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Huang CJ, Wu TL, Zheng PX, Ou JY, Ting CL, Lin YC. Complete Genome Sequence Resource of Pectobacterium colocasium Strain F1-1 that Causes Soft Rot Disease of Taro. Plant Dis 2023:PDIS09222198A. [PMID: 36451306 DOI: 10.1094/pdis-09-22-2198-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Pectobacterium colocasium is a recently named, narrow-host-range phytopathogenic bacterium causing soft rot of taro (Colocasium esculenta). It is found on the Chinese mainland and the island of Taiwan. Taro is a domesticated crop with a long history of cultivation in Taiwan and the Pacific islands. However, not much was known about Pectobacterium spp. from taro, especially from the islands in the Pacific. Herein, we report a high-quality, completely annotated genome sequence of P. colosacium strain F1-1. The 4,816,345 bp genome, which was assembled with Illumina and Nanopore reads with 217× and 311× coverage, respectively, consists of one chromosome and no plasmid. This completely circularized genome will aid future studies in comparative genomics, evolution, and pathogenicity of P. colocasium. This genome resource will also be helpful for developing strategies to control P. colocasium in taro.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Chien-Jui Huang
- Department of Plant Medicine, National Chiayi University, Chiayi 600355, Taiwan
| | - Ting-Li Wu
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Chao-Ling Ting
- Crop Improvement Division, Miaoli District Agricultural Research and Extension Station, Council of Agriculture, Executive Yuan, Guannan, Miaoli 363201, Taiwan
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
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Lin CS, Hsu CT, Yuan YH, Zheng PX, Wu FH, Cheng QW, Wu YL, Wu TL, Lin S, Yue JJ, Cheng YH, Lin SI, Shih MC, Sheen J, Lin YC. DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration. Plant Physiol 2022; 188:1917-1930. [PMID: 35088855 PMCID: PMC8968427 DOI: 10.1093/plphys/kiac022] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 05/24/2023]
Abstract
Wild tomatoes (Solanum peruvianum) are important genomic resources for tomato research and breeding. Development of a foreign DNA-free clustered regularly interspaced short palindromic repeat (CRISPR)-Cas delivery system has potential to mitigate public concern about genetically modified organisms. Here, we established a DNA-free CRISPR-Cas9 genome editing system based on an optimized protoplast regeneration protocol of S. peruvianum, an important resource for tomato introgression breeding. We generated mutants for genes involved in small interfering RNAs biogenesis, RNA-DEPENDENT RNA POLYMERASE 6 (SpRDR6), and SUPPRESSOR OF GENE SILENCING 3 (SpSGS3); pathogen-related peptide precursors, PATHOGENESIS-RELATED PROTEIN-1 (SpPR-1) and PROSYSTEMIN (SpProSys); and fungal resistance (MILDEW RESISTANT LOCUS O, SpMlo1) using diploid or tetraploid protoplasts derived from in vitro-grown shoots. The ploidy level of these regenerants was not affected by PEG-Ca2+-mediated transfection, CRISPR reagents, or the target genes. By karyotyping and whole genome sequencing analysis, we confirmed that CRISPR-Cas9 editing did not introduce chromosomal changes or unintended genome editing sites. All mutated genes in both diploid and tetraploid regenerants were heritable in the next generation. spsgs3 null T0 regenerants and sprdr6 null T1 progeny had wiry, sterile phenotypes in both diploid and tetraploid lines. The sterility of the spsgs3 null mutant was partially rescued, and fruits were obtained by grafting to wild-type (WT) stock and pollination with WT pollen. The resulting seeds contained the mutated alleles. Tomato yellow leaf curl virus proliferated at higher levels in spsgs3 and sprdr6 mutants than in the WT. Therefore, this protoplast regeneration technique should greatly facilitate tomato polyploidization and enable the use of CRISPR-Cas for S. peruvianum domestication and tomato breeding.
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Affiliation(s)
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Hsuan Yuan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Xing Zheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Qiao-Wei Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Lin Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ting-Li Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Steven Lin
- Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan
| | - Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311, China
| | - Ying-Huey Cheng
- Plant Pathology Division, Taiwan Agricultural Research Institute, Taichung 413, Taiwan
| | - Shu-I Lin
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 106, Taiwan
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Huang CJ, Wu TL, Zheng PX, Ou JY, Ni HF, Lin YC. Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. citri. Front Microbiol 2021; 12:731711. [PMID: 34557177 PMCID: PMC8453159 DOI: 10.3389/fmicb.2021.731711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/28/2021] [Accepted: 08/18/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Worldwide citrus production is severely threatened by Asiatic citrus canker which is caused by the proteobacterium Xanthomonas citri subsp. citri. Foliar sprays of copper-based bactericides are frequently used to control plant bacterial diseases. Despite the sequencing of many X. citri strains, the genome diversity and distribution of genes responsible for metal resistance in X. citri subsp. citri strains from orchards with different management practices in Taiwan are not well understood. Results: The genomes of three X. citri subsp. citri strains including one copper-resistant strain collected from farms with different management regimes in Taiwan were sequenced by Illumina and Nanopore sequencing and assembled into complete circular chromosomes and plasmids. CRISPR spoligotyping and phylogenomic analysis indicated that the three strains were located in the same phylogenetic lineages and shared ∼3,000 core-genes with published X. citri subsp. citri strains. These strains differed mainly in the CRISPR repeats and pathogenicity-related plasmid-borne transcription activator-like effector (TALE)-encoding pthA genes. The copper-resistant strain has a unique, large copper resistance plasmid due to an unusual ∼40 kbp inverted repeat. Each repeat contains a complete set of the gene cluster responsible for copper and heavy metal resistance. Conversely, the copper sensitive strains carry no metal resistance genes in the plasmid. Through comparative analysis, the origin and evolution of the metal resistance clusters was resolved. Conclusion: Chromosomes remained constant among three strains collected in Taiwan, but plasmids likely played an important role in maintaining pathogenicity and developing bacterial fitness in the field. The evolution of pathogenicity factors and horizontal gene transfer events were observed in the three strains. These data suggest that agricultural management practices could be a potential trigger for the evolution of citrus canker pathogens. The decrease in the number of CRISPR repeats and pthA genes might be the result of adaptation to a less stressful environment. The metal resistance genes in the copper resistant X. citri strain likely originated from the Mauritian strain not the local copper-resistant X. euvesicatoria strain. This study highlights the importance of plasmids as 'vehicles' for exchanging genetic elements between plant pathogenic bacteria and contributing to bacterial adaptation to the environment.
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Affiliation(s)
- Chien-Jui Huang
- Department of Plant Medicine, National Chiayi University, Chiayi, Taiwan
| | - Ting-Li Wu
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Hui-Fang Ni
- Department of Plant Protection, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
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Hsieh CL, Hsieh SY, Huang HM, Lu SL, Omori H, Zheng PX, Ho YN, Cheng YL, Lin YS, Chiang-Ni C, Tsai PJ, Wang SY, Liu CC, Noda T, Wu JJ. Nicotinamide Increases Intracellular NAD + Content to Enhance Autophagy-Mediated Group A Streptococcal Clearance in Endothelial Cells. Front Microbiol 2020; 11:117. [PMID: 32117141 PMCID: PMC7026195 DOI: 10.3389/fmicb.2020.00117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 10/10/2019] [Accepted: 01/20/2020] [Indexed: 12/16/2022] Open
Abstract
Group A streptococcus (GAS) is a versatile pathogen that causes a wide spectrum of diseases in humans. Invading host cells is a known strategy for GAS to avoid antibiotic killing and immune recognition. However, the underlying mechanisms of GAS resistance to intracellular killing need to be explored. Endothelial HMEC-1 cells were infected with GAS, methicillin-resistant Staphylococcus aureus (MRSA) and Salmonella Typhimurium under nicotinamide (NAM)-supplemented conditions. The intracellular NAD+ level and cell viability were respectively measured by NAD+ quantification kit and protease-based cytotoxicity assay. Moreover, the intracellular bacteria were analyzed by colony-forming assay, transmission electron microscopy, and confocal microscopy. We found that supplementation with exogenous nicotinamide during infection significantly inhibited the growth of intracellular GAS in endothelial cells. Moreover, the NAD+ content and NAD+/NADH ratio of GAS-infected endothelial cells were dramatically increased, whereas the cell cytotoxicity was decreased by exogenous nicotinamide treatment. After knockdown of the autophagy-related ATG9A, the intracellular bacterial load was increased in nicotinamide-treated endothelial cells. The results of Western blot and transmission electron microscopy also revealed that cells treated with nicotinamide can increase autophagy-associated LC3 conversion and double-membrane formation during GAS infection. Confocal microscopy images further showed that more GAS-containing vacuoles were colocalized with lysosome under nicotinamide-supplemented conditions than without nicotinamide treatment. In contrast to GAS, supplementation with exogenous nicotinamide did not effectively inhibit the growth of MRSA or S. Typhimurium in endothelial cells. These results indicate that intracellular NAD+ homeostasis is crucial for controlling intracellular GAS infection in endothelial cells. In addition, nicotinamide may be a potential new therapeutic agent to overcome persistent infections of GAS.
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Affiliation(s)
- Cheng-Lu Hsieh
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Ying Hsieh
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsuan-Min Huang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shiou-Ling Lu
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Osaka, Japan
| | - Hiroko Omori
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Po-Xing Zheng
- Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Ning Ho
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Lin Cheng
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Yee-Shin Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology & Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Pei-Jane Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Ying Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chuan Liu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Pediatrics, College of Medicine, National Cheng Kung University and Hospital, Tainan, Taiwan
| | - Takeshi Noda
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Osaka, Japan
| | - Jiunn-Jong Wu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
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Borgers K, Ou JY, Zheng PX, Tiels P, Van Hecke A, Plets E, Michielsen G, Festjens N, Callewaert N, Lin YC. Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine. BMC Genomics 2019; 20:561. [PMID: 31286858 PMCID: PMC6615170 DOI: 10.1186/s12864-019-5909-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG Tokyo 172-1 as Russia BCG-1, reference genomes exist, not for BCG Danish. In this study, we set out to determine the completely assembled genome sequence for BCG Danish and to establish a workflow for genome characterization of engineering-derived vaccine candidate strains. RESULTS By combining second (Illumina) and third (PacBio) generation sequencing in an integrated genome analysis workflow for BCG, we could construct the completely assembled genome sequence of BCG Danish 1331 (07/270) (and an engineered derivative that is studied as an improved vaccine candidate, a SapM KO), including the resolution of the analytically challenging long duplication regions. We report the presence of a DU1-like duplication in BCG Danish 1331, while this tandem duplication was previously thought to be exclusively restricted to BCG Pasteur. Furthermore, comparative genome analyses of publicly available data for BCG substrains showed the absence of a DU1 in certain BCG Pasteur substrains and the presence of a DU1-like duplication in some BCG China substrains. By integrating publicly available data, we provide an update to the genome features of the commonly used BCG strains. CONCLUSIONS We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of the BCG Danish vaccine strain. The BCG Danish WHO reference genome will serve as a reference for future engineered strains and the established workflow can be used to enhance BCG vaccine standardization.
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Affiliation(s)
- Katlyn Borgers
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, 74145 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 74145 Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, 74145 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 74145 Taiwan
| | - Petra Tiels
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Annelies Van Hecke
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Evelyn Plets
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Gitte Michielsen
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Nele Festjens
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Nico Callewaert
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, 74145 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 74145 Taiwan
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Hsieh CL, Huang HM, Hsieh SY, Zheng PX, Lin YS, Chiang-Ni C, Tsai PJ, Wang SY, Liu CC, Wu JJ. NAD-Glycohydrolase Depletes Intracellular NAD + and Inhibits Acidification of Autophagosomes to Enhance Multiplication of Group A Streptococcus in Endothelial Cells. Front Microbiol 2018; 9:1733. [PMID: 30123194 PMCID: PMC6085451 DOI: 10.3389/fmicb.2018.01733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 03/30/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022] Open
Abstract
Group A Streptococcus (GAS) is a human pathogen causing a wide spectrum of diseases, from mild pharyngitis to life-threatening necrotizing fasciitis. GAS has been shown to evade host immune killing by invading host cells. However, how GAS resists intracellular killing by endothelial cells is still unclear. In this study, we found that strains NZ131 and A20 have higher activities of NADase and intracellular multiplication than strain SF370 in human endothelial cells (HMEC-1). Moreover, nga mutants of NZ131 (SW957 and SW976) were generated to demonstrate that NADase activity is required for the intracellular growth of GAS in endothelial cells. We also found that intracellular levels of NAD+ and the NAD+/NADH ratio of NZ131-infected HMEC-1 cells were both lower than in cells infected by the nga mutant. Although both NZ131 and its nga mutant were trapped by LC3-positive vacuoles, only nga mutant vacuoles were highly co-localized with acidified lysosomes. On the other hand, intracellular multiplication of the nga mutant was increased by bafilomycin A1 treatment. These results indicate that NADase causes intracellular NAD+ imbalance and impairs acidification of autophagosomes to escape autophagocytic killing and enhance multiplication of GAS in endothelial cells.
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Affiliation(s)
- Cheng-Lu Hsieh
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsuan-Min Huang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Ying Hsieh
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Xing Zheng
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Yee-Shin Lin
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology & Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Pei-Jane Tsai
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Ying Wang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chuan Liu
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jiunn-Jong Wu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
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Li HY, Kao CY, Lin WH, Zheng PX, Yan JJ, Wang MC, Teng CH, Tseng CC, Wu JJ. Characterization of CRISPR-Cas Systems in Clinical Klebsiella pneumoniae Isolates Uncovers Its Potential Association With Antibiotic Susceptibility. Front Microbiol 2018; 9:1595. [PMID: 30061876 PMCID: PMC6054925 DOI: 10.3389/fmicb.2018.01595] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 02/26/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022] Open
Abstract
Prokaryotic CRISPR-Cas systems limit the acquisition of genetic elements and provide immunity against invasive bacteriophage. The characteristics of CRISPR-Cas systems in clinical Klebsiella pneumoniae isolates are still unknown. Here, 97 K. pneumoniae genomes retrieved from the Integrated Microbial Genomes & Microbiomes genome database and 176 clinical isolates obtained from patients with bloodstream (BSI, n = 87) or urinary tract infections (UTI, n = 89) in Taiwan, were used for analysis. Forty out of ninety-seven genomes (41.2%) had CRISPR-Cas systems identified by the combination of CRISPRFinder and cas1 gene sequence alignment. The phylogenetic trees revealed that CRISPR-Cas systems in K. pneumoniae were divided into two types (type I-E, 23; subtype I-E∗, 17) based on the sequences of Cas1 and Cas3 proteins and their location in the chromosome. The distribution of type I-E and I-E∗ CRISPR-Cas systems was associated with the multilocus sequence typing and the pulsed-field gel electrophoresis results. Importantly, no CRISPR-Cas system was identified in published genomes of clonal complex 258 isolates (ST11 and ST258), which comprise the largest multi-drug resistant K. pneumoniae clonal group worldwide. PCR with cas-specific primers showed that 30.7% (54/176) of the clinical isolates had a CRISPR-Cas system. Among clinical isolates, more type I-E CRISPR-Cas systems were found in UTI isolates (BSI, 5.7%; UTI, 11.2%), and subtype I-E∗ CRISPR-Cas systems were dominant in BSI isolates (BSI, 28.7%; UTI, 15.7%) (p = 0.042). Isolates which had subtype I-E∗ CRISPR-Cas system were more susceptible to ampicillin-sulbactam (p = 0.009), cefazolin (p = 0.016), cefuroxime (p = 0.039), and gentamicin (p = 0.012), compared to the CRISPR-negative isolates. The strains containing subtype I-E∗ CRISPR-Cas systems had decreased numbers of plasmids, prophage regions, and acquired antibiotic resistance genes in their published genomes. Here, we first revealed subtype I-E∗ CRISPR-Cas system in K. pneumoniae potentially interfering with the acquisition of phages and plasmids harboring antibiotic resistance determinants, and thus maintained these isolates susceptible to antibiotics.
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Affiliation(s)
- Hsin-Yu Li
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, Taipei, Taiwan
| | - Cheng-Yen Kao
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, Taipei, Taiwan
| | - Wei-Hung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Jing-Jou Yan
- Department of Pathology, Cheng Ching Hospital at Chung Kang, Taichung, Taiwan
| | - Ming-Cheng Wang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Hao Teng
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chin-Chung Tseng
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jiunn-Jong Wu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, Taipei, Taiwan
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Zheng PX, Chan YC, Chiou CS, Hsieh CL, Chiang-Ni C, Wu JJ. Highly prevalent emmSTG840.0 and emmSTC839.0 types of erythromycin non-susceptible group G Streptococcus isolated from bacteremia in southern Taiwan. J Microbiol Immunol Infect 2017; 50:831-838. [PMID: 28711431 DOI: 10.1016/j.jmii.2016.12.010] [Citation(s) in RCA: 4] [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: 07/26/2016] [Revised: 12/09/2016] [Accepted: 12/27/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND/PURPOSE Group G Streptococcus (GGS) infections in human have increased. Treatment relied on antibiotic therapy, including erythromycin. However, information regarding the dominant strains and erythromycin susceptibility in GGS bacteremia is limited. METHODS A total of 134 GGS were isolated from patients with bacteremia in a university hospital of southern Taiwan during 1993-2010. The erythromycin susceptibility was determined by disc diffusion and agar dilution assays. The bacterial species was determined by MALDI-TOF. The presence of erythromycin-resistant genes and emm types were determined by polymerase chain reaction and sequence. The clonal spreading was analyzed by pulsed-field gel electrophoresis with SmaI or SgrAI digestion. RESULTS The annual erythromycin non-susceptible rate varied, with an average of 40.3%. All erythromycin non-susceptible strains belonged to the Streptococcus dysgalactiae. No erythromycin non-susceptible strains belong to the anginosus group. The most prevalent erythromycin-resistant gene was mefA (57.4%), followed by ermB (37%), and ermA (3.7%). The N terminal hyper variable region of emm was sequenced to determine the emm type, and only S. dysgalactiae had the emm gene. The most prevalent emm types were emmSTG840.0 (17.2%), emmSTG485.0 (10.4%), and emmSTC839.0 (9.0%). 73% and 47% of the strains with only mefA and ermB belonged to emmSTG840.0 and emmSTC839.0 types, respectively. Pulsed-field gel electrophoresis showed that different clones of emmSTG840.0 and emmSTC839.0 strains were spread in this region during the 18 years of surveillance. CONCLUSION Our data indicate that there were dominant emm types with erythromycin non-susceptibility in S. dysgalactiae isolated from bacteremia in Taiwan, and thus constant surveillance is warranted.
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Affiliation(s)
- Po-Xing Zheng
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Yuen-Chi Chan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Shun Chiou
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan
| | - Cheng-Lu Hsieh
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Jiunn-Jong Wu
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan.
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9
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Chen HM, Zheng PX, Wang LR, Wu JJ, Yan JJ. Multilocus sequence typing of carbapenemase-producing Enterobacter cloacae bloodstream isolates between 2002 and 2013 in a Taiwanese university hospital. J Glob Antimicrob Resist 2017; 9:135-137. [PMID: 28576741 DOI: 10.1016/j.jgar.2017.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/14/2017] [Accepted: 05/21/2017] [Indexed: 11/29/2022] Open
Affiliation(s)
- Hung-Mo Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Po-Xing Zheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Li-Rong Wang
- Center for Infection Control, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Jiunn-Jong Wu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Jing-Jou Yan
- Department of Pathology, Cheng Ching Hospital, Taichung, Taiwan; Department of Pathology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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10
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Yan JJ, Wang MC, Zheng PX, Tsai LH, Wu JJ. Associations of the major international high-risk resistant clones and virulent clones with specific ompK36 allele groups in Klebsiella pneumoniae in Taiwan. New Microbes New Infect 2015; 5:1-4. [PMID: 25834737 PMCID: PMC4366441 DOI: 10.1016/j.nmni.2015.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 12/19/2014] [Accepted: 01/23/2015] [Indexed: 01/07/2023] Open
Abstract
This study was conducted to investigate the association between ompK36 variants and international high-risk clones in Klebsiella pneumoniae. Fifty-nine sequence types (STs) divided into four ompK36 allele groups (groups A to D) were identified among 185 K. pneumoniae isolates. The major high-risk clones (29 ST11, 13 ST15, 7 ST37 and 1 ST147 isolates) were assigned to group A, while 6 STs (15 ST23, 2 ST65, 3 ST86, 1 ST163, 1 ST373 and 2 ST375 isolates) associated with pyogenic liver abscess were assigned to group C. The genotyping assay developed in this study may be useful for screening of epidemic STs.
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Affiliation(s)
- J J Yan
- Department of Pathology, National Cheng Kung University College of Medicine and Hospital, Taiwan
| | - M C Wang
- Department of Internal Medicine, National Cheng Kung University College of Medicine and Hospital, Taiwan
| | - P X Zheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Taiwan
| | - L H Tsai
- Department of Pathology, National Cheng Kung University College of Medicine and Hospital, Taiwan ; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Taiwan
| | - J J Wu
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Taiwan
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11
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Zheng PX, Fang HY, Yang HB, Tien NY, Wang MC, Wu JJ. Lactobacillus pentosus strain LPS16 produces lactic acid, inhibiting multidrug-resistant Helicobacter pylori. J Microbiol Immunol Infect 2014; 49:168-74. [PMID: 24874430 DOI: 10.1016/j.jmii.2014.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 02/08/2023]
Abstract
BACKGROUND/PURPOSE Helicobacter pylori is a human gastric pathogen. Antibiotic resistance of H. pylori has become a problem increasing the failure of H. pylori eradication. Therefore alternative approaches are required. The aim of this study was to evaluate the anti-H. pylori activity of Lactobacillus pentosus strain LPS16 and the mechanism of its killing effect. METHODS The anti-H. pylori activity of LPS16 was determined by the disc diffusion test and time killing assay. High-performance liquid chromatography analysis was used to analyze the secreted compounds of LPS16. Sixty H. pylori strains isolated from different gastric diseases, having different antibiotic susceptibility were collected to analyze the spectrum of anti-H. pylori activity of LPS16. Adhesion ability of LPS16 to gastric epithelial cell lines was assayed by flow cytometry. RESULTS The anti-H. pylori activity of LPS16 depended on the secreted component, and lactic acid mediated bactericidal activity against H. pylori. The bactericidal activity did not vary significantly among the strains isolated from different diseases having different antibiotic susceptibility. Moreover, LPS16 can adhere on gastric epithelial cell lines AKG and MKN45. CONCLUSION L. pentosus strain LPS16 had the broad-spectrum anti-H. pylori activity, suggesting that it can be used to prevent H. pylori infection.
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Affiliation(s)
- Po-Xing Zheng
- Institutes of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin-Yi Fang
- Department of Biotechnology, College of Pharmacy and Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | - Hsiao-Bai Yang
- Department of Pathology, Ton-Yen General Hospital, Hsinchu, Taiwan
| | - Nai-Yueh Tien
- Department of Biotechnology, College of Pharmacy and Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | - Ming-Cheng Wang
- Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Jiunn-Jong Wu
- Institutes of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signal Research, National Cheng Kung University, Tainan, Taiwan.
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12
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Chiang-Ni C, Zheng PX, Wang S, Tsai PJ, Kuo CF, Chuang WJ, Lin YS, Liu CC, Wu JJ. Invasive hypermucoid variant of group AStreptococcusis defective in growth and susceptible to DNA-damaging treatments. Pathog Dis 2013; 70:194-201. [DOI: 10.1111/2049-632x.12114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/16/2013] [Accepted: 11/06/2013] [Indexed: 11/26/2022] Open
Affiliation(s)
- Chuan Chiang-Ni
- Department of Microbiology and Immunology; College of Medicine; Chang Gung University; Taoyuan Taiwan
| | - Po-Xing Zheng
- Institute of Basic Medical Sciences; College of Medicine; National Cheng Kung University; Tainan Taiwan
| | - Shuying Wang
- Department of Microbiology and Immunology; College of Medicine; National Cheng Kung University; Tainan Taiwan
| | - Pei-Jane Tsai
- Department of Medical Laboratory Science and Biotechnology; College of Medicine; National Cheng Kung University; Tainan Taiwan
| | - Chih-Feng Kuo
- Department of Nursing; I-Shou University; Yanchao Campus Kaohsiung Taiwan
| | - Woei-Jer Chuang
- Department of Biochemistry; College of Medicine; National Cheng Kung University; Tainan Taiwan
| | - Yee-Shin Lin
- Department of Microbiology and Immunology; College of Medicine; National Cheng Kung University; Tainan Taiwan
| | - Ching-Chuan Liu
- Department of Pediatrics; College of Medicine; National Cheng Kung University; Tainan Taiwan
| | - Jiunn-Jong Wu
- Institute of Basic Medical Sciences; College of Medicine; National Cheng Kung University; Tainan Taiwan
- Department of Medical Laboratory Science and Biotechnology; College of Medicine; National Cheng Kung University; Tainan Taiwan
- Center of Infectious Disease and Signaling Research; College of Medicine; National Cheng Kung University; Tainan Taiwan
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13
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Wang CH, Chiang-Ni C, Kuo HT, Zheng PX, Tsou CC, Wang S, Tsai PJ, Chuang WJ, Lin YS, Liu CC, Wu JJ. Peroxide responsive regulator PerR of group A Streptococcus is required for the expression of phage-associated DNase Sda1 under oxidative stress. PLoS One 2013; 8:e81882. [PMID: 24312597 PMCID: PMC3849366 DOI: 10.1371/journal.pone.0081882] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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: 07/18/2013] [Accepted: 10/17/2013] [Indexed: 12/17/2022] Open
Abstract
The peroxide regulator (PerR) is a ferric uptake repressor-like protein, which is involved in adaptation to oxidative stress and iron homeostasis in group A streptococcus. A perR mutant is attenuated in surviving in human blood, colonization of the pharynx, and resistance to phagocytic clearance, indicating that the PerR regulon affects both host environment adaptation and immune escape. Sda1 is a phage-associated DNase which promotes M1T1 group A streptococcus escaping from phagocytic cells by degrading DNA-based neutrophil extracellular traps. In the present study, we found that the expression of sda1 is up-regulated under oxidative conditions in the wild-type strain but not in the perR mutant. A gel mobility shift assay showed that the recombinant PerR protein binds the sda1 promoter. In addition, mutation of the conserved histidine residue in the metal binding site of PerR abolished sda1 expression under hydrogen peroxide treatment conditions, suggesting that PerR is directly responsible for the sda1 expression under oxidative stress. Our results reveal PerR-dependent sda1 expression under oxidative stress, which may aid innate immune escape of group A streptococcus.
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Affiliation(s)
- Chih-Hung Wang
- Departments of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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14
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Chiang-Ni C, Zheng PX, Tsai PJ, Chuang WJ, Lin YS, Liu CC, Wu JJ. Environmental pH changes, but not the LuxS signalling pathway, regulate SpeB expression in M1 group A streptococci. J Med Microbiol 2011; 61:16-22. [PMID: 21890514 DOI: 10.1099/jmm.0.036012-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The autoinducer-2/LuxS signalling pathway participates in quorum sensing in diverse bacterial species. In group A streptococci (GAS), LuxS has been shown to be involved in regulating the expression of several important virulence factors. Streptococcal pyrogenic exotoxin B (SpeB), a cysteine protease that has important roles in GAS pathogenesis, is positively regulated by LuxS in M3 and M5 strains. In the present study, it was found that the supernatant harvested from an overnight culture stimulated M1 strains to express speB. However, mutation of the luxS gene in M1 strains or treating M1 strains with luxS mutant culture supernatant did not affect speB expression, indicating that the LuxS pathway is not involved in regulation of speB expression in M1 strains. In addition, the acid property of culture broth was found to be able to stimulate M1 strains to express speB in the same LuxS-independent manner. These results indicate that speB expression in M1 strains is induced by environmental pH changes but is not regulated by the LuxS signalling pathway.
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Affiliation(s)
- Chuan Chiang-Ni
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Po-Xing Zheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Pei-Jane Tsai
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Woei-Jer Chuang
- Department of Biochemistry, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Yee-Shin Lin
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Ching-Chuan Liu
- Department of Pediatrics, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Jiunn-Jong Wu
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan, ROC.,Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
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15
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Wu H, Cai BC, Zheng PX, Zhao CZ, Yuan ZR. [Effect of processing on the alkaloids in Strychnos nux-vomica L]. Zhongguo Zhong Yao Za Zhi 1994; 19:277-9, 319. [PMID: 7945866] [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: 01/28/2023]
Abstract
The contents of strychnine, brucine, isostrychnine and isobrucine in different processed products of Strychnos nux-vomica were determined by TLC-densitometry. The relationship of the contents of strychnos alkaloids with processing methods was studied.
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Affiliation(s)
- H Wu
- Nanjing College of Traditional Chinese Medicine
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