36 results on '"Ye Tao"'
Search Results
2. A case report of sepsis associated coagulopathy after percutaneous nephrostomy
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Duan, Juan, Ye, Tao, Yang, Yueyue, Zhou, Yiping, Yang, Shengyu, and Wang, Yueli
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- 2024
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3. Insulin resistance, coronary artery lesion complexity and adverse cardiovascular outcomes in patients with acute coronary syndrome
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Chen, Qiang, Xiong, Shiqiang, Ye, Tao, Gao, Yanxiang, Wang, Jian, Li, Xingliang, Li, Yike, Cui, Caiyan, Liu, Hanxiong, Zhang, Zhen, Cai, Lin, and Zheng, Jingang
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- 2024
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4. SIRT1 mediates the inhibitory effect of Dapagliflozin on EndMT by inhibiting the acetylation of endothelium Notch1
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Wang, Weijie, Li, Yilan, Zhang, Yanxiu, Ye, Tao, Wang, Kui, Li, Shuijie, and Zhang, Yao
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- 2023
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5. Triglyceride-glucose index is associated with recurrent revascularization in patients with type 2 diabetes mellitus after percutaneous coronary intervention
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Chen, Qiang, Xiong, Shiqiang, Zhang, Zhen, Yu, Xiuqiong, Chen, Yingzhong, Ye, Tao, Yang, Siqi, Qi, Lingyao, Chen, Xu, Liu, Hanxiong, Zheng, Jingang, and Cai, Lin
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- 2023
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6. Mechanical properties evaluation of metacarpophalangeal joint prosthesis with new titanium-nickel memory alloy: a cadaver study
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Guo, Minzheng, Qi, Baochuang, Li, Jun, Shi, Xiangwen, Ni, Haonan, Shi, Hongxin, Ren, Junxiao, Zhou, Xizong, Ye, Tao, Yao, Ling, Xu, Yongqing, Zhang, Meichao, and Li, Chuan
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- 2023
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7. Chondrocyte-derived exosomes promote cartilage calcification in temporomandibular joint osteoarthritis
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Liu, Qian, Wang, Ruoxin, Hou, Shujie, He, Feng, Ma, Yuanjun, Ye, Tao, Yu, Shibin, Chen, Hongwei, Wang, Helin, and Zhang, Mian
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- 2022
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8. Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy
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Niewiadomska-Cimicka, Anna, Hache, Antoine, Le Gras, Stéphanie, Keime, Céline, Ye, Tao, Eisenmann, Aurelie, Harichane, Imen, Roux, Michel J., Messaddeq, Nadia, Clérin, Emmanuelle, Léveillard, Thierry, and Trottier, Yvon
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- 2022
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9. Expression profiles, biological functions and clinical significance of circRNAs in bladder cancer
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Yang, Xiaoqi, Ye, Tao, Liu, Haoran, Lv, Peng, Duan, Chen, Wu, Xiaoliang, Jiang, Kehua, Lu, Hongyan, Xia, Ding, Peng, Ejun, Chen, Zhiqiang, Tang, Kun, and Ye, Zhangqun
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- 2021
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10. Mortality effects of heat waves vary by age and area: a multi-area study in China
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Zhang, Lingyan, Zhang, Zhao, Ye, Tao, Zhou, Maigeng, Wang, Chenzhi, Yin, Peng, and Hou, Bin
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- 2018
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11. Indicators for prediction of Mycobacterium tuberculosis positivity detected with bronchoalveolar lavage fluid
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Liu, Xi, Hou, Xing-Fang, Gao, Lei, Deng, Guo-Fang, Zhang, Ming-Xia, Deng, Qun-Yi, Ye, Tao-Sheng, Yang, Qian-Ting, Zhou, Bo-Ping, Wen, Zhi-Hua, Liu, Hai-Ying, Kornfeld, Hardy, and Chen, Xin-Chun
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- 2018
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12. The clinical assessment of amyotrophic lateral sclerosis patients’ prognosis by ZNF512B gene, neck flexor muscle power score and body mass index (BMI)
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Ying Zhang, Ling-Yu Cai, Ye Tao, Li Wang, Ling-Ling Song, Sen-Lin Mao, and Chun-Jiang Yu
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0301 basic medicine ,Male ,medicine.medical_specialty ,Neurology ,Single-nucleotide polymorphism ,Polymorphism, Single Nucleotide ,lcsh:RC346-429 ,Body Mass Index ,Manual Muscle Testing ,03 medical and health sciences ,BMI ,0302 clinical medicine ,Internal medicine ,medicine ,Humans ,Mass index ,Neurochemistry ,Muscle Strength ,Amyotrophic lateral sclerosis ,Muscle, Skeletal ,lcsh:Neurology. Diseases of the nervous system ,Alleles ,Aged ,Risk allele ,business.industry ,Amyotrophic Lateral Sclerosis ,General Medicine ,Middle Aged ,medicine.disease ,Prognosis ,Zinc finger protein 512B gene ,Single nucleotide polymorphism ,030104 developmental biology ,Neck flexor muscle power score ,Disease Progression ,Female ,Neurology (clinical) ,Neurosurgery ,business ,Carrier Proteins ,Body mass index ,030217 neurology & neurosurgery ,Neck ,Research Article - Abstract
Background Assessment on the prognosis of amyotrophic lateral sclerosis (ALS) is becoming a focus of research in recent years since there is no effective treatment. The aim of the research is to explore the major factors involving in prognosis of ALS patients through long-term follow-up. Methods ALS patients’ DNA extracted from peripheral blood white cells were detected for the risk allele by single nucleotide polymorphism (SNP) analysis. Neck flexor muscle score and body mass index (BMI) were recorded during Medical Research Council follow-up using manual muscle testing method. Results ALS patients with risk alleles (C) deteriorated rapidly with poor clinical outcome. It seemed that the higher neck flexor muscle strength score in ALS patients with the longer survival time but without significant correlation (p > 0.05). The lower the basal body mass index, the shorter the survival time and the faster deterioration (p 0.05). Conclusion The risk (C) allele of the SNP (rs2275294) in the ZNF512B gene, cervical flexor muscle power and body weight index might have clinical potential for ALS prognostication, since these indicators is so simple to perform that they might be very suitable for primary clinics and even community medical institutions to carry out.
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- 2018
13. Construction of a high density SNP linkage map of kelp (Saccharina japonica) by sequencing Taq I site associated DNA and mapping of a sex determining locus
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Li Guo, Sun Juan, Xia Li, Ye Tao, Ning Zhang, Nan Zhao, Linan Zhang, Jinsa Chen, Xiaojie Li, Guanpin Yang, Jie Peng, and Liang Zeng
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Genotyping Techniques ,Genetic Linkage ,Quantitative Trait Loci ,SNP ,Genomics ,Locus (genetics) ,Single-nucleotide polymorphism ,Saccharina japonica ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,Genetic linkage ,Genetics ,Sex determining locus ,Deoxyribonucleases, Type II Site-Specific ,Binding Sites ,biology ,Linkage map ,RAD ,Chromosome Mapping ,Sequence Analysis, DNA ,Sex Determination Processes ,biology.organism_classification ,SNP genotyping ,Kelp ,Microsatellite ,Germ Cells, Plant ,Biotechnology ,Research Article ,Microsatellite Repeats - Abstract
Background Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns. Results We constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400–500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595. Conclusions A high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1371-1) contains supplementary material, which is available to authorized users.
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- 2015
14. High-density genetic map construction and QTLs analysis of grain yield-related traits in Sesame (Sesamum indicum L.) based on RAD-Seq techonology
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Minmin Yang, Huihui Ma, Wenxiong Wu, Kun Wu, Yang Zuo, Yingzhong Zhao, Ye Tao, and Hongyan Liu
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Genetic Markers ,Genotype ,Genetic Linkage ,Grain yield-related traits ,Population ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Genomics ,Plant Science ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,RAD-seq ,Sesamum ,Genetic map ,Genetic linkage ,education ,Sesame ,Genetics ,Expressed Sequence Tags ,Expressed sequence tag ,education.field_of_study ,biology ,business.industry ,food and beverages ,RIL ,Chromosome Mapping ,Sequence Analysis, DNA ,QTLs ,biology.organism_classification ,Biotechnology ,Phenotype ,Genetic marker ,business ,Edible Grain ,Genome, Plant ,Research Article ,Microsatellite Repeats - Abstract
Background Sesame (Sesamum indicum L., 2n = 26) is an important oilseed crop with an estimated genome size of 369 Mb. The genetic basis, including the number and locations of quantitative trait loci (QTLs) of sesame grain yield and quality remain poorly understood, due in part to the lack of reliable markers and genetic maps. Here we report on the construction of a hitherto most high-density genetic map of sesame using the restriction-site associated DNA sequencing (RAD-seq) combined with 89 PCR markers, and the identification of grain yield-related QTLs using a recombinant inbred line (RIL) population. Result In total, 3,769 single-nucleotide polymorphism (SNP) markers were identified from RAD-seq, and 89 polymorphic PCR markers were identified including 44 expressed sequence tag-simple sequence repeats (EST-SSRs), 10 genomic-SSRs and 35 Insertion-Deletion markers (InDels). The final map included 1,230 markers distributed on 14 linkage groups (LGs) and was 844.46 cM in length with an average of 0.69 cM between adjacent markers. Using this map and RIL population, we detected 13 QTLs on 7 LGs and 17 QTLs on 10 LGs for seven grain yield-related traits by the multiple interval mapping (MIM) and the mixed linear composite interval mapping (MCIM), respectively. Three major QTLs had been identified using MIM with R2 > 10.0% or MCIM with ha2 > 5.0%. Two co-localized QTL groups were identified that partially explained the correlations among five yield-related traits. Conclusion Three thousand eight hundred and four pairs of new DNA markers including SNPs and InDels were developed by RAD-seq, and a so far most high-density genetic map was constructed based on these markers in combination with SSR markers. Several grain yield-related QTLs had been identified using this population and genetic map. We report here the first QTL mapping of yield-related traits with a high-density genetic map using a RIL population in sesame. Results of this study solidified the basis for studying important agricultural traits and implementing marker-assisted selection (MAS) toward genetic improvement in sesame. Electronic supplementary material The online version of this article (doi:10.1186/s12870-014-0274-7) contains supplementary material, which is available to authorized users.
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- 2014
15. Association between alcohol intake and the risk of pancreatic cancer: a dose-response meta-analysis of cohort studies.
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Ye-Tao Wang, Ya-Wen Gou, Wen-Wen Jin, Mei Xiao, Hua-Ying Fang, Wang, Ye-Tao, Gou, Ya-Wen, Jin, Wen-Wen, Xiao, Mei, and Fang, Hua-Ying
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ALCOHOL drinking & health , *RISK factors of pancreatic cancer , *CONFIDENCE intervals , *MEDICAL databases , *META-analysis , *ALCOHOLS (Chemical class) , *DIABETES , *ALCOHOL drinking , *ENERGY metabolism , *PANCREATIC tumors , *SYSTEMATIC reviews , *BODY mass index - Abstract
Background: Studies examining the association between alcohol intake and the risk of pancreatic cancer have given inconsistent results. The purpose of this study was to summarize and examine the evidence regarding the association between alcohol intake and pancreatic cancer risk based on results from prospective cohort studies.Methods: We searched electronic databases consisting of PubMed, Ovid, Embase, and the Cochrane Library identifying studies published up to Aug 2015. Only prospective studies that reported effect estimates with 95% confidence intervals (CIs) for the risk of pancreatic cancer, examining different alcohol intake categories compared with a low alcohol intake category were included. Results of individual studies were pooled using a random-effects model.Results: We included 19 prospective studies (21 cohorts) reporting data from 4,211,129 individuals. Low-to-moderate alcohol intake had little or no effect on the risk of pancreatic cancer. High alcohol intake was associated with an increased risk of pancreatic cancer (risk ratio [RR], 1.15; 95% CI: 1.06-1.25). Pooled analysis also showed that high liquor intake was associated with an increased risk of pancreatic cancer (RR, 1.43; 95% CI: 1.17-1.74). Subgroup analyses suggested that high alcohol intake was associated with an increased risk of pancreatic cancer in North America, when the duration of follow-up was greater than 10 years, in studies scored as high quality, and in studies with adjustments for smoking status, body mass index, diabetes mellitus, and energy intake..Conclusions: Low-to-moderate alcohol intake was not significantly associated with the risk of pancreatic cancer, whereas high alcohol intake was associated with an increased risk of pancreatic cancer. Furthermore, liquor intake in particular was associated with an increased risk of pancreatic cancer. [ABSTRACT FROM AUTHOR]- Published
- 2016
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16. The effect of methamphetamine abuse on dental caries and periodontal diseases in an Eastern China city.
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Ye, Tao, Sun, Dongliang, Dong, Guangying, Xu, Guangjie, Wang, Ligang, Du, Jinjin, Ren, Pengcheng, and Yu, Shibin
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DENTAL calculus ,DENTAL caries ,METHAMPHETAMINE ,ORAL hygiene ,NONPARAMETRIC statistics ,PERIODONTAL disease ,PERIODONTAL pockets ,QUESTIONNAIRES ,RISK assessment ,TOOTH care & hygiene ,DRUG abusers ,CROSS-sectional method ,SEVERITY of illness index ,DATA analysis software ,INHALATION injuries ,PHARMACODYNAMICS - Abstract
Background: Dental diseases are among the most frequently reported health problems in drug abusers. However, few studies have been conducted on oral health of methamphetamine (meth) abusers in China. The aim of the present study was to investigate the caries and periodontal health profile of former meth abusers in Eastern China. Methods: A cross-sectional study was conducted on 162 former meth abusers in the male Zhoushan Compulsory Detoxification Center. A standardized questionnaire, which collected information about age, drug-use duration / pattern, oral hygiene habit and systemic diseases, was administered. Then, a dental examination was performed to investigate the severity of dental caries and periodontal diseases. In evaluating dental caries, the prevalence of dental caries, the scores of decayed teeth (DT), missing teeth (MT), filled teeth (FT), and decayed, missing, filled teeth (DMFT) were recorded. In evaluating periodontal diseases, community periodontal index (CPI), and the prevalence of gingival bleeding, dental calculus, periodontal pocket and loose teeth, were recorded. Additionally, the non-parametric test was adopted to analyze the potential risk factors via SPSS. Results: All the participants abused meth by inhalation. The mean scores of DT, MT, FT and DMFT in the former meth users were 2.72 ± 2.78, 3.07 ± 3.94, 0.33 ± 1.03 and 6.13 ± 5.20 respectively. The prevalence of gingival bleeding, dental calculus, periodontal pocket and loose teeth was 97.53%, 95.68%, 51.23% and 9.26% respectively. The DT, DMFT and CPI scores in those who had abused meth for longer than 4 years were significantly higher than those who abused for less than 4 years (P = 0.039, 0.045, P < 0.001, respectively). The DT score in those who brushed their teeth more than twice a day were significantly lower than those who brushed less (P = 0.018). Conclusions: The status of caries and periodontal diseases among former male meth users in Eastern China was poor. Prolonged drug abuse and lower frequency of tooth brushing may be the risk factors of their poor status of caries and periodontal diseases. [ABSTRACT FROM AUTHOR]
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- 2018
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17. Genetic polymorphism of scrA gene of Streptococcus mutans isolates is not associated with biofilm formation in severe early childhood caries.
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Yan Zhou, Lixia Yu, Ye Tao, Qinghui Zhi, and Huancai Lin
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BIOFILMS ,BIOLOGICAL assay ,BIOTIC communities ,CHI-squared test ,COMPUTER software ,DENTAL caries in children ,DNA ,GENES ,GENETIC polymorphisms ,GENTIAN violet ,GENETIC mutation ,POLYMERASE chain reaction ,STREPTOCOCCUS mutans ,CASE-control method ,SEQUENCE analysis - Abstract
Background: To explore and analyse the association between biofilm and the genetic polymorphisms of scrA gene of EnzymeIIscr found in clinical isolates of Streptococcus mutans (S. mutans) from severe early childhood caries (S-ECC) in 3 years old children. Methods: Clinical strains of S. mutans were conserved from a previous study. Thirty strains of S. mutans from the S-ECC group and 30 strains of S. mutans from the caries free (CF) group were selected. Biomass and viability of biofilm formed by the strains were evaluated by crystal violet and alamar blue assay. Genomic DNA was extracted from the S. mutans isolates. PCR was conducted to amplify scrA gene. After purified and sequenced the PCR products, BioEdit sofeware was used to analyse the sequence results. A chi-square test was used to compare the results. Results: Compared to the CF group, the biomass of S-ECC group was higher (P = 0.0424). However, the viability of the two groups showed no significant difference. All 60 clinically isolated S. mutans strains had a 1995 base pair (bp) scrA gene. Forty-nine point mutations were identified in scrA from the 60 clinical isolates. There were 17 missense point mutations at the 10, 65, 103, 284, 289, 925, 1444, 1487, 1494, 1508, 1553, 1576, 1786, 1822, 1863, 1886, and 1925 bp positions. The other 32 mutations were silent point mutations. No positions were found at active sites of ScrA. The statistic analyse showed no significant missense mutation rates between the two groups. Conclusions: There was no association between biofilm and genetic polymorphisms of scrA from S. mutans with S-ECC in 3 years old children. [ABSTRACT FROM AUTHOR]
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- 2017
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18. Upregulation of the long noncoding RNA UCA1 affects the proliferation, invasion, and survival of hypopharyngeal carcinoma.
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Ye Qian, Dayu Liu, Shengda Cao, Ye Tao, Dongmin Wei, Wenming Li, Guojun Li, Xinliang Pan, and Dapeng Lei
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NON-coding RNA ,CELL proliferation ,HYPOPHARYNGEAL cancer ,ONCOGENES ,LYMPHATIC diseases - Abstract
Background: Several long noncoding RNAs (lncRNAs) are involved in oncogenesis. Methods and Results: Our microarray analysis showed that numerous lncRNAs are dysregulated in hypopharyngeal squamous cell carcinoma (HSCC) tumor tissues as compared with normal tissues. Among those lncRNAs, urothelial carcinoma-associated 1 (UCA1) has been found to have an oncogenic role in HSCC. We confirmed the upregulation of UCA1 in HSCC by assessing its expression levels in a cohort of 53 patient tumors and paired non-tumor samples. In addition, we found that high UCA1 expression was significantly associated with advanced T category, late clinical stage, greater lymphatic invasion, and worse prognosis. Furthermore, in vitro experiments demonstrated that UCA1 functioned as an oncogene by promoting the proliferation and invasion and preventing the apoptosis of HSCC cells. Conclusions: Taken together, our findings for the first time identify the role of UCA1 as a tumor promoter and a prometastatic factor in HSCC, demonstrating that UCA1 is a potential prognostic biomarker and therapeutic target in HSCC. [ABSTRACT FROM AUTHOR]
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- 2017
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19. Kudiezi injection mitigates myocardial injury induced by acute cerebral ischemia in rats.
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Xuemei Liu, Ye Tao, Fengli Wang, Ting Yao, Chen Fu, Hong Zheng, Yan Yan, Xiao Liang, Xiangning Jiang, and Yunling Zhang
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CEREBRAL ischemia ,CORONARY heart disease prevention ,TISSUE analysis ,ANIMAL experimentation ,BLOOD testing ,BRAIN ,ENZYME-linked immunosorbent assay ,HEART beat ,HERBAL medicine ,HISTOLOGICAL techniques ,CHINESE medicine ,MITOCHONDRIA ,POLYMERASE chain reaction ,RATS ,RESEARCH funding ,RNA ,STATISTICS ,T-test (Statistics) ,DATA analysis ,OXIDATIVE stress ,DESCRIPTIVE statistics ,ONE-way analysis of variance ,DRUG administration ,DRUG dosage ,PREVENTION - Abstract
Background: Kudiezi (KDZ) injection is commonly used in traditional Chinese medicine as treatment for cerebral infarction and angina pectoris. The present study investigated the therapeutic effects of KDZ injection on myocardial injury induced by acute cerebral ischemia and the possibly protective mechanisms. Methods: Rats were divided into three groups: sham, 6h-ischemia, and KDZ treatment (KDZ). The neurological deficits were determined by the Garcia score. The cerebral infarct volume was measured by 2,3,5-triphenyltetrazolium chloride (TTC) staining, and brain water content was also evaluated. Serum creatinine kinase (CK), lactate dehydrogenase (LDH), and creatine kinase-myocardial band (CK-MB) activity, myocardial tissue malondialdehyde (MDA) levels, L-Glutathione (GSH) levels, and superoxide dismutase (SOD) activity as well as mitochondrial cytochrome c oxidase (COX) activity were determined. Mitochondrial COX I and COX III mRNA expressions of myocardial tissues were measured by RT-PCR. Results: Impaired neurological function and brain edema were observed in the 6h-ischemia group. TTC staining showed that the 6h-ischemia group had larger infarct zones than the sham group. Myocardial ischemic changes (widened myocardial cell gap, cracks, and obvious edema) were detected in the 6h-ischemia group compared with the sham group, with elevated serum CK-MB activity and CK and LDH levels. Electrocardiography showed lower medium frequency (MF) and high frequency (HF) in the 6h-ischemia group compared with the sham group. In myocardial tissue, COX activity was elevated in the 6h-ischemia compared with the sham group, while SOD, GSH, and MDA levels, and COX I and COX III mRNA expressions remained unchanged. KDZ injection decreased neurological impairment, brain edema, gaps between cells, and infarct size. Compared with the 6h-ischemia group, it reduced serum CK-MB activity and CK and LDH levels, and MDA levels in myocardial tissue. KDZ significantly increased GSH levels, SOD activity, and mitochondria COX activity and the expression of COX I and COX III mRNA in myocardial tissue compared with the sham group. Conclusion: KDZ injection had a protective effect against cerebral ischemia in rats. KDZ injection could also alleviate myocardial injury after acute cerebral ischemia in rats. The possible mechanisms involve the regulation of the oxidative stress/antioxidant capacity after cerebral ischemia. [ABSTRACT FROM AUTHOR]
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- 2017
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20. The relationship between children's oral health-related behaviors and their caregiver's social support.
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Rong Min Qiu, Ye Tao, Yan Zhou, Qing Hui Zhi, and Huan Cai Lin
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CAREGIVERS ,HEALTH behavior in children ,ORAL hygiene ,QUESTIONNAIRES ,SNACK foods ,TOOTH care & hygiene ,MATHEMATICAL variables ,MULTIPLE regression analysis ,SOCIAL support ,CROSS-sectional method - Abstract
Background: Social support might play a role in helping people adopt healthy behaviors and improve their health. Stronger social support from mothers has been found to be positively related to higher tooth brushing frequency in 1- to 3-year-old children. However, little is known regarding the relationship between the caregiver's social support and the oral health-related behaviors of 5-year-old children in China. This study aimed to investigate this relationship. Methods: A cross-sectional study was conducted among 1332 5-year-old children and their caregivers in Guangzhou, southern China. Data were collected using questionnaires that were completed by the caregivers and the children's caries status were examined. The caregivers' social support was measured using the Social Support Rating Scale. The measurements of the children's oral health-related behaviors included the frequencies of sugary snack intake and tooth brushing, utilization of dental services, and patterns of dental visits. Univariate and multiple logistic regression analyses were used to analyze the relationships between the variables. Results: No association was found between the caregiver's social support and the child's oral health-related behaviors in a multiple logistic regression analysis. However, other factors, particularly the oral health-related behaviors of the caregiver, were found to be significantly linked to the child's oral health-related behaviors. Conclusions: The oral health-related behaviors of 5-year-old children in Guangzhou are unrelated to the caregiver's social support but are related to other specific factors, particularly the caregiver's oral health-related behaviors. [ABSTRACT FROM AUTHOR]
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- 2016
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21. A case of lipoprotein glomerulopathy with thrombotic microangiopathy due to malignant hypertension
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Yuan Yang, Yu Wu, Ye Tao, Xiaohan Chen, Zhangxue Hu, Xiaoxia Liu, Baohe Wang, and Ping Fu
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medicine.medical_specialty ,Pathology ,Thrombotic microangiopathy ,Adolescent ,Anemia ,Malignant hypertension ,medicine.medical_treatment ,Renal function ,Case Report ,APOE Kyoto ,Lipoprotein glomerulopathy ,urologic and male genital diseases ,Gastroenterology ,Diagnosis, Differential ,chemistry.chemical_compound ,Internal medicine ,medicine ,Humans ,Creatinine ,Proteinuria ,business.industry ,Thrombotic Microangiopathies ,medicine.disease ,Uremia ,Treatment Outcome ,chemistry ,Nephrology ,Hypertension ,Female ,Kidney Diseases ,Hemodialysis ,medicine.symptom ,business ,Nephrotic syndrome - Abstract
Background Lipoprotein glomerulopathy (LPG) is a rare inherited renal disease characterized by intraglomerular lipoprotein within the lumina of severely dilated glomerular capillaries. The common clinical presentation of LPG includes proteinuria or nephrotic syndrome. Hypertension and anemia were thought to be mild in LPG. Thrombotic microangiopathy (TMA) in LPG has not been previously reported. In this report, we present a patient with LPG that developed TMA. To the best of our knowledge, this is the first report of TMA in LPG. Case presentation Four years ago (2005), a 19-year-old Chinese woman was diagnosed with nephrotic syndrome and provided prednisone treatment. A combination of prednisone and cyclophosphamide did not have any effect and was discontinued after six months. Although she was steroid-resistant, over the next subsequent three years, she maintained normal renal function without anemia and thrombocytopenia. In February 2009, she had a severe headache and blurry vision and presented at a local hospital with severe hypertension. Blood pressure was 220/160 mmHg. Laboratory data showed hemoglobin 3.8 g/dL; platelet counts 29×109/L; urinary protein 7.90 g/d; total bilirubin 29.9 umol/L; indirect bilirubin 28.2 umol/L; LDH 1172 U/L; ALB 2.66 g/dL; urea nitrogen 52 mg/dL; serum creatinine 3.2 mg/dL; triglyceride 253 mg/dL; total cholesterol 273 mg/dL. ANA, ds-DNA, ANCA, anti-GBM antibody and anticardiolipin were all negative. A renal biopsy revealed LPG with TMA. Genetic evaluation showed the patient carried the APOE Kyoto mutation. Adequate control of blood pressure improved microangiopathic anemia and thrombocytopenia, however, renal function did not improve and she eventually developed uremia and became hemodialysis dependent. Conclusion We report on a rare case of TMA probably due to malignant hypertension in LPG. Early lipid-lowering and antihypertensive treatment may improve outcome. The pathophysiologic relationship between LPG and TMA should be investigated further.
- Published
- 2013
22. Endogenous siRNAs and piRNAs derived from transposable elements and genes in the malaria vector mosquito Anopheles gambiae.
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Biryukova, Inna and Ye, Tao
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SMALL interfering RNA , *ANOPHELES gambiae , *MOSQUITO vectors , *TRANSPOSONS , *INSECT genetics - Abstract
Background: The siRNA and piRNA pathways have been shown in insects to be essential for regulation of gene expression and defence against exogenous and endogenous genetic elements (viruses and transposable elements). The vast majority of endogenous small RNAs produced by the siRNA and piRNA pathways originate from repetitive or transposable elements (TE). In D. melanogaster, TE-derived endogenous siRNAs and piRNAs are involved in genome surveillance and maintenance of genome integrity. In the medically relevant malaria mosquito Anopheles gambiae TEs constitute 12-16% of the genome size. Genetic variations induced by TE activities are known to shape the genome landscape and to alter the fitness in An. gambiae. Results: Here, using bioinformatics approaches we analyzed the small RNA data sets from 6 libraries formally reported in a previous study and examined the expression of the mixed germline/somatic siRNAs and piRNAs produced in adult An. gambiae females. We characterized a large population of TE-derived endogenous siRNAs and piRNAs, which constitutes 56-60% of the total siRNA and piRNA reads in the analysed libraries. Moreover, we identified a number of protein coding genes producing gene-specific siRNAs and piRNAs that were generally expressed at much lower levels than the TE-associated small RNAs. Detailed sequence analysis revealed that An. gambiae piRNAs were produced by both "ping-pong" dependent (TE-associated piRNAs) and independent mechanisms (genic piRNAs). Similarly to D. melanogaster, more than 90% of the detected piRNAs were produced from TE-associated clusters in An. gambiae. We alsofound that biotic stress as blood feeding and infection with Plasmodium parasite, the etiological agent of malaria, modulated the expression levels of the endogenous siRNAs and piRNAs in An. gambiae. Conclusions: We identified a large and diverse set of the endogenously derived siRNAs and piRNAs that share common and distinct aspects of small RNA expression across insect species, and inferred their impact on TE and gene activity in An. gambiae. The TE-specific small RNAs produced by both the siRNA and piRNA pathways represent an important aspect of genome stability and genetic variation, which might have a strong impact on the evolution of the genome and vector competence in the malaria mosquitoes. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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23. Genetic polymorphisms of the sortase A gene and social-behavioural factors associated with caries in children: a case-control study.
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Li Xia Yu, Ye Tao, Rong Min Qiu, Yan Zhou, Qing Hui Zhi, and Huan Cai Lin
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DENTAL caries ,CHI-squared test ,CHILD behavior ,CONFIDENCE intervals ,DNA ,GENES ,GENETIC polymorphisms ,HUMAN genome ,GENETIC mutation ,POLYMERASE chain reaction ,QUESTIONNAIRES ,RESEARCH funding ,STATISTICS ,T-test (Statistics) ,LOGISTIC regression analysis ,MULTIPLE regression analysis ,CASE-control method ,DATA analysis software ,ODDS ratio ,CHILDREN ,GENETICS - Abstract
Background: Streptococcus mutans (S. mutans) is the primary etiological agent of dental caries. Sortase is a transpeptidase that anchors several surface proteins to the S. mutans cell wall and has been shown to play a major role in cariogenicity. The purpose of this study was to explore the genetic polymorphisms of the sortase gene (srtA) and the social-behavioural factors associated with dental caries in children with S. mutans. Methods: In this case-control study, 121 S. mutans strains were separately selected from caries-free children and high-severity caries children for sequencing of the srtA gene. Social and behavioural data were collected by self-administered questionnaires. Genomic DNA was extracted from S. mutans strains and amplified by PCR to obtain the srtA gene. The purified PCR products were sequenced and analysed for mutations with ABI Variant Reporter software. The distribution of missense mutations and the mean of social-behavioural factors were compared between the groups. A multiple logistic regression model was used to control for confounding factors. Results: The mutation frequencies at loci 168 (P = 0.023) and 470 (P = 0.032) were significantly different between the groups. The best-fitting model showed that greater age, high frequencies of solid sugar consumption, prolonged breastfeeding, a high proportion of visible plaque, and S. mutans with a T at locus 168 of the srtA gene were associated with high-severity caries in children (P < 0.05). Children carrying a G at locus 168 of S. mutans had a decreased risk for high-severity caries (OR = 0.32, 95% CI = 0.12-0.86) compared with those carrying a T. Conclusions: The present study suggested that the locus 168 missense mutation of the srtA gene may correlate with caries susceptibility in children with S. mutans. In addition, age, duration of breastfeeding, solid sugar consumption, and poor oral hygiene contributed to this complex disease. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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- View/download PDF
24. Sphenopalatine ganglion stimulation with one acupuncture needle for moderate-severe persistent allergic rhinitis: study protocol for a multicenter randomized controlled trial.
- Author
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Lu Zhang, Lei Li, Da-Zhuo Shi, Lu-Quan Chen, Kai-Min Zheng, Kai Cheng, Ye Tao, Hai-Yan Guo, Shu-Liang Li, Jing Liu, Feng Xu, and Jian-Wu Shen
- Subjects
PTERYGOPALATINE ganglion ,ALLERGIC rhinitis ,INFLAMMATION ,NOSE diseases ,RHINITIS ,ALTERNATIVE medicine ,ACUPUNCTURE - Abstract
Background: Allergic rhinitis is a symptomatic allergic disease of the nose that affects 10 to 20% of the global population. Chinese otolaryngologists use one acupuncture needle to stimulate the sphenopalatine ganglion because of its potential advantages for treating moderate-severe persistent allergic rhinitis compared with traditional Chinese acupuncture (verum acupuncture); however, little evidence is available to support the wide clinical use thus far. Therefore, we propose a protocol for a parallel, multicenter, assessor-blinded, randomized controlled trial to evaluate sphenopalatine ganglion stimulation with one acupuncture needle compared to verum acupuncture for treatment of moderate-severe persistent allergic rhinitis. Methods: In the trial, 96 patients previously diagnosed with moderate-severe persistent allergic rhinitis and meeting all inclusion criteria will be allocated to one of two equal therapeutic groups by using a computer-generated randomization list. The interventional group will receive sphenopalatine ganglion stimulation with one acupuncture needle for 4 weeks (once or twice weekly, total four to eight sessions); attending physicians will decide whether the second session is required in a week by examining signs and symptoms. The control group will receive individualized verum acupuncture for 4 weeks (twice weekly, total eight sessions). Follow-up evaluations will be performed 1 month later. The primary outcome measure is the change in the total nasal symptom score from the baseline to week 4. The secondary outcome measures include onset time and duration of effectiveness in every session, change in number of days with moderate-severe persistent allergic rhinitis from the baseline to week 8, change in total immunoglobulin E level and eosinophil count in venous blood from the baseline to week 4, change in Rhinoconjunctivitis Quality of Life Questionnaire score from the baseline to week 4, and clinical waiting time. Discussion: The trial should provide evidence for the benefits of sphenopalatine ganglion stimulation with one acupuncture needle for treating moderate-severe persistent allergic rhinitis, including better change in total nasal symptom score, faster onset time, longer duration of effectiveness, and shorter treatment time. Trial registration: Current Controlled Trials: ISRCTN21980724 (registered on 27 March 2014). [ABSTRACT FROM AUTHOR]
- Published
- 2015
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25. Construction of a high density SNP linkage map of kelp (Saccharina japonica) by sequencing Taq I site associated DNA and mapping of a sex determining locus.
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Ning Zhang, Linan Zhang, Ye Tao, Li Guo, Juan Sun, Xia Li, Nan Zhao, Jie Peng, Xiaojie Li, Liang Zeng, Jinsa Chen, and Guanpin Yang
- Subjects
SINGLE nucleotide polymorphisms ,SACCHARINA ,NUCLEOTIDE sequencing ,GENETIC sex determination ,LOCUS (Genetics) ,BROWN algae - Abstract
Background: Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns. Results: We constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400-500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595. Conclusions: A high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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26. High-density genetic map construction and QTLs analysis of grain yield-related traits in Sesame (Sesamum indicum L.) based on RAD-Seq techonology.
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Kun Wu, Hongyan Liu, Minmin Yang, Ye Tao, Huihui Ma, Wenxiong Wu, Yang Zuo, and Yingzhong Zhao
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PLANT gene mapping ,SESAME ,GRAIN yields ,OILSEEDS ,LOCUS in plant genetics ,NUCLEOTIDE sequencing ,SINGLE nucleotide polymorphisms - Abstract
Background: Sesame (Sesamum indicum L., 2n = 26) is an important oilseed crop with an estimated genome size of 369 Mb. The genetic basis, including the number and locations of quantitative trait loci (QTLs) of sesame grain yield and quality remain poorly understood, due in part to the lack of reliable markers and genetic maps. Here we report on the construction of a hitherto most high-density genetic map of sesame using the restriction-site associated DNA sequencing (RAD-seq) combined with 89 PCR markers, and the identification of grain yield-related QTLs using a recombinant inbred line (RIL) population. Result: In total, 3,769 single-nucleotide polymorphism (SNP) markers were identified from RAD-seq, and 89 polymorphic PCR markers were identified including 44 expressed sequence tag-simple sequence repeats (EST-SSRs), 10 genomic-SSRs and 35 Insertion-Deletion markers (InDels). The final map included 1,230 markers distributed on 14 linkage groups (LGs) and was 844.46 cM in length with an average of 0.69 cM between adjacent markers. Using this map and RIL population, we detected 13 QTLs on 7 LGs and 17 QTLs on 10 LGs for seven grain yield-related traits by the multiple interval mapping (MIM) and the mixed linear composite interval mapping (MCIM), respectively. Three major QTLs had been identified using MIM with R2 > 10.0% or MCIM with ha 2 > 5.0%. Two co-localized QTL groups were identified that partially explained the correlations among five yield-related traits. Conclusion: Three thousand eight hundred and four pairs of new DNA markers including SNPs and InDels were developed by RAD-seq, and a so far most high-density genetic map was constructed based on these markers in combination with SSR markers. Several grain yield-related QTLs had been identified using this population and genetic map. We report here the first QTL mapping of yield-related traits with a high-density genetic map using a RIL population in sesame. Results of this study solidified the basis for studying important agricultural traits and implementing marker-assisted selection (MAS) toward genetic improvement in sesame. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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27. Factors related to children's caries: a structural equation modeling approach.
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Rong Min Qiu, Lo, Edward C. M., Qing Hui Zhi, Yan Zhou, Ye Tao, and Huan Cai Lin
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DENTAL caries ,CHILDREN'S health ,SOCIAL status ,CAREGIVERS ,NUTRITION & oral health ,STRUCTURAL equation modeling - Abstract
Background: Dental caries among preschool children is highly prevalent in many less-developed countries. Methods: A model which explored the factors related to children's dental caries was tested in this study using structural equation modeling. Caregivers of children aged 5 years were surveyed on their socioeconomic status, and their oral health knowledge, attitudes and practices. In addition, information on their children's oral health practices, dental insurance and dental service utilization were collected. Examination of caries was conducted on all children who returned fully completed questionnaires. Results: The results showed that socioeconomic factors influenced children's oral health practices through the impact of caregivers' oral health knowledge and practices; that caregivers' oral health knowledge affected children's oral health practices through the influence of caregivers' oral health attitudes and practices; and finally, that children's oral health practices were linked directly to their caries. Conclusion: The findings have important applications for promoting policies aimed at advancing children's oral health. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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28. Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using Insertion-Deletion (InDel) and Simple Sequence Repeat (SSR) markers.
- Author
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Kun Wu, Minmin Yang, Hongyan Liu, Ye Tao, Ju Mei, and Yingzhong Zhao
- Abstract
Background: Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design. Results: Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines. Conclusions: This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic drift or selection during breeding processes. Comparative analysis of allele distribution revealed genetic divergence between improved cultivars and landraces, as well as between cultivars released in different years. These results will be useful for assessing cultivars and for marker-assisted breeding in sesame. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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29. A case of lipoprotein glomerulopathy with thrombotic microangiopathy due to malignant hypertension.
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Yu Wu, Xiaohan Chen, Yuan Yang, Baohe Wang, Xiaoxia Liu, Ye Tao, Ping Fu, and Zhangxue Hu
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KIDNEY glomerulus diseases ,LIPOPROTEINS ,THROMBOTIC microangiopathies ,MALIGNANT hypertension ,GENETIC disorders ,STEROID drugs ,DRUG resistance - Abstract
Background: Lipoprotein glomerulopathy (LPG) is a rare inherited renal disease characterized by intraglomerular lipoprotein within the lumina of severely dilated glomerular capillaries. The common clinical presentation of LPG includes proteinuria or nephrotic syndrome. Hypertension and anemia were thought to be mild in LPG. Thrombotic microangiopathy (TMA) in LPG has not been previously reported. In this report, we present a patient with LPG that developed TMA. To the best of our knowledge, this is the first report of TMA in LPG. Case presentation: Four years ago (2005), a 19-year-old Chinese woman was diagnosed with nephrotic syndrome and provided prednisone treatment. A combination of prednisone and cyclophosphamide did not have any effect and was discontinued after six months. Although she was steroid-resistant, over the next subsequent three years, she maintained normal renal function without anemia and thrombocytopenia. In February 2009, she had a severe headache and blurry vision and presented at a local hospital with severe hypertension. Blood pressure was 220/ 160 mmHg. Laboratory data showed hemoglobin 3.8 g/dL; platelet counts 29×109/L; urinary protein 7.90 g/d; total bilirubin 29.9 umol/L; indirect bilirubin 28.2 umol/L; LDH 1172 U/L; ALB 2.66 g/dL; urea nitrogen 52 mg/dL; serum creatinine 3.2 mg/dL; triglyceride 253 mg/dL; total cholesterol 273 mg/dL. ANA, ds-DNA, ANCA, anti-GBM antibody and anticardiolipin were all negative. A renal biopsy revealed LPG with TMA. Genetic evaluation showed the patient carried the APOE Kyoto mutation. Adequate control of blood pressure improved microangiopathic anemia and thrombocytopenia, however, renal function did not improve and she eventually developed uremia and became hemodialysis dependent. Conclusion: We report on a rare case of TMA probably due to malignant hypertension in LPG. Early lipid-lowering and antihypertensive treatment may improve outcome. The pathophysiologic relationship between LPG and TMA should be investigated further. [ABSTRACT FROM AUTHOR]
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- 2013
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30. Identical twins:one with anti-glomerular basement membrane glomerulonephritis,the other with systemic lupus erythematosus.
- Author
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Xiaoxia Liu, Yu Wu, Yuan Yang, Jue Wang, Ye Tao, Ping Fu, and Zhangxue Hu
- Subjects
GLOMERULAR filtration rate ,GLOMERULONEPHRITIS ,SYSTEMIC lupus erythematosus ,IMMUNE system ,HEMATURIA ,CREATININE - Abstract
Background Anti-glomerular basement membrane (GBM) glomerulonephritis and systemic lupus erythematosus (SLE) are both disorders of the immune system; however, they are known as distinct diseases. Till now no clinical evidence suggests the genetic relationship between these two diseases. Herein, we present two identical twins; one was diagnosed as anti-GBM glomerulonephritis, the other SLE. This is the first clinical report on the genetic relationship between these two diseases. Case presentation A 25-year-old female was admitted complaining of intermittent gross hematuria for 6 months and elevated serum creatinine for 1 month. She denied hemoptysis. Laboratory examinations showed hemoglobin 7.4 g/dL, serum creatinine 7.15 mg/dL and albumin 2.8 g/dL. Urinalysis showed hematuria (484 RBCs per high-power field) and proteinuria 4+. Antinuclear antibody, complement levels and ANCAs were all normal. Renal ultrasound showed normalsized kidneys without obstruction or masses. Serum anti-GBM antibody assay showed 119.70 RU/mL (normal range, <20 RU/mL). Chest X-ray was normal. She was diagnosed as anti- GBM glomerulonephritis and received plasma exchange (2000-3000 ml plasma/exchange, 5 turns), methylprednisolone 0.5 g for three days, plus cyclophosphamide. Although serum anti-GBM antibodies decreased gradually to a normal range, her renal function did not improve. One month later, her identical twin sister was diagnosed as SLE based on malar erythema, arthralgia, antinuclear antibody positive with liter 1:1000, and Anti-Smith (Sm) antibody ++. Anti-GBM antibody and complements were within normal ranges. Further study showed these twins were HLA-DRB1*1501 homozygotes. Conclusion The presence of identical twins having anti-GBM nephritis and SLE respectively provides clinical evidence to support that anti-GBM nephritis and lupus may share a common genetic background to some extent, while environment may contribute to disease evolution in part. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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31. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.
- Author
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Huaan Yang, Ye Tao, Zequn Zheng, Chengdao Li, Sweetingham, Mark W., and Howieson, John G
- Subjects
- *
PLANT breeding , *GENETIC markers , *LUPINUS angustifolius , *DISEASE resistance of plants - Abstract
Background: In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results: Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. Conclusions: We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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32. Cell-specific occupancy of an extended repertoire of CREM and CREB binding loci in male germ cells.
- Author
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Martianov, Igor, Choukrallah, Mohamed-Amin, Krebs, Arnaud, Ye, Tao, Legras, Stephanie, Rijkers, Erikjan, Van Ijcken, Wilfred, Jost, Bernard, Sassone-Corsi, Paolo, and Davidson, Irwin
- Subjects
GERM cells ,TRANSCRIPTION factors ,LOCUS (Genetics) ,SPERMIOGENESIS in animals ,RNA polymerases - Abstract
Background: CREB and CREM are closely related factors that regulate transcription in response to various stress, metabolic and developmental signals. The CREMt activator isoform is selectively expressed in haploid spermatids and plays an essential role in murine spermiogenesis. Results: We have used chromatin immunoprecipitation coupled to sequencing (ChIP-seq) to map CREM and CREB target loci in round spermatids from adult mouse testis and spermatogonia derived GC1-spg cells respectively. We identify more than 9000 genomic loci most of which are cell-specifically occupied. Despite the fact that round spermatids correspond to a highly specialised differentiated state, our results show that they have a remarkably accessible chromatin environment as CREM occupies more than 6700 target loci corresponding not only to the promoters of genes selectively expressed in spermiogenesis, but also of genes involved in functions specific to other cell types. The expression of only a small subset of these target genes are affected in the round spermatids of CREM knockout animals. We also identify a set of intergenic binding loci some of which are associated with H3K4 trimethylation and elongating RNA polymerase II suggesting the existence of novel CREB and CREM regulated transcripts. Conclusions: We demonstrate that CREM and CREB occupy a large number of promoters in highly cell specific manner. This is the first study of CREM target promoters directly in a physiologically relevant tissue in vivo and represents the most comprehensive experimental analysis of CREB/CREM regulatory potential to date. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
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33. Elevated LRRK2 autophosphorylation in brain-derived and peripheral exosomes in LRRK2 mutation carriers.
- Author
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Wang S, Liu Z, Ye T, Mabrouk OS, Maltbie T, Aasly J, and West AB
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- Aged, Case-Control Studies, Cohort Studies, DNA-Binding Proteins cerebrospinal fluid, DNA-Binding Proteins genetics, DNA-Binding Proteins metabolism, DNA-Binding Proteins urine, Endosomal Sorting Complexes Required for Transport cerebrospinal fluid, Endosomal Sorting Complexes Required for Transport genetics, Endosomal Sorting Complexes Required for Transport metabolism, Endosomal Sorting Complexes Required for Transport urine, Female, Genetic Predisposition to Disease, HEK293 Cells, Humans, Male, Membrane Proteins cerebrospinal fluid, Membrane Proteins urine, Middle Aged, Norway, Parkinson Disease cerebrospinal fluid, Parkinson Disease pathology, Parkinson Disease urine, Phosphorylation genetics, Serine genetics, Serine metabolism, Severity of Illness Index, Transcription Factors cerebrospinal fluid, Transcription Factors genetics, Transcription Factors metabolism, Transcription Factors urine, Brain metabolism, Gene Expression Regulation genetics, Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 genetics, Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 metabolism, Mutation genetics, Parkinson Disease genetics
- Abstract
Missense mutations in the leucine-rich repeat kinase 2 (LRRK2) gene can cause late-onset Parkinson disease (PD). LRRK2 mutations increase LRRK2 kinase activities that may increase levels of LRRK2 autophosphorylation at serine 1292 (pS1292) and neurotoxicity in model systems. pS1292-LRRK2 protein can be packaged into exosomes and measured in biobanked urine. Herein we provide evidence that pS1292-LRRK2 protein is robustly expressed in cerebral spinal fluid (CSF) exosomes. In a novel cohort of Norwegian subjects with and without the G2019S-LRRK2 mutation, with and without PD, we quantified levels of pS1292-LRRK2, total LRRK2, and other exosome proteins in urine from 132 subjects and in CSF from 82 subjects. CSF and urine were collected from the same morning clinic visit in 55 of the participants. We found that total LRRK2 protein concentration was similar in exosomes purified from either CSF or urine but the levels did not correlate. pS1292-LRRK2 levels were higher in urinary exosomes from male and female subjects with a LRRK2 mutation. Male LRRK2 mutation carriers without PD had intermediate pS1292-LRRK2 levels compared to male carriers with PD and controls. However, female LRRK2 mutation carriers without PD had the same pS1292-LRRK2 levels compared to female carriers with PD. pS1292-LRRK2 levels in CSF exosomes were near saturated in most subjects, ten-fold higher on average than pS1292-LRRK2 levels in urinary exosomes, irrespective of LRRK2 mutation status or PD diagnosis. These results provide insights into the effects of LRRK2 mutations in both the periphery and brain in a well-characterized clinical population and show that LRRK2 protein in brain exosomes may be much more active than in the periphery in most subjects.
- Published
- 2017
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34. Association between alcohol intake and the risk of pancreatic cancer: a dose-response meta-analysis of cohort studies.
- Author
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Wang YT, Gou YW, Jin WW, Xiao M, and Fang HY
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- Alcohol Drinking adverse effects, Alcohols toxicity, Body Mass Index, Diabetes Mellitus epidemiology, Diabetes Mellitus pathology, Energy Metabolism, Female, Humans, Male, North America, Pancreatic Neoplasms chemically induced, Risk Factors, Alcohol Drinking epidemiology, Alcohol Drinking pathology, Pancreatic Neoplasms epidemiology, Pancreatic Neoplasms pathology
- Abstract
Background: Studies examining the association between alcohol intake and the risk of pancreatic cancer have given inconsistent results. The purpose of this study was to summarize and examine the evidence regarding the association between alcohol intake and pancreatic cancer risk based on results from prospective cohort studies., Methods: We searched electronic databases consisting of PubMed, Ovid, Embase, and the Cochrane Library identifying studies published up to Aug 2015. Only prospective studies that reported effect estimates with 95% confidence intervals (CIs) for the risk of pancreatic cancer, examining different alcohol intake categories compared with a low alcohol intake category were included. Results of individual studies were pooled using a random-effects model., Results: We included 19 prospective studies (21 cohorts) reporting data from 4,211,129 individuals. Low-to-moderate alcohol intake had little or no effect on the risk of pancreatic cancer. High alcohol intake was associated with an increased risk of pancreatic cancer (risk ratio [RR], 1.15; 95% CI: 1.06-1.25). Pooled analysis also showed that high liquor intake was associated with an increased risk of pancreatic cancer (RR, 1.43; 95% CI: 1.17-1.74). Subgroup analyses suggested that high alcohol intake was associated with an increased risk of pancreatic cancer in North America, when the duration of follow-up was greater than 10 years, in studies scored as high quality, and in studies with adjustments for smoking status, body mass index, diabetes mellitus, and energy intake.., Conclusions: Low-to-moderate alcohol intake was not significantly associated with the risk of pancreatic cancer, whereas high alcohol intake was associated with an increased risk of pancreatic cancer. Furthermore, liquor intake in particular was associated with an increased risk of pancreatic cancer.
- Published
- 2016
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35. Tip60 complex binds to active Pol II promoters and a subset of enhancers and co-regulates the c-Myc network in mouse embryonic stem cells.
- Author
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Ravens S, Yu C, Ye T, Stierle M, and Tora L
- Abstract
Background: Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip60 as reflected in a genome-wide context is not yet well understood., Results: Gel filtration of nuclear mESCs extracts indicate incorporation of Tip60 into large molecular complexes and exclude the existence of large quantities of "free" Tip60 within the nuclei of ESCs. Thus, monitoring of Tip60 binding to the genome should reflect the behaviour of Tip60-containing complexes. The genome-wide mapping of Tip60 binding in mESCs by chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) shows that the Tip60 complex is present at promoter regions of predominantly active genes that are bound by RNA polymerase II (Pol II) and contain the H3K4me3 histone mark. The coactivator HAT complexes, Tip60- and Mof (KAT8)-containing (NSL and MSL), show a global overlap at promoters, whereas distinct binding profiles at enhancers suggest different regulatory functions of each essential HAT complex. Interestingly, Tip60 enrichment peaks at about 200 bp downstream of the transcription start sites suggesting a function for the Tip60 complexes in addition to histone acetylation. The comparison of genome-wide binding profiles of Tip60 and c-Myc, a somatic cell reprogramming factor that binds predominantly to active genes in mESCs, demonstrate that Tip60 and c-Myc co-bind at 50-60 % of their binding sites. We also show that the Tip60 complex binds to a subset of bivalent developmental genes and defines a set of mESC-specific enhancer as well as super-enhancer regions., Conclusions: Our study suggests that the Tip60 complex functions as a global transcriptional co-activator at most active Pol II promoters, co-regulates the ESC-specific c-Myc network, important for ESC self-renewal and cell metabolism and acts at a subset of active distal regulatory elements, or super enhancers, in mESCs.
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- 2015
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36. Transcriptome-wide analysis of microRNA expression in the malaria mosquito Anopheles gambiae.
- Author
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Biryukova I, Ye T, and Levashina E
- Subjects
- Animals, Anopheles metabolism, Base Sequence, Chromosomes, Insect genetics, Cluster Analysis, Conserved Sequence, Female, Gene Duplication, Gene Expression Profiling, Genes, Insect, Insect Vectors metabolism, MicroRNAs metabolism, Multigene Family, Postprandial Period, Sequence Analysis, RNA, Anopheles genetics, Insect Vectors genetics, MicroRNAs genetics, Transcriptome
- Abstract
Background: microRNAs (miRNAs) are a highly abundant class of small noncoding regulatory RNAs that post-transcriptionally regulate gene expression in multicellular organisms. miRNAs are involved in a wide range of biological and physiological processes, including the regulation of host immune responses to microbial infections. Small-scale studies of miRNA expression in the malaria mosquito Anopheles gambiae have been reported, however no comprehensive analysis of miRNAs has been performed so far., Results: Using small RNA sequencing, we characterized de novo A. gambiae miRNA repertoire expressed in adult sugar- and blood-fed females. We provided transcriptional evidences for 123 miRNAs, including 58 newly identified miRNAs. Out of the newly described miRNAs, 19 miRNAs are homologs to known miRNAs in other insect species and 17 miRNAs share sequence similarity restricted to the seed sequence. The remaining 21 novel miRNAs displayed no obvious sequence homology with known miRNAs. Detailed bioinformatics analysis of the mature miRNAs revealed a sequence variation occurring at their 5'-end and leading to functional seed shifting in more than 5% of miRNAs. We also detected significant sequence heterogeneity at the 3'-ends of the mature miRNAs, mostly due to imprecise processing and post-transcriptional modifications. Comparative analysis of arm-switching events revealed the existence of species-specific production of dominant mature miRNAs induced by blood feeding in mosquitoes. We also identified new conserved and fragmented miRNA clusters and A. gambiae-specific miRNA gene duplication. Using miRNA expression profiling, we identified the differentially expressed miRNAs at an early time point after regular blood feeding and after infection with the rodent malaria parasite Plasmodium berghei. Significant changes were detected in the expression levels of 4 miRNAs in blood-fed mosquitoes, whereas 6 miRNAs were significantly upregulated after P. berghei infection., Conclusions: In the current study, we performed the first systematic analysis of miRNAs in A. gambiae. We provided new insights on mature miRNA sequence diversity and functional shifts in the mosquito miRNA evolution. We identified a set of the differentially expressed miRNAs that respond to normal and infectious blood meals. The extended set of Anopheles miRNAs and their isoforms provides a basis for further experimental studies of miRNA expression patterns and biological functions in A. gambiae.
- Published
- 2014
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