173 research outputs found
Abstract 4650: Mutation detection by target sequence analyses using tissue-specific panels in esophageal squamous cell carcinoma
No full textAbstract
Whole-exome sequencing (WES) studies on esophageal squamous cell carcinoma (ESCC) have revealed that only a small number of frequently mutated genes, such as TP53, NOTCH1, NRF2, and ZNF750, are present in individual tumors, whereas hundreds of others less frequently mutated genes are accumulated. The mutation detection rate by target sequence analyses is an important factor for clinical sequence in the course of ESCC treatment. This study aimed to evaluate the mutation detection rates of several target sequence analyses for ESCC. Ten pairs of surgically or endoscopically acquired tumor tissues and corresponding peripheral blood mononuclear cells were obtained from ESCC patients. We used three types of target sequence panels for mutation screening in 10 ESCC patients as follows: 1) Cancer Hotspot Panel (CHPv2), targeting mutation hotspot regions in the most common 50 human cancer genes that are frequently mutated (panel size: 22,027 bp), for five patients; 2) TP53 Panel, covering all exons of TP53 (panel size: 2,359 bp), for five patients; and 3) ESCC Panel, originally designed to target 31 frequently mutated genes in ESCC (panel size: 210,570 bp), for seven patients. Four missense and two nonsense mutations in TP53 were detected in CHPv2 and the TP53 Panel. Furthermore, one missense mutation in FBXW7 and one intronic mutation in the vicinity of exon 8 in TP53 were also observed in CHPv2 and the TP53 Panel, respectively. In the ESCC Panel, 47 mutations in 17 genes were detected in seven patients. The mutation detection rates by the TP53 Panel, CHPv2, and ESCC Panel were 593.0/Mb, 63.5/Mb, and 30.4/Mb, respectively. These mutation detection rates were more than 20-fold higher than that of WES, which has been reported to be 3.1/Mb for ESCC. These results suggest that tissue-specific cancer-related gene panels are a highly effective approach for mutation detection in ESCC.
Citation Format: Takeshi Iwaya, Fumitaka Endo, Kohei Kume, Yasushi Sasaki, Takashi Tokino, Satoshi Nishizuka. Mutation detection by target sequence analyses using tissue-specific panels in esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4650. doi:10.1158/1538-7445.AM2017-4650</jats:p
3次元ハイゼンベルグスピングラスのスティッフネス(京大基礎研短期研究計画「フラストレーションとカイラル秩序」,研究会報告)
No full textこの論文は国立情報学研究所の電子図書館事業により電子化されました
Abstract 5683: Evaluation of the utilization of blood collection tubes for cell-free DNA research
No full textAbstract
Many studies have been conducted investigating cell-free DNA (cfDNA) for disease diagnosis. To prevent cellular DNA release into the plasma, plasma separation within 2 hours of blood collection is required, when utilizing the most commonly used type of tube (BD Vacutainer® CPTTM; CPT). These temporal restrictions render operations requiring plasma separation a laborious task. It has been demonstrated that Cell-Free DNA BCT® tubes (Streck Inc; BCTs) prevented nucleated cell disruption. The use of BCTs may enable us to separate plasma without temporal restrictions. The aim of this study was to evaluate changes in DNA levels in plasma after preservation using two types of collection tubes. Samples were drawn from 7 healthy donors into CPTs and BCTs, and stored at room temperature. Plasma was separated immediately (d0), and on days 3, 6, 9, 12, and 14 after blood collection. The concentrations of DNA in the extracted plasma samples were measured. Blood stored in CPTs showed increases in plasma DNA concentrations over time. The mean DNA concentrations at each time-point were 0.39 (d0), 2.96 (d3), 40.4 (d6), 84.9 (d9), 91.4 (d12), and 94.9 ng/μl (d14). However, plasma DNA levels remained stable in BCTs from 6 days. There were significant differences between the DNA concentrations in BCTs on d0 (0.74 [0.43-1.44] ng/µl) and d14 (1.78 [0.63-4.20] ng/µl) (p = 0.0378). Although significant differences were only observed between d0 and d14 in BCTs, the amount of plasma DNA gradually increased after d6. Furthermore, obvious color changes in the plasma were observed, and the boundary between plasma and PBMCs became unclear over time. These results indicate that BCTs may yield stable cfDNA samples for up to 6 days after blood collection. BCTs may be a novel collection tube for cfDNA research, including liquid biopsies in cancer patients.
Citation Format: Fumitaka Endo, Takeshi Iwaya, Takehiro Chiba, Mizunori Yaegashi, Kei Sato, Kohei Kume, Atsuhiro Arisue, Yutaka Nishinari, Ryoko Kawagishi, Takenori Segawa, Satoshi Nishizuka, Akira Sasaki. Evaluation of the utilization of blood collection tubes for cell-free DNA research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5683. doi:10.1158/1538-7445.AM2017-5683</jats:p
724 Ultra high speed Observations of Dynamic Interfatial Crack-tip Propagation in Composite Materials
No full text
Improvement of Production and Isolation of Human Neuraminidase-1 in Cellulo Crystals
No full textIn cellulo crystallization is a developing technique to provide crystals for protein structure determination, particularly for proteins that are difficult to prepare by in vitro crystallization. This method has a key advantage: It requires neither a protein purification step nor a crystallization step. However, there is still no systematic strategy for improving the technique of in cellulo crystallization because the process occurs spontaneously. Here we report a protocol to produce and extract in cellulo crystals of human lysosomal neuraminidase-1 (NEU1) in human cultured cells. Overexpression of NEU1 protein by the retransfection of cells pretransfected with neu1-overexpressing plasmid improved the efficiency of NEU1 crystallization. Microscopic analysis revealed that NEU1 proteins were not crystallized in the lysosome but in the endoplasmic reticulum (ER). Screening of the buffer conditions used to extract crystals from cells further improved the crystal yield. The optimal pH was 7.0, which corresponds to the pH in the ER. Use of a high-yield flask with a large surface area also yielded more crystals. These optimizations enabled us to execute a serial femtosecond crystallography experiment with a sufficient number of crystals to generate a complete data set. Optimization of the in cellulo crystallization method was thus shown to be possible.Accepted Author ManuscriptBN/Arjen Jakobi La
Alteration of N-linked oligosaccharide structures of human chorionic gonadotropin β -subunit by disruption of disulfide bonds
No full textThe human chorionic gonadotropin β-subunit (hCGβ) is a glycoprotein in which 12 cysteine residues pair to form six intramolecular disulfide bonds. In order to elucidate the effect of each disulfide bond on glycosylation of the molecule, we analysed structures of asparagine-linked oligosaccharides of various recombinant hCGβ produced in Chinese hamster ovary (CHO) cells: wild-type hCGβ (βWT) and mutants in which any one of the six intramolecular disulfide bonds had been disrupted by site-directed mutagenesis. SDS-PAGE analysis of βWT and these mutants before and after digestion with endoglycosidase F and H revealed structural changes in the oligosaccharide moieties of some mutants. In addition, structural analysis of oligosaccharides obtained from metabolically labeled βWT and a mutant showed that the mutant contained additional high mannose type oligosaccharides. These results suggest that elimination of a specific disulfide bond, resulting in a change in the protein conformation, disturbs the normal assembly of the mature complex type oligosaccharides in the hCGβ molecule. Abbreviations: hCGβ, human chorionic gonadotropin β-subunit; βWT, wild type hCGβ; CHO, Chinese hamster ovary; Endo-H, endoglycosidase H; Endo-F, endoglycosidase F名古屋大学博士学位論文 学位の種類 : 博士(医学)(論文) 学位授与年月日:平成9年2月28日 森脇崇之氏の博士論文として提出され
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