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Yang SH, Seo J, Koo Y. Alginate and fucoidan changes the bacterial community in different directions and the alginate or fucoidan degrading bacteria isolated from paddy soil promotes the plant growth. Arch Microbiol 2021; 203:5183-5192. [PMID: 34345977 DOI: 10.1007/s00203-021-02480-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/15/2021] [Accepted: 07/07/2021] [Indexed: 12/01/2022]
Abstract
Seaweed and its extracts have been developed as fertilizers because they possess plant-growth-promoting and antibacterial compounds. For use as fertilizers, the major carbohydrates in seaweed, including fucoidan and alginate, need to be efficiently digested in the soil. We isolated fucoidan/alginate degrading bacteria from paddy soil and verified its use as a biofertilizer. Results show that Stenotrophomonas pavanii has a high alginate degrading activity, and also stimulating melon, pepper, and tomato growth. The growth stimulation effect of the bacteria was enhanced by alginate treatment. Bacillus sp. was isolated as a fucoidan degrading bacterium and this bacterium was also able to stimulate melon growth. Using 16S ribosomal DNA analysis, fucoidan/alginate resistant or susceptible bacteria were successively selected. Bacteria with increased population due to fucoidan and alginate had specificity to each carbohydrate, whereas those with decreased population showed susceptibility to both carbohydrates. This report demonstrates some bacteria for their use as biofertilizers with seaweed and demonstrated that a high throughput method is efficient in identifying bacteria with specific properties.
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Affiliation(s)
- So Hee Yang
- Department of Agricultural Chemistry, Chonnam National University, Gwangju, 61186, South Korea
| | - Jeongwon Seo
- Department of Agricultural Chemistry, Chonnam National University, Gwangju, 61186, South Korea
| | - Yeonjong Koo
- Department of Agricultural Chemistry, Chonnam National University, Gwangju, 61186, South Korea.
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2
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A Novel Acetaldehyde Dehydrogenase with Salicylaldehyde Dehydrogenase Activity from Rhodococcus ruber Strain OA1. Curr Microbiol 2017; 74:1404-1410. [PMID: 28849423 DOI: 10.1007/s00284-017-1333-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 08/10/2017] [Indexed: 10/19/2022]
Abstract
Salicylaldehyde dehydrogenase (sALDH) can oxidize salicylaldehyde, which is an intermediate in the naphthalene catabolism in bacteria. However, genes encoding sALDH have not been discovered so far in Rhodococcus. Here, we report the discovery of a novel aldehyde dehydrogenase (ALDH) gene in the naphthalene degrader Rhodococcus ruber OA1 based on phylogenetic analysis. Interestingly, apart from ALDH activity, ALDH of R. ruber OA1 (OA1-ALDH) also showed sALDH activity. Moreover, its sALDH specific activity was higher than its ALDH specific activity. Based on a comparison with the ALDH of Thermomonospora curvata DSM 43,183, a putative active site Cys123 and NAD+ binding site Asn263 were proposed in R. ruber OA1. Multiple alignment of OA1-ALDH with ALDHs from other organisms indicated that the residues Ser122 and Ala124 might influence the enzyme activity and substrate specificity that render OA1-ALDH the ability to catalyze salicylaldehyde better than acetaldehyde. These results support the possibility that OA1-ALDH plays the role of sALDH in the oxidation of salicylaldehyde to salicylate in R. ruber OA1. In summary, our study would contribute to the understanding of the structure and roles of ALDH in Rhodococcus.
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Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches. PLoS One 2017; 12:e0174614. [PMID: 28346815 PMCID: PMC5367889 DOI: 10.1371/journal.pone.0174614] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/13/2017] [Indexed: 11/26/2022] Open
Abstract
Honeybees face many parasites and pathogens and consequently rely on a diverse set of individual and group-level defenses to prevent disease. The crop microbiota of Apis mellifera, composed of 13 Lactic Acid Bacterial (LAB) species within the genera Lactobacillus and Bifidobacterium, form a beneficial symbiotic relationship with each other and the honeybee to protect their niche and their host. Possibly playing a vital role in honeybee health, it is important that these honeybee specific Lactic Acid Bacterial (hbs-LAB) symbionts can be correctly identified, isolated and cultured, to further investigate their health promoting properties. We have previously reported successful identification to the strain level by culture-dependent methods and we recently sequenced and annotated the genomes of the 13 hbs-LAB. However, the hitherto applied techniques are unfortunately very time consuming, expensive and not ideal when analyzing a vast quantity of samples. In addition, other researchers have constantly failed to identify the 13 hbs-LAB from honeybee samples by using inadequate media and/or molecular techniques based on 16S rRNA gene sequencing with insufficient discriminatory power. The aim of this study was to develop better and more suitable methods for the identification and cultivation of hbs-LAB. We compared currently used bacterial cultivation media and could for the first time demonstrate a significant variation in the hbs-LAB basic requirements for optimal growth. We also present a new bacterial identification approach based on amplicon sequencing of a region of the 16S rRNA gene using the Illumina platform and an error correction software that can be used to successfully differentiate and rapidly identify the 13 hbs-LAB to the strain level.
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Cendron L, Ramazzina I, Puggioni V, Maccacaro E, Liuzzi A, Secchi A, Zanotti G, Percudani R. The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism. Biochemistry 2016; 55:6421-6432. [DOI: 10.1021/acs.biochem.6b00881] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Laura Cendron
- Department
of Biomedical Sciences, University of Padova, Padova, Italy
| | | | | | | | | | - Andrea Secchi
- Department
of Chemistry, University of Parma, Parma, Italy
| | - Giuseppe Zanotti
- Department
of Biomedical Sciences, University of Padova, Padova, Italy
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5
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Amidani D, Tramonti A, Canosa AV, Campanini B, Maggi S, Milano T, di Salvo ML, Pascarella S, Contestabile R, Bettati S, Rivetti C. Study of DNA binding and bending by Bacillus subtilis GabR, a PLP-dependent transcription factor. Biochim Biophys Acta Gen Subj 2016; 1861:3474-3489. [PMID: 27640111 DOI: 10.1016/j.bbagen.2016.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/02/2016] [Accepted: 09/11/2016] [Indexed: 12/23/2022]
Abstract
BACKGROUND GabR is a transcriptional regulator belonging to the MocR/GabR family, characterized by a N-terminal wHTH DNA-binding domain and a C-terminal effector binding and/or oligomerization domain, structurally homologous to aminotransferases (ATs). In the presence of γ-aminobutyrate (GABA) and pyridoxal 5'-phosphate (PLP), GabR activates the transcription of gabT and gabD genes involved in GABA metabolism. METHODS Here we report a biochemical and atomic force microscopy characterization of Bacillus subtilis GabR in complex with DNA. Complexes were assembled in vitro to study their stoichiometry, stability and conformation. RESULTS The fractional occupancy of the GabR cognate site suggests that GabR binds as a dimer with Kd of 10nM. Upon binding GabR bends the DNA by 80° as measured by anomalous electrophoretic mobility. With GABA we observed a decrease in affinity and conformational rearrangements compatible with a less compact nucleo-protein complex but no changes of the DNA bending angle. By employing promoter and GabR mutants we found that basic residues of the positively charged groove on the surface of the AT domain affect DNA affinity. CONCLUSIONS The present data extend current understanding of the GabR-DNA interaction and the effect of GABA and PLP. A model for the GabR-DNA complex, corroborated by a docking simulation, is proposed. GENERAL SIGNIFICANCE Characterization of the GabR DNA binding mode highlights the key role of DNA bending and interactions with bases outside the canonical direct repeats, and might be of general relevance for the action mechanism of MocR transcription factors.
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Affiliation(s)
- Davide Amidani
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parma, Italy
| | - Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy; Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | | | | | - Stefano Maggi
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parma, Italy
| | - Teresa Milano
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Bettati
- Dipartimento di Neuroscienze, Università di Parma, Parma, Italy; National Institute of Biostructures and Biosystems, Rome, Italy
| | - Claudio Rivetti
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parma, Italy.
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6
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Identification of Salmonella enterica Typhimurium and variants using a novel multiplex PCR assay. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Chen W, Yang J, You C, Liu Z. Diversity of Cronobacter spp. isolates from the vegetables in the middle-east coastline of China. World J Microbiol Biotechnol 2016; 32:90. [PMID: 27116956 DOI: 10.1007/s11274-016-2033-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/14/2016] [Indexed: 11/30/2022]
Abstract
Cronobacter spp. has caused life-threatening neonatal infections mainly resulted from consumption of contaminated powdered infant formula. A total of 102 vegetable samples from retail markets were evaluated for the presence of Cronobacter spp. Thirty-five presumptive Cronobacter isolates were isolated and identified using API 20E and 16S rDNA sequencing analyses. All isolates and type strains were characterized using enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), and genetic profiles of cluster analysis from this molecular typing test clearly showed that there were differences among isolates from different vegetables. A polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) based on the amplification of the gyrB gene (1258 bp) was developed to differentiate among Cronobacter species. A new PCR-RFLP assay based on the amplification of the gyrB gene using Alu I and Hinf I endonuclease combination is established and it has been confirmed an accurate and rapid subtyping method to differentiate Cronobacter species. Sequence analysis of the gyrB gene was proven to be suitable for the phylogenetic analysis of the Cronobacter strains, which has much better resolution based on SNPs in the identification of Cronobacter species specificity than PCR-RFLP and ERIC-PCR. Our study further confirmed that vegetables are one of the most common habitats or sources of Cronobacter spp. contamination in the middle-east coastline of China.
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Affiliation(s)
- Wanyi Chen
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Synergetic Innovation Center of Food Safety and Nutrition, 1518 West Jiangchang Rd., Shanghai, 200436, China
| | - Jielin Yang
- Shanghai Entry-Exit Inspection and Quarantine Bureau, 1208 Minsheng Rd., Shanghai, 200135, China
| | - Chunping You
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Synergetic Innovation Center of Food Safety and Nutrition, 1518 West Jiangchang Rd., Shanghai, 200436, China
| | - Zhenmin Liu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Synergetic Innovation Center of Food Safety and Nutrition, 1518 West Jiangchang Rd., Shanghai, 200436, China.
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Baeshen MN, Al-Attas SG, Ahmed MM, Hanafy AAELMEL, Anwar Y, Alotibi IA, Baeshen NA. The effect of Rhazya strictaaqueous leaves extract on MRSA genotypes in Jeddah province. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2015.1124739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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9
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Draft Genome Sequences of Four Genetically Distinct Human Isolates of Streptococcus dysgalactiae subsp. equisimilis. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01139-15. [PMID: 26430051 PMCID: PMC4591323 DOI: 10.1128/genomea.01139-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
β-Hemolytic group C and group G streptococci (GCS-GGS; Streptococcus dysgalactiae subsp. equisimilis) emerged as human pathogens in the late 1970s. We report here the draft genome sequences of four genetically distinct human strains of GCS-GGS isolated between the 1960s and 1980s. Comparative analysis of these genomes may provide a deeper understanding of GCS-GGS genome and virulence evolution.
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10
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Chen W, Yu S, Ren J, Shi C, Hang F, Guo B. Development of a PCR Assay for Rapid Detection of C
ronobacter sakazakii
from Powdered Infant Formula Using a Target Sequence Identified by Comparative Genomic Analysis. J Food Saf 2015. [DOI: 10.1111/jfs.12185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Wanyi Chen
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd.; 1518 West Jiangchang Rd Shanghai 200436 China
| | - Shuijing Yu
- School of Resources and Environment; Jiangxi University of Science and Technology; Ganzhou Jiangxi China
| | - Jing Ren
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd.; 1518 West Jiangchang Rd Shanghai 200436 China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety; School of Agriculture & Biology; State Key Lab of Microbial Metabolism; Shanghai Jiao Tong University; Shanghai China
| | - Feng Hang
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd.; 1518 West Jiangchang Rd Shanghai 200436 China
| | - Benheng Guo
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd.; 1518 West Jiangchang Rd Shanghai 200436 China
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Puggioni V, Dondi A, Folli C, Shin I, Rhee S, Percudani R. Gene Context Analysis Reveals Functional Divergence between Hypothetically Equivalent Enzymes of the Purine–Ureide Pathway. Biochemistry 2014; 53:735-45. [DOI: 10.1021/bi4010107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vincenzo Puggioni
- Laboratory
of Biochemistry, Molecular Biology, and Bioinformatics, Department
of Life Sciences, University of Parma, Italy
| | - Ambra Dondi
- Laboratory
of Biochemistry, Molecular Biology, and Bioinformatics, Department
of Life Sciences, University of Parma, Italy
| | - Claudia Folli
- Department
of Food Science, University of Parma, Italy
| | - Inchul Shin
- Department
of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Sangkee Rhee
- Department
of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Riccardo Percudani
- Laboratory
of Biochemistry, Molecular Biology, and Bioinformatics, Department
of Life Sciences, University of Parma, Italy
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12
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Novel Approaches of Genomic DNA Isolation for Identification of Cultivable Bacteria. Jundishapur J Microbiol 2013. [DOI: 10.5812/jjm.8339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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13
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Amano M, Ohkusu K, Kusaba K, Ikeda H, Nagasawa Z, Aoki Y, Kawamura Y, Kobatake S, Tanaka T, Matsuura S, Ezaki T. Quantitative Microarray-Based DNA-DNA Hybridization Assay for Measuring Genetic Distances among Bacterial Species and Its Application to the Identification of FamilyEnterobacteriaceae. Microbiol Immunol 2013; 49:255-63. [PMID: 15781999 DOI: 10.1111/j.1348-0421.2005.tb03727.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative DNA-DNA hybridization to measure the genetic distances among bacterial species is indispensable for taxonomical determination. In the current studies, we developed a method to determine bacterial DNA relatedness on a glass microarray. Reference DNAs representing a total 93 species of Enterobacteriaceae were arrayed on a glass microplate, and signal intensities were measured after 2 hr of hybridization with Cy3-labeled bacterial DNAs. All immobilized DNAs from members of the family Enterobacteriaceae were identified by this method except for DNAs from Yersinia pseudotuberculosis and Y. pestis. These results suggest that quantitative microarray hybridization could be an alternative to conventional DNA-DNA hybridization for measuring chromosome relatedness among bacterial species.
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Affiliation(s)
- Makoto Amano
- Osaka Research Laboratories, Wako Pure Chemical Industries, Ltd., Amagasaki, Hyogo, Japan
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14
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Chen W, Ai L, Yang J, Ren J, Li Y, Guo B. Molecular Typing of Cronobacter
Strains from Food in China by Enterobacterial Repetitive Intergenic Consensus Sequence PCR (ERIC-PCR) and Sequence Analysis of the gyrB
Gene. J Food Saf 2013. [DOI: 10.1111/jfs.12068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wanyi Chen
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd; 1518 West Jiangchang Rd Shanghai 200436 China
| | - Lianzhong Ai
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd; 1518 West Jiangchang Rd Shanghai 200436 China
| | - Jielin Yang
- Shanghai Entry-Exit Inspection and Quarantine Bureau; Shanghai China
| | - Jing Ren
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd; 1518 West Jiangchang Rd Shanghai 200436 China
| | - Yunfei Li
- School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai China
| | - Benheng Guo
- State Key Laboratory of Dairy Biotechnology; Technology Center of Bright Dairy & Food Co., Ltd; 1518 West Jiangchang Rd Shanghai 200436 China
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15
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Chen W, Ai L, Yang J, Ren J, Li Y, Guo B. Development of a PCR assay for rapid detection ofCronobacterspp. from food. Can J Microbiol 2013; 59:656-61. [PMID: 24102218 DOI: 10.1139/cjm-2013-0243] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The occurrence of outbreaks of necrotizing meningitis caused by Cronobacter spp. in neonates highlights the need for rapid detection and accurate identification of this pathogenic species. The gold standard for isolation and identification of Cronobacter spp. from powdered infant formula is time consuming and labor intensive. The gyrB gene that encodes the B subunit of DNA gyrase (topoisomerase type II) was found to be suitable for the identification of Cronobacter spp. A region of the gyrB gene of 38 Cronobacter spp. strains and 5 Enterobacter spp. strains was amplified and sequenced, and a pair of primers was designed and synthesized based on the sequence of the gyrB gene. A polymerase chain reaction (PCR) system was developed and optimized to detect Cronobacter spp. The PCR assay amplified a 438 bp DNA product from all 38 Cronobacter spp. strains tested but not from 34 other bacteria. The detection limit was 1.41 pg/PCR (equivalent 282 genomic copies) when the genomic DNA of Cronobacter sakazakii ATCC 29544 was 10-fold diluted. Infant formula powders from 3 different commercial brands were inoculated with strains ATCC 29544 at a level of 56 colony-forming units, and the target fragment were produced after samples were enriched for 6 h at 37 °C. Twenty-five food samples were evaluated by the PCR assay and the conventional method. A PCR product of the expected size was obtained from 3 samples; however, Cronobacter spp. strains were isolated from only 2 samples by the conventional method. This method is a useful tool for rapid identification of Cronobacter spp. in food and potentially environmental samples.
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Affiliation(s)
- Wanyi Chen
- State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co., Ltd., 1518 West Jiangchang Road, Shanghai 200436, People’s Republic of China
| | - Lianzhong Ai
- State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co., Ltd., 1518 West Jiangchang Road, Shanghai 200436, People’s Republic of China
| | - Jielin Yang
- Shanghai Entry-Exit Inspection and Quarantine Bureau, 1208 Minsheng Road, Shanghai 200135, People’s Republic of China
| | - Jing Ren
- State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co., Ltd., 1518 West Jiangchang Road, Shanghai 200436, People’s Republic of China
| | - Yunfei Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People’s Republic of China
| | - Benheng Guo
- State Key Laboratory of Dairy Biotechnology, Technology Center of Bright Dairy & Food Co., Ltd., 1518 West Jiangchang Road, Shanghai 200436, People’s Republic of China
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Fine-Coulson K, Reaves BJ, Karls RK, Quinn FD. The role of lipid raft aggregation in the infection of type II pneumocytes by Mycobacterium tuberculosis. PLoS One 2012; 7:e45028. [PMID: 23024786 PMCID: PMC3443240 DOI: 10.1371/journal.pone.0045028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 08/11/2012] [Indexed: 11/18/2022] Open
Abstract
Dynamic, cholesterol-dense regions of the plasma membrane, known as lipid rafts (LR), have been observed to develop during and may be directly involved in infection of host cells by various pathogens. This study focuses on LR aggregation induced in alveolar epithelial cells during infection with Mycobacterium tuberculosis (Mtb) bacilli. We report dose- and time-dependent increases in LR aggregation after infection with three different strains at multiplicities of infection of 1, 10 and 100 from 2-24 hr post infection (hpi). Specific strain-dependent variations were noted among H37Rv, HN878 and CDC1551 with H37Rv producing the most significant increase from 15 aggregates per cell (APC) to 27 APC at MOI 100 during the 24 hour infection period. Treatment of epithelial cells with Culture Filtrate Protein, Total Lipids and gamma-irradiated whole cells from each strain failed to induce the level of LR aggregation observed during infection with any of the live strains. However, filtered supernatants from infected epithelial cells did produce comparable LR aggregation, suggesting a secreted mycobacterial product produced during infection of host cells is responsible for LR aggregation. Disruption of lipid raft formation prior to infection indicates that Mtb bacilli utilize LR aggregates for internalization and survival in epithelial cells. Treatment of host cells with the LR-disruption agent Filipin III produced a nearly 22% reduction in viable bacteria for strains H37Rv and HN878, and a 7% reduction for strain CDC1551 after 6 hpi. This study provides evidence for significant mycobacterial-induced changes in the plasma membrane of alveolar epithelial cells and that Mtb strains vary in their ability to facilitate aggregation and utilization of LR.
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Affiliation(s)
- Kari Fine-Coulson
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Barbara J. Reaves
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Russell K. Karls
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Frederick D. Quinn
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Liu B, Zhou X, Zhang L, Liu W, Dan X, Shi C, Shi X. Development of a novel multiplex PCR assay for the identification of Salmonella enterica Typhimurium and Enteritidis. Food Control 2012. [DOI: 10.1016/j.foodcont.2012.01.062] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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18
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Molecular typing of Vibrio parahaemolyticus isolates from the middle-east coastline of China. Int J Food Microbiol 2011; 153:402-12. [PMID: 22225982 DOI: 10.1016/j.ijfoodmicro.2011.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 11/28/2011] [Accepted: 12/04/2011] [Indexed: 11/23/2022]
Abstract
The occurrence of outbreaks of Vibrio parahaemolyticus gastroenteritis in China highlights the need for strain characterization and subtyping of this pathogenic species. A total of 56 epidemiologically-unrelated strains of V. parahaemolyticus were isolated from clinical samples, seafood and various environmental sites in the middle-east coastline of China from 2006 to 2008. The isolates were characterized using four molecular typing methods, including ribotyping, enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), pulsed-field gel electrophoresis (PFGE), and sequence analysis of the gyrB gene. Genetic profiles of cluster analysis from these molecular typing tests clearly showed that there were differences in potential pathogenicity among isolates from seafood and its environments. Genetic characterization of two isolates (F13 and QS2) that originated from seafood demonstrated that they were potentially pathogenic. Discriminatory indices of four typing methods for the 56 V. parahaemolyticus isolates were differentiated by Simpson's Index of Diversity. The discriminatory index of ERIC-PCR typing was maximal (D=0.942), while that of sequence analysis of the gyrB gene was minimal (D=0.702). The discriminatory ability was greatly enhanced (D=0.966) when ERIC-PCR was coupled with sequence analysis of the gyrB gene. These results suggest that ERIC-PCR combined with sequence analysis of gyrB gene may be a reliable, rapid typing strategy for V. parahaemolyticus strains.
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Atashpaz S, Khani S, Barzegari A, Barar J, Vahed SZ, Azarbaijani R, Omidi Y. A robust universal method for extraction of genomic DNA from bacterial species. Microbiology (Reading) 2010. [DOI: 10.1134/s0026261710040168] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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20
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FAN YILING, PAN FENG, PAOLI GEORGEC, XIAO YONGHONG, SHENG HAIHUI, SHI XIANMING. DEVELOPMENT OF A MULTIPLEX PCR METHOD FOR DETECTION OF THE GENES ENCODING 16S rRNA, COAGULASE, METHICILLIN RESISTANCE AND ENTEROTOXINS INSTAPHYLOCOCCUS AUREUS. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1745-4581.2008.00144.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Sánchez B, Rodríguez M, Casado EM, Martín A, Córdoba JJ. Development of an efficient fungal DNA extraction method to be used in random amplified polymorphic DNA-PCR analysis to differentiate cyclopiazonic acid mold producers. J Food Prot 2008; 71:2497-503. [PMID: 19244904 DOI: 10.4315/0362-028x-71.12.2497] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A variety of previously established mechanical and chemical treatments to achieve fungal cell lysis combined with a semiautomatic system operated by a vacuum pump were tested to obtain DNA extract to be directly used in randomly amplified polymorphic DNA (RAPD)-PCR to differentiate cyclopiazonic acid-producing and -nonproducing mold strains. A DNA extraction method that includes digestion with proteinase K and lyticase prior to using a mortar and pestle grinding and a semiautomatic vacuum system yielded DNA of high quality in all the fungal strains and species tested, at concentrations ranging from 17 to 89 ng/microl in 150 microl of the final DNA extract. Two microliters of DNA extracted with this method was directly used for RAPD-PCR using primer (GACA)4. Reproducible RAPD fingerprints showing high differences between producer and nonproducer strains were observed. These differences in the RAPD patterns did not differentiate all the strains tested in clusters by cyclopiazonic acid production but may be very useful to distinguish cyclopiazonic acid producer strains from nonproducer strains by a simple RAPD analysis. Thus, the DNA extracts obtained could be used directly without previous purification and quantification for RAPD analysis to differentiate cyclopiazonic acid producer from nonproducer mold strains. This combined analysis could be adaptable to other toxigenic fungal species to enable differentiation of toxigenic and non-toxigenic molds, a procedure of great interest in food safety.
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Affiliation(s)
- Beatriz Sánchez
- Higiene y Seguridad Alimentaria, Facultad de Veterinaria, Universidad de Extremadura, Avda. de la Universidad s/n Cáceres, Spain
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22
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Ramazzina I, Cendron L, Folli C, Berni R, Monteverdi D, Zanotti G, Percudani R. Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases. J Biol Chem 2008; 283:23295-304. [PMID: 18550550 DOI: 10.1074/jbc.m801195200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hydrolytic cleavage of the hydantoin ring of allantoin, catalyzed by allantoinase, is required for the utilization of the nitrogen present in purine-derived compounds. The allantoinase gene (DAL1), however, is missing in many completely sequenced organisms able to use allantoin as a nitrogen source. Here we show that an alternative allantoinase gene (puuE) can be precisely identified by analyzing its logic relationship with three other genes of the pathway. The novel allantoinase is annotated in structure and sequence data bases as polysaccharide deacetylase for its homology with enzymes that catalyze hydrolytic reactions on chitin or peptidoglycan substrates. The recombinant PuuE protein from Pseudomonas fluorescens exhibits metal-independent allantoinase activity and stereospecificity for the S enantiomer of allantoin. The crystal structures of the protein and of protein-inhibitor complexes reveal an overall similarity with the polysaccharide deacetylase beta/alpha barrel and remarkable differences in oligomeric assembly and active site geometry. The conserved Asp-His-His metal-binding triad is replaced by Glu-His-Trp, a configuration that is distinctive of PuuE proteins within the protein family. An extra domain at the top of the barrel offers a scaffold for protein tetramerization and forms a small substrate-binding cleft by hiding the large binding groove of polysaccharide deacetylases. Substrate positioning at the active site suggests an acid/base mechanism of catalysis in which only one member of the catalytic pair of polysaccharide deacetylases has been conserved. These data provide a structural rationale for the shifting of substrate specificity that occurred during evolution.
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Affiliation(s)
- Ileana Ramazzina
- Department of Biochemistry and Molecular Biology and Mathematics, University of Parma, 43100, Parma, Italy
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23
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Alfieri B, Folloni S, Elviri L, Gobbo M, Berni R, Folli C. Cloning, E. coli overexpression, purification and binding properties of TraA and TraC, two proteins involved in the pheromone-dependent conjugation process in enterococci. Protein Expr Purif 2008; 60:198-204. [PMID: 18468916 DOI: 10.1016/j.pep.2008.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 03/12/2008] [Accepted: 03/14/2008] [Indexed: 11/25/2022]
Abstract
The bacteriocin encoding plasmid pPD1 from Enterococcus faecalis is involved in a mating response to the sex pheromone cPD1 produced by recipient bacterial cells devoid of pPD1. Previous studies showed that cPD1 is internalized into donor cells in a process in which TraC plays the role of cell surface pheromone receptor. Inside the recipient cells, the pheromone binds to the plasmid-encoded cytoplasmic protein TraA, able to recognize specific DNA sequences and to modulate the conjugation process. To avoid self-induction of the conjugation process, donor cells produce the inhibitor iPD1, which competes with cPD1. This study was designed to produce recombinant TraA and TraC in a functionally active state and to evaluate their main functional properties. We have isolated the sequences encoding TraA and TraC from the plasmid pPD1 and cloned them in suitable expression vectors. The two recombinant proteins were successfully obtained in a soluble form using Escherichia coli as expression host and a T7 inducible expression system. TraC and TraA were purified to homogeneity by three or two chromatographic steps, respectively, leading to a final yield up to 4mg/l of cell culture for TraC and up to 10mg/l of cell culture for TraA. The ability of TraA and TraC to bind the specific pheromone and inhibitor peptides has been assessed by means of ESI-mass spectrometry. Moreover, the ability of recombinant TraA to bind DNA has been demonstrated by means of electrophoretic mobility shift assay. Overall these results are consistent with the heterologously expressed TraC and TraA being functionally active.
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Affiliation(s)
- Beatrice Alfieri
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, Viale Usberti 23/A, 43100 Parma, Italy
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24
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Jones JC, Rogers TJ, Brookmeyer P, Dunne WM, Storch GA, Coopersmith CM, Fraser VJ, Warren DK. Mupirocin resistance in patients colonized with methicillin-resistant Staphylococcus aureus in a surgical intensive care unit. Clin Infect Dis 2007; 45:541-7. [PMID: 17682986 DOI: 10.1086/520663] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Accepted: 05/23/2007] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Nasal colonization with methicillin-resistant Staphylococcus aureus (MRSA) can be a precursor to serious infection, and decolonization with topical mupirocin has been studied as a means of preventing clinical infection. Mupirocin resistance in patients with MRSA has been reported, usually in the context of widespread mupirocin use. METHODS Patients admitted to a surgical intensive care unit (SICU) had nasal swab cultures for MRSA performed at admission, weekly, and at discharge in an active surveillance program. Collected MRSA isolates were tested for mupirocin resistance, and molecular analysis was performed. Clinical data on the characteristics and outcomes of the patients who stayed in the SICU for >48 h were collected prospectively. RESULTS Of the 302 MRSA isolates available for testing, 13.2% were resistant to mupirocin, with 8.6% having high-level resistance (minimum inhibitory concentration, >or=512 microg/mL) and 4.6% having low-level resistance (minimum inhibitory concentration, 8-256 microg/mL). Patients admitted to the SICU for >48 h who were colonized with mupirocin-resistant MRSA were more likely to have been admitted to our hospital during the previous year (P=.016), were older (P=.009), and had higher in-hospital mortality (16% vs. 33%; P=.027), compared with patients colonized with mupirocin-susceptible MRSA. Molecular analysis of the mupirocin-resistant isolates revealed that 72.5% of isolates contained staphylococcal cassette chromosome mec II. Repetitive sequence polymerase chain reaction typing revealed that high-level mupirocin resistance was present in multiple clonal groups. The rate of mupirocin use hospital-wide during the study period was 6.08 treatment-days per 1000 patient-days. CONCLUSIONS We documented a high rate of mupirocin resistance in MRSA isolates from SICU patients, despite low levels of in-hospital mupirocin use.
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Affiliation(s)
- Jeffrey C Jones
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA.
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25
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Lin AE, Davies JE. Occurrence of highly fluoroquinolone-resistant and methicillin-resistant Staphylococcus aureus in domestic animals. Can J Microbiol 2007; 53:925-9. [PMID: 17898848 DOI: 10.1139/w07-062] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe phenotypic and genotypic analyses carried out on multidrug-resistant Staphylococcus aureus isolated from domestic animals. The sequence type ST239 methicillin-resistant Staphylococcus aureus isolated from dogs were highly resistant to fluoroquinolones, and new combinations of GyrA and GrlA mutations were identified. These findings are consistent with a role for animal carriage in the dissemination of important human pathogens in the community.
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Affiliation(s)
- Ann E Lin
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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26
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Kido H, Micic M, Smith D, Zoval J, Norton J, Madou M. A novel, compact disk-like centrifugal microfluidics system for cell lysis and sample homogenization. Colloids Surf B Biointerfaces 2007; 58:44-51. [PMID: 17499489 DOI: 10.1016/j.colsurfb.2007.03.015] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2007] [Accepted: 03/19/2007] [Indexed: 11/29/2022]
Abstract
In this paper, we present the design and characterization of a novel platform for mechanical cell lysis of even the most difficult to lyse cell types on a micro or nanoscale (maximum 70 microL total volume). The system incorporates a machined plastic circular disk assembly, magnetic field actuated microfluidics, centrifugal cells and tissue homogenizer and centrifugation system. The mechanism of tissue disruption of this novel cell homogenization apparatus derives from the relative motion of ferromagnetic metal disks and grinding matrices in a liquid medium within individual chambers of the disk in the presence of an oscillating magnetic field. The oscillation of the ferromagnetic disks or blades produces mechanical impaction and shear forces capable of disrupting cells within the chamber both by direct action of the blade and by the motion of the surrounding lysis matrix, and by motion induced vortexing of buffer fluid. Glass beads or other grinding media are integrated into each lysis chamber within the disk to enhance the transfer of energy from the oscillating metal blade to the cells. The system also achieves the centrifugal elimination of solids from each liquid sample and allows the elution of clarified supernatants via siphoning into a collection chamber fabricated into the plastic disk assembly. This article describes system design, implementation and validation of proof of concept on two samples--Escherichia coli and Saccharomyces cerevisiae representing model systems for cells that are easy and difficult to lyse, respectively.
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Affiliation(s)
- Horacio Kido
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, Irvine, CA 92697-3975, USA.
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27
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Redecke L, Brehm MA, Bredehorst R. Cloning and characterization of dihydrofolate reductase from a facultative alkaliphilic and halotolerant bacillus strain. Extremophiles 2006; 11:75-83. [PMID: 17021659 DOI: 10.1007/s00792-006-0013-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Accepted: 06/30/2006] [Indexed: 10/24/2022]
Abstract
Elucidation of the molecular basis of the stability of enzymes from extremophilic organisms is of fundamental importance for various industrial applications. Due to the wealth of structural data from various species, dihydrofolate reductase (DHFR, EC 1.5.1.3) provides an excellent model for systematic investigations. In this report, DHFR from alkaliphilic Bacillus halodurans C-125 was cloned and expressed in E. coli. Functional analyses revealed that BhDHFR exhibits the most alkali-stable phenotype of DHFRs characterized so far. Optimal enzyme activity was observed in a slightly basic pH region ranging from 7.25 to 8.75. Alkali-stability is associated with a remarkable resistance to elevated temperatures (half-life of 60 min at 52.5 degrees C) and to high concentrations of urea (up to 3 M). Although the secondary structure shows distinct similarities to those of mesophilic DHFR molecules, BhDHFR exhibits molecular features contributing to its alkaliphilic properties. Interestingly, the unique phenotype is diminished by C-terminal addition of a His-tag sequence. Therefore, His-tag-derivatized BhDHFR offers the opportunity to obtain deeper insights into the specific mechanisms of alkaliphilic adaption by comparison of the three dimensional structure of both BhDHFR molecules.
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Affiliation(s)
- Lars Redecke
- Institute of Biochemistry and Food Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
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28
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TANG JUNNI, SHI XIANMING, SHI CHUNLEI, CHEN HUANCHUN. CHARACTERIZATION OF A DUPLEX POLYMERASE CHAIN REACTION ASSAY FOR THE DETECTION OF ENTEROTOXIGENIC STRAINS OF STAPHYLOCOCCUS AUREUS. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1745-4581.2006.00047.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Liao RS, Storch GA, Buller RS, Orscheln RC, Mardis ER, Armstrong JR, Dunne WM. Blinded comparison of repetitive-sequence PCR and multilocus sequence typing for genotyping methicillin-resistant Staphylococcus aureus isolates from a children's hospital in St. Louis, Missouri. J Clin Microbiol 2006; 44:2254-7. [PMID: 16757633 PMCID: PMC1489435 DOI: 10.1128/jcm.00690-06] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We performed a blinded study to compare repetitive-sequence PCR and multilocus sequence typing for genotyping hospital- and community-acquired methicillin-resistant Staphylococcus aureus (MRSA). The MRSA strains that were sequence type 8 (ST8), staphylococcal cassette chromosome mec (SCCmec) type IV, and Panton-Valentine leukocidin-positive clustered separately from those that were ST5 and SCCmec type II.
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Affiliation(s)
- Robert S Liao
- Department of Pathology, Washington University School of Medicine, St. Louis, MO 63110, USA
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30
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Micek ST, Dunne M, Kollef MH. Pleuropulmonary complications of Panton-Valentine leukocidin-positive community-acquired methicillin-resistant Staphylococcus aureus: importance of treatment with antimicrobials inhibiting exotoxin production. Chest 2005; 128:2732-8. [PMID: 16236949 DOI: 10.1378/chest.128.4.2732] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Four patients with pleuropulmonary complications attributed to community-acquired methicillin-resistant Staphylococcus aureus (CAMRSA) positive for Panton-Valentine leukocidin (PVL) are described. These patients presented to Barnes-Jewish Hospital with severe necrotizing pneumonia, empyema, ARDS-complicating pneumonia, and ventilator-associated pneumonia-complicating acute pancreatitis, respectively. The first three patients had influenza-like illnesses preceding their PVL-positive CAMRSA infections. In all four cases, PVL-positive CAMRSA was isolated from respiratory secretions, and from blood cultures in three of the individuals. Antimicrobial therapy was inappropriate initially in all four patients. Three patients failed to respond to subsequent treatment with vancomycin, including two patients with persistent bacteremia despite at least 48 h of treatment with vancomycin. These patients were subsequently treated with antimicrobials inhibiting exotoxin production (linezolid or clindamycin) with good clinical results. Clinicians should be aware of PVL-positive CAMRSA due to the rapid and severe progression of pleuropulmonary complications associated with this infection. Additionally, specific antimicrobial therapy directed against CAMRSA differs from the traditional antimicrobial agents prescribed for community-acquired pneumonia. Antimicrobial agents that specifically inhibit exotoxin production appear to be the preferred treatment agents.
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Affiliation(s)
- Scott T Micek
- Clinical Pharmacy Department, Barnes-Jewsih Hospital, St. Louis, MO, USA
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31
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Ruiz-Barba JL, Maldonado A, Jiménez-Díaz R. Small-scale total DNA extraction from bacteria and yeast for PCR applications. Anal Biochem 2005; 347:333-5. [PMID: 16266685 DOI: 10.1016/j.ab.2005.09.028] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 09/20/2005] [Accepted: 09/21/2005] [Indexed: 11/29/2022]
Affiliation(s)
- José Luis Ruiz-Barba
- Departamento de Biotecnología de Alimentos, Instituto de la Grasa, Consejo Superior de Investigaciones Científicas (CSIC), 41012 Seville, Spain.
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Niwa T, Kawamura Y, Katagiri Y, Ezaki T. Lytic enzyme, labiase for a broad range of Gram-positive bacteria and its application to analyze functional DNA/RNA. J Microbiol Methods 2005; 61:251-60. [PMID: 15722152 DOI: 10.1016/j.mimet.2004.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2004] [Revised: 12/09/2004] [Accepted: 12/13/2004] [Indexed: 11/17/2022]
Abstract
The lytic activity of labiase and achromopeptidase for bacterial DNA/RNA extraction were compared. Rapid lysis of many bacterial strains was observed with labiase followed by SDS treatment. Both labiase and achromopeptidase showed high lytic activity against bacterial strains with the A1alpha chemotype (e.g., Aerococcus viridans) and the A3alpha chemotype (e.g., Staphylococcus epidermidis) for cell wall peptidoglycan structures. The lytic activity of labiase was higher than that of achromopeptidase against strains with the A1gamma chemotype (e.g., Bacillus subtilis). The activity of labiase was not detrimentally affected with increasing NaCl concentration. Labiase lysates were successfully used for rapid extraction of DNA and RNA, whereas achromopeptidase lysates degraded RNA. The DNA and RNA obtained were successfully used for 16S rRNA amplification and real-time RT-PCR detection. It is concluded that labiase is useful for rapid lysis of a wide variety of Gram-positive bacteria and can be used for DNA/RNA isolation protocols.
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Affiliation(s)
- Takashi Niwa
- Department of Microbiology, Regeneration and Advanced Medical Science, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
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33
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Kang HP, Dunne WM. Stability of repetitive-sequence PCR patterns with respect to culture age and subculture frequency. J Clin Microbiol 2003; 41:2694-6. [PMID: 12791907 PMCID: PMC156572 DOI: 10.1128/jcm.41.6.2694-2696.2003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To examine the stability of repetitive-sequence (rep) PCR profiles, six species of bacteria were subcultured to blood agar plates and DNA was extracted from the cultures after 24, 48, and 72 h of incubation at 35 degrees C. In addition, the same species were subcultured to fresh blood plates daily and DNA was extracted from the cultures after growth of 5, 10, and 15 subcultures, respectively. rep PCR analysis demonstrated that all rep PCR fingerprints from a single species were identical.
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Affiliation(s)
- Hyunseok Peter Kang
- Division of Laboratory Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Oumouna M, Jaso-Friedmann L, Evans DL. Activation of nonspecific cytotoxic cells (NCC) with synthetic oligodeoxynucleotides and bacterial genomic DNA: binding, specificity and identification of unique immunostimulatory motifs. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2002; 26:257-269. [PMID: 11755675 DOI: 10.1016/s0145-305x(01)00068-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We have analyzed the effects of synthetic oligodeoxynucleotides (sODNs) and bacterial DNA (bDNA) on the in vitro activation of NCC. Teleost NCC recognition of DNA appeared to differ from that which occurs in higher vertebrates. NCC contain at least two different receptor specificities for DNA. Both oligodeoxyguanosine 20-mers (dG20) and 5'-TGCTGCTTGTGCTTGTGCTT-3' (4GC-2T) bound specifically to NCC. The existence of different receptor specificities was indicated by reciprocal cold target inhibition experiments. dG20 competed with 4GC-2T binding but sODNs composed of GpC or CpG nests did not compete with recognition by NCC of the dG20. ODN binding by NCC primarily depended on the presence of GpC or CpG nests with a preference for -G- serving as the anchor nucleotide. Secondarily, and similar to models of ODN activation in mammals, palindrome sequences of pu-pu-CpG-py-py activated NCC cytotoxicity. Additional analysis of the requirements for ODN activation indicated that guanosine could not substitute for adenosine as a purine spacer and that CpG motifs containing flanking thymidine (i.e.-GTCpGTT-) augmented the activity of the sODN containing this flanking base. Other evidence for the participation of both G and C in the recognition of specific nucleotides by NCC was that poly-dC20, dA20 or dT20 had no activating properties. Methylation of all cytosine nucleotides within an ODN abrogated activation. A canonical ODN motif of 5'-C/AT/AGCTT-3' can now be suggested for teleosts. Additional studies were done to examine the effects of in vitro treatment of NCC with bDNA. bDNA from three different disease isolates of Streptococcus iniae activated NCC cytotoxicity. Treatment of the bDNA with DNase abrogated the enhancement of cytotoxicity. Also, treatment of NCC with eukaryotic DNA had no effects on cytotoxicity. These studies suggested that NCC recognize bacterial nonmethylated DNA. The consequences of these interactions may be increased innate and acquired anti-bacterial immunity.
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Affiliation(s)
- M Oumouna
- Department of Medical Microbiology and Parasitology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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