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Abstract Several studies reveal that allergic rhinitis (AR) is a significant risk factor of systemic lupus erythematosus (SLE). However, studies investigating the common pathogenesis linking AR and SLE are lacking. Our study aims to search for the shared biomarkers and mechanisms that may provide new therapeutic targets for preventing AR from developing SLE. GSE50223 for AR and GSE103760 for SLE were downloaded from the Gene Expression Omnibus (GEO) database to screen differentially expressed genes (DEGs). The Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to explore the functions of shared DEGs. Hub genes were screened by cytoHubba (a plugin of Cytoscape) and validated in another two datasets. Gene set enrichment analysis (GSEA) and single-sample Gene set enrichment analysis (ssGSEA) algorithm were applied to understand the functions of hub gene. ENTPD1 was validated as a hub gene between AR and SLE. GSEA results revealed that ENTPD1 was associated with KRAS_SIGNALING_UP pathway in AR and related to HYPOXIA, TGF_BETA_SIGNALING and TNFA_SIGNALING_VIA_NFKB pathways in SLE. The expression of ENTPD1 was positively correlated with activated CD8 T cell in both diseases. Thus, ENTPD1 may be a novel therapeutic target for preventing AR from developing SLE.

Refining effect of B4C nanoparticles in ZL108 alloy on Fe-rich phase was studied in this work. It was observed that B4C nanoparticles apparently refines the size of the Fe-rich phases and partially transforms Fe-rich phases morphology from hollow polyhedron to petal-like shape. The DSC results show that B4C nanoparticles does not affect the initial nucleation temperature of the Fe-rich phase. However, the addition of B4C nanoparticles to ZL108 alloy inhibits the growth of Fe-rich phase. The TEM results confirm that the addition of B4C nanoparticles alters the lattice parameter of Fe-rich phase due to incorporation of C atoms, thereby suppressing the growth of the Fe-rich phase and ultimately leading to its refinement. From the perspective of fracture behavior, the addition of B4C nanoparticles remarkably reduces the stress concentration of Fe-rich phase, and the elongation of the alloy increases by 25.3%. These findings provide a new perspective for further research and development to refine Fe-rich phase.

BackgroundSoil salinization is one of the significant factors limiting high crop yields and expansion of arable land, seriously affecting global agricultural production. Rice is an essential food crop throughout the world, and its seedlings are particularly susceptible to salt stress, which can directly affect the growth and development of rice and its final yield. We used the natural population as the material for genome-wide association study (GWAS) and the recombinant inbred line (RIL) population from CD (salt sensitive)/WD20342 (salt tolerant) hybridization as the material for linkage analysis.ResultsThe degree of salt tolerance was evaluated by using the relative root length (RRL), relative root number (RRN), relative root fresh weight (RRFW), and relative root dry weight (RRDW) as indicators. Fifteen and six major quantitative trait loci (QTLs) were identified by GWAS and linkage analysis, respectively. Meanwhile, the GWAS identified the lead SNP (Chr2_22340368), which was located within qRRL2 and qRRDW2 identified by linkage analysis. GWAS, combined with linkage analysis, selected a 196-kb overlapping region on chromosome 2, including 22 candidate genes. LOC_Os02g36880 was discovered as the candidate gene involved in salt tolerance by haplotype analysis, qRT-PCR, and sequence analysis. The score of salinity toxicity (SST) and seedling survival rate (SSR) were determined for CRISPR/Cas9 mutants (CR-1 and CR-15) and wild-type (ZH11), respectively.ConclusionThe phenotypic validation indicated that LOC_Os02g36880 negatively regulated the salt tolerance at the seedling stage. This study provides resources for breeding Japonica rice to improve its response to salt stress.

BackgroundAntibody-drug conjugates (ADCs) have emerged as the focus and hotspots in the cancer field, yet the accompanying ocular toxicity has often been underestimated. We aimed to comprehensively and comparatively analyze the risk of ocular toxicity associated with various ADCs using the FDA Adverse Event Reporting System (FAERS) database.MethodsData were extracted from the FAERS database from Q3 2011 to Q3 2023. We analyzed the clinical characteristics of ADCs-related ocular adverse events (AEs). These data were further mined by proportional analysis and Bayesian approach to detect signals of ADCs-induced ocular AEs. Moreover, the time to onset of ocular toxicity was also evaluated.ResultsA total of 1,246 cases of ocular AEs were attributed to ADCs. Ocular toxicity signals were observed in patients treated with belantamab mafodotin, brentuximab vedotin, enfortumab vedotin, mirvetuximab soravtansine, sacituzumab govitecan, trastuzumab deruxtecan, and trastuzumab emtansine. Of these, belantamab mafodotin, trastuzumab emtansine, and mirvetuximab soravtansine, whose payloads are microtubule polymerization inhibitors, were more susceptible to ocular toxicity. The ten most common ADCs-related ocular AEs signals are keratopathy [ROR = 1,273.52, 95% CI (1,129.26–1,436.21)], visual acuity reduced [ROR = 22.83, 95% CI (21.2–24.58)], dry eye [ROR = 9.69, 95% CI (8.81–10.66)], night blindness [ROR = 259.87, 95% CI (228.23–295.89)], vision blurred [ROR = 1.78, 95% CI (1.57–2.02)], photophobia [ROR = 10.45, 95% CI (9.07–12.05)], foreign body sensation in eyes [ROR = 23.35, 95% CI (19.88–27.42)], ocular toxicity [ROR = 144.62, 95% CI (117.3–178.32)], punctate keratitis [ROR = 126.21, 95% CI (101.66–156.69)], eye disorder [ROR = 2.71, 95% CI (2.21–3.32)]. In terms of onset time, sacituzumab govitecan displayed an earlier onset of 21 days, while trastuzumab deruxtecan exhibited the latest onset of 223 days.ConclusionADCs may increase the risk of ocular toxicity in cancer patients, leading to serious mortality. With the widespread application of newly launched ADCs, combining the FAERS data with other data sources is crucial for monitoring the ocular toxicity of ADCs. In addition, novel ocular toxicity signals not documented in product labeling were detected. Further research will be necessary to validate our findings in the future.

Long-term denervation-induced atrophy and fibrosis of skeletal muscle due to denervation leads to poor recovery of muscle function. Studies have shown that the transforming growth factor-β1 (TGF-β1)-Smad signaling pathway plays a central role in muscle atrophy and fibrosis. Recent studies demonstrate the role of microRNAs (miRs) in various pathological conditions, including muscle regeneration. miR-21 has been shown to play a dynamic role in inflammatory responses and in accelerating injury responses to fibrosis. We used both RNA sequencing and quantitative RT-PCR strategies to examine the alternations of miRNAs during denervation-induced gastrocnemius muscle atrophy and fibrosis. Our data showed that MiR-21 was upregulated in denervated gastrocnemius muscle tissue, and TGF-β1treatment increased miR-21 expression. Inhibition of miR-21 reduced gastrocnemius muscle fibrosis and significantly downregulated the expression of p-SMAD2/3 and the fibrosis-associated markers TGF-β1, connective tissue growth factor, alpha smooth muscle actin. Masson's trichrome staining revealed that atrophy and fibrosis in gastrocnemius muscle tissue were reduced in the miR-21 inhibition group compared to the control group. We confirmed that SMAD7 is a direct target of miR-21 using a dual luciferase assay. Furthermore, Immunofluorescence and Western blot analyses revealed that miR-21 inhibition reduced SMAD2/3 phosphorylation and nuclear translocation. While SMAD7-siRNA abolished the effect. Consequently, the discovery that miR-21 regulates the atrophy and fibrosis of the gastrocnemius muscle offers a possible therapeutic approach for their management.

Abstract The role of 5-methylcytosine (m5C) in tumor initiation and progression has been increasingly recognized. However, the precise association between the regulation of m5C and the progression, metastasis, and prognosis of head and neck squamous cell carcinoma (HNSCC) has not yet been fully explored. Data from 545 HNSCC patients obtained from The Cancer Genome Atlas (TCGA) database were analyzed. Unsupervised cluster analysis was conducted using the expression levels of m5C regulatory genes. Additionally, gene set variation analysis (GSVA), single-sample gene set enrichment analysis (ssGSEA), and Cox regression analysis were utilized. Quantitative reverse transcription polymerase chain reaction (RT-qPCR), colony formation assay, transwell experiments and western blots were performed in the HNSCC cell line UM-SCC-17B to assess the expression and functional role of one of the novel signatures, CNFN. Significant expression differences were found in m5C regulatory genes between tumor and normal tissues in HNSCC. Two distinct m5C modification patterns, characterized by substantial prognostic differences, were identified. Cluster-2, which exhibited a strong association with epithelial-mesenchymal transition (EMT), was found to be associated with a poorer prognosis. Based on the m5C clusters and EMT status, differentially expressed genes (DEGs) were identified. Using DEGs, an 8-gene signature (CAMK2N1, WNT7A, F2RL1, AREG, DEFB1, CNFN, TGFBI, and CAV1) was established to develop a prognostic model. The performance of this signature was validated in both the training and external validation datasets, demonstrating its promising efficacy. Furthermore, additional investigations using RT-qPCR on clinical specimens and experimental assays in cell lines provided compelling evidence suggesting that CNFN, one of the genes in the signature, could play a role in HNSCC progression and metastasis through the EMT pathway. This study highlighted the role of m5C in HNSCC progression and metastasis. The relationship between m5C and EMT has been elucidated for the first time. A robust prognostic model was developed for accurately predicting HNSCC patients’ survival outcomes. Potential molecular mechanisms underlying these associations have been illuminated through this research.

Fibrosis is a complex pathological process that can lead to the permanent loss of biological function, with P2ry2 playing a crucial role in this process. Long non-coding RNAs (lncRNAs) have been reported to play an critically important role in the fibrotic process. However, it remains unclear whether lncRNAs can regulate fibrosis through P2ry2. In this study, we detected the expression of the long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (lnc-MALAT1). We investigated the expression patterns of lnc-MALAT1 and P2ry2 in denervated skeletal muscle, a classical model of fibrosis. Additionally, we utilized a TGF-β-mediated fibrosis model in NIH/3T3 cells to examine the effects of lnc-MALAT1 and P2ry2 on fibroblast activation and the underlying regulatory mechanisms in vitro. Our results demonstrated that the expression levels of lnc-MALAT1 and P2ry2 were consistently elevated in denervated skeletal muscle, correlating with the degree of fibrosis. In vitro experiments confirmed the regulatory effect of lnc-MALAT1 on P2ry2. Furthermore, we identified miR-335-3p as a potential key molecule in the regulatory relationship of lnc-MALAT1/P2ry2. Dual luciferase reporter assays and AGO2-RIP verified the molecular sponging effect of lnc-MALAT1 on miR-335-3p. Additionally, we validated the regulation of the lnc-MALAT1/miR-335-3p/P2ry2 axis through experimental approaches. In conclusion, our study identified a crucial role of lnc-MALAT1/miR-335-3p/P2ry2 axis in fibroblast activation, providing a promising treatment option against the fibrosis.

Drought stress poses a significant threat to rice production, necessitating the identification of genes associated with drought tolerance. This study employed a combination of genome-wide association study (GWAS) and linkage mapping to pinpoint seedling drought tolerance genes in Japonica rice. Using the leaf rolling scale (LRS) as the phenotypic index, we assessed rice drought tolerance under polyethylene glycol-induced drought during the seedling stage. A lead SNP C8_28933410 by GWAS was identified, which was located within qLRS-8-1 identified by linkage mapping on chromosome 8. Combing the LD block analyses and QTL interval, a 138.6 kb overlap interval was considered as the candidate region. Haplotype analysis, qRT-PCR, sequence analysis, and mutant phenotype verification led to the speculation that LOC_Os08g05520 is a candidate gene associated with drought tolerance. Our findings provide a valuable reference for breeders aiming to enhance rice drought tolerance.

Abstract Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency.

Low-temperature chilling is a major abiotic stress leading to reduced rice yield and is a significant environmental threat to food security. Low-temperature chilling studies have focused on physiological changes or coding genes. However, the competitive endogenous RNA mechanism in rice at low temperatures has not been reported. Therefore, in this study, antioxidant physiological indices were combined with whole-transcriptome data through weighted correlation network analysis, which found that the gene modules had the highest correlation with the key antioxidant enzymes superoxide dismutase and peroxidase. The hub genes of the superoxide dismutase-related module included the UDP-glucosyltransferase family protein, sesquiterpene synthase and indole-3-glycerophosphatase gene. The hub genes of the peroxidase-related module included the WRKY transcription factor, abscisic acid signal transduction pathway-related gene plasma membrane hydrogen-ATPase and receptor-like kinase. Therefore, we selected the modular hub genes and significantly enriched the metabolic pathway genes to construct the key competitive endogenous RNA networks, resulting in three competitive endogenous RNA networks of seven long non-coding RNAs regulating three co-expressed messenger RNAs via four microRNAs. Finally, the negative regulatory function of the WRKY transcription factor OsWRKY61 was determined via subcellular localization and validation of the physiological indices in the mutant.

Under uncertain environments, how to characterize individual preferences more naturally and aggregate parameters better have been hot research topics in multiple attribute decision making (MADM). Fuzzy set theory provides a better mathematical tool to deal with uncertain data, which promotes substantial extended studies. In this paper, we propose a hybrid fuzzy set model by combining a linguistic interval-valued spherical fuzzy set with a soft set for MADM. The emergence of a linguistic interval-valued spherical fuzzy soft set (LIVSFSS) not only handles qualitative information and provides more freedom to decision makers, but also solves the inherent problem of insufficient parameterization tools for fuzzy set theory. To tackle the application challenges, we introduce the basic concepts and define some operations of LIVSFSS, e.g., the “complement”, the “AND”, the “OR”, the “necessity”, the “possibility” and so on. Subsequently, we prove De Morgan’s law, associative law, distribution law for operations on LIVSFSS. We further propose the linguistic weighted choice value and linguistic weighted overall choice value for MADM by taking parameter weights into account. Finally, the MADM algorithm and parameter reduction algorithm are provided based on LIVSFSS, together with examples and comparisons with some existing algorithms to illustrate the rationality and effectiveness of the proposed algorithms.

Salinity stress is one of the major abiotic stresses affecting crop growth and production. Rice is an important food crop in the world, but also a salt-sensitive crop, and the rice seedling stage is the most sensitive to salt stress, which directly affects the final yield formation. In this study, two RIL populations derived from the crosses of CD (salt-sensitive)/WD (salt-tolerant) and KY131 (salt-sensitive)/XBJZ (salt-tolerant) were used as experimental materials, and the score of salinity toxicity (SST), the relative shoot length (RSL), the relative shoot fresh weight (RSFW), and the relative shoot dry weight (RSDW) were used for evaluating the degree of tolerance under salt stress in different lines. The genetic linkage map containing 978 and 527 bin markers were constructed in two RIL populations. A total of 14 QTLs were detected on chromosomes 1, 2, 3, 4, 7, 9, 10, 11, and 12. Among them, qSST12-1, qSST12-2, and qRSL12 were co-localized in a 140-kb overlap interval on chromosome 12, which containing 16 candidate genes. Furthermore, transcriptome sequencing and qRT-PCR were analyzed in CD and WD under normal and 120 mM NaCl stress. LOC_Os12g29330, LOC_Os12g29350, LOC_Os12g29390, and LOC_Os12g29400 were significantly induced by salt stress in both CD and WD. Sequence analysis showed that LOC_Os12g29400 in the salt-sensitive parents CD and KY131 was consistent with the reference sequence (Nipponbare), whereas the salt-tolerant parents WD and XBJZ differed significantly from the reference sequence both in the promoter and exon regions. The salt-tolerant phenotype was identified by using two T3 homozygous mutant plants of LOC_Os12g29400; the results showed that the score of salinity toxicity (SST) of the mutant plants (CR-3 and CR-5) was significantly lower than that of the wild type, and the seedling survival rate (SSR) was significantly higher than that of the wild type, which indicated that LOC_Os12g29400 could negatively regulate the salinity tolerance of rice at the seedling stage. The results lay a foundation for the analysis of the molecular mechanism of rice salinity tolerance and the cultivation of new rice varieties.

To explore suitable synthesis parameters of efficient graft copolymerization on wool, the disulfide bonds in wool chains were reduced to sulfhydryl groups by the treatment of thioglycolic acid to wool, and then wool-g-poly(glycidyl methacrylate) was prepared by graft copolymerization of wool with glycidyl methacrylate by building a redox system between sulfhydryl groups and ammonium persulfate. The wool-g-poly(glycidyl methacrylate) was characterized by the analyses of Fourier transform infrared spectroscopy, scanning electron microscopy, thermogravimetric and x-ray diffraction. Influences of molar concentrations of monomer and initiator as well as reaction temperature on grafting ratios were investigated. The experimental results showed that the sulfhydryl groups/ammonium persulfate redox system built could effectively initiate graft polymerization of lipophilic glycidyl methacrylate on the wool surface in an aqueous medium. The suitable process parameters of graft copolymerization were: 0.6 mmol/L molar concentration of glycidyl methacrylate, 3.0 mmol/L molar concentration of ammonium persulfate, and reaction temperature of 50 ℃. At the suitable parameters, the grafting ratio of wool-g-poly(glycidyl methacrylate) showed a maximum value of 195.8 %, indicating an efficient graft copolymerization was achieved. The copolymerization could reduce the degree of crystallinity of wool. The wool-g-poly(glycidyl methacrylate) had higher thermal stability than raw wool at a temperature of below 406 ℃ by performing the thermogravimetric analysis. Based on the results, we successfully built new sulfhydryl groups on the wool/ammonium persulfate redox system, prepared the wool-g-poly(glycidyl methacrylate), and this work will lay an important foundation for the application of wool-g-poly(glycidyl methacrylate) in the textile field.

BackgroundSalinity tolerance plays a vital role in rice cultivation because the strength of salinity tolerance at the seedling stage directly affects seedling survival and final crop yield in saline soils. Here, we combined a genome-wide association study (GWAS) and linkage mapping to analyze the candidate intervals for salinity tolerance in Japonica rice at the seedling stage.ResultsWe used the Na+ concentration in shoots (SNC), K+ concentration in shoots (SKC), Na+/K+ ratio in shoots (SNK), and seedling survival rate (SSR) as indices to assess the salinity tolerance at the seedling stage in rice. The GWAS identified the lead SNP (Chr12_20864157), associated with an SNK, which the linkage mapping detected as being in qSK12. A 195-kb region on chromosome 12 was selected based on the overlapping regions in the GWAS and the linkage mapping. Based on haplotype analysis, qRT-PCR, and sequence analysis, we obtained LOC_Os12g34450 as a candidate gene.ConclusionBased on these results, LOC_Os12g34450 was identified as a candidate gene contributing to salinity tolerance in Japonica rice. This study provides valuable guidance for plant breeders to improve the response of Japonica rice to salt stress.

Abstract With the expansion of the epidemic, online multimedia teaching has become a common trend. The reasoning model of multimedia teaching evaluation is a useful tool to infer the result of teaching effects and predict the tendency. However, the ambiguity in the linguistic-valued evaluation leads to reasoning problems always in the context with uncertainty. To make the reasoning model better deal with multiple and multidimensional reasoning problems in uncertainty environment, while considering both positive evidence and negative evidence at the same time, this paper mainly focuses on a linguistic truth-valued intuitionistic fuzzy layered aggregation (LTV-IFLA) reasoning method. First, based on the layered linguistic truth-valued intuitionistic fuzzy lattice (LTV-IFL), we realize aggregating the linguistic truth-valued information through the layered average aggregation (LAA) operator presented by this paper. Furthermore, a layered weighted average aggregation (LWAA) operator is proposed to consider setting different weights to achieve personalization of the reasoning results. Finally, a multiple multidimensional reasoning model which simulates the reasoning of human language is presented to illustrate the method’s rationality and validity.

Abstract Background Plant height is a key factor in the determination of rice yield since excessive height can easily cause lodging and reduce yield. Therefore, the identification and analysis of plant height-related genes to elucidate their physiological, biochemical, and molecular mechanisms have significant implications for rice breeding and production. Results High-throughput quantitative trait locus (QTL) sequencing analysis of a 638-individual F2:3 mapping population resulted in the identification of a novel height-related QTL (qPH9), which was mapped to a 2.02-Mb region of Chromosome 9. Local QTL mapping, which was conducted using 13 single nucleotide polymorphism (SNP)-based Kompetitive allele-specific PCR (KASP) markers for the qPH9 region, and traditional linkage analysis, facilitated the localization of qPH9 to a 126-kb region that contained 15 genes. Subsequent haplotype and sequence analyses indicated that OsPH9 was the most probable candidate gene for plant height at this locus, and functional analysis of osph9 CRISPR/Cas9-generated OsPH9 knockout mutants supported this conclusion. Conclusion OsPH9 was identified as a novel regulatory gene associated with plant height in rice, along with a height-reducing allele in ‘Dongfu-114’ rice, thereby representing an important molecular target for rice improvement. The findings of the present study are expected to spur the investigation of genetic mechanisms underlying rice plant height and further the improvement of rice plant height through marker-assisted selection.

Abstract Bortezomib, a proteasome inhibitor, proved potent in the treatment of recurrent multiple myeloma or mantle cell lymphoma. However, slow progress was made when it was applied to treat solid tumors. We discovered that different head and neck squamous cell carcinoma (HNSCC) cell lines had significantly different sensitivities to bortezomib, and also demonstrated that individual relatively sensitive HNSCC cell lines had fewer ΔNp63α expressions. Based on these findings, we speculated that ΔNp63α may be a key factor in the resistance of HNSCC cells to bortezomib. ΔNp63α knockdown made HNSCC more sensitive to bortezomib, while ΔNp63α overexpression made it more resistant. RNA sequencing (RNA-seq) analysis of ΔNp63α-knockdown cells revealed clear alterations in the subset of genes that were associated with oxidative stress and antioxidant defense. The gene CYGB was downregulated significantly. CHIP-seq detection showed that CYGB was the transcriptional regulatory site of ΔNp63α. CHIP-PCR showed evidence of ΔNp63α binding. The detection of the dual-luciferase reporter gene demonstrated that ΔNp63α significantly enhanced the CYGB promoter activity. Furthermore, we confirmed that CYGB plays a role in clearing excess ROS induced by bortezomib to inhibit HNSCC apoptosis. Consequently, ΔNp63α regulated the expression of CYGB in HNSCC. CYGB was the target of transcription regulation of ΔNp63α. It reduced apoptosis by clearing excess ROS produced by bortezomib, and thus exerted drug resistance.

Abstract Background Rice (Oryza sativa L.) is one of the most widely grown food crops, and its yield and quality are particularly important for a warm-saturated diet. Cold stress restricts rice growth, development, and yield; however, the specific mechanism of cold tolerance in rice remains unknown. Results The analysis of leaf physiological and photosynthetic characteristics showed that the two rice varieties were significantly affected by cold stress, but the cold-tolerant variety KY131 had more stable physiological characteristics, maintaining relatively good photosynthetic capacity. To better explore the transcriptional regulation mechanism and biological basis of rice response to cold stress, a comprehensive analysis of the rice transcriptome and lipidome under low temperature and control temperature conditions was carried out. The transcriptomic analysis revealed that lipid metabolism, including membrane lipid and fatty acid metabolism, may be an important factor in rice cold tolerance, and 397 lipid metabolism related genes have been identified. Lipidomics data confirmed the importance of membrane lipid remodeling and fatty acid unsaturation for rice adaptation to cold stress. This indicates that the changes in the fluidity and integrity of the photosynthetic membrane under cold stress lead to the reduction of photosynthetic capacity, which could be relieved by increased levels of monogalactosyldiacylglycerol that mainly caused by markedly increased expression of levels of 1,2-diacylglycerol 3-beta-galactosyltransferase (MGD). The upregulation of phosphatidate phosphatase (PAP2) inhibited the excessive accumulation of phosphatidate (PA) to produce more phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG), thereby preventing of membrane phase transition under cold stress. In addition, fatty acid β-oxidation is worth further study in rice cold tolerance. Finally, we constructed a metabolic model for the regulatory mechanism of cold tolerance in rice, in which the advanced lipid metabolism system plays a central role. Conclusions Lipidome analysis showed that membrane lipid composition and unsaturation were significantly affected, especially phospholipids and galactolipids. Our study provides new information to further understand the response of rice to cold stress.

Improving rice yield is one of the most important food issues internationally. It is an undeniable goal of rice breeding, and the effective panicle number (EPN) is a key factor determining rice yield. Increasing the EPN in rice is a major way to increase rice yield. Currently, the main quantitative trait locus (QTL) for EPN in rice is limited, and there is also limited research on the gene for EPN in rice. Therefore, the excavation and analysis of major genes related to EPN in rice is of great significance for molecular breeding and yield improvement. This study used japonica rice varieties Dongfu 114 and Longyang 11 to construct an F5 population consisting of 309 individual plants. Two extreme phenotypic pools were constructed by identifying the EPN of the population, and QTL-seq analysis was performed to obtain three main effective QTL intervals for EPN. This analysis also helped to screen out 34 candidate genes. Then, EPN time expression pattern analysis was performed on these 34 genes to screen out six candidate genes with higher expression levels. Using a 3K database to perform haplotype analysis on these six genes, we selected haplotypes with significant differences in EPN. Finally, five candidate genes related to EPN were obtained.

The Green Revolution gene sd1 has been used extensively in modern rice breeding, especially in indica cultivars. However, elite sd1 alleles and related germplasm resources used for japonica rice breeding have not been identified, and extensive efforts are needed for japonica rice breeding to obtain new dwarfing sources. Data from MBKbase-Rice revealed seven sd1 haplotypes in indica and four in japonica rice. Two new sd1 alleles were identified in indica rice. In 295 japonica accessions from northeast Asia, except for the weak functional allele SD1-EQ, sd1-r was the major allele, reducing plant height in comparison with SD1-EQ. Japonica germplasm resources carrying reported sd1 alleles were identified by genotype searching and further verified by literature search, genealogical analysis, and dCaps markers. Pedigrees and geographic distribution showed that sd1-r is an excellent allele widely used in northern China and Tohoku in Japan, and sd1-j is commonly used in east China and Kyushu in Japan. Dongnong- and Xiushui-series cultivars carrying sd1-r and sd1-j, respectively, are essential branches of the backbone parents of Chinese japonica rice, Akihikari and Ce21, with the largest number of descendants and derived generations. In semi-dwarf japonica rice breeding, sd1-d was introgressed into Daohuaxiang 2 (DHX2). Dwarf and semi-dwarf lines carrying sd1-d were selected and designated as 1279 and 1280, respectively, after withstanding typhoon-induced strong winds and heavy rains in 2020, and are anticipated to become useful intermediate materials for future genetic research and breeding. This work will facilitate the introduction, parental selection, and marker-assisted breeding, and provide a material basis for the next step in identifying favorable genes that selected together with the sd1 alleles in japonica backbone parents.

Abstract Background This study investigated the role of lncRNA CASC15 in laryngeal squamous cell carcinoma (LSCC). Methods This study included 58 LSCC patients. Both tumor (LSCC) and adjacent (within 3 cm around tumors) non-tumor tissues from 3 different sites of each patient were collected. CCK-8 assay was used to determine cell proliferation. The expression levels of proteins and mRNAs were determined by Western blotting analysis and qRT-PCRs, respectively. Results CASC15 was upregulated in LSCC and high expression levels of CASC15 predicted poor survival. In LSCC tissues, CASC15 was negatively correlated with miR-365 but positively correlated with cyclin D1. In LSCC cells, overexpression of CASC15 resulted in downregulation of miR-365 and upregulation of cyclin D1. Overexpression of miR-365 did not affect the expression of CASC15 but downregulated cyclin D1. Overexpression of Cyclin D1 did not affect the expression of miR-365 and CASC15. Overexpression of CASC15 and cyclin D1 led to promoted, while overexpression of miR-365 led to inhibited LSCC cell proliferation. In addition, overexpression of miR-365 reduced the effects of overexpression of CASC15. Conclusion Therefore, CASC15 upregulates cyclin D1 by downregulating miR-365 in LSCC to promote cell proliferation.

Grain length (GL) is one of the crucial determinants of rice yield and quality. However, there is still a shortage of knowledge on the major genes controlling the inheritance of GL in japonica rice, which severely limits the improvement of japonica rice yields. Here, we systemically measured the GL of 667 F2 and 1570 BC3F3 individuals derived from two cultivated rice cultivars, Pin20 and Songjing15, in order to identify the major genomic regions associated with GL. A novel major QTL, qGL9.1, was mapped on chromosome 9, which is associated with the GL, using whole-genome re-sequencing with bulked segregant analysis. Local QTL linkage analysis with F2 and fine mapping with the recombinant plant revealed a 93-kb core region on qGL9.1 encoding 15 protein-coding genes. Only the expression level of LOC_Os09g26970 was significantly different between the two parents at different stages of grain development. Moreover, haplotype analysis revealed that the alleles of Pin20 contribute to the optimal GL (9.36 mm) and GL/W (3.31), suggesting that Pin20 is a cultivated species carrying the optimal GL variation of LOC_Os09g26970. Furthermore, a functional-type mutation (16398989-bp, G>A) located on an exon of LOC_Os09g26970 could be used as a molecular marker to distinguish between long and short grains. Our experiments identified LOC_Os09g26970 as a novel gene associated with GL in japonica rice. This result is expected to further the exploration of the genetic mechanism of rice GL and improve GL in rice japonica varieties by marker-assisted selection.

Abstract Background Skeletal muscle atrophy and fibrosis are pathological conditions that contribute to morbidity in numerous conditions including aging, cachexia, and denervation. Muscle atrophy is characterized as reduction of muscle fiber size and loss of muscle mass while muscle fibrosis is due to fibroblasts activation and excessive production of extracellular matrix. Purinergic receptor P2Y2 has been implicated in fibrosis. This study aims to elucidate the roles of P2Y2 in sleketal muscle atrophy and fibrosis. Methods Primary muscle fibroblasts were isolated from wild type and P2Y2 knockout (KO) mice and their proliferating and migrating abilities were assessed by CCK-8 and Transwell migration assays respectively. Fibroblasts were activated with TGF-β1 and assessed by western blot of myofibroblast markers including α-SMA, CTGF, and collagen I. Muscle atrophy and fibrosis were induced by transection of distal sciatic nerve and assessed using Masson staining. Results P2Y2 KO fibroblasts proliferated and migrated significantly slower than WT fibroblasts with or without TGF-β1.The proliferation and ECM production were enhanced by P2Y2 agonist PSB-1114 and inhibited by antagonist AR-C118925. TGF-β1 induced fibrotic activation was abolished by P2Y2 ablation and inhibited by AKT, ERK, and PKC inhibitors. Ablation of P2Y2 reduced denervation induced muscle atrophy and fibrosis. Conclusions P2Y2 is a promoter of skeletal muscle atrophy and activation of fibroblasts after muscle injury, which signaling through AKT, ERK and PKC. P2Y2 could be a potential intervention target after muscle injury.

Abstract Background Cold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular rice breeding. Results In this study, we employed high-throughput quantitative trait locus sequencing (QTL-seq) analyses in a 460-individual F2:3 mapping population to identify major QTL genomic regions governing cold tolerance at the seedling stage in rice. A novel major QTL (qCTS6) controlling the survival rate (SR) under low-temperature conditions of 9°C/10 days was mapped on the 2.60-Mb interval on chromosome 6. Twenty-seven single-nucleotide polymorphism (SNP) markers were designed for the qCST6 region based on re-sequencing data, and local QTL mapping was conducted using traditional linkage analysis. Eventually, we mapped qCTS6 to a 96.6-kb region containing 13 annotated genes, of which seven predicted genes contained 13 non-synonymous SNP loci. Quantitative reverse transcription PCR analysis revealed that only Os06g0719500, an OsbZIP54 transcription factor, was strongly induced by cold stress. Haplotype analysis confirmed that +376 bp (T>A) in the OsbZIP54 coding region played a key role in regulating cold tolerance in rice. Conclusion We identified OsbZIP54 as a novel regulatory gene associated with rice cold-responsive traits, with its Dongfu-104 allele showing specific cold-induction expression serving as an important molecular variation for rice improvement. This result is expected to further exploration of the genetic mechanism of rice cold tolerance at the seedling stage and improve cold tolerance in rice varieties by marker-assisted selection.

Transcranial alternating current stimulation (tACS) applies a sinusoidal oscillating current to modulate intrinsic oscillatory activity. Relevant studies of tACS have indicated that tACS can increase spontaneous brain activity in the occipital area. However, few studies have compared the effects of tACS with different current intensities on spontaneous brain activity in the occipital region. In this study, 10-Hz tACS was delivered to the occipital region at different current intensities (i.e., 1 and 2 mA). We investigated the effect of the tACS on both eyes-open and eyes-closed resting-state electroencephalography (EEG). A total of 20 subjects and fifteen subjects were recruited to participate in the 1-mA tACS experiment and the 2-mA tACS experiment, respectively. Ten subjects participated in both experiments. The experimental results demonstrated that both 1-mA tACS and 2-mA tACS could increase occipital resting-state EEG activities. For the eyes-open condition, alpha activity elicited by 2-mA tACS increased significantly greater than that elicited by 1-mA tACS, while 1-mA tACS could produce greater alpha activity compared to 2 mA for the eyes-closed condition. These results suggested that the optimal current intensity might be different for the eyes-open and eyes-closed resting-state conditions, laying a foundation for the subsequent study of occipital tACS on task-state EEG activities.

Water shortages and nitrogen (N) fertilizer overuse limit japonica rice production in Northeastern China. The interactions between water-saving irrigation and nitrogen management on rice root and shoot growth is still our research focus. Here, japonica rice (DN425) was subjected to the irrigation methods W1 (flooding irrigation), W2 [mild alternate wetting and drying irrigation (AWD); −10 kPa], W3 (severe AWD; −30 kPa), and different N fertilizer ratios were applied in different growth stages, namely, N1 (6:3:1:0), N2 (5:3:1:1), and N3 (4:3:2:1). From jointing to full heading stages, the highest photosynthate production capacity and root activity were obtained under W1N2. AWD markedly affected the root system and resulted in root senescence at later growth stages. Grain yield and N utilization efficiency were closely and positively correlated with the relative water content, crop growth rate (CGR), leaf area duration (LAD), the increase rate of root length density, root surface area density, and root volume density (RVD) from the jointing to full heading stages. This positive correlation was also observed in the increased rate of root bleeding sap (RBS) under W1N2 and CGR under W2N3. From full heading to maturity stages, N2 could promote root growth, LAD, and CGR under AWD to a greater extent than those under the other treatments. Water use efficiency (WUE) and N uptake efficiency (NUpE) were both negatively associated with the decreased rate of RVD, root dry weight (RDW), and RBS. They were closely and positively correlated with the increased rate of RDW and CGR. Our results suggested that W2N2 treatment delayed root senescence, maintained leaf photosynthesis, optimized the crop growth rate from full heading to maturity stages, and improved grain yield. The optimal grain yield, WUE, and NUpE were achieved at the irrigation water amount and topdressing fertilizer ratio of 41.40–50.34 × 102 and 31.20–34.83 kg ha–1, respectively.

Nitrogen-based nutrients are the main factors affecting rice growth and development. As the nitrogen (N) application rate increased, the nitrogen use efficiency (NUE) of rice decreased. Therefore, it is important to understand the molecular mechanism of rice plant morphological, physiological, and yield formation under low N conditions to improve NUE. In this study, changes in the rice morphological, physiological, and yield-related traits under low N (13.33 ppm) and control N (40.00 ppm) conditions were performed. These results show that, compared with control N conditions, photosynthesis and growth were inhibited and the carbon (C)/N and photosynthetic nitrogen use efficiency (PNUE) were enhanced under low N conditions. To understand the post-translational modification mechanism underlying the rice response to low N conditions, comparative phosphoproteomic analysis was performed, and differentially modified proteins (DMPs) were further characterized. Compared with control N conditions, a total of 258 DMPs were identified under low N conditions. The modification of proteins involved in chloroplast development, chlorophyll synthesis, photosynthesis, carbon metabolism, phytohormones, and morphology-related proteins were differentially altered, which was an important reason for changes in rice morphological, physiological, and yield-related traits. Additionally, inconsistent changes in level of transcription and protein modification, indicates that the study of phosphoproteomics under low N conditions is also important for us to better understand the adaptation mechanism of rice to low N stress. These results provide insights into global changes in the response of rice to low N stress and may facilitate the development of rice cultivars with high NUE by regulating the phosphorylation level of carbon metabolism and rice morphology-related proteins.

Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.

To provide the basis for thermal conductivity regulation of vermicular graphite cast iron (VGI), a new theoretical method consisting of shape interpolation, unit cell model and numerical calculation was proposed. Considering the influence of the graphite anisotropy and interfacial contact thermal conductivity (ICTC), the effective thermal conductivity of a series of unit cell models was calculated by numerical calculation based on finite difference. The effects of microstructure on effective thermal conductivity of VGI were studied by shape interpolation. The experimental results were in good agreement with the calculated ones. The effective thermal conductivity of VGI increases in power function with the decrease in graphite shape parameter, and increases linearly with the increase in graphite volume fraction and thermal conductivity of matrix. When the graphite volume fraction increases by 1%, the thermal conductivity of nodular cast iron increases by about 0.18 W/(m·K), while that of gray cast iron increases by about 3 W/(m·K). The thermal conductivity of cast iron has the same sensitivity to the thermal conductivity of matrix regardless of the graphite shape parameter. The thermal conductivity of matrix increased by 15 W/(m·K) and the thermal conductivity of cast iron increased by about 12 W/(m·K). Moreover, the more the graphite shape deviates from the sphere, the greater the enhancement effect of graphite anisotropy on thermal conductivity than the hindrance effect of interface between graphite and matrix. This work can provide guidance for the development of high thermal conductivity VGI and the study of thermal conductivity of composites containing anisotropic dispersed phase particles with complex shapes.

Drought stress at jointing and booting phases of plant development directly affects plant growth and productivity in rice. Limited by natural factors, the jointing and booting stages in rice varieties are known to overlap in high-latitude areas that are more sensitive to water deficit. However, the regulation of photosynthetic carbon fixation and sucrose metabolism in rice leaves under different degrees of drought stress remains unclear. In this study, rice plants were subjected to three degrees of drought stress (−10, −25, −and 40 kPa) for 15 days during the jointing-booting stage, we investigated photosynthetic carbon sequestration and sucrose metabolism pathways in rice leaves and analyzed key genes and regulatory networks using transcriptome sequencing in 2016. And we investigated the effects of drought stress on the growth periods of rice with overlapping growth periods in 2016 and 2017. The results showed that short-term drought stress promoted photosynthetic carbon fixation. However, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) activity significantly decreased, resulting in a significant decrease in photosynthetic rate. Drought stress increased the maximum activity of fructose-1,6-bisphosphate aldolase (FBA). FBA maintains the necessary photosynthetic rate during drought stress and provides a material base after the resumption of irrigation in the form of controlling the content of its reaction product triose phosphate. Drought stress significantly affected the activities of sucrose synthase (SuSase) and sucrose phosphate synthase (SPS). Vacuoles invertase (VIN) activity increased significantly, and the more severe the drought, the higher the VIN activity. Severe drought stress at the jointing-booting stage severely restricted the growth process of rice with overlapping growth stages and significantly delayed heading and anthesis stages. Transcriptome analysis showed that the number of differentially expressed genes was highest at 6–9 days after drought stress. Two invertase and four β-amylase genes with time-specific expression were involved in sucrose-starch metabolism in rice under drought stress. Combined with weighted gene co-expression network analysis, VIN and β-amylase genes up-regulated throughout drought stress were regulated by OsbZIP04 and OsWRKY62 transcription factors under drought stress. This study showed that any water deficit at the jointing-booting stage would have a serious effect on sucrose metabolism in leaves of rice with overlapping growth stages.

Abstract Background Salt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited. Results Here, an F2:3 population derived from a cross between IR36 (salt-sensitive) and Weiguo (salt-tolerant) was used to identify salt-tolerant QTL interval at the bud burst stage using a whole-genome sequencing-based QTL-seq containing 40 extreme salt-tolerant and 40 extreme salt-sensitive individuals. A major QTL, qRSL7, related to relative shoot length (RSL) was detected on chromosome 7 using ΔSNP index algorithms and Euclidean Distance (ED) algorithms. According to single nucleotide polymorphisms (SNPs) between the parents, 25 Kompetitive allele-specific PCR (KASP) markers were developed near qRSL7, and regional QTL mapping was performed using 199 individuals from the F2:3 population. We then confirmed and narrowed down qRSL7 to a 222 kb genome interval. Additionally, RNA sequencing (RNA-seq) was performed for IR36 and Weiguo at 36 h after salt stress and control condition at the bud burst stage, and 5 differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Furthermore, sequence analysis revealed a 1 bp Indel difference in Os07g0569700 (OsSAP16) between IR36 and Weiguo. OsSAP16 encodes a stress-associated protein whose expression is increased under drought stress. Conclusion These results indicate that OsSAP16 was the candidate gene of qRSL7. The results is useful for gene cloning of qRSL7 and for improving the salt tolerance of rice varieties by marker assisted selection (MAS).

Abstract Background Salinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. In this study, we combined linkage mapping and a genome-wide association study (GWAS) to analyze the genetic structure of this trait in japonica rice at the bud stage. Results A population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) for the root length under control condition (RL), alkaline stress (ARL) and relative root length (RRL) at the bud stage. A major QTL related to alkali tolerance at the rice bud stage, qAT11, was detected on chromosome 11. Interestingly, a GWAS identified a lead SNP (Chr_21,999,659) in qAT11 that was significantly associated with alkaline tolerance. After filtering by linkage disequilibrium (LD), haplotype analysis, quantitative real-time PCR, we obtained three candidate genes (LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390). In addition, we performed phenotype verification on the CRISPR/Cas9 mutant of LOC_Os11g37390. Conclusion Based on these results, LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390 were the candidate genes contributing to alkaline tolerance in japonica rice. This study provides resources for breeding aimed at improving rice responses to alkalinity stress.

Low temperatures stress is one of the important factors limiting rice yield, especially during rice anther development, and can cause pollen sterility and decrease grain yield. In our study, low-temperature stress decreased pollen viability and spikelet fertility by affecting the sugar, nitrogen and amino acid contents of anthers. We performed RNA-seq and ISO-seq experiments to study the genome-wide transcript expression profiles in low-temperature anthers. A total of 4,859 differentially expressed transcripts were detected between the low-temperature and control groups. Gene ontology enrichment analysis revealed significant terms related to cold tolerance. Hexokinase and glutamate decarboxylase participating in starch and sucrose metabolism may play important roles in the response to cold stress. Using weighted gene co-expression network analysis, nine hub transcripts were found that could improve cold tolerance throughout the meiosis period of rice: Os02t0219000-01 (interferon-related developmental regulator protein), Os01t0218350-00 (tetratricopeptide repeat-containing thioredoxin), Os08t0197700-00 (luminal-binding protein 5), Os11t0200000-01 (histone deacetylase 19), Os03t0758700-01 (WD40 repeat domain-containing protein), Os06t0220500-01 (7-deoxyloganetin glucosyltransferase), Pacbio.T01382 (sucrose synthase 1), Os01t0172400-01 (phospholipase D alpha 1), and Os01t0261200-01 (NAC domain-containing protein 74). In the PPI network, the protein minichromosome maintenance 4 (MCM4) may play an important role in DNA replication induced by cold stress.

Abstract Necrosis induces strong inflammation with undesirable implications in clinics compared with apoptosis. Fortunately, the switch between necrosis and apoptosis could be realized by tailoring the appropriate structural properties of gold nano rods (GNRs) that could precisely modulate cell death pathways. Herein, the intracellular interaction between GNRs and organelles is monitored and it is found that lysosomes dominates necrosis/apoptosis evoking. Then the surface molecule density of GNRs, which is first defined as ρsurf. molecule (Nsurf. molecules/(a × π × Diameter × Length)), mediates lysosome activities as the membrane permeabilization (LMP), the Cathepsin B and D release, the cross‐talk between lysosome and different organelles, which selectively evokes apoptosis or necrosis and the production of TNF‐α from macrophages. GNRs with small ρsurf. molecule mainly induce apoptosis, while with large ρsurf. molecule they greatly contribute to necrosis. Interestingly, necrosis can be suppressed by GNRs with higher ρsurf. molecule due to the overexpression of key protease caspase 8, which cleaves the RIP1‐RIP3 complex and activates caspase 3 followed by necrosis to apoptosis transition. This investigation indicates that the ρsurf. molecule greatly affects the utility of nanomaterials and different structural properties of nanomaterials have different implications in clinics.

Rice salt tolerance at the germination stage directly affects the germination rate and seedling establishment of rice directly seeded in saline soils, which in turn affects yield. In this study, we determined the relative germination potential (RGP) and relative germination index (RGI) under 200 mM salt stress and control conditions using 295 japonica rice accessions. Statistical analysis showed extensive phenotypic variations under salt stress conditions. Twenty-one varieties with an RGP ≥ 80% and an RGI ≥ 80% were screened. Based on genotypic data including, 788,396 single-nucleotide polymorphisms (SNPs), 40 quantitative trait loci (QTL) were localized on rice chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12, which were shown to be significantly associated with rice salt tolerance at the germination stage, including 20 for RGP and 20 for RGI, using genome-wide association analysis. Six QTL with ≥ 3 consecutive significant SNP loci and localized in the same LD interval were selected for further analysis. Four rice genes (LOC_Os01g04920, LOC_Os10g38350, LOC_Os10g38470, and LOC_Os10g38489) were selected as important candidates for salt tolerance based on haplotype analysis and functional annotation. The findings could facilitate the development of valuable rice varieties for direct seeding in salinized soil and improve japonica rice salt tolerance at the germination stage through molecular breeding.

Drought stress at jointing–booting directly affects plant growth and productivity in rice. Limited by natural factors, the jointing and booting stages of short-growth-period rice varieties are highly overlapped in high-latitude areas, which are more sensitive to water deficit. However, little is known about the dry matter translocation in rice and the strategies of starch synthesis and filling of superior and inferior grains under different drought stress was unclear. In this study, the rice plants were subjected to three degrees of drought stress (−10 kPa, −25 kPa, −40 kPa) for 15 days during the jointing–booting stage; we investigated dry matter accumulation and translocation, grain filling and enzyme activities to starch synthesis of superior and inferior grains in rice with overlapping growth stages from 2016 to 2017. The results showed that drought stress significantly reduced dry matter accumulation in the stems and leaves. Mild and moderate drought increased dry matter translocation efficiency. However, severe drought stress largely limited the dry matter accumulation and translocation. A large amount of dry matter remains in vegetative organs under severe drought stress. The high content in NSC in stem and sheath plays a key role in resisting drought stress. The drought stress at jointing–booting directly caused a change in the grain filling strategy. Under moderate and severe drought, the grain-filling active period of the superior grains was shortened to complete the necessary reproductive growth. The grain-filling active period of the inferior grains was significantly prolonged to avoid a decrease in grain yield. The significant decrease in the grain-filling rate of the superior and inferior grains caused a reduction in the thousand-grain weight. In particular, the influence of the grain-filling rate of inferior grains on the thousand-grain weight was more significant. Drought stress changed the starch synthesis strategies of the superior and inferior grains. Soluble starch synthase and starch branching enzyme activities of inferior grains increased significantly under drought stress. GBSS activity was not sensitive to drought stress. Therefore, amylose content was decreased and amylopectin synthesis was enhanced under drought stress, especially in inferior grains.

Rice (Oryza sativa L.) is an important crop in China. Although it is known that its yield is restricted by nitrogen (N) supply, the response of the root system to N supply specifically has not been systematically explored. This study aimed to investigate the effect of N uptake on grain yield to clarify the relationships between root morphophysiological traits and N uptake, and to understand relation between phytohormones and root morphophysiological traits. Two N-efficient absorption cultivars (NEAs) and two N-inefficient absorption cultivars (NIAs) were grown in the field, and three N conditions, deficient N (60 kg ha–1), intermediate N (180 kg ha–1), and sufficient N (240 kg ha–1), were applied during the growing season. The results showed higher dry matter and grain yield in NEAs than in NIAs, which was mainly attributed to increased N uptake in the mid- and late growth stages under all N conditions. And NEAs have different root regulation methods to obtain higher N accumulation and yield under different N supply conditions. Under lower N conditions, compared with NIAs, NEAs shown greater total root length, root oxidation activity, and root active absorbing surface area and smaller root diameter owing to higher indole-3-acetic acid and cytokinin content and lower 1-aminocyclopropane-1-carboxylic acid content in the early growth stages to respond to low N stress faster, laying a morphophysiological basis for its high N-uptake capacity in the mid- and late growth stages. Under higher N conditions, NEAs had higher root oxidation activity and root active absorbing surface area for N uptake and yield formation owing to higher abscisic acid and cytokinin content in the mid- and late growth stages, which improved the seed setting rate, thereby increasing the rice grain yield. These results suggest that NEAs can optimize the morphophysiological characteristics of roots through phytohormone regulation to adapt to different nutrient conditions, thereby promoting N accumulation and yield formation in rice.

Over-application of nitrogen (N) fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high N use efficiency (NUE) reduce fertilizer requirements, enabling sustainable agriculture. Genome-wide association study (GWAS) analysis of N absorption and utilization traits under low and high N conditions was performed to obtain 12 quantitative trait loci (QTLs) based on genotypic data including 151,202 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 267 japonica rice varieties. Eighteen candidate genes were obtained by integrating GWAS and transcriptome analyses; among them, the functions of OsNRT2.4, OsAMT1.2, and OsAlaAT genes in N transport and assimilation have been identified, and OsJAZ12 and OsJAZ13 also play important roles in rice adaptation to abiotic stresses. A NUE-related candidate gene, OsNAC68, was identified by quantitative real-time PCR (qRT-PCR) analyses. OsNAC68 encodes a NAC transcription factor and has been shown to be a positive regulator of the drought stress response in rice. Overexpression of OsNAC68 significantly increased rice NUE and grain yield under deficient N conditions, but the difference was not significant under sufficient N conditions. NUE and grain yield significantly decreased under both N supply conditions in the osbnac68 mutant. This study provides crucial insights into the genetic basis of N absorption and utilization in rice, and a NUE-related gene, OsNAC68, was cloned to provide important resources for rice breeding with high NUE and grain yield.

Abstract Background Salinity-alkalinity stress is one of the major factors limiting rice production. The damage caused by alkaline salt stress to rice growth is more severe than that caused by neutral salt stress. At present, the genetic resources (quantitative trait loci (QTLs) and genes) that can be used by rice breeders to improve alkalinity tolerance are limited. Here, we assessed the alkalinity tolerance of rice at the seedling stage and performed a genome-wide association study (GWAS) based on genotypic data including 788,396 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 295 japonica rice varieties. Results We used the score of alkalinity tolerance (SAT), the concentrations of Na+ and K+ in the shoots (SNC and SKC, respectively) and the Na+/K+ ratio of shoots (SNK) as indices to assess alkalinity tolerance at the seedling stage in rice. Based on population structure analysis, the japonica rice panel was divided into three subgroups. Linkage disequilibrium (LD) analysis showed that LD decay occurred at 109.77 kb for the whole genome and varied between 13.79 kb and 415.77 kb across the 12 chromosomes, at which point the pairwise squared correlation coefficient (r 2) decreased to half of its maximum value. A total of eight QTLs significantly associated with the SAT, SNC and SNK were identified by genome-wide association mapping. A common QTL associated with the SAT, SNC and SNK on chromosome 3 at the position of 15.0 Mb, which explaining 13.36~13.64% of phenotypic variation, was selected for further analysis. The candidate genes were filtered based on LD decay, Gene Ontology (GO) enrichment, RNA sequencing data, and quantitative real-time PCR (qRT-PCR) analysis. Moreover, sequence analysis revealed one 7-bp insertion/deletion (indel) difference in LOC_Os03g26210 (OsIRO3) between the alkalinity-tolerant and alkalinity-sensitive rice varieties. OsIRO3 encodes a bHLH-type transcription factor and has been shown to be a negative regulator of the Fe-deficiency response in rice. Conclusion Based on these results, OsIRO3 maybe a novel functional gene associated with alkalinity tolerance in japonica rice. This study provides resources for improving alkalinity tolerance in rice, and the functional molecular marker could be verified to breed new rice varieties with alkalinity tolerance via marker-assisted selection (MAS).

Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.

Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice. The identification of cold-tolerance quantitative trait loci (QTL) in species that can stably tolerate cold environments is crucial for the molecular breeding of rice with such traits. In our study, high-throughput QTL-sequencing analyses were performed in a 460-individual F2:3 mapping population to identify the major QTL genomic regions governing cold tolerance at the bud-bursting (CTBB) stage in rice. A novel major QTL, qCTBB9, which controls seed survival rate (SR) under low-temperature conditions of 5°C/9 days, was mapped on the 5.40-Mb interval on chromosome 9. Twenty-six non-synonymous single-nucleotide polymorphism (nSNP) markers were designed for the qCTBB9 region based on re-sequencing data and local QTL mapping conducted using traditional linkage analysis. We mapped qCTBB9 to a 483.87-kb region containing 58 annotated genes, among which six predicted genes contained nine nSNP loci. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that only Os09g0444200 was strongly induced by cold stress. Haplotype analysis further confirmed that the SNP 1,654,225 bp in the Os09g0444200 coding region plays a key role in regulating the cold tolerance of rice. These results suggest that Os09g0444200 is a potential candidate for qCTBB9. Our results are of great significance to explore the genetic mechanism of rice CTBB and to improve the cold tolerance of rice varieties by marker-assisted selection.

Abstract Long non‐coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. The spectacular progress made in next‐generation sequencing technologies has enabled a genome‐wide identification of lncRNAs in multiple plant species. In this study, a genome‐wide lncRNA sequencing technology was used to identify cold‐responsive lncRNAs at the booting stage in rice by comparing a tolerant variety, Kongyu131 (KY131) and a sensitive variety, Dongnong422 (DN422). A total of 1485 lncRNAs were identified, and 566 of these lncRNAs were defined as differential lncRNAs by comparing four samples. GO and KEGG enrichment analyses were performed, focusing on the cis‐ and trans‐ target genes of the differential lncRNAs. To identify cold‐responsive genes, a meta‐analysis was used to integrate 35 cold‐tolerant QTLs at the booting stage. In summary, 12 candidate genes and their target lncRNAs were identified by qRT‐PCR. LncTar was used to identify the interaction between lncRNAs and the candidate genes. In addition, 130 rice cultivars with rich genetic diversity were collected to verify the association of candidate genes with cold‐resistance. The results revealed that five SNPs in LOC_Os07g42940, three SNP and one InDel in LOC_Os02g03410 were associated with cold‐resistance at a significant level using association analysis. This study provides new gene resources and insights into cold‐resistance research for rice.

Heavy metal exposure is a serious environmental stress in plants. However, plants have evolved several strategies to improve their heavy metal tolerance. Heavy metal-associated proteins (HMPs) participate in heavy metal detoxification. Here, we identified 46 and 55 HMPs in rice and Arabidopsis, respectively, and named them OsHMP 1–46 and AtHMP 1–55 according to their chromosomal locations. The HMPs from both plants were divided into six clades based on the characteristics of their heavy metal-associated domains (HMA). The HMP gene structures and motifs varied greatly among the different classifications. The HMPs had high collinearity and were segmentally duplicated. A cis-element analysis revealed that the HMPs may be regulated by different transcription factors. An expression profile analysis disclosed that only eight OsHMPs were constitutive in rice tissues. Of these, the expression of OsHMP37 was far higher than that of the other seven genes while OsHMP28 was expressed exclusively in the roots. For Arabidopsis, nine AtHMPs presented with very high transcript levels in all organs. Most of the selected OsHMPs were differentially expressed in various tissues under different heavy metal stresses. Only OsHMP09, OsHMP18, and OsHMP22 showed higher expression levels in all tissues under different heavy metal stresses. In contrast, most of the selected AtHMPs had nearly constant expression levels in different tissues under various heavy metal stresses. The AtHMP20, AtHMP23, AtHMP25, AtHMP31, AtHMP35, AtHMP46 expression levels under different heavy metal stresses were higher in the leaves and roots. The foregoing discoveries elucidated HMP evolution in monocotyledonous and dicotyledonous plants and may helpful functionally characterize HMPs in the future.

Human papillomavirus (HPV) activates E2F1-driven transcription via the E7-RB-E2F1 pathway. A polymorphism in the 3’ UTR of E2F1 gene may disrupt a binding site for miRNA and may affect its transcription level, thus modifying the susceptibility to radiotherapy and outcomes through this pathway. We evaluated the association of a polymorphism at the 3’UTR miRNA binding site of E2F1 gene (rs3213180) with risk of recurrence of SCCOP in a cohort of 1008 patients. Log-rank test and univariate and multivariable Cox models were used to evaluate the associations. Compared with patients with E2F1-rs3213180 GG homozygous genotype, the patients with E2F1-rs3213180GC + CC variant genotypes had significantly better disease-free survival (log-rank P

Abstract Background Cold stress can cause serious abiotic damage that limits the growth, development and yield of rice. Cold tolerance during the booting stage of rice is a key factor that can guarantee a high and stable yield under cold stress. The cold tolerance of rice is controlled by quantitative trait loci (QTLs). Based on the complex genetic basis of cold tolerance in rice, additional efforts are needed to detect reliable QTLs and identify candidate genes. In this study, recombinant inbred lines (RILs) derived from a cross between a cold sensitive variety, Dongnong422, and strongly cold-tolerant variety, Kongyu131, were used to screen for cold-tolerant loci at the booting stage of rice. Results A novel major QTL, qPSST6, controlling the percent seed set under cold water treatment (PSST) under the field conditions of 17 °C cold water irrigation was located on the 28.4 cM interval on chromosome 6. Using the combination of bulked-segregant analysis (BSA) and next-generation sequencing (NGS) technology (Seq-BSA), a 1.81 Mb region that contains 269 predicted genes on chromosome 6 was identified as the candidate region of qPSST6. Two genes, LOC_Os06g39740 and LOC_Os06g39750, were annotated as “response to cold” by gene ontology (GO) analysis. qRT-PCR analysis revealed that LOC_Os06g39750 was strongly induced by cold stress. Haplotype analysis also demonstrate a key role of LOC_Os06g39750 in regulating the PSST of rice, suggesting that it was the candidate gene of qPSST6. Conclusions The information obtained in this study is useful for gene cloning of qPSST6 and for breeding cold-tolerant varieties of rice using marker assisted selection (MAS).

It has been widely considered that reversing epithelial-to-mesenchymal transition (EMT) is a potential access to restrain cancer progression and therapeutic resistance. Here, we aim to uncover the novel mechanisms by which we can reverse EMT and inhibit metastasis in laryngeal squamous cell carcinoma (LSCC). We show that miR-98 is significantly reduced in both LSCC specimens and cell lines. Over-expression of miR-98 inhibits the EMT-related gene expression and metastasis and invasive behavior in LSCC in vitro, as well as reduces lung metastasis in mouse model. In the mechanistically study, miR-98 directly targets HMGA2 in mediating EMT. HMGA2 knock down by si-RNA method declines several EMT-related genes expression and LSCC migration and invasion. In parallel, overexpression of HMGA2 transforms LSCC cells to acquire stem cell-like features. Furthermore, we reveal that HMGA2-mediated EMT is closely linked with the expression of POSTN that inhibits EMT, as a tumor suppressor, by gene profiling analyses. POSTN is transcriptionally repressed by HMGA2. In clinic, the HMGA2 mRNA level is negatively correlated with the miR-98 level in LSCC patient cohort. In conclusion, our study confers a powerful signal: miR-98-HMGA-POSTN in LSCC, which is able to reverse EMT and inhibit metastasis, underlining the therapeutic potential of this signal.

Objective: To investigate immune-related genetic background in bilateral sudden sensorineural hearing loss (SSNHL). Case report and methods: The case is a 45-year-old man presenting with a 7-year history of bilateral profound SSNHL. Blood biochemical testing demonstrated increased levels of total cholesterol (5.88 mmol/L). Tests for hepatitis B showed a positive antibody against the hepatitis B core antigen. Complement C3 was below the normal value, and complement C4 and IgG were in the lower range of normal values. CT images showed a normal inner ear and vestibular aqueduct but round window membranous ossification on both sides. A total number of 232 immune-associated genes were sequenced using the next generation sequencing technique. Results: Mutations were detected in 5 genes, including the phosphoinositide 3-kinase catalytic subunit delta (PIK3CD), caspase recruitment domain-containing protein 9 (CARD9), complement factor H-related (CFHR2), immunoglobulin lambda-like polypeptide 1 Protein (IGLL1), and transmembrane channel-like gene family 8 (TMC8). In the PIK3CD gene, a C896T substitute in exon 7 was detected. This mutation causes primary immunodeficiency and is an autosomal dominant disease. Conclusion: The PIK3CD C896T mutation responsible for primary immunodeficiency may contribute to the onset of bilateral SSNHL with subsequent rapid progression.

ObjectivesTo investigate the surgical outcomes of different uvulopalatopharyngoplasty (UPPP).Methods All subjects underwent overnight polysomnography and were evaluated using the Epworth sleepiness scale (ESS), the Quebec sleep questionnaire and the snoring scale at the baseline and 3 and 12 months following operation. The primary endpoint was the overall effective rate representing the sum of the surgical success rate and effective rate.ResultsThe overall effective rate at 12 months post surgery was 55.6% for simple UPPP, 95.8% for UPPP+GA, and 92.3% for UPPP+TBA. The surgical success rate at 3 and 12 months postoperation for UPPP+GA or UPPP+TBA was significantly higher than simple UPPP (P