Identification and Functional Characterization of the SaMYB113 Gene in Solanum aculeatissimum.

The MYB transcription factors (TFs) have substantial functions in anthocyanin synthesis as well as being widely associated with plant responses to various adversities. In the present investigation, we found an unreported MYB TF from Solanum aculeatissimum (a wild relative of eggplant) and named it SaMYB113 in reference to its homologous gene. Bioinformatics analysis demonstrated that the open reading frame of SaMYB113 was 825 bp in length, encoding 275 amino acids, with a typical R2R3-MYB gene structure, and predicted subcellular localization in the nucleus. Analysis of the tissue-specific expression pattern through qRT-PCR showed that the SaMYB113 was expressed at a high level in young stems as well as leaves of S. aculeatissimum. Transgenic Arabidopsis and tobacco plants overexpressing SaMYB113 pertinent to the control of the 35S promoter exhibited a distinct purple color trait, suggesting a significant change in their anthocyanin content. Furthermore, we obtained three tobacco transgenic lines with significant differences in anthocyanin accumulation and analyzed the differences in anthocyanin content by LC-MS/MS. The findings demonstrated that overexpression of SaMYB113 caused tobacco to have considerably raised levels of several anthocyanin components, with the most significant increases in delphinidin-like anthocyanins and cyanidin-like anthocyanins. The qRT-PCR findings revealed significant differences in the expression levels of structural genes for anthocyanin synthesis among various transgenic lines. In summary, this study demonstrated that the SaMYB113 gene has a substantial impact on anthocyanin synthesis, and overexpression of the SaMYB113 gene leads to significant modifications to the expression levels of a variety of anthocyanin-synthesizing genes, which leads to complex changes in anthocyanin content and affects plant phenotypes. This present research offers the molecular foundation for the research of the mechanism of anthocyanin formation within plants, as well as providing some reference for the improvement of traits in solanum crops.

Genome-Wide Analysis of C-Repeat Binding Factor Gene Family in Capsicum baccatum and Functional Exploration in Low-Temperature Response.

Capsicum baccatum is a close relative of edible chili peppers (Capsicum annuum) with high economic value. The CBF gene family plays an important role in plant stress resistance physiology. We detected a total of five CBF genes in the C. baccatum genome-wide sequencing data. These genes were scattered irregularly across four chromosomes. The genes were categorized into three groupings according to their evolutionary relationships, with genes in the same category showing comparable principles for motif composition. The 2000 bp upstream of CbCBF contains many resistance-responsive elements, hormone-responsive elements, and transcription factor binding sites. These findings emphasize the crucial functions of these genes in responding to challenging conditions and physiological regulation. Analysis of tissue-specific expression revealed that CbCBF3 exhibited the greatest level of expression among all tissues. Under conditions of low-temperature stress, all CbCBF genes exhibited different levels of responsiveness, with CbCBF3 showing a considerable up-regulation after 0.25 h of cold stress, indicating a high sensitivity to low-temperature response. The importance of the CbCBF3 gene in the cold response of C. baccatum was confirmed by the use of virus-induced gene silencing (VIGS) technology, as well as the prediction of its protein interaction network. To summarize, this study conducts a thorough bioinformatics investigation of the CbCBF gene family, showcases the practicality of employing VIGS technology in C. baccatum, and confirms the significance of the CbCBF3 gene in response to low temperatures. These findings provide significant references for future research on the adaptation of C. baccatum to low temperatures.

Cu(II)-Catalyzed Enantioselective Aza-Friedel-Crafts Reaction of 1-Naphthols and Electron-Rich Phenols with Isatin-Derived Ketimines.

New chiral ligands could be obtained by introducing proline moieties and imidazoline moieties to binaphthyl skeletons. The chiral ligands exhibited balanced rigidity and flexibility which could allow the change of the conformations during the reactions on one hand, and could provide sufficient asymmetric induction on the other. The proline moiety could act as a linker connecting the binaphthyl skeletons and the imidazoline moieties as well as a coordinating group for the central metal, and the electronic and steric properties of the imidazoline groups could be carefully fine-tuned by the use of different substituents. In the presence of Cu(II) catalyst bearing such chiral ligands, aza-Friedel-Crafts reaction of 1-naphthols and electron-rich phenols with isatin-derived ketimines provided the desired products with good to excellent yields and up to 99 % ee. The reactions showed good scalability, and excellent ee could still be obtained when the reaction was carried out in gram-scale.

New Binaphthyl-Proline-Based Chiral Ligands Bearing Imidazoline Groups: Design, Synthesis, and Their Application in Enantioselective Conjugate Addition of 4-Hydroxycoumarin and Related Nucleophiles to ß,γ-Unsaturated α-Ketoesters.

This paper describes the design and application of new binaphthyl-proline-based chiral ligands bearing imidazoline functional groups. These chiral ligands incorporate the advantages of both the binaphthyl and proline skeletons, they are featured with regulatable electronic and steric properties for the imidazoline functional groups, and form chiral complexes with different metal salts such as cuprous acetate. In the presence of an appropriate amount of a chiral catalyst, enantioselective conjugate addition of 4-hydroxycoumarin or related nucleophiles to different ß,γ-unsaturated α-ketoesters proceeded readily, giving the desired products in high yield (up to 99%) and excellent enantiomeric excess (up to 99%).

Copper(II)-Catalyzed Enantioselective Aza-Friedel-Crafts Reaction of Indoles with Isatin-Derived N-Boc-Ketimines.

The copper(II)-catalyzed enantioselective aza-Friedel-Crafts reaction of indoles with isatin-derived N-Boc-ketimines was developed by using tunable chiral O-N-N tridentate ligands derived from BINOL and proline. In general, the reaction afforded chiral 3-indolyl-3-aminooxindoles under mild conditions in high yields (83-97%) with excellent ee (69-99%).

Enantioselective Friedel-Crafts Alkylation of Indoles with ß,γ-Unsaturated α-Ketoesters Catalyzed by New Copper(I) Catalysts.

New Cu(I) catalysts are effective in enantioselective Friedel-Crafts alkylation of a variety of indoles with different ß,γ-unsaturated α-ketoesters. A control study shows that such a catalyst system is less sensitive to air, and the reactions can be carried out without special cares such as glovebox operation or moisture/oxygen-free conditions. Preliminary computation results suggest that there exists π-π stacking between the substrate and the catalyst, and such an interaction seems to play a role in stabilizing the reaction intermediate and enhancing the stereoselectivity of the reactions. The desired products can be obtained in up to 98% yield at 99% enantiomeric excess. The same high enantioselectivity can be observed when the reaction is carried in a gram scale, indicating a good scalability of the catalyst system in enantioselective Friedel-Crafts alkylation of different indoles with ß,γ-unsaturated α-ketoesters.

Enantioselective Michael addition of malonates to ß,γ-unsaturated α-ketoesters catalysed by Cu(II) complexes bearing binaphthyl-proline hybrid ligands.

High yields (up to 96%) and high ee (up to 92%) were achieved for chiral copper(II) complex-catalysed enantioselective Michael addition of malonates to ß,γ-unsaturated-α-ketoesters. The chiral ligands took advantage of both the binaphthyl and the proline moieties, and substituents with different electronic and steric features could be tolerated. The reactions could be carried out under mild conditions, and a gram scale reaction could be realised without the loss of yield and enantioselectivity.

Predicting HIV drug resistance using weighted machine learning method at target protein sequence-level.

Acquired immune deficiency syndrome (AIDS) is a fatal disease caused by human immunodeficiency virus (HIV). Although 23 different drugs have been available, the treatment of AIDS remains challenging because the virus mutates very quickly which can lead to drug resistance. Therefore, predicting drug resistance before treatment is crucial for individual treatments. Here, based on HIV target protein sequence information, we analyzed 21-drug resistance caused by mutated residues using machine learning (ML) methods. To transform target sequences into numeric vectors, seven physicochemical properties were used, which can well represent the interacting characteristics of target proteins. Then, principal component analysis (PCA) method was adopted to reduce the feature dimensionality. Random forest (RF) and support vector machine (SVM) based on three different kernel functions, including linear, polynomial and radial basis function (RBF), were all employed. By comparisons, we found that RBF-based SVM method gives a comparative performance with RF model. Further, we added the weight information to RBF-based SVM method by four different weight evaluation methods of RF, eXtreme Gradient Boosting (XGB), CfsSubsetEval and ReliefFAttributeEval, respectively. Results show that the RF-weighted RBF-based SVM yield the superior performance and 13 out of 21 drug models provide the correlation coefficients (R2) over 0.8 and 3 of them are higher than 0.9. Finally, position-specific importance analysis indicates that most of the mutation residues with high RF weight scores are proved to be closely related with drug resistance, which has been revealed in previous reports. Overall, we can expect that this method can be a supplementary tool for predicting HIV drug resistance for newly discovered mutations. Here, based on HIV target protein sequence information, we analyzed 21-drug resistance caused by mutated residues using machine learning (ML) methods by fusing the weight information of different mutation positions.

An effective seven-CpG-based signature to predict survival in renal clear cell carcinoma by integrating DNA methylation and gene expression.

AIMS: Currently, using clinicopathological risk factors only is not far from effective to evaluate the risk of disease progression in renal clear cell carcinoma (KIRC) patients. Molecular biomarkers might improve risk stratification of KIRC. DNA methylation occurs the whole process of tumor development and transcriptional disorders are also one of the important characteristics of tumor. Hence, this study aims to develop an effective and independent prognostic signature for KIRC patients by Integrating DNA methylation and gene expression. MAIN METHODS: Difference analysis was conducted on DNA methylation sites and gene expression data. The Spearman's rank correlation and univariate Cox regression analysis were used to screen out the CpG sites that related with RNAs' expression and KIRC patients' overall survival. Then, a five-CpG-based prognostic classifier was established using LASSO Cox regression method. KEY FINDINGS: The seven-CpG-based classifier can successfully divide KIRC patients into high-risk from low-risk groups, even after adjustment for standard clinical prognostic factors, such as age, stage, gender and grade. Moreover, the seven-CpG-based signature was more effective as independent prognostic factors than the combined model of these clinical factors. Six differential mRNA genes corresponding to the seven CpG sites are all related to human cancers by functional exploration. The gene functional and pathway enrichment analysis found that genes in immune-related pathways were remarkably different in high and low-risk groups. SIGNIFICANCE: The new seven-CpG-based signature could helpfully provide insights into the underlying mechanism of KIRC and may be a powerful independent biomarker for predicting of the survival of KIRC patients.

In vivo effects of dexmedetomidine on immune function and tumor growth in rats with ovarian cancer through inhibiting the p38MAPK/NF-κB signaling pathway.

OBJECTIVES: During this study, we aimed to analyze the correlation between dosages of dexmedetomidine (DEX) and the p38MAPK/NF-κB signaling pathway, and their effects on immune function and tumor growth in rats with ovarian cancer (OC). METHODS: A total of 100 rats were selected for the purposes of the study. The normal group consisted of 20 rats, while the remaining 80 rats were utilized for OC model establishment purposes, and further assigned into the model, 0.2 DEX, 1 DEX and 5 DEX groups (based on respective dosages of DEX, n=20 per group). The tumor inhibition rate was calculated. Positive expressions of p38 and NF-κB in ovarian tissues were examined by means of immunohistochemical staining. Cell transformation as well as lymphocyte proliferation rates were measured using MTT. Cell cycle and apoptosis of CD4+ and CD8+ cells were determined by flow cytometry. Serum levels of IL-2 and TNF-α were detected using ELISA, while qRT-PCR and western blotting methods were used to analyze mRNA and protein expressions of p38 and NF-κB. RESULTS: Compared with the normal group, the other four groups exhibited up-regulated IL-2, TNF-α serum levels as well as up regulated expressions of p38, NF-κB65 mRNA and protein; while the respective percentages of both CD4+ and CD8+ T cells exhibited down-regulated rates. The other four groups displayed increases in tumor weight and cell apoptosis, as well as decreased levels of cell proliferation and transformation rates. The aforementioned findings of the study ultimately highlighted a greater tendency among the three DEX groups in comparison to the model group. CONCLUSION: The findings of the study suggest that a particular dosage of DEX may act to enhance the immune function of rats with OC by inhibiting the p38MAPK/NF-κB signaling pathway.

Protective effect of autophagy on endoplasmic reticulum stress induced apoptosis of alveolar epithelial cells in rat models of COPD.

During the present study, we explored the protective effects of autophagy on endoplasmic reticulum (ER) stress (ERS) induced apoptosis belonging to alveolar epithelial cells (AECs) in rat models with chronic obstructive pulmonary disease (COPD). Fifty-six 12-week-old male Sprague-Dawley (SD) rats were randomly assigned into the COPD group (rats exposed to cigarette smoke (CS)), the 3-methyladenine (3-MA) intervention group (COPD rats were administrated with 10 mg/kg autophagy inhibitors), the chloroquine (CQ)-intervention group (COPD rats were administrated 40 mg/kg CQ), and the control group (rats breathed in normal saline). The forced expiratory volume in 0.3 s/forced vital capacity (FEV0.3/FVC%), inspiratory resistance (RI), and dynamic lung compliance (Cdyn) were measured and recorded. The expressions of PKR-like ER kinase (PERK) and CCAAT/enhancer-binding protein-homologous protein (CHOP) were detected by immunohistochemistry. The cell apoptotic rates of AECs were analyzed by terminal deoxynucleotidyl transferase (TdT) mediated dUTP-biotin nick end-labeling (TUNEL) staining. The expression levels of light chain 3 (LC3-II), p62, Beclin-1, ATG5, ATG7, Caspase-12, and Caspase-3 were detected by Western blotting. Results showed that the COPD group exhibited a lower FEV0.3/FVC% and Cdyn, and a higher RI than the control group. Compared with the control group, the integrated optical density (IOD) values of PERK and CHOP, the apoptotic rate of AECs, and expressions of LC3-II, Beclin-1, ATG5, ATG7, Caspase-3, and Caspase-12 expressions were significantly higher, whereas p62 expression was significantly lower in the COPD group. Based on the results obtained during the present study, it became clear that the inhibition of autophagy could attenuate the ERS-induced apoptosis of AECs in rats with COPD.