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Xia Y, Wang J, Fang X, Dou T, Han L, Yang C. Combined analysis of metagenomic data revealed consistent changes of gut microbiome structure and function in inflammatory bowel disease. J Appl Microbiol 2021; 131:3018-3031. [PMID: 34008889 DOI: 10.1111/jam.15154] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/13/2021] [Accepted: 05/12/2021] [Indexed: 12/11/2022]
Abstract
AIMS To reveal the consistency and discrepancy in the gut microbial structure and function in inflammatory bowel disease (IBD) patients from different regions. METHODS AND RESULTS Gut microbes, antibiotic resistance genes (ARGs) and virulence factors genes (VFGs) were analysed using metagenome data from three cohorts. The abundance of Escherichia coli extensively increased in IBD patients, whereas Subdoligranulum unclassified decreased dramatically in IBD patients from three countries. Escherichia coli showed a positive correlation with multiple ARGs and VFGs in cohorts from China and the United States, including multidrug-related resistance genes and Capsule and LOS-related virulence factors genes. Escherichia coli biofilm synthesis pathways significantly enriched in IBD patients from three different regions. Notably, Subdoligranulum unclassified and Eubacterium hallii were negatively related to ARGs and VFGs. CONCLUSIONS Consistent changes of microbiome structure and function were observed in IBD patients from three different regions. As pathogenic bacteria, E. coli may accelerate IBD progression through encapsulation in biofilms by upregulating antibiotic resistance in Crohn's disease patients. Subdoligranulum unclassified and E. hallii may be beneficial for IBD patients and could serve as potential probiotics for IBD treatment. SIGNIFICANCE AND IMPACT OF THE STUDY This work dispels worries about the regional differences in gut microbial changes in IBD patients and provides useful guidance for more rational microbiome-based therapies.
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Affiliation(s)
- Y Xia
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - J Wang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China.,Department of Scientific Research, KMHD, Shenzhen, China
| | - X Fang
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - T Dou
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - L Han
- Department of Scientific Research, KMHD, Shenzhen, China
| | - C Yang
- Department of Scientific Research, KMHD, Shenzhen, China
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Xi J, Wang X, Yue D, Dou T, Wu Q, Lu J, Liu Y, Yu W, Qiao K, Lin J, Luo S, Li J, Du A, Dong J, Chen Y, Luo L, Yang J, Niu Z, Liang Z, Zhao C, Lu J, Zhu W, Zhou Y. 5' UTR CGG repeat expansion in GIPC1 is associated with oculopharyngodistal myopathy. Brain 2021; 144:601-614. [PMID: 33374016 DOI: 10.1093/brain/awaa426] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/20/2020] [Accepted: 10/05/2020] [Indexed: 11/14/2022] Open
Abstract
Oculopharyngodistal myopathy is a late-onset degenerative muscle disorder characterized by ptosis and weakness of the facial, pharyngeal, and distal limb muscles. A recent report suggested a non-coding trinucleotide repeat expansion in LRP12 to be associated with the disease. Here we report a genetic study in a Chinese cohort of 41 patients with the clinical diagnosis of oculopharyngodistal myopathy (21 cases from seven families and 20 sporadic cases). In a large family with 12 affected individuals, combined haplotype and linkage analysis revealed a maximum two-point logarithm of the odds (LOD) score of 3.3 in chromosomal region chr19p13.11-p13.2 and narrowed the candidate region to an interval of 4.5 Mb. Using a comprehensive strategy combining whole-exome sequencing, long-read sequencing, repeat-primed polymerase chain reaction and GC-rich polymerase chain reaction, we identified an abnormal CGG repeat expansion in the 5' UTR of the GIPC1 gene that co-segregated with disease. Overall, the repeat expansion in GIPC1 was identified in 51.9% independent pedigrees (4/7 families and 10/20 sporadic cases), while the repeat expansion in LRP12 was only identified in one sporadic case (3.7%) in our cohort. The number of CGG repeats was <30 in controls but >60 in affected individuals. There was a slight correlation between repeat size and the age at onset. Both repeat expansion and retraction were observed during transmission but somatic instability was not evident. These results further support that non-coding CGG repeat expansion plays an essential role in the pathogenesis of oculopharyngodistal myopathy.
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Affiliation(s)
- Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xilu Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dongyue Yue
- Department of Neurology, Jing'an District Center Hospital of Shanghai, Shanghai, 200040, China
| | - Tonghai Dou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qunfeng Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jun Lu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yiqi Liu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Wenbo Yu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Kai Qiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jie Lin
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Sushan Luo
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jing Li
- Department of Radiology, Jing'an District Center Hospital of Shanghai, Shanghai, 200040, China
| | - Ailian Du
- Department of Neurology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China
| | - Jihong Dong
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yan Chen
- Department of Neurology, Tongji Hospital, Tongji University, Shanghai, 200065, China
| | - Lijun Luo
- Department of Neurology, Wuhan No.1 Hospital, Wuhan, 430021, China
| | - Jie Yang
- Department of Neurology, Wuhan No.1 Hospital, Wuhan, 430021, China
| | - Zhenmin Niu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Zonghui Liang
- Department of Radiology, Jing'an District Center Hospital of Shanghai, Shanghai, 200040, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
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3
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Abstract
1. Egg-laying performance reflects the overall reproductive performance of breeding hens. The genetic traits for egg-laying performance have low or medium heritability, and, depending on the period involved, usually ranges from 0.16 to 0.64. Egg-laying in chickens is regulated by a combination of environmental, endocrine and genetic factors. 2. The main endocrine factors that regulate egg-laying are gonadotropin-releasing hormone (GnRH), prolactin (PRL), follicle-stimulating hormone (FSH) and luteinising hormone (LH). 3. In the last three decades, many studies have explored this aspect at a molecular genetic level. Recent studies identified 31 reproductive hormone-based candidate genes that were significantly associated with egg-laying performance. With the development of genome-sequencing technology, 64 new candidate genes and 108 single nucleotide polymorphisms (SNPs) related to egg-laying performance have been found using genome-wide association studies (GWAS), providing novel insights into the molecular genetic mechanisms governing egg production. At the same time, microRNAs that regulate genes responsible for egg-laying in chickens were reviewed. 4. Research on endocrinological and genetic factors affecting egg-laying performance will greatly improve the reproductive performance of chickens and promote the protection, development, and utilisation of poultry. This review summarises studies on the endocrine and genetic factors of egg-laying performance in chickens from 1972 to 2019.
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Affiliation(s)
- Y Du
- College of Animal Science and Technology, Yunnan Agricultural University , Kunming, Yunnan, The People's Republic of China
| | - L Liu
- School of Forensic Medicine, Kunming Medical University , Kunming, Yunnan, The People's Republic of China
| | - Y He
- College of Animal Science and Technology, Yunnan Agricultural University , Kunming, Yunnan, The People's Republic of China
| | - T Dou
- College of Animal Science and Technology, Yunnan Agricultural University , Kunming, Yunnan, The People's Republic of China
| | - J Jia
- College of Animal Science and Technology, Yunnan Agricultural University , Kunming, Yunnan, The People's Republic of China
| | - C Ge
- College of Animal Science and Technology, Yunnan Agricultural University , Kunming, Yunnan, The People's Republic of China
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Sun J, Luo S, Song J, Huang J, Cai S, Zhu W, Zhou L, Xi J, Lin J, Lu J, Xu M, Dou T, Zhao C, Qiao K. Electromyographic Features in a Chinese Cohort With Hereditary Skeletal Muscle Channelopathies. J Clin Neurophysiol 2020; 37:231-238. [DOI: 10.1097/wnp.0000000000000635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Zhao C, Pan T, Dou T, Liu J, Liu C, Ge Y, Zhang Y, Yu X, Mitrovic S, Lim R. Making global river ecosystem health assessments objective, quantitative and comparable. Sci Total Environ 2019; 667:500-510. [PMID: 30833248 DOI: 10.1016/j.scitotenv.2019.02.379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/21/2019] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Abstract
Assessing and comparing global river ecosystem health in an objective and quantitative way remains a major challenge. In this study the widely-used semi-quantitative methods Rapid Biological assessment Protocols (RBPs) was used to determine the health of rivers. The findings were then compared to the results derived from our new UAV (Unmanned aerial vehicles) orthophotographic imagery method. This method quantitatively and objectively assesses river ecosystem health. As a comparison, our method was used to quantitatively measure distance and areas of a range of hydrological and biological attributes thus improving the accuracy of distance- and area-related indices, consequently avoiding subjective errors in these estimations that is fraught in methods like the RBPs. To strengthen the objectivity of the assessment the weights of these indices were objectively determined using the entropy weighting method. This new method was then tested using 9551 UAV orthophotographs taken over six field campaigns. It performed satisfactorily, showing that in our study area the health status of mountain rivers was the best with the highest score of 0.94 out of 1.0. Temporally, the health of the river was better in summer (0.65) compared with that in autumn (0.40). Changes in river ecosystem health were driven by variations in biology and water quality. In contrast the outputs of RBPs, especially in relation to distance and area indices, had ~ 20% uncertainty due to visual errors and subjectivity in estimations by observers. The UAV orthophotographic imaging method proposed in this study can improve the ability to compare the health of rivers across different periods and regions throughout the globe.
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Affiliation(s)
- C Zhao
- College of Water Sciences, Beijing Normal University, Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, Beijing 100875, PR China; ICube, UdS, CNRS (UMR 7357), 300 Bld Sebastien Brant, CS 10413, 67412 Illkirch, France
| | - T Pan
- School of Geography, Beijing Normal University, Beijing 100875, PR China
| | - T Dou
- Jinan Survey Bureau of Hydrology and Water Resources, Jinan 250013, PR China
| | - J Liu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - C Liu
- College of Water Sciences, Beijing Normal University, Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, Beijing 100875, PR China.
| | - Y Ge
- Jinan Survey Bureau of Hydrology and Water Resources, Jinan 250013, PR China
| | - Y Zhang
- School of Geography, Beijing Normal University, Beijing 100875, PR China
| | - X Yu
- School of Geography, Beijing Normal University, Beijing 100875, PR China
| | - S Mitrovic
- School of Life Sciences, Faculty of Science, University of Technology, Sydney, NSW 2007, Australia
| | - R Lim
- School of the Environment, Faculty of Science, University of Technology, Sydney, NSW 2007, Australia
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Luo S, Xu M, Sun J, Qiao K, Song J, Cai S, Zhu W, Zhou L, Xi J, Lu J, Ni X, Dou T, Zhao C. Identification of gene mutations in patients with primary periodic paralysis using targeted next-generation sequencing. BMC Neurol 2019; 19:92. [PMID: 31068157 PMCID: PMC6505267 DOI: 10.1186/s12883-019-1322-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 04/29/2019] [Indexed: 02/02/2023] Open
Abstract
Background Primary periodic paralysis is characterized by recurrent quadriplegia typically associated with abnormal serum potassium levels. The molecular diagnosis of primary PP previously based on Sanger sequencing of hot spots or exon-by-exon screening of the reported genes. Methods We developed a gene panel that includes 10 ion channel-related genes and 245 muscular dystrophy- and myopathy-related genes and used this panel to diagnose 60 patients with primary periodic paralysis and identify the disease-causing or risk-associated gene mutations. Results Mutations of 5 genes were discovered in 39 patients (65.0%). SCN4A, KCNJ2 and CACNA1S variants accounted for 92.5% of the patients with a genetic diagnosis. Conclusions Targeted next-generation sequencing offers a cost-effective approach to expand the genotypes of primary periodic paralysis. A clearer genetic profile enables the prevention of paralysis attacks, avoidance of triggers and the monitoring of complications. Electronic supplementary material The online version of this article (10.1186/s12883-019-1322-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sushan Luo
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Minjie Xu
- Key Laboratory of Contraceptives and Devices, Shanghai Institute of Planned Parenthood Research, institute of Reproduction and development, Fudan University, Shanghai, 200032, China
| | - Jian Sun
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Kai Qiao
- Department of clinical electrophysiology, Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jie Song
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Shuang Cai
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Lei Zhou
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xiaohua Ni
- Key Laboratory of Contraceptives and Devices, Shanghai Institute of Planned Parenthood Research, institute of Reproduction and development, Fudan University, Shanghai, 200032, China
| | - Tonghai Dou
- State Key Laboratory of Genetic Engineering, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, 200433, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, 200040, China. .,Department of Neurology, Jing'an District Center Hospital of Shanghai, Shanghai, 200040, China.
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Wang L, Dou T, Li S, Liu Y. Transcriptome profiling and pathway analysis of the effects of mono-(2-ethylhexyl) phthalate in mouse Sertoli cells. Exp Ther Med 2019; 17:2821-2829. [PMID: 30906470 DOI: 10.3892/etm.2019.7239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 01/28/2019] [Indexed: 01/12/2023] Open
Abstract
Phthalates are confirmed to have toxic effects on the reproductive system and are likely to have further damaging actions in humans. The present study explored the molecular mechanisms of the toxic effect of mono-(2-ethylhexyl) phthalate (MEHP) on mouse Sertoli cells. Cell apoptosis and proliferation assays were used to assess the effects of MEHP on the TM4 Sertoli cell line derived from mouse testes. TM4 cells were treated with two doses of MEHP or left untreated as a control group, followed by RNA extraction and analysis using high-throughput transcriptome sequencing technology. The gene expression profile obtained was then subjected to a bioinformatics analysis to explore the molecular mechanisms of reproductive toxicity. The results revealed that 528 and 269 genes were upregulated in the high- and low-dose MEHP groups of cells compared with the control group, while 148 and 173 genes were downregulated. Gene ontology (GO) analysis indicated that the differently expressed genes were associated with the GO term 'extracellular region' of the cellular component domain in the high and low MEHP groups. Compared with the control group, eight common pathway changes were identified in the high- and low-dose MEHP groups, including 'terpenoid backbone biosynthesis'. Reverse transcription-quantitative polymerase chain reaction analysis was used to validation, and hermetic effects were observed for certain genes. These results provide an important basis and experimental data for further research into the mechanisms of phthalate-induced toxicity.
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Affiliation(s)
- Liqiang Wang
- Key Laboratory of Public Health Safety of The Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, P.R. China.,College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai 201318, P.R. China
| | - Tonghai Dou
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Shuguang Li
- Key Laboratory of Public Health Safety of The Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, P.R. China
| | - Yang Liu
- Shanghai Institute of Quality Inspection and Technical Research, National Quality Supervision and Inspection Center for Food Products (Shanghai), Shanghai 200233, P.R. China
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Liu Y, Chen W, Yu Y, Zhang Q, Qu Q, Duan W, Zhao Y, Weng S, Zhao G, Dou T. Identification and characterisation of bifidobacteria in infant formula milk powder obtained from the Chinese market. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Dou T, Aerts H, Coroller T, Mak R. Radiomic-Based Phenotyping of Tumor Core and Rim to Predict Survival in Nonsmall Cell Lung Cancer. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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Thomas DH, Ruan D, Williams P, Lamb J, White BM, Dou T, O’Connell D, Lee P, Low DA. Is there an ideal set of prospective scan acquisition phases for fast-helical based 4D-CT? Phys Med Biol 2016; 61:N632-N641. [DOI: 10.1088/0031-9155/61/23/n632] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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O'Connell D, Thomas D, Dou T, Yang L, Lamb J, Lewis J, Ruan D, Lee P, Low D. SU-D-202-06: Prospective Free-Breathing CT Scan Selection for 5DCT. Med Phys 2016. [DOI: 10.1118/1.4955646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Yang L, O'Connell D, Lee P, Shaverdian N, Kishan A, Lewis J, Dou T, Thomas D, Qi X, Low D. SU-F-J-135: Tumor Displacement-Based Binning for Respiratory-Gated Time-Independent 5DCT Treatment Planning. Med Phys 2016. [DOI: 10.1118/1.4956043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Dou T, Ruan D, Heinrich M, Low D. TH-CD-202-06: A Method for Characterizing and Validating Dynamic Lung Density Change During Quiet Respiration. Med Phys 2016. [DOI: 10.1118/1.4958161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Low D, Thomas D, Dou T, Lee P, Lewis J, O'Connell D. PO-0880: Clinical implementation of 5DCT workflow. Radiother Oncol 2016. [DOI: 10.1016/s0167-8140(16)32130-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Guo J, Ma M, Qu L, Shen M, Dou T, Wang K. Estimation of genetic parameters related to eggshell strength using random regression models. Br Poult Sci 2016; 56:645-50. [DOI: 10.1080/00071668.2015.1113503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Chen C, Yao Y, Zhang L, Xu M, Jiang J, Dou T, Lin W, Zhao G, Huang M, Zhou Y. A Comprehensive Analysis of the Transcriptomes of Marssonina brunnea and Infected Poplar Leaves to Capture Vital Events in Host-Pathogen Interactions. PLoS One 2015. [PMID: 26222429 PMCID: PMC4519268 DOI: 10.1371/journal.pone.0134246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Understanding host-pathogen interaction mechanisms helps to elucidate the entire infection process and focus on important events, and it is a promising approach for improvement of disease control and selection of treatment strategy. Time-course host-pathogen transcriptome analyses and network inference have been applied to unravel the direct or indirect relationships of gene expression alterations. However, time series analyses can suffer from absent time points due to technical problems such as RNA degradation, which limits the application of algorithms that require strict sequential sampling. Here, we introduce an efficient method using independence test to infer an independent network that is exclusively concerned with the frequency of gene expression changes. Results Highly resistant NL895 poplar leaves and weakly resistant NL214 leaves were infected with highly active and weakly active Marssonina brunnea, respectively, and were harvested at different time points. The independent network inference illustrated the top 1,000 vital fungus-poplar relationships, which contained 768 fungal genes and 54 poplar genes. These genes could be classified into three categories: a fungal gene surrounded by many poplar genes; a poplar gene connected to many fungal genes; and other genes (possessing low degrees of connectivity). Notably, the fungal gene M6_08342 (a metalloprotease) was connected to 10 poplar genes, particularly including two disease-resistance genes. These core genes, which are surrounded by other genes, may be of particular importance in complicated infection processes and worthy of further investigation. Conclusions We provide a clear framework of the interaction network and identify a number of candidate key effectors in this process, which might assist in functional tests, resistant clone selection, and disease control in the future.
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Affiliation(s)
- Chengwen Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China
- Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Ye Yao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Center for Computational Systems Biology and School of Mathematical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Liang Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China
| | - Minjie Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China
| | - Jianping Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China
| | - Tonghai Dou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Wei Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Center for Computational Systems Biology and School of Mathematical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Guoping Zhao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China
| | - Minren Huang
- Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, People’s Republic of China
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China
- * E-mail:
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Dou T, Ramos-Mendez J, Piersimoni P, Giacometti V, Penfold S, Censor Y, Faddegon B, Low D, Schulte R. SU-E-J-148: Tools for Development of 4D Proton CT. Med Phys 2015. [DOI: 10.1118/1.4924233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Penfold S, Casiraghi M, Dou T, Schulte R, Censor Y. SU-E-T-33: A Feasibility-Seeking Algorithm Applied to Planning of Intensity Modulated Proton Therapy: A Proof of Principle Study. Med Phys 2015. [DOI: 10.1118/1.4924394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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19
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Ruan D, Dou T, Thomas D, Low D. MO-FG-204-02: Reference Image Selection in the Presence of Multiple Scan Realizations. Med Phys 2015. [DOI: 10.1118/1.4925423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Dou T, Thomas D, O'Connell D, Lamb J, Low D. TH-CD-303-04: A Method for Assessing Ground-Truth Accuracy of a Motion Model Based 4DCT Technique. Med Phys 2015. [DOI: 10.1118/1.4926239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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21
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Jiang J, Gu J, Zhang L, Zhang C, Deng X, Dou T, Zhao G, Zhou Y. Comparing Mycobacterium tuberculosis genomes using genome topology networks. BMC Genomics 2015; 16:85. [PMID: 25766780 PMCID: PMC4342819 DOI: 10.1186/s12864-015-1259-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 01/20/2015] [Indexed: 11/25/2022] Open
Abstract
Background Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. Results In this work, we introduce a ‘Genome Topology Network’ (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of ‘unfixed ortholog’ has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). Conclusions The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/, and allows re-annotating the ‘lost’ genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes were found to be affected by SVs in M. tuberculosis genomes. We believe that the GTN method will be suitable for the exploration of genomic SVs in connection with biological features of bacterial strains, and that GTN-based phylogenetic analysis will provide additional insights into whole genome-based phylogenetic analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1259-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jianping Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
| | - Jianlei Gu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
| | - Liang Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
| | - Chenyi Zhang
- School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - Xiao Deng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, 215123, People's Republic of China.
| | - Tonghai Dou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China.
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
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Thomas D, Tan J, Neylon J, Dou T, Jani S, Lamb J, Low D. TH-C-18A-11: Investigating the Minimum Scan Parameters Required to Generate Free-Breathing Fast-Helical CT Scans Without Motion-Artifacts. Med Phys 2014. [DOI: 10.1118/1.4889635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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23
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Dou T, Thomas D, Lamb J, Low D. SU-D-17A-05: A Method to Determine the Accuracy of a Proposed Breathing Motion Model-Based 4DCT Technique. Med Phys 2014. [DOI: 10.1118/1.4887898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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24
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Dou T, Thomas D, Lamb J, Low D. SU-E-J-25: Analysis of Commercial 4DCT Flaws and the Potential Benefits of a New Technique for Irregular Breathing Patients. Med Phys 2014. [DOI: 10.1118/1.4888076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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25
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Abstract
Interferon gamma (IFNG) is a major cytokine and plays crucial roles in pathogen clearance. About the course of evolution of IFNG, it has been reported that IFNG is being subjected to adaptive selection, which is proved at the level of gene. Neighbor-joining method was used to reconstruct the phylogenetic tree of all IFNG protein-coding sequences. The pair-wise computation of Ka/Ks between every exon homologs, branch-specific model, and site-specific model of the likelihood method were performed to detect positive selection of IFNG. We reported, for the first time, that the signal peptide region of IFNG is under significant positive selection, evolving faster than other parts. We provide evidence at the level of individual exon and individual amino acid site that IFNG is under adaptive evolution, which establishes the basis for further researches about IFNG.
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Affiliation(s)
- Zhengshi Wang
- a Department of General Surgery, Ren Ji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai , China
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26
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Wang Z, Zhong M, Fu M, Dou T, Bian Z. Evidence of positive selection at codon sites localized in the C-terminal peptide of ORC6. Biotechnol Lett 2014; 36:251-6. [DOI: 10.1007/s10529-013-1371-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/30/2013] [Indexed: 11/29/2022]
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27
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Low D, Thomas D, Lamb J, Lee P, Gaudio S, Jani S, Dou T, White B, Wu X. OC-0501: Comparison between existing and proposed 4DCT protocols. Radiother Oncol 2014. [DOI: 10.1016/s0167-8140(15)30606-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Dou T, Morele D, Low D. SU-E-T-20: Validating That the Gamma Dose Distribution Comparison Defaults to the Distance-To-Agreement (DTA) Test in Steep Dose Gradients for Clinical Dose Distributions. Med Phys 2013. [DOI: 10.1118/1.4814454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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29
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Santhanam A, Dou T, Min Y, Meeks S, Kupelian P. SU-E-J-73: Effect of 4D-CT Image Artifacts On the 3D Lung Registration Accuracy: A Parametric Study Using a GPU-Accelerated Multi-Resolution Multi-Level Optical Flow. Med Phys 2013. [DOI: 10.1118/1.4814285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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31
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Xu Z, Dou C, Dou T, Gu Y, Wu S, Song Y, Xing H. 59P Mammary Duct Endoscopy with Saline Lavage for Breast Cancer Prevention and Homeostasis Maintenance in Middle Aged Women. Ann Oncol 2012. [DOI: 10.1016/s0923-7534(19)65704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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32
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Xu J, Dou T, Liu C, Fu M, Huang Y, Gu S, Zhou Y, Xie Y. The evolution of alternative splicing exons in vascular endothelial growth factor A. Gene 2011; 487:143-50. [PMID: 21782909 DOI: 10.1016/j.gene.2011.06.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 06/12/2011] [Accepted: 06/18/2011] [Indexed: 12/13/2022]
Abstract
The C-terminus alternative splicing in VEGFA (vascular endothelial growth factor A) is known for its impact on physiological and pathological angiogenesis. Based on our prediction and RT-PCR verification, we identified anti-angiogenic VEGFA165b isoforms in mouse and rabbit for the first time. We also found that the relative expression level of VEGFA165b isoform had been increasing from rodents to human, and exon8b may have experienced a minor-to-major form exon conversion, possibly correlated with its gain-of-function. It is suggested that introduction of alternative splicing exons (esp. exon6 and exon8b) made important contributions to the transcriptional diversity of VEGFA and played a crucial role in the evolution of its regulatory mechanism.
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Affiliation(s)
- Jiaxi Xu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
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33
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Tenn S, Ruan D, Dou T, Low D. SU-E-T-108: EBT2 Film Based Dosimetry Incorporating Correction for Spatial-Temporal Dose Response Variation. Med Phys 2011. [DOI: 10.1118/1.3612059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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34
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Gu X, Wang H, Wang A, Dou T, Qi P, Ji Q, Li H, Gao C. An intronic polymorphism rs2237062 in the CXCL14 gene influences HBV-related HCC progression in Chinese population. Mol Biol Rep 2011; 39:797-803. [PMID: 21556757 DOI: 10.1007/s11033-011-0801-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 04/29/2011] [Indexed: 01/06/2023]
Abstract
CXCL14 (C-X-C motif chemokine ligand 14) is a conserved member of chemokine family and functions as a chemoattractant for multiplicate immunocytes. CXCL14 expression is constitutive in normal tissues, but absent in wide range of epithelial tumors. Many reports have claimed its important role in tumorigenesis and vascularization. An association between rs2237062 polymorphism and hepatocellular carcinoma (HCC) susceptibility was found in patients with chronic HCV infection in Japanese population. Here we analyzed, by using a polymerase chain reaction-ligation detection reaction (PCR-LDR), the polymorphism in 202 non-HCC patients with HBV infection, 361 HBV-related HCC patients and 407 healthy controls. The aim was to detect the possible association of this single-nucleotide polymorphism (SNP) with HBV-related HCC susceptibility and progression. However, no association was found between rs2237062 polymorphism and susceptibility to HBV infection or HBV-related HCC. Intriguingly, our stratification analysis revealed that HBV-related HCC patients in advanced phase (TNM-II-IV stage) had significantly higher C allele frequency at this polymorphism than patients at early stage (TNM-I stage) (33.5% vs. 25.7%), and its odds ratio reached 1.47 (95% CI 1.06-2.04, P = 0.021). These results suggest that the rs2237062 polymorphism in the CXCL14 gene might influence HBV-related HCC progression in Chinese population.
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Affiliation(s)
- Xing Gu
- Department of Laboratory Medicine, Eastern Hepatobiliary Hospital, Second Military Medical University, Shanghai 200438, People's Republic of China
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35
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Chen H, Zhou L, Wan G, Dou T, Tian J. BMI1 promotes the progression of laryngeal squamous cell carcinoma. Oral Oncol 2011; 47:472-81. [PMID: 21482478 DOI: 10.1016/j.oraloncology.2011.03.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 02/16/2011] [Accepted: 03/12/2011] [Indexed: 10/18/2022]
Abstract
BMI1 is highly expressed in several malignant tumors, and its expression level is associated with tumor progression, proliferation, and prognosis. However, no published studies have examined the role of BMI1 in laryngeal squamous cell carcinoma (SCC). Expression of BMI1 in primary tumors was analyzed by immunofluorescence staining, real-time PCR, and Western blotting. BMI1 was knocked down, and proliferation, apoptosis, and cell cycle assays were performed. Sensitivity to radiochemotherapy was evaluated, and tumorigenicity assays were performed in vivo. BMI1 was highly expressed in laryngeal SCCs. BMI1 promoted cell proliferation and tumor progression, and inhibited apoptosis due to influences on the cell cycle. More importantly, BMI1 suppressed the sensitization of laryngeal Hep2 cells to radiochemotherapy. BMI1 is essential to maintain the proliferation and progression of laryngeal SCCs. Therefore, depletion of BMI1 may be a potential therapeutic option for cancer management.
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Affiliation(s)
- Hui Chen
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye and ENT Hospital of Fudan University, Shanghai, China
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36
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Tang W, Dou T, Zhong M, Wu Z. Dysregulation of Claudin family genes in colorectal cancer in a Chinese population. Biofactors 2011; 37:65-73. [PMID: 21294205 DOI: 10.1002/biof.138] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 11/15/2010] [Indexed: 12/18/2022]
Abstract
Claudins play an important role in tumor metastasis and in invasiveness of colorectal cancer (CRC). We have evaluated the relationship between CRC and expression of the claudin genes in Chinese patients with CRC. We measured CLDN1 and CLDN7 mRNA using quantitative PCR, and protein levels with immunohistochemistry in cancer tissues and adjacent normal tissue. Cancer tissues had significantly higher levels of CLDN1, and significantly lower levels of CLDN3, CLDN4, and CLDN7 than did normal tissue. CLDN3, CLDN4, and CLDN7 expression levels were higher in CRC of the protruded type than in CRC of the infiltrative type. Expression of CLDN7 correlated with lymph node metastasis. Stage N0 cancer tissues had higher levels of CLDN7 than did stages N1 and N2, suggesting that CLDN7 expression was closely related to the extent of lymph node metastasis. CLDN1 protein was upregulated, but CLDN7 protein was downregulated in cancer tissues when compared with expression in adjacent normal tissues. In conclusion, CLDN3, CLDN4, and CLDN7 were significantly downregulated, whereas CLDN1 was significantly upregulated in CRC. The altered expression of claudin genes may play a role in the initiation and development of CRC.
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Affiliation(s)
- Weijun Tang
- Department of General Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shangai, People's Republic of China
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37
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Wu Q, Zhan X, Dou T, Chen H, Fan W, Zhou K, Zhang H, Zheng H, Cai Y, Zhao Y, Huang F, Zhou L, Mao Y, Lu D. CTLA4 A49G Polymorphism Shows Significant Association With Glioma Risk in a Chinese Population. Biochem Genet 2010; 49:190-201. [DOI: 10.1007/s10528-010-9398-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 08/25/2010] [Indexed: 10/18/2022]
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38
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Chen H, Zhou L, Dou T, Wan G, Tang H, Tian J. BMI1'S maintenance of the proliferative capacity of laryngeal cancer stem cells. Head Neck 2010; 33:1115-25. [DOI: 10.1002/hed.21576] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2010] [Indexed: 12/28/2022] Open
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39
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Dou T, Xu J, Gao Y, Gu J, Ji C, Xie Y, Zhou Y. Evolution of peroxisome proliferator-activated receptor gamma alternative splicing. Front Biosci (Elite Ed) 2010; 2:1334-43. [PMID: 20515805 DOI: 10.2741/e193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisome proliferator-activated receptor gamma (PPAR gamma) plays an important role in the control of energy balance and lipid and glucose homeostasis. Different transcript variants were investigated not only in human but also in other vertebrates. To look into the evolutionary changes of these variants, we analyzed the genomic sequences of PPAR gamma genes from several vertebrate species, as well as their mRNA and EST data. Several potential alternative splicing exons at the 5'-end of the PPAR gamma gene were identified. The 5'-end of the PPAR gamma gene is discovered to be evolutionarily active and recruits new exons via different strategies. Moreover, it is shown that the only coding alternative exon (exon B) processes much higher Ka/Ks compared with its constitutive counterparts. In addition, its Ka/Ks is greater than 1 in the rat, mouse, and rabbit, indicating adaptive evolution and possible energy storage related gain-of-function for the exon.
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Affiliation(s)
- Tonghai Dou
- Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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40
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Dou T, Wu Q, Chen X, Ribas J, Ni X, Tang C, Huang F, Zhou L, Lu D. A polymorphism of microRNA196a genome region was associated with decreased risk of glioma in Chinese population. J Cancer Res Clin Oncol 2010; 136:1853-9. [PMID: 20229273 DOI: 10.1007/s00432-010-0844-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 02/15/2010] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play important roles in regulation of eukaryotic gene expression. Aberrant expression and structural alternation of miRNAs are considered to participate in tumorigenesis and cancer development. Recently, different genotypes of miR-196a polymorphisms (SNP, rs11614913) were found to be associated with the survival of patients with lung cancer and increased risk of breast cancer. To further investigate whether this polymorphism may influence glioma risk or not, we examined the SNP allele frequency in Chinese population. Our data shows the genotype CC of miR-196a (rs11614913) polymorphism is associated with decreased risk of glioma in the Chinese population (OR = 0.74, 95% CI:0.56-0.98). Furthermore, a significant association was observed between this genotype and glioma risk in the subgroups of adult glioma (OR = 0.73, 95% CI:0.55-0.98), male glioma (OR = 0.69, 95% CI:0.48-0.99) and patients with glioblastoma (OR = 0.58, 95% CI:0.37-0.91). This was the first study investigating the association between the miR-196a rs11614913 and glioma risk. Compared with the results from previous studies in lung cancer and breast cancer, our data suggest a different genotype association in glioma. This may be related to the diversity on the tissue origin, tumor type, tumorigenesis, and developing process.
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Affiliation(s)
- Tonghai Dou
- Department of Microbiology School of Life Sciences, Fudan University, Shanghai 200433, China
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41
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Zheng H, Zhou L, Dou T, Han X, Cai Y, Zhan X, Tang C, Huang J, Wu Q. Genome-wide prediction of G protein-coupled receptors in Verticillium spp. Fungal Biol 2010; 114:359-68. [PMID: 20943146 DOI: 10.1016/j.funbio.2010.02.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 01/11/2010] [Accepted: 02/24/2010] [Indexed: 11/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are critical factors in regulating morphogenesis, mating, infection and virulence in fungi. In this study, various computational strategies were applied to identify GPCR-like proteins from the genomes of both Verticillium dahliae and Verticillium albo-atrum. The putative GPCRs were distributed over 13 classes, and significantly, three of those represented novel classes of GPCR-like proteins in fungi. The three novel GPCRs had high levels of identity to their counterparts in higher eukaryotes, including Homo sapiens. The numbers of GPCR-like proteins in the two Verticillium spp. were similar to those seen in other filamentous fungi, such as Magnaporthe grisea, Neurospora crassa and Fusarium graminearum. Additionally, the carbon/amino acid receptors were divided into three different subclasses, indicating that differences among the GPCRs existed not only among different classes but also within classes. In conclusion, the identification and classification of GPCRs and their homology to some well-studied fungi will be an important starting point for future research in Verticillium spp.
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Affiliation(s)
- Hongxia Zheng
- Department of Biomedicine, School of Life Science, East China Normal University, Shanghai, China
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Gu X, Qi P, Zhou F, Ji Q, Wang H, Dou T, Zhao Y, Gao C. An intronic polymorphism in the corticotropin-releasing hormone receptor 2 gene increases susceptibility to HBV-related hepatocellular carcinoma in Chinese population. Hum Genet 2009; 127:75-81. [PMID: 19813023 DOI: 10.1007/s00439-009-0750-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 09/17/2009] [Indexed: 01/26/2023]
Abstract
Corticotropin-releasing hormone receptor 2 (CRHR2) plays a role in both the central nervous system (CNS) and the peripheral nervous system. CRHR2 together with its ligands, urocortins (Ucns) and corticotropin-releasing hormone (CRH), functions as a mediator of inflammatory response and inhibitor of angiogenesis. Recently, it has been reported to be expressed in many human cancers. An association between rs2267716 polymorphism in the CRHR2 gene and susceptibility to hepatocellular carcinoma (HCC) was found in patients with chronic hepatitis C virus (HCV) infection. In the present study we analyzed, using a polymerase chain reaction-ligation detection reaction (PCR-LDR), the rs2267716 polymorphism in 364 hepatitis B virus (HBV)-related HCC patients, 196 non-HCC patients with HBV infection, and 404 healthy controls. The aim was to detect the possible association of this single-nucleotide polymorphism (SNP) with susceptibility to HBV-related HCC. Significant differences of rs2267716 allele were detected between HBV-related HCC patients and healthy controls (OR = 1.55, 95% CI 1.13-2.15, P = 0.007) or non-HCC patients with HBV infection (OR = 1.61, 95% CI 1.13-2.31, P = 0.009). These results suggest that the rs2267716 polymorphism in the CRHR2 gene might influence the risk of developing HCC in patients with HBV infection in Chinese population.
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Affiliation(s)
- Xing Gu
- Department of Laboratory Medicine, Eastern Hepatobiliary Hospital, Second Military Medical University, 200438 Shanghai, People's Republic of China
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43
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Dou T, Ji C, Gu S, Chen F, Xu J, Ye X, Ying K, Xie Y, Mao Y. Cloning and Characterization of a novel splice variant of humanRab18gene (RAB18). ACTA ACUST UNITED AC 2009; 16:230-4. [PMID: 16147880 DOI: 10.1080/10425170500061681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Rab GTPase proteins are a kind of small GTP-binding proteins, which functions mainly focus on regulating interacellular trafficking pathways during vesicular transport. To date, 60 distinct human RAB proteins have been identified. RAB18 gene is discovered from endothelial cells. Its function is considered as endosomes and plasma membrane recycling. Research indicates RAB18 may relate to inflammation and some kinds of tumor. Here we report a splice variant of RAB18, which is 2571 bp in length and has an open reading frame coding a predicted 235 amino-acids protein. RT-PCR shows that the cDNA has different expression pattern with RAB18 and is highly expressed in testis.
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Affiliation(s)
- Tonghai Dou
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
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44
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Xu J, Peng Z, Li R, Dou T, Xu W, Gu G, Liu Y, Kang Z, Tao H, Zhang JH, Ostrowski RP, Lu J, Sun X. Normoxic induction of cerebral HIF-1α by acetazolamide in rats: Role of acidosis. Neurosci Lett 2009; 451:274-8. [DOI: 10.1016/j.neulet.2009.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 01/05/2009] [Accepted: 01/06/2009] [Indexed: 11/28/2022]
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Chen F, Ji C, Dou T, Zheng N, Qiu R, Peng J, Fang W, Feng C, Xie Y, Mao Y. Cloning and characterization of a novel splice variant of human U2AF1L3 gene. ACTA ACUST UNITED AC 2007; 17:282-6. [PMID: 17312947 DOI: 10.1080/10425170600807744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Pre-mRNA splicing allows individual genes to produce multiple protein isoforms with diverse functions. Recognition of functional splice sites in pre-mRNAs is very important in this splicing process and requires some protein auxiliary factors such as U2 small nuclear ribonucleoprotein auxiliary factor small subunit (U2AF35, encoded by U2AF1). By its RNA binding domains, U2AF35 interacts with U2AF65 to bind 3' splice site of pre-mRNA and initiates splicing. Another protein, which is named as U2AF1-like3 (U2AF1L3), shows high similarity with U2AF35 and may have related function in pre-mRNA splicing. Here, we report a splice variant of U2AF1L3, which is 767 bp in length and has an open reading frame (ORF) coding a predicted 181 amino acids protein. Reverse transcription-PCR (RT-PCR) shows that this isoform has different expression pattern with U2AF1L3 and is highly expressed in heart, brain and lung.
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Affiliation(s)
- Fei Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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Duan A, Gao J, Xu C, Wang D, Zhao Z, Dou T, Chung KH. Quantum chemistry of adsorption and hydrogenation of DBT and carbazole on NiMoS using ZINDO/I method. Molecular Simulation 2007. [DOI: 10.1080/08927020601133375] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Dou T, Gu S, Liu J, Chen F, Zeng L, Guo L, Xie Y, Mao Y. Isolation and characterization of ubiquitin-activating enzyme E1-domain containing 1, UBE1DC1. Mol Biol Rep 2006; 32:265-71. [PMID: 16328888 DOI: 10.1007/s11033-005-4822-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2005] [Indexed: 12/16/2022]
Abstract
Ubiquitin and other ubiquitin-like proteins play important roles in post-translational modification. They are phylogenetically well-conserved in eukaryotes. Activated by other proteins, ubiquitin and ubiquitin-like proteins can covalently modify target proteins. The enzymes responsible for the activation of this modification have been known to include UBA1, SAE2, UBA3, SAE1 and ULA1. Here we report a new ubiquitin activating enzyme like cDNA, named ubiquitin activating enzyme E1-domain containing 1 (UBE1DC1), whose cDNA is 2654 base pairs in length and contains an open reading frame encoding 404 amino acids. The UBE1DC1 gene consists of 12 exons and is located at human chromosome 3q22. The result of RT-PCR showed that UBE1DC1 is expressed in most of human tissues.
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Affiliation(s)
- Tonghai Dou
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, People's Republic of China
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Dou T, Ji C, Gu S, Xu J, Xu J, Ying K, Xie Y, Mao Y. Co-evolutionary analysis of insulin/insulin like growth factor 1 signal pathway in vertebrate species. FRONT BIOSCI-LANDMRK 2006; 11:380-8. [PMID: 16146739 DOI: 10.2741/1805] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Insulin/insulin like growth factor 1 signaling pathway plays an essential role on the regulation of variant, interrelated and fundamental processes, such as metabolism, growth, reproduction and aging. This pathway is highly conserved during evolution. We analyzed eight vertebrate species' insulin/insulin like growth factor 1 pathway and examined the co-evolutionary relationship between different protein components by quantifying similarity of phylogenetic trees. The collected species include Takifugu rubripes, Danio rerio, Xenopus laevis, Gallus gallus, Mus musculus, Rattous norvegicus, Pan troglodytes and Homo sapiens. Results show that interacting proteins in this pathway share highly co-evolutionary relationship while contrarily the proteins without interaction have low co-evolutionary relationship. We also predict some receptor and ligand partners enjoy highly binding potential in corresponding species' pathway.
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Affiliation(s)
- Tonghai Dou
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, PR China
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Dou T, Chen S, Ji C, Xie Y, Mao Y. Co-evolution analysis on endocrine research: a methodological approach. Endocrine 2005; 28:187-92. [PMID: 16388092 DOI: 10.1385/endo:28:2:187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 08/31/2005] [Accepted: 09/06/2005] [Indexed: 11/11/2022]
Abstract
The rapid growth of different kinds of biological information allows a good opportunity to analyze the co-evolutionary characteristics in endocrine regulatory pathways. Data ranging from kinds of species' genome, gene sequence, protein structure, and expression profile of different organisms can reveal the inner co-evolutionary relationship of ligands, receptors, and other related molecules. In return, these co-evolutionary characteristics can help us determine uncharacterized ligands and receptors, annotate gene functions, highlight amino acid residues with biochemical significance, and identify regulated genes in the endocrine process. Encouraging examples in this field, although at their starting stage, have emerged. Here we focus on recent progress in endocrine-related co-evolution research from a methodological approach.
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Affiliation(s)
- Tonghai Dou
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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Dou T, Gu S, Zhou Z, Ji C, Zeng L, Ye X, Xu J, Ying K, Xie Y, Mao Y. Note: Isolation and Characterization of a Jerky and JRK/JH8 Like Gene, Tigger Transposable Element Derived 7, TIGD7. Biochem Genet 2004; 42:279-85. [PMID: 15487591 DOI: 10.1023/b:bigi.0000034428.95802.35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tonghai Dou
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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