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Effects of microbial DNA on human DNA profiles generated using the PowerPlex ® 16 HS system. J Forensic Leg Med 2017; 52:208-214. [PMID: 28963943 DOI: 10.1016/j.jflm.2017.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/21/2022]
Abstract
Most crime scenes are not sterile and therefore may be contaminated with environmental DNA, especially if a decomposing body is found. Collecting biological evidence from this individual will yield DNA samples mixed with microbial DNA. This also becomes important if postmortem swabs are collected from sexually assaulted victims. Although genotyping kits undergo validation tests, including bacterial screens, they do not account for the diverse microbial load during decomposition. We investigated the effect of spiking human DNA samples with known concentrations of DNA from 17 microbe species associated with decomposition on DNA profiles produced using the Promega PowerPlex® HS system. Two species, Bacillus subtilis and Mycobacterium smegmatis, produced an extraneous allele at the TPOX locus. When repeated with the PowerPlex® Fusion kit, the extra allele no longer amplified with these two species. This experiment demonstrates that caution should be exhibited if microbial load is high and the PowerPlex® 16HS system is used.
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152
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Yu X, Torzewska A, Zhang X, Yin Z, Drzewiecka D, Cao H, Liu B, Knirel YA, Rozalski A, Wang L. Genetic diversity of the O antigens of Proteus species and the development of a suspension array for molecular serotyping. PLoS One 2017; 12:e0183267. [PMID: 28817637 PMCID: PMC5560731 DOI: 10.1371/journal.pone.0183267] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/01/2017] [Indexed: 11/18/2022] Open
Abstract
Proteus species are well-known opportunistic pathogens frequently associated with skin wound and urinary tract infections in humans and animals. O antigen diversity is important for bacteria to adapt to different hosts and environments, and has been used to identify serotypes of Proteus isolates. At present, 80 Proteus O-serotypes have been reported. Although the O antigen structures of most Proteus serotypes have been identified, the genetic features of these O antigens have not been well characterized. The O antigen gene clusters of Proteus species are located between the cpxA and secB genes. In this study, we identified 55 O antigen gene clusters of different Proteus serotypes. All clusters contain both the wzx and wzy genes and exhibit a high degree of heterogeneity. Potential functions of O antigen-related genes were proposed based on their similarity to genes in available databases. The O antigen gene clusters and structures were compared, and a number of glycosyltransferases were assigned to glycosidic linkages. In addition, an O serotype-specific suspension array was developed for detecting 31 Proteus serotypes frequently isolated from clinical specimens. To our knowledge, this is the first comprehensive report to describe the genetic features of Proteus O antigens and to develop a molecular technique to identify different Proteus serotypes.
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Affiliation(s)
- Xiang Yu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Agnieszka Torzewska
- Department of Immunobiology of Bacteria, Department of General Microbiology Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Xinjie Zhang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Zhiqiu Yin
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Dominika Drzewiecka
- Department of Immunobiology of Bacteria, Department of General Microbiology Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Hengchun Cao
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Bin Liu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Yuriy A. Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Antoni Rozalski
- Department of Immunobiology of Bacteria, Department of General Microbiology Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Lei Wang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
- * E-mail:
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153
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Xu J, Bai Y, Fan T, Zheng X, Cai Y. Expression, purification, and characterization of a membrane-bound D-amino acid dehydrogenase from Proteus mirabilis JN458. Biotechnol Lett 2017; 39:1559-1566. [PMID: 28676939 DOI: 10.1007/s10529-017-2388-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 06/19/2017] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To characterize a novel membrane-bound D -amino acid dehydrogenase from Proteus mirabilis JN458 (PmDAD). RESULTS The recombinant PmDAD protein, encoding a peptide of 434 amino acids with a MW of 47.7 kDa, exhibited broad substrate specificity with D -alanine the most preferred substrate. The K m and V max values for D -alanine were 9 mM and 20 μmol min-1 mg-1, respectively. Optimal activity was at pH 8 and 45 °C. Additionally, this PmDAD generated H2O2 and exhibited 68 and 60% similarity with E. coli K12 DAD and Pseudomonas aeruginosa DAD, respectively, with low degrees of sequence similarity with other bacterial DADs. CONCLUSIONS D-Amino acid dehydrogenase from Proteus mirabilis JN458 was expressed and characterized for the first time, DAD was confirmed to be an alanine dehydrogenase.
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Affiliation(s)
- Jinjin Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Taiping Fan
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China.,Department of Pharmacology, University of Cambridge, Cambridge, CB2 1T, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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155
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Drzewiecka D, Arbatsky NP, Kondakova AN, Shashkov AS, Knirel YA. Structures and serospecificity of threonine-containing O polysaccharides of two clinical isolates belonging to the genus Proteus and their classification into O11 subserogroups. J Med Microbiol 2016; 65:1260-1266. [PMID: 27902374 DOI: 10.1099/jmm.0.000360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two clinical isolates from Polish patients, Proteus mirabilis 9B-m and Proteus genomospecies 3J-r, were found to be serologically related to P mirabilis O11. However, serological studies involving ELISA and Western blotting methods, using lipopolysaccharides (LPSs) extracted from the strains as antigens and native or adsorbed rabbit polyclonal O antisera, specific to the studied strains, revealed slight differences in the cross-reactivity and specificity of the two studied Proteus isolates, when compared to P. mirabilis O11. Two different O polysaccharides containing N-(d-galacturonoyl)-l-threonine were isolated from the LPSs of the isolates. Their structures were determined by chemical analysis and NMR spectroscopy and found to be related to the P. mirabilis O11 antigen structure established earlier, the 9B-m structure differing in the absence of the lateral glucose residue and the 3J-r structure in non-stoichiometric O-acetylation of the threonine residue only. Thus, the Proteus O11 serogroup should be divided into two subgroups: O11a, represented by the 9B-m isolate and O11a, b possessing the additional b epitope, containing the lateral residue of glucose and formed by the 3J-r isolate as well as P. mirabilis 25/57 belonging to O11 serogroup so far. O11a is the sixth new serotype found in Proteus spp. strains recently isolated from patients in central Poland.
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Affiliation(s)
- Dominika Drzewiecka
- Department of General Microbiology, Institute of Microbiology, Biotechnology and Immunology, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt, 47, 119991 Moscow, Russia
| | - Anna N Kondakova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt, 47, 119991 Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt, 47, 119991 Moscow, Russia
| | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt, 47, 119991 Moscow, Russia
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156
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Drzewiecka D, Shashkov AS, Arbatsky NP, Knirel YA. Immunochemical characterization of the O antigens of two Proteus strains, O8-related antigen of Proteus mirabilis 12 B-r and O2-related antigen of Proteus genomospecies 5/6 12 B-k, infecting a hospitalized patient in Poland. Microbiology (Reading) 2016; 162:789-797. [DOI: 10.1099/mic.0.000274] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dominika Drzewiecka
- Department of General Microbiology, Institute of Microbiology, Biotechnology and Immunology, University of Łódź,90-237 Łódź,Poland
| | - Alexander S. Shashkov
- N. D. Zelinsky Institute of Organic Chemistry,Russian Academy of Sciences, 119991 Moscow,Russia
| | - Nikolay P. Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry,Russian Academy of Sciences, 119991 Moscow,Russia
| | - Yuriy A. Knirel
- N. D. Zelinsky Institute of Organic Chemistry,Russian Academy of Sciences, 119991 Moscow,Russia
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