Pub Date : 2016-09-01DOI: 10.13343/J.CNKI.WSXB.20150538
Zhiping Deng, Hao Chen, San-feng Chen
Objective Paenibacillus sp. 1-49 is a nitrogen-fixing bacterium that has the potential as a fertilizer. However, it grows poorly (OD600≤1) in both mineral medium and rich medium. To achieve high-yield biomass, we optimized fermentation medium for Paenibacillus sp. 1-49. Methods Plackett-Burman Design and Central Composite Design in response surface methodology were used to optimize medium composition. Results The optimal fermentation medium contained:(per liter) 36.22 g Sucrose, 5.31 g Tryptone, 10.92 g Yeast Extract, 0.51 g MgSO4, 3.5 g NaCl, 0.02 g Na2MoO4 and 0.02 g FeSO4. The maximum OD600 of 10.280±0.009 was obtained in shake flask fermentation, reached 94.6% of the predicted value. Conclusion We succeeded in using a response surface methodology to optimize the fermentation medium for Paenibacillus sp. 1-49. Our results will be useful for largescale fermentation of this strain and other Paenibacillus spp.
{"title":"Medium optimization for nitrogen fixer Paenibacillus sp. 1-49.","authors":"Zhiping Deng, Hao Chen, San-feng Chen","doi":"10.13343/J.CNKI.WSXB.20150538","DOIUrl":"https://doi.org/10.13343/J.CNKI.WSXB.20150538","url":null,"abstract":"Objective\u0000Paenibacillus sp. 1-49 is a nitrogen-fixing bacterium that has the potential as a fertilizer. However, it grows poorly (OD600≤1) in both mineral medium and rich medium. To achieve high-yield biomass, we optimized fermentation medium for Paenibacillus sp. 1-49.\u0000\u0000\u0000Methods\u0000Plackett-Burman Design and Central Composite Design in response surface methodology were used to optimize medium composition.\u0000\u0000\u0000Results\u0000The optimal fermentation medium contained:(per liter) 36.22 g Sucrose, 5.31 g Tryptone, 10.92 g Yeast Extract, 0.51 g MgSO4, 3.5 g NaCl, 0.02 g Na2MoO4 and 0.02 g FeSO4. The maximum OD600 of 10.280±0.009 was obtained in shake flask fermentation, reached 94.6% of the predicted value.\u0000\u0000\u0000Conclusion\u0000We succeeded in using a response surface methodology to optimize the fermentation medium for Paenibacillus sp. 1-49. Our results will be useful for largescale fermentation of this strain and other Paenibacillus spp.","PeriodicalId":67785,"journal":{"name":"微体古生物学报","volume":"61 1","pages":"1415-25"},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88760323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-08-04DOI: 10.13343/J.CNKI.WSXB.20150500
Nanping Jiang, Wei Liu, Yan Li, Zhihong Xie
Objective Azorhizobium caulinodans ORS571 can fix nitrogen not only as a free-living organism and an associative-symbiotic bacterium by colonizing the root surface of non-leguminous plants, but also as a symbiotic bacterium by interacting with leguminous plant Sesbania rostrata. Due to its ability to grow and fix nitrogen under three conditions, A. caulinodans uses sophisticated chemotaxis signal transduction systems to transform environmental cues into corresponding behavioral responses. Chemotaxis appears crucial for the growth of A. caulinodansin complicated environment and the construction of associative relationship with the plant. However, little is known about the chemotactic pathway of A. caulinodans. Thus, our study aimed to compare the chemotaxis-like genes of A. caulinodans with those of well-studied species. Methods NCBI protein BLAST was used for searching sequence similarity with default parameter values against the genomes of A. caulinodans. HMMER3, based on Pfam database, was used for comparative analyses of methyl-accepting chemotaxis protein (MCP). Results There was a major chemotaxis cluster in A. caulinodans and the CheR methylated MCPs independently of pentapeptide motif. There were 43 MCP homologs containing diverse signal-sensing architectures in A. caulinodans. In addition, cytoplasmic domains of these MCPs were all composed of 38 heptad repeats. Conclusion Despite the extremely high homology presented between the chemotactic system of A. caulinodans and those of well-studied species, A. caulinodans shows its own unique characteristics. The classification of these chemotactic pathways by comparative genomics enables us to better understand how A. caulinodansresponds to changes in environment via exquisite signal transductions in chemotaxis system.
{"title":"Comparative genomic and protein sequence analyses of the chemotaxis system of Azorhizobium caulinodans.","authors":"Nanping Jiang, Wei Liu, Yan Li, Zhihong Xie","doi":"10.13343/J.CNKI.WSXB.20150500","DOIUrl":"https://doi.org/10.13343/J.CNKI.WSXB.20150500","url":null,"abstract":"Objective\u0000Azorhizobium caulinodans ORS571 can fix nitrogen not only as a free-living organism and an associative-symbiotic bacterium by colonizing the root surface of non-leguminous plants, but also as a symbiotic bacterium by interacting with leguminous plant Sesbania rostrata. Due to its ability to grow and fix nitrogen under three conditions, A. caulinodans uses sophisticated chemotaxis signal transduction systems to transform environmental cues into corresponding behavioral responses. Chemotaxis appears crucial for the growth of A. caulinodansin complicated environment and the construction of associative relationship with the plant. However, little is known about the chemotactic pathway of A. caulinodans. Thus, our study aimed to compare the chemotaxis-like genes of A. caulinodans with those of well-studied species.\u0000\u0000\u0000Methods\u0000NCBI protein BLAST was used for searching sequence similarity with default parameter values against the genomes of A. caulinodans. HMMER3, based on Pfam database, was used for comparative analyses of methyl-accepting chemotaxis protein (MCP).\u0000\u0000\u0000Results\u0000There was a major chemotaxis cluster in A. caulinodans and the CheR methylated MCPs independently of pentapeptide motif. There were 43 MCP homologs containing diverse signal-sensing architectures in A. caulinodans. In addition, cytoplasmic domains of these MCPs were all composed of 38 heptad repeats.\u0000\u0000\u0000Conclusion\u0000Despite the extremely high homology presented between the chemotactic system of A. caulinodans and those of well-studied species, A. caulinodans shows its own unique characteristics. The classification of these chemotactic pathways by comparative genomics enables us to better understand how A. caulinodansresponds to changes in environment via exquisite signal transductions in chemotaxis system.","PeriodicalId":67785,"journal":{"name":"微体古生物学报","volume":"12 1","pages":"1256-65"},"PeriodicalIF":0.0,"publicationDate":"2016-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80465511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-07-04DOI: 10.13343/J.CNKI.WSXB.20150410
Jie Xu, Yalin Yang, Yang Liu, Chao Ran, Juan Li, Suxu He, Li Xu, Xhunxiang Ai, Zhigang Zhou
Objective We isolated bacterial strains with chitin-degrading activity from the digesta of large yellow croakers (Pseudosciaena crocea) fed with chitin-enriched trash fish, and characterized potential chitinases thereof. Methods Chitin-degrading strains were screened with colloidal chitin agar from the digesta of P. crocea fed with trash fish. The chitinase gene (chi-X) was cloned and expressed in Escherichia coli, and the enzymatic properties of the chitinase (CHI-X) were characterized. Results A Citrobacter freundii strain with chitin-degrading activity was isolated. The chitinase gene encodes a protein containing 493 amino acid residues, with a proposed glycoside hydrolase family-18 catalytic domain. CHI-X could hydrolyze colloidal chitin. The optimal pH for CHI-X was 4.0 at optimal temperature (60 ℃). CHI-X was active over a broad pH range, with around 90% of the activity maintained after incubation at pH between 3.0 and 11 for 1 h. The enzymatic activity of CHI-X was stimulated by Mn2+, Li+, and K+, but inhibited by Ag+. The enzyme was stable after treatment by proteases and grouper intestinal juice. CHI-X hydrolyzes colloidal chitin into GlcNAc and (GlcNAc)2. Furthermore, an synergic effect was observed between CHIX and ChiB565 (a chitinase from Aeromonas veronii B565) on colloidal chitin. Conclusion CHI-X from intestinal bacterium may be potentially used as feed additive enzyme for warm water marine fish.
{"title":"Characterization of an exo-chitinase from a Citrobacter strain isolated from the intestine content of large yellow croakers.","authors":"Jie Xu, Yalin Yang, Yang Liu, Chao Ran, Juan Li, Suxu He, Li Xu, Xhunxiang Ai, Zhigang Zhou","doi":"10.13343/J.CNKI.WSXB.20150410","DOIUrl":"https://doi.org/10.13343/J.CNKI.WSXB.20150410","url":null,"abstract":"Objective\u0000We isolated bacterial strains with chitin-degrading activity from the digesta of large yellow croakers (Pseudosciaena crocea) fed with chitin-enriched trash fish, and characterized potential chitinases thereof.\u0000\u0000\u0000Methods\u0000Chitin-degrading strains were screened with colloidal chitin agar from the digesta of P. crocea fed with trash fish. The chitinase gene (chi-X) was cloned and expressed in Escherichia coli, and the enzymatic properties of the chitinase (CHI-X) were characterized.\u0000\u0000\u0000Results\u0000A Citrobacter freundii strain with chitin-degrading activity was isolated. The chitinase gene encodes a protein containing 493 amino acid residues, with a proposed glycoside hydrolase family-18 catalytic domain. CHI-X could hydrolyze colloidal chitin. The optimal pH for CHI-X was 4.0 at optimal temperature (60 ℃). CHI-X was active over a broad pH range, with around 90% of the activity maintained after incubation at pH between 3.0 and 11 for 1 h. The enzymatic activity of CHI-X was stimulated by Mn2+, Li+, and K+, but inhibited by Ag+. The enzyme was stable after treatment by proteases and grouper intestinal juice. CHI-X hydrolyzes colloidal chitin into GlcNAc and (GlcNAc)2. Furthermore, an synergic effect was observed between CHIX and ChiB565 (a chitinase from Aeromonas veronii B565) on colloidal chitin.\u0000\u0000\u0000Conclusion\u0000CHI-X from intestinal bacterium may be potentially used as feed additive enzyme for warm water marine fish.","PeriodicalId":67785,"journal":{"name":"微体古生物学报","volume":"123 1","pages":"1089-1104"},"PeriodicalIF":0.0,"publicationDate":"2016-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78176402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2009-05-14DOI: 10.1504/IJEP.2009.025129
Guang-wei Li, He Liu, Feng Zhang, G. Du, Jian Chen
The V2 region of the 16S ribosomal DNA of the ammonia-oxidizing bacteria (AOB) was amplified directly from the environmental sample by using the specific PCR primers. The purified PCR product was cloned into T-vector and was identified as 16S rDNA fragment of AOB by sequencing and Real-time PCR method. Then, the recombined plasmid was used as standard molecule sample in Real-time PCR for AOB quantification. The numbers of the AOB were monitored in samples of both aerobic granular sludge and activated sludge influenced by PCP by using Real-time PCR. The results showed that the numbers of AOB in aerobic granular sludge and activated sludge were 4.28 x 10(7) 5.44 x 10(6) cells/g dried sludge and 2.51 x 10(9) +/- 8.61 x 10(8) cells/g dried sludge without PCP in the reactors, respectively. With the increase of PCP concentration (from 0mg/L to 50mg/L), the numbers of AOB in both types of sludge had no obvious change( P > 0.05) . The numbers of AOB had no obvious correlation with ammonia removal ( P > 0.05) . The main effect of PCP on AOB in both types of sludge was to inhibit their metabolic activity.
{"title":"[Real time PCR quantification of ammonia-oxidizing bacteria in aerobic granular sludge and activated sludge influenced by pentachlorophenol].","authors":"Guang-wei Li, He Liu, Feng Zhang, G. Du, Jian Chen","doi":"10.1504/IJEP.2009.025129","DOIUrl":"https://doi.org/10.1504/IJEP.2009.025129","url":null,"abstract":"The V2 region of the 16S ribosomal DNA of the ammonia-oxidizing bacteria (AOB) was amplified directly from the environmental sample by using the specific PCR primers. The purified PCR product was cloned into T-vector and was identified as 16S rDNA fragment of AOB by sequencing and Real-time PCR method. Then, the recombined plasmid was used as standard molecule sample in Real-time PCR for AOB quantification. The numbers of the AOB were monitored in samples of both aerobic granular sludge and activated sludge influenced by PCP by using Real-time PCR. The results showed that the numbers of AOB in aerobic granular sludge and activated sludge were 4.28 x 10(7) 5.44 x 10(6) cells/g dried sludge and 2.51 x 10(9) +/- 8.61 x 10(8) cells/g dried sludge without PCP in the reactors, respectively. With the increase of PCP concentration (from 0mg/L to 50mg/L), the numbers of AOB in both types of sludge had no obvious change( P > 0.05) . The numbers of AOB had no obvious correlation with ammonia removal ( P > 0.05) . The main effect of PCP on AOB in both types of sludge was to inhibit their metabolic activity.","PeriodicalId":67785,"journal":{"name":"微体古生物学报","volume":"448 1","pages":"136-40"},"PeriodicalIF":0.0,"publicationDate":"2009-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82933869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2006-10-01DOI: 10.3760/CMA.J.ISSN.1008-1372.2008.11.010
Yi Zheng, Hai-bo Luo, B. Gao, Laiqiang Huang
The function of NS4B is incompletely understood. The aim of the study is to understand the influence of NS4B on anti-viral response. After cell line stably expressing NS4B established, the influence of IFN-alpha of different concentration on VSV was studied using plaque assay; cell expression profiling caused by NS4B was studied using DNA microarray, and the IFNGR1 fluorescence intensity was analyzed. Our data showed that HCV-NS4B could suppress immuno-associated gene expression, in particular, IFN-gamma receptor signal transduction-related genes. Taken together, NS4B could play some roles in HCV resistance to IFN therapy.
{"title":"[Inhibition of IFN-gamma receptor signaling by hepatitis C virus non-structural protein NS4B].","authors":"Yi Zheng, Hai-bo Luo, B. Gao, Laiqiang Huang","doi":"10.3760/CMA.J.ISSN.1008-1372.2008.11.010","DOIUrl":"https://doi.org/10.3760/CMA.J.ISSN.1008-1372.2008.11.010","url":null,"abstract":"The function of NS4B is incompletely understood. The aim of the study is to understand the influence of NS4B on anti-viral response. After cell line stably expressing NS4B established, the influence of IFN-alpha of different concentration on VSV was studied using plaque assay; cell expression profiling caused by NS4B was studied using DNA microarray, and the IFNGR1 fluorescence intensity was analyzed. Our data showed that HCV-NS4B could suppress immuno-associated gene expression, in particular, IFN-gamma receptor signal transduction-related genes. Taken together, NS4B could play some roles in HCV resistance to IFN therapy.","PeriodicalId":67785,"journal":{"name":"微体古生物学报","volume":"20 1","pages":"802-6"},"PeriodicalIF":0.0,"publicationDate":"2006-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75130567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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