as a control measure in limiting virus spread, particularly in dental settings. Here, the efficacy of SARS-CoV-2 inactivation by seven commercially available mouthwashes with a range of active ingredients were evaluated in vitro. We demonstrate [≥]4.1 to [≥]5.5 log10 reduction in SARS-CoV-2 titre following a one minute treatment with commercially available mouthwashes containing 0.01-0.02% stabilised hypochlorous acid or 0.58% povidone iodine, and non-specialist mouthwashes with both alcohol-based and alcohol-free formulations designed for home use. In contrast, products containing 1.5% hydrogen peroxide or 0.2% chlorhexidine gluconate were ineffective against SARS-CoV-2 in these tests. This study contributes to the growing body of evidence surrounding virucidal efficacy of mouthwashes/oral rinses against SARS-CoV-2, and has important applications in reducing risk associated with aerosol generating procedures in dentistry and potentially for infection control more widely.

microbiology↗

bioRxiv2020

Heme is crucial for medium-dependent metronidazole resistance in clinical isolates of C. difficile

Until recently, metronidazole was the first-line treatment for Clostridioides difficile infection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases. Here, we investigate resistance to metronidazole in a collection of clinical isolates of C. difficile. We find that nearly all isolates demonstrate a heme-dependent increase in the minimal inhibitory concentration for metronidazole, which in some cases leads to isolates being qualified as resistant (MIC > 2 mg/L). Moreover, whole genome sequence analysis reveals a single nucleotide polymorphism in the heme responsive gene hsmA, which defines a metronidazole resistant lineage of PCR ribotype 010 / multilocus sequence type 15 isolates that also includes pCD-METRO containing strains. Together our data demonstrate that heme is crucial for medium-dependent metronidazole resistance in C. difficile.

microbiology↗