Biology subjects

Wright, A.

Publications and source records attributed to Wright, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Disruption of cAMP Signalling and RNA Regulation Confers Cefiderocol Resistance in Acinetobacter baumannii

Cefiderocol is a siderophore-conjugated cephalosporin used to treat severe multidrug-resistant Gram-negative infections. Its recent prioritisation for US national preparedness underscores its clinical importance, yet resistance can emerge despite apparent in vitro susceptibility. Here, we identify two regulatory routes to cefiderocol resistance in carbapenem-resistant Acinetobacter baumannii (CRAB): mutation of the cAMP-producing adenylate cyclase CavA and truncation of the glycine-rich RNA-binding domain of the post-transcriptional regulator Hfq. These variants occurred in contemporary clinical isolates, conferred resistance in a murine CRAB lung-infection model and imposed minimal fitness costs. In Escherichia coli, deletion of the CavA orthologue cyaA increased competitive fitness during sub-inhibitory cefiderocol exposure. Hfq-CLASH and integrated omics revealed Hfq-dependent regulation of Fur-associated iron homeostasis in A. baumannii. Under iron limitation, truncated-Hfq induced a defence-primed state that attenuated siderophore uptake and reduced cefiderocol activity. These findings identify bacterial regulatory state and iron availability as determinants of cefiderocol susceptibility, with implications for resistance surveillance and susceptibility testing.

microbiology↗

bioRxiv2026

Haplotype-phased, chromosome-level, annotated genome assembly of the soybean rust pathogen Phakopsora pachyrhizi

Phakopsora pachyrhizi, the causal agent of soybean rust, is among the most aggressive and economically impactful pathogens affecting soybean (Glycine max) production worldwide. As a dikaryotic rust fungus, P. pachyrhizi maintains its genetic information as two discrete haplotypes that are sequestered within separate nuclei for most of its life cycle as it reproduces asexually via the production of infectious urediniospores. Previous genomes of three P. pachyrhizi isolates collected in South America revealed a large genome with a high transposable element content, measuring up to 1.25 Gb and 93%, respectively. Although these efforts provided valuable foundational resources, the complexity of the genome resulted in highly fragmented assemblies. Here, we generated a highly contiguous, substantially improved, annotated genome resource from the P. pachyrhizi isolate LA04-1, collected during the initial outbreak of soybean rust in the continental United States in 2004. The assembly is haplotype-phased, with each haplotype assembled into 18 chromosomes totaling 572 Mb and 569 Mb in size. The isolate contains unique mating-type genes and does not share haplotype genomes with any available isolates with whole-genome sequencing datasets. This resource will be valuable to future investigations into the underlying mechanisms of virulence in this important plant pathogen.

genomics↗

bioRxiv2026

A Compact, Standalone & Battery-Powered 3D Organoid-on-Chip System with Programmable Flow Control

Organoids-on-chip combine the 3D complex microenvironment and cellular composition of organoids with microfluidic flow, increasing nutrient-waste exchange and mimicking the contributions of in vivo interstitial and vascular flow. However, the widespread adoption of organoid-on-chip platforms is limited by the lack of incubator-friendly flow control systems. Existing approaches often rely on commercially available syringe or peristaltic pumps, but these are bulky, lack scalability, and present a significant barrier for clinical translation. To circumvent these issues, we present the Compact Active Perfusion Standalone Organoid-on-Chip (CAPS-OC) platform, a fully integrated and battery-powered microfluidic system capable of culturing organoids in active media flow. To achieve this, we introduce a novel low-power mechanism of pressure pulse generation using an off-the-shelf compact rotary actuator (CRA), and package it into a compact electromechanical assembly. This assembly provides timed pneumatic inputs to achieve programmable control of membrane-based peristaltic pumps, with [~]100 {micro}L/hr dynamic range achieved on a custom microfluidic organoid chip. We biologically validated this system by culturing pancreatic cancer organoids derived from a KrasLSL-G12D/+; Trp53LSL-R172H/WT; Pdx1-Cre (KPC) genetically engineered mouse model. We found that our chip enhances proliferation and helps sustain a population of larger (>150 {micro}m) organoids compared to standard dome based static culture. Additionally, through immunostaining, we observe that KPC organoids cultured in the chip show more aggressive PDAC phenotype with reduced nuclear expression of GATA6, whereas organoids in static culture retain less aggressive classical- like subtype. Finally, testing of a RAS inhibitor drug, daraxonrasib, on the KPC organoids on chip showed size-based sensitivity elucidating the impact of active perfusion on the drug diffusion kinetics. Altogether, we establish CAPS-OC as a valuable tool for the bioengineering community and for clinically translating organoid model systems.

bioengineering↗

bioRxiv2026

Multi-site phenotypic characterisation of Kisumu colonies for comparison of insecticide susceptibility between testing centres

Testing of insecticides and insecticide-based vector control tools relies on the use of bioassays whereby insects are exposed and mortality, or another relevant entomological endpoint, is measured. To be able to compare results between products and across time and space standard laboratory strains are used. Insecticide-susceptible strains are often used as comparators in studies involving insecticide-resistant populations. Kisumu is a long-established, widely-used insecticide-susceptible strain of Anopheles gambiae. In this study, 16 facilities across different countries exposed their Kisumu colonies aged 3-5 days to four insecticides (permethrin, alpha-cypermethrin, DDT and pirimiphos-methyl) at a range of concentrations in WHO tube assays to assess susceptibility. Insecticide-treated filter papers were made at the Liverpool School of Tropical Medicine and sent to testing centres, along with a standard protocol and testing conditions requirements, to standardise testing as much as possible. A first observation was that DDT results were affected by the use of Risella oil, the WHO-recommended carrier oil but immiscible in acetone, leading to uneven coating of papers and increased variability in bioassay results (40x variance between colonies). Bioassay data generated by the testing facilities suggest a wide range of susceptibility to different insecticides between colonies of Kisumu: LC50 values between colonies differed, though not significantly, by up to 4x for permethrin, 6x for pirimiphos-methyl, and 15x for alpha-cypermethrin. Some colonies are classified as insecticide resistant based on the WHO definition of <98% mortality on exposure to a discriminating concentration. The assumption that Kisumu is a standard susceptible strain, consistent between facilities is challenged, which has implications when comparing results between studies. We propose genotypic analysis of the colonies to identify signs of resistance markers indicative of contamination from resistant strains or wild mosquitoes, and generation of guidance to support the maintenance and monitoring of susceptible mosquito strains.

zoology↗

bioRxiv2026

Voluntary wheel running provides pain relief but transiently exacerbates gait impairments in male and female mice with unilateral osteoarthritis

ObjectivePhysical activity is a first-line therapeutic intervention for managing osteoarthritis-related pain and functional impairment. However, the growing literature questions the long-term relevance of exercise-induced improvements in patients, while pre-clinical research evidence base is limited by reliance on stressful, forced exercise paradigms which do not reflect voluntary engagement. Here, we aimed to investigate the effects of voluntary wheel running on the pain experience in mice with joint pain. DesignWe investigated the impact of free access to a running wheel on sensory, functional and affective outcomes following unilateral intra-articular injection of monoiodoacetate in single-housed male and female C57Bl/6J mice. ResultsMonoiodoacetate injection transiently reduced running activity in both sexes; however, females rapidly resumed and sustained high activity levels over a two-month period, while males showed a progressive decline in running distance. Active males and females showed improvements in the monoiodoacetate-induced hindpaw secondary mechanical hypersensitivity. Moreover, mechanical thresholds positively correlated with the distance ran after injury, suggesting a functional relationship between exercise and secondary pain relief. However, access to a wheel temporarily exacerbated several monoiodoacetate-induced gait impairments in both sexes. Finally, while there were no obvious effects of running on anxio-depressive-like behaviours or cognitive functioning, exercise significantly impacted stress-induced faecal output and phenotypic regulation of body weight. ConclusionsOur findings suggest that persistent loading of an injured knee joint may compromise functional outcomes independently of pain relief away from the joint, underscoring a critical consideration for exercise-based therapeutic strategies in osteoarthritis.

animal behavior and cognition↗

bioRxiv2025

React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase.

The Reactome Pathway Knowledgebase (www.reactome.org) provides expert-curated information on human biological pathways, molecular interactions, and disease mechanisms. However, its complex data model and keyword-based search interface present accessibility barriers for non-expert users. In contrast, general-purpose conversational AI systems offer intuitive natural language interfaces but lack the domain-specificity, transparent sourcing, and factual reliability required for scientific applications. To address this gap, we developed React-to-Me (https://reactome.org/chat), a domain-specific conversational assistant that enables users to query Reactome using natural language while maintaining scientific rigor and source traceability. React-to-Me integrates hybrid retrieval-augmented generation (RAG) with constrained language model generation to ensure that all responses are grounded in curated Reactome content and directly linked to corresponding knowledgebase entries. When internal coverage is insufficient, the system defers to trusted external biomedical sources rather than generating speculative or unverified content. Computational benchmarking confirmed that combining semantic vector search with keyword-based matching substantially improved contextual grounding and factual precision relative to dense-only retrieval baselines. In blinded expert evaluations, grounded responses were more likely to receive higher quality ratings than ungrounded counterparts, with significant gains in factual accuracy, biological specificity, and mechanistic depth. User surveys further indicated strong satisfaction with ease of use, citation reliability, and factual accuracy. These findings demonstrate that domain-specific grounding can markedly improve the reliability and usability of conversational AI for biological knowledge exploration. React-to-Me provides a transparent and scientifically robust interface for accessing and exploring Reactome content and is freely available at https://reactome.org/chat. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/693752v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1ef0d73org.highwire.dtl.DTLVardef@15c2d4dorg.highwire.dtl.DTLVardef@a2338corg.highwire.dtl.DTLVardef@e639fd_HPS_FORMAT_FIGEXP M_FIG C_FIG

scientific communication and education↗

bioRxiv2025

Imaging progenitor cell differentiation during central nervous system remyelination using an MRI gene reporter

Demyelination, the loss of the myelin sheath from around otherwise intact axons, occurs in several diseases, most notably multiple sclerosis (MS). Demyelinated axons that are not remyelinated are vulnerable to irreversible degeneration and therefore therapies that enhance remyelination have been sought. However, there remains a paucity of suitable outcome measures to assess their efficacy. Magnetic Resonance Imaging (MRI) is a non-invasive imaging modality that is used both preclinically and clinically for the assessment of anatomy and tissue function. Here we describe an MRI technique for following the differentiation of oligodendrocyte progenitor cells (OPCs) into oligodendrocytes during the spontaneous regenerative process of remyelination in vivo. OPCs were transduced in situ with a lentiviral vector expressing an organic anion transporting polypeptide (Oatp1a1) under the control of the differentiation-specific Myelin Basic Protein (MBP) promoter. Oatp1a1 mediates cell uptake of a gadolinium-based MRI contrast agent (Primovist), allowing detection of the cells in T1-weighted MR images. Uptake of the contrast agent is restricted to MBP-expressing cells, which is most highly expressed during myelin sheath formation, thereby allowing progenitor-mediated, and potentially oligodendrocyte-mediated, remyelination to be monitored non-invasively in vivo using MRI. These findings provide the foundation for the development of direct methods for assessing the efficacy of pro-remyelination therapies.

neuroscience↗

bioRxiv2025

OmniShim - a vendor-independent B0 Shimming software toolbox

PurposeTo introduce the OmniShim Toolbox, a software package designed to calibrate and perform B0 shimming in user-defined regions of interest across systems from different vendors, supporting various shim orders. MethodsIn this study, we systematically compared the performance of vendor-implemented B0 shim routines with our custom developed OmniShim toolbox, designed to improve static magnetic field homogeneity. Single-voxel magnetic resonance spectroscopy (MRS) data were acquired from the prefrontal cortex and occipital lobe, while magnetic resonance spectroscopic imaging (MRSI) data were collected from regions above and below the corpus callosum in healthy volunteers. Measurements were conducted on both 3T and 7T MR systems to evaluate the robustness and scalability of each B0 shimming strategy across different field strengths. Additionally, functional MRI (fMRI) data were acquired at 7T to assess the impact of improved shimming on EPI data quality and BOLD contrast. ResultsThe OmniShim Toolbox demonstrated superior B0 homogeneity across all applications and field strength, leading to reduced signal dropout in fMRI and MRSI data, significantly improved spectral linewidths in SV MRS and MRSI data as well improved detection of neural networks by resting state fMRI. ConclusionThe proposed OmniShim Toolbox offers a robust and flexible approach to control B0 inhomogeneity, resulting in substantial improvements in image quality and spectral resolution. These enhancements benefit a broad range of MR applications.

bioengineering↗

bioRxiv2025

TRACC-PHYSIO: Time-domain Resolution-Aligned Cross-Correlation to estimate PHYSIOlogical coupling and time delays in dynamic MRI

Physiological brain pulsations, primarily driven by cardiac and respiratory activity, play a key role in driving neurofluid circulation and waste clearance. Capturing the temporal dynamics of cardiac- and respiratory-driven brain pulsations (0.2-1.5 Hz) requires fast imaging with TRs near 100 ms, which is often unachievable in functional MRI or dynamic diffusion MRI. As a result, valuable physiological information remains hidden in these datasets. Here, we introduce TRACC-PHYSIO, a time-domain analytical framework designed to quantify physiological coupling and pulse time delays in dynamic MRI without requiring a fast acquisition. TRACC-PHYSIO uses cross-correlation to detect co-fluctuations between slowly sampled dynamic MRI data and simultaneously recorded physiological waveforms. It measures two key metrics: the peak Coupling Coefficient (peak CorrCoeff), quantifying the strength of co-fluctuations, and the TimeDelay, reflecting the relative arrival time of the physiological impulse in the brain with millisecond-level temporal resolution. The primary aim of this study is to validate TRACC-PHYSIO through systematic simulations that model realistic dynamic MR signals with mixed physiological components. We comprehensively evaluate TRACC-PHYSIOs performance under a wide range of conditions, including varying cardiac-to-respiratory composition ratios, TRs, and acquisition times. Results demonstrate that TRACC-PHYSIO can robustly assess coupling strengths and time delays for both cardiac (TRACC-Cardiac) and respiratory (TRACC-Respiratory) components, even in datasets with long TRs up to 3 seconds. By enabling a reliable time-domain coupling analysis, TRACC-PHYSIO opens new avenues for revealing brain pulsation mechanisms and elucidating the physiological drivers of neurofluid dynamics in health and disease. This stimulation study provides a valuable reference for interpreting TRACC-PHYSIO results and understanding associated uncertainties in future applications. Highlights- TRACC-PHYSIO is a time-domain method developed to estimate cardiac and respiratory coupling and their pulsation time delays in dynamic MRI without requiring high temporal resolution. - TRACC-PHYSIO was validated through systematic simulations across varying physiological compositions and MR acquisition parameters. - Results demonstrated that TRACC-PHYSIO reliably quantifies cardiac and respiratory components in dynamic MR signals. - The stimulation study provides a useful reference for interpreting TRACC-PHYSIO results and understanding associated uncertainties in future applications.

bioengineering↗

bioRxiv2025

Comparative analysis of shared and unique mechanisms important for diverse strains of Pasteurella multocida to cause systemic infection in mice

Pasteurella multocida is a Gram-negative bacterium that causes a range of distinct diseases in livestock animals. Different P. multocida diseases are associated with different capsule and lipopolysaccharide (LPS) types, but little else is known about what underpins this disease specificity. In this study, we utilised transposon-directed insertion site sequencing (TraDIS) to identify genes in two diverse P. multocida strains that are required for growth in rich media, and genes important for survival during systemic infections in BALB/c mice. Analysis of growth in heart infusion broth showed that the fowl cholera isolate VP161 (capsule type A and LPS type L1) and the bovine haemorrhagic septicaemia isolate M1404 (capsule type B and LPS type L2) shared 461 genes essential for growth in rich media, with 95% of these present in all publicly available closed P. multocida genomes. In vivo fitness analysis identified 63 and 94 genes important for VP161 and M1404 survival in BALB/c mice, respectively. Only 35 homologs were identified as important for survival in both strains, showing that conserved biological systems can be differentially important for different P. multocida strains. Investigation of proteins involved in the catabolite response showed that an active cyclic-adenosine monophosphate (cAMP) receptor protein (CRP) was required for maximal fitness in M1404. Furthermore, disrupting CRP or cAMP production also reduced capsule production in M1404, but increased capsule production in VP161, demonstrating that these P. multocida strains have different regulatory systems for crucial virulence factors. Author SummaryPasteurella multocida is an important livestock pathogen, causing several distinct severe diseases in many different livestock animals. P. multocida can spread rapidly throughout animal populations, with peracute infections causing death within 48 h, resulting in large outbreaks with high mortality. Host predilection and disease presentation often correlate with the capsule and lipopolysaccharide type produced by the causative strain. However, the processes that allow certain strains to cause a particular disease are not well understood. In this study, we have comprehensively identified genes required for two P. multocida strains to cause systemic infection in mice, showing that these diverse strains have differential requirements for survival during a systemic infection. This information is crucial for understanding P. multocida diseases and for the development of new strategies to combat infection.

microbiology↗

bioRxiv2025

Plasma membrane rather than endosomal Gq signaling drives transcriptional activity by the viral chemokine receptor US28 in glioblastoma

US28 is a human cytomegalovirus-encoded chemokine receptor homologue that has high agonist-independent activity, internalizes constitutively, and plays an oncomodulatory role in glioblastoma. As G protein signaling was originally believed to strictly occur at the plasma membrane, it has been assumed that US28s constitutive Gq/11 signaling is mediated by a minor population at the plasma membrane. However, accumulating evidence shows that some GPCRs activate G proteins from intracellular organelles, such as endosomes. Importantly, endosomal rather than plasma membrane G protein signaling has been associated with transcriptional activity. Here, we demonstrate that the endosomal US28 population robustly activates Gq/11, and thus, provides the major contribution of Gq/11 signaling. Surprisingly, US28 signaling at the plasma membrane rather than from endosomes primarily drives upregulation of gene expression involved in cell proliferation and inflammatory responses that are associated with glioblastoma and cancer. Our findings highlight the crucial role of receptor signaling location in cellular responses.

cell biology↗

bioRxiv2025

The extended language network: Language selective brain areas whose contributions to language remain to be discovered

Although language neuroscience has largely focused on core left frontal and temporal brain areas and their right-hemisphere homotopes, numerous other areas--cortical and subcortical--have been implicated in linguistic processing. However, these areas contributions to language remain unclear given that the evidence for their recruitment comes from diverse paradigms, many of which conflate language processing with perceptual, motor, or task-related cognitive processes. Using fMRI data from 772 participants (438 females, 334 males) performing an extensively validated language localizer paradigm that isolates language processing from other processes, we a) delineate a comprehensive set of areas that respond reliably to language across written and auditory modalities, and b) evaluate these areas selectivity for language relative to a demanding non-linguistic task. In line with prior claims, many areas outside the core fronto-temporal network respond during language processing, and most of them show selectivity for language relative to general task demands. These language-selective areas of the extended language network include areas around the temporal poles, in the medial frontal cortex, in the hippocampus, and in the cerebellum, among others. Although distributed across many parts of the brain, the extended language-selective network still only comprises a small fraction (<5%) of the grey matter volume, challenging the view that the entire brain processes language. These newly identified language-selective areas can now be systematically characterized to decipher their contributions to language processing, including testing whether these contributions differ from those of the core language areas. Significance statementLanguage processing consistently recruits a left-lateralized fronto-temporal brain network, but language tasks often additionally engage areas outside this core system. In an fMRI dataset of 772 participants performing a validated language localizer task, we identified 17 brain areas outside the core fronto-temporal network that respond to both auditory and written language. Most of these areas show selectivity for language, including regions in the temporal poles, medial frontal cortex, hippocampus, and cerebellum. Despite its large number of components, this extended language network still only takes up a small fraction of the grey matter volume, challenging the view that the entire brain processes language. These findings lay the foundation for systematic characterization of these newly identified non-canonical language areas.

neuroscience↗

bioRxiv2025

Incorporating continuous characters in joint estimation of dicynodont phylogeny

Continuous characters have received comparatively little attention in Bayesian phylogenetic estimation. This is predominantly because they cannot be modeled by a standard phylogenetic Q-matrix approach due to their non-discrete nature. In this paper, we explore the use of continuous traits under two Brownian motion models to estimate a phylogenetic tree for Dicynodontia, a well-studied group of early synapsids (stem mammals) in which both discrete and continuous characters have been extensively used in parsimony-based tree reconstruction. We examine the differences in phylogenetic signal between a continuous trait partition, a discrete trait partition, and a joint analysis with both types of characters. We find that continuous and discrete traits contribute substantially different signal to the analysis, even when other parts of the model (clock and tree) are held constant. Tree topologies resulting from the new analyses differ strongly from the established phylogeny for dicynodonts, highlighting continued difficulty in incorporating truly continuous data in a Bayesian phylogenetic framework.

evolutionary biology↗

bioRxiv2024

Chromosomal fusion drives sex chromosome evolution in treehoppers despite long-term X chromosome conservation

Sex chromosomes follow distinct evolutionary trajectories compared to the rest of the genome. In many cases, sex chromosomes (X and Y, or Z and W) significantly differentiate from one another resulting in heteromorphic sex chromosome systems. Such heteromorphic systems are thought to act as an evolutionary trap that prevents subsequent turnover of the sex chromosome system. For old, degenerated sex chromosome systems in which turnover is unlikely, chromosomal fusion with an autosome may be one way that sex chromosomes can refresh their sequence content. We investigated these dynamics using treehoppers (hemipteran insects of the family Membracidae), which ancestrally have XX/X0 sex chromosomes. We assembled the first chromosome-level treehopper genome from Umbonia crassicornis and employed comparative genomic analyses of 12 additional treehopper species to analyze X chromosome variation across different evolutionary timescales. We find that the X chromosome is largely conserved, with one exception being an X-autosome fusion in Calloconophora caliginosa. We also compare the ancestral treehopper X with other X chromosomes in Auchenorrhyncha (the clade containing treehoppers, leafhoppers, spittlebugs, cicadas, and planthoppers), revealing X conservation across more than 300 million years. These findings shed light on chromosomal evolution dynamics in treehoppers and the role of chromosomal rearrangements in sex chromosome evolution. SignificanceThe evolutionary forces underlying sex chromosome stability versus turnover have been challenging to disentangle. We present the first chromosome-level treehopper genome and find evidence of long-term X chromosome conservation within treehoppers - and among treehoppers and other hemipteran insects. A key exception is the evolution of neo-XX/XY sex chromosomes via an X-autosome fusion. Sex chromosome-autosome fusions may play an important role in the evolution of otherwise trapped (i.e., old and degenerated) sex chromosome systems.

evolutionary biology↗

bioRxiv2024

Delivery determinants of an Acinetobacter baumannii type VI secretion system bifunctional peptidoglycan hydrolase.

Acinetobacter baumannii is a Gram-negative opportunistic pathogen that is a common cause of nosocomial infections. The increasing development of antibiotic resistance in this organism is a global health concern. The A. baumannii clinical isolate AB307-0294 produces a type VI secretion system (T6SS) that delivers three antibacterial cargo effector proteins (Tse15, Tde16 and Tae17) that give this strain a competitive advantage against other bacteria in polymicrobial environments. These effectors are delivered via specific non-covalent interactions with the T6SS needle tip proteins VgrG15, VgrG16 and VgrG17, respectively. Here we determine the molecular function of the Tae17 effector protein and define the regions of Tae17 and VgrG17 essential for its delivery. Specifically, we show that Tae17 is a multidomain, bifunctional peptidoglycan-degrading enzyme. Tae17 has both lytic transglycosylase activity, which targets the peptidoglycan sugar backbone, and amidase activity, which targets the sugar-peptide bonds. Moreover, we show that the transglycosylase activity was more important for killing Escherichia coli. Using deletion constructs and bacterial two-hybrid analyses, we identify that amino acids 1051-1085 of the VgrG17 needle tip protein and amino acids 1-162 of the Tae17 effector protein are necessary for the Tae17:VgrG17 interaction. Furthermore, we identify the VgrG17 amino acids G1069 and W1075 as crucial for the delivery of Tae17; the first time such specific delivery determinants of T6SS cargo effectors have been defined. This study provides molecular insight into how the T6SS allows A. baumannii strains to gain dominance in polymicrobial communities and thus improve their chances of survival and transmission. IMPORTANCEWe have shown that the Acinetobacter baumannii T6SS effector Tae17 is a modular, bifunctional, peptidoglycan-degrading enzyme that has both lytic transglycosylase and amidase activity. Both activities contribute to the ability to degrade peptidoglycan, but the glycosyltransferase activity was more important for the interbacterial killing of Escherichia coli. We have defined the specific regions of Tae17 and its cognate delivery protein VgrG17 that are necessary for the non-covalent interactions and, for the first time, identified specific amino acids essential for delivery. This work contributes to our molecular understanding of bacterial competition strategies in polymicrobial environments and may provide a window to the design of new therapeutic approaches for combating infection by A. baumannii.

microbiology↗

bioRxiv2023

Predicting hypersensitivity and comorbid depressive-like behavior in late stages of joint disease using early weight bearing deficit

Chronic pain is a hallmark of joint diseases and is often accompanied by negative affective symptoms such as low mood, anxiety and memory dysfunction. Whether these may be the results of the more obvious sensory and functional symptoms of joint pain is poorly understood and this likely contributes to the difficulty in adequately managing this condition. Here, we have used two mouse models to address this lack of knowledge. Using a model of ankle inflammation and a model of knee osteoarthritis, we found that these models of joint pain induced weight bearing deficits of different magnitude but relatively similar mechanical allodynia that lasted at least 3 months. However, the models were accompanied by very different affective outcomes, as only the model of knee osteoarthritis, that led to significant early changes in activity and sleep patterns, was accompanied by an increase in negative affective behaviors, including cognitive impairments and depressive-like behavior. The models also had different molecular profiles at both spinal and hippocampal levels. Importantly, the functional outcomes measured in the early stages of the disease stage strongly correlated with sensory and emotional profiles at 3 months, suggesting that early functional measures may be used as predictors of the long-term symptoms associated with persistent joint pain. In conclusion, the predictive value of early measures of functional impact of joint disease could prove useful in the clinics for adapted therapeutic approaches for the prevention of emotional comorbidities and better pain management for patients with joint pain.

neuroscience↗

bioRxiv2023

FAIR Header Reference genome: A TRUSTworthy standard

The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability, and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST). The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility, and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHRs design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.

bioinformatics↗

bioRxiv2023

Structure of a Rhs effector clade domain identifies new mechanistic insights into type VI secretion system toxin delivery.

The type VI secretion system (T6SS) is a molecular machine utilised by many Gram-negative bacteria to deliver antibacterial toxins directly into adjacent bacteria, often providing a competitive advantage. Rearrangement hotspot (Rhs) effectors are known T6SS cargo effectors, but the precise delivery and activation of these toxins is poorly defined. We present the structure of a novel T6SS Rhs effector (Tse15) from the multidrug resistant nosocomial pathogen Acinetobacter baumannii. Tse15 forms a triple layered y-cocoon Rhs domain with an N-terminal -helical clade domain and an unfolded C-terminal toxin domain located entirely inside the Rhs cage. We identify that Tse15 is cleaved into three domains, through two independent auto-cleavage events involving aspartyl protease activity for toxin self-cleavage and a nucleophilic glutamic acid for the cleavage of the N-terminal clade domain. Proteomic analyses showed that the N-terminal clade and toxin domains, but not the y-strand rich Rhs cage, are delivered outside of the cell, suggesting a novel mechanism for Rhs toxin delivery and activation. Our findings suggest that this delivery mechanism requires an interaction between the N-terminal clade and toxin domains, with the clade domain acting as the internal chaperone to mediate tethering of the toxin to the T6SS machinery. Conservation of the clade domain in other Gram-negative bacteria suggest this may be a common mechanism for T6SS toxin delivery.

microbiology↗