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Chen LG, Lan T, Zhang S, Zhao M, Luo G, Gao Y, Zhang Y, Du Q, Lu H, Li B, Jiao B, Hu Z, Ma Y, Zhao Q, Wang Y, Qian W, Dai J, Jiao Y. A designer synthetic chromosome fragment functions in moss. Nat Plants 2024; 10:228-239. [PMID: 38278952 DOI: 10.1038/s41477-023-01595-7] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/22/2023] [Indexed: 01/28/2024]
Abstract
Rapid advances in DNA synthesis techniques have enabled the assembly and engineering of viral and microbial genomes, presenting new opportunities for synthetic genomics in multicellular eukaryotic organisms. These organisms, characterized by larger genomes, abundant transposons and extensive epigenetic regulation, pose unique challenges. Here we report the in vivo assembly of chromosomal fragments in the moss Physcomitrium patens, producing phenotypically virtually wild-type lines in which one-third of the coding region of a chromosomal arm is replaced by redesigned, chemically synthesized fragments. By eliminating 55.8% of a 155 kb endogenous chromosomal region, we substantially simplified the genome without discernible phenotypic effects, implying that many transposable elements may minimally impact growth. We also introduced other sequence modifications, such as PCRTag incorporation, gene locus swapping and stop codon substitution. Despite these substantial changes, the complex epigenetic landscape was normally established, albeit with some three-dimensional conformation alterations. The synthesis of a partial multicellular eukaryotic chromosome arm lays the foundation for the synthetic moss genome project (SynMoss) and paves the way for genome synthesis in multicellular organisms.
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Affiliation(s)
- Lian-Ge Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Tianlong Lan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Shuo Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mengkai Zhao
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Guangyu Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yi Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuliang Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qingwei Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Houze Lu
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Bimeng Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bingke Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhangli Hu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qiao Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Junbiao Dai
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, China.
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2
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Li X, Chen Z, Zhang G, Lu H, Qin P, Qi M, Yu Y, Jiao B, Zhao X, Gao Q, Wang H, Wu Y, Ma J, Zhang L, Wang Y, Deng L, Yao S, Cheng Z, Yu D, Zhu L, Xue Y, Chu C, Li A, Li S, Liang C. Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions. Sci China Life Sci 2020; 63:1688-1702. [PMID: 32303966 DOI: 10.1007/s11427-019-1682-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/16/2020] [Indexed: 12/31/2022]
Abstract
Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies (GWAS). Several rice populations have been re-sequenced in the past decade; however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.
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Affiliation(s)
- Xiuxiu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guomin Zhang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Hongwei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Qin
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ming Qi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bingke Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianfeng Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Wang
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunyu Wu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China.,Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095, China
| | - Juntao Ma
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Liyan Zhang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yongli Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Lingwei Deng
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Shanguo Yao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhukuang Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Lihuang Zhu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongbiao Xue
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225009, China. .,Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095, China.
| | - Shigui Li
- Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Yu H, Lu L, Jiao B, Liang C. Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. Bioinformatics 2019; 35:361-364. [PMID: 30032165 DOI: 10.1093/bioinformatics/bty642] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2023] Open
Abstract
Motivation The complex cellular networks underlying phenotypes are formed by the interacting gene modules. Building and analyzing genome-wide and high-quality Gene Co-expression Networks (GCNs) is useful for uncovering these modules and understanding the phenotypes of an organism. Results Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, we discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. We explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, we discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. Our study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding. Availability and implementation The analyzed gene expression data, reconstructed GCNs, modules and detailed annotations can be freely downloaded from ftp://47.94.193.106/pub. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hua Yu
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Lu
- School of Computer and Information Engineering, NanTong Institute of Technology, Nantong, China
| | - Bingke Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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4
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Yu H, Jiao B, Lu L, Wang P, Chen S, Liang C, Liu W. NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples. PLoS One 2018; 13:e0192613. [PMID: 29425247 PMCID: PMC5806890 DOI: 10.1371/journal.pone.0192613] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/27/2018] [Indexed: 01/10/2023] Open
Abstract
Accurately reconstructing gene co-expression network is of great importance for uncovering the genetic architecture underlying complex and various phenotypes. The recent availability of high-throughput RNA-seq sequencing has made genome-wide detecting and quantifying of the novel, rare and low-abundance transcripts practical. However, its potential merits in reconstructing gene co-expression network have still not been well explored. Using massive-scale RNA-seq samples, we have designed an ensemble pipeline, called NetMiner, for building genome-scale and high-quality Gene Co-expression Network (GCN) by integrating three frequently used inference algorithms. We constructed a RNA-seq-based GCN in one species of monocot rice. The quality of network obtained by our method was verified and evaluated by the curated gene functional association data sets, which obviously outperformed each single method. In addition, the powerful capability of network for associating genes with functions and agronomic traits was shown by enrichment analysis and case studies. In particular, we demonstrated the potential value of our proposed method to predict the biological roles of unknown protein-coding genes, long non-coding RNA (lncRNA) genes and circular RNA (circRNA) genes. Our results provided a valuable and highly reliable data source to select key candidate genes for subsequent experimental validation. To facilitate identification of novel genes regulating important biological processes and phenotypes in other plants or animals, we have published the source code of NetMiner, making it freely available at https://github.com/czllab/NetMiner.
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Affiliation(s)
- Hua Yu
- Nantong Medical College and School of Pharmacy, Nantong University, Nantong, China
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: , , (HY); (CL); (WL)
| | - Bingke Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Lu
- Nantong Polytechnic College, Nantong, China
| | - Pengfei Wang
- Nantong Medical College and School of Pharmacy, Nantong University, Nantong, China
| | - Shuangcheng Chen
- Nantong Medical College and School of Pharmacy, Nantong University, Nantong, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: , , (HY); (CL); (WL)
| | - Wei Liu
- Nantong Medical College and School of Pharmacy, Nantong University, Nantong, China
- * E-mail: , , (HY); (CL); (WL)
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5
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Tu Q, Hao J, Zhou X, Yan L, Dai H, Sun B, Yang D, An S, Lv L, Jiao B, Chen C, Lai R, Shi P, Zhao X. CDKN2B deletion is essential for pancreatic cancer development instead of unmeaningful co-deletion due to juxtaposition to CDKN2A. Oncogene 2017; 37:128-138. [PMID: 28892048 PMCID: PMC5759028 DOI: 10.1038/onc.2017.316] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 01/24/2017] [Revised: 06/07/2017] [Accepted: 07/31/2017] [Indexed: 12/28/2022]
Abstract
Pancreatic cancer is among the deadliest malignancies; however, the genetic events that lead to pancreatic carcinogenesis in adults remain unclear. In vivo models in which these genetic alterations occur in adult animals may more accurately reflect the features of human cancer. In this study, we demonstrate that inactivation of Cdkn2b (p15ink4b) is necessary for induction of pancreatic cancer by oncogenic KRASG12D expression and inactivation of Tp53 and Cdkn2a in adult mouse pancreatic ductal cells (P60 or older). KRASG12D overexpression in these cells activated transforming growth factor-β signaling and expression of CDKN2B, which, along with CDKN2A, led to cellular senescence and protected cells from KRAS-mediated transformation via inhibition of retinoblastoma phosphorylation. These results show a critical role of CDKN2B inactivation in pancreatic carcinogenesis, and provide a useful adult animal model by genetic engineering via lentiviral delivery.
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Affiliation(s)
- Q Tu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - J Hao
- State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - X Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - L Yan
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming Primate Research Center, Chinese Academy of Sciences, Kunming, China
| | - H Dai
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - B Sun
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - D Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - S An
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - L Lv
- Kunming Primate Research Center, Chinese Academy of Sciences, Kunming, China
| | - B Jiao
- State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - C Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - R Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - P Shi
- State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - X Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Kunming, China.,Kunming Primate Research Center, Chinese Academy of Sciences, Kunming, China.,KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
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6
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Jin X, Liu K, Jiao B, Wang X, Huang S, Ren W, Zhao K. Vincristine promotes migration and invasion of colorectal cancer HCT116 cells through RhoA/ROCK/ Myosin light chain pathway. Cell Mol Biol (Noisy-le-grand) 2016; 62:91-96. [PMID: 27894406 DOI: 10.14715/cmb/2016.62.12.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 11/26/2016] [Indexed: 11/18/2022]
Abstract
Vincristine is an antitumor vinca alkaloid isolated from vinca rosea, and is a medication used to treat a number of types of cancer. In this study, we investigated the impact of vincristine on oncogenic phenotypes of human colorectal cancer HCT116 cells. MTT assay demonstrated that vincristine showed a obviously inhibitory effect on cell growth compared to non-treated cells. However, Transwell assay showed that vincristine promoted migration and invasion of HCT116 cells in vitro in a concentration-dependent manner between 0.5 and 15 μM vincristine treatment, whereas cell growth showed no remarkable difference within the same concentration range. Additionally, Western blot analysis showed that vincristine significantly elevated RhoA activity and Myosin light chain (MLC) phosphorylation, suggesting the involvement of RhoA/ROCK pathway in the vincristine-induced enhancement of cellular motility. Furthermore, we found that both the siRNA for RhoA and ROCK inhibitor Y27632 attenuated the phosphorylation of MLC, as well as vincristine-induced migration and invasion. These data indicate that vincristine enhanced migration and invasion of HCT116 cells possibly through stimulating RhoA/ROCK/MLC signaling pathway.
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Affiliation(s)
- X Jin
- Department of cancer rehabilitation center, Ningbo senile rehabilitation hospital and cancer rehabilitation center, Ningbo, Zhejiang, China.
| | - K Liu
- Department of general surgery, Mingzhou Hospital of Ningbo, Ningbo, China
| | - B Jiao
- Department of general surgery, Mingzhou Hospital of Ningbo, Ningbo, China
| | - X Wang
- Department of general surgery, Mingzhou Hospital of Ningbo, Ningbo, China
| | - S Huang
- Department of general surgery, Mingzhou Hospital of Ningbo, Ningbo, China
| | - W Ren
- Department of general surgery, Mingzhou Hospital of Ningbo, Ningbo, China
| | - K Zhao
- Department of general surgery, Mingzhou Hospital of Ningbo, Ningbo, China
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7
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Liu P, Jiao B, Zhang R, Zhao H, Zhang C, Wu M, Li D, Zhao X, Qiu Q, Li J, Ren R. Palmitoylacyltransferase Zdhhc9 inactivation mitigates leukemogenic potential of oncogenic Nras. Leukemia 2015; 30:1225-8. [PMID: 26493479 DOI: 10.1038/leu.2015.293] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- P Liu
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - B Jiao
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - R Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - H Zhao
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - C Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - M Wu
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - D Li
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - X Zhao
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Q Qiu
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - J Li
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - R Ren
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Collaborative Innovation Center of Hematology, Collaborative Innovation Center of System Biology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Biology, Brandeis University, Waltham, MA, USA
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8
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Li Q, Jiao B, Zhou F, Tan Q, Ma Y, Luo L, Zhai J, Luan Q, Li C, Wang G, Gao T. Comparative study of photodynamic therapy with 5%, 10% and 20% aminolevulinic acid in the treatment of generalized recalcitrant facial verruca plana: a randomized clinical trial. J Eur Acad Dermatol Venereol 2013; 28:1821-6. [PMID: 24267796 DOI: 10.1111/jdv.12319] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 10/11/2013] [Indexed: 11/28/2022]
Abstract
BACKGROUND Generalised recalcitrant facial verruca plana responds poorly to current therapeutic options, including cryotherapy, topical drugs and carbon dioxide (CO2 ) laser. Case reports and uncontrolled studies suggested that topical photodynamic therapy (PDT) is effective choice of treatment free from potential complications associated with invasive therapies. AIMS To investigate the efficacy and safety of PDT with different concentrations of photosensitiser in the treatment of verruca plana. MATERIALS & METHODS The two sides of a subject's face were separately randomized to receive aminolevulinic acid (ALA) of 5%, 10% or 20% concentration. All patients were irradiated with 633-nm red light for 339 J/cm(2) total dose. Complete response (CR) rate was assessed on Week 4, 8, and 16 respectively. RESULTS The mean overall clearance rate was 74.1%, 68.8%, and 64.6% on Week 4, 8, and 12, respectively, in the 110 treated sides. The CR rate was lower in the 5%-ALA group than in the 10%-ALA group (14.3% vs. 33.3%, p < 0.05) and 20%-ALA group (14.3% vs. 26.3%, p < 0.05) after 12 weeks. The mean severity of pain measured by visual analogue scale (VAS) scoring was 3.8 (range: 2 to 10, depending on the lesion location). The overall recurrence rate was 16.7% (4/24) on Week 12. Hyperpigmentation was observed in 61% (67/110) of all treated sides. On Week 4, 8, and 16, hyperpigmentation was more developed in the 20%-ALA group than in the other two groups (p < 0.05). DISCUSSION In terms of complete clearance rate, the 5% ALA-PDT group was significantly inferior to the 10% and 20% ALA-PDT groups at each follow-up. In contrast, the 20% ALA group showed a higher incidence rate of transient hyperpigmentation than the other two groups. CONCLUSIONS This randomised clinical trial suggests that PDT with ALA of 10% concentration offers better efficacy and safety than 5% or 20% concentration for generalised recalcitrant facial verruca plana.
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Affiliation(s)
- Q Li
- Department of Dermatology at Xijing Hospital, Fourth Military Medical University, Xi'an, China
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Lu S, Wang S, Geng S, Ma S, Liang Z, Jiao B. Upregulation of microRNA-224 confers a poor prognosis in glioma patients. Clin Transl Oncol 2012; 15:569-74. [PMID: 23263909 DOI: 10.1007/s12094-012-0972-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/14/2012] [Indexed: 10/27/2022]
Abstract
OBJECTIVE MicroRNA-224 (miR-224) has been consistently reported to be dysregulated in various human malignancies and can potentially affect many cancer-related cellular processes, including transcription, cell differentiation, cell death, growth, and cell proliferation. However, its roles in human glioma have not been reported. The aim of this study was to explore the expression pattern, clinical significance, and prognostic value of miR-224 in glioma patients using large cohorts. METHODS Quantitative real-time polymerase chain reaction analysis was used to characterize the expression patterns of miR-224 in 108 glioma and 20 normal brain tissues. The associations of miR-224 expression with clinicopathological factors and prognosis of glioma patients were also statistically analyzed. RESULTS miR-224 expression is significantly upregulated in glioma tissues compared with normal brain tissues (P < 0.001). In addition, high expression of miR-224 was significantly associated with advanced pathological grade (P = 0.006) and low Karnofsky performance score (KPS, P = 0.01). Moreover, Kaplan-Meier survival analysis showed that high miR-224 expression group had significantly shorter disease-free survival (DFS) and overall survival (OS) rates than low miR-224 expression group (both P < 0.001). Multivariate analysis with the Cox's proportional hazards model revealed that high expression of miR-224 (P = 0.006 and P = 0.01, respectively) and advanced pathological grade (both P = 0.02) were independent factors for shorter DFS and OS. Furthermore, subgroup analyses showed that miR-224 expression was significantly associated with poor DFS and OS in glioma patients with high pathological grades (for grade III-IV: P < 0.001 and P = 0.005, respectively). CONCLUSIONS MiR-224 is upregulated and confers a poor prognosis in glioma patients.
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Affiliation(s)
- S Lu
- Department of Neurosurgery, Second Hospital of Hebei Medical University, No. 215, Hepingxi Road, Shijiazhuang, 050000, Hebei, China
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Jiao B, Zhang YH, Cheng YN, Gao JJ, Zhang QZ. A low-dose combination of valsartan and low molecular weight heparin better improved glomerular permeability than did high-dose monotherapy in rats with diabetic nephropathy. Drug Discov Ther 2012; 5:119-24. [PMID: 22466240 DOI: 10.5582/ddt.2011.v5.3.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Diabetic nephropathy is the most common and severe renal complication of diabetes mellitus. The present study sought to investigate the renoprotective effects of a combination therapy of valsartan and low molecular weight heparin (LMWH) in rats with diabetic nephropathy induced by uninephrectomy and streptozotocin. The animals were divided into five groups as follows: sham-operated rats, diabetic control rats, diabetic rats treated with 20 mg/kg/day valsartan, diabetic rats treated with 600 IU/kg/day LMWH, diabetic rats treated with a combination of valsartan and LMWH (valsartan 10 mg/kg/day and LMWH 300 IU/kg/day). The treatment regimen was maintained for 8 weeks. Treatment with valsartan, LMWH, or a combination of the two had no significant effect on blood glucose levels. However, the urine protein excretion levels significantly decreased for the three drug treatment groups; the most dramatic decreases were observed in the combination treatment group. Kidney histology was examined using periodic acid-Schiff staining and immunohistochemical staining of extracellular matrix proteins. Results indicated that histopathology improved markedly in the three drug treatment groups; combination therapy had an equal or better effect than monotherapy in terms of decreasing the abnormal thickness of the glomerular basal membrane, the ratio of the area of the mesangial region with respect to the total area of renal glomeruli, and the accumulation of collagen IV and laminin in kidney tissue. In addition, serum levels of transforming growth factor-β1 (TGF-β1) also markedly decreased in the drug treatment groups according to ELISA. However, there were no significant differences between the combination therapy group and monotherapy group. These results suggest that a combination of valsartan and LMWH at half the dose used in monotherapy is better at improving glomerular permeability in rats with diabetic nephropathy.
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Affiliation(s)
- B Jiao
- Department of Pharmacology, School of Pharmaceutical Science, Shandong University, Ji'nan, Shandong, China
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Jiao B, Wang YS, Cheng YN, Gao JJ, Zhang QZ. Valsartan attenuated oxidative stress, decreased MCP-1 and TGF-β1 expression in glomerular mesangial and epithelial cells induced by high-glucose levels. Biosci Trends 2012; 5:173-81. [PMID: 21914953 DOI: 10.5582/bst.2011.v5.4.173] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Our previous studies revealed that valsartan, an angiotensin II type I receptor blocker, exhibited renoprotective effects through decreasing urine protein excretion levels due to improving glomerular permeability in rats with diabetic nephropathy (DN). In this study, we sought to investigate the underlying mechanisms in perspectives of oxidative stress, transforming growth factor beta-1 (TGF-β1) and monocyte chemoattractant protein-1 (MCP-1) expressions in glomerular mesangial cells (GMCs) and glomerular epithelial cells (GECs) since their roles are well-established in the development and progression of DN. High-glucose levels significantly increased oxidative stress in GMCs and GECs, as evidenced by enhanced generation of reactive reactive oxygen species (ROS), reduced levels of glutathione (GSH) and antioxidant enzyme superoxide dismutase (SOD), and increased production of malondialdehyde (MDA). Treatment with valsartan significantly restored the levels of those oxidative stress relevant molecules. Furthermore, valsartan obviously diminished the expression of proinflammatory cytokine MCP-1 in GMCs and GECs induced by high-glucose levels both at mRNA and protein levels, as determined by real-time PCR, immunocytochemistry, western blotting, and ELISA. In addition, the increased expressions of TGF-β1 mRNA and protein induced by high-glucose level were also abrogated by valsartan treatment in GMCs, as evaluated by real-time PCR and ELISA. These results suggest that the renoprotective effects of valsartan may be related to its potential in decreasing oxidative stress and the expressions of MCP-1 and TGF-β1 in GMCs and GECs.
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Affiliation(s)
- B Jiao
- Department of Pharmacology, School of Pharmaceutical Science, Shandong University, Ji'nan, China.
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Lu X, Cao X, Liu X, Jiao B. Marine Microbes-Derived Anti-Bacterial Agents. Mini Rev Med Chem 2010; 10:1077-90. [DOI: 10.2174/1389557511009011077] [Citation(s) in RCA: 8] [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] [Received: 07/22/2010] [Accepted: 07/25/2010] [Indexed: 11/22/2022]
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Xu H, Guo T, Guo YF, Zhang JE, Li Y, Feng W, Jiao B. Characterization and Protection on Acute Liver Injury of a Polysaccharide MP-I from Mytilus Coruscus. Glycobiology 2007; 18:97-103. [DOI: 10.1093/glycob/cwm116] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Zhang Q, Miao Z, Guo Z, Dong F, Xiong Z, Wu X, Chen D, Li C, Jiao B. Optical readout uncooled infrared imaging detector using knife-edge filter operation. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11801-007-7014-2] [Citation(s) in RCA: 6] [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: 11/28/2022]
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Li D, Jiao B, Zhu Y. [Effect and mechanism of garlic juice and hydrogen peroxide on the degradation of lipopolysaccharide]. Zhonghua Kou Qiang Yi Xue Za Zhi 2000; 35:333-5. [PMID: 11780236] [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] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE To elucidate the effect and mechanism of garlic juice and hydrogen peroxide on the degradation of lipopolysaccharide (LPS). METHODS Hot phenol-water method, phenol-chloroform-petroleum ether procedure, limulus lysate test, lowry's ash spetrographical examination and gas-liquid chromatography etc. were used in this study. RESULTS The sequence of degradation effect was 30% hydrogen peroxide (H), the most powerful, followed by garlic juice (G), 1:1 diluted G and 3% H, their effects were dose dependent and G group was time dependent. The mechanism of H on LPS degradation was fractionization of phosphoryl in position 1 from lipid A, while that of G was complex, it could bound LPS molecule and influenced its effect besides LPS hydrolysis. CONCLUSION The study may imply that the degradation position and mechanism on LPS are different and remain to be elucidated.
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Affiliation(s)
- D Li
- Department of Oral Medicine, School of Stomatology, Shanghai Second Medical University, Shanghai 200011, China
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Li Z, Jiao B, Qian H, Qian X, Mo B. [The application of Apo-1/Fas to evaluate apoptosis of myocardial cells in patients with congestive heart failure]. Zhonghua Nei Ke Za Zhi 1999; 38:168-70. [PMID: 11798644] [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] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE To study the changes of serum level of Apo-1/Fas in patients with congestive heart failure (CHF) and evaluate apoptosis of failing myocardial cells. METHODS Strepavidin-Biotin ELISA was used to determine serum level of Apo-1/Fas, interleukin-6 (IL-6) and tumor necrosis factor (TNF alpha) in 60 patients with CHF. Cardiac ejection fraction (EF) of the patients were measured by acusson 128XP/10 echocardiograph. RESULTS Serum levels of Apo-1/Fas and TNF alpha in class III and IV patients with CHF were significantly higher than those in class I and II (P < 0.01). Serum levels of IL-6 in all the patients were obviously higher than those in controls (P < 0.05 and 0.01) and the levels in class III and IV patients were significantly higher than those in class I and II (P < 0.05). Serum levels of Apo-1/Fas in patients with EF < 55 percent were higher than in those with EF > 55 percent (P < 0.05). CONCLUSION Serum level of Apo-1/Fas in patients with CHF reflects a state of apoptosis in failing myocardial cells. IL-6 and TNF alpha have important effects on immune regulation of myocardial cell apoptosis.
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Affiliation(s)
- Z Li
- Department of Cardiovascular, Zhujiang Hospital, First Military Medical University, Guangzhou 510282
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Wang H, Gao X, Jiao B. Ultraphatological observation on the small brain abscess caused by cysticerci of taenia a solium: a double · necrosis (apoptosis) theory about the formation and development of the abscesses. Parasitol Int 1998. [DOI: 10.1016/s1383-5769(98)81043-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: 11/25/2022]
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Li L, Chen H, Xi Y, Wang X, Han G, Zhou Y, Yang D, Zhao W, Feng Z, Jiao B. Comparative observation on effect of electric acupuncture of neiguan (P 6) at chen time versus xu time on left ventricular function in patients with coronary heart disease. J TRADIT CHIN MED 1994; 14:262-5. [PMID: 7877334] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Paired experimental design was adopted in this experiment for comparative observation on effect of electric acupuncture (EA) of Neiguan (P 6) at Chen Time (7 a.m. to 9 a.m.) versus Xu Time (7 p.m. to 9 p.m.) on left ventricular function in patients with coronary heart disease (CHD). The results show that EA performed at Chen Time could improve the left ventricular function of CHD patients as indicated by shortening of PEPI and decrease of PEPI/LVETI ratio; on the contrary, EA performed at Xu Time prolonged PEPI and raised PEPI/LVETI ratio in CHD patients, suggesting impairment of left ventricular function.
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