miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants. In the last few years, the oligonucleotide microarray is one high-throughput and robust method for detecting miRNA expression. However, the approach is restricted to detecting the expression of known miRNAs. Second-generation sequencing is an inexpensive and high-throughput sequencing method. This new method is a promising tool with high sensitivity and specificity and can be used to measure the abundance of small-RNA sequences in a sample. Hence, the expression profiling of miRNAs can involve use of sequencing rather than an oligonucleotide array. Additionally, this method can be adopted to discover novel miRNAs.</p> <p>Results</p> <p>This work presents a systematic approach, miRExpress, for extracting miRNA expression profiles from sequencing reads obtained by second-generation sequencing technology. A stand-alone software package is implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. The software is also a database-supported, efficient and flexible tool for investigating miRNA regulation. Moreover, we demonstrate the utility of miRExpress in extracting miRNA expression profiles from two Illumina data sets constructed for the human and a plant species.</p> <p>Conclusion</p> <p>We develop miRExpress, which is a database-supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel miRNAs.</p

Adenovirus-mediated delivery of bFGF small interfering RNA increases levels of connexin 43 in the glioma cell line, U251

BACKGROUND: bFGF is an important growth factor for glioma cell proliferation and invasion, while connexin 43 is implicated in the suppression of glioma growth. Correspondingly, gliomas have been shown to have reduced, or compromised, connexin 43 expression. METHODS: In this study, a bFGF-targeted siRNA was delivered to the glioma cell line, U251, using adenovirus (Ad-bFGF-siRNA) and the expression of connexin 43 and its phosphorylation state were evaluated. U251 cells were infected with Ad-bFGF-siRNA (100, 50, or 25 MOI), and infection with adenovirus expressing green fluorescent protein (Ad-GFP) at 100 MOI served as a control. Western blotting and immunofluorescence were used to detect the expression levels, phosphorylation, and localization of connexin 43 in U251 cells infected, and not infected, with Ad-bFGF-siRNA. RESULTS: Significantly higher levels of connexin 43 were detected in U251 cells infected with Ad-bFGF-siRNA at 100 and 50 MOI than in cells infected with Ad-GFP, and the same amount of connexin 43 was detected in Ad-GFP-infected and uninfected U251 cells. Connexin 43 phosphorylation did not differ between Ad-bFGF-siRNA-infected and uninfected U251 cells. However, the ratio of phosphorylated to unphosphorylated connexin 43 in Ad-bFGF-siRNA cells was lower, and connexin 43 was predominantly localized to the cytoplasm. Using a scrape loading dye transfer assay, more Lucifer Yellow was transferred to neighboring cells in the Ad-bFGF-siRNA treated group than in the control group. CONCLUSION: To our knowledge, this is the first description of a role for connexin 43 in the inhibition of U251 growth using Ad-bFGF-siRNA

Diaqua­bis(norfloxacinato)manganese(II) 2,2′-bipyridine solvate tetra­hydrate

In the crystal structure of the title compound {systematic name: diaqua­bis[1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydro­quinoline-3-carboxyl­ato]manganese(II) 2,2′-bipyridine solvate tetra­hydrate}, [Mn(C16H17FN3O3)2(H2O)2]·C10H8N2·4H2O, the pyridone O atom and one carboxyl­ate O atom of the two norfloxacin ligands are bound to the MnII ion, which is located on an inversion centre, and occupy equatorial positions, while two aqua O atoms lie in apical positions, resulting in a distorted octa­hedral geometry. The crystal packing is stabilized by N—H⋯O and O—H⋯O hydrogen-bonding interactions

Bis(2-amino-3H-benzothia­zolium) bis­(7-oxabicyclo­[2.2.1]heptane-2,3-dicarboxyl­ato)cobaltate(II) hexa­hydrate

In the crystal structure of the title salt, (C7H7N2S)2[Co(C8H8O5)2]·6H2O, the heterocyclic N atom of the 2-amino­benzothia­zole mol­ecule is protonated. The CoII atom is situated on an inversion centre and exhibits a slightly distorted octa­hedral CoO6 coordination defined by the bridging O atoms of the bicyclo­heptane unit and four carboxyl­ate O atoms of two symmetry-related and fully deprotonated ligands. The crystal packing is stabilized by N—H⋯O hydrogen bonds between the cations and anions and by O—H⋯O hydrogen bonds including the crystal water mol­ecules

Isospin-conserving hadronic decay of the Ds1(2460){D_{s1}(2460)} into Dsπ+π−{D_s\pi^+\pi^-}

The internal structure of the charm-strange mesons $D_{s0}^*(2317)$ and $D_{s1}(2460)$ are subject of intensive studies. Their widths are small because they decay dominantly through isospin-breaking hadronic channels $D_{s0}^*(2317)^+\to D_s^+\pi^0$ and $D_{s1}(2460)^+\to D_s^{*+}\pi^0$. The $D_{s1}(2460)$ can also decay into the hadronic final states $D_s^+\pi\pi$, conserving isospin. In that case there is, however, a strong suppression from phase space. We study the transition $D_{s1}(2460)^+\to D_s^+\pi^+\pi^-$ in the scenario that the $D_{s1}(2460)$ is a $D^*K$ hadronic molecule. The $\pi\pi$ final state interaction is taken into account through dispersion relations. We find that the ratio of the partial widths of the $\Gamma(D_{s1}(2460)^+\to D_s^+\pi^+\pi^-)/\Gamma(D_{s1}(2460)^+\to D_s^{*+}\pi^0)$ obtained in the molecular picture is consistent with the existing experimental measurement. More interestingly, we demonstrate that the $\pi^+\pi^-$ invariant mass distribution shows a double bump structure, which can be used to disentangle the hadronic molecular picture from the compact state picture for the $D_{s1}(2460)^+$. Predictions on the $B_{s1}^0\to B_s^0\pi^+\pi^-$ are also made.Comment: 16 pages, 5 figure

Bis(2-amino-3H-benzothia­zolium) bis­(7-oxabicyclo­[2.2.1]heptane-2,3-di­carbox­yl­ato)manganate(II) hexa­hydrate

In the crystal structure of the title salt, (C7H7N2S)2[Mn(C8H8O5)2]·6H2O, the heterocyclic N atom of the 2-amino­benzothia­zole mol­ecule is protonated. The MnII atom (site symmetry ) has a slightly distorted octa­hedral MnO6 coordination defined by the bridging O atoms of the bicyclo­heptane unit and four carboxyl­ate O atoms of two symmetry-related and fully deprotonated ligands. The crystal packing is stabilized by N—H⋯O hydrogen bonds between the cations and anions and by O—H⋯O hydrogen bonds including the crystal water mol­ecules

catena-Poly[[diaqua­manganese(II)]-μ-7-oxabicyclo­[2.2.1]heptane-2,3-dicarboxyl­ato]

In the title polymer, [Mn(C8H8O5)(H2O)2]n, the MnII atom is in a distorted octa­hedral coordination mode, binding to the bridging O atom of the bicyclo­heptane unit, two O atoms from corresponding carboxyl­ate groups, one carboxyl­ate O atom from a symmetry-related bridging ligand and two water O atoms. This arrangement leads to the formation of polymeric chains propagating parallel to [001]. The crystal structure is stabilized by several O—H⋯O hydrogen-bonding inter­actions involving the coordinated water mol­ecules as donors and the carboxyl­ate O atoms as acceptors

Designing Pt-based electrocatalysts with high surface energy

The reactivity of an electrocatalyst depends strongly on its surface structure. Pt-based electrocatalysts of nanocrystals (NCs) enclosed with high-index facets contain a large density of catalytically active sites formed from step and kink atoms on the facets and exhibit intrinsically superior activity. However, the Pt-based NCs of high-index facets do possess a high surface energy and are thermodynamically metastable, leading to a big challenge in their shape-controlled synthesis. To overcome the challenge, kinetic–thermodynamic control of crystal growth is indispensable and is currently realized mainly by electrochemical methods and surfactant-based wet chemical approaches. This Perspective reviews recent progresses in Pt-based electrocatalysts of monometallic and bimetallic NCs of high surface energy with different morphologies of convex or concave tetrahexahedron, trapezohedron, trisoctahedron, hexoctahedron, etc. Remarkable electrocatalytic performance of these NCs has been demonstrated. Despite the considerable progress already made, the electrocatalysts of NCs with high surface energy still hold significant future opportunities in both fundamental understanding and practical applications