De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes

Prunus subgenus Cerasus (Mill) A. Gray, commonly known as cherries and cherry blossoms, possesses significant edible and ornamental value. However, the mitochondrial genomes (mitogenomes) of cherry species remain largely unexplored. Here, we successfully assembled the mitogenomes of five cherry species (P. campanulata, P. fruticosa, P. mahaleb, P. pseudocerasus, and P. speciosa), revealing common circular structures. The assembled mitogenomes exhibited sizes ranging from 383,398 bp to 447,498 bp, with GC content varying between 45.54% and 45.76%. A total of 62 to 69 genes were annotated, revealing variability in the copy number of protein-coding genes (PCGs) and tRNA genes. Mitogenome collinearity analysis indicated genomic rearrangements across Prunus species, driven by repetitive sequences, particularly dispersed repeats. Additionally, the five cherry species displayed highly conserved codon usage and RNA editing patterns, highlighting the evolutionary conservation of the mitochondrial PCGs. Phylogenetic analyses confirmed the monophyly of subg. Cerasus, although notable phylogenetic incongruences were observed between the mitochondrial and plastid datasets. These results provide significant genomic resources for forthcoming studies on the evolution and molecular breeding of cherry mitogenomes, enhancing the overall comprehension of mitogenome structure and evolution within Prunus

The LDL1/2-HDA6 Histone Modification Complex Interacts With TOC1 and Regulates the Core Circadian Clock Components in Arabidopsis

In Arabidopsis, the circadian rhythm is associated with multiple important biological processes and maintained by multiple interconnected loops that generate robust rhythms. The circadian clock central loop is a negative feedback loop composed of the core circadian clock components. TOC1 (TIMING OF CAB EXPRESSION 1) is highly expressed in the evening and negatively regulates the expression of CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)/LHY (LATE ELONGATED HYPOCOTYL). CCA1/LHY also binds to the promoter of TOC1 and represses the TOC1 expression. Our recent research revealed that the histone modification complex comprising of LYSINE-SPECIFIC DEMETHYLASE 1 (LSD1)-LIKE 1/2 (LDL1/2) and HISTONE DEACETYLASE 6 (HDA6) can be recruited by CCA1/LHY to repress TOC1 expression. In this study, we found that HDA6, LDL1, and LDL2 can interact with TOC1, and the LDL1/2-HDA6 complex is associate with TOC1 to repress the CCA1/LHY expression. Furthermore, LDL1/2-HDA6 and TOC1 co-target a subset of genes involved in the circadian rhythm. Collectively, our results indicate that the LDL1/2-HDA6 histone modification complex is important for the regulation of the core circadian clock components

Identification of a cellular senescence-related-lncRNA (SRlncRNA) signature to predict the overall survival of glioma patients and the tumor immune microenvironment

Background: Gliomas are brain tumors that arise from glial cells, and they are the most common primary intracranial tumors with a poor prognosis. Cellular senescence plays a critical role in cancer, especially in glioma. In this study, we constructed a senescence-related lncRNA (SRlncRNA) signature to assess the prognosis of glioma.Methods: The Cancer Genome Atlas was used to collect SRlncRNA transcriptome profiles and clinical data about glioma. Patients were randomized to training, testing, and whole cohorts. LASSO and Cox regression analyses were employed to construct the SRlncRNA signature, and Kaplan–Meier (K-M) analysis was performed to determine each cohort’s survival. Receiver operating characteristic (ROC) curves were applied to verify the accuracy of this signature. Gene set enrichment analysis was used to visualize functional enrichment (GSEA). The CIBERSORT algorithm, ESTIMATE and TIMER databases were utilized to evaluate the differences in the infiltration of 22 types of immune cells and their association with the signature. RT–qPCR and IHC were used to identify the consistency of the signature in tumor tissue.Results: An SRlncRNA signature consisting of six long non-coding RNAs (lncRNAs) was constructed, and patients were divided into high-risk and low-risk groups by the median of their riskscore. The KM analysis showed that the high-risk group had worse overall survival, and the ROC curve confirmed that the riskscore had more accurate predictive power. A multivariate Cox analysis and its scatter plot with clinical characteristics confirmed the riskscore as an independent risk factor for overall survival. GSEA showed that the GO and KEGG pathways were mainly enriched in the immune response to tumor cells, p53 signaling pathway, mTOR signaling pathway, and Wnt signaling pathway. Further validation also yielded significant differences in the risk signature in terms of immune cell infiltration, which may be closely related to prognostic differences, and qRT–PCR and IHC confirmed the consistency of the expression differences in the major lncRNAs with those in the prediction model.Conclusion Our findings indicated that the SRlncRNA signature might be used as a predictive biomarker and that there is a link between it and immune infiltration. This discovery is consistent with the present categorization system and may open new avenues for research and personalized therapy

Numerical Study on the Disturbance Effect of Short-Distance Parallel Shield Tunnelling Undercrossing Existing Tunnels

The construction of new tunnels poses a threat to the operational safety of closely existing tunnels, and the construction mode of parallel undercrossing over short distances has the most significant impact. In this study, a new double-line shield tunnel parallel undercrossing of existing tunnels in Hefei, China, is taken as an example. A three-dimensional (3D) numerical model using FLAC3D finite difference software was established. The dynamic construction of the new double-line shield tunnel undercrossing the existing subway tunnel over a short distance and in parallel was simulated. The pattern of existing tunnel settlement and change in lining stress caused by the shield tunnelling process were analyzed. The reliability of simulation was verified through field-monitoring data. Finally, based on the numerical model, the effects of change in stratum sensitivity on the settlement of existing tunnel, lining internal force, and surface settlement are discussed. The results show that during shield tunnelling, the maximum ground settlement is 3.9 mm, the maximum settlement at the arch waist of existing tunnel near the new tunnel is 7.75 mm, and the maximum vault settlement is 5.38 mm. The maximum stress of lining of existing tunnel before the excavation is 7.798 × 105 Pa. After the construction of double-line shield tunnel, the maximum stress of lining is 1.124 × 106 Pa, an increase of 44% than that before the construction. The surface settlement and tunnel settlement are sensitive to the weakening of soil layer strength, and lining stress is not affected by the weakening of soil layer strength. The field-monitoring results are consistent with the numerical simulation results, and the model calculation is reliable. This study plays an important role in ensuring construction safety and optimizing the construction risk control of a tunnel

Numerical Study on the Disturbance Effect of Short-Distance Parallel Shield Tunnelling Undercrossing Existing Tunnels

The construction of new tunnels poses a threat to the operational safety of closely existing tunnels, and the construction mode of parallel undercrossing over short distances has the most significant impact. In this study, a new double-line shield tunnel parallel undercrossing of existing tunnels in Hefei, China, is taken as an example. A three-dimensional (3D) numerical model using FLAC3D finite difference software was established. The dynamic construction of the new double-line shield tunnel undercrossing the existing subway tunnel over a short distance and in parallel was simulated. The pattern of existing tunnel settlement and change in lining stress caused by the shield tunnelling process were analyzed. The reliability of simulation was verified through field-monitoring data. Finally, based on the numerical model, the effects of change in stratum sensitivity on the settlement of existing tunnel, lining internal force, and surface settlement are discussed. The results show that during shield tunnelling, the maximum ground settlement is 3.9 mm, the maximum settlement at the arch waist of existing tunnel near the new tunnel is 7.75 mm, and the maximum vault settlement is 5.38 mm. The maximum stress of lining of existing tunnel before the excavation is 7.798 × 105 Pa. After the construction of double-line shield tunnel, the maximum stress of lining is 1.124 × 106 Pa, an increase of 44% than that before the construction. The surface settlement and tunnel settlement are sensitive to the weakening of soil layer strength, and lining stress is not affected by the weakening of soil layer strength. The field-monitoring results are consistent with the numerical simulation results, and the model calculation is reliable. This study plays an important role in ensuring construction safety and optimizing the construction risk control of a tunnel.</jats:p