Plants tailor their architecture to warm temperatures through the central transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4). Here, we dissect how structured and disordered regions of PIF4 contribute to its function in thermomorphogenesis. A long N-terminal intrinsically disordered region (IDR) enables PIF4 to form low-mobility condensates. Within this IDR, we identify an acidic transactivation domain (TAD) and an extended basic segment that carries a nuclear-localization signal and the canonical basic motif of the basic helix-loop-helix (bHLH) domain. The basic segment is both necessary and sufficient to drive PIF4 condensate formation, while the TAD tunes condensate properties. Strikingly, alanine substitutions that abolish TAD-mediated transactivation, disrupt DNA binding, or greatly reduce phase-separation propensity have no significant effect on thermomorphogenetic hypocotyl elongation. By contrast, substituting twelve basic residues within the basic segment, which disrupts both DNA binding and HLH-mediated oligomerization, abolishes thermo-induced hypocotyl growth. These findings suggest that PIF4's oligomerization competence contributes significantly to thermomorphogenesis by enabling partner recruitment, allowing DNA-binding and transactivation functions to be supplied in trans.

How nuclear condensates encode cell-signaling dynamics remains unclear. Photobodies (PBs) in Arabidopsis offer a genetically tractable paradigm. PBs are light- and temperature-sensing nuclear condensates organized by the thermosensitive photoreceptor phytochrome B (phyB). Recent advances have clarified PB composition and illuminated PB formation and function. phyB is the dominant component and provides scaffold-like determinants that recruit selective signaling partners as primary clients (direct phyB binders) and secondary clients (recruited via primaries), spanning transcription/splicing regulators, E3-ligase components, kinases/phosphatases, and chaperones. These clients connect phyB condensates to diverse environmental and hormonal pathways, positioning PBs as a central hub for signaling integration. PB assembly is driven by condensation encoded in phyB's output module and modulated by its photosensory module, coupling assembly/dissolution to photostate and temperature. PBs nucleate nonrandomly at preferred seeding sites, producing spatially distinct classes with different occurrence frequencies and thermosensitivities. PB formation partitions signaling between PBs and the surrounding nucleoplasm, establishing a 2-compartment photosensory system. Within this architecture, dynamic sequestration in PBs tunes nucleoplasmic transcription factor stability and activity to expand signaling dynamic range and extends phyB control into the night by stabilizing active phyB. We propose that PBs function as an autoregulatory rheostat, dialing nucleoplasmic light sensitivity in proportion to incident irradiance and thereby enabling continuous discrimination of light-intensity changes across multiple orders of magnitude. We suggest that this 2-compartment logic illustrates a general role of membraneless organelles in signaling: using dense-phase dynamics to adjust pathway sensitivity and output in the surrounding dilute phase.

Branching regulation and biomass accumulation are key determinants of tobacco productivity and bioenergy potential, yet the molecular mechanisms underlying branching control in tobacco remain poorly understood. Here, we characterize the ntmbd1 mutant derived from EMS mutagenesis, which exhibits excessive basal branching and altered plant architecture. SSR mapping and whole-genome sequencing identify a nonsense mutation in ntmbd1 leading to truncation of the encoded P450 protein. NtMBD1 is predominantly expressed in the shoot apical meristem, flower, and root, where its localization to the endoplasmic reticulum suggests a role in ER-associated regulatory processes. Phylogenetic analysis reveals that NtMBD1 in cultivated tobacco originates from its ancestral species Nicotiana sylvestris, while its homolog from N. tomentosiformis is likely lost during evolution. Functional validation shows that NtMBD1 is required for axillary bud suppression, as CRISPR disruption in N. tabacum and N. benthamiana phenocopies the branching defect, while heterologous complementation of the Arabidopsis max1 mutant confirms its conserved function; moreover, complementation of the ntmbd1 mutant restores normal architecture and biomass traits. Collectively, these findings reveal NtMBD1 as a key regulator of branching and plant architecture, providing new insights into its molecular and evolutionary roles and offering potential applications in crop improvement and sustainable bioenergy development.

Abstract The tumor microenvironment (TME) actively contributes to pancreatic ductal adenocarcinoma (PDAC) pathogenesis through dynamic bidirectional tumor–stroma interactions. In this study, we demonstrated that ATM-deficient tumor epithelium reprograms the TME in a genotype-specific manner to enhance cancer aggressiveness. In genetically engineered mouse models, pancreatic stellate cell and cancer-associated fibroblast (CAF) coculture systems, single-nucleus multiomics, and human PDAC models, tumoral loss of ATM serine/threonine kinase drove CAFs toward αSMA+ myofibroblastic (myCAF) differentiation, independently of p53 status. The myCAFs, in turn, promoted cancer aggressiveness and chemoresistance. Mechanistically, ATM deficiency increased reactive oxygen species and contractility signaling, enhancing TGFβ1 secretion. Pharmacologic TGFβ inhibition reversed myCAF differentiation, sensitized tumors to chemotherapy, and impaired tumor progression in both murine and human ATM-null models. These findings reveal that ATM-deficient tumors shape a cancer-promoting niche via TGFβ signaling and identify dual targeting of intrinsic and extrinsic vulnerabilities as a promising precision oncology strategy. Significance: TGF-β-driven myofibroblastic stromal differentiation in ATM-deficient pancreatic cancer generates a genotype-specific tumor microenvironment, providing a targetable axis and highlighting the need to integrate epithelial genotype and stromal context in pancreatic cancer therapy.

Thoracic aortic dissection (TAD) is a life-threatening vascular pathology with limited therapeutic options. The role of the small molecule STF083010, a novel IRE1α RNase-specific inhibitor, in TAD has not yet been defined. We aimed to target the IRE1α-XBP1s axis pharmacologically using STF083010, and evaluate its therapeutic potential in the occurrence and progression of TAD. Using a β-aminopropionitrile monofumarate (BAPN)-induced murine TAD model combined with interleukin 1β (IL1β)-stimulated vascular smooth muscle cells (VSMCs), we systematically evaluated the effects of STF083010 on the development of TAD as well as VSMCs' phenotypic switching and vascular inflammation. Our study reveals that STF083010 administration significantly attenuates TAD formation in vivo. Furthermore, we identified STF083010 confers VSMCs with resistance to IL1β-induced VSMCs inflammation and phenotypic switching. Mechanistically, STF083010 restrains IRE1α-XBP1s axis and suppresses NLRP3 inflammasome activation-dependent pyroptosis, further inhibiting VSMCs phenotypic switching and inflammatory activation, and eventually alleviates the progress of TAD. Our findings establish STF083010 as a potential molecule drug for the prevention of TAD and provide mechanistic insights for developing innovative therapies in aortic pathologies.

FERONIA (FER) receptor kinase is a critical regulator in balancing plant growth and stress responses. As an active kinase, FER phosphorylates many proteins to regulate their stability, nuclear accumulation, and condensation in diverse biological processes. Phytochrome B (phyB) is a thermosensitive red/far-red photoreceptor that can switch between an inactive Pr and an active Pfr conformer via light-dependent interconversion and temperature-dependent Pfr-to-Pr thermal reversion (Pfr-to-Pr). The phyB N-terminal extension (NTE, aa1–90) plays an essential role in stabilizing Pfr, and NTE phosphorylation at multiple sites can decrease Pfr stability, thereby serving as a critical control for light sensitivity. However, direct experimental demonstration of kinase(s) responsible for NTE phosphorylation and their site specificity is lacking. Here we show that FER phosphorylates Ser24 and Ser25 of phyB NTE. Genetic analysis demonstrates that FER modulates phyB-mediated responses to red light and temperature. While the fer-4 mutant is hypersensitive to red light-inhibited hypocotyl growth and less sensitive to warm temperature-induced hypocotyl elongation, the fer-4 phyB-9 double mutant largely mimics phyB-9 , supporting a function of FER to tune down phyB activity via NTE phosphorylation. Consistently, phosphosite mutational analysis showed that phosphorylation at Ser24 and Ser25 destabilizes phyB Pfr by accelerating thermal reversion and reduces phyB photobody formation and signaling output. Together, these results reveal a direct link between FER and phyB, in which FER phosphorylates Ser24 and Ser25 of phyB NTE to fine-tune light and temperature responses.

A novel Gram-stain-positive, rod-shaped bacterium with peritrichous flagella, designated C159T, was isolated from tomato rhizosphere soil. Growth of strain C159T occurred at 4-45 °C, pH 6.0-10.0 and in the presence of 0-5% NaCl. Based on 16S rRNA gene sequence analysis, strain C159T belongs to the genus Pseudoneobacillus and has a sequence similarity of 98.70% with Pseudoneobacillus rhizosphaerae JJ-79T. The whole genome of strain C159T was 4.65 Mb, with a DNA G+C content of 38.65 mol%. The average nucleotide identity between strain C159T and P. rhizosphaerae JJ-79T was 75.31%, and the digital DNA-DNA hybridization value was 19.6%, supporting its designation as a novel species of the genus Pseudoneobacillus. The major respiratory quinone of strain C159T was menaquinone 7; the major fatty acids were iso-C14:0, iso-C15:0 and anteiso-C15:0; and the major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on its phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain C159T represents a novel species in the genus Pseudoneobacillus, for which the name Pseudoneobacillus rhizolycopersici sp. nov. is proposed. The type strain is C159T (=GDMCC 1.5552T=KCTC 43820T). In addition, strain C159T possesses the ability to produce indole-3-acetic acid (33.72 mg·l-1) and to mineralize insoluble organic phosphorus. In a pot experiment, this strain demonstrated a plant growth-promoting effect of 22.68-44.49% and a disease suppression efficacy of 89.29% against bacterial wilt of tomato caused by Ralstonia solanacearum. The above results confirm that strain C159T is a novel multifunctional rhizobacterium for the biocontrol of tomato bacterial wilt.

Background Osteoarthritis (OA) is characterized by persistent inflammation, extracellular matrix (ECM) degradation, and impaired autophagy. Corilagin is a natural ellagitannin with anti-inflammatory properties, but its effects on OA remain unclear. Methods IL-1β-stimulated primary mouse chondrocytes were used to evaluate the effects of Corilagin on cell viability, ECM metabolism, inflammation, signaling pathways, and autophagic flux. Transcriptomic analysis and the autophagy inhibitor 3-methyladenine (3-MA) were used to investigate the underlying mechanisms. Therapeutic efficacy was further assessed in a destabilization of the medial meniscus-induced mouse OA model. Results Corilagin restored chondrocyte proliferation and increased Aggrecan, collagen II, and SOX9 expression while reducing MMP3, MMP13, iNOS, and COX2 levels. Mechanistically, Corilagin inhibited PI3K/AKT/mTOR and NF-κB signaling, reduced p65 nuclear translocation, and restored autophagic flux, as evidenced by increased Beclin-1 and LC3 II/I levels and decreased p62 accumulation. 3-MA partially abolished these protective effects. In vivo, intra-articular Corilagin administration reduced osteophyte formation, cartilage erosion, proteoglycan loss, OARSI scores, and MMP13 and p62 expression, while restoring Aggrecan expression. Conclusion Corilagin alleviates experimental OA by suppressing inflammatory and catabolic responses and restoring autophagy through inhibition of the NF-κB and PI3K/AKT/mTOR pathways.

Abstract Intraflagellar transport (IFT) is essential for cilia, and its dysfunction drives ciliopathies and systemic ageing. However, the in vivo dynamics of individual components in the IFT complexes remain obscured, leaving the mechanisms of age-dependent IFT failure largely unknown. Here, we report a dual-color super-resolution imaging strategy to dissect the structural integrity and kinetics of IFT trains in the sensory cilia of young and aged Caenorhabditis elegans . We show that IFT complexes are not static entities. Instead, distinct components undergo dynamic dissociation within IFT trains. This intra-complex dissociation causes a remarkable reduction in IFT velocity and is significantly exacerbated in the cilia of aged worms. Mechanistically, we identify the conserved TRiC/CCT chaperonin complex and daf-19 /RFX, the master transcription factor driving IFT genes, as critical regulators of IFT stability. We demonstrate that their age-dependent downregulation drives the progressive IFT component dissociation. Our findings re-frame the IFT complex as a highly dynamic assembly, uncover a new dimension of IFT regulation, and identify the progressive uncoupling of IFT components as a key driver of ciliary dysfunction during ageing.

Covalent organic frameworks are a class of crystalline porous polymers with well-defined skeletons and ordered pores, making them attractive for structural design and synthesis. Progress in chemistry over the past two decades has greatly enabled our capability of designed synthesis of framework materials. However, a key fundamental issue that how reaction systems select a specific topology from isomers and what structural parameters determine the formation of the topology remains unclear. Here, we unveil a feasible design strategy for the selective formation of polygonal topology in the framework synthesis. We focused on tetragonal and Kagome topologies as they are the most challenging topology isomers to be selectively synthesized. We observed that electron-deficient monomers form Kagome frameworks and electron-rich units produce tetragonal skeletons. This finding provides the structural guidance for de novo synthesis of Kagome and tetragonal frameworks selectively. Remarkably, the framework topology exerts profound electronic effects on photoconductivity and photocatalytic activity, leading to the finding of exceptional hydrogen evolution systems.

Phosphorus (P) availability in acidic red soils is primarily driven by phosphate-solubilizing bacteria (PSB), particularly those harboring the phoD and pqqC genes. However, the differential effect of soil pH on the community structure, interaction networks, and functional contributions of these two key PSB taxa remains unclear. In this study, we analyzed soil chemical properties as well as PSB abundance and community across typical acidic red soil regions. Our findings revealed that soil pH was the sole edaphic factor significantly correlated with the absolute abundance of both phoD and pqqC genes, showing a positive correlation with phoD but a negative correlation with pqqC. Redundancy analysis showed that the phoD-harboring community was influenced by a broader set of soil chemical properties, while the pqqC-harboring community was more exclusively and strongly shaped by pH and specific P fractions. Co-occurrence network analysis further demonstrated that non-acidic conditions (pH >= 5.5) promoted more complex and stable networks for the phoD-harboring community, whereas acidic conditions (pH < 5.5) intensified connectivity within the pqqC-harboring community. Random forest analysis revealed that pqqC-harboring bacteria explained a substantially greater proportion of available P (AP) variation (an incremental contribution of 14.72%) than did phoD-harboring bacteria (an incremental contribution of 3.50%). Further, core pqqC-harboring species belonging to the phylum Actinomycetota, particularly the genus Trebonia, were strongly positively correlated with AP content. In conclusion, our study suggests an association between pqqC-harboring bacteria (particularly Actinomycetota) and phosphorus availability in acidic red soils, offering a basis for targeted screening of PSB to improve soil fertility.

Abstract Photobodies (PBs) are phytochrome B (phyB)-organized nuclear condensates that nucleate at defined subnuclear seeding sites and decrease in number with warming. How cells set PB number—and, more broadly, condensate number—remains poorly understood. Here we show that phyB’s output module (OPM) functions as a universal nucleator for all site-defined PB types, whereas the photosensory module (PSM) attenuates this activity, enabling environmental control. Consistently, missense substitutions in OPM genetically separate intrinsic nucleation potency from PSM-mediated regulation. Unexpectedly, the constitutively active phyB Y276H allele defines a hypoactive nucleation state, supporting graded active conformations with distinct nucleation potency. Temperature tunes PB number through two separable inputs—phyB thermal reversion (nucleator state) and temperature-responsive seeding-site efficacy—whose contributions vary across sites and cell types. Together, these results distinguish nucleation control (number) from growth control (size) and show that condensate number is jointly determined by nucleator state and seeding-site efficacy.

Rotator cuff injuries are a common cause of shoulder pain with limited treatment options. Recent studies highlight inflammation's role in tendinopathy. GLP-1R agonists have shown anti-inflammatory effects in various diseases, but their role in rotator cuff injuries is unclear. This study investigates Liraglutide's (LIRA) effects on tendon cell inflammation, apoptosis, and endoplasmic reticulum stress in vitro and its therapeutic effects on rat rotator cuff repair in vivo. LIRA significantly inhibits IL-1β-induced inflammation, enhances tendon cell anabolism, and upregulates the AMPK/SIRT1 pathway. Mechanistically, GLP-1R interacts with SIRT1 to prevent tendon cell apoptosis and endoplasmic reticulum stress. LIRA effectively promotes tissue regeneration and restores biomechanical strength in a rat rotator cuff injury model. These findings suggest LIRA's therapeutic potential for rotator cuff repair and highlight GLP-1R activation as a key mechanism.

Organic solvent nanofiltration (OSN) requires membranes to have exquisite pore structures and excellent solvent resistance to alter energy-intensive separation processes. Here, we report a scalable “living nanosheet” strategy for synthesizing covalent organic framework (COF) membranes with robust laminar structures. COF nanosheets and residual monomers are collectively cast onto smooth substrates, followed by heating in an enclosed environment. The slow shear-flows make COF nanosheets accurately aligned into laminar structures while avoiding possible distortion. The COF nanosheets are still “living”, so that they can continue to react with remaining monomers upon heating, further healing the intercrystalline defects and stabilizing the laminar membranes. This strategy allows upscalable preparation of membranes with a large area of up to 600 cm 2 . The resulting COF membranes exhibit ultrahigh permeability (1.1 × 10 4  L m −2 h −1 bar −1 nm for methanol) and a sharp molecular weight cutoff (360 Da), outperforming state-of-the-art OSN membranes. Notably, it achieves a sharp and durable separation process of photosensitizers (e.g., 98.3% rejection of TMPyP4 tosylate) and >92% solvent recovery. This work establishes a versatile approach for scalable synthesis of COF membranes, enabling energy-efficient molecular separations in pharmaceutical and chemical industries.

Objective To study the effect of CCR1 and its ligands on macrophage polarization and evaluate its effect on chondrocytes in relieving the progression of osteoarthritis. Methods: RAW cells were polarized to M1/M2 subtype, and then different concentrations of BX471 were added to selectively inhibit CCR1. The polarization of the cells was detected by RT-qPCR, immunofluorescence and flow cytometry. CCL5 and CCL7 genes were silenced by SiRNA and its role in macrophage polarization was analyzed. Macrophage conditioned medium was further used to stimulate chondrocytes. Histological observation was carried out on models of medial meniscus (DMM) with or without BX471 treatment. Results: We found that blocking of CCR1 and silencing of its ligand, CCL5 and CCL7, reduced the polarization of M1 macrophages. In terms of mechanism, we found that blocking CCR1 could reduce the activation of NF-κB pathway and inhibit the phosphorylation of IKK, IκBα and P65. In addition, blocking of CCR1 could also reduce cartilage injury induced by macrophage conditioned medium. In vivo, blocking of CCR1 reduced the infiltration and accumulation of M1 macrophages and alleviated articular cartilage injury. Conclusion: CCL5/CCL7-CCR1 axis was involved in macrophage polarization, and blocking it could reduce synovitis and alleviate the process of OA.

Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises serious privacy concerns. Here we introduce FedProt, the first privacy-preserving tool for collaborative differential protein abundance analysis of distributed data, which utilizes federated learning and additive secret sharing. In the absence of a multicenter patient-derived dataset for evaluation, we created two: one at five centers from E. coli experiments and one at three centers from human serum. Evaluations using these datasets confirm that FedProt achieves accuracy equivalent to the DEqMS method applied to pooled data, with completely negligible absolute differences no greater than 4 × 10 −12 . By contrast, −log 10 P computed by the most accurate meta-analysis methods diverged from the centralized analysis results by up to 25–26.

Polycyclic aromatic hydrocarbons (PAHs), recognized as teratogenic and carcinogenic pollutants, exhibit moderate-to-high acute toxicity and long-term detrimental effects on aquatic organisms. However, conventional monitoring methods often fail to detect early-stage sublethal impacts of PAHs, potentially due to limited disruption of intrinsic circadian rhythms during initial exposure periods. To investigate the physiological responses of aquatic species to PAHs, we employed real-time biomonitoring to evaluate metabolic alterations in juvenile zebrafish (Danio rerio), including oxygen consumption rate (OR), carbon dioxide excretion rate (CR), ammonia-nitrogen excretion rate (AE), respiratory quotient (RQ), and ammonia quotient (AQ), alongside their circadian rhythmicity under PAH exposure. Two representative PAHs, phenanthrene (Phe) and pyrene (Pyr), were tested at 10%×LC50(96 h) concentrations (Phe: 102 µg/mL; Pyr: 70.6 µg/mL) over a 7-day exposure period. Comparative analysis revealed significant PAH-induced suppression of OR and CR, while AE was markedly enhanced, resulting in elevated RQ and AQ. Despite these metabolic responses, circadian rhythms remained intact across all parameters. These findings indicate that PAHs induce transient metabolic dysregulation without perturbing core circadian mechanisms, highlighting the feasibility of zebrafish metabolic profiling as a sensitive tool for aquatic PAH monitoring.

Microbial communities perform myriad functions in various environments, including the mammalian gut. These functions are largely based on the metabolic activity of microbial communities, which arises from the individual members’ contributions and their interactions. However, microbial functions and interactions are often inferred from simplified systems such as pure or pairwise cultures. Larger communities, in particular, are mainly analysed by metagenomics and the activity is deduced from the genetic potential of their community members. Although these approaches allow detailed insights into compositions, pairwise interactions and potential functions, they neglect the complexities of microbial communities, as evident in higher-order relationships, competition outcomes and the regulatory influence of environmental factors and other community members. Here, we study a mouse gut community along a gradient of complexity - from monocultures, to in vitro communities, to the mouse gut, to probe how bacteria adapt metabolically to their biotic and abiotic environments. Using metaproteomics to analyze realized bacterial niches and metabolic modeling to infer community interactions, we found that bacteria substantially modify their carbon source usage, biosynthetic activities, and protein allocation when grown in communities versus isolation. Furthermore, communities themselves adapted to their growth environment, changing in functionality as well as in the metabolic network between members. Host-associated communities isolated from the mouse gut invested in resource acquisition and utilized a broader spectrum of carbon sources, resulting in a large increase of predicted interactions between them. Our findings demonstrate the remarkable adaptability of microbes and microbial communities across environmental contexts. This underscores the critical need to study microbiomes under near-natural conditions and incorporate context-specific data into functional analyses. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 865615 Deutsche Forschungsgemeinschaft, https://ror.org/018mejw64, 395357507, 390713860, INST 95/1435-1 FUGG

Obesity has emerged as a global health challenge, closely associated with multiple metabolic diseases, such as cardiovascular diseases, type 2 diabetes, and non-alcoholic fatty liver disease. The traditional “calories-in minus calories-out” paradigm is no longer sufficient to explain the heterogeneity of obesity; consequently, a growing body of research has turned its focus to epigenetic regulation—particularly chemical modifications at the RNA level. N6-methyladenosine (m6A) modification is one of the most abundant epigenetic modifications on RNA, which dynamically regulates the methylation reaction in specific sequences on mRNA through methyltransferases (writers), demethylases (erasers), and binding proteins (readers). Accumulating evidence in recent years has revealed that m6A modification plays a pivotal role in the pathogenesis and progression of obesity, particularly through its regulation of key biological processes, such as adipocyte differentiation, lipid metabolism, and energy homeostasis. Given its critical involvement in metabolic dysregulation, targeting m6A-related mechanisms may offer novel therapeutic avenues for obesity management. This review systematically summarizes the current understanding of m6A modification in obesity, elucidates its underlying molecular mechanisms, and evaluates its potential as a therapeutic target. By integrating recent advances in the field, we aim to provide new perspectives for the development of innovative strategies in obesity treatment.