Search Results (467)

Tubulins are essential cytoskeletal components involved in plant cell division and expansion, yet their evolutionary dynamics across plant lineages and potential roles in horticultural seed/kernel development remain insufficiently understood. Here, we identified 2535 tubulin-related genes from 97 plant genomes and performed an integrated phylogenomic analysis. Phylogenetic and synteny network analyses resolved four ancient clades, including α-, β-,γ-tubulin and FtsZ, all of which were predominantly subjected to purifying selection. The α- and β-tubulin subfamilies exhibited lineage-specific expansion in angiosperms, particularly in eudicots, and these expansions were associated with ancient WGD and WGT events while retaining relatively conserved chromosomal contexts. By employing a pyramid-structured microsynteny framework across 12 Rosaceae genomes, we further traced the orthologous conservation and lineage-specific rearrangements of tubulin loci, with Prunus armeniaca as a reference. Spatiotemporal transcriptome profiling of Siberian apricot and kernel apricot revealed a group of tubulin genes highly expressed during key stages of kernel development, highlighting PaTUA1 as a priority candidate gene. Transient overexpression of PaTUA1 in wounded developing apricot kernels was associated with short-term increases in average phytohormone concentrations, including IAA, GA₃, BR, and cytokinins. Together, these results suggest that PaTUA1 represents a promising candidate gene associated with hormone-related responses during apricot kernel development, providing a basis for future functional validation rather than direct evidence of kernel-size determination. Full article

Although previous studies have indicated that heme oxygenase 1 (HO1/HY1) regulates the flowering time via the photoperiod pathway, the specific mechanism is still elusive. Here, we found that the Arabidopsis hy1-100 mutant displayed early flowering, and the characteristic expression patterns of several master genes involved in the autonomous pathway were altered. Notably, the transcript levels of FLOWERING LOCUS C (AtFLC) gene declined developmentally in both wild-type and hy1-100 mutant, with a more pronounced fold reduction observed in the mutant. Genetic evidence further underlined that hy1-100/FLCOE plants partially reversed the early flowering phenomenon of hy1-100 mutant, suggesting that AtHO1 regulated flowering at least partially through the AtFLC-involved autonomous pathway, as supported by changes in FLOWERING LOCUS T (AtFT) and SUPPRESSOR OF OVEREXPRESSION OF CO1 (AtSOC1) transcripts. Further analysis of hy1-100/ft mutants revealed that hy1-100/ft and ft mutants displayed similar late flowering phenotypes, accompanied by downregulated APETALA1 (AtAP1) and AtSOC1, indicating that AtFT played a crucial role in AtHO1-regulated flowering. Two key conclusions are drawn: first, the loss of AtHO1 function promotes early flowering in Arabidopsis, which was genetically linked to the autonomous pathway regulating AtFLC expression; second, AtFT was an essential downstream factor mediating AtHO1-regulated flowering. Full article

Lentiviral vectors (LVs) are indispensable tools in cell and gene therapy. Rising demand has created a global shortage of LVs, driving the development of novel packaging approaches. We report a novel vector packaging approach using autonomously replicating cytoplasmic RNAs (replicons) to express packaging proteins. Yellow fever virus (YFV) was used as a source of replicons encoding the HIV-1 Gag–Pol polyprotein together with reporter or selectable markers. YFV replicons were able to establish chronic infection in HEK293FT cells. Replicons expressing HIV-1 Gag–Pol containing the wild-type HIV-1 protease caused strong cytotoxicity, which prevented the selection of polyclonal cell pools harboring the replicon. In contrast, a replicon carrying the T26S mutation in the HIV-1 protease gene showed no measurable cytotoxic effects, enabling the generation of stable replicon-containing cell pools. The replicon cell pools were established using antibiotic selection and maintained Gag-Pol expression for at least ten passages under selection pressure. Using these first-generation replicon cell pools as packaging cells, LV production required only transient transfection of a transfer vector, a Tat/Rev plasmid, and an envelope plasmid. Yields reached ~10⁶ TU/mL prior to concentration and ~10⁹ TU from multilayer cell stacks, which fall within the range typically reported for conventional transient transfection systems under similar culture conditions. The resulting vectors efficiently transduced target cells, and no replication-competent lentivirus (RCL) was detected using a two-phase RCL assay with p24 ELISA detection. This demonstrator platform utilizing replicon cell pools represents a novel approach for LV packaging. Full article

Choy Sum (Brassica rapa subsp. chinensis var. parachinensis), also known as flowering Chinese cabbage, is an important stalk vegetable in Asia. However, the unique regulatory mechanism governing its “easy-bolting yet susceptible to premature bolting” trait remains poorly understood. The phosphatidyl ethanolamine-binding protein (PEBP) family serves as a central regulator of bolting, flowering, and growth development in plants. But this gene family has not been systematically identified and studied in Choy Sum yet. Therefore, this study systematically identified and analyzed the members of the PEBP gene family in Choy Sum using bioinformatics, transcriptomics, real-time fluorescence quantification, subcellular localization, and transgenic techniques. A total of 12 BcPEBP genes were identified and categorized into three subfamilies: FT-like, TFL1-like, and MFT-like. Phylogenomic analyses revealed family expansion through whole-genome duplication with strong purifying selection. Most members have highly conserved core motifs and gene structures. Protein sequence alignment showed that BcFT-2 and BcTFL-2 underwent non-synonymous mutations at key residues. The analysis of cis-acting elements suggests that the BcPEBP gene may be influenced by complex hormone and light regulatory networks. Expression profiling demonstrated leaf-specific upregulation of BcFT-1/2 during development and shoot apices-predominant expression of BcTFL1 genes, and the expression between homologous genes of BcTFL1-1/3 is more refined. Subcellular localization confirmed dual nuclear and plasma membrane targeting of BcFT-1/2 proteins. Overexpression of BcFT-1/2 in transgenic Arabidopsis promotes flowering. These findings establish BcPEBP genes as key bolting regulators and provide molecular targets for breeding-improved varieties. Full article

Nitzschia sp., a diatom isolated from Paposo (Antofagasta, northern Chile), was evaluated as a biological solution for removing kaolinite-type clay minerals from recycled process water in large-scale copper mining. Optimization of culture conditions to maximize extracellular polymeric substance (EPS) production revealed that supplementing with 0.1 gL⁻¹ of glucose yielded the highest EPS levels on day 17, reaching 1285 ± 58.9 mgL⁻¹ (control equal to 237.8 ± 34 mgL⁻¹ on day 17). However, maximum dry weight biomass productivity was achieved in the presence of sodium carbonate at a concentration of 1 gL⁻¹ (319 ± 12.5 mgL⁻¹d⁻¹), significantly exceeding the productivity of the control group (242.7 ± 5.4 mgL⁻¹d⁻¹). Notably, low glucose supplementation enhanced EPS synthesis. Application of control-derived EPS of 1 gL⁻¹ rapidly decreased kaolinite initial turbidity from ~2024 FNU to ~354 ± 0.74 FNU within one minute. Even more glucose-derived EPS (1 gL⁻¹) further reduced turbidity to ~22.2 ± 0.1 FNU at 5 min, achieving a flocculation efficiency of ~98.9% after 15 min. Genomic analysis and KEGG annotation identified abundant genes for EPS and carbohydrate metabolism, including numerous glycosyltransferases, glycoside hydrolases, and multiple copies of UDP-glucose 4-epimerase, consistent with strong polysaccharide-biosynthesis capacity. Physicochemical characterization (particle sizing, HPLC, SEM, zeta-potential and FT-IR) showed EPS comprised mainly of rhamnose, fucose, arabinose, xylose and glucose, featuring functional groups (–OH, C=O/COO–, O-acetyl, uronic/guluronic signatures) that interact with kaolinite to promote aggregation. These findings demonstrate that Nitzschia-derived EPS, especially from glucose-supplemented cultures, represent promising sustainable bioflocculants for treating kaolinite-contaminated recycled water in mining operations. Full article

As plant factories with artificial lighting (PFALs) expand beyond leafy greens to include flowering crops, understanding the role of light quantity and quality in regulating plant development becomes increasingly important. This study investigated how far-red (FR) radiation and daily light integral (DLI) influences flowering time, plant morphology, and FLOWERING LOCUS T (FT) gene expression in petunia. Four facultative commercial cultivars and one obligate long-day model cultivar, ‘Mitchell Diploid’, were grown under two DLI conditions with a gradient of FR radiation. Increasing FR consistently accelerated flowering across both DLI conditions without reducing flower bud number, branch number, or shoot fresh weight at harvest. Higher DLI generally produced more compact plants by reducing plant height and canopy area, whereas increasing FR promoted stem elongation, particularly in ‘Mitchell Diploid’. Cultivar responses varied substantially, indicating that genotype is an important factor when applying FR-based lighting strategies. To explore potential molecular mechanisms associated with FR-induced flowering acceleration, the expression levels of five petunia homologs, PhFT1 to PhFT5, were analyzed across developmental stages under low and supplemental FR conditions. PhFT2-5 expression was generally associated with flower initiation, with PhFT2 showing the strongest positive relationship with flowering and responsiveness to supplemental FR, whereas PhFT1 showed a decreasing trend over time and was not positively associated with flowering. Overall, this study demonstrates that FR radiation can be used to accelerate petunia flowering in PFAL production without compromising key quality traits and suggests that specific FT homologs, particularly PhFT2, may contribute to FR-mediated flowering regulation. Full article

To investigate the coordinated role of RALF1 and eIF4E1 within the FER signaling module in regulating root hair elongation and stress responses in Arabidopsis thaliana, we constructed a ralf1/eif4e1 double mutant via conventional hybridization. Although the roles of the RALF1 and eIF4E1 genes are well known, the simultaneous absence of them remains poorly characterized. The double mutant exhibited significantly reduced root hair numbers and elongation and heightened sensitivity to ABA, Cd²⁺, and NaCl stress. The ralf1/eif4e1 double mutant exhibited delayed flowering time and higher numbers of rosette leaves. Fluorescence quantitative PCR analyses revealed that several key genes involved in regulating flowering such as FT, LFY and SOC reached maximum levels in wild-type plants. However, other genes that regulated floral meristem exhibited higher expression levels in the ralf1 mutant, followed by in wild-type plants. This work provides new insight into the RALF1-FERONIA-eIF4E1 module, demonstrating that it converges environmental cues to coordinately regulate root hair elongation, stress responses, and flowering time in Arabidopsis. Full article

The immunomodulatory potential of natural polysaccharides is often limited by their structural complexity and high molecular weight. In this study, DFIP-A3-1 (M_w = 8.68 × 10³ g/mol) was obtained from the leaves of Isatis indigotica Fort. by ultrafiltration, DEAE-650M, and Sephadex G-100 chromatography, followed by acid degradation. Fortunately, DFIP-A3-1 exhibited the most potent immunostimulatory activity in vitro. HPGPC, HPSEC-MALLS-RID, GC-MS, FT-IR, Congo red tests, SEM, and AFM were used to characterize their structure, and 1D/2D NMR was used for further investigation of DFIP-A3-1 for in-depth structural clarification. DFIP-A3-1 was primarily composed of Rha and Gal. Based on methylation and NMR analyses, the structure of DFIP-A3-1 was elucidated as follows: →1)-β-Galp-(4→1,4)-α-Rhap-(2→1,4)-α-Rhap-(2→1)-β-Galp-(6→1)-β-Galp-(6→1,6)-β-Galp-(3→1,6)-β-Galp-(3→. Furthermore, DFIP-A3-1 was found to exhibit a triple-helix conformation. DFIP-A3-1 markedly upregulated the secretion of NO, IL-6, and TNF-α and enhanced the mRNA expression levels of their related genes in RAW 264.7 cells. Moreover, DFIP-A3-1 activated p-IκBα, p-p65, and TLR4, while co-treatment with TAK-242 markedly suppressed the expression of these pathway-related proteins. All of the aforementioned findings suggested that DFIP-A3-1 is a promising natural immunomodulatory drug deserving of additional research and use. Full article

5-Fluorouracil (5-FU) is a cornerstone chemotherapeutic agent that is extensively utilized in the management of malignancies; however, its clinical utility is constrained by its narrow therapeutic index and dose-limiting toxicities. The study aimed to study the hepato-nephroprotective effects of epigallocatechin gallate (EGCG) and EGCG mediated selenium nanoparticles and their effect in mitigating the toxicity induced by 5-FU. EGCG-functionalized selenium nanoparticles (EGCG-SeNPs) were produced by mixing sodium selenite, with EGCG acting as both the reducing and stabilizing agent. Nanoparticles were characterized using UV-vis spectroscopy, FT-IR, dynamic light scattering, zeta potential analysis, and transmission electron microscopy. 35 adult rats were randomly assigned to control, 5-FU, 5-FU + Na₂SeO₃, 5-FU + EGCG, and 5-FU + EGCG-SeNPs groups. Hepatorenal toxicity was induced by intraperitoneal 5-FU administration during the final five days of the experiment. Serum biochemical markers, tissue oxidative stress, antioxidant enzyme, inflammatory cytokine levels, and apoptosis-related gene expression were evaluated. Immunohistochemical analysis of Nrf2 and Keap1 and histopathological examination of tissues were performed. 5-FU induced severe hepatorenal toxicity, evidenced by marked elevations in liver and kidney function biomarkers, excessive oxidative stress, inflammatory cytokine overproduction, NF-κB activation, and apoptotic signaling. Treatment with EGCG-SeNPs markedly ameliorated 5-FU-induced hepatic and renal dysfunction, restoring liver enzyme and kidney biomarker levels to near-normal levels more effectively than EGCG or sodium selenite alone. EGCG-SeNPs significantly suppressed lipid peroxidation, NGAL, and inflammatory mediators while robustly enhancing antioxidant defenses and activating the Nrf2/HO-1 pathway with concomitant Keap-1 downregulation, strongly inhibited NF-κB signaling, normalized cytokine balance, reduced poly (ADP-ribose) (PAR) activation, and attenuated apoptosis. EGCG–SeNPs confer superior protection against 5-FU–induced hepatorenal toxicity compared to EGCG or inorganic selenium alone. The potent protective effects of EGCG–SeNPs are mediated through coordinated antioxidant, anti-inflammatory, and anti-apoptotic mechanisms, primarily via activation of the Nrf2/HO-1 axis and suppression of NF-κB signaling. Full article

Chinese cabbage is one of the major vegetable crops in northern Asia. Its leaves are the major organ for photosynthesis and production, and leaf color directly influences its yield and quality. Here, we obtained a pale green mutant pgm3. This mutant line was derived from EMS mutagenesis of Chinese cabbage DH line FT. pgm3 exhibited chlorosis and etiolation, delayed growth, reduced photosynthetic pigment content and net photosynthetic rates, and impaired development of the chloroplast inner membrane system. Genetic analysis revealed that the pale green phenotype was controlled by a single recessive nuclear gene, Brpgm3. Mutmap analysis indicated that Brpgm3 is located on a 13.9 Mb region in A03. Within this region, a single SNP (A03: 7194530) with an SNP-index of 1, located in BraA03g015750.3C (BrClpC1), was identified from 40 differential SNPs. KASP genotyping demonstrated that the SNP co-segregated with the pale green phenotype in the F₂ population. Sanger sequencing confirmed a G-to-A SNP in exon 4 of BrClpC1, which resulted in an amino acid substitution from S to G. Furthermore, multiple sequence alignment of homologs from 28 species demonstrated that this mutated residue is highly conserved. BrClpC1 was predominantly expressed in leaves and exhibited the highest transcript abundance among the nine members of the Class I Clp gene family in Brassica rapa. This is the first report identifying ClpC1 in Brassica crops. Our results not only confirmed BrClpC1 as a strong candidate gene for the pale green mutant of Chinese cabbage, but also highlighted BrClpC1 as a target for chloroplast biology research in Brassica crops. Full article

Background: Tartary buckwheat (Fagopyrum tataricum) serves as an excellent model for studying plant water adaptation mechanisms due to its exceptional drought tolerance. While aquaporins (AQPs) mediate the transmembrane transport of water and solutes in plants, their fine-tuned regulatory networks underlying stress resilience in Tartary buckwheat remain largely elusive. Methods: Here, we combined bioinformatics and transcriptomics to systematically identify 30 highly conserved FtAQP genes at the genome-wide level. Results: Cross-validated by qRT-PCR, our analysis revealed their distinct expression patterns across different organs. Based on our transcriptomic data, we hypothesize that FtAQP family members potentially participate in a coordinated whole-plant water management network through differential spatiotemporal expression. Specifically, the robust transcription of FtAQP8, FtAQP12, and FtAQP28 in roots is associated with the initial water uptake process. As water undergoes long-distance transport, the synergistic upregulation of FtAQP13, FtAQP17, FtAQP20, and FtAQP29 in the stem suggests a potential role in facilitating critical lateral water flow. Furthermore, during reproductive development, FtAQP27 exhibits extreme tissue specificity in floral organs, implying its possible involvement in maintaining local osmotic homeostasis. Furthermore, the promoter regions of FtAQPs are highly enriched with cis-acting elements responsive to light, abscisic acid (ABA), and cold stress, suggesting they are intimately regulated by a coupling of endogenous phytohormones and environmental cues. Conclusions: Ultimately, this study provides valuable insights into the potential molecular basis of multidimensional water regulation in Tartary buckwheat, and identifies candidate genetic targets for improving water use efficiency in dryland agriculture through the precise manipulation of aquaporins. Collectively, while these observational findings provide valuable predictive models, future in vivo experimental validations are required to confirm their exact biological functions. Full article

IQ67-domain (IQD) proteins are plant-specific calmodulin (CaM)/calmodulin-like (CML) targets implicated in the spatial organization of Ca²⁺ signaling, yet their roles in tartary buckwheat (Fagopyrum tataricum) remain largely unexplored. Here, we identified 24 FtIQD genes and classified them into six phylogenetic subfamilies. FtIQDs show uneven chromosomal distribution and mainly arise from segmental duplication under purifying selection. Promoter analysis revealed the enrichment of MYB-, light-, and ABA-related cis-elements. To link FtIQDs with rutin variation, we performed an FtIQD-focused association analysis using whole-genome resequencing data from altitude-stratified panels of up to 220 accessions. Under additive, dominant, and recessive models, multiple significant SNPs (p < 1 × 10⁻⁵) were detected near a subset of FtIQD loci, showing clear model- and environment-dependent patterns. Recurrent loci included FtIQD22, FtIQD02, FtIQD16, and FtIQD19. RNA-seq under PEG-induced drought stress, tissue expression patterns, pathway co-expression, and qRT–PCR further prioritized FtIQD19. FtIQD19–GFP showed predominant nuclear localization with additional filamentous/peripheral signals, and yeast two-hybrid assays identified FtCaM7.2 as the strongest interactor among representative CaMs. Structural modeling of the FtIQD19–FtCaM7.2 complex suggested testable residue-level interaction features. Collectively, this work provides a foundational FtIQD resource and highlights candidate Ca²⁺/CaM–IQD modules potentially associated with altitude-dependent rutin variation in tartary buckwheat. Full article

Environmental pH plays a critical role in microbial fermentation processes. Weizmannia coagulans attracts particular attention for exceptional acid tolerance and lactic acid productivity. Yet acidic stress impacts on its cell division regulation remain unclear. Here, a critical pH value (pH 4.20) for growth inhibition of the Gram-positive bacterium Weizmannia coagulans strain BC99 was first established. Transcriptomic analysis of metabolic pathways was then performed. The multi-layered regulatory network underlying acid stress-induced cell division was elucidated. Integrated transcriptomic and physiological analyses reveal that acid stress triggers multigene expression reprogramming. This drives core metabolic network reorganization, coordinately regulating division processes. RNA-seq analysis demonstrated acid stress triggered differential expression of division genes (FtsZ/Q downregulation), ATP synthase suppression, and peptidoglycan transport reduction, while enhancing membrane rigidification (Cfa) and magnesium homeostasis (CorA). The PhoPR dual-component system emerged as a central regulator, inhibiting septal assembly via RipA hydrolase and RpsU ribosomal suppression while rerouting carbon flux to glycolysis, elucidating bacterial acid adaptation mechanisms. Collectively, these adaptive changes prioritize cell survival over active proliferation under acidic conditions. This study provides molecular insights into how W. coagulans preserves viability under acid stress, offering a theoretical basis for optimizing its performance in probiotic applications. Full article

Soybean (Glycine max) is a critically important crop for oil, protein, feed, and food security in China. Expanding soybean cultivation into high-latitude regions represents one of the most direct and effective strategies to increase total production. In the present study, we employed KASP (Kompetitive Allele-Specific PCR) marker technology to systematically analyze 18 variant loci across 14 flowering-time genes in 443 soybean germplasm accessions adapted to high-latitude conditions in Arctic Village (Beiji Cun), Mohe City (>53° N), northeastern China. Our results revealed clear functional-tier-dependent selection gradients: key mutation sites (frequency > 96%) in upstream photoreceptors and core circadian clock genes, such as E2 and GmPRR3a, were nearly fixed in the population, whereas downstream flowering genes such as GmFT5b and GmFT2b remained under dynamic selection. Combinatorial analysis of early-maturity allelic variants identified 178 distinct genotype combinations, including six dominant types (n ≥ 10). Field phenotypic analysis demonstrated that the cumulative number of early-maturity alleles was significantly negatively correlated with flowering time, with specific allele combinations such as FT5a^A + FKF1b-hap3^T exhibiting particularly strong flower-promoting effects. A set of 80 highly enriched super-early-maturity accessions, including extreme materials such as MHL22002, were identified, providing valuable genetic resources and a theoretical framework for elucidating the flowering regulatory mechanisms of high-latitude soybean and for breeding super-early-maturing varieties. Full article

Basalt fiber-reinforced concrete (BFRC) exhibits superior mechanical performance, durability, and environmental benefits, making it a promising material for promoting green and low-carbon construction. This study develops a novel multi-objective mix design optimization method for BFRC under cost and carbon emission constraints, presents a framework that considers tensile strength (f_t) as a core design objective, and establishes high-precision strength prediction models via gene expression programming (GEP). Material cost and carbon emission functions were formulated based on market data, while compressive strength (f_c) and tensile strength (f_t) prediction models were established using using GEP implemented in MATLAB 2018b with seven mix design variables, including cement dosage, aggregate parameters, and basalt fiber (BF) characteristics (diameter, length, and dosage). Multiple constraints covering material quantities, mix ratios, workability, and density were incorporated into the optimization model, which was solved via the non-dominated sorting genetic algorithm II (NSGA-II). The method identifies the optimal cement dosage, aggregate proportions, and BF dosage to maximize tensile strength (f_t) while minimizing cost and carbon emissions. Computational results suggest that within the target strength range of 30–60 MPa, the proposed design yields reductions of 10–20% in carbon emissions and 12–18% in costs compared to conventional methods, offering potential advantages for sustainable construction. Unlike existing multi-objective studies, which focus on compressive strength, this work addresses critical factors of tensile strength (f_t) and prediction inaccuracy, proposing a systematic low-carbon design framework for potential BFRC applications. Full article