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Zhang, Z.

Publications and source records attributed to Zhang, Z..

At least 271 records · Page 15Linked to original sources

Nonlinear Relationships of Fibrin Network Structure as a Function of Fibrinogen and Thrombin Concentrations for Purified Fibrinogen and Plasma Clots

BackgroundFibrinogen levels are associated with bleeding disorders and thrombotic disease. Thrombin converts fibrinogen to fibrin, producing the load-bearing fibrin scaffold that governs clot mechanics and transport. ObjectiveQuantitatively map how initial fibrinogen and thrombin concentrations, [Fgn]0 and [T[h]r]0, determine fibrin architecture in human plasma and a purified fibrinogen system. MethodsScanning electron microscopy was used to quantify single-fiber morphology--fiber diameter and branch-to-branch segment length from a standardized sample-preparation protocol. Confocal microscopy was used to quantify network architecture--projected fiber density and pore/bubble size. Results and ConclusionsAcross plasma and purified systems, fibrin structural parameters were quantitatively captured by compact multiplicative scaling laws of the form Y = k[Fgn]0[T[h]r]0{beta}. Unlike prior studies, which examined narrower condition ranges without establishing predictive equations across a systematic fibrinogen-thrombin concentration matrix, this framework defines distinct, quantitative roles for fibrinogen and thrombin in fibrin assembly. The magnitudes and signs of the exponents and {beta} indicate that thrombin primarily controls individual fiber growth kinetics, strongly shortening branch-to-branch segment length and modestly thinning fibers, whereas fibrinogen primarily controls space filling, strongly increasing fiber density, reducing pore/bubble size, and thickening fibers. For matched [Fgn]0 and [T[h]r]0, compared to plasma clots, purified fibrinogen formed denser networks with thinner and shorter fibers, suggesting that the plasma biochemical environment partially inhibits thrombin activity. Fiber length analysis further suggests that each thrombin molecule nucleates one fiber segment. Together, these parameterized scaling relations provide a predictive quantitative framework linking clot composition to fibrin microstructure in plasma and purified fibrinogen clots.

biophysics↗

Isolation and Characterization of a Novel Calcium-Precipitating Alkali-Tolerant Lysinibacillus sphaericus in Local Urban Environment

Concrete is an extensively used construction material in infrastructures due to cost-effectiveness and durability. However, its low tensile strength makes it prone to cracking, posing persistent maintenance challenges. Traditional repair methods are often expensive and difficult to implement, especially for critical structures. Recent studies propose a potential solution involving alkaliphilic or alkali-tolerant calcium-carbonate producing bacteria in aiding concrete crack repair through microbial-induced calcium carbonate precipitation (MICP) via urea hydrolysis. Considering the adaptive nature of bacteria, we hypothesize that naturally occurring concrete-inhabiting microbes possess properties crucial for mending cracks. Therefore, this study aims to isolate and evaluate these inherent microbes and their MICP ability. Six concrete samples were collected and cultured on Alkaline Nutrient Agar for microbial isolation. Urease activity was assessed phenotypically and genotypically. MICP activity was observed and validated under Scanning Electron Microscope/Energy Dispersive Spectroscopy (SEM/EDS). Out of the 49 isolates cultured, Lysinibacillus sphaericus PUMA0250 emerges as the most promising isolate for practical implementation, showing high pH survivability in an in-house formulated concrete agar medium (pH 12.6). L. sphaericus PUMA0250 exhibited MICP activity via urea hydrolysis and harbored all crucial genes involved in urease-mediated MICP. SEM/EDS analysis confirmed the structure and composition of the produced calcium carbonate precipitate. This study demonstrates the potential of L. sphaericus PUMA0250 to be incorporated into concrete to assess its healing efficiency. Its ability to thrive in the alkaline concrete environment and produce calcium by-products may aid concrete crack repair, opening microbiological avenues for sustainable and efficient concrete repair methodologies. IMPORTANCEAlthough concrete is widely used in construction, the construction material is prone to cracking, leading to costly repairs and structural degradation. This study isolated Lysinibacillus sphaericus PUMA0250 from tropical urban concrete, that can survive the highly alkaline environment typical of concrete structures in equatorial climate. Importantly, it produces calcium carbonate, a mineral that can help in concrete repair. These findings contribute to our understanding of how microbes that naturally produce calcium carbonate by-products can be used to repair concrete. For such applications, microbes must be able to withstand extreme conditions, including high pH and low nutrient availability. Our discovery of a resilient, native isolate highlights the potential of tropical concrete microbiomes as sources for self-healing construction technologies. This work lays the foundation for more sustainable, low-maintenance building materials and opens new possibilities in microbiology-driven solutions for urban infrastructure challenges.

microbiology↗

Layer-by-Layer Polymeric Films: A Novel Approach to Buccal GLP-1 Delivery

Buccal delivery offers a promising alternative to oral drug administration by enabling direct systemic absorption and avoiding first-pass metabolism. Multilayer polymeric films represent a promising strategy for the sequential delivery of drug and absorption enhancer in the oral cavity. Here, dual- and triple-layer films were fabricated via slot-die coating, incorporating a GLP-1 receptor agonist (GLP-1-RA) and the penetration enhancer sodium glycodeoxycholate (GDC). These were co-loaded in dual-layer films or compartmentalized in triple-layer films. Scanning electron microscopy and optical coherence tomography confirmed well-defined, distinct layers with thicknesses suitable for buccal administration (339 {+/-} 10.24 {micro}m and 487 {+/-} 36.5 {micro}m for dual- and triple-layer films, respectively). Both designs exhibited good mucoadhesion and mucosal compatibility, and preserved the secondary structure of GLP-1-RA. In vitro release studies showed rapid diffusion of GDC and GLP-1-RA from dual-layer films, whereas triple-layer films enabled sustained, sequential release of GDC and GLP-1-RA. Ex vivo porcine buccal mucosa studies showed higher GLP-1-RA and GDC flux from triple-layer films compared to dual-layer films. The films also did not compromise epithelial integrity, in contrast to the direct application of GLP-1-RA and GDC, which caused significant epithelial disruption. These results demonstrate that multilayer film architecture and spatial layering can be harnessed to control release kinetics, maximize peptide penetration, and minimize tissue stress, offering a versatile platform for safe and effective peptide delivery. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/700335v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@76858borg.highwire.dtl.DTLVardef@1397e74org.highwire.dtl.DTLVardef@19d1841org.highwire.dtl.DTLVardef@a369c5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

Amyloid precursor protein interacts with the mitochondrial phosphatase PGAM5 and regulates mitochondrial respiration

Amyloid Precursor Protein (APP) has been reported to partially localize to mitochondria, and mitochondrial dysfunction is a key feature of Alzheimers disease; however, the mechanisms linking APP to mitochondrial functions remain incompletely defined. In this study, we identified an interaction between APP and phosphoglycerate mutase family member 5 (PGAM5), a mitochondrial protein phosphatase. We confirmed their endogenous interaction in mouse brain tissue and determined that APP and PGAM5 are both present at mitochondria-ER contact sites (MERCS) and. Using in vitro binding assays, we demonstrate a direct interaction between the linker region of APP and a region of PGAM5 that includes the Kelch-like ECH-associated protein 1 (Keap-1) binding domain. PGAM5 is known to anchor a portion of Nuclear factor erythroid 2 p45-related factor 2 (Nrf2) through Keap1 at the outer mitochondrial membrane and regulates mitochondrial respiration and stress responses. We found that the Nrf2-regulated genes Hmox1 (Heme oxygenase-1) and Nqo1 (NADH:quinone oxidoreductase 1), which are involved in mitochondrial respiration, are downregulated in APP KO astrocytes. Accordingly, mitochondria isolated from the brains of APP knockout (KO) mice have impaired substrate-specific respiration and electron transport chain (ETC) function. Together, these findings suggest that APP supports mitochondrial respiration by binding to PGAM5 and modulating Keap1-Nrf2 signaling.

neuroscience↗

Molecular Imaging of Collagen Turnover in Myocardial Infarction

Cardiac fibrosis is a key contributor to cardiomyopathy after myocardial infarction (MI). Existing imaging techniques can detect established fibrotic changes; however, they lack sensitivity for ongoing collagen turnover--a dynamic process involving the denaturation of collagen triple helix. Molecular imaging of this process could enhance risk assessment and aid in the development of anti-fibrotic treatments. This study aimed to evaluate 99mTc-(HE)-(GPO), a radiotracer designed to target denatured collagen, as a biomarker of collagen turnover after MI. Methods99mTc-(HE)-(GPO) incorporates glycine-proline-hydroxyproline (GPO) repeats and can hybridize with denatured single- or double-stranded collagen. MI was induced in mice by ligation of the left anterior descending artery; sham-operated animals served as controls. At 2 weeks post-MI, animals underwent myocardial perfusion imaging or contrast-enhanced CT to detect the infarct zone, followed by SPECT/CT imaging using 99mTc-(HE)-(GPO) or a control scrambled tracer. Tracer uptake was quantified in vivo and ex vivo with gamma counting and autoradiography. Different aspects of fibrosis were examined by tissue analysis, along with autoradiography with a matrix metalloproteinase-targeted radiotracer, 99mTc-RYM1. Tracer binding was also assessed in human cardiac tissue through ex vivo autoradiography. Results99mTc-(HE)-(GPO) SPECT/CT revealed significantly higher tracer uptake in the infarct zone of MI mice compared to the remote zone and sham controls (P < 0.0001 for both). Tracer uptake was confirmed by autoradiography, which showed a strong correlation between SPECT and autoradiography (R = 0.81, P < 0.01). The scrambled tracer exhibited minimal cardiac uptake, demonstrating the specificity of 99mTc-(HE)-(GPO) signal. Denatured collagen staining and 99mTc-RYM1 autoradiography showed similar patterns as ex vivo 99mTc-(HE)-(GPO) autoradiography, while the ratio of denatured collagen to procollagen in the infarct zone significantly increased from day 3 to 2 weeks post-MI. Finally, 99mTc-(HE)-(GPO) bound to human fibrotic (but not normal) cardiac tissue. Conclusion99mTc-(HE)-(GPO) enables non-invasive detection of denatured collagen as a marker of collagen remodeling in vivo, offering a promising tool for assessing fibrotic remodeling after MI. Collagen, procollagen, and denatured collagen, along with MMP activation, exhibit distinct patterns, and their combined imaging may provide a comprehensive molecular fingerprint of cardiac fibrosis, advancing personalized management of cardiomyopathy.

bioengineering↗

Asymmetric partition of the O-GlcNAcome in mitosis ensures binary cell fate decision

Many cellular components undergo biased segregation during stem cell division, but whether such order extends to the proteome has remained unknown. Using our real-time O-GlycoTracer, we find that O-GlcNAcylated proteins (the O-GlcNAcome) segregate asymmetrically during Drosophila neuroblast mitosis, predisposing the two daughters to distinct fates. The daughter that preserves stem cell identity inherits most of the O-GlcNAcome. This asymmetric partition requires putative O-GlcNAc readers, notably 14-3-3 proteins. We further identify the nuclear pore complex (NPC) as a major O-GlcNAc substrate in neuroblasts; Nup153, located in the nuclear basket, shows O-GlcNAc-dependent biased inheritance. Perturbing multiple steps in this segregation pathway disrupts neuroblast differentiation, reduces brain size, and causes adult learning deficits. These findings reveal a coordinated O-GlcNAc-driven mechanism for proteome-level asymmetric inheritance during neural stem cell division, with implications for neurodevelopmental disorders linked to OGT or 14-3-3 mutations.

cell biology↗

A dual-factor complex governs archaeal ribosome hibernation by sensing energy status

Efficient coupling of cellular energy status to ribosome regulation is fundamental for cellular survival. Here, we identify the Archaeal Ribosome regulatory Complex (ARC)--a previously uncharacterized dual-factor complex comprising ARC-P and ARC-A. Cryo-EM reveals that ARC anchors to the small ribosomal subunit, establishing a stringent blockade of the tRNA and mRNA paths via an electrostatic wedge mechanism. This hibernation state is modulated by energy status: the complex remains stably associated under low-energy conditions, whereas ATP binding triggers rapid mobilization. Genetic analyses demonstrate that ARC acts as a translational brake essential for preserving ribosomal structural integrity, with ARC-A serving as the primary inhibitory factor. Notably, while the loss of ARC accelerates growth, it impairs recovery in proportion to stress severity. Phylogenomic analysis identifies ARC as an evolutionarily novel and widely distributed dual-factor system, revealing a conserved regulatory strategy for metabolic-translational coupling across diverse archaea. Our findings define a fundamental strategy where modular complexes integrate metabolic sensing with mechanical sequestration to balance growth and persistence.

biochemistry↗

A methylome-derived m6-dAMP trigger assembles a PUA-Cal-HAD immune filament that depletes dNTPs to abort phage infection

Bacteria must distinguish phage attack from normal homeostatic processes, yet the danger signals that trigger many defence systems remain unknown. Here, we show that a PUA-Calcineurin-CE-HAD module from Escherichia coli ECOR28 confers broad anti-phage protection by binding Dam-methylated deoxyadenosine monophosphate (m6-dAMP) generated during phage-induced chromosome degradation. Ligand binding converts a preassembled PUA-Calcineurin-CE hexamer loaded with six HAD phosphatases into a polymerising filament. The filament acts as a high-flux dNTP sink through a two-enzyme cascade: HAD first dephosphorylates dATP to dADP, and Calcineurin-CE then converts dADP to dAMP. dNTP collapse halts phage replication and enforces abortive infection. Multiple mobile-element DNA mimic proteins block filament assembly, revealing a direct phage counter-defence. More broadly, our findings extend a conserved, cross-kingdom paradigm of immune filament assembly to nucleotide-depletion antiviral defence and suggest modified-nucleotide sensing by related PUA-Calcineurin-CE modules as a widespread, underappreciated bacterial strategy.

microbiology↗

The overall and sequence-specific degradation of soil extracellular 16S rRNA genes across China: rates and influential factors

While extracellular DNA persistence substantially influences soil microbiome investigations, its degradation kinetics remain poorly quantified. Here, we developed a primer-labeled DNA approach coupled with microcosm incubation to determine the overall and sequence-specific degradation rates of extracellular DNA amplicon fragments across China. We observed substantial variations in the overall degradation rates of extracellular 16S rRNA gene amplicon fragments among the study sites, with degradation rate constants ranging from 0.05 to 0.16 day-1. The overall degradation rate constants showed significant correlations with soil moisture content, prokaryotic abundance, prokaryotic community profiles, and mean annual precipitation (MAP). The significant influences of moisture content on the overall degradation rates were further verified by a moisture gradient microcosm experiment. The sequence-specific degradation rate constant profiles were additionally correlated with pH, nitrogen content, and mean annual temperature (MAT). Furthermore, propidium monoazide (PMA)-based exclusion of extracellular DNA signals significantly altered soil prokaryotic abundance, richness, and prokaryotic community profiles, and the pool sizes of sequence-specific extracellular 16S rRNA gene amplicon fragments were significantly correlated with their respective degradation rates. This study developed a methodology for determining the overall and sequence-specific degradation rates of extracellular DNA amplicon fragments, highlighting the profound influences of extracellular DNA on soil microbial research and informing the optimization of environmental DNA technologies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/699460v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@b1b3e2org.highwire.dtl.DTLVardef@98f334org.highwire.dtl.DTLVardef@1870650org.highwire.dtl.DTLVardef@1af7105_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

Poly(A)-tail-length-dependent surveillance of viral RNA by PABPC1 orchestrates broad-spectrum antiviral defense

RNA processing and modification are critical for virus replication and pathogenesis, yet how the host exploits viral RNA features--particularly the poly(A) tail--for antiviral defense remains unclear. Through multi-omics integration and systematic functional screening, we identify the poly(A)-binding protein PABPC1 as a broad-spectrum restriction factor against multiple coronaviruses. We demonstrate that PABPC1 preferentially binds viral RNAs bearing short poly(A) tails--distinct from the longer and more heterogeneous host poly(A) tails--and, in a poly(A)-length-dependent manner, recruits the mitochondrial exonuclease EXD2 to assemble a degradative RNA-protein complex. Both the recognition and subsequent degradation of viral RNA strictly depend on poly(A) tail length, enabling selective decay of short-tailed viral transcripts while sparing host mRNAs. Importantly, inflammatory signaling enhances the expression of PABPC1 and EXD2, suggesting its role as an inducible host defense pathway activated during viral infection. Capitalizing on this discovery, we engineered a synthetic fusion protein mimicking the PABPC1-EXD2 complex and achieved efficient delivery using lipid nanoparticles (LNPs). This rationally designed therapeutic exhibits robust suppression of coronavirus replication in both cellular and murine models. Collectively, our findings uncover a novel host antiviral strategy that targets a conserved viral RNA structural element and provide a conceptual framework for developing host-derived and broad-spectrum anti-coronavirus therapeutics.

microbiology↗

Exercise-Induced Epoxy-Eicosanoids Promote Cardiomyocyte Proliferation and Post-Infarction Repair via NR4A1

BACKGROUNDMyocardial infarction (MI) causes irreversible cardiomyocyte loss that exceeds the adult hearts regenerative capacity, leading to adverse remodeling and heart failure. While exercise provides cardiovascular protection, the mechanisms underlying exercise-induced cardiac repair remain unclear. METHODSPlasma levels of free fatty acids and polyunsaturated fatty acid metabolites were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). RNA sequencing was performed to identify differentially expressed genes and enriched pathways. NR4A1 was knocked down in mice via tail vein injection of AAV9 carrying shRNA targeting NR4A1 (AAV9-shNR4A1). The role of 17,18-EEQ was evaluated by continuous subcutaneous infusion via osmotic minipump; the involvement of the cAMP-PKA-CREB axis was assessed using specific pharmacological inhibitor. Molecular analyses included ELISA, immunofluorescence staining, QPCR, and western blotting. Additionally, clinical samples were collected from 36 endurance-trained athletes and 30 sedentary individuals (age 18-22, male) for comparative analysis. RESULTSHere we demonstrate that preventive aerobic training promotes post-MI cardiomyocyte proliferation and confers cardioprotection by reducing fibrosis area and improving cardiac function. Targeted lipidomics revealed that exercise elevates circulating epoxyeicosatetraenoic acids (EEQs), particularly 17,18-EEQ; osmotic pump delivery of 17,18-EEQ mimicked the protective effects of exercise, reducing infarct burden and enhancing proliferation markers (Ki67, pH3, Aurora B). Transcriptomic analysis identified NR4A1 as the most prominent up-regulated mRNA under exercise induction; AAV9-mediated NR4A1 knockdown abolished exercise-mediated cardioprotection and proliferative benefits, establishing NR4A1 as essential for exercise-driven repair. Phosphoproteomic profiling revealed that 17,18-EEQ activates the PKA-CREB pathway to induce NR4A1 expression; pharmacological inhibition of adenylyl cyclase, PKA, or CREB phosphorylation reversed EEQ-mediated cardioprotection and proliferation, confirming pathway necessity. Dietary supplementation with eicosapentaenoic acid (EPA), the metabolic precursor of 17,18-EEQ, amplified exercise-induced cardioprotection by enhancing EEQ biosynthesis. CONCLUSIONOur study identifies 17,18-EEQ as an exercise-derived exerkine that promotes cardiomyocyte proliferation and post-MI repair through a PKA-CREB-NR4A1 signaling axis, advancing our understanding of exercise cardioprotection and myocardial regeneration mechanisms while providing novel therapeutic targets for cardiac intervention. What IS New?O_LIAerobic exercise enhances post-myocardial infarction cardiac repair by upregulating the cardio-protective lipid mediator 17,18-EEQ and its downstream effector NR4A1. C_LIO_LI17,18-EEQ promotes cardiomyocyte proliferation and cardiac repair through activation of the cAMP-PKA-NR4A1 signaling axis. C_LIO_LICombining aerobic exercise with omega-3 fatty acid supplementation synergistically improves cardiac remodeling and functional recovery after ischemic injury. C_LI What Are the Clinical Implications?O_LITargeting endogenous cardiomyocyte proliferation represents a promising therapeutic strategy for cardiac regeneration after ischemic injury. C_LIO_LIDietary supplementation with omega-3 fatty acids may be a clinically feasible approach to amplify exercise-induced cardioprotection and improve outcomes after myocardial infarction. C_LI

physiology↗

Development of Integrin α5β1-targeted PET/NIR imaging probes for glioblastoma intraoperative navigation and intracavity targeted radionuclide therapy

Incomplete extent of tumor resection is the major factor of glioblastoma recurrence, leading to its poor prognosis. Developing therapies that enable the minimal tumor cell remnant during surgical resection is a major challenge to combat this aggressive cancer. This study develops a glioblastoma integrin 5{beta}1-selective peptide binder through series strategy screening and labeling it with 68Ga, indocyanine green (ICG), or 177Lu for efficacious multimodal treatment. This strategy combines positron emission tomography (PET) imaging for preoperative diagnosis, intraoperative NIR-II fluorescence-guided surgery for maximal tumor resection, and followed by intracavity targeted radionuclide therapy for elimination of residual tumor cells. We identified GR, with five arginine mutation, exhibiting superior integrin 5{beta}1 binding affinity and brain penetration. [68Ga]GR demonstrated substantial tumor uptake and prolonged retention time in both mouse models and tissues from glioblastoma patients. The guidance of ICG-GR achieved accurately intraoperative tumor imaging and maximal tumor resection in orthotopic mouse glioblastoma models. Notably, combining intracavity administration of [177Lu]GR following ICG-GR guiding resection markedly inhibited tumor growth and reduced possibility of tumor recurrence compared with surgery alone (unguided or ICG-GR-guided) or unguided surgery followed by [177Lu]GR. Therefore, we have reported the integrin 5{beta}1-targeted radionuclide and optical agents for maximal elimination of tumor cells during surgical resection in glioblastoma patients. HIGHLIGHTSO_LIGR is a glioblastoma-specific peptide with both favorable binding affinity superior brain penetration. C_LIO_LIICG-GR is a glioblastoma-targeted NIR probe enabling maximal surgical resection. C_LIO_LIICG-GR-guided surgery with [177Lu]GR-based adjuvant therapy allows robust elimination of tumor cells. C_LI

cancer biology↗

Unifying constraints linking protein folding and native dynamics decoded from AlphaFold

The interplay between protein folding and native dynamics remains a central question in biophysics. Analyzing an extensive set of AlphaFold-predicted structures, we uncover a robust relationship between folding topology (contact order) and native dynamics (fluctuation entropy), showing that long-range contacts that slow folding also restrict conformational flexibility across protein sizes and taxonomic groups. Scaling analysis reveals that this relationship, together with its chain-length dependence, is consistent with power-law-like trends, reflecting common organizing constraints of protein architecture. Across species, increasing organismal complexity is associated with proteome-wide shifts toward lower contact order and higher fluctuation entropy. Together, evidence from folding, stability, and functional dynamics converges on unifying constraints, revealing an intrinsic physical organizing principle captured by AI models.

bioinformatics↗

Single-cell transcriptomic landscapes reveal cell-type-specific regulatory mechanisms of nutrient accumulation and transport in wheat grain

To elucidate the transcriptional regulatory mechanisms underlying wheat grain development, we constructed single-cell transcriptomic atlases of wheat grains at 4 and 8 days after pollination (DAP) using single-nucleus RNA sequencing. A total of 58,546 high-quality nuclei were clustered into 16 distinct cell populations representing all major seed tissues, including the embryo, aleurone layer, transfer cells, endosperm, inner pericarp, seed coat, and embryo surrounding region. Comparative analysis revealed a dynamic transcriptional reprogramming from growth-related pathways at DAP 4 to nutrient accumulation at DAP 8, which coincided with shifts in the expression of hormone signaling and organ development genes, as well as starch and storage protein genes. Pseudotime trajectory analysis identified two major differentiation branches, highlighting distinct roles in nutrient storage and support. Notably, the transcription factor TaMADS58 was found to regulate pericarp cell number while simultaneously enhancing protein content and processing quality. Concurrently, TaJEKLL, specifically expressed in nucellar projection cells, was demonstrated to influence nucellar projection development and nutrient transport. Natural variation in TaMADS58 and TaJEKLL revealed their potential to decouple yield from quality traits, offering promising applications for crop improvement. Collectively, this study provides a high-resolution single-cell resource for wheat seed biology and demonstrates that investigating gene expression with spatiotemporal precision at the single-cell level can facilitate the discovery of key genes for precisely regulating individual traits.

plant biology↗

PAR-Driven Condensation Maintains Stalled Replication Fork Stability

Poly(ADP-ribose) (PAR) is a nucleic acid-like heterogeneous polymer in nature. Recently, it was found to engage in liquid-liquid phase separation (LLPS), generating condensates as an emerging class of subcellular structures with pivotal functions in response to stimuli. As a post-translational modification catalyzed by PAR polymerases (PARPs), PAR is known to modulate many key events in cells. However, its involvement in biomolecular condensation remains elusive. Through an imaging-based screening of small molecules with diverse biological activities, we here discovered that PAR undergoes LLPS upon inhibiting proteasome in different types of cells, resulting in co-condensation of PAR with proteasome and ubiquitin chains in nucleus. This unprecedented co-condensation is dependent on PARP2 not PARP1 and requires K6-linked ubiquitylation. PAR is shown for the first time to directly interact with ubiquitin chains. Notably, stalled DNA replication forks arose from proteasome inhibition are co-localized with PAR-proteasome-ubiquitin chain condensates. By attenuating replication and stabilizing stalled replication forks, PAR-proteasome-ubiquitin chain condensates sustain genomic integrity under proteasomal stress. This work demonstrates a self-protective mechanism in stressed cells and provides fundamental understanding of PAR condensation in cell biology.

biochemistry↗

The Red Rice Bran Extract (RRBE) Mitigates Photoaging by Targeting Mitochondrial Oxidative Stress and Regulating Thermal Damage Responses

The photoprotective efficacy of natural skin-active complexes is well recognized, yet their ap-plication is often hindered by the challenge of deciphering their complex, multi-component, and multi-target mechanisms. To bridge the gap between established phenotypes and molecular mechanisms, we developed an AI-driven integrated platform that combines phytochemical profiling, network pharmacology, and deep learning-based target prediction with rigorous biophysical validation. We applied this platform to investigate RRBE, a bioactive complex refined from red rice bran extract. In vivo clinical studies confirmed that RRBE significantly accelerates the resolution of UV-induced erythema, while cellular and 3D tissue models demonstrated robust suppression of oxidative stress and DNA damage responses. To decode its material basis, the platform deconstructed RRBE into 10 distinct chemical modules. Leveraging our SCOPE-DTI deep learning model for global target prediction, we identified flavonoids (Module 1) and phenolic acids (Module 10) as the primary bioactive drivers relevant to photoprotection. These computational predictions were structurally supported by molecular docking and definitively validated in a physiological environment via Cellular Thermal Shift Assay-Mass Spectrometry (CETSA-MS). Mechanistically, RRBE functions through a synergistic polypharmacology: (1) Module 1 components, represented by procyanidin B2, target NDUFA7 to stabilize mitochondrial function and mitigate ROS; (2) Module 10 components, exemplified by caffeic acid, ferulic acid, and p-coumaric acid, engage FKBP11 and HSP90AA1 to regulate protein homeostasis and stress responses. This work not only deciphers the polypharmacological basis of RRBEs photoprotective action but also validates a scalable "AI-guided, cell-validated" discovery pipeline, offering a rational paradigm for uncovering the protective benefits of complex natural extracts.

systems biology↗

On-virion structural dynamics reveal temperature- and receptor-coordinated activation of an alphacoronavirus spike

Human alphacoronaviruses primarily infect the human upper respiratory tract, yet how physiological temperature and receptor-binding coordinate viral spike (S) protein activation remain unclear. Using cryo-electron tomography and subtomogram averaging, we directly visualized the structural dynamics of S on human coronavirus 229E (HCoV-229E) virions under physiologically relevant temperatures and in the presence of the host receptor human aminopeptidase N (hAPN). We identified two prefusion S2 conformations, compact and loose, that interconvert reversibly by temperature, revealing intrinsic S2 "breathing" on virions. Receptor-binding domain (RBD)-up conformations are rare on apo virions but are promoted at physiological temperature and stabilized upon receptor binding. hAPN can bind bivalently to neighboring S, forming Gemini S-hAPN complexes. Receptor incubation further promotes conversion from prefusion to postfusion S, an effect enhanced at 33. Together, our results demonstrate an optimized temperature for the HCoV-229E viral fitness, establish temperature and receptor binding as synergistic regulators of alphacoronavirus S activation and define an integrated, on-virion model of S conformational transitions during viral entry. These findings provide a structural framework for understanding alphacoronavirus infectivity.

microbiology↗

DNA sequence quantitatively encodes CTCF-binding affinity at genome scale

CTCF is a central architectural protein that shapes 3D genome organization through sequence-specific DNA binding, but how DNA sequence quantitatively determines CTCF-binding strength remains poorly understood. Progress has been hampered by the lack of large, high-quality measurements of binding affinity. Here, we experimentally determine in vitro CTCF-binding affinity for 276,765 DNA sequences derived from the human genome, generating a comprehensive quantitative landscape of CTCF-DNA interactions. Leveraging these data, we develop DeepCTCF, a deep learning model that predicts CTCF-binding strength directly from DNA sequence and enables quantitative interpretation of CTCF motif grammar. Using this framework, we systematically dissect how specific sequence features modulate CTCF-binding affinity and generate quantitative predictions for disease-associated variants that alter CTCF binding. Together, this study defines general principles by which DNA sequence encodes CTCF-binding affinity and provides a quantitative framework for interpreting regulatory sequence variation. TeaserMapping how DNA encodes CTCF binding reveals quantitative rules across over 1{per thousand} of the human genome.

genomics↗