Biology subjects

Yang, J.

Publications and source records attributed to Yang, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Accounting for DNA Recovery and Cell Culturability Enhances Quantitative Compatibility of Molecular and Legiolert Assays for Legionella pneumophila

Disagreement between molecular and culture-based assays for Legionella pneumophila detection is widely reported, yet comparisons have largely been based on direct assay-derived concentrations or binary positive/negative outcomes. However, it remains unclear whether molecular-culture disagreement reflects concentration-level incompatibility or unaccounted methodological and physiological differences related to DNA recovery and cell culturability. In this study, we also observed disagreement between molecular and Legiolert assays in source and finished drinking water samples collected from eight full-scale drinking water systems across the United States. Molecular thresholds adjusted for DNA recovery and cell culturability only partially resolved these discrepancies. We therefore developed a probabilistic Monte Carlo framework that incorporates sample-specific DNA recovery and cell culturability to evaluate the quantitative consistency of culturable L. pneumophila concentrations estimated by molecular and Legiolert assays. Quantitatively consistent and inconsistent samples occurred across both binary concordant and discordant classifications, demonstrating that positive/negative agreement poorly reflects concentration-level comparability. Overall, molecular and Legiolert assays showed strong quantitative consistency once sample-specific DNA recovery and cell culturability were considered. A small proportion of persistent inconsistencies at specific sampling sites, coupled with atypical microbial indicators, suggest that sample heterogeneity likely contributed to the remaining discrepancies. These findings demonstrate that integrating DNA recovery and cell culturability enhanced quantitative consistency between molecular and Legiolert assays and supports the use of molecular methods as rapid quantitative tools to complement culture-based L. pneumophila monitoring. SynopsisAccounting for DNA recovery and cell culturability revealed broad quantitative compatibility between molecular and Legiolert assays for Legionella pneumophila in drinking water. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/739452v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1e01cdcorg.highwire.dtl.DTLVardef@86bbc2org.highwire.dtl.DTLVardef@190fc66org.highwire.dtl.DTLVardef@1aa9ec8_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Assessing Microcirculation Impairment in Ischemic Stroke Mice Using Arteriovenous Co-fluctuation Analysis

Accurate assessment of cerebral hemodynamics impairment traditionally relies on arterial metrics, yet often overlooks venous drainage and arteriovenous dynamics, thereby limiting the evaluation of ischemia-induced microvascular dysfunction. To address this limitation, we implemented a signal-averaging framework, combined with co-fluctuation analysis, to extract predominantly arterial and venous hemodynamic signals and construct a dynamic arteriovenous co-fluctuation index that quantifies frame-by-frame coordination between arterial inflow and venous outflow activity. This time-resolved index enables spatial characterization of large-scale cortical arteriovenous coordination beyond conventional static correlation-based analyses. Comparative analyses between healthy controls and acute ischemic stroke mice demonstrated that the arteriovenous co-fluctuation index sensitively detects disruption of vascular coordination, revealing a slower state transition that occurs alongside distinct temporal abnormalities and regional heterogeneity between ischemic core and penumbral regions. These findings underscore the utility of arteriovenous coordination as a sensitive indicator of microcirculatory dysfunction, offering a practical analytical tool for assessing stroke-induced microvascular impairment.

neuroscience↗

bioRxiv2026

GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution

BackgroundDissecting the genetic basis of cell-type-specific gene regulation during gametogenesis remains a major challenge. Population-level studies mask cellular heterogeneity, while the extreme data sparsity of single-cell profiling has precluded robust genetic mapping. ResultsWe present GAMETE (Genetic Architecture Mapping of Epigenetic Traits at single-nucleus resolution), an integrated framework combining MPS-ATAC-seq, a high-throughput single-nucleus ATAC-seq method, with robust computational approaches for genotype inference and genetic mapping from sparse single-nucleus data. Applying GAMETE to hybrid rice pollen, we simultaneously profiled chromatin accessibility and inferred the genotypes of 4,887 individual haploid nuclei, revealing distinct chromatin landscapes across pollen cell types. This uncovered an unexpected elevation of chromatin accessibility at gypsy retrotransposons in microspores preceding their silencing in sperm cells, exposing a surveillance gap that may contribute to genome expansion. The synchronized profiling enabled us to construct a single-cell recombination map, map segregation distortion loci and trace their developmental origins, and identify 16,113 chromatin accessibility QTLs (caQTLs), 48.6% of which exhibited pronounced cell-type specificity. Analysis of introgression lines supported a cell-type-specific trans-acting caQTL regulating the pollen-essential gene DTM1. ConclusionsThis work establishes GAMETE as a broadly applicable framework for dissecting the genetic architecture of chromatin accessibility during gametogenesis without the need for subsequent generations.

genomics↗

bioRxiv2026

EZSolver: Template-free prediction of polar enzymatic mechanisms via bidirectional flow matching and search

Predicting enzymatic reaction mechanisms is critical for understanding enzyme function and for designing and discovering new enzymes. Current computational predictors rely on deterministic, rule-based dictionaries, which perform well on in-distribution tasks but fail to generalize to out-of-distribution (OOD) chemistry. To address this limitation, we present EZSolver, a template-free, generative framework for polar enzymatic mechanism prediction. Powered by a flow matching predictor (EZFlow) and navigated by an evaluator-guided bidirectional beam search, EZSolver learns the chemistry of electron redistribution instead of memorizing rigid templates. Evaluated across diverse enzyme classes, EZSolver achieves a 60.0% accuracy and an 84.6% chemical plausibility rate for full mechanism prediction of unseen polar enzymatic reactions. While rule-based models collapse without predefined templates, EZSolver successfully extrapolates chemical knowledge to infer uncatalogued pathways, as demonstrated during rigorous OOD benchmarking. By illuminating enzymatic chemical mechanisms, EZSolver helps pave the way for automated prediction of enzyme function and discovery and design of novel biocatalysts for sustainable chemistry. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/737313v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1b0ad92org.highwire.dtl.DTLVardef@535a71org.highwire.dtl.DTLVardef@56e846org.highwire.dtl.DTLVardef@1ab76ec_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Designing Fidelity of CRISPR-Cas Endonucleases by Kinetic Insights

Finding high-fidelity CRISPR-Cas variants is critical for both the precision of in vitro DNA detection and the safety of in vivo gene-editing therapeutics. However, the large size of the Cas enzyme and the distinct selection criteria between its natural evolution and clinical practice lead to extensive experimental trials and limited success rate for de novo design, directed evolution, protein language model (PLM)-based filtering. Here, we present a PLM-assisted physics-driven approach that utilizes atomistic molecular dynamics simulations and automated path searching to efficiently obtain the complete kinetic insights, including the transition state structures, for the conformational changes of Cas before DNA cleavage. We show that these kinetic insights can pinpoint a few fidelity-diminishing protein residues during the early stage of target recognition, and have led to SpyCas9 and FnCas12a variants with ultra-high fidelity surpassing previously reported counterparts at minimal cost of a few wet-lab trials.

biophysics↗

bioRxiv2026

A vascular chip for disease-relevant flow shear stress topology

Vascular chips have advanced endothelial mechanobiology by enabling controlled responses to hemodynamic cues, yet disease-relevant wall shear stress (WSS) modeling remains limited. Simplified one-dimensional flow shear systems, designed mainly for physiological mechanobiology, miss the topological organization of pathological flow, whereas patient-specific vascular models capture complex hemodynamics but sacrifice generality and imaging compatibility. Here we develop a programmable vascular chip that converts disease-associated WSS topology into a physiologically parameterized experimental input. The device reconstructs a representative pathological shear-topology field on endothelial layer, supports stationary and physiologically paced oscillatory flow modes, and integrates matched unidirectional-shear references within the same chip. Using this system, we show that oscillatory WSS topology destabilizes endothelial monolayers, drives asymmetric collective emergent behaviors, impairs actin-nuclear mechanotransduction, accompanied by nuclear softening and enhanced perinuclear nanoparticle uptake. Integrated live-cell imaging, fluorescence analysis, Brillouin microscopy, and transport assays enable multimodal phenotyping across collective, subcellular mechanical and functional scales. By making disease-relevant WSS topology experimentally controllable, this vascular-chip framework bridges computational hemodynamics and experimental mechanomedicine, supporting standardized vascular disease modeling and functional screening.

bioengineering↗

bioRxiv2026

Lack of co-ordination of stomatal, hydraulic and leaf browning traits in 16 perennial Australian grass species of differing climate origins

Grasslands are vulnerable to increasing drought with global warming, but process-based models lack the mechanistic knowledge required to predict the magnitude of drought impacts. While a plant hydraulics framework has been successful in advancing process understanding of drought responses in trees, and how drought responses vary across rainfall gradients, similar approaches have rarely been applied to grasses. Here, we quantified the progression of key drought response processes in sixteen dominant perennial grasses (seven C3 and nine C4) with differing climatic origins across eastern Australia. We found that stomatal closure, hydraulic impairment and leaf browning occurred concurrently, in contrast to the progressive sequence typically observed in trees. We also found that drought response traits were not correlated with species climate of origin. The early impairment of leaf hydraulic conductance and leaf browning along with the lack of correlation with climate of origin suggest that grasses may employ fundamentally different strategies to adapt to low water availability than trees. These results highlight the need for grass-specific parameterization of drought responses in process-based models.

ecology↗

bioRxiv2026

A Metabolic Enzyme, Pyruvate Carboxylase, Functions as a Sequence-Selective Small RNA Sensor for Antiviral Immunity

Interleukin-27 (IL-27) is an anti-HIV cytokine that induces 14 novel microRNAs (miRNAs) in primary CD4(+) T cells. We previously reported that transfection of two of these miRNA mimics, miRTC10 and miRTC14 into human primary macrophages, differentially induced interferon (IFN)-2, -8, -13, and -{lambda}1 expression. However, the mechanism underlying this activation remains unclear. Here, we demonstrate that miRTC14 does not directly target canonical IFN-regulatory genes but instead engages with pyruvate carboxylase (PC) and laboratory of genetics and physiology-2 (LGP2/DHX58) as direct binding partner proteins. Functional analysis revealed that miRTC14 transfection induces IFN expression by more than 100-fold (p<0.001), whereas PC or LGP2 depletion by siRNAs markedly attenuated this response (50-100-fold reduction, p<0.01). Reconstitution of PC and LGP2 in deficient HEK293 cells restored miRTC14-driven IFN induction. Notably, IFN activation depended on sequence features at the duplex termini. However, PC-miRTC14-LGP2 axis activates TBK1-dependent phosphorylation of IRF3/7, similarly to canonical RNA sensors (RIG-I/MDA5), but this process induced differential IFN subtype. These findings establish PC as a miRNA-binding protein and define a previously unrecognized RNA-sensing mechanism, linking metabolic enzymes to RNA sequence-dependent innate immunity. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/735367v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@ea70d3org.highwire.dtl.DTLVardef@1953a73org.highwire.dtl.DTLVardef@305f16org.highwire.dtl.DTLVardef@1b2daff_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO microRNA sequence-dependent activation of innate immunity by pyruvate carboxylase (PC). PC-miRTC14-LGP2 axis induces TBK1 phosphorylation via an as-yet-unidentified adapter(s). The activated TBK1 (p-TBK1) subsequently phosphorylates IRF3 and/or IRF7 leading to selective IFN subtypes (IFN-2, IFN-8, IFN-13, and IFN-{lambda}1). (Created in BioRender. Kariyawasam, U. (2027) https://BioRender.com/u82s04p) C_FIG

immunology↗

bioRxiv2026

Therapy-induced senescent-like cancer cells drive macrophage-mediated immunosuppression in cholangiocarcinoma

Cholangiocarcinoma (CCA) is a lethal biliary cancer in which chemoresistance is nearly universal, and its tumor immune microenvironment is dominated by immunosuppressive tumor-associated macrophages (TAMs) that exclude cytotoxic CD8+ T cells. How tumor cells sustain this immunosuppressive state during chemotherapy is undefined. Here we demonstrate that therapy-induced senescent-like (Sen-L) cancer cells accumulate after gemcitabine/cisplatin in human and murine CCA, are predominantly cancer cells, and predict shorter survival. Genetic elimination of Sen-L cancer cells reduces tumor burden, lowers TAM abundance, and restores intratumoral CD8+ T cells, establishing them as causal drivers. Growth differentiation factor 15 (GDF-15) is the dominant Sen-L-secreted factor and reprograms macrophages to suppress CD8+ T cells through the non-canonical receptor TGFBR2 and STAT6, and p16-restricted Gdf15 silencing phenocopies Sen-L elimination. Combined with chemotherapy, Sen-L elimination improves survival beyond chemotherapy alone. These findings establish Sen-L cancer cells and their GDF-15 output as causal, targetable drivers of macrophage-mediated immune evasion in CCA. SIGNIFICANCE STATEMENTTherapy-induced senescent-like cancer cells, not stromal cells, are the dominant senescent-like and immunosuppressive population in cholangiocarcinoma, and their elimination restores antitumor immunity. GDF-15 is their dominant secreted effector and engages a non-canonical macrophage receptor, TGFBR2, identifying a cancer-cell-to-macrophage axis and a Sen-L-elimination strategy to restore chemosensitivity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/734341v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@7d3fd8org.highwire.dtl.DTLVardef@ea9efborg.highwire.dtl.DTLVardef@16ba16borg.highwire.dtl.DTLVardef@132b821_HPS_FORMAT_FIGEXP M_FIG Graphical abstract. Senescent-like CCA cells promote tumor immunosuppression through TAMs polarization by GDF-15 C_FIG

Cancer Biology↗

bioRxiv2026

Acquisition of Stickland-metabolizing bacteria during infancy prevents Clostridium botulinum infection

Infant botulism is caused by intestinal colonization with Clostridium botulinum, whereas healthy adults are resistant. Although the gut microbiota has long been implicated in protection against C. botulinum, its bacterial basis has remained unknown. Here, we show that specific amino acid-metabolizing bacteria confer resistance to C. botulinum colonization through nutrient competition. Longitudinally collected human infant microbiotas exhibited a transition from susceptibility to resistance after transplantation into germ-free mice. 5-Aminovalerate marked the resistant microbiota, implicating Stickland metabolism. Resistant microbiotas were enriched in Stickland-metabolizing Clostridia, including Clostridioides difficile. Metabolomics revealed overlapping amino acid utilization, and C. difficile suppressed C. botulinum expansion through amino acid competition. These findings demonstrate that acquisition of Stickland-metabolizing Clostridia during infancy prevents C. botulinum infection through competition for shared amino-acid-dependent nutritional niches.

microbiology↗

bioRxiv2026

Metabolically engineered oilcane reshapes rhizosphere microbial guilds while preserving broad functional capacity

Metabolic engineering of crops can redirect host carbon flux, but its consequences for microbiomes remain unclear. Here, we show that engineering oilcane for triacylglycerol (TAG) accumulation reshapes rhizosphere microbial guilds across greenhouse and field environments while preserving functional capacity. Using 36 rhizosphere metagenomes from wild-type sugarcane and engineered oilcane accessions, we reconstructed metagenome-assembled genomes and linked community turnover with shifts in functional potential. Oilcane rhizospheres exhibited taxonomic restructuring relative to wild-type plants, driven primarily by turnover rather than nestedness and marked by genotype-dependent replacement of microbial guilds. These patterns were strongest in accession 1566 and amplified under field conditions. Despite these compositional shifts, broad patterns of functional potential remained similarly distributed, whereas pathway-level differences were evident in energy production and conversion, lipid transport and metabolism, secondary metabolite biosynthesis, transport and catabolism, and signal transduction. These findings extend evaluation of engineered crops beyond host traits alone to include microbiome-scale responses.

microbiology↗

bioRxiv2026

Targeted Photodegradation of Misfolded Proteins via Self-photosensitizing with Molecularly Produced Light

Misfolded proteins are tightly associated with various neurodegenerative diseases, and removing these misfolded proteins is one of the actively pursued approaches for seeking therapeutics for these diseases. In this study, we demonstrated that molecularly produced light (molecular light) from ADLumin-5, a self-photosensitizing chemiluminescence compound, could induce photo-oxidation and photodegradation of misfolded proteins, including beta-amyloid, tau, alpha-synucleins, and TDP-43 proteins in vitro. We validated the oxidation and degradation via LC-MS, MADLI-MS, and western blotting. Using beta-amyloid as a showcase, we demonstrated that, upon photo-oxidation and photodegradation, the toxicities of this misfolded protein were significantly reduced. To investigate the therapeutic effects of ADLumin-5 in vivo, we used the 5xFAD mouse model for longitudinal treatment for 4 months. In vivo molecular imaging results indicated that ADLumin-5 could reduce the accumulation of beta-amyloid proteins. Our study presents a novel approach to seek therapeutics for neurodegenerative disease via molecular light-induced degradation of misfolded proteins. In addition, because ADLumin-5 is dual-functional--enabling both photodegradation and in vivo imaging of misfolded protein changes--it can be considered a photo-theranostic agent for neurodegenerative diseases, representing a novel approach to drug discovery for neurodegenerative diseases.

neuroscience↗

bioRxiv2026

Upregulation of ATP-purinergic P2x2 receptors in the cochlea over-amplifies hearing sensitivity leading to hyperacusis and attenuation by antagonists

Hearing hypersensitivity (hyperacusis) is a common hearing stress and can cause many psychological diseases, e.g., anxiety, learning disabilities, and attention-deficit/hyperactivity disorder (ADHD). Here, we report an unexpected finding that the upregulation of P2x2 ATP-purinergic receptors in the cochlea links to hyperacusis generation. We found that P2x2 expression in the cochlea but not in auditory centers was upregulated in the hyperacusis generated by Cx26 deficiency. Overexpression of P2x2 in the cochlea also caused hyperacusis. Conversely, downregulation of P2x2 expression or administration of P2x2 antagonists attenuated hyperacusis. We further found that upregulation of P2x2 receptors in the cochlea increased outer hair cell (OHC) electromotility through the post-transcription functional modulation to potentiate active cochlear amplification leading to hearing hypersensitivity. Such enhancements in OHC electromotility and active cochlear amplification were also suppressed by P2x2 receptor antagonists. Overall, these findings demonstrate that P2x2-mediated ATP-purinergic signaling in the cochlea plays a critical role in hyperacusis generation; targeting P2x2 receptors can attenuate hyperacusis stress, which may also offer a therapeutic strategy for other related psychological comorbidities. Significance statementHearing hypersensitivity is a common hearing stress and can cause many other psychological disorders. However, little is known about the underlying genetic and cellular mechanisms. Also, it lacks efficient drugs for their treatments in the clinic. In this study, we found that upregulation of P2x2 ATP-purinergic receptors in the cochlea can potentiate outer hair cell electromotility, which is an active cochlear amplifier in mammals and can increase hearing sensitivity and frequency selectivity, through post-transcription functional modulation to enhance active cochlear amplification leading to hearing hypersensitivity. These enhancements can be inhibited by administrations of P2x2 receptor antagonists both in vitro and in vivo. These findings revealed a new genetic and cellular mechanism underlying hyperacusis generation and opened a new avenue to develop an efficient therapy for this common hearing stress and other associated psychological comorbidities.

physiology↗

bioRxiv2026

Enzyme-Linked Cycloaddition Assay (ELCA) for rapid, ultra-sensitive monitoring of secreted sialoglycoproteins

Glycosylation of proteins is central to cell signaling, immune function, and pathogen interactions, yet existing methods for monitoring glycan changes require specialized instrumentation and primarily report on membrane-anchored, rather than secreted, glycoproteins, with a slow turnover. Here, we present the Enzyme-Linked Cycloaddition Assay (ELCA), a click chemistry-based platform for ultra-sensitive detection and semi-quantitative analysis of secreted sialoglycoproteins. By metabolically incorporating an azide-modified sialic acid into newly synthesized glycoproteins and capturing labeled material via strain-promoted cycloaddition, ELCA quantifies aggregate sialylation using a microplate reader-compatible, ELISA-like workflow. We demonstrate that the secreted glycoproteome responds rapidly to pharmacological perturbation, with changes detectable within hours. Benchmarking against common glycosylation inhibitors and profiling cytokine-driven macrophage polarization further establishes ELCAs sensitivity and temporal resolution. Compatible with serum-containing conditions and requiring no specialized instrumentation, ELCA provides a broadly accessible tool for rapid, cost-effective monitoring of secreted glycoprotein dynamics.

biochemistry↗

bioRxiv2026

Low Shear Modeled Microgravity Induces Unexpected Motility Phenotypes in Salmonella Typhimurium

Bacteria routinely exhibit unexpected phenotypic and molecular changes in response to spaceflight and spaceflight-analogue conditions, yet the mechanisms by which they sense and respond to these low fluid shear environments are not fully elucidated. We previously demonstrated that spaceflight and low shear modeled microgravity (LSMMG) altered motility and chemotaxis gene expression in Salmonella enterica serovar Typhimurium (S. Typhimurium), raising the possibility that flagella mediate responses of the pathogen to these environments. Herein, we investigated whether LSMMG culture alters S. Typhimurium motility and examined the role of flagella in regulating pathogenesis-associated stress and infection phenotypes. LSMMG enhanced the swimming motility of wild-type S. Typhimurium relative to 1xg controls; a trend which persisted even in the absence of the global stress response regulators Hfq and RpoS. This finding was unexpected, as {Delta}hfq mutants are typically defective for motility under conventional culture conditions. Motility was also observed in the flagella-deficient {Delta}flhDC mutant following LSMMG and 1xg culture, although the relative motility pattern differed relative to wild-type. Collectively, these results indicate that flagella contribute to LSMMG-enhanced motility, but are not strictly required under these conditions. Conditioned supernatant exchange demonstrated that LSMMG-induced motility changes are cell-intrinsic rather than mediated by extracellular factors. While flagella were dispensable for many pathogenesis-related phenotypes tested, their deletion selectively altered the magnitude of LSMMG-associated thermal stress and intracellular survival in human intestinal epithelial cells. Together, these findings demonstrate that motility and pathogenesis-related responses in S. Typhimurium are governed by multiple regulatory pathways that differentially respond to LSMMG and 1xg conditions. IMPORTANCESpaceflight and spaceflight-analogue conditions alter bacterial physiology in unexpected ways that are important for pathogenesis, yet the mechanisms by which bacteria sense and respond to low fluid shear environments remain incompletely understood. This study shows that low shear modeled microgravity (LSMMG) enhances Salmonella Typhimurium motility and produces unexpected motility phenotypes in mutants lacking Hfq or the flagellar master regulator FlhDC. These findings indicate that flagellar biosynthesis contributes to LSMMG-enhanced motility but is not strictly required for motility under these conditions. We also suggest that flagella influence the magnitude of selected stress and infection phenotypes rather than serving as an absolute requirement for LSMMG responsiveness. Together, these results highlight the complexity of bacterial mechanotransduction under simulated microgravity conditions and advances our understanding of how a foodborne pathogen adapts to physiological low fluid shear environments encountered both in space and during terrestrial infection of the intestinal tract.

microbiology↗

bioRxiv2026

FALCON: Closed-Loop Multi-Objective Optimization of Lipid Nanoparticles for Cell-Selective mRNA Delivery

Efficient, cell type-selective delivery of genetic payloads remains a central challenge in the development of gene and cell therapies. Lipid nanoparticles (LNPs) offer a versatile delivery platform, but their optimization is hindered by reliance on brute-force screening methods that are laborious, resource-intensive, and focus on single targets. Here, we present FALCON (Framework for Active Learning-driven Compositional Optimization of Nanoparticles), a closed-loop pipeline that leverages iterative screening, surrogate modeling, and multi-objective optimization to accelerate LNP compositional design. In B cell-targeted validation experiments, FALCON-optimized LNPs achieved a 1.8-fold increase in splenic B cell transfection in vivo compared with reference compositions. When optimized for selectivity, FALCON LNPs displayed an 84-fold improvement in selective transfection of splenic B cells over off-target liver populations and enabled spleen-tropic behavior across factorial panels of varying ionizable and helper lipid chemistries. In vaccine studies, these LNPs induced higher IgG2c antibody titers and a more Th1-biased immune profile. FALCON was also deployed to optimize LNPs for myeloid cell-selective delivery, achieving enhanced in vivo selectivity following systemic administration both across and within spleen and liver compartments. Our results establish FALCON as a useful tool for data-driven design of LNP compositions for precision gene delivery.

bioengineering↗

bioRxiv2026

Ventricular Expansion Couples Hyperosmotic Stress to Thirst

Thirst is thought to arise from osmotic signals detected by circumventricular organs, yet how hyperosmotic stress activates mechanosensitive channels remains unclear because cell shrinkage should reduce membrane tension. Here we identify a brain-scale mechanical signal that couples systemic osmotic stress to drinking. In mice, hypertonic saline rapidly increased serum and cerebrospinal fluid osmolality, expanded the lateral ventricles, and promoted water intake. Relieving or blocking ventricular deformation attenuated drinking without eliminating osmotic gradients. Hyperosmotic challenge also produced localized deformation of periventricular cells, where spatial transcriptomics revealed candidate mechanosensitive channels, including Tmem63b and Piezo1. Thus, ventricular expansion provides a mechanical component of osmotic thirst, uncovering an osmo-mechanical layer of interoceptive regulation.

neuroscience↗

bioRxiv2026

α-synuclein pathology drives multi-scale reorganization of fronto-limbic networks and cognitive flexibility in the common marmoset

Understanding how -synuclein misfolding and spreading affect brain systems is central to synucleinopathy research, yet evidence from primate models remains limited. Here, we combined histology, awake structural MRI, awake resting-state fMRI, regional homogeneity, actimetry and touchscreen behavioral testing to longitudinally track the consequences of striatal -synuclein seeding in the common marmoset. Phosphorylated -synuclein inclusions were detected from 2 months post-injection and spread progressively to distributed cortical and subcortical regions bilaterally, accompanied by regionally specific structural atrophy. Functional imaging revealed widespread disruption of large-scale networks, particularly within fronto-limbic circuits, alongside reductions in local functional coherence. Despite the absence of overt motor or sleep deficits, animals exhibited a selective impairment in cognitive flexibility, with preserved learning and task engagement. These findings indicate that striatal -synuclein seeding induces a multi-scale reorganization of brain networks preferentially affecting circuits supporting cognitive flexibility and limbic processing, establishing a primate platform for studying early stages of synucleinopathy.

animal behavior and cognition↗