Biology subjects

Qi, H.

Publications and source records attributed to Qi, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Dual phage sensing activates an RNA-targeting reverse transcriptase for anti-phage defense

Defense-associated reverse transcriptases (DRTs) mediate diverse antiphage responses, yet how they sense phage infection and couple unconventional DNA synthesis to antiviral effector activation remains poorly understood. Here, we characterize DRT4 as a dual-sensor immune system that integrates two distinct phage-derived signals. Cryo-EM analysis reveals that DRT4 assembles into a dimer-of-trimers hexamer, with each protomer catalyzing protein-primed, template-independent synthesis of a covalently linked ssDNA product. DRT4 displays a strong preference for purine nucleotides, determined by base-specific interactions within the polymerase active site. Using phage escape genetics, we identify two independent activators of DRT4: the phage ribonucleotide reductase NrdAB, which increase intracellular dNTP levels, and the SSB-like protein 0087, which directly binds the DRT4-generated ssDNA. Activated DRT4 exhibits dNTP-dependent RNase activity, linking phage sensing to RNA cleavage and abortive infection. Together, our findings show DRT4-generated ssDNA as a signaling intermediate that integrates phage-induced metabolic changes with direct recognition of viral replication proteins, revealing how protein-primed DNA synthesis can be repurposed for infection sensing and antiviral effector activation.

microbiology↗

bioRxiv2026

Somatotopic Organization of the Ventroposterior Nucleus of the Thalamus in Macaque Monkeys with Dorsal Spinal Cord Injuries Sustained During Early Postnatal Development

Injuries to peripheral nerves or the spinal cord lead to changes in the topographic organization in the brain at multiple levels along the sensory pathways. In adult monkeys large-scale deafferentations due to transection of the dorsal columns of the spinal cord at cervical levels result in large-scale reorganizations such that the deafferented neurons in the hand representation of somatosensory cortical area 3b start responding to anatomically distant body parts such as the chin. However, reorganization following dorsal column injuries depends upon the age at the time of the injury. The somatotopy of areas 3b, 1 and 2 in macaque monkeys with injuries sustained on or before postnatal day (PND) 5 is very normal-like. Whereas in monkeys with injuries sustained between PND9 and PND12, a large extent of the deafferented somatosensory cortex remains unresponsive to peripheral touch, with neurons at only a few sites responding to touch on the face or arm. Here we determined the organization of the ventroposterior nucleus (VPN) of the thalamus in four of these monkeys (Macaca radiata, 3 females, 1 male) that received lesions of the dorsal columns on PND 3, 5 and 9. We show that the nature of reorganization of VPN largely resembles that of the somatosensory cortex. Somatotopy is normal-like after lesions on PND3 and 5, whereas after lesion on PND9, the deprived neurons are largely unresponsive to peripheral touch, with a limited expansion of the chin representation.

neuroscience↗

bioRxiv2026

CHAIR an antigen-resolved antibody-reactome resource for healthy adult immune aging

Antigen-recognition histories accumulate across adult life, but existing human aging resources largely emphasize host-state measurements rather than antigen-resolved humoral memory. We present CHAIR, the Chinese Healthy Aging Immune Resource, which integrates self-antigen, human virome and toxin/virulence-factor PhIP-seq with routine clinical measurements and T/B/NK phenotyping in clinically screened adults aged 20-94 years. The resource framework includes 1,008 unique PhIP-seq samples, 995 clinical records, 977 T/B/NK records and 853 participants with all three layers. Across modeled spaces comprising 23,584 self-antigen targets, 210 virome targets and 1,258 virulence-factor source targets, most measured antibody-reactivity architecture was consistent with broad preservation within domains, whereas age- and sex-associated signals were concentrated in focal targets and modules. Together, CHAIR provides a traceable, antigen-resolved reference framework based on clinically screened adults for investigating focal humoral remodeling across healthy adult aging.

immunology↗

bioRxiv2026

SEEKER: A genome-scale library-on-library screening platform for deciphering T cell recognition of antigen

Decoding which antigens activate a given T cell receptor (TCR) is a central challenge in immunology. We present SEEKER, a functional genome-scale library-on-library screening platform built on three elements: a Jurkat-derived T-APC cell (TAPCell) that combinatorially expresses one TCR and one peptide-MHC drawn from separate libraries together with an NFAT activation reporter; encapsulation of single TAPCells in a thermos-reversible hydrogel for isolated clonal expansion, so recognition is read out as intraclonal activation; and dual-asymmetric PCR that links TCR- and pMHC-encoding sequences into a heritable unit, enabling progressive hit enrichment over screening rounds. SEEKER interrogates ~10^8 TCR-pMHC combinations per run without prior knowledge. Screening joint-infiltrating CD8+ T cells from HLA-B*27+ ankylosing spondylitis patients against proteome-wide libraries validated 53 TCR-peptide pairs, uncovered extensive cross-recognition of self and common viral epitopes, and revealed highly polyreactive T cells recognizing up to 80 autoantigens, implicating virus-triggered poly-autoreactivity in multi-organ autoimmune diseases.

immunology↗

bioRxiv2026

ERBB2 establishes the timing of progesterone priming required for uterine receptivity

Progesterone is essential for establishing uterine receptivity and sustaining early pregnancy. However, how the uterus acquires the competence to respond to progesterone at the appropriate time remains poorly understood. Here we show that ERBB2 governs the timing of progesterone responsiveness required for uterine receptivity. In endometrial samples from women with recurrent spontaneous abortion (RSA), ERBB2 is downregulated specifically in the stromal compartment, accompanied by a parallel reduction in stromal progesterone receptor (PGR). Uterine deletion of Erbb2 in mice blunts the rise of stromal PGR at the onset of the receptive window, deferring implantation and impairing decidualization despite normal circulating progesterone and estrogen. Epithelial deletion has no such effect, placing the requirement in the stroma. High-dose progesterone fails to rescue the phenotype; advancing progesterone priming by 24 hours restores stromal PGR, HAND2, Bmp2, and on-time implantation. Collectively, the present study provides evidence that ERBB2 directs the temporal window of stromal progesterone priming by setting the threshold for PGR induction, thereby synchronizing the maternal-fetal interface and safeguarding pregnancy.

developmental biology↗

bioRxiv2026

Conserved and specialized features of thalamocortical wiring revealed by single-cell projection mapping in mouse and marmoset

Across mammals, brain regions can duplicate, expand, and diversify, requiring long-range connectivity to accommodate species-specific specializations while preserving globally ordered wiring. This challenge is especially pronounced in primate thalamocortical circuits, where select cortical fields and their thalamic partners have expanded disproportionately. Although gene expression in the thalamus follows broad and conserved gradients, how thalamocortical projections are organized at single-neuron resolution, and how this organization is reshaped by expansion, remain unknown. Here, we investigate thalamocortical projection organization by in situ sequencing and BARseq projection mapping in marmosets and mice. We profiled the gene expression of 1.5 million marmoset neurons and jointly measured gene expression and cortical projections in 708 marmoset and 1,518 mouse neurons that spanned multiple thalamic nuclei. In both species, projections of individual neurons targeted diverse areas that together spanned a large fraction of the cortex. Comparing projections at the single-neuron level and local neighborhood level revealed that marmoset thalamocortical projections were more spatially segregated, producing a point-to-point architecture. Strikingly, this local specialization coexisted with a conserved gradient that predominated over discrete anatomical borders: In the higher-order sensory thalamus of both species, gene expression and projections varied continuously across nucleus borders, and borders had only a small effect on projections. Furthermore, in both marmoset and mouse, gene expression gradients were associated with the anteroposterior locations of cortical targets. These results reconcile discrete nucleus and gradient-based models of thalamic organization and suggest that primate circuit specialization is superimposed on a conserved molecular-projection gradient.

neuroscience↗

bioRxiv2026

BARseq3: a modular system for integrating spatial multi-omics and cellular barcoding in single cells

Understanding cellular identity requires multimodal measurements in single cells. Cellular barcoding provides powerful tools for recording the properties or history of individual cells in nucleic acids, while spatial omics techniques enable the measurement of a growing list of molecular features at micron resolution in tissue. However, existing methods that integrate these approaches in single samples are limited in the modalities they support, their flexibility, and efficiency. Here, we present BARseq3, a modular system that combines cellular barcoding with high-efficiency spatial transcriptomics and translatomics at subcellular resolution in tissue. BARseq3 is compatible with fixed samples, immunostaining, diverse species, and can be easily extended to include other spatial assays, enabling a multimodal understanding of cellular identity.

genomics↗

bioRxiv2026

Antiviral reverse transcriptase-primase synthesizes protein-templated DNA

Defense-associated reverse transcriptases (DRTs) are widespread in bacteria1,2, but how multi-domain DRTs containing RT and additional catalytic activities coordinate antiviral defense remains unclear. Here we show that DRT7, which contains both reverse transcriptase (RT) and primase-polymerase (PP) domains, provides broad-spectrum anti-phage immunity through abortive infection and can be activated by a phage-encoded putative transcriptional regulator. Upon activation, DRT7 synthesizes long, protein-primed, palindromic poly(A)/poly(T)-rich duplex-like DNA. Cryo-electron microscopy structures reveal that RT initiates protein-primed, protein-templated, sequence-specific poly(T) synthesis through an arginine-rich recognition pocket without requiring a complementary nucleic acid template, thereby converting DRT7 from an inactive closed dimer to an active open dimer. The RT-produced poly(T) then serves as both primer and template for PP-mediated poly(A) extension, with iterative handoff between RT and PP generating palindromic, alternating poly(A)/poly(T) ssDNA tracts that assemble into fold-back duplex-like DNA. These findings uncover an unexpected antiviral strategy based on protein self-templating, sequence-specific duplex-like DNA synthesis and reveal how coupling RTs with additional catalytic activities expands the functional scope of nucleic acid synthesis pathways.

microbiology↗

bioRxiv2026

A Multi-Objective Scoring (MOS) Framework for Detecting Cross-Modal Spatial Similarity: Conceptual and Direct Formulations

Spatial multi-omics methods allow researchers to study complex biological systems by integrating multiple molecular layers while preserving their spatial organization. However, integrating spatial transcriptomics and mass spectrometry imaging (MSI) remains challenging due to the differences between the two modalities, including sampling geometry, spatial resolution, signal scaling, and measurement principles. For example, 10x Genomics Visium captures transcriptomic data on a discrete hexagonal grid of spots; however, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) produces dense Cartesian pixel maps of molecular distributions. These differences make exact spatial co-registration difficult and limit the effectiveness of single-metric similarity approaches. Here, we introduce a Multi-Objective Scoring (MOS) framework designed to detect cross-modal spatial similarity without requiring exact pixel-to-pixel alignment. The MOS framework integrates multiple complementary spatial descriptors into a unified similarity score, including coordinate-based metrics (value correlation, importance-based Intersection-over-Union (IoU), and importance-map correlation) and descriptor-based metrics that capture higher-order spatial organization, such as spatial histograms, radial profiles, quadrant statistics, and Morans I spatial autocorrelation. These metrics are combined through a weighted ensemble model. This model calculates the weights using synthetic spatial datasets that simulate realistic tissue geometry, sampling differences, and spatial distortions. The framework was applied to a spatial multi-omics dataset from murine brain tissue, integrating spatial transcriptomics with MALDI-MSI lipidomics across young and aged control and Alzheimers disease (AD) models. Synthetic data validation results demonstrated strong pattern-matching performance (96.14% accuracy), and application to experimental data identified several MSI analyte features whose spatial distributions closely matched transcriptomic patterns. In particular, strong and reproducible associations were observed between myelin-related genes (Mbp and Plp1) and multiple analyte features enriched in white matter regions. Overall, whether applied conceptually or directly, the MOS framework provides a strong strategy for cross-modal spatial integration and offers a scalable tool for discovering spatial relationships across diverse multi-omics datasets and facilitating hypothesis generation.

biochemistry↗

bioRxiv2026

Continental-scale multi-omics reveals a distinct microbial-viral biome in sandy beach ecosystems structured by tidal zonation

Sandy beaches are dynamic coastal interfaces shaped by strong physical forcing and intense exchange between marine and terrestrial environments, yet their microbiomes remain poorly resolved at the genomic scale. Here we present a genome-resolved survey of microbial and viral communities across sandy beaches spanning a continental-scale latitudinal gradient along the Chinese coastline. By integrating cross-shore sampling, coastal geochemistry and large-scale multi-omics, we generated 978 metagenomes, 63 viromes and 72 metatranscriptomes, reconstructing 13,337 metagenome-assembled genomes and 38,255 viral populations. Sandy beach microbiomes exhibit exceptionally high genomic novelty, with more than 90% of species-level genomes representing previously undescribed taxa, suggesting that permeable coastal sediments constitute a distinct microbial and viral reservoir. Tidal zonation emerged as a dominant ecological driver structuring microbial diversity, metabolic strategies and virus-host interactions across cross-shore gradients. Genome-resolved analyses revealed systematic metabolic shifts from oxic heterotrophy in supratidal sediments toward increasingly chemolithotrophic and autotrophic pathways toward the low-intertidal and subtidal zone. Sandy beach microbiomes further encode broad potential for hydrocarbon and plastic transformation, together with diverse biosynthetic and antibiotic resistance repertoires that may mediate microbial chemical interactions. Together, these findings identify sandy beaches as a previously under-recognized microbial-viral biome shaped by tidal forcing, providing insight into microbiome evolution and coastal ecosystem resilience under increasing anthropogenic pressure.

microbiology↗

bioRxiv2026

Knockdown of the long isoform of the prolactin receptor selectively targets pathogenic immune cells and averts lupus nephritis

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by chronic inflammation in multiple organ systems. While a clinical association between elevated levels of the hormone/cytokine, prolactin (PRL), and exacerbation of SLE has been recognized for some time, little is known about the mechanisms through which PRL affects the course of this disease. Here, we show that immune cells in SLE have aberrant splicing of the prolactin receptor (PRLR) such that the ratio of the long to short splice variants is increased. To determine whether the change in PRLR isoform expression was causal in this disease, we used a splice-modulating oligomer (SMO) that knocked down expression of the long splice variant (LFPRLR). Using patient samples ex vivo, SLE-prone mice in vivo, high-dimensional flow cytometry and single-cell RNA-sequencing, we demonstrate that the aberrant PRLR isoform expression in SLE both directly and indirectly drives production of autoreactive immune cell phenotypes. Thus, LFPRLR knockdown decreased the expression of type I interferon signaling/response genes known to be biomarkers and hub genes for SLE, reduced immunoglobulins with signatures considered autoreactive, and averted glomerular kidney damage in SLE-prone mice. Importantly, LFPRLR knockdown reduced pathogenic B cells and other immune subsets that drive B-cell activation, without negative impact on healthy donor counterparts. Current treatments for SLE adversely affect healthy cells and do not concurrently eradicate multiple pathogenic immune subsets. Since LFPRLR SMO does not share these disadvantages, knockdown of the LFPRLR represents a potential treatment strategy for SLE that merits further investigation. Graphical AbstractThe LFPRLR represents an attractive therapeutic target in SLE. (Left) In addition to increased pituitary/circulating PRL, individuals with SLE exhibit aberrant increases in the production of autocrine/paracrine PRL by immune cells, and in their expression of specifically the long isoform (LF) of the PRLR. (Middle) Expression of the LFPRLR specifically enhances autoreactive immunophenotypes and promotes lupus nephritis. (Right) A splice modulating oligomer (SMO), that prevents synthesis of only the LFPRLR but not the short PRLR isoforms, reduces pathogenic immunophenotypes without affecting the normal counterparts of immune cells.

immunology↗

bioRxiv2026

MNS induces antiviral protection and suppresses inflammation

BackgroundIdentifying safe and broad-spectrum antiviral and anti-inflammatory agents remains an urgent need in infectious and inflammatory diseases. Here, we demonstrated that MNS (NSC170724), a small-molecule nitrovinyl benzodioxole, enhanced antiviral defense while limiting excessive inflammation. MethodsThe antiviral activity of MNS was evaluated in multiple cell lines and mouse infection models across DNA and RNA viruses. Virus-induced and LPS-induced inflammatory responses were assessed using RT-qPCR, ELISA and western blotting. Bulk RNA-seq and ATAC-seq were performed to define transcriptional and epigenetic mechanisms. ResultsMNS significantly suppressed viral infection in vitro and improved survival in four lethal viral infection models, accompanied by reduced viral loads and attenuated tissue injury. MNS also diminished virus-triggered and LPS-triggered inflammatory cytokine production in macrophages and multiple mouse organs, and protected mice from LPS-induced endotoxic lethality. Multi-omics profiling showed that MNS broadly repressed LPS-induced inflammatory transcriptional programs and reversed chromatin accessibility gains across promoters and transcription start sites. Joint analysis of RNA-seq and ATAC-seq data demonstrated consistent downregulation of pivotal inflammatory pathways, such as NF-{kappa}B, Toll-like receptor, and TNF signaling. ConclusionsWith potent activity against viral replication and inflammation in cellular and animal models, MNS emerges as a promising candidate for the treatment of viral infections and hyperinflammatory conditions.

systems biology↗

bioRxiv2025

β-catenin-independent regulation by TCF7L2 underlies isoform redundancy during embryonic thalamic development

Alternative promoter usage generates multiple transcription factor isoforms during brain development, yet their functional significance remains poorly defined. One such example is TCF7L2, a transcription factor critical for the development of the thalamus and recurrently affected by de novo mutations in autism spectrum disorder. TCF7L2 exists in two isoforms driven from different promoters: the long isoform (L-TCF7L2) with the {beta}-catenin-binding domain, and the shorter isoform (S-TCF7L2), lacking this domain and classically considered a dominant-negative regulator of the L isoform. We investigated the role of TCF7L2 isoforms in thalamic development using total and isoform-specific knockout strategies. Integrated phenotypic and transcriptomic analyses revealed functional redundancy of TCF7L2 isoforms during embryogenesis. {beta}-catenin subcellular localization and chromatin occupancy uncovered a developmental switch in TCF7L2 activity, from a {beta}-catenin-independent and isoform-redundant mode in the embryonic thalamus to a {beta}-catenin-dependent program postnatally. More broadly, these findings point to distinct embryonic and postnatal regulatory strategies, with alternative promoter usage potentially supporting robust availability of regulatory proteins during brain development.

neuroscience↗

bioRxiv2025

Evolutionarily Conserved T-tubule-Mitochondria Contacts in Striated Muscle

The intricate architecture of skeletal muscle is essential for its contractile function, with the spatial organization of organelles such as T-tubules and mitochondria playing a crucial role in maintaining muscle performance and health1,2. T-tubules propagate electrical signals deep into muscle fibers to ensure synchronous contraction, while mitochondria provide the necessary energy for muscle contraction3-5. Previous studies have extensively documented the interactions between T-tubules and the sarcoplasmic reticulum (SR), which are essential for excitation-contraction coupling6,7. However, the detailed spatial relationship between T-tubules and mitochondria has remained relatively unexplored. In this study, we utilized zebrafish and mice as model organisms to investigate the contacts between T-tubules and mitochondria. Using array tomography, deep learning-based analysis, and advanced microscopy techniques, we discovered extensive membrane contact sites, termed T-tubule-Mitochondria (TTM) contacts. These contacts are evolutionarily conserved across vertebrates, including skeletal and cardiac muscles. Our findings reveal a previously unrecognized, intimate spatial coupling between T-tubules and mitochondria, with significant implications for muscle physiology and pathology. Understanding these TTM contacts could provide new insights into the mechanisms underlying muscle function and the development of muscle-related diseases.

cell biology↗

bioRxiv2025

Isolation of the first cultured representative from a deep-branching phylum in serpentinite-hosted ecosystems

Serpentinization drives abiotic synthesis of organics (e.g., hydrocarbon) potentially conducive to the emergence of life, making serpentinite-hosted systems and associated microbial community key windows into nature of lifes origin. Although cultivation-independent studies uncovered the Candisdatus Bipolaricaulota widely distributed in serpentinizing environments, cultivation of this phylum has been unsuccessful. Here we cultured the first pure strain, J31, of Ca. Bipolaricaulota from the Lost City hydrothermal field, a well-characterized marine serpentinite system, using hydrocarbons as the primary nutrient source. As an early-branching bacterial lineage, strain J31 exhibits an unusual morphology composed of a central rod and elongated Toga-like extensions at both ends, and divides by binary fission. Strain J31 absorbs hexadecane through Toga ends via coordinated processes resembling inhalation and swallowing, after which hexadecane is efficiently transported to the central rod in the vesicle-like structures and subsequently converted into membrane lipids to support Toga synthesis and cellular growth. Hydrocarbon-degrading capability is widespread among the globally distributed members of Ca. Bipolaricaulota. Strain J31 colonizes serpentine minerals, facilitating the utilization of hydrocarbons derived from serpentines and promoting the release of soluble iron and silicon, thereby linking microbial activity to geochemical cycling. Thus, our study presents a novel strategy for cultivating deep-branching bacteria and offers insights into the metabolic foundations of early life on Earth--and potentially on other rocky planets undergoing serpentinization.

microbiology↗

bioRxiv2025

ISKNV-pORF71 hijacks outer mitochondrial membrane-localized VDAC2 to the nucleus, enhancing apoptosis by disrupting mitochondrial membrane permeability

Infectious spleen and kidney necrosis virus (ISKNV), the type species of the genus Megalocytivirus within the family Iridoviridae, is one of the most devastating pathogens affecting global teleost populations. Our previous study confirmed that ISKNV-pORF71 (p71/VP71) is a viral virulence factor by constructing a recombinant virus with ISKNV orf071 deletion (ISKNV-{Delta}71). In the present study, we further found that compared with ISKNV-WT, the ISKNV-{Delta}71 mutant is more capable of maintaining mitochondrial membrane potential, alleviating mitochondrial membrane permeabilization, preserving mitochondrial membrane integrity, sustaining lower cytochrome c release, and thereby reducing the apoptosis rate of infected cells. Further investigations demonstrated a strong interaction between p71 and the outer mitochondrial membrane (OMM)-localized voltage-dependent anion channel 2 (VDAC2). At the subcellular level, p71 and mandarin fish VDAC2 (mfVDAC2) are originally localized to the nucleus and mitochondria, respectively. However, in cells co-transfected with p71 and mfVDAC2, robust nuclear translocation of mfVDAC2 was verified. Endogenous mfVDAC2 was also confirmed to undergo nuclear translocation upon ISKNV-WT infection. In the zebrafish infection model, zebrafish VDAC2 (zfVDAC2)--but not zfVDAC-1 or zfVDAC-3--was observed to translocate into the nucleus through interaction with p71. Using CRISPR/Cas9 technology, VDAC2-knockout zebrafish were successfully constructed. Infection experiments showed that ISKNV-{Delta}71 exhibits significantly reduced lethality to both wild-type zebrafish and zfVDAC2-knockout zebrafish. In conclusion, our findings reveal that p71 exerts its function during ISKNV infection by hijacking VDAC2 into the nucleus, which alters mitochondrial membrane permeability and enhances ISKNV-induced apoptosis. The phenotypic characteristics of VDAC2 knockout (vdac-/-) zebrafish were also thoroughly analyzed and discussed. Author summaryVDAC2, a well-characterized cellular protein localized to the outer mitochondrial membrane (OMM), plays critical roles in viral pathogenesis and antiviral immune escape. Previous studies have shown that VDAC2 interacts directly or indirectly with viral proteins or functions as a functional receptor to modulate viral pathogenesis; however, few studies have demonstrated that VDAC2 is hijacked from its native OMM to other organelles. Our study here provides robust evidence that cellular VDAC2 is rerouted from its original OMM to the nucleus through interaction with ISKNV p71, thereby altering viral pathogenesis. This work offers novel insights into the role of VDAC2 in pathogen virulence. As far as we know, this is the first report demonstrating that host VDAC2 is hijacked into the nucleus by a viral protein to subsequently modulate the viral life cycle. Collectively, these findings advance our understanding of the active regulation of host functional proteins by iridoviruses.

microbiology↗

bioRxiv2025

Hydration Network Drives Activation and G Protein Selectivity in GPR174

G protein-coupled receptor 174 (GPR174), a key modulator of autoimmune responses, maintains immune homeostasis through distinct G protein signaling pathways, particularly Gs and Gi. Although the structural mechanism of lysophosphatidylserine (LysoPS)-activated GPR174 in the Gs pathway has been characterized, how hydration-mediated interactions influence GPR174 activation and signaling selectivity remains unclear. Here, we determined high-resolution cryo-electron microscopy (cryo-EM) structures of LysoPS-activated GPR174 bound to Gs (2.0 [A]) and Gi (3.4 [A]), revealing a continuous hydration-mediated signaling transduction network that bridges the sodium-binding pocket, NPxxY and DRY motifs, and the G protein-binding interface. This network stabilizes the active-state conformation of GPR174 and dynamically reshapes the intracellular cavity, thereby enabling differential engagement of Gs and Gi. Molecular dynamics simulations and functional assays demonstrated that the hydration network is essential for receptor activation and selectively modulates G protein coupling. To evaluate its conservation, we performed sequence alignment and structural analysis across class A GPCRs, defining three hydration cavities: the conserved water cavity (CWC), the junction water cavity (JWC), and the extended water cavity (EWC), whose hydration is determined by residue properties at position 5.58. Together, our study reveals a hydration-driven molecular mechanism that underlies the activation of GPR174 and its dual G protein selectivity. These findings advance the understanding of hydration-mediated signaling in GPR174 and provide a framework for investigating water-mediated regulation across class A GPCRs.

biophysics↗

bioRxiv2025

Context Shapes Fear: Habituation of Innate Defensive Behaviours Depends on Environmental Context

The capacity of animals to rapidly and appropriately respond to potential threats is critical for survival. In many species, this involves innate defensive behaviours, such as escape or freezing. But not all threats are dangerous. Habituation - a form of non-associative learning - allows animals to filter out irrelevant stimuli and thereby avoid unnecessary energy expenditure. While it is well known that context can influence behavioural responses to associative learning, whether non-associative forms of learning, such as habituation, are also context-dependent is unclear. Here, we address this issue in mice by examining the role of environmental context on habituation of defensive behaviours to threatening visual stimuli. We first developed a protocol leading to rapid (within minutes) and stable (at least one week) habituation of freezing responses to slowly sweeping visual stimuli, resembling an aerial predator moving across the sky. Using this protocol, we tested the impact of environmental context on habituation of freezing responses, finding that changing the environmental context led to a significant and reversible reduction in habituation. In summary, we find that environmental context plays a critical role in determining the impact of habituation on visually evoked innate defensive behaviours. These findings reveal a previously unrecognised flexibility in defensive responses to visual threats, extending the influence of environmental context to non-associative learning. HighlightsO_LIMice freeze in response to sweeping visual stimuli, resembling an aerial predator. C_LIO_LIHabituation to sweeping visual stimuli could be induced rapidly and remained stable over time. C_LIO_LIHabituation to sweeping visual stimuli depended on environmental context. C_LIO_LIContext-specific habituation was reversible. C_LI

animal behavior and cognition↗