22 results on '"00303842"'
Search Results
2. The Conservation of Average Entropy Production Rate in a Model of Signal Transduction: Information Thermodynamics Based on the Fluctuation Theorem
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00303842, Tsuruyama, Tatsuaki, 00303842, and Tsuruyama, Tatsuaki
- Abstract
Cell signal transduction is a non-equilibrium process characterized by the reaction cascade. This study aims to quantify and compare signal transduction cascades using a model of signal transduction. The signal duration was found to be linked to step-by-step transition probability, which was determined using information theory. By applying the fluctuation theorem for reversible signal steps, the transition probability was described using the average entropy production rate. Specifically, when the signal event number during the cascade was maximized, the average entropy production rate was found to be conserved during the entire cascade. This approach provides a quantitative means of analyzing signal transduction and identifies an effective cascade for a signaling network. more...
- Published
- 2018
Catalog
3. Human Sox4 facilitates the development of CXCL13-producing helper T cells in inflammatory environments
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50402920, 70782407, 60806793, 00303842, 10252462, 40294938, Yoshitomi, Hiroyuki, Kobayashi, Shio, Miyagawa-Hayashino, Aya, Okahata, Akinori, Doi, Kohei, Nishitani, Kohei, Murata, Koichi, Ito, Hiromu, Tsuruyama, Tatsuaki, Haga, Hironori, Matsuda, Shuichi, Toguchida, Junya, 50402920, 70782407, 60806793, 00303842, 10252462, 40294938, Yoshitomi, Hiroyuki, Kobayashi, Shio, Miyagawa-Hayashino, Aya, Okahata, Akinori, Doi, Kohei, Nishitani, Kohei, Murata, Koichi, Ito, Hiromu, Tsuruyama, Tatsuaki, Haga, Hironori, Matsuda, Shuichi, and Toguchida, Junya more...
- Published
- 2018
4. Information thermodynamics of the cell signal transduction as a Szilard engine
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00303842, Tsuruyama, Tatsuaki, 00303842, and Tsuruyama, Tatsuaki
- Abstract
A cell signaling system is in a non-equilibrium state, and it includes multistep biochemical signaling cascades (BSCs), which involve phosphorylation of signaling molecules, such as mitogen-activated protein kinase (MAPK) pathways. In this study, the author considered signal transduction description using information thermodynamic theory. The ideal BSCs can be considered one type of the Szilard engine, and the presumed feedback controller, Maxwell’s demon, can extract the work during signal transduction. In this model, the mutual entropy and chemical potential of the signal molecules can be redefined by the extracted chemical work in a mechanicochemical model, Szilard engine, of BSC. In conclusion, signal transduction is computable using the information thermodynamic method. more...
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- 2018
5. Information Thermodynamics Derives the Entropy Current of Cell Signal Transduction as a Model of a Binary Coding System
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00303842, Tsuruyama, Tatsuaki, 00303842, and Tsuruyama, Tatsuaki
- Abstract
The analysis of cellular signaling cascades based on information thermodynamics has recently developed considerably. A signaling cascade may be considered a binary code system consisting of two types of signaling molecules that carry biological information, phosphorylated active, and non-phosphorylated inactive forms. This study aims to evaluate the signal transduction step in cascades from the viewpoint of changes in mixing entropy. An increase in active forms may induce biological signal transduction through a mixing entropy change, which induces a chemical potential current in the signaling cascade. We applied the fluctuation theorem to calculate the chemical potential current and found that the average entropy production current is independent of the step in the whole cascade. As a result, the entropy current carrying signal transduction is defined by the entropy current mobility. more...
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- 2018
6. CCL2 as a potential therapeutic target for clear cell renal cell carcinoma
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00607749, 00303842, Arakaki, Ryuichiro, Yamasaki, Toshinari, Kanno, Toru, Shibasaki, Noboru, Sakamoto, Hiromasa, Utsunomiya, Noriaki, Sumiyoshi, Takayuki, Shibuya, Shinsuke, Tsuruyama, Tatsuaki, Nakamura, Eijiro, Ogawa, Osamu, Kamba, Tomomi, 00607749, 00303842, Arakaki, Ryuichiro, Yamasaki, Toshinari, Kanno, Toru, Shibasaki, Noboru, Sakamoto, Hiromasa, Utsunomiya, Noriaki, Sumiyoshi, Takayuki, Shibuya, Shinsuke, Tsuruyama, Tatsuaki, Nakamura, Eijiro, Ogawa, Osamu, and Kamba, Tomomi more...
- Abstract
We previously reported that the pVHL-atypical PKC-JunB pathway contributed to promotion of cell invasiveness and angiogenesis in clear cell renal cell carcinoma (ccRCC), and we detected chemokine (C-C motif) ligand-2 (CCL2) as one of downstream effectors of JunB. CCL2 plays a critical role in tumorigenesis in other types of cancer, but its role in ccRCC remains unclear. In this study, we investigated the roles and therapeutic potential of CCL2 in ccRCC. Immunohistochemical analysis of CCL2 expression for ccRCC specimens showed that upregulation of CCL2 expression correlated with clinical stage, overall survival, and macrophage infiltration. For functional analysis of CCL2 in ccRCC cells, we generated subclones of WT8 cells that overexpressed CCL2 and subclones 786-O cells in which CCL2 expression was knocked down. Although CCL2 expression did not affect cell proliferation in vitro, CCL2 overexpression enhanced and CCL2 knockdown suppressed tumor growth, angiogenesis, and macrophage infiltration in vivo. We then depleted macrophages from tumor xenografts by administration of clodronate liposomes to confirm the role of macrophages in ccRCC. Depletion of macrophages suppressed tumor growth and angiogenesis. To examine the effect of inhibiting CCL2 activity in ccRCC, we administered CCL2 neutralizing antibody to primary RCC xenografts established from patient surgical specimens. Inhibition of CCL2 activity resulted in significant suppression of tumor growth, angiogenesis, and macrophage infiltration. These results suggest that CCL2 is involved in angiogenesis and macrophage infiltration in ccRCC, and that CCL2 could be a potential therapeutic target for ccRCC. more...
- Published
- 2016
7. Neuoroprotective efficacies by KUS121, a VCP modulator, on animal models of retinal degeneration
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00739089, 00303842, 80204329, Hasegawa, Tomoko, Muraoka, Yuki, Ikeda, Hanako Ohashi, Tsuruyama, Tatsuaki, Kondo, Mineo, Terasaki, Hiroko, Kakizuka, Akira, Yoshimura, Nagahisa, 00739089, 00303842, 80204329, Hasegawa, Tomoko, Muraoka, Yuki, Ikeda, Hanako Ohashi, Tsuruyama, Tatsuaki, Kondo, Mineo, Terasaki, Hiroko, Kakizuka, Akira, and Yoshimura, Nagahisa more...
- Abstract
Retinitis pigmentosa (RP) is one of the leading causes of adult blindness and has no established therapy. We have shown that valosin-containing protein (VCP) modulators, Kyoto University Substances (KUSs), ameliorated abnormally low ATP levels by inhibiting the ATPase of VCP, thereby protected several types of cells, including retinal neurons, from cell death-inducing insults. In this study, we found that KUS121, one of the VCP modulators, effectively protects photoreceptors both morphologically and functionally, in two animal models of retinal degeneration, rd12 mice and RP rabbits with a rhodopsin (Pro347Leu) mutation. In rd12 mice, KUS121 suppressed the loss of photoreceptors, not only rods but also cones, as well as the visual function deterioration. Significant protective effects existed even when the medication was started in later stages of the disease. In RP rabbits, KUS121 suppressed thinning of the outer nuclear layer and maintained visual function. In the retinas treated with KUS121, suppression of endoplasmic reticulum stress, activation of mammalian target of rapamycin and suppression of disease-Associated apoptosis were evident. The ability of KUS121 to protect photoreceptors, especially cones, even in later stages of the disease may contribute to the preservation of central vision in RP patients, which is important for quality of vision. more...
- Published
- 2016
8. Aquaporin-3 potentiates allergic airway inflammation in ovalbumin-induced murine asthma
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90771733, 00303842, 20639140, 10432395, Ikezoe, Kohei, Oga, Toru, Honda, Tetsuya, Hara-Chikuma, Mariko, Ma, Xiaojun, Tsuruyama, Tatsuaki, Uno, Kazuko, Fuchikami, Jun Ichi, Tanizawa, Kiminobu, Handa, Tomohiro, Taguchi, Yoshio, Verkman, Alan S., Narumiya, Shuh, Mishima, Michiaki, Chin, Kazuo, 90771733, 00303842, 20639140, 10432395, Ikezoe, Kohei, Oga, Toru, Honda, Tetsuya, Hara-Chikuma, Mariko, Ma, Xiaojun, Tsuruyama, Tatsuaki, Uno, Kazuko, Fuchikami, Jun Ichi, Tanizawa, Kiminobu, Handa, Tomohiro, Taguchi, Yoshio, Verkman, Alan S., Narumiya, Shuh, Mishima, Michiaki, and Chin, Kazuo more...
- Abstract
Oxidative stress plays a pivotal role in the pathogenesis of asthma. Aquaporin-3 (AQP3) is a small transmembrane water/glycerol channel that may facilitate the membrane uptake of hydrogen peroxide (H[2]O[2]). Here we report that AQP3 potentiates ovalbumin (OVA)-induced murine asthma by mediating both chemokine production from alveolar macrophages and T cell trafficking. AQP3 deficient (AQP3[-/-]) mice exhibited significantly reduced airway inflammation compared to wild-type mice. Adoptive transfer experiments showed reduced airway eosinophilic inflammation in mice receiving OVA-sensitized splenocytes from AQP3[-/-] mice compared with wild-type mice after OVA challenge, consistently with fewer CD4[+]T cells from AQP3[-/-] mice migrating to the lung than from wild-type mice. Additionally, in vivo and vitro experiments indicated that AQP3 induced the production of some chemokines such as CCL24 and CCL22 through regulating the amount of cellular H[2]O[2] in M2 polarized alveolar macrophages. These results imply a critical role of AQP3 in asthma, and AQP3 may be a novel therapeutic target. more...
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- 2016
9. Neuroprotective effects of VCP modulators in mouse models of glaucoma
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00739089, 00303842, 80204329, Nakano, Noriko, Ikeda, Hanako Ohashi, Hasegawa, Tomoko, Muraoka, Yuki, Iwai, Sachiko, Tsuruyama, Tatsuaki, Nakano, Masaki, Fuchigami, Tomohiro, Shudo, Toshiyuki, Kakizuka, Akira, Yoshimura, Nagahisa, 00739089, 00303842, 80204329, Nakano, Noriko, Ikeda, Hanako Ohashi, Hasegawa, Tomoko, Muraoka, Yuki, Iwai, Sachiko, Tsuruyama, Tatsuaki, Nakano, Masaki, Fuchigami, Tomohiro, Shudo, Toshiyuki, Kakizuka, Akira, and Yoshimura, Nagahisa more...
- Abstract
Glaucoma is a major cause of adult blindness due to gradual death of retinal ganglion cells. Currently, no therapeutics are available for the protection of these cells from the cell death. We have recently succeeded in synthesizing novel compounds, KUSs (Kyoto University Substances), which can reduce cellular ATP consumption by specifically inhibiting the ATPase activities of VCP, a major ATPase in the cell, and we have shown that KUSs could mitigate the disease progression of rd10, a mouse model of retinitis pigmentosa, without any apparent side effects. Here we show that KUSs (e.g. KUS121 and KUS187) can prevent antimycin- and oligomycin-induced ATP depletion, endoplasmic reticulum (ER) stress, and cell death in neuronally differentiated PC12 cells. Furthermore, KUSs manifest significant efficacies on several mouse models of glaucoma. KUS administration prevented or mitigated ER stress and subsequent apoptotic cell death of retinal ganglion cells in an acute injury mouse model of retinal ganglion cell loss, which was induced with N-methyl-D-aspartate. In a mouse model of glaucoma with high intraocular pressure, KUSs prevented the typical glaucoma pathologies, i.e. enlargement of optic disc cupping and thinning of the retinal nerve fiber layer. KUSs also preserved visual functions in GLAST knockout mice, a mouse model for chronic retinal ganglion cell loss. We propose "ATP maintenance" via inhibition of ATPase activities of VCP as a promising new neuroprotective strategy for currently incurable eye diseases, such as glaucoma. more...
- Published
- 2016
10. Matrix metalloproteinase-10: A novel biomarker for idiopathic pulmonary fibrosis
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10432395, 20639140, 00303842, 20464216, 90771733, 60344454, 20359805, Sokai, Akihiko, Handa, Tomohiro, Tanizawa, Kiminobu, Oga, Toru, Uno, Kazuko, Tsuruyama, Tatsuaki, Kubo, Takeshi, Ikezoe, Kohei, Nakatsuka, Yoshinari, Tanimura, Kazuya, Muro, Shigeo, Hirai, Toyohiro, Nagai, Sonoko, Chin, Kazuo, Mishima, Michiaki, 10432395, 20639140, 00303842, 20464216, 90771733, 60344454, 20359805, Sokai, Akihiko, Handa, Tomohiro, Tanizawa, Kiminobu, Oga, Toru, Uno, Kazuko, Tsuruyama, Tatsuaki, Kubo, Takeshi, Ikezoe, Kohei, Nakatsuka, Yoshinari, Tanimura, Kazuya, Muro, Shigeo, Hirai, Toyohiro, Nagai, Sonoko, Chin, Kazuo, and Mishima, Michiaki more...
- Published
- 2015
11. Role of IL13RA2 in Sunitinib Resistance in Clear Cell Renal Cell Carcinoma.
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00607749, 80511881, 00303842, 20402836, Shibasaki, Noboru, Yamasaki, Toshinari, Kanno, Toru, Arakaki, Ryuichiro, Sakamoto, Hiromasa, Utsunomiya, Noriaki, Inoue, Takahiro, Tsuruyama, Tatsuaki, Nakamura, Eijiro, Ogawa, Osamu, Kamba, Tomomi, 00607749, 80511881, 00303842, 20402836, Shibasaki, Noboru, Yamasaki, Toshinari, Kanno, Toru, Arakaki, Ryuichiro, Sakamoto, Hiromasa, Utsunomiya, Noriaki, Inoue, Takahiro, Tsuruyama, Tatsuaki, Nakamura, Eijiro, Ogawa, Osamu, and Kamba, Tomomi more...
- Abstract
Vascular endothelial growth factor (VEGF) and mammalian target of rapamycin are well-known therapeutic targets for renal cell carcinoma (RCC). Sunitinib is an agent that targets VEGF receptors and is considered to be a standard treatment for metastatic or unresectable clear cell RCC (ccRCC). However, ccRCC eventually develops resistance to sunitinib in most cases, and the mechanisms underlying this resistance are not fully elucidated. In the present study, we established unique primary xenograft models, KURC1 (Kyoto University Renal Cancer 1) and KURC2, from freshly isolated ccRCC specimens. The KURC1 xenograft initially responded to sunitinib treatment, however finally acquired resistance. KURC2 retained sensitivity to sunitinib for over 6 months. Comparing gene expression profiles between the two xenograft models with different sensitivity to sunitinib, we identified interleukin 13 receptor alpha 2 (IL13RA2) as a candidate molecule associated with the acquired sunitinib-resistance in ccRCC. And patients with high IL13RA2 expression in immunohistochemistry in primary ccRCC tumor tends to have sunitinib-resistant metastatic site. Next, we showed that sunitinib-sensitive 786-O cells acquired resistance in vivo when IL13RA2 was overexpressed. Conversely, shRNA-mediated knockdown of IL13RA2 successfully overcame the sunitinib-resistance in Caki-1 cells. Histopathological analyses revealed that IL13RA2 repressed sunitinib-induced apoptosis without increasing tumor vasculature in vivo. To our knowledge, this is a novel mechanism of developing resistance to sunitinib in a certain population of ccRCC, and these results indicate that IL13RA2 could be one of potential target to overcome sunitinib resistance. more...
- Published
- 2015
12. A case of maxillary sarcoma in a chimpanzee (Pan troglodytes).
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90396226, 70237139, 80396225, 00303842, Fujisawa, M, Udono, T, Nogami, E, Hirosawa, M, Morimura, N, Saito, A, Seres, M, Teramoto, M, Nagano, K, Mori, Y, Uesaka, H, Nasu, K, Tomonaga, M, Idani, G, Hirata, S, Tsuruyama, T, Matsubayashi, K, 90396226, 70237139, 80396225, 00303842, Fujisawa, M, Udono, T, Nogami, E, Hirosawa, M, Morimura, N, Saito, A, Seres, M, Teramoto, M, Nagano, K, Mori, Y, Uesaka, H, Nasu, K, Tomonaga, M, Idani, G, Hirata, S, Tsuruyama, T, and Matsubayashi, K more...
- Abstract
Oral malignancy is rare in chimpanzees. A 34-year-old female chimpanzee (Pan troglodytes) at Kumamoto Sanctuary, Japan, had developed it. Treatment is technically difficult for chimpanzees while malignant neoplasm is seemingly rising in captive populations. Widespread expert discussion, guidelines for treatment, especially for great apes in terminal stages is urgently needed. more...
- Published
- 2014
13. The effectiveness and limitations of triphenyltetrazolium chloride to detect acute myocardial infarction at forensic autopsy.
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00303842, 90711466, 20330582, 10252462, 90217175, Kakimoto, Yu, Tsuruyama, Tatsuaki, Miyao, Masashi, Abiru, Hitoshi, Sumiyoshi, Shinji, Kotani, Hirokazu, Haga, Hironori, Tamaki, Keiji, 00303842, 90711466, 20330582, 10252462, 90217175, Kakimoto, Yu, Tsuruyama, Tatsuaki, Miyao, Masashi, Abiru, Hitoshi, Sumiyoshi, Shinji, Kotani, Hirokazu, Haga, Hironori, and Tamaki, Keiji more...
- Abstract
Triphenyltetrazolium chloride (TTC) is one of the most conventional stains to detect infarcted area of the heart in animal experiments. However, its availability and limitations have not been thoroughly discussed in the forensic field. Here, authors stained human hearts with TTC soon after the harvest. Photographs of the samples were analyzed using image analysis software, which evaluated the occupying ratio of the stained area on the surface of each slice. The results showed that the stainability of TTC declines with the length of the postmortem interval (PMI). Specimens reacted well to TTC within 1.5 days after death and then decreased the stainability logarithmically with PMI (y = - 0.294 In (x) + 1.0441; x = PMI, y = TTC-stained area, total myocardial area, R = 0.5673). Samples with old myocardial infarction produced clear TTC contrast; normal tissue is vivid red, and fibrotic myocardium is white discoloration. In acute myocardial infarction cases where death occurred within 9 hours after the attack, however, the detection of infarcted area was very difficult even when PMI was less than 1.5 days. In summary, the TTC method may be useful within 1.5 days after death, but short suffering period before death disturbs its staining efficiency. more...
- Published
- 2013
14. Stromal plasma cells expressing immunoglobulin G4 subclass in non-small cell lung cancer.
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90573676, 80378645, 00303842, 60252962, 10252462, Fujimoto, Masakazu, Yoshizawa, Akihiko, Sumiyoshi, Shinji, Sonobe, Makoto, Kobayashi, Masashi, Koyanagi, Itsuko, Aini, Wulamujiang, Tsuruyama, Tatsuaki, Date, Hiroshi, Haga, Hironori, 90573676, 80378645, 00303842, 60252962, 10252462, Fujimoto, Masakazu, Yoshizawa, Akihiko, Sumiyoshi, Shinji, Sonobe, Makoto, Kobayashi, Masashi, Koyanagi, Itsuko, Aini, Wulamujiang, Tsuruyama, Tatsuaki, Date, Hiroshi, and Haga, Hironori more...
- Abstract
Inflammatory cell infiltration in tumor stroma may represent the interaction between the tumor and the immune system. The significance of immunoglobulin (Ig) G4+ plasmacytic infiltration, however, is poorly understood. Here, we analyzed the number of stromal IgG4+ plasma cells and the IgG4/IgG ratio of plasma cells in 294 primary non-small cell lung cancers (NSCLCs) using tissue microarray (TMA) and conventional surgical specimens. In TMA, 35 (12%) cases of NSCLC revealed more than 20 IgG4+ plasma cells per high-power field. In surgical specimens, most (97%) of those IgG4+ plasma cell-enriched cases showed obliterative phlebitis or arteritis, one of the key morphologic features of IgG4-related disease, within or at the periphery of the tumor. Clinically, none of the patients showed symptoms associated with IgG4-related systemic diseases. In patients with stage I squamous cell carcinoma, IgG4-enriched stroma was significantly associated with a favorable prognosis (P = .04). In conclusion, considerable IgG4+ plasma cell infiltration can be seen in a minority of cases of NSCLC and might contribute to prognostic modulation of NSCLC. more...
- Published
- 2013
15. Frequent hepatocyte chimerism in long-term human liver allografts independent of graft outcome.
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80549618, 00303842, 90217175, 40252449, 10252462, Aini, Wulamujiang, Miyagawa-Hayashino, Aya, Ozeki, Munetaka, Tsuruyama, Tatsuaki, Tamaki, Keiji, Uemoto, Shinji, Haga, Hironori, 80549618, 00303842, 90217175, 40252449, 10252462, Aini, Wulamujiang, Miyagawa-Hayashino, Aya, Ozeki, Munetaka, Tsuruyama, Tatsuaki, Tamaki, Keiji, Uemoto, Shinji, and Haga, Hironori more...
- Abstract
Microchimerism after liver transplantation is considered to promote graft tolerance or tissue repair, but its significance is controversial. By using multiplex polymerase chain reaction (PCR) of short tandem repeat (STR) loci after laser capture microdissection of hepatocyte nuclei, we compared the proportions of recipient-derived hepatocytes in long-term stable liver allografts and late dysfunctional allografts caused by chronic rejection or idiopathic post-transplantation hepatitis. Through fluorescence in situ hybridization (FISH), we also analyzed the presence of recipient-derived Y-positive hepatocytes in the biopsies of livers transplanted from female donors to male recipients. The study population comprised 24 pediatric liver transplant recipients who survived with the initial graft, whose 10-year protocol biopsy records were available, and who had normal liver function (stable graft, SG; n=13) or a late dysfunctional graft (LDG; n=11) with similar follow-up periods (mean 10.8years in the SG group and 11.2years in the LDG group). STR analysis revealed that hepatocyte chimerism occurred in 7 of 13 (54%) SGs and 5 of 11 (45%) LDGs (p=0.68). The proportion of hepatocyte chimerism was low, with a mean of 3% seen in 2 of 3 female-to-male transplanted livers (one each of SG and LDG). In conclusion, hepatocyte chimerism was a constant event. The extent of engraftment of recipient-derived hepatocytes does not seem to correlate with the degree of hepatic injury in long-term liver allografts. more...
- Published
- 2013
16. Bile canalicular abnormalities in the early phase of a mouse model of sclerosing cholangitis.
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90711466, 80549618, 20330582, 00303842, 90217175, Miyao, Masashi, Ozeki, Munetaka, Abiru, Hitoshi, Manabe, Sho, Kotani, Hirokazu, Tsuruyama, Tatsuaki, Tamaki, Keiji, 90711466, 80549618, 20330582, 00303842, 90217175, Miyao, Masashi, Ozeki, Munetaka, Abiru, Hitoshi, Manabe, Sho, Kotani, Hirokazu, Tsuruyama, Tatsuaki, and Tamaki, Keiji more...
- Abstract
[Background]The bile canaliculus is the smallest and first biliary channel and is formed by two or three adjacent hepatocytes. Previous studies of chronic cholangiopathies such as primary sclerosing cholangitis have focused on the bile ductules. However, little is known about the pathological alterations in bile canaliculi in the early phase of cholangiopathies. [Aim]To characterize the bile canalicular morphology in the early phase of sclerosing cholangitis we used 3, 5-diethoxycarbonyl-1, 4-dihydrocollidine-induced mouse model of sclerosing cholangitis. [Methods]Mice were fed a diet with 3, 5-diethoxycarbonyl-1, 4-dihydrocollidine (0.1%). Serum biochemical, histological, immunohistochemical, and electron microscopic analyses were performed 1, 2, 4, and 7 days after feeding. [Results]All experimental groups showed significantly increased serum aspartate aminotransferase, alanine aminotransferase, and alkaline phosphatase levels. From day 1, bile canalicular abnormalities such as dilatation and meandering and loss of microvilli were observed. After bile canalicular abnormalities had appeared, substantial infiltration of inflammatory cells was observed amongst the necrotic cells and periductal region. After these inflammatory changes, cholangiocytes proliferated in the portal area and formed ductular reactions. Finally, periductal fibrosis appeared. [Conclusion]This study provides novel evidence of the occurrence of bile canalicular abnormalities during the early phase of sclerosing cholangitis. more...
- Published
- 2013
17. Dialysis Purification of Integrase-DNA Complexes Provides High-Resolution Atomic Force Microscopy Images: Dimeric Recombinant HIV-1 Integrase Binding and Specific Looping on DNA.
- Author
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00303842, 80549618, 90217175, Tsuruyama, Tatsuaki, Nakai, Tonau, Ohmori, Rei, Ozeki, Munetaka, Tamaki, Keiji, Yoshikawa, Kenichi, 00303842, 80549618, 90217175, Tsuruyama, Tatsuaki, Nakai, Tonau, Ohmori, Rei, Ozeki, Munetaka, Tamaki, Keiji, and Yoshikawa, Kenichi more...
- Abstract
It remains difficult to obtain high-resolution atomic force microscopy images of HIV-1 integrase bound to DNA in a dimeric or tetrameric fashion. We therefore constructed specific target DNAs to assess HIV-1 integrase binding and purified the complex by dialysis prior to analysis. Our resulting atomic force microscopy analyses indicated precise size of binding human immunodeficiency virus type 1 (HIV-1) recombinant integrase in a tetrameric manner, inducing formation of a loop-like or figure-eight-like secondary structure in the target DNA. Our findings regarding the target DNA secondary structure provide new insights into the intermediate states of retroviral integration. more...
- Published
- 2013
18. In Vitro HIV-1 LTR Integration into T-Cell Activation Gene CD27 Segment and the Decoy Effect of Modified-Sequence DNA.
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00303842, Ohmori, Rei, Tsuruyama, Tatsuaki, 00303842, Ohmori, Rei, and Tsuruyama, Tatsuaki
- Abstract
Integration into the host genome is an essential step in the HIV-1 life cycle. However, the host genome sequence that is favored by HIV-1 during integration has never been documented. Here, we report that CD27, a T cell activation gene, includes a sequence that is a target for in vitro HIV-1 cDNA integration. This sequence has a high affinity for integrase, and the target nucleotides responsible for this higher affinity were identified using a crystal microbalance assay. In experiments involving a segment of the CD27 gene, integration converged in the target nucleotides and flanking sequence DNA, indicating that integration is probably dependent upon the secondary structure of the substrate DNA. Notably, decoy modified CD27 sequence DNAs in which the target nucleotides were replaced suppressed integration when accompanying the original CD27 sequence DNA. Our identified CD27 sequence DNA is useful for investigating the biochemistry of integrase and for in vitro assessment of integrase-binding inhibitors. more...
- Published
- 2012
19. In vitro murine leukemia retroviral integration and structure fluctuation of target DNA.
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00303842, Tsuruyama, Tatsuaki, Liu, Weizhi, Yoshikawa, Kenichi, 00303842, Tsuruyama, Tatsuaki, Liu, Weizhi, and Yoshikawa, Kenichi
- Abstract
Integration of the retroviral genome into host DNA is a critical step in the life cycle of a retrovirus. Although assays for in vitro integration have been developed, the actual DNA sequences targeted by murine leukemia retrovirus (MLV) during in vitro reproduction are unknown. While previous studies used artificial target sequences, we developed an assay using target DNA sequences from common MLV integration sites in Stat5a and c-myc in the genome of murine lymphomas and successfully integrated MLV into the target DNA in vitro. We calculated the free energy change during folding of the target sequence DNA and found a close correlation between the calculated free energy change and the number of integrations. Indeed, the integrations closely correlated with fluctuation of the structure of the target DNA segment. These data suggest that the fluctuation may generate a DNA structure favorable for in vitro integration into the target DNA. The approach described here can provide data on the biochemical properties of the integration reaction to which the target DNA structure may contribute. more...
- Published
- 2012
20. Transmesenteric hernia due to double-loop formation in the small intestine: a fatal case involving a toddler.
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20330582, 80549618, 00303842, 90217175, Kakimoto, Yu, Abiru, Hitoshi, Kotani, Hirokazu, Ozeki, Munetaka, Tsuruyama, Tatsuaki, Tamaki, Keiji, 20330582, 80549618, 00303842, 90217175, Kakimoto, Yu, Abiru, Hitoshi, Kotani, Hirokazu, Ozeki, Munetaka, Tsuruyama, Tatsuaki, and Tamaki, Keiji more...
- Abstract
We report a unique case of transmesenteric hernia resulting in death, which went undiagnosed during a recent hospital visit. The victim was a 2.5-year-old girl who - with the exception of chronic constipation - had no medical history. One night she complained of abdominal pains and was taken to a pediatric hospital where doctors performed an abdominal X-ray and echography. No significant findings suggesting bowel obstruction (e.g. air-fluid levels or dilation of the bowel) were obtained on examinations and bloody feces were not observed in this particular episode. As her abdominal pain gradually attenuated, the doctor allowed her to return home. A few hours later, she lost consciousness and expired despite resuscitation efforts attempted at an emergency hospital. A subsequent autopsy revealed that the small bowel had herniated through a defect in the mesentery resulting in two consecutive and inversely forming loops, in which each loop protruded on either side of the mesentery. This rare morphological anatomy seems to have progressed in a two-step process. The girl's mild abdominal pain was likely induced by herniation and formation of the first intestinal loop, followed by severe shock occurring when the subsequent intestinal segment invaginated into the same defect forming the second loop on the opposite side of the mesentery. This case illustrates the difficulty of diagnosing transmesenteric hernia due to the presentation of unspecific symptoms; especially in infants and toddlers. Furthermore, this report demonstrates the value of a complete autopsy in cases of sudden and unexpected deaths involving children. more...
- Published
- 2012
21. Pituitary abscess presenting a very rapid progression: report of a fatal case.
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20330582, 90711466, 80549618, 00303842, 90217175, Kotani, Hirokazu, Abiru, Hitoshi, Miyao, Masashi, Kakimoto, Yu, Kawai, Chihiro, Ozeki, Munetaka, Tsuruyama, Tatsuaki, Tamaki, Keiji, 20330582, 90711466, 80549618, 00303842, 90217175, Kotani, Hirokazu, Abiru, Hitoshi, Miyao, Masashi, Kakimoto, Yu, Kawai, Chihiro, Ozeki, Munetaka, Tsuruyama, Tatsuaki, and Tamaki, Keiji more...
- Abstract
Pituitary abscess is a rare disease presenting with nonspecific clinical symptoms, and diagnosis is often difficult. This disease is potentially life-threatening, but most cases have a chronic and indolent course. We report a case of a 60-year-old man with a pituitary abscess associated with pituitary adenoma who died 5 days after the onset of clinical symptoms without a definitive diagnosis. Postmortem computed tomography and autopsy findings revealed a sellar mass with cystic change and extension toward the optic chiasm. Histopathology of the lesion demonstrated an abscess with suppurative meningitis and encephalitis. The disturbance of the cardiac autonomic nervous system because of hypothalamus involvement was suggested as the cause of rapid progression and death. This case provides useful information for clinicians to avoid a lethal outcome. more...
- Published
- 2012
22. In vitro HIV-1 selective integration into the target sequence and decoy-effect of the modified sequence.
- Author
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00303842, 90641639, Tsuruyama, Tatsuaki, Nakai, Tonau, Hiratsuka, Takuya, Jin, Guang, Nakamura, Takuro, Yoshikawa, Kenichi, 00303842, 90641639, Tsuruyama, Tatsuaki, Nakai, Tonau, Hiratsuka, Takuya, Jin, Guang, Nakamura, Takuro, and Yoshikawa, Kenichi more...
- Abstract
Although there have been a few reports that the HIV-1 genome can be selectively integrated into the genomic DNA of cultured host cell, the biochemistry of integration selectivity has not been fully understood. We modified the in vitro integration reaction protocol and developed a reaction system with higher efficiency. We used a substrate repeat, 5'-(GTCCCTTCCCAGT)(n)(ACTGGGAAGGGAC)(n)-3', and a modified sequence DNA ligated into a circular plasmid. CAGT and ACTG (shown in italics in the above sequence) in the repeat units originated from the HIV-1 proviral genome ends. Following the incubation of the HIV-1 genome end cDNA and recombinant integrase for the formation of the pre-integration (PI) complex, substrate DNA was reacted with this complex. It was confirmed that the integration selectively occurred in the middle segment of the repeat sequence. In addition, integration frequency and selectivity were positively correlated with repeat number n. On the other hand, both frequency and selectivity decreased markedly when using sequences with deletion of CAGT in the middle position of the original target sequence. Moreover, on incubation with the deleted DNAs and original sequence, the integration efficiency and selectivity for the original target sequence were significantly reduced, which indicated interference effects by the deleted sequence DNAs. Efficiency and selectivity were also found to vary discontinuously with changes in manganese dichloride concentration in the reaction buffer, probably due to its influence on the secondary structure of substrate DNA. Finally, integrase was found to form oligomers on the binding site and substrate DNA formed a loop-like structure. In conclusion, there is a considerable selectivity in HIV-integration into the specified sequence; however, similar DNA sequences can interfere with the integration process, and it is therefore difficult for in vivo integration to occur selectively in the actual host genome DNA. more...
- Published
- 2010
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