Search Results (62)

Soil salinity is a serious abiotic stressor threatening global agriculture, currently affecting nearly 20% of irrigated land, with projections suggesting that almost 50% of cultivated areas may be impacted by 2050. Plant growth-promoting rhizobacteria (PGPR) and Silicon (Si) have been widely investigated for their individual roles in improving plant tolerance to salinity, yet their combined application—particularly using Si nanoparticles (SiNPs), remains underexplored. This review synthesizes current knowledge on PGPR, SiNPs, and their synergistic effects in mitigating salinity stress, with emphasis on physiological, biochemical, and molecular mechanisms. Special attention is given to Si-mediated regulation of stress-responsive genes (e.g., RD29B, DREB2b, RAB18, HKT1, WRKY TFs, CAT, POD) and PGPR-induced gene expression (e.g., GmST1, GmLAX3, NHX1, NRT2.2, GR), which are directly linked to ion homeostasis, osmolyte accumulation, and antioxidant activation. In addition, crop-specific case studies and emerging molecular insights are highlighted to demonstrate practical applications. Despite these promising findings, significant challenges remain, including the stability of nanoformulations, microbial compatibility, and the lack of field-scale validation under diverse agro-climatic conditions. This review highlights knowledge gaps and briefly outlines future directions for the integrated use of PGPR and SiNPs as sustainable strategies to enhance crop resilience under salinity stress. Full article

Nicotinamide adenine dinucleotide (NAD⁺) serves as a critical cofactor in redox reactions and metabolic transformations catalyzed by NAD-dependent enzymes and is essential for bacterial survival and virulence. The biosynthesis of NAD⁺ in the cariogenic pathogen Streptococcus Sobrinus (S. sobrinus), a pivotal participant in oral cavities of children and adolescents with a history of caries, has yet to be explored. Bioinformatics, genetics, and biochemical techniques were used to identify NAD⁺ biosynthesis pathways and corresponding regulator in S. Sobrinus. S. sobrinus lacks de novo NAD⁺ synthesis pathway but comprises NA and Nam salvage pathway I (PncA-PncB-NadD-NadE) and PnuC-NadR salvage pathway III. NiaY and PnuC were involved in the salvage pathways. N-terminal domain of SsNrtR regulator was identified as DNA-binding domain binding to the pnuC and pncB probe, and addition of ADP-ribose reversed the binding of SsNrtR to the target promoters to regulate NAD⁺ salvage pathways. C-terminal domain of SsNrtR was non-catalytic, consistent with loss of Nudix motif conservation. Furthermore, the abrogation of niaR compromised multiple pathogenic traits, including cellular proliferation, acidogenesis, and the architecture/mechanical integrity of biofilms. Consequently, this mutant exhibited attenuated virulence in a rat caries model. Our findings conclusively demonstrate that SsNrtR-mediated regulation of NAD⁺ homeostasis is a critical determinant of the cariogenic potential of S. sobrinus. This study identifies SsNrtR as a previously uncharacterized NAD⁺-responsive regulator that integrates metabolic homeostasis with the control of virulence in Streptococcus sobrinus. These findings elucidate a novel metabolic–virulence regulatory axis in this species and position SsNrtR as a promising target for the development of anti-caries interventions. Full article

Nitrogen assimilation is vital for apple growth, yield, and quality, with nitrate reductase (NIA), nitrite reductase (NIR), glutamine synthetase (GS), and glutamate synthase (GOGAT) serving as key regulatory enzymes. This study systematically identified these four gene families in apple (Malus domestica) through genome-wide analysis and examined their expression patterns under nitrate treatment. In total, 13 genes were identified, 2 MdNIAs, 1 MdNIR, 7 MdGSs, and 3 MdGOGATs, with gene lengths ranging from 2577 to 27736 base pairs (bp); MdGLT1A had the longest coding sequence (6627 bp). The encoded proteins contained 355–2208 amino acids, with predicted isoelectric points (pIs) between 5.55 and 6.63. Subcellular localization analysis predicted distinct compartmentalization: MdNIA1A in peroxisomes; MdGS1 in the cytosol; MdNIR1, MdGS2, and MdGLU1 in chloroplasts; and MdGLT1 in mitochondria/chloroplasts. Functional site prediction revealed multiple phosphorylation and glycosylation sites, with ATP/GTP-binding motifs present only in certain MdGOGAT proteins. Protein interaction analysis suggested close associations among these genes and possible interactions with NRT2.1/2.2. Chromosomal mapping showed their distribution across eight chromosomes, while promoter analysis identified diverse cis-acting regulatory elements (e.g., ABRE and G-box). Under nitrate treatment (0–12 h), these genes exhibited distinct expression dynamics: MdNIA1A and B were rapidly induced (0–6 h) and maintained high expression; MdNIR1 peaked at 6 h and then declined; MdGS1.1B was activated after 6 h; and MdGS2A, MdGLU1, and MdGLT1A/B peaked at 6 h before decreasing. Therefore, these results elucidate the structural and functional divergence of nitrogen assimilation genes in apple and provide a basis for understanding nitrogen utilization mechanisms and developing nitrogen-efficient breeding strategies. Full article

Salix suchowensis is an ideal model organism for investigating nitrogen (N) transport mechanisms due to its low N-input requirements. Accurate quantification of gene expression is essential for elucidating these processes, with quantitative real-time PCR (RT-qPCR) being the preferred method. However, the identification of stable reference genes for normalization in Salix suchowensis under varying N conditions remains unresolved. In this study, thirteen commonly employed candidate reference genes were evaluated across root, stem, and leaf tissues, under four N treatments (NH₄NO₃, NH₄⁺, NO₃⁻, and N deficiency). Five genes (UBQ1, UBQ3, 18S, H2A2, and H2B2) were excluded due to poor amplification efficiency or irregular melting curves. The remaining eight genes were further assessed for expression stability using the geNorm, NormFinder, and BestKeeper algorithms. Integrated ranking via RefFinder identified EF1α, EFβ, and αTUB as the most stable reference genes. GeNorm analysis suggested that two reference genes were sufficient for reliable normalization. Validation using the N-responsive gene SsAMT1 and SsNRT2 confirmed the stability of EF1α, EFβ, and αTUB as suitable reference genes. Based on comprehensive stability assessments and experimental validation, we recommended EF1α + αTUB as optimal reference gene pairs for RT-qPCR normalization under varying N conditions. Furthermore, the consistent expression of EF1α and αTUB across nine willow genotypes highlighted their broader applicability within Salix species. This study provides valuable methodological guidance for advancing molecular research on N transport in woody perennial plants. Full article

The development of a new salt–alkaline-tolerant hybrid japonica rice is crucial for enhancing japonica rice supply and ensuring national food security. Utilizing molecular marker-assisted selection (MAS) technology combining Kompetitive Allele-Specific PCR (KASP) markers and a gene breeding chip, the salt-tolerant gene SKC1 was introgressed into a rice genotype Fan 14. This led to the development of Shenyanhui 1, a new high-quality, strongly heterotic, and salt-tolerant japonica restorer line. Subsequently, the high-quality, salt-tolerant japonica three-line hybrid rice variety Shenyanyou 1 was developed by crossing the BT-type japonica cytoplasmic male sterile (CMS) line Shen 21A with the restorer line Shenyanhui 1. Shenyanyou 1 carries the major salt tolerance gene SKC1, exhibiting excellent salt tolerance with seedling stage salt tolerance reaching level 5. Under precise salt tolerance evaluation throughout its growth cycle, Shenyanyou 1 achieved a yield of 3640.5 kg/hm², representing an extremely significant increase of 20.7% over the control variety Yandao 21. Shenyanyou 1 exhibits superior grain quality, meeting the Grade 3 high-quality rice standards issued by the Ministry of Agriculture. Shenyanyou 1 has good comprehensive resistance, aggregating rice blast resistance genes such as Pi2, Pita, Pizt and LHCB5, bacterial blight resistance genes Xa26/Xa3, stripe blast resistance gene STV11, semi-dwarf gene Sdt97, nitrogen-efficient utilization gene NRT1.1B, the light repair activity enhancement gene qUVR-10, the cold resistance gene qLTG3-1, and the iron tolerance gene OsFRO1. It has good resistance to biotic and abiotic stresses. This paper details the breeding process, key agronomic traits, salt tolerance, yield performance, and grain quality characteristics of Shenyanyou 1. Full article

BeiDou navigation satellite system (BDS) precise point positioning (PPP)-B2b has significant potential for application in meteorological fields, such as standalone water vapor monitoring in depopulated area without Internet. In this study, the practical ability of water vapor monitoring using the BDS PPP-B2b service is illustrated through a continuously operated water vapor monitoring system in Wuhan, China, with a 25-day experiment in 2025. Original observations from the Global Positioning System (GPS) and BDS are collected and processed in the near real-time (NRT) mode using ephemeris from the PPP-B2b service. Precipitable water vapor PWV monitored with B2b ephemeris are evaluated with radiosonde and ERA5 reanalysis, respectively. Taking PWV from radiosonde observations as the reference, RMS of PWV based on B2b ephemeris varies from 3.71 to 4.66 mm for different satellite combinations. While those values are with a range from 3.95 to 4.55 mm when compared with ERA5 reanalysis. These values are similar to those processed with the real-time ephemeris from the China Academy of Science (CAS). In general, this study demonstrates that the practical accuracy of water vapor monitored based on the BDS PPP-B2b service can meet the basic demand for operational meteorology for the first time. This will provide a scientific reference for its wide promotion to meteorological applications in the near future. Full article

This study investigates the impact of response time on ability estimation within an Item Response Theory (IRT) framework, introducing time-sensitive formulations to enhance student assessment accuracy. Seven models were evaluated, including standard 1PL-IRT and six response-time-adjusted variants: TP-IRT, STP-IRT, TWD-IRT, NRT-IRT, DTA-IRT, and ART-IRT. Three optimization techniques—Maximum Likelihood Estimation (MLE), full parameter optimization, and K-fold Cross-Validation (CV)—were employed to assess model performance. Empirical validation was conducted using data from 150 students solving 30 mathematics items on the “TestYourself” platform, integrating response accuracy and timing metrics. Student abilities (θ), item difficulties (b), and time–effect parameters (λ) were estimated using the L-BFGS-B algorithm to ensure numerical stability. The results indicate that subtractive models, particularly DTA-IRT, achieved the lowest AIC/BIC values, highest AUC, and improved parameter stability, confirming their effectiveness in penalizing excessive response times without disproportionately affecting moderate-speed students. In contrast, multiplicative models (TWD-IRT, ART-IRT) exhibited higher variability, weaker generalizability, and increased instability, raising concerns about their applicability in adaptive testing. K-fold CV further validated the robustness of subtractive models, emphasizing their suitability for real-world assessments. These findings highlight the importance of incorporating response time as an additive factor to improve ability estimation while maintaining fairness and interpretability. Future research should explore multidimensional IRT extensions, behavioral response–time analysis, and adaptive testing environments that dynamically adjust item difficulty based on response behavior. Full article

Apple (Malus domestica Borkh.) is an economically important fruit. The use of nitrate by plants plays a crucial role in their growth and development, and its absorption and dispersal are controlled by nitrate transport proteins (NRTs). In this study, we investigated the potential function of MdNRT2.4 under low-nitrogen (N) stress by overexpressing it in tobacco. Compared with plants treated with a normal nitrogen level (5 mM), the MdNRT2.4 overexpression lines under low-N stress (0.25 mM) exhibited significantly greater plant height and width, as well as larger leaves and a higher leaf density, than wild-type plants, suggesting that the overexpression of MdNRT2.4 enhances the low-N tolerance of tobacco. Enhanced antioxidant enzyme activities in the MdNRT2.4 overexpression plant lines promoted the scavenging of reactive oxygen species, which reduced damage to their cell membranes. GUS staining of pMdNRT2.4::GUS-transformed Arabidopsis thaliana lines showed that MdNRT2.4 was expressed in the roots, vascular bundles, seeds in fruit pods, and young anther sites, suggesting that MdNRT2.4 mediates the transport of nitrate to these tissues, indicating that MdNRT2.4 might promote nitrate utilization in apple and improve its tolerance to low-N stress. Experiments using yeast one-hybrid and dual-luciferase assays revealed that MdbHLH3 binds to the MdNRT2.4 promoter and activates its expression. MdbHLH3 belongs to the basic helix–loop–helix (bHLH) transcription factor (TF). It is speculated that MdbHLH3 may interact with the promoter of MdNRT2.4 to regulate N metabolism in plants and enhance their low-N tolerance. This study establishes a theoretical framework for investigating the regulatory mechanisms of low-N responsive molecules in apple, while simultaneously providing valuable genetic resources for molecular breeding programs targeting low-N tolerance. Full article

Rice is a major crop for half of the world’s population, and nitrogen (N) fertilizers play a crucial role in its production. However, imbalanced N fertilizer uses and traditional fertilization practices have led to low nitrogen use efficiency (NUE), increased N footprints, and reduced rice yields and farmers’ income. There are limited studies where the integration of both agronomic and molecular advancements to enhance NUE is discussed, particularly in developing countries. This review highlights novel agronomic and molecular strategies to enhance NUE, rice yields, and profitability, while minimizing environmental impact. The agronomic strategies include the 4R Nutrient Stewardship framework, enhanced efficiency nitrogen fertilizers (EENFs), nano-fertilizers, biochar-based fertilizers, biological N fixation, and sensor-based fertilizer management in major rice-growing countries. The molecular mechanisms focus on N uptake, assimilation, and utilization, highlighting the role of hormones, key genes, transcription factors (TFs), and regulatory pathways. Moreover, we examine promising rice genotypes and cultivars with improved NUE and grain yield. Additionally, this paper offers deep insights into recent advancements in molecular genetics, such as multi-omics approaches (transcriptomics, metabolomics, and metagenomics), the Genome-Wide Association Study (GWAS), Quantitative Traits Loci mapping (QTLs), Single Nucleotide Polymorphisms (SNPs) analysis, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas9)-mediated genome editing, which serve as valuable tools for developing rice cultivars with enhanced NUE and grain yield. Full article

Cytomegalovirus (CMV) infection in pregnant women is one of the most common causes of congenital infection in children. It is often asymptomatic but can lead to serious complications, including progressive sensorineural hearing loss. Profound hearing loss is an indication for cochlear implantation (CI). Electrode impedance and neural response telemetry (NRT) thresholds can be measured to confirm correct electrode placement and speech processor programming. Background/Objectives: The aim of the study is to evaluate the hearing outcome of children with profound sensorineural hearing loss or deafness due to cCMV infection after CI compared to a control group of children born with other causes of congenital hearing loss and to identify prognostic factors predicting the outcome of patients with hearing loss due to cCMV infection after CI. Methods: A retrospective study was conducted in patients implanted between 2016 and 2023 at the Department of Otolaryngology of the Institute of the Polish Mother’s Memorial Hospital Research Institute in Łódź. Pre- and postoperative hearing levels, electrode impedance and neural response telemetry (NRT) thresholds were compared. The degree of pre-implantation hearing loss was assessed by the level of the recorded V-wave in the ABR test. Post-implantation hearing assessment was based on the last available free-field tonal audiometry measurement. Impedance measurements were included: intraoperative, 1, 6, 12 months after CI, respectively, and NRT thresholds. Results: The final analysis included 84 patients with profound sensorineural hearing loss and complete audiological follow-up data: 13 patients with congenital CMV (cCMV) infection and 71 patients with other causes of deafnes. The analysis included 175 implanted ears: 17 in the CMV group and 158 in the control group. The age at implantation ranged from 1 to 11 years in the CMV and from 1 to 13 years in the control group. Mean preoperative hearing thresholds were 94.54 dB in the CMV group and 97.04 dB in the control group. At the most recent postoperative evaluation, mean thresholds improved to 33.83 dB and 36.42 dB, respectively. No statistically significant differences were observed between the groups. Mean intraoperative NRT values were 79.74 in the CMV group and 86.90 in the non-CMV group. Final NRT values were 129.77 and 130.76, respectively. Mean impedance values measured intraoperatively and at 1, 6 and 12 months postoperatively were 11.09 kOhm, 13.40 kOhm, 8.35 kOhm and 8.25 kOhm in the CMV group; and 12.28 kOhm, 14.06 kOhm, 9.60 kOhm and 8.00 kOhm in the control group, respectively. Conclusions: CI in children with deafness caused by cCMV infection is an effective treatment option. Initial electrical impedance values of the electrodes increase after implant activation and decrease in subsequent months of follow-up, suggesting the absence of active adhesion processes in the cochlea. Full article

‘Dianheyou615’ (DHY615) is an elite Dian (D1)-type hybrid japonica rice variety, renowned for its high yield, exceptional grain quality, and unique adaptability to both irrigated and rainfed conditions in the Yungui Plateau of southwestern China. However, the genetic mechanisms underlying the agronomic performance of the D1-type hybrid japonica rice remain unclear. In this study, a comprehensive analysis of ‘DHY615’’s agronomic performance, genetic genealogy, and molecular genetic foundation was conducted to dissect its desirable traits for upland rainfed cultivation across diverse ecological environments. The main findings indicate that ‘DHY615’ possesses 6432 heterozygous SNPs, with 57.48% and 14.43% located in the promoter and coding regions, respectively, potentially affecting key phenotypic traits. High-impact SNPs variants and numerous well-known functional genes were identified, such as OsAAP6, GS3, Sd1, Rf1, BADH2, BPh14, Rymv1, OsFRO1, NRT1.1B, SKC1, OsNCED2, and qUVR-10, which are likely linked to traits including plant architecture, grain yield, grain quality, and resistance to various biotic and abiotic stresses (e.g., disease, cold, drought, salt, high iron, and high UV radiation). Notably, ‘Nan615’ harbors a greater number of functional allele variants compared to ‘H479A’, which potentially explaining its superior grain yield and remarkable adaptability. This study offers novel and valuable insights into the molecular genetic foundation of the plateau D1-type hybrid japonica rice, underscoring its potential for sustainable rice production across diverse ecological zones, especially with its unparalleled high-altitude adaptability to rainfed upland planting. Full article

The global shortage of protein resources has highlighted microbial processes as a promising solution for protein production. Photosynthetic bacteria (PSB) offer advantages in protein synthesis, yet the mechanisms underlying nitrogen conversion to protein remain insufficiently understood. To clarify these mechanisms, nitrogen metabolism-related genes and networks were analyzed using high-throughput sequencing. Synthetic sugar wastewater served as the initial substrate. The results showed that at a nitrogen concentration of 200 mg/L with a combined NH₄-N + NO₃-N supply, the nitrogen conversion rate reached 3.3, and protein production peaked at 130.35 mg/(L·d). Under these conditions, 68.4% of the utilized nitrogen originated from NH₄-N, and 31.6% from NO₃-N, leading to an increase in pro-N to 12.46 mg. Transcriptome analysis revealed high expression of nirK, norB, and nosZ, confirming significant denitrification, while the absence of nitrate reductase, GLDH, GDH, and GltS in Rp. palustris corresponded to a lower protein yield of 53.28 mg/(L·d). Additionally, genes related to nitrogen transport (amtB, nrtABC), ammonium assimilation (glnA, gltB, gltD), and nitrate reduction (nasA, narB) were upregulated, facilitating nitrogen utilization. These findings provide insights into optimizing nitrogen utilization for improved protein synthesis in PSB-based wastewater treatment. Full article

The TGA (TGACG motif-binding factor) transcription factors are integral to root growth and development, and are pivotal in mediating plant responses to abiotic stresses. Nonetheless, their role in the nutrient absorption processes of banana plants has not been extensively investigated. This research conducted a comprehensive analysis of the MaTGA gene family, emphasizing their physicochemical characteristics, phylogenetic relationships, gene duplication events, promoter cis-regulatory elements and protein interaction networks. Furthermore, this study investigated the expression patterns of MaTGA family members under varying nitrogen conditions. A total of 18 MaTGA members were identified within the banana genome, each encoding proteins characterized by the presence of bZIP and DOG domains. These genes exhibited an uneven distribution across eight chromosomes. Phylogenetic analysis further classified the MaTGA family into four distinct subgroups (I–IV), consisting of three, seven, three, and five members, respectively. An analysis of promoter cis-elements indicated that over 50% of the MaTGA gene family members contain hormone-responsive elements associated with abscisic acid (ABRE), ethylene (ERE), and salicylic acid (SARE), in addition to stress-responsive elements related to drought (MBS) and low temperature (LTR). Regarding gene expression, MaTGA7, MaTGA8, and MaTGA15 exhibited significantly elevated expression levels in the leaves and roots relative to other tissues. Under varying nitrogen conditions, 13 members, including MaTGA7 and MaTGA8, demonstrated the highest expression levels under reduced nitrogen (70%) treatment, followed by low nitrogen (20%) conditions, and the lowest expression levels were observed under nitrogen-deficient conditions. These findings imply that MaTGA genes may play crucial roles in enhancing nitrogen use efficiency. Protein interaction predictions suggest that MaTGA7, MaTGA8, and MaTGA15 may interact with nitrogen-related proteins, including Nitrate Transporter 2 (NRT2.1 and NRT2.2), NIN-Like Protein 7 (NLP7), and Nitrate Transporter 1.1 (NPF6.3). In summary, MaTGA7, MaTGA8, and MaTGA15 are likely involved in the processes of nitrogen absorption and utilization in bananas. The present findings establish a basis for subsequent investigations into the functional roles of MaTGA genes in augmenting nutrient use efficiency and mediating responses to abiotic stresses in banana plants. Full article

Methylation plays an important role in regulating crop development, but little is known about how methylation regulates plant architecture in rapeseed (Brassica napus L.). Here, we examined how methylation affects the thickness-of-pod-canopy (TPC) trait in rapeseed by performing genome-wide methylation analysis of two extreme TPC lines. In flower buds, 26 genes had significantly higher methylation levels in the high-TPC samples compared to the low-TPC samples, resulting in significantly reduced gene expression. By contrast, in the stem apex samples, the promoter regions of 22 genes were hypermethylated in the high- vs. low-TPC samples. The promoters of 19 and 21 genes had significantly reduced methylation levels in the flower bud and stem apex, respectively, of the high- vs. low-TPC samples, resulting in significantly higher expression levels. Some of these differentially expressed genes are associated with TPC-related traits, such as BnaC01g12960D (NRT1.8). In addition, 14 important genes related to growth and development were differentially regulated between the two groups due to miRNA-mediated differences in methylation levels in their promoters. For example, hypermethylation in the promoter region of BnaCnng64040D (Lipase family protein), mediated by miR159, led to significantly reduced gene expression in flower buds of high-TPC vs. low-TPC lines. These results, together with our previously generated RNA-seq and miRNA profiling data, indicate that both methylation and miRNAs are perhaps involved in regulating the expression of genes, thereby affecting the TPC trait in B. napus, providing a reference for uncovering the molecular mechanism regulating this crucial trait. Full article

Nitrogen is an essential nutrient that frequently determines the growth rate of fungi. Nitrate transporter proteins (Nrts) play a crucial role in the cellular absorption of nitrate from the environment. Entomopathogenic fungi (EPF) have shown their potential in the biological control of pests. Thus, comprehending the mechanisms that govern the pathogenicity and stress tolerance of EPF is helpful in improving the effectiveness and practical application of these fungal biocontrol agents. In this study, we utilized homologous recombination to create MaNrtB deletion mutants and complementation strains. We systematically investigated the biological functions of the nitrate transporter protein gene MaNrtB in M. acridum. Our findings revealed that the disruption of MaNrtB resulted in delayed conidial germination without affecting conidial production. Stress tolerance assays demonstrated that the MaNrtB disruption strain was more vulnerable to UV-B irradiation, hyperosmotic stress, and cell wall disturbing agents, yet it exhibited increased heat resistance compared to the wild-type strain. Bioassays on the locust Locusta migratoria manilensis showed that the disruption of MaNrtB impaired the fungal virulence owing to the reduced appressorium formation on the insect cuticle and the attenuated growth in the locust hemolymph. These findings provide new perspectives for understanding the pathogenesis of EPF. Full article