Biology subjects

Luo, Y.

Publications and source records attributed to Luo, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

A life-history axis of resource acquisition in bacteria: depolymerisation versus uptake

Microbial decomposition of complex organic matter is a major control on the global carbon cycle, and its efficiency hinges on how microbes acquire resources. Decomposition requires costly extracellular enzymes to break down complex polymers, whereas the resulting soluble products are captured far more cheaply through membrane transporters. How microbes balance investment between these two processes is a fundamental axis of microbial life history, yet it has remained difficult to quantify across their vast diversity. Using genomic repertoires for carbohydrate depolymerisation and uptake, we developed a simple ratio distinguishing depolymerisation-optimised from uptake-optimised strategies, and applied it to more than 249,000 environmental and host-associated bacterial genomes. These strategies were strongly phylogenetically structured and differed by habitat, with uptake-optimised bacteria unexpectedly more prevalent in diffusion-limited soils than in aquatic environments. In an 18-month field-scale plant litter decomposition experiment, uptake-optimised bacteria dominated during early decomposition, when fungi were more abundant and strongly expressed hydrolytic enzymes, shifting towards depolymerisation-optimised bacteria at later stages. A simple genomic ratio therefore captures ecologically meaningful resource-acquisition strategies that vary with phylogeny, habitat and successional stage. The balance of these strategies could shape community-level extracellular enzyme investment, with consequences for decomposition and carbon cycling.

microbiology↗

bioRxiv2026

Information contracts determine what inverse perturbation benchmarks measure

Inverse perturbation benchmarks rank interventions toward a desired cellular state, but high accuracy can answer a different question from biological prioritization. We present InverseBench, which makes candidate information and endpoint construction explicit, and FSTN, a linear pipeline evaluated under it. With identical inputs, candidates and validation, nested ridge reaches Spearman 0.959 for a transcriptional principal-component proxy but 0.445 for independently measured K562 growth fitness across 7,354 genes. Controlled response-entry availability across seven tasks gives heterogeneous gains, 0.442 for CD4 activation and 0.116 for external fitness. Yet predefined shortlist comparisons show no primary-cutoff penalty in K562 or a melanoma co-culture screen, and secondary cutoffs reverse the K562 ordering. FSTN's nonnegative set selector recovers 0.840 of measured two-gene constituents in three picks, against 0.771 for an unconstrained greedy. The framework separates proxy reconstruction, response-informed prioritization and unseen-intervention ranking: an endpoint-dependent accuracy gap does not by itself mean worse biological decisions.

bioinformatics↗

bioRxiv2026

Super-resolution imaging flow cytometry

Organelle architecture is a key determinant of cellular state. However, its heterogeneity remains difficult to quantify at population scale because conventional imaging flow cytometry is diffraction-limited. Here we present super-resolution imaging flow cytometry (SR-IFC), a high-throughput structured-illumination platform combining stroboscopic excitation, microfluidic hydrodynamic focusing and AI-assisted reconstruction. From three phase-shifted frames acquired along the flow axis, SR-IFC reconstructs images with approximately 118-nm isotropic in-plane resolution, about two-fold beyond the diffraction limit, at up to approximately 720 cells per second. In microbiology, SR-IFC resolves individual lipid droplets in nitrogen-starved Euglena gracilis and reveals spatial reorganization during lipid biogenesis missed by diffraction-limited imaging. In immunology, it maps activation-associated mitochondrial remodeling across primary human CD8+ T-cell differentiation, including a transient networked state. SR-IFC thus provides a broadly applicable platform for population-scale super-resolution phenotyping across diverse areas of biology.

bioengineering↗

bioRxiv2026

NeuroPilot: Longitudinal intravital neural imaging across scales and modalities through an agentic platform

Longitudinal intravital imaging is essential for understanding how neural populations evolve across behavioral states, yet converting large-scale recordings into biological insight remains a fundamental challenge because neural signals are degraded by noise, non-rigid motion, and heterogeneous recording conditions. Here we introduce NeuroPilot, an agentic framework that transforms neural imaging analysis into a closed-loop, context-aware process, integrating a multimodal large language model with callable computational imaging modules to adaptively coordinate workflows from raw recordings to population-level readouts. Across heterogeneous imaging and experimental regimes, NeuroPilot restores motion-degraded recordings and supports consistent neural signal recovery, detection, and tracking in challenging deep-brain, freely moving, and longitudinal settings. These enable neuronal population tracking across spinal stimulation paradigms, deep-brain imaging, and continuous 24-hour mPFC recordings aligned with spontaneous sleep-wake behavior. By converting heterogeneous intravital recordings into stable population activity maps, NeuroPilot supports behavioral decoding and reveals structured neural dynamics across behavioral states and transitions. NeuroPilot establishes a scalable agentic paradigm for neural imaging analysis, expanding experimental access to the measurement, visualization, and interpretation of neural population activity.

neuroscience↗

bioRxiv2026

Contrasting gene gain and loss shape metabolic diversification in the Ralstonia solanacearum species complex

Metabolic repertoires are continually remodeled by gene acquisition and loss, but how these contrasting processes jointly generate phenotypic diversity within bacterial species complexes remains poorly understood. Here, we elucidated the genetic and evolutionary basis of the classical biovar phenotypes of the Ralstonia solanacearum species complex (RSSC), which are defined by differential utilization of three hexitols (sorbitol, mannitol, and dulcitol) and three disaccharides (lactose, maltose, and cellobiose). Although this classification has been used for over half a century, the genetic determinants and evolutionary origins of these phenotypes have not been systematically resolved. Machine-learning analysis of genomic data from 250 RSSC strains with documented biovar phenotypes, combined with genome-wide association analysis and gene deletion, identified the smoEFGK gene cluster and flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase (FADGDH) as the major determinants of hexitol and disaccharide utilization, respectively. Comparative phylogenomics revealed fundamentally different evolutionary histories of these loci. An ancestral smoEFGK system was lost early in RSSC evolution and subsequently reacquired by the ancestor of phylotype I through horizontal transfer from a Burkholderia-related lineage, whereas vertically inherited FADGDH underwent recurrent, independent losses across multiple RSSC lineages. Extending the analysis to 1,082 RSSC strains further showed that disaccharide-utilization capacity was significantly depleted among monocot-associated strains after accounting for phylogenetic relatedness and geographic origin. Together, these findings reveal how contrasting trajectories of gene gain and loss can reshape bacterial metabolic repertoires, generate lineage-associated phenotypic diversity, and potentially contribute to ecological differentiation.

genomics↗

bioRxiv2026

FlyAnatoView: Visualization of Drosophila Single-cell RNA-seq Datasets on Anatomographs

Single-cell RNA sequencing (scRNA-seq) is a powerful approach for measuring the transcriptomic landscape at single-cell resolution. However, while scRNA-seq data reveals what genes each cell expresses, they do not indicate where that cell was located within the tissue or organ, anatomically. We developed FlyAnatoView (https://www.flyrnai.org/tools/rna_seq_base/web/svg_files/), a resource that projects scRNA-seq data onto anatomical diagrams, restoring this missing spatial context.

bioinformatics↗

bioRxiv2026

Reconstructing donor genotypes from scRNA-seq for downstream eQTL and HLA-TCR analysis

Single-cell eQTL studies can reveal heterogeneous genetic effects on gene expression that vary with cell type, but their wider application has been constrained by the frequent absence of matched genotype data. Here, we present single-cell Transcriptome Allelic Prediction and Association Studies (scTAPAS), a bioinformatic framework for reconstructing donor genotypes directly from single-cell RNA-sequencing reads and downstream genetic analysis. Applying scTAPAS to 5' single-cell RNA-sequencing data from the COVID-19 Multi-omic Blood Atlas (COMBAT), we show that reference-based imputation of sparse RNA-derived genetic information generates genotype dosages sufficiently accurate for association testing. Despite testing only 18.0% of the variants available from conventional array-based genotyping and imputation, scTAPAS recovers 68.6% of cell type-eGene pairs identified using conventional array-based genotypes, with strong concordance in effect sizes. We further show that scTAPAS-derived variants can support imputation of classical HLA alleles and enable HLA-aware QTL analyses, including associations between HLA variation and TCR repertoire at single-cell resolution. Using matched single-cell TCR-sequencing data, we identify CD4+ T cell-specific associations between HLA class II alleles and T-cell receptor (TCR) Va; gene segment usage, highlighting the potential of analyses that complement TCR sequencing at single-cell resolution with HLA types. These results show that genetic information recovered from single-cell RNA sequencing data can support both regulatory and immunogenetic association analyses, expanding the discovery potential of single-cell cohorts for which conventional genotyping or HLA typing is unavailable.

bioinformatics↗

bioRxiv2026

Rank-based integration identifies convergent disease mechanisms across omics

The rapid growth of omics studies offers new opportunities to uncover disease mechanisms, yet findings from individual studies or single omics may be influenced by cohort-, platform- and layer-specific variation. Integrating evidence across studies and omics layers can reveal robust biological signals that are reproducible across molecular layers, but differences in assay platforms, sample sizes and feature coverage complicate direct combination of summary statistics. Here we present the Omics Rank-Based Integration Tool (ORBIT), a direction-aware framework for prioritizing concordant signals across omics layers using only within-dataset feature ranks and effect directions. ORBIT tests directional rank consistency across omics layers against a closed-form variance-gamma null distribution while accounting for inter-dataset correlation and incomplete feature overlap. Simulations show that ORBIT maintains well-calibrated false-positive rates under inter-omics correlation, increasing numbers of omics layers and missingness, while detecting concordant signals with increasing power as the number of layers grows. We applied ORBIT to tubulointerstitial transcriptomic data from patients with chronic kidney disease in the C-PROBE cohort and proteomic data from the Kidney Precision Medicine Project, identifying a concordant injury programme marked by inflammatory and fibrotic remodeling together with impaired energy metabolism. We also used ORBIT to integrate ten transcriptomic, four proteomic and one translatomic datasets in dilated cardiomyopathy heart tissue, identifying extracellular matrix remodeling and mitochondrial energy failure as the dominant concordant biological programmes. In both diseases, ORBIT prioritized concordant genes and identified pathways that were not significant in any single omics layer alone. These results show that directional rank integration can be used for integrating heterogeneous omics summary data and prioritizing robust molecular mechanisms.

bioinformatics↗

bioRxiv2026

An accumbal cholinergic ISR-HCN2 axis sustains maladaptive cue motivation

Environmental cues associated with rewarding outcomes can exert persistent control over behavior long after the reward is absent, yet the cellular adaptations that stabilize such maladaptive motivation remain unclear. Here we identify nucleus accumbens cholinergic interneurons (CINs) as causal regulators of persistent cue-driven seeking. Self-administration of addictive drugs or high-fat reward, but not sucrose, selectively increased CIN pacemaker firing. Cocaine-paired cues evoked rapid acetylcholine release in the nucleus accumbens core, and bidirectional manipulation of CINs suppressed or enhanced cue-induced cocaine seeking. Mechanistically, cocaine experience engaged the integrated stress response (ISR) in CINs, increased HCN2 expression and Ih, and stabilized a hyperexcitable state. CIN-specific ISR suppression or HCN2 knockdown reduced cocaine seeking, whereas HCN2 overexpression enhanced it. Local HCN blockade and systemic treatment with the clinically approved HCN blocker ivabradine reduced cue-driven seeking across addictive-drug and high-fat-reward paradigms while sparing sucrose seeking. These findings identify an ISR-HCN2-dependent cholinergic mechanism that stabilizes maladaptive cue-driven motivation and nominate HCN-dependent excitability as a tractable target for therapeutic intervention.

neuroscience↗

bioRxiv2026

Functional reorganization of large-scale brain systems underlies emotion regulation maturation

Emotion regulation via cognitive reappraisal is essential for socioemotional development and mental health, yet the organizational logic of its supporting brain systems across youth remains unclear. Using a large multisite cohort, we demonstrate that maturation of reappraisal capacity reflects reorganization of a distributed architecture rather than progressive strengthening of prefrontal control. Reappraisal robustly reduced negative affect, with non-linear gains concentrated between 6 and 10.5 years. Bayesian systems identification resolved this architecture into four functionally distinct systems-reappraisal-specific, common-appraisal, modifiable-emotion, and non-modifiable-emotion components-spanning prefrontal-control, salience, default-mode and dorsal-attention networks. Age-related variation in anterior temporal cortex, emerged as essential hub, statistically accounted for developmental gains in reappraisal success. Multivariate modelling together with intersubject analyses further identified a cross-site-generalizable whole-brain reappraisal signature and revealed an age-dependent shift in brain-behaviour coupling, with neurobehavioural convergence increasing with age. These findings establish distributed network reorganization as a core mechanism of emotion regulation development and provide mechanistic targets for stage-matched interventions.

neuroscience↗

bioRxiv2026

STAT1 sets microglial neutral-lipid content independently of lipid-handling transcriptional programs

Inflammatory activation and lipid remodeling are linked features of microglial states, but how inflammatory transcription factors shape microglial lipid handling is unclear. Here we show that STAT1 sets neutral-lipid content in microglia through a route not predicted by lipid-handling transcription. Acute STAT1 depletion in primary microglia lowered neutral-lipid content while lipid-uptake and lipid-storage programs were induced, and interferon-{gamma} activation moved inflammatory transcription in the opposite direction yet lowered lipid content alike. Single-cell transcriptomic and chromatin profiling of Stat1- and Irf1-deficient mice showed that STAT1 and IRF1 organize overlapping inflammatory and lipid-handling programs, with genome-wide accessibility changes that did not predict transcriptional output at individual lipid-handling loci. Microglia co-expressing STAT1 and APOE recurred across Alzheimer's disease and multiple sclerosis datasets. Transcriptional program engagement is therefore separable from cellular lipid state, and lipid-handling gene expression cannot be read as a proxy for microglial lipid content.

neuroscience↗

bioRxiv2026

Mammalian TMC Family Proteins are Mechanically Gated Ion Channels

Every known life form senses and reacts to mechanical forces. These mechanical stimuli can be converted into electrical signals by mechanically gated ion channels, a transduction cascade pivotal to numerous physiological functions including touch, hearing, mechanical pain, circulation, gastrointestinal function, and mechanical loading in various tissues. Despite continuous efforts, numerous mechanically gated ion channels with the mechanotransduction process underlying these physiological functions remain unidentified. Here, we focused on the transmembrane channel-like (TMC) protein family expressed in the cultured cells to identify those with potential mechanosensitive activity. Remarkably, in contrast to human TMC1/2 (HsTMC1/2), human TMC3-8 (HsTMC3-8) proteins are localized to the plasma membrane when heterologously expressed in the cultured cells. Further experiments revealed that mechanical poking stimuli can effectively activate HsTMC3-8. In addition, HsTMC3-8 induced stretch-activated currents and elicited well-resolved single-channel activities in response to negative pressure stimulation. The mutants near the putative pore region altered reversal potentials (Erev) of HsTMC3-8, suggesting that TMC3-8 are likely pore-forming subunits of ion channels. In summary, we proposed that TMC proteins are the largest mammalian mechanically gated ion channel family.

neuroscience↗

bioRxiv2026

PKA can adopt structural or enzymatic roles depending on its anchoring site

Protein kinase A (PKA) is a central mediator of cAMP signaling whose spatial specificity is conferred by A-kinase anchoring proteins (AKAPs). However, functions of individual anchored PKA pools are difficult to resolve as current approaches cannot isolate anchoring at defined sites. Here, we develop a SpyCatcher-SpyTag-based replacement strategy enabling direct comparison of AKAP function with and without type II PKA regulatory (RII) subunit anchoring in intact signaling environments. Anchoring RII to AKAP79 or AKAP1 produced distinct phosphorylation-dependent effects, including catalytic subunit membrane recruitment and mitochondrial morphology regulation. In contrast, MAP2-anchored RII drove phosphorylation-independent microtubule straightening, increased formation of widely spaced bundles, and supported dendritic arborization. This structural function was recapitulated by native MAP2-RII binding and required an intact cAMP-binding pocket in the second cyclic nucleotide-binding domain. These findings establish that AKAP-bound PKA can function as either an enzymatic or structural component and provide a generalizable strategy to dissect compartmentalized kinase signaling.

molecular biology↗

bioRxiv2026

Structure and energy transfer of a minimal PSI-LHCI supercomplex with FNR binding from a terrestrial eustigmatophyte

Soil microalgae endure harsh terrestrial stressors, such as intense light. Eustigmatophytes are an independent evolutionary branch within stramenopiles and occupy diverse aquatic and terrestrial environments, but the structural organization of their photosynthetic apparatus remains poorly understood. Here, we determined the cryo-electron microscopy structure of a photosystem I-light-harvesting complex I (PSI-LHCI) supercomplex bound with ferredoxin-NADP+ oxidoreductase (FNR) from the terrestrial eustigmatophyte Vischeria stellata at 2.44 [A] resolution. The supercomplex contains a monomeric PSI core associated with only three LHCI subunits, representing the smallest PSI-LHCI reported among structurally characterized red-lineage PSI complexes composed of violaxanthin-Chl a proteins (VCPs). The three VCPIs with distinct structure features and arrangements form a compact belt along the PsaL-PsaI-PsaM side of PSI. The structure also resolves a 43-residue N-terminal segment of FNR (FNR-N) bound to the PSI stromal surface, which is stabilized by both a eustigmatophyte-conserved insertion in PsaL and the N-terminal region of PsaD. In contrast, the catalytic region of FNR was not resolved, suggesting conformational flexibility. Computational simulations indicate potential excitation-energy-transfer pathways connecting the three VCPI subunits to the PSI core and highlight lineage-specific pigments that maintain energetic connectivity within the exceptionally compact antenna. Our analysis further reveals conservation of FNR tethering despite pronounced diversification of antenna size and organization. These findings uncover a modular evolutionary principle in which PSI acceptor-side organization is retained while the light-harvesting antenna is extensively remodeled, providing a framework for understanding the diversification of photosynthetic energy conversion across ecological transitions.

plant biology↗

bioRxiv2026

The cellular and genetic basis of inflorescence divergence between maize and teosinte

The domestication of maize from teosinte involved dramatic remodeling of the ear, yet the cellular and genetic bases of this transformation remain unclear. Here, we generate a single-nucleus and spatial transcriptome atlas of developing maize and teosinte ears. Comparative analysis reveals divergence in cob-associated cell types, with enhanced cytokinin signaling and reduced growth-inhibitory signals collectively driving cob thickening and enlargement in maize. We further demonstrate that domestication expanded the spatial expression domain of key transcription factors in maize meristem cells, enhancing the potential for increasing kernel number. Additionally, we verified a major domestication gene, ZmSPD1, in which two nonsynonymous SNPs differentiate maize from teosinte and alter jasmonic acid (JA) levels in the ear, thereby suppressing spikelet abortion to effectively double kernel production. These findings provide a cell-resolved mechanistic framework for how cob architecture and kernel number were shaped during maize domestication, offering new insights into the formation of key agronomic traits.

plant biology↗

bioRxiv2026

Neural control of respiration in Drosophila

Adaptive control of breathing is essential for life, yet the neural circuits that couple respiration to locomotion and internal physiological state remain poorly understood. Insects regulate gas exchange through spiracles: valve-like openings in the cuticle that allow oxygen uptake while minimizing water loss. We find that spiracle opening in Drosophila is dynamically matched to flight power and reduced by dehydration. We identify the motor neurons that innervate the spiracle muscles and show that their optogenetic activation closes all eighteen spiracles and rapidly limits flight power. Inhibitory interneurons transmit descending flight commands to the spiracle motor neurons, opening spiracles in proportion to metabolic demand. A parallel interoceptive pathway converges on the same interneurons to close the spiracles and suppress flight. Feedforward descending commands thus couple flight power to spiracle opening, while interoceptive feedback pathways close spiracles to balance oxygen supply against water loss. This compact circuit architecture may reflect a general solution for matching respiration to the competing demands of locomotion and water conservation.

neuroscience↗

bioRxiv2026

Anti-Z-NA antibodies can distinguish accessible Z-form states across DNA, RNA, and DNA-RNA substrates

Left-handed (Z-form) double-stranded nucleic acid conformers (Z-DNA and Z-RNA, collectively called Z-NA) are molecular patterns recognized by ADAR1 and ZBP1, which are sensor proteins involved in innate immunity. Monoclonal antibodies raised against Z-DNA, such as Z22 and Z-D11, are employed as probes for the study of Z-NAs, but their substrate specificity and functional equivalence remain unclear. Here, we used biochemical, biophysical, and structural approaches to compare the binding modes and target specificies of Z22 and Z-D11, using Z-prone CG-rich dsDNA, dsRNA, and DNA-RNA hybrids as substrates. Both antibodies failed to form stable complexes with short CG-rich dsRNA under conditions compatible with antibody stability, which suggests that they are unable to induce A-to-Z transitions in dsRNA. In contrast, both antibodies robustly complexed with dsDNA and DNA-RNA hybrid substrates. Cryo-EM structural analysis confirmed that both antibodies interact with Z-NA through a conserved interaction network, and demonstrated that complexes between the antibodies and DNA-RNA hybrids adopted distinct higher-order organizations. Z22 retained binding to both Z-DNA and Z-RNA segments, whereas Z-D11 displayed substrate-dependent organization and was restricted to Z-DNA segments Molecular modelling provided mechanistic explanation for the differences in Z-RNA binding ability between the two antibodies, which was confirmed in situ with ADAR1-depleted, IAV- infected and JTE607-treated cells. We also demonstrate that Z-D11, in contrast to previously described Z22, is unable to induce B-to-Z-transitions in short d(CG)6 oligos under physiological conditions. Together, these results show that anti Z-NA monoclonal antibodies are not functionally interchangeable: whereas Z22 recognizes pre-formed Z-RNA, Z-DNA- RNA hybrids, and Z-DNA, Z-D11 recognizes Z-DNA, and DNA segments in Z-DNA-RNA hybrids. These differences are dictated by substrate composition, local geometry, and conformational accessibility, which also likely impact their ability to induce NA structural transitions. These findings have important implications for interpreting antibody-based detection of left-handed nucleic acids in biological systems.

biophysics↗

bioRxiv2026

Engineered Amphiregulin Promotes Tissue Healing via Dual Regenerative and Immunomodulatory Functions in Tissue-Resident Non-Immune Cells

Amphiregulin (AREG), a growth factor prominently expressed by immune cells, has emerged as an important mediator of tissue healing. However, its therapeutic potential and immunomodulatory effects remain elusive. Here, we engineered an optimized AREG (eAREG) with enhanced signaling and show that it promotes robust skin repair and muscle regeneration in murine models. Beyond its growth factor function, eAREG acts on tissue-resident non-immune cells to suppress inflammation-induced chemokine programs, thereby limiting the recruitment of pro-inflammatory immune cells. We further demonstrate that eAREG constrains chromatin accessibility at regulatory regions of key chemokine genes, revealing an epigenetic mechanism of immune regulation operating within non-immune tissue compartments. Importantly, the regenerative and immunomodulatory effects of eAREG are preserved in diabetic mice with elevated inflammation and impaired healing. Together, these findings identify eAREG as a dual-function regenerative biologic and establish a design principle for regenerative therapies that integrate morphogenic signaling with immunomodulation mediated by tissue-resident cells.

immunology↗