Two new megastigmane glycosides from the leaves of Nicotiana tabacum and their anti-inflammatory activities.

Two new megastigmane glycosides, (6 R,7E,9R)-3-oxo-α-ionyl-9-O-α-L-rhamnopyranosyl-(1''→4')-ß-D-glucopyranoside (1) and (6 R,7E,9R)-3-oxo-α-ionyl-9-O-ß-D-glucopyranosyl-(1''→6')-ß-D-glucopyranoside (2), together with six known analogues (3-8) were isolated from the leaves of Nicotiana tabacum. The structures of all metabolites were determined by comprehensive analysis of NMR and MS spectroscopic data as well as by comparison with those of previously reported. The in vitro anti-inflammatory activity of all isolates was evaluated using a lipopolysaccharide (LPS)-induced RAW264.7 cell inflammatory model, and the compounds 1, 3, 7, and 8 exhibited inhibition of LPS-induced NO production in RAW264.7 macrophage cells with IC50 values of 42.3-61.7 µM (positive control, dexamethasone, IC50 = 21.3 ± 1.2 µM).

oppHeatmap: Rendering Various Types of Heatmaps for Omics Data.

Heatmaps are preferred visualization modes for biologists to display high-dimensional information from high-throughput omics data. Many software including website services and R packages are available to generate various types of customized heatmaps. Here, we describe oppHeatmap (omics pilot platform of heatmap), a new tool constructed to render different kinds of heatmaps through MATLAB. oppHeatmap is available for plotting ordinary heatmaps, hierarchical clustering, TreeMaps, microplates graph, sample correlation (full heatmap and upper and lower triangle parts), gene correlation (between columns or tables), and polar heatmaps. oppHeatmap can support the modification of borders, fonts, and colors to customize the final plots. oppHeatmap can not only read data from Microsoft Excel to generate specific heatmaps but also make Excel heatmaps by coloring each cell in Excel. The graphs can be stored in SVG (supported vector graph) format and modified by other SVG recognition software. oppHeatmap is designed by MATLAB AppDesigner with GUI (graphical user interface) operation. The program for oppHeatmap was available at https://github.com/HangZhouSheep/oppHeatmap .are diagramed by All kinds of heatmaps oppHeatmap. The main function of oppHeatmap is to enable visualization of two types of heatmaps and a total of 11 graphs. The first type is a heatmap with a polar or rectangular coordinate system, including ordinary heatmap, microplates graph, polar heatmap, and Excel heatmap. The last one involves writing the heatmap in Excel and others in MATLAB. The second type is with rearranged rows and columns, which includes hierarchical clustering, TreeMaps, and sample/gene correlation between columns or rows. All plots support row standardization for better color contrast. Eleven base functions implement heatmap plotting in the command line environment of MATLAB. GUI designed by AppDesigner supports the interactive construction of heatmaps.

Survey of Acetylation for Thermoanaerobacter tengcongensis.

Non-histone protein acetylation is involved in key cellular processes both in eukaryotes and prokaryotes. Acetylation in bacteria is used to modify proteins involved in metabolism and allow the bacteria to adapt to their environment. TTE (Thermoanaerobacter tengcongensis) is an anaerobic, thermophilic saccharolytic bacterium that grows at extreme temperature range between 50 and 80 â„ƒ. The annotated TTE proteome contains less than 3000 proteins. We analyzed the proteome and acetylome of TTE using 2DLC-MS/MS (2-dimensional liquid chromatography mass spectrum). We evaluated the ability of mass spectrometry technology to cover a relatively small proteome as much as possible. And we also observed wide spread of acetylation in TTE, which changed under different temperatures. A total of 2082 proteins were identified, which accounts for about 82% of the database. A total of 2050 (~ 98%) proteins were quantified in at least one culture condition and 1818 proteins were quantified in all 4 conditions. The result also consisted 3457 acetylation sites corresponding to 827 distinct proteins, which covered 40% of the proteins identified. Bioinformatics analysis reported that proteins related to replication, recombination, repair, and extracellular structure cell wall biogenesis had more than half members acetylated, while energy production, carbohydrate transport, and metabolism related proteins were least acetylated. Our result suggested that acetylation affects the ATP-related energy metabolism and energy-dependent biosynthesis process. Comparing the enzymes related with lysine acetylation and acetyl-CoA (acetyl-coenzyme A) metabolism, we suggested that the acetylation of TTE took a non-enzymatic mechanism and affected by abundance of acetyl-CoA.

oppOntology: a MATLAB Toolbox for Enrichment Analysis.

Biologists often use systems of ontologies to classify gene lists obtained by high-throughput gene or protein-sequencing instruments, and then enrichment scores were used to rank the ontology system. Therefore, the important molecular functional categories related to the phenotype can be conveniently viewed in the ontology system. Since the birth of GO (Gene Ontology) organization, various types of ontology software have been developed to calculate enrichment scores for the target gene list in the GO system. Herein, we provide an enrichment calculation application oppOntology (Omics Pilot Platform for Ontology) developed by MATLAB. oppOntology supports simultaneous calculation of multiple samples with manifold enrichment scores (GeneCount, GeneRatio, EnrichFactor, HypergeometricTest, and FisherExactTest). oppOntology can not only calculate enrichment scores for generic functional databases, such as GO, KEGG, HPO, and MsigDB, but also for self-defined functional category databases and customized GO Slim. Moreover, oppOntology supports online mapping of KEGG pathway diagrams in a batch way. The GUI (Graphical User Interface) of oppOntology is developed on the architecture of AppDesigner in MATLAB, and all input and output files are Microsoft Excel. oppOntology is an independent, easy-to-use enrichment calculation software, that can be available at https://github.com/HangZhouSheep/oppOntology .

opplncRNA: A MATLAB Package for Comprehensive Pathway Analysis of lncRNA-miRNA-mRNA in Humans.

The discovery of new lncRNAs (long noncoding RNAs) and their regulatory pathways has always been a hotspot in the field of ceRNA (competing endogenous RNA). Herein, we report opplncRNA (Omics Pilot Platform of lncRNA), a novel and rapid tool for investigating lncRNA-miRNA-mRNA interactions based on the architecture of MATLAB AppDesigner. opplncRNA is useful to analyze the regulatory interaction networks of lncRNA with a friendly GUI (graphical user interface). There are three lncRNA databases (ENCORI, LncBase, and miRcode) about lncRNA-miRNA interactions that have been integrated into opplncRNA, as well as seven miRNA databases (miRcode, ENCORI, TarBase, miRTarBase, miRDB, miRanda, and miRecords) about miRNA-mRNA interactions as also. opplncRNA can read expression data from any profile techniques, such as microarray or RNA-seq. Then, the relationships between lncRNA-miRNA and miRNA-mRNA can be directly calculated through the profile data of lncRNA, miRNA, and mRNA by the threshold of correlation coefficients. Integrated databases can be used to filter calculation outcomes to obtain more reliable pathways. Moreover, opplncRNA has the functionality of directly demonstrating 3 layers network from lncRNA to mRNA in command line form.

Ki20227 aggravates apoptosis, inflammatory response, and oxidative stress after focal cerebral ischemia injury.

The survival of microglia depends on the colony-stimulating factor-1 receptor (CSF1R) signaling pathway under physiological conditions. Ki20227 is a highly selective CSF1R inhibitor that has been shown to change the morphology of microglia. However, the effects of Ki20227 on the progression of ischemic stroke are unclear. In this study, male C57BL/6 mouse models of focal cerebral ischemic injury were established through the occlusion of the middle cerebral artery and then administered 3 mg/g Ki20227 for 3 successive days. The results revealed that the number of ionized calcium-binding adaptor molecule 1/bromodeoxyuridine double positive cells in the infarct tissue was reduced, the degree of edema was increased, neurological deficits were aggravated, infarct volume was increased, and the number of peri-infarct Nissl bodies was reduced. The number of terminal deoxynucleotidyl transferase dUTP nick-end labeling-positive cells in the peri-infarct tissue was increased. The expression levels of Bax and Cleaved caspase-3 were up-regulated. Bcl-2 expression was downregulated. The expression levels of inflammatory factors and oxidative stress-associated factors were increased. These findings suggested that Ki20227 blocked microglial proliferation and aggravated the pathological progression of ischemia/reperfusion injury in a transient middle cerebral artery occlusion model. This study was approved by the Animal Ethics Committee of Lanzhou University Second Hospital (approval No. D2020-68) on March 6, 2020.

Bilateral Dysplastic Gangliocytoma with Concurrent Polyostotic Fibrous Dysplasia: A Case Report and Literature Review.

BACKGROUND: Dysplastic gangliocytoma is a sporadic cerebellar benign tumor with the characteristics of hamartoma and true tumor, also known as Lhermitte-Duclos disease (LDD). Bone fibrous dysplasia (FD) is a slowly progressive self-limited benign bone tissue disease. Cowden syndrome, an autosomal dominant genetic disorder caused by germline mutations in the PTEN gene, is considered to be closely related to dysplastic gangliocytoma. McCune-Albright syndrome is a disease characterized by café-au-lait skin macules, polyostotic FD, and precocious puberty. The etiologic mechanism of both conditions is not yet clear. We report a rare case of bilateral dysplastic gangliocytoma with concurrent polyostotic FD. CASE DESCRIPTION: We describe a 16-year-old boy with both LDD and FD. He presented for medical examination with headache and poor eyesight. Magnetic resonance imaging revealed proliferation of the skull and abnormal signals in the cerebellum, and supratentorial hydrocephalus. Subtotal resection of the cerebellar tumor was performed, and the diagnosis of LDD and FD was confirmed by histopathology. No other abnormal changes were found in systemic medical examination and no PTEN gene mutation was found in the genetic analysis; therefore, the diagnoses of Cowden syndrome and McCune-Albright syndrome were excluded. CONCLUSIONS: LDD and FD are 2 rare diseases, and the simultaneous occurrence of the 2 conditions has not been reported before, to our knowledge. Our report challenges the etiology of the 2 diseases and the relationship between them, hoping to provide a reference for the study of the 2 diseases.