Biology subjects

Yang, J.

Publications and source records attributed to Yang, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Goat Milk-derived Extracellular Vesicles modulate glial responses in vitro and attenuate neuroinflammation in vivo

Milk-derived extracellular vesicles (MEV) represent a naturally derived, potentially scalable platform for immunomodulation, yet their effects on central nervous system (CNS) glial inflammation at defined particle-to-cell ratios remain insufficiently characterized. Here, we investigated the immunomodulatory effects of goat milk-derived MEV in cellular and murine models of neuroinflammation. MEV-enriched preparations were obtained by sequential filtration, ultrafiltration, and size-exclusion chromatography, and characterized by scanning electron microscopy, nanoparticle tracking analysis, and dynamic light scattering. In LPS-stimulated BV2 microglia-like cells, MEV at 250 and 2500 particles per cell significantly reduced CD40 expression. In primary rat mixed glial cultures, microglia, astrocytes, and oligodendrocytes internalized MEV. At 250 particles per cell, MEV significantly reduced CD40 and IL1{beta} gene expression at the mixed-culture level. In both cellular models, MEV also increased markers associated with an M2-like microglial phenotype under resting conditions. Following intrathecal administration in healthy mice, MEV did not induce significant changes in the inflammatory gene markers assessed at 8 h. In an LPS-induced mouse model of neuroinflammation, intrathecal MEV administration reduced CD40 protein expression towards control levels within 24 h and shifted the inflammatory marker profile towards a pro-resolutive state, as indicated by increased Arg1 levels and elevated CD206/CD86 and IL10/IL6 ratios. These findings identify goat milk-derived MEV-enriched preparations as potential modulators of CNS glial inflammation and support further investigation of their therapeutic potential.

neuroscience↗

bioRxiv2026

Stabilizing gas in aqueous liquids with metal-organic frameworks for persistent acoustic transduction

Gas is the most efficient mediator of acoustic energy owing to its high compressibility, yet its thermodynamic instability in aqueous environments makes it inherently transient, limiting sustained ultrasound-biological interfacing. Here, we show that gas can be stabilized, confined, and manipulated in the liquid phase to function as a persistent acoustic transducer. By trapping gas within designed microporous metal-organic framework (MOF) nanocrystals, interfacial forces establish a stable ternary-phase equilibrium that suppresses water intrusion and prevents gas collapse, enabling reversible, non-destructive oscillations under ultrasound stimulation and providing design principles for stabilizing gas in liquid environments. By leveraging high-resolution ultra-high-speed digital image correlation (DIC), we unveil the previously inaccessible spatiotemporal dynamics of confined gas oscillations within these nanotransducers under ultrasound stimulation, revealing localized amplification of the surrounding acoustic field and establishing a quantitative structure-function relationship for programmable acoustic transduction. These aqueous-phase gas nanotransducers exhibit sustained acoustic amplification over millions of excitation cycles and remain functional after prolonged storage (>2 years) under physiological conditions. In vitro and in vivo, this platform enables long-term ultrasound imaging and sustained, non-invasive neuromodulation by converting confined gas oscillations into persistent and amplified mechanical actuation. Our findings establish a generalizable design framework for stabilizing gas in liquid environments to achieve persistent and programmable acoustic transduction, thereby enabling sustained ultrasound-biological interfacing and opening opportunities for gas-based therapeutics.

bioengineering↗

bioRxiv2026

IL-27 Reduces Cell-Surface LDLR in Human Macrophages and Restricts VSV-G-Pseudotyped HIV infection

The low-density lipoprotein receptor (LDLR) is a major cellular receptor for vesicular stomatitis virus glycoprotein (VSV-G), which is widely used to pseudotyped virus vectors. A replication incompetent VSV-G-pseudotyped HIV (VSV-G-HIVLuc) has been used in HIV infection studies. Although IL-27-polarized macrophages induce multiple antiviral genes and resist replication-competent HIV infection, their impact on VSV-GHIVLuc infection has not been studied. Here, we evaluated the role of IL-27 polarization on VSV-G-HIVLuc infection. Infection was monitored by luciferase activity. Cell-surface LDLR was analyzed by flow cytometry. LDLR transcripts and protein expression were quantified by qRT-PCR and Western blotting, respectively. Viral binding was assessed by measuring cell-associated p24 antigen, while post-entry events were evaluated by quantifying late reverse-transcription products. VSV-G-HIVLuc infection in IL-27-polarized M-CSF-induced macrophages (27M-Mac) and IL-27-polarized GM-CSFinduced macrophages (27GM-Mac) was reduced to 5.8{+/-}0.4% and 5.9{+/-}2.1%, respectively (both p<0.0001), compared to unpolarized macrophages. 27M-Mac and 27GM-Mac reduced cell-surface LDLR to 38.3{+/-}2.6% (p<0.01) and 31.4{+/-}3.2% (p<0.01). Western blotting showed that total LDLR protein decreased to 48{+/-}0.8% in 27M-Mac (p<0.01), whereas 27GM-Mac showed no significant change. However, LDLR transcripts increased approximately 1.6-1.9-fold following IL-27 treatment in both macrophage types (p<0.01). Viral binding to 27M-Mac decreased modestly, while binding to 27GM-Mac decreased significantly to 67.5 {+/-} 7.5% of that to GM-Mac (p<0.05, n=3). In contrast, late reverse-transcription products decreased to 23{+/-}2.1% (p<0.0001) and 44{+/-}1.5% (p<0.0001). These findings demonstrate that IL-27 downregulates cell-surface LDLR expression in macrophages despite increasing LDLR transcript abundance, suggesting that IL-27 restricts VSV-G-pseudotyped Lentiviral infection through both receptor-associated and additional post-entry mechanisms.

immunology↗

bioRxiv2026

Using XCiMS to Quantify the Benefits of Ion Mobility Spectrometry for Untargeted Metabolomics

Integrating ion mobility spectrometry (IMS) with liquid chromatography-mass spectrometry (LC-MS) has the potential to improve untargeted metabolomics workflows, but assessing the benefits of IMS has been challenging due to a paucity of software solutions to process raw LC-IMS-MS data in a manner that enables direct comparison with LC-MS data. We developed the XCiMS software to collapse 4D data into pseudo-3D data. Peak detection is then performed in the pseudo-3D space, followed by targeted extraction of 4D signals from 3D-guided regions of interest. Here, we applied XCiMS to estimate the potential of IMS for untargeted metabolomics when analyzing human plasma. First, we assessed the number of metabolites that are uniquely resolved by LC-IMS-MS but not LC-MS. Although as many as 50% of 3D peaks produce multiple 4D peaks when using high-resolution IMS, few represent newly resolved structural isomers. We found that the increase in features due to IMS was mostly caused by charge isomers and ion clusters. Second, we investigated the impact of IMS on metabolite identification. When using a 16-minute chromatographic separation, we found that IMS can decrease the frequency of chimeric MS/MS by about half. We conclude that while IMS adds considerable complexity to untargeted metabolomics data without resolving a large number of additional structural isomers relative to a standard LC-MS experiment, it does facilitate metabolite identification by decreasing chimeric spectra and providing CCS values for library searching.

bioinformatics↗

bioRxiv2026

Erythrocyte extravasation drives ferroptosis and inflammatory amplification in eccentric contraction-induced skeletal muscle injury via the heme-HO-1-iron axis

Eccentric contraction-induced skeletal muscle injury is a common sports-related condition characterized by pain, impaired muscle function, slow recovery, and frequent recurrence, yet treatment remains symptomatic and mechanism-based targets are lacking. Although microvascular disruption and erythrocyte extravasation characterize severe muscle strain, the metabolic fate of extravasated erythrocytes has received little attention. In hemorrhagic and hemolytic conditions, erythrocyte-derived heme can activate heme oxygenase-1 (HO-1)-mediated iron release and ferroptosis, potentially amplifying inflammation; however, whether this pathway contributes to eccentric muscle injury remains unknown. To address this gap, we established a parameter-controlled rat model in which the gastrocnemius underwent 0, 50, 100, or 150 eccentric stretch repetitions. Muscle torque, gait, weight-bearing, endurance, pain threshold, histopathology, microcirculatory perfusion, macrophage polarization, and heme, ferrous iron, glutathione (GSH), malondialdehyde (MDA), glutathione peroxidase 4 (GPX4), and pro-inflammatory cytokine levels were assessed. Increasing repetitions produced graded functional impairment, myofiber damage, erythrocyte extravasation, inflammatory infiltration, and microcirculatory disturbance. Heme accumulation was accompanied by HO-1 upregulation in perivascular CD68-positive (CD68) macrophages, muscle iron accumulation, GSH and GPX4 depletion, elevated MDA, and increased M1 macrophage and cytokine levels. These findings suggest a potential heme-HO-1-iron-ferroptosis-associated inflammatory mechanism in eccentric muscle injury, providing a rationale for mechanistic validation and targeted therapeutic development. Keywords: Eccentric contraction-induced muscle injury; Erythrocyte extravasation; Heme oxygenase-1; Ferroptosis; Macrophage polarization

immunology↗

bioRxiv2026

OmniRE-seq: A Dual-Method Framework for Decoding RNA Editing Dynamics in Disease and Therapy

RNA editing is a widespread post-transcriptional modification involved in transcriptome diversity and disease regulation. However, its quantification remains technically challenging. We present OmniRE-seq, a dual-framework combining RE-seq for bulk and scRE-seq for single-cell RNA-seq data, enabling multi-level quantification, differential analysis, and functional annotation of RNA editing. Using RE-seq, we profile editing alterations across diverse contexts -- including murine sepsis, MDS, drug-treated melanoma, and colorectal cancer -- demonstrating the utility of locus-, gene-, and burden-level metrics in capturing biologically meaningful differences. scRE-seq further resolves cell-type-specific editing patterns by aggregating cells of shared identity into pseudo-bulk units (Spots), enhancing editing signal while preserving cellular resolution in colorectal cancer. Integrated bulk and single-cell analysis identified convergent editing signals and therapeutic targets, exemplified in a mouse model of thymic atrophy treated with Ganoderma lucidum spores. Together, OmniRE-seq offers a standardized and scalable toolkit for dissecting RNA editing landscapes across resolution levels, advancing both mechanistic discovery and translational application in precision medicine.

bioinformatics↗

bioRxiv2026

RiboDFM: Robust RNA sequence design using backbone-conditioned discrete flow matching

Designing RNA sequences that fold into predefined 3D structures is central to RNA engineering, yet it remains challenging due to the scarcity of experimentally determined structures and the complex sequence-structure relationships. Here, we present RiboDFM, a backbone-conditioned discrete flow-matching framework for RNA sequence design. RiboDFM progressively resolves fully masked sequences by integrating a geometric backbone encoder, an auxiliary base-pairing prediction head, and language model representations into a discrete flow sampler. To expand our training data, we supplemented experimental structures with a large-scale collection of trRosettaRNA2-predicted models. Across diverse benchmarks, RiboDFM achieves high sequence recovery and generates sequences with greater tertiary-structure self-consistency than existing methods. RiboDFM also performs strongly on aptamer-focused design tasks. Finally, beyond sequence generation, the nucleotide probabilities derived from RiboDFM' s flow trajectory serve as an intrinsic measure of sequence-structure compatibility. This enables reliable confidence estimation for designed sequences, as well as reference-free, zero-shot assessment of predicted structure models. Together, these results establish RiboDFM as an effective framework for structure-based RNA sequence design.

bioinformatics↗

bioRxiv2026

The effects of DNA repair factor-Cas9 fusions on homing drive performance

CRISPR-based homing gene drives achieve super-Mendelian inheritance by converting wild-type alleles into drive alleles through homology-directed repair (HDR). However, competing end-joining repair can generate resistance alleles that limit drive spread. Although fusing Cas9 to DNA repair-associated proteins has improved HDR in conventional genome editing systems, its effectiveness in gene drives remains unclear. Here, we systematically evaluated in Drosophila melanogaster eight Cas9 fusion constructs previously reported to improve HDR in other systems. Although none of the fusion constructs significantly increased HDR-associated signals in S2 cells, several candidates retained relatively high activity comparable to standard Cas9. These candidates were then tested in vivo across multiple split drive systems, regulatory elements, target loci, and parental sexes. Cas9-POLD3 significantly increased female drive inheritance in contexts with low baseline efficiency or substantial nonfunctional resistance formation, likely by increasing effective cutting rate and potentially also by biasing repair outcomes toward drive conversion. Cas9-Geminin degron generally maintained germline drive performance while reducing embryo resistance. Together, these findings identify Cas9-POLD3 and Cas9-Geminin degron as complementary, context-specific tools for enhancing drive conversion and limiting embryo resistance, respectively. These results highlight the importance of matching fusion modules to the regulatory and genetic context of individual drive systems.

genetics↗

bioRxiv2026

SMAD3-driven cell state transitions underpin immunoresistance in bladder cancer

Despite the clinical success of anti-PD-1/PD-L1 immunotherapy in a subset of patients with high-risk bladder cancer (BLCA), most tumors remain refractory to treatment. We hypothesized that immunotherapy resistance is encoded within the intrinsic signaling state of BLCA cells and arises through specific cell-state transitions that precede therapeutic exposure. To test this hypothesis, we applied a cell State Transition Assessment and Regulation (cSTAR) framework to identify key signaling modules and aberrant causal network connections that (i) drive oncogenic progression and acquisition of aggressive phenotypes and (ii) govern BLCA cell susceptibility to T cell-mediated cytotoxicity. cSTAR analysis identified TGF{beta}/SMAD3 signaling as the principal driver of both oncogenic transformation and immunoresistance in BLCA cells. Inhibiting SMAD3 sensitized BLCA cells to PD-1-expressing Jurkat cells and primary human CD4+ T cell-mediated cytotoxicity through suppression of autophagy and activation of multiple cell death pathways. By integrating cell state transition analysis with functional immune co-culture assays, our work demonstrates that tumor cell state transitions control sensitivity to T cell killing, complementing established immune-intrinsic mechanisms of immunotherapy response.

systems biology↗

bioRxiv2026

Population genomics of Actinobacillus pleuropneumoniae reveals lineage-associated K:O antigen and Apx toxin diversity

Actinobacillus pleuropneumoniae (APP) is the causative agent of porcine pleuropneumonia, causing high mortality and morbidity and substantial economic losses in the swine industry. Nineteen capsular (K) serotypes, defined by variation in capsular polysaccharide (CPS) biosynthesis loci, ten O serotypes, defined by variation in lipopolysaccharide (LPS) biosynthesis loci, characteristic Apx toxin profiles, and genomic diversity have been increasingly described; however, relationships among genomic lineage, surface antigen genotype, and Apx toxin repertoire remain incompletely resolved. Here, we analyzed 328 APP genomes, including 153 newly sequenced isolates and 175 public genomes from 21 countries. Core-genome SNP phylogeny and FastBAPS identified 23 genomic lineages. Nineteen capsular K types and 10 O-antigen types formed 26 K:O genotypes, of which 24 were restricted to a single lineage. Adjusted Wallace analysis showed greater concordance of K:O genotype with lineage than K type alone (0.881 versus 0.759), and with ApxI, ApxII and ApxIII genotype (0.949 versus 0.787). ApxIVA related sequence was detected in all genomes, while 56 complete loci revealed recurrent length variation within the N-terminus or the RTX repeat rich region and an additional divergent ApxIVA related homolog. In conclusion, our comprehensive population genomic study gives a more informative picture of APP genomics and virulence-associated diversity, providing a useful genomic basis for future diagnostic test and vaccine development.

genomics↗

bioRxiv2026

CucurbitAgent: An AI agent for exploring cucurbit multi-omics resources

Functional genomics in crops increasingly depends on integrating information from an extensive literature and heterogeneous multi-omics datasets. Large language models (LLMs) offer a powerful approach to synthesizing these resources and revealing hidden connections across datasets; however, they frequently hallucinate, producing plausible but unsupported claims, when responding to gene-specific queries. Here, we present CucurbitAgent, an AI research agent for functional genomics in the Cucurbitaceae, a major family of horticultural crops. CucurbitAgent integrates multi-omics resources from nine cultivated cucurbit species and more than 18,000 publications, encompassing approximately 256,000 genes, tissue-resolved expression profiles, over 16 million natural genetic variants, and roughly 242,000 predicted protein structures with more than 14 million predicted binding-site residue annotations. Responses link retrieved evidence to source records, including gene entries, expression measurements, structural predictions, and literature passages. On a curated benchmark of 50 tasks assessed by domain experts under blinded conditions, CucurbitAgent achieved an overall pairwise win rate of 96.0% against nine general-purpose LLMs, based on weighted scores for factual accuracy, completeness, relevance, and traceability. The platform is freely available at https://cucurbitagent.com and supports queries in 37 languages collectively spoken by an estimated 70% or more of the world's population. CucurbitAgent not only unifies evidence retrieval and interpretation but also reveals latent associations across datasets, helping researchers formulate testable hypotheses and substantially accelerating candidate-gene research. Its framework is readily transferable to other crops and, more broadly, provides a blueprint for building specialized agents in any domain.

bioinformatics↗

bioRxiv2026

Early-life human lymphopoiesis generates a distinct B-cell lineage

We characterize the first wave of human B-lymphopoiesis across gestation (n=42 donors) and identify a developmentally and functionally distinct B-cell lineage that shapes antibody specificity before birth. The earliest lymphoid progenitors engage an evolutionarily conserved genetic program enriched for imprinted genes associated with embryogenesis in mice and humans. These progenitors arise in the yolk sac and acquire Early B-cell Factor 1 (EBF1) in the embryonic liver, initiating B-lymphopoiesis before Hematopoietic Stem Cells emerge. Functionally, these early-life B-lymphoid progenitors (eBLPs; CD81hiTdT-IL3R+) respond to IL-3 to promote B-cell fate commitment and generate two waves of stereotyped public B-cell receptor (BCR) repertoires, shaping adaptive immunity at birth. The same molecular program and public BCRs are recapitulated during B-cell differentiation from pluripotent stem cells in vitro and after transplantation into humanized mice, where they generate antibody-secreting cells and SOX4+ B cells resembling infant lymphocytes. Developmental origin therefore intrinsically programs B-cell identity and antibody specificity.

immunology↗

bioRxiv2026

A multimodal precision oncology platform integrating genomics,single-cell transcriptomics, and functional drug screening expandstherapeutic options in pediatric brain tumors

Precision oncology for pediatric brain tumors mainly relies on clinically validated, targetable genomic alterations, which are often sparse, yield few matched therapies, and do not guide chemotherapy selection. We developed a tiered framework in which deep whole-genome sequencing and single-cell RNA sequencing extend targeted-therapy selection, with ex vivo functional drug screening supporting selection of both targeted therapies and chemotherapies. We applied it to 17 children with malignant CNS tumors. The approach expanded recommendations beyond genomics: functional screening provided every patient with at least one high-confidence targeted-therapy or chemotherapy nomination, while single-cell RNA sequencing identified an average of 37 druggable gene targets per patient, producing a fourfold increase in high-confidence targeted-therapy recommendations. In an exploratory analysis, functional classifications were directionally consistent with outcomes in 8 of 10 evaluable cases, although combination treatments and radiation precluded causal attribution. Single-cell profiling also identified subclone-specific vulnerabilities, supporting prospective evaluation of the platform's feasibility and predictive utility.

cancer biology↗

bioRxiv2026

A 21-Color Spectral Flow Cytometry Panel for Comprehensive Immunophenotyping of Rat Tissues and a Companion 9-Color T-Cell Functional Assay

Although rats are crucial translational research models due to their immunological homology and surgical feasibility, the scarcity of conjugated antibodies has hampered high-dimensional immune profiling. To bridge this gap, we created a synergistic two-panel method that uses full-spectral flow cytometry: a 21-color comprehensive immunophenotyping panel and a 9-color intracellular cytokine staining (ICS) panel. The 21-color panel navigates the limited fluorophore pool and maps innate and adaptive lineages at high resolution. While it can be used to profile neutrophils and monocytes in peripheral blood it reaches its full potential in lymphoid organs, allowing for the simultaneous evaluation of tissue-resident macrophages, dendritic cells, T cell differentiation (including Tregs), and APC function. Based on this phenotypic paradigm, the 9-color ICS panel dissects effector T cell activation and Th1/Th2/Th17 cytokine production. Furthermore, we reserved the PE color during panel creation, allowing for the use of antibodies and probes with PE or comparable fluorophores in conjunction with this panel, hence increasing overall flexibility. This combination technique, designed for rat peripheral blood, spleen, and lymph nodes, combines panoramic phenotyping with functional analysis, offering an adaptable foundation for complicated tissue microenvironments in tumor immunology, rheumatology, and autoimmunity research.

immunology↗

bioRxiv2026

An Inducible Model of RPE-Associated Hydroxyapatite Mineralization with Relevance to Drusen Formation in Age-Related Macular Degeneration

A cardinal feature of nonexudative age-related macular degeneration (AMD) is the accumulation of drusen between the retinal pigment epithelium (RPE) and Bruch's membrane, yet the mechanisms that initiate and promote drusen formation remain to be fully understood. Hydroxyapatite (HAP), a calcium-phosphate mineral identified within human drusen, has been proposed to contribute to drusen nucleation and is associated with increased likelihood of RPE atrophy. However, mechanistic studies providing insight into RPE-associated mineralization have been limited by a lack of easy-to-use and manipulatable culture models. Here, we established a rapid, inducible ARPE-19-based model of HAP mineralization. We found that ARPE-19 cells cultured in minimum essential media (MEM) supplemented with nicotinamide (NIC), sodium phosphate, and ascorbic acid (NaPAA) reproducibly formed HAP positive deposits, whereas mineralization was not observed while using standard DMEM/F12 medium, DMEM/F12 with NaPAA, MEM-NIC medium, or MEM-NIC medium with alternative osteogenic supplements (such as beta-glycerophosphate, ascorbic acid, and dexamethasone). Scanning electron microscopy with energy dispersive X ray spectroscopy demonstrated that the formed deposits were enriched in calcium (Ca) and phosphorus (P) with Ca/P ratios comparable to drusen-associated HAP deposits from AMD donor tissue. ARPE-19-based HAP deposits were also closely associated with neutral lipid-rich material, staining positive for BODIPY around their core structure. Bulk RNA sequencing of mineralized ARPE-19 cells revealed extracellular matrix, angiogenic, inflammatory, and metabolic transcriptional changes in the absence of strong enrichment of canonical osteogenic pathways. Co-treatment of mineralizing cells with either pyrophosphate, EDTA, or sodium citrate significantly reduced mineral deposition, but these approaches were not able to reverse it. Together, these findings establish a tractable RPE mineralization model that recapitulates key features of AMD-associated HAP and provides a platform for investigating mechanisms of drusen-associated mineral formation.

cell biology↗

bioRxiv2026

Paired single-nucleus and spatial transcriptomics of the lung adenocarcinoma invasion sequence reveal niche domains and candidate reversal compounds

Lung adenocarcinoma (LUAD) develops through a defined morphological sequence from atypical adenomatous hyperplasia (AAH) to invasive adenocarcinoma, but the transcriptional programmes accompanying this transition have mostly been characterised in bulk tissue or in tumour tissue alone. We profiled paired samples spanning the full sequence by single-nucleus RNA sequencing (413,697 nuclei, 23 patients) and spatial transcriptomics (56 Visium sections, 25 patients), asking how the transcriptional state of the tissue changes as invasion proceeds and whether that state can be reversed in silico by known perturbations. The atlas resolves into 39 second-level subtypes and the tissue into seven recurring niche-domain archetypes (K* = 7), six of which are ordinary lung structures and only one of which is restricted to invasive disease. A confound then shaped the remaining analyses: domain identity, marker stability and the apparent stage-dependence of the spatial programmes all scale with sequencing depth, and depth is in these sections a proxy for tissue density rather than a purely technical artefact (rho=-0.89 between a domain's depth and the fraction of its markers surviving depth matching). Several apparently positive results disappeared once depth was matched. The invasive domain's ECM/interstitial identity survives that check: within patients the fibroblast ECM programme is higher in invasive disease in 20 of 22 paired cases (P=0.0033 against random gene sets), and the result is unchanged when the genes added by hand are removed and under every leave-one-out variant. Querying a patient-paired disease axis against the LINCS compound library with three scoring schemes returned 34 compounds in common, dominated by PI3K/mTOR inhibitors, with a split-half reproducibility of rho=0.962 against a permutation null of +/-0.045 and an agreement of rho=0.735 between a single-cell-derived and a spatially derived axis. A positive control, the recovery of known regulators of an official benchmark (TBXT ranked 1st of 8,450), establishes that the pipeline recovers true positives, so the negative results reported here are properties of the data rather than of the method. Those negatives are stated explicitly: single-cell copy-number inference produced no usable malignant/non-malignant separator, the cohort-level spatial copy-number difference did not survive depth matching, a developmental trajectory ran opposite to that of the source study, gene-level prediction returned no signal on the pooled axis and only one perturbation survives compartment-wise gating, and a ligand-level analysis produced no usable pair.

cancer biology↗

bioRxiv2026

CryoCodex: learning discrete structural representations for cryo-EM map post-processing

Cryo-EM maps frequently suffer from weak structural signals, spatially variable quality, and noise, complicating interpretation and downstream modeling. Existing post-processing approaches treat density enhancement, quality assessment, and masking as separate tasks, often amplifying residual noise or introducing local artifacts. Here, we present CryoCodex, a unified framework that jointly performs density enhancement, local quality estimation, and molecular masking. CryoCodex introduces a multi-head, multi-scale vector-quantization module that projects encoder-derived latent features onto a shared codebook of structural prototypes. By imposing discrete constraints across feature subspaces and spatial scales, the codebook suppresses stochastic noise while preserving recurrent structural patterns. On a non-redundant test set of 126 experimental maps spanning 3-8 [A], CryoCodex outperformed four representative methods, achieving a mean map-model FSC-0.5 of 3.93 [A] versus 4.62 [A] for EMReady2 and 6.87 [A] for the deposited maps. Downstream automated de novo model building with Phenix further confirmed the quality of the CryoCodex-enhanced maps. These gains extended to maps containing nucleic acids, where CryoCodex produced the best map-model agreement and improved model building. Half-map cross-validation indicated that these improvements are anchored to experimental data rather than driven by half-map-specific noise or structural hallucination. CryoCodex also delivered reliable local quality estimates and molecular masks within the same framework. Together, these results establish CryoCodex as a practical tool for cryo-EM map post-processing and structural determination in challenging cases.

bioinformatics↗

bioRxiv2026

Patronin condensation integrates recognition, protection and organization of microtubule minus ends

Microtubule minus ends are central to non-centrosomal microtubule organization, yet how their recognition, protection and molecular organization are integrated remains unclear. Here we show that Drosophila Patronin forms dynamic condensates at microtubule minus ends through a prion-like domain (PrLD). PrLD-mediated condensation cooperates with the CKK domain and a second CKK-independent recognition region to convert weak or broadly distributed microtubule-binding activities into persistent minus-end recognition and tracking. Replacing the PrLD with a heterologous phase-separating HNRNPA1 IDR restores minus-end targeting, indicating that condensation capacity rather than PrLD primary sequence is critical. Patronin condensates further form a protective cap that resists minus-end depolymerization and recruit the cytoskeletal regulators Sas-4, Katanin and Ena. Disrupting PrLD multivalency impairs Patronin localization at multiple developmental sites and causes early organismal lethality. Thus, Patronin condensation creates a physiologically essential microtubule minus-end compartment coupling end recognition, stabilization and cytoskeletal organization.

cell biology↗