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

Temperature-dependent free radical reaction in water

Temperature-dependent free radical reactions were investigated using nitroxyl radicals as redox probes. Reactions of two types of nitroxyl radicals, TEMPOL (4-hydroxyl-2,2,6,6-tetramethylpiperidine-N-oxyl) and carbamoyl-PROXYL (3-carbamoyl-2,2,5,5-tetramethylpyrrolidine-N-oxyl), were tested in this paper. Heating a solution containing a nitroxyl radical and a reduced form of glutathione (GSH) caused temperature-dependent decay of electron paramagnetic resonance (EPR) signal of the nitroxyl radical. Heating a solution of the corresponding hydroxylamine form of the nitroxyl radical showed EPR signal recovery. The GSH-dependent reduction of nitroxyl radicals at 70°C was suppressed by antioxidants, spin trapping agents, and/or bubbling N2 gas, although heating carbamoyl-PROXYL with GSH showed temporarily enhanced signal decay by bubbling N2 gas. Since SOD could restrict the GSH-dependent EPR signal decay of TEMPOL, O2•− is related with this reaction. O2•− was probably generated from dissolved oxygen in the reaction mixture. Oxidation of the hydroxylamines at 70°C was also suppressed by bubbling N2 gas. Heating a solution of spin trapping agent, DMPO (5,5-dimethyl-1-pyrroline-N-oxide) showed a temperature-dependent increase of the EPR signal of the hydroxyl radical adduct of DMPO. Synthesis of hydroxyl radical adduct of DMPO at 70°C was suppressed by antioxidants and/or bubbling N2 gas. The results suggested that heating an aqueous solution containing oxygen can generate O2•−

Telmisartan improves nonalcoholic steatohepatitis in medaka (Oryzias latipes) by reducing macrophage infiltration and fat accumulation

We investigated the efficacy of the antihypertensive drug telmisartan (Tel) and the mechanisms underlying the progression from simple steatosis to nonalcoholic steatohepatitis (NASH) in a medaka (Oryzias latipes) NASH model. We used the NASH activity score (NAS) developed in humans to assess the histology of the medaka NASH model and found that NAS increased with time. Further, TUNEL-positive apoptosis hepatocytes were found in the medaka NASH model. Tel administration resulted in the increased expression of liver peroxisome proliferator-activated receptor-γ, carnitine palmitoyltransferase 1 and acyl-CoA oxidase 1 and decreased the number of 8-hydroxydeoxyguanosine-positive hepatocytes and the migration of macrophages positive for diastase-periodic-acid-Schiff. Medaka NAS was improved by Tel administration but fatty acid content was not affected. Tel reduced the infiltration of macrophages into the liver and ameliorated NASH pathology

Development of a deep-sea laser-induced breakdown spectrometer for in situ multi-element chemical analysis

Spectroscopy is emerging as a technique that can expand the envelope of modern oceanographic sensors. The selectivity of spectroscopic techniques enables a single instrument to measure multiple components of the marine environment and can form the basis for versatile tools to perform in situ geochemical analysis. We have developed a deep-sea laser-induced breakdown spectrometer (ChemiCam) and successfully deployed the instrument from a remotely operated vehicle (ROV) to perform in situ multi-element analysis of both seawater and mineral deposits at depths of over 1000 m. The instrument consists of a long-nanosecond duration pulse-laser, a spectrometer and a high-speed camera. Power supply, instrument control and signal telemetry are provided through a ROV tether. The instrument has two modes of operation. In the first mode, the laser is focused directly into seawater and spectroscopic measurements of seawater composition are performed. In the second mode, a fiber-optic cable assembly is used to make spectroscopic measurements of mineral deposits. In this mode the laser is fired through a 4 m long fiber-optic cable and is focused onto the target’s surface using an optical head and a linear stage that can be held by a ROV manipulator. In this paper, we describe the instrument and the methods developed to process its measurements. Exemplary measurements of both seawater and mineral deposits made during deployments of the device at an active hydrothermal vent field in the Okinawa trough are presented. Through integration with platforms such as underwater vehicles, drilling systems and subsea observatories, it is hoped that this technology can contribute to more efficient scientific surveys of the deep-sea environment

Serotonin transporter gene polymorphism may be associated with functional dyspepsia in a Japanese population

<p>Abstract</p> <p>Background</p> <p>Although familial clustering of functional dyspepsia (FD) has been reported, the role of genetics in the susceptibility to FD is still not well understood. In the present study, the association between serotonin transporter (SERT) gene (<it>SLC6A4</it>) polymorphism and FD was explored.</p> <p>Methods</p> <p>Subjects were divided into either a postprandial distress syndrome (PDS) group or an epigastric pain syndrome (EPS) group according to the Rome III criteria. The healthy controls were those who had visited a hospital for an annual health check-up. The presence of the <it>SLC6A4 </it>promoter polymorphism, <it>5-hydroxytryptamin transporter gene linked polymorphic region </it>(<it>5-HTTLPR</it>), was then evaluated, and logistic regression analysis was used to test all variables.</p> <p>Results</p> <p>The <it>5-HTTLPR </it>genotype distribution was 448 SS, 174 SL, and 24 LL in controls and 30 SS, 20 SL, and 3 LL in FD subjects. No significant correlation was found between the <it>5-HTTLPR </it>genotype and FD. When the genotypes and subtypes of FD were exploratory evaluated, the SL genotype was significantly associated with PDS [odds ratio (OR) = 2.24, 95% confidence interval (CI); 1.16-4.32, <it>P </it>= 0.034 after Bonferroni correction] compared to the SS genotype adjusted for sex and age. Comparison of the SS genotype with the SL/LL genotype also showed a significant association of genotype with PDS (OR = 2.32, 95% CI; 1.23-4.37, <it>P </it>= 0.009).</p> <p>Conclusion</p> <p>The present results suggest that <it>5-HTTLPR </it>L allele may influence the susceptibility to PDS.</p

Automated detection method of thoracic aorta calcification from non-contrast CT images using mediastinal anatomical label map

Progression of thoracic aortic calcification (TAC) has been shown to be associated with hard cardiovascular events including stroke and all-cause mortality as well as coronary events. In this study, we propose an automated detection method of TACs of non-contrast CT images using mediastinal anatomical label map. This method consists of two steps: (1) the construction of a mediastinal anatomical label map, and (2) the detection of TACs using the intensity and the mediastinal anatomical label map. The proposed method was applied to two non-contrast CT image datasets: 24 cases of chronic thromboembolic pulmonary hypertension (CTEPH) and 100 non-CTEPH cases of low-dose CT screening. The method was compared with two-dimensional U-Nets and the Swin UNETR. The results showed that the method achieved significantly higher F1 score of 0.937 than other methods for the non-CTEPH case dataset (p-value < 0.05, pairwise Wilcoxon signed rank test with Bonferroni correction)

EPR based Estimation of Radiation-Induced Reactive Oxygen Species

Generation of reactive oxygen species (ROS) is considered as essential trigger of biological effects of ionizing radiations, and may be deeply linked with the radiation quality.Amounts of total oxidation reactions (i.e. oxidative free radical species, •OH and HO2•), H2O2 generations, Oxygen consumptions, and •OH generations induced by X-ray, 20 keV/μm carbon beam, and 80 keV/μm carbon beam were estimated using EPR based techniques.Total oxidation reactions were estimated as 3, 1.3, and 0.66 μmol/L/Gy, amount of H2O2 generations were 0.2, 0.57, and 0.35 μmol/L/Gy, oxygen consumptions were 0.4, 0.39, and 0.15 μmol/L/Gy for X-ray, 20 keV/μm carbon beam, and 80 keV/μm carbon beam, respectively. The ratio of H2O2 generation per oxygen consumption were increased with LET, and were 0.5, 1.46, 2.33 for X-ray, 20 keV/μm carbon beam, and 80 keV/μm carbon beam, respectively. The •OH generations expected to be localized on the track/range of the radiation beam/ray, and both sparse (≈ 3.3 mM) and very dense (> 1.7 M) •OH generations were suggested. Percentage of sparse •OH generation decreased with LET becoming higher.The SFRBM\u27s 23rd Annual Meeting, a joint meeting with the Society for Free Radical Research International (SFRBM/SFRRI 2016

Detection of an H-alpha Emission Line on a Quasar, RX J1759.4+6638, at z=4.3 with AKARI

We report the detection of an H-alpha emission line in the low resolution spectrum of a quasar, RX J1759.4+6638, at a redshift of 4.3 with the InfraRed Camera (IRC) onboard the AKARI. This is the first spectroscopic detection of an H-alpha emission line in a quasar beyond z=4. The overall spectral energy distribution (SED) of RX J1759.4+6638 in the near- and mid-infrared wavelengths agrees with a median SED of the nearby quasars and the flux ratio of F(Ly-alpha)/F(H-alpha) is consistent with those of previous reports for lower-redshift quasars.Comment: 9pages, 3 figures, Publications of the Astronomical Society of Japan, in pres

Modulation of anti-cancer drug sensitivity through the regulation of mitochondrial activity by adenylate kinase 4

Background: Adenylate kinase is a key enzyme in the high-energy phosphoryl transfer reaction in living cells. An isoform of this enzyme, adenylate kinase 4 (AK4), is localized in the mitochondrial matrix and is believed to be involved in stress, drug resistance, malignant transformation in cancer, and ATP regulation. However, the molecular basis for the AK4 functions remained to be determined. Methods: HeLa cells were transiently transfected with an AK4 small interfering RNA (siRNA), an AK4 short hairpin RNA (shRNA) plasmid, a control shRNA plasmid, an AK4 expression vector, and a control expression vector to examine the effect of the AK4 expression on cell proliferation, sensitivity to anti-cancer drug, metabolome, gene expression, and mitochondrial activity. Results: AK4 knockdown cells treated with short hairpin RNA increased ATP production and showed greater sensitivity to hypoxia and anti-cancer drug, cis-diamminedichloro-platinum (II) (CDDP). Subcutaneous grafting AK4 knockdown cells into nude mice revealed that the grafted cells exhibited both slower proliferation and reduced the tumor sizes in response to CDDP. AK4 knockdown cell showed a increased oxygen consumption rate with FCCP treatment, while AK4 overexpression lowered it. Metabolome analysis showed the increased levels of the tricarboxylic acid cycle intermediates, fumarate and malate in AK4 knockdown cells, while AK4 overexpression lowered them. Electron microscopy detected the increased mitochondrial numbers in AK4 knockdown cells. Microarray analysis detected the increased gene expression of two key enzymes in TCA cycle, succinate dehydrogenase A (SDHA) and oxoglutarate dehydrogenease L (OGDHL), which are components of SDH complex and OGDH complex, supporting the metabolomic results. Conclusions: We found that AK4 was involved in hypoxia tolerance, resistance to anti-tumor drug, and the regulation of mitochondrial activity. These findings provide a new potential target for efficient anticancer therapies by controlling AK4 expression