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De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress

Dan-Qing Tian, Xiao-Yun Pan, Yong-Ming Yu, Wei-Yong Wang, Fei Zhang, Ya-Ying Ge, Xiao-Lan Shen, Fu-Quan Shen, Xiao-Jing Liu
2013 BMC Genomics  
Anthurium andraeanum is one of the most popular tropical flowers. In temperate and cold zones, a much greater risk of cold stress occurs in the supply of Anthurium plants. Unlike the freeze-tolerant model plants, Anthurium plants are particularly sensitive to low temperatures. Improvement of chilling tolerance in Anthurium may significantly increase its production and extend its shelf-life. To date, no previous genomic information has been reported in Anthurium plants. Results: Using Illumina
more » ... quencing technology, we generated over two billion base of high-quality sequence in Anthurium, and demonstrated de novo assembly and annotation of genes without prior genome information. These reads were assembled into 44,382 unigenes (mean length = 560 bp). Based on similarity search with known protein in the non-redundant (nr) protein database, 27396 unigenes (62%) were functionally annotated with a cut-off E-value of 10 -5 . Further, DGE tags were mapped to the assembled transcriptome for gene expression analysis under cold stress. In total, 4363 differentially expressed genes were identified. Among these genes, 292, 805 and 708 genes were up-regulated after 1-h, 5-h and 24-h cold treatment, respectively. Then we mapped these cold-induced genes to the KEGG database. Specific enrichment was observed in photosynthesis pathway, metabolic pathways and oxidative phosphorylation pathway in 1-h cold-treated plants. After a 5-h cold treatment, the metabolic pathways and oxidative phosphorylation pathway were significantly identified as the top two pathways. After 24-h cold treatment, mRNA surveillance pathway, RNA transport pathway and plant-pathogen interaction pathway were significantly enriched. Together, a total of 39 cold-inducible transcription factors were identified, including subsets of AP2/ERF, Zinc figure, NAC, MYB and bZIP family members. Conclusion: Our study is the first to provide the transcriptome sequence resource for Anthurium plants, and demonstrate its digital gene expression profiling under cold conditions using the assembled transcriptome data for reference. These data provides a valuable resource for genetic and genomic studies under abiotic conditions for Anthurium plants.
doi:10.1186/1471-2164-14-827 pmid:24267953 pmcid:PMC4046746 fatcat:irwnsb6m4vacbltacicfk2leeu

Shock wave velocity measurement in the Al2O3under ultrahigh pressure

Feng Wang, Xiao-Shi Peng, Shen-Ye Liu, Yong-Sheng Li, Xiao-Hua Jiang, Yong-Kun Ding
2011 Chinese Physics B  
In indirect-drive experiment, the blank effect caused by X-rays from Hohlraum will show the dark area in time scale of optical streak camera (OSC). This blank effect, which was a serious problem in indirect-drive shock wave experiments, has been explained by the semiconductor model. The X-rays cause the band to band transition and the probe laser is absorbed by the intraband transition, which leads to a dark region in time scale of the OSC image. In the experiment, the reflectivity of shock
more » ... front was measured to be about 50% at shock wave velocity 32 km/s and was compared to the theoretical calculations with the Drude free electron model. From the experimental data, it is found that the blank effect can be avoided at radiation temperature of 170 eV if the Al layer is thicker than 60 µm.
doi:10.1088/1674-1056/20/6/065202 fatcat:uofy4zng65clvouksa23nceiiy

The role of autophagy during murine primordial follicle assembly

Yuan-Chao Sun, Yong-Yong Wang, Xiao-Feng Sun, Shun-Feng Cheng, Lan Li, Yong Zhao, Wei Shen, Hong Chen
2018 Aging  
doi:10.18632/aging.101376 pmid:29410391 pmcid:PMC5842841 fatcat:gdj7bq2v3bgelen3lddo4633tm

Current status of studies on genome-wide gene-gene interactions

Jia-Wei SHEN, Xiao-Han HU, Yong-Yong SHI
2011 Hereditas (Beijing)  
Complex diseases have affected human's health throughout the world. Hundreds of studies show that complex diseases are caused by multiple loci. Currently, genome-wide association studies(GWAS) only focus on the single locus that contributes to the susceptibility of a certain disease. However, the interaction between genes could be one of the main factors that lead to complex traits. This fact has initiated scientists to propose some algorithms to detect these interactions, such as the penalized
more » ... logistic regression model, multifactor dimensionality reduction method, set association analysis method, Bayesian networks analysis method and random forest. However, these algorithms are of high complexity, hypothesis-driven, causing over fitting of data, or not sensible of data at low dimensions. In this paper, we reviewed these algorithms, and then demonstrated a new algorithm based on GPU to provide a powerful strategy to analyze gene-gene interaction in genome-wide association datasets. This algorithm is of low computing complexity, free of hypothesis, not affected by single locus marginal effect, and also of high stability and speed.
doi:10.3724/sp.j.1005.2011.00820 pmid:21831799 fatcat:r4iuwio7vjflrixxqocdvslacy

Parallel evolution ofIDH2gene in cetaceans, primates and bats

Wei-Ming Ai, Shao-Bo Chen, Xiao Chen, Xue-Juan Shen, Yong-Yi Shen
2013 FEBS Letters  
Cetaceans and primates both have large brains that require large amounts of aerobic energy metabolism. In bats, the cost of flight makes locomotion energetically demanding. These mammalian groups may represent three independent evolutionary origins of an energy-demanding lifestyle in mammals. IDH2 encodes an enzyme in the tricarboxylic acid cycle in the mitochondrion, which plays a key role in aerobic energy metabolism. In this study, we cloned and sequenced this gene in two cetaceans, and 19
more » ... t species, and compared the data with available primate sequences to test its evolution. We found significant signals of parallel evolution in this gene among these three groups. Parallel evolution of this gene may reflect their parallel evolution towards a higher demand for energy.
doi:10.1016/j.febslet.2013.12.005 pmid:24374336 fatcat:m3lhhls5ybbmphvrvkaqfxrrey

Direct interaction and cooperative role of tumor suppressor p16 with band 3 (AE1)

Guo-Hui Fu, Yong Wang, Yu-Hui Xi, Wei-Wei Shen, Xiao-Yan Pan, Wu-Zhong Shen, Xiao-Shu Jiang, Guo-Qiang Chen
2005 FEBS Letters  
By using the C-terminal 112-residue of band 3 to screen the K562 cDNA library, we find that the p16 interacts with band 3, which was confirmed both in yeast and in mammalian cells. Functional experiments show that p16 facilitates the movement of band 3 to plasma membrane with increased anion transport activity in 293t cells. Moreover, expression of endogenous p16 in 293t cells was increased at 24 and 36 h after transfection with band 3. Our findings provide a novel regulation pathway for both band 3 and p16.
doi:10.1016/j.febslet.2005.02.063 pmid:15811326 fatcat:uzs6svaq25hqzdjcg6r36yzsym

Acupuncture De-qi: From Characterization to Underlying Mechanism

Shi-Peng Zhu, Li Luo, Ling Zhang, Song-Xi Shen, Xiao-Xuan Ren, Meng-Wei Guo, Jia-Min Yang, Xiao-Yu Shen, Yong-Si Xu, Bo Ji, Jiang Zhu, Xiao-Hong Li (+1 others)
2013 Evidence-Based Complementary and Alternative Medicine  
De-qi refers to the participant's subjective sensations and objective body responses as well as the acupuncturist's perceptions while the acupuncturist needles certain acupoints in the participant's body. In recent years, De-qi is getting increasing attention of the researchers and many efforts have been made to understand its mechanism. By the broad literature survey, this paper explores the subjective De-qi sensation of the patients, its influencing factors, and the resulting physiological
more » ... ponses. The purpose of this paper is expected to find out a possible mechanism of De-qi and to provide certain scientific evidence for acupuncture fundamental research and clinical practice.
doi:10.1155/2013/518784 pmid:24194782 pmcid:PMC3781993 fatcat:xtm2tl5cynef3if4uhinmym7wi

mmeta: AnRPackage for Multivariate Meta-Analysis

Shen Luo, Yong Chen, Xiao Su, Haitao Chu
2014 Journal of Statistical Software  
Yong Chen's research was partially supported by a start-up fund from the University of Texas School of Public Health. Haitao Chu was supported in part by the U.S.  ... 
doi:10.18637/jss.v056.i11 fatcat:bypcgwikovckpboccnjo75zena

Peli1 Contributions in Microglial Activation, Neuroinflammatory Responses and Neurological Deficits Following Experimental Subarachnoid Hemorrhage

Xue-Ping Huang, Jian-Hua Peng, Jin-Wei Pang, Xiao-Cui Tian, Xin-Shen Li, Yue Wu, Yong Li, Yong Jiang, Xiao-Chuan Sun
2017 Frontiers in Molecular Neuroscience  
Peli1 has been suggested to have a microglial cell-specific role in mediating TLR-induced pro-inflammatory cytokine and chemokine expression (Xiao et al., 2013) .  ...  The activities of MyD88-dependent MAPK in microglia could be downregulated by Peli1 on experimental autoimmune encephalomyelitis (EAE; Xiao et al., 2013) .  ... 
doi:10.3389/fnmol.2017.00398 pmid:29249938 pmcid:PMC5714869 fatcat:sm6vwpqhwrd7zm4dwsnczk4k5a

Mycobacterial Lipoprotein Z Triggers Efficient Innate and Adaptive Immunity for Protection Against Mycobacterium tuberculosis Infection

Yingying Chen, Jia-ni Xiao, Yong Li, Yang-jiong Xiao, Yan-qing Xiong, Ying Liu, Shu-jun Wang, Ping Ji, Guo-ping Zhao, Hao Shen, Shui-hua Lu, Xiao-yong Fan (+1 others)
2019 Frontiers in Immunology  
Mycobacterial lipoproteins are considered to be involved in both virulence and immunoregulatory processes during Mycobacterium tuberculosis (M.tb) infection. In our previous investigations on the immunoreactivity of more than 30 M.tb proteins in active TB patients, we identified mycobacterial lipoprotein Z (LppZ) as one of the most immune dominant antigens. How LppZ triggers immune responses is still unclear. In this study, we analyzed LppZ-mediated innate and adaptive immunity using a murine
more » ... r pouch model and an M.tb infection model, respectively. We found that LppZ could not only recruit inflammatory cells but also induce the production of proinflammatory cytokines inside the pouches. LppZ could also induce strong Th1 responses following immunization and confer protection against challenge with M.tb virulent strain H37Rv at a similar level to BCG vaccination but with less pathological damage in the lungs. Furthermore, we revealed the presence of LppZ-specific functional CD4 + T cells in the lungs of the challenged mice that were capable of secreting double or triple cytokines, including IFN-γ, IL-2, and TNF-α. Our study thus demonstrates that LppZ is of strong immunogenicity during M.tb infection in both humans and mice and has the ability to trigger effective innate and cellular immunity. Considering the limitations of candidate antigens in the pipeline of TB vaccine development, LppZ-mediated immune protection against M.tb challenge in the mouse model implies its potential application in vaccine development.
doi:10.3389/fimmu.2018.03190 fatcat:dnafszbmsjhhpe6jf5527lravi

Inherently improper surface parametric supports

Eng-Wee Chionh, Xiao-Shan Gao, Li-Yong Shen
2006 Computer Aided Geometric Design  
We identify a class of monomial supports from which any rational parametrizations for surfaces are improper. These inherently improper surface parametric supports are called improper supports and they can be characterized by a simple necessary and sufficient condition. The constructive proof of this condition can be implemented to detect and correct improper parametrizations due to improper supports. Our results also extend to rational parametric representations of hypersurfaces with arbitrary dimensions.
doi:10.1016/j.cagd.2006.06.002 fatcat:gbswclnza5hmdhod77oytgcn5q

The antiproliferative effects of somatostatin receptor subtype 2 in breast cancer cells

Yong He, Xiao-mei Yuan, Ping Lei, Sha Wu, Wei Xing, Xiao-li Lan, Hui-fen Zhu, Tao Huang, Guo-bing Wang, Rui An, Yong-xue Zhang, Guan-xin Shen
2009 Acta Pharmacologica Sinica  
Author contribution Guan-xin SHEN and Yong HE designed research; Yong HE, Xiao-mei YUAN, Ping LEI, Sha WU, Wei XING and Xiao-li LAN performed research; Tao HUANG, Guo-bing WANG, Rui AN, Yong-xue ZHANG  ...  contributed new analytical tools and reagents; Xiao-mei YUAN and Hui-fen ZHU analyzed data; Yong HE, Xiao-mei YUAN and Ping LEI wrote the paper.  ... 
doi:10.1038/aps.2009.59 pmid:19575008 pmcid:PMC4006656 fatcat:zwjdasuiuvazvp652zp7lvulpy

Dissipative optomechanics of a single-layer graphene in a microcavity [article]

Lin-Da Xiao, Yu-Feng Shen, Yong-Chun Liu, Meng-Yuan Yan, Yun-Feng Xiao
2014 arXiv   pre-print
Lin-Da Xiao was supported by The Presents Fund for Undergraduate Research of Peking University. Yu-Feng Shen was supported by The Beijing Undergraduate Innovational Experimentation Program.  ... 
arXiv:1411.2202v2 fatcat:7k3w35sdjnh6lmckbiv4fbv3km

Shock experiment with sandwiched target in laser indirect-drive experiment

Wang Feng, Peng Xiao-Shi, Liu Shen-Ye, Jiang Xiao-Hua, Xu Tao, Ding Yong-Kun, Zhang Bao-Han
2011 Wuli xuebao  
doi:10.7498/aps.60.115203 fatcat:pel7rmn3xfft7dsyqndh3vibgu

Pulmonary sarcomatoid carcinoma: a

Xiao-yong Shen, Zhi-feng Lin, Qiang Lin, Zhen Ruan, Hai-long Huang, Chao-qiang Ju, Jin Wang
2013 Contemporary Oncology  
Sarcomatoid carcinoma (SC) is a rare primary malignant tumor in which both carcinomatous and sarcomatous elements occur. It can occur in many different organs and anatomical locations, such as the skin, thyroid gland, bone, urinary tract, breast, pancreas, liver and other areas. Of them, pulmonary sarcomatoid carcinoma (PSC) is a rare malignant cancer composed of sarcoma and sarcoma-like tumors with spindle or giant cell features. Here a case of a 75-yearold Chinese man with a six-month history
more » ... of cough and hemoptysis is reported. Chest X-ray showed a tumor shadow in the left lung field. Chest computed tomography (CT) scan showed a lobulated mass in his left hilum and even the left pulmonary artery. Pleomorphic interstitial cells were found by bronchoscopic brushing. To establish a definitive diagnosis for PSC, a left pneumonectomy was performed. The pathological stage was IIB (pT2N1M0) based on the tumor node metastasis (TNM) staging system. The tumor's pathology, histology, immunohistochemistry and treatment methods are discussed. K Ke ey y w wo or rd ds s: : lung neoplasms; carcinoma; diagnosis; treatment.
doi:10.5114/wo.2013.34375 pmid:23788993 pmcid:PMC3685364 fatcat:h2wgjce7hvalbh3oiexmrn7t7u
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