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81.
82.
Aniruddha Chatterjee Yuichi Ozaki Peter A Stockwell Julia A Horsfield Ian M Morison Shinichi Nakagawa 《Epigenetics》2013,8(9):979-989
Reduced representation bisulfite sequencing (RRBS) has been used to profile DNA methylation patterns in mammalian genomes such as human, mouse and rat. The methylome of the zebrafish, an important animal model, has not yet been characterized at base-pair resolution using RRBS. Therefore, we evaluated the technique of RRBS in this model organism by generating four single-nucleotide resolution DNA methylomes of adult zebrafish brain. We performed several simulations to show the distribution of fragments and enrichment of CpGs in different in silico reduced representation genomes of zebrafish. Four RRBS brain libraries generated 98 million sequenced reads and had higher frequencies of multiple mapping than equivalent human RRBS libraries. The zebrafish methylome indicates there is higher global DNA methylation in the zebrafish genome compared with its equivalent human methylome. This observation was confirmed by RRBS of zebrafish liver. High coverage CpG dinucleotides are enriched in CpG island shores more than in the CpG island core. We found that 45% of the mapped CpGs reside in gene bodies, and 7% in gene promoters. This analysis provides a roadmap for generating reproducible base-pair level methylomes for zebrafish using RRBS and our results provide the first evidence that RRBS is a suitable technique for global methylation analysis in zebrafish. 相似文献
83.
Caiyong Chen Daniel Garcia-Santos Yuichi Ishikawa Alexandra Seguin Liangtao Li Katherine H. Fegan Gordon J. Hildick-Smith Dhvanit I. Shah Jeffrey D. Cooney Wen Chen Matthew J. King Yvette Y. Yien Iman J. Schultz Heidi Anderson Arthur J. Dalton Matthew L. Freedman Paul D. Kingsley James Palis Barry H. Paw 《Cell metabolism》2013,17(3):343-352
Highlights? Snx3 is highly expressed in vertebrate hematopoietic tissues ? Silencing of Snx3 results in anemia and hemoglobin defects in vertebrates ? Snx3 and Vps35 physically interact with Tfrc ? Snx3 is required for endosomal recycling of Tf-Tfrc complex 相似文献
84.
85.
Quanhai Li Kiyoko Kawamura Shan Yang Shinya Okamoto Hiroshi Kobayashi Yuji Tada Ikuo Sekine Yuichi Takiguchi Masato Shingyouji Koichiro Tatsumi Hideaki Shimada Kenzo Hiroshima Masatoshi Tagawa 《PloS one》2013,8(8)
Interferons (IFNs) have been tested for the therapeutic effects in various types of malignancy, but mechanisms of the anti-tumors effects and the differential biological activities among IFN members are dependent on respective cell types. In this study, we examined growth inhibitory activities of type I and III IFNs on 5 kinds of human mesothelioma cells bearing wild-type p53 gene, and showed that type I IFNs but not type III IFNs decreased the cell viabilities. Moreover, growth inhibitory activities and up-regulated expression levels of the major histocompatibility complexes class I antigens were greater with IFN-β than with IFN-α treatments. Cell cycle analyses demonstrated that type I IFNs increased S- and G2/M-phase populations, and subsequently sub-G1-phase fractions. The cell cycle changes were also greater with IFN-β than IFN-α treatments, and these data collectively showed that IFN-β had stronger biological activities than IFN-α in mesothelioma. Type I IFNs-treated cells increased p53 expression and the phosphorylation levels, and activated apoptotic pathways. A combinatory use of IFN-β and cisplatin or pemetrexed, both of which are the current first-line chemotherapeutic agents for mesothelioma, produced synergistic anti-tumor effects, which were also evidenced by increased sub-G1-phase fractions. These data demonstrated firstly to our knowledge that IFN-β produced synergistic anti-tumor effects with cisplatin or pemetrexed on mesothelioma through up-regulated p53 expression. 相似文献
86.
87.
Koshiishi Yuichi Murata-Okubo Michiko Fujisawa Shin-ichiro Shimoi Gaku Hirayama Hiroki Kameyama Yuichi Souma Kousaku Wada Kenta 《Molecular biology reports》2020,47(4):2521-2527
Molecular Biology Reports - The emu (Dromaius novaehollandiae) is a useful poultry animal farmed for fat, meat, and eggs. Genetic structure and relationships among farmed emu populations in Japan... 相似文献
88.
Hayuki Sugimoto Yuichi Nakajima Ayaka Motoyama Erina Katagiri Takeshi Watanabe Kazushi Suzuki 《Biopolymers》2020,111(1):e23339
Chitin-binding protein 21 (CBP21) from Serratia marcescens is a lytic polysaccharide monooxygenase that contains a copper ion as a cofactor. We aimed to elucidate the unfolding mechanism of CBP21 and the effects of Cu2+ on its structural stability at pH 5.0. Thermal unfolding of both apo- and holoCBP21 was reversible. ApoCBP21 unfolded in a simple two-state transition manner. The peak temperature of the DSC curve, tp, for holoCBP21 (74.4°C) was about nine degrees higher than that for apoCBP21 (65.6°C). The value of tp in the presence of excess Cu2+ was around 75°C, indicating that Cu2+ does not dissociate from the protein molecule during unfolding. The unfolding mechanism of holoCBP21 was considered to be as follows: N∙Cu2+ ⇌ U∙Cu2+, where N and U represent the native and unfolded states, respectively. Urea-induced equilibrium unfolding analysis showed that holoCBP21 was stabilized by 35 kJ mol−1 in terms of the Gibbs energy change for unfolding (pH 5.0, 25°C), compared with apoCBP21. The increased stability of holoCBP21 was considered to result from the structural stabilization of the protein-Cu2+ complex itself. 相似文献
89.
Yoshiteru Sasaki Soichi Sano Masaki Nakahara Shigeo Murata Kohei Kometani Yuichi Aiba Shinji Sakamoto Yoshihiro Watanabe Keiji Tanaka Tomohiro Kurosaki Kazuhiro Iwai 《The EMBO journal》2013,32(18):2463-2476
The linear ubiquitin chain assembly complex (LUBAC) plays a crucial role in activating the canonical NF‐κB pathway, which is important for B‐cell development and function. Here, we describe a mouse model (B‐HOIPΔlinear) in which the linear polyubiquitination activity of LUBAC is specifically ablated in B cells. Canonical NF‐κB and ERK activation, mediated by the tumour necrosis factor (TNF) receptor superfamily receptors CD40 and TACI, was impaired in B cells from B‐HOIPΔlinear mice due to defective activation of the IKK complex; however, B‐cell receptor (BCR)‐mediated activation of the NF‐κB and ERK pathways was unaffected. B‐HOIPΔlinear mice show impaired B1‐cell development and defective antibody responses to thymus‐dependent and thymus‐independent II antigens. Taken together, these data suggest that LUBAC‐mediated linear polyubiquitination is essential for B‐cell development and activation, possibly via canonical NF‐κB and ERK activation induced by the TNF receptor superfamily, but not by the BCR. 相似文献
90.
Distribution pattern, threats and conservation of fish biodiversity in the East Tiaoxi, China 总被引:1,自引:0,他引:1
Jianhua Li Liangliang Huang Tatsuro Sato Limin Zou Ke Jiang Tetsukazu Yahara Yuichi Kano 《Environmental Biology of Fishes》2013,96(4):519-533
East Tiaoxi River is one of the largest inflowing rivers into Taihu Lake, and the fish fauna in the river is poorly understood. In the present study, an extensive survey of fish was conducted in October and November 2009, May and September 2010 and May 2011 covering a total of 55 sites along the whole river. A total of 84 freshwater fish species belonging to 8 orders, 18 families and 52 genera have been recorded. Among these are 35 species endemic to China, and 3 newly recorded exotic species. The fish composition varies greatly from headwaters to downstream. Based on cluster analysis with presence-absence data, the East Tiaoxi River is divided into four regions, specifically, the upper reach, middle-up reach, middle reach and lower reach. It is observed that species richness and the proportion of omnivorous species increased from upstream to downstream while the proportion of invertivorous species decreased consequently. Habitat alteration, overfishing, pollution and inland navigation adversely affect the fish diversity and ecosystem functioning in the East Tiaoxi River. To protect fish diversity more effectively in the area, the conservation of fish biodiversity in the North Tiaoxi River and Middle Tiaoxi River should be considered as a priority. Meanwhile, shallow zones or backwater areas should be created in the middle-lower reaches. Furthermore, river restoration, in terms of habitat creation, should be considered to protect the structure and diversity of fish communities, halt the progressive deterioration of freshwater ecosystems and sustain a valuable ecological resource for humans. 相似文献