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Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome
Li‑Qin Xie,Ping‑Lan Wang,Shen‑Hua Jiang,Ze Zhang,Hua‑Hao Zhang 한국유전학회 2018 Genes & Genomics Vol.40 No.5
TC1/Mariner transposons belong to class II transposable elements (TEs) that use DNA-mediated “cut and paste” mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (Bombyx mori) has a large amount of TC1/Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 TC1/Mariner (Bmmar) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members of TC1/Mariner were grouped into five subgroups: Mariner, Tc1, maT, DD40D and DD41D/E. Of these five subgroups, maT rather than Mariner possessed most members of TC1/Mariner (51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed that Bmmar15 (DD40D) formed a new basal subgroup of TC1/Mariner element in insects, which was referred to as bmori. Furthermore, we concluded that DD40D appeared to intermediate between mariner and Tc1. Finally, we estimated the insertion time for each copy of TC1/Mariner in the silkworm and found that most of members were dramatically amplified during a period from 0 to 1 mya. Moreover, the detailed functional data analysis showed that Bmmar1, Bmmar6 and Bmmar9 had EST evidence and intact transposases. These implied that TC1/Mariner might have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution of TC1/Mariner in the insect genomes.
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Jing Shen,Jilin Zhang,Jian Wan,Li Zhou,Ming Jiang 보안공학연구지원센터 2014 International Journal of Database Theory and Appli Vol.7 No.6
Stencils are finite-difference algorithms for solving large-scale and high-dimension partial differential equations. Due to the data dependences among the iterative statements in Stencils, traditional Stencil computations are be executed serially, rather than in parallel. It’s challenging to design an effective and scalable Stencil parallelized method. To address the issue of 3D data space computing, we present a serial execution model based on multi-layers symmetric Stencil method and time skewing techniques. Within this model, the iteration space is divided to multiple tiles based on time skewing, where the executive process is ordered by the sequence of tiles, and the nodes in each individual tile can be swept repeatedly to improve the data locality. In addition, we propose a novel 3D iterative space alternate tiling Stencil parallel method, which subdivides the iteration space along high dimension, and changes the execution sequence of tiles to reduce the data dependency and communication cost, where the partial order of tiles is still guaranteed. Experimental results demonstrate our proposed alternative tiling parallel method achieves better parallel efficiency and scalability compared with the domain-decomposition methods.
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A Survey of the Geographic Distribution of Ophiocordyceps sinensis
Yi Li,Xiao-Liang Wang,Lei Jiao,Yi Jiang,Hui Li,Si-Ping Jiang,Ngarong Lhosumtseiring,Shen-Zhan Fu,Cai-Hong Dong,Yu Zhan,Yi-Jian Yao 한국미생물학회 2011 The journal of microbiology Vol.49 No.6
Ophiocordyceps sinensis is one of the best known fungi in Traditional Chinese Medicine. Many efforts have been devoted to locating the production areas of this species resulting in various reports; however, its geographic distribution remains incompletely understood. Distribution of O. sinensis at the county level is clarified in this work based on both a literature search and fieldwork. More than 3600 publications related to O. sinensis were investigated, including scientific papers, books, and online information. Herbarium specimens of O. sinensis and field collections made by this research group during the years 2000-2010 were examined to verify the distribution sites. A total of 203 localities for O. sinensis have been found, of which 106 are considered as confirmed distribution sites, 65 as possible distribution sites, 29 as excluded distribution sites and three as suspicious distribution sites. The results show that O. sinensis is confined to the Tibetan Plateau and its surrounding regions, including Tibet, Gansu, Qinghai, Sichuan, and Yunnan provinces in China and in certain areas of the southern flank of the Himalayas, in the countries of Bhutan, India and Nepal, with 3,000 m as the lowest altitude for the distribution. The fungus is distributed from the southernmost site in Yulong Naxi Autonomous County in northwestern Yunnan Province to the northernmost site in the Qilian Mountains in Qilian County, Qinghai Province, and from the east edge of the Tibetan Plateau in Wudu County, Gansu Province to the westernmost site in Uttarakhand, India. The clarification of the geographic distribution of O. sinensis will lay the foundation for conservation and sustainable use of the species.
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Zong, Li-Ju,Zhang, You-Zhong,Yang, Xing-sheng,Jiang, Jie,Cui, Bao-Xia,Qiao, Yun-Bo,Li, Li,Jiang, Kan,Zhang, Wen-Jing,Kong, Bei-Hua,Shen, Keng Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.5
Purpose: The study was designed to: (1) investigate the prevalence of high-risk human papillomavirus (HR-HPV) infection and cervical neoplasia; and (2) evaluate clinical performance of visual inspection with acetic acid/ Lugol's iodine (VIA /VILI), Pap smear, high-risk human papillomavirus (HR-HPV) DNA test for detecting cervical intraepithelial neoplasia grade 2 or worse (CIN2+) and (3) explore appropriate screening approach in rural areas of Shandong Province. Materials and Methods: A total of 3,763 eligible women from Yiyuan County in Yimeng mountainous areas of rural Shandong, China, were enrolled and underwent Pap smear, HR-HPV DNA testing by Hybrid Capture 2 (HC2), and VIA /VILI tests. Women positive in any test were referred to colposcopy and biopsy as indicated. Results: The prevalence of HR-HPV infection among all enrolled women was 11.1% and that in healthy women was 9.9%. In total 33 cases of CIN1, 16 cases of CIN2, 6 cases of CIN3 but none of cervical cancer were detected and the crude prevalence of CIN2+ was 0.58%. For detecting CIN2+, the sensitivity of HR-HPV DNA testing, VIA/VILI, Pap smear was 90.9%, 77.3%, 81.8%, respectively. Pap smear had the best specificity of 98.2%, followed by HR-HPV DNA testing with specificity of 89.4%, VIA/VILI had the lowest specificity of 81.2%. Colposcopy referral rate of HR-HPV DNA testing, VIA/VILI, Pap smear was 11.1%, 18.5%, 2.3%, respectively. Conclusions: Our results suggest that HR-HPV DNA testing alone might be appropriate for primary cervical cancer screening in rural low-resource areas of Shandong Province, China.
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Luo, Jia,Shen, Linyuan,Gan, Mailin,Jiang, Anan,Chen, Lei,Ma, Jideng,Jin, Long,Liu, Yihui,Tang, Guoqing,Jiang, Yanzhi,Li, Mingzhou,Li, Xuewei,Zhang, Shunhua,Zhu, Li Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.8
Objective: Investigation of muscle growth at different developmental stages is an appropriate strategy for studying the mechanisms underlying muscle development and differences in phenotypes. In particular, the muscle development mechanisms and the difference between the fastest and slowest growth rates. Methods: In this study, we used a growth curve model to fit the growth inflection point (IP) of QingYu pigs and compared differences in the long non-coding RNA (lncRNA) transcriptome of muscle both at the growth IP and plateau phase (PP). Results: The growth curve of the QingYu pig had a good fit (R<sup>2</sup> = 0.974) relative to a typical S-curve and reached the IP at day 177.96. At the PP, marbling, intramuscular fat, and monounsaturated fatty acids had increased significantly and the percentage of lean muscle and polyunsaturated fatty acids had decreased. A total of 1,199 mRNAs and 62 lncRNAs were differentially expressed at the IP compared with the PP. Additional to gene ontology and Kyoto encyclopedia of genes and genomes pathway analyses, these differentially expressed protein coding genes were principally related to muscle growth and lipid metabolism. Conclusion: Our results suggest that the identified differentially expressed lncRNAs, could play roles in muscle growth, fat deposition and regulation of fatty acid composition at the IP and PP.
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Shen Tianli,Wu Yunhua,Wang Xingjie,Wang Zijun,Li Enmeng,Zhou Cancan,Yue Chenyang,Jiang Zhengdong,Wei Guangbing,Lian Jie,Xu Qinhong,Li Xuqi 생화학분자생물학회 2022 Experimental and molecular medicine Vol.54 No.-
Peritoneal adhesions (PAs) are a serious complication of abdominal surgery and negatively affect the quality of life of millions of people worldwide. However, a clear molecular mechanism and a standard therapeutic strategy for PAs have not been established. Here, we developed a standardized method to mimic the pathological changes in PAs and found that sirtuin 3 (SIRT3) expression was severely decreased in adhesion tissues, which was consistent with our bioinformatics analysis and patient adhesion tissue analysis. Thus, we hypothesized that activating SIRT3 could alleviate postsurgical PAs. Sirt3-deficient (Sirt3−/−) mice exhibited many more PAs after standardized abdominal surgery. Furthermore, compared with wild-type (Sirt3+/+) mice, Sirt3-deficient (Sirt3−/−) mice showed more prominent reactive oxygen species (ROS) accumulation, increased levels of inflammatory factors, and exacerbated mitochondrial damage and fragmentation. In addition, we observed NLRP3 inflammasome activation in the adhesion tissues of Sirt3−/− but, not Sirt3+/+ mice. Furthermore, mesothelial cells sorted from Sirt3−/− mice exhibited impaired mitochondrial bioenergetics and redox homeostasis. Honokiol (HKL), a natural compound found in several species of the genus Magnolia, could activate SIRT3 in vitro. Then, we demonstrated that treatment with HKL could reduce oxidative stress and the levels of inflammatory factors and suppress NLRP3 activation in vivo, reducing the occurrence of postsurgical PAs. In vitro treatment with HKL also restored mitochondrial bioenergetics and promoted mesothelial cell viability under oxidative stress conditions. Taken together, our findings show that the rescue of SIRT3 by HKL may be a new therapeutic strategy to alleviate and block postsurgical PA formation.
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Development of analysis program for direct containment heating
Jiang Herui,Shen Geyu,Meng Zhaoming,Li Wenzhe,Yan Ruihao 한국원자력학회 2022 Nuclear Engineering and Technology Vol.54 No.8
Direct containment heating (DCH) is one of the potential factors leading to early containment failure. DCH is closely related to safety analysis and containment performance evaluation of nuclear power plants. In this study, a DCH prediction program was developed to analyze the DCH loads of containment vessel. The phenomenological model of debris dispersal, metal oxidation reaction, debris-atmospheric heat transfer and hydrogen jet burn was established. Code assessment was performed by comparing with several separate effect tests and integral effect tests. The comparison between the predicted results and experimental data shows that the program can predict the key parameters such as peak pressure, temperature, and hydrogen production in containment well, and for most comparisons the relative errors can be maintained within 20%. Among them, the prediction uncertainty of hydrogen production is slightly larger. The analysis shows that the main sources of the error are the difference of time scale and the oxidation of cavity debris
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Dynamics of excitons and carriers at the NPB/C60 interface by transient photocurrents
Li Ping,De Yang Xiu,Wu Bo,Zhang Yu,Jiang Ze Zhuan,Bao Xi,Huang Hai Shen 한국물리학회 2020 Current Applied Physics Vol.20 No.5
The transient photocurrent (TPC) technique was performed to explore the dynamics of excitons and carriers at organic active layer/buffer layer interfaces. A special device with ITO/PEIE/NPB/C60/Al structure was designed to study the interfacial processes at the NPB/C60 interface. An external electrical field was provided to neutralize the built-in electrical field of the device. Interestingly, a new phenomenon was observed, wherein the polarity of the TPC changed from negative to positive under an external electrical field. The initial negative signal was ascribed to exciton separation by the built-in field in C60, and the subsequent positive signal can be attributed to the diffusion of electrons that accumulate at the NPB/C60 interface. TPC measurements shown that further increasing the external electrical field causes polarity to change twice. Analyzing the two changes in polarity revealed that the NPB did not only extract holes from C60 but also provided an effective interface for exciton dissociation.
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