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Zhang J, Wang QH, Miao BB, Wu RX, Li QQ, Tang BG, Liang ZB, Niu SF. Liver transcriptome analysis reveal the metabolic and apoptotic responses of Trachinotus ovatus under acute cold stress. Fish & Shellfish Immunology 2024; 148:109476. [PMID: 38447780 DOI: 10.1016/j.fsi.2024.109476] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/07/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
Trachinotus ovatus is an economically important fish and has been recommended as a high-quality aquaculture fish breed for the high-quality development of sea ranches in the South China Sea. However, T. ovatus shows intolerance to low temperature, greatly limiting the extension of farming scale, reducing production efficiency in winter, and increasing farming risks. In this study, liver transcriptome analysis was investigated in T. ovatus under acute low temperature conditions (20 and 15 °C) using RNA sequencing (RNA-Seq) technology. Inter-groups differential expression analysis and trend analysis screened 1219 DEGs and four significant profiles (profiles 0, 3, 4, and 7), respectively. GO enrichment analysis showed that these DEGs were mainly related to metabolic process and cell growth and death process. KEGG enrichment analysis found that DEGs were mainly associated with lipid metabolism, carbohydrate metabolism, and cell growth and death, such as gluconeogenesis, glycolysis, fatty acid oxidation, cholesterol biosynthesis, p53 signaling pathway, cell cycle arrest, and apoptotic cell death. Moreover, protein-protein interaction networks identified two hub genes (FOS and JUNB) and some important genes related to metabolic process and cell growth and death process, that corresponding to enrichment analysis. Overall, gluconeogenesis, lipid mobilization, and fatty acid oxidation in metabolic process and cell cycle arrest and apoptotic cell death in cell growth and death process were enhanced, while glycolysis, liver glycogen synthesis and cholesterol biosynthesis in metabolic process were inhibited. The enhancement or attenuatment of metabolic process and cell growth and death process is conducive to maintain energy balance, normal fluidity of cell membrane, normal physiological functions of liver cell, enhancing the tolerance of T. ovatus to cold stress. These results suggested that metabolic process and cell growth and death process play important roles in response to acute cold stress in the liver of T. ovatus. Gene expreesion level analysis showed that acute cold stress at 15 °C was identified as a critical temperature point for T. ovatus in term of cellular metabolism alteration and apoptosis inducement, and rewarming intervention should be timely implemented above 15 °C. Our study can provide theoretical support for breeding cold-tolerant cultivars of T. ovatus, which is contributed to high-quality productions fish production.
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Affiliation(s)
- Jing Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China
| | - Qing-Hua Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China
| | - Qian-Qian Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Bao-Gui Tang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, 524025, China.
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Deng WJ, Li QQ, Shuai HN, Wu RX, Niu SF, Wang QH, Miao BB. Whole-Genome Sequencing Analyses Reveal the Evolution Mechanisms of Typical Biological Features of Decapterus maruadsi. Animals (Basel) 2024; 14:1202. [PMID: 38672351 PMCID: PMC11047736 DOI: 10.3390/ani14081202] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Decapterus maruadsi is a typical representative of small pelagic fish characterized by fast growth rate, small body size, and high fecundity. It is a high-quality marine commercial fish with high nutritional value. However, the underlying genetics and genomics research focused on D. maruadsi is not comprehensive. Herein, a high-quality chromosome-level genome of a male D. maruadsi was assembled. The assembled genome length was 716.13 Mb with contig N50 of 19.70 Mb. Notably, we successfully anchored 95.73% contig sequences into 23 chromosomes with a total length of 685.54 Mb and a scaffold N50 of 30.77 Mb. A total of 22,716 protein-coding genes, 274.90 Mb repeat sequences, and 10,060 ncRNAs were predicted, among which 22,037 (97%) genes were successfully functionally annotated. The comparative genome analysis identified 459 unique, 73 expanded, and 52 contracted gene families. Moreover, 2804 genes were identified as candidates for positive selection, of which some that were related to the growth and development of bone, muscle, cardioid, and ovaries, such as some members of the TGF-β superfamily, were likely involved in the evolution of typical biological features in D. maruadsi. The study provides an accurate and complete chromosome-level reference genome for further genetic conservation, genomic-assisted breeding, and adaptive evolution research for D. maruadsi.
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Affiliation(s)
| | | | | | | | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (W.-J.D.); (Q.-Q.L.); (H.-N.S.); (R.-X.W.); (Q.-H.W.); (B.-B.M.)
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Han FY, Wu RX, Miao BB, Niu SF, Wang QH, Liang ZB. Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus. Animals (Basel) 2024; 14:434. [PMID: 38338077 PMCID: PMC10854985 DOI: 10.3390/ani14030434] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Smallhead hairtail (Eupleurogrammus muticus) is an important marine economic fish distributed along the northern Indian Ocean and the northwest Pacific coast; however, little is known about the mechanism of its genetic evolution. This study generated the first genome assembly of E. muticus at the chromosomal level using a combination of PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. The final assembled genome size was 709.27 Mb, with a contig N50 of 25.07 Mb, GC content of 40.81%, heterozygosity rate of 1.18%, and repetitive sequence rate of 35.43%. E. muticus genome contained 21,949 protein-coding genes (97.92% of the genes were functionally annotated) and 24 chromosomes. There were 143 expansion gene families, 708 contraction gene families, and 4888 positively selected genes in the genome. Based on the comparative genomic analyses, we screened several candidate genes and pathways related to whip-like tail formation, innate immunity, and DNA repair in E. muticus. These findings preliminarily reveal some molecular evolutionary mechanisms of E. muticus at the genomic level and provide important reference genomic data for the genetic studies of other trichiurids.
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Affiliation(s)
- Fang-Yuan Han
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Ben-Ben Miao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China;
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Qing-Hua Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China;
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
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Wang QH, Wu RX, Ji JN, Zhang J, Niu SF, Tang BG, Miao BB, Liang ZB. Integrated Transcriptomics and Metabolomics Reveal Changes in Cell Homeostasis and Energy Metabolism in Trachinotus ovatus in Response to Acute Hypoxic Stress. Int J Mol Sci 2024; 25:1054. [PMID: 38256129 PMCID: PMC10815975 DOI: 10.3390/ijms25021054] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Trachinotus ovatus is an economically important mariculture fish, and hypoxia has become a critical threat to this hypoxia-sensitive species. However, the molecular adaptation mechanism of T. ovatus liver to hypoxia remains unclear. In this study, we investigated the effects of acute hypoxic stress (1.5 ± 0.1 mg·L-1 for 6 h) and re-oxygenation (5.8 ± 0.3 mg·L-1 for 12 h) in T. ovatus liver at both the transcriptomic and metabolic levels to elucidate hypoxia adaptation mechanism. Integrated transcriptomics and metabolomics analyses identified 36 genes and seven metabolites as key molecules that were highly related to signal transduction, cell growth and death, carbohydrate metabolism, amino acid metabolism, and lipid metabolism, and all played key roles in hypoxia adaptation. Of these, the hub genes FOS and JUN were pivotal hypoxia adaptation biomarkers for regulating cell growth and death. During hypoxia, up-regulation of GADD45B and CDKN1A genes induced cell cycle arrest. Enhancing intrinsic and extrinsic pathways in combination with glutathione metabolism triggered apoptosis; meanwhile, anti-apoptosis mechanism was activated after hypoxia. Expression of genes related to glycolysis, gluconeogenesis, amino acid metabolism, fat mobilization, and fatty acid biosynthesis were up-regulated after acute hypoxic stress, promoting energy supply. After re-oxygenation for 12 h, continuous apoptosis favored cellular function and tissue repair. Shifting from anaerobic metabolism (glycolysis) during hypoxia to aerobic metabolism (fatty acid β-oxidation and TCA cycle) after re-oxygenation was an important energy metabolism adaptation mechanism. Hypoxia 6 h was a critical period for metabolism alteration and cellular homeostasis, and re-oxygenation intervention should be implemented in a timely way. This study thoroughly examined the molecular response mechanism of T. ovatus under acute hypoxic stress, which contributes to the molecular breeding of hypoxia-tolerant cultivars.
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Affiliation(s)
- Qing-Hua Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (Q.-H.W.); (R.-X.W.); (J.-N.J.); (J.Z.); (B.-G.T.); (B.-B.M.); (Z.-B.L.)
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (Q.-H.W.); (R.-X.W.); (J.-N.J.); (J.Z.); (B.-G.T.); (B.-B.M.); (Z.-B.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Jiao-Na Ji
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (Q.-H.W.); (R.-X.W.); (J.-N.J.); (J.Z.); (B.-G.T.); (B.-B.M.); (Z.-B.L.)
| | - Jing Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (Q.-H.W.); (R.-X.W.); (J.-N.J.); (J.Z.); (B.-G.T.); (B.-B.M.); (Z.-B.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (Q.-H.W.); (R.-X.W.); (J.-N.J.); (J.Z.); (B.-G.T.); (B.-B.M.); (Z.-B.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Bao-Gui Tang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (Q.-H.W.); (R.-X.W.); (J.-N.J.); (J.Z.); (B.-G.T.); (B.-B.M.); (Z.-B.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (Q.-H.W.); (R.-X.W.); (J.-N.J.); (J.Z.); (B.-G.T.); (B.-B.M.); (Z.-B.L.)
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (Q.-H.W.); (R.-X.W.); (J.-N.J.); (J.Z.); (B.-G.T.); (B.-B.M.); (Z.-B.L.)
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Li QQ, Zhang J, Wang HY, Niu SF, Wu RX, Tang BG, Wang QH, Liang ZB, Liang YS. Transcriptomic Response of the Liver Tissue in Trachinotus ovatus to Acute Heat Stress. Animals (Basel) 2023; 13:2053. [PMID: 37443851 DOI: 10.3390/ani13132053] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Trachinotus ovatus is a major economically important cultured marine fish in the South China Sea. However, extreme weather and increased culture density result in uncontrollable problems, such as increases in water temperature and a decline in dissolved oxygen (DO), hindering the high-quality development of aquaculture. In this study, liver transcriptional profiles of T. ovatus were investigated under acute high-temperature stress (31 °C and 34 °C) and normal water temperature (27 °C) using RNA sequencing (RNA-Seq) technology. Differential expression analysis and STEM analysis showed that 1347 differentially expressed genes (DEGs) and four significant profiles (profiles 0, 3, 4, and 7) were screened, respectively. Of these DEGs, some genes involved in heat shock protein (HSPs), hypoxic adaptation, and glycolysis were up-regulated, while some genes involved in the ubiquitin-proteasome system (UPS) and fatty acid metabolism were down-regulated. Our results suggest that protein dynamic balance and function, hypoxia adaptation, and energy metabolism transformation are crucial in response to acute high-temperature stress. Our findings contribute to understanding the molecular response mechanism of T. ovatus under acute heat stress, which may provide some reference for studying the molecular mechanisms of other fish in response to heat stress.
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Affiliation(s)
- Qian-Qian Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jing Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Hong-Yang Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Bao-Gui Tang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Qing-Hua Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yan-Shan Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
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Wu RX, Miao BB, Han FY, Niu SF, Liang YS, Liang ZB, Wang QH. Chromosome-Level Genome Assembly Provides Insights into the Evolution of the Special Morphology and Behaviour of Lepturacanthus savala. Genes (Basel) 2023; 14:1268. [PMID: 37372448 DOI: 10.3390/genes14061268] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled L. savala genome was 790.02 Mb with contig N50 and scaffold N50 values of 19.01 Mb and 32.77 Mb, respectively. The assembled sequences were anchored to 24 chromosomes by using Hi-C data. Combined with RNA sequencing data, 23,625 protein-coding genes were predicted, of which 96.0% were successfully annotated. In total, 67 gene family expansions and 93 gene family contractions were detected in the L. savala genome. Additionally, 1825 positively selected genes were identified. Based on a comparative genomic analysis, we screened a number of candidate genes associated with the specific morphology, behaviour-related immune system, and DNA repair mechanisms in L. savala. Our results preliminarily revealed mechanisms underlying the special morphological and behavioural characteristics of L. savala from a genomic perspective. Furthermore, this study provides valuable reference data for subsequent molecular ecology studies of L. savala and whole-genome analyses of other trichiurid fishes.
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Affiliation(s)
- Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Fang-Yuan Han
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yan-Shan Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Qing-Hua Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
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Jin Y, Mao Y, Niu SF, Pan Y, Zheng WH, Wang J. Molecular characterisation and biological activity of an antiparasitic peptide from Sciaenops ocellatus and its immune response to Cryptocaryon irritans. Mol Immunol 2021; 141:1-12. [PMID: 34781186 DOI: 10.1016/j.molimm.2021.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 11/20/2022]
Abstract
Cryptocaryon irritans, a holotrichous ciliate parasitic protozoan, can trigger marine white spot disease and cause substantial economic losses in mariculture. However, methods of preventing and curing the disease have negatively affect fish, human, other organisms, and the natural environment. The antiparasitic activity of some antimicrobial peptides (AMPs) has garnered extensive attention of scholars. In this study, we identified and characterised a novel antiparasitic peptide, named So-pis, from Sciaenops ocellatus. The sequence analysis, structural features, and tissue distribution suggested that So-pis is genetically related to the piscidins family. However, So-pis showed a relatively low overall conservation compared with other known piscidins. So-pis is abound in glycine residues (22.7 %) and it has a neutral isoelectric point, weak amphipathicity, relatively long α-helix, and high hydrophobicity. These key elements are responsible for its biological activity. Quantitative real-time polymerase chain reaction (qRT-PCR) data indicated that So-pis is a typically gill-expressed peptide. The expression of So-pis in the gill, skin, spleen, and head kidney could be regulated during C. irritans infection, thereby implicating a role of So-pis in immune defence against C. irritans. The synthetic So-pis had limited or no antimicrobial activity against bacterial and yeasts but exhibited potent antiparasitic activity against C. irritans in vitro. The activity of synthetic So-pis against erythrocytes was less potent than its antiparasitic activity against C. irritans. These results indicated that So-pis might be one of the crucial defence cytokines against C. irritans in the red drum. Cumulatively, our data suggested that So-pis might be a potential candidate for developing a novel, effective, and safe therapeutic agent against marine white spot disease.
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Affiliation(s)
- Yuan Jin
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian, 352103, China; National Marine Environmental Monitoring Center, Dalian, Liaoning, 116023, China
| | - Yong Mao
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian, 352103, China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Ying Pan
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian, 352103, China
| | - Wei-Hao Zheng
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian, 352103, China
| | - Jun Wang
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian, 352103, China.
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Miao BB, Niu SF, Wu RX, Liang ZB, Tang BG, Zhai Y, Xu XQ. Gene Expression Profile and Co-Expression Network of Pearl Gentian Grouper under Cold Stress by Integrating Illumina and PacBio Sequences. Animals (Basel) 2021; 11:ani11061745. [PMID: 34208015 PMCID: PMC8230743 DOI: 10.3390/ani11061745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 04/06/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary In this study, we investigated the liver transcriptomic responses of pearl gentian grouper towards cold stress. Some cold-related key genes and biological pathways were screened, of which energy-related metabolic pathways and genes had higher expression levels under cold stress. This suggested that energy homeostasis plays a crucial role in the physiological adjustments of pearl gentian grouper when exposed to the cold stress environment. Our results will expedite the understanding of different fishes adaptive mechanisms to profound environmental temperature changes and provide insights into the molecular breeding of cold-tolerant pearl gentian grouper varieties. Abstract Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying cold stress remains largely elusive. This study thus investigated the liver transcriptomic responses of pearl gentian grouper by comparing the gene expression of cold stress groups (20, 15, 12, and 12 °C for 6 h) with that of control group (25 °C) using PacBio SMRT-Seq and Illumina RNA-Seq technologies. In SMRT-Seq analysis, a total of 11,033 full-length transcripts were generated and used as reference sequences for further RNA-Seq analysis. In RNA-Seq analysis, 3271 differentially expressed genes (DEGs), two low-temperature specific modules (tan and blue modules), and two significantly expressed gene sets (profiles 0 and 19) were screened by differential expression analysis, weighted gene co-expression networks analysis (WGCNA), and short time-series expression miner (STEM), respectively. The intersection of the above analyses further revealed some key genes, such as PCK, ALDOB, FBP, G6pC, CPT1A, PPARα, SOCS3, PPP1CC, CYP2J, HMGCR, CDKN1B, and GADD45Bc. These genes were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and endocrine system pathways. All these pathways were linked to biological functions relevant to cold adaptation, such as energy metabolism, stress-induced cell membrane changes, and transduction of stress signals. Taken together, our study explores an overall and complex regulation network of the functional genes in the liver of pearl gentian grouper, which could benefit the species in preventing damage caused by cold stress.
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Affiliation(s)
- Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
- Correspondence:
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
| | - Bao-Gui Tang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
- Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524025, China
| | - Yun Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
| | - Xue-Qi Xu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (B.-B.M.); (S.-F.N.); (Z.-B.L.); (B.-G.T.); (Y.Z.); (X.-Q.X.)
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Niu SF, Wu RX, Zhai Y, Zhang HR, Li ZL, Liang ZB, Chen YH. Demographic history and population genetic analysis of Decapterus maruadsi from the northern South China Sea based on mitochondrial control region sequence. PeerJ 2019; 7:e7953. [PMID: 31681517 PMCID: PMC6822595 DOI: 10.7717/peerj.7953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 01/02/2019] [Accepted: 09/26/2019] [Indexed: 11/24/2022] Open
Abstract
Late Pleistocene climate oscillations are believed to have greatly influenced the distribution, population dynamics, and genetic variation of many marine organisms in the western Pacific. However, the impact of the late Pleistocene climate cycles on the demographic history and population genetics of pelagic fish in the northern South China Sea (SCS) remains largely unexplored. In this study, we explored the demographic history, genetic structure, and genetic diversity of Decapterus maruadsi, a typical pelagic fish, over most of its range in the northern SCS. A 828–832 bp fragment of mitochondrial control region were sequenced in 241 individuals from 11 locations. High haplotype diversity (0.905–0.980) and low nucleotide diversity (0.00269–0.00849) was detected, revealing low levels of genetic diversity. Demographic history analysis revealed a pattern of decline and subsequent rapid growth in the effective population size during deglaciation, which showed that D. maruadsi experienced recent demographic expansion after a period of low effective population size. Genetic diversity, genetic structure, and phylogenetic relationship analysis all demonstrated that no significant genetic differentiation existed among the populations, indicating that D. maruadsi was panmictic throughout the northern SCS. Periodic sea-level changes, fluctuation of the East Asian Monsoon, and Kuroshio variability were responsible for the population decline and expansion of D. maruadsi. The demographic history was the primary reason for the low levels of genetic diversity and the lack of significant genetic structure. The life history characteristics and ocean currents also had a strong correlation with the genetic homogeneity of D. maruadsi. However, the genetic structure of the population (genetic homogeneity) is inconsistent with biological characteristics (significant difference), which is an important reminder to identify and manage the D. maruadsi population carefully.
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Affiliation(s)
- Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yun Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Hao-Ran Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Zhong-Lu Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yu-Hang Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
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10
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Wu RX, Miao BB, Niu SF, Zhai Y, Zhang HR, Liu F, Ou CX. The second complete mitogenome of Scolopsis ciliata (Perciformes, Nemipteridae) to analyze control region structure and intraspecific variation. Mitochondrial DNA B Resour 2019; 4:3520-3522. [PMID: 33366067 PMCID: PMC7707376 DOI: 10.1080/23802359.2019.1675546] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/25/2019] [Indexed: 11/12/2022] Open
Abstract
In this study, we reported the complete mitogenome of Scolopsis ciliata sampled from the Beibu Gulf, South China Sea. It was 16,734 bp in length and contained 37 canonical mitochondrial genes and 2 non-coding regions. Fifty-one single nucleotide polymorphisms and five insertion and deletions were detected between two S. ciliata mitogenomes, suggesting a high level of intraspecific genetic variation in the species. The control region contained termination associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-A), and conserved sequence block domain (CSB-1, CSB-2, and CSB-3). The phylogenetic analysis of 21 complete mitogenome sequences well supports the phylogenetic position of S. ciliata and reveals the phylogenetic relationship of the genus Scolopsis.
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Affiliation(s)
- Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Yun Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Hao-Ran Zhang
- School of Life Sciences, East China Normal University, Shanghai, P. R. China
| | - Fang Liu
- Guangdong Leizhou Rare Marine Life National Nature Reserve, Zhanjiang, Guangdong, P. R. China
| | - Chun-Xiao Ou
- Guangdong Leizhou Rare Marine Life National Nature Reserve, Zhanjiang, Guangdong, P. R. China
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11
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Wu RX, Zhai Y, Miao BB, Niu SF, Zhang HR, Liu F, Ou CX. The second complete mitogenome of Nemipterus virgatus to dissect control region structure and phylogenetic problem of the superfamily Sparoidea (Teleostei, Perciformes). Mitochondrial DNA B Resour 2019; 4:3409-3411. [PMID: 33366016 PMCID: PMC7707243 DOI: 10.1080/23802359.2019.1674708] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 09/25/2019] [Indexed: 11/16/2022] Open
Abstract
In this study, we determined the complete mitogenome of Nemipterus virgatus of which the length was 17,073 bp, including 37 canonical mitochondrial genes and 2 non-coding regions. The control region contained termination associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-A), conserved sequence block domain (CSB-1, CSB-2, and CSB-3), and tandem repeat sequence domain (TTD). Nine single nucleotide polymorphisms and three insertion of tandem repeat sequence (each length in 28 bp) were detected between two N. virgatus mitogenomes. The phylogenetic analysis showed that the families Nemipteridae, Sparidae, Centracanthidae, and Lethrinidae did not gather into a monophyly of superfamily Sparoidea in the neighbor-joining tree.
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Affiliation(s)
- Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Yun Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P. R. China
| | - Hao-Ran Zhang
- School of Life Sciences, East China Normal University, Shanghai, P. R. China
| | - Fang Liu
- Guangdong Leizhou Rare Marine Life National Nature Reserve, Zhanjiang, Guangdong, P. R. China
| | - Chun-Xiao Ou
- Guangdong Leizhou Rare Marine Life National Nature Reserve, Zhanjiang, Guangdong, P. R. China
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12
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Wu RX, Zhai Y, Niu SF, Liu J, Miao BB, Liu F, Ou CX. Complete mitochondrial genome of yellowback seabream, Dentex hypselosomus and phylogenetic analysis of the family Sparidae. Mitochondrial DNA B Resour 2019; 4:2441-2442. [PMID: 33365577 PMCID: PMC7687427 DOI: 10.1080/23802359.2019.1637298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 12/03/2022] Open
Abstract
The complete mitogenome sequence of Dentex hypselosomus was amplified by designing 15 primer pairs. The circle genome was 16,618 bp in size and the overall base composition was 27.04% of A, 26.38% of T, 17.08% of G, and 29.50 of C, with significant anti-G bias. The complete mitogenome of D. hypselosomus encodes 37 canonical mitochondrial genes, two non-coding regions, an L-strand replication region (OL), and a control region (D-loop). The D-loop contained termination sequence domain (TAS), central conserved domains (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-A), and conserved sequence blocks (CSB-1, CSB-2, and CSB-3). Phylogenetic analysis of nine sparid species well supported the phylogenetic position of D. hypselosomus and revealed the phylogenetic relationship of the family Sparidae at the level of mitochondrial genomes.
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Affiliation(s)
- Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, P.R. China
| | - Yun Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang, P.R. China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, P.R. China
| | - Jing Liu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P.R. China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, P.R. China
| | - Fang Liu
- Guangdong Leizhou Rare Marine Life National Nature Reserve, Zhanjiang, P.R. China
| | - Chun-Xiao Ou
- Guangdong Leizhou Rare Marine Life National Nature Reserve, Zhanjiang, P.R. China
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13
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Zhai Y, Niu SF, Wu RX, Miao BB, Liu F, Ou CX. Complete mitochondrial genome and phylogenetic relationship of ornate threadfin bream, Nemipterus hexodon (Perciformes, Nemipteridae). Mitochondrial DNA B Resour 2019; 4:2506-2508. [PMID: 33365602 PMCID: PMC7687645 DOI: 10.1080/23802359.2019.1640081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 11/01/2022] Open
Abstract
The complete mitochondrial genome of the ornate threadfin bream, Nemipterus hexodon, was first determined by the pairs-walking sequencing in this study. The circular mtDNA molecule was 17,115 bp in size and the overall nucleotide composition of H-stand was A (29.55%), T (27.36%), G (16.08%), and C (27.01%), with a slight bias towards A + T. The complete mitogenome encoded 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions (an origin of L-strand replication and a control region). The Bayesian tree supported the phylogenetic position of N. hexodon, which provided useful information for phylogenetic relationship in genus Nemipterus.
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Affiliation(s)
- Yun Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P.R. China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P.R. China
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P.R. China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, P.R. China
| | - Fang Liu
- Guangdong Leizhou Rare Marine Life National Nature Reserve, Zhanjiang, Guangdong, P.R. China
| | - Chun-Xiao Ou
- Guangdong Leizhou Rare Marine Life National Nature Reserve, Zhanjiang, Guangdong, P.R. China
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14
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Wu RX, Zhang HR, Niu SF, Zhai Y, Liu XF. Development of polymorphic microsatellites for Sillago sihama based on next-generation sequencing and transferability to Sillago japonica. Genet Mol Res 2016; 15:gmr-15-04-gmr.15049046. [PMID: 27886349 DOI: 10.4238/gmr15049046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sillago sihama (Forsskål, 1775), a commercially important marine fishery species in the Indo-West Pacific, is being developed as a target species for aquaculture and stock enhancement in China. However, due to the limitations of traditional isolation methods, the available microsatellite loci, or simple sequence repeats (SSRs), of S. sihama lack diversity. We used a stepwise approach including Illumina sequencing, primer screening, and SSR marker validation to develop diverse SSRs for S. sihama. A total of 853.48 Mb clean sequences were assembled with high coverage and sequencing depth, and 27,288 potential SSRs were identified. A set of 18 novel SSR markers with four type motifs including 11 di-, 1 tri-, 5 tetra-, and 1 hexanucleotide repeats were successfully isolated. The ranges of number of alleles per locus and observed and expected heterozygosities were 5-24, 0.226-0.968, and 0.319-0.950, respectively. The diversity parameters exhibited high levels of polymorphism in these 18 loci. Three loci with the presence of both null alleles and inbreeding showed significant deviation from Hardy-Weinberg equilibrium after Bonferroni correction. Moreover, 13 loci developed in S. sihama showed high transferability to the closely related species Sillago japonica. The polymorphic SSR markers developed in this study may serve as valuable tools for further basic and applied research on the genetic resources of S. sihama as well as S. japonica. Our results indicate that this approach, based on next-generation sequencing technology, is convenient, cost-effective, and suitable for SSR marker isolation in other sillaginid fishes.
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Affiliation(s)
- R X Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - H R Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - S F Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Y Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - X F Liu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
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15
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Liu HT, Wang J, Mao Y, Liu M, Niu SF, Qiao Y, Su YQ, Wang CZ, Zheng ZP. Identification and expression analysis of a new invertebrate lysozyme in Kuruma shrimp (Marsupenaeus japonicus). Fish Shellfish Immunol 2016; 49:336-343. [PMID: 26723264 DOI: 10.1016/j.fsi.2015.12.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
Lysozyme is an important component of the innate immunity system against invading pathogens. An invertebrate (i-type) lysozyme from the hepatopancreas of Kuruma shrimp Marsupenaeus japonicus (Mj-ilys) was identified. The full-length cDNA of Mj-ilys was 580bp with a 429 bp open reading frame encoding a 142 amino acid polypeptide. The encoded polypeptide was predicted to have a 17 amino acid signal peptide, and a 125 amino acid mature protein with a theoretical mass of 14.099 kDa and an isoelectric point (pI) of 4.18. A Destabilase conserved domain was predicted in Mj-ilys amino acid sequences which may be stable by 10 cysteine residues forming 5 disulfide bonds. Mj-ilys may loss the muramidase and isopeptidase activities due to the lack of the key catalytic residues. Mj-ilys had high homologous of 80-82% with i-type lysozymes of penaeid shrimps. It was first grouped with other i-type lysozyme of shrimps and crabs in a phylogenetic tree predicted by the Neighbor-Joining method. Mj-ilys mRNA was expressed mainly in hepatopancreas and almost undetectable in other tissues. The mRNA expression of Mj-ilys were all found from fertilized eggs to post-larvae of 17 days (PL17), and its expression exhibited significant differences among each developmental stage. After white spot syndrome virus (WSSV) challenge (3.6 × 10(8) virions/μl), the time-dependent expression pattern of Mj-ilys in hepatopancreas and gills showed significantly different. These results indicated that Mj-ilys is potentially involved in the ontogenesis and immune defense in Kuruma shrimp.
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Affiliation(s)
- Hong-Tao Liu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jun Wang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Min Liu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Su-Fang Niu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Ying Qiao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yong-Quan Su
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, Fujian 361102, China.
| | | | - Zhi-Peng Zheng
- Putian Tian-ran-xing Agricultural Development Co. Ltd., Putian, Fujian 351100, China
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16
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Zhou QJ, Su YQ, Niu SF, Liu M, Qiao Y, Wang J. Discovery and molecular cloning of piscidin-5-like gene from the large yellow croaker (Larimichthys crocea). Fish Shellfish Immunol 2014; 41:417-420. [PMID: 25263194 DOI: 10.1016/j.fsi.2014.09.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/09/2014] [Accepted: 09/17/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Qi-Jia Zhou
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Yong-Quan Su
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Su-Fang Niu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Min Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Ying Qiao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Jun Wang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China.
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17
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Niu SF, Jin Y, Xu X, Qiao Y, Wu Y, Mao Y, Su YQ, Wang J. Characterization of a novel piscidin-like antimicrobial peptide from Pseudosciaena crocea and its immune response to Cryptocaryon irritans. Fish Shellfish Immunol 2013; 35:513-524. [PMID: 23727503 DOI: 10.1016/j.fsi.2013.05.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 04/22/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
Piscidins, important components of the innate (nonspecific) immunity system in fish, have potent, broad-spectrum antimicrobial and antiparasitic activities. In this study, we reported a novel antimicrobial cationic peptide from Pseudosciaena crocea. Although this peptide exhibited a genomic (3 exons and 2 introns) and propeptide (signal peptide, mature peptide and prodomain) organization, conserved signal peptide (22 amino acids) and consensus motif I-X5-H-X4-I-H identical to the reported fish piscidins, Pc-pis showed a relatively low overall conservation with other known piscidins, which was obviously embodied in the amino acid composition of the peptide. Pc-pis is strikingly rich in glycine residues (27.3%), which disrupted the amphipathic structure of the peptide. Relative quantitative real-time PCR revealed that Pc-pis is a typically gill-expressed peptide. The sequence analysis, structural features and tissue distribution suggested that Pc-pis was genetically related to the piscidins family and might be a novel piscidin-like antimicrobial peptide. Quantitative PCR analysis revealed that the expression of Pc-pis in the spleen, head-kidney, liver, intestine, skin and gill could be regulated during Cryptocaryon irritans infection and post C. irritans falling off, implicating a role for Pc-pis in immune defense against C. irritans and secondary bacterial infections. Synthetic Pc-pis exhibited broad-spectrum activity against bacteria, fungi and C. irritans in parasitic stages. These results provided the first evidence of piscidins antiparasitic activity against marine fish ectoparasites C. irritants trophonts and further indicated that Pc-pis might be an important component of the P. crocea innate immune system against C. irritans and secondary bacterial infections. Thus, these data provided new insights into P. crocea innate immunity against external protozoan parasite and microbial infections and facilitate the evaluation of Pc-pis as a therapeutic agent against pathogen invasion.
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Affiliation(s)
- Su-Fang Niu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
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Chen X, Su YQ, Wang J, Liu M, Niu SF, Zhong SP, Qiu F. Isolation and identification of the immune-relevant ribosomal protein L10 (RPL10/QM-like gene) from the large yellow croaker Pseudosciaena crocea (Pisces: Sciaenidae). Genet Mol Res 2012; 11:3755-65. [PMID: 23096695 DOI: 10.4238/2012.october.15.7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In order to investigate the immune role of ribosomal protein L10 (RPL10/QM-like gene) in marine fish, we challenged the large yellow croaker Pseudosciaena (= Larimichthys) crocea, the most important marine fish culture species in China, by injection with a mixture of the bacteria Vibrio harveyi and V. parahaemolyticus (3:1 in volume). Microarray analysis and real-time PCR were performed 24 and 48 h post-challenge to isolate and identify the QM-like gene from the gill P. crocea (designated PcQM). The expression level of the PcQM gene did not changed significantly at 24 h post-challenge, but was significantly downregulated at 48 h post-challenge, suggesting that the gene had an immune-modulatory effect in P. crocea. Full-length PcQM cDNA and genomic sequences were obtained by rapid amplification of cDNA ends (RACE)-PCR. The sequence of the PcQM gene clustered together with those of other QM-like genes from other aquatic organisms, indicating that the QM-like gene is highly conserved in teleosts.
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Affiliation(s)
- X Chen
- Department of Marine technology, College of Ocean, Nantong University, Nantong, China
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Zhu GF, Sun B, Niu SF, Cai YY, Lin K, Lindwall R, Robertson B. Combined surfactant therapy and inhaled nitric oxide in rabbits with oleic acid-induced acute respiratory distress syndrome. Am J Respir Crit Care Med 1998; 158:437-43. [PMID: 9700118 DOI: 10.1164/ajrccm.158.2.9711107] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Intratracheal administration of surfactant and inhaled nitric oxide (INO) have had variable effects in clinical trials on patients with acute respiratory distress syndrome (ARDS). We hypothesized that combined treatment with exogenous surfactant and INO may have effects in experimental ARDS. After intravenous infusion of oleic acid in adult rabbits and 4-6 h of ventilation, there was more than a 40% reduction in both dynamic compliance (Cdyn) of the respiratory system and functional residual capacity (FRC), a 50% increment of respiratory resistance (Rrs), a 70% reduction in PaO2 /FIO2, and an increase in intrapulmonary shunting (Q S/Q T) from 4.4 to 33.5%. The animals were then allocated to groups receiving (1) neither surfactant nor INO (control), (2) 100 mg/kg of surfactant (S) administered intratracheally, (3) 20 ppm INO (NO), or (4) 100 mg/kg of surfactant and 20 ppm INO (SNO), and subsequently ventilated for 6 h. After the period of ventilation, the animal lungs were used for analysis of disaturated phosphatidylcholine (DSPC) and total proteins (TP) in bronchoalveolar lavage fluid (BALF), and for determination of alveolar volume density (VV). The animals in the control group had the lowest survival rate, and no improvement in lung mechanics and blood oxygenation, whereas those in the S group had a modest but statistically significant improvement in Cdyn, Rrs, PaO2 and FRC, reduced Q S/Q T, lowered minimum surface tension (gammamin) of BALF, and increased DSPC/ TP and alveolar VV. The NO group had increased PaO2 and reduced Q S/Q T. The SNO group showed improved Cdyn, Rrs, FRC, DSPC/TP, alveolar VV, and gammamin of BALF comparable to the S group, but there was a further increase in survival rate and PaO2, and additional reduction in Q S/Q T and TP in BALF. These results indicate that, in this animal model of ARDS, a combination of surfactant therapy and INO is more effective than either treatment alone.
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Affiliation(s)
- G F Zhu
- Children's Hospital Research Institute; Department of Pulmonology, Zhongshan Hospital, Shanghai Medical University, Shanghai 200032, China
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20
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Bai CX, Niu SF, Zhang HX. [The effects of sodium nitroprusside and almitrine bismesylate on blood gases, hemodynamics and oxygen delivery in patients with cor pulmonale]. Zhonghua Nei Ke Za Zhi 1993; 32:388-91. [PMID: 8269771] [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: 01/29/2023]
Abstract
The effects of sodium nitroprusside and almitrine bismesylate on blood gases, hemodynamics and oxygen delivery were respectively studied in twenty-one and eighteen patients with cor pulmonale. The treatment of sodium nitroprusside resulted in significant decrease in pulmonary artery pressure. Although physiological shunt was increased (from 12.6 +/- 10.5 to 20.1 +/- 10.9%, P < 0.01) and arterial oxygen tension was decreased (from 12.6 +/- 4.0 to 9.9 +/- 2.5 kPa, P < 0.01) in patients undergoing mechanical ventilation, cardiac index (from 44.8 +/- 10.5 to 53.3 +/- 12.8 ml.s-1/m-2, P < 0.05) and oxygen delivery index (from 7.8 +/- 1.7 to 9.2 +/- 2.3 ml.s-1/m-2, P < 0.05) were improved. After treatment with almitrine bismesylate, improvement of arterial oxygen tension was observed in patients with spontaneous breathing (from 6.7 +/- 0.6 to 7.8 +/- 0.6 kPa, P < 0.05) and undergoing mechanical ventilation (from 10.9 +/- 1.9 to 13.4 +/- 2.5 kPa, P < 0.01), but increment of mean pulmonary artery pressure (from 3.8 to 0.5 and 3.1 +/- 0.8 to 6.3 +/- 0.7 and 3.6 +/- 0.9 kPa, respectively, P < 0.01) was noted.
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Affiliation(s)
- C X Bai
- Department of Pulmonary Medicine, Zhongshan Hospital, Shanghai Medical University
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21
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Cai YY, Niu SF, Bai CX. [A comparison between nasotracheal and orotracheal intubation in treating chronic obstructive pulmonary disease complicated by respiratory failure]. Zhonghua Nei Ke Za Zhi 1992; 31:332-4, 380. [PMID: 1286580] [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: 12/26/2022]
Abstract
Endotracheal intubation and mechanical ventilation were given to 100 COPD patients complicated by respiratory failure from Dec. 1977 to May 1990. Among them 42 were intubated through mouth. The tubes were kept from 1 to 6 days. In only 8 cases (19.0%) the tubes could be withdrawn according to the criterion, and 25 patients (59.0%) were tracheostomized. Nasotracheal intubation were given to 58 patients. The tubes were kept from 1 to 220 days and could be withdrawn in 39 cases (81.0%), with an incidence higher than that in patients intubated orotracheally (P < 0.01). Tracheostomy mas given to 6 patients intubated nasotracheally (10.3%), being fewer than in patients intubated through mouth (P < 0.01). Although the tubes have been kept for longer time, the duration of hospitalization was not prolonged.
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Affiliation(s)
- Y Y Cai
- Dept. of Chest Medicine, Zhongshan Hospital, Shanghai Medical University
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Bai CX, Niu SF, Xu FP. [A study of measuring cardiac output in patients during mechanical ventilation with CO2 rebreathing method]. Zhonghua Nei Ke Za Zhi 1992; 31:220-2, 254-5. [PMID: 1425000] [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: 12/27/2022]
Abstract
Measurement of cardiac output with CO2 rebreathing method and thermodilution method was carried out in seven COPD patients undergoing mechanical ventilation. Mixed venous PCO2 could be measured reasonably well with CO2 rebreathing method. There was a very significant positive correlation between the CO2 method and thermodilution method for measuring cardiac output (r = 0.9130, P < 0.01). The change of cardiac output before and after infusion of sodium nitroprusside could be reflected by CO2 rebreathing method. We conclude that the cardiac output in COPD patients undergoing mechanical ventilation could be measured reasonably well with CO2 rebreathing method.
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Affiliation(s)
- C X Bai
- Department of Chest Medicine, Zhongshan Hospital, Shanghai Medical University
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23
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Shen X, Niu SF, Cai YY. [A clinical trial of treating asthma of moderate severity with beclomethasone dipropionate aerosol]. Zhonghua Nei Ke Za Zhi 1991; 30:536-8, 593. [PMID: 1806334] [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: 12/28/2022]
Abstract
In order to investigate the efficacy of steroid inhalation in treating asthma of moderate severity, a single-blind, randomized short-term (3-4 weeks) trial was performed in 25 asthmatics uncontrolled by salbutamol inhalation, oral aminophylline and beta 2-agonist. 22 patients finished the trial. Among them, twelve received beclomethasone dipropionate 300 mcg/day and ten received placebo. There was significant improvement in asthmatic symptoms and pulmonary function (FEV1.0, V50, V25) in the group treated with steroid inhalation at the end of this trial, whereas no significant changes were observed in the placebo group. The results demonstrated that steroid inhalation could effectively control asthma of moderate severity.
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Affiliation(s)
- X Shen
- Department of Pulmonary Medicine, Zhongshan Hospital, Shanghai Medical University
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24
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Cai YY, Xu FP, Niu SF. [Effects of external diaphragm pacing on transdiaphragmatic pressure, ventilation and arterial blood gases in healthy volunteers]. Zhonghua Nei Ke Za Zhi 1990; 29:730-2, 765-6. [PMID: 2092956] [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: 12/30/2022]
Abstract
The effects of external diaphragm pacing (EDP) were studied in seven healthy volunteers. During EDP the movement of both left and right hemidiaphragms increased on average 1.28 and 1.30 cm respectively. The transdiaphragmatic pressure also increased from 8.63 +/- 1.576 cm H2O to 15.18 +/- 1.946 cm H2O (P less than 0.01). Inductive plethysmography showed that with EDP the mean inspiratory flow rate increased from 308 +/- 28.6 ml/sec. to 454 +/- 36.6 ml/sec. (P less than 0.01), but there was no change in respiratory rate, inspiratory time and the ratio of inspiratory time to respiratory cycle. Both tidal volume and minute volume of ventilation increased from 419 +/- 33.9 ml to 691 +/- 71.5 ml (P less than 0.01) and from 7.02 +/- 0.74 l/min. to 10.14 +/- 0.73 l/min. (P less than 0.01) respectively. Accompanied with the change of ventilation, the consumption of oxygen and the production of CO2 also increased from 258 +/- 14.9 ml/min. to 310 +/- 15.0 ml/min. (P less than 0.05) and from 228 +/- 11.4 ml/min. to 299 +/- 25.9 ml/min. (P less than 0.05) respectively. Consequently PaCO2 reduced from 5.24 +/- 0.22 kPa to 4.27 +/- 0.25 kPa (P less than 0.05), whereas PaO2 increased from 12.7 +/- 0.32 kPa to 14.5 +/- 0.42 kPa (P less than 0.01).
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Affiliation(s)
- Y Y Cai
- Department of Chest Medicine, Zhongshan Hospital, Shanghai Medical University
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25
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Xu FP, Cai YY, Niu SF. [The effects of almitrine bismesylate in chronic obstructive pulmonary disease with CO2 retention]. Zhonghua Nei Ke Za Zhi 1990; 29:479-81, 511. [PMID: 2128259] [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: 12/30/2022]
Abstract
Ten cases of chronic obstructive pulmonary disease (COPD) were examined before and 2 hours after oral administration of 150 mg of almitrine bismesylate while breathing 31% oxygen. The agent induced a rise in mouth occlusion pressure (P 0.1) from 2.67 +/- 0.64 cmH2O to 3.74 +/- 1.02 cmH2O (P less than 0.01). However the central inspiratory drive and ventilation response to hypercapnia did not change after taking almitrine. VT/Ti increased from 0.32 +/- 0.06 L/sec. to 0.40 +/- 0.08 L/sec. (P less than 0.01) and RR, Ti, Ti/Ttot were not changed, so VT and VE increased from 0.37 +/- 0.10 L to 0.42 +/- 0.16 L (P less than 0.05) and from 7.70 +/- 1.72 L to 8.85 +/- 2.28 L (P less than 0.05) respectively. VA also increased from 3.34 +/- 0.06 L to 4.14 +/- 0.86 L (P less than 0.01). Analysis of blood gases showed a marked increase in PaO2 from 88.70 +/- 16.19 mmHg to 109.10 +/- 25.57 mmHg (P less than 0.05) and a decrease in PaCO2 from 61.73 +/- 12.15 mmHg to 54.01 +/- 10.37 mmHg (P less than 0.05). Our results suggested that almitrine bismesylate could improve the blood gases in COPD patients with CO2 retention as it is a respiratory stimulant which might act through a peripheral mechanism.
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Affiliation(s)
- F P Xu
- Department of Chest Medicine, Zhongshan Hospital, Shanghai Medical University
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Niu SF, Sixt R, Bake B. Non-uniform lung elastic properties and the slope of the alveolar plateau. Bull Eur Physiopathol Respir 1987; 23:163-9. [PMID: 3607330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Dispersion of elastic properties within the lungs may contribute to the creation of a sloping alveolar plateau of the single-breath N2 washout curve. In this study we have systematically explored the behaviour of a simple two-compartment lung model with non-uniform pressure-volume characteristics. The inhomogeneity was expressed in terms of the ratio between the shape constants (k1/k2) of the compartmental pressure-volume curves and the ratio between compartmental RV/TLC (R-RV/TLC). The model simulations indicate that normal slope magnitudes can be achieved with a moderate degree of inhomogeneity (k1/k2 and R-RV/TLV = 2). The model simulations also show that a phase II-like shape of the curve--of non dead space origin--may occur and furthermore that single-breath TLC determinations increasingly underestimate true TLC as the R-RV/TLC deviates from unity. For a given degree of inhomogeneity, the model predicts the slope to increase with overall RV/TLC and k but decrease with TLC. The relations between these overall factors and the slope of phase III are also found in a patient group, where these factors explain approximately 61% of the slope variance.
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Niu SF. [The clinical evaluation of FEV1% in COPD patients]. Zhonghua Jie He He Hu Xi Xi Ji Bing Za Zhi 1985; 8:345-7, 373. [PMID: 3836841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Xu SF, Lu WX, Zhou KR, He XP, Niu SF, Xu WM, Zhang AZ, Weber E, Chang JK. The analgesic and respiratory depressant actions of metorphamide in mice and rabbits. Neuropeptides 1985; 6:121-31. [PMID: 4000426 DOI: 10.1016/0143-4179(85)90103-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Metorphamide (MET) elicited a potent, dose-dependent analgesia and respiratory depression in mice and rabbits. MET induced-analgesia was naloxone reversible and potentiated by bestatin. Naloxonazine, a relatively selective mu 1 blocker, at certain dosage (50 micrograms per rabbit, icv), could abolish the analgesia but not the respiratory inhibition produced by MET. Our result indicates that mu 1 receptors mediate the MET induced-analgesia but not its respiratory effect. Since MET is a mu- and kappa-ligand with very low delta activity, the MET induced respiratory depression may be mediated by mu 2 or kappa binding sites.
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