1
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Van Caenegem W, Haelewaters D. New insights into the DNA extraction and PCR amplification of minute ascomycetes in the genus Laboulbenia (Pezizomycotina, Laboulbeniales). IMA Fungus 2024; 15:14. [PMID: 38863065 PMCID: PMC11167896 DOI: 10.1186/s43008-024-00146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in axenic culture, and lack of reliable and cost-efficient DNA extraction protocols. In particular, the genus Laboulbenia is notorious for low success with DNA extraction and polymerase chain reaction (PCR) amplification. This is attributed to the presence of melanin, a molecule known to inhibit PCR, in the cells. We evaluated the efficacy of a standard single cell-based DNA extraction protocol by halving the recommended amount of reagents to reduce the cost per extraction and adding bovine serum albumin (BSA) during the multiple displacement amplification step to reverse the effect of melanin. A total of 196 extractions were made, 111 of which were successful. We found that halving the reagents used in the single cell-based extraction kit did not significantly affect the probability of successful DNA extraction. Using the halved protocol reduces cost and resource consumption. Moreover, there was no significant difference in the probability of successfully extracting DNA based on whether BSA was added or not, suggesting that the amount of melanin present in cells of the thallus has no major inhibitory effect on PCR. We generated 277 sequences from five loci, but amplification of the internal transcribed spacer region, the mitochondrial small subunit rDNA, and protein-coding genes remains challenging. The probability of successfully extracting DNA from Laboulbeniales was also impacted by specimen storage methods, with material preserved in > 95% ethanol yielding higher success rates compared to material stored in 70% ethanol and dried material. We emphasize the importance of proper preservation of material and propose the design of Laboulbeniales-specific primers to overcome the problems of primer mismatches and contaminants. Our new insights apply not only to the genus Laboulbenia; Laboulbeniales generally are understudied, and the vast majority of species remain unsequenced. New and approachable molecular developments will benefit the study of Laboulbeniales, helping to elucidate the true diversity and evolutionary relationships of these peculiar microfungi.
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Affiliation(s)
- Warre Van Caenegem
- Research Group Mycology, Department of Biology, Ghent University, Ghent, 9000, Belgium.
| | - Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, Ghent, 9000, Belgium.
- Meise Botanic Garden, Meise, 1860, Belgium.
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic.
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3
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Hymus CM, Baxter FO, Ta H, Tran T, de Sousa C, Mountford NS, Tay JW. A comparison of six adhesive tapes as tape lifts for efficient trace DNA recovery without the transfer of PCR inhibitors. Leg Med (Tokyo) 2024; 67:102330. [PMID: 37802731 DOI: 10.1016/j.legalmed.2023.102330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
Tape-lifting is a non-destructive method employed in the laboratory to recover and collect trace DNA evidence from crime scene exhibits with porous surfaces. The success of tape-lifting is a balance between capturing the biological material and compatibility with downstream DNA extraction processes to ensure efficient release of the tape-lifted material during DNA extraction. In this study, six commercially available low-, regular- and high-tack adhesive tapes were evaluated. The low-tack S183 tape and the highly adhesive S-Hold tape were compared for DNA recovery efficiency from different materials commonly encountered in casework. All tape-lifts were processed using PrepFiler Express™ BTA and AutoMate Express™ Forensic DNA extraction systems, DNA samples quantitated by Quantifiler TRIO, amplified using Powerplex® 21 and VeriFiler™ PLUS (VFP), and analysed on a 3500xl genetic analyser to evaluate the quality of the resultant STR profiles obtained. The more adhesive S-Hold tape recovered comparable or more DNA than the low-tack S183 tape from the majority of materials tested. However, STR profiles obtained from S183 tape-lifts were of markedly higher quality compared to S-Hold tape-lifts. This was most evident for towel, denim and printed chiffon, where S-Hold samples exhibited severe PCR inhibition, with VFP internal quality markers confirming the presence of inhibitors. The findings suggest that strong adhesion is not necessarily beneficial for tape-lifting, as the low tack S183 tape was able to efficiently recover cellular material from the surface of porous substrates commonly encountered in casework, while avoiding the co-transfer of PCR-inhibitory substances from the sampled material.
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Affiliation(s)
- Colby M Hymus
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Fiona O Baxter
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Hoan Ta
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Teresa Tran
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Clare de Sousa
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Nicholas S Mountford
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia
| | - Jasmine W Tay
- Forensic Biology Department, PathWest Laboratory Medicine, Western Australia, Australia.
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4
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Haarkötter C, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Saiz M, Lorente JA, Álvarez JC. A comparison of five DNA extraction methods from degraded human skeletal remains. Forensic Sci Int 2023; 348:111730. [PMID: 37224759 DOI: 10.1016/j.forsciint.2023.111730] [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: 03/24/2023] [Revised: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023]
Abstract
Extracting DNA from degraded human remains poses a challenge for any forensic genetics laboratory, as it requires efficient high-throughput methods. While little research has compared different techniques, silica in suspension has been identified in the literature as the best method for recovering small fragments, which are often present in these types of samples. In this study, we tested five DNA extraction protocols on 25 different degraded skeletal remains. Including the humerus, ulna, tibia, femur, and petrous bone. The five protocols were organic extraction by phenol/chloroform/isoamyl alcohol, silica in suspension, High Pure Nucleic Acid Large Volume silica columns (Roche), InnoXtract™ Bone (InnoGenomics), and PrepFiler™ BTA with AutoMate™ Express robot (ThermoFisher). We analysed five DNA quantification parameters (small human target quantity, large human target quantity, human male target quantity, degradation index, and internal PCR control threshold), and five DNA profile parameters (number of alleles with peak height higher than analytic and stochastic threshold, average relative fluorescence units (RFU), heterozygous balance, and number of reportable loci) were analysed. Our results suggest that organic extraction by phenol/chloroform/isoamyl alcohol was the best performing method in terms of both quantification and DNA profile results. However, Roche silica columns were found to be the most efficient method.
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Affiliation(s)
- Christian Haarkötter
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - Xiomara Gálvez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain.
| | - Diana C Vinueza-Espinosa
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - María Isabel Medina-Lozano
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - María Saiz
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - José Antonio Lorente
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - Juan Carlos Álvarez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
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5
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Bandehpour M, Dehghani N, Jaliani HZ, Asadi-Saghandi A. Modified Phenol/Chloroform-Free DNA Isolation from Yeast and Other Fungi by Non-Enzymatic Salting Out Method. Curr Protoc 2023; 3:e749. [PMID: 37097192 DOI: 10.1002/cpz1.749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
The most commonly used fungal DNA extraction techniques require enzymatic digestion or hazardous chemicals. Here, we describe a quick non-enzymatic salt-out method that we developed for isolating high-quality DNA from various fungal species. DNA was extracted from four species of typical fungi, including Saccharomyces cerevisiae, Hansenula polymorpha, Candida albicans, and Aspergillus flavus. Results that we obtained from agarose gel electrophoresis and spectrophotometry verified the integrity, high quality, and purity of the extracted DNAs. Also, PCR amplification and restriction enzyme digestion confirmed the efficiency of the extracted DNAs in molecular biology applications. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Yeast and fungal cultivation for DNA extraction Basic Protocol 2: Modified salting out DNA extraction protocol Support Protocol 1: PCR amplification of extracted genomes Support Protocol 2: Digestion with restriction enzyme.
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Affiliation(s)
- Mojgan Bandehpour
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Niloofar Dehghani
- Department of Advanced Medical Sciences and Technologies, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hossein Zarei Jaliani
- Protein Engineering Laboratory, Department of Medical Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Abolghasem Asadi-Saghandi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Advanced Medical Sciences and Technologies, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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6
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Optimization of an approach to detect low-concentration MNV-1 and HAV from soil-rich or non-soil post-washing water containing various PCR inhibitory substances. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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7
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Liu Z, Simayijiang H, Wang Q, Yang J, Sun H, Wu R, Yan J. DNA and protein analyses of hair in forensic genetics. Int J Legal Med 2023; 137:613-633. [PMID: 36732435 DOI: 10.1007/s00414-023-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China.
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8
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Forsberg J, Ayoub C. Differential Extraction with Purification via Organic/Microcon ® and Promega DNA IQ™ Methods. Methods Mol Biol 2023; 2685:103-117. [PMID: 37439978 DOI: 10.1007/978-1-0716-3295-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The differential extraction method allows for the separation of sperm cell DNA from non-sperm cell DNA by incorporating two separate lysis steps. This is crucial in forensic casework, as sexual assault samples frequently deal with a mixture of seminal fluid and other body fluids. After performing a differential lysis, DNA extraction can be completed through a variety of methods. In addition to the differential lysis, two methods will be described in this chapter for DNA purification: Organic (Phenol)/Microcon® purification and purification with the Promega DNA IQ™ System.
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Affiliation(s)
| | - Caitlin Ayoub
- Virginia Department of Forensic Science, Richmond, VA, USA
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9
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Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution. Microbiol Spectr 2022; 10:e0225522. [PMID: 36377933 PMCID: PMC9769501 DOI: 10.1128/spectrum.02255-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The major aquatic interface between host and environment in teleost finfish species is the gill. The diversity of this infraclass, high complexity of the organ, and its direct exposure to the surrounding environment make it an ideal candidate for furthering our understanding of the intertwined relationships between host and microbiome. Capturing the structure and diversity of bacterial communities from this low-biomass, inhibitor-rich tissue can, however, prove challenging. Lessons learned in doing so are directly applicable to similar sample types in other areas of microbiology. Through the development of a quantitative PCR assay for both host material and 16S rRNA genes, we tested and developed a robust method for low-biomass sample collection which minimized host DNA contamination. Quantification of 16S rRNA facilitated not only the screening of samples prior to costly library construction and sequencing but also the production of equicopy libraries based on 16S rRNA gene copies. A significant increase in diversity of bacteria captured was achieved, providing greater information on the true structure of the microbial community. Such findings offer important information for determining functional processes. Results were confirmed across fresh, brackish, and marine environs with four different fish species, with results showing broad homology between samples, demonstrating the robustness of the approach. Evidence presented is widely applicable to samples similar in composition, such as sputum or mucus, or those that are challenging due to the inherent inclusion of inhibitors. IMPORTANCE The interaction between the fish gill and surrounding bacteria-rich water provides an intriguing model for examining the interaction between the fish, free-floating bacteria, and the bacterial microbiome on the gill surface. Samples that are inherently low in bacteria, or that have components that inhibit the ability to produce libraries that identify the components of microbial communities, present significant challenges. Gill samples present both of these types of challenges. We developed methods for quantifying both the bacterial and host DNA material and established a sampling method which both reduced inhibitor content and maximized bacterial diversity. By quantifying and normalizing bacteria prior to library construction, we showed significant improvements with regards to the fidelity of the final data. Our results support wide-ranging applications for analyzing samples of similar composition, such as mucus and sputum, in other microbiological spheres.
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10
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Zhou Y, Cui W, Wu B, Zhu B. Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination. Electrophoresis 2022; 43:1899-1910. [PMID: 35856743 DOI: 10.1002/elps.202100313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/28/2022] [Accepted: 07/08/2022] [Indexed: 12/14/2022]
Abstract
In an attempt to increase the discrimination capacity (DC) and reduce the adventitious match probability, a 6-dye multiplex Y-chromosomal short tandem repeat (Y-STR) panel named Y34plex was constructed that combined 25 Y-chromosomal markers (DYS456, DYS627, DYS390, DYS570, DYS635, DYS385a/b, DYS448, DYS437, DYS533, DYS449, DYS481, DYS392, DYS391, DYS389I, DYS460, YGATAH4, DYS438, DYS389II, DYS19, DYS458, DYF387S1a/b, DYS439, DYS393, DYS576, and DYS518) in widely used commercial kits, with nine highly polymorphic Y-STR loci (DYS557, DYS527a/b, DYS593, DYS444, DYS596, DYS643, DYS447, DYS549, and DYS645). The Y34plex is a promising type system to distinguish both unrelated and related male individuals due to the incorporation of rapidly mutated Y-STR loci. A validation study of the Y34plex was performed and followed the guidelines of the Scientific Working Group on DNA analysis methods. Results show that full Y-STR profiles were obtained from male/female DNA mixtures with 125 pg of male DNA in the presence of 50 ng of female DNA. The ability to tolerate polymerase chain reaction inhibitors commonly contained in forensic casework samples demonstrated the applicability and robustness of the Y34plex. Compared with the Yfiler Plus kit, the novel panel showed an increased power of discrimination in Chinese Wuxi Han population (n = 434). The overall haplotype diversity of the Y34plex was 0.999606, whereas DC value was 0.956221, which is suitable for use on forensic paternal investigation.
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Affiliation(s)
- Yongsong Zhou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China
| | - Bofeng Zhu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, P. R. China
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11
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Development of an effective method of human DNA extraction from soil as forensic evidence. Forensic Sci Int 2022; 335:111284. [DOI: 10.1016/j.forsciint.2022.111284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/21/2022]
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12
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Dronina J, Samukaite-Bubniene U, Ramanavicius A. Advances and insights in the diagnosis of viral infections. J Nanobiotechnology 2021; 19:348. [PMID: 34717656 PMCID: PMC8556785 DOI: 10.1186/s12951-021-01081-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.
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Affiliation(s)
- Julija Dronina
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Urte Samukaite-Bubniene
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Arunas Ramanavicius
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania.
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13
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Liu C, Huang D, Yang L, Wu S, Shen X, Pedersen-Bjergaard S, Huang C. Removal of Polymerase Chain Reaction Inhibitors by Electromembrane Extraction. Anal Chem 2021; 93:11488-11496. [PMID: 34383461 DOI: 10.1021/acs.analchem.1c01689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polymerase chain reaction (PCR) technology has become the cornerstone of DNA analysis. However, special samples (e.g., forensic samples, soil, food, and mineral medicine) may contain powerful PCR inhibitors. High levels of inhibitors can hardly be sufficiently removed by conventional DNA extraction approaches and may result in the complete failure of PCR. In this work, the removal of PCR inhibitors by electromembrane extraction (EME) was investigated for the first time. To demonstrate the universality of the approach, EME formats with and without supported membranes (termed parallel-EME and μ-EME, respectively) were employed, and both anionic [humic acid (HA)] and cationic (Ca2+) PCR inhibitors were used as models. During EME, charged inhibitors in the sample migrate into the liquid membrane in the presence of an electric field and might further leech into the waste solution, while PCR analytes remain in the sample. After EME, the clearance values for HA at 0.2 and 2.5 mg mL-1 were 94 and 85%, respectively, and that for Ca2+ (275 mM) was 63%. Forensic PCR-short tandem repeat (PCR-STR) genotyping showed that EME significantly reduced the interference by HA in PCR-STR analysis and displayed a higher HA purge capability compared to existing methods. Furthermore, by combining EME with liquid-liquid extraction or solid-phase extraction, satisfactory STR profiles were obtained from HA-rich blood samples. In addition, false-negative reports of bacterial detection in mineral medicine and shrimps were avoided after the removal of Ca2+ by μ-EME. Our research demonstrates the great potential of EME for the purification of DNA samples containing high-level PCR inhibitors and opens up a new application direction for EME.
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Affiliation(s)
- Cong Liu
- Department of Forensic Medicine, Huazhong University of Science and Technology, Hangkong Road #13, Wuhan 430030, China
| | - Daixin Huang
- Department of Forensic Medicine, Huazhong University of Science and Technology, Hangkong Road #13, Wuhan 430030, China
| | - Liuqian Yang
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Hangkong Road #13, Wuhan 430030, China
| | - Shifan Wu
- Department of Forensic Medicine, Huazhong University of Science and Technology, Hangkong Road #13, Wuhan 430030, China
| | - Xiantao Shen
- State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Hangkong Road #13, Wuhan 430030, China
| | - Stig Pedersen-Bjergaard
- School of Pharmacy, University of Oslo, P.O. Box 1068 Blindern, Oslo 0316, Norway.,Faculty of Health and Medical Sciences, School of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Chuixiu Huang
- Department of Forensic Medicine, Huazhong University of Science and Technology, Hangkong Road #13, Wuhan 430030, China
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14
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Koprinarova M. Methods To Improve Molecular Detection of Salmonella in Complex Herbal Matrices Containing Inhibitors. J Food Prot 2021; 84:1309-1314. [PMID: 33561204 DOI: 10.4315/jfp-20-262] [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: 07/05/2020] [Accepted: 02/06/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Salmonella is one of the main causes of foodborne diseases worldwide. Molecular tests such as the PCR assay are rapid and sensitive and are increasingly becoming the preferred method for pathogen detection. However, the presence in the analyzed samples of substances that reduce the sensitivity of the assay or totally inhibit PCR amplification might result in failure of pathogen detection. Using a multiplex real-time PCR assay, I investigated the detection of Salmonella enterica serovar Typhimurium in three herbal matrices containing inhibiting substances: (i) chamomile (Matricaria recutita), (ii) sage (Salvia officinalis), and (iii) mint (Menthae piperitae). Internal positive controls in the multiplex PCR reactions indicated the degree of inhibition. All three herbs inhibited PCR amplification at the standard matrix concentration (10% suspension). I applied and compared four approaches for overcoming the negative effect of the matrices on the PCR detection of Salmonella. The efficiency strongly depended on the matrix and the method used for removing the inhibitory substances. By using a series of centrifugation steps combined with a direct PCR, I removed the PCR inhibitors and successfully detected the pathogen in each of the tested matrices. This approach did not significantly decrease the sensitivity of the PCR assay, and the detection of the pathogen was with a quantification cycle delay of only 1.48 ± 1.05 cycles compared with the control. Thus, the proposed simple, efficient, reliable, quick, and cost-effective method allowed for removal of PCR inhibitors and subsequent detection of foodborne bacterial pathogens in complex matrices containing PCR inhibitors. HIGHLIGHTS
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Affiliation(s)
- Miglena Koprinarova
- Institute of Molecular Biology "Acad. Roumen Tsanev," Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
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15
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Buchner D, Beermann AJ, Leese F, Weiss M. Cooking small and large portions of “biodiversity‐soup”: Miniaturized DNA metabarcoding PCRs perform as good as large‐volume PCRs. Ecol Evol 2021. [DOI: 10.1002/ece3.7753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Dominik Buchner
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
| | - Arne J. Beermann
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
| | - Florian Leese
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
| | - Martina Weiss
- Aquatic Ecosystem Research University of Duisburg‐Essen Essen Germany
- Centre for Water and Environmental Research (ZWU) University of Duisburg‐Essen Essen Germany
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16
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De Smet M, Ramaekers K, Verhoeven E, Vermeulen S, Bekaert B. Influence of ink and smoke ATM security systems on dactyloscopy and subsequent DNA analysis after detonation. Forensic Sci Int Genet 2021; 54:102540. [PMID: 34111720 DOI: 10.1016/j.fsigen.2021.102540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/04/2021] [Accepted: 05/25/2021] [Indexed: 11/28/2022]
Abstract
Automated Teller Machine bombings are an increasing societal problem that are often committed using Improvised Explosive Devices. The evolution in IEDs and the negative consequences for society require new security measures to prevent these crimes. Ink staining and security smoke devices are added to cash cassettes, in order to protect ATMs and prevent ATM bombings. Traces found at crime scenes, such as fingerprints and DNA, can contribute to the identification of perpetrators. However, the effect of ink staining and security smoke devices on dactyloscopy and DNA profiling is still unknown. In the current study, we demonstrate that procedures using Citrus Cleaner or sulfosalicylic acid were successful in removing ink and security smoke deposited on plastic plates but did result in the massive loss of fingerprint information as only a low number (4%) of good quality fingerprints were recovered after smoke contamination. Secondly, security ink Sun Blue ES2, but not SICPA Green and Sun Blue ES1, had a significant impact on DNA profiling success. DNA concentrations obtained from blood spiked swabs decreased with increasing ink concentration resulting in a complete loss of genotype information with the addition of ≥10 μl Sun Blue ES2. No noticeable PCR inhibition or DNA degradation was detected during quantification, but a decreased efficiency of DNA extraction could not be excluded. Security smoke, on the other hand, does not seem to have a significant influence on DNA analysis. Precautions must therefore be taken in order to avoid contaminating DNA swabs with ink during sampling. Thirdly, only a single negative impression of a glove in ink and a single glove print were able to be visualized with white fingerprint powder on detonated cash cassettes. In conclusion, the detection of glove prints and fingerprints is limited and security ink, contrary to smoke, after detonation can have a negative influence on downstream DNA analysis procedures.
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Affiliation(s)
- Margot De Smet
- KU Leuven - University of Leuven, Department of Imaging and Pathology, Leuven, Belgium
| | - Kato Ramaekers
- KU Leuven - University of Leuven, Department of Imaging and Pathology, Leuven, Belgium
| | - Elke Verhoeven
- Technical and Scientific Police, Federal Judicial Police, Leuven, Belgium
| | - Steve Vermeulen
- Technical and Scientific Police, Federal Judicial Police, Leuven, Belgium
| | - Bram Bekaert
- KU Leuven - University of Leuven, Department of Imaging and Pathology, Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium.
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17
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Integration of microfluidic sample preparation with PCR detection to investigate the effects of simultaneous DNA-Inhibitor separation and DNA solution exchange. Anal Chim Acta 2021; 1160:338449. [PMID: 33894958 DOI: 10.1016/j.aca.2021.338449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/23/2021] [Accepted: 03/21/2021] [Indexed: 11/20/2022]
Abstract
In this paper, we applied a curved-channel microfluidic device to separate DNA from PCR-inhibitor-containing water and simultaneously wash them into clean water for detection using a portable PCR thermocycler. Environmental DNA (eDNA) sampling has become an effective surveying approach for detecting rare organisms. However, low concentration eDNA molecules may be masked by PCR inhibitors during amplification and detection, increasing the risk of false negatives. Therefore, technologies for on-site DNA separation and washing are urgently needed. Our device consisted of a half-circle microchannel with a DNA-inhibitor sample inlet, a clean buffer inlet, and multiple outlets. By using the flow-induced inertial forces, 10 μm DNA-conjugated microparticles were focused at the inner-wall of the curved microchannel while separation from 1 μm inhibitor-conjugated microparticles and DNA washing were achieved simultaneously with the Dean flow. We achieved singleplex focusing, isolation and washing of 10 μm particles at an efficiency of 94.5 ± 2.0%. In duplex experiments with 1 μm and 10 μm particles, larger particles were washed with an efficiency of 92.1 ± 1.6% and a purity of 79 ± 2%. By surface-functionalizing the microparticles with affinity groups against Atlantic salmon DNA and humic acid (HA), and processing samples of various concentrations in our device, we achieved an effective purification and detection of DNA molecules using the portable PCR thermocycler. Our method significantly decreased PCR quantitation cycles from Cq > 38 to Cq = 30.35 ± 0.5, which confirmed enhancement of PCR amplification. The proposed device takes a promising step forward in sample preparation towards an integrated device that can be used for simultaneous purification and solution exchange of DNA in point-of-need environmental monitoring applications.
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18
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Takasaki K, Aihara H, Imanaka T, Matsudaira T, Tsukahara K, Usui A, Osaki S, Doi H. Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding. PLoS One 2021; 16:e0250162. [PMID: 33961651 PMCID: PMC8104373 DOI: 10.1371/journal.pone.0250162] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/01/2021] [Indexed: 11/19/2022] Open
Abstract
Environmental DNA (eDNA) analysis is a novel approach for biomonitoring and has been mostly used in clear water. It is difficult to detect eDNA in turbid water as filter clogging occurs, and environmental samples contain various substances that inhibit the polymerase chain reaction (PCR) and affect the accuracy of eDNA analysis. Therefore, we applied a pre-filtration method to better detect the fish species (particularly pale chub, Opsariichthys platypus) present in a water body by measuring eDNA in environmental samples containing PCR inhibitors. Upon conducting 12S rRNA metabarcoding analysis (MiFish), we found that pre-filtration did not affect the number or identities of fish species detected in our samples, but pre-filtration through pore sizes resulted in significantly reduced variance among replicate samples. Additionally, PCR amplification was improved by the pre-filtration of environmental samples containing PCR inhibitors such as humic substances. Although this study may appear to be a conservative and ancillary experiment, pre-filtration is a simple technique that can not only improve the physical properties of water, such as turbidity, but also the quality of eDNA biomonitoring.
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Affiliation(s)
- Kazuto Takasaki
- Research and Development Division, FASMAC Co., Ltd., Atsugi, Kanagawa, Japan
| | - Hiroki Aihara
- Biotechnological Research Support Division, FASMAC Co., Ltd., Atsugi, Kanagawa, Japan
| | - Takanobu Imanaka
- Biotechnological Research Support Division, FASMAC Co., Ltd., Atsugi, Kanagawa, Japan
| | - Takahiro Matsudaira
- Biotechnological Research Support Division, FASMAC Co., Ltd., Atsugi, Kanagawa, Japan
| | - Keita Tsukahara
- Biotechnological Research Support Division, FASMAC Co., Ltd., Atsugi, Kanagawa, Japan
| | - Atsuko Usui
- Biotechnological Research Support Division, FASMAC Co., Ltd., Atsugi, Kanagawa, Japan
| | - Sora Osaki
- Biotechnological Research Support Division, FASMAC Co., Ltd., Atsugi, Kanagawa, Japan
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, Kobe, Hyogo, Japan
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19
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Huang C, Mahboubat BY, Ding Y, Yang Q, Wang J, Zhou M, Wang X. Development of a rapid Salmonella detection method via phage-conjugated magnetic bead separation coupled with real-time PCR quantification. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Assurian A, Murphy H, Shipley A, Cinar HN, DA Silva A, Almeria S. Assessment of Commercial DNA Cleanup Kits for Elimination of Real-Time PCR Inhibitors in the Detection of Cyclospora cayetanensis in Cilantro. J Food Prot 2020; 83:1863-1870. [PMID: 32722800 DOI: 10.4315/jfp-20-139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/09/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT Inhibited reactions have occasionally been observed when cilantro samples were processed for the detection of Cyclospora cayetanensis using quantitative real-time PCR (qPCR). Partial or total inhibition of PCR reactions, including qPCR, can occur, leading to decreased sensitivity or false-negative results. If inhibition occurs, this implies the need for additional purification or cleanup treatments of the extracted DNA to remove inhibitors prior to molecular detection. Our objective was to evaluate the performance of five commercial DNA cleanup kits (QIAquick purification kit from Qiagen [kit 1], OneStep PCR inhibitor removal by Zymo Research [kit 2], NucleoSpin genomic DNA cleanup XS from Macherey-Nagel [kit 3], DNA IQ system by Promega [kit 4], and DNeasy PowerPlant pro kit from Qiagen [5]) to minimize qPCR inhibition using the U.S. Food and Drug Administration-validated Bacteriological Analytical Manual (BAM) Chapter 19b method for detection of C. cayetanensis in cilantro samples containing soil. Each of the five commercial DNA cleanup kits evaluated was able to reduce the qPCR internal amplification control cycle threshold values to those considered to be normal for noninhibited samples, allowing unambiguous interpretation of results in cilantro samples seeded at both a high oocyst level (200 oocysts) and a low oocyst level (10 oocysts). Of the five kits compared, kits 1, 2, and 3 did not show significant differences in the detection of C. cayetanensis, while significantly higher cycle threshold values, indicating lower recovery of the target DNA, were observed from kits 4 and/or 5 in samples seeded with 200 and 10 oocysts (P < 0.05). This comparative study provides recommendations on the use of commercial cleanup kits which could be implemented when inhibition is observed in the detection of C. cayetanensis in cilantro samples using the BAM Chapter 19b method. HIGHLIGHTS
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Affiliation(s)
- Angela Assurian
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, Maryland 20740
| | - Helen Murphy
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, 8301 Muirkirk Road, Laurel, Maryland 20805, USA
| | - Alicia Shipley
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, Maryland 20740
| | - Hediye Nese Cinar
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, 8301 Muirkirk Road, Laurel, Maryland 20805, USA
| | - Alexandre DA Silva
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, 8301 Muirkirk Road, Laurel, Maryland 20805, USA
| | - Sonia Almeria
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, 8301 Muirkirk Road, Laurel, Maryland 20805, USA.,(ORCID: https://orcid.org/0000-0002-0558-5488 [S.A.])
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21
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Zhu H, Zhang H, Xu Y, Laššáková S, Korabečná M, Neužil P. PCR past, present and future. Biotechniques 2020; 69:317-325. [PMID: 32815744 PMCID: PMC7439763 DOI: 10.2144/btn-2020-0057] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.
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Affiliation(s)
- Hanliang Zhu
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Haoqing Zhang
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Ying Xu
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Soňa Laššáková
- Institute of Biology & Medical Genetics, First
Faculty of Medicine, Charles University & General University Hospital in
Prague, Purkyně Institute, Albertov 4, Praha 2 128 00, Czech
Republic
| | - Marie Korabečná
- Institute of Biology & Medical Genetics, First
Faculty of Medicine, Charles University & General University Hospital in
Prague, Purkyně Institute, Albertov 4, Praha 2 128 00, Czech
Republic
| | - Pavel Neužil
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
- Brno University of Technology, Central European Institute
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Electrical
Engineering and Communications, Technická 3058/10, 616 00 Brno,
Czech Republic
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22
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Norris L, Lawler N, Hunkapiller A, Mulrooney DM, Kent ML, Sanders JL. Detection of the parasitic nematode, Pseudocapillaria tomentosa, in zebrafish tissues and environmental DNA in research aquaria. JOURNAL OF FISH DISEASES 2020; 43:1087-1095. [PMID: 32720361 DOI: 10.1111/jfd.13220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Although zebrafish continue to increase in popularity as a vertebrate animal model for biomedical research, chronic infectious diseases in laboratory populations remain prevalent. The presence of pathogens such as Pseudocapillaria tomentosa, a parasitic nematode found in the intestine of infected zebrafish, can significantly influence experimental endpoints and negatively impact reproducibility of research findings. Thus, there is a need for screening tests for zebrafish with the sensitivity to detect even low levels of pathogens present in tissues. Assays based on the detection of DNA are commonly used for such screening tests. Newer technologies such as digital PCR provide an opportunity to improve the sensitivity and precision of these assays, so they can be reliably used to detect pathogen DNA in water, reducing the need for lethal testing. We have designed a qPCR-based assay with the sensitivity to detect less than 5 copies of the P. tomentosa SSU-rDNA gene in tissues of infected zebrafish and environmental DNA from aquarium water housing infected fish. In addition, we adapted this test to a dPCR platform to provide a precise quantification of P. tomentosa DNA and demonstrate the resistance of this assay to inhibitors commonly found in freshwater aquaria.
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Affiliation(s)
- Lauren Norris
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Noah Lawler
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Andree Hunkapiller
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Donna M Mulrooney
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Michael L Kent
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Justin L Sanders
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
- Oregon Veterinary Diagnostic Laboratory, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
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23
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Chen Y, Liu Y, Shi Y, Ping J, Wu J, Chen H. Magnetic particles for integrated nucleic acid purification, amplification and detection without pipetting. Trends Analyt Chem 2020; 127:115912. [PMID: 32382202 PMCID: PMC7202819 DOI: 10.1016/j.trac.2020.115912] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleic acid amplification based detection plays an important role in food safety, environmental monitoring and clinical diagnosis. However, traditional nucleic acid detection process involves transferring liquid from one tube to another by pipetting. It requires trained persons, equipped labs and consumes lots of time. The ideal nucleic acid detection is integrated, closed, simplified and automated. Magnetic particles actuated by magnetic fields can efficiently adsorb nucleic acids and promote integrated nucleic acid assays without pipetting driven by pumps and centrifuges. We will comprehensively review magnetic particles assisted integrated system for nucleic acid detection and hope it can inspire further related study.
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Key Words
- ATP, adenosine triphosphate
- DLS, dynamic light scattering
- FMR, ferromagnetic resonance
- GTC, guanidinium thiocyanate
- ICP-AES, inductively coupled plasma atomic emission spectroscopy
- IFAST, immiscible filtration assisted by surface tension
- Immiscible interface
- Integrated detection
- LAMP, loop-mediated isothermal amplification
- Magnetic particles
- Nucleic acid
- PCR, polymerase chain reaction
- PEG, polyethylene glycol
- POCT, point-of-care testing
- RPA, recombinase polymerase amplification
- SQUID, superconducting quantum interference device magnetometer
- TEM, transmission electron microscopy
- XRD, X-Ray diffraction
- qPCR, quantitative PCR
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Affiliation(s)
- Yanju Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Yang Liu
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Ya Shi
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China
| | - Huan Chen
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
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24
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Petty DR, Hassan OA, Barker CS, O'Neill SS. Rapid BRAF Mutation Testing in Pigmented Melanomas. Am J Dermatopathol 2020; 42:343-348. [PMID: 31833840 DOI: 10.1097/dad.0000000000001592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BRAF mutations are present in ∼40%-60% of melanomas, and targeted therapy in advanced-stage melanoma is associated with improvement in overall and progression-free survival. Accordingly, BRAF mutation determination is standard-of-care in metastatic melanoma, and a rapid, accurate assay is desirable. Melanin can present unique challenges due to inhibition of the polymerase chain reaction. The novel cartridge-based Idylla platform offers rapid molecular oncology testing; however, a formal evaluation of the impact of melanin on testing heretofore has not been explored. In this study, we evaluated the performance of Idylla BRAF mutation detection in 23 melanomas including resections, small biopsies, and cytology cell blocks. Pathologists assigned each case a pigment score from 0 to 2 based on extent of melanin content. Samples with a pigment score of 2 were successfully resulted, thus demonstrating that high melanin content did not inhibit the assay. Sensitivity and specificity of BRAF mutation detection were 100% compared with reference laboratory testing. Tissue input requirements were low, with the Idylla successfully detecting a BRAF mutation in cell block material containing only ∼400 tumor cells. The assay was simple and quick to perform, with total hands-on time of 5-10 minutes and instrument time ∼90 minutes. In summary, the Idylla BRAF mutation assay provides rapid, robust testing for melanomas with high melanin content, including samples with limited material. The assay requires minimal technical expertise, making mutation status determination accessible in a range of clinical laboratory settings. The total assay time of <2 hours facilitates prompt results to guide patient care decisions.
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Affiliation(s)
- Danielle R Petty
- Department of Pathology, Wake Forest Baptist Medical Center, Winston-Salem, NC
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25
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Turingan RS, Tan E, Jiang H, Brown J, Estari Y, Krautz-Peterson G, Selden RF. Developmental Validation of the ANDE 6C System for Rapid DNA Analysis of Forensic Casework and DVI Samples. J Forensic Sci 2020; 65:1056-1071. [PMID: 32040208 PMCID: PMC7383818 DOI: 10.1111/1556-4029.14286] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/01/2020] [Accepted: 01/06/2020] [Indexed: 12/13/2022]
Abstract
A developmental validation was performed to demonstrate reliability, reproducibility, and robustness of the ANDE Rapid DNA Identification System for processing of crime scene and disaster victim identification (DVI) samples. A total of 1705 samples were evaluated, including blood, oral epithelial samples from drinking containers, samples on FTA and untreated paper, semen, bone, and soft tissues. This study was conducted to address the FBI’s Quality Assurance Standards on developmental validation and to accumulate data from a sufficient number of unique donors and sample types to meet NDIS submission requirements for acceptance of the ANDE Expert System for casework use. To date, no Expert System has been approved for such samples, but the results of this study demonstrated that the automated Expert System performs similarly to conventional laboratory data analysis. Furthermore, Rapid DNA analysis demonstrated accuracy, precision, resolution, concordance, and reproducibility that were comparable to conventional processing along with appropriate species specificity, limit of detection, performance in the presence of inhibitors. No lane‐to‐lane or run‐to‐run contamination was observed, and the system correctly identified the presence of mixtures. Taken together, the ANDE instrument, I‐Chip consumable, FlexPlex chemistry (a 27‐locus STR assay compatible with all widely used global loci, including the CODIS core 20 loci), and automated Expert System successfully processed and interpreted more than 1200 unique samples with over 99.99% concordant CODIS alleles. This extensive developmental validation data provides support for broad use of the system by agencies and accredited forensic laboratories in single‐source suspect‐evidence comparisons, local database searches, and DVI.
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Affiliation(s)
| | - Eugene Tan
- ANDE Corporation, 266 Second Avenue, Waltham, MA, 02451
| | - Hua Jiang
- ANDE Corporation, 266 Second Avenue, Waltham, MA, 02451
| | - Jessi Brown
- ANDE Corporation, 266 Second Avenue, Waltham, MA, 02451
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26
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Jue E, Witters D, Ismagilov RF. Two-phase wash to solve the ubiquitous contaminant-carryover problem in commercial nucleic-acid extraction kits. Sci Rep 2020; 10:1940. [PMID: 32029846 PMCID: PMC7004994 DOI: 10.1038/s41598-020-58586-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/02/2020] [Indexed: 11/09/2022] Open
Abstract
The success of fundamental and applied nucleic acid (NA) research depends on NA purity, but obtaining pure NAs from raw, unprocessed samples is challenging. Purification using solid-phase NA extractions utilizes sequential additions of lysis and wash buffers followed by elution. The resulting eluent contains NAs and carryover of extraction buffers. Typically, these inhibitory buffers are heavily diluted by the reaction mix (e.g., 10x dilution is 1 µL eluent in 9 µL reaction mix), but in applications requiring high sensitivity (e.g., single-cell sequencing, pathogen diagnostics) it is desirable to use low dilutions (e.g., 2x) to maximize NA concentration. Here, we demonstrate pervasive carryover of inhibitory buffers into eluent when several commercial sample-preparation kits are used following manufacturer protocols. At low eluent dilution (2-2.5x) we observed significant reaction inhibition of polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and reverse transcription (RT). We developed a two-phase wash (TPW) method by adding a wash buffer with low water solubility prior to the elution step. The TPW reduces carryover of extraction buffers, phase-separates from the eluent, and does not reduce NA yield (measured by digital PCR). We validated the TPW for silica columns and magnetic beads by demonstrating significant improvements in performance and reproducibility of qPCR, LAMP, and RT reactions.
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Affiliation(s)
- Erik Jue
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd., Pasadena, CA, 91125, United States
| | - Daan Witters
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd., Pasadena, CA, 91125, United States
| | - Rustem F Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd., Pasadena, CA, 91125, United States.
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd., Pasadena, CA, 91125, United States.
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Totoiu CA, Phillips JM, Reese AT, Majumdar S, Girguis PR, Raston CL, Weiss GA. Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens. PLoS One 2020; 15:e0225807. [PMID: 31999723 PMCID: PMC6992170 DOI: 10.1371/journal.pone.0225807] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 01/06/2020] [Indexed: 12/25/2022] Open
Abstract
DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species.
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Affiliation(s)
- Christian A. Totoiu
- Department of Chemistry, University of California, Irvine, California, United States of America
| | - Jessica M. Phillips
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Aspen T. Reese
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Sudipta Majumdar
- Department of Chemistry, University of California, Irvine, California, United States of America
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Colin L. Raston
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Gregory A. Weiss
- Department of Chemistry, University of California, Irvine, California, United States of America
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, United States of America
- Department of Pharmaceutical Sciences, University of California, Irvine, California, United States of America
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28
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Liu C, Wu S, Yan Y, Dong Y, Shen X, Huang C. Application of magnetic particles in forensic science. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115674] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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29
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Validation study and forensic applications of investigator 24plex QS Kit. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Zeng X, Elwick K, Mayes C, Takahashi M, King JL, Gangitano D, Budowle B, Hughes-Stamm S. Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success. Int J Legal Med 2018; 133:51-58. [PMID: 30341454 DOI: 10.1007/s00414-018-1955-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/12/2018] [Indexed: 11/24/2022]
Abstract
Skeletal remains recovered from missing persons' cases are often exposed to harsh environmental conditions resulting in the DNA being damaged, degraded, and/or the samples containing PCR inhibitors. In this study, the efficacy of common extraction methods was evaluated to remove high levels of PCR inhibitors commonly encountered with human remains, and their downstream compatibility with the two leading sequencing chemistries and platforms for human identification purposes. Blood, hair, and bone samples were spiked with high levels of inhibitors commonly identified in each particular substrate in order to test the efficiency of various DNA extraction methods prior to sequencing. Samples were extracted using three commercial extraction kits (DNA IQ™, DNA Investigator, and PrepFiler® BTA), organic (blood and hair only), and two total demineralization protocols (bone only)). Massively parallel sequencing (MPS) was performed using two different systems: Precision ID chemistry and a custom AmpliSeq™ STR and iiSNP panel on the Ion S5™ System and the ForenSeq DNA Signature Prep Kit on the MiSeq FGx™. The overall results showed that all DNA extraction methods were efficient and are fully compatible with both MPS systems. Key performance indicators such as STR and SNP reportable alleles, read depth, and heterozygote balance were comparable for each extraction method. In samples where CE-based STRs yielded partial profiles (bone), MPS-based STRs generated more complete or full profiles. Moreover, MPS panels contain more STR loci than current CE-based STR kits and also include SNPs, which can further increase the power of discrimination obtained from these samples, making MPS a desirable choice for the forensic analysis of such challenging samples.
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Affiliation(s)
- Xiangpei Zeng
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA
| | - Kyleen Elwick
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA.
| | - Carrie Mayes
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA
| | - Maiko Takahashi
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA
| | - David Gangitano
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA
| | - Sheree Hughes-Stamm
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA
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31
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Taylor SL, O'Farrell HE, Simpson JL, Yang IA, Rogers GB. The contribution of respiratory microbiome analysis to a treatable traits model of care. Respirology 2018; 24:19-28. [PMID: 30282116 DOI: 10.1111/resp.13411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/13/2018] [Accepted: 09/09/2018] [Indexed: 12/15/2022]
Abstract
The composition of the airway microbiome in patients with chronic airway diseases, such as severe asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and cystic fibrosis (CF), has the potential to inform a precision model of clinical care. Patients with these conditions share overlapping disease characteristics, including airway inflammation and airflow limitation. The clinical management of chronic respiratory conditions is increasingly moving away from a one-size-fits-all model based on primary diagnosis, towards care targeting individual disease traits, and is particularly useful for subgroups of patients who respond poorly to conventional therapies. Respiratory microbiome analysis is an important potential contributor to such a 'treatable traits' approach, providing insight into both microbial drivers of airways disease, and the selective characteristics of the changing lower airway environment. We explore the potential to integrate respiratory microbiome analysis into a treatable traits model of clinical care and provide a practical guide to the application and clinical interpretation of respiratory microbiome analysis.
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Affiliation(s)
- Steven L Taylor
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Hannah E O'Farrell
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Jodie L Simpson
- Respiratory and Sleep Medicine, Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Ian A Yang
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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32
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Elwick K, Mayes C, Hughes-Stamm S. Comparative sensitivity and inhibitor tolerance of GlobalFiler® PCR Amplification and Investigator® 24plex QS kits for challenging samples. Leg Med (Tokyo) 2018; 32:31-36. [DOI: 10.1016/j.legalmed.2018.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 01/16/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
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Stoop B, Defaux PM, Utz S, Zieger M. Touch DNA sampling with SceneSafe Fast™ minitapes. Leg Med (Tokyo) 2017; 29:68-71. [DOI: 10.1016/j.legalmed.2017.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 04/26/2017] [Accepted: 10/25/2017] [Indexed: 11/28/2022]
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34
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Influence of mucinous and necrotic tissue in colorectal cancer samples on KRAS mutation analysis. Pathol Res Pract 2017; 213:606-611. [DOI: 10.1016/j.prp.2017.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 12/21/2022]
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35
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Desmyter S, De Cock G, Moulin S, Noël F. Organic extraction of bone lysates improves DNA purification with silica beads. Forensic Sci Int 2017; 273:96-101. [DOI: 10.1016/j.forsciint.2017.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/23/2016] [Accepted: 02/02/2017] [Indexed: 11/17/2022]
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36
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Pîrlea S, Puiu M, Răducan A, Oancea D. Permanganate-assisted removal of PCR inhibitors during the DNA Chelex extraction from stained denim samples. Int J Legal Med 2016; 131:323-331. [PMID: 27595149 DOI: 10.1007/s00414-016-1443-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/23/2016] [Indexed: 11/25/2022]
Abstract
In this study, it was demonstrated that the DNA Chelex extraction combined with the permanganate assisted-oxidation is highly efficient in removing the PCR inhibitors often found in clothing materials, such as phthalocyanine. The extraction assays were conducted in saliva, blood and epithelial cells samples mixed with three oxidation-resistant dye copper(II) α-phthalocyanine, copper(II) β-phthalocyanine and tetrasulfonated copper(II) β-phthalocyanine. After DNA amplification, all samples were able to provide full DNA profiles. The permanganate/Chelex system was tested further on denim-stained samples and displayed the same ability to remove the PCR inhibitors from the commercial textile materials.
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Affiliation(s)
- Sorina Pîrlea
- National Forensic Science Institute, Şoseaua Ştefan cel Mare 13-15, sect. 2, 020123, Bucharest, Romania
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania
| | - Mihaela Puiu
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania
| | - Adina Răducan
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania.
| | - Dumitru Oancea
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania
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37
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Nilsson M, Grånemo J, Buś MM, Havsjö M, Allen M. Comparison of DNA polymerases for improved forensic analysis of challenging samples. Forensic Sci Int Genet 2016; 24:55-59. [DOI: 10.1016/j.fsigen.2016.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/25/2016] [Accepted: 05/29/2016] [Indexed: 11/24/2022]
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38
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Comparative Methods to Improve the Detection of BRAF V600 Mutations in Highly Pigmented Melanoma Specimens. PLoS One 2016; 11:e0158698. [PMID: 27466810 PMCID: PMC4965116 DOI: 10.1371/journal.pone.0158698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/20/2016] [Indexed: 12/04/2022] Open
Abstract
Genotyping BRAF in melanoma samples is often challenging. The presence of melanin greatly interferes with thermostable DNA polymerases and/or nucleic acids in traditional polymerase chain reaction (PCR)-based methods. In the present work, we evaluated three easy-to-use strategies to improve the detection of pigmented DNA refractory to PCR amplification. These pre-PCR processing methods include the addition of bovine serum albumin (BSA), the dilution of DNA, and the purification of DNA using the NucleoSpin® gDNA Clean-up XS Kit. We found that BRAF genotyping in weakly and moderately pigmented samples was more efficient when the sample was processed with BSA or purified with a NucleoSpin® gDNA Clean-up XS Kit prior to PCR amplification. In addition, the combination of both methods resulted in successful detection of BRAF mutation in pigmented specimens, including highly pigmented samples, thereby increasing the chance of patients being elicited for anti-BRAF treatment. These solutions to overcome melanin-induced PCR inhibition are of tremendous value and provide a simple solution for clinical chemistry and routine laboratory medicine.
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39
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Chen M, Wu BL, Chen T, Liu Z, Deng ZL, Peng L. The impact of different DNA extraction methods on the analysis of microbial diversity of oral saliva from healthy youths by polymerase chain reaction-denaturing gradient gel electrophoresis. J Dent Sci 2016; 11:54-58. [PMID: 30894946 PMCID: PMC6395153 DOI: 10.1016/j.jds.2015.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/06/2015] [Indexed: 11/11/2022] Open
Abstract
Background/purpose Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), as a conventional molecular technique, was utilized to analyze the diversity of oral microbiota. However, studies found that the results of PCR-DGGE were affected by the DNA isolation method. This study compared QIAamp DNA Micro Kit extraction method with the phenol and chloroform extraction method for DNA isolation of saliva of healthy youths and analyzed PCR-DGGE fingerprints. Materials and methods In the first stage, samples were divided into two after collection from eight health youths. Two methods were used to isolate the DNA for PCR-DGGE analysis. In the second stage, another 16 samples were collected from 14 youths. The better method, QIAamp DNA Micro Kit, was used to isolate the DNA for PCR-DGGE analysis. The cluster analysis was performed with unweighted pair-group method with arithmetic means. Results The results in the first stage showed that the QIAamp DNA Micro Kit extraction method was more suitable for DNA extraction of saliva than the phenol-chloroform extraction method. In the second stage, the bands were changed into numbers “0”, “1”, and “2” to analyze the similarity of samples according to the bands' lightness. The similarity indices of different periods from the same individual showed that the microbiological composition was very similar (>0.95), while those from different individuals varied greatly (<0.90). Conclusion PCR-DGGE was more accurate in assessing oral microbial diversity by QIAamp DNA Micro Kit. Different individuals had large differences in oral microbial diversity but also had some common microbial dominant communities.
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Affiliation(s)
- Ming Chen
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Bu-Ling Wu
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Ting Chen
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhao Liu
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Zi-Long Deng
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
| | - Ling Peng
- Department of Stomatology, Nanfang Hospital, College of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
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40
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Barbano R, Pasculli B, Coco M, Fontana A, Copetti M, Rendina M, Valori VM, Graziano P, Maiello E, Fazio VM, Parrella P. Competitive allele-specific TaqMan PCR (Cast-PCR) is a sensitive, specific and fast method for BRAF V600 mutation detection in Melanoma patients. Sci Rep 2015; 5:18592. [PMID: 26690267 PMCID: PMC4686972 DOI: 10.1038/srep18592] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/23/2015] [Indexed: 12/31/2022] Open
Abstract
BRAF codon 600 mutation testing of melanoma patients is mandatory for the choice of the most appropriate therapy in the clinical setting. Competitive allele specific TaqMan PCR (Cast-PCR) technology allows not only the selective amplification of minor alleles, but it also blocks the amplification of non-mutant allele. We genotyped codon 600 of the BRAF gene in 54 patients’ samples by Cast-PCR and bidirectional direct sequence analysis. All the mutations detected by sequencing were also identified by Cast-PCR. In addition, Cast-PCR assay detected four samples carrying mutations and was able to clearly identify two mutations of uncertain interpretation by Sanger sequencing. The limit of detection of Cast-PCR was evaluated by constructing dilution curves of BRAFV600E and BRAFV600K mutated clinical samples mixed with a not-mutated specimens. Both mutations could be detected until a 1:100 mutated/not mutated ratio. Cloning and sequencing of the clones was used to confirm mutations on representative discrepant cases. Cast PCR performances were not affected by intratumour heterogeneity, and less affected by melanin content. Our results indicate that Cast-PCR is a reliable diagnostic tool for the identification of melanoma patients as eligible to be treated with TKIs and might be implemented in the clinical setting as elective screening method.
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Affiliation(s)
- Raffaela Barbano
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Barbara Pasculli
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Michelina Coco
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Andrea Fontana
- Biostatic Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Massimiliano Copetti
- Biostatic Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Michelina Rendina
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy.,Department of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Vanna Maria Valori
- Department of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Paolo Graziano
- Department of Pathology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG) 71013, Italy
| | - Evaristo Maiello
- Department of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Vito Michele Fazio
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy.,CIR Laboratory for Molecular Medicine and Biotechnology, University Campus Biomedico, Rome 00128, Italy
| | - Paola Parrella
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
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