Biology subjects

Yin, H.

Publications and source records attributed to Yin, H..

At least 19 recordsLinked to original sources

bioRxiv2026

In situ loading of biologics on and tissue redirection of circulating extracellular vesicles with an anchoring nanobody

Extracellular vesicles (EVs) are promising nanocarriers of therapeutic macromolecules, but ex vivo production, cargo loading and quality control constrains clinical translation. Here we demonstrate that NEV3, an EV-anchoring nanobody identified by phage display, binds EVs from multiple sources through interactions involving fibronectin and loads diverse proteins onto EVs, resulting in enhanced intracellular delivery and biological activities in vitro and in vivo. Conjugating NEV3 to target proteins hijacks circulating EVs, prolonging circulation and altering tissue distribution in vivo. When fused with an GFP nanobody or protein A, NEV3 enabled simultaneous capture and loading of circulating GFP or immunoglobulin G (IgG) antibodies on endogenous EVs with enhanced intracellular delivery in vitro and redistribution to liver in vivo. Intravenous protein A-NEV3 significantly reduced circulating IgG and anti-dsDNA antibodies in systemic lupus erythematosus mice with improved survival and reduced pathologies. Intravenous anti-transferrin receptor-protein A-NEV3 redirected circulating EVs to muscle and alleviated muscle pathologies in dystrophin-deficient mdx mice. Our study demonstrates that NEV3 enables in situ loading of protein therapeutics and tissue-specific delivery of circulating EVs, providing a modular strategy for loading cargo onto and redirecting circulating EVs in vivo.

bioengineering↗

bioRxiv2026

Development of CYP8B1-specific inhibitors for metabolic diseases

Changes in bile acids (BAs) balance lead to various metabolic diseases, yet current treatment options targeting these changes remain severely limited. CYP8B1 (cytochrome P450, family 8, subfamily B, polypeptide 1) is a liver-exclusive enzyme that controls the synthesis of 12-hydroxylated (12-OH) BAs. Inhibiting CYP8B1 is an attractive therapeutic strategy for attenuating 12-OH BA levels, remodeling the gut microbiota and thereby ameliorating metabolic diseases. CYP8B1-specific inhibitors are currently lacking due to structural similarities between the active site of CYP8B1 and other CYPs, and the lack of suitable high-throughput screening (HTS) assays. Herein, we developed a highly sensitive, and specific enzyme-coupled fluorescence assay to detect CYP8B1 activity, making it ideal for HTS. Employing this assay, structure-based drug design by protein X-ray crystallography, structure-activity relationship (SAR) analyses, and in vitro and in vivo validation, we developed novel CYP8B1-specific small molecule inhibitors. The lead candidate alters BA composition, favorably remodels the gut microbiota, and corrects metabolic disease in a metabolic dysfunction-associated steatotic liver disease (MASLD) mouse model. These findings reveal that pharmacologically inhibiting CYP8B1 is able to reshape the BA and gut microbiota profiles and effectively ameliorates metabolic diseases. Overall, CYP8B1-specific inhibitors represent a first-in-class promising, safe and effective therapeutic strategy against metabolic disorders.

pharmacology and toxicology↗

bioRxiv2026

Defense-associated reverse transcriptases synthesize DNA in a telomerase-like manner

Defense-associated reverse transcriptases (DRTs) constitute an emerging class of bacterial defense systems that harness reverse-transcriptase activity to generate cDNA products and counter phage infection. A distinct subset of DRT10 systems evolutionarily related to telomerase generates tandem-repeat DNA to confer antiphage immunity. Here, we biochemically characterize the reverse transcription activity of DRT10 and determine cryo-EM structures of DRT10-ncRNA complex in three functional states, revealing an unanticipated 2:1 RT:ncRNA assembly mode. Two DRT10 protomers dimerize through a central pair of interlocked {beta}-hairpins and are further embraced by a single ncRNA. This architecture distinguishes DRT10 from previously characterized DRT complexes, which either lack an ncRNA component or exhibit an equivalent stoichiometry of RT:ncRNA. Strikingly, despite the nearly identical conformations of the two DRT10 protomers, cDNA product density was resolved in only one catalytic pocket, revealing different product occupancy within the dimer. Moreover, along with flanking linkers, the stem loops of the ncRNA as fixed points to supply steric barriers help define the template boundary. These findings reveal a distinctive ncRNA-mediated DRT10 dimeric assembly and establish a mechanistic framework for protein-primed reverse transcription constrained by the length of the RNA flanking linker.

biochemistry↗

bioRxiv2026

Multiple introductions shaped genomic diversity and demographic history of invasive box tree moth (Cydalima perspectalis) populations in North America

The box tree moth (Cydalima perspectalis) is an invasive pest of boxwood plants (Buxus spp.) that has rapidly expanded across Europe and, since its first detection in Canada in 2018, across North America. Understanding its introduction pathways and early population structure is critical for effective surveillance and management. We integrated genome-wide single nucleotide polymorphism (SNP), mitochondrial cytochrome c oxidase I (COI), and morphological data to investigate the early invasion history of C. perspectalis across North America. Genome-wide analyses revealed pronounced genetic differentiation between North American and European populations, together with substantial genetic structure within North America. Delaware was genetically distinct from other North American populations and showed greater affinity with European populations, consistent with a separate introduction history. In contrast, New York, Massachusetts, Michigan, Ohio, and Ontario showed greater genetic similarity, suggesting shared ancestry and/or regional connectivity, whereas Virginia and West Virginia exhibited additional differentiation. Mitochondrial data supported shared ancestry among most North American populations, while Delaware shared a haplotype group with the Croatian European population. D-statistic analyses identified asymmetric allele sharing among several North American and European populations, consistent with multiple introductions and subsequent admixture. Morphometric analyses revealed significant geographic variation in several body and wing traits. Together, these complementary datasets indicate that multiple introductions, regional genetic structuring, and admixture have shaped the North American invasion. These findings highlight the value of integrating genomic approaches with nursery and border surveillance to identify introduction pathways and inform targeted containment and long-term management of this emerging horticultural pest.

genomics↗

bioRxiv2026

scOLAR: Ontology-Anchored Open-Set Annotation of Single-Cell RNA-seq Data

Single-cell RNA sequencing profiles cellular heterogeneity at atlas scale, making automated annotation essential. However, target datasets often contain novel cell types missing from incomplete references. We present scOLAR, an ontology-guided open-set framework that learns prototypes over the Cell Ontology and uses both reference and target expression to annotate known classes while detecting unfamiliar populations. Guided by ontology hierarchies and decision-boundary regularization, scOLAR penalizes coarse-lineage misclassification and groups novel cells without requiring predefined cluster counts. Across benchmarks, scOLAR achieves a novelty-detection AUROC of 0.9726 and an average precision of 0.9871, enabling structured post-hoc lineage-level interpretation of populations absent from the reference.

bioinformatics↗

bioRxiv2026

Tracking claim changes from preprint to publication across 72,644 biomedical studies using large language models

Preprints now disseminate a large share of biomedical research before peer review. Because they have not yet passed peer review, some scientists regard preprint claims as unverified or potentially unreliable, yet how much those claims change before publication has so far been quantified only in smaller cohorts, with results that vary by field and topic. Here, we compiled every bioRxiv preprint posted between 2018 and 2025 that we could match by DOI to a peer-reviewed published version, yielding 72,644 preprint-publication pairs. Using a large language model (Claude Sonnet 4.6), we parsed every preprint-publication abstract pair into one primary and two secondary claims, and classified each pair for content change (unchanged, minor, major) and hedging shift (more cautious, more confident, unchanged). On a validation subsample, the model agreed with two independent domain experts about as well as the experts agreed with each other (Cohens kappa 0.63 to 0.66). The primary claim was unchanged in 39.9% of abstracts, minorly revised in 50.0%, and substantially revised in only 10.2%. Hedging shifts were uncommon and asymmetric, with twice as many claims becoming more cautious as more confident (8.4% vs 4.2%). Major revisions were more frequent after long peer review (14.1% in the slowest versus 7.0% in the fastest tertile of review time) and declined over the study period (17.0% in 2019 to 5.7% in 2024). Over the same period, biomedical papers that were never posted as preprints were retracted at roughly twice the rate of those that were. Together, these data show that the move from preprint to peer-reviewed publication leaves the central claims of most biomedical abstracts intact, indicating that preprints are a reliable source of biomedical research.

scientific communication and education↗

bioRxiv2026

Development of Deep-Learning Models that Predict Quantitative Protein-Ligand Interac-tions in Glycobiology as a part of a Capstone Course

Glycans coat the surface of all cells, and every glycan is recognised by specific glycan-binding proteins (GBPs). There are no general tools that can accurately estimate the binding strength between glycan and GBP from the amino acid sequence of the GBP and the molecular structure of the glycan, represented as SMILES string. We describe models for predicting such binding strengths developed as a part of a Capstone Course at the University of Alberta. The models are trained on a dataset that combines BindingDB, a published database of small-molecule protein interactions, and data from glycan arrays measured by Consortium of Functional Glycomics (CFG). In this hybrid dataset of protein-ligand interactions the ligands are both glycans from CFG and small molecules from BindingDB; similarly, proteins include GBP and proteins from BindingDB. Three models are presented (i) ProMax which fuses ESM-2, MolFormer, and MolCLR features; (ii) APEX which constrains learning to a predetermined form, a physical model of binding; (iii) UltraMax adds inter-atomic distances for the ligands. To address the datasets severe long-tail distribution, the models employ tail-aware losses for rare high-binding instances. Trained and evaluated on approximately one million protein-ligand pairs using hold-out splits for unseen molecules, the three models provide a unified framework for quantitative glycan-protein binding prediction. We observed that learning glycan-protein binding is harder than the similar task of learning small-molecule-protein interactions. Simple mirror-inversion tests led us to postulate that insufficient use of chiral features is an important source of difficulty in learning these interactions.

bioinformatics↗

bioRxiv2026

NF1 deficiency induces metabolic reprogramming and epithelial-mesenchymal transition in glioblastoma

BackgroundMetabolic reprogramming is a common occurrence in tumor cells, where enhanced glycolysis promotes cell growth, invasion and migration. NF1 is tumor suppressor gene that downregulates the encoded neurofibromin protein. However, the effects of NF1 on energy metabolism and epithelial-mesenchymal transition (EMT) in glioblastoma multiforme (GBM), as well as the underlying molecular mechanisms, remain unclear. MethodsCRISPR/Cas9 gene editing technology was employed to construct GBM cell lines with NF1 gene mutations. Metabolomics was utilized to examine the impact of NF1 on metabolic remodeling in GBM. The Seahorse XF24 extracellular flux analyzer was used to detect the effect of NF1 knockdown on glycolysis and mitochondrial oxidative phosphorylation in GBM cells. Wound healing assay and Transwell chamber assay were utilized to detect the effect of NF1 on GBM cell invasion. Orthotopic tumor model in nude mice was established to explore the role of NF1 in vivo. In addition, Co-IP, western blotting, and immunofluorescence were used to explore the changes of key enzymes in glycolysis and mitochondrial oxidative phosphorylation and the relationship between NF1 and MFN1. ResultsThe expression of NF1 is decreased in glioma tissues and is significantly correlated with patient prognosis. NF1 knockdown may promote the invasion, migration, and EMT of GBM cells. At the same time, the activation of the AKT/mTOR signaling pathway promotes aerobic glycolysis in GBM cells, promotes mitochondrial division through targeted regulation of MFN1, and inhibits mitochondrial oxidative phosphorylation. NF1 deficiency promotes EMT in GBM cells by enhancing aerobic glycolysis and mitochondrial division. ConclusionNF1 deficiency promotes GBM glycolysis by activating the AKT/mTOR signaling pathway and inhibits the mitochondrial oxidative phosphorylation by regulating MFN1; NF1 deletion promotes GBM EMT by remodeling the pattern of energy metabolism.

Cancer Biology↗

bioRxiv2026

Near-Infrared-II Chemo-Optogenetics for Deep-Brain Stimulation

Precise activation of ion channels enables fine-tuned control of neuronal excitability, providing a powerful strategy for dissecting and modulating neural circuits. Although optogenetics offers high spatiotemporal neuronal manipulation with cell-type specificity, its reliance on visible light (400-650 nm) limits tissue penetration to millimeter depths, restricting applications in deep-brain stimulation. Here we report a near-infrared-II (NIR-II)-sensitive calcium channel, HaloNeu, created by genetically fusing a circularly permuted HaloTag (cpHaloTag) to the thermo-sensitive transient receptor potential vanilloid 1 (TRPV1) and covalently conjugating NIR-II photothermal nanotransducers (HPN). The HaloNeu enables non-invasive neuromodulation at depths up to 1.0 cm at ultralow laser power ([~]60 mW/cm2) and up to 5.0 cm under the safe exposure limit ([~]1 W/cm2) with 1064 nm laser illumination. Remarkably, HaloNeu maintains stable, on-demand neuron-specific modulation for over two months in vivo, providing sustained activation of ventral tegmental area (VTA) circuits and effective alleviation of Parkinsonian symptoms in mouse models. These results establish HaloNeu as a robust and versatile platform for cell-type-specific, deep-tissue, and chronic neuromodulation, with broad implications for neuroscience and neurotherapeutics.

neuroscience↗

bioRxiv2026

Generation of functional vasculature from engraftable human pluripotent stem cell-derived progenitors

The ability to revascularize target tissues and organs through cell-based therapy would provide a novel approach for the treatment of a range of ischemic disorders including cardiovascular diseases, stroke and peripheral artery disease. Towards this goal, we have identified a human pluripotent stem cell (hPSC)-derived vascular progenitor (VP) population generated via an epicardial intermediate with functional engraftment properties. VP cells efficiently engraft the mammary fat pad and hind limb skeletal muscle of NSG recipient mice and form vessel-like structures that integrate with the host vasculature. In an ischemic hind limb mouse model, VPs generate extensive vascular grafts that improve perfusion, restore some function and preserve muscle integrity over a three-month period post-transplant. Single-cell transcriptomic and flow cytometric analyses show that the VP population, initially identified by the co-expression of CD140b, CD13 and KDR, displays an epicardial lineage signature and expresses a spectrum of genes and proteins indicative of vascular progenitor stage cells. Together, these findings demonstrate that it is possible to revascularize both normal and ischemic tissue through the transplantation of an appropriate hPSC-derived progenitor and in doing so, lay the foundation for developing cell-based therapy approaches to treat ischemic diseases. Graphical Abstract LegendHuman pluripotent stem cells are differentiated through an epicardial intermediate to generate vascular progenitor (VP) cells characterized by expression of CD140b, CD13 and KDR. These VP cells demonstrate the capacity to engraft both mammary fat pad and skeletal muscle tissue where they form stable perfused vascular networks. In a hindlimb ischemia model, VP cell transplantation restores blood flow and improves functional outcomes. eTOC BlurbFernandes et al. develop a protocol to generate engraftable vascular progenitors from human pluripotent stem cells through an epicardial intermediate. These cells form functional vessels in vivo, restore perfusion in ischemic tissue, and demonstrate tissue-specific adaptation while maintaining endothelial identity, providing a foundation for therapeutic revascularization. HighlightsO_LIA staged differentiation protocol generates vascular progenitors (VPs) from hPSCs via an epicardial intermediate. C_LIO_LIVP cells form stable, perfused vascular networks following transplantation into multiple tissue sites. C_LIO_LIVP cell therapy with or without VEGF nanoparticles restores perfusion and improves functional outcomes in hindlimb ischemia. C_LIO_LISingle-cell analysis reveals tissue-specific adaptation while maintaining endothelial identity. C_LI

cell biology↗

bioRxiv2026

Correlation, Regression, and Growth Curve Analyses of Body Weight and Body Measurements in Female Jiangyue Donkeys

ObjectiveThis study aimed to systematically analyze the correlation between body weight and body measurement traits and the growth pattern of female Jiangyue donkeys. MethodsA total of 484 female Jiangyue donkeys were selected to determine their body weight (Y) and 11 body measurement traits, including withers height (X1), body length (X2), chest circumference (X3), cannon circumference (X4), head length (X5), neck length (X6), chest width (X7), chest depth (X8), rump height (X9), rump length (X10) and rump width (X11). SPSS 27.0 statistical software was used to conduct descriptive statistics, correlation and regression analysis on body weight and body measurement traits, and the optimal regression equation between them was established by the stepwise method and validated. Furthermore, four growth curve models (Logistic, Gompertz, Brody and Von Bertalanffy) were used to fit the body weight of 241 female Jiangyue donkeys at different months of age. ResultsThe body weight of female Jiangyue donkeys was significantly positively correlated with all body measurement traits (p<0.01), with the highest correlation coefficient observed for chest circumference. The optimal regression equations for body weight established by stepwise regression yielded R{superscript 2} values of 0.918 and 0.844 for growing and adult donkeys, respectively (p<0.01). Among the four growth curve models, the Von Bertalanffy model exhibited the best fitting effect (R{superscript 2}=0.99992), with an estimated asymptotic body weight of 184.41 kg, which was close to the measured values of growing female donkeys. ConclusionThe regression models for body weight estimation and the Von Bertalanffy growth curve model for growth pattern evaluation established in this study can serve as effective tools and production management of female Jiangyue donkeys.

genetics↗

bioRxiv2026

Multi-omic profiling of human antibody-secreting cells reveals diverse subsets sustain durable humoral immunity

Antibody-secreting cells (ASCs) provide humoral immunity that can mediate lifelong protection against pathogens. Current classifications cannot delineate the heterogenous functionalities, tissue residencies, and lifespans of human ASC subsets, impeding clinical translation. We applied multi-omic sequencing, spatial proteomics, and functional assays to discover and characterize human bone marrow (BM) ASC subsets. We identified two peripheral subsets (ASCp) also present in blood and three BM-resident subsets (ASCr), comprising a maturation continuum associated with increased mitochondrial networking, diminished antibody secretion, differential transcription factor motif accessibility, and preferential co-localization in homotypic niches. CD19+9+ASCr and CD19-ASCr exhibited poor recovery years after BM transplantation, indicating a strong dependence on supportive niches. Childhood vaccine antigens were recognized by long-lived ASCr subsets in adults and by immature HLA-DR+ASCp, implying ASCs can differentiate without recent antigen exposure. Our results provide new insights into ASC identity, maturation, and longevity and a generalizable framework for study and manipulation of human ASCs.

immunology↗

bioRxiv2026

Mouse behavioral genomics identifies Creld1 as a gatekeeper of somatosensation

Somatosensation enables the perception of touch, temperature, pain, and itch. These sensory modalities are mediated by primary sensory neurons in the dorsal root ganglion (DRG), which convert physical and chemical stimuli into electrical signals using specialized molecular sensors, including the touch sensor PIEZO2 (Ref1,2) and temperature sensors such as TRPV1 (Ref3,4), coupled with downstream voltage-gated sodium channels (Nav) like Nav1.7 (Ref5,6). However, the full repertoire of molecular components involved in somatosensory processing remains incompletely identified. Here, we developed an efficient postnatal CRISPR-Cas9 knockout platform to screen DRG-expressed genes via AAV9-sgRNA delivery. Combining this approach with behavioral assays of somatosensory responses, we validated the roles of PIEZO2 and TRPV1 in sensing gentle touch and noxious heat, respectively, and the broad involvement of Nav1.7 in distinct somatosensory modalities. Remarkably, a targeted screen of 20 DRG-expressed genes identified the Cysteine-rich with EGF-like domains 1 (Creld1) as a master regulator of somatosensation. Either sgRNA-mediated postnatal knockout or tamoxifen-induced Cre-mediated deletion of Creld1 in DRG neurons resulted in profound behavioral deficits in touch, temperature, pain, and itch perception, while its overexpression enhanced touch and thermal responses. Mechanistically, Creld1 functions as a novel auxiliary regulator of Nav for controlling the excitability of DRG neurons. The biochemical interaction and functional modulation of Nav by mouse Creld1 are mediated via its C-terminal transmembrane region. Notably, this domain is conserved in mouse Creld1 and some isoforms of human CRELD1, resulting in an isoform-dependent regulation of Nav1.7. Together, this work establishes a robust postnatal screening platform for somatosensory genomics and identifies Creld1 as a master regulator of somatosensory function, and provides novel therapeutic strategy for pain and itch treatment.

neuroscience↗

bioRxiv2026

KuafuPrimer: Machine learning empowers the design of 16S amplicon sequencing primers toward minimal bias for bacterial communities

Amplicon sequencing protocol targeting the 16S rRNA gene is a widely used and cost-effective method for exploring bacterial communities. However, its performance is often limited by primer bias arising from the arbitrary use of universal primers across diverse microbial communities and habitats. We propose KuafuPrimer to design the optimal 16S rRNA gene primers toward minimal bias for targeted bacterial communities, using few-shot machine learning to guide the primer design procedure based on a small number of samples. Simulations on 809 samples across 26 representative environments and habitats showed that KuafuPrimer-designed primers outperformed the universal primers in taxonomic accuracy, achieving an averaged 16.31% relative reduction in primer bias, with reductions up to 46.08% in plant samples. Notably, KuafuPrimer detected 29 rare and key taxa undetectable by the universal primers. Validation with 317 longitudinal gut microbiota samples demonstrated that KuafuPrimer-designed primers consistently outperformed the universal primers across temporal, individual, and cohort levels, with relative bias reductions of 5.03%, 3.53%, and 3.10%, respectively. Finally, in real PCR experiments on human gut samples from Clostridioides difficile-infected and healthy groups showed that polymerase chain reaction products using KuafuPrimer-designed primers correlated better with metagenomic data compared to the universal primers. More importantly, KuafuPrimer successfully detected Clostridioides difficile, the key pathogen missed by the universal primers, highlighting its potential for improving clinical diagnostics. In summary, KuafuPrimer provides a machine learning-based primer design strategy for targeted bacterial communities, with demonstrated utility in large-scale microbiome initiatives, longitudinal surveys and clinical diagnostics.

bioinformatics↗

bioRxiv2026

Basal ganglia output dynamically controls skilled forelimb kinematics in real time

The substantia nigra pars reticulata (SNr), the principal output nucleus of the basal ganglia, is traditionally viewed as a binary gate that permits actions through disinhibition. However, this framework fails to explain the fluid, high-dimensional control required for skilled behavior. Using high-resolution 3D kinematic tracking and automated behavioral classification, we show that SNr population activity paradoxically increases during skilled forelimb reaching and scales with motif-specific kinematics. Systematic optogenetic and chemogenetic perturbations reveal that the SNr bidirectionally controls movement vigor and online kinematics. Remarkably, a transient 12.5 ms pause is sufficient to abort a motor program, while a 12.5 ms burst enhances velocity and reshapes trajectories without altering sequence identity. Calcium imaging at single-neuron resolution further confirms that endogenous SNr dynamics represent real-time 3D kinematics. These findings demonstrate that SNr output does not merely gate movement initiation but continuously regulates the stability and kinematic evolution of skilled actions, expanding the functional framework of basal ganglia output from binary selection to the real-time dynamical control of motor execution. HighlightsO_LISNr activity paradoxically increases and scales with motor motif kinematics C_LIO_LIBidirectional SNr control of action vigor for skilled forelimb reaching C_LIO_LIBrief SNr pauses or bursts reshape online motor execution C_LIO_LIThe SNr acts as a continuous controller for real-time motor execution C_LI

neuroscience↗

bioRxiv2026

Mitochondria Organize Gap Junctions to Enable Neural Circuit Scaling

Neural circuits must maintain function during dramatic growth-driven expansion. While chemical synapses can be independently reorganized in pre- and postsynaptic neurons, gap junctions physically couple partner cells, requiring coordinated spatial redistribution--a process whose mechanisms remain unknown. Using the C. elegans mechanosensory circuit, we show that gap junctions undergo stereotyped developmental reorganization, transitioning from clustered to dispersed configurations as partner neurites elongate. Forward genetic screening identified RIC-7, a mitochondrial adaptor protein, as essential for this redistribution. Loss of RIC-7 prevents gap junction dispersal, trapping partner neurites at clustered sites and severely impairing electrical transmission. Mechanistically, RIC-7 directs mitochondrial positioning to gap junctions, where mitochondria recruit the microtubule-organizing component PTRN-1 to locally enhance microtubule dynamics. Disrupting mitochondrial transport (miro-1;mtx-2 mutants) or PTRN-1 function phenocopies ric-7 defects, while metabolic dysfunction does not, establishing a non-metabolic role for mitochondria in organizing synaptic architecture. Remarkably, RIC-7 expression in one neuron alone suffices to restore gap junction and partner neurite distribution across both coupled cells. Structural modeling suggests mechanical adhesion between docked hemichannels enables this coordinated reorganization. These findings establish mitochondria as mobile organizers of synaptic spatial architecture, demonstrate that proper junction distribution is essential for electrical transmission efficacy, and reveal how cell-autonomous mechanisms can achieve bilateral structural coordination during circuit growth.

neuroscience↗

bioRxiv2026

The parafascicular nucleus of the thalamus orchestrates coordinated skeletomotor, autonomic, and aversive state transitions

The parafascicular nucleus (Pf), part of the intralaminar thalamic nuclei, has been implicated in diverse functions such as attention, nociception, and behavioral flexibility, yet its precise contributions to behavior remain poorly defined. In this study, we used optogenetics in male and female mice to study the role of Pf projection neurons using high-resolution and continuous measures to quantify both skeletomotor and autonomic behavioral outputs as well as motivational valence. We showed that selective Pf stimulation resulted in wide-ranging effects, including ipsiversive turning, facial and whisker movements, pupil constriction, and heart rate reduction. Finally, we found that Pf stimulation could be highly aversive, as mice showed strong place aversion to areas where stimulation was delivered. Together our results indicate that Pf outputs can ultimately influence both skeletomotor outputs like turning and autonomic outputs like pupil constriction. The latter parasympathetic responses may be directly related to the role of the Pf in regulating motivational and emotional valence. These findings broaden our understanding of Pf function and suggest it may serve as a major hub for the integration of behavioral state feedback and top-down command of a variety of effectors. Significance statementThis study demonstrates that the parafascicular nucleus (Pf) of the thalamus plays a critical role in coordinating both skeletomotor and autonomic responses, as evidenced by optogenetic stimulation in mice triggering rapid ipsilateral turning, facial movements, pupil constriction, and heart rate reduction. The findings reveal that Pf activation induces an aversive state, highlighting its involvement in motivational valence. These insights expand our understanding of Pfs top-down regulatory influence on behavior.

neuroscience↗

bioRxiv2026

A dual-color miniature endoscope for calcium imaging in behaving mice

Calcium imaging with miniature endoscopes has become an essential tool in neuroscience, but conventional miniscopes typically record signals from only a single calcium indicator. Here, we present a dual-color miniature endoscope (miniscope) that enables simultaneous calcium imaging from two neuronal populations using spectrally distinct genetically encoded indicators. In freely moving mice, we used this system to record activity from striatal neurons of the direct (dSPN) and indirect (iSPN) pathways. We showed that dSPNs were activated earlier than iSPNs during contraversive movements, with dSPNs preferentially active during acceleration and iSPNs during deceleration. During ipsiversive turns, however, this temporal relationship was reversed. These findings indicate that dSPNs and iSPNs are not concurrently active, but instead exhibit complementary, direction-dependent dynamics that govern movement velocity. Our dual-color miniscope provides a compact, cost-effective platform for simultaneous two-population imaging, offering new opportunities to dissect coordinated activity across neural circuits in freely behaving animals.

neuroscience↗