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Sugarcane ( Saccharum officinarum L.) is a sugar crop capable of ratoon cultivation, and its ratooning ability directly relates to sugarcane production costs and planting benefits. Sugarcane ridges with missing seedlings and gaps are an important reason for the reduction in the number of effective stalks and the years of ratooning of ratoon sugarcane. Therefore, analyzing the differences and correlations in important agronomic traits during yield formation within ratoon sugarcane populations after replanting treatment is of paramount importance for guiding ratoon cultivation. In this study, the 3rd-year ratoon sugarcane of the main varieties Guiliu 2 (GL2), Guitang 44 (GT44), and Yuetang 00236 (YT236), which are widely cultivated, served as the target population for replenishment. Using stem cuttings of Guifu 98-296 (GF296) as the replanting material, replanting treatment was applied to sugarcane ridges with missing seedlings and gaps in the planting plots of the after mentioned three varieties. Unreplanted populations served as their respective controls (CK). At harvest in the 3rd, 4th, and 5th ratoon years, data on important agronomic traits and sucrose content of the sugarcane populations under the replanting and non-replanting treatments were investigated. An analysis was conducted to ascertain the differences and correlations among agronomic trait indicators. The economic benefits of the replanting treatment and CK were calculated. The findings of the study demonstrated that the number of effective stalks in the replanted populations of GL2, GT44, and YT236 was significantly higher than in the non-replanted control groups (CK), with an increase ranging from 10.72 to 45.26%. The yield of both the replanted and CK groups for GL2, GT44, and YT236 decreased by 9.56–54.14% with prolonged the years of ratooning. Conversely, the yield of the replanted populations increased by 28.19–158.61% over extended ratooning years. Significant variations were observed in plant height, stem diameter, and single-stalk weight among the original ratoon sugarcane varieties (GL2, GT44, YT236) and their respective CK groups across different ratooning years. In the non-replanted groups, the number of effective stalks exhibited a highly significant negative correlation with the years of ratooning (correlation coefficients: GL2: − 0.907, GT44: − 0.931, YT236: − 0.756), and yield also showed a highly significant negative correlation with the years of ratooning (GL2: − 0.915, GT44: − 0.905, YT236: − 0.930). Notably, after replanting, the negative correlation between the years of ratooning and both yield and effective stalk number was eliminated, indicating improved population structure. Furthermore, the replanted GL2, GT44, and YT236 populations exhibited increased economic benefits, with cumulative net income gains over three ratooning seasons of 48,120.80 CNY ha −1 , 46,765.80 CNY ha −1 , and 42,398.60 CNY ha −1 , respectively. In conclusion, GF296 replanting effectively extended the years of ratooning by three years, substantially enhanced economic returns, and is suitable for large-scale implementation. The present study provides a theoretical basis for constructing high-yield populations, maximising ratoon potential, and achieving high-efficiency cultivation.

Background Although extensive breeding efforts are ongoing in sugarcane ( Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.

The Jinsha River Basin (JRB) is the largest hydropower base in China, serving as the main source of the Western Route of China’s South-to-North Water Diversion Project. Under the influence of the reservoirs operation and climate change, the general hydrological regime in the JRB has been altered. Although the change process can be determined through a runoff time-series analysis and hydrological simulation, the individual impacts of the reservoirs have not been quantified. This study aimed to clarify the impact of the reservoirs in the JRB on the runoff, flood, and drought processes using a framework coupling long short-term memory (LSTM) and flood drought assessment techniques. The results are as follows: (1) From 1998 to 2020, reservoirs in the JRB changed the average daily runoff at Pingshan Station by −5.64%, +10.95%, and −10.93% at the annual and seasonal (dry and rainy) scales, respectively. (2) The operation of dams reduces the risk of flood disasters effectively. Compared with the natural river flow, the flood frequency decreased by 7.69%, and the total flow over the threshold was reduced by 37.86%. (3) The operation of dams has changed the duration and severity of drought, reducing extreme drought and increasing moderate and severe drought. In conclusion, the reservoirs in the JRB have positive effects on water resource regulation, and their mitigation of floods and extreme drought provides security for the middle and lower reaches of the Yangtze River. This study provides a reference for the LSTM modeling of reservoir basins, quantifying the impact of reservoirs on runoff, flood, and drought in the JRB.

Hantaan virus (HTNV), a Hantavirus serotype that is prevalent in Asia, causes hemorrhagic fever with renal syndrome (HFRS) with high mortality in human race. However, the pathogenesis of HTNV infection remains elusive. Circular RNAs (circRNAs), a new type of non-coding RNAs, play a crucial role in various pathogenic processes. Nevertheless, circRNA expression profiles and their effects on pathogenesis of HTNV infection are still completely unknown. In the present study, RNA sequencing was performed to analyze the circRNA, microRNA (miRNA), and mRNA expression profiles in HTNV-infected and mock-infected human umbilical vein endothelial cells (HUVECs). A total of 70 circRNAs, 66 miRNAs, and 788 mRNAs were differently expressed. Several differentially expressed RNAs were validated by RT-qPCR. Moreover, we verified that some differentially expressed RNAs, such as circ_0000479, miR-149-5p, miR-330-5p, miR-411-3p, RIG-I, CMPK2, PARP10, and GBP1, promoted or inhibited HTNV replication. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis demonstrated that the host genes of differentially expressed circRNAs were principally involved in the innate immune response, the type I interferon (IFN) signaling pathway, and the cytokine-mediated signaling pathway. Additionally, the circRNA-miRNA-mRNA regulatory network was integrally analyzed. The data showed that there were many circRNA-miRNA-mRNA interactions in HTNV infection. By dual-luciferase reporter assay, we confirmed that circ_0000479 indirectly regulated RIG-I expression by sponging miR-149-5p, hampering viral replication. This study for the first time presents a comprehensive overview of circRNAs induced by HTNV and reveals that a network of enriched circRNAs and circRNA-associated competitive endogenous RNAs (ceRNAs) is involved in the regulation of HTNV infection, thus offering new insight into the mechanisms underlying HTNV-host interaction.

Background Following the outbreak of the COVID-19 pandemic, a change in the incidence and transmission of respiratory pathogens was observed. Here, we retrospectively analyzed the impact of COVID-19 on the epidemiologic characteristics of Mycoplasma pneumoniae infection among children in Chengdu, one of the largest cities of western China. Method M. pneumoniae infection was diagnosed in 33,345 pediatric patients with respiratory symptoms at the Chengdu Women’s & Children’s Central Hospital between January 2017 and December 2020, based on a serum antibody titer of ≥1:160 measured by the passive agglutination assay. Differences in infection rates were examined by sex, age, and temporal distribution. Results Two epidemic outbreaks occurred between October-December 2017 and April-December 2019, and two infection peaks were detected in the second and fourth quarters of 2017, 2018, and 2019. Due to the public health response to COVID-19, the number of positive M. pneumoniae cases significantly decreased in the second quarter of 2020. The number of M. pneumoniae infection among children aged 3–6 years was higher than that in other age groups. Conclusions Preschool children are more susceptible to M. pneumoniae infection and close contact appears to be the predominant factor favoring pathogen transmission. The public health response to COVID-19 can effectively control the transmission of M. pneumoniae .

As the most common type of renal cell carcinoma (RCC), the renal clear cell carcinoma (ccRCC) is highly malignant and insensitive to chemotherapy or radiotherapy. Although systemic immunotherapies have been successfully applied to ccRCC in recent years, screening for patients who can benefit most from these therapies is still essential and challenging due to immunological heterogeneity of ccRCC patients. To this end, we implemented a series of deep investigation on the expression and clinic data of ccRCC from The Cancer Genome Atlas (TCGA) International Consortium for Cancer Genomics (ICGC). We identified a total of 946 immune-related genes that were differentially expressed. Among them, five independent genes, including SHC1, WNT5A, NRP1, TGFA, and IL4R, were significantly associated with survival and used to construct the immune-related prognostic differential gene signature (IRPDGs). Then the ccRCC patients were categorized into high-risk and low-risk subgroups based on the median risk score of the IRPDGs. IRPDGs subgroups displays distinct genomic and immunological characteristics. Known immunotherapy-related genes show different mutation burden, wherein the mutation rate of VHL was higher than 40% in the two IRPDGs subgroups, and SETD2 and BAP1 mutations differed most between two groups with higher frequency in the high-risk subgroup. Moreover, IRPDGs subgroups had different abundance in tumor-infiltrating immune cells (TIICs) with distinct immunotherapy efficacy. Plasma cells, regulatory cells (Tregs), follicular helper T cells (Tfh), and M0 macrophages were enriched in the high-risk group with a higher tumor immune dysfunction and rejection (TIDE) score. In contrast, the low-risk group had abundant M1 macrophages, mast cell resting and dendritic cell resting infiltrates with lower TIDE score and benefited more from immune checkpoint inhibitors (ICI) treatment. Compared with other biomarkers, such as TIDE and tumor inflammatory signatures (TIS), IRPDGs demonstrated to be a better biomarker for assessing the prognosis of ccRCC and the efficacy of ICI treatment with the promise in screening precise patients for specific immunotherapies.

Primary cilia dyskinesia (PCD) is a rare genetic disease caused by ciliary structural or functional defects. It causes severe outcomes in patients, including recurrent upper and lower airway infections, progressive lung failure, and randomization of heterotaxy. To date, although 50 genes have been shown to be responsible for PCD, the etiology remains elusive. Meanwhile, owing to the lack of a model mimicking the pathogenesis that can be used as a drug screening platform, thereby slowing the development of related therapies. In the current study, we identified compound mutation of DNAH9 in a patient with PCD with the following clinical features: recurrent respiratory tract infections, low lung function, and ultrastructural defects of the outer dynein arms (ODAs). Bioinformatic analysis, structure simulation assay, and western blot analysis showed that the mutations affected the structure and expression of DNAH9 protein. Dnah9 knock-down (KD) mice recapitulated the patient phenotypes, including low lung function, mucin accumulation, and increased immune cell infiltration. Immunostaining, western blot, and co-immunoprecipitation analyses were performed to clarify that DNAH9 interacted with CCDC114/GAS8 and diminished their protein levels. Furthermore, we constructed an airway organoid of Dnah9 KD mice and discovered that it could mimic the key features of the PCD phenotypes. We then used organoid as a drug screening model to identify mitochondrial-targeting drugs that can partially elevate cilia beating in Dnah9 KD organoid. Collectively, our results demonstrated that Dnah9 KD mice and an organoid model can recapture the clinical features of patients with PCD and provide an excellent drug screening platform for human ciliopathies.

Background The nasal epithelium, as part of a continuous and integrated airway epithelium, provides a more accessible sample source than the bronchial epithelium. However, the similarities and differences in gene expression patterns and immune responses between these two sites have not been extensively studied. Results Four lines of matched nasal and bronchial airway epithelial cells obtained from the four patients were embedded in Matrigel and cultured in thechemically defined medium to generate patient-derived nasal organoids (NO) and bronchial organoids (BO). Histologic examination of nasal organoid tissue revealed high similarity and a reduced ciliary beat frequency compared to bronchial organoid tissue. Whole exome sequencing revealed that over 99% of single nucleotides were shared between the NO and matched BO and there was a 95% overlap in their RNA transcriptomes. RNA sequencing analysis of differentially expressed genes indicated a significant reduction in the immune response in NO. RSV infection revealed more productive replication in NO, with a downregulated immune pathway identified by RNA sequencing analysis and upregulated levels of pro-inflammatory cytokines in culture supernatants in NO compared to BO. Conclusions NO and BO serve as robust in vitro models, faithfully recapitulating the biological characteristics of upper respiratory epithelial cells. The different regions of respiratory epithelial cells exhibit distinct immune responses, underscoring their complementary roles in exploring airway immune mechanisms and disease pathophysiology.

Background and Objectives: The clinical prognosis and survival prediction of glioma based on gene signatures derived from heterogeneous tumor cells are unsatisfactory. This study aimed to construct an immune gene-related prognostic score model to predict the prognosis of glioma and identify patients who may benefit from immunotherapy. Methods: 23 immune-related genes (IRGs) associated with glioma prognosis were identified through weighted gene co-expression network analysis (WGCNA) and Univariate Cox regression analysis based on large-scale RNA-seq data. Eight IRGs were retained as candidate predictors and formed an immune gene-related prognostic score (IGRPS) by multifactorial Cox regression analysis. The potential efficacy of immune checkpoint blockade (ICB) therapy of different subgroups was compared by The Tumor Immune Dysfunction and Exclusion (TIDE) algorithm. We further adopted a series of bioinformatic methods to characterize the differences in clinicopathological features and the immune microenvironment between the different risk groups. Finally, a nomogram integrating IGRPS and clinicopathological characteristics was built to accurately predict the prognosis of glioma. Results: Patients in the low-risk group had a better prognosis than those in the high-risk group. Patients in the high-risk group showed higher TIDE scores and poorer responses to ICB therapy, while patients in the low-risk group may benefit more from ICB therapy. The distribution of age and tumor grade between the two subgroups was significantly different. Patients with low IGRPS harbor a high proportion of natural killer cells and are sensitive to ICB treatment. While patients with high IGRPS display relatively poor prognosis, a higher expression level of DNA mismatch repair genes, high infiltrating of immunosuppressive cells, and poor ICB therapeutic outcomes. Conclusions: We demonstrated that the IGRPS model can independently predict the clinical prognosis as well as the ICB therapy responses of glioma patients, thus having important implications on the design of immune-based therapeutic strategies.