MetaSquare: An integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification

MOTIVATION: Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. 16S rRNA sequence databases like SILVA, RDP, EzBioCloud and HOMD used in downstream bioinformatic pipelines have limitations on either the sequence redundancy or the delay on new sequence recruitment. To improve the 16S rRNA gene-based taxonomic classification, we merged these widely used databases and a collection of novel sequences systemically into an integrated resource. RESULTS: MetaSquare version 1.0 is an integrated 16S rRNA sequence database. It is composed of more than 6 million sequences and improves taxonomic classification resolution on both long-read and short-read methods. AVAILABILITY AND IMPLEMENTATION: Accessible at https://hub.docker.com/r/lsbnb/metasquare_db and https://github.com/lsbnb/MetaSquare. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Hispolon Protects against Acute Liver Damage in the Rat by Inhibiting Lipid Peroxidation, Proinflammatory Cytokine, and Oxidative Stress and Downregulating the Expressions of iNOS, COX-2, and MMP-9

The hepatoprotective potential of hispolon against carbon tetrachloride (CCl4)-induced liver damage was evaluated in preventive models in rats. Male rats were intraperitoneally treated with hispolon or silymarin once daily for 7 consecutive days. One hour after the final hispolon or silymarin treatment, the rats were injected with CCl4. Administration with hispolon or silymarin significantly decreased the alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels in serum and increased the activities of superoxide dismutase (SOD), catalase, glutathione peroxidase (GPx), and glutathione (GSH) content and decreased the malondialdehyde (MDA) content in liver compared with CCl4-treated group. Liver histopathology also showed that hispolon reduced the incidence of liver lesions induced by CCl4. In addition, hispolon decreased nitric oxide (NO) production and tumor necrosis factor (TNF-α), inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) activation in CCl4-treated rats. We also examined the involvement of matrix metalloproteinase (MMP)-9 in the development of CCl4-induced liver damage in rats. Hispolon inhibited the expression of MMP-9 protein, indicating that MMP-9 played an important role in the development of CCl4-induced rat liver damage. Therefore, we speculate that hispolon protects rats from liver damage through their prophylactic redox balancing ability and anti-inflammation capacity

Comparison of Skull Motions in Six Degrees of Freedom Between Two Head Supports During Frameless Radiosurgery by CyberKnife

Introduction: Maintaining immobilization to minimize skull motion is important during frameless radiosurgery. This study aimed to compare the intrafractional skull motions between two head supports.Methods: With 6D skull tracking system, 4,075 image records from 45 patients receiving radiosurgery by CyberKnife were obtained. Twenty-three patients used TIMO head supports (CIVCO) (Group A) and twenty-two patients used Silverman head supports (CIVCO) with MoldCare cushions (ALCARE) (Group B). The skull motions in X (superior-inferior), Y (right-left), Z (anterior-posterior) axes, 3D (three-dimensional) vector, Roll, Pitch and Yaw between the two groups were compared and the margins of planning target volume were estimated.Results: The translational motions in Group A were similar in three axes at initial but became different after 10 min, and those in Group B were less prominent in the Y axis. The rotational errors in Group A were most obvious in Yaw, but those in Group B were stationary in three axes. The motions in the X axis, 3D vector, Pitch and Yaw in Group B were significantly smaller than those in Group A; conversely, the motions in the Z axis in Group B were larger. To cover the 95% confidence intervals, margins of 0.77, 0.79, and 0.40 mm in the X, Y, and Z axes, respectively, were needed in Group A, and 0.69, 0.50, and 0.51 mm were needed in Group B.Conclusions: Both head supports could provide good immobilization during the frameless radiosurgery. Silverman head support with MoldCare cushion was better than TIMO head support in the superior-inferior direction, 3D vector, Pitch and Yaw axes, but worse in the anterior-posterior direction

Role of the Diphosphine Chelate in Emissive, Charge-Neutral Iridium(III) Complexes

A class of neutral tris-bidentate Ir(III) metal complexes incorporating a diphosphine as a chelate is prepared and characterized here for the first time. Treatment of [Ir(dppb)(tht)Cl3] (1) with fppzH afforded the dichloride complexes, trans-(Cl,Cl)[Ir(dppb)(fppz)Cl2] (2) and cis-(Cl,Cl)[Ir(dppb)(fppz)Cl2] (3). The reaction of 3 with the dianionic chelate precursor bipzH2 or mepzH2, in DMF gave the complex [Ir(dppb)(fppz)(bipz)] (4) or [Ir(dppb)(fppz)(mepz)] (5), respectively. In contrast, a hydride complex [Ir(dppb)(fppz)(bipzH)H] (6) was isolated instead of 4 in protic solvent, namely: DGME. All complexes 2 - 6 are luminescent in powder forms and thin films where the dichlorides (2, 3) emit with maxima at 590-627 nm (orange) and quantum yields (Q.Y.s) up to 90% whereas the tris-bidentate (4, 5) and hydride (6) complexes emit at 455-458 nm (blue) with Q.Y.s up to 70%. Hybrid TD-DFT calculations showed considerable MLCT contribution to the orange-emitting 2 and 3 but substantial ligand-centered 3ππ* transition character in the blue-emitting 4 - 6. The dppb does not participate to these radiative transitions in 4 - 6, but it provides the rigidity and steric bulk needed to promote the luminescence by suppressing the self-quenching in the solid state. Fabrication of an OLED with dopant 5 gave a deep blue CIE chromaticity of (0.16, 0.15). Superior blue emitters, which are vital in OLED applications, may be found in other neutral Ir(III) complexes containing phosphine chelates

Retroperitoneoscopic laparo-endoscopic single-site radical nephrectomy (RLESS-RN): initial experience with a homemade port

We successfully performed 6 LESS radical nephrectomy via the retroperitoneal approach (RLESS) using the Alexis wound retractor as a single access with conventional laparoscopic instruments. The results demonstrated that our RLESS technique of radical nephrectomy is a safe and feasible procedure for management of localized renal cancer

Mitochondrial oxidative phosphorylation complex regulates NLRP3 inflammasome activation and predicts patient survival in nasopharyngeal carcinoma

© 2020 Chung et al. We previously reported that tumor inflammasomes play a key role in tumor control and act as favorable prognostic markers in nasopharyngeal carcinoma (NPC). Activated inflammasomes frequently form distinguishable specks and govern the cellular secretion of IL-1β. However, we know little about the biological and biochemical differences between cells with and without apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) speck formation. In this study, we used proteomic iTRAQ analysis to analyze the proteomes of NPC cells that differ in their ASC speck formation upon cisplatin treatment. We identified proteins that were differentially over-expressed in cells with specks, and found that they fell into two Gene ontology (GO) pathways: mitochondrial oxidative phosphorylation (OxPhos) and ubiquinone metabolism. We observed up-regulation of various components of the OxPhos machinery (including NDUFB3, NDUFB8 and ATP5B), and subsequently found that these changes lead to mitochondrial ROS (mtROS) production, which promotes the formation and activation of NLRP3 inflammasomes and subsequent pyroptosis. In NPC patients, better local recurrence-free survival was significantly associated with high-level expression of NDUFB8 (p = 0.037) and ATP5B (p = 0.029), as examined using immunohistochemistry. However, there were no significant associations between the expression of NDUFB8 and ATP5B with overall survival of NPC patients. Together, our results demonstrate that up-regulated mitochondrial OxPhos components are strongly associated with NLRP3 inflammasome activation in NPC. Our findings further suggest that high-level expression of OxPhos components could be markers for local recurrence and/or promising therapeutic targets in patients with NPC