1
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Habib HN, Saleh WMM, Gheni QJ. Genetic profiling of HSP70 gene in local Iraqi goats. BRAZILIAN JOURNAL OF VETERINARY MEDICINE 2022; 44:e004121. [PMID: 36212990 PMCID: PMC9536216 DOI: 10.29374/2527-2179.bjvm004121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 09/18/2022] [Indexed: 11/10/2022] Open
Abstract
Animals display numerous physiological and behavioral responses that reduce the effects of heat stress. Moreover, genetic variance is strongly associated with responses to heat stress, including variants of heat shock proteins (HSPs) that are necessary for thermoregulation and stress resistance. Herein, we performed the molecular profiling of the HSP70 gene, and its polymorphism was demonstrated as a possible factor in the stress tolerance of local Iraqi goats. A number of different mutations were found owing to seven main polymorphisms. Results indicated the occurrence of silent and missense mutations in sequences obtained for Iraqi local goats. Genetic diversity was observed in the HSP70 gene of Iraqi local goats on the basis of phylogenetic-tree analysis as some mutations occurred once whereas others occurred multiple times. The polymorphisms LC616787, LC616788, and LC616791 were combined with the reference gene in the same branch, whereas polymorphisms (LC616785 and LC616786) and (LC616789 and LC616790) met in different branches, respectively. Moreover, all studied proteins had mismatches in their three-dimensional structures. Therefore, the presence of specific genetic differences within the HSP70 gene in Iraqi goats can increase the possibility of selecting animals more suitable to various levels of stress.
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Affiliation(s)
- Hassan Nima Habib
- Biotechnology and Molecular Genetics, PhD, Department of Animal Production, College of Agriculture, University of Basrah, Basrah, Iraq
| | - Wessam Monther Mohammed Saleh
- Veterinarian, PhD, Department of Internal and Preventive Medicine, College of Veterinary, Medicine, University of Basrah, Basrah, Iraq,Correspondence Wessam Monther Mohammed Saleh Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Basrah 57 Baghdad Street Basrah, Iraq E-mail: ;
| | - Qutaiba Jassim Gheni
- Veternarian, PhD, Department of Animal Production, College of Agriculture, University of Basrah, Basrah, Iraq
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2
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Díaz T, Ortega-Pinazo J, Martínez B, Jiménez A, Gómez-Zumaquero JM, Caracuel Z, Hortas ML, Ferro P. Measurement of yield and quality of DNA in human buffy coat is extraction method dependent. Prep Biochem Biotechnol 2022:1-8. [PMID: 36121058 DOI: 10.1080/10826068.2022.2119574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
During the last few years, an important element in the improvement of the molecular biology techniques has been the necessity for availability of high quality and functionality DNA. Several DNA extraction procedures with different results in both performance and quality, have been proposed. In this study our objective was to determine the most reliable extraction method that balances DNA quantity, and to assess the sample quantification of the fluorometric DNA quantification methods. For this, blood extracted by venopunction from 20 healthy volunteers was used to obtain DNA from buffy coat, and 4 commercial DNA extraction kits were assessed as well as two fluorometric DNA quantification methods with protocols of different complexity. Results suggest that manual methods achieve higher quality and larger yields of DNA. DNA purity obtained with the 4 extraction kits evaluated through the 260/280 and 260/230 ratio showed that the Qiacube kit fulfilled the criteria established in this work, followed very close by the Flexigene kit. On the other hand, the fluorometric DNA methods used in the samples quantification showed a higher variability when using QuantiFlour method, obtaining better results probably due to the simplicity of this protocol.
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Affiliation(s)
- T Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - J Ortega-Pinazo
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga-IBIMA, UGC Neurociencias, Hospital Regional Universitario de Málaga, Malaga, Spain
| | - B Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - A Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - J M Gómez-Zumaquero
- Genomic ECAI, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - Z Caracuel
- Costa del Sol Sanitary Agency, Sanitary District of Málaga, Malaga, Spain
| | - M L Hortas
- Costa del Sol Sanitary Agency, Sanitary District of Málaga, Malaga, Spain
| | - P Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain.,Unidad Clínica de Endocrinología y Nutrición, Hospital Universitario Virgen de la Victoria, Málaga, Spain
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3
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Harbusch NS, Bozic M, Konrad PM, Winkler M, Kessler HH. Evaluation of a new extraction platform in combination with molecular assays useful for monitoring immunosuppressed patients. J Clin Virol 2018; 108:59-63. [PMID: 30248619 DOI: 10.1016/j.jcv.2018.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/10/2018] [Accepted: 09/09/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND In the immunosuppressed, detection of viral reactivation at the earliest convenience and molecular monitoring are of paramount importance. Nucleic acid extraction has a major impact on the reliability of results obtained from molecular assays. OBJECTIVES The aim of this study was to investigate the accuracy of the new EMAG® nucleic acid extraction platform and to compare the performance of the new platform to that of the standard NucliSENS® easyMAG® instrument in the routine clinical laboratory. STUDY DESIGN For accuracy testing, reference material and for comparison studies, clinical specimens were used. In addition, a lab-flow analysis including estimation of hands-on time and that for automated extraction was performed. RESULTS When accuracy was tested, all 89 results obtained were found to be concordant with the results expected. When 648 clinical results were compared, 85.7% were found to be within ±0.5 log10 unit, 9.5% between ±0.5 and ±1.0 log10 unit, and 4.8% more than ±1.0 log10 unit. The overall time required for nucleic acid extraction of 8 samples in parallel was 94 min for the fully automated extraction mode and 82 min for the partly automated mode with the new platform, and 73 min with the standard instrument. Hands-on time was found to be shorter with the new platform. CONCLUSIONS The extraction performance of both platforms was found to be similar for EDTA whole blood, BAL, and urine specimens. The total turn-around time for nucleic acid extraction was found to be longer with the EMAG® platform, whereas hands-on time was reduced.
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Affiliation(s)
- Nora S Harbusch
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Michael Bozic
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Petra M Konrad
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Michaela Winkler
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Harald H Kessler
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria.
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4
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A simple, rapid and economic manual method for human sperm DNA extraction in genetic and epigenetic studies. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2018. [DOI: 10.1016/j.mefs.2017.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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5
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Zulkifli SN, Rahim HA, Lau WJ. Detection of contaminants in water supply: A review on state-of-the-art monitoring technologies and their applications. SENSORS AND ACTUATORS. B, CHEMICAL 2018; 255:2657-2689. [PMID: 32288249 PMCID: PMC7126548 DOI: 10.1016/j.snb.2017.09.078] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 05/12/2023]
Abstract
Water monitoring technologies are widely used for contaminants detection in wide variety of water ecology applications such as water treatment plant and water distribution system. A tremendous amount of research has been conducted over the past decades to develop robust and efficient techniques of contaminants detection with minimum operating cost and energy. Recent developments in spectroscopic techniques and biosensor approach have improved the detection sensitivities, quantitatively and qualitatively. The availability of in-situ measurements and multiple detection analyses has expanded the water monitoring applications in various advanced techniques including successful establishment in hand-held sensing devices which improves portability in real-time basis for the detection of contaminant, such as microorganisms, pesticides, heavy metal ions, inorganic and organic components. This paper intends to review the developments in water quality monitoring technologies for the detection of biological and chemical contaminants in accordance with instrumental limitations. Particularly, this review focuses on the most recently developed techniques for water contaminant detection applications. Several recommendations and prospective views on the developments in water quality assessments will also be included.
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Affiliation(s)
| | - Herlina Abdul Rahim
- Faculty of Electrical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Woei-Jye Lau
- Advanced Membrane Technology Research Centre (AMTEC), Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
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6
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Kalousová M, Levová K, Kuběna AA, Jáchymová M, Franková V, Zima T. Comparison of DNA isolation using salting-out procedure and automated isolation (MagNA system). Prep Biochem Biotechnol 2017; 47:703-708. [DOI: 10.1080/10826068.2017.1303613] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marta Kalousová
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Kateřina Levová
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Aleš A. Kuběna
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Marie Jáchymová
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Věra Franková
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Tomáš Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
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7
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Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System. J Clin Microbiol 2016; 55:291-301. [PMID: 27847371 DOI: 10.1128/jcm.01126-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/02/2016] [Indexed: 11/20/2022] Open
Abstract
Francisella tularensis is a potential bioterrorism agent that is highly infectious at very low doses. Diagnosis of tularemia by blood culture and nucleic acid-based diagnostic tests is insufficiently sensitive. Here, we demonstrate a highly sensitive F. tularensis assay that incorporates sample processing and detection into a single cartridge suitable for point-of-care detection. The assay limit of detection (LOD) and dynamic range were determined in a filter-based cartridge run on the GeneXpert system. F. tularensis DNA in buffer or CFU of F. tularensis was spiked into human or macaque blood. To simulate detection in human disease, the assay was tested on blood drawn from macaques infected with F. tularensis Schu S4 at daily intervals. Assay detection was compared to that with a conventional quantitative PCR (qPCR) assay and blood culture. The assay LOD was 0.1 genome equivalents (GE) per reaction and 10 CFU/ml F. tularensis in both human and macaque blood. In infected macaques, the assay detected F. tularensis on days 1 to 4 postinfection in 21%, 17%, 60%, and 83% of macaques, respectively, compared to conventional qPCR positivity rates of 0%, 0%, 30%, and 100% and CFU detection of blood culture at 0%, 0%, 0%, and 10% positive, respectively. Assay specificity was 100%. The new cartridge-based assay can rapidly detect F. tularensis in bloodstream infections directly in whole blood at the early stages of infection with a sensitivity that is superior to that of other methods. The simplicity of the automated testing procedures may make this test suitable for rapid point-of-care detection.
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8
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Mölsä M, Kalin-Mänttäri L, Tonteri E, Hemmilä H, Nikkari S. Comparison of four commercial DNA extraction kits for the recovery of Bacillus spp. spore DNA from spiked powder samples. J Microbiol Methods 2016; 128:69-73. [PMID: 27435532 DOI: 10.1016/j.mimet.2016.07.013] [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: 05/18/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 11/28/2022]
Abstract
Bacillus spp. include human pathogens such as Bacillus anthracis, the causative agent of anthrax and a biothreat agent. Bacillus spp. form spores that are physically highly resistant and may remain active over sample handling. We tested four commercial DNA extraction kits (QIAamp DNA Mini Kit, RTP Pathogen Kit, ZR Fungal/Bacterial DNA MiniPrep, and genesig Easy DNA/RNA Extraction kit) for sample inactivation and DNA recovery from two powders (icing sugar and potato flour) spiked with Bacillus thuringiensis spores. The DNA was analysed using a B. thuringiensis-specific real-time PCR assay. The detection limit was 3×10(1)CFU of spiked B. thuringiensis spores with the QIAamp DNA Mini, RTP Pathogen, and genesig Easy DNA/RNA Extraction kits, and 3×10(3)CFU with the ZR Fungal/Bacterial DNA MiniPrep kit. The results showed that manual extraction kits are effective and safe for fast and easy DNA extraction from powder samples even in field conditions. Adding a DNA filtration step to the extraction protocol ensures the removal of Bacillus spp. spores from DNA samples without affecting sensitivity.
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Affiliation(s)
- Markos Mölsä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland.
| | | | - Elina Tonteri
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Heidi Hemmilä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Simo Nikkari
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
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9
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Lai XH, Zhao LF, Chen XM, Ren Y. Rapid Identification and Characterization of Francisella by Molecular Biology and Other Techniques. Open Microbiol J 2016; 10:64-77. [PMID: 27335619 PMCID: PMC4899538 DOI: 10.2174/1874285801610010064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/22/2022] Open
Abstract
Francisella tularensis is the causative pathogen of tularemia and a
Tier 1 bioterror agent on the CDC list. Considering the fact that some
subpopulation of the F. tularensis strains is more virulent, more
significantly associated with mortality, and therefore poses more threat to
humans, rapid identification and characterization of this subpopulation strains
is of invaluable importance. This review summarizes the up-to-date developments
of assays for mainly detecting and characterizing F. tularensis and a
touch of caveats of some of the assays.
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Affiliation(s)
- Xin-He Lai
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Long-Fei Zhao
- College of Life Sciences, Key Laboratory of Plant-Microbe Interactions of Henan, Shangqiu Normal University, Shangqiu, Henan, 476000, PR China
| | - Xiao-Ming Chen
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China ; Department of Pediatric Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yi Ren
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA
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10
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Hua F, Zhang P, Zhang F, Zhao Y, Li C, Sun C, Wang X, Yang R, Wang C, Yu A, Zhou L. Development and evaluation of an up-converting phosphor technology-based lateral flow assay for rapid detection of Francisella tularensis. Sci Rep 2015; 5:17178. [PMID: 26608358 PMCID: PMC4660431 DOI: 10.1038/srep17178] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/27/2015] [Indexed: 01/11/2023] Open
Abstract
Francisella tularensis is a potential biowarfare/bioterrorism agent and zoonotic pathogen that causes tularemia; thus, surveillance of F. tularensis and first-level emergency response using point-of-care testing (POCT) are essential. The UPT-LF POCT assay was established to quantitatively detect F. tularensis within 15 min, and the sensitivity of the assay was 10(4) CFU · mL(-1) (100 CFU/test). The linear quantitative range covered five orders of magnitude, and the coefficients of variation were less than 10%. Except Shigella dysenteriae, UPT-LF showed excellent specificity to four strains that are also potential biowarfare/bioterrorism agents and 13 food-borne pathogenic strains. Samples with pH 2-13, high ion strengths (≥ 2 mol · L(-1) solution of KCl and NaCl), high viscosities (≤ 50 mg · mL(-1) PEG20000 or ≥ 20% glycerol), and high concentrations of biomacromolecules (≥ 400 mg · mL(-1) bovine serum albumin or ≥ 80 mg · mL(-1) casein) showed little influence on the assay. For practical utilization, the tolerance limits for seven powders and eight viscera were determined, and operation errors of liquid measurement demonstrated a minor influence on the strip. Ftu-UPT-LF is a candidate POCT method because of its excellent sensitivity, specificity, and stability in complex samples, as well as low operation error.
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Affiliation(s)
- Fei Hua
- Laboratory of Analytical Microbiology, State Key Laboratory of
Pathogen and Biosecurity, Beijing Institute of Microbiology and
Epidemiology, Beijing
100071, P.R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No.
BZ0329), Beijing
100071, P.R. China
- Department of Etiology, Taishan Medical University,
Taian
271000, P.R. China
- Clinical Diagnostic Center, 302nd Hospital of the
People’s Liberation Army, Beijing
100039, P.R. China
| | - Pingping Zhang
- Laboratory of Analytical Microbiology, State Key Laboratory of
Pathogen and Biosecurity, Beijing Institute of Microbiology and
Epidemiology, Beijing
100071, P.R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No.
BZ0329), Beijing
100071, P.R. China
| | - Fuli Zhang
- Radiation Oncology Department, Beijing Military General
Hospital, Beijing
100700, P.R. China
| | - Yong Zhao
- Laboratory of Analytical Microbiology, State Key Laboratory of
Pathogen and Biosecurity, Beijing Institute of Microbiology and
Epidemiology, Beijing
100071, P.R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No.
BZ0329), Beijing
100071, P.R. China
| | - Chunfeng Li
- Laboratory of Analytical Microbiology, State Key Laboratory of
Pathogen and Biosecurity, Beijing Institute of Microbiology and
Epidemiology, Beijing
100071, P.R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No.
BZ0329), Beijing
100071, P.R. China
- Department of Clinical Laboratory, Chinese People’s
Liberation Army General Hospital, Beijing
100853, P.R. China
| | - Chongyun Sun
- Laboratory of Analytical Microbiology, State Key Laboratory of
Pathogen and Biosecurity, Beijing Institute of Microbiology and
Epidemiology, Beijing
100071, P.R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No.
BZ0329), Beijing
100071, P.R. China
- Department of Clinical Laboratory, Chinese People’s
Liberation Army General Hospital, Beijing
100853, P.R. China
| | - Xiaochen Wang
- Laboratory of Analytical Microbiology, State Key Laboratory of
Pathogen and Biosecurity, Beijing Institute of Microbiology and
Epidemiology, Beijing
100071, P.R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No.
BZ0329), Beijing
100071, P.R. China
- College of Animal Science and Technology, Jilin Agricultural
University, Changchun
130118, P.R. China
| | - Ruifu Yang
- Laboratory of Analytical Microbiology, State Key Laboratory of
Pathogen and Biosecurity, Beijing Institute of Microbiology and
Epidemiology, Beijing
100071, P.R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No.
BZ0329), Beijing
100071, P.R. China
| | - Chengbin Wang
- Department of Clinical Laboratory, Chinese People’s
Liberation Army General Hospital, Beijing
100853, P.R. China
| | - Ailian Yu
- Department of Etiology, Taishan Medical University,
Taian
271000, P.R. China
| | - Lei Zhou
- Laboratory of Analytical Microbiology, State Key Laboratory of
Pathogen and Biosecurity, Beijing Institute of Microbiology and
Epidemiology, Beijing
100071, P.R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No.
BZ0329), Beijing
100071, P.R. China
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Bowman S, Roffey P, McNevin D, Gahan ME. Evaluation of commercial DNA extraction methods for biosecurity applications. AUST J FORENSIC SCI 2015. [DOI: 10.1080/00450618.2015.1106585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Psifidi A, Dovas CI, Bramis G, Lazou T, Russel CL, Arsenos G, Banos G. Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. PLoS One 2015; 10:e0115960. [PMID: 25635817 PMCID: PMC4312062 DOI: 10.1371/journal.pone.0115960] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/28/2014] [Indexed: 12/21/2022] Open
Abstract
Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.
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Affiliation(s)
- Androniki Psifidi
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Chrysostomos I. Dovas
- Microbiology and Infectious Diseases Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Bramis
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Thomai Lazou
- Food safety Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Claire L. Russel
- Department of Clinical Veterinary Sciences, University of Bristol, Langford House, Langford, Bristol, United Kingdom
| | - Georgios Arsenos
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Banos
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Scotland’s Rural College, Edinburgh, United Kingdom
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13
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Seo SH, Lee YR, Ho Jeon J, Hwang YR, Park PG, Ahn DR, Han KC, Rhie GE, Hong KJ. Highly sensitive detection of a bio-threat pathogen by gold nanoparticle-based oligonucleotide-linked immunosorbent assay. Biosens Bioelectron 2014; 64:69-73. [PMID: 25194798 DOI: 10.1016/j.bios.2014.08.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 08/07/2014] [Accepted: 08/19/2014] [Indexed: 01/08/2023]
Abstract
Francisella (F.) tularensis causes the zoonotic disease tularemia and categorized as one of the highest-priority biological agents. The sensing approaches utilized by conventional detection methods, including enzyme-linked immunosorbent assay (ELISA), are not sensitive enough to identify an infectious dose of this high-risk pathogen due to its low infective dose. As an attempt to detect F. tularensis with high sensitivity, we utilized the highly sensitive immunoassay system named gold nanoparticle-based oligonucleotide-linked immunosorbent assay (GNP-OLISA) which uses antibody-gold nanoparticles conjugated with DNA strands as a signal generator and RNA oligonucleotides appended with a fluorophore as a quencher for signal amplification. We modified the GNP-OLISA for the detection F. tularensis to utilize one antibody for both the capture of the target and for signal generation instead of using two different antibodies, which are usually employed to construct the antibody sandwich in the ELISA. The GNP-OLISA showed 37-fold higher sensitivity compared with ELISA and generated very consistent detection results in the sera. In addition, the detection specificity was not affected by the presence of non-target bacteria, suggesting that GNP-OLISA can be used as a sensitive detection platform for monitoring high-risk pathogens thereby overcoming the limit of the conventional assay system.
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Affiliation(s)
- Sang-Hwan Seo
- Division of High-Risk Pathogen Research, Center for Infectious Diseases, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongwon, Chungcheongbuk-do 363-951, Republic of Korea
| | - Young-Ran Lee
- Division of High-Risk Pathogen Research, Center for Infectious Diseases, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongwon, Chungcheongbuk-do 363-951, Republic of Korea
| | - Jun Ho Jeon
- Division of High-Risk Pathogen Research, Center for Infectious Diseases, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongwon, Chungcheongbuk-do 363-951, Republic of Korea
| | - Yi-Rang Hwang
- Division of High-Risk Pathogen Research, Center for Infectious Diseases, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongwon, Chungcheongbuk-do 363-951, Republic of Korea
| | - Pil-Gu Park
- Division of High-Risk Pathogen Research, Center for Infectious Diseases, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongwon, Chungcheongbuk-do 363-951, Republic of Korea
| | - Dae-Ro Ahn
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea; Department of Biological Chemistry, KIST Campus, Korea University of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Ki-Cheol Han
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Gi-Eun Rhie
- Division of High-Risk Pathogen Research, Center for Infectious Diseases, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongwon, Chungcheongbuk-do 363-951, Republic of Korea
| | - Kee-Jong Hong
- Division of High-Risk Pathogen Research, Center for Infectious Diseases, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongwon, Chungcheongbuk-do 363-951, Republic of Korea.
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Enzymatic treatment of specimens before DNA extraction directly influences molecular detection of infectious agents. PLoS One 2014; 9:e94886. [PMID: 24936792 PMCID: PMC4061000 DOI: 10.1371/journal.pone.0094886] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/20/2014] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Biological samples, pharmaceuticals or food contain proteins, lipids, polymers, ammoniums and macromolecules that alter the detection of infectious agents by DNA amplification techniques (PCR). Moreover the targeted DNA has to be released from the complex cell walls and the compact nucleoprotein matrixes and cleared from potential inhibitors. The goal of the present work was to assess the efficiency of enzymatic pretreatments on infectious agents to make DNA available for further extraction and amplification. METHODS Staphylococcus epidermidis, Streptococcus mitis, Propionibacterium acnes, Escherichia coli, Pseudomonas aeruginosa, Candida albicans, Aspergillus niger and Fusarium solani were mixed with an internal control virus and treated with: 1) proteinase K; 2) lyticase and 3) lyticase followed by proteinase K. DNAs was manually extracted using the QIAmp DNA Mini kit or the MagNA Pure Compact automate. DNA extraction yields and the inhibitors were assessed with a phocid Herpesvirus. Bacterial detection was performed using TaqMan real-time PCR and yeasts and filamentous Fungi with HRM (real-time PCR followed by high-resolution melting analysis). RESULTS Viral DNA was released, extracted and detected using manual and automatic methods without pre enzymatic treatments. Either the manual or the automatic DNA extraction systems did not meet the sensitivity expectations if enzymatic treatments were not performed before: lyticase for Fungi and Proteinase K for Bacteria. The addition of lyticase and proteinase K did not improve results. For Fungi the detection after lyticase was higher than for Proteinase K, for which melting analysis did not allow fungal specification. DISCUSSION Columns and magnetic beads allowed collecting DNA and separate PCR inhibitors. Detection rates cannot be related to DNA-avidity of beads or to elution but to the lack of proteolysis.
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Gonçalves-de-Albuquerque SDC, Pessoa E Silva R, de Morais RCS, Trajano-Silva LAM, Régis-da-Silva CG, Brandão-Filho SP, de Paiva-Cavalcanti M. Tracking false-negative results in molecular diagnosis: proposal of a triplex-PCR based method for leishmaniasis diagnosis. J Venom Anim Toxins Incl Trop Dis 2014; 20:16. [PMID: 24808911 PMCID: PMC4012836 DOI: 10.1186/1678-9199-20-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/07/2014] [Indexed: 11/26/2022] Open
Abstract
Background Molecular biological methods have become increasingly relevant to the diagnosis and control of infectious diseases, such as leishmaniasis. Since various factors may affect the sensitivity of PCR assays, including DNA yield and purity, an optimal extraction method is pivotal. Losses of a parasite’s DNA during extraction may significantly impair its detection by PCR and lead to false-negative results. This study proposes a triplex PCR assay targeting the parasite’s DNA, an external control (pUC18) and an internal control (G3PD) for accurate diagnosis of leishmaniasis. Results Two primer pairs were designed to detect the plasmid pUC18 and a triplex PCR assay targeting the Leishmania braziliensis kinetoplast DNA, the external control and the internal control was standardized. The triplex PCR assay was assessed for its ability to detect the three target DNA fragments simultaneously. PCR products from pUC18 DNA resulted in bands of 368 (P1) and 316 (P2) base pairs (bp). The triplex PCR optimized with the chosen external control system (P1) allowed the simultaneous detection of the internal control (G3PD – 567 bp) as well as of small quantities (10 pg) of the target parasite’s DNA, detected by amplification of a 138 bp product. Conclusions The new tool standardized herein enables a more reliable interpretation of PCR results, mainly by contributing to quality assurance of leishmaniasis diagnosis. Furthermore, after simple standardization steps, this protocol could be applied to the diagnosis of other infectious diseases in reference laboratories. This triplex PCR enables the assessment of small losses during the DNA extraction process, problems concerning DNA degradation (sample quality) and the detection of L. braziliensis kDNA.
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Affiliation(s)
| | - Rômulo Pessoa E Silva
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
| | - Rayana Carla Silva de Morais
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
| | | | - Carlos Gustavo Régis-da-Silva
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
| | - Sinval Pinto Brandão-Filho
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
| | - Milena de Paiva-Cavalcanti
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
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Hutchins AS, Astwood MJ, Saah JR, Michel PA, Newton BR, Dauphin LA. Evaluation of automated and manual DNA purification methods for detecting Ricinus communis DNA during ricin investigations. Forensic Sci Int 2014; 236:10-5. [PMID: 24529769 DOI: 10.1016/j.forsciint.2013.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 11/26/2013] [Accepted: 12/10/2013] [Indexed: 11/25/2022]
Abstract
In April of 2013, letters addressed to the President of United States and other government officials were intercepted and found to be contaminated with ricin, heightening awareness about the need to evaluate laboratory methods for detecting ricin. This study evaluated commercial DNA purification methods for isolating Ricinus communis DNA as measured by real-time polymerase chain reaction (PCR). Four commercially available DNA purification methods (two automated, MagNA Pure compact and MagNA Pure LC, and two manual, MasterPure complete DNA and RNA purification kit and QIAamp DNA blood mini kit) were evaluated. We compared their ability to purify detectable levels of R. communis DNA from four different sample types, including crude preparations of ricin that could be used for biological crimes or acts of bioterrorism. Castor beans, spiked swabs, and spiked powders were included to simulate sample types typically tested during criminal and public health investigations. Real-time PCR analysis indicated that the QIAamp kit resulted in the greatest sensitivity for ricin preparations; the MasterPure kit performed best with spiked powders. The four methods detected equivalent levels by real-time PCR when castor beans and spiked swabs were used. All four methods yielded DNA free of PCR inhibitors as determined by the use of a PCR inhibition control assay. This study demonstrated that DNA purification methods differ in their ability to purify R. communis DNA; therefore, the purification method used for a given sample type can influence the sensitivity of real-time PCR assays for R. communis.
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Affiliation(s)
- Anne S Hutchins
- Bioterrorism and Emerging Pathogens Unit, North Carolina State Laboratory of Public Health, Raleigh, NC 27607, USA
| | | | - J Royden Saah
- Bioterrorism and Emerging Pathogens Unit, North Carolina State Laboratory of Public Health, Raleigh, NC 27607, USA
| | - Pierre A Michel
- Bioterrorism Rapid Response and Advanced Technology (BRRAT) Laboratory, Laboratory Preparedness and Response Branch (LPRB), Division of Preparedness and Emerging Infections (DPEI), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA
| | | | - Leslie A Dauphin
- Bioterrorism Rapid Response and Advanced Technology (BRRAT) Laboratory, Laboratory Preparedness and Response Branch (LPRB), Division of Preparedness and Emerging Infections (DPEI), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA.
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Comparative evaluation of eleven commercial DNA extraction kits for real-time PCR detection of Bacillus anthracis spores in spiked dairy samples. Int J Food Microbiol 2013; 170:29-37. [PMID: 24291177 DOI: 10.1016/j.ijfoodmicro.2013.10.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 09/02/2013] [Accepted: 10/26/2013] [Indexed: 11/23/2022]
Abstract
Spores of Bacillus anthracis are highly resistant and can survive conditions used for food preservation. Sample size and complexity represent the major hurdles for pathogen detection in food-related settings. Eleven commercial DNA extraction kits were evaluated for detection of B. anthracis spores by quantitative real-time PCR (qPCR) in dairy products. DNA was extracted from serial dilutions of B. anthracis spores in milk powder, cream cheese, whole milk and buttermilk. Three kits (QIAamp DNA mini kit, Invisorb Food kit I and II) were determined to produce the lowest limit of detections (LODs) with equally good performance. These kits employed lysozyme and proteinase K treatments or proteinase K in combination with cethyltrimethylamonium bromide-mediated (CTAB) precipitation of cell debris for cell disruption and DNA release. The LODs for these three kits were determined as 10(2) spores/ml of distilled water, 10(3)s pores/20 mg of powdered milk and 10(4) spores/100 mg of cream cheese, respectively. Performance testing of the QIAamp DNA mini kit demonstrated a good reproducibility and appropriate detection limits from 10(3)/ml for butter milk, 10(4)/ml for whole milk and 10(4)/100 mg for low fat cream cheese. However, DNA extraction efficiency was strongly inhibited by cream cheese with higher fat contents with an increased LOD of 10(6)/100 mg spores. This study demonstrated that qPCR detection depends directly on the appropriate DNA extraction method for an individual food matrix and bacterial agent.
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van Belkum A, Durand G, Peyret M, Chatellier S, Zambardi G, Schrenzel J, Shortridge D, Engelhardt A, Dunne WM. Rapid clinical bacteriology and its future impact. Ann Lab Med 2012; 33:14-27. [PMID: 23301218 PMCID: PMC3535192 DOI: 10.3343/alm.2013.33.1.14] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/10/2012] [Indexed: 02/01/2023] Open
Abstract
Clinical microbiology has always been a slowly evolving and conservative science. The sub-field of bacteriology has been and still is dominated for over a century by culture-based technologies. The integration of serological and molecular methodologies during the seventies and eighties of the previous century took place relatively slowly and in a cumbersome fashion. When nucleic acid amplification technologies became available in the early nineties, the predicted "revolution" was again slow but in the end a real paradigm shift did take place. Several of the culture-based technologies were successfully replaced by tests aimed at nucleic acid detection. More recently a second revolution occurred. Mass spectrometry was introduced and broadly accepted as a new diagnostic gold standard for microbial species identification. Apparently, the diagnostic landscape is changing, albeit slowly, and the combination of newly identified infectious etiologies and the availability of innovative technologies has now opened new avenues for modernizing clinical microbiology. However, the improvement of microbial antibiotic susceptibility testing is still lagging behind. In this review we aim to sketch the most recent developments in laboratory-based clinical bacteriology and to provide an overview of emerging novel diagnostic approaches.
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Affiliation(s)
- Alex van Belkum
- BioMérieux SA, Unit Microbiology, R&D Microbiology, La Balme Les Grottes, France
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Verheyen J, Kaiser R, Bozic M, Timmen-Wego M, Maier BK, Kessler HH. Extraction of viral nucleic acids: Comparison of five automated nucleic acid extraction platforms. J Clin Virol 2012; 54:255-9. [DOI: 10.1016/j.jcv.2012.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 02/02/2023]
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