Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.).

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.

Comparative transcriptome profiling of resistant and susceptible sugarcane genotypes in response to the airborne pathogen Fusarium verticillioides.

Fusarium verticillioides is the pathogen associated with pokkah boeng disease (PBD), the most significant airborne disease of sugarcane. The molecular mechanisms that regulate the defense responses of sugarcane towards this fungus are not yet fully known. Samples of 'YT 94/128' (resistant, R) and 'GT 37' (susceptible, S) inoculated with F. verticillioides on the 14 days post-inoculation were used to analyze the transcriptome to screen R genes. In total, 80.93 Gb of data and 76,175 Unigenes were obtained after assembling the sequencing data, and comparisons of Unigenes with NR, Swiss-prot, KOG, and KEGG databases confirmed 42,451 Unigenes. The analysis of differentially expression genes (DEGs) in each sample revealed 9092 DEGs in 'YT 94/128,' including 8131 up-regulated DEGs and 961 down-regulated DEGs; there were 9829 DEGs in 'GT 37,' including 7552 up-regulated DEGs and 2277 down-regulated DEGs. The identified DEGs were mainly involved in catalytic enzyme activity, cell protease, hydrolytic enzymes, peptide enzyme, protein metabolism process of negative regulation, phenylpropanoid metabolism, extracellular region, aldehyde dehydrogenase, endopeptidase, REDOX enzyme, protein kinases, and phosphoric acid transferase categories. KEGG pathway clustering analysis showed that the DEGs involved in resistance were significantly related to metabolic pathways of phenylpropanoid biosynthesis, cutin, suberine and wax biosynthesis, nitrogenous metabolism, biosynthesis of secondary metabolites, and plant-pathogen interactions. This application of transcriptomic data clarifies the mechanism of interactions between sugarcane and F. verticillioides, which can help to reveal disease-related metabolic pathways, molecular regulatory networks, and key genes involved in sugarcane responses to F. verticillioides.

Uniform, Fully Connected, High-Quality Monocrystalline Freestanding Perovskite Oxide Films Fabricated from Recyclable Substrates.

Releasing epitaxial perovskite oxide films from their native oxide substrates produces high quality, 2D-material-like monocrystalline freestanding oxide membranes, as potential key components for the next-generation electronic devices. Two major obstacles still limit their practical applications: macroscopic material defects (mainly cracks) that lowers uniformity and yield, and the high cost of the consumed oxide substrates. Here, a two-step film transfer method and a substrate recycling method enable repetitive fabrication of millimeter-scale, fully-connected freestanding oxide films of various chemical compositions from the same substrates; arrays of capacitor and resistor devices based on these oxides transferred on silicon indicate high uniformity, low sample-to-sample variation, and satisfactory electrical connectivity. The two-step transfer suppresses crack formation by avoiding buckling-delamination-type relaxation of epitaxial strain, and the key point to achieve substrate reuse is to remove the residual Al species bonded to the substrate surfaces. The mitigation of such long-lasting issues in freestanding oxide fabrication techniques may eventually pave roads toward future industrial-grade devices, as well as enabling many research opportunities in fundamental physics.

Screening of Sugarcane Proteins Associated with Defense against Leifsonia xyli subsp. xyli, Agent of Ratoon Stunting Disease.

Sugarcane is the most important sugar crop and one of the leading energy-producing crops in the world. Ratoon stunting disease (RSD), caused by the bacterium Leifsonia xyli subsp. xyli, poses a huge threat to ratoon crops, causing a significant yield loss in sugarcane. Breeding resistant varieties is considered the most effective and fundamental approach to control RSD in sugarcane. The exploration of resistance genes forms the foundation for breeding resistant varieties through molecular technology. The pglA gene is a pathogenicity gene in L. xyli subsp. xyli, encoding an endopolygalacturonase. In this study, the pglA gene from L. xyli subsp. xyli and related microorganisms was analyzed. Then, a non-toxic, non-autoactivating pglA bait was successfully expressed in yeast cells. Simultaneously the yeast two-hybrid library was generated using RNA from the L. xyli subsp. xyli-infected sugarcane. Screening the library with the pglA bait uncovered proteins that interacted with pglA, primarily associated with ABA pathways and the plant immune system, suggesting that sugarcane employs these pathways to respond to L. xyli subsp. xyli, triggering pathogenicity or resistance. The expression of genes encoding these proteins was also investigated in L. xyli subsp. xyli-infected sugarcane, suggesting multiple layers of regulatory mechanisms in the interaction between sugarcane and L. xyli subsp. xyli. This work promotes the understanding of plant-pathogen interaction and provides target proteins/genes for molecular breeding to improve sugarcane resistance to L. xyli subsp. xyli.

Assessment of the rhizosphere fungi and bacteria recruited by sugarcane during smut invasion.

Whip smut is one of the most serious and widely spread sugarcane diseases. Plant-associated microbes play various roles in conferring advantages to the host plant. Understanding the microbes associated with sugarcane roots will help develop strategies for the biocontrol of smut. Therefore, the present study explored microbe-mediated sugarcane response to smut invasion via 16S rRNA and ITS metabarcoding survey of the rhizosphere soils of resistant and susceptible sugarcane varieties. The bacterial and fungal diversity in the rhizosphere soils differed between the resistant and susceptible varieties. The bacterial genera Sphingomonas, Microcoleus_Es-Yyy1400, Marmoricola, Reyranella, Promicromonospora, Iamia, Phenylobacterium, Aridibacter, Actinophytocola, and Edaphobacter and one fungal genus Cyphellophora were found associated with smut resistance in sugarcane. Detailed analysis revealed that the majority of bacteria were beneficial, including the actinomycete Marmoricola and Iamia and Reyranella with denitrification activity. Analysis of bacterial network interaction showed that three major groups interacted during smut invasion. Meanwhile, seven of these genera appeared to interact and promote each other's growth. Finally, functional annotation based on the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database predicted that the abundant bacteria are dominated by oxygenic photoautotrophy, photoautotrophy, and phototrophy functions, which may be related to smut resistance in sugarcane. The present study thus provides new insights into the dynamics of the sugarcane rhizosphere microbial community during smut invasion.

Variety-Specific Flowering of Sugarcane Induced by the Smut Fungus Sporisorium scitamineum.

Sugarcane smut is the most severe sugarcane disease in China. The typical symptom is the emerging of a long, black whip from the top of the plant cane. However, in 2018, for the first time we observed the floral structures of sugarcane infected by smut fungus in the planting fields of China. Such smut-associated inflorescence in sugarcane was generally curved and short, with small black whips emerging from glumes of a single floret on the cane stalk. Compatible haploid strains, named Ssf1-7 (MAT-1) and Ssf1-8 (MAT-2), isolated from teliospores that formed black whips in inflorescence of sugarcane were selected for sexual mating assay, ITS DNA sequencing analysis and pathogenicity assessment. The isolates Ssf1-7 and Ssf1-8 showed stronger sexual mating capability than the reported Sporisorium scitamineum strains Ss17 and Ss18. The ITS DNA sequence of the isolates Ssf1-7 and Ssf1-8 reached 100% similarity to the isolates of S. scitamineum strains available in GenBank. Inoculating Ssf1-7 + Ssf1-8 to six sugarcane varieties, i.e., GT42, GT44, GT49, GT55, LC05-136 and ROC22, resulted in different smut morphological modifications. The symptoms of floral structure only occurred in LC05-136, indicating that the flowering induction by S. scitamineum is variety-specific. Furthermore, six selected flowering-related genes were found to be differentially expressed in infected Ssf1-7 + Ssf1-8 LC05-13 plantlets compared to uninfected ones. It is concluded that the flowering induction by S. scitamineum depends on specific fungal race and sugarcane variety, suggesting a specific pathogen-host interaction and expression of some flowering-related genes.

Machine learning models to predict in-hospital mortality in septic patients with diabetes.

Background: Sepsis is a leading cause of morbidity and mortality in hospitalized patients. Up to now, there are no well-established longitudinal networks from molecular mechanisms to clinical phenotypes in sepsis. Adding to the problem, about one of the five patients presented with diabetes. For this subgroup, management is difficult, and prognosis is difficult to evaluate. Methods: From the three databases, a total of 7,001 patients were enrolled on the basis of sepsis-3 standard and diabetes diagnosis. Input variable selection is based on the result of correlation analysis in a handpicking way, and 53 variables were left. A total of 5,727 records were collected from Medical Information Mart for Intensive Care database and randomly split into a training set and an internal validation set at a ratio of 7:3. Then, logistic regression with lasso regularization, Bayes logistic regression, decision tree, random forest, and XGBoost were conducted to build the predictive model by using training set. Then, the models were tested by the internal validation set. The data from eICU Collaborative Research Database (n = 815) and dtChina critical care database (n = 459) were used to test the model performance as the external validation set. Results: In the internal validation set, the accuracy values of logistic regression with lasso regularization, Bayes logistic regression, decision tree, random forest, and XGBoost were 0.878, 0.883, 0.865, 0.883, and 0.882, respectively. Likewise, in the external validation set 1, lasso regularization = 0.879, Bayes logistic regression = 0.877, decision tree = 0.865, random forest = 0.886, and XGBoost = 0.875. In the external validation set 2, lasso regularization = 0.715, Bayes logistic regression = 0.745, decision tree = 0.763, random forest = 0.760, and XGBoost = 0.699. Conclusion: The top three models for internal validation set were Bayes logistic regression, random forest, and XGBoost, whereas the top three models for external validation set 1 were random forest, logistic regression, and Bayes logistic regression. In addition, the top three models for the external validation set 2 were decision tree, random forest, and Bayes logistic regression. Random forest model performed well with the training and three validation sets. The most important features are age, albumin, and lactate.

Clinical characteristics and antibiotics treatment in suspected bacterial infection patients with COVID-19.

Coronavirus disease 2019 (COVID-19) pandemic has brought challenges to health and social care systems. However, the empirical use of antibiotics is still confusing. Presently, a total of 1123 patients with COVID-19 admitted to Renmin Hospital of Wuhan University was included in this retrospective cohort study. The clinical features, complications and outcomes were compared between the suspected bacterial infection and the no evidence of bacterial infection. The risk factors of mortality and the incidence of acute organ injury were analyzed. As a result, 473 patients were selected to suspected bacterial infection (SI) group based on higher white blood cell count and procalcitonin or bacterial pneumonia on chest radiography. 650 patients were selected to the no evidence of bacterial infection (NI) group. The SI group had more severely ill patients (70.2% vs. 39.8%), more death (20.5% vs. 2.2%), and more acute organ injury (40.2% vs. 11.2%). Antibiotics were found associated with improved mortality and an increased risk for acute organ injury in hospitalized patients with COVID-19. Intravenous moxifloxacin and meropenem increased the death rate in patients with suspected bacterial infection, while oral antibiotics reduced mortality in this group. Moreover, penicillin and meropenem treatments were associated with increased mortality of the patients with no evidence of bacterial infection. In conclusion, patients with suspected bacterial infection were more likely to have negative clinical outcomes than those without bacterial infection. Empirical use of antibiotics may not have the expected benefits.

AMPK/SIRT1 Pathway is Involved in Arctigenin-Mediated Protective Effects Against Myocardial Ischemia-Reperfusion Injury.

Arctigenin, one of the active ingredients extracted from Great Burdock (Arctium lappa) Achene, has been found to relieve myocardial infarction injury. However, the specific mechanism of Arctigenin against myocardial infarction remains largely unknown. Here, both acute myocardial ischemia-reperfusion injury (AMI/R) rat model and oxygen glucose deprivation (OGD)-induced myocardial cell injury model were constructed to explore the underlying role of AMPK/SIRT1 pathway in Arctigenin-mediated effects. The experimental data in our study demonstrated that Arctigenin ameliorated OGD-mediated cardiomyocytes apoptosis, inflammation and oxidative stress in a dose-dependent manner. Besides, Arctigenin activated AMPK/SIRT1 pathway and downregulated NF-κB phosphorylation in OGD-treated cardiomyocytes, while inhibiting AMPK or SIRT1 by the Compound C (an AMPK inhibitor) or SIRT1-IN-1 (a SIRT1 inhibitor) significantly attenuated Arctigenin-exerted protective effects on cardiomyocytes. In the animal experiments, Arctigenin improved the heart functions and decreased infarct size of the AMI/R-rats, accompanied with downregulated oxidative stress, inflammation and apoptotic levels in the heart tissues. What's more, Arctigenin enhanced the AMPK/SIRT1 pathway and repressed NF-κB pathway activation. Taken together, our data indicated that Arctigenin reduced cardiomyocytes apoptosis against AMI/R-induced oxidative stress and inflammation at least via AMPK/SIRT1 pathway.