ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences

<p>Abstract</p> <p>Background</p> <p>Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can narrow down key regulatory elements. Repeat masking processes are often performed before alignment to mask insertion sequences such as transposable elements (TEs). However, recently such TEs have been reported to influence the gene regulatory network evolution. Therefore, an alignment approach that is robust to TE insertions is meaningful for finding novel conserved TFBSs in TEs.</p> <p>Results</p> <p>We constructed a web server 'ReAlignerV' for complex alignment of genomic sequences. ReAlignerV returns ladder-like schematic alignments that integrate predicted TFBSs and the location of TEs. It also provides pair-wise alignments in which the predicted TFBS sites and their names are shown alongside each sequence. Furthermore, we evaluated false positive aligned sites by focusing on the species-specific TEs (SSTEs), and found that ReAlignerV has a higher specificity and robustness to insertions for sequences having more than 20% TE content, compared to LAGAN, AVID, MAVID and BLASTZ.</p> <p>Conclusion</p> <p>ReAlignerV can be applied successfully to TE-insertion-rich sequences without prior repeat masking, and this increases the chances of finding regulatory sequences hidden in TEs, which are important sources of the regulatory network evolution. ReAlignerV can be accessed through and downloaded from <url>http://genet.med.kagawa-u.ac.jp/</url>.</p

Effects of vasoactive intestinal contractor (VIC) and endothelin on intracellular calcium level in neuroblastoma NG108-15 cells

AbstractEffects on [Ca2+]i levels of endothelin-1 (ET) and vasoactive intestinal contractor peptide (VIC), which is a novel member of the endothelin family, were examined in fura 2-loaded neuroblastoma NG108-15 cells. VIC was found to be a very effective stimulus for intracellular Ca2+ mobilization and to be more potent than ET. Intracellular calcium response to sequential addition of two stimulants exhibited the homologous desensitization of either ET or VIC, but no heterologous desensitization between ET and VIC. This indicates evidence suggesting that these two peptides act through distinct receptors

An All-Recombinant Protein-Based Culture System Specifically Identifies Hematopoietic Stem Cell Maintenance Factors.

Hematopoietic stem cells (HSCs) are considered one of the most promising therapeutic targets for the treatment of various blood disorders. However, due to difficulties in establishing stable maintenance and expansion of HSCs in vitro, their insufficient supply is a major constraint to transplantation studies. To solve these problems we have developed a fully defined, all-recombinant protein-based culture system. Through this system, we have identified hemopexin (HPX) and interleukin-1α as responsible for HSC maintenance in vitro. Subsequent molecular analysis revealed that HPX reduces intracellular reactive oxygen species levels within cultured HSCs. Furthermore, bone marrow immunostaining and 3D immunohistochemistry revealed that HPX is expressed in non-myelinating Schwann cells, known HSC niche constituents. These results highlight the utility of this fully defined all-recombinant protein-based culture system for reproducible in vitro HSC culture and its potential to contribute to the identification of factors responsible for in vitro maintenance, expansion, and differentiation of stem cell populations

Theory of tunneling spectroscopy in superconducting Sr2RuO4

A theory for tunneling spectroscopy in normal metal /insulator/triplet superconductor junction is presented. We assume two kinds of non-unitary triplet superconducting states which are the most promising states for Sr$_{2}$RuO$_{4}$. The calculated conductance spectra showzero-bias peaks as well as gap structures. The existences of residual components in the spectra reflect the non-unitary properties of superconducting states.Comment: 5pages, 4figures(included), to be published in Phys.Rev.B 56, (1997

Observation of domain wall bimerons in chiral magnets

Topological defects embedded in or combined with domain walls have been proposed in various systems, some of which are referred to as domain wall skyrmions or domain wall bimerons. However, the experimental observation of such topological defects remains an ongoing challenge. Here, using Lorentz transmission electron microscopy, we report the experimental discovery of domain wall bimerons in chiral magnet Co-Zn-Mn(110) thin films. By applying a magnetic field, multidomain structures develop, and simultaneously, chained and isolated bimerons arise as the localized state between the domains with the opposite in-plane components of net magnetization. The multidomain formation is attributed to magnetic anisotropy and dipolar interaction, and domain wall bimerons are stabilized by the Dzyaloshinskii-Moriya interaction. In addition, micromagnetic simulations show that domain wall bimerons appear for a wide range of conditions in chiral magnets with cubic magnetic anisotropy. Our results promote further study in various fields of physics.Comment: 30 pages, 10 figures (including Supplementary Materials

グラス ファイバー デ ホキョウ サレタ コウキョウド コンポジット レジン オ モチイタ 3 ユニット ブリッジ チリョウ ニツイテ

Mechanical strength to withstand occlusal force is required to the crown restorations of molars. Ag-Pd-Au alloy has been used as the acceptable material of the National Health Insurance system in Japan. However, the metallic color of prosthesis does not meet the aesthetic requirements of the patients, and there is also a problem to the provider side of the treatment that the price fluctuation is large by soaring material costs. A fiber reinforced metal-less bridge is proposed to resolve these problems and we began clinical application of this prosthetic treatment from September, 2012 on the approval of Tokushima University Hospital ethics committee. So far, six patients have been treated with 8 fiber reinforced bridges, and this treatment in Tokushima University Hospital was approved in Shikoku Regional Bureau of Health and Welfare as the advanced medical. We have followed the treatment for a maximum of more than two years, and it has been passed successfully with patient's satisfaction. Slightly problems which were caused in the hybrid resin material, could be easily solved by the direct procedures. This clinical results in short term suggested that the fiber reinforced metalless bridge have a sufficiently high therapeutic effect as a prosthetic method

Development of Kupffer cell targeting type-I interferon for the treatment of hepatitis via inducing anti-inflammatory and immunomodulatory actions

Because of its multifaceted anti-inflammatory and immunomodulatory effects, delivering type-I interferon to Kupffer cells has the potential to function as a novel type of therapy for the treatment of various types of hepatitis. We report herein on the preparation of a Kupffer cell targeting type-I interferon, an albumin-IFNα2b fusion protein that contains highly mannosylated N-linked oligosaccharide chains, Man-HSA(D494N)-IFNα2b, attached by combining albumin fusion technology and site-directed mutagenesis. The presence of this unique oligosaccharide permits the protein to be efficiently, rapidly and preferentially distributed to Kupffer cells. Likewise IFNα2b, Man-HSA(D494N)-IFNα2b caused a significant induction in the mRNA levels of IL-10, IL-1Ra, PD-L1 in RAW264.7 cells and mouse isolated Kupffer cells, and these inductions were largely inhibited by blocking the interferon receptor. These data indicate that Man-HSA(D494N)-IFNα2b retained the biological activities of type-I interferon. Man-HSA(D494N)-IFNα2b significantly inhibited liver injury in Concanavalin A (Con-A)-induced hepatitis model mice, and consequently improved their survival rate. Moreover, the post-administration of Man-HSA(D494N)-IFNα2b at 2 h after the Con-A challenge also exerted hepato-protective effects. In conclusion, this proof-of-concept study demonstrates the therapeutic effectiveness and utility of Kupffer cell targeting type-I interferon against hepatitis via its anti-inflammatory and immunomodulatory actions

Josephson current in s-wave superconductor / Sr_2RuO_4 junctions

The Josephson current between an s-wave and a spin-triplet superconductor Sr$_2$RuO$_4$ (SRO) is studied theoretically. In spin-singlet / spin-triplet superconductor junctions, there is no Josephson current proportional to $\sin \phi$ in the absence of the spin-flip scattering near junction interfaces, where $\phi$ is a phase-difference across junctions. Thus a dominant term of the Josephson current is proportional to $\sin 2\phi$ . The spin-orbit scattering at the interfaces gives rise to the Josephson current proportional to $\cos\phi$, which is a direct consequence of the chiral paring symmetry in SRO