Biology subjects

Jones, J.

Publications and source records attributed to Jones, J..

At least 19 recordsLinked to original sources

bioRxiv2026

The molecular basis of hard cornification in the keratinized jaw sheaths and keratodonts of anuran tadpoles

Hard cornification is the developmental process that produces the hardened epidermal structures that characterize tetrapod diversity, including scales, feathers, hair, and claws. This process relies on keratin proteins and additional reinforcing proteins that assemble, cross-link, and strengthen tissues to become mechanically resilient. Although the molecular composition of hard cornified tissues is known to vary among tetrapods, the program is least understood in amphibians. Within frogs, hard cornification occurs in the mouthparts of most tadpoles and in the nuptial pads, hindfoot claws, and foot tubercles of some adults. We characterized transcriptomic profiles of Bombina orientalis tadpoles at three developmental stages before, during, and after mouthpart cornification. We identified 25 keratin genes orthologous to amniote hard keratins in the B. bombina genome, 18 of which are upregulated in cornifying larval mouthparts. Furthermore, two of these hard keratin paralogs and an amphibian epidermal differentiation gene exhibit distinct spatial expression patterns within the jaw sheaths and keratodonts evidenced by in situ hybridization, suggesting they have discrete functional roles. The newly discovered diversity of the hard keratin repertoire in Bombina , and the concurrent expression of many of these paralogs in tadpole mouthparts, suggests that anuran hard cornification is much more complex than adult cornified traits thus far characterized in Xenopus frogs. Our results also challenge the notion that the diversification of keratins in Amphibia is primarily associated with the transition to more terrestrial habits, and may instead be shaped, in part, by the novel feeding apparatus of aquatic tadpoles.

evolutionary biology↗

bioRxiv2026

Design and Application of a μSiM Outer Blood-Retinal Barrier (OBRB) Model as a Drug Development Tool

The outer blood-retinal barrier (OBRB) is the primary interface through which systemically circulating drugs reach the retina. A tool that measures delivery across this barrier would support the development of targeted therapies as alternatives to repeated intravitreal injection, and the screening of drugs that reach the retina as an off-target toxicity. Such a tool should deliver drugs fluidically through a vascular compartment, measure transport across the retinal pigment epithelium (RPE), and display disease phenotypes relevant to efficacy. Here we adapt the SiM platform, which places epithelium and endothelium in direct juxtaposition across a permeable, optically transparent silicon nitride nanomembrane. ARPE-19 and human umbilical vein endothelial cells (HUVECs) were used as development cell sources. ARPE-19 monocultures reached a transepithelial electrical resistance of 68 {+/-} 26 {Omega} cm2 by 28 days, and ARPE-19 + HUVEC co-cultures reached a small-molecule permeability of 6.34 {+/-} 1.3 x 10-4 cm min-1 within 14 days, a state reported elsewhere only after longer culture. The barriers developed an intervening basement membrane. Drugs perfused through the basal vascular channel crossed into an open apical well, where sampling and mass spectrometry showed transport correlating with lipophilicity, as reported in vivo. The device also displayed two clinically relevant phenotypes. Digoxin at a clinically toxic concentration reduced viability in the co-barrier by about half and doubled permeability. In a vascularized configuration, VEGF drove endothelial invasion of the RPE layer, as seen in neovascular AMD. The SiM-OBRB therefore satisfies basic design criteria for measurement of drug bioavailability, toxicity, and efficacy.

bioengineering↗

bioRxiv2026

Metagenomic analysis of the effects of European bison Bison bonasus (Linnaeus, 1758) presence on soil community structure and function in West Blean and Thornden Woods, Kent

The reintroduction of extinct or endangered species to restore ecosystem function is an essential aspect of rewilding. The Wilder Blean Project at West Blean and Thornden Woods in Canterbury, UK, is committed to rewilding natural processes and enhancing biodiversity in one of England's oldest and largest areas of ancient woodland. The introduction of European bison (Bison bonasus) is an important part of the project. However, how the reintroduction of large herbivores influences local biodiversity and ecosystem functions during the early stages of rewilding remains poorly understood. Soil samples were collected from the same sampling sites before and two years after bison were reintroduced and profiled by metagenomic sequencing using Oxford Nanopore Technologies sequencing platforms. The results showed that the alpha diversity of soil organisms did not change significantly before and after the introduction of European bison, while beta diversity showed modest shifts in community composition. The relative abundance of some nitrogen-fixing and photosynthetic microbial genera showed declines in the 2024 Bison Area, while the mycorrhizal fungus genus Rhizophagus was significantly less abundant than in the 2024 Control Area. Despite relatively stable taxonomic diversity, functional composition differed significantly between the 2022 and 2024 Bison areas and among the 2024 rewilding treatments, revealing a decoupling between taxonomic diversity and functional composition. Amino acid synthesis pathways and carbon metabolism pathways were significantly enriched. These findings highlight the potential of long-read Oxford Nanopore metagenomics to reveal functional shifts that may not be apparent from taxonomic diversity alone. Although these early-stage responses cannot yet predict long-term rewilding trajectories, continued longitudinal monitoring integrating microbial, soil physicochemical, and ecosystem-level measurements will be essential to determine the persistence and ecological significance of these functional shifts.

ecology↗

bioRxiv2026

Integrated multi-omics profiling of gut bacterial extracellular vesicles links cargo composition to host transcriptional responses

Bacterial extracellular vesicles (bEVs) enable gut microbiota to deliver bioactive cargo to host cells, yet the specific bacterial producers have not been systematically identified. Here, we profiled stool-derived bEVs from healthy individuals using metaproteomic profiling, revealing that vesiculation is widespread across gut bacterial phyla. We selected a subset of vesiculating species, showing that bEVs localize to distinct tissues in vivo, including extraintestinal sites such as lung, liver, kidney, and bone, suggesting roles beyond the gastrointestinal tract. We profiled intestinal epithelial cells and macrophages after endocytosing bEVs from various species, uncovering pronounced, cell-type-specific responses. For example, Bacteroides fragilis bEVs promote anti-inflammatory mitochondrial-telomeric regulation, while a set of commensal-derived bEVs contribute to epithelial survival and structural renewal. By combining proteomic, lipidomic, and metabolomic cargo profiling with transcriptional output, we find that specific Bacteroidota-derived protein cargo activates cytoprotective stress defenses while attenuating inflammatory signaling. Together, these findings establish a multi-layered comparative atlas of bEV composition, uptake, and host response, providing a framework for understanding bEV-mediated microbiome-host communication.

microbiology↗

bioRxiv2026

The Two Tube Volatile Assay: a non-contact benchtop bioassay for monitoring susceptibility to transfluthrin

IntroductionProgress against malaria has stalled since 2015, with insecticide resistance a key driver. Spatial emanators release volatile insecticides into the air, exposing mosquitoes through a route distinct from the tarsal contact used by treated nets, indoor residual spraying, and standard bioassays. Transfluthrin is currently monitored using the WHO bottle bioassay, which combines contact and vapour exposure and cannot isolate airborne effects. A scalable, vapour-only method is needed to characterise susceptibility to volatile pyrethroids. MethodsWe adapted the WHO tube bioassay to deliver non-contact transfluthrin vapour exposure without contacting treated papers. Non-blood-fed female Anopheles were exposed to acetone control or transfluthrin papers at 0.005, 0.1 and 2 mg/paper. Knockdown was recorded over 60 minutes and mortality at 24 hours. Testing spanned three laboratories (LSTM, AIRID and KEMRI) using susceptible reference and resistant lab colonies. Dose response models estimated EC{square}{square} for knockdown (EC{square}{square}KD) and mortality (EC{square}{square}Mort), with resistance ratios (RR) against the local susceptible reference. ResultsThe assay generated clear concentration- and time-dependent responses. At LSTM, Kisumu gave an EC{square}{square}KD of 0.052 and EC{square}{square}Mort of 0.054 mg/paper; Siaya was comparable (RR{square}{square}KD 1.17, RR{square}{square}Mort 0.89), whereas Tiassale 13 and KDR showed reduced susceptibility (RR{square}{square}KD 2.42 and 2.85; RR{square}{square}Mort 5.56 and 6.65). At AIRID, the resistant Cove strain did not reach 50% knockdown or mortality. At KEMRI, Siaya showed reduced susceptibility (RR{square}{square}KD 3.36/RR{square}{square}Mort 5.65). Kisumu at AIRID and KEMRI was comparable to LSTM (EC{square}{square}KD 0.007/EC{square}{square}Mort 0.030; EC{square}{square}KD 0.044/EC{square}{square}Mort 0.023). Despite inter-laboratory variation, susceptible strains remained distinguishable from resistant ones. Lower RRs than for contact pyrethroids suggest contact-based phenotypes may not predict vapour susceptibility. ConclusionThe assay provides a practical benchtop method using standard WHO hardware, distinguishing susceptible from resistant strains across three laboratories. Twenty-four-hour mortality is the recommended endpoint, 60-minute knockdown secondary. Not yet validated, it provides a foundation for further validation and adaptation to other actives.

zoology↗

bioRxiv2026

Osteopontin Mediates Uterine Artery Dysfunction in Hypertensive Pregnancy

BackgroundSuccessful pregnancy requires substantial maternal cardiovascular adaptation, including expansion and remodelling of the uterine arteries to support increased nutrient flow to the fetus. Hypertension is associated with impaired uterine artery remodelling and increased risk of fetal growth restriction and other adverse outcomes, yet the mechanisms driving vascular dysfunction in hypertensive pregnancy remain incompletely understood. Osteopontin, a matricellular protein, is implicated in vascular pathology in hypertension, positioning it as a candidate mediator of impaired uterine artery adaptation during hypertensive pregnancy. MethodsUterine artery remodelling was compared between pregnant normotensive Wistar-Kyoto (WKY) rats and spontaneously hypertensive stroke-prone rats (SHRSP), a model of chronic hypertension. To determine the role of osteopontin in this process, an osteopontin-deficient SHRSP strain was characterized. Uterine artery blood flow was assessed by Doppler ultrasound, arterial structure was evaluated by histology, and molecular differences were identified by RNA sequencing. Fetal weight and length were measured at mid and late gestation. ResultsCompared with WKY, SHRSP fetuses were smaller, and uterine arteries exhibited inward hypertrophic remodelling, characterized by increased wall thickness, reduced lumen area, and elevated resistance index. SHRSP uterine arteries also showed increased expression of inflammatory and vascular pathology-associated genes, including osteopontin. In osteopontin-deficient SHRSP, uterine arteries had larger lumen areas, decreased resistance index, and reduced expression of inflammation-associated genes. Fetal growth was also improved in osteopontin-deficient SHRSP pregnancies. ConclusionsThese findings identify osteopontin as a contributor to impaired uterine artery adaptation and suggest that reduced osteopontin may improve vascular remodelling and fetal growth in hypertensive pregnancies.

developmental biology↗

bioRxiv2026

A direct SCN-to-DMH output pathway organizes circadian behavioral timing

Circadian rhythms in behavior depend on the suprachiasmatic nucleus (SCN), but how SCN timekeeping is transmitted to downstream circuits that organize daily behavioral rhythms remains poorly defined. The dorsomedial hypothalamus (DMH) has been implicated in circadian behavioral output, but lesion studies cannot determine whether the DMH contributes through local molecular timekeeping or through intact neurons that relay SCN-derived timing signals. Here, we combined DMH neuronal ablation, local molecular clock disruption, retrograde and intersectional tracing, single-cell RNA sequencing, and intersectional optogenetics to define and test a direct SCN-to-DMH output pathway. DMH neuronal ablation disrupted locomotor activity rhythms, whereas DMH Cry1/2 disruption did not, indicating that intact DMH neurons, but not local molecular timekeeping, are required for locomotor rhythmicity. Retrograde tracing identified a sparse population of DMH-projecting SCN neurons concentrated in the dorsal SCN. These neurons showed minimal overlap with canonical AVP- and VIP-expressing SCN populations and were most strongly represented in a Prokr2/Vipr2-expressing transcriptional cluster. Repeated activation of DMH-projecting SCN neurons entrained locomotor rhythms, produced persistent phase shifts after stimulation ended, and compressed the temporal distribution of activity during entrainment. Together, these findings identify sparse, molecularly distinct DMH-projecting SCN neurons capable of organizing circadian locomotor timing.

neuroscience↗

bioRxiv2026

Alcohol and Opioids Modulate Excitatory Inputs to the SCN

BackgroundDisturbance of circadian rhythms is a hallmark of substance use disorders, with depressant drugs often causing soporific effects such as reduced sleep latency. The suprachiasmatic nucleus (SCN) of the hypothalamus is the central circadian pacemaker in mammals, regulating daily rhythms in physiology and behavior. However, the cellular mechanisms through which depressants alter SCN function remain poorly defined. MethodsWe used whole-cell patch clamp electrophysiology in acute brain slices to examine how alcohol and opioids modulate excitatory glutamatergic transmission onto SCN neurons. Ethanol effects were examined both acutely and following chronic exposure paradigms. Optogenetic stimulation was used to activate either RHT input or -opioid receptor-expressing (MOR) terminals, and MOR agonists were used to assess opioid-mediated effects on synaptic transmission. ResultsWe show that acute application of ethanol paradoxically enhances SCN firing rates. In contrast, chronic alcohol exposure reduces glutamatergic drive. We also found that activating MOR+ terminals produced bidirectional modulation of SCN firing and that MOR+ inputs formed functional glutamatergic synapses onto SCN neurons. Notably, this transmission could be suppressed by the MOR agonists DAMGO and fentanyl. ConclusionsTogether, these findings reveal that both alcohol and opioids modulate glutamatergic input to the SCN. This work establishes the SCN as a novel target of depressant substances and highlights glutamatergic transmission as a key point of vulnerability in circadian dysregulation associated with substance use.

neuroscience↗

bioRxiv2026

Circadian modulation of spontaneous dopamine release shapes reward-evoked signaling in the nucleus accumbens

The circadian system is an important regulator of reward-related neural function and behavior. Dopamine (DA) release in the nucleus accumbens is a key component of reward processing, yet how circadian timing shapes DA release in relation to reward behavior remains unclear. Here, we investigated circadian rhythms in DA release and reward behavior using long-term fiber photometry paired with an automated reward delivery and measurement system. We found two distinct circadian rhythms in DA release: spontaneous DA, reflecting ongoing DA release not associated with reward, and reward-evoked DA, reflecting transient DA response during reward. Spontaneous DA peaked during the early subjective day, whereas reward-evoked peak DA peaked near the day-to-night transition. Both rhythms were distinct from reward behavior, which peaked during the early subjective night. Linear modeling further showed that the relationship between reward-evoked DA and reward behavior depended on circadian time, with greater DA responses occurring between late subjective day and early subjective night. Spontaneous baseline and reward-evoked DA were also negatively correlated, and this relationship was likewise modulated across circadian time. Together, these findings support a model in which circadian modulation of baseline DA may alter the gain of reward-evoked signaling, amplifying DA responses across behaviorally relevant times of day.

neuroscience↗

bioRxiv2026

Charting developmental trajectories of dynamic brain networks during emotional face processing

Emotional face processing is a critical component in the development of social cognition through childhood. The neural mechanisms supporting this development can be understood by tracking age-related changes in brain activity. Prior work in this area with MEG relies on static, bandlimited, or region-specific measures, which do not capture the dynamic, distributed nature of brain activity. Here we used Dynamic Network Modes (DyNeMo) to analyze MEG data from a large cohort of typically developing individuals (N=224, ages 5-40) during an emotional faces vigilance task. DyNeMo is a data-driven, generative modelling approach which captures functional networks as a set of whole-brain spatiospectral "modes" whose relative mixture (i.e., activation levels) can change dynamically in response to stimuli. We inferred six modes from the MEG data and characterized developmental trajectories in task-related activation and mode connectivity. Across modes we observed distinct developmental trajectories in both measures. With respect to mode activation, a visual mode and a frontotemporal mode (whose labels reflect their respective spatial profiles) increased nonlinearly with age; meanwhile, activation in temporal and sensorimotor modes decreased linearly with age. Meanwhile, connectivity broadly increased with age in all modes, but with different degrees of nonlinearity. These results suggest developmental dissociations between different modes (e.g., visual versus sensorimotor), as well as within individual modes (task-related mode activation versus connectivity). These results provide a comprehensive and complex picture of functional network development underlying emotional face processing. Significance StatementBrain networks supporting social cognition undergo profound changes from childhood through adolescence to adulthood. However, current understanding of how these networks develop has been limited by conventional analyses of brain imaging data, which typically provide a static picture of brain activity. Here we leveraged a cutting-edge, data-driven modeling approach (DyNeMo) to characterize age-related changes in distributed and dynamic networks supporting emotional face processing, in a large cohort of children and young adults (N=224). We inferred six functional networks whose activation levels changed rapidly in response to emotional faces. Network activation and connectivity exhibited profound and distinct non-linear changes with age, indicating that emotional face processing is supported by complex interactions among multiple dynamic networks, each with different maturational trajectories.

neuroscience↗

bioRxiv2026

An integrated workflow for long-term fiber photometry analysis

Long-term fiber photometry enables measurement of neural dynamics across hours to days, but these recordings create analytical and reproducibility challenges that are not well addressed by tools developed for short, stimulus-locked experiments. Here we present a software environment for long-term photometry analysis organized around a structured, revisitable workflow for run execution, inspection, and post-run refinement. The software separates correction retuning from downstream event reanalysis, allowing both signal correction and event-analysis settings to be revised after the initial run. We show that correction choice can substantially change the corrected signal itself and that post-run reanalysis can revise event-detection outcomes. The software also preserves tonic and phasic outputs and supports inspection of the same recording at both multiday and session-level scales. Together, these capabilities provide a practical workflow for more interpretable, revisitable, and reproducible analysis of long-term photometry recordings.

neuroscience↗

bioRxiv2026

Sentinel plants enable quantitative monitoring of bioavailable nitrate in soils and microbial environments

Microbial transformations of nitrogen in soils strongly influence plant nutrition and ecosystem function, yet these processes remain difficult to monitor. Existing approaches rely largely on destructive soil sampling and laboratory analysis, limiting the ability to track nitrate dynamics in situ. Here, we engineer "sentinel plants," genetically encoded plant biosensors that convert nitrate perception into a quantitative signal reporting plant-accessible nitrate. The sensor uses a synthetic nitrate-responsive promoter coupled to a ratiometric luciferase reporter, enabling high-dynamic-range measurements. Sentinel plants exhibit a dose-dependent, reversible nitrate response with high specificity over alternative nitrogen sources. In agricultural soils from multiple California field sites, sensor output closely tracked analytically measured nitrate concentrations and resolved nitrate amendments without destructive extraction. Beyond environmental sensing, sentinel plants enabled screening of nitrogen-fixing microbial communities and the detection of microbially generated nitrate in both liquid culture and soil systems. Using this platform, we identified a minimal three-member microbial consortium capable of converting atmospheric nitrogen into nitrate via sequential nitrogen fixation and nitrification. This consortium increased tissue nitrate accumulation and plant fresh weight, demonstrating that sentinel plants can both monitor nitrate availability and identify microbial communities that enhance plant growth. Significance StatementNitrogen availability in soils fluctuates across space and time, yet most measurements rely on extracting soil samples and analyzing them in the laboratory. Such measurements provide only snapshots of nitrogen status and do not necessarily reflect the nitrogen that plants themselves experience. Here, we engineer plants that act as living nitrate sensors by converting nitrate perception into a measurable optical signal. Because these sensors operate within intact plants, they report nitrate availability as integrated through plant uptake and physiology rather than through chemical extraction alone. Using this platform, we tracked nitrate levels in agricultural soils and identified a minimal microbial consortium capable of converting atmospheric nitrogen into plant-available nitrate. This plant-based sensing strategy enables direct monitoring of nitrogen dynamics in soils and microbial environments, providing a platform for identifying microbial communities that enhance nitrogen availability for crops.

bioengineering↗

bioRxiv2026

Widely circulating pyrethroid resistance mechanisms reduce the efficacy of transfluthrin and pose a risk for mosquito-borne disease control with spatial emanators

Spatial emanators (SE) are a promising complement to existing tools for preventing mosquito transmitted diseases. In 2025, the WHO updated the WHO Guidelines for Malaria to include a conditional recommendation for the indoor use of prequalified SE products in malaria control. Both prequalified, and many other SE products contain the volatile pyrethroid transfluthrin, which shares the same target site as other (contact/solid phase) pyrethroids. Therefore, an assessment of cross resistance is critical to predict effectiveness against mosquitoes with existing pyrethroid resistance. Our results show that resistance to solid phase pyrethroids is correlated with resistance to transfluthrin in Anopheles and Aedes species. Moreover, commonly-selected resistance mechanisms including target site mutations and over-expression of P450 detoxification enzymes can confer resistance to transfluthrin. Furthermore, we show that resistant mosquitoes are less impacted by transfluthrin in terms of flight activation (irritancy) and reduced blood feeding inhibition, with the response correlating with resistance strength. Transfluthrin did not elicit an electroantennography response in Anopheles gambiae and surgically ablating mosquitoes antennae did not result in differences in flight activation upon transfluthrin exposure, suggesting the antennae are not required for transfluthrin to elicit behavioral responses. These results provide new insight regarding the mode of action of transfluthrin and the risk of resistance reducing transfluthrins efficacy in vector control interventions.

pharmacology and toxicology↗

bioRxiv2026

Diurnality reconfigures circadian network dynamics in the suprachiasmatic nucleus

Diurnal and nocturnal mammals occupy opposite temporal niches, but whether the suprachiasmatic nucleus (SCN), the central circadian pacemaker, follows the same intrinsic rules for timing adjustment and network coordination across species is unknown. Because SCN clock gene rhythms and population-level activity measurements look broadly similar across species, the prevailing interpretation in comparative studies has been that temporal niche differences are implemented upstream or downstream of the SCN. However, these coarse readouts do not test how clock resetting depends on circadian phase or how neuronal timing is coordinated across SCN space. Here, we combined long-duration ex vivo SCN recordings with optogenetic stimulation to compare SCN network dynamics in the nocturnal mouse (Mus musculus) and the diurnal four-striped grass mouse (Rhabdomys pumilio). Rhabdomys SCN molecular clock rhythms exhibited a longer intrinsic period and, under the same daily stimulation protocol, converged on a larger absolute phase angle relative to the stimulus. Molecular clock phase response curves differed in overall structure across circadian time between species, including pronounced early subjective day delays in Rhabdomys when Mus responses were minimal. Phase mapping of single-cell SCN calcium rhythms revealed species-specific spatial timing organization, with a graded dorsomedial-to-ventrolateral phase progression in Rhabdomys and a sharper transition in Mus. The Mus and Rhabdomys SCN can thus appear similar by coarse readouts yet diverge in phase-dependent molecular clock resetting and network timing organization. These results indicate that models placing temporal niche divergence solely outside the SCN are mechanistically incomplete.

neuroscience↗

bioRxiv2025

Stable Inheritance of Transgene and Yellow Fluorescent Protein Gene Expression in Progeny of Transgenic Cacao (Theobroma cacao) Plants

Genetic engineering tools have the potential to rapidly and precisely improve the genome of slow-to-breed cacao. We previously developed an efficient protocol for transforming cacao using cotyledonary explants derived from secondary somatic embryos via Agrobacterium tumefaciens. In this study, we demonstrate that our transformation protocol is successful in elite cultivars, INIAPG-038 and Matina 1-6, producing fertile seeds with stable visual marker inheritance regardless of whether the transgenic plants were used as the pollen or ovule donor. Three vectors were used in the transformations, each containing genes for enhanced yellow fluorescent protein (eyfp) and neomycin phosphotransferase II (nptII). Three transgenic INIAPG-038 events and one transgenic Matina 1-6 event were used to evaluate seed fertility and the stability of transgene inheritance in cacao seeds and plants. The T1 progeny of these four transgenic events were analyzed for YFP expression and transgene presence. YFP expression segregated at a 1:1 ratio in all events when the transgenic plants were crossed with non-transgenic plants, while a 3:1 segregation was observed when transgenic events were crossed with each other. The transgenic plants exhibited a normal phenotype compared to non-transgenic control plants, producing seeds with a 97% germination rate.

plant biology↗

bioRxiv2025

Histological techniques for the visualisation and identification of polymicrobial communities in mucosal tissue

Sequencing studies have generated masses of data linking mucosal bacteria to health and disease, particularly in organs such as the colon, mouth and stomach. However, extracting microbial DNA from mucosal sites with lower bacterial biomass can introduce significant variation given the heterogeneity of bacterial colonisation within pathological microenvironments. Therefore, a histological technique that identifies mucosal samples with high microbial mass samples prior to applying sequencing technologies, would increase reproducibility and reduce issues of low signal: noise ratios commonly observed during 16S rRNA gene sequencing. Using RNAscope technology, we have previously shown that non-H. pylori bacteria invade the gastric lamina propria in H. pylori-infected patients diagnosed with chronic gastritis and gastric intestinal metaplasia. However, RNAscope technology is costly and time consuming. Here, using gastric tissue from patients with Helicobacter pylori-associated precancer and cancer, we applied the use of a modified Gram stain technique to identify gastric tissue with high bacterial biomass. We validated the presence of bacteria using custom-designed RNAscope probes on consecutive tissue sections and then we visualised bacteria within a polymicrobial community at the Phylum, Kingdom and Genus taxonomic levels. This study validates the cost-effective modified Gram stain as an efficient way to select samples with high microbial biomass for downstream applications investigating host-microbiota relationships.

microbiology↗

bioRxiv2025

Structural basis for constitutive activation of oncogenic gp130 mutants in human inflammatory hepatocellular adenomas

Inflammatory hepatocellular adenomas (IHCAs) are benign liver tumors primarily driven by somatic mutations in the gp130 receptor, resulting in its constitutive activation. To uncover the structural mechanisms underlying this activation, we employed cryo-electron microscopy and mutagenesis to study five representative IHCAs-associated gp130 mutants and two engineered mutants with ligand-independent activity. Most mutants formed "X"-shaped dimers through a 3D domain-swapping mechanism, characterized by large juxtamembrane separations and reliant on D1 domain-mediated "tip-to-tip" interactions for dimer clustering and activation. A rare mutant displayed a distinct "Y"-shaped dimer conformation, with closely aligned juxtamembrane domains enabling direct activation independent of dimer clustering. These findings highlight the diversity of gp130 mutant activation mechanisms and provide a foundation for developing therapeutic strategies targeting aberrant gp130 signaling in IHCAs.

biochemistry↗

bioRxiv2025

FOXI3 Promotes Migration and Proliferation in Prostate Cancer Bone Metastases, Modulated by FGF8.

Studies have shown that all men who die from prostate cancer exhibit bone involvement, highlighting the clinical significance of bone metastases. Previously, we demonstrated that prostate cancer exhibits elevated expression of FOXI3; a transcription factor critical to bone development. However, its functional role in prostate cancer progression remains unexplored. In this study, we explored FOXI3 expression in human prostate cancer tissues and cell lines. Immunohistochemical analysis revealed a significant association between FOXI3 expression, tumor pathology, and increasing tumor grade. Analysis of publicly available gene expression data from prostate cancer patients showed that that FOXI3 is markedly elevated in bone metastases and strongly correlates with FGF8, suggesting a potential bone-specific regulatory interaction between these factors. Consistent with this, treatment of bone-derived prostate cancer cells with FGF8 increased FOXI3 RNA expression, whereas no such effect was observed in a brain-metastatic cell line. Further, we demonstrated that FGF8-FOXI3 axis regulates bone-derived prostate cancer cell migration and proliferation in a FOXI3 dependent manner. Together, our findings demonstrate a pro-metastatic role of FOXI3 in prostate cancer progression.

cancer biology↗