Gut function exhibits 24 h (circadian) rhythmicity, in part driven by intrinsic clocks within intestinal epithelial cells (IECs). The gut microbiome also demonstrates circadian rhythms in composition and function, important for maintenance of metabolic, immune and gut health. Here, we determined the influence of feeding behaviour on the 24 h colonic landscape using an interval feeding paradigm, whereby food intake was partitioned equally across the 24 h day. RNAseq analysis revealed that the IEC intrinsic clock persists in the absence of diurnal feeding rhythms; however, a subset of key transcripts loses rhythmicity, demonstrating that cell extrinsic temporal cues contribute significantly to the maintenance of the rhythmic gut transcriptome. Furthermore, interval-fed mice demonstrated a striking loss of rhythms in secretory IgA, a critical regulator of the temporal landscape of the gut microbiome. In keeping, rhythmicity within the microbiota and microbial-derived short chain fatty acids was significantly diminished. This work highlights the importance of daily rhythms in feeding behaviour for the maintenance of rhythmic processes within the gut, with implications for metabolic and immune health.
Cell-to-cell communication is essential for maintaining homeostasis and coordinating complex biological processes in multicellular organisms. Classically, cells communicate using secreted peptides and metabolites and through cell contact-dependent signaling. Emerging studies over the past 20 years indicate that many cell types, including innate immune cells such as macrophages, participate in a process called intercellular mitochondria transfer, in which macrophages either donate their own mitochondria to other cells or accept mitochondria originating from another cell type. This raises the intriguing possibility that macrophages use mitochondria transfer as a mechanism of cell-to-cell communication. In this review, we describe the distinct mechanisms and functional roles of mitochondria transfer in macrophages across different organ systems and highlight how this biology contributes to health maintenance and disease pathogenesis.
Voltage-gated sodium channels (VGSCs) mediate neuronal excitability and synaptic transmission and are functionally relevant targets for volatile anaesthetic (VA) actions. Here, we show that multiple VAs at clinically relevant concentrations share binding sites on NavMs, a prokaryotic VGSC. Sevoflurane, a representative VA, interacts with NavMs and NaChBac with functional effects paralleling those on human VGSCs, including modulation of channel inactivation. X-ray crystallography of purified NavMs reveals an atomic-resolution VA binding site in a VGSC, in which sevoflurane displaces lipid to occupy a membrane-embedded hydrophobic pocket. Alanine substitution of an invariant tyrosine within this binding pocket abolishes sevoflurane binding and eliminates the sevoflurane-induced hyperpolarising shift of steady-state inactivation. Sevoflurane modulates both fast and slow inactivation of human Nav1.1, demonstrating VA modulation of steady-state slow inactivation in a neuronal VGSC. Supporting evidence shows that VAs interact with homologous sites in human VGSCs. These findings define a VA binding site in VGSCs that supports a membrane-assisted pathway for modulating channel gating and neuronal activity in general anaesthesia.
The use of advanced analytics in public health policy remains hindered by a disconnect between researchers, policymakers and technical experts. Bridging this gap requires intentional knowledge translation strategies that facilitate interdisciplinary collaboration and real-world application of research findings. Hackathons, which bring together diverse stakeholders in a time-bound, solution-oriented format, offer an approach to address this challenge. In January 2025, the MRC Centre for Global Infectious Disease Analysis and the Centre for Epidemiological Modelling and Analysis at the University of Nairobi organised the Bridging the Gap Hackathon, designed to strengthen collaboration between academia, policy and public health practitioners in Kenya. The hackathon convened researchers, software engineers and policymakers to co-develop data-driven tools to tackle public health challenges identified by Kenya's Ministry of Health and the Directorate of Veterinary Services. Over five days and using a structured multi-stage process, six interdisciplinary teams developed prototype solutions to improve outbreak surveillance, vaccine deployment, data quality monitoring and health workforce estimation. This paper reflects on the hackathon's structure, participant experiences and project outcomes, highlighting key lessons for future knowledge translation initiatives. Our findings suggest that hackathons can serve as effective platforms for accelerating interdisciplinary research impact, fostering engagement between policymakers and researchers and promoting the development of solutions to public health issues.
Pregnant women are vulnerable to sexually transmitted infections (STIs), which can lead to adverse pregnancy outcomes. Evidence on STI prevalence and determinants among pregnant women in peri-urban Malawi remains limited. This study aimed to determine human immunodeficiency virus (HIV) and syphilis prevalence, identify associated factors and assess antenatal care (ANC) service quality among pregnant women in Blantyre peri-urban health facilities. A cross-sectional mixed-methods study was conducted at three peri-urban health centers (Zingwangwa, Ndirande, and Limbe). Quantitative data were retrospectively collected from facility records between January and June 2022 to determine STI diagnoses. Structured questionnaires assessed contributing factors and ANC service quality. Among 5,634 pregnant women tested for HIV, the prevalence of serologically detected HIV was 10.4% (95% confidence interval (CI): 9.7-11.3). Among 2,983 women tested for syphilis, the prevalence was 11.1% (95% CI: 10.0-12.3). The prevalence varied significantly by facility (p < 0.001), with the highest burden recorded at Limbe (HIV: 12.5%, 95% CI: 11.1-13.9; syphilis: 14.8%, 95% CI: 12.8-16.9), versus Ndirande (HIV: 10.5%, 95% CI: 9.1-12.1; syphilis: 8.4%, 95% CI: 6.7-10.3) and Zingwangwa (HIV: 7.5%, 95% CI: 6.2-8.9; syphilis: 8.9%, 95% CI: 7.0-11.0). Among women tested for both infections (n = 2,917), co-infection prevalence was 2.0% (95% CI: 1.6-2.6). Among 91 interviewed women (aged 14-43 years), unemployment (odds ratio (OR) 2.74, 95% CI: 1.07-7.03; p = 0.033) and lack of partner treatment (OR 2.83, 95% CI: 1.12-7.19; p = 0.025) were significantly associated with STI positivity. Although most participants were satisfied with ANC services, 64% reported that their partners were not treated, and no formal follow-up system existed, revealing gaps in partner management. The high HIV and syphilis prevalence highlights a pressing public health concern. Strengthening antenatal screening, improving partner management and implementing targeted interventions are essential to reduce HIV and syphilis burden among pregnant women in peri-urban Blantyre.
The development and progression of respiratory diseases are influenced by both the local pulmonary microenvironment and the intestinal ecosystem. Research on the gut-lung axis has shown that diverse small-molecule metabolites produced or modified by the gut microbiota can cross the intestinal barrier and enter the systemic circulation, where they may modulate immune-cell response thresholds, functional polarisation, and inflammatory dynamics in the distal lung. The local respiratory microbiota may also contribute to the pulmonary metabolic microenvironment, although its role in metabolite production and immune regulation remains less clearly defined. This review summarises the metabolic features of the gut and respiratory microbiota, focusing on the production, systemic distribution, and immunomodulatory mechanisms of microbiota-associated metabolites, including short-chain fatty acids, other short-chain carboxylic acids, and amino acid-derived metabolites, with attention to their effects on respiratory immune-cell populations. These mechanisms include metabolite-sensing G protein-coupled receptor signalling, histone deacetylase inhibition, and aryl hydrocarbon receptor-dependent mucosal immune programmes. At the disease level, current evidence suggests that these metabolites mainly influence viral infections, bacterial infections, and chronic inflammatory lung diseases by regulating immune-response intensity, persistence, and tissue tolerance, rather than directly mediating pathogen clearance. Finally, this review discusses the key challenges and future directions for moving from associative studies to causal validation and translational applications.
We have been funded to examine post-incarceration health and social outcomes for all people incarcerated in New South Wales, Australia, 2000-2022; assess treatment and services for drug dependence and serious mental illness; and project the impact of expanding intervention coverage. We will use a linked cohort, the Prison Outcomes STudy (POST), which we also describe. The POST cohort was established using linked administrative data for all adults (≥ 18 years) admitted to full-time custody in New South Wales, 2000-2022. Custody records were probabilistically linked to 18 health, justice and mortality datasets. We report baseline sociodemographic and custody characteristics and the frequency of key post-release events. 200,486 adults, 15% women (n = 30,698), were incarcerated, with 2,282,367 person-years of follow-up and 11% (257,545 person-years) of follow-up spent in custody. First Nations people comprised 27% of the cohort. Half (48%) of the cohort (n = 95,563) had at least one contact with community mental health services, and 27% (n = 54,100) had received alcohol and other drug treatment. POST will provide population-wide evidence on health and social outcomes after custody, including the effects of treatment for drug dependence and serious mental illness. We will compare across subgroups and the outcomes of post-release service engagement. Mathematical modelling will test the impact of expanding access to care in prison and post-release on outcomes in the community. POST will inform policy and service responses across justice, health and community settings to reduce harms among people who experience incarceration.
Lymphatic vessels perform diverse functions, ranging from fluid homeostasis to immune regulation, and arise from multiple cellular origins to form organ-specific networks. Despite their importance in kidney disease and transplant immunity, the origins of kidney lymphatics are unknown. Using genetic lineage tracing in mice, we identify two origins of kidney lymphatics. Most kidney lymphatics arise from a Tie2+ endothelial origin shared by other organs. However, Osr1+ mesoderm generates approximately 15% of kidney lymphatics, without contributing to heart, mesentery, and skin lymphatics. Interrogating single-cell transcriptomics data of mice and humans reveals lymphatic progenitors within Osr1+ mesoderm. Lymphatic clusters forming by de novo assembly originate from both Osr1+ and Tie2+ lineages. Deleting the lymphatic specification gene Prox1 in Osr1+ mesoderm reduces lymphatic cluster number, impairing overall lymphatic network complexity, with lower glomerular number. Thus, an Osr1+ mesodermal origin contributes to organ-specific lymphatic assembly, with consequences for kidney health, disease, and regeneration.
SEMA6A is a transmembrane protein that plays a role in axon guidance and cell migration. Sema6a null mice have cerebral anatomical defects and altered social interactions and working memory. However, the phenotypes associated with loss of SEMA6A function have not been clearly defined in humans. Here we describe 11 individuals who are heterozygous for putatively damaging variants affecting SEMA6A. All of these individuals (100%) had neurodevelopmental phenotypes that included developmental delay, intellectual disability, and/or autism spectrum disorder. Abnormal behaviors were seen in 73% with oppositional defiant disorder being diagnosed in 27% and acting out, overeating, and tantrums each being described in 18% of individuals. Disorders of attention were documented in 45%. Among the six individuals who had a brain MRI, 50% had at least one abnormal finding. Of the eight SEMA6A variants with known inheritance, five were inherited. Taken together, our data suggest that loss of SEMA6A function may be associated with an increased risk of neurodevelopmental phenotypes, abnormal behaviors, disorders of attention, and brain anomalies. Additional studies will be needed to determine if SEMA6A haploinsufficiency is best characterized as an autosomal dominant disorder with incomplete penetrance or as a risk factor for these phenotypes.
The twin-arginine translocation (Tat) system is a mechanistically unique protein transport pathway moving folded proteins across membranes. It is found in all domains of life and is essential for bacterial virulence and plant photosynthesis. The membrane proteins, TatA, TatB and TatC form a core complex to which substrate proteins bind, triggering the recruitment of additional TatA protomers to form the transport site. Here we present cryo-electron microscopy structures of the prototypical TatBC complex from Escherichia coli and the atypical complexes from Nitratifactor salsuginis and Myxococcus xanthus in a resting state, alongside TatAC substrate-bound TatBC and TatABC complexes from E. coli in the early stages of transport. These structures demonstrate that substrate proteins associate with the core complex solely through their N-terminal signal peptides. The Tat targeting sequences of the signal peptides make specific contacts with TatC, and the peptide body is clamped by TatB. The core complex contains highly tilted transmembrane helices that drive extreme local membrane thinning. On the basis of our structures and biochemical and functional analyses, we propose a model for the early steps in Tat transport.
Ultra-low-field (ULF) MRI facilitates neuroimaging access, yet its application in early infancy is constrained by low resolution and contrast, and the limited suitability of existing segmentation tools. In this work we introduce and validate miniMORPH, an open-source pipeline for automated brain volumetry from 0.064T T2-weighted MRI acquired across infancy and toddlerhood. ULF scans were acquired from infants aged 2 to 27 months across two cohorts in South Africa and Uganda. Age-specific templates and priors were used to segment major brain tissues and substructures. Validation used two high-field (HF) references: (i) expert manual HF segmentations for key ROIs across ages, and (ii) automated HF segmentations from SuperSynth on paired HF-ULF scans. We quantified (a) between-subject ordering across modalities using Pearson's correlation (r) and (b) systematic scaling differences using percentage error (PE) and time-corrected percentage error (CPE), stratifying performance by cohort and age. Face validity was also tested via mixed-effects models of age, sex, and birthweight. miniMORPH generated anatomically plausible segmentations of major brain regions across infancy. In paired HF-ULF comparisons, between-subject ordering was generally preserved across many ROIs, with stronger correspondence in the South African cohort than in the Ugandan cohort at 12 months. Systematic scaling offsets were most evident in CSF-rich or boundary-sensitive compartments, with consistently negative CPE for ventricles and cerebellum. Performance varied with age, showing the greatest variability at 3 months. miniMORPH successfully captured regional age-related growth trajectories. Sex-dependent volumetric differences were widespread but attenuated after intracranial volume correction. Low birthweight infants exhibited reduced regional volumes and altered growth trajectories. Taken together, these findings indicate that miniMORPH enables volumetric analysis of ULF infant MRI and preserves between-subject variation suitable for developmental and group analyses. ROI- and cohort-specific offsets, particularly in CSF-rich regions, may require calibration when absolute volumes are needed. The pipeline is openly available at https://github.com/UNITY-Physics/fw-minimorph.
Healthy sleep is electrographically defined by oscillations that drive alternating up- and down-states that regulate neuronal excitability. Slow oscillations-the hallmark rhythm of deep nonrapid eye movement sleep, temporally organize faster, more focal rhythms, including thalamocortical sleep spindles and hippocampal sharp-wave ripples. These cascading rhythms have been implicated as a critical activity-dependent mechanism that binds coordinated neuronal activity to support systems-level consolidation of previous experience into long-term memory. Epilepsy is a disease characterized by sporadic pathologic neuronal activity, including interictal epileptiform discharges and seizures. Epileptic activity is frequently potentiated during sleep, but the interactions with specific graphoelements that comprise sleep microarchitecture are complex. Critically, the diverse ways in which epileptic activity interdigitates with sleep microstructure imply that epileptiform activity can distort and disrupt the same sleep rhythms that normally support memory consolidation. Cognitive comorbidities are common in epilepsy, and impairments in memory consolidation are increasingly recognized. In this review, we synthesize leading evidence on the complex interactions between sleep microarchitecture and interictal epileptiform discharges. We first summarize electrophysiologic data on how slow oscillations interact with spindles and interictal epileptiform discharges and then assemble these findings into a unifying framework for interictal epileptiform discharge-slow oscillation-spindle dynamics. Finally, we review evidence on how disruption of these sleep oscillations can contribute to cognitive dysfunction in epilepsy and highlight implications for developmental and epileptic encephalopathies.
Chemical proteomics approaches often yield low peptide recovery because they aim to enrich low-abundance proteins. Poor sample handling further reduces recovery through peptide adsorption to plastic surfaces and losses due to vacuum evaporation. We systematically mapped these losses across buffers, volumes, plastics and pH, then developed an Evotip-compatible handling protocol that minimizes adsorption and removes the need for vacuum evaporation. Losses to plastic adsorption and vacuum evaporation were most apparent at low inputs (< 200 ng) and with larger volumes (> 20 µL) but were also dependent on acidification as well as the buffer and plastic used. The optimized workflow: direct acidification of peptides, frozen storage if needed, and direct loading onto Evotips, resulted in up to ∼90-fold gains versus workflows incorporating vacuum concentration steps, a common practice in proteomics sample preparation, when peptide input was limited to 10 ng. This optimized sample handling method enables high-throughput chemical proteomics by reducing manual handling steps and enables the characterization of low abundance proteins previously lost during sample preparation.
To evaluate the association between prematurity and dental caries occurrence at four years of age and to assess whether variables related to dental development, tooth eruption, and oral healthcare mediate this association. A longitudinal study was conducted using data from the 2015 Pelotas (RS) Birth Cohort. The outcome was dental caries at four years, classified using ICDAS. Gestational age at birth was estimated by ultrasonography examination in 3 407 (79.7%) cases, with 3 242 (75.8%) performed during the 1st or 2nd trimester. Mediating variables included enamel defects, number of teeth at 12 months, oral hygiene practices, sugar consumption, and maternal guidance. The variables were selected using a directed acyclic graph (DAG). Associations were estimated using Poisson regression models, and mediation was assessed through structural equation modelling (SEM). Analyses were performed using STATA 18.0. Children born before 34 weeks had a 40% lower incidence of caries at four years compared to those born after 39 weeks, and those born between 37 and 38 weeks had a 20% lower incidence. The number of teeth mediated this relationship, indicating that lower gestational age was associated with fewer teeth at 12 months and a lower occurrence of caries. The findings highlight the importance of early dental monitoring and suggest preventive programs starting with the eruption of the first tooth, given its relevance in the occurrence of caries.
Hyperactivating mutations in guanylyl cyclase C (GC-C) are monogenic causes of early-onset inflammatory bowel disease, familial diarrheal syndrome and congenital secretory diarrhea. The mechanisms linking elevated cGMP levels to immune imbalance remain poorly defined. Here, using a preclinical model of a disease-associated GC-C mutation, we observe pleiotropic alterations in the small intestinal epithelium. Transcriptomic and functional analyses revealed impaired Paneth and goblet cell differentiation, compromised barrier integrity, heightened epithelial permeability, and increased proinflammatory cytokine levels. Intestinal organoids from mutant mice exhibited amplified cGMP responses to GC-C ligands and defects in secretory lineage specification, confirming cell-autonomous mechanisms. Strikingly, oral zinc administration suppressed aberrant GC-C activity, normalized cGMP levels and restored barrier function. These findings highlight the central role of epithelial cGMP signaling in coordinating barrier integrity and immune-epithelial interactions, and identify zinc as a tractable therapeutic strategy for GC-C-mediated intestinal disorders.
Under low concentrations of antibiotics causing DNA damage, Escherichia coli bacteria can trigger stochastically a stress response known as the SOS response. While the expression of this stress response can make individual cells transiently able to overcome antibiotic treatment, it can also delay cell division, thus impacting the whole population's ability to grow and survive. In order to study the trade-offs that emerge from this phenomenon, we propose a bi-type age-structured population model that captures the phenotypic plasticity observed in the stress response. Individuals can belong to two types: either a fast-dividing but prone to death "vulnerable" type, or a slow-dividing but "tolerant" type. We study the survival probability of the population issued from a single cell as well as the population growth rate in constant and periodic environments. We show that the sensitivity of these two different notions of fitness with respect to the parameters describing the phenotypic plasticity differs between the stochastic approach (survival probability) and the deterministic approach (population growth rate). Moreover, under a more realistic configuration of periodic stress, our results indicate that maximal population growth can only be achieved through fine-tuning simultaneously both the induction of the stress response and the repair efficiency of the damage caused by the antibiotic.
The inward rectifying human potassium channel 7.1 (Kir7.1) is a vital ion channel involved in maintaining cellular homoeostasis and electrical signalling across various tissues and organs, activated by phosphatidylinositol 4,5-bisphosphate (PIP2). A genetically inherited loss-of-function mutation in Kir7.1 (R162W) has been linked to the rare retinal disease Snowflake Vitreoretinal Degeneration (SVD), for which there are currently no curative treatment options. Here, the cryo-EM structures of wild type Kir7.1 and the R162W disease-related variant are presented, which unveil the molecular basis of SVD: the reorientation of the mutant tryptophan side chains into the pore impedes the flow of potassium ions, which would result in the loss of Kir7.1 transport function. Furthermore, this investigation shows that PIP2 binding widens the helix bundle crossing gate diameter, even in the absence of a docked cytoplasmic domain. This observation contrasts with other Kir-PIP₂ complexes and suggests that Kir7.1 may adopt an intermediate conformation during channel activation. These findings provide a structural basis for Kir7.1 loss of function in SVD and provide a framework for future therapeutic development.
Family members of survivors of critical illness are known to experience adverse outcomes in the months following the critical care admission, which can impact their physical, social and emotional health. This protocol describes the Family or Caregiver Outcomes after critical illness (FOCUS) study, which aims to develop a core outcome set (COS) for trials involving family members of critical care patients across the continuum of care. A modified Delphi consensus process with researcher, clinician and patient/caregiver stakeholder groups and consensus meetings for ratification of findings, resolving uncertainty and developing an action plan for COS implementation. The FOCUS COS will inform relevant stakeholders about important outcomes for family members of critical care patients and may enhance the future design and conduct of trials in this area. This study has been approved by the University of Cambridge Psychology Research Ethics Committee. The COS will be disseminated through peer-reviewed publications and engagement with key stakeholders. COMET database (https://comet-initiative.org/Studies/Details/1977).
Pneumonia is the leading infectious disease killer worldwide and commonly requires admission to critical care. Despite its prevalence, the underpinning biology of severe pneumonia remains incompletely understood. Here we perform multifaceted assessments of bronchoalveolar transcriptome, cytokines, microbiology, and clinical features to biologically characterise a cohort of patients with suspected severe pneumonia. Our data implicate three lung-restricted transcriptionally defined severe pneumonia endotypes (termed 'Pneumotypes' (Pn)). All three Pneumotypes have comparable clinical presentations and severity of respiratory failure but experience divergent outcomes. Pn1, the most common, is characterised by low alveolar cytokines, expanded tolerogenic macrophages and epithelial damage. Pn3 is characterised by immature neutrophil infiltration, IL-6-STAT3 activation and longer duration of mechanical ventilation. Pn2 displays the fastest resolution, exhibiting a balanced immune response and epithelial-endothelial repair signatures. We identify and validate mechanistically distinct phenotypes in the lungs of patients with suspected pneumonia and acute lung injury, implicating targets for personalised therapy.
Risk stratification for advanced colorectal polyps typically relies on colonoscopy and/or pathology findings. However, there is growing interest in whether noninvasive features available prior to colonoscopy can help identify patients at higher risk. Such approaches may enhance clinical decision-making by prioritizing surveillance for individuals most likely to harbor high-risk polyps, when colonoscopy resources are limited while potentially reducing unnecessary procedures in lower-risk patients. Importantly, the use of noninvasive, pre-procedural information may also help promote more equitable access to risk stratification, particularly in settings where colonoscopy resources are limited or unevenly distributed. We aimed to develop and externally validate machine learning models to predict high-risk colorectal polyps using only noninvasive, pre-colonoscopy demographic, clinical, and behavioral features in a diverse, predominantly African American, urban cohort. We conducted a retrospective cohort study using demographic, lifestyle, and comorbidity data from patients who underwent colonoscopy at Howard University Hospital to develop and validate several machine learning models, including neural networks, random forest, support vector machines (SVM), Naïve Bayes, logistic regression, decision trees, k-nearest neighbors (KNN), and XGBoost, for predicting high-risk colorectal polyps. High-risk polyps (HRP) were defined as villous or tubullovillous adenomas, high-grade dysplasia, polyps ≥ 10 mm in size, and/or the presence of ≥ 3 polyps per procedure; all other cases were classified as low-risk polyps (LRP). The dataset included 4,681 patients from 2015 to 2022 used for internal validation and 1,562 patients from 2023 to 2024 used for external validation. Model performance was evaluated using the area under the receiver operating characteristic curve (ROC-AUC), precision-recall area under the curve (PR-AUC), accuracy, precision, recall, and F1 score. Model interpretability and feature contribution were assessed using SHapley Additive exPlanations (SHAP). Overall predictive performance was moderate using noninvasive pre-colonoscopy features. The neural network demonstrated the strongest overall discrimination, achieving the highest internal validation performance (ROC-AUC 0.78, PR-AUC 0.75, accuracy 0.72), but showed reduced performance in the external cohort (ROC-AUC 0.67, accuracy 0.66), suggesting potential overfitting or temporal feature drift. In contrast, simpler models including Naïve Bayes, SVM, and XGBoost exhibited lower internal performance (ROC-AUC 0.54-0.59) but more stable generalization to the external cohort (ROC-AUC 0.52-0.63; accuracy approximately 0.53-0.60). Model interpretability analysis using SHAP identified age, smoking status, sex, occupation, race, colonoscopy indication, and family history of colorectal cancer as the most influential predictors, highlighting contributions from both traditional clinical and sociodemographic factors. Prediction of HRP using routine pre-colonoscopy data is feasible but demonstrates limited generalizability across cohorts. These findings highlight the clinical potential and limitations of pre-procedural risk modeling, especially in diverse, underserved populations. Integration of additional data modalities may be required to achieve clinically robust and equitable prediction tools.