Biology subjects

Brown, J.

Publications and source records attributed to Brown, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Personalised prediction of anomalous bone regeneration in multiple myeloma patients

Recent advances in immunotherapies have dramatically extended the lives of patients with multiple myeloma, resulting in a growing population of elderly patients suffering from damage to their vertebrae caused by this blood cancer. Clinicians typically intervene to fill in these lytic lesions in an attempt to reduce the risk of vertebral collapse and spinal cord injury, however observations of rapid bone regeneration post-cancer treatment suggest that surgery may not always be required. Here we develop a series of mechanistic computational models, optimised using cohorts of healthy volunteer and patient data, to show that vertebrae of recovering multiple myeloma patients rapidly strengthen in a manner not entirely explained by known bone remodelling mechanisms. Furthermore, using pathways informed by genomics data and patient-specific bone biomarkers, we demonstrate the potential for these models to provide personalised predictions of bone disease trajectory.

bioengineering↗

bioRxiv2026

Global, single-cell-resolution of antiviral defenses in marine prokaryoplankton

Background Growing evidence suggests that variation in resistance to viral infections by marine prokaryoplankton enables the coexistence of both viral and host populations. Recent experimental work on model organisms has revealed dozens of novel antiviral defense mechanisms. This diversity has prompted the hypothesis of the pan-immunity model, in which diverse defenses are a shared resource among closely related individuals to broaden the population's resistance and minimize an individual's burden. The composition and abundance of such defense pools in natural microbial communities, however, remain largely unknown. Here, we begin to parameterize resistance in marine prokaryotes and define their defense repertoire by quantifying antiviral defenses across thousands of randomized single-amplified genomes (SAGs) from a global collection of seawater samples. Results Prokaryoplankton SAGs contained an average of 1.1 defenses, with dark ocean (200 m - 11 km) prokaryotes having a slightly higher genomic load of defenses as compared to the sunlit, surface ocean. The number of defenses per cell was taxon-specific, with little or no relationship to depth, taxon abundance, estimated maximal growth rate, or viral infection rate. The most numerous and taxonomically widespread defenses were restriction modification systems, followed by dGTPase (mostly in Pelagibacterales) in the sunlit ocean and AbiU (mostly in Nitrososphaerales) in the dark ocean. Most other defense types were rare (< 0.1% SAGs) yet distributed across distant taxa (> 3 phyla). We found evidence for the cross-domain exchange of the most common defense system, RM II, between archaea and bacteria, which improves our understanding of the biology of this prevalent defense and could be consequential in predicting target motifs for connecting viruses with potential hosts in epigenetic studies. Conclusions Collectively, these results suggest lineages restrict genomic real estate for defenses yet enable extensive lateral transfer, potentially for the maintenance of defense variation at the community level rather than only among closely related individuals. This study provides a quantitative atlas of prokaryoplankton immunity toward grounding our understanding of virus-microbe interactions in the Earth's largest biome, the open ocean.

microbiology↗

bioRxiv2026

Large oncosomes reprogram bone marrow mesenchymal stem cells to establish a pre-metastatic niche

Metastatic progression depends on the systemic remodeling of distant tissues before tumor cell arrival, yet the cancer-derived signals that orchestrate this process remain poorly understood. Large oncosomes (LOs) are atypically large (>1 um), tumor-derived extracellular vesicles shed by invasive cancer cells. Here, we demonstrate that LOs function as systemic mediators of pre-metastatic niche formation by activating innate immune sensing in bone marrow mesenchymal stem cells (BM-MSCs). Systemic administration of prostate- and breast cancer-derived LOs to immunocompetent tumor-bearing mice did not affect primary tumor growth but increased metastatic burden. LOs induced a robust, dose-dependent interferon-driven inflammatory program, characterized by interferon-stimulated genes and neutrophil chemokines. Mechanistically, this response was driven by LO-associated nucleic acids activating convergent cytosolic DNA- and RNA-sensing pathways in recipient stromal cells. LO-conditioned BM-MSCs promoted the accumulation and polarization of neutrophils toward an immunosuppressive, polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) phenotype. In vivo, genetic suppression of LO shedding in tumor cells reduced PMN-MDSC accumulation in the bone marrow, which was reverted by systemic LO administration. Together, these findings establish LOs as specialized carriers of immunomodulatory signals that reprogram the bone marrow microenvironment to support metastatic colonization, identifying a previously unrecognized mechanism linking tumor vesiculation to immune remodeling at distant sites.

cancer biology↗

bioRxiv2026

Ontological Analysis of Brain Proteostasis Highlights the Sex-Dependent Trajectory of ApoE Isoform-Specific Regulation

Apolipoprotein E (ApoE) is the strongest genetic predictor of Alzheimers disease (AD) risk, with ApoE4 increasing and ApoE2 decreasing risk relative to ApoE3. Using a global LC-MS proteomic approach, we integrated protein abundance and kinetics in Human-APOE knock-in mice for young (3-month) and aged (18-month) cohorts to quantify the changes in steady-state proteostasis. By mapping 6,052 identified proteins and 3,986 associated turnover rates into ontological groups, we observed that vesicle trafficking and mitochondrial dysregulation occur as early as 3 months in ApoE4 mice accompanied by hyperactive metabolism that eventually reduces with age. In contrast, young and old ApoE2 mice retain similar signatures to ApoE3 mice in metabolic, mitochondrial, cellular regulation, and membrane trafficking ontologies. We found that females had more isoform-induced ontological changes relative to ApoE3, providing insight into sex-dependent vulnerabilities. Our global proteomic approach for ApoE proteostasis crucially unifies independent literature observations while providing turnover kinetics to uncover the underlying mechanism behind abundance changes. Data are available via ProteomeXchange with identifier PXD079261. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/735293v1_ufig2.gif" ALT="Figure 1000"> View larger version (45K): org.highwire.dtl.DTLVardef@28ebfforg.highwire.dtl.DTLVardef@9dc6f2org.highwire.dtl.DTLVardef@704577org.highwire.dtl.DTLVardef@e0b0e2_HPS_FORMAT_FIGEXP M_FIG C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/735293v1_ufig1.gif" ALT="Figure 1001"> View larger version (48K): org.highwire.dtl.DTLVardef@17d0474org.highwire.dtl.DTLVardef@af771borg.highwire.dtl.DTLVardef@1b49f67org.highwire.dtl.DTLVardef@14d3aa2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Characterisation of Peripheral Blood B Cell Receptor Repertoire in Severe Eosinophilic Asthma and EGPA

BackgroundSevere eosinophilic asthma (SEA), eosinophilic granulomatosis with polyangiitis (EGPA) and nasal polyposis (NP) are immune-mediated diseases characterised by eosinophilic inflammation. However, there is also increasing interest in the potential pathological roles of autoantibodies in these diseases. Understanding their B cell receptor (BCR) repertoires may provide valuable insights into disease mechanisms, and potential role of B cells in their pathology. MethodsWe conducted BCR repertoire sequencing using peripheral blood from 43 patients, comprising SEA with nasal polyps (SEA+NP), SEA without nasal polyps (SEA-NP), and EGPA, along with 16 healthy controls (HCs). ResultsCompared to HCs, patients with EGPA exhibited increased relative proportions of IgA1, IgG1, IgG2, and IgG4 subclasses. Similarly, SEA-NP patients demonstrated significantly high proportion of IgG2 sequences. Notably, the IgG4 subclass was significantly elevated across all patient groups compared to HCs. Patients receiving anti-IL-5/5R biologic treatments showed increased relative proportions of IgA2 and IgG2 subclasses compared to untreated patients. Some variation across participant groups in mean somatic hypermutation and mutation frequency was evident. 1,508 clones shared across patients, but not healthy controls, were evident though the majority showed low clonal expansion. Nevertheless, a few shared clones did show either high prevalence across patients and/or higher clonal expansion. ConclusionChanges in BCR repertoires in SEA/EGPA are consistent with a pattern of a more mature B cell component in the periphery and with the T2 inflammatory response observed in SEA and EGPA. BCR clonotypes shared across patients were evident, however, whether such clonotypes are pathological in SEA/EGPA requires further investigation.

immunology↗

bioRxiv2026

Electrical stimulation precisely reproduces naturalistic spiking activity in complete and intermixed neural populations in the primate retina

Neurostimulation technologies have the potential to restore complex brain functions by evoking naturalistic patterns of neural activity. However, faithfully mimicking the brains natural neural code in diverse neuron types remains an unsolved challenge. Here we exploit focal electrical stimulation and recording to reproduce natural visual signals at cellular resolution in two intermixed and oppositely-tuned neural populations in the isolated macaque retina. We calibrated and delivered electrical stimulation sequences to precisely mimic recorded visually-evoked responses to natural images in complete populations of ~50 ON and OFF parasol cells uniformly sampling ~4{degrees} x 4{degrees} of visual angle. Distinct and opposing visually-evoked response patterns in the two intermixed populations were closely replicated spike-by-spike in 5 retinal preparations using electrical stimulation, reproducing spike trains with 51 {+/-} 17% lower variability than repeated presentations of the same visual stimulus. Focal electrical stimulation also replicated traveling waves of neural activity in response to visual motion, and highly structured artificial response patterns. These findings demonstrate for the first time that neurostimulation can match or exceed biological signaling fidelity in large, complete and intermixed neural populations.

bioengineering↗

bioRxiv2026

Data mining reveals the diversity of prophage endolysins targeting pathogenic enterococci

Antimicrobial resistance (AMR) poses a critical global health threat, with enterococci among the leading contributors due to their intrinsic and acquired resistance to antibiotics. Clinically relevant species, including Enterococcus faecalis and Enterococcus faecium, as well as the emerging poultry pathogen Enterococcus cecorum, highlight the need for alternative therapeutics across human and agricultural settings. Bacteriophages and their derived enzymes, particularly endolysins, offer promising antibacterial strategies but challenges such as phage resistance and limited lysin diversity hinder their application. In this study, we performed a large-scale analysis of prophage-encoded endolysins across these three enterococcal opportunistic pathogens, characterizing over 48,000 sequences. We identified 33 distinct domain architectures combining diverse catalytic and cell wall-binding domains, including novel putative cell wall binding domains. These findings expand the known diversity of enterococcal lysins and provide a comprehensive resource for the rational design of stable, recombinant "enzybiotics" to combat multidrug-resistant enterococcal infections. Data summaryAll genomes analysed in this work are available through Genbank. The data mining strategy was carried out open-access software available through GitHub as described in the Methods section. The raw output of the search and sequences obtained after each filtering step are provided in Supplementary Files 1 and 2. Modelling data related to figure 6 is provided in supplementary File 3. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/720912v1_fig6.gif" ALT="Figure 6"> View larger version (42K): org.highwire.dtl.DTLVardef@16ea8f5org.highwire.dtl.DTLVardef@16883aorg.highwire.dtl.DTLVardef@149d360org.highwire.dtl.DTLVardef@1d47ec1_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 6.C_FLOATNO BSD is predicted to be a novel cell wall binding domain. A, Alignment of amino acid sequences encoding the BSD. B, Structural alignment of AlphaFold predictions. C, A box plot quantifying the ligand ipTM scores of 25 Efm and Efs muropeptide dockings for various domains / proteins, and the custom-calculated docking consistency scores for each of those 25 predictions. The results have been visually grouped into predicted binders and predicted non-binders by comparing ipTM and docking consistency scores to known binders (LysM, SH3) and random proteins (GFP, RNBR). D, Docking of Efs muropeptide (gold) into the binding pocket of BSD (blue), including any predicted hydrogen bonding. C_FIG Impact statementAntimicrobial resistant enterococci threaten therapeutic options in both medicine and agriculture. Yet, the therapeutic potential of bacteriophage-derived endolysins (enzybiotics) is limited by an incomplete understanding of their natural diversity. By analysing more than 48,000 prophage encoded lysins from E. faecalis, E. faecium, and E. cecorum, this study provides the most extensive characterization of enterococcal lysin architectures to date. The identification of 34 distinct domain organizations, including a previously unrecognized cell wall-binding domain, substantially broadens the known functional repertoire of these enzymes. This work fills a major knowledge gap and offers a foundational resource for engineering stable, targeted enzybiotics to combat multidrug resistant enterococcal infections.

microbiology↗

bioRxiv2026

Molecularly defined subpopulations of leptin receptor neurons dissociate the control of food intake from blood pressure

While previous studies have suggested that leptin regulates cardiovascular function independently of body weight, the specific leptin receptor (Lepr)-expressing neurons that mediate these distinct effects remain unknown. We found that genes located in blood pressure (BP)-associated genome-wide association study loci were regulated by leptin in Lepr and glucagon-like peptide-1 receptor (Glp1r)-expressing (LeprGlp1r) neurons. Ablating Lepr from these cells decreased BP despite causing hyperphagic obesity. Single-cell and spatial transcriptomics revealed that LeprGlp1r neurons segregate into two distinct subpopulations of cells located in the arcuate nucleus (ARC) and dorsomedial hypothalamic nucleus (DMH). Activating ARC LeprGlp1r neurons suppressed food intake without impacting energy expenditure or cardiovascular function. Conversely, DMH LeprGlp1r neurons increased energy utilization and BP without altering food intake. Our results identify distinct LeprGlp1r neuron subpopulations that dissociate the control of food intake from outputs related to sympathetic tone, including BP, suggesting the potential therapeutic utility of targeting of these subpopulations independently.

physiology↗

bioRxiv2026

Direct-to-Biology Enables Rapid Identification of Potent FBXO22 Degraders

Proteolysis Targeting Chimeras (PROTACs) are heterobifunctional molecules that bring a ubiquitin E3 ligase into proximity of a target protein to polyubiquitinate and degrade the target. PROTACs act catalytically, offering distinct advantages over conventional inhibitors and are the subject of intense study. The development of PROTACs involves extensive optimization of the chemical moiety linking two different protein-binding chemotypes, often requiring the synthesis, purification and testing of hundreds of PROTAC candidates. We used this approach to rapidly explore the landscape of targeted degradation of four different targets in parallel, combining and comparing a recently reported FBXO22-recruiting chemical warhead with warheads for the commonly used CRBN and VHL E3 ligases. Using a limited number of compounds (175 compounds in total) we observed no FBXO22-dependent degradation of these four targets. However, our libraries generated potent FBXO22 homo-PROTACs inducing self-degradation, as well as CRBN- and VHL-mediated degraders of FBXO22.

cell biology↗

bioRxiv2026

PTPN1/2 inhibits alveolar macrophage-mediated control of lung metastasis

Metastasis remains the leading cause of cancer mortality, yet effective therapies are limited. While therapeutic responses are influenced by organ-specific immune microenvironments, strategies to pharmacologically modulate these niches remain poorly defined. Here, using the clinical-stage inhibitor ABBV-CLS-484 (AC484) as a chemical probe, we demonstrate that systemic PTPN1/2 inhibition remodels the pulmonary myeloid landscape, specifically activating alveolar macrophages (AMs) toward a tumoricidal state. Integrated single-cell/spatial transcriptomics and functional assays reveal that AC484 promotes AM accumulation within metastatic lesions, elevates their IFN{gamma} production and responsiveness, and enhances their tumor-killing activity. Depletion of AMs diminishes the anti-metastatic efficacy of AC484. Mechanistically, inhibiting PTPN1/2 by AC484 amplifies IFN{gamma}-STAT1 signaling in AMs, while disrupting this pathway impairs their tumor control capability. These findings delineate a distinct innate immune axis where PTPN1/2 acts as a molecular "brake" on AM activation, suggesting that pharmacologically unleashing tissue-resident macrophages offers a therapeutic strategy to overcome metastatic progression, particularly in microenvironments where adaptive immunity is insufficient. SignificanceAMs are potent anti-metastatic immune effectors functionally constrained by PTPN1/2. Pharmacologically inhibiting PTPN1/2 amplifies their IFN{gamma}-STAT1 signaling and tumoricidal activity, establishing a strategy to reactivate tissue-resident immunity against metastasis.

immunology↗

bioRxiv2026

MicroRNA-sensing plasmid system for dynamic control of functional ion channel expression

Gene therapy offers the potential for long-term treatment or cures for a range of chronic diseases. However, permanent gene therapy expression may not be desirable. Efforts have been made to create systems which can be switched on/off by stimuli including light, designer drugs, or cellular contexts such as increased electrical activity. Here, we designed a novel plasmid system in which ion channel expression, and therefore function, is regulated by microRNA (miR) - an endogenous class of short noncoding RNAs which negatively regulate gene expression via binding the 3 untranslated region of target transcripts. We modified an existing voltage-gated potassium channel gene therapy with a binding cassette for miR-193a-3p, and transfected this miR-193-OFF system in neuro2A cells. Co-transfection with an inhibitor or mimic of miR-193a-3p respectively enhanced or repressed expression of our transgene, assessed using a GFP marker. Using whole-cell voltage clamp, we observed enhanced voltage-gated potassium currents in cells co-transfected with a miR-193a-3p inhibitor, compared with a non-targeting control oligonucleotide. Together, this demonstrates the concept of a novel miR-mediated molecular switch which can bias therapeutic ion channel expression based on a specific miR signal. As miRs are a ubiquitous molecular mechanism, our approach could be applied to a wide range of cellular and disease contexts, potentially expanding gene therapy to new patient populations.

neuroscience↗

bioRxiv2026

Identification of novel inhibitors of Mycobacterium smegmatis growth through genome-wide overexpression of Cluster P3 mycobacteriophage Xavia genes

We examined whether genes encoded by the mycobacteriophage Xavia disrupt growth of Mycobacterium smegmatis, a widely used mycobacterial model. Seventy-one Xavia genes were individually expressed using an inducible plasmid system and assessed for effects on colony formation. Two genes were lethal even without induction, indicating toxicity under basal expression. Induction of sixteen additional genes reduced bacterial growth, spanning structural proteins, lysogeny regulators, DNA-associated enzymes, a lysis protein, and several genes with no known function. These findings expand functional insights into mycobacteriophage gene repertoires and identify candidates for future mechanistic studies. AbstractBacteriophage genomes encode large numbers of genes with no known function, and many of these genes affect essential host processes when expressed in a heterologous system. For mycobacteriophages, genome-wide overexpression in Mycobacterium smegmatis provides a direct way to identify proteins that impair growth and to determine which mycobacterial pathways are sensitive to phage gene products. To evaluate the cytotoxic potential of the Cluster P3 phage Xavia, a lineage that has not undergone functional screening, we constructed an arrayed pExTra library containing 71 predicted Xavia genes under control of the anhydrotetracycline inducible promoter pTet. All constructs were sequence-verified and transformed into M. smegmatis, and induction allowed measurement of gene-specific effects on growth. Two genes prevented recovery of transformants, suggesting toxicity under basal promoter leakiness. Inducible expression of 16 additional genes impaired growth, and these inhibitory proteins include structural components, regulators of lysogeny, enzymes of DNA metabolism, a lysis factor, and several proteins with no known function. Four of the strongest inhibitors were genes with no known function. These results extend functional screening into the previously untested P3 branch of Actinobacteriophages and identify new proteins that require mechanistic analysis.

microbiology↗

bioRxiv2025

EcoKMER: One-stop shop for spatio-temporal metagenomic exploration using DataFed

Spatially distributed environmental sampling generates highly complex and multidimensional datasets illuminating key insights into microbial diversity, evolutionary-coevolutionary processes, and host-pathogen interactions. While these sampling methods generate high value datasets, dataset size, the dataset integration, visualization, analysis, and provenance tracking present significant bottlenecks to scientific discovery. To address this bottleneck, we developed EcoKMER, an R-Shiny front-end application designed to streamline metagenomic data accessibility and provide geospatial context to data in support of hypothesis-driven investigations into environmental sampling, supported by DataFed as its back-end data management platform. EcoKMER enables interactive visualization and filtering of harmonized metagenomic data and metadata using an interoperable approach, allowing users to extract spatially distributed sample-based metadata on top of environmental parameters such as geolocation, temperature, pH, for investigating ecological changes across time and space enhancing sample processing methods. As an example, we deployed this tool to track analysis of metagenomes from the organisms in the Salish Sea Estuary, consistent with existing community-accepted standards. Built on top of DataFed, a flexible and robust scientific data management system built for data lakehouse architectures, EcoKMER is positioned as a powerful tool to improve sampling strategy decision making, accelerate new insights for collaborative biological and environmental research, and fostering AI-ready analyses designed to enhance discovery and guidance for bioeconomic engineering. The published manuscript is available at https://www.osti.gov/biblio/3412938

bioinformatics↗

bioRxiv2025

Biofilm formation during pneumococcal carriage imprints naturally acquired humoral immunity

Streptococcus pneumoniae (Spn) colonization of the nasopharynx is a prerequisite for transmission and invasive disease. To investigate how repeated asymptomatic colonization shapes immunity and influences bacterial traits, we developed the Repeated Asymptomatic Murine Pneumococcal Colonization (RAMPC) model using strains belonging to serotypes: 2 (D39), 3 (WU2), and 4 (TIGR4). Sequential colonization revealed strain- and exposure-order-dependent effects on bacterial burden, with initial colonization yielding robust carriage and subsequent exposures resulting in diminished burden and rapid clearance. Humoral profiling demonstrated antigenic imprinting: the first colonizing strain largely determined IgG and IgA specificity, with minimal diversification after repeated exposures. Reactivity was strongest for biofilm-associated antigens correlating with each strains biofilm-forming capacity. Using TIGR4 mutants deficient in biofilm formation, we confirmed that in vivo aggregate formation drives humoral responses. Human sera from naturally colonized adults mirrored these findings, favoring biofilm antigens independent from capsule. Protection was demonstrated as triple-colonized mice exhibited reduced mortality and bacteremia following pneumococcal pneumonia challenge. Moreover, the initial colonizing strain influenced protection against heterologous infection, underscoring the lasting imprint of the biofilm phenotype on immunity. Finally, IgA responses in nasal-associated lymphoid tissue paralleled serum IgA patterns, validating systemic measurements as a proxy for mucosal immunity. Collectively, these results reveal that biofilm formation during colonization is a key determinant of humoral immunity and protection, providing insight into pneumococcal biology and informing strategies to design next-generation interventions. Author summaryStreptococcus pneumoniae (Spn) is a leading cause of pneumonia, meningitis, and sepsis, yet its primary lifestyle is asymptomatic colonization of the nasopharynx. Understanding how colonization shapes immunity and bacterial physiology is critical for predicting disease risk and improving future vaccines. Using a novel murine model of repeated colonization and human sera from naturally colonized adults, we show that humoral immunity is strongly biased toward antigens expressed during biofilm growth, the predominant mode of Spn in the nasopharynx, rather than planktonic forms. This response is strain-dependent and imprinted by the first colonizing strain, influencing subsequent exposures and protection against pneumonia. Importantly, biofilm formation, not capsule, drives immune recognition revealing a key link between bacterial physiology and host immunity. These findings provide fundamental insight into pneumococcal biology and the host response, suggesting that targeting biofilm-associated antigens may improve vaccine design or strategies to prevent transmission and invasive disease.

microbiology↗

bioRxiv2025

Physical, chemical, and structural properties of human gastric organoid-derived mucus

The gastric mucus layer protects the epithelium from gastric acid and ingested pathogens. However, studies of human gastric mucus have been limited due to poor accessibility of native human mucus and the abundance of contaminants in these samples. Here, we explored the potential of human gastric organoids as models for mucus production. Immunofluorescence staining confirmed that the organoids produced mucus containing MUC5AC and MUC6. The luminal mucus had viscoelastic properties similar to those of native human gastric mucus, as determined by particle tracking microrheology. To collect organoid-produced gastric mucus, termed bioengineered gastric mucus (BGM), organoids were cultured as monolayers at the air-liquid interface (ALI), and apically-secreted mucus was harvested and analyzed by MUC5AC ELISA, proteomics, CryoFE-SEM, and bulk rheometry. BGM contained high-molecular weight molecules also found in native gastric mucus, including MUC5AC. Proteomic analysis confirmed that BGM contained MUC5AC, MUC6, MUC1, and other stomach-specific molecules such as gastricsin, olfactomedin 4, and gastrokine. CryoFE-SEM showed that both BGM and native mucus had a porous structure and a characteristic honeycomb scaffold. Bulk rheometry confirmed that BGM exhibited shear thinning and predominantly elastic behavior, consistent with native mucus. Collectively, these findings indicate that BGM is an accessible alternative to native gastric mucus that can be produced on-demand for in vitro studies. New and NoteworthyWe demonstrate the structural and functional similarities of organoid-derived gastric mucus and native mucus collected from human patients. The bioengineered gastric mucus mimics its native counterpart in its proteomic profile, physical architecture, and viscoelasticity. This work highlights the translational potential of organoid-derived mucus for functional investigations of the human gastric mucus layer.

cell biology↗

bioRxiv2025

Adaptive evolution of Candida maltosa improves the bioconversion of depolymerized plastic feedstock by targeting biosurfactant production

Thermal oxo-degradation (TOD) of plastic can transform plastic waste into fermentable feedstocks. Bioconversion of the TOD products could be used as feedstocks in a biorefinery concept and lead to new avenues for plastic waste upcycling. Previous work demonstrated this concept with high density polyethylene (HDPE), the most abundant type of plastic, and identified the nonconventional yeast Candida maltosa as a promising candidate for this application. Here we describe the evolution of an improved strain of C. maltosa and characterize the uptake mechanisms of TOD products from HDPE (TOD_HDPE). Batch cultures in series passaged at the mid-exponential growth phase applied a selective pressure for faster growth and resulted in a >100% increase in specific growth rate when using TOD_HDPE as a carbon source. The evolved strain was compared to the parent strain to identify the cellular and biochemical changes associated with the improved phenotype and the uptake mechanisms involved in the bioconversion of TOD_HDPE. This comparison found that C. maltosa secretes biosurfactants capable of solubilizing hydrocarbons. The adaptive evolution resulted in changes in biosurfactant production that translated to improved emulsification of alkanes and increased solubilization of fatty alcohols and alkanes. In addition to the changes in metabolites, the study identified increases in membrane permeability associated with a reduction in ergosterol that may also play a role in the improved phenotype. These findings support the development of C. maltosa and other potential microbial cell factories for plastic biorefineries and may inform future design strategies.

microbiology↗

bioRxiv2025

Arabidopsis arenosa influences its microbiome as a serpentine soil adaptation strategy

There is growing evidence that microbes can facilitate plant growth in metal-rich soils. However, our current understanding of how plants recruit their microbiomes under abiotic stress remains incomplete. Serpentine soils are elementally skewed, with high concentrations of magnesium and nickel, often accompanied by other heavy metals, which can limit calcium availability and present unique challenges to plant growth. These soils are also nutrient-poor, prone to erosion, and have low water-holding capacity. To date, the mechanisms by which plants adapt to serpentine soils remain poorly understood and the role of plant-associated microbiomes in this process has not been described. Here, we focus on Arabidopsis arenosa populations adapted to serpentine conditions and investigate their bacterial and fungal microbiomes to better understand the role of plant-associated microbes in serpentine adaptation. We show that serpentine soils harbour distinct plant-associated microbiomes across different plant niches and that the plant genetic background plays a key role in shaping microbial community composition. Finally, we identify serpentine-specific bacterial and fungal variants that may contribute to plant adaptation under these challenging soil conditions.

ecology↗

bioRxiv2025

HIF-1α and RhoA Drive Enhanced Motility and Aerotaxis of Polyaneuploid Prostate Cancer Cells in Hypoxia

Most cancer deaths result from metastasis, yet only a rare subset of tumor cells can complete this process. Among these, polyaneuploid cancer cells (PACCs), which arise via endoreplication under stressors such as hypoxia, are implicated as metastatic drivers, but how they acquire this potential is poorly understood. Here, we show that prostate cancer-derived PACCs exhibit features predictive of invasion and intravasation. Time-lapse fluorescence microscopy and single-cell tracking under hypoxia revealed that PACCs migrated significantly farther than Non-PACCs, consistent with local invasion. PACC trajectories showed a strong tendency to migrate toward oxygen, consistent with aerotaxis and predictive of intravasation. siRNA-mediated knockdown demonstrated that the enhanced motility and aerotaxis of hypoxic PACCs require both HIF-1and RhoA, with RhoA expression suppressed upon HIF-1 inhibition. Altogether, we propose a HIF-1[->] RhoA [->] motility/aerotaxis mechanism enabling PACCs to escape hypoxic cores, invade tissue, and access vasculature, highlighting them as a uniquely invasive subpopulation with implications for anti-metastatic therapies.

cancer biology↗