35 results on '"You, Yu"'
Search Results
2. Active targeting of orthotopic glioma using biomimetic liposomes co-loaded elemene and cabazitaxel modified by transferritin
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Li, Jie, Zeng, Huamin, You, Yu, Wang, Rongrong, Tan, Tiantian, Wang, Weiming, Yin, Liyan, Zeng, Zhaowu, Zeng, Yiying, and Xie, Tian
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- 2021
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3. Shengmai Yin formula modulates the gut microbiota of spleen-deficiency rats
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You, Yu, Luo, Lin, You, Yanyan, Lin, Yanjun, Hu, Huiling, Chen, Yunhui, Fu, Chaomei, and Xie, Tian
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- 2020
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4. HBV X protein-based therapeutic vaccine accelerates viral antigen clearance by mobilizing monocyte infiltration into the liver in HBV carrier mice
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Horng, Jau-Hau, Lin, Wei-Hsiang, Wu, Chang-Ru, Lin, You-Yu, Wu, Li-Ling, Chen, Ding-Shinn, and Chen, Pei-Jer
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- 2020
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5. Predictors of five-year relapse rates of youths with substance abuse who underwent a family-oriented therapy program
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You, Yu-Han, Lu, Shing-Fang, Tsai, Chih-Pu, Chen, Mei-Yen, Lin, Chin-Yin, Chong, Mian-Yoon, Chou, Wen-Jiun, Chen, Yi-Syuan, and Wang, Liang-Jen
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- 2020
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6. Rifampin resistance and its fitness cost in Riemerella anatipestifer
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Sun, Jiakai, Zhu, Dekang, Xu, Jinge, Jia, Renyong, Chen, Shun, Liu, Mafeng, Zhao, Xinxin, Yang, Qiao, Wu, Ying, Zhang, Shaqiu, Liu, Yunya, Zhang, Ling, Yu, Yanling, You, Yu, Wang, Mingshu, and Cheng, Anchun
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- 2019
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7. Retraction Note: MicroRNA-31-5p regulates chemosensitivity by preventing the nuclear location of PARP1 in hepatocellular carcinoma
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Que, Ke-ting, Zhou, Yun, You, Yu, Zhang, Zhen, Zhao, Xiao-ping, Gong, Jian-ping, and Liu, Zuo-jin
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- 2019
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8. Growth characteristics of the novel goose parvovirus SD15 strain in vitro
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Zhang, Jinyue, Liu, Peng, Wu, Yuanyuan, Wang, Mingshu, Jia, Renyong, Zhu, Dekang, Liu, Mafeng, Yang, Qiao, Wu, Ying, Zhao, Xinxin, Zhang, Shaqiu, Liu, Yunya, Zhang, Ling, Yu, Yanling, You, Yu, Chen, Shun, and Cheng, Anchun
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- 2019
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9. RETRACTED ARTICLE: MicroRNA-31-5p regulates chemosensitivity by preventing the nuclear location of PARP1 in hepatocellular carcinoma
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Que, Ke-ting, Zhou, Yun, You, Yu, Zhang, Zhen, Zhao, Xiao-ping, Gong, Jian-ping, and Liu, Zuo-jin
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- 2018
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10. HBV X protein-based therapeutic vaccine accelerates viral antigen clearance by mobilizing monocyte infiltration into the liver in HBV carrier mice
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Wei Hsiang Lin, Jau Hau Horng, Ding-Shinn Chen, Li Ling Wu, Chang Ru Wu, You Yu Lin, and Pei-Jer Chen
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0301 basic medicine ,Male ,Hepatitis B virus ,Endocrinology, Diabetes and Metabolism ,T cell ,medicine.medical_treatment ,Clinical Biochemistry ,lcsh:Medicine ,medicine.disease_cause ,Chronic hepatitis B ,Monocytes ,Hepatitis B Antigens ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Immune system ,Antigen ,medicine ,Animals ,Pharmacology (medical) ,Hepatitis B Vaccines ,Viral Regulatory and Accessory Proteins ,Hepatic innate immunity ,Molecular Biology ,business.industry ,Research ,Biochemistry (medical) ,lcsh:R ,virus diseases ,Cell Biology ,General Medicine ,Immunotherapy ,Myeloid cell ,Vaccine therapy ,digestive system diseases ,Vaccination ,Mice, Inbred C57BL ,HBx ,030104 developmental biology ,medicine.anatomical_structure ,Liver ,Immunology ,Mice, Inbred CBA ,Trans-Activators ,030211 gastroenterology & hepatology ,business - Abstract
Background Hepatitis B virus (HBV) persistently infected about 250 million people worldwide, and a curative treatment remains an unmet medical need. Among many approaches to treat chronic hepatitis B (CHB), therapeutic vaccines have been developed for two decades, but none have yielded promising results in clinical trials. Therefore, dissection of HBV clearance mechanisms during therapeutic vaccination in appropriate models, which could give rise to new curative therapies, is urgently needed. Growing evidence indicates that prolonged and intensive exposure of antigen-specific T cells to viral antigens is a major cause of T cell exhaustion, and decreases anti-HBV immunity efficacy of therapeutic vaccination. HBV X protein (HBx) is expressed at low levels, and the understanding of its immunogenicity and potential in therapeutic CHB vaccines is limited. Methods HBV genome sequences from CHB patients were cloned into a pAAV plasmid backbone and transfected into immunocompetent mouse hepatocytes through hydrodynamic injection. Mice carrying > 500 IU/mL serum HBV surface antigen (HBs) for more than 4 weeks were considered HBV carriers mimicking human CHB and received 3 doses of weekly HBx vaccine by subcutaneous immunization. Serum HBV clearance was evaluated by monitoring serum HBs and HBV-DNA titers. Residual HBV in the liver was evaluated by western blotting for HBV core antigen. The splenic antigen-specific T cell response was quantified by a 15-mer overlapping peptide-stimulated interferon-γ enzyme-linked immunospot assay. Blood and hepatic immune cells were quantified by flow cytometric analysis. Results Our HBx-based vaccine induced systemic HBx-specific CD4+ and CD8+ T cell responses in HBV carrier mice and demonstrated significant HBs and HBV-DNA elimination. The protective effect persisted for at least 30 days without additional booster immunization. Different infiltrating myeloid cell subsets, each with distinctive roles during immune-mediated HBV clearance, were found in the liver of vaccinated mice. During vaccine therapy, inflammatory monocyte depletion resulted in sustained HBV clearance inhibition, whereas phagocytic monocyte-derived macrophage and Kupffer cell elimination resulted in only transient inhibition of vaccine-induced HBV clearance. Conclusions We report the potential role of HBx as a major immunogen in an HBV therapeutic vaccine and the significance of a liver-infiltrating monocyte subset during hepatic viral clearance.
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- 2020
11. MicroRNA-31-5p regulates chemosensitivity by preventing the nuclear location of PARP1 in hepatocellular carcinoma
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Que, Ke-ting, Zhou, Yun, You, Yu, Zhang, Zhen, Zhao, Xiao-ping, Gong, Jian-ping, and Liu, Zuo-jin
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Hepatocellular carcinoma ,Research ,microRNA-31-5p ,PARP1 ,Chemosensitivity - Abstract
Background MicroRNAs (miRNAs) posttranscriptionally regulate gene expression and thereby contribute to the modulation of numerous complex and disease-relevant cellular processes, including cell proliferation, cell motility, apoptosis and stress response. miRNA-31-5p is encoded on a genomic fragile site, 9p21.3, which is reportedly lost in many hepatocellular carcinoma (HCC) tumors. Based on previous findings, we hypothesized that miR-31-5p alters chemosensitivity and that miR-31-5p mimics may influence sensitivity to chemotherapeutics in HCC as well as in a variety of other cancers. Methods MiR-31-5p and PARP1 in HCC tissues were tested by RT-PCR and histological analysis, respectively. Next, clonogenic assay and western blot were used to detect miR-31-5p and PARP1 to modulate sensitivity to OXA-based chemotherapy. The distribution of OXA in the nuclear and intracellular was detected by ICP-MS. Coimmunoprecipitation was used to characterize the protein-protein interaction between PARP1 and ABCB9. A xenograft nude mouse model was used to examine the in vivo effects of miR-31-5p. Results Reintroduction of miR-31-5p into miR-31-5p-null Hep3B cells significantly enhanced clonogenic resistance to oxaliplatin. Although miR-31-5p re-expression increased chemoresistance, it paradoxically increased the relative intracellular accumulation of oxaliplatin. This effect was coupled with a significantly decreased intranuclear concentration of oxaliplatin by ICP-MS. miR-31-5p prevents the nuclear location of PARP1 detected by immunofluorescence, histological analysis and Western blotting analysis. We subsequently identified an indirect miR-31-5p-mediated upregulation of ABCB9, which is a transporter associated with drug accumulation in lysosomes, along with an increased uptake of oxaliplatin to lysosomes; these phenomena were associated with a downregulation of PARP1, a bipotential transcriptional regulator with multiple miR-31-5p binding sites. However, the indirect overexpression of ABCB9 promoted cellular chemosensitivity, suggesting that miR-31-5p promotes chemoresistance largely via an ABCB9-independent mechanism. Conclusions Overall, our data suggest that the loss of miR-31-5p from HCC tumors promotes chemosensitivity, and this knowledge may be prognostically beneficial in the context of therapeutic sensitivity. Electronic supplementary material The online version of this article (10.1186/s13046-018-0930-0) contains supplementary material, which is available to authorized users.
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- 2018
12. Signature of circular RNAs in human induced pluripotent stem cells and derived cardiomyocytes
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Zhen-Ao Zhao, Wei Lei, Xing Fang, Junjie Yang, Junwei Liu, Zhenya Shen, Wenbo Deng, Shijun Hu, Tingting Feng, and You Yu
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0301 basic medicine ,Gene isoform ,Cardiomyopathy, Dilated ,Calcium Channels, L-Type ,Induced Pluripotent Stem Cells ,Medicine (miscellaneous) ,Cardiomyocyte ,030204 cardiovascular system & hematology ,Biology ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Sodium-Calcium Exchanger ,lcsh:Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Circular RNA ,Humans ,lcsh:QD415-436 ,Myocytes, Cardiac ,Human Induced Pluripotent Stem Cells ,Induced pluripotent stem cell ,Cells, Cultured ,Adaptor Proteins, Signal Transducing ,lcsh:R5-920 ,Research ,Wnt signaling pathway ,RNA ,Cell Differentiation ,Cell Biology ,RNA, Circular ,Non-coding RNA ,Cell biology ,030104 developmental biology ,Molecular Medicine ,Stem cell ,lcsh:Medicine (General) ,Protein Kinases ,Biomarkers - Abstract
Background Circular RNAs (circRNAs) are regarded as a novel class of noncoding RNA regulators. Although a number of circRNAs have been identified by bioinformatics analysis of RNA-seq data, tissue and disease-specific circRNAs are still to be uncovered to promote their application in basic research and clinical practice. The purpose of this study was to explore the circRNA profiles in human induced pluripotent stem cells (hiPSCs) and hiPSC-derived cardiomyocytes (hiPSC-CMs), and to identify cardiac or disease-specific circRNAs. Methods hiPSCs were generated from fibroblasts, and then further differentiated to hiPSC-CMs by modulating WNT signaling in RPMI+B27 medium. Following high-throughput RNA sequencing, circRNAs were extracted and quantified by a combined strategy known as CIRCexplorer. Integrative analysis was performed to illuminate the correlation between circRNAs and their parental linear isoforms. Cardiac and disease-specific expression of circRNAs was confirmed by quantitative reverse-transcription PCR. Results In this study, a total of 5602 circRNAs were identified in hiPSCs and hiPSC-CMs. Our data indicated, for the first time, more enriched expression of circRNAs in differentiated cardiomyocytes than in undifferentiated hiPSCs. In addition to the host gene-dependent expression, our integrative analysis also identified a number of circRNAs showing host gene-independent expression in hiPSCs and hiPSC-CMs. CircRNAs including circSLC8A1, circCACNA1D, circSPHKAP and circALPK2 showed cardiac-selective expression during cardiac differentiation and human heart-specific enrichment in fetal tissues. Furthermore, circSLC8A1 abnormally increased in heart tissues from patients suffering from dilated cardiomyopathy. Conclusions CircRNAs are highly enriched in hiPSC-differentiated CMs, and cardiac-specific circRNAs such as circSLC8A1, circCACNA1D, circSPHKAP and circALPK2 may serve as biomarkers of CMs. Detection of the excessive expression of circSLC8A1 provides a potential approach for pathological status indication of heart disease. Electronic supplementary material The online version of this article (10.1186/s13287-018-0793-5) contains supplementary material, which is available to authorized users.
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- 2018
13. Efficacy and safety of Qing-Feng-Gan-Ke Granules in patients with postinfectious cough: study protocol of a novel-design phase III placebo-controlled, double-blind randomized trial
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Wei Liu, Liangji Liu, Su-yun Li, Hongli Jiang, Yunqing Zhong, Faguang Jin, Bing Mao, You-yu Long, Rui-ming Zhang, and Liying Cui
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Adult ,medicine.medical_specialty ,Adolescent ,MEDLINE ,Traditional Chinese medicine ,Placebo ,law.invention ,Study Protocol ,Young Adult ,Randomized controlled trial ,law ,Medicine ,Humans ,Young adult ,Montelukast ,Aged ,business.industry ,General Medicine ,Middle Aged ,Clinical trial ,Clinical research ,Complementary and alternative medicine ,Cough ,Physical therapy ,business ,medicine.drug ,Drugs, Chinese Herbal - Abstract
Postinfectious cough (PIC) is a common condition that affects millions of people worldwide every year. There is Western medicine for this condition but the treatment effect is often incomplete. Traditional Chinese medicine (TCM) has been increasingly prescribed for patients with PIC. Preliminary trials on Qing-Feng-Gan-Ke-Granules (QFGKG) conveyed promising results in treating PIC. This protocol describes an ongoing phase III randomized controlled clinical trial, designed according to a novel methodology of “one study, one primary outcome”, with the objective of evaluating the efficacy and safety of QFGKG in patients suffering from PIC. This is a multicenter, phase III, randomized, double-blind, parallel-group, placebo-controlled clinical trial, comprising two simultaneously conducted study parts, part A and part B, intending to investigate two primary outcomes, i.e. time to cough resolution and cough symptom score, respectively. A total of 480 patients, aged 18 to 65 years, who complain of an ongoing persistent cough that has been lasting ≥3 weeks, will be recruited from six participating sites and then randomized to receive QFGKG 12.0 g twice daily or placebo 12.0 g twice daily. Each part will enroll 240 patients, with 180 patients being allocated to the QFGKG group and 60 to the placebo group. Although traditional Chinese medicine is a structured intervention that has shown some promise in treating persistent cough, existing unconvincing evidence has noted limitations. This is a rare well-designed and rigorously-controlled, randomized, double-blind trial to evaluate the effects and safety of a Chinese herbal medicine in patients with postinfectious cough, providing tangible benefits for clinical research. Results of this trial are inclined to be conjectured as more truthful by implementing separate study parts that specifically estimate exclusive primary outcome. It will not only provide robust clinical evidence on the efficacy and safety of QFGKG for postinfectious cough, but will also provide a critical piece of information on the availability and superiority of a novel methodology for future clinical trials. The current trial is ongoing with recruitment of the predetermined number of patients being in progress. The two parts of this trial were separately registered with the Chinese Clinical Trial Registry: ChiCTR-TRC-13003278 (part A); and ChiCTR-TRC-13003337 (part B).
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- 2015
14. Comparative analysis reveals the Genomic Islands in Pasteurella multocida population genetics: on Symbiosis and adaptability.
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Zhu, Dekang, He, Jiao, Yang, Zhishuang, Wang, Mingshu, Jia, Renyong, Chen, Shun, Liu, Mafeng, Zhao, Xinxin, Yang, Qiao, Wu, Ying, Zhang, Shaqiu, Liu, Yunya, Zhang, Ling, Yu, Yanling, You, Yu, Chen, Xiaoyue, and Cheng, Anchun
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GENOMICS ,PASTEURELLA multocida ,POPULATION genetics ,PATHOGENIC microorganisms ,BACTERIAL population ,PROTEINS - Abstract
Background: Pasteurella multocida (P. multocida) is a widespread opportunistic pathogen that infects human and various animals. Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria acquire large fragments of foreign genes. However, the effects of GIs on P. multocida are unknown in the evolution of bacterial populations. Results: Ten avian-sourced P. multocida obtained through high-throughput sequencing together with 104 publicly available P. multocida genomes were used to analyse their population genetics, thus constructed a pan-genome containing 3948 protein-coding genes. Through the pan-genome, the open evolutionary pattern of P. multocida was revealed, and the functional components of 944 core genes, 2439 accessory genes and 565 unique genes were analysed. In addition, a total of 280 GIs were predicted in all strains. Combined with the pan-genome of P. multocida, the GIs accounted for 5.8% of the core genes in the pan-genome, mainly related to functional metabolic activities; the accessory genes accounted for 42.3%, mainly for the enrichment of adaptive genes; and the unique genes accounted for 35.4%, containing some defence mechanism-related genes. Conclusions: The effects of GIs on the population genetics of P. multocida evolution and adaptation to the environment are reflected by the proportion and function of the pan-genome acquired from GIs, and the large quantities of GI data will aid in additional population genetics studies. [ABSTRACT FROM AUTHOR]
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- 2019
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15. Treatment and outcomes of tumor-induced osteomalacia associated with phosphaturic mesenchymal tumors: retrospective review of 12 patients.
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Qing-yao Zuo, Hong Wang, Wei Li, Xiao-hui Niu, Yan-hong Huang, Jia Chen, Yu-hua You, Bao-yue Liu, Ai-min Cui, Wei Deng, Zuo, Qing-Yao, Wang, Hong, Li, Wei, Niu, Xiao-Hui, Huang, Yan-Hong, Chen, Jia, You, Yu-Hua, Liu, Bao-Yue, Cui, Ai-Min, and Deng, Wei
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HEALTH outcome assessment ,OSTEOMALACIA ,VITAMIN D deficiency ,RETROSPECTIVE studies ,HYPOPHOSPHATEMIA ,THERAPEUTICS ,LONGITUDINAL method ,PARANEOPLASTIC syndromes ,PHOSPHATES ,SOFT tissue tumors ,TREATMENT effectiveness ,CONNECTIVE tissue tumors - Abstract
Background: Tumor-induced osteomalacia (TIO) is a rare paraneoplastic syndrome characterized by severe hypophosphatemia and osteomalacia. Nonspecific symptoms make the diagnosis elusive. In addition, locating the responsible tumor(s) is challenging. The aim of this study was to investigate the clinical management and outcomes of TIO.Methods: The clinical features, diagnostic procedures, treatment, and outcomes of 12 patients were reviewed retrospectively.Results: The cohort comprised six men and six women (mean age 45.5 ± 9.9 years, range 23-61 years). The mean duration of disease was 3.7 ± 2.6 years. All patients manifested progressive bone pain, muscle weakness, and/or difficulty walking. Serum phosphorus concentrations were low in all patients (mean 0.42 ± 0.12 mmol/L). Technetium-99m octreotide scintigraphy was performed in 11 patients and showed lesions in the right distal femur, left femoral head, and right tibial plateau, respectively, in three patients. Magnetic resonance imaging (MRI) was negative for lesions in one patient. Two patients underwent biopsies that showed negative histopathology. Two patients, at 2 years and 8 months, respectively, after having negative technetium-99m octreotide studies, underwent 18F-fluorodeoxyglucose positron emission tomography/computed tomography (CT), which revealed lesions in the sacrum and soft tissue of the left palm, respectively. One tumor was detected by CT and MRI. Overall, lesion sites were the head (two patients, 16.7%), thoracic and lumbar region (two, 16.7%), pelvis (three, 25%), lower limbs (four, 33.3%), and upper limbs (one, 8.3%). All patients underwent surgery, and histopathology showed phosphaturic mesenchymal tumors in each. Postoperatively, serum phosphorus concentrations normalized within 2-7 days in 11 patients. With follow-ups of 1-41 months, surgery was effective in 10 patients. One patient developed local recurrence and another had metastases.Conclusions: Locating tumors responsible for tumor-induced osteomalacia is often challenging. Although complete tumor resection confers a good prognosis in most patients, surveillance for recurrence and metastasis is necessary. Before surgery or when surgery is not indicated, oral phosphate can alleviate symptoms and metabolic imbalance. [ABSTRACT FROM AUTHOR]- Published
- 2017
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16. De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.
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You-Yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen, and Hurng-Yi Wang
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METAGENOMICS , *HEPATITIS B virus , *GENETIC polymorphisms , *NUCLEOTIDES , *ALGORITHMS - Abstract
Background: The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data. Results: In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods. Conclusions: Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies. [ABSTRACT FROM AUTHOR]
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- 2017
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17. Does training improve diagnostic accuracy and inter-rater agreement in applying the Berlin radiographic definition of acute respiratory distress syndrome? A multicenter prospective study.
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Jin-Min Peng, Chuan-Yun Qian, Xiang-You Yu, Ming-Yan Zhao, Shu-Sheng Li, Xiao-Chun Ma, Yan Kang, Fa-Chun Zhou, Zhen-Yang He, Tie-He Qin, Yong-Jie Yin, Li Jiang, Zhen-Jie Hu, Ren-Hua Sun, Jian-Dong Lin, Tong Li, Da-Wei Wu, You-Zhong An, Yu-Hang Ai, and Li-Hua Zhou
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CHEST X rays ,CLINICAL competence ,CLINICAL trials ,COMPARATIVE studies ,LONGITUDINAL method ,RESEARCH methodology ,MEDICAL cooperation ,RESEARCH ,RESEARCH evaluation ,ADULT respiratory distress syndrome ,EVALUATION research ,TEACHING ,RESEARCH bias ,DIAGNOSIS ,STANDARDS - Abstract
Background: Poor inter-rater reliability in chest radiograph interpretation has been reported in the context of acute respiratory distress syndrome (ARDS), although not for the Berlin definition of ARDS. We sought to examine the effect of training material on the accuracy and consistency of intensivists' chest radiograph interpretations for ARDS diagnosis.Methods: We conducted a rater agreement study in which 286 intensivists (residents 41.3%, junior attending physicians 35.3%, and senior attending physician 23.4%) independently reviewed the same 12 chest radiographs developed by the ARDS Definition Task Force ("the panel") before and after training. Radiographic diagnoses by the panel were classified into the consistent (n = 4), equivocal (n = 4), and inconsistent (n = 4) categories and were used as a reference. The 1.5-hour training course attended by all 286 intensivists included introduction of the diagnostic rationale, and a subsequent in-depth discussion to reach consensus for all 12 radiographs.Results: Overall diagnostic accuracy, which was defined as the percentage of chest radiographs that were interpreted correctly, improved but remained poor after training (42.0 ± 14.8% before training vs. 55.3 ± 23.4% after training, p < 0.001). Diagnostic sensitivity and specificity improved after training for all diagnostic categories (p < 0.001), with the exception of specificity for the equivocal category (p = 0.883). Diagnostic accuracy was higher for the consistent category than for the inconsistent and equivocal categories (p < 0.001). Comparisons of pre-training and post-training results revealed that inter-rater agreement was poor and did not improve after training, as assessed by overall agreement (0.450 ± 0.406 vs. 0.461 ± 0.575, p = 0.792), Fleiss's kappa (0.133 ± 0.575 vs. 0.178 ± 0.710, p = 0.405), and intraclass correlation coefficient (ICC; 0.219 vs. 0.276, p = 0.470).Conclusions: The radiographic diagnostic accuracy and inter-rater agreement were poor when the Berlin radiographic definition was used, and were not significantly improved by the training set of chest radiographs developed by the ARDS Definition Task Force.Trial Registration: The study was registered at ClinicalTrials.gov (registration number NCT01704066 ) on 6 October 2012. [ABSTRACT FROM AUTHOR]- Published
- 2017
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18. Comparative genomic analysis between newly sequenced Brucella suis Vaccine Strain S2 and the Virulent Brucella suis Strain 1330.
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Dong-dong Di, Hai Jiang, Li-li Tian, Jing-li Kang, Wen Zhang, Xin-ping Yi, Feng Ye, Qi Zhong, Bo Ni, You-yu He, Lin Xia, Yao Yu, Bu-yun Cui, Xiang Mao, and Wei-xing Fan
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GENOMICS ,BRUCELLA suis ,BRUCELLOSIS ,VACCINES ,NUCLEOTIDE sequencing - Abstract
Background: Brucellosis is a bacterial disease caused by Brucella infection. In the late fifties, Brucella suis vaccine strain S2 with reduced virulence was obtained by serial transfer of a virulent B. suis biovar 1 strain in China. It has been widely used for vaccination in China since 1971. Until now, the mechanisms underlie virulence attenuation of S2 are still unknown. Results: In this paper, the whole genome sequencing of S2 was carried out by Illumina Hiseq2000 sequencing method. We further performed the comparative genomic analysis to find out the differences between S2 and the virulent Brucella suis strain 1330. We found premature stops in outer membrane autotransporter omaA and eryD genes. Single mutations were found in phosphatidylcholine synthase, phosphorglucosamine mutase, pyruvate kinase and FliF, which have been reported to be related to the virulence of Brucella or other bacteria. Of the other different proteins between S2 and 1330, such as Omp2b, periplasmic sugar-binding protein, and oligopeptide ABC transporter, no definitive implications related to bacterial virulence were found, which await further investigation. Conclusions: The data presented here provided the rational basis for designing Brucella vaccines that could be used in other strains. [ABSTRACT FROM AUTHOR]
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- 2016
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19. BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori.
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Qiu-Zhong Zhou, Bindan Zhang, Quan-You Yu, and Ze Zhang
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NON-coding RNA ,EUKARYOTES ,RNA sequencing ,SILKWORMS ,MICRORNA - Abstract
Background: Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori). Description: In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. Conclusions: We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. [ABSTRACT FROM AUTHOR]
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- 2016
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20. Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon
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Chu Fang Lo, Guang Hsiung Kou, Ming Chen, En Min You, Gwo Chin Ma, Hung Yu Shu, You Yu Lin, Shiao Wei Huang, Dongying Wu, Tze Tze Liu, Takashi Aoki, Hon-Tsen Yu, Shih-Feng Tsai, Keh Ming Wu, and Ikuo Hirono
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lcsh:QH426-470 ,lcsh:Biotechnology ,Retrotransposon ,Genome ,Penaeus monodon ,Open Reading Frames ,Penaeidae ,lcsh:TP248.13-248.65 ,Genetics ,Animals ,Genome size ,Genomic organization ,Genomic Library ,biology ,Base Sequence ,Genomics ,Sequence Analysis, DNA ,biology.organism_classification ,Shrimp ,Fosmid ,lcsh:Genetics ,Microsatellite ,Female ,Biotechnology ,Research Article ,Microsatellite Repeats ,Plasmids - Abstract
Background The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses. Results We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome. Conclusions The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.
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- 2011
21. Single cell transcriptome analysis upon MCF-7 breast cancer
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Yu-Chang Su, Tzu-Han Chen, Hong-Chih Kuo, Lock Ying Seng, Shih-Hao Chen, Chung-Hsuan Chen, You-Yu Lin, Kuo Ping Chiu, and Yih-Shien Chiang
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Genetics ,education.field_of_study ,Population ,Cancer ,Computational biology ,Epigenome ,Biology ,medicine.disease ,Human genetics ,Transcriptome ,Breast cancer ,MCF-7 ,Cancer cell ,Poster Presentation ,medicine ,education ,human activities - Abstract
Background During cancer progression, the genome and epigenome of each cancer cell mutate constantly, leading to a diverse transcriptome in a cancer tissue. Such diversity results in variations in drug response among individual cancer cells and is responsible for poor prognosis. It is therefore important to reveal the diversity in the transcriptome profiles of single cancer cells, in order to further understand how the diversified cancer cells interplay to make a cancer cell population capable of escaping immune surveillance and respond poorly to drug treatment. Materials and methods Here, we adopt the recently published single cell transcriptome (SCT) analysis protocol and evaluate its reliability using RNA- seq approach on analysis of housekeeping (HK) gene expression as a control, and describe four SCT libraries and one 5,000-cell transcriptome library generated from MCF-7 breast cancer cells. Results
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- 2010
22. Characterization of 13 multi-drug resistant Salmonella serovars from different broiler chickens associated with those of human isolates
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Lan-Ho Chiu, Chien-Shun Chiou, Chean-Ping Wu, Chao-Chin Chang, Cheng-Hsun Chiu, Chang-You Yu, Chien-Yu Lee, Yan-Ming Horn, Chishih Chu, and Chia-Ming Yeh
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Serotype ,Microbiology (medical) ,Salmonella ,animal structures ,Tetracycline ,lcsh:QR1-502 ,Microbial Sensitivity Tests ,Biology ,medicine.disease_cause ,Microbiology ,lcsh:Microbiology ,H-2 Antigens ,Cloaca ,Ampicillin ,Drug Resistance, Multiple, Bacterial ,Research article ,medicine ,Enrofloxacin ,Prevalence ,Animals ,Humans ,Serotyping ,Poultry Diseases ,Antigens, Bacterial ,Salmonella Infections, Animal ,Virology ,Anti-Bacterial Agents ,Electrophoresis, Gel, Pulsed-Field ,Parasitology ,embryonic structures ,Salmonella Infections ,Bacterial antigen ,Chickens ,medicine.drug - Abstract
Background Salmonella are frequently isolated from chickens and their products. Prevalent serogroups and serovars of Salmonella as well as their genotypes and antibiograms were determined for cloacal samples from 1595 chickens. To understand the possible serovar and H antigens for transmission between chicken and human, serovars and their H antigens of 164 chicken and 5314 human isolates were compared. Results Prevalence of Salmonella differed among chicken lines and ages. Chicken and human isolates belonged mainly to serogroup B, C1, C2-C3, D, and E. 13 serovars and 66 serovars were identified for chicken and human isolates respectively. The common serovars for chicken and human isolates were S. Typhimurium, S. Enteritidis, S. Albany, S. Derby, and S. Anatum and shared common H1 antigens "g complex; i; e,h; and z4,z24" and H2 antigens "1 complex and -". In human isolates, H1 antigen "i" and H2 antigen "-" were common in all serogroups. In chicken, antimicrobial susceptibility differed among serogroups, serovars and three counties. All isolates were susceptible to cefazolin and ceftriaxone, but highly resistant to ampicillin, chloramphenicol, flumequine, streptomycin, sulfamethoxazole-trimethoprim, and tetracycline. Except those isolates of serogroup C1 of Chick group and serogroup G, all isolates were multi-drug resistance. Only S. Kubacha, S. Typhimurium, S. Grampian, and S. Mons were resistant to ciprofloxacin and/or enrofloxacin. Conclusion In chicken, prevalent serogroups and serovars were associated with chicken ages, lines and regions; and flouroquinolone-resistant and MDR isolates emerged. H1 antigens "g complex and i" and H2 antigens "1 complex and -" might be important for transmission of Salmonella between chicken and human.
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- 2010
23. The small heat shock protein (sHSP) genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genes
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Zhong-Huai Xiang, Quan-You Yu, Xue-zhi Li, Hirohisa Kishino, Ze Zhang, and Zi-Wen Li
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Insecta ,Evolution ,Molecular Sequence Data ,Sequence alignment ,Genes, Insect ,Genome ,Evolution, Molecular ,Phylogenetics ,Bombyx mori ,Heat shock protein ,QH359-425 ,Animals ,Amino Acid Sequence ,Heat shock ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Bombyx ,Genetics ,biology ,fungi ,biology.organism_classification ,Heat-Shock Proteins, Small ,Drosophila melanogaster ,Sequence Alignment ,Research Article - Abstract
Background Small heat shock proteins (sHSPs) are products of heat shock response and of other stress responses, and ubiquitous in all three domains of life, archaea, bacteria, and eukarya. They mainly function as molecular chaperones to protect proteins from being denatured in extreme conditions. Study on insect sHSPs could provide some insights into evolution of insects that have adapted to diverse niches in the world. Results Taking advantage of the newly assembled genome sequence, we performed a genome-wide analysis of the candidate sHSP genes in the silkworm, Bombyx mori. Based on known silkworm sHSP sequences, we identified 16 silkworm sHSP genes. Most of them are distributed on two silkworm chromosomes 5 and 27, respectively. 15 of 16 silkworm sHSPs have expression evidence. The comparative analysis of insect sHSPs from B. mori, Drosophila melanogaster, Apis mellifera, Tribolium castaneum, and Anopheles gambiae revealed that there is only one orthologous cluster whereas remaining clusters are species-specific on the phylogenetic tree. This suggested that most of sHSPs might have diverged in function across insects investigated. In addition, the data presented in this study also revealed that sHSPs in the insect orthologous cluster are highly conserved in both sequence and expression pattern. In sum, insect sHSPs show a completely different evolutionary pattern from that found in vertebrate sHSPs. Conclusion B. mori has the largest number of insect sHSP genes characterized to date, including 16 genes. The inference that most species-specific sHSPs might have diverged in function across insects investigated will help us understand the adaptability of these insects to diverse environments.
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- 2009
24. Comparative analysis of the silk gland transcriptomes between the domestic and wild silkworms.
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Shou-Min Fang, Bi-Li Hu, Qiu-Zhong Zhou, Quan-You Yu, and Ze Zhang
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SILKWORMS ,PROTEIN synthesis ,GENE expression ,GENOMICS ,BIOLOGICAL adaptation - Abstract
Background: Bombyx mori was domesticated from the Chinese wild silkworm, Bombyx mandarina. Wild and domestic silkworms are good models in which to investigate genes related to silk protein synthesis that may be differentially expressed in silk glands, because their silk productions are very different. Here we used the mRNA deep sequencing (RNA-seq) approach to identify the differentially expressed genes (DEGs) in the transcriptomes of the median/posterior silk glands of two domestic and two wild silkworms. Results: The results indicated that about 58% of the total genes were expressed (reads per kilo bases per million reads (RPKM) ≥ 1) in each silkworm. Comparisons of the domestic and wild silkworm transcriptomes revealed 32 DEGs, of which 16 were up-regulated in the domestic silkworms compared with in the wild silkworms, and the other 16 were up-regulated in the wild silkworms compared with in the domestic silkworms. Quantitative real-time polymerase chain reaction (qPCR) was performed for 15 randomly selected DEGs in domestic versus wild silkworms. The qPCR results were mostly consistent with the expression levels determined from the RNA-seq data. Based on a Gene Ontology (GO) enrichment analysis and manual annotation, five of the up-regulated DEGs in the wild silkworms were predicted to be involved in immune response, and seven of the up-regulated DEGs were related to the GO term "oxidoreductase activity", which is associated with antioxidant systems. In the domestic silkworms, the up-regulated DEGs were related mainly to tissue development, secretion of proteins and metabolism. Conclusions: The up-regulated DEGs in the two domestic silkworms may be involved mainly in the highly efficient biosynthesis and secretion of silk proteins, while the up-regulated DEGs in the two wild silkworms may play more important roles in tolerance to pathogens and environment adaptation. Our results provide a foundation for understanding the molecular mechanisms of the silk production difference between domestic and wild silkworms. [ABSTRACT FROM AUTHOR]
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- 2015
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25. Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon.
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Shiao-Wei Huang, You-Yu Lin, En-Min You, Tze-Tze Liu, Hung-Yu Shu, Keh-Ming Wu, Shih-Feng Tsai, Chu-Fang Lo, Guang-Hsiung Kou, Gwo-Chin Ma, Ming Chen, Dongying Wu, Takashi Aoki, Ikuo Hirono, and Hon-Tsen Yu
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PENAEUS monodon , *SHRIMPS , *GENOMICS , *GENE libraries , *NUCLEOTIDE sequence - Abstract
Background: The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses. Results: We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self- BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained proteincoding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome. Conclusions: The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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26. High prevalence of plasmid-mediated 16S rRNAmethylase gene rmtB among Escherichia coliclinical isolates from a Chinese teaching hospital.
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Fang-you Yu, Dan Yao, Jing-ye Pan, Chong Chen, Zhi-qiang Qin, Parsons, Chris, Le-he Yang, Qiao-qiao Li, Xueqing Zhang, Di Qu, and Liang-xing Wang
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RNA , *METHYLTRANSFERASES , *AMINOGLYCOSIDES , *ESCHERICHIA coli , *GENES - Abstract
Background: Recently, production of 16S rRNA methylases by Gram-negative bacilli has emerged as a novel mechanism for high-level resistance to aminoglycosides by these organisms in a variety of geographic locations. Therefore, the spread of high-level aminoglycoside resistance determinants has become a great concern. Methods: Between January 2006 and July 2008, 680 distinct Escherichia coli clinical isolates were collected from a teaching hospital in Wenzhou, China. PCR and DNA sequencing were used to identify 16S rRNA methylase and extended-spectrum β-lactamase (ESBL) genes, including armA and rmtB, and in situ hybridization was performed to determine the location of 16S rRNA methylase genes. Conjugation experiments were subsequently performed to determine whether aminoglycoside resistance was transferable from the E. coli isolates via 16S rRNA methylase-bearing plasmids. Homology of the isolates harboring 16S rRNA methylase genes was determined using pulse-field gel electrophoresis (PFGE). Results: Among the 680 E. coli isolates, 357 (52.5%), 346 (50.9%) and 44 (6.5%) isolates were resistant to gentamicin, tobramycin and amikacin, respectively. Thirty-seven of 44 amikacin-resistant isolates harbored 16S rRNA methylase genes, with 36 of 37 harboring the rmtB gene and only one harboring armA. The positive rates of 16S rRNA methylase genes among all isolates and amikacin-resistant isolates were 5.4% (37/680) and 84.1% (37/44), respectively. Thirty-one isolates harboring 16S rRNA methylase genes also produced ESBLs. In addition, high-level aminoglycoside resistance could be transferred by conjugation from four rmtB-positive donors. The plasmids of incompatibility groups IncF, IncK and IncN were detected in 34, 3 and 3 isolates, respectively. Upstream regions of the armA gene contained ISCR1 and tnpU, the latter a putative transposase gene,. Another putative transposase gene, tnpD, was located within a region downstream of armA. Moreover, a transposon, Tn3, was located upstream of the rmtB. Nineteen clonal patterns were obtained by PFGE, with type H representing the prevailing pattern. Conclusion: A high prevalence of plasmid-mediated rmtB gene was found among clinical E. coli isolates from a Chinese teaching hospital. Both horizontal gene transfer and clonal spread were responsible for the dissemination of the rmtB gene. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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27. Molecular characterization of Staphylococus aureus isolates causing skin and soft tissue infections (SSTIs).
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Dan Yao, Fang-you Yu, Zhi-qiang Qin, Chun Chen, Su-su He, Zeng-qiang Chen, Xue-qing Zhang, and Liang-xing Wang
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- *
STAPHYLOCOCCUS aureus infections , *DRUG resistance in microorganisms , *SOFT tissue injuries , *SKIN diseases - Abstract
Background: Staphylococcus aureus, particularly methicillin-resistant S. aureus (MRSA), is an important cause of pyogenic skin and soft tissue infections (SSTIs). The aim of present study is to investigate the molecular characteristic of Staphylococcus aureus isolates isolated from the pus samples from the patients with purulent skin and soft tissue infections in Wenzhou, China. Methods: Between December 2002 and June 2008, a total of 111 nonduplicate S. aureus isolates were collected from the pus samples of the patients with SSTIs in a teaching hospital in Wenzhou, China. All the tested isolates were confirmed as S. aureus using a Staph SPA agglutination kit, Gram's stain and a Vitek-60 microbiology analyzer. The homology among the tested isolates was determined by pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing (MLST) was used to determine the sequence types (STs) of the selected isolates. The genotypes of SCCmec were determined by a multiplex PCR in the MRSA isolates. Panton-Valentine leukocidin (PVL) genes and mecA were also determined by another multiplex PCR. Results: Among the 111 S. aureus isolates, 48 and 63 isolates were community-acquired and hospital-acquired respectively. Sixty isolates were confirmed as MRSA harboring mecA detected by PCR. A total of 32 PFGE clonal types were obtained by PFGE, with 10 predominant patterns (types A to J). Twenty-five different STs including ST398 and three novel STs were found among 51 selected isolates. The main STs were ST239, ST1018, ST59, ST7 and ST88. Of 60 MRSA isolates, SCCmec II, III, IV and SCCmec V were found in three, 50, three and two isolates, respectively. The positive rates of PVL genes in overall isolates, HA-isolates, CA-isolates, MRSA isolates and MSSA isolates were 23.4% (26/111), 20.6% (13/63), 27.1% (13/48), 21.7% (13/60) and 25.5% (13/51), respectively. Eight (33.3%, 8/24) of 24 CA-MRSA isolates and 5 (13.9%, 5/36) of 36 HA-MRSA isolates were positive for PVL genes. ST239-MRSA-SCCmecIII and ST1018-MRSASCCmecIII clones were found to be main clones and spread between community and hospital. Conclusion: S. aureus isolates causing SSTIs showed considerable molecular heterogeneity and harbored high prevalence of PVL genes. Clonal spread was responsible for the dissemination of the isolates of S. aureus associated with SSTIs. [ABSTRACT FROM AUTHOR]
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- 2010
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28. Annotation and expression of carboxylesterases in the silkworm, Bombyx mori.
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Quan-You Yu, Cheng Lu, Wen-Le Li, Zhong-Huai Xiang, and Ze Zhang
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- *
GENE expression , *XENOBIOTICS , *GENOMES , *METABOLITES , *SILKWORMS - Abstract
Background: Carboxylesterase is a multifunctional superfamily and ubiquitous in all living organisms, including animals, plants, insects, and microbes. It plays important roles in xenobiotic detoxification, and pheromone degradation, neurogenesis and regulating development. Previous studies mainly used Dipteran Drosophila and mosquitoes as model organisms to investigate the roles of the insect COEs in insecticide resistance. However, genome-wide characterization of COEs in phytophagous insects and comparative analysis remain to be performed. Results: Based on the newly assembled genome sequence, 76 putative COEs were identified in Bombyx mori. Relative to other Dipteran and Hymenopteran insects, alpha-esterases were significantly expanded in the silkworm. Genomics analysis suggested that BmCOEs showed chromosome preferable distribution and 55% of which were tandem arranged. Sixty-one BmCOEs were transcribed based on cDNA/ESTs and microarray data. Generally, most of the COEs showed tissue specific expressions and expression level between male and female did not display obvious differences. Three main patterns could be classified, i.e. midgut-, head and integument-, and silk gland-specific expressions. Midgut is the first barrier of xenobiotics peroral toxicity, in which COEs may be involved in eliminating secondary metabolites of mulberry leaves and contaminants of insecticides in diet. For head and integument-class, most of the members were homologous to odorant-degrading enzyme (ODE) and antennal esterase. RT-PCR verified that the ODE-like esterases were also highly expressed in larvae antenna and maxilla, and thus they may play important roles in degradation of plant volatiles or other xenobiotics. Conclusion: B. mori has the largest number of insect COE genes characterized to date. Comparative genomic analysis suggested that the gene expansion mainly occurred in silkworm alpha-esterases. Expression evidence indicated that the expanded genes were specifically expressed in midgut, integument and head, implying that these genes may have important roles in detoxifying secondary metabolites of mulberry leaves, contaminants in diet, and odorants. Our results provide some new insights into functions and evolutionary characteristics of COEs in phytophagous insects. [ABSTRACT FROM AUTHOR]
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- 2009
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29. Region- or state-related differences in expression and activation of extracellular signal-regulated kinases (ERKs) in naïve and pain-experiencing rats.
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She-Wei Guo, Ming-Gang Liu, Ya-Li Long, Li-Ying Ren, Zhuo-Min Lu, Hou-You Yu, Jun-Feng Hou, Hua Li, Cui-Ying Gao, Xiu-Yu Cui, Yang-Yuan An, Junfa Li, Lan-Feng Zhao, and Jun Chen
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MITOGEN-activated protein kinases ,PROTEIN kinases ,NEUROPLASTICITY ,DEVELOPMENTAL neurobiology ,EVOKED potentials (Electrophysiology) ,MEDICAL sciences - Abstract
Background: Extracellular signal-regulated kinase (ERK), one member of the mitogen-activated protein kinase (MAPK) family, has been suggested to regulate a diverse array of cellular functions, including cell growth, differentiation, survival, as well as neuronal plasticity. Recent evidence indicates a role for ERKs in nociceptive processing in both dorsal root ganglion and spinal cord. However, little literature has been reported to examine the differential distribution and activation of ERK isoforms, ERK1 and ERK2, at different levels of pain-related pathways under both normal and pain states. In the present study, quantitative blot immunolabeling technique was used to determine the spatial and temporal expression of ERK1 and ERK2, as well as their activated forms, in the spinal cord, primary somatosensory cortex (SI area of cortex), and hippocampus under normal, transient pain and persistent pain states. Results: In naïve rats, we detected regional differences in total expression of ERK1 and ERK2 across different areas. In the spinal cord, ERK1 was expressed more abundantly than ERK2, while in the SI area of cortex and hippocampus, there was a larger amount of ERK2 than ERK1. Moreover, phosphorylated ERK2 (pERK2), not phosphorylated ERK1 (pERK1), was normally expressed with a high level in the SI area and hippocampus, but both pERK1 and pERK2 were barely detectable in normal spinal cord. Intraplantar saline or bee venom injection, mimicking transient or persistent pain respectively, can equally initiate an intense and long-lasting activation of ERKs in all three areas examined. However, isoform-dependent differences existed among these areas, that is, pERK2 exhibited stronger response than pERK1 in the spinal cord, whereas ERK1 was more remarkably activated than ERK2 in the S1 area and hippocampus. Conclusion: Taken these results together, we conclude that: (1) under normal state, while ERK immunoreactivity is broadly distributed in the rat central nervous system in general, the relative abundance of ERK1 and ERK2 differs greatly among specific regions; (2) under pain state, either ERK1 or ERK2 can be effectively phosphorylated with a long-term duration by both transient and persistent pain, but their response patterns differ from each other across distinct regions; (3) The long-lasting ERKs activation induced by bee venom injection is highly correlated with our previous behavioral, electrophysiological, morphological and pharmacological observations, lending further support to the functional importance of ERKs-mediated signaling pathways in the processing of negative consequences of pain associated with sensory, emotional and cognitive dimensions. [ABSTRACT FROM AUTHOR]
- Published
- 2007
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30. Difference in long-term relapse rates between youths with ketamine use and those with stimulants use.
- Author
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Wang, Liang-Jen, Chen, Mei-Yen, Lin, Chin-Yin, Chong, Mian-Yoon, Chou, Wen-Jiun, You, Yu-Han, Tsai, Chih-Pu, Chen, Yi-Syuan, and Lu, Shing-Fang
- Abstract
Background: Understanding the relapse risk among different illicit drugs is vital for developing an adequate relapse prevention policy. Therefore, the current study aims to explore the potential difference in long-term relapse rates between youths who use ketamine and those who use stimulants (3,4-Methylenedioxymethamphetamine [MDMA] or methamphetamine).Methods: The study's participants included 92 youths with ketamine use (ketamine group, mean age: 16.0 years) and 43 youths with MDMA/methamphetamine use (stimulants group, mean age: 16.1 years) that had undergone a family-oriented treatment program in a medical center in Taiwan. All participants were followed up for a maximum of 7 years in order to observe their long-term outcomes with regard to substance use relapse.Results: During the follow-up period, compared to the 34.8% relapse rate in ketamine users, their counterparts who used MDMA or methamphetamine had a significantly higher relapse rate (60.5%, Adjusted HR = 1.86, 95%CI: 1.06-3.28, p = 0.032). Of the youths in the ketamine group that relapsed, 65.6% continued to use ketamine in their relapse event, while 34.4% switched to MDMA or methamphetamine. Among the relapsing youths in the stimulants group, 84.6% continued to use MDMA or methamphetamine in their relapse event, while 15.4% switched to ketamine (p = 0.042).Conclusions: Compared to adolescents who use ketamine, those using MDMA or methamphetamine had higher relapse rates and were more likely to use the same type of drug upon relapsing. These results can serve as a crucial reference for developing relapse prevention policies of illicit drugs for the youth population. [ABSTRACT FROM AUTHOR]- Published
- 2018
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31. Combined treatment with bone marrow mesenchymal stem cells and methylprednisolone in paraquat-induced acute lung injury.
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Yang, Huang, Wen, Yin, Hou-You, Yu, Yu-Tong, Wang, Chuan-Ming, Liu, Jian, Xiong, and Lu, Hao
- Abstract
Background: To evaluate the efficacy of combined treatment with bone marrow mesenchymal stem cell (BMSC) transplantation and methylprednisolone (MP) to treat paraquat (PQ)-induced acute lung injury.Materials and Methods: A total of 102 female rats were randomly divided into five groups: PQ, BMSC, MP, BMSC + MP and normal control. After 14 days of PQ poisoning, the survival of rats, wet/dry weight ratio of lung tissue, serum levels of tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, IL-10, malondialdehyde (MDA) and superoxidase dismutase (SOD), and the expression of nuclear factor (NF)-кB p65 in lung tissue were determined.Results: Rats in BMSC and BMSC + MP groups survived. BMSC transplantation significantly decreased the wet/dry weight ratio of lung tissue, down-regulated NF-кB p65 expression in lung tissue, lowered serum levels of TNF-α, IL-1β, IL-6 and MDA, and increased serum levels of IL-10 and SOD. These changes were particularly significant on days 7-14 after PQ poisoning. The above changes were more significant in the MP group on days 1-3 after PQ poisoning, compared with those of the BMSC group. However, the BMSC + MP group showed more significant changes on days 1-14 after PQ poisoning than those of both BMSC and MP groups.Conclusions: MP inhibits the inflammatory response, reduces the products of lipid peroxidation and promotes survival of transplanted BMSC, thus improving the intermediate and longer term efficacy of BMSC transplantation for treatment of PQ-induced lung injury. [ABSTRACT FROM AUTHOR]- Published
- 2013
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32. Treatment and outcomes of tumor-induced osteomalacia associated with phosphaturic mesenchymal tumors: retrospective review of 12 patients.
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Zuo QY, Wang H, Li W, Niu XH, Huang YH, Chen J, You YH, Liu BY, Cui AM, and Deng W
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- Adult, Cohort Studies, Female, Follow-Up Studies, Humans, Hypophosphatemia blood, Hypophosphatemia surgery, Male, Middle Aged, Neoplasms, Connective Tissue blood, Neoplasms, Connective Tissue surgery, Osteomalacia blood, Osteomalacia diagnostic imaging, Osteomalacia surgery, Paraneoplastic Syndromes blood, Paraneoplastic Syndromes surgery, Phosphates blood, Retrospective Studies, Soft Tissue Neoplasms blood, Soft Tissue Neoplasms surgery, Treatment Outcome, Hypophosphatemia diagnostic imaging, Neoplasms, Connective Tissue diagnostic imaging, Paraneoplastic Syndromes diagnostic imaging, Soft Tissue Neoplasms diagnostic imaging
- Abstract
Background: Tumor-induced osteomalacia (TIO) is a rare paraneoplastic syndrome characterized by severe hypophosphatemia and osteomalacia. Nonspecific symptoms make the diagnosis elusive. In addition, locating the responsible tumor(s) is challenging. The aim of this study was to investigate the clinical management and outcomes of TIO., Methods: The clinical features, diagnostic procedures, treatment, and outcomes of 12 patients were reviewed retrospectively., Results: The cohort comprised six men and six women (mean age 45.5 ± 9.9 years, range 23-61 years). The mean duration of disease was 3.7 ± 2.6 years. All patients manifested progressive bone pain, muscle weakness, and/or difficulty walking. Serum phosphorus concentrations were low in all patients (mean 0.42 ± 0.12 mmol/L). Technetium-99m octreotide scintigraphy was performed in 11 patients and showed lesions in the right distal femur, left femoral head, and right tibial plateau, respectively, in three patients. Magnetic resonance imaging (MRI) was negative for lesions in one patient. Two patients underwent biopsies that showed negative histopathology. Two patients, at 2 years and 8 months, respectively, after having negative technetium-99m octreotide studies, underwent
18 F-fluorodeoxyglucose positron emission tomography/computed tomography (CT), which revealed lesions in the sacrum and soft tissue of the left palm, respectively. One tumor was detected by CT and MRI. Overall, lesion sites were the head (two patients, 16.7%), thoracic and lumbar region (two, 16.7%), pelvis (three, 25%), lower limbs (four, 33.3%), and upper limbs (one, 8.3%). All patients underwent surgery, and histopathology showed phosphaturic mesenchymal tumors in each. Postoperatively, serum phosphorus concentrations normalized within 2-7 days in 11 patients. With follow-ups of 1-41 months, surgery was effective in 10 patients. One patient developed local recurrence and another had metastases., Conclusions: Locating tumors responsible for tumor-induced osteomalacia is often challenging. Although complete tumor resection confers a good prognosis in most patients, surveillance for recurrence and metastasis is necessary. Before surgery or when surgery is not indicated, oral phosphate can alleviate symptoms and metabolic imbalance.- Published
- 2017
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33. De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.
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Lin YY, Hsieh CH, Chen JH, Lu X, Kao JH, Chen PJ, Chen DS, and Wang HY
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- DNA, Viral genetics, Hepatitis B virus genetics, High-Throughput Nucleotide Sequencing, Software, Algorithms, Metagenomics methods
- Abstract
Background: The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data., Results: In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods., Conclusions: Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies.
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- 2017
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34. Comparative genomic analysis between newly sequenced Brucella suis Vaccine Strain S2 and the Virulent Brucella suis Strain 1330.
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Di DD, Jiang H, Tian LL, Kang JL, Zhang W, Yi XP, Ye F, Zhong Q, Ni B, He YY, Xia L, Yu Y, Cui BY, Mao X, and Fan WX
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- Brucella suis pathogenicity, Chromosomes, Bacterial, Comparative Genomic Hybridization, Computational Biology methods, Gene Order, Genes, Bacterial, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Virulence genetics, Brucella Vaccine genetics, Brucella suis genetics, Genome, Bacterial, Genomics methods
- Abstract
Background: Brucellosis is a bacterial disease caused by Brucella infection. In the late fifties, Brucella suis vaccine strain S2 with reduced virulence was obtained by serial transfer of a virulent B. suis biovar 1 strain in China. It has been widely used for vaccination in China since 1971. Until now, the mechanisms underlie virulence attenuation of S2 are still unknown., Results: In this paper, the whole genome sequencing of S2 was carried out by Illumina Hiseq2000 sequencing method. We further performed the comparative genomic analysis to find out the differences between S2 and the virulent Brucella suis strain 1330. We found premature stops in outer membrane autotransporter omaA and eryD genes. Single mutations were found in phosphatidylcholine synthase, phosphorglucosamine mutase, pyruvate kinase and FliF, which have been reported to be related to the virulence of Brucella or other bacteria. Of the other different proteins between S2 and 1330, such as Omp2b, periplasmic sugar-binding protein, and oligopeptide ABC transporter, no definitive implications related to bacterial virulence were found, which await further investigation., Conclusions: The data presented here provided the rational basis for designing Brucella vaccines that could be used in other strains.
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- 2016
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35. Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon.
- Author
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Huang SW, Lin YY, You EM, Liu TT, Shu HY, Wu KM, Tsai SF, Lo CF, Kou GH, Ma GC, Chen M, Wu D, Aoki T, Hirono I, and Yu HT
- Subjects
- Animals, Base Sequence, Female, Microsatellite Repeats genetics, Open Reading Frames genetics, Sequence Analysis, DNA, Genomic Library, Genomics, Penaeidae genetics, Plasmids genetics
- Abstract
Background: The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses., Results: We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome., Conclusions: The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.
- Published
- 2011
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