Transcriptomic analysis reveals GA3 is involved in regulating flavonoid metabolism in grape development for facility cultivation.

Gibberellin, as one of the pivotal plant growth regulators, can improve fruit quality by altering fruit size and secondary metabolite content. Flavonoids are the most abundant secondary metabolites in grapes, which influence the color and quality of the fruit. However, the molecular mechanism of whether and how GA3 affects flavonoid metabolism has not been reported, especially for the 'Red globe' grape with delayed cultivation in Hexi corridor. In the present study, the 'Red globe' grape grown in delayed facilities was sprayed with 20, 40, 60, 80 and 100 mg/L GA3 at berries pea size (BPS), veraison (V) and berries ripe (BR), respectively. The results showed that the berry weight, soluble sugar content and secondary metabolite content (the flavonoid content, anthocyanin content and polyphenol content) at BR under 80 mg/L GA3 treatment were remarkably increased compared with other concentration treatments. Therefore, RNA sequencing (RNA-seq) was used to analyze the differentially expressed genes (DEGS) and pathways under 80 mg/L GA3 treatment at three periods. GO analysis showed that DEGs were closely related to transporter activity, cofactor binding, photosynthetic membrane, thylakoid, ribosome biogenesis and other items. The KEGG enrichment analysis found that the DEGs were mainly involved in flavonoid biosynthesis and phenylpropanoid biosynthesis, indicating GA3 exerted an impact on the color and quality of berries through these pathways. In conclusion, GA3 significantly increased the expression of genes related to flavonoid synthesis, enhanced the production of secondary metabolites, and improved fruit quality. In addition, these findings can provide a theoretical basis for GA3 to modulate the accumulation and metabolism of flavonoids in grape fruit.

mTOR Signaling Pathway in Bone Diseases Associated with Hyperglycemia.

The interplay between bone and glucose metabolism has highlighted hyperglycemia as a potential risk factor for bone diseases. With the increasing prevalence of diabetes mellitus worldwide and its subsequent socioeconomic burden, there is a pressing need to develop a better understanding of the molecular mechanisms involved in hyperglycemia-mediated bone metabolism. The mammalian target of rapamycin (mTOR) is a serine/threonine protein kinase that senses extracellular and intracellular signals to regulate numerous biological processes, including cell growth, proliferation, and differentiation. As mounting evidence suggests the involvement of mTOR in diabetic bone disease, we provide a comprehensive review of its effects on bone diseases associated with hyperglycemia. This review summarizes key findings from basic and clinical studies regarding mTOR's roles in regulating bone formation, bone resorption, inflammatory responses, and bone vascularity in hyperglycemia. It also provides valuable insights into future research directions aimed at developing mTOR-targeted therapies for combating diabetic bone diseases.

Molecular cloning and functional characterization of MhHEC2-like genes in Malus halliana reveals it enhances Fe (iron) deficiency tolerance.

The basic helix-loop-helix (bHLH) family, as one of the largest families of transcription factors (TFs) in plants, plays crucial roles in regulating growth, development, and abiotic stress responses. However, studies on the association of the bHLH genes with apple iron (Fe) deficiency are limited. Here, multiple bHLH genes that responded to Fe deficiency were selected for quantitative real-time PCR in Malus halliana. The results showed that the expression of HEC2-like gene exerted more values compared to other genes under Fe deficiency stress, but the mechanism by which it regulates Fe deficiency stress is unclear. Subsequently, MhHEC2-like gene (ID: 103,455,961) was cloned from M. halliana for functional identification. We found that both transgenic Arabidopsis thaliana and tobacco displayed less chlorosis and more robust growth than wild-type (WT) controls under Fe deficiency stress. At the same time, the overexpressed apple calli grew prominently larger and better under Fe deficiency compared to the wild type. On the other hand, physiological index measurements revealed that overexpressed MhHEC2-like gene enhanced tolerance to Fe deficiency stress in A. thaliana and tobacco by promoting the synthesis of photosynthetic pigments, improving antioxidant enzyme activity, and enhancing Fe reduction, and strengthened tolerance to Fe deficiency stress in apple calli by reducing pH, boosting Fe reduction, and increasing antioxidant enzyme activity. To sum up, the overexpression of MhHEC2-like gene strengthened tolerance to Fe deficiency stress in Arabidopsis thaliana, tobacco, and apple calli.

Saline-alkali stress tolerance is enhanced by MhPR1 in Malus halliana leaves as shown by transcriptomic analyses.

MAIN CONCLUSION: qRT-PCR analysis showed that MhPR1 was strongly induced by saline-alkali stress. Overexpression of MhPR1 enhanced tolerance to saline-alkali stress in transgenic tobacco (Nicotiana tabacum L.) and apple calli. Abstract: Soil salinization seriously threaten apple growth in Northwest loess plateau of China. Malus halliana has developed special system to adapt to saline-alkali environmental stress. To obtain a more detailed understanding of the adaptation mechanisms involved in M. halliana, a transcriptomic approach was used to analyze the leaves' pathways in the stress and its regulatory mechanisms. RNA-Seq showed that among the 16,246 investigated unigenes under saline-alkali stress, 7268 genes were up-regulated and 8978 genes were down-regulated. KEGG analysis indicated that most of the enriched saline-alkali-responsive genes were mainly involved in plant hormone, calcium signal transduction, amino acids, carotenoid and flavonoids biosynthesis, carbon and phenylalanine metabolism, and other secondary metabolites. Expression profile analysis by quantitative real-time PCR confirmed that the maximum up-regulation of MhPR1 under saline-alkali stress was 7.1 folds in leaves. Overexpression of MhPR1 enhanced tolerance to saline-alkali stress in transgenic tobacco (Nicotiana tabacum L.) and apple calli. Taken together, our results demonstrate that MhPR1 encodes a saline-alkali-responsive transcriptional activator and provide valuable information for further study of PR1 functions in apple.

Genome-wide analysis of the bZIP gene lineage in apple and functional analysis of MhABF in Malus halliana.

MAIN CONCLUSION: 51 MdbZIP genes were identified from the apple genome by bioinformatics methods. MhABF-OE improved tolerance to saline-alkali stress in Arabidopsis, indicating it is involved in positive regulation of saline-alkali stress response. Saline-alkali stress is a major abiotic stress limiting plant growth all over the world. Members of the bZIP family play an important role in regulating gene expression in response to many kinds of biotic and abiotic stress, including salt stress. According to the transcriptome data, 51 MdbZIP genes responding to saline-alkali stress were identified in apple genome, and their gene structures, conserved protein motifs, phylogenetic analysis, chromosome localization, and promoter cis-acting elements were analyzed. Based on transcriptome data analysis, a MdbZIP family gene (MD15G1081800), which was highly expressed under stress, was selected to isolate and named as MhABF. Expression profile analysis by quantitative real-time PCR confirmed that the expression of MhABF in the leaves of Malus halliana was 10.6-fold higher than that of the control (0 days) after 2 days of stress. Then an MhABF gene was isolated from apple rootstock M. halliana. CaMV35S promoter drived MhABF gene expression vector was constructed to infect Arabidopsis with Agrobacterium-mediated infection. And overexpression MhABF gene plants were obtained. Compared with wild type, transgenic plants grew better under saline-alkali stress and the MhABF-OE lines showed higher chlorophyll content, POD, SOD and CAT activity, which indicated that they had strong resistance to stress. These results indicate that MhABF plays an important role in plant resistance to saline-alkali stress, which lays a foundation for further study on the functions in apple.

Transcriptome analysis reveals wax and phytohormone metabolism potentially involved in shooting shrivelling of apple branches overwinter.

Shoot shrivelling severely threatens growth and development of deciduous trees in the northern hemisphere, and we observed that there was a significant difference in shoot shrivelling rate between different apple varieties in practice. In this study, we investigated the anatomical and physiological characteristics of branches from different germplasm resources combined with an analysis of the transcriptome. Transcriptomes of samples treated in the initial dormancy, deep dormancy and freeze-thaw periods were generated and characterised. In three different periods, 7233 differentially expressed genes (DEGs) were identified including 3538 upregulated genes and 3695 downregulated genes. DEGs related to plant hormone signal transduction, starch and sucrose metabolism, cutin, suberin and wax biosynthesis were significantly enriched. Physiological characterisation showed that dormancy overwinter can induce the accumulation of soluble sugar and starch, shoot shrivelling rate of 'Fuji' was 2.31times that of the 'Delicious'; and the critical water content of 'Delicious' was significantly higher than 'Fuji'. Phytohormone contents and proportions varied irregularly according to the overwintering phase among two varieties. Wax content, morphology and composition also exhibited difference. In conclusion, branch microstructure, phytohormone and wax metabolism all determined the overwintering performance of trees and phytohormones can regulate wax metabolism to ensure normal overwintering of trees.

Discovering genetic linkage between periodontitis and type 1 diabetes: A bioinformatics study.

Background: Relationship between periodontitis (PD) and type 1 diabetes (T1D) has been reported, but the detailed pathogenesis requires further elucidation. This study aimed to reveal the genetic linkage between PD and T1D through bioinformatics analysis, thereby providing novel insights into scientific research and clinical treatment of the two diseases. Methods: PD-related datasets (GSE10334, GSE16134, GSE23586) and T1D-related datasets(GSE162689)were downloaded from NCBI Gene Expression Omnibus (GEO). Following batch correction and merging of PD-related datasets as one cohort, differential expression analysis was performed (adjusted p-value <0.05 and ∣log2 fold change| > 0.5), and common differentially expressed genes (DEGs) between PD and T1D were extracted. Functional enrichment analysis was conducted via Metascape website. The protein-protein interaction (PPI) network of common DEGs was generated in The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Hub genes were selected by Cytoscape software and validated by receiver operating characteristic (ROC) curve analysis. Results: 59 common DEGs of PD and T1D were identified. Among these DEGs, 23 genes were commonly upregulated, and 36 genes were commonly downregulated in both PD- and T1D-related cohorts. Functional enrichment analysis indicated that common DEGs were mainly enriched in tube morphogenesis, supramolecular fiber organization, 9 + 0 non-motile cilium, plasma membrane bounded cell projection assembly, glomerulus development, enzyme-linked receptor protein signaling pathway, endochondral bone morphogenesis, positive regulation of kinase activity, cell projection membrane and regulation of lipid metabolic process. After PPI construction and modules selection, 6 hub genes (CD34, EGR1, BBS7, FMOD, IGF2, TXN) were screened out and expected to be critical in linking PD and T1D. ROC analysis showed that the AUC values of hub genes were all greater than 70% in PD-related cohort and greater than 60% in T1D-related datasets. Conclusion: Shared molecular mechanisms between PD and T1D were revealed in this study, and 6 hub genes were identified as potential targets in treating PD and T1D.

Different biomechanical effects of clear aligners in bimaxillary space closure under two strong anchorages: finite element analysis.

BACKGROUND: Clear aligner (CA) treatment has been gaining popularity, but the biomechanical effects of CAs in bimaxillary dentition have not been thoroughly investigated. Direct and indirect strong anchorages are two common anchorage control methods, but the underlying biomechanical mechanism has not yet been elucidated. This study aimed to investigate the different biomechanical effects of CAs in closing the bimaxillary space under different anchorage controls, further instructing the compensation strategies design and strong anchorage choice in clinical practice. METHODS: Three-dimensional (3D) bimaxillary models of different anchorage controls were created based on cone-beam computed tomography and intraoral scan data. Four first premolars were extracted using 3D modeling software. Finite element analysis was conducted to simulate the space closure process of the CAs. RESULTS: In the two strong anchorage groups, the bimaxillary dentition presented different movement patterns during the space closure process, and the lower dentition was more vulnerable to elastic force. From the vertical view, direct strong anchorage with elastic force had the advantage of flattening the longitudinal occlusal curve and resisting the roller-coaster effects, whereas indirect strong anchorage could lead to a deep longitudinal occlusal curve. From the sagittal view, indirect strong anchorage with metallic ligaments had a greater instantaneous anchorage protection effect, particularly in the lower dentition, which reduced the mesial movement of the posterior teeth by nearly four times that of the direct anchorage group. In addition, indirect strong anchorage presented better anterior teeth torque/tipping control, while direct strong anchorage could aggravate lingual tipping of the upper central incisors. Due to the differences in anterior-posterior anchorage and arch shape, compared with the upper dentition, anchorage preservation and vertical control effects were amplified in the lower dentition. CONCLUSIONS: The biomechanical effects of CAs differed between the two strong anchorage groups. Due to the differences in dentition morphology, anterior-posterior anchorage, and dental arch shape, CAs present different biomechanical effects in bimaxillary space closure. Orthodontists should consider the corresponding mechanical compensation according to specific anchorage control methods and dentitions.

The Potential Therapeutic Role of Mesenchymal Stem Cells-Derived Exosomes in Osteoradionecrosis.

As one of the most serious complications of radiotherapy, osteoradionecrosis (ORN) seriously affects the quality of life of patients and even leads to death. Vascular injury and immune disorders are the main causes of bone lesions. The traditional conservative treatment of ORN has a low cure rate and high recurrent. Exosomes are a type of extracellular bilayer lipid vesicles secreted by almost all cell types. It contains cytokines, proteins, mRNA, miRNA, and other bioactive cargos, which contribute to several distinct processes. The favorable biological functions of mesenchymal stem cells-derived exosomes (MSC exosomes) include angiogenesis, immunomodulation, bone regeneration, and ferroptosis regulation. Exploring the characteristic of ORN and MSC exosomes can promote bone regeneration therapies. In this review, we summarized the current knowledge of ORN and MSC exosomes and highlighted the potential application of MSC exosomes in ORN treatment.

Using k-dependence causal forest to mine the most significant dependency relationships among clinical variables for thyroid disease diagnosis.

Numerous data mining models have been proposed to construct computer-aided medical expert systems. Bayesian network classifiers (BNCs) are more distinct and understandable than other models. To graphically describe the dependency relationships among clinical variables for thyroid disease diagnosis and ensure the rationality of the diagnosis results, the proposed k-dependence causal forest (KCF) model generates a series of submodels in the framework of maximum spanning tree (MST) and demonstrates stronger dependence representation. Friedman test on 12 UCI datasets shows that KCF has classification accuracy advantage over the other state-of-the-art BNCs, such as Naive Bayes, tree augmented Naive Bayes, and k-dependence Bayesian classifier. Our extensive experimental comparison on 4 medical datasets also proves the feasibility and effectiveness of KCF in terms of sensitivity and specificity.