Biology subjects

He, J.

Publications and source records attributed to He, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

A tunnel microtract organ for T cell progenitor homing is formed by neural crest morphogenesis via Sox10-Cdc42 axis

Thymic colonization by T cell progenitors (TCPs) is essential for adaptive immunity, yet the guiding tissues remain elusive. Here, we unveiled a tunnel microtract (TMT) as an organ indispensable in TCPs homing in both zebrafish and mouse. Disruption of TMT leads to compromised T cell development. Specifically, the zebrafish TMT were positioned bilaterally beneath the fifth branchial levator muscle, connecting the thymus and kidney. They are semi-coiled, non-vascular, non-lymphatic tubes of epithelial signatures. Impressively, Sox10 activates Cdc42 to promote F-actin remodeling in neural crest cells (NCCs), leading to precise elongation and tight packaging of a low-permeability TMT. Remarkably, a homologous CD34 TMT was observed in mice, which bilaterally enveloped the embryonic thymus and extended into the thyroid cartilage. Sox10-Cdc42 signalling functioned recapitulatively in NCC morphogenesis during its construction. These findings establish TMT as an unappreciated NCC-derived organ in TCPs homing, with implications in T cell development and immune disorders.

developmental biology↗

bioRxiv2026

MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

Spatial transcriptomics has emerged as a transformative approach for elucidating tissue architecture, cellular heterogeneity, and disease mechanisms by preserving the spatial context of gene expression in cells. Despite these advances, many spatial transcriptomic methods underperform in archival or clinically relevant specimens, particularly formalin-fixed, paraffin-embedded (FFPE) tissues, where RNA degradation and crosslinking hinder transcript detection. To address these challenges, we developed Multiplexed Error Robust Fluorescence In Situ Hybridization 2.0 (MERFISH 2.0), an optimized spatial transcriptomic imaging chemistry to enhance profiling of fragmented and highly crosslinked RNA. Across diverse human and mouse tissues preserved as fresh-frozen, fixed-frozen, and FFPE specimens, MERFISH 2.0 substantially increased transcript detection sensitivity by up to [~]8-fold relative to MERFISH 1.0 while preserving quantitative concordance (Pearson r [≥] 0.8 across tissues). In archived fresh-frozen human brain samples, MERFISH 2.0s enhanced sensitivity improved transcript recovery, enhanced cell type resolution and spatial analyses. In low quality archival FFPE human breast cancer specimen, MERFISH 2.0 revealed additional cell populations, novel cell clusters, refined tumor-immune architecture, and increased detection of gene-gene and cell-cell interactions relative to MERFISH 1.0, underscoring the impact of improved sensitivity on downstream spatial analysis. By substantially expanding robust transcript detection to degraded and archival samples, MERFISH 2.0 enables scalable, cohort-level spatial transcriptomic analysis across clinically relevant tissue collections.

genomics↗

bioRxiv2026

PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery

The convergence of large language model-powered autonomous agent systems and single-cell biology promises a paradigm shift in biomedical discovery. However, existing biological agent systems, building upon single-agent architectures, are narrowly specialized or overly general, limiting applications to routine analyses. We introduce PantheonOS (https://PantheonOS.stanford.edu), an evolvable, privacy-preserving multi-agent framework designed to reconcile generality with domain specificity. Critically, PantheonOS enables agentic code evolution, allowing evolving state-of-the-art batch correction and our reinforcement-learning augmented gene panel selection algorithms to achieve super-human performance. PantheonOS drives biological discoveries across systems: uncovering asymmetric paracrine Cer1-Nodal inhibition in proximal-distal axis formation of novel early mouse embryo 3D data; integrating human fetal heart multi-omics with whole-heart data to reveal molecular programs underpin heart diseases; and adaptively selecting virtual cell models to predict cardiac regulatory and perturbation effects. Together, PantheonOS points towards a future where scientific discoveries are increasingly driven by self-evolving AI systems across biology and beyond. Websitehttps://pantheonos.stanford.edu Ecosystemhttps://github.com/aristoteleo SummaryLarge language model-powered agent systems are driving a paradigm shift in scientific discovery by automating, scaling, and accelerating data analysis. This transformation is particularly profound in biology, where the rapid expansion of single-cell and spatial genomics has effectively reshaped the field into a data-intensive science. However, existing biological agent systems are typically constrained to single-agent designs, are narrowly specialized, or are overly general without sufficient domain expertise, limiting their applicability to routine or shallow analyses. Here, we introduce PantheonOS (https://pantheonos.stanford.edu), an evolvable, privacy-preserving, and general-purpose multi-agent framework designed to reconcile generality with deep domain specificity. PantheonOS provides an abstract, extensible architecture that enables customized agent composition and supports end-to-end single-cell and multi-omics analysis, spanning reinforcement-learning-augmented gene panel design, raw FASTQ processing, multimodal data integration, and three-dimensional spatial genomics reconstruction. Central to this framework, Pantheon-Evolve enables agentic code evolution, allowing the system to autonomously improve state-of-the-art batch-correction algorithms and new reinforcement-learning based gene panel design algorithms, achieving performance beyond manually designed baselines. We demonstrate the power of PantheonOS across multiple biological domains. In early mouse embryogenesis, PantheonOS automatically reconstructs three-dimensional spatial gene expression landscapes and resolves asymmetric Cer1 expression and paracrine Cer1-Nodal inhibition, revealing a robust proximal-distal axis at embryonic day six (E6.0). In human development, PantheonOS integrates fetal heart single-cell multi-omics with whole-heart 3D MERFISH+ data at post-conception week 12, uncovering spatially resolved molecular programs underlying heart disease ontogeny. Finally, an intelligent model-routing mechanism enables PantheonOS to adaptively select optimal virtual cell models across heterogeneous tasks, revealing minimal regulatory networks of cardiogenesis and predicting spatially resolved perturbation effects in the developing heart. Together, PantheonOS establishes a foundation for fully automated, evolvable, and domain-aware agentic analysis in genomics, and points toward a future in which scientific discovery is increasingly driven by self-improving AI systems across biology and beyond.

bioinformatics↗

bioRxiv2026

Variant-to-gene mapping identifies ARHGEF12 as a primary open-angle glaucoma effector gene

Primary open-angle glaucoma (POAG), a leading cause of irreversible blindness worldwide, has a strong genetic basis. The Primary Open-Angle African Ancestry Glaucoma Genetics study previously identified 46 risk loci associated with this disease. To pinpoint causal variants and their corresponding effector genes, we analyzed gene expression, chromatin accessibility, and conformation in two ocular cell types: trabecular meshwork cells (hTMCs) and retinal ganglion cells derived from induced pluripotent stem cells (hiPSC-RGCs). We identified 24 candidate genes in hTMCs and 56 in hiPSC-RGCs. Several prioritized genes showed altered mRNA expression, implicating pathways involved in oxidative stress, tissue homeostasis, neuronal maintenance, and retinal degeneration. Among these genes, ARHGEF12 was selected for further validation because local and distal promoter interactions nominated it in both cell types, and prior evidence reproducibly links it to POAG. While its role in hTMCs is established, its function in RGCs is unclear. hiPSC-RGCs generated from a POAG donor homozygous for the risk allele exhibited reduced ARHGEF12 expression, altered morphology, and disrupted neuronal activity. By linking POAG risk loci to candidate effector genes in ocular cell types, this study provides a framework for functional evaluation of additional POAG risk variants.

genomics↗

bioRxiv2026

Distinct Biological and Biomechanical Features in TMJ and Knee Cartilages

The temporomandibular joint (TMJ) and the knee joint are two of the most frequently used joints in the body, with the mandibular condylar cartilage (MCC) and the articular cartilage (AC) covering the joint bone surfaces, respectively. Compromised MCC functions lead to various temporomandibular disorders (TMD), including TMJ osteoarthritis (TMJ OA); however, the mechanisms governing MCC homeostasis and its biomechanical properties are still poorly understood. In this study, we comprehensively compared the biological and biomechanical features of the MCC and AC in mice. Histological analysis on P1, P21, 3-month, and 10-month mice revealed the most drastic structural differences between MCC and AC at occlusion establishment (P21), with MCC found to be more susceptible to age-associated cartilage degeneration. Immunostaining revealed differentially distributed cartilage extracellular matrix components in MCC and AC, including collagen type I, II, and X, and highly enriched expression of several key transcriptional factors at the posterior region of the MCC, including sex determining region Y-box 9 (SOX9), runt-related transcription factor 2 (RUNX2), and scleraxis (SCX). The posterior MCC also houses a group of long-lasting, slow-proliferative cells, as evidenced by the BrdU/EdU incorporation assay, suggesting the presence of a potential stem/progenitor cell niche at the posterior TMJ. Unbiased nanoindentation analysis revealed distinct biomechanical features between these joint cartilages. MCC exhibits a significantly lower elastic modulus (EIT) than AC, with the highest EIT observed at the anterior TMJ, which is oppositely associated with the fibrous layer thickness, but positively correlated with the ratio of the collagen type X-positive matrix in the cartilaginous layer. Altogether, this study provides a basic understanding of the biological and biomechanical features of the cartilaginous tissues in two important joints, which may facilitate our understanding of the physiology in the TMJ and knee joint, and support the applications of mouse models to study TMJ dysfunctions.

developmental biology↗

bioRxiv2026

MG53 Protects Against Intestinal Inflammation by Inhibiting NLRP3 Inflammasome Activation

Background and ObjectivesInflammatory bowel disease (IBD) involves dysregulated immune responses and chronic intestinal inflammation. The nod-like receptor pyrin domain-containing 3 (NLRP3) inflammasome plays a critical role in IBD pathogenesis, but regulatory mechanisms remain not fully understood. Mitsugumin 53 (MG53, also known as TRIM72), originally identified as a critical membrane repair protein, has emerged as a novel regulator of inflammatory processes. To investigate the protective role of MG53 in colitis and elucidate its mechanisms in regulating NLRP3 inflammasome activation in IBD. MethodsWe used dextran sodium sulfate (DSS)-induced colitis models comparing MG53 knockout (MG53-/-) and wild-type (WT) mice, assessing disease severity, MG53 tissue uptake, and therapeutic effects of recombinant human MG53 (rhMG53). In vitro studies examined rhMG53s effects on NLRP3 inflammasome activation, caspase-1 cleavage, interleukin-1{beta} (IL-1{beta}) secretion, and MG53-NLRP3 interactions. ResultsMG53-/- mice showed more severe colitis with increased weight loss, higher disease activity scores, shortened colons, and greater inflammation. DSS treatment induced the accumulation of circulating MG53 in inflamed colonic tissue. rhMG53 administration ameliorated colitis severity in MG53-/- mice and dose-dependently suppressed NLRP3 inflammasome activation in vitro. MG53 interacted with NLRP3 and reduced apoptosis-associated speck-like protein containing a CARD (ASC) speck formation and NLRP3 oligomerization without affecting upstream signaling or NLRP3 stability. ConclusionMG53 is a physiological regulator of NLRP3 inflammasome activation that protects against colitis, suggesting therapeutic potential for IBD.

immunology↗

bioRxiv2026

Inhibition of KDM5A/B promotes antitumor innate immune responses in HHV-8/KSHV2 positive B-cell lymphomas

Summary/AbstractHistone methylation is a dynamic and reversible epigenetic modification that critically controls the progression of human diseases, including infections and cancers. Here we reported that histone lysine demethylases (KDMs) in the KDM5 family KDM5A/B play profound roles in suppressing lytic reactivation of oncogenic human herpesvirus 8 (HHV-8), i.e., Kaposis sarcoma-associated herpesvirus (KSHV), as well as antiviral/antitumor innate immune responses in KSHV-infected B-cell lymphomas. We showed that KSHV lytic replication decreases KDM5A/B protein stability by enhancing their K-48 linked polyubiquitination while KDM5A/B depletion facilitates KSHV lytic reactivation. Mechanistic studies illustrated that KDM5A/B associate with KSHV LANA protein and dampen its chromatin association at both KSHV viral lytic promoter and promoters of antitumor immune-responsive genes (IRGs). In comparisons to normal B cells, KDM5A/B expression significantly increased in B-cell lymphoma cells, including KSHV-positive primary effusion lymphoma (PEL). We demonstrated that KDM5A/B inhibition remarkably induces both KSHV lytic reactivation and innate immune responses in PEL cells, resulting in a strong viral oncolytic effect, both in vitro in cell cultures and in vivo using a PEL xenograft mouse model. Overall, our studies identified the novel functions of KDM5A/B to silence KSHV lytic replication and antiviral/antitumor innate immune responses, which can be blocked to benefit the treatment of KSHV-associated B-cell lymphomas that are usually aggressive and difficult to treat.

microbiology↗

bioRxiv2026

Pan-genome and multi-omics analyses reveal the genomic basis of symbiotic evolution in the mycoheterotrophic medicinal orchid Gastrodia elata

Mycoheterotrophy represents an extreme evolutionary strategy in which plants abandon photosynthesis and become obligately dependent on fungal partners for carbon and nutrients. Gastrodia elata, a medicinal orchid forming long-term symbioses with Armillaria and Mycena, provides a compelling system to investigate the genomic basis of obligate plant-fungus mutualism. Here, we generate a chromosome-level genome assembly (1.09 Gb) of a dark-red G. elata accession and construct a pan-genome from 12 Gastrodia accessions to dissect the evolutionary consequences of mycoheterotrophy. Phylogenomic analyses reveal pervasive hybridization across cultivated germplasm and demonstrate that tuber morphology more accurately reflects intraspecific relationships than stem color, challenging the traditional color-based taxonomy. Comparative genomic analyses reveal a pronounced degeneration of photosynthetic capacity. We detect no intact nuclear-encoded rbcS loci, which would preclude assembly of the Rubisco holoenzyme and thus canonical Calvin-Benson carbon fixation. Notably, a subset of photosynthesis-related genes is retained and transcriptionally active, suggesting their co-option into non-photosynthetic regulatory roles. Despite millions of years of intimate association with fungal partners, we detect no evidence of fungal-derived horizontal gene transfer based on a multi-step phylogenomic validation pipeline, indicating that G. elata-fungus mutualism is sustained through metabolic exchange rather than genetic integration. We further identify the Gastrodia antifungal protein (GAFP) gene family as a key molecular innovation underlying symbiotic homeostasis. The recently derived Class 1 GAFP lineage exhibits distinct domain architecture, tandem expansion, and elevated expression, consistent with enhanced regulation of fungal overgrowth. Finally, we delineate a specialized nutrient-acquisition framework adapted to obligate heterotrophy, in which fungal trehalose hydrolysis supplies hexose carbon via an expanded sugar transporter protein (STP) repertoire, while organic nitrogen is assimilated through amino acid and oligopeptide transporters coupled with urease-mediated conversion, compensating for the loss of nitrate uptake and reduction pathways. Together, these results establish a pan-genomic blueprint for symbiotic adaptation and reductive genome evolution in G. elata.

genomics↗

bioRxiv2026

Evolutionary genomics of local adaptation, climate vulnerability, and linarin metabolism in Opisthopappus longilobus

Global climate change and human activities are posing substantial threats to biodiversity. The genus Opisthopappus (O. taihangensis and O. longilobus), endemic to Chinas Taihang Mountains, possesses great ecological, ornamental and medicinal value. However, it is confronted with the pressures of habitat fragmentation and climate change. Here, we present the first haplotype-resolved, chromosome-scale genome assembly of O. longilobus ([~]2.95 Gb) and re-sequence 115 individuals across its range. Comparative analyses show Opisthopappus is sister to Artemisia-Chrysanthemum, with Opisthopappus and Chrysanthemum diverging at 5.15-5.18 million years ago. A profound genetic divergence is evident between O. taihangensis and O. longilobus, resulting in two distinct lineages within each species, driven by geography and climate. Our analyses indicate restricted gene flow, low diversity, and recurrent demographic bottlenecks collectively contribute to their endangerment. By integrating population genomics and environmental variables, we identified 4,437 core adaptive genes linked to water deprivation, and metabolism. Genomic offset predicts higher maladaptation risk in populations under drastic climate change. Furthermore, diverged promoters of two O-methyltransferase genes, OMT250 and OMT310, likely underlie the differential acacetin/linarin accumulation between C. morifolium and O. longilobus. These findings advance understanding of Opisthopappus evolution and climate vulnerability, offering a model for genomics-guided biodiversity conservation.

plant biology↗

bioRxiv2026

Gn1a rice promotes symbiotic fish growth via reprogramming soil microbiome

Rice-fish symbiotic ecosystems significantly contribute to world food supply. Mutation in rice (Oryza sativa) quantitative trait locus Gn1a, encoding a cytokinin oxidase/dehydrogenase (OsCKX2), leads to cytokinin accumulation in plant, which promotes tillering and panicle branching to achieved higher yield and also shows a selective effect on soil microbial composition. Given that the growth of aquatic animals can be shaped by their surrounding microbial communities, we asked whether adjusting rice cytokinin levels might synergistically boosts both rice yield and fish growth. Herein, we co-cultured common carp (Cyprinus carpio) with ckx2 rice plants to determine the effect of cytokinins on fish. Surprisingly, compared to wild-type plants, the ckx2 plants enhanced nearly 10% fish growth and improved fish antibacterial capacity against Aeromonas hydrophila and Edwardsiella tarda. In fact, the growth-promoting effect on fish requires mediation by the soil microbiota. Mechanistically, ckx2 plants secreted more cytokinins into soil to reprogram the microbial composition, which subsequently translocated to fish gut and modulated the keystone microbes in gut to facilitate short-chain fatty acid production and carbohydrate degradation. These findings provide the first evidence that rice-derived cytokinins exert a cross-kingdom growth-promoting effect on fish, providing a boosting dual-production strategy for advancing rice-fish symbiotic ecosystem.

plant biology↗

bioRxiv2026

Chromatin context-dependent deacetylation by the asymmetric Rpd3L

The regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone deacetylase (HDAC) complex that dynamically adapt to chromatin states to reinforce transcriptional silencing, yet the mechanisms governing the catalytic activation in chromatin context-dependent manner remain unclear. Here we present the cryo-EM structure of Rpd3L bound to both mono- and di-nucleosome substrate at near-atomic resolution, uncovering a substrate-guided allosteric activation mechanism. Rpd3L adopts an asymmetric architecture, in which the proximal catalytic module anchors the first nucleosome, while the Sin3 PAH domains engage linker DNA to reposition a second nucleosome. This spatial configuration brings the distal catalytic module into proximity with chromatin and unlocks its latent deacetylase activity. Biochemical and mass spectrometry analyses confirm that dual nucleosome engagement selectively enhances Rpd3L activity and broadens substrate specificity. Together, these findings establish a hierarchical mechanism by which Rpd3L interprets histone modifications and nucleosome organization to modulate its enzymatic output at promoter regions. Our study provides a framework for understanding higher-order chromatin repression mechanisms by chromatin-regulation complexes and co-repressors.

molecular biology↗

bioRxiv2026

GraphESMStable: A Deep Learning Framework for Protein Stability Prediction Fusing Pre-trained Sequence Models and Graph Neural Networks

Predicting protein stability is fundamental, yet existing computational methods often face limitations in generalization, reliance on single data modalities, and challenges with complex multi-point mutations. To address these, we propose GraphESMStable, a novel deep learning framework for predicting protein mutation-induced thermal stability changes. GraphESMStable integrates rich evolutionary context from a frozen pre-trained protein sequence language model with fine-grained three-dimensional structural geometry captured by a trainable Graph Neural Network. A sophisticated residue-level cross-attention mechanism facilitates the deep fusion of these distinct modal representations. The framework features a dedicated prediction head capable of predicting an entire single-point mutation landscape in a single forward pass, and an Epistasis Decoder explicitly modeling non-additive effects for multi-point mutations. Trained exclusively on a large-scale dataset, GraphESMStable achieves state-of-the-art performance, outperforming baselines across a diverse suite of independent evaluation benchmarks. This includes superior generalization on multiple stability datasets, cross-metric generalization to thermal melting prediction, and a significant lead in predicting double mutation epistatic effects. Furthermore, it demonstrates robust performance in predicting human pathogenic mutation stability and achieves substantial improvements in low-sample fitness prediction tasks. Our ablation studies confirm the synergistic benefits of this cross-modal fusion. GraphESMStable represents a significant advancement towards building highly generalizable and efficient foundational models for protein stability prediction, offering broad applicability in protein design and biomedical research.

bioengineering↗

bioRxiv2026

APIPred Web 1.0: A Web Platform to Predict Potential Aptamer Sequences for Protein targets

Aptamers are short single-stranded nucleic acids that bind protein targets with high specificity and are increasingly used in diagnostics and therapeutics, yet experimental discovery remains slow and variable in success. This creates a demand for computational systems that not only score candidate binders but also generate experimentally usable libraries under biologically meaningful constraints. Here, we present APIPred Web 1.0, a unified web platform that integrates constraint-aware aptamer library generation, machine learning- based aptamer- protein interaction prediction, and DNA secondary-structure analysis within a user-facing workflow. Users submit a target protein aminoacid sequence and define an aptamer template in a PREFIX - [VARIABLE] - SUFFIX format with real-time validation of key biological constraints (GC content and homopolymer limits). On the backend, sequences are converted into model- compatible features via optimized k-mer encodings (aptamer) and pseudo amino acid composition (PAAC) descriptors (protein), followed by inference with a trained XGBoost predictor. APIPred Web 1.0 improves the computational efficiency by applying precomputed protein features, vectorized batch processing (hundreds of sequences per batch), optimized XGBoost DMatrix inference, and a bounded heap that retains only the top 25 candidates during generation. The platform then computes minimum free energy (MFE) structures using ViennaRNA with parallel folding and returns ranked list of the top candidates with log-transformed interaction scores, complete sequences (variable region highlighted), dot-bracket structures, MFE values, and interactive 2D visualizations via persistent result links. In a demonstration study targeting CD64 protein, the platform produced 25 putative binders from a custom 40- nucleotide library and enabled selection of structurally diverse candidates for experimental testing. Flow cytometry showed specific binding to CD64-expressing THP-1 cells with minimal signal in Ramos control cells. Collectively, APIPred Web 1.0 offers a reproducible, structure-informed, and computationally efficient pipeline for rapid generation of aptamer candidates against target proteins for downstream experimental validation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=50 SRC="FIGDIR/small/697194v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1c1ca4dorg.highwire.dtl.DTLVardef@1c8b23dorg.highwire.dtl.DTLVardef@12dfe2dorg.highwire.dtl.DTLVardef@8a7c8f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Histone Demethylase KDM6B Promotes Postnatal Oligodendrocyte Development and Cortical Myelination

Myelination in the postnatal cortex requires epigenetic programs that activate oligodendrocyte gene networks. Here we show that the histone H3K27me3 demethylase KDM6B promotes this process in vivo. Conditional Kdm6b deletion (Kdm6b-cKO) in Emx1 dorsal telencephalic progenitors caused delayed cortical myelination. Lineage-specific RNA-seq revealed that the oligodendrocyte master regulator Sox10 was significantly reduced, as well as myelination effectors, indicating impaired oligodendrocyte maturation. Chromatin immunoprecipitation assays of the same lineage showed increased H3K27me3 at promoter-proximal regions of Sox10, consistent with loss of KDM6B-mediated de-repression. Temporally controlled Sox10 induction partially rescued myelination in Kdm6b-cKO mice. These findings define a KDM6B[->]SOX10 axis that licenses oligodendrocyte development and cortical myelination by removing repressive H3K27me3 and sustaining active chromatin, with implications for KDM6B-related neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

Optical Limits in Skin Reflectance Measurement: Quantifying Melanin-Dependent Constraints on Erythema Detection

As skin color measurement shifts from subjective classification to quantitative assessment, the assumption that objective measures are unbiased requires scrutiny. We provide a physics-informed framework for interpreting visible-range skin measurements, clarifying terminology, describing light-chromophore interactions, and surveying tools and output metrics. The physics of light-tissue interaction constrains what any visible-range observation can reveal: melanin and hemoglobin absorb across overlapping wavelengths, and as melanin increases, hemoglobins signature is masked. By analyzing over 15,000 spectra from the International Skin Spectra Archive, we demonstrate that this attenuation is systematic and most severe in the darkest skin, where data are scarcest. These limits arise from the physical properties of skins biological constituents and consequently apply to any sensor operating in the visible range. We conclude with guidance on analytical methods, sampling strategies, and extended wavelengths to improve measurement validity across the full range of human skin pigmentation. Graphical AbstractObjective skin measurements are not inherently unbiased: melanins broadband absorption progressively masks hemoglobins spectral signature, reducing the sensitivity of visible-range erythema detection in darker skin. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/696093v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@23ef00org.highwire.dtl.DTLVardef@11ff875org.highwire.dtl.DTLVardef@1f0eed4org.highwire.dtl.DTLVardef@cfca53_HPS_FORMAT_FIGEXP M_FIG C_FIG Summary PointsO_LIVisible-range skin reflectance measurements capture real optical information but do not directly measure chromophore concentrations; interpreting these signals requires understanding light-tissue interactions. C_LIO_LIMelanin and hemoglobin absorb at overlapping wavelengths, creating optical entanglement that limits the separability of pigmentation and erythema signals from reflectance data. C_LIO_LIHemoglobin spectral signatures are systematically attenuated as melanin increases, reducing the sensitivity of erythema detection in darker skin. This represents objective bias arising from physics, not subjective bias in assessment. C_LIO_LIDerivative analysis of full reflectance spectra can reveal hemoglobin-related structure that persists in darker skin even when standard indices show no signal. C_LIO_LIMelanin index distributions should be reported to assess sample representativeness, as demographic diversity does not guarantee adequate coverage of the pigmentation range relevant to optical measurement. C_LI LimitationsO_LISpectral overlap between melanin and hemoglobin is a physical property of these chromophores; no visible-range instrument or algorithm can fully overcome this constraint. C_LIO_LIThese optical limits apply to any visible-range sensor, including spectrophotometers, clinical photography, and AI systems trained on photographic data. C_LIO_LIExisting datasets remain sparse at the high end of the melanin index distribution, limiting validation of measurement approaches in the darkest skin. C_LI

bioengineering↗

bioRxiv2025

AI Identifies Broadly Neutralizing Antibodies from an IGHV1-69 Public Antibody Class Exerting Continued Selection Over SARS-CoV-2

R1-32-like public antibodies, characterized by shared IGHV1-69/IGLV1-40 usage, are elicited in more than 50% of individuals with COVID-19 and have been implicated in driving recurrent mutations at L452SARS2 and F490SARS2 within their convergent epitope in the SARS-CoV-2 spike receptor-binding domain. These mutations effectively mediate escape from non-affinity-matured R1-32-like antibodies with germline-like sequences. Here, we characterize four affinity-matured R1-32-like antibodies, C092, C807, BD56-104, and BD56-597, that tolerate L452SARS2 and F490SARS2 mutations. We show that this tolerance arises from residues introduced by somatic hypermutation at convergent positions across multiple CDR loops and surrounding regions, thereby creating additional contacts that reinforce epitope binding. An unusual N354SARS2 glycosylation site, which emerged in BA.2.86 and became fixed in its descendants, is linked to escape from affinity-matured R1-32-like antibodies, implying ongoing selection by this public antibody class. Using an AI model trained on integrated structural, neutralization, and binding data, we further identified ZL525, an ultrapotent R1-32-like antibody with pan-SARS-CoV-2 variant activity, including against the highly evasive KP.3 variant carrying the N354SARS2 glycosylation, and broad sarbecovirus cross-reactivity extending to SARS-CoV-1. Together, these findings show how affinity maturation enables public antibodies to adapt to viral antigenic drift, reveal their role in shaping SARS-CoV-2 antigenic evolution, and demonstrate the potential of AI-empowered strategies for discovering broadly neutralizing antibodies.

immunology↗

bioRxiv2025

Treatment of Huntington's disease with a pan-HTT-targeting CRISPR nuclease

Huntingtons disease (HD) is an inherited neurodegenerative disorder caused by an expansion of a CAG trinucleotide repeat in the huntingtin (HTT) gene, which leads to a mutant protein that destroys neurons in the brain. Despite intense effort, there remains no approved disease-modifying therapy for HD. Here we develop a pan-HTT-targeting CRISPR-Cas9 system that, when delivered to the striatum of R6/2 and YAC128 mice by AAV5, lowered mutant HTT mRNA and protein by 55-80% via its induction of frameshift-inducing indel mutations in HTT exon 1. Cas9 targeting improved motor coordination and locomotor activity, decreased anxiety-like deficits, reduced clasping and weight loss, limited striatal atrophy, and decreased the formation of intranuclear inclusions immunoreactive for the mutant HTT protein. In Hu21/21 mice, which carry the wild-type human HTT gene in lieu of the mouse ortholog, Cas9 lowered the HTT protein by 44% but induced no measurable behavioral deficits and had no adverse effect on neuronal viability, though its targeting was associated with neuroinflammation. Altogether, our results demonstrate the ability for a newly developed pan-HTT-targeting Cas9 system to affect HD-related phenotypes across models and provides insights into its tolerability.

bioengineering↗

bioRxiv2025

A coherent feed-forward loop fine-tunes KatG to maintain redox homeostasis in mycobacteria

Bacteria survive and reproduce in fluctuating environments by balancing their basic physiological needs, such as relying on iron-containing enzymes to detoxify reactive oxygen species (ROS) while conserving scarce iron. Understanding the regulatory networks that balance these conflicting needs is key to deciphering bacterial adaptability. Here, we identify a coherent feed-forward loop in mycobacteria that integrates the transcriptional regulator FurA3, the small RNA MrsI, RNA sponge FutR, and the catalase-peroxidase KatG. This circuit fine-tunes antioxidant responses according to iron availability. Under iron limitation, the iron-containing enzyme KatG is dually repressed by FurA3 transcriptionally and by MrsI post-transcriptionally, which conserves iron at the cost of antioxidant capacity. However, when iron deprivation coincides with oxidative stress, the circuit triggers an emergency response: H2O2 inactivates FurA3, relieving transcriptional repression of katG and futR, while induced FutR sequesters MrsI to post-transcriptionally derepress katG expression, enabling rapid KatG synthesis for effective peroxide detoxification. Our findings reveal a tightly regulated network that allows mycobacteria to balance iron homeostasis and oxidative stress defense, providing mechanistic insights into bacterial physiological trade-offs.

microbiology↗