Biology subjects

Baker, S.

Publications and source records attributed to Baker, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Colistin resistance-mediated lipopolysaccharide modification in Klebsiella pneumoniae modulates host inflammatory response

Resistance to the polymyxin antimicrobial colistin in Gram-negative bacteria is associated with a modification of the immunogenic lipid A moiety of the lipopolysaccharide (LPS). Chromosomal and plasmid-borne colistin resistance results in the addition of L-Ara4N and pEtN groups to lipopolysaccharide (LPS), respectively. Here, using THP-1 cells, we studied the impact of different LPS modifications of Klebsiella pneumoniae in stimulating host immune response. K. pneumoniae clinical isolates were screened for colistin resistance using broth microdilution (BMD) and the MALDIxin test. LPS was extracted from colistin-resistant isolates and used to stimulate differentiated THP-1 cells. Luminex cytokine assay measured the immune induction via a panel of proinflammatory cytokines. Out of a collection of 72 clinical K. pneumoniae, eight (11.1%) exhibited phenotypic colistin resistance with a minimum inhibitory concentration (MIC) of 8 to 64 mg/L. In total, five isolates possessed genes associated with polymyxin resistance; three isolates had a mutation in the pmrB gene, and two were mcr-8.1 positive. MALDIxin demonstrated that all eight phenotypic colistin-resistant isolates elaborated peaks at m/z 1,955 and m/z 2,193, indicating an L-Ara4N group of LPS modification. For two mcr-8.1 positive isolates, LPS had a pEtN group. The LPS modification positively correlated with colistin MIC (correlation coefficient, r= 0.6 and R2= 0.4). Compared to the native structure, LPS modification was associated with greater production of IL-1{beta}, IL-6, and CXCL-8 (p<0.001). The pEtN-conjugated LPS triggered a significantly greater production of TNF-, IL-6, and CXCL-8 compared to L-Ara4N (p<0.05). This study reveals that the colistin MIC value can significantly predict lipid A modification in clinical K. pneumoniae, and differences in resistance-mediated lipid A modification result in variation in the immunological response. This study highlights the potential of dynamic host-pathogen interaction in the context of colistin resistance.

microbiology↗

bioRxiv2026

RNAquarium: an archive-scale atlas of zebrafish gene expression coupled with pan-taxonomic profiling reveals diverse viral drivers of transcriptomic states

Zebrafish RNA-seq studies span diverse developmental, physiological, and disease contexts, yet most analyses remain confined to individual experiments and disregard the non-zebrafish component of the data. We present RNAquarium, a scalable framework for joint transcriptomic and metatranscriptomic analysis of RNA-seq data and apply it to all publicly available zebrafish RNA-seq datasets in the Sequence Read Archive. This resource captures transcriptomic structure across development and tissues, reveals diverse microbial and viral associations, and identifies previously undescribed zebrafish viruses including a close relative of human influenza B virus linked to distinct host transcriptional states. We further demonstrate that archive-scale transcriptomes can support foundation-model training and prediction of infection-associated transcriptomic signatures. RNAquarium provides an open framework and interactive portal for exploring the breadth of zebrafish gene expression patterns and associated taxa profiled across a large re-search community and establishes a generalizable strategy for integrating transcriptomic and metatranscriptomic analyses across the diversity of life represented in public sequencing archives.

genomics↗

bioRxiv2026

Screening metatranscriptomes for ultrastable RNA secondary structures reveals hidden bacteriophages and novel capsid nanomaterials

Metatranscriptomics has transformed our view of RNA bacteriophage diversity, revealing vast numbers of single-stranded RNA (ssRNA) phages whose protein capsids can be engineered for biotechnology applications. However, many ssRNA phages remain hidden from current detection methods, which require protein-level similarity to known phages. Here we show that RNA structure provides an additional signal for the detection of ssRNA phages in metatranscriptomes, including hidden phages missed by prior protein-based methods. By computationally folding each contig and screening for exceptionally stable RNA secondary structures, we find evidence of thousands of previously unrecognized phages encoding novel coat proteins. We express a library of 12,000 such coat proteins in E. coli and find that most assemble into nuclease-resistant capsids. We determine the 3D structure of one such capsid by cryo-electron microscopy and demonstrate that it can be disassembled and reassembled in vitro to package heterologous RNA--a key step toward repurposing these particles as RNA delivery vehicles. We compile the newly discovered ssRNA phages with previously known ones into a database that contains sequence and structural information for over 460,000 unique RNA molecules and over 100,000 distinct coat proteins, providing a comprehensive resource for microbiology and nanomaterials research.

biochemistry↗

bioRxiv2026

Development and evaluation of a dual target glycoconjugate vaccine against Shigella sonnei

BackgroundShigellosis morbidity and mortality, combined with the increase in multidrug-resistant infections make Shigella vaccine development a global imperative. Glycoconjugate vaccines that couple immunogenic O-antigen to protein derived from Shigella may provide broader protection across Shigella species and serogroups. Such an approach also circumvents immunotolerance arising from repeated use of the same carrier. Here we use bioconjugation, exploiting an oligosaccharyltransferase (OST) enzyme to couple O-antigen and carrier protein in vivo, to generate a "double-hit" Shigella glycoconjugate vaccine. MethodGlycoconjugates were synthesised in E. coli SDB1 cells expressing S. sonnei O-antigen, the OST PglS, and one of two Shigella carrier proteins. Recombinant glycoconjugate was purified using anion exchange chromatography and then used to immunise mice. Antibody responses were measured and compared by ELISA. ResultsWhen co-produced in E. coli, PglS was able to transfer the cloned S. sonnei O-antigen onto three carrier proteins, modified to accept glycans from the PglS transferase enzymes- the standard bioconjugate carrier ExoA and two immunogenic Shigella-specific outer membrane proteins, EmrK and MdtA. Production of MdtA or ExoA glycoconjugates for immunisation studies utilised successive rounds of anion exchange chromatography, to remove unglycosylated material and obtain highly purified glycoconjugate proteins for us in vaccination. Analysis of murine sera following immunisation revealed an IgG response was raised against both carrier protein and the S. sonnei O-antigen for each glycoconjugate. ConclusionA novel, conserved Shigella protein can be utilised as an effective carrier for the generation of a "double-hit", immunogenic Shigella glycoconjugate vaccine that elicits IgG responses to both carrier protein and S. sonnei O-antigen.

microbiology↗

bioRxiv2026

Intracellular Mechanosensation in Intestinal Smooth Muscle: Piezo1 Complexes Amplify Signaling Beyond the Surface

Mechanosensation is fundamentally viewed as a plasma membrane phenomenon. We challenge this paradigm by introducing intracellular mechanosensation in intestinal smooth muscle. We hypothesized that a distinct, organelle-based signaling axis exists to amplify mechanotransduction from the inside out. To test this, we investigated whether Piezo1, a canonical plasma membrane mechanosensor, also operates within the cell. Using tissue-level wire myography, high-resolution confocal microscopy, proximity ligation assays, and patch-clamp electrophysiology on freshly dissociated cells, we identified a functional intracellular signaling hub that starts at the sarcoplasmic reticulum (SR). Unlike surface transduction, this intracellular mechanism relies on a nanoscale multiprotein complex (<40 nm) comprising an SR sensor (intra-Piezo1) and an amplifier (Ryanodine Receptor, RyR), coupled with a PM effector (large-conductance, Ca2+-activated K+ channels, i.e., BKCa channels). Activating this intracellular complex generated massive BK-mediated outward currents independent of extracellular Ca{superscript 2} but strictly dependent on internal SR Ca{superscript 2} stores, confirming intrinsic organellar mechanotransduction. Within this complex, intra-Piezo1 and RyR are positioned to operate as a coupled SR Ca{superscript 2} release unit that activates BK channels at SR-PM junctions, driving potent membrane hyperpolarization that reduces smooth muscle contractility, revealing the intra-Piezo1 complex as a molecular brake on excitation. These findings demonstrate that mechanotransduction is not confined to the cell surface. Instead, a specialized Sensor-Amplifier-Effector complex originating at intracellular organelles amplifies cellular sensitivity to physical force, providing a critical gain-control system that restrains smooth muscle excitability and regulates GI motility. Key PointsO_LIIntracellular organelles contribute to mechanosensory signaling in GI smooth muscle cells, complementing plasma membrane mechanisms. C_LIO_LIIntra-Piezo1 form a nanoscale signaling complex (<40nm) on the sarcoplasmic reticulum (SR), linking the mechanosensor Piezo1 with RyR and large conductance, Ca2+-activated K+ channels. C_LIO_LIUnlike surface sensors, this intracellular complex functions via a "Sensor-Amplifier-Effector" mechanism in which intra-Piezo1 detects mechanical stress and triggers SR Ca2+ release, thereby activating a nearby RyR and large-conductance, Ca2+-activated K+ channel. C_LIO_LIEngaging this intracellular Piezo1-mediated axis significantly dampens smooth muscle contractility, identifying a critical gain-control system essential for regulating GI motility. C_LI

physiology↗

bioRxiv2026

Nonlinear Relationships of Fibrin Network Structure as a Function of Fibrinogen and Thrombin Concentrations for Purified Fibrinogen and Plasma Clots

BackgroundFibrinogen levels are associated with bleeding disorders and thrombotic disease. Thrombin converts fibrinogen to fibrin, producing the load-bearing fibrin scaffold that governs clot mechanics and transport. ObjectiveQuantitatively map how initial fibrinogen and thrombin concentrations, [Fgn]0 and [T[h]r]0, determine fibrin architecture in human plasma and a purified fibrinogen system. MethodsScanning electron microscopy was used to quantify single-fiber morphology--fiber diameter and branch-to-branch segment length from a standardized sample-preparation protocol. Confocal microscopy was used to quantify network architecture--projected fiber density and pore/bubble size. Results and ConclusionsAcross plasma and purified systems, fibrin structural parameters were quantitatively captured by compact multiplicative scaling laws of the form Y = k[Fgn]0[T[h]r]0{beta}. Unlike prior studies, which examined narrower condition ranges without establishing predictive equations across a systematic fibrinogen-thrombin concentration matrix, this framework defines distinct, quantitative roles for fibrinogen and thrombin in fibrin assembly. The magnitudes and signs of the exponents and {beta} indicate that thrombin primarily controls individual fiber growth kinetics, strongly shortening branch-to-branch segment length and modestly thinning fibers, whereas fibrinogen primarily controls space filling, strongly increasing fiber density, reducing pore/bubble size, and thickening fibers. For matched [Fgn]0 and [T[h]r]0, compared to plasma clots, purified fibrinogen formed denser networks with thinner and shorter fibers, suggesting that the plasma biochemical environment partially inhibits thrombin activity. Fiber length analysis further suggests that each thrombin molecule nucleates one fiber segment. Together, these parameterized scaling relations provide a predictive quantitative framework linking clot composition to fibrin microstructure in plasma and purified fibrinogen clots.

biophysics↗

bioRxiv2025

Stable fusion of bone marrow-derived cells with Purkinje neurons enables long-term nuclear integration and neuronal repair

Developing effective strategies to replace or restore injured neurons could significantly revolutionise the treatment of currently incurable neurodegenerative disorders. Studies have shown that bone marrow-derived cells (BMDCs) can migrate into the brain and fuse with damaged Purkinje neurons (PNs), restoring their structure and function. Yet, despite over two decades of research, the temporal dynamics and functional stability of these fusion events in vivo remain poorly defined, largely due to reliance on static, post-mortem histological analyses that provide only a single snapshot in time. Here, using in vivo two-photon imaging of the intact cerebellum in EGFP-bone marrow chimeric mice, we visualised the dynamics of BMDC-PN interactions both in real time and longitudinally to monitor the physiological characteristics of fused PNs. Notably, we provide definitive evidence that fused cells are not transient but remain stable over extended periods in the living brain. Moreover, we demonstrate sustained transcriptional activity of donor-derived genes within fused PNs, indicating partial or complete functional integration of the BMDC nucleus. Given their accessibility and genetic tractability, BMDCs represent a practical and promising platform for targeted delivery of therapeutic genes to PNs, opening new avenues for treating neurodegenerative disease.

neuroscience↗

bioRxiv2025

Advancing Knock-In Approaches for Robust Genome Editing in Zebrafish

Precise genome editing remains a major challenge in functional genomics, particularly for generating knock-in (KI) alleles in model organisms. Here, we introduce the mini-golden system, a versatile Golden Gate-based subcloning platform that enables rapid assembly of donor constructs containing homology arms and a gene of interest. This system offers a library of middle entry vectors including diverse genes, enhancing the preparation of donor minicircles for KI applications. Using the mini-golden system, we efficiently generated a foxd3CreER KI zebrafish line, allowing conditional recombination in neural crest cells. To further improve genome editing precision, we developed a synthetic exon-based donor template strategy combined with fluorescence screening. Using this approach, we successfully engineered a targeted isoleucine-to-valine substitution (Ile-to-Val) in hbaa1.2, one of the two adult hemoglobin alpha genes in zebrafish. Importantly, despite the high sequence similarity between hbaa1.2 and its paralog hbaa1.1, our strategy specifically edited hbaa1.2, demonstrating the effectiveness of the synthetic exon approach. This method minimized undesired recombination and significantly improved the identification of lines carrying the edited genome. Together, we provide a robust toolkit for efficient and precise genome engineering in zebrafish, with broad applicability to other model systems.

developmental biology↗

bioRxiv2025

Origins and diversity of Exmoor ponies: A mitogenome framework for assessing maternal lineage diversification in endangered pony breeds

In response to growing concerns over human-driven biodiversity loss, rewilding efforts increasingly employ semi-wild herbivores to restore ecosystems. The Exmoor pony is often cited as an ancient breed retaining primitive traits suited for such projects, yet its genetic history remains underexplored. We combined studbook records, mitochondrial DNA (mtDNA) D-loop, and whole mitogenome sequences to evaluate maternal lineage diversity for improved management recommendations and the phylogenetic placement of Exmoor ponies among modern and ancient breeds. We also assessed whether data from multiple breeds already available based on D-loop sequences could be organised into a useful framework for resolving the complex history of modern horse breeds. We identified eight mtDNA haplotypes among 88 Exmoor pony samples, representing all extant maternal lines. While phylogenetic trees based on D-loop sequences lacked resolution, clustering published sequences to a mitogenome-derived haplogroup framework allowed assessment of the distribution and relationships of lineages across diverse horse populations, including ancient DNA samples and Przelwalskis horses. The most basal lineages of Exmoors were traced back to the Pleistocene, supporting their ancient origin and status as a primitive population, with a possible ancestral role in the development of some modern breeds. The founder lineages were found to be polyphyletic, with more derived haplogroups representing subsequent mixture with other domestic horse breeds. Although nuclear genome sequencing is needed to fully assess levels of admixture, we identified new haplotypes, along with rare or basal haplotypes that could be prioritised for conservation in rewilding studies. Our results highlight the potential for broad testing of hypotheses about origins and relationships among horse breeds using short regions of DNA mapped onto a more robust phylogenetic framework resolved through comparison of whole mitogenomes.

evolutionary biology↗

bioRxiv2025

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae, a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in length in infant and adult guts, and other microbiomes. Of 19 complete plasmid genomes, one was reconstructed from an E. coli isolate; others were linked to species of Citrobacter and Enterobacter via analysis of genome modification patterns. The detection of related plasmids in different Enterobacteriaceae, conjugation machinery, and more diverse modified motifs in certain plasmids compared to hosts suggests that these elements are self-transmissible, with a broad host range. The plasmids encode multi-drug efflux systems and potential secreted effectors. Up to 208 tRNAs are encoded and include sequence variants that may counter tRNA-centric defense mechanisms. Overall, the vast megaplasmid coding capacity may broaden host range, increase competitiveness, control invasion by other elements, and counter programmed cell death.

microbiology↗

bioRxiv2025

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

BACKGROUNDCiprofloxacin resistant Klebsiella pneumoniae is common or emerging in many geographies, and knowledge of local resistance rates is important for empirical therapy. Whilst there are known K. pneumoniae ciprofloxacin resistance determinants, there is a lack of systematic data on the effect of determinants, alone and in combination, and there are no publicly accessible tools for predicting resistance from whole genome sequence data. METHODSThe KlebNET-GSP AMR Genotype-Phenotype Group aggregated a matched genotype-phenotype dataset of n=12,167 K. pneumoniae species complex (KpSC) isolates from 27 countries between 2001-2021. We developed a rules-based classifier to predict ciprofloxacin resistance by categorizing the number of quinolone resistance determining regions mutations in gyrA and parC, the number of plasmid-mediated quinolone resistance genes, and the presence/absence of aac(6')-Ib-cr (which can acetylate ciprofloxacin). Predictive performance was assessed using the discovery dataset, for which we re-phenotyped discrepant isolates; and validated using externally contributed datasets (n=7,030 KpSC isolates). RESULTSThe rules-based classifier predicted R vs S/I with categorical agreement, sensitivity, and specificity >96%, and major/very major error rates <4%. Performance was similar across diverse KpSC sources (human, animal, other), species, and intra-species lineages. External validation of the classifier yielded overall 93.12% categorical agreement [95% confidence interval (CI), 92.50-93.74%], 8.65% major errors [95% CI, 7.34-9.97%], and 6.20% very major errors [95% CI, 5.51-6.90%]. We implemented the classifier in Kleborate, a command-line tool that is integrated into the Pathogenwatch web platform. Using this to assess the global distribution of ciprofloxacin resistance determinants in KpSC genomes available in Pathogenwatch (n=31,319, from 109 countries between years 2000-2023), we observed a significant positive association between national quinolone consumption rates and predicted ciprofloxacin resistance (R2=0.20, p=0.004). CONCLUSIONS Ciprofloxacin resistance phenotypes can be reasonably predicted from genotypes, which is sufficient for informing surveillance. However, unexplained resistance remains and accuracy is insufficient for clinical applications. We demonstrate the value of aggregating genotype-phenotype data to explore resistance mechanisms and develop predictors, but highlight complexities in combining phenotype data from different assays and standards.

genomics↗

bioRxiv2025

Electrophysiological Characteristics of Epidural Spinal Signals in Preclinical Models of Spinal Cord Stimulation

ObjectivesEpidural stimulation of the spinal cord evokes distinct electrophysiological responses that can be recorded epidurally. Here, we characterized evoked compound action potentials (ECAPs), doublets (secondary or tertiary ECAPs, likely of different physiological origin than primary ECAPs), evoked synaptic activity potentials (ESAPs), and electromyographic (EMG) signals in preclinical models. Our objective was to clarify the features and distinct physiological origins of these signals, in order to advance mechanistic studies and support clinical applications of spinal cord stimulation (SCS) therapy. Materials and MethodsAdult male Sprague-Dawley rats (300-440 g) were implanted with two epidural leads (caudal and rostral; each with eight electrodes) and received monopolar, biphasic stimulation (200 s pulse width) at 2 and 50 Hz, with current increased stepwise to motor threshold. Rhesus macaques (11.5 and 10.2 kg) were implanted with a single 12-electrode epidural lead and stimulated using either tripolar, triphasic pulses at 10 Hz (100 s) or tripolar, biphasic pulses at 3 Hz (80 s) up to 3xECAP threshold. Recordings were taken from non-stimulating electrodes. ResultsECAPs and EMG signals were recorded across multiple spinal segments in both rats (L1-T7) and macaques (L2-T11). Doublets presented as complex waveforms with multiple negative peaks, two in rats and three in macaques, likely representing distinct ECAPs at T11-T6 in a rat and L1-T11 in macaques. ESAPs, detectable in rats, showed anatomical specificity, over the L1/T13 vertebrae with peak responses at L1. Signal analysis included activation thresholds, amplitudes, latencies, and conduction velocities. ConclusionsThis study outlines electrophysiological signals evoked by SCS in terms of their waveform, recruitment thresholds, and putative physiological origins. We propose that, to the extent these signals reflect different aspects of spinal processing and may serve as biomarkers of dysregulated nociceptive pathways, as well as indicators of SCS efficacy or potential side effects.

neuroscience↗

bioRxiv2025

Measuring the selective packaging of RNA molecules by viral coat proteins in cells

Some RNA viruses package their genomes with extraordinary selectivity, assembling protein capsids around their own viral RNA while excluding nearly all host RNA. How the assembling proteins distinguish viral RNA from host RNA is not fully understood, but RNA structure is thought to play a key role. To test this idea, we perform in-cellulo packaging experiments using bacteriophage MS2 coat proteins and a variety of RNA molecules in E. coli. In each experiment, plasmid-derived RNA molecules with a specified sequence compete against the cellular transcriptome for packaging by plasmid-derived coat proteins. Following this competition, we quantify the total amount and relative composition of the packaged RNA using electron microscopy, interferometric scattering microscopy, and high-throughput sequencing. By systematically varying the input RNA sequence and measuring changes in packaging outcomes, we are able to directly test competing models of selective packaging. Our results rule out a longstanding model in which selective packaging requires the well-known TR stem-loop, and instead support more recent models in which selectivity emerges from the collective interactions of multiple coat proteins and multiple stem-loops distributed across the RNA molecule. These findings establish a framework for understanding selective packaging in a range of natural viruses and virus-like particles, and lay the groundwork for engineering synthetic systems that package specific RNA cargoes. Significance StatementBacteriophage MS2 packages its RNA genome into protective protein shells called capsids while excluding nearly all host-cell RNA. Engineering synthetic capsids with similar selectivity could enable a broad range of RNA-based technologies, including CRISPR gene editing systems, mRNA vaccines, and other emerging RNA-based therapeutics. Our study shows that selective packaging in MS2 is not dictated by a single, high-affinity RNA-protein interaction but instead emerges from the collective interactions of multiple coat proteins and an ensemble of stem-loops distributed across the RNA molecule. By establishing these collective interactions as the basis of selectivity, our findings provide a foundation for engineering synthetic capsids capable of selectively packaging target RNAs for next-generation RNA-based technologies.

biophysics↗

bioRxiv2025

Epidermal Resident Memory T Cell Fitness Requires Antigen Encounter in the Skin

CD8+ tissue resident memory T cells (TRM) develop from effectors that seed peripheral tissues where they persist providing defense against subsequent challenges. TRM persistence requires autocrine TGF{beta} transactivated by integrins expressed on keratinocytes. TRM precursors that encounter antigen in the epidermis during development outcompete bystander TRM for TGF{beta} resulting in enhanced persistence. ScRNA-seq analysis of epidermal TRM revealed that local antigen experience in the skin resulted in an enhanced differentiation signature in comparison with bystanders. Upon recall, TRM displayed greater proliferation dictated by affinity of antigen experienced during epidermal development. Finally, local antigen experienced TRM differentially expressed TGF{beta}RIII, which increases avidity of the TGF{beta}RI/II receptor complex for TGF{beta}. Selective ablation of Tgfbr3 reduced local antigen experienced TRM capacity to persist, rendering them phenotypically like bystander TRM. Thus, antigen driven TCR signaling in the epidermis during TRM differentiation results in a lower TGF{beta} requirement for persistence and increased proliferative capacity that together enhance epidermal TRM fitness.

immunology↗

bioRxiv2025

Corticospinal, reticulospinal, and motoneuronal contributions to fatigability during a sustained contraction of the elbow flexors

Synaptic input to the motoneuron pool is altered during fatiguing muscle contractions. In humans, the corticospinal tract is often studied, with equivocal findings regarding its role in the reduction of force. To date, the involvement of the reticulospinal tract during states of fatigue has not been explored. Fourteen participants (28{+/-}6 years, nine males) visited the laboratory twice, first for a familiarisation, then an experimental trial. Participants completed a 5-min sustained elbow flexor contraction at an intensity eliciting 40% of the EMG recorded during a maximal isometric voluntary contraction (MVC). Before, during, and after the contraction, transcranial magnetic stimulation and electrical cervicomedullary stimulation were used to elicit motor evoked potentials (MEPs) and cervicomedullary evoked potentials during the silent period (SP-CMEPs) respectively, with CMEPs also being evoked in combination with a startling acoustic sound (CMEPcon). Electrical stimulation of the brachial plexus was used to evoke maximal compound action potentials of the elbow flexors (Mmax). The 5-min contraction induced a 53% loss of force (p<0.001), with no change in background EMG ([~]4% Mmax, p=0.293). Neither MEP amplitude (p=0.246) nor CMEPcon ratio (p=0.489) were altered during the contraction. Whereas CMEP and SP-CMEP amplitudes were reduced by [~]20 and 50%, respectively (p<0.001) and remained depressed post-task. The results suggest that neither corticospinal nor reticulospinal tract excitability was altered during a 5-min constant-EMG task at 40% maximal EMG. Instead, the aetiology of the neural contribution to fatigability appeared to be primarily related to the loss of motoneuron excitability.

neuroscience↗

bioRxiv2025

Enhanced virulence and stress tolerance are signatures of epidemiologically successful Shigella sonnei

Shigellosis is a leading cause of diarrhoeal deaths worldwide, with Shigella sonnei increasingly implicated as a dominant agent. S. sonnei is divided into five monophyletic lineages all sharing a single O-antigen, yet most contemporary infections are caused by just a few clonal sub-lineages within globally dominant Lineage 3 that are quite distinct from the widely used Lineage 2 laboratory strain 53G. Factors underlying the success of these globally dominant lineages remain poorly understood in part due to a lack of complete genome sequences and available animal models. Here, we utilise a novel reference collection of representative Lineage 1, 2 and 3 isolates with complete genome sequences, and find that epidemiologically successful S. sonnei harbour fewer genes encoding putative immunogenic components whilst key virulence-associated regions (such as the type three secretion system and O-antigen) remain highly conserved. Using a zebrafish infection model, we discover that Lineage 3 isolates are most virulent, driven by significantly increased dissemination and a greater neutrophil response. We show that Lineage 3 isolates have increased tolerance to complement-mediated killing and acidic conditions alongside upregulated expression of group four capsule synthesis genes. Consistent with these observations, infection of primary human neutrophils revealed that Lineage 3 isolates are more tolerant of phagosomal killing. Together, our findings link the epidemiological success of S. sonnei to heightened virulence and stress tolerance and highlight zebrafish as a valuable platform to illuminate factors underlying establishment of Shigella epidemiological success.

microbiology↗

bioRxiv2025

A public resource of 15 genomically characterised representative strains of Shigella sonnei

Shigella sonnei is rapidly emerging as the dominant agent of shigellosis, an enteric disease responsible for a significant burden of morbidity and mortality worldwide. Whole-genome sequencing of S. sonnei isolated over the last three decades has revealed phylogenomic diversity within the population and the emergence of multiple lineages associated with distinct epidemiological patterns such as resistance to critical antimicrobials and/or transmission within different groups. However most experimental work on S. sonnei biology and pathogenicity has focused on a single laboratory strain (53G), which is phylogenetically distant from currently circulating strains. Here we introduce a set of 15 phylogenetically diverse and epidemiologically relevant S. sonnei isolates made available through publicly accessible culture collections as a resource for laboratory science. We present their complete whole-genome sequences, including the pINV invasion plasmid (missing from a large proportion of public genome data due to loss during laboratory culture). Finally, the characterisation and comparison of these complete genome sequences highlight evidence for ongoing adaptive evolution in S. sonnei, featuring the accumulation of insertion sequences, gene pseudogenisation and structural variation. Significance as a BioResource to the communityGenomic analysis of Shigella has historically been challenging due to presence of hundreds of repetitive sequence elements (which can cause fragmented assemblies) and loss of the pINV invasion plasmid (essential to virulence) during laboratory culture. Furthermore, most experimental work on S. sonnei pathogenicity uses a lab strain that is phylogenetically distant from circulating isolates. To support S. sonnei experimental and in silico research and increase its relevance to current clinical problems, we report here the complete, high-quality genome sequences of 15 S. sonnei isolates, each selected to represent distinct sub-clades of epidemiological interest. We also make the corresponding strains publicly available in national reference culture collections. Data summaryAll sequencing reads and complete assemblies have been deposited into the National Center for Biotechnology Information (NCBI) database (accessions to be determined). Genome assemblies and Bakta annotations used in the analysis can be found in Figshare (https://doi.org/10.6084/m9.figshare.28302986) together with Mauve multiple-sequence alignments for the chromosome and pINV plasmid sequences, and genome-scale metabolic models produced for each strain. Pure cultures of all strains were deposited in the publicly accessible National Collection of Type Cultures (NCTC, UK) or the "Collection de lInstitut Pasteur" (CIP, France) (accessions to be determined).

microbiology↗

bioRxiv2024

Imaging synaptic density in ageing and Alzheimer's Disease with -SynVesT-1

Monitoring synaptic injury in neurodegenerative diseases may provide new insights into the evolution of the degenerative process as well as a potential mechanism to target for preservation of function. Synaptic density imaging with PET is a relatively new approach to this issue. However, there are remaining questions about technical approaches to data analysis including reference region selection, and how specific phenotypic presentations and symptoms of Alzheimers Disease (AD) are reflected in alterations in synaptic density. MethodsUsing an SV2A PET ligand radiolabeled with the 18F isotope ([18F]-SynVesT-1) we performed sensitivity analyses to determine the optimal reference tissue modelling approach to derive whole brain ratio images. Using these whole brain images from a sample of young adults, older adults, and patients with varied phenotypic presentations of AD we then contrast regional SV2A density and in vivo AD biomarkers. ResultReference tissue optimisation concluded that a cerebellar grey matter reference region is best for deriving whole brain ratio images. Using these whole brain ratio images, we find a strong inverse association between [18F]-SynVesT-1 PET uptake and amyloid beta and tau PET deposition. Finally, we find that individuals with lower temporal grey matter volume but higher temporal [18F]-SynVesT-1 PET uptake show preserved performance on the MMSE. Conclusions[18F]-SynVesT-1 PET shows a close association with in vivo AD pathology and preserved SV2A density may be a possible marker for resilience to neurodegeneration.

neuroscience↗