ExonMiner: Web service for analysis of GeneChip Exon array data

<p>Abstract</p> <p>Background</p> <p>Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer.</p> <p>Results</p> <p>We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1) data normalization, (2) statistical analysis based on two-way ANOVA, (3) finding transcripts with significantly different splice patterns, (4) efficient visualization based on heatmaps and barplots, and (5) meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers.</p> <p>Conclusion</p> <p>ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL <url>http://ae.hgc.jp/exonminer</url>. Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers.</p

Immunoregulatory effects triggered by immunobiotic Lactobacillus jensenii TL2937 strain involve efficient phagocytosis in porcine antigen presenting cells

Background: Immunobiotic Lactobacillus jensenii TL2937 modulates porcine mononuclear phagocytes from Peyer?s patches (PPMPs) and induces a differential production of pro- and anti-inflammatory cytokines in response to Toll-like receptor (TLR)-4 activation. Objective: In view of the important role played by phagocytosis in the activation of antigen presenting cells (APCs), the aim of the present work was to examine the interaction of TL2937 with porcine PPMPs focusing on phagocytosis. In addition, this study aimed to investigate whether the effects of L. jensenii TL2937 in porcine blood monocyte-derived dendritic cells (MoDCs) are similar to those found in PPMPs considering that MoDCs do not recapitulate all functions of mucosal APCs. Results: studies showed a high ability of porcine CD172a+ PPMPs to phagocytose L. jensenii TL2937. Interestingly, our results also revealed a reduced capacity of the non-immunomodulatory L. plantarum TL2766 to be phagocytosed by those immune cells. Phagocytosis of L. jensenii TL2937 by porcine PPMPs was partially dependent on TLR2. In addition, we demonstrated that TL2937 strain was able to improve the expression of IL-1, IL-12 and IL-10 in immature MoDCs resembling the effect of this immunobiotic bacterium on PPMPs. Moreover, similarly to PPMPs those immunomodulatory effects were related to the higher capacity of TL2937 to be phagocytosed by immature MoDCs. Conclusions: Microbial recognition in APCs could be effectively mediated through ligand-receptor interactions that then mediate phagocytosis and signaling. For the immunobiotic strain TL2937, TLR2 has a partial role for its interaction with porcine APCs and it is necessary to investigate the role of other receptors. A challenge for future research will be advance in the full understanding of the molecular interactions of immunobiotic L. jensenii TL2937 with porcine APCs that will be crucial for the successful development of functional feeds for the porcine host. This study is a step in that direction.Fil: Tsukida, Kohichiro. Tohoku University; JapónFil: Takahashi, Takuya. Tohoku University; JapónFil: Iida, Hikaru. Tohoku University; JapónFil: Kanmani, Paulraj. Tohoku University; JapónFil: Suda, Yoshihito. Miyagi University; JapónFil: Nochi, Tomonori. Tohoku University; JapónFil: Ohwada, Shuichi. Tohoku University; JapónFil: Aso, Hisashi. Tohoku University; JapónFil: Ohkawara, Sou. Meiji Seika Pharma Co., Ltd. Agricultural & Veterinary Division; JapónFil: Makino, Seiya. Meiji Co., Ltd. Division of Research and Development; JapónFil: Kano, Hiroshi. Meiji Co., Ltd. Division of Research and Development; JapónFil: Saito, Tadao. Tohoku University; JapónFil: Villena, Julio Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Kitazawa, Haruki. Tohoku University; Japó

Modulation of porcine intestinal epitheliocytes immunetranscriptome response by Lactobacillus jensenii TL2937

In order to evaluate probiotic strains applicable for the beneficial immunomodulation of the porcine gut (immunobiotics), we previously developed a porcine intestinal epitheliocyte cell line (PIE cells). Here, transcriptomic studies using PIE cells were performed considering that this information would be valuable for understanding the mechanisms involved in the protective activity of the immunobiotic strain Lactobacillus jensenii TL2937 against intestinal inflammatory damage in pigs. In addition, those studies would provide criteria for selecting biomarkers for the screening of new immunobiotic strains. We performed microarray analysis to investigate the transcriptomic response of PIE cells to the challenge with heat-stable Enterotoxigenic Escherichia coli (ETEC) pathogen-associated molecular patterns (PAMPs) and, the changes induced by L. jensenii TL2937 in that response. The approach allowed us to obtain a global overview of the immune genes involved in the response of PIE cells to heat-stable ETEC PAMPs. We observed that L. jensenii TL2937 differently modulated gene expression in ETEC PAMPs-challenged PIE cells. Microarray and RT-PCR analysis indicated that the most remarkable changes in PIE cells transcriptomic profile after heat-stable ETEC PAMPs challenge were observed in chemokines, adhesion molecules, complement and coagulation cascades factors. In addition, an anti-inflammatory effect triggered by TL2937 strain in PIE cells was clearly demonstrated. The decrease in the expression of chemokines (CCL8, CXCL5, CXCL9, CXCL10, and CXCL11), complement (C1R, C1S, C3, and CFB), and coagulation factors (F3) by L. jensenii TL2937 supports our previous reports on the immunoregulatory effect of this strain. These results provided clues for the better understanding of the mechanism underlying host-immunobiotic interaction in the porcine host. The comprehensive transcriptomic profiles of PIE cells provided by our analyses successfully identified a group of genes, which could be used as prospective biomarkers for the screening and evaluation of new anti-inflammatory immunobiotics for the prevention of inflammatory intestinal disorders in pigs.Fil: Kobayashi, Hisakazu. Tohoku University; JapónFil: Albarracín, Leonardo Miguel. Tohoku University; Japón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Sato, Nana. Tohoku University; JapónFil: Kanmani, Paulraj. Tohoku University; JapónFil: Kober, Humayun A.K.M.. Tohoku University; Japón. Chittagong Veterinary and Animal Sciences University. Department of Dairy and Poultry Science; BangladeshFil: Ikeda-Ohtsubo, Wakako. Tohoku University; JapónFil: Suda, Yoshihito. Miyagi University; JapónFil: Nochi, Tomonori. Tohoku University; JapónFil: Aso, Hisashi. Tohoku University; JapónFil: Makino, Seiya. Meiji Co., Ltd. Food Science Research Labs.; JapónFil: Kano, Hiroshi. Meiji Co., Ltd. Food Science Research Labs.; JapónFil: Ohkawara, Sou. Meiji Seika Pharma Co., Ltd. Agricultural and Veterinary Division; JapónFil: Saito, Tadao. Tohoku University; JapónFil: Villena, Julio Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina. Tohoku University; JapónFil: Kitazawa, Haruki. Tohoku University; Japó

Open Access

Cost-effective length and timing of school closure during an influenza pandemic depend on the severit

イレウスカン ノ カンリ ニ チュウモク シタ カキイセキ ニヨル ショクジセイ イレウス ノ 1レイ

Intestinal food-induced obstruction is a rare disease. Diospyrobezoar is one of the main causes. The structure has characteristic CT findings of clear wedge and internal cavernous low density area. Diospyrobezoar sometimes exist with other stones. A 60s-year-old man with abdominal pain and vomiting was introduced to our hospital. CT scan showed the dilated small intestine and two round structures with 3.5cm and 2.5cm in minor axis in the ileum. The patient had been having dried persimmons habitually in this season without artificial teeth. Based on these findings, intestinal diospyrobezoar obstruction was diagnosed. Depressurization by a balloon-tipped long tube was performed prior to surgery. The long tube and 2 structures in the intestine were detected under the laparoscopic examination, and the small intestine at 30cm oral side from two structures was pulled-out through the umbilical incision. Another stone was led to the other one to the oral side manually and a longitudinal incision was made on the anal side of the stones. Not only 2 stones that were identified preoperatively but also 4 small stones were removed. Surgery should be needed to treat diospyrobezoar ileus with a 3.0cm stone in minor axis, and it is essential to consider multiple stones

Embedded DRAM using c-axis-aligned crystalline In-Ga-Zn oxide FET with 1.8V-power-supply voltage

An embedded memory using c-axis aligned crystalline In-Ga-Zn oxide (CAAC-IGZO) FETs with an extremely low off-state current on the order of yoctoamperes (yA) (yocto- is a metric prefix denoting a factor of 10-24) is known as a potential next-generation memory [1][2]. A dynamic oxide semiconductor RAM (DOSRAM), where each memory cell is composed of one CAAC-IGZO FET and one capacitor, enables long data retention and long interval of refresh operations with an advantage of extremely low off-state current of the CAAC-IGZO FET. However, negative backgate voltage (Vbg) and word-line driving voltages of 0/3.3 V (VSSL/VDDH) had been required for an access transistor of the memory cell to satisfy high on-state current and low off-state current. This work shows that DOSRAM operates with 1.8 V-power supply voltage by using a novel driving method. Figure 1 shows Vg-Id performance of a CAAC-IGZO FET used as a cell transistor. The threshold voltage (Vth) of the CAAC-IGZO FET is controlled by changing a level of Vbg, whereas Vth of the Si FET is controlled by channel doping. Figure 2 shows a block diagram of a prototyped DOSRAM. The refresh rate in DOSRAM mainly depends on the leakage current of cell transistors. To reduce the refresh rate to once an hour, the off-state current of the cell transistors on a non-selected word line needs to be reduced to 200 zeptoamperes (zA) per FET (zepto- is a metric prefix denoting a factor of 10-21) or lower at 85C. The required Vbg is -7.0 V to achieve such an off-state current at Vg 0 V, for example. To obtain approx. 100 MHz-driving frequency, the required on-state current is at least several microamperes. The voltage level difference in the word line, VDDH VSSL, is a factor that determines the on-state current, and in this work is fixed to 3.3 V so that the combination of Vbg and the word line voltage is optimized. The application of negative voltage to the word line enables the leakage current of the cell transistor to be maintained low even when Vbg is increased. For example, whereas the existing driving method meets the above off-state current value with Vbg -7.0 V and the VSSL 0 V, the novel driving method meets the value with Vbg 0 V and VSSL -1.5 V. In the novel driving method, VDDH 1.8 V. There has been a report of a reduction in leakage current of a memory cell by application of negative voltage to a top gate in DRAM using Si CMOS [3]. In contrast to it, DOSRAM including CAAC-IGZO FETs with L 60 nm has a leakage current of 200 zA or lower, which is 7-digit lower than that of the DRAM using Si CMOS, and enables longer data retention. The evaluation results of the prototyped DOSRAM verify that a reduction in power-supply voltage from 3.3 V to 1.8 V is possible in terms of operation and data retention. This suggests a highly compatible and efficient configuration of an embedded DRAM and a logic circuit where signals can be transmitted with low VDD. References [1] S. H. Wu, et al., IEEE Symp. VLSI Tech., pp. 166-167, 2017. [2] T. Ishizu, et al., IEEE Symp. VLSI Cir., pp. 162-163, 2017. [3] F. Hamzaoglu et al., IEEE Journal of Solid-State Circuits, vol. 50, no. 1, pp. 150-157, Jan. 2015

An Angiotensin II Type 1 Receptor Blocker Prevents Renal Injury via Inhibition of the Notch Pathway in Ins2 Akita Diabetic Mice

Recently, it has been reported that the Notch pathway is involved in the pathogenesis of diabetic nephropathy. In this study, we investigated the activation of the Notch pathway in Ins2 Akita diabetic mouse (Akita mouse) and the effects of telmisartan, an angiotensin II type1 receptor blocker, on the Notch pathway. The intracellular domain of Notch1 (ICN1) is proteolytically cleaved from the cell plasma membrane in the course of Notch activation. The expression of ICN1 and its ligand, Jagged1, were increased in the glomeruli of Akita mice, especially in the podocytes. Administration of telmisartan significantly ameliorated the expression of ICN1 and Jagged1. Telmisartan inhibited the angiotensin II-induced increased expression of transforming growth factor β and vascular endothelial growth factor A which could directly activate the Notch signaling pathway in cultured podocytes. Our results indicate that the telmisartan prevents diabetic nephropathy through the inhibition of the Notch pathway