Biology subjects

Chen, Y.

Publications and source records attributed to Chen, Y..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

G4All: a database of experimentally confirmed G-quadruplex-forming sequences

G-quadruplexes (G4s) are non-canonical nucleic acid structures with critical roles in gene regulation, genomic stability, and disease, making them prime targets for therapeutic and biotechnological applications. However, the absence of a curated, centralized, experimentally validated repository of short (mostly synthetic) G4-forming sequences, paired with appropriate single-stranded or hairpin controls, has limited reproducibility and hindered progress in the field. Here, we introduce G4All, a comprehensive, curated database of G4-forming short DNA and RNA sequences, complemented by rigorously selected non-G4 controls, all studied under roughly similar experimental conditions (around 100 mM potassium ion at near neutral pH). G4All consolidates sequences validated by diverse experimental methods, including circular dichroism, NMR, UV spectroscopy, with standardized annotations for topology, thermal stability, and experimental conditions. By providing both positive and negative datasets, G4All enables rigorous comparative analyses, assay benchmarking, and the development of predictive models. The database supports a broad range of applications, from fundamental studies of G4 biophysics to the rational design of aptamers, as well as benchmarking prediction algorithms. Future developments will expand G4All to include user-submitted datasets and more RNA sequences. Freely accessible, G4All offers a searchable interface and downloadable datasets, establishing a community-driven hub to accelerate discovery and standardization in G4 research. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/743020v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@111d015org.highwire.dtl.DTLVardef@74447corg.highwire.dtl.DTLVardef@13c5642org.highwire.dtl.DTLVardef@432469_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Endogenous APOBEC3B Promotes CHK1 Inhibitor Sensitivity

APOBEC3B (A3B) is a single-stranded DNA cytosine deaminase overexpressed in cancer, where it causes genomic DNA damage and mutations associated with tumor evolution. Enforced A3B overexpression triggers a dependency on the replication-stress response in different cellular models. However, whether endogenous A3B in cancer cells might yield a similar vulnerability is unclear. Here, we investigate how endogenous A3B expression and catalytic activity affect sensitivity to CHK1 inhibition, using two cancer cell lines, JHOC5 and U2OS. A3B-expressing cancer cells are sensitive to two chemically distinct CHK1 inhibitors, GDC-0575 and Prexasertib. CHK1 inhibitor sensitivity is reduced by A3B CRISPR knockout and restored by re-expressing wildtype A3B in knockout cells. Moreover, an endogenous A3B-E255A catalytic mutant generated by homology-directed repair phenocopies the reduced CHK1 inhibitor sensitivity of A3B-null cells, demonstrating a DNA deamination-dependent mechanism. CHK1 inhibition induces replication-associated DNA damage and cell-cycle perturbation dependent on A3B expression. As a result, A3B-expressing cells accumulate more pan-nuclear {gamma}H2AX, aberrant DNA-content profiles, and an expanded EdU-negative S-phase population, which are hallmarks of stalled DNA replication. In comparison, A3B-null and A3B-E255A cells retain defined cell-cycle distributions and are less sensitive to CHK1 inhibition. Together, these findings identify endogenous A3B-catalyzed deamination as a therapeutically actionable source of replication-associated DNA damage that renders tumor cells selectively dependent on CHK1 function. Statement of significanceAPOBEC3B causes mutations in cancer cells and simultaneously imposes DNA replication stress. This combines to sensitize tumor cells to chemical inhibitors of the DNA damage response kinase CHK1.

cancer biology↗

bioRxiv2026

Defining the genetic landscape of acid and oxidative stress tolerance in Streptococcus mutans by pooled CRISPR interference screening

Bacterial stress tolerance is a fundamental ecological adaptation that enables survival, competitive fitness, and persistent colonization under fluctuating environmental conditions. Dental caries remains a major global health burden. As an etiologic agent in caries, Streptococcus mutans (S. mutans) has the ability to adapt to sudden and substantial acid and oxidative stress. Nevertheless, the genome-wide genetic programs that support these stress tolerances remain incompletely defined. Herein, we established a xylose-inducible, genome-wide pooled CRISPR interference (CRISPRi) platform in S. mutans and performed parallel functional screens under acidic conditions (pH 5.0) and low-dose hydrogen peroxide (H{square}O{square}) stress. Using predefined screening thresholds, we identified 422 genes whose repression reduced fitness during acid challenge and 337 genes whose repression reduced fitness during H{square}O{square} exposure. Functional and network analyses revealed that stress tolerance is strongly constrained by core physiological processes, including RNA (particularly transfer RNA) metabolism, macromolecule maintenance, and damage repair. Comparative analyses further indicated that growth-associated pathways displayed opposite trends between the two stresses, consistent with a stress-dependent allocation trade-off. These two complementary findings redefine the dual-stress adaptation paradigm of S. mutans: stress resistance is not determined merely by canonical stress signaling, but requires intact core physiological modules, and bacteria tune resource allocation dynamically to adapt to divergent stress microenvironments. Collectively, the present study provides a comparative, genome-scale functional map of acid- and oxidative-stress tolerance in a key oral pathogen and identifies genetic determinants for mechanistic studies and anti-caries interventions.

microbiology↗

bioRxiv2026

A benchmarking framework for single-cell genome-scale metabolic model construction

Single-cell genome-scale metabolic models (scGEMs) enable characterization of metabolic heterogeneity underlying cellular states and phenotypes. However, methodological choices during scGEM construction can substantially alter model structure and predictions, challenging the reliability and comparability of resulting analyses. Here, we established a systematic benchmark to assess three key construction factors: data preprocessing method, model extraction method (MEM) and gene expression threshold. We evaluated 26 strategies representing different combinations of these factors across nine scRNA-seq datasets in three dimensions: accuracy, sensitivity to expression perturbation and computational feasibility. We found that MEM had the greatest influence on most accuracy metrics, data preprocessing strongly influenced the discrimination of cellular identities, and expression threshold balanced model completeness and cellular specificity. These findings indicate that strategy performance varies across evaluation criteria. Our benchmark provides practical guidance for strategy selection and an empirical basis for standardized evaluation and future scGEM method development.

systems biology↗

bioRxiv2026

Spatiotemporal coordination of specialized cerebellar networks supports episodic memory in older adults

Episodic memory decline in ageing is typically attributed to the cortico-hippocampal system, yet the cerebellums specific contribution via cerebellar-cerebral circuits remains underexplored. We analysed task-based fMRI data from 821 older adults, including a longitudinal subset of 78 participants followed for four years. Using sparse dictionary learning on task-responsive activity, we identified three non-motor networks: a bilateral lobule VI/Crus I mnemonic-monitoring network, a right lobule Crus I/II default-mode-aligned network, and a right lobule VIIb/VIIIa evidence-evaluation network. While network recruitment varied with task demands and associated with memory performance, phase-specific static cerebellar-cerebral functional connectivity showed stable organization but limited behavioural specificity. In contrast, dynamic functional connectivity patterns effectively distinguished memory-performance groups. Crucially, greater instability in dynamic functional connectivity during encoding predicted longitudinal retrieval slowing. These findings suggest that preserved episodic memory in older adults is supported by the spatiotemporal coordination of specialized cerebellar networks with distributed cerebral networks.

neuroscience↗

bioRxiv2026

Benchmarking Deep Learning Predictions of Mutation-Induced Fold Switching

Many proteins are known to adopt multiple distinct folded states which are often associated with key functional behavior. A predictive understanding of the properties of such fold-switching or metamorphic proteins can provide insights into protein dynamics and energetics, and enable the design of complex protein functions and molecular machines. Recently developed deep learning modeling tools, including AlphaFold, have led to dramatic increases in accuracy for prediction of protein structures from sequence, but their performance for prediction of point mutant effects or fold switching is unclear. Here we present a systematic NMR-characterized dataset of mutants of the GA/GB model fold-switching system and use it to evaluate whether current structure prediction and design methods can predict mutation-induced changes in fold state. We measured fold-state populations for variants at three key positions that differentially stabilize the 3, 4{beta}+, mixed, or unfolded states, generating a quantitative experimental benchmark for mutation-level fold switching. Using this benchmark to assess and compare a panel of deep learning and physics-based modeling and design algorithms, we found that this benchmark revealed variable and position-dependent performance across methods, with certain AlphaFold2-based algorithms were able to predict mutant effects at individual sites, indicating some understanding of physical effects of residue substitutions. Additional comparisons of predictions with experimentally measured stability changes further highlighted position-dependent success and general challenges for predictive algorithms. Together, this study provides a new benchmark for mutation-induced fold switching and reveals the current capabilities and limitations of deep learning models for predicting mutation-dependent protein conformational states.

biophysics↗

bioRxiv2026

Integrative spatial profiling of 3D genome organization and gene expression in tissue

The interplay between 3D genome architecture and transcriptional activity is fundamental to gene regulation. However, existing methodologies cannot simultaneously measure these modalities within intact tissues, limiting our understanding of how genome organization coordinates transcriptional programs across diverse cell types and spatial microenvironments. Here, we introduce Spatial Hi-C-RNA, a spatial multi-omics technology that enables the genome-wide co-mapping of chromatin conformation and transcriptome directly from the same tissue section at near- single-cell resolution. Applied to the mouse embryo and adult brains, Spatial Hi-C-RNA generated high-resolution tissue maps revealing that chromatin organization and gene expression jointly define spatially coherent domains aligned with histological structures. While concordant features were observed across modalities, distinct domain patterns also emerged, indicating that chromatin structure and transcription each contribute complementary layers of spatial regulation. We further demonstrated the robustness and biological insight of Spatial Hi-C-RNA in human melanoma, where both modalities delineated tumor boundaries and microenvironmental niches. Notably, chromatin maps revealed fine-scale tumor subdomains undetectable by transcriptomic profiling alone, highlighting the added resolution provided by spatial chromatin architecture. Integrated analysis revealed that multiscale 3D genome features, from A/B compartments and topologically associating domains to chromatin loops, are closely coupled with domain- and cell-type-specific transcriptional programs. In addition, Spatial Hi-C-RNA resolves spatiotemporal dynamics underlying embryonic lineage specification and tumor progression. Together, these capabilities extend the spatial omics landscape beyond transcriptome and epigenome profiling to the level of chromatin organization, establishing an integrative framework for understanding tissue biology across development and disease.

genomics↗

bioRxiv2026

Discovery of a regulatory node that coordinates cell envelope assembly in mycobacteria

Mycobacteria possess a complex double-membrane cell envelope critical for survival and pathogenesis. Proper assembly of this architecture requires the biosynthesis and transport of major components, including arabinogalactan (AG) polysaccharides and mycolic acids (MAs), but how these processes are effectively coordinated is unknown. Here, we discover an essential membrane complex that serves as a regulatory node in mycobacterial envelope biogenesis. The acyltransferase TmaT and the arabinofuranosyltransferase AftD physically interact; cryo-EM structures reveal a 1:1 stoichiometry, and present a novel fold for TmaT, featuring a central channel that binds co-factor for acetylation in the periplasm. We establish that the TmaT-AftD interaction, and the catalytic activities of both enzymes, are required for MA transport across the cell envelope, as well as AG ligation to the cell wall, the final stage of AG biosynthesis. The TmaT-AftD complex coordinates the two major envelope assembly pathways, presenting a structural vulnerability for future anti-mycobacterial drug development.

biochemistry↗

bioRxiv2026

Genomic Population Structure of Atlantic surfclams: Cryptic Taxonomic Units and Population Connectivity

The Atlantic surfclam, Spisula solidissima solidissima supports multimillion dollar harvests in the western North Atlantic, including Georges Bank and Mid-Atlantic Bight populations along the continental shelf. Surfclam populations in this part of the Exclusive Economic Zone (3-200 nm from shore) are managed as a single unit, but demographic connectivity has never been tested directly. This study analyzed >8,500 SNPs in 548 Atlantic surfclams sampled across the USA harvested range to infer population structure, genomic diversity, and gene flow patterns. Genomic analyses included eight sampled and 10 reference Spisula solidissima similis samples, a morphologically cryptic nominal subspecies previously known only from nearshore habitats. Novel morphologically cryptic population structure was identified in S.s. solidissima. One operational taxonomic unit (OTU-A) was found only in the inshore region of southern New England, south of Cape Cod. The other population unit, OTU-B, was found offshore and in Cape Cod Bay. The federal fishing grounds only had OTU-B clams. Populations within each OTU were connected by gene flow, justifying current fishery management practices. Nearshore state waters had mixed OTU stocks. Hybridization was analyzed between the two OTUs and between the two subspecies based on nuclear SNPs and asymmetrical mitochondrial DNA introgression. Finally, we demonstrated the utility of a novel SNP panel for diagnosing all three taxa and their hybrids.

evolutionary biology↗

bioRxiv2026

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

East Asian populations, representing over 20% of the global population, remain critically underrepresented in human genomic studies, limiting our understanding of population-stratified genetic variation and its implications for health and disease. Here we present the first phase of the Asian Pan-Genome project (APG), comprising 320 nearly complete, fully phased haploid genome assemblies from 160 East Asian individuals. These assemblies achieve unprecedented quality, with an average contig N50 of 144.3 megabase pairs and an average quality value of 64.5. Leveraging these superior assemblies, we reveal previously uncharacterized diversity in human repeatome, including population-stratified patterns in centromere satellites and rDNA arrays. Compared to existing global human genome assemblies, the newly generated genomes supplement 152 million base pairs of novel sequences, 355 gene gains, 18,300 structural variation loci and 26 large euchromatic inversions missing from current human pangenomes. We perform population stratification analyses of structural variations, and further resolve the structural haplotypes of complex genomic regions such as Major Histocompatibility Complex and Survival Motor Neuron loci across global pangenomes, exemplifying tandem-duplicate and inversion-rich complex locus architectures in the human genome, respectively. This resource provides a critical foundation for human genetic studies, especially for East Asian populations, promoting more accurate variant discovery, reducing bias, and ultimately advancing the equity and efficacy of genomic medicine.

genomics↗

bioRxiv2026

A missing PEPC1 exaptation restricts C₄ evolution in palms (Arecaceae)

O_LIC4 and CAM photosynthesis evolved repeatedly across angiosperms, yet the four palm species examined here -- representing three of five Arecaceae subfamilies ([~]2,600 species total) -- all lack both. We hypothesized that this reflects the absence of PEPC1, a phosphoenolpyruvate carboxylase isoform required for C4 carbon fixation initiation and present in commelinids (Poaceae + Bromeliaceae) but whose distribution across monocots is unknown. C_LIO_LIWe surveyed six core C4 enzyme families by HMMER profiling across nine plant genomes -- four palms (Cocos nucifera, Elaeis guineensis, Phoenix dactylifera, Nypa fruticans), two grasses, one bromeliad, one basal monocot, and one fern. We constructed maximum-likelihood PEPC phylogenies and performed codon-based branch-site likelihood ratio tests using PAML. C_LIO_LIAll six enzyme families were present in palms. PEPC1 was detected in all commelinids (rice, maize, pineapple) but absent from all four palm species and outgroups. No palm PEPC sequence fell within the PPC-1 clade. Molecular dating indicates the Arecaceae-commelinid divergence ([~]120 Mya) predates PEPC1 origin ([~]105 Mya). Branch-site tests on the maize C4-PEPC1 branch were marginally significant (2{Delta}l = 3.03, p {approx} 0.082). C_LIO_LIThe absence of PEPC1 represents an ancestral molecular barrier that likely precluded C4 evolution in palms. This identifies a lineage-specific gene duplication as a constraint on photosynthetic pathway evolution in a major tropical plant lineage. C_LI

plant biology↗

bioRxiv2026

LIFU-Responsive Nanocomplexes Deliver PDGF-BB mRNA for Plaques Stabilization via Neovascularization Modulation

BackgroundPathological intraplaque neovascularization, vascular leakage, and fibrous cap thinning contribute to vulnerable atherosclerotic plaque rupture. Platelet- derived growth factor-BB (PDGF-BB) has been shown to promote pericyte recruitment, thereby stabilizing the microvascular structure, and to induce phenotypic modulation of vascular smooth muscle cells (VSMCs), which enhances fibrous cap thickness and reinforces plaque stability. Nevertheless, systemic protein delivery is limited by rapid clearance and potential off-target effects. MethodsWe developed PDGF-BB mRNA-loaded lipid nanoparticle-poly(lactic-co- glycolic acid) nanobubble complexes (LNPmRNA@PLGA) and used low-intensity focused ultrasound (LIFU) to enhance plaque-targeted delivery. Cellular uptake, PDGF- BB expression, vascular mural-cell responses, plaque histology, hemodynamics, and proteomic changes were evaluated in vitro and in ApoE-/-Fbn1C1041G+/- mice. ResultsLIFU enhanced nanocomplex uptake and PDGF-BB expression, promoted vascular smooth muscle cell proliferation, migration, and phenotypic switching, and increased pericyte coverage. In vivo, LIFU plus LNPmRNA@PLGA reduced the plaque vulnerability index by 78.2% and the neovascularization area by 67.3% compared with controls, while increasing collagen deposition and improving carotid hemodynamics. ConclusionsLIFU-responsive delivery of PDGF-BB mRNA stabilized vulnerable plaques by promoting neovessel maturation and strengthening the fibrous cap. This strategy provides a spatially controlled framework for therapeutic remodeling of high-risk atherosclerotic plaques. Research Perspective What New Question Does This Study Raise?O_LICan spatially controlled PDGF-BB mRNA delivery simultaneously mature intraplaque neovessels and reinforce the fibrous cap without the systemic effects associated with recombinant PDGF-BB? C_LI What Question Should Be Addressed Next?O_LIFuture studies should define the therapeutic window, durability, and long-term safety of LIFU-triggered PDGF-BB mRNA delivery in large-animal models that more closely reproduce human plaque rupture. C_LI

pharmacology and toxicology↗

bioRxiv2026

Adipocyte Expression of O-Glycoprotein Procollagen C-Endopeptidase Enhancer Protein 2 (PCPE2): Mechanisms Linking Fibrosis and Beiging of White Adipose Tissue

BackgroundProcollagen C-endopeptidase enhancer protein 2 (Pcpe2) has been primarily investigated in collagen processing during wound healing and is assumed to function similarly to Pcpe1 in the extracellular matrix (ECM). Our studies suggest that Pcpe2 has unique structural and functional features not shared with Pcpe1. MethodsTo study the role of Pcpe2 in adipose tissue remodeling, we created adipose tissue-specific knockout of Pcpe2 (TgAd+Pcpe2KO) and adipose tissue-specific Pcpe2 overexpressing (TgAd+Pcpe2Ox) mice and performed in vivo and ex vivo experiments. ResultsWe show that TgAd+Pcpe2KO mice are resistant to WD-induced obesity and exhibit reductions in body and fat pad mass. Promethion cage studies showed no significant differences in lean mass or food intake, yet WD-fed TgAd+Pcpe2KO mice exhibited significantly higher energy expenditure than negative Cre littermate controls. WD-fed TgAd+Pcpe2KO mice also showed reduced plasma glucose and lipoprotein lipid concentrations compared to controls. While markers of adipose tissue inflammation were reduced in WD-fed TgAd+Pcpe2KO mice. Examination of mature adipocytes from white adipose tissue showed that WD consumption greatly stimulated Pcpe2 expression, while no change in Pcpe2 expression in the stromal vascular cells was noted. However, in VAT precursor cells (PCs), the CD140b+ population showed a shift from fibroadipogenic precursors towards adipocyte PCs in TgAd+Pcpe2KO mice. This shift in PCs may account for the attenuation of local inflammation and fibrosis in the absence of Pcpe2. Ex vivo differentiation of adipose PCs showed that loss of Pcpe2 enhanced adipocyte differentiation, reducing TGF{beta}-like signaling via pSmad2/3, and increasing mitochondrial function. Furthermore, unlike Pcpe1, Pcpe2 contains a mucin-like linker domain with nine sites of O-linked glycosylation which may regulate receptor signaling at the plasma membrane. ConclusionsOur results show the ECM O-glycoprotein Pcpe2 is a robust marker of unhealthy adipose tissue expansion in humans and mice and contributes to inflammation and fibrosis associated with WD-induced obesity.

cell biology↗

bioRxiv2026

Microbial Metabolites Potentiate MAIT Cell Anti-Tumor Immunity Against Solid Tumors

Mucosal-associated invariant T (MAIT) cells sense riboflavin metabolites through the monomorphic antigen-presenting molecule MR1, providing a unique opportunity to therapeutically mobilize a broadly shared T cell population without genetic engineering. Here, we show that the highly potent microbial metabolites, 5-OP-RU and 5-OE-RU, can be exploited as pharmacologic precision immune activators to drive human MAIT cell responses against solid tumors. Ligand stimulation in human co-culture systems elicited robust MAIT cell cytotoxicity, inflammatory cytokine secretion, and transcriptional states transformation. In vivo administration of riboflavin ligands 5-OP-RU significantly suppressed tumor growth in xenograft liver cancer models. Metabolite-driven MAIT activation also reprogrammed the local immune landscape, enhancing effector function and overcoming features of the immunosuppressive niche by markedly eliminating tumor-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs) within the tumor microenvironment (TME). These findings reveal that microbial riboflavin metabolites can power and redirect MAIT cells to solid tumors, establishing MR1-metabolite signaling as a tractable therapeutic axis for liver cancer and other solid malignancies.

cancer biology↗

bioRxiv2026

Symmetry-breaking flow bifurcation as an under-recognised haemodynamic factor in valve-associated thrombosis

Venous thrombosis commonly develops near venous valve pockets, where disturbed hemodynamics and reduced washout create spatially heterogeneous flow environments. Conventional descriptions of this region emphasize continuously varying quantities such as velocity, shear stress, recirculation, and residence time, but do not address whether post-valve flow can transition between distinct organized states. Here, we combine computational and experimental vein-on-a-chip approaches to resolve Reynolds-number-dependent post-valve flow organization and its downstream transport consequences. In a geometrically symmetric rigid valve, increasing Reynolds number triggered a symmetrybreaking transition from a centered jet to a persistent asymmetric flow state, with repeatable separation between the increasing- and decreasing-Reynolds-number branches under transient forcing. Valve compliance delayed this transition by increasing the effective opening and reducing local inertial forcing, whereas a small bilateral geometric bias promoted earlier branch selection. Fluid-structure interaction further showed that, after symmetry breaking, unequal hydrodynamic loading generated unequal leaflet deformation, providing a mechanism for structural reinforcement of the selected flow state. The Reynolds-number-dependent ordering was reproduced experimentally and remained detectable in whole blood. Downstream transport of RBC-scale particles exhibited a delayed but persistent lateral redistribution relative to the velocity-field response. These results identify post-valve symmetry breaking as a flow-state transition regulated by local inertial forcing, valve mechanics, and geometric bias. Venous-valve hemodynamics can therefore transition between distinct flow states, providing a physical basis for how small mechanical or geometric differences can generate persistent transport heterogeneity relevant to thrombosis.

biophysics↗

bioRxiv2026

Photo-thermal Bidirectional Coupling Model for Transcranial Photobiomodulation

BackgroundAccurate optical-field simulation is critical for precise dosage delivery in transcranial photobiomodulation (tPBM). Current simulations neglect photon absorption-induced tissue heating which leads to temperature-dependent alterations of the optical field, thus fails to account for the bidirectional photo-thermal coupling effect. ObjectiveThis paper aims to establish a dynamic photo-thermal couple model that rigorously quantifies the bidirectional interaction between tissue heating and light propagation, and improves the optical dose prediction. ModelWe propose a Photo-Thermal bidirectional coupling Model (PTM). First, the Pennes Bioheat Equation (PBE) is employed to model the thermal response induced by photon absorption. Second, a Real-time temperature-dependent Absorption coefficient Model (RAM) is newly developed to quantify the thermal effect. Third, the PBE and RAM are integrated into the photon diffusion equation, forming the PTM. Finally, this coupled framework is solved temporally by an unconditionally stable Crank-Nicolson scheme. SimulationsBenchmarking against an analytical solution (two-layer cylindrical domain) demonstrates that PTM reduces the temperature prediction error by over 2.35% compared to the uncoupled baseline. Simulations using a realistic head model reveal that, compared to PTM, uncoupled modeling underestimates energy deposition by 150 J/m3 and overestimates photon fluence by 3 J/m2 within just one minute, and such discrepancies will be amplified with increasing exposure duration and power. Furthermore, the PTM identifies a 1.43-mm advantage in penetration depth for pulsed-wave over continuous-wave modality under iso-energy conditions, a key insight enabled by the coupled modeling approach. ConclusionThe PTM provides a high-fidelity simulation framework that captures the dynamic, bidirectional photo-thermal coupling in tPBM, explicitly quantifying the thermal feedback ignored by current models and thereby enabling more reliable treatment optimization and safer clinical translation.

neuroscience↗

bioRxiv2026

Decoding the oxytocinergic and behavioral signatures of milk ejection

Oxytocin-mediated milk ejection (ME) is pivotal to effective breastfeeding and productive health, yet behaviorally decoding and revealing neural mechanisms of ME remains challenging. Here, we combined in vivo calcium imaging and intramammary pressure recording to uncover the temporal connections between episodic activity of oxytocin neurons and ME in conscious lactating rats. Leveraging the association and behavioral responses in dam and pup, we developed a supervised machine learning framework (ME Decoder) to enable automated analyses of ME. Inspired by its interpretable features, we defined the activity-coupled dam-pup interactions (ADPI), manifested by high kyphosis of the dam followed by pup treading and stretch, as the behavioral signatures of ME. By ME Decoder and ADPI analyses, we detected reduced ME but unaffected activity of oxytocinergic neurons after systemic blockade of oxytocin receptor. Our study uncovers the oxytocinergic and behavioral signatures of ME and provides a generalizable approach for further investigation.

neuroscience↗

bioRxiv2026

Two-locus CRISPR toxin-antidote gene drive for confined population modification

Gene drive systems enable rapid spread of desired transgenes throughout populations. Advances in CRISPR technology have facilitated the construction of toxin-antidote gene drives, which utilize a CRISPR nuclease as the toxin to disrupt an essential wild-type gene alongside a recoded version of the same gene as the antidote. Because these systems propagate by eliminating wild-type alleles rather than directly copying themselves like homing drives, they typically exhibit introduction thresholds, allowing them to be confined to target populations. Previous work developed the efficient Toxin-Antidote Recessive Embryo (TARE) drive, but its threshold may be too low in challenging confinement scenarios. Here, we constructed a 2-locus TARE drive system. It has underdominance characteristics, yielding a higher introduction threshold, even when drive performance is ideal. It targets the essential but haplosufficient genes hairy and sim using two different drives at different genomic locations, each targeting the gene that the other rescues. Our system involved two linked elements together with rare homology-directed repair-mediated drive conversion, reducing the threshold to compensate for fitness costs. The system showed high efficiency in individual crosses. When released into multigenerational cage populations above the introduction threshold, the drive successfully and rapidly modified the entire population, and when below this threshold, it was eliminated. Our findings indicate that 2-locus TARE drives represent promising tools for effective and strongly confined population modification.

genetics↗