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Qiu, J.

Publications and source records attributed to Qiu, J..

At least 37 records · Page 2Linked to original sources

Mononuclear myeloid cells mount an adaptive protective response to intracerebral haemorrhage by activation of NRF2

Following intracerebral haemorrhage (ICH), secondary injury contributes to negative outcomes. Here, we describe inter-dependent injurious and adaptive-protective pathways that form a therapeutically modifiable ICH response. In perihaematomal tissue from post-mortem ICH patients, transcriptomic analysis pointed to concurrent perihaematomal activation of the cytoprotective stress-induced transcription factor NRF2 and activation of interferon responses, with mononuclear myeloid cells (microglia and monocyte-derived cells, MMCs) and astrocytes contributing to this signature. In vitro, microglia-astrocyte-neuron co-culture studies revealed that microglial NRF2 activation was induced by clot-conditioned medium and could influence the interferon pathway in both microglia themselves as well as astrocytes. In vivo, MMC-specific deletion of NRF2 inhibited NRF2 target-gene induction, exacerbated interferon pathway activation following ICH, and impaired functional recovery. Pharmacological NRF2 activation suppressed interferon pathway induction post-ICH, and direct interferon pathway antagonism rescued neurological recovery deficits caused by MMC-specific NRF2 deficiency. Thus, augmenting NRF2- or inhibiting interferon-signalling may improve outcomes after ICH.

neuroscience↗

Multi-Scale Tri-Modal Histology Dataset Integrating Tumor Morphology, Immune Patterns, and Clinical Outcomes

Accurate prognostic assessment of prostate cancer (PCa) requires an integrated understanding of tissue morphology-encompassing cell structure, glandular architecture, and tissue organization-and the immune environment. We present Prostate-TriMod, a novel tri-modal histology dataset designed to integrate high-resolution visual morphology with spatial tissue maps, immune infiltration patterns, and clinical outcomes. This dataset, generated from the Cell DIVE multiplexed imaging platform, consists of three synchronized modalities: (1) multiscale virtual H&E tiles (224px, 256px, 512px, and 2040px) providing visual morphological context, (2) spatial tissue maps identifying cancerous/non-cancerous epithelial cells, stroma and immune cell populations (via TOPAZ and CAT models), and (3) text captions generated from single-cell data and patterns. The dataset includes comprehensive clinical annotations, including Grade Groups and biochemical recurrence (BCR) status. By providing high-fidelity alignment between visual features, spatial tissue maps, and textual descriptions, Prostate-TriMod empowers the development of advanced multimodal AI frameworks. We expect this resource to support reuse in multimodal representation learning, spatial analysis, and benchmarking studies that link histology morphology and immune context to clinical outcomes in prostate cancer.

bioinformatics↗

Astrocytes transform the transcriptomic and epigenetic landscape of developing cortical neurons to promote activity via intrinsic excitability control

Astrocytes are implicated in neuronal development and function, particularly of synapses, but their genome-wide impact is unclear. We show that cortical astrocytes trigger epigenetic remodelling in developing cortical neurons and widespread transcriptomic changes distinct from neurons intrinsic developmental trajectory. These changes can cause an emergence of neuronal firing activity independent of functional excitatory synaptogenesis. The mechanism is via through astrocyte-derived signals causing the transcriptional repression of inwardly-rectifying K+-channels (Kirs), causing a pro-excitatory shift in intrinsic properties. This places neurons in a zone of excitability whereupon cell-autonomous homeostatic control was activated, also associated with Kir regulation. Astrocyte-induced neuronal genes were enriched for schizophrenia, epilepsy, ADHD and Alzheimers disease risk, disorders associated with circuit imbalance. Thus, astrocyte-to-neuron signaling can alter firing via intrinsic properties in addition to the classical synaptogenic mechanism. The opposing actions of astrocytes and neuronal activity in regulating neuronal intrinsic properties may prevent hyper- or hypo-activity in neuronal circuits

neuroscience↗

Land-use intensity overrides grazing and precipitation effects on soil microbial communities in a subtropical agroecosystem

Global change drivers are reshaping agroecosystems and their sustained functions worldwide. While soil microorganisms underpin the resilience of these systems, the individual and interactive effects of multiple anthropogenic stressors on microbial community structure and function using large-scale field experiments remain poorly understood. Here, we utilize a full-factorial field experiment in a subtropical agroecosystem to investigate how land-use intensity, cattle grazing intensity, and altered precipitation regimes interact to shape soil microbiomes. Combining microbiome sequencing with network analyses and functional bioinformatics, we evaluated effects of these drivers on prokaryotic and fungal diversity, composition, predicted functional profiles, and community structure. Land-use intensity emerged as the primary driver of microbial responses, explaining 25% and 13% of the total variation in community composition for prokaryotes and fungi, respectively. Compared to intensively managed pastures, semi-natural pastures had significantly different community composition for prokaryotes and fungi and exhibited 22% higher fungal diversity. Semi-natural pastures were enriched with decomposer-associated taxa and metabolic pathways related to energy and lipid metabolism indicating enhanced microbial activity. Surprisingly, intensively managed pastures showed higher network modularity but lower network richness, suggesting a trade-off between community compartmentalization and complexity under intensive land management. Grazing and precipitation manipulations induced core microbiome changes within land-use intensities but had no impact on overall community structure and no significant interactions with land-use. Together, these findings suggest that long-term land-use legacies exert a persistent influence on soil microbial community structure, function, and organization, shaping the context within which other global change drivers operate in subtropical agroecosystems.

ecology↗

Autoluminescence characteristics of 25 Phalaenopsis orchids following transient transformation with eFBP2

Engineering autoluminescent plants, especially horticultural crops, has recently emerged as a promising research area, with one current approach involving the transgenic introduction of fungal bioluminescence pathway genes. Although autoluminescent plants such as tobacco and petunia have been created, it remains unclear whether all horticultural plants have the potential to be autoluminescent after genetic modification, especially those having flowers with dark colors and thick cuticles. To understand whether, and what if any, floral traits affect autoluminescence potential, we assess the autoluminescence characteristics of 25 representative Phalaenopsis cultivars after transient transformation of fungal bioluminescence pathway genes, alongside several key morphological and biochemical traits. Our results demonstrate that autoluminescence characteristics are correlated with floral color lightness, organ textures and epidermal cell types. In contrast, the content of the substrates of luciferin--caffeic acid and tyrosine, and the infiltration ease of inoculation solution into floral organs after injection, have limited effects on autoluminescence characteristics. Autoluminescence intensity can be reasonably predicted using five floral traits investigated, as 80.4% of variation can be explained by these traits. Our study not only identifies specific Phalaenopsis cultivars with high potential for developing autoluminescent lines but also provides a selection framework applicable to other horticultural crops.

plant biology↗

Glucose-dependent signalling pathways regulate TE differentiation in bovine embryos

Glucose uptake and metabolism increase markedly during the transition from morula to blastocyst. However, the functional roles of glucose during this process in bovine embryos remain incompletely understood. Here, we demonstrate that glucose specifically modulates trophectoderm (TE) differentiation without affecting the inner cell mass (ICM), acting through Hippo signalling via the hexosamine biosynthetic pathway (HBP) and the pentose phosphate pathway (PPP) rather than glycolysis. Consistently, scRNA-seq analysis reveals that unlike glycolysis-related genes, which show only stage-specific changes, HBP- and PPP-related genes exhibit significant differential expression between the TE and ICM lineages. Furthermore, we found that glucose deprivation does not impair pyruvate uptake or intracellular pyruvate levels in blastocysts, yet it significantly depletes the terminal metabolites of the HBP and PPP. Together, these findings reveal that glucose-dependent regulation of TE differentiation is conserved in bovine embryos.

developmental biology↗

Identification of Human Transferrin Receptor as an Entry Co-receptor for Parvovirus B19 Infection of Human Erythroid Progenitor Cells

Parvovirus B19 (B19V), a member of the genus Erythroparvovirus within the Parvoviridae family, infects human erythroid progenitor cells (EPCs) of bone marrow and fetal liver, and causes various hematological disorders. The minor capsid protein VP1 of B19V contains a unique N-terminal region (VP1u) that facilitates virus binding and internalization into EPCs via its receptor-binding domain (RBD). We previously identified tyrosine protein kinase receptor UFO (AXL) as a proteinaceous receptor for B19V infection of EPCs. In this study, we employed an ascorbate peroxidase 2 (APEX2)-based proximity labeling method to identify host proteins that are associated with B19V VP1u during entry. This analysis revealed human transferrin receptor 1 (hTfR) as a key host protein associated with VP1u. hTfR knockdown in UT7/Epo-S1 cells, a B19V-permissive human megakaryoblastoid leukemia cell line, showed significantly reduced B19V internalization and replication. Biolayer interferometry (BLI) assays confirmed a direct interaction between B19V VP1u and hTfR extracellular domain (ECD). Inhibition of VP1u interaction with hTfR ECD, either by a monoclonal antibody targeting the apical domain of the ECD or human ferritin, a natural ligand of hTfR that binds the apical domain, significantly reduced VP1u binding to hTfR, as well as B19V internalization and B19V replication in ex vivo-expanded EPCs. Furthermore, mutant RBD proteins that bear amino acid substitutions in the three helical domains nearly abolished RBD binding to hTfR and significantly reduced the ability to inhibit B19V infection of EPCs. Collectively, our findings establish hTfR as a B19V entry co-receptor that mediates B19V internalization into its natural host EPCs. SignificanceB19V causes severe hematological disorders, including transient aplastic crisis, chronic pure red cell aplasia, and hydrops fetalis, by selectively infecting erythroid progenitor cells (EPCs). Despite its clinical impact, no approved antivirals or vaccines exist, largely due to limited understanding of viral entry mechanisms. A unique feature of B19V is the externalization of the VP1 unique region (VP1u) from the viral capsid, which mediates receptor engagement. Our prior studies identified AXL as an attachment receptor for B19V. Here, we identify that human transferrin receptor 1 (hTfR) acts as a critical co-receptor that directly binds VP1u and promotes viral internalization. Inhibition of the VP1u-hTfR interaction by competitive binding of hTfR with either an anti-hTfR monoclonal antibody or human ferritin significantly reduces B19V internalization and replication in ex vivo-expanded EPCs, highlighting a link between VP1u binding to the apical domain of hTfR and viral internalization. RBD mutants that disrupt its interaction with hTfR barely inhibited B19V infection in EPCs. These findings support a receptor-switch model in which AXL mediates attachment and hTfR drives internalization. Defining these mechanisms provides a foundation for developing antiviral strategies targeting B19V entry into EPCs.

microbiology↗

Paternal behavior is controlled by preoptic Trpc5 neurons

Male parenting behavior is highly conserved and activated only after offspring are born. Here we show that the behavioral switch from infanticide in virgin male mice to caregiving in wild-type sires is associated with enhanced expression and activation of Transient receptor potential channel 5 (Trpc5) in estrogen receptor (Esr1)-expressing neurons in the hypothalamic medial preoptic area (MPOA). While selective deletion of Trpc5 from Esr1MPOA neurons diminishes paternal behavior in sires, overexpression of Trpc5 in these neurons converts the otherwise infanticidal virgin males to exhibit care to pups. Mechanistically, Trpc5-dependent changes in neuronal excitability underlie fatherhood-associated Esr1MPOA neuron plasticity. Notably, Trpc5 overexpression also enhances escape behavior and elicits exploratory diving behavior, suggesting that these neurons control a broader adaptive parenting response in males. These findings establish a Trpc5-dependent MPOA neural signal as a critical regulator of paternal behavior.

neuroscience↗

The BRCA1-A complex restricts replication fork reversal-dependent DNA repair in ATM deficient cells

Ataxia Telangiectasia Mutated (ATM) kinase deficiency results in cancer susceptibility and drug sensitivity. Deficiency in either the BRCA1 interacting A complex or XRCC4/Ligase 4 confers resistance to Topoisomerase I or PARP1 inhibitors in ATM-deficient cells. This suggests that BRCA1-A directs toxicity to fork-damaging agents in ATM mutated cells vis-a-vis illegitimate end-joining. Here, we show that ATM inhibition triggers combined SUMO and ubiquitin mediated BRCA1-A damaged fork recognition to restrict end-resection and cause Topoisomerase I inhibitor hypersensitivity. BRCA1-A deficient cells display elevated chromatin accessibility and nuclease activity at damaged forks, coupled with restored resection and drug resistance. Electron microscopy evidence demonstrates that ATM inhibition prevents replication fork reversal, which is restored by BRCA1-A loss to generate substrates for end resection. These findings reveal that BRCA1-A enforces a restrictive chromatin state to suppress the genesis of resection substrates, implicating fork reversal as a key determinant of chemotherapy response in ATM deficient cells.

cell biology↗

CsFDL1-CsFTL3 complex represses CsFTL3 via negative feedback to fine-tune flowering in Chrysanthemum seticuspe

In many flowering plants, the transition from vegetative growth to reproductive development is regulated by seasonal changes in photoperiod. Under inductive photoperiods, leaves produce the florigen FT (FLOWERING LOCUS T), which is transported to the shoot apex to promote flowering. The photoperiod is known to have a major effect on the flowering of chrysanthemum. In the perennial short-day (SD) plant Chrysanthemum seticuspe, the expression of CsFTL3 (FT-like gene) does not increase immediately after shifting from long-day (LD) to SD conditions but gradually accumulates under continuous SD conditions, peaking during inflorescence development. However, the underlying mechanism remains elusive. We show that CsFDL1 (an ortholog of FD) and CsFTL3 exhibit a significant inverse expression pattern in leaves during the initial stage of short-day inductions. Furthermore, the expression of CsFTL3 is upregulated in the leaves of CsFDL1-knockdown transgenic lines. CsFDL1 is expressed in leaves and forms a complex with CsFTL3 to recognize several TCGA- and ACGT-containing motifs in the CsFTL3 promoter. The CsFTL3-CsFDL1 complex downregulates CsFTL3 expression, thereby preventing its excessive induction by SD signals and inhibiting precocious floral transition. This study reveals that CsFDL1 acts as a key early repressor in the photoperiodic flowering pathway of chrysanthemum leaf, mediating negative feedback regulation by forming a complex with CsFTL3 to achieve precise temporal control of short-day-dependent flowering responses.

plant biology↗

THIK-1 channel mediates microglial glucose sensing and modulates AgRP neurons

Microglia play essential roles in maintaining energy homeostasis, and their dysfunction contributes to metabolic disease. Although high-fat diet (HFD) exposure induces microglial activation, the underlying mechanisms remain poorly defined. Here, we identified a previously unrecognized role for THIK-1 channel in mediating glucose sensing of microglia in arcuate nucleus of the hypothalamus (ARH), during HFD-induced obesity. Pharmacological inhibition of THIK-1 channel with tetrapentylammonium (TPA) suppresses feeding and attenuates body-weight gain in diet induced obese mice. Mechanistically, inhibition of agouti-related peptide (AgRP) neurons is indispensable for TPA-induced hypophagia. Moreover, THIK-1 inhibition promotes microglial phagocytosis of perineuronal nets (PNNs), leading to reduced AgRP neuronal activity and feeding suppression. Together, these findings establish THIK-1 as a critical glucose sensor in hypothalamic microglia and uncover a microglia-dependent pathway through which overnutrition modulates AgRP neuronal activity via PNN remodeling to regulate energy balance, highlighting THIK-1 as a potential therapeutic target for treatment of diet-induced obesity.

neuroscience↗

TRPV4 Inhibition by a Natural Product Mediates Analgesia

The transient receptor potential vanilloid 4 (TRPV4) channel, a polymodal calcium-permeable cation channel, is activated by diverse stimuli, including hyposmolarity, moderate heat, mechanical stress, and acidic pH. TRPV4 plays a critical role in the onset and progression of pain and is implicated in multiple pathological conditions, positioning it as an attractive therapeutic target. However, the development of TRPV4-targeted therapeutics has been hindered by limited mechanistic understanding of its inhibition. Here, the natural product (R)-1-(3-ethylphenyl)ethane-1,2-diol (AH001) is identified as a potent, subtype-selective TRPV4 inhibitor. A potential gating mechanism of TRPV4 inhibition is proposed through a combination of structural analyses and site-directed mutagenesis. Electrophysiological studies and cryo-electron microscopy (cryo-EM) further reveal that AH001s glucuronide metabolite, AHP, retains robust TRPV4 inhibitory activity, providing a critical structural basis for rational optimization of AH001 as a lead compound. Notably, AH001 demonstrated significant efficacy in reducing neuronal hyperexcitability in dorsal root ganglia (DRGs) and produced pronounced analgesic effects across multiple pain models, highlighting its therapeutic potential in pain relief. This study offers critical structural and mechanistic insights into TRPV4 inhibition and lays the groundwork for the structure-based design of TRPV4-targeted therapeutics.

biochemistry↗

Transforming a Fragile Protein Helix into an Ultrastable Scaffold via a Hierarchical AI and Chemistry Framework

The rational design of proteins that maintain structural integrity under concurrent thermal, mechanical, and chemical stress remains a challenge in molecular engineering. We present a hierarchical framework that transforms an -helical domain into an ultrastable scaffold by integrating AI-guided design with foundational chemical principles. This approach progresses from global architectural reinforcement, using multiple AI tools to create a stabilized four-helix bundle, to local chemical tuning, where AlphaFold3 guides the installation of salt bridges and metal-coordination motifs. A computational pipeline using physics-based screening such as molecular dynamics (MD) simulations efficiently distilled millions of designs into a minimal candidate set. The resulting -helical proteins exhibit unprecedented multi-axis stability, with mechanical unfolding forces exceeding 200 pN, thermal resilience >100 {degrees}C, and high resistance to chemical denaturants. By systematically dissecting the contributions of hydrophobic packing, electrostatics, and metal coordination, we establish a general blueprint for imparting extreme robustness. This work bridges AI-driven structural generation with chemical precision, advancing the creation of durable proteins for mechanistic studies and synthetic biology.

biophysics↗

Redirection of SARS-CoV-2 to phagocytes by intranasal sACE2-Fc as a universal decoy confers complete prophylactic protection

The rapid evolution of SARS-CoV-2 and other respiratory RNA viruses limits the success of current vaccines and antibody-based therapies. Engineered decoy receptors based on soluble angiotensin-converting enzyme 2 (sACE2) offer promising alternatives. Clinical-grade recombinant sACE2 inhibits SARS-CoV-2 replication in vitro but shows limited clinical success. This study reports an optimized sACE2 mutant fused to human IgG1 Fc (B5-D3), which redirects virus-decoy complexes to lysosomal degradation in macrophages. Intranasal prophylactic delivery of B5-D3 confers complete protection in SARS-CoV-2-infected K18-hACE2 mice. Abrogation of Fc effector functions compromises antiviral protection, indicating that Fc-mediated uptake of virus-decoy complexes is critical. Transcriptomic analysis suggests that B5-D3 induces early immune activation in lungs of infected mice. Bio-distribution and flow cytometry reveal selective targeting of airway phagocytes. In vitro assays confirm lysosomal degradation of virus-decoy complexes by macrophages without productive infection. These findings reveal a distinct antiviral mechanism via phagocytic clearance, supporting refined regimens for decoy treatments against SARS-CoV-2 and potentially other respiratory viruses.

immunology↗

Morphomolecular Longitudinal Endoscopy of Carcinogenesis

Current diagnostic approaches for head and neck cancer rely primarily on white-light endoscopy and tissue biopsy, providing only static, episodic assessments that fail to capture dynamic changes in tumour biology over time. This absence of continuous, detailed molecular and microscopic structural information makes early identification of dysplasia or cancer difficult and can delay critical treatment. Here, we introduce a unified, label-free endoscopic platform that combines Raman spectroscopy (RS) and optical coherence tomography (OCT) within a miniaturised, forward-viewing fibre-optic probe. This integration enables simultaneous video-rate OCT imaging and subsecond RS acquisition linking morphological and molecular tissue trajectories in vivo. We developed an explainable AI-based fusion framework that learns joint temporal representations of biochemical and structural features to classify tissue states while highlighting the most influential predictors. In a longitudinal 4NQO-induced murine model of carcinogenesis, the system tracked epithelial transformation in real-time from hyperplasia through dysplasia to neoplasia. By capturing temporally resolved morphomolecular trajectories in vivo, this platform establishes a new paradigm for early cancer detection and real-time surveillance, supporting timely and individualised clinical decision-making.

bioengineering↗

RAD18 Methylation by the Methyltransferase SETD6 Attenuates DNA Breaks

This study investigated the interaction between the SETD6 lysine methyltransferase and RAD18, a key protein in the DNA damage repair pathway. SETD6 belongs to the SET-domain-containing family of proteins, which are known to catalyze protein methylation, a post-translational modification that plays a critical role in regulating protein function, stability, and interactions. Using protein microarray technology, we identified RAD18 as an interactor and substrate of SETD6. We confirmed this interaction through ELISA and immunoprecipitation assays, demonstrating that SETD6 directly binds and methylates RAD18. Using mass spectrometry and site-directed mutagenesis, we identified that RAD18 undergoes mono-methylation at the K73 and K406 residues. Furthermore, we found that RAD18 methylation affects its nuclear localization. Specifically, SETD6 KO cells exhibited increased nuclear RAD18 levels, suggesting that methylation status influences RAD18s shuttling between the cytoplasm and nucleus. Notably, depletion of SETD6 led to elevated markers of DNA damage ({gamma}H2AX) and increased DNA breaks, as evidenced by comet assays. Restoring SETD6 activity significantly reduced DNA damage, while a catalytic inactive mutant did not have this effect, underscoring the importance of SETD6s enzymatic function. Overall, our results demonstrate that SETD6-mediated methylation of RAD18 is essential for attenuating DNA breaks, thereby regulating its cellular localization and function in maintaining genomic integrity.

molecular biology↗

Complex I Governs Iron Levels in Bat Mitochondria to Couple Respiration with Lipid Metabolism

The evolution of mitochondrial respiration has been implicated in the remarkable adaptations of bats, including powered flight, longevity and viral tolerance. However, the mechanisms coordinating mitochondrial respiration with lipid metabolism--a critical energy source for flight--remain poorly understood. Here, we discovered that complex I inhibition triggered iron overload into bat mitochondria, inducing a burst of reactive oxygen species (ROS). This iron translocation relied on the VDAC-MCU axis and mitochondrial membrane potential. Intriguingly, disrupting VDAC oligomerization enhanced iron uptake in a complex I-dependent manner. Mitochondrial iron translocation perturbed fatty acid oxidation and upregulated linoleic acid species, which promoted the reversible accumulation of lipid droplets, suggesting metabolic plasticity crucial for bat energetics. Our findings establish complex I as a pivotal regulatory hub that directly couples respiratory efficiency to lipid metabolism by governing mitochondrial iron levels. This mechanism may represent a key evolutionary adaptation supporting the unique metabolic demands of bat physiology. HIGHLIGHTSComplex I inhibition induces unique mitochondrial ROS burst in bat cells. Mitochondrial iron overload is the primary trigger of complex I-linked ROS burst. VDAC-MCU axis couples membrane potential to drive mitochondrial iron influx. Mitochondrial iron translocation remodels lipid metabolism in bat cells.

cell biology↗

Widespread distribution of the BpfA-carrying bacteria involved in the bisphenol F degradation in Pseudomonadota and Actinomycetota

The global use of bisphenol F (BPF) has led to widespread environmental contamination, posing significant threats to ecosystems and human health. However, the genes involved in BPF degradation remained unknown. In this study, a novel oxidase gene, bpfA, was obtained from strain Microbacterium sp. F2 through a four-step purification strategy. BpfA is classified as a member of the 4-phenol oxidizing (4PO) subfamily and contains a conserved FAD-binding domain (Asp152 and His393) as well as a Tyr-Tyr-Arg triad (Tyr93, Tyr474, Arg475). BpfA catalyzes the conversion of BPF to 4,4-dihydroxydibenzophenone (DHBP) through a series of three consecutive reactions. In addition, BpfA exhibits catalytic activity towards 4-alkylphenols, such as vanillyl alcohol (VA), 4-n-propylguaiacol (4PG), and 4-(methoxymethyl)phenol (4MOP). BpfA homologs are widely distributed in the environment, particularly in soil. Bioinformatics-based taxonomic profiling revealed that BpfA homologs are widely distributed in metagenomes from cultivated land and forests, mainly belonging to Pseudomonadota and Actinomycetota. This study enhances our understanding of the microbial degradation mechanism of BPF, elucidates the catalytic function of the novel oxidase gene bpfA and its distribution pattern in the environment, and provides important insights into the evolutionary origin of BPF degradation genes and the targeted mining of environmental microbial resources.

microbiology↗