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Search Results: 1 - 10 of 3112 matches for " Yuki Ito "
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Denaturation of DNA in Ternary Mixed Solution of Water/Hydrophilic/Hydrophobic Organic Solvent  [PDF]
Yuki Ito, Kazuhiko Tsukagoshi, Akira Kobayashi
Journal of Analytical Sciences, Methods and Instrumentation (JASMI) , 2017, DOI: 10.4236/jasmi.2017.72004
Abstract: Denaturation was examined for the first time in a ternary mixed solution of water/hydrophilic/ hydrophobic organic solvent using λ-DNA and a plasmid as models. The absorbance of λ-DNA and the plasmid at 260 nm gradually increased for several days up to 1.68 and 1.38 times the initial values, respectively, in a water/acetonitrile/ethyl acetate (15:3:2, volume ratio) mixed solution, whereas there was little change in a water/acetonitrile (15:3, volume ratio) mixed solution. The plasmid treated with the ternary mixed solution was also examined with agarose gel electrophoresis. These experimental data indicated that λ-DNA changed from a double helix structure to a single helix structure and that the plasmid partially transformed to generate a denaturation bubble in the structure. The new idea of using the ternary mixed solution first enabled the interaction of the hydrophobic organic solvent (e.g., ethyl acetate) molecule with the double helical structure of DNA, leading to specific slow-proceeding denaturation.
Simplified Intraoperative Goal-Directed Therapy Using the FloTrac/Vigileo System: An Analysis of Its Usefulness and Safety  [PDF]
Kenji Ito, Miho Ito, Aki Ando, Yuki Sakuma, Toshiyasu Suzuki
Open Journal of Anesthesiology (OJAnes) , 2017, DOI: 10.4236/ojanes.2017.71001
Abstract: Purpose: We investigated whether the simplified intraoperative Goal-Directed Therapy (GDT) could improve the factors affecting medical costs, and contribute in standardizing intraoperative fluid management. Methods: The enrolled patients underwent esophagectomy, pancreatoduodenectomy, or aortic stent grafting in 2012, and between March 2013 and October 2014. We conducted a comparison study on the effects of GDT, between the before-GDT historical control group (n = 100) and GDT group (n = 100). The hemodynamic indices used for control group patients were conventional: Blood pressure, heart rate, and urine output. For GDT group, additionally, we used stroke volume variation (SVV) and stroke volume index (SVI). The primary outcomes were the length of intensive care unit (ICU) stay and hospital stay (LOS). Regression analysis was used to identify factors affecting LOS. The secondary outcomes were the albumin use, the fluid amount administered, and the variation in the fluid administration rate. Results: The control and GDT groups comprised 96 and 99 patients, respectively. The patient characteristics were similar. The length of ICU stay was significantly shorter (2.1 ± 2.1 days vs. 2.8 ± 1.9 days, P = 0.0009) and LOS was shorter but without statistical significance (24.5 ± 17.7 days vs. 27.7 ± 20.1 days, P = 0.21) in the GDT group than in the control group. The fluid amount administered and the presence/ absence of albumin use were factors affecting LOS. The variation of the fluid administration rate was significantly lower in the GDT group.
PPAR- and DEHP-Induced Cancers
Yuki Ito,Tamie Nakajima
PPAR Research , 2008, DOI: 10.1155/2008/759716
Abstract: Di(2-ethylhexyl)phthalate (DEHP) is a widely used plasticizer and a potentially nongenotoxic carcinogen. Its mechanism had been earlier proposed based on peroxisome proliferator-activated receptor (PPAR) because metabolites of DEHP are agonists. However, recent evidence also suggests the involvement of non-PPAR multiple pathway in DEHP-induced carcinogenesis. Since there are differences in the function and constitutive expression of PPAR among rodents and humans, species differences are also thought to exist in the carcinogenesis. However, species differences were also seen in the lipase activity involved in the first step of the DEHP metabolism, which should be considered in DEHP-induced carcinogenesis. Taken together, it is very difficult to extrapolate the results from rodents to humans in the case of DEHP carcinogenicity. However, PPAR-null mice or mice with human PPAR gene have been developed, which may lend support to make such a difficult extrapolation. Overall, further mechanical study on DEHP-induced carcinogenicity is warranted using these mice.
Design of Phosphonium-Type Zwitterion as an Additive to Improve Saturated Water Content of Phase-Separated Ionic Liquid from Aqueous Phase toward Reversible Extraction of Proteins
Yoritsugu Ito,Yuki Kohno,Nobuhumi Nakamura,Hiroyuki Ohno
International Journal of Molecular Sciences , 2013, DOI: 10.3390/ijms140918350
Abstract: We designed phosphonium-type zwitterion (ZI) to control the saturated water content of separated ionic liquid (IL) phase in the hydrophobic IL/water biphasic systems. The saturated water content of separated IL phase, 1-butyl-3-methyimidazolium bis(trifluoromethanesulfonyl)imide, was considerably improved from 0.4 wt% to 62.8 wt% by adding N, N, N-tripentyl-4-sulfonyl-1-butanephosphonium-type ZI (P 555C4S). In addition, the maximum water content decreased from 62.8 wt% to 34.1 wt% by increasing KH 2PO 4/K 2HPO 4 salt content in upper aqueous phosphate buffer phase. Horse heart cytochrome c (cyt. c) was dissolved selectively in IL phase by improving the water content of IL phase, and spectroscopic analysis revealed that the dissolved cyt. c retained its higher ordered structure. Furthermore, cyt. c dissolved in IL phase was re-extracted again from IL phase to aqueous phase by increasing the concentration of inorganic salts of the buffer solution.
High Incidence of Null-Type Mutations of the TP53 Gene in Japanese Patients with Head and Neck Squamous Cell Carcinoma  [PDF]
Yasuhiro Ebihara, Miwako Iwai, Ken Akashi, Takeshi Ito, Go Omura, Yuki Saito, Masafumi Yoshida, Mizuo Ando, Takahiro Asakage, Tatsuya Yamasoba, Yoshinori Murakami
Journal of Cancer Therapy (JCT) , 2014, DOI: 10.4236/jct.2014.57075
Abstract:

Objective: Molecular targeting therapy has not been generally established in head and neck squamous cell carcinoma (HNSCC) except for cetuximab treatment for targeting epidermal growth factor receptor (EGFR). We analyzed alterations of the TP53, KRAS2, and EGFR genes in Japanese HNSCC to identify subpopulations of tumors potentially susceptible or not susceptible to specific therapy based on their genetic alterations. Materials and Methods: A total of 56 Japanese subjects were included in this study. Genomic DNA of exons 5 - 9 of the TP53, exons 1 and 2 of the KRAS2, exons 19 - 22 of the EGFR, and their flanking sequences were amplified by polymerase chain reaction (PCR) followed by direct sequencing. Splicing variants of EGFR were examined by reverse transcription (RT)-PCR. Results: Mutations of the TP53 and KRAS genes were detected in 25 (45%) and 2 (4%) of 56 HNSCC cases, respectively, while neither mutation nor splicing variant of EGFR was observed. The

Identification of DNA-Dependent Protein Kinase Catalytic Subunit (DNA-PKcs) as a Novel Target of Bisphenol A
Yuki Ito, Takumi Ito, Satoki Karasawa, Teruya Enomoto, Akihiro Nashimoto, Yasuyoshi Hase, Satoshi Sakamoto, Tsuneyo Mimori, Yoshihisa Matsumoto, Yuki Yamaguchi, Hiroshi Handa
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050481
Abstract: Bisphenol A (BPA) forms the backbone of plastics and epoxy resins used to produce packaging for various foods and beverages. BPA is also an estrogenic disruptor, interacting with human estrogen receptors (ER) and other related nuclear receptors. Nevertheless, the effects of BPA on human health remain unclear. The present study identified DNA-dependent protein kinase catalytic subunit (DNA-PKcs) as a novel BPA-binding protein. DNA-PKcs, in association with the Ku heterodimer (Ku70/80), is a critical enzyme involved in the repair of DNA double-strand breaks. Low levels of DNA-PK activity are previously reported to be associated with an increased risk of certain types of cancer. Although the Kd for the interaction between BPA and a drug-binding mutant of DNA-PKcs was comparatively low (137 nM), high doses of BPA were required before cellular effects were observed (100–300 μM). The results of an in vitro kinase assay showed that BPA inhibited DNA-PK kinase activity in a concentration-dependent manner. In M059K cells, BPA inhibited the phosphorylation of DNA-PKcs at Ser2056 and H2AX at Ser139 in response to ionizing radiation (IR)-irradiation. BPA also disrupted DNA-PKcs binding to Ku70/80 and increased the radiosensitivity of M059K cells, but not M059J cells (which are DNA-PKcs-deficient). Taken together, these results provide new evidence of the effects of BPA on DNA repair in mammalian cells, which are mediated via inhibition of DNA-PK activity. This study may warrant the consideration of the possible carcinogenic effects of high doses of BPA, which are mediated through its action on DNA-PK.
An Empirical Investigation of Common Sense of Land Use from a Statistical Approach  [PDF]
Yuki Hanashima
Journal of Geographic Information System (JGIS) , 2012, DOI: 10.4236/jgis.2012.42014
Abstract: Recently, ontological study has been one of the key concerns of geographic information science, a number of studies have been conducted in both of philosophical and knowledge engineering approach. Some studies pointed out the importance of human cognition and social context for development of ontologies. This paper presents empirical investigation of common sense of land use categories for development of suitable ontologies for each cultural or speech communities. Distinctions and characteristics in perceiving land use categories were described by a psychological method that was submitted to Japanese graduate and undergraduate students. In addition the results were analyzed using corresponddence analysis, a statistical technique for categorical data. This analysis serves to clarify the dominant determining factors for land use categories.
Bacterial Cells Carrying Synthetic Dual-Function Operon Survived Starvation
Yuki Matsumoto,Yoichiro Ito,Saburo Tsuru,Bei-Wen Ying,Tetsuya Yomo
Journal of Biomedicine and Biotechnology , 2011, DOI: 10.1155/2011/489265
Abstract: A synthetic dual-function operon with a bistable structure was designed and successfully integrated into the bacterial genome. Bistability was generated by the mutual inhibitory structure comprised of the promoters Ptet and Plac and the repressors LacI and TetR. Dual function essential for cell growth was introduced by replacing the genes (i.e., hisC and leuB) encoding proteins involved in the biosynthesis of histidine and leucine from their native chromosomal locations to the synthetic operon. Both colony formation and population dynamics of the cells carrying this operon showed that the cells survived starvation and the newly formed population transited between the two stable states, representing the induced hisC and leuB levels, in accordance with the nutritional status. The results strongly suggested that the synthetic design of proto-operons sensitive to external perturbations is practical and functional in native cells.
Highly Sensitive Determination of Hydrogen Peroxide and Glucose by Fluorescence Correlation Spectroscopy
Satoshi Watabe,Yuki Sakamoto,Mika Morikawa,Ryuichi Okada,Toshiaki Miura,Etsuro Ito
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0022955
Abstract: Because H2O2 is generated by various oxidase-catalyzed reactions, a highly sensitive determination method of H2O2 is applicable to measurements of low levels of various oxidases and their substrates such as glucose, lactate, glutamate, urate, xanthine, choline, cholesterol and NADPH. We propose herein a new, highly sensitive method for the measurement of H2O2 and glucose using fluorescence correlation spectroscopy (FCS).
Nutrient-Regulated Antisense and Intragenic RNAs Modulate a Signal Transduction Pathway in Yeast
Masafumi Nishizawa,Tae Komai,Yuki Katou,Katsuhiko Shirahige,Takehiko Ito,Akio Toh-e
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0060326
Abstract: The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to a change in nutrient availability. The PHO system is a well-studied case in the transcriptional regulation responding to nutritional changes in which a set of genes (PHO genes) is expressed to activate inorganic phosphate (Pi) metabolism for adaptation to Pi starvation. Pi starvation triggers an inhibition of Pho85 kinase, leading to migration of unphosphorylated Pho4 transcriptional activator into the nucleus and enabling expression of PHO genes. When Pi is sufficient, the Pho85 kinase phosphorylates Pho4, thereby excluding it from the nucleus and resulting in repression (i.e., lack of transcription) of PHO genes. The Pho85 kinase has a role in various cellular functions other than regulation of the PHO system in that Pho85 monitors whether environmental conditions are adequate for cell growth and represses inadequate (untimely) responses in these cellular processes. In contrast, Pho4 appears to activate some genes involved in stress response and is required for G1 arrest caused by DNA damage. These facts suggest the antagonistic function of these two players on a more general scale when yeast cells must cope with stress conditions. To explore general involvement of Pho4 in stress response, we tried to identify Pho4-dependent genes by a genome-wide mapping of Pho4 and Rpo21 binding (Rpo21 being the largest subunit of RNA polymerase II) using a yeast tiling array. In the course of this study, we found Pi- and Pho4-regulated intragenic and antisense RNAs that could modulate the Pi signal transduction pathway. Low-Pi signal is transmitted via certain inositol polyphosphate (IP) species (IP7) that are synthesized by Vip1 IP6 kinase. We have shown that Pho4 activates the transcription of antisense and intragenic RNAs in the KCS1 locus to down-regulate the Kcs1 activity, another IP6 kinase, by producing truncated Kcs1 protein via hybrid formation with the KCS1 mRNA and translation of the intragenic RNA, thereby enabling Vip1 to utilize more IP6 to synthesize IP7 functioning in low-Pi signaling. Because Kcs1 also can phosphorylate these IP7 species to synthesize IP8, reduction in Kcs1 activity can ensure accumulation of the IP7 species, leading to further stimulation of low-Pi signaling (i.e., forming a positive feedback loop). We also report that genes apparently not involved in the PHO system are regulated by Pho4 either dependent upon or independent of the Pi conditions, and many of the latter genes are involved in stress response. In S. cerevisiae, a large-scale cDNA analysis and mapping of RNA polymerase II binding using a high-resolution tiling array have identified a large number of antisense RNA species whose functions are yet to be clarified. Here we have shown that nutrient-regulated antisense and intragenic RNAs as well as direct regulation of structural gene transcription function in the response to nutrient availability. Our findings also imply that Pho4 is present in the nucleus even under high-Pi conditions to activate or repress transcription, which challenges our current understanding of Pho4 regulation.
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