BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes

<p>Abstract</p> <p>Background</p> <p>Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest.</p> <p>Description</p> <p>BPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ) and Unweighted Pair-Group Method using Arithmetic averages (UPGMA). Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint.</p> <p>Conclusion</p> <p>BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by annotations make BPhyOG a powerful web server for genomic and genetic studies. It is freely available at <url>http://cmb.bnu.edu.cn/BPhyOG</url>.</p

Cluster Synchronization of Stochastic Complex Networks with Markovian Switching and Time-Varying Delay via Impulsive Pinning Control

This paper studies the cluster synchronization of a kind of complex networks by means of impulsive pinning control scheme. These networks are subject to stochastic noise perturbations and Markovian switching, as well as internal and outer time-varying delays. Using the Lyapunov-Krasovskii functional, Itö’s formula, and some linear matrix inequalities (LMI), several novel sufficient conditions are obtained to guarantee the desired cluster synchronization. At the end of this writing, a numerical simulation is given to demonstrate the effectiveness of those theoretical results

Deciphering of interactions between platinated DNA and HMGB1 by hydrogen/deuterium exchange mass spectrometry

A high mobility group box 1 (HMGB1) protein has been reported to recognize both 1,2-intrastrand crosslinked DNA by cisplatin (1,2-cis-Pt-DNA) and monofunctional platinated DNA using trans-[PtCl2(NH3)(thiazole)] (1-trans-PtTz-DNA). However, the molecular basis of recognition between the trans-PtTz-DNA and HMGB1 remains unclear. In the present work, we described a hydrogen/deuterium exchange mass spectrometry (HDX-MS) method in combination with docking simulation to decipher the interactions of platinated DNA with domain A of HMGB1. The global deuterium uptake results indicated that 1-trans-PtTz-DNA bound to HMGB1a slightly tighter than the 1,2-cis-Pt-DNA. The local deuterium uptake at the peptide level revealed that the helices I and II, and loop 1 of HMGB1a were involved in the interactions with both platinated DNA adducts. However, docking simulation disclosed different H-bonding networks and distinct DNA-backbone orientations in the two Pt-DNA-HMGB1a complexes. Moreover, the Phe37 residue of HMGB1a was shown to play a key role in the recognition between HMGB1a and the platinated DNAs. In the cis-Pt-DNA-HMGB1a complex, the phenyl ring of Phe37 intercalates into a hydrophobic notch created by the two platinated guanines, while in the trans-PtTz-DNA-HMGB1a complex the phenyl ring appears to intercalate into a hydrophobic crevice formed by the platinated guanine and the opposite adenine in the complementary strand, forming a penta-layer π–π stacking associated with the adjacent thymine and the thiazole ligand. This work demonstrates that HDX-MS associated with docking simulation is a powerful tool to elucidate the interactions between platinated DNAs and proteins

Enhanced cycling stability of Li–O2 batteries by using a polyurethane/SiO2/glass fiber nanocomposite separator

A considerable improvement in the cycle performance of aprotic Li–O2 batteries was achieved by using a polyurethane/SiO2 gel nanoparticles/glass fiber (PU/SiO2/GF) nanocomposite separator, where a persistent capability of 1000 mA h g−1 was maintained for at least 300 charge/discharge cycles in a DMSO electrolyte with 1 M LiClO4 and 0.05 M LiI. In comparison, the cell with a conventional GF separator in the same experimental setup only run for 60 cycles. SEM, XRD and FT-IR analyses indicate that the corrosion and dendritic growth of the Li anode were significantly inhibited during the charge/discharge cycling, and the eventual failure of the Li–O2 batteries was attributed to the cathode passivation caused by the accumulation of the discharge product, which blocked the transfer of oxygen and electrolyte to the MWNTs cathode

Pseudo almost automorphic behavior of solutions to a semi-linear fractional differential equation

In this paper, we shall deal with $mu$-pseudo almost automorphic solutions to a semi-linear fractional differential equation by new concept of $mu$-pseudo almost automorphic functions presented recently. We first establish some new properties of $mu$-pseudo almost automorphic functions, and then we apply the results obtained to prove some existence theorems combined with the Leray-Schauder alternative theorem

2-Methyl­carbamoyl-4-{4-[3-(trifluoro­meth­yl)benzamido]phen­oxy}pyridinium 4-methyl­benzene­sulfonate monohydrate

The asymmetric unit of the title compound, C21H17F3N3O3 +·C7H7O3S−·H2O, contains two formula units. In one of the cations, the pyridinium and trifluoro­methyl benzene rings form dihedral angles of 87.42 (8) and 45.92 (8)°, respectively, with the central benzene ring [79.56 (8) and 43.52 (8)° in the other cation]. In the crystal structure, N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds link the ions and water mol­ecules, forming a three-dimensional network

3,3′-Dibromo-1,1′-[ethyl­enedioxy­bis(nitrilo­methyl­idyne)]dibenzene

In the centrosymmetric title compound, C16H14Br2N2O2, the intra­molecular interplanar distance between the parallel benzene rings is 1.305 (3) Å, while the inter­molecular interplanar distance (between neighbouring mol­ecules) is 3.463 (3) Å, exhibiting obvious strong inter­molecular π–π stacking inter­actions