Search Results (295)

Background: Safflower (Carthamus tinctorius L.) is a high-value economic crop with broad applications in agriculture, industry, and traditional medicine. Seed germination and seedling establishment are critical stages in the safflower life cycle, as they directly influence subsequent seedling establishment, survival, and plant growth. However, the transcriptomic dynamics and regulatory mechanisms underlying these processes remain largely unexplored, and the functional roles of long non-coding RNAs (lncRNAs) in this context are also poorly understood. Methods: In this study, transcriptome sequencing was performed across five developmental stages from seed germination to seedling establishment in safflower, followed by a comprehensive transcriptomic analysis and lncRNA identification. Results: Transcriptome sequencing identified a total of 3027 lncRNAs, including 940 natural antisense transcript (NAT)-pair-associated lncRNAs, which were classified into the divergent, convergent, and chimeric categories. Among these, 767 lncNATs were differentially expressed. Further analysis identified 542 NAT pairs in which both the protein-coding gene and its corresponding lncNAT exhibited a differential expression across the five developmental stages. A functional enrichment analysis of the predicted target genes of these lncRNAs suggested their involvement in photosynthesis and hormone-related responses. An enrichment analysis of differentially expressed genes (DEGs) across developmental stages further revealed the significant enrichment of photosynthesis and plant hormone signal transduction-related pathways, suggesting that these pathways are closely associated with safflower seed germination and seedling establishment. A further analysis of photosynthesis-related genes, particularly the expression patterns of LHC family members, suggested that Stage 3 may represent an important developmental transition associated with the optimization of the light-harvesting capacity during early seedling establishment, whereas plant-hormone-related genes are involved in regulating seed germination and subsequent leaf growth during seedling establishment. In addition, a weighted gene co-expression network analysis (WGCNA) identified candidate transcription factors associated with photomorphogenesis and plant hormone responses in safflower. Conclusions: This study advances our understanding of the regulatory mechanisms underlying safflower seed germination and subsequent growth and provides valuable molecular resources for future safflower breeding programs. Full article

Potato (Solanum tuberosum L.) is the world’s fourth-largest staple crop. Alkaline salt stress is a major abiotic stress factor that severely limits the growth, yield, and quality of potatoes; however, little is known about the molecular basis of potatoes’ response to alkaline salt stress or the stress-alleviation mechanism mediated by 24-epibrassinoside. In this study, we conducted a genome-wide identification of the potato miR482 family and analyzed its response patterns under alkaline salt stress and 24-epibrassinoside-mediated stress relief. We identified a total of 9 mature stu-miR482 sequences and 5 precursor sequences; all precursors form typical stable hairpin structures and exhibit high evolutionary conservation among Solanaceae plants. Promoter analysis revealed multiple cis-acting elements in the promoter region associated with light signaling, plant hormones, and stress signaling. A total of 64 potential target genes were predicted, encompassing transcription factors, disease resistance, and signal transduction-related genes, forming a complex regulatory network. Phenotypic analysis confirmed that EBR significantly alleviates the growth inhibition in potatoes induced by alkaline salt stress. qRT-PCR analysis indicated that stu-miR482a-5p is the primary stress-responsive member in leaves; stu-miR482d-3p/5p exhibited the strongest regulatory response to EBR in roots; in potato stolons, all members of the miR482 family were significantly upregulated under alkaline salt stress, with stu-miR482d-5p showing extremely significant upregulation across all treatment groups. In summary, this study represents the first systematic characterization of the potato miR482 family, revealing its tissue differential functions in alkaline salt stress and EBR-mediated stress relief. Full article

Protein kinases have key roles in cells as they regulate diverse signal transduction pathways. Mitogen-activated protein kinase (MAPK) signaling route modulates several processes, such as cell proliferation, cell programming, metabolic changes and stress responses. Within the group of proteins participating in this pathway, the MAPK kinase (MEK1) is a dimeric, 393-residue-long, dual-specificity protein kinase that phosphorylates both tyrosine and threonine residues. In this study, we explored the conformational changes occurring during the unfolding of MEK1, by using orthogonal biophysical techniques. Intrinsic fluorescence, extrinsic 8-anilinonapthalene-1-sulfonic acid (ANS) fluorescence, dynamic light scattering (DLS), and far-ultraviolet (UV) circular dichroism (CD) showed that the protein acquired a native-like conformation within a narrow pH range (8.0 to 9.0). Urea and guanidinium hydrochloride (GdmCl) denaturations followed by intrinsic and ANS fluorescence and far-UV CD, at pH 8.1, where the protein acquired a native-like conformation, showed that: (i) the apparent conformational stability of isolated MEK1 was low; and (ii) the unfolding occurred through the presence of intermediates. The presence of several unfolding intermediates was also evidenced through: (i) differential scanning calorimetry (DSC) in the absence of the ligand ATP; and (ii) unfolding simulations with the help of computational techniques based on constraint network analysis (CNA). We propose that the apparent low stability of this protein was related to its flexibility and modulates its ability to interact with diverse molecular partners. Full article

Ultraviolet (UV) light is emerging as an important tool for biosensing, biomedical signal readout, and dose monitoring because of its strong and selective interactions with nucleic acids, proteins, and other biological components. This review summarizes recent progress in UV sensing-guided biomedical systems, with emphasis on three interconnected directions: label-free and surface-weighted imaging, wearable and embedded UV dosimetry, and sensor-assisted therapeutic guidance. Representative examples include ultraviolet photoacoustic microscopy (UV-PAM) for label-free nuclear imaging, microscopy with ultraviolet surface excitation (MUSE) for rapid slide-free histology-like readout, epidermal and flexible UV dosimeters for skin-level exposure quantification, and UV therapeutic platforms that are increasingly supported by sensing, dosimetry, and feedback for safer dose delivery. Across these applications, we emphasize the shared biosensing principles of signal generation, optical or acoustic transduction, quantitative readout, calibration, and feedback-informed decision support. We also discuss the role of artificial intelligence in virtual staining, image enhancement, domain correction, dose prediction, and decision support. The review concludes with key translational challenges in standardization, uncertainty quantification, multimodal integration, and feedback-driven system design. Overall, this sensing-centered perspective helps define the role of UV technologies more clearly within biosensors-oriented biomedical engineering. Full article

Extending the fruiting season of Annona squamosa L. requires overcoming autumn and winter flowering declines. This study investigates the efficacy of light-quality regulation technologies and their temperature dependence for floral induction. Field surveys initially identified temperature as the primary climatic factor governing flowering. Under suboptimal autumn temperatures, red light (R-660) night-break (NB) treatments significantly enhanced shoot growth and flowering compared to other light spectra. Transcriptomic analysis revealed 2027 upregulated and 341 downregulated transcripts consistently regulated by R-660, with significant enrichment in the plant hormone signal transduction pathway. Furthermore, R-660 upregulated cold response genes (e.g., CBFs, WRKYs, ERD7), which are associated with the maintenance of vegetative vigor under suboptimal autumn temperatures. However, mid-winter R-660 NB failed to induce flowering without supplemental greenhouse heating. Ultimately, warm ambient temperature is the absolute prerequisite for A. squamosa floral induction, with R-660 serving as a highly effective seasonal supplement to extend autumn flowering. Full article

To investigate the differences in reactive oxygen species (ROS) metabolism and signal transduction between the illuminated and non-illuminated surfaces of mangoes exposed to red light, this study used “Tainong No.1” mangoes as the test material, setting up three groups: mango exposed to red light, mango without red light and mango in darkness. The study measured maturity physiological indicators, ROS content, antioxidant enzyme activity, non-enzymatic substances, and combinations with DIA proteomics analysis. The results showed that red light exposure promoted the overall ripening of mangoes, and there was almost no difference in ripening between mango exposed to red light and mango without red light. Red light mainly induced rapid accumulation of hydrogen peroxide in the peel of the irradiated area and stimulated the synthesis of superoxide anion in the pulp. The antioxidant capacity of both the irradiated and non-irradiated areas was enhanced. Key proteins in the ROS signaling pathways such as Rab11, LRK-RLK, and PIN3 were significantly upregulated. In summary, red light promotes synchronous ripening of mango fruits by coordinately regulating the ROS homeostasis of the tissue, and provides new insights into the use of light signals for regulating fruit metabolism. Full article

The tissue regeneration of sea cucumber (Apostichopus japonicus) involves precise intercellular signal pathway transduction and gene expression regulation. This study investigated the function of the Notch signaling pathway in A. japonicus papilla regeneration and its modulation by LED light of varying intensities. We detected the expression patterns of Notch signaling pathway-related genes and their downstream cell proliferation-related genes during papilla regeneration, and further verified the pathway function via gene silencing, combined with histological analyses to explore LED-mediated effects. Gene expression assays revealed that AjNotch, AjSu(H), AjHes1, AjCyclinA, AjCyclinD and AjCDK8 were significantly upregulated at 28 days post papilla excision (p < 0.05). LED light treatment accelerated papilla regeneration in a light intensity-dependent manner, with the most pronounced promotion at 2000 lx (p < 0.05). Moreover, LED light treatment was associated with altered expression of Notch signaling pathway genes and their downstream proliferation-related genes in a light intensity-dependent manner. Gene silencing of AjNotch significantly downregulated its downstream target genes (p < 0.05), attenuated the regenerative promotion of LED light, and reduced cell proliferation rate (p < 0.05). These findings suggest that the Notch signaling pathway is pivotal for A. japonicus papilla regeneration, and LED light modulates papilla regeneration with concurrent changes in the expression of Notch pathway-related genes. This study provides novel insights into the function of the Notch signaling pathway in echinoderm regenerative development. Full article

When in contact with microbes or other pathogens plants develop an induced defense response. This reaction is triggered by pathogen-derived molecules that provoke the so-called microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) or pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI). Recognition of a MAMP or PAMP by a pattern recognition receptor (PRR) activates rapid downstream signaling, manifested in, e.g., a rise in the cytosolic Ca²⁺ concentration. As a consequence, defense-related genes are expressed and antimicrobial substances are produced. There is also evidence that Ca²⁺-induced responses show a refractory behavior in plant cells, as the reaction to an identical stimulus applied shortly after the first one is strongly suppressed, if it can be observed at all. Subsequent elicitations over a longer period of time, on the other hand, can trigger stronger Ca²⁺ responses, which lead to so-called “defense priming”. Although refractory behavior has been documented in various plant cell types, its underlying function and causative mechanisms remain unclear. In this review article we give an overview of the refractory machinery, including elicitors, receptors, typical Ca²⁺ responses, and signal transduction pathways. We shed light on possible explanatory scenarios and address open questions. Full article

Light and drought antagonistically regulate stomatal movement, yet the mechanisms for integrating these conflicting signals remain unclear. In this study, the stomatal aperture and photosynthetic parameters under red light (RL), blue light (BL), and white light in different water regimes were evaluated. Transcriptome analysis was conducted during a 0–6 h period of BL exposure, with or without drought, to explore the molecular mechanisms underlying BL and drought-mediated stomatal movement. Under non-drought conditions, BL significantly enhanced stomatal conductance, transpiration rate, and stomatal aperture. After drought stress, BL-treated seedlings exhibited the greatest reductions in these indicators. Transcriptomic analysis revealed that both BL-responsive genes and drought-responsive genes were significantly enriched in overlapping pathways related to plant hormone signal transduction, and biological processes of water/fluid transport. Among these, the aquaporin gene CsPIP2;3 was identified as a core node in the crosstalk between BL and drought signals, and a potential key regulator of stomatal movement. Tissue-specific expression analysis showed its highest expression in mature leaves; GUS staining further confirmed its expression in guard cells and vascular bundles, while subcellular localization verified the plasma membrane localization of its encoded protein. The transcriptomic data provide novel insights into the mechanisms underlying stomatal movement regulated by BL and drought. Full article

C3H-type zinc finger proteins play essential roles in plant responses to abiotic stresses, as well as in the regulation of growth, development, and signal transduction. Birch (Betula platyphylla Suk.), an ecologically adaptable tree species widely distributed in northern regions, has not yet been systematically characterized for its C3H gene family. In this study, a total of 15 BpC3Hs were identified from a genome-wide analysis of birch. Their physiochemical properties, gene structures, conserved motifs and domains were systematically analyzed. Promoter analysis identified cis-acting elements associated with stress responses, hormone signaling, and developmental regulation. Transcriptome data further showed that most BpC3Hs were responsive to salt, drought, high/low-temperature stresses, and light/dark treatment, and showed differential expression patterns in tension wood and opposite wood. Additionally, they displayed stage-specific expression patterns during male inflorescence development. This study lays a foundation for future functional characterization of the C3H gene family in birch and its application in molecular breeding for stress resistance. Full article

(1) Background: The “Bider” marking refers to the symmetrical black stripes distributed on the shoulder blades of Dun Mongolian horses, representing an ancestral trait of significant genetic value. However, the molecular mechanisms underlying its formation remain unclear. This study aims to elucidate the molecular basis of these markings by comparing transcriptomic differences in skin tissues from variously pigmented areas of Mongolian horses’ “Bider” patterns. (2) Methods: Using three Dun Mongolian horses as subjects, skin tissue samples were collected from their shoulders (dark-marked and light-marked areas), dorsal midline, and croup regions for transcriptome sequencing. Differentially expressed genes were identified based on sequencing data, followed by Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Key findings were validated through quantitative reverse transcription polymerase chain reaction (qRT-PCR). (3) Results: The sequencing yielded approximately 893 million high-quality clean reads, with an overall alignment rate exceeding 96%. A total of 140 to 775 differentially expressed genes were identified. GO enrichment analysis revealed that these genes were significantly enriched in biological processes related to pigment metabolism, skin and hair follicle development, signal transduction (including calcium and cyclic guanosine monophosphate (cGMP) signaling), and immune regulation. KEGG analysis further indicated that multiple pathways closely associated with pigment regulation, including the calcium signaling pathway, tyrosine metabolism, cyclic adenosine monophosphate (cAMP) signaling pathway, and melanoma pathway, were significantly enriched across different tissue comparison groups, suggesting their potential key roles in coat color phenotype formation. The reliability of the sequencing data was corroborated by the results of qRT-PCR validation. (4) Conclusions: This study conducted a transcriptome analysis of skin samples from various pigmented regions of the Dun Mongolian horse’s Bider marking, revealing that the formation of this marking is associated with the differential expression of numerous genes and is co-regulated by multiple pigment-related signaling pathways. Full article

Plant cysteine oxidase (PCO) catalyzes the oxidation of cysteine residues in the N-degron pathway, thereby regulating the stability and activity of the seventh group of ethylene response factors (ERF-VII), which play a crucial role in reactive oxygen species (ROS)-mediated signal transduction. By regulating the degradation of ERF-VII, the PCO family genes control hormone signaling, which is highly valuable for plant growth and abiotic stress responses. However, systematic studies on PCO genes in Medicago sativa, a key forage legume, remain lacking. Herein, 35 MsPCO genes were identified from the alfalfa (Medicago sativa) genome, and their biological characteristics were comprehensively analyzed via bioinformatics approaches. The results showed that MsPCO genes are asymmetrically distributed across 18 chromosomes and clustered into 5 subgroups phylogenetically. Most MsPCO proteins are hydrophilic and localized in the cytoplasm. A total of 56 duplication events were detected, with most duplicated pairs undergoing purifying selection (Ka/Ks analysis). Collinearity analysis revealed close evolutionary relationships between Medicago sativa and Medicago truncatula, Arabidopsis thaliana or Glycine max. Promoter cis-acting elements in MsPCO genes are involved in light response, stress adaptation, hormone signaling, and growth regulation. Transcriptomic data indicated differential expression of MsPCO genes under abiotic stresses. MsPCO20 is dispersed throughout the cell membrane and nucleus, whereas MsPCO19 is localized to the nucleus, according to subcellular localization experiments. These findings provide candidate genes and a theoretical basis for further functional characterization of PCO genes in alfalfa. Full article

In the past two decades, important progress has allowed a better understanding of how light signals are perceived by plants, not only as a source of energy for photosynthesis but also as environmental cues that modulate growth, development, and stress responses. These advances open up promising prospects for light-based treatments in agriculture. This review synthesizes recent scientific findings on the application of specific wavelengths (from ultraviolet to infrared) to improve crop yield, quality, and resilience. The analysis focuses on controlled environment agriculture, where most experimental data have been generated and where the integration of lighting strategies is technically more feasible compared to open-field settings. Preharvest: we explore how spectral quality, intensity, and duration can be used to modulate plant growth, photosynthesis, defense pathways, and the accumulation of nutritional compounds. Postharvest: the focus shifts to how light can help maintain visual and nutritional quality, regulate ripening, limit pathogen development, and extend shelf-life. The review emphasizes plant photoreceptors and signal transduction pathways, as well as technical parameters such as spectrum selection, application timing, and lighting configuration. A selection of recent patents illustrates how fundamental research is being translated into deployable, energy-efficient lighting technologies for sustainable crop management. Full article

Since the first synthetic macrocyclic receptors were shown to bind ions selectively, supramolecular host–guest chemistry has enabled the translation of molecular recognition events into physical signals. Early coupling of such receptors to ion-sensitive field-effect transistors established a bridge between supramolecular chemistry and solid-state electronics. Today, this bridge is rebuilt in iontronics, where ions carry information through nanoconfined media and ionic transport becomes highly sensitive to electrostatic gradients, surface charge, and surface molecular interactions. As a result, ionic flux can serve as an efficient transduction mechanism that responds precisely, reversibly, and rapidly to changes in the chemical environment. Within this regime, host–guest chemistry offers a powerful means to exert direct control over ionic behavior, allowing molecular recognition to modulate conductance, rectification, and ion selectivity, thereby conferring practical function to nanofluidic systems. This review highlights systems in which host molecules act as chemical actuators that modulate nanochannel surface chemistry, thereby regulating ionic flux and enabling reversible, tunable, and stimulus-responsive behaviors. We survey architectures in which crown ethers, calixcrowns, pillararenes, and related hosts are integrated into solid-state nanochannels, emphasizing representative achievements such as biological-level Na⁺/K⁺ selectivity in crown ether-based systems and nanomolar-level detection of ions using calixcrowns- and pillararene-functionalized nanochannels. Finally, we discuss how temperature, pH, light, and redox state act as external stimuli that reversibly switch between conductive states, yielding ion-selective platforms for sensing and ion sieving. Full article

Light-induced membrane fusion has become a pivotal technique for constructing and functionalizing synthetic cells by enabling precise control over membrane merging events. Traditional fusion approaches that rely on chemical, physical, and mechanical stimuli frequently lack both specificity and reversibility, limiting their utility in mimicking dynamic cellular processes. Here, we review advances employing photosensitive molecules and optogenetic tools that facilitate spatiotemporally controlled fusion of lipid and polymer vesicles, enabling dynamic content exchange and membrane remodeling. These approaches have enhanced synthetic cell assembly, molecular transport, and signal transduction, with applications extending to drug delivery and biosensing. Despite challenges in efficiency and biocompatibility, ongoing innovations in photosensitizer design and light activation strategies promise to expand the capabilities of synthetic biology platforms. This work underscores the potential of light-induced fusion to advance the development of intelligent nanomaterials and functional synthetic cellular systems. Full article