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Tang JJ, Zhong ZH, Li ZC, Guo QK, Li SY, Guo YX, Jiang B, Li AX. Quantitative detection of parasitic ciliate Cryptocaryon irritans in seawater with an optimized sample processing method. JOURNAL OF FISH DISEASES 2022; 45:623-630. [PMID: 35176179 DOI: 10.1111/jfd.13587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
The protozoan Cryptocaryon irritans is one of the most important ectoparasites of marine fish, causing 'white spot disease' and mass mortality in aquaculture. To accurately predict disease outbreaks and develop prevention strategies, improved detection methods are required that are sensitive, convenient and rapid. In this study, a pair of specific primers based on the C. irritans 18S rRNA gene was developed and used in a real-time PCR (qPCR) assay. This assay was able to detect five theronts in 1 L of natural seawater. Furthermore, a linear model was established to analyse the log of Ct value and parasite abundance in seawater (y = -2.9623x + 24.2930), and the coefficient of determination (R2 ) value was 0.979. A lysis buffer was optimized for theront DNA extraction and used for storage sample. This method was superior to the commercial water DNA kit, and there was no significant degradation of DNA at room temperature for 24-96 hr. A dilution method was developed to manage qPCR inhibitors and used to investigate natural seawater samples in a net cage farm with diseased fish, and the findings were consistent with the actual situation. This study provides a valuable tool for assisting in the early monitoring and control of cryptocaryoniasis in aquaculture.
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Affiliation(s)
- Jia-Jia Tang
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhi-Hong Zhong
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhi-Cheng Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qing-Kai Guo
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Shi-Yu Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yi-Xuan Guo
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Biao Jiang
- Innovative Institute of Animal Healthy breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - An-Xing Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals and Institute of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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2
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Detection of Cancer Mutations by Urine Liquid Biopsy as a Potential Tool in the Clinical Management of Bladder Cancer Patients. Cancers (Basel) 2022; 14:cancers14040969. [PMID: 35205727 PMCID: PMC8870091 DOI: 10.3390/cancers14040969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/02/2022] [Accepted: 02/11/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary The management of bladder cancer faces multiple challenges concerning the diagnostic and follow-up approaches. The standard diagnostic examination comprises invasive cystoscopy. Urine cytology and recently proposed urine-based biomarkers have been unable to replace cystoscopy, thus prompting calls for improvements. Here, we explore urine liquid biopsy to detect cancer mutations and subsequently evaluate the utility of urine as a suitable specimen for diagnosing bladder cancer. Our results show that the analysis of pre- and postoperative urine with a cost-effective 127-gene panel enables the characterization of tumor mutations. These findings provide cumulative evidence in support of the results of previous studies that testing urine for mutations is a useful strategy to complement the clinical management of bladder cancer patients. Abstract The standard diagnostic and follow-up examination for bladder cancer is diagnostic cystoscopy, an invasive test that requires compliance for a long period. Urine cytology and recent biomarkers come short of replacing cystoscopy. Urine liquid biopsy promises to solve this problem and potentially allows early detection, evaluation of treatment efficacy, and surveillance. A previous study reached 52–68% sensitivity using small-panel sequencing but could increase sensitivity to 68–83% by adding aneuploidy and promoter mutation detection. Here, we explore whether a large 127-gene panel alone is sufficient to detect tumor mutations in urine from bladder cancer patients. We recruited twelve bladder cancer patients, obtained preoperative and postoperative urine samples, and successfully analyzed samples from eleven patients. In ten patients, we found at least one mutation in bladder-cancer-associated genes, i.e., a promising sensitivity of 91%. In total, we identified 114 variants, of which 90 were predicted as nonbenign, 30% were associated with cancer, and 13% were actionable according to the CIViC database. Sanger sequencing of the patients’ formalin-fixed, paraffin-embedded (FFPE) tumor tissues confirmed the findings. We concluded that incorporating urine liquid biopsy is a promising strategy in the management of bladder cancer patients.
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Nauwelaerts SJD, Van Geel D, Delvoye M, De Cremer K, Bernard A, Roosens NHC, De Keersmaecker SCJ. Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva? J Biomol Tech 2021; 31:27-35. [PMID: 32042275 DOI: 10.7171/jbt.20-3101-004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic epidemiology requires an appropriate approach to measure genetic variation within the population. The aim of this study was to evaluate the characteristics and genotyping results of DNA extracted from 2 human DNA sources, selected for their rapid and noninvasive sampling, and the use of simple and standardized protocols that are essential for large-scale epidemiologic studies. Saliva and urine samples were collected at the same day from 20 subjects aged 9-10 yr. Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping was performed targeting CC16 A38G and uteroglobin-related protein 1 (UGRP1)-112G/A. Saliva was found to provide the highest yield and concentration of total DNA extracted. Salivary DNA showed higher purity and a significantly less degraded state compared to urinary DNA. Consequently, the salivary DNA gave better genotyping results than urinary DNA. Therefore, if the choice exists, saliva is the preferred noninvasive matrix for genotyping purposes in large-scale genetic epidemiologic studies. Only in particular cases using urine could nevertheless be considered useful, although specific limitations need to be taken into account.
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Affiliation(s)
- Sarah J D Nauwelaerts
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium.,Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Dirk Van Geel
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Maud Delvoye
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Koen De Cremer
- Platform Chromatography and Mass Spectrometry, Sciensano, 1050 Brussels, Belgium; and
| | - Alfred Bernard
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
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4
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Streleckiene G, Reid HM, Arnold N, Bauerschlag D, Forster M. Quantifying cell free DNA in urine: comparison between commercial kits, impact of gender and inter-individual variation. Biotechniques 2019; 64:225-230. [PMID: 29793362 DOI: 10.2144/btn-2018-0003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA can enter the blood circulation from living cells by extracellular vesicles or at cell death, and pass into urine through the kidney barrier. Urine can be collected non-invasively, making it an interesting source of cell-free DNA (cfDNA) for research studies and ultimately for clinical diagnostics. However, there is currently a lack of data on the quantity and variability of cfDNA in urine. Here, we benchmark two commercial urine cfDNA isolation kits with respect to the quantity of DNA, the labor time, and cost. The results show distinctive differences between each kit. Furthermore, the cfDNA amount from the same probands varied strongly from day to day and may be higher in female samples than in male samples (p = 0.003).
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Affiliation(s)
- Greta Streleckiene
- Institute for Digestive Research, Lithuanian University of Health Sciences, Eiveniu Str. 2, LT-50009 Kaunas, Lithuania.,Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
| | - Hayley M Reid
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
| | - Norbert Arnold
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Schleswig-Holstein, D-24105 Kiel, Germany.,Department of Gynecology & Obstetrics, University Hospital of Schleswig-Holstein, Christian-Albrechts-Universität zu Kiel, D-24105 Kiel, Germany
| | - Dirk Bauerschlag
- Department of Gynecology & Obstetrics, University Hospital of Schleswig-Holstein, Christian-Albrechts-Universität zu Kiel, D-24105 Kiel, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Schleswig-Holstein, D-24105 Kiel, Germany
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Aoki K, Tanaka H, Kawahara T. Multiplexed Microsphere Suspension-Array Assay for Urine Mitochondrial DNA Typing by C-Stretch Length in Hypervariable Regions. J Clin Med Res 2018; 10:552-561. [PMID: 29904439 PMCID: PMC5997413 DOI: 10.14740/jocmr3302w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/10/2018] [Indexed: 11/11/2022] Open
Abstract
Background The standard method for personal identification and verification of urine samples in doping control is short tandem repeat (STR) analysis using nuclear DNA (nDNA). The DNA concentration of urine is very low and decreases under most conditions used for sample storage; therefore, the amount of DNA from cryopreserved urine samples may be insufficient for STR analysis. We aimed to establish a multiplexed assay for urine mitochondrial DNA typing containing only trace amounts of DNA, particularly for Japanese populations. Methods A multiplexed suspension-array assay using oligo-tagged microspheres (Luminex MagPlex-TAG) was developed to measure C-stretch length in hypervariable region 1 (HV1) and 2 (HV2), five single nucleotide polymorphisms (SNPs), and one polymorphic indel. Based on these SNPs and the indel, the Japanese population can be classified into five major haplogroups (D4, B, M7a, A, D5). The assay was applied to DNA samples from urine cryopreserved for 1 - 1.5 years (n = 63) and fresh blood (n = 150). Results The assay with blood DNA enabled Japanese subjects to be categorized into 62 types, exhibiting a discriminatory power of 0.960. The detection limit for cryopreserved urine was 0.005 ng of nDNA. Profiling of blood and urine pairs revealed that 5 of 63 pairs showed different C-stretch patterns in HV1 or HV2. Conclusions The assay described here yields valuable information in terms of the verification of urine sample sources employing only trace amounts of recovered DNA. However, blood cannot be used as a reference sample.
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Affiliation(s)
- Kimiko Aoki
- Anti-doping Research Laboratory, Japan Chemical Analysis Center, 6-39-4, Minami Senju, Arakawa-ku, Tokyo, 116-0003, Japan.,Nihon Pharmaceutical University, 10281, Komuro, Inamachi, Kitaadachi-gun, Saitama 362-0806, Japan
| | - Hiroyuki Tanaka
- Anti-doping Research Laboratory, Japan Chemical Analysis Center, 6-39-4, Minami Senju, Arakawa-ku, Tokyo, 116-0003, Japan
| | - Takashi Kawahara
- Anti-doping Research Laboratory, Japan Chemical Analysis Center, 6-39-4, Minami Senju, Arakawa-ku, Tokyo, 116-0003, Japan
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Ng HH, Ang HC, Hoe SY, Lim ML, Tai HE, Soh RCH, Syn CKC. Simple DNA extraction of urine samples: Effects of storage temperature and storage time. Forensic Sci Int 2018; 287:36-39. [PMID: 29627711 DOI: 10.1016/j.forsciint.2018.03.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 11/18/2022]
Abstract
Urine samples are commonly analysed in cases with suspected illicit drug consumption. In events of alleged sample mishandling, urine sample source identification may be necessary. A simple DNA extraction procedure suitable for STR typing of urine samples was established on the Promega Maxwell® 16 paramagnetic silica bead platform. A small sample volume of 1.7mL was used. Samples were stored at room temperature, 4°C and -20°C for 100days to investigate the influence of storage temperature and time on extracted DNA quantity and success rate of STR typing. Samples stored at room temperature exhibited a faster decline in DNA yield with time and lower typing success rates as compared to those at 4°C and -20°C. This trend can likely be attributed to DNA degradation. In conclusion, this study presents a quick and effective DNA extraction protocol from a small urine volume stored for up to 100days at 4°C and -20°C.
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Affiliation(s)
- Huey Hian Ng
- DNA Profiling Laboratory, Applied Sciences Group, Health Sciences Authority, 3 Biopolis Drive, 138623, Singapore.
| | - Hwee Chen Ang
- DNA Profiling Laboratory, Applied Sciences Group, Health Sciences Authority, 3 Biopolis Drive, 138623, Singapore
| | - See Ying Hoe
- DNA Profiling Laboratory, Applied Sciences Group, Health Sciences Authority, 3 Biopolis Drive, 138623, Singapore
| | - Mae-Lynn Lim
- DNA Profiling Laboratory, Applied Sciences Group, Health Sciences Authority, 3 Biopolis Drive, 138623, Singapore
| | - Hua Eng Tai
- DNA Profiling Laboratory, Applied Sciences Group, Health Sciences Authority, 3 Biopolis Drive, 138623, Singapore
| | - Richard Choon Hock Soh
- Central Narcotics Bureau, Ministry of Home Affairs, 393 New Bridge Road, 088763, Singapore
| | - Christopher Kiu-Choong Syn
- DNA Profiling Laboratory, Applied Sciences Group, Health Sciences Authority, 3 Biopolis Drive, 138623, Singapore
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Mendy M, Lawlor RT, van Kappel AL, Riegman PHJ, Betsou F, Cohen OD, Henderson MK. Biospecimens and Biobanking in Global Health. Clin Lab Med 2018; 38:183-207. [PMID: 29412882 PMCID: PMC11232505 DOI: 10.1016/j.cll.2017.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biobanks provide a critical infrastructure to support research in human health. Biospecimens and their accompanying data are increasingly needed to support biomedical research and clinical care. The original text was initially published in the Handbook for Cancer Research in Africa. The value of this publication is great as it underlines the importance of biobanks in Africa as a key resource to increase quality scientific research and participate in global health research. Therefore, a revision to extend these principles to other low resource contexts, to include updated material and references and add the topic of biobank sustainability were relevant.
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Affiliation(s)
- Maimuna Mendy
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, Lyon 69372, France
| | - Rita T Lawlor
- ARC-Net Applied Research on Cancer Centre, University of Verona, Piazzale LA Scuro 10, Verona 37134, Italy
| | | | - Peter H J Riegman
- Department of Pathology, Tissue Bank, Erasmus MC, Dr Molewaterplein 40, Rotterdam 3015, The Netherlands
| | - Fay Betsou
- Integrated BioBank of Luxembourg, 6 rue Nicolas Ernest Barble, Luxembourg L-1210, Luxembourg
| | - Oliver D Cohen
- AGEIS EA 7407 Laboratory, Medical School of Grenoble, Joseph Fourier University, Domaine de la Merci, La Tronche 38700, France
| | - Marianne K Henderson
- Center for Global Health, National Cancer Institute, NIH, DHHS, 9609 Medical Center Drive, Room 3W534, Bethesda, MD 20892, USA.
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8
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Jung M, Kristiansen G, Dietrich D. DNA Methylation Analysis of Free-Circulating DNA in Body Fluids. Methods Mol Biol 2018; 1708:621-641. [PMID: 29224167 DOI: 10.1007/978-1-4939-7481-8_32] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circulating cell-free DNA in body fluids is an analyte of great interest in basic and clinical research. The analyses of DNA methylation and hydroxymethylation patterns in body fluids might allow one to determine the certain state of a disease, in particular of cancer. DNA methylation biomarkers in liquid biopsies, i.e. blood plasma samples, may help optimizing personalized therapy for individual patients. DNA methylation analyses of specific loci usually require a bisulfite conversion of the DNA, which requires a sufficiently high amount of DNA at the appropriate concentration. However, free-circulating DNA is generally low concentrated. Therefore, high volumes of body fluids need to be analyzed. This high volume needs to be reduced in order to facilitate the bisulfite conversion. In addition, disease-related free-circulating DNA is even less abundant than normal DNA in the total amount of free-circulating DNA. Accordingly, analytical and pre-analytical methods are needed, which permit an accurate and sensitive quantification of single methylated DNA copies in the presence of unmethylated DNA in abundance.This protocol describes two methods for DNA enrichment from body fluids: DNA extraction by means of magnetic beads and polymer-mediated enrichment of DNA. Subsequent bisulfite conversion is achieved by means of a high-speed conversion protocol. Adaptions of the workflow required for the analysis of hydroxymethylation via oxidation 5-hydroxymethylcytosines to 5-formylcytosines prior to the bisulfite conversion are introduced. A quantitative real-time PCR based on the methylation-specific and HeavyMethyl PCR methodologies is introduced. This qPCR assay allows for an accurate and sensitive quantification of single copies of the DNA methylation biomarkers SHOX2 and SEPT9 in blood plasma. Specific issues regarding the analysis of body fluids and respective trouble shooting approaches are discussed.
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Affiliation(s)
- Maria Jung
- Institute of Pathology, University Hospital Bonn (UKB), Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Glen Kristiansen
- Institute of Pathology, University Hospital Bonn (UKB), Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Dimo Dietrich
- Institute of Pathology, University Hospital Bonn (UKB), Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
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White RM, Mitchell JM, Hart ED, Evans A, Meaders M, Norsworthy SE, Hayes ED, Flegel R, Maha GC, Shaffer MD, Hall EM, Rogers K. Assessment of the stability of DNA in specimens collected under conditions for drug testing-A pilot study. Forensic Sci Int 2017; 283:41-46. [PMID: 29248811 DOI: 10.1016/j.forsciint.2017.11.011] [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: 06/28/2017] [Revised: 09/23/2017] [Accepted: 11/06/2017] [Indexed: 10/18/2022]
Abstract
For forensic biological sample collections, the specimen donor is linked solidly to his or her specimen through a chain of custody (CoC) sometimes referenced as a chain of evidence. Rarely, a donor may deny that a urine or oral fluid (OF) specimen is his or her specimen even with a patent CoC. The goal of this pilot study was to determine the potential effects of short-term storage on the quality and quantity of DNA in both types of specimen under conditions that may be encountered with employment-related drug testing specimens. Fresh urine and freshly collected oral fluid all produced complete STR profiles. For the "pad" type OF collectors, acceptable DNA was extractable both from the buffer/preservative and the pad. Although fresh urine and OF produced complete STR profiles, partial profiles were obtained after storage for most samples. An exception was the DNA in the Quantisal OF collector, from which a complete profile was obtained for both freshly collected OF and stored OF.
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Affiliation(s)
- Robert M White
- RTI International, Center for Forensic Sciences, Bldg. 7, P.O. Box 12194, 3040 E. Cornwallis Road, Research Triangle Park, North Carolina 27709-2194, United States.
| | - John M Mitchell
- RTI International, Center for Forensic Sciences, Bldg. 7, P.O. Box 12194, 3040 E. Cornwallis Road, Research Triangle Park, North Carolina 27709-2194, United States
| | - E Dale Hart
- RTI International, Center for Forensic Sciences, Bldg. 7, P.O. Box 12194, 3040 E. Cornwallis Road, Research Triangle Park, North Carolina 27709-2194, United States
| | - Amy Evans
- RTI International, Center for Forensic Sciences, Bldg. 7, P.O. Box 12194, 3040 E. Cornwallis Road, Research Triangle Park, North Carolina 27709-2194, United States
| | - Meredith Meaders
- RTI International, Center for Forensic Sciences, Bldg. 7, P.O. Box 12194, 3040 E. Cornwallis Road, Research Triangle Park, North Carolina 27709-2194, United States
| | - Sarah E Norsworthy
- RTI International, Center for Forensic Sciences, Bldg. 7, P.O. Box 12194, 3040 E. Cornwallis Road, Research Triangle Park, North Carolina 27709-2194, United States
| | - Eugene D Hayes
- Substance Abuse and Mental Health Service Administration (SAMHSA/CBHSQ), Division of Workplace Programs, 5600 Fishers Lane, 16N02, Rockville, MD 20857, United States
| | - Ron Flegel
- Substance Abuse and Mental Health Service Administration (SAMHSA/CBHSQ), Division of Workplace Programs, 5600 Fishers Lane, 16N02, Rockville, MD 20857, United States
| | - George C Maha
- Laboratory Corporation of America Holdings, 1440 York Court, Burlington, North Carolina 27215-3361, United States
| | - Megan D Shaffer
- Laboratory Corporation of America Holdings, 1440 York Court, Burlington, North Carolina 27215-3361, United States
| | - Erin M Hall
- Laboratory Corporation of America Holdings, 1440 York Court, Burlington, North Carolina 27215-3361, United States
| | - Kelley Rogers
- Laboratory Corporation of America Holdings, 1440 York Court, Burlington, North Carolina 27215-3361, United States
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Soupé-Gilbert ME, Bierque E, Geroult S, Teurlai M, Goarant C. Continuous Excretion of Leptospira borgpetersenii Ballum in Mice Assessed by Viability Quantitative Polymerase Chain Reaction. Am J Trop Med Hyg 2017; 97:1088-1093. [PMID: 28722586 PMCID: PMC5637600 DOI: 10.4269/ajtmh.17-0114] [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] [Received: 02/14/2017] [Accepted: 05/14/2017] [Indexed: 12/22/2022] Open
Abstract
Rodents are the main reservoir animals of leptospirosis. In this study, we characterized and quantified the urinary excretion dynamics of Leptospira by Mus musculus infected with 2 × 108 virulent Leptospira borgpetersenii serogroup Ballum. Each micturition was collected separately in metabolic cages, at 12 time points from 7 to 117 days post-infection (dpi). We detected Leptospira in all urine samples collected (up to 8 per time point per mouse) proving that Leptospira excretion is continuous with ca. 90% live L. borgpetersenii Ballum, revealed by viability quantitative polymerase chain reaction. Microscopic visualization by Live/Dead fluorescence confirmed this high proportion of live bacteria and demonstrated that L. borgpetersenii Ballum are excreted, at least partly, as bacterial aggregates. We observed two distinct phases in the excretion dynamics, first an increase in Leptospira concentration shed in the urine between 7 and 63 dpi followed by a plateau phase from 63 dpi onward, with up to 3 × 107Leptospira per mL of urine. These two phases seem to correspond to progressive colonization of renal tubules first, then to stable cell survival and maintenance in kidneys. Therefore, chronically infected adult mice are able to contaminate the environment via urine at each micturition event throughout their lifetime. Because Leptospira excretion reached its maximum 2 months after infection, older rodents have a greater risk of contaminating their surrounding environment.
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Affiliation(s)
- Marie-Estelle Soupé-Gilbert
- Institut Pasteur International Network, Institut Pasteur in New Caledonia, Leptospirosis Research and Expertise Unit, Nouméa Cedex, New Caledonia
| | - Emilie Bierque
- Institut Pasteur International Network, Institut Pasteur in New Caledonia, Leptospirosis Research and Expertise Unit, Nouméa Cedex, New Caledonia
| | - Sophie Geroult
- Institut Pasteur International Network, Institut Pasteur in New Caledonia, Leptospirosis Research and Expertise Unit, Nouméa Cedex, New Caledonia
| | - Magali Teurlai
- Institut Pasteur International Network, Institut Pasteur in New Caledonia, Epidemiology and Infectious Research and Expertise Unit, Nouméa Cedex, New Caledonia
| | - Cyrille Goarant
- Institut Pasteur International Network, Institut Pasteur in New Caledonia, Leptospirosis Research and Expertise Unit, Nouméa Cedex, New Caledonia
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11
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Aoki K, Tanaka H, Ueki M. DNA typing for personal identification of urine after long-term preservation for testing in doping control. Drug Test Anal 2016; 9:1116-1123. [DOI: 10.1002/dta.2126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 10/21/2016] [Accepted: 10/21/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Kimiko Aoki
- Anti-Doping Research Laboratory, Japan Chemical Analysis Center; 6-39-4, Minami Senju, Arakawa-ku Tokyo 116-0003 Japan
- Nihon Pharmaceutical University; 10281, Komuro, Inamachi, Kitaadachi-gun Saitama 362-0806 Japan
| | - Hiroyuki Tanaka
- Anti-Doping Research Laboratory, Japan Chemical Analysis Center; 6-39-4, Minami Senju, Arakawa-ku Tokyo 116-0003 Japan
| | - Makoto Ueki
- Anti-Doping Research Laboratory, Japan Chemical Analysis Center; 6-39-4, Minami Senju, Arakawa-ku Tokyo 116-0003 Japan
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12
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Choong E, Schulze JJ, Ericsson M, Rane A, Ekström L. Discordant genotyping results using DNA isolated from anti-doping control urine samples. Drug Test Anal 2016; 9:994-1000. [DOI: 10.1002/dta.2103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/21/2016] [Accepted: 10/01/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Eva Choong
- Department Laboratory Medicine; Division of Clinical Pharmacology, Karolinska Institutet; Stockholm Sweden
| | - Jenny J Schulze
- Department Laboratory Medicine; Division of Clinical Pharmacology, Karolinska Institutet; Stockholm Sweden
| | - Magnus Ericsson
- Department Laboratory Medicine; Division of Clinical Pharmacology, Karolinska Institutet; Stockholm Sweden
| | - Anders Rane
- Department Laboratory Medicine; Division of Clinical Pharmacology, Karolinska Institutet; Stockholm Sweden
| | - Lena Ekström
- Department Laboratory Medicine; Division of Clinical Pharmacology, Karolinska Institutet; Stockholm Sweden
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13
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Yao W, Mei C, Nan X, Hui L. Evaluation and comparison of in vitro degradation kinetics of DNA in serum, urine and saliva: A qualitative study. Gene 2016; 590:142-8. [PMID: 27317895 DOI: 10.1016/j.gene.2016.06.033] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/12/2016] [Accepted: 06/14/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Cell-free DNA is naturally degraded in various bodily fluids. The aim of this study was to determine the degradation kinetics of DNA, with and without protein, in serum, urine and saliva. METHODS Naked DNA and DNA-protein complex were prepared, added to the samples to be analysed and incubated at 37°C and room temperature for various lengths of time. Alleles of 20 short tandem repeat loci were amplified from the incubated samples, and clearance models were generated from the mean peak areas. RESULTS Plotting the natural logarithm of DNA concentration against the incubation time produced a linear relationship. The half-lives of DNA with and without protein in serum were 157.6min and 30.8min at 37°C, 330.5min and 70.5min at room temperature, respectively. The half-lives of DNA with protein in saliva were 175.6min and 251.3min at 37°C and room temperature, respectively. However, the half-lives of DNA in urine (both with and without protein) were too short to detect. CONCLUSIONS The kinetics of DNA degradation in serum and saliva followed a first-order clearance model. Urine had the strongest effect on DNA degradation, and the half-lives of DNA with protein were relatively longer than those of naked DNA.
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Affiliation(s)
- Wang Yao
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China; Wuxi Maternal and Child Health Hospital Affiliated Nanjing Medical University, 214002 Wuxi, Jiangsu, China
| | - Chen Mei
- Dalian Blood Centre, Dalian, China
| | - Xiao Nan
- Dalian Blood Centre, Dalian, China
| | - Liu Hui
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China.
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El Bali L, Diman A, Bernard A, Roosens NHC, De Keersmaecker SCJ. Comparative study of seven commercial kits for human DNA extraction from urine samples suitable for DNA biomarker-based public health studies. J Biomol Tech 2015; 25:96-110. [PMID: 25365790 DOI: 10.7171/jbt.14-2504-002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at -20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies.
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Affiliation(s)
- Latifa El Bali
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and ; Louvain Center for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, Brussels, Belgium
| | - Aurélie Diman
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and
| | - Alfred Bernard
- Louvain Center for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, Brussels, Belgium
| | - Nancy H C Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and
| | - Sigrid C J De Keersmaecker
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium; and
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15
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Devesse L, Syndercombe Court D, Cowan D. Determining the authenticity of athlete urine in doping control by DNA analysis. Drug Test Anal 2015; 7:912-8. [DOI: 10.1002/dta.1785] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 01/23/2015] [Accepted: 02/12/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Laurence Devesse
- The Drug Control Centre; King's College London, Franklin-Wilkins Building; 150 Stamford Street London SE1 9NH UK
| | - Denise Syndercombe Court
- The Drug Control Centre; King's College London, Franklin-Wilkins Building; 150 Stamford Street London SE1 9NH UK
| | - David Cowan
- The Drug Control Centre; King's College London, Franklin-Wilkins Building; 150 Stamford Street London SE1 9NH UK
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Ammerlaan W, Trezzi JP, Mathay C, Hiller K, Betsou F. Method Validation for Preparing Urine Samples for Downstream Proteomic and Metabolomic Applications. Biopreserv Biobank 2014; 12:351-7. [DOI: 10.1089/bio.2014.0013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Jean-Pierre Trezzi
- Integrated BioBank of Luxemburg (IBBL), Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), Luxembourg
| | - Conny Mathay
- Integrated BioBank of Luxemburg (IBBL), Luxembourg
| | - Karsten Hiller
- Luxembourg Centre for Systems Biomedicine (LCSB), Luxembourg
| | - Fay Betsou
- Integrated BioBank of Luxemburg (IBBL), Luxembourg
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17
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Hilhorst M, Theunissen R, van Rie H, van Paassen P, Tervaert JWC. DNA extraction from long-term stored urine. BMC Nephrol 2013; 14:238. [PMID: 24168031 PMCID: PMC4231352 DOI: 10.1186/1471-2369-14-238] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 10/17/2013] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Traditionally, for DNA analyses, DNA is recovered from buffy coats. Since DNA in urine has been reported to deteriorate quickly, this option is often not considered. To complete our DNA database in patients with ANCA-associated vasculitis, we aimed to extract DNA from stored urine. METHODS Urine was stored at the time of kidney biopsy from patients included in our regional kidney biopsy database, who had given informed consent for further study. Urine was subsequently filtered, dialyzed, concentrated and freeze dried and finally resolubilized and centrifuged. DNA was extracted using the high pure PCR template preparation kit (Roche Diagnostics). Next, concentration and purity were determined by Nanodrop analysis and by Quant-iT analysis. RESULTS One hundred and eighty-one patients with ANCA-associated vasculitis were included. Of 114 patients (63%), DNA was available. From 53 of the remaining 67 patients, stored urine was available. Of the 53 samples that were processed, 46 (86.8%) yielded DNA with a mean concentration of 258.7 ng/μL (range 33.2-529) with a mean purity ratio of 1.81 (λ 260/280). CONCLUSION DNA extraction from fresh urine has been described before, yielding DNA usable for PCR analysis in healthy subjects. Storage of fresh urine at 4 °C or lower temperatures results in significant degradation of the DNA, making recovery of DNA more difficult with longer periods of storage. In the current study, we demonstrated that DNA could be retrieved from subsequently filtered, dialyzed, concentrated and freeze dried urine that was stored at room temperature. In addition, we demonstrated that this DNA could be used for PCR analysis. This method is useful when no other material from these patients is available.
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Affiliation(s)
| | | | | | | | - Jan Willem Cohen Tervaert
- Clinical & Experimental Immunology, Maastricht University, P,O, Box 5800, 6202 AZ Maastricht, The Netherlands.
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do Nascimento C, Muller K, Sato S, Albuquerque Junior RF. Effect of sample storage time on detection of hybridization signals in Checkerboard DNA–DNA hybridization. Can J Microbiol 2012; 58:502-6. [DOI: 10.1139/w2012-021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Long-term sample storage can affect the intensity of the hybridization signals provided by molecular diagnostic methods that use chemiluminescent detection. The aim of this study was to evaluate the effect of different storage times on the hybridization signals of 13 bacterial species detected by the Checkerboard DNA–DNA hybridization method using whole-genomic DNA probes. Ninety-six subgingival biofilm samples were collected from 36 healthy subjects, and the intensity of hybridization signals was evaluated at 4 different time periods: (1) immediately after collecting (n = 24) and (2) after storage at –20 °C for 6 months (n = 24), (3) for 12 months (n = 24), and (4) for 24 months (n = 24). The intensity of hybridization signals obtained from groups 1 and 2 were significantly higher than in the other groups (p < 0.001). No differences were found between groups 1 and 2 (p > 0.05). The Checkerboard DNA–DNA hybridization method was suitable to detect hybridization signals from all groups evaluated, and the intensity of signals decreased significantly after long periods of sample storage.
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Affiliation(s)
- Cássio do Nascimento
- Department of Dental Materials and Prosthodontics, Faculty of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Katia Muller
- Faculty of Dentistry, McGill University, Montréal, Quebec, Canada
| | - Sandra Sato
- Department of Dental Materials and Prosthodontics, Faculty of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Rubens Ferreira Albuquerque Junior
- Department of Dental Materials and Prosthodontics, Faculty of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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Shan Z, Zhou Z, Chen H, Zhang Z, Zhou Y, Wen A, Oakes KD, Servos MR. PCR-ready human DNA extraction from urine samples using magnetic nanoparticles. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 881-882:63-8. [DOI: 10.1016/j.jchromb.2011.11.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 11/15/2011] [Accepted: 11/27/2011] [Indexed: 11/28/2022]
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20
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Implications of storing urinary DNA from different populations for molecular analyses. PLoS One 2009; 4:e6985. [PMID: 19746164 PMCID: PMC2735781 DOI: 10.1371/journal.pone.0006985] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Accepted: 08/19/2009] [Indexed: 02/04/2023] Open
Abstract
Background Molecular diagnosis using urine is established for many sexually transmitted diseases and is increasingly used to diagnose tumours and other infectious diseases. Storage of urine prior to analysis, whether due to home collection or bio-banking, is increasingly advocated yet no best practice has emerged. Here, we examined the stability of DNA in stored urine in two populations over 28 days. Methodology Urine from 40 (20 male) healthy volunteers from two populations, Italy and Zambia, was stored at four different temperatures (RT, 4°C, −20°C & −80°C) with and without EDTA preservative solution. Urines were extracted at days 0, 1, 3, 7 and 28 after storage. Human DNA content was measured using multi-copy (ALU J) and single copy (TLR2) targets by quantitative real-time PCR. Zambian and Italian samples contained comparable DNA quantity at time zero. Generally, two trends were observed during storage; no degradation, or rapid degradation from days 0 to 7 followed by little further degradation to 28 days. The biphasic degradation was always observed in Zambia regardless of storage conditions, but only twice in Italy. Conclusion Site-specific differences in urine composition significantly affect the stability of DNA during storage. Assessing the quality of stored urine for molecular analysis, by using the type of strategy described here, is paramount before these samples are used for molecular prognostic monitoring, genetic analyses and disease diagnosis.
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Green C, Huggett JF, Talbot E, Mwaba P, Reither K, Zumla AI. Rapid diagnosis of tuberculosis through the detection of mycobacterial DNA in urine by nucleic acid amplification methods. THE LANCET. INFECTIOUS DISEASES 2009; 9:505-11. [DOI: 10.1016/s1473-3099(09)70149-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Chen JW, Uboh CE, Soma LR, Li X, Guan F, You Y. Microsatellite loci in urine supernatant and stored samples from racehorses. Am J Vet Res 2009; 70:648-57. [DOI: 10.2460/ajvr.70.5.648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Díaz S, Kienast ME, Villegas-Castagnasso EE, Pena NL, Manganare MM, Posik D, Peral-García P, Giovambattista G. Substitution of Human for Horse Urine Disproves an Accusation of Doping*. J Forensic Sci 2008; 53:1145-8. [DOI: 10.1111/j.1556-4029.2008.00797.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
This study examined the cellular origin and concentration of nuclear DNA in human urine. Ten subjects provided two entire, first-morning voids: one as a single specimen and one as a consecutive series of samples. The serial samples were centrifuged, organically extracted, and quantified by slot-blot analysis. Total DNA concentrations ranged from 0.02 to 21.3 ng/mL for the males and 25.0 to 96.9 ng/mL for the females. The female samples were found to contain numerous vaginal epithelial cells. DNA was detected in all of the serial samples of nine subjects; however, the DNA concentrations varied considerably. With six subjects, the DNA concentration of the first serial sample was at least three times greater than that of the entire void. DNA was only detected in the first 21% of the void from one male subject. The results of this study have implications for the collection of urine samples.
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Affiliation(s)
- Donald J Johnson
- School of Criminal Justice and Criminalistics, California State University, Los Angeles, CA 90032, USA.
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25
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Dash B, Afriyie-Gyawu E, Huebner HJ, Porter W, Wang JS, Jolly PE, Phillips TD. Determinants of the variability of aflatoxin-albumin adduct levels in Ghanaians. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2007; 70:58-66. [PMID: 17162498 DOI: 10.1080/15287390600748880] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Hepatocellular carcinoma (HCC) is a multifactorial disease with various host and environmental factors involved in its etiology. Of these, aflatoxin exposure has been established as an important risk factor in the development of HCC; the presence of aflatoxin-albumin (AA) adducts in the blood serves as a valuable biomarker of human exposure. In this study, the relationship between a variety of different HCC host factors and the incidence of AA adduct levels was examined in a Ghanaian population at high risk for HCC. These factors included age, gender, hepatitis virus B (HVB) and hepatitis C virus (HCV) status, and genetic polymorphisms in both microsomal epoxide hydrolase (mEH) and glutathione S-transferases (GSTs). Blood samples were analyzed for AA adducts and HBV and HCV status. GSTM1 and GSTT1 deletion polymorphisms and mEH exon 3 and exon 4 single-nucleotide polymorphisms (SNPs) were determined from urine samples. In univariate analysis, age, HBV and HVC status, and GSTT1 and mEH exon 3 genotypes were not associated with AA adduct levels. However, mean adduct levels were significantly higher in both females and individuals typed heterozygous for mEH exon 4 (vs. wild types). Stratification analysis also showed that gender along with mEH exon 4 genotype and HBV status had a significant effect on adduct levels. Both females typed HBsAg+ and males with mEH exon 4 heterozygote genotypes showed significantly higher adduct levels as compared to the HBsAg- and wild types, respectively. Understanding the relationships between these host factors and the variability in aflatoxin-adduct levels may help in identifying susceptible populations in developing countries and for targeting specific public health interventions for the prevention of aflatoxicoses in populations with HCC and chronic liver diseases.
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Affiliation(s)
- B Dash
- Faculty of Toxicology, Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
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HAUSKNECHT ROLAND, GULA ROMAN, PIRGA BARTOSZ, KUEHN RALPH. Urine - a source for noninvasive genetic monitoring in wildlife. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01622.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Dash B, Afriyie-Gyawu E, Huebner HJ, Porter W, Wang JS, Jolly PE, Phillips TD. Noninvasive identification of interindividual variation in xenobiotic-metabolizing enzymes: implications for cancer epidemiology and biomarker studies. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2006; 69:1203-16. [PMID: 16754536 DOI: 10.1080/15287390500354938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In this study, DNA extracted from frozen urine was used in the analysis of polymorphisms in genes coding for xenobiotic-metabolizing enzymes (XMEs). These included single-nucleotide polymorphisms (SNP) in microsomal epoxide hydrolase (mEH), that is, substitutions of tyrosine by histidine in codon 113 (Y113H) and histidine by arginine in codon 139 (H139R), and deletion polymorphisms in glutathione S-transferase (GST) M1 and T1 genes. The concentration of DNA extracted from urine of a Ghanaian population (n = 91) exposed to aflatoxins in their diet ranged from 82.5 to 573 ng/ml urine. Polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) procedures were used for the characterization of mEH polymorphisms, whereas a multiplex PCR method was utilized to identify GST deletion polymorphisms. In total, 91% and 94% of 91 samples were genotyped for mEH exon 3 and exon 4 polymorphisms, respectively. In the multiplex analysis of GST polymorphisms, 94% and 91% of 91 individuals were genotyped for GSTM1 and GSTT1 polymorphisms, respectively. The polymorphisms in the mEH exon 4, GSTM1 and GSTT1, were not in Hardy-Weinberg equilibrium (HWE) except for mEH exon 3. Representative genotypes identified by PCR-RFLP were cloned and sequenced, then confirmed by comparison with reference sequences of human DNA published in the GenBank BLAST database. These results demonstrate that XMEs can be genotyped from urine with reliable accuracy and may be useful in cancer and molecular epidemiology studies.
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Affiliation(s)
- B Dash
- Faculty of Toxicology, Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458, USA
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Giacomazzi S, Leroi F, Joffraud JJ. Comparison of three methods of DNA extraction from cold-smoked salmon and impact of physical treatments. J Appl Microbiol 2005; 98:1230-8. [PMID: 15836493 DOI: 10.1111/j.1365-2672.2005.02574.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To compare three bacterial DNA extraction procedures on cold-smoked salmon (CSS) and assess the impact on their efficiency of two physical treatments of the food matrix, ionizing irradiation and freezing. METHODS AND RESULTS As molecular methods for bacterial detection have become an important analytical tool, we compared bacterial DNA extraction procedures on CSS. Working with frozen and irradiated CSS, we obtained negative responses from samples known to be highly contaminated. Thus, we decided to study the impact of these two physical treatments on bacterial DNA extraction procedures. The efficiency of bacterial DNA extraction directly from the fish matrix suspension was measured by an rpoB PCR-based reaction. The results demonstrated that the DNeasy tissue extraction kit (Qiagen, Courtaboeuf, France) was the most efficient and reproducible method. We also showed that freezing and ionizing irradiation have a negative impact on DNA extraction. This was found probably not to be due to inhibition as the PCR reaction remained negative after adding BSA to the PCR mix reaction. CONCLUSIONS The extraction kit was the most efficient method. Physical treatments were shown to hamper bacterial DNA extraction. SIGNIFICANCE AND IMPACT OF THE STUDY Attention must be paid to molecular bacterial detection on food products subject to freezing or to ionizing irradiation.
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Affiliation(s)
- S Giacomazzi
- Laboratoire de Génie Alimentaire, IFREMER Nantes, Rue de l'Ile d'Yeu, Nantes cedex, France
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A Simple Method of DNA Extraction and STR Typing from Urine Samples Using a Commercially Available DNA/RNA Extraction Kit. J Forensic Sci 2003. [DOI: 10.1520/jfs2002184] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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van der Hel OL, van der Luijt RB, Bueno de Mesquita HB, van Noord PAH, Slothouber B, Roest M, van der Schouw YT, Grobbee DE, Pearson PL, Peeters PHM. Quality and quantity of DNA isolated from frozen urine in population-based research. Anal Biochem 2002; 304:206-11. [PMID: 12009697 DOI: 10.1006/abio.2002.5634] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In several population-based studies in the past urine samples were collected and stored for future research. We set out to determine the reliability of using such samples for genotyping DNA markers in epidemiologic research. A source of DNA extracted from exfoliated nucleated cells in urine is provided by the DOM cohort, in which specimens were collected 15-25 years ago. We have examined the quality of the DNA in 48 of these samples by measuring the amount of DNA isolated and its ability to provide an adequate PCR template for amplicons of different lengths. MTHFR polymorphism was analyzed in 644 specimens to determine the inter- and intraobserver reproducibility. Although the DNA amount was variable, 26 to 89% of the samples, depending both on the length of the PCR amplicon and on PCR conditions, yielded a visible PCR product. The intra- and interobserver agreements were comparable (kappa 0.86 and 0.88, respectively). Our results demonstrate that frozen urine samples can be used for DNA typing studies in women after prolonged periods of storage, but with sometimes unpredictable results. Ultimately, the genotype success rate was 89.3%. Urine collection can be considered as a useful method of obtaining DNA in large cohort studies and other circumstances when blood samples cannot be obtained or have not been stored.
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Affiliation(s)
- Olga L van der Hel
- Julius Center for General Practice and Patient Oriented Research, University Medical Center, 3508 GA Utrecht, The Netherlands.
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Affiliation(s)
- T A Brettell
- Forensic Science Bureau, New Jersey State Police, West Trenton 08628, USA
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Valiere N, Taberlet P. Urine collected in the field as a source of DNA for species and individual identification. Mol Ecol 2000; 9:2150-2. [PMID: 11123627 DOI: 10.1046/j.1365-294x.2000.11142.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- N Valiere
- Laboratoire de Biologie des Populations d'Altitude, CNRS UMR 5553, Université Joseph Fourier, F-38041 Grenoble Cedex 9, France
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