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Scali M, Spinsanti G, Vignani R. Validation of a simplified small-scale DNA extraction protocol from wine by quantitative real-time PCR. 3 Biotech 2024; 14:145. [PMID: 38706928 PMCID: PMC11065827 DOI: 10.1007/s13205-024-03992-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/17/2024] [Indexed: 05/07/2024] Open
Abstract
In the present study, we compared a simplified small-scale purification protocol to obtain DNA admixtures out of wine, with our large-scale published method. The extraction methods must provide DNA free of PCR inhibitors, that can interfere with DNA amplification. To evaluate the efficiency of grapevine's nuclear DNA extraction from wine, the new protocol was also compared in terms of purity and yield to the DNA obtained out of grapevine's (Vitis vinifera) leaf tissue, using a commercial kit. Two single-copy nuclear genes, nine-cis-epoxy carotenoid dioxygenase 2 (NCED2), and prefoldin subunit 5-like (PS5) were amplified in DNA extracted from wine and grapevine by real-time TaqMan PCR to determine the presence of inhibitors in relation to the diversity of starting biological matrix. This study showed that the small-scale, simpler method for extracting DNA from wine produced effective results in terms of inhibitor presence and purity. Furthermore, even though the initial biological matrix was more complicated, the grapevine nuclear DNA that was removed from wine was qualitatively equivalent to the DNA that was isolated from the leaves. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03992-x.
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Affiliation(s)
- Monica Scali
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Giacomo Spinsanti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Rita Vignani
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
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2
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Parkins MD, Lee BE, Acosta N, Bautista M, Hubert CRJ, Hrudey SE, Frankowski K, Pang XL. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin Microbiol Rev 2024; 37:e0010322. [PMID: 38095438 PMCID: PMC10938902 DOI: 10.1128/cmr.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024] Open
Abstract
Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.
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Affiliation(s)
- Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O’Brien Institute of Public Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole Acosta
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria Bautista
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Provincial Health Laboratory, Alberta Health Services, Calgary, Alberta, Canada
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3
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Nwe MK, Jangpromma N, Taemaitree L. Evaluation of molecular inhibitors of loop-mediated isothermal amplification (LAMP). Sci Rep 2024; 14:5916. [PMID: 38467647 PMCID: PMC10928092 DOI: 10.1038/s41598-024-55241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a cost-effective and easy-to-perform assay that enables the direct detection of DNA. Its use in point-of-care diagnostic tests is growing, while it has the potential to be used in presumptive on-the-field forensic tests. Samples are often collected from complex matrices that contain high levels of contaminants. Herein, we evaluate the effect of seven common DNA amplification inhibitors on LAMP - bile salts, calcium chloride, hematin, humic acid, immunoglobulin G, tannic acid and urea. We study the effect of each inhibitor individually in real-time detection systems coupled with end-point measurements to delineate their inhibitory effects from the matrix in which they may be found. Our studies show LAMP inhibitors generally delay the onset of amplicon formation and quench fluorescence at similar or higher concentrations compared to PCR, but that end-point measurements of LAMP amplicons are unaffected. This is important as LAMP amplicons can be detected in non-fluorometric ways thus contributing to the assertions that LAMP is more robust to inhibitors than PCR.
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Affiliation(s)
- May Khat Nwe
- Department of Integrated Science, Forensic Science Program, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nisachon Jangpromma
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Lapatrada Taemaitree
- Department of Integrated Science, Forensic Science Program, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.
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4
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Xu EY, Schneper LM, Notterman DA. A novel metric to improve mismatched primer selection and quantification accuracy in amplifying DNA repeats for quantitative polymerase chain reactions. PLoS One 2023; 18:e0292559. [PMID: 37812635 PMCID: PMC10561853 DOI: 10.1371/journal.pone.0292559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/23/2023] [Indexed: 10/11/2023] Open
Abstract
In quantitative polymerase chain reaction (qPCR) experiments, primers containing mismatches with respect to the template are widely used in measuring repetitive DNA elements. Primer-template mismatches may lead to underestimation of the input sample quantity due to inefficient annealing and amplification. But how primer-template mismatches affect quantification accuracy has not been rigorously investigated. In this study, we performed a series of qPCR experiments in which we tested three pairs of mismatched telomere primers (tel1/tel2, tel1b/tel2b and telg/telc) and two pairs of perfect-match reference gene primers (36B4-F/-R and IFNB1-F/-R) at three different primer concentrations under four cycling conditions. Templates used were genomic DNA from two human cell lines and oligo duplexes which contained telomere sequences, reference gene sequences, or both. We demonstrated that the underestimation of input sample quantity from reactions containing mismatched primers was not due to lower amplification efficiency (E), but due to ineffective usage of the input sample. We defined a novel concept of amplification efficacy (f) which quantifies the effectiveness of input sample amplification by primers. We have modified the conventional qPCR kinetic formula to include f, which corrects the effects of primer mismatches. We demonstrated that reactions containing mismatched telomere primer pairs had similar efficiency (E), but varying degrees of reduced efficacy (f) in comparison to those with the perfect-match gene primer pairs. Using the quantitative parameter f, underestimation of initial target by telomere primers can be adjusted to provide a more accurate measurement. Additionally, we found that the tel1b/tel2b primer set at concentration of 500 nM and 900 nM exhibited the best amplification efficacy f. This study provides a novel way to incorporate an evaluation of amplification efficacy into qPCR analysis. In turn, it improves mismatched primer selection and quantification accuracy in amplifying DNA repeats using qPCR methods.
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Affiliation(s)
- Eugenia Y. Xu
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Lisa M. Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
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5
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Vajpayee K, Dash HR, Parekh PB, Shukla RK. PCR inhibitors and facilitators - Their role in forensic DNA analysis. Forensic Sci Int 2023; 349:111773. [PMID: 37399774 DOI: 10.1016/j.forsciint.2023.111773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/01/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023]
Abstract
Since its inception, DNA typing technology has been practiced as a robust tool in criminal investigations. Experts usually utilize STR profiles to identify and individualize the suspect. However, mtDNA and Y STR analyses are also considered in some sample-limiting conditions. Based on DNA profiles thus generated, forensic scientists often opine the results as Inclusion, exclusion, and inconclusive. Inclusion and exclusion were defined as concordant results; the inconclusive opinions create problems in conferring justice in a trial- since nothing concrete can be interpreted from the profile generated. The presence of inhibitor molecules in the sample is the primary factor behind these indefinite results. Recently, researchers have been emphasizing studying the sources of PCR inhibitors and their mechanism of inhibition. Furthermore, several mitigation strategies- to facilitate the DNA amplification reaction -have now found their place in the routine DNA typing assays with compromised biological samples. The present review paper attempts to provide a comprehensive review of PCR inhibitors, their source, mechanism of inhibition, and ways to mitigate their effect using PCR facilitators.
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Affiliation(s)
- Kamayani Vajpayee
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Hirak Ranjan Dash
- National Forensic Science University, New Delhi Campus, New Delhi, India
| | - Prakshal B Parekh
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Ritesh K Shukla
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India.
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Han YJ, Liu LY, Rong Z, Zhang QZ, Cheng P, Xu GJ, Wang DF, Zhou Z, Wang SQ. Rapid genotyping of 32 insertion/deletion panel for human identification using fluorogenic probes-based multiplex real-time PCR. Anal Biochem 2023; 674:115208. [PMID: 37315679 DOI: 10.1016/j.ab.2023.115208] [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: 03/29/2023] [Revised: 05/17/2023] [Accepted: 06/04/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Insertion and deletion polymorphisms (InDels) have considerable potential in the field of forensic genetics because of their low mutation rate and small amplicons. At present, InDel polymorphisms detection based on the technique of capillary electrophoresis is the main technique used in forensic DNA laboratory. However, this method is complicated and time-consuming, and is not suitable for rapid on-site paternity and personal identification. Next-generation sequencing analysis of InDels polymorphisms requires expensive instruments, large upfront reagent and supply costs, computational requirements and complex bioinformatics, increased the time to obtain results. Thus, there is an urgent need to establish a method to provide reliable, rapid, sensitive and economical genotyping for InDels. METHOD A rapid InDels (32 InDels) panel was established using fluorogenic probes-based multiplex real-time PCR with microfluidic test cartridge and portable real-time PCR instrument. Then, we performed several validation studies including concordance, accuracy, sensitivity, stability, species specificity. RESULTS It showed that the complete genotypes could be obtained from ≥100 pg of input DNA and from a series of challenging samples with high accuracy and specificity within 90 min. CONCLUSION This method provides a rapid and cost-effective solution for InDels genotyping and personal identification in portable format.
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Affiliation(s)
- Yong-Jun Han
- Bioinformatics Center of AMMS, Beijing 100850, China
| | - Li-Yan Liu
- Bioinformatics Center of AMMS, Beijing 100850, China
| | - Zhen Rong
- Bioinformatics Center of AMMS, Beijing 100850, China
| | | | - Peng Cheng
- Bioinformatics Center of AMMS, Beijing 100850, China
| | - Guo-Juan Xu
- Bioinformatics Center of AMMS, Beijing 100850, China
| | | | - Zhe Zhou
- Bioinformatics Center of AMMS, Beijing 100850, China
| | - Sheng-Qi Wang
- Bioinformatics Center of AMMS, Beijing 100850, China.
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Agboola O, Bakre B, Oladokun O, Ayeni AO, Fayomi OSI, Odunlami O, Sadiku R, Adeniyi A, Popoola P. Effect of dissolved CO2 and Syzygium malaccense leaf DNA concentrations on carbon steel within a carbonic acid equilibrium. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02268-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kim YS, Kim J, Na W, Sung GH, Baek SK, Kim YK, Kim GR, Hu HJ, Park JH. Development of a Microneedle Swab for Acquisition of Genomic DNA From Buccal Cells. Front Bioeng Biotechnol 2022; 10:829648. [PMID: 35252137 PMCID: PMC8895340 DOI: 10.3389/fbioe.2022.829648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
A swab is a tool for obtaining buccal DNA from buccal mucus for biological analysis. The acquisition of a sufficient amount and high quality of DNA is an important factor in determining the accuracy of a diagnosis. A microneedle swab (MN swab) was developed to obtain more oral mucosal tissues non-invasively. Eight types of MN swabs were prepared with varying combinations of patterns (zigzag or straight), number of MNs, intervals of MNs, and sharpness of tips. When MN swab was applied up to 10 times, the tissue amount and DNA yield increased compared to commercial swabs. A zigzag pattern of microneedles was found to be more efficient than a straight pattern and increasing the number of microneedles in an array increased the DNA yield. The MN swab collected about twice the DNA compared to the commercial swab. In an in vivo test using mini pigs, the lower cycle threshold values of mucosal samples collected with MN swabs compared to samples collected with commercial swabs indicated that a greater amount of DNA was collected for SNP genotyping. A polymer MN swab is easy to manufacture by a single molding process, and it has a greater sampling capacity than existing commercial swabs.
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Affiliation(s)
- Yun-Seo Kim
- Department of Bionano Technology and Gachon BioNano Research Institute, Gachon University, Seongnam, South Korea
| | - JeongHyeon Kim
- Department of Bionano Technology and Gachon BioNano Research Institute, Gachon University, Seongnam, South Korea
| | - Woonsung Na
- Laboratory of Veterinary Virology, College of Veterinary Medicine, Chonnam National University, Gwangju, South Korea
| | - Gil-Hwan Sung
- QuadMedicine R and D Centre, QuadMedicine Co., Ltd., Seongnam, South Korea
| | - Seung-Ki Baek
- QuadMedicine R and D Centre, QuadMedicine Co., Ltd., Seongnam, South Korea
| | | | | | - Hae-Jin Hu
- Endomics, Inc., Seongnam, South Korea
- *Correspondence: Hae-Jin Hu, ; Jung-Hwan Park,
| | - Jung-Hwan Park
- Department of Bionano Technology and Gachon BioNano Research Institute, Gachon University, Seongnam, South Korea
- *Correspondence: Hae-Jin Hu, ; Jung-Hwan Park,
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9
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Diagnostic armamentarium of infectious keratitis: A comprehensive review. Ocul Surf 2021; 23:27-39. [PMID: 34781020 PMCID: PMC8810150 DOI: 10.1016/j.jtos.2021.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 01/23/2023]
Abstract
Infectious keratitis (IK) represents the leading cause of corneal blindness worldwide, particularly in developing countries. A good outcome of IK is contingent upon timely and accurate diagnosis followed by appropriate interventions. Currently, IK is primarily diagnosed on clinical grounds supplemented by microbiological investigations such as microscopic examination with stains, and culture and sensitivity testing. Although this is the most widely accepted practice adopted in most regions, such an approach is challenged by several factors, including indistinguishable clinical features shared among different causative organisms, polymicrobial infection, long diagnostic turnaround time, and variably low culture positivity rate. In this review, we aim to provide a comprehensive overview of the current diagnostic armamentarium of IK, encompassing conventional microbiological investigations, molecular diagnostics (including polymerase chain reaction and mass spectrometry), and imaging modalities (including anterior segment optical coherence tomography and in vivo confocal microscopy). We also highlight the potential roles of emerging technologies such as next-generation sequencing, artificial intelligence-assisted platforms. and tele-medicine in shaping the future diagnostic landscape of IK.
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10
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Advanced methods for RNA recovery from petroleum impacted soils. MethodsX 2021; 8:101503. [PMID: 34754774 PMCID: PMC8563465 DOI: 10.1016/j.mex.2021.101503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/28/2021] [Indexed: 11/29/2022] Open
Abstract
Microbially-mediated hydrocarbon degradation is well documented. However, how these microbial processes occur in complex subsurface petroleum impacted systems remains unclear, and this knowledge is needed to guide technologies to enhance microbial degradation effectively. Analysis of RNA derived from soils impacted by petroleum liquids would allow for analysis of active microbial communities, and a deeper understanding of the dynamic biochemistry occurring during site remediation. However, RNA analysis in soils impacted with petroleum liquids is challenging due to: (A) RNA being inherently unstable, and (B) petroleum impacted soils containing problematic levels of polymerase chain reaction (PCR) inhibitors that must be removed to yield high-purity RNA for downstream analysis. A previously published soil wash pretreatment step and a commercially available DNA extraction kit protocol were combined and modified to be able to purify RNA from soils containing petroleum liquids.A key modification involved reformulation of the pretreatment solution via replacing water as the diluent with a commercially-available RNA preservation solution. Methods were developed and demonstrated using cryogenically preserved soils from three former petroleum refineries. Results showed the new soil washing approach had no adverse effects on RNA recovery but did improve RNA quality, by PCR inhibitor removal, which in turn allows for characterization of active microbial communities present in petroleum impacted soils. In summary, our method for extracting RNA from petroleum-impacted soils provides a promising new tool for resolving metabolic processes at sites as they progress toward restoration via natural and/or engineered remediation.
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11
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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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12
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Lau MJ, Hoffmann AA, Endersby-Harshman NM. A diagnostic primer pair to distinguish between wMel and wAlbB Wolbachia infections. PLoS One 2021; 16:e0257781. [PMID: 34555085 PMCID: PMC8459989 DOI: 10.1371/journal.pone.0257781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
Detection of the Wolbachia endosymbiont in Aedes aegypti mosquitoes through real-time polymerase chain reaction assays is widely used during and after Wolbachia releases in dengue reduction trials involving the wMel and wAlbB strains. Although several different primer pairs have been applied in current successful Wolbachia releases, they cannot be used in a single assay to distinguish between these strains. Here, we developed a new diagnostic primer pair, wMwA, which can detect the wMel or wAlbB infection in the same assay. We also tested current Wolbachia primers and show that there is variation in their performance when they are used to assess the relative density of Wolbachia. The new wMwA primers provide an accurate and efficient estimate of the presence and density of both Wolbachia infections, with practical implications for Wolbachia estimates in field collected Ae. aegypti where Wolbachia releases have taken place.
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Affiliation(s)
- Meng-Jia Lau
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
| | - Ary A. Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Nancy M. Endersby-Harshman
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
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13
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Liu P, Amin N, Miah R, Foster T, Raj S, Corpuz MJB, Rahman M, Willetts J, Moe CL. A method for correcting underestimation of enteric pathogen genome quantities in environmental samples. J Microbiol Methods 2021; 189:106320. [PMID: 34478762 DOI: 10.1016/j.mimet.2021.106320] [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: 07/08/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Exposure to enteric pathogens in the environment poses a serious risk for infection and disease. The accurate detection and quantification of enteric pathogens in environmental samples is critical for understanding pathogen transport and fate and developing risk assessment models. In this study, we successfully applied TaqMan real-time PCR assays to quantitatively detect five human-specific pathogens (Shigella/EIEC, Salmonella Typhi, Vibrio cholera, Norovirus, and Giardia) in samples from open drains, canals, floodwater, septic tanks, and anaerobic baffled reactors (ABR) collected in Mirpur, Dhaka, Bangladesh from April to October 2019. Overall, the grab and sediment samples showed low inhibition but the ultrafiltration samples collected from open drain had significantly higher (P = 0.0049) degree of PCR inhibition (median Ct = 31.06) compared to the extraction controls (Ct = 28.54). We developed a two-step method to adjust underestimation of pathogen quantities due to PCR inhibition and non-optimum PCR efficiency. Compared to other sample types, ultrafiltration samples demonstrated a wide range of concentration increase (1.0%-182.5%) by pathogens after adjusting for PCR inhibition and non-optimum efficiencies. These quantitative qPCR assays are successful in quantifying multiple enteric pathogens in environmental samples, and the adjustment method would be useful for correcting underestimates of pathogen quantities due to partial PCR inhibition and non-optimum efficiency.
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Affiliation(s)
- Pengbo Liu
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA..
| | - Nuhu Amin
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh..
| | - Rana Miah
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh..
| | - Tim Foster
- Institute for Sustainable Futures, University of Technology Sydney, Australia..
| | - Suraja Raj
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA..
| | - Maria Julia Bianca Corpuz
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA..
| | - Mahbubur Rahman
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh..
| | - Juliet Willetts
- Institute for Sustainable Futures, University of Technology Sydney, Australia..
| | - Christine L Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA..
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14
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Untergasser A, Ruijter JM, Benes V, van den Hoff MJB. Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data. BMC Bioinformatics 2021; 22:398. [PMID: 34433408 PMCID: PMC8386043 DOI: 10.1186/s12859-021-04306-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/22/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The analyses of amplification and melting curves have been shown to provide valuable information on the quality of the individual reactions in quantitative PCR (qPCR) experiments and to result in more reliable and reproducible quantitative results. IMPLEMENTATION The main steps in the amplification curve analysis are (1) a unique baseline subtraction, not using the ground phase cycles, (2) PCR efficiency determination from the exponential phase of the individual reactions, (3) setting a common quantification threshold and (4) calculation of the efficiency-corrected target quantity with the common threshold, efficiency per assay and Cq per reaction. The melting curve analysis encompasses smoothing of the observed fluorescence data, normalization to remove product-independent fluorescence loss, peak calling and assessment of the correct peak by comparing its melting temperature with the known melting temperature of the intended amplification product. RESULTS The LinRegPCR web application provides visualization and analysis of a single qPCR run. The user interface displays the analysis results on the amplification curve analysis and melting curve analysis in tables and graphs in which deviant reactions are highlighted. The annotated results in the tables can be exported for calculation of gene-expression ratios, fold-change between experimental conditions and further statistical analysis. Web-based LinRegPCR addresses two types of users, wet-lab scientists analyzing the amplification and melting curves of their own qPCR experiments and bioinformaticians creating pipelines for analysis of series of qPCR experiments by splitting its functionality into a stand-alone back-end RDML (Real-time PCR Data Markup Language) Python library and several companion applications for data visualization, analysis and interactive access. The use of the RDML data standard enables machine independent storage and exchange of qPCR data and the RDML-Tools assist with the import of qPCR data from the files exported by the qPCR instrument. CONCLUSIONS The combined implementation of these analyses in the newly developed web-based LinRegPCR ( https://www.gear-genomics.com/rdml-tools/ ) is platform independent and much faster than the original Windows-based versions of the LinRegPCR program. Moreover, web-based LinRegPCR includes a novel statistical outlier detection and the combination of amplification and melting curve analyses allows direct validation of the amplification product and reporting of reactions that amplify artefacts.
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Affiliation(s)
- Andreas Untergasser
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany. .,European Molecular Biology Laboratory (EMBL), Genomics Core Facility, 69117, Heidelberg, Germany.
| | - Jan M Ruijter
- Department of Medical Biology, Amsterdam University Medical Centres, Academic Medical Center, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, 69117, Heidelberg, Germany
| | - Maurice J B van den Hoff
- Department of Medical Biology, Amsterdam University Medical Centres, Academic Medical Center, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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15
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Song Y, Kim YT, Choi Y, Kim H, Yeom MH, Kim Y, Lee TJ, Lee KG, Im SG. All-in-One DNA Extraction Tube for Facilitated Real-Time Detection of Infectious Pathogens. Adv Healthc Mater 2021; 10:e2100430. [PMID: 34050626 DOI: 10.1002/adhm.202100430] [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: 03/07/2021] [Revised: 04/29/2021] [Indexed: 12/23/2022]
Abstract
An "all-in-one tube" platform is developed, where the genetic analysis involving DNA extraction, amplification, and detection can be performed in a single tube. The all-in-one tube consists of a polymerase chain reaction (PCR) tube in which the inner surface is conformally modified with a tertiary-amine-containing polymer to generate a strong electrostatic interaction with DNA. The all-in-one tube provides high DNA capture efficiency exceeding 80% from Escherichia coli O157: H7 pathogen at a wide range of DNA amount from 0.003 to 3 ng. Indeed, the use of the surface-functionalized PCR tube enables direct amplification and detection of the surface-captured DNA without the modification of standard real-time PCR instrument. Besides, this platform has sensitivity, selectivity, and reliability enough for accurate detection at the minimal infective dose of both gram-positive and negative pathogens. The all-in-one tube enables the direct molecular diagnosis, substantially reducing the labor-intensive pathogen detection steps while providing high compatibility with the currently established real-time PCR instruments, and illustrates its on-site applicability with convenience expandable to various genetic analyses including food safety testing, forensic analysis, and clinical diagnosis.
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Affiliation(s)
- Younseong Song
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Yong Tae Kim
- Department of Chemical Engineering & Biotechnology Korea Polytechnic University 237 Sangidaehak‐ro Siheung‐si 15073 Republic of Korea
| | - Yunho Choi
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Hogi Kim
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Min Hee Yeom
- Nanobio Application Team National NanoFab Center 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Yesol Kim
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Tae Jae Lee
- Nanobio Application Team National NanoFab Center 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Kyoung G. Lee
- Nanobio Application Team National NanoFab Center 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
- KAIST Institute for NanoCentury Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
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16
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Ramezani A. CtNorm: Real time PCR cycle of threshold (Ct) normalization algorithm. J Microbiol Methods 2021; 187:106267. [PMID: 34116107 DOI: 10.1016/j.mimet.2021.106267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/05/2021] [Accepted: 06/06/2021] [Indexed: 11/25/2022]
Abstract
In relative quantification with Real Time PCR (qRT-PCR,), accurate analysis requires equal amplification efficiency for both genes (Gene of interest and reference gene) and equal threshold values for all the samples. In this quantification method the expression level in treated samples will be calculated in comparison to the control group. We conducted the present study to design an algorithm for converting the data obtained from different runs containing identical standard samples into one run with the same amplification efficiency and threshold value. For this purpose, two formulas were designed; one to convert the amplification efficiency of the each run to 100%, and the other one for converting data from different runs into one run. Utilizing these two formulas, an algorithm was developed and named CtNorm. The online version of CtNorm algorithm is available at http://ctnorm.sums.ac.ir/. We used qRT-PCR technique to validate the accuracy of the designed algorithm for the normalization of four different human internal control genes. Normalizing the Ct values obtained from separate runs with the CtNorm algorithm has eliminated the differences and the average of the Ct values has become similar to the condition in which all the samples were amplified in a single run. The CtNorm algorithm could be utilized for equalizing the Ct values of several qRT-PCR runs with the same standard samples. The algorithm has also the ability to convert the amplification efficiency to 100% which is useful in absolute and relative quantification.
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Affiliation(s)
- Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
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17
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Ekka MM, Arya L, Patel BC. A systematic evaluation of 'Bidi - a hand-rolled cigarette' as a forensic DNA evidence. Forensic Sci Int 2021; 324:110821. [PMID: 34000618 DOI: 10.1016/j.forsciint.2021.110821] [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: 02/03/2021] [Revised: 04/10/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
Bidis are small handmade cigarettes consisting of ~0.2 g of tobacco flakes rolled in a dried leaf of 'Tendu' (Diospyros melanoxylon) or Piliostigma racemosum and tied with a thin thread. They have gained worldwide popularity among smokers and are often collected as forensic DNA evidence from crime scenes and processed similarly to cigarette butts. However, bidi's composition and manufacturing process differs distinctly from the cigarette, and hence the optimal processing for DNA analysis should not be assumed to be similar to cigarette butts. In the present study, the methodical evaluation of the bidi for DNA analysis is reported and an additional process of cell elution from bidi stubs prior to DNA extraction is systematically compared with the direct lysis of bidi stubs which is identical to the standard practice in forensic labs for cigarette butts. In terms of cell recovery from bidi stubs, the SDS based Cell Elution Buffer (CEB) proved to be better than Tween20 based CEB. The three components (cell-elute, supernatant, and processed stub) obtained after the cell elution process of smoked bidi stubs showed varying amounts of DNA. The cell-elute and processed stub exhibited high quality DNA, resulting in 90-100% of the samples giving a full STR profile. On the contrary, the directly lysed stubs yielded high quantity but low quality of DNA, resulting in only 40% of the samples with full STR profiles. The cell elution process enables three components namely cell-elute, supernatant and processed stub from the same bidi to be used for forensic DNA analysis, although the cell-elute proved to be the best source of DNA for STR profiling. The current study demonstrates that the additional cell elution process proved to be an essential step prior to DNA extraction procedure for bidi stubs.
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Affiliation(s)
- Molina Madhulika Ekka
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar 382007, Gujarat, India
| | - Lakshita Arya
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar 382007, Gujarat, India
| | - Bhargav C Patel
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar 382007, Gujarat, India.
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18
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Ruijter JM, Barnewall RJ, Marsh IB, Szentirmay AN, Quinn JC, van Houdt R, Gunst QD, van den Hoff MJB. Efficiency Correction Is Required for Accurate Quantitative PCR Analysis and Reporting. Clin Chem 2021; 67:829-842. [PMID: 33890632 DOI: 10.1093/clinchem/hvab052] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/19/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Quantitative PCR (qPCR) aims to measure the DNA or RNA concentration in diagnostic and biological samples based on the quantification cycle (Cq) value observed in the amplification curves. Results of qPCR experiments are regularly calculated as if all assays are 100% efficient or reported as just Cq, ΔCq, or ΔΔCq values. CONTENTS When the reaction shows specific amplification, it should be deemed to be positive, regardless of the observed Cq. Because the Cq is highly dependent on amplification efficiency that can vary among targets and samples, accurate calculation of the target quantity and relative gene expression requires that the actual amplification efficiency be taken into account in the analysis and reports. PCR efficiency is frequently derived from standard curves, but this approach is affected by dilution errors and hampered by properties of the standard and the diluent. These factors affect accurate quantification of clinical and biological samples used in diagnostic applications and collected in challenging conditions. PCR efficiencies determined from individual amplification curves avoid these confounders. To obtain unbiased efficiency-corrected results, we recommend absolute quantification with a single undiluted calibrator with a known target concentration and efficiency values derived from the amplification curves of the calibrator and the unknown samples. SUMMARY For meaningful diagnostics or biological interpretation, the reported results of qPCR experiments should be efficiency corrected. To avoid ambiguity, the Minimal Information for Publications on Quantitative Real-Time PCR Experiments (MIQE) guidelines checklist should be extended to require the methods that were used (1) to determine the PCR efficiency and (2) to calculate the reported target quantity and relative gene expression value.
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Affiliation(s)
- Jan M Ruijter
- Department of Medical Biology, Amsterdam University Medical Centres, Location Academic Medical Center, Amsterdam, the Netherlands
| | - Rebecca J Barnewall
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.,NSW Department of Primary Industries), Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Ian B Marsh
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Narellan, NSW, Australia
| | | | - Jane C Quinn
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.,NSW Department of Primary Industries), Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Robin van Houdt
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, Amsterdam, the Netherlands
| | - Quinn D Gunst
- Department of Medical Biology, Amsterdam University Medical Centres, Location Academic Medical Center, Amsterdam, the Netherlands
| | - Maurice J B van den Hoff
- Department of Medical Biology, Amsterdam University Medical Centres, Location Academic Medical Center, Amsterdam, the Netherlands
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19
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Xu J, Wang J, He S, Su X, Zhong Z, Zhong W, Yan L, Huang S, Yang J, Gao R, Zhang J, Zeng J, Zhang D, Li T, Zhang S, Ge S, Zhang J, Xia N. Accurate nucleic acid quantification in a single sample tube without the need for calibration. Anal Chim Acta 2021; 1167:338599. [PMID: 34049623 DOI: 10.1016/j.aca.2021.338599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/14/2021] [Accepted: 04/28/2021] [Indexed: 12/18/2022]
Abstract
Convenient and accurate nucleic acid quantification (NAQ) is crucial to clinical diagnosis, forensic medicine, veterinary medicine and food analysis. However, traditional NAQ relies on the preparation of a laborious, time-consuming and expensive calibration curve, which would also propagate pipette errors through serially dilutions. Besides, traditional NAQ is run in different tubes, which introduces bias from random tube-to-tube variations and is unable to detect inhibitors from biological samples. To solve these problems, a single-tube quantitative PCR (stqPCR) technique is proposed which enables accurate quantification without the need for a calibration curve. In this method, an internal quantitative standard DNA (IQS-DNA) for quantification was screened out by co-amplification with the target DNA. Then the difference between the quantification cycle value (ΔCq) of the IQS-DNA and the target DNA was used for NAQ. The method permitted high accuracy quantification with reliable data for concentrations in plasmid, serum standard, and clinical samples being confirmed (R2 values of 0.9951, 0.9889, and 0.9727, slope values of 1.011, 1.028, and 0.9327, and intercept values of -0.06037, -0.1486, and 0.3325, respectively). Accurate NAQ could also be achieved by stqPCR even though inhibitors were present in a sample; however, in the case of using a commercial assay kit, satisfactory performance was only attained after the same sample was diluted some 32-fold. Moreover, integration of the present method into a microfluidic system could achieve super-fast NAQ in less than 30 min and achieve super-fast "sample in, quantitative answer out" testing in less than 40 min. Thus, the stqPCR method present here would promote the development of NAQ in the laboratory and on site.
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Affiliation(s)
- Jiasu Xu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Jin Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China; School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Shuizhen He
- Haicang Hospital of Xiamen, Xiamen, 361026, China
| | - Xiaosong Su
- Xiang'an Hospital of Xiamen University, Xiamen, 361102, China
| | - Zecheng Zhong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Weibo Zhong
- Xiamen Innovax Biotech CO., LTD., Xiamen, 361022, China
| | - Lizhen Yan
- Haicang Hospital of Xiamen, Xiamen, 361026, China
| | - Shaolei Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Jiayu Yang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Runxin Gao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Jianbin Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Juntian Zeng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Dongxu Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Shiyin Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China.
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China.
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, 361102, China; School of Life Sciences, Xiamen University, Xiamen, 361102, China
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20
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Iwalokun BA, Olalekan A, Adenipekun E, Ojo O, Iwalokun SO, Mutiu B, Orija O, Adegbola R, Salako B, Akinloye O. Improving the Understanding of the Immunopathogenesis of Lymphopenia as a Correlate of SARS-CoV-2 Infection Risk and Disease Progression in African Patients: Protocol for a Cross-sectional Study. JMIR Res Protoc 2021; 10:e21242. [PMID: 33621190 PMCID: PMC7935252 DOI: 10.2196/21242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/05/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic, caused by SARS-CoV-2, continues to impact health systems throughout the world with serious medical challenges being imposed on many African countries like Nigeria. Although emerging studies have identified lymphopenia as a driver of cytokine storm, disease progression, and poor outcomes in infected patients, its immunopathogenesis, as well as environmental and genetic determinants, remain unclear. Understanding the interplay of these determinants in the context of lymphopenia and COVID-19 complications in patients in Africa may help with risk stratification and appropriate deployment of targeted treatment regimens with repurposed drugs to improve prognosis. OBJECTIVE This study is designed to investigate the role of vitamin D status, vasculopathy, apoptotic pathways, and vitamin D receptor (VDR) gene polymorphisms in the immunopathogenesis of lymphopenia among African people infected with SARS-CoV-2. METHODS This cross-sectional study will enroll 230 participants, categorized as "SARS-CoV-2 negative" (n=69), "COVID-19 mild" (n=32), "hospitalized" (n=92), and "recovered" (n=37), from two health facilities in Lagos, Nigeria. Sociodemographic data, travel history, and information on comorbidities will be obtained from case files and through a pretested, interview-based structured questionnaire. Venous blood samples (5 mL) collected between 8 AM and 10 AM and aliquoted into EDTA (ethylenediaminetetraacetic acid) and plain tubes will be used for complete blood count and CD4 T cell assays to determine lymphopenia (lymphocyte count <1000 cells/µL) and CD4 T lymphocyte levels, as well as to measure the concentrations of vitamin D, caspase 3, soluble vascular cell adhesion molecule-1 (sVCAM-1), and soluble Fas ligand (sFasL) using an autoanalyzer, flow cytometry, and ELISA (enzyme-linked immunosorbent assay) techniques. Genomic DNA will be extracted from the buffy coat and used as a template for the amplification of apoptosis-related genes (Bax, Bcl-2, BCL2L12) by polymerase chain reaction (PCR) and genotyping of VDR (Apa1, Fok1, and Bsm1) gene polymorphisms by the PCR restriction fragment length polymorphism method and capillary sequencing. Total RNA will also be extracted, reverse transcribed, and subsequently quantitated by reverse transcription PCR (RT-PCR) to monitor the expression of apoptosis genes in the four participant categories. Data analyses, which include a test of association between VDR gene polymorphisms and study outcomes (lymphopenia and hypovitaminosis D prevalence, mild/moderate and severe infections) will be performed using the R statistical software. Hardy-Weinberg equilibrium and linkage disequilibrium analyses for the alleles, genotypes, and haplotypes of the genotyped VDR gene will also be carried out. RESULTS A total of 45 participants comprising 37 SARS-CoV-2-negative and 8 COVID-19-recovered individuals have been enrolled so far. Their complete blood counts and CD4 T lymphocyte counts have been determined, and their serum samples and genomic DNA and RNA samples have been extracted and stored at -20 °C until further analyses. Other expected outcomes include the prevalence and distribution of lymphopenia and hypovitaminosis D in the control (SARS-CoV-2 negative), confirmed, hospitalized, and recovered SARS-CoV-2-positive participants; association of lymphopenia with CD4 T lymphocyte level, serum vitamin D, sVCAM-1, sFasL, and caspase 3 levels in hospitalized patients with COVID-19; expression levels of apoptosis-related genes among hospitalized participants with COVID-19, and those with lymphopenia compared to those without lymphopenia; and frequency distribution of the alleles, genotypes, and haplotypes of VDR gene polymorphisms in COVID-19-infected participants. CONCLUSIONS This study will aid in the genotypic and phenotypic stratification of COVID-19-infected patients in Nigeria with and without lymphopenia to enable biomarker discovery and pave the way for the appropriate and timely deployment of patient-centered treatments to improve prognosis. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/21242.
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Affiliation(s)
| | - Adesola Olalekan
- Department of Medical Laboratory Sciences, Faculty of Basic Medical Science, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Eyitayo Adenipekun
- Department of Medical Laboratory Sciences, Faculty of Basic Medical Science, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Olabisi Ojo
- Department of Natural Sciences, Albany State University, Georgia, GA, United States
| | | | - Bamidele Mutiu
- Department of Medical Microbiology & Parasitology, College of Medicine, Lagos State University, Lagos, Nigeria
| | - Oluseyi Orija
- Department of Public Health, National University, San Diego, CA, United States
| | - Richard Adegbola
- Microbiology Department, Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | - Oluyemi Akinloye
- Department of Medical Laboratory Sciences, Faculty of Basic Medical Science, College of Medicine, University of Lagos, Lagos, Nigeria
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21
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Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology of Prorocentrum minimum (Dinophyceae), a Harmful Algal Species. Microorganisms 2021; 9:microorganisms9030510. [PMID: 33670984 PMCID: PMC7997176 DOI: 10.3390/microorganisms9030510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Prorocentrum minimum is a species of marine dinoflagellate that occurs worldwide and can be responsible for harmful algal blooms (HABs). Some studies have reported it to produce tetrodotoxin; however, results have been inconsistent. qPCR and molecular barcoding (amplicon sequencing) using high-throughput sequencing have been increasingly applied to quantify HAB species for ecological analyses and monitoring. Here, we isolated a strain of P. minimum from eastern Australian waters, where it commonly occurs, and developed and validated a qPCR assay for this species based on a region of ITS rRNA in relation to abundance estimates from the cultured strain as determined using light microscopy. We used this tool to quantify and examine ecological drivers of P. minimum in Botany Bay, an estuary in southeast Australia, for over ~14 months in 2016–2017. We compared abundance estimates using qPCR with those obtained using molecular barcoding based on an 18S rRNA amplicon. There was a significant correlation between the abundance estimates from amplicon sequencing and qPCR, but the estimates from light microscopy were not significantly correlated, likely due to the counting method applied. Using amplicon sequencing, ~600 unique actual sequence variants (ASVs) were found, much larger than the known phytoplankton diversity from this region. P. minimum abundance in Botany Bay was found to be significantly associated with lower salinities and higher dissolved CO2 levels.
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22
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Nairz M, Bellmann-Weiler R, Ladstätter M, Schüllner F, Zimmermann M, Koller AM, Blunder S, Naschberger H, Klotz W, Herold M, Kerndler S, Jeske M, Haschka D, Petzer V, Schroll A, Sonnweber T, Tancevski I, Fritsche G, de Araujo MEG, Stasyk T, Huber LA, Griesmacher A, Theurl I, Weiss G. Overcoming limitations in the availability of swabs systems used for SARS-CoV-2 laboratory diagnostics. Sci Rep 2021; 11:2261. [PMID: 33500503 PMCID: PMC7838421 DOI: 10.1038/s41598-021-81782-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/03/2021] [Indexed: 01/21/2023] Open
Abstract
The diagnosis of COVID-19 relies on the direct detection of SARS-CoV-2 RNA in respiratory specimens by RT-PCR. The pandemic spread of the disease caused an imbalance between demand and supply of materials and reagents needed for diagnostic purposes including swab sets. In a comparative effectiveness study, we conducted serial follow-up swabs in hospitalized laboratory-confirmed COVID-19 patients. We assessed the diagnostic performance of an in-house system developed according to recommendations by the US CDC. In a total of 96 serial swabs, we found significant differences in the accuracy of the different swab systems to generate a positive result in SARS-CoV-2 RT-PCR, ranging from around 50 to 80%. Of note, an in-house swab system was superior to most commercially available sets as reflected by significantly lower Ct values of viral genes. Thus, a simple combination of broadly available materials may enable diagnostic laboratories to bypass global limitations in the supply of swab sets.
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Affiliation(s)
- Manfred Nairz
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria.
| | - Rosa Bellmann-Weiler
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Miriam Ladstätter
- Hospital Pharmacy, University Hospital of Innsbruck, Innsbruck, Austria
| | - Falko Schüllner
- Hospital Pharmacy, University Hospital of Innsbruck, Innsbruck, Austria
| | - Martina Zimmermann
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Anna-Maria Koller
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Silvia Blunder
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Helene Naschberger
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Werner Klotz
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Manfred Herold
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Sylvia Kerndler
- Hospital Pharmacy, University Hospital of Innsbruck, Innsbruck, Austria
| | - Martina Jeske
- Hospital Pharmacy, University Hospital of Innsbruck, Innsbruck, Austria
| | - David Haschka
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Verena Petzer
- Department of Internal Medicine V, Hematology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Schroll
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Thomas Sonnweber
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Ivan Tancevski
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Gernot Fritsche
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Mariana E G de Araujo
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Taras Stasyk
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas A Huber
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Griesmacher
- Central Institute of Medical and Chemical Laboratory Diagnostics, University Hospital of Innsbruck, Innsbruck, Austria
| | - Igor Theurl
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Pneumology, Medical University of Innsbruck, Anichstr. 35, 6020, Innsbruck, Austria
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Lee D, Cho S, Chae S, Choi W, Han M. Evaluation of a test method to detect hepatitis A virus in salted shellfish. J Food Saf 2021. [DOI: 10.1111/jfs.12883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deog‐Yong Lee
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases Korea Disease Control and Prevention Agency Cheonhju Republic of Korea
| | - Seung‐Rye Cho
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases Korea Disease Control and Prevention Agency Cheonhju Republic of Korea
| | - Su‐Jin Chae
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases Korea Disease Control and Prevention Agency Cheonhju Republic of Korea
| | - Wooyoung Choi
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases Korea Disease Control and Prevention Agency Cheonhju Republic of Korea
| | - Myung‐Guk Han
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases Korea Disease Control and Prevention Agency Cheonhju Republic of Korea
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24
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Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter. Sci Rep 2020; 10:21531. [PMID: 33298993 PMCID: PMC7725969 DOI: 10.1038/s41598-020-77304-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/10/2020] [Indexed: 11/29/2022] Open
Abstract
Environmental DNA (eDNA) is increasingly popular as a useful non-invasive method to monitor and study biodiversity and community structure in freshwater and marine environments. To effectively extract eDNA from the filter surface is a fundamental factor determining the representativeness of the samples. We improved the eDNA extraction efficiency of an established Sterivex method by 12- to 16-fold using a larger volume of lysis buffer mix coupled with backflushing the cartridges. The DNeasy extraction column could be overloaded when the environmental sample input is high, possibly due to a higher nonspecific binding present in environmental samples, thus resulting in a relatively lower quantity measured. Therefore, we included an internal control DNA in the extraction to monitor the extraction and purification efficiencies in field samples, which is crucial for quantification of original eDNA concentration. The use of Takara Probe qPCR Mix supplemented with protein-based additives improved the robustness of the real time PCR assay on inhibitor-rich environmental samples, but prior purification by Qiagen PowerClean Pro Cleanup kit could be essential for inhibitor-rich water samples, even though the recovery rate was unexpectedly low (average 33.0%). The improved extraction and quantification complement the qualitative analyses including metabarcoding and metagenomics in field application.
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25
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Gouker FE, Guo Y, Pooler MR. Using acetone for rapid PCR-amplifiable DNA extraction from recalcitrant woody plant taxa. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11403. [PMID: 33344094 PMCID: PMC7742202 DOI: 10.1002/aps3.11403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/17/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Quick and effective DNA extraction from plants for subsequent PCR amplification is sometimes challenging when working across diverse plant taxa that may contain a variety of inhibitory compounds. Time-consuming methods may be needed to overcome these inhibitory effects as well as the effects of various preservation and collection methods to extract DNA from leaf samples. Our objective was to develop a rapid DNA extraction protocol that could be used with diverse plant taxa to produce high-quality DNA suitable for downstream PCR applications. METHODS AND RESULTS We tested the efficacy of acetone in extracting DNA from fresh, frozen, oven-dried, acetone-fixed, and herbarium leaf material of 22 species from 16 woody and herbaceous plant families. An improved simplified DNA extraction protocol was developed using acetone-fixed leaf material. The addition of 1% sodium dodecyl sulfate solution resulted in the optimal extraction from all tissue samples. The DNA resulting from the extraction protocol was readily amplified using real-time PCR assays. CONCLUSIONS The protocol described here resulted in the extraction of DNA from recalcitrant plant species that was of sufficient quality and quantity for PCR amplification, as indicated by the low threshold cycle values from real-time assays. This method is simple, fast, and cost-effective, and is a reliable tool for extracting high-quality DNA from plant material containing PCR inhibitors.
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Affiliation(s)
- Fred E. Gouker
- U.S. Department of Agriculture Agricultural Research ServiceU.S. National Arboretum, Floral and Nursery Plants Research UnitBeltsvilleMarylandUSA
| | - Yonghong Guo
- U.S. Department of Agriculture Agricultural Research ServiceU.S. National Arboretum, Floral and Nursery Plants Research UnitBeltsvilleMarylandUSA
| | - Margaret R. Pooler
- U.S. Department of Agriculture Agricultural Research ServiceU.S. National Arboretum, Floral and Nursery Plants Research UnitBeltsvilleMarylandUSA
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26
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Simon N, Shallat J, Williams Wietzikoski C, Harrington WE. Optimization of Chelex 100 resin-based extraction of genomic DNA from dried blood spots. Biol Methods Protoc 2020; 5:bpaa009. [PMID: 32665976 PMCID: PMC7334876 DOI: 10.1093/biomethods/bpaa009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/11/2020] [Accepted: 04/24/2020] [Indexed: 11/13/2022] Open
Abstract
Dried blood spots (DBS) are widely utilized as part of universal newborn screening and as a means of transporting samples from field sites. We use DBS from African field sites to assess for rare maternal-fetal cell exchange during pregnancy known as microchimerism. We aimed to develop a protocol to maximize the quantity of high-quality genomic DNA (gDNA) extracted from DBS. The total gDNA yield obtained from control DBS utilizing a Qiagen-based protocol and a Chelex® 100 resin-based protocol was first compared. Variations of the Chelex® protocol were subsequently tested to develop an optimized protocol. The gDNA was quantified by qPCR targeting the human beta-globin gene. DNA yield for a given experimental condition was normalized to a Chelex® control performed on the same day, and the total yields were compared using a Student's t-test. The control Chelex® protocol yielded 590% more DNA than the QIAamp® DNA Blood Mini Kit . The absolute efficiency of the control Chelex® protocol was 54%, compared to an absolute efficiency of 9% for the QIAamp® DNA Blood Mini Kit. Modification of the Chelex® protocol to include a second heat precipitation from the same DBS increased the gDNA yield by 29% (P < 0.001). Our optimized protocol including this modification increased the absolute efficiency of extraction to 68%. The gDNA extracted using the Chelex® protocol was stable through repeated freeze-thaw cycles. In a mock microchimerism experiment, rare donor alleles at a frequency of 10 in 100 000 could be identified in gDNA from DBS extracted using the optimized Chelex® protocol. Our findings may be of significance for a diverse range of applications that utilize DBS and require high-quality DNA, including newborn screening programs, pathogen and drug resistance screening from remote field sites, forensics, and rare allele detection.
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Affiliation(s)
- Neta Simon
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Jaclyn Shallat
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Whitney E Harrington
- Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
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27
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Khairil Mokhtar NF, El Sheikha AF, Azmi NI, Mustafa S. Potential authentication of various meat-based products using simple and efficient DNA extraction method. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:1687-1693. [PMID: 31803942 DOI: 10.1002/jsfa.10183] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND The growth of halal food consumption worldwide has resulted in an increase in the request for halal authentication. DNA-based detection using powerful real-time polymerase chain reaction (PCR) technique has been shown to be highly specific and sensitive authentication tool. The efficient DNA extraction method in terms of quality and quantity is a backbone step to obtain successful real-time PCR assays. In this study, different DNA extraction methods using three lysis buffers were evaluated and developed to recommend a much more efficient method as well as achieve a successful detection using real-time PCR. RESULTS The lysis buffer 2 (LB2) has been shown to be the best lysis buffer for DNA extraction from both raw and processed meat samples comparing to other lysis buffers tested. Hence, the LB2 has been found to be ideal to detect meat and porcine DNAs by real-time PCR using pairs of porcine specific primers and universal primers which amplified at 119 bp fragment and 93 bp fragment, respectively. This assay allows detection as low as 0.0001 ng of DNA. Higher efficiency and sensitivity of real-time PCR via a simplified DNA extraction method using LB2 have been observed, as well as a reproducible and high correlation coefficient (R2 = 0.9979) based on the regression analysis of the standard curve have been obtained. CONCLUSION This study has established a fast, simple, inexpensive and efficient DNA extraction method that is feasible for raw and processed meat products. This extraction technique allows an accurate DNA detection by real-time PCR and can also be implemented to assist the halal authentication of various meat-based products available in the market. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Nur Fadhilah Khairil Mokhtar
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Aly Farag El Sheikha
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, 25 University Private Ottawa, ON K1N, 6N5, Canada
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang, China
- Department of Food Science and Technology, Faculty of Agriculture, Minufiya University, 32511 Shibin El Kom, Minufiya Government, Egypt
| | - Nur Izzah Azmi
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Shuhaimi Mustafa
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
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Trubl G, Roux S, Solonenko N, Li YF, Bolduc B, Rodríguez-Ramos J, Eloe-Fadrosh EA, Rich VI, Sullivan MB. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ 2019; 7:e7265. [PMID: 31309007 PMCID: PMC6612421 DOI: 10.7717/peerj.7265] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/07/2019] [Indexed: 11/29/2022] Open
Abstract
Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1–2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were successfully recovered by using the Accel-NGS 1S Plus Library Kit. While ssDNA viruses were identified in all three soil types, none were identified in the samples that used bead-beating, suggesting this lysis method may impact recovery. Further, 13 ssDNA vOTUs were identified compared to 582 dsDNA vOTUs, and the ssDNA vOTUs only accounted for ∼4% of the assembled reads, implying dsDNA viruses were dominant in these samples. This optimized approach was combined with the previously published viral resuspension protocol into a sample-to-virome protocol for soils now available at protocols.io, where community feedback creates ‘living’ protocols. This collective approach will be particularly valuable given the high physicochemical variability of soils, which will may require considerable soil type-specific optimization. This optimized protocol provides a starting place for developing quantitatively-amplified viromic datasets and will help enable viral ecogenomic studies on organic-rich soils.
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Affiliation(s)
- Gareth Trubl
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America.,Current affiliation: Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States of America
| | - Simon Roux
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, United States of America
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Josué Rodríguez-Ramos
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America.,Current affiliation: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States of America
| | - Emiley A Eloe-Fadrosh
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, United States of America
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, United States of America.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States of America
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Machado MC, Vimbela GV, Nilsson M, Dallaire S, Wu R, Tripathi A. Rapid electrophoretic recovery of DNA from dried blood spots. Electrophoresis 2019; 40:1812-1819. [PMID: 31095765 DOI: 10.1002/elps.201800363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 03/31/2019] [Accepted: 04/23/2019] [Indexed: 11/09/2022]
Abstract
Large-scale genetic screening of neonatal dried blood spots for episomal DNA has a great potential to lower patient mortality and morbidity through early diagnosis of primary immunodeficiencies. However, DNA extraction from the surface of dried blood spots remains one of the most time consuming, costly, and labor-intensive parts of DNA analysis. In the present study, we developed and optimized a rapid methodology using only 50 V and heat to extract episomal DNA from dried blood spots prepared from diagnostic cord blood samples. This electric field DNA extraction is the first methodology to use an electric field to extract episomal DNA from a dried blood spot. This 25-minute procedure has one of the lowest times for the extraction of episomal DNA found within the literature and this novel procedure not only negates the need for costly treatment and wash steps, but reduces the time of manual procedures by more than 30 min while retaining the 75-80% of the yield. Combined with real-time PCR, this novel method of electric field extraction not only provides an effective tool for the large scale genetic analysis of neonates, but a key step forward in the simplification and standardization of diagnostic testing.
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Affiliation(s)
- Mary C Machado
- Center for Biomedical Engineering, School of Engineering Brown University, Providence, RI
| | - Gina V Vimbela
- Center for Biomedical Engineering, School of Engineering Brown University, Providence, RI
| | | | | | - Rongcong Wu
- PerkinElmer, 940 Winter Street, Waltham, Massachusetts, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering Brown University, Providence, RI
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30
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Paulino PG, Pires MS, Silva CBD, Peckle M, Costa RLD, Vitari GLV, Abreu APMD, Almosny NRP, Massard CL, Santos HA. Comparison of heat shock protein 70 kDa and 18S rDNA genes for molecular detection and phylogenetic analysis of Babesia vogeli from whole blood of naturally infected dogs. Ticks Tick Borne Dis 2018; 9:556-562. [PMID: 29409719 DOI: 10.1016/j.ttbdis.2018.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 01/11/2018] [Accepted: 01/24/2018] [Indexed: 11/30/2022]
Abstract
A total of 300 blood samples of domiciliated dogs in rural and urban areas of southeast Rio de Janeiro State, Brazil, were used to compare the 18S ribosomal DNA region (18S rDNA) and the heat shock protein 70 kDa (hsp70) gene for molecular detection of Babesia vogeli and to perform a phylogenetic study comparing the two genes for B. vogeli classification. Using conventional polymerase chain reaction (cPCR) of 18S rDNA and hsp70 sequences, we were able to detect B. vogeli with the same sensitivity (96.15%) and specificity (99.63%). However, sequencing revealed one false positive (Rangelia sp.) for 18S rDNA that was not detected by hsp70. This is the first report of an organism closely related to the Rangelia vitalii parasite of dogs in Brazil. In the hsp70-cPCR and hsp70-qPCR comparison, 15.66% of samples were considered positive by quantitative (q)PCR, significantly more than was detected by cPCR (8.66%). In addition to the high conservation of the 18S rDNA, phylogenetic analysis showed that the hsp70 gene can be used to describe phylogenetic relationships between canine piroplasmids with more accuracy than 18S rDNA. According to these findings, the qPCR method has greater sensitivity than cPCR for detection of B. vogeli in naturally infected dogs. The hsp70-qPCR detection limit was 10 copies, with an efficiency of 100.30% and a determination coefficient (R2) of 0.998. The development of this qPCR method provides a highly sensitive approach for B. vogeli molecular detection and a tool that is capable of quantifying parasitemia levels in whole blood samples from dogs. The primers and probes were designed to be specific for B. vogeli, though analytical specificity of the assay has not been tested in vitro with DNA of certain Babesia species that infect dogs. The hsp70 gene is a precise molecular marker for Babesia phylogeny, especially species that infect dogs.
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Affiliation(s)
- Patrícia G Paulino
- Department of Epidemiology and Public Health Veterinary Institute, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcus S Pires
- Department of Animal Parasitology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudia B da Silva
- Department of Epidemiology and Public Health Veterinary Institute, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maristela Peckle
- Department of Animal Parasitology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata L da Costa
- Department of Animal Parasitology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriela L V Vitari
- Department of Epidemiology and Public Health Veterinary Institute, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Paula M de Abreu
- Department of Animal Parasitology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nádia R P Almosny
- Departament of Veterinary Clinic and Pathology, Federal Fluminense University, Niteroi, Brazil
| | - Carlos L Massard
- Department of Animal Parasitology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Huarrisson A Santos
- Department of Epidemiology and Public Health Veterinary Institute, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil.
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Patel K, Nagel M, Wesolowski M, Dees S, Rivera-Milla E, Geldmacher C, Dheda K, Hoelscher M, Labugger I. Evaluation of a Urine-Based Rapid Molecular Diagnostic Test with Potential to Be Used at Point-of-Care for Pulmonary Tuberculosis: Cape Town Cohort. J Mol Diagn 2017; 20:215-224. [PMID: 29269279 DOI: 10.1016/j.jmoldx.2017.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 10/02/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022] Open
Abstract
Tuberculosis (TB) diagnosis among sputum-scarce patients is time consuming. Thus, a nonsputum diagnostic alternative is urgently needed. The Mycobacterium tuberculosis-specific transrenal (Tr) DNA from urine is a potential target for TB diagnostics. In this study, a new urine-based Tr-DNA molecular assay was evaluated for diagnosis of pulmonary tuberculosis among 428 adults suspected of having pulmonary TB (164 HIV positive, 263 HIV negative) from Cape Town, South Africa. Tr-DNA was isolated from 4 mL of EDTA urine, and a rapid, double-stranded, primer-based PCR method was performed targeting the Mycobacterium tuberculosis-specific direct repeat region. Each Tr-DNA eluate was tested in triplicate using an automated molecular analyzer with controls included in each test. With liquid culture used as the gold standard, the Tr-DNA assay showed sensitivity of 42.9% (n = 75/175; 95% CI, 35.4%-50.5%) and specificity of 88.6% (n = 210/237; 95% CI, 83.9%-92.4%). Among HIV-infected patients with TB, sensitivity and specificity were 45.2% and 89.0%, respectively. The combination of smear microscopy and Tr-DNA increased the sensitivity to 83.8% (smear microscopy alone, 75.1%), with 96.6% specificity. This study indicates that Tr-DNA has a moderate specificity with low sensitivity for diagnosis of pulmonary TB. Despite low sensitivity, this diagnostic test may have potential in combination with smear microscopy to support TB diagnosis in HIV-endemic regions, where sputum-scarce patients are common.
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Affiliation(s)
- Krutarth Patel
- Alere Technologies GmbH, Jena, Germany; Center for International Health, University of Munich, Munich, Germany.
| | | | | | | | | | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany; German Center for Infection Research, Munich, Germany
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology & Clinical Immunology, Department of Medicine and UCT Lung Institute, University of Cape Town, Cape Town, South Africa
| | - Michael Hoelscher
- Center for International Health, University of Munich, Munich, Germany; Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany; German Center for Infection Research, Munich, Germany
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Fabre AL, Luis A, Colotte M, Tuffet S, Bonnet J. High DNA stability in white blood cells and buffy coat lysates stored at ambient temperature under anoxic and anhydrous atmosphere. PLoS One 2017; 12:e0188547. [PMID: 29190767 PMCID: PMC5708797 DOI: 10.1371/journal.pone.0188547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/30/2017] [Indexed: 01/28/2023] Open
Abstract
Conventional storage of blood-derived fractions relies on cold. However, lately, ambient temperature preservation has been evaluated by several independent institutions that see economic and logistic advantages in getting rid of the cold chain. Here we validated a novel procedure for ambient temperature preservation of DNA in white blood cell and buffy coat lysates based on the confinement of the desiccated biospecimens under anoxic and anhydrous atmosphere in original hermetic minicapsules. For this validation we stored encapsulated samples either at ambient temperature or at several elevated temperatures to accelerate aging. We found that DNA extracted from stored samples was of good quality with a yield of extraction as expected. Degradation rates were estimated from the average fragment size of denatured DNA run on agarose gels and from qPCR reactions. At ambient temperature, these rates were too low to be measured but the degradation rate dependence on temperature followed Arrhenius’ law, making it possible to extrapolate degradation rates at 25°C. According to these values, the DNA stored in the encapsulated blood products would remain larger than 20 kb after one century at ambient temperature. At last, qPCR experiments demonstrated the compatibility of extracted DNA with routine DNA downstream analyses. Altogether, these results showed that this novel storage method provides an adequate environment for ambient temperature long term storage of high molecular weight DNA in dehydrated lysates of white blood cells and buffy coats.
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Affiliation(s)
- Anne-Lise Fabre
- Imagene, R&D department, Université de Bordeaux, ENSTBB, 146 Rue Léo Saignat, Bordeaux, France
- Imagene, production platform, Rue Henri Desbruères, Genopole campus 1, Bât 6, Evry, France
- * E-mail:
| | - Aurélie Luis
- Imagene, R&D department, Université de Bordeaux, ENSTBB, 146 Rue Léo Saignat, Bordeaux, France
| | - Marthe Colotte
- Imagene, production platform, Rue Henri Desbruères, Genopole campus 1, Bât 6, Evry, France
| | - Sophie Tuffet
- Imagene, R&D department, Université de Bordeaux, ENSTBB, 146 Rue Léo Saignat, Bordeaux, France
| | - Jacques Bonnet
- Imagene, R&D department, Université de Bordeaux, ENSTBB, 146 Rue Léo Saignat, Bordeaux, France
- Institut Bergonié- Université de Bordeaux, INSERM U1218, 229 Cours de l'Argonne, Bordeaux, France
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Uzair A, Rasool N, Wasim M. Evaluation of different methods for DNA extraction from human burnt bones and the generation of genetic profiles for identification. MEDICINE, SCIENCE, AND THE LAW 2017; 57:159-166. [PMID: 28820349 DOI: 10.1177/0025802417723808] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bone exposure to heat in the presence of moisture breaks the phosphodiester bonds of the backbone, leaving sheared DNA in bone cells. This also limits the possibility of generating a complete profile of the victim. With the increasing incidence of fire outbreaks over the past few years, a paradigm shift to establish identity has been observed, from morphological identification of victims to STR profiling. For this study, 10 bone samples were taken from burnt human bodies that were recovered from different fire outbreak scenes. The DNA from these burnt human tissues was isolated using four different extraction methods: the organic extraction method, the total demineralisation method, the Qiagen kit method, and the Chelex extraction method. STR profiles of victims were generated on a genetic analyser using an AmpFlSTR Identifiler® Plus Kit and analysed on Gene Mapper ID-X. DNA isolated from bones using the total demineralisation extraction method and organic extraction method was of the highest quality due to the efficient removal of inhibitors. DNA obtained using these two methods successfully generated the STR profiles of the victims. The quality of isolated DNA obtained through the Qiagen kit was comparatively low, but STR profiles of the victims were successfully generated. The Chelex kit failed to extract good quality DNA of high quantity from the burnt bones, encountering inhibition in all samples at varying degrees. This study concludes that total demineralisation and the Qiagen kit are sophisticated and reliable methods to obtain a good yield of DNA from burnt human bones, which can be used for the identification of victims.
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Affiliation(s)
- Anum Uzair
- 1 66920 Institute of Biochemistry and Biotechnology (IBBT) , UVAS, Pakistan
| | - Nouman Rasool
- 2 Department of Life Sciences, University of Management and Technology, Pakistan
| | - Muhammad Wasim
- 1 66920 Institute of Biochemistry and Biotechnology (IBBT) , UVAS, Pakistan
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Vázquez D, Cutrín JM, Olveira JG, Dopazo CP. Design and validation of a RT-qPCR procedure for diagnosis and quantification of most types of infectious pancreatic necrosis virus using a single pair of degenerated primers. JOURNAL OF FISH DISEASES 2017; 40:1155-1167. [PMID: 28026015 DOI: 10.1111/jfd.12590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 06/06/2023]
Abstract
Infectious pancreatic necrosis virus (IPNV) is an important virus which affects the salmonid aquaculture industry worldwide; therefore, it is important to develop rapid and reliable methods of diagnosis to detect the disease at early stages. Nowadays, RT-qPCR is replacing other methods because it provides additional information on the viral load, which is important to have a better understanding of the virus replication level and of the stage of the infection and its risk level. The main problem stems from the high diversity of this virus, which can compromise the reliability of the diagnosis. In this study, we have designed an RT-qPCR procedure for diagnosis and quantification of IPNV based on a single pair of primers targeted to segment B. The procedure has been validated, in vitro and in vivo, testing two different types of standards against seven reference strains and 23 field isolates from different types. The procedure is reliable for the detection of any type, with a detection limit of 31 TCID50 mL-1 , 50 pfu mL-1 or 66 RNA copies mL-1 , depending on the standard. All the standard curves showed high reliability (R2 > 0.95). The results support the high reliability of this new procedure for the diagnosis and quantification of IPNV.
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Affiliation(s)
- D Vázquez
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - J M Cutrín
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - J G Olveira
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - C P Dopazo
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Lin HT, Okumura T, Yatsuda Y, Ito S, Nakauchi H, Otsu M. Application of Droplet Digital PCR for Estimating Vector Copy Number States in Stem Cell Gene Therapy. Hum Gene Ther Methods 2017; 27:197-208. [PMID: 27763786 PMCID: PMC5111482 DOI: 10.1089/hgtb.2016.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Stable gene transfer into target cell populations via integrating viral vectors is widely used in stem cell gene therapy (SCGT). Accurate vector copy number (VCN) estimation has become increasingly important. However, existing methods of estimation such as real-time quantitative PCR are more restricted in practicality, especially during clinical trials, given the limited availability of sample materials from patients. This study demonstrates the application of an emerging technology called droplet digital PCR (ddPCR) in estimating VCN states in the context of SCGT. Induced pluripotent stem cells (iPSCs) derived from a patient with X-linked chronic granulomatous disease were used as clonable target cells for transduction with alpharetroviral vectors harboring codon-optimized CYBB cDNA. Precise primer–probe design followed by multiplex analysis conferred assay specificity. Accurate estimation of per-cell VCN values was possible without reliance on a reference standard curve. Sensitivity was high and the dynamic range of detection was wide. Assay reliability was validated by observation of consistent, reproducible, and distinct VCN clustering patterns for clones of transduced iPSCs with varying numbers of transgene copies. Taken together, use of ddPCR appears to offer a practical and robust approach to VCN estimation with a wide range of clinical and research applications.
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Affiliation(s)
- Huan-Ting Lin
- 1 Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan .,2 Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan
| | - Takashi Okumura
- 2 Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan
| | | | - Satoru Ito
- 3 Life Science Division, Bio-Rad Laboratories , Tokyo, Japan
| | - Hiromitsu Nakauchi
- 1 Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan .,4 Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford, California
| | - Makoto Otsu
- 1 Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan .,2 Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan
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Brzobohatá K, Drozdová E, Smutný J, Zeman T, Beňuš R. Comparison of Suitability of the Most Common Ancient DNA Quantification Methods. Genet Test Mol Biomarkers 2017; 21:265-271. [DOI: 10.1089/gtmb.2016.0197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Kristýna Brzobohatá
- Laboratory of Biological and Molecular Anthropology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Eva Drozdová
- Laboratory of Biological and Molecular Anthropology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Smutný
- Biovendor, Laboratory Medicine, Brno, Czech Republic
| | - Tomáš Zeman
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Radoslav Beňuš
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
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Luchi N, Capretti P, Pazzagli M, Pinzani P. Powerful qPCR assays for the early detection of latent invaders: interdisciplinary approaches in clinical cancer research and plant pathology. Appl Microbiol Biotechnol 2016; 100:5189-204. [PMID: 27112348 DOI: 10.1007/s00253-016-7541-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/07/2016] [Accepted: 04/10/2016] [Indexed: 12/29/2022]
Abstract
Latent invaders represent the first step of disease before symptoms occur in the host. Based on recent findings, tumors are considered to be ecosystems in which cancer cells act as invasive species that interact with the native host cell species. Analogously, in plants latent fungal pathogens coevolve within symptomless host tissues. For these reasons, similar detection approaches can be used for an early diagnosis of the invasion process in both plants and humans to prevent or reduce the spread of the disease. Molecular tools based on the evaluation of nucleic acids have been developed for the specific, rapid, and early detection of human diseases. During the last decades, these techniques to assess and quantify the proliferation of latent invaders in host cells have been transferred from the medical field to different areas of scientific research, such as plant pathology. An improvement in molecular biology protocols (especially referring to qPCR assays) specifically designed and optimized for detection in host plants is therefore advisable. This work is a cross-disciplinary review discussing the use of a methodological approach that is employed within both medical and plant sciences. It provides an overview of the principal qPCR tools for the detection of latent invaders, focusing on comparisons between clinical cancer research and plant pathology, and recent advances in the early detection of latent invaders to improve prevention and control strategies.
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Affiliation(s)
- Nicola Luchi
- National Research Council (IPSP-CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019, Sesto Fiorentino Firenze, Italy
| | - Paolo Capretti
- National Research Council (IPSP-CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019, Sesto Fiorentino Firenze, Italy
- Department of Agri-Food Productions and Environmental Sciences (DiSPAA), University of Florence, Piazzale delle Cascine 28, Florence, Italy
| | - Mario Pazzagli
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence, Viale Pieraccini, 6, 50139, Firenze, Italy
| | - Pamela Pinzani
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence, Viale Pieraccini, 6, 50139, Firenze, Italy.
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Grass G, Ahrens B, Schleenbecker U, Dobrzykowski L, Wagner M, Krüger C, Wölfel R. Technical Note: Simple, scalable, and sensitive protocol for retrieving Bacillus anthracis (and other live bacteria) from heroin. Forensic Sci Int 2016; 259:32-5. [DOI: 10.1016/j.forsciint.2015.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/19/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
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Nadkarni A, Burns JA, Gandolfi A, Chowdhury MA, Cartularo L, Berens C, Geacintov NE, Scicchitano DA. Nucleotide Excision Repair and Transcription-coupled DNA Repair Abrogate the Impact of DNA Damage on Transcription. J Biol Chem 2016; 291:848-61. [PMID: 26559971 PMCID: PMC4705403 DOI: 10.1074/jbc.m115.685271] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/23/2015] [Indexed: 11/06/2022] Open
Abstract
DNA adducts derived from carcinogenic polycyclic aromatic hydrocarbons like benzo[a]pyrene (B[a]P) and benzo[c]phenanthrene (B[c]Ph) impede replication and transcription, resulting in aberrant cell division and gene expression. Global nucleotide excision repair (NER) and transcription-coupled DNA repair (TCR) are among the DNA repair pathways that evolved to maintain genome integrity by removing DNA damage. The interplay between global NER and TCR in repairing the polycyclic aromatic hydrocarbon-derived DNA adducts (+)-trans-anti-B[a]P-N(6)-dA, which is subject to NER and blocks transcription in vitro, and (+)-trans-anti-B[c]Ph-N(6)-dA, which is a poor substrate for NER but also blocks transcription in vitro, was tested. The results show that both adducts inhibit transcription in human cells that lack both NER and TCR. The (+)-trans-anti-B[a]P-N(6)-dA lesion exhibited no detectable effect on transcription in cells proficient in NER but lacking TCR, indicating that NER can remove the lesion in the absence of TCR, which is consistent with in vitro data. In primary human cells lacking NER, (+)-trans-anti-B[a]P-N(6)-dA exhibited a deleterious effect on transcription that was less severe than in cells lacking both pathways, suggesting that TCR can repair the adduct but not as effectively as global NER. In contrast, (+)-trans-anti-B[c]Ph-N(6)-dA dramatically reduces transcript production in cells proficient in global NER but lacking TCR, indicating that TCR is necessary for the removal of this adduct, which is consistent with in vitro data showing that it is a poor substrate for NER. Hence, both global NER and TCR enhance the recovery of gene expression following DNA damage, and TCR plays an important role in removing DNA damage that is refractory to NER.
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Affiliation(s)
- Aditi Nadkarni
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - John A Burns
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - Alberto Gandolfi
- the Dipartimento di Matematica e Informatica "Ulisse Dini," Università di Firenze, 50134 Firenze, Italy, the Division of Science, New York University Abu Dhabi, Post Office Box 129188, Abu Dhabi, United Arab Emirates
| | - Moinuddin A Chowdhury
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - Laura Cartularo
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - Christian Berens
- the Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Jena, Germany, 07743, and
| | - Nicholas E Geacintov
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003
| | - David A Scicchitano
- From the Departments of Biology and Chemistry, New York University, New York, New York 10003, the Division of Science, New York University Abu Dhabi, Post Office Box 129188, Abu Dhabi, United Arab Emirates
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40
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Li M, Ishiguro Y, Kageyama K, Zhu Z. A simple method for normalization of DNA extraction to improve the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR. Lett Appl Microbiol 2015; 61:179-85. [PMID: 25970140 DOI: 10.1111/lam.12441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED Most of the current research into the quantification of soil-borne pathogenic oomycetes lacks determination of DNA extraction efficiency, probably leading to an incorrect estimation of DNA quantity. In this study, we developed a convenient method by using a 100 bp artificially synthesized DNA sequence derived from the mitochondrion NADH dehydrogenase subunit 2 gene of Thunnus thynnus as a control to determine the DNA extraction efficiency. The control DNA was added to soils and then co-extracted along with soil genomic DNA. DNA extraction efficiency was determined by the control DNA. Two different DNA extraction methods were compared and evaluated using different types of soils, and the commercial kit was proved to give more consistent results. We used the control DNA combined with real-time PCR to quantify the oomycete DNAs from 12 naturally infested soils. Detectable target DNA concentrations were three to five times higher after normalization. Our tests also showed that the extraction efficiencies varied on a sample-to-sample basis and were <50%. Therefore, the method introduced here is simple and useful for the accurate quantification of soil-borne pathogenic oomycetes. SIGNIFICANCE AND IMPACT OF THE STUDY Oomycetes include many important plant pathogens. Accurate quantification of these pathogens is essential in the management of diseases. This study reports an easy method utilizing an external DNA control for the normalization of DNA extraction by real-time PCR. By combining two different efficient soil DNA extraction methods, the developed quantification method dramatically improved the results. This study also proves that the developed normalization method is necessary and useful for the accurate quantification of soil-borne plant pathogenic oomycetes.
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Affiliation(s)
- M Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Y Ishiguro
- River Basin Research Center, Gifu University, Gifu, Japan
| | - K Kageyama
- River Basin Research Center, Gifu University, Gifu, Japan
| | - Z Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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41
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Eichmiller JJ, Miller LM, Sorensen PW. Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish. Mol Ecol Resour 2015; 16:56-68. [DOI: 10.1111/1755-0998.12421] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Jessica J. Eichmiller
- Department of Fisheries Wildlife and Conservation Biology; Minnesota Aquatic Invasive Species Research Center; University of Minnesota; Twin Cities Saint Paul MN 55108 USA
| | - Loren M. Miller
- Department of Fisheries Wildlife and Conservation Biology; Minnesota Aquatic Invasive Species Research Center; University of Minnesota; Twin Cities Saint Paul MN 55108 USA
- Minnesota Department of Natural Resources; Saint Paul MN 55155 USA
| | - Peter W. Sorensen
- Department of Fisheries Wildlife and Conservation Biology; Minnesota Aquatic Invasive Species Research Center; University of Minnesota; Twin Cities Saint Paul MN 55108 USA
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42
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Barbarić L, Bačić I, Grubić Z. Powdered Activated Carbon: An Alternative Approach to Genomic DNA Purification. J Forensic Sci 2015; 60:1012-5. [PMID: 25929735 DOI: 10.1111/1556-4029.12773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/24/2014] [Accepted: 07/30/2014] [Indexed: 11/29/2022]
Abstract
Forensic evidence samples are routinely found as stains on various substrates, which may contain substances known to inhibit polymerase chain reaction (PCR). The goal of this study was to evaluate post-Chelex(®) 100 purification using powdered activated carbon (PAC). Mock crime scene DNA extracts were analyzed using quantitative PCR and short tandem repeat (STR) profiling to test the DNA recovery and inhibitor removal using PAC with those of the Amicon(®) Ultra 100K. For extracted bloodstains on soil and wood substrates, PAC and Amicon(®) Ultra 100K generated similar DNA yield and quality. Moreover, the two methods significantly decreased the concentration of humic substances and tannins compared to nonpurified extracts (p < 0.001). In instances where extracts contained indigo dye (bloodstains on denim), Amicon(®) Ultra 100K performed better than PAC due to improved amplifiability. Efficient adsorption of humic substances and tannins, which are common inhibitors, indicates PAC's potential application in the purification of high-template DNA extracts.
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Affiliation(s)
- Lucija Barbarić
- Ivan Vučetić Forensic Science Center, General Police Directorate, Ministry of the Interior of the Republic of Croatia, Ilica 335, 10000, Zagreb, Croatia
| | - Ivana Bačić
- Ivan Vučetić Forensic Science Center, General Police Directorate, Ministry of the Interior of the Republic of Croatia, Ilica 335, 10000, Zagreb, Croatia
| | - Zorana Grubić
- Tissue Typing Center, University Hospital Center Zagreb, Kišpatićeva 12, 10000, Zagreb, Croatia
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43
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Xu C, Dong W, Shi S, Cheng T, Li C, Liu Y, Wu P, Wu H, Gao P, Zhou S. Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques. Mol Ecol Resour 2015; 15:1366-74. [DOI: 10.1111/1755-0998.12413] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 03/21/2015] [Accepted: 04/04/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Shuo Shi
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
- College of Life Science; Hebei Normal University; Shijiazhuang 050024 China
| | - Tao Cheng
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Changhao Li
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yanlei Liu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Ping Wu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Hongkun Wu
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Peng Gao
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
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Abstract
The technology of Single Nucleotide Polymorphism (SNP) detection has evolved steadily through mobility shift studies, mass cleavage product evaluations, heterodimer differences in chemical, conformational, and enzymatic properties, mass spectroscopy and sequencing, to allele-specific hybridization probe methods. Each method presented challenges of labor intensity, unreliable efficiencies, complicated optimizations, and issues of sample quantity and quality. Concurrently the value of SNP detection in basic research and personalized medicine has continued to grow. Accessing the secrets of genetic individuality is the next frontier in moving medicine from the description of very low frequency and highly deleterious nucleotide changes to the study of very low frequency polymorphisms, lower penetrance polymorphisms, and polymorphisms with public health importance. High-Resolution Melting (HRM) analysis of SNP status became an option for high throughput settings with the development of double-stranded dyes that do not interfere with PCR amplification in saturation, eliminate dye jumping, and nearest neighbor sequence changes influence melt temperature via amplicon strand locking chemistry. This method is able to distinguish transitions, transversions, and identify novel changes at or near the SNP of interest rapidly, inexpensively, and without post-amplification assay techniques or extensive technical interpretation of data. For probe or solid matrix based assays, the investigator initially defines a set of target sequences for binding. These assays are not only difficult due to the optimization of binding conditions but are unable to detect sequences that were not included in the design, often have marginalized binding due to a "one size fits all" reaction, and are not distinct in the case of heterozygotes.
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Affiliation(s)
- Carol M Bruzzone
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA,
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45
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Kalle E, Kubista M, Rensing C. Multi-template polymerase chain reaction. BIOMOLECULAR DETECTION AND QUANTIFICATION 2014; 2:11-29. [PMID: 27896140 PMCID: PMC5121205 DOI: 10.1016/j.bdq.2014.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 12/12/2022]
Abstract
PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.
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Affiliation(s)
- Elena Kalle
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Allmas alle 5, 75007 Uppsala, Sweden
| | - Mikael Kubista
- TATAA Biocenter, Odinsgatan 28, 41103 Göteborg, Sweden; Institute of Biotechnology, Czech Academy of Sciences
| | - Christopher Rensing
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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Nixon GJ, Svenstrup HF, Donald CE, Carder C, Stephenson JM, Morris-Jones S, Huggett JF, Foy CA. A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods. BIOMOLECULAR DETECTION AND QUANTIFICATION 2014; 2:4-10. [PMID: 27896139 PMCID: PMC5121211 DOI: 10.1016/j.bdq.2014.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/06/2014] [Accepted: 11/12/2014] [Indexed: 12/20/2022]
Abstract
Molecular diagnostic measurements are currently underpinned by the polymerase chain reaction (PCR). There are also a number of alternative nucleic acid amplification technologies, which unlike PCR, work at a single temperature. These ‘isothermal’ methods, reportedly offer potential advantages over PCR such as simplicity, speed and resistance to inhibitors and could also be used for quantitative molecular analysis. However there are currently limited mechanisms to evaluate their quantitative performance, which would assist assay development and study comparisons. This study uses a sexually transmitted infection diagnostic model in combination with an adapted metric termed isothermal doubling time (IDT), akin to PCR efficiency, to compare quantitative PCR and quantitative loop-mediated isothermal amplification (qLAMP) assays, and to quantify the impact of matrix interference. The performance metric described here facilitates the comparison of qLAMP assays that could assist assay development and validation activities.
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Affiliation(s)
- Gavin J. Nixon
- LGC, Queens Road, Teddington, UK
- Corresponding author at: Molecular and Cell Biology, LGC, Queens Road, Teddington, UK.
| | | | | | - Caroline Carder
- Medicine Clinical Board, University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Stephen Morris-Jones
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
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47
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Lee SB, McCord B, Buel E. Advances in forensic DNA quantification: a review. Electrophoresis 2014; 35:3044-52. [PMID: 25088961 DOI: 10.1002/elps.201400187] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/27/2014] [Accepted: 07/27/2014] [Indexed: 01/11/2023]
Abstract
This review focuses upon a critical step in forensic biology: detection and quantification of human DNA from biological samples. Determination of the quantity and quality of human DNA extracted from biological evidence is important for several reasons. Firstly, depending on the source and extraction method, the quality (purity and length), and quantity of the resultant DNA extract can vary greatly. This affects the downstream method as the quantity of input DNA and its relative length can determine which genotyping procedure to use-standard short-tandem repeat (STR) typing, mini-STR typing or mitochondrial DNA sequencing. Secondly, because it is important in forensic analysis to preserve as much of the evidence as possible for retesting, it is important to determine the total DNA amount available prior to utilizing any destructive analytical method. Lastly, results from initial quantitative and qualitative evaluations permit a more informed interpretation of downstream analytical results. Newer quantitative techniques involving real-time PCR can reveal the presence of degraded DNA and PCR inhibitors, that provide potential reasons for poor genotyping results and may indicate methods to use for downstream typing success. In general, the more information available, the easier it is to interpret and process the sample resulting in a higher likelihood of successful DNA typing. The history of the development of quantitative methods has involved two main goals-improving precision of the analysis and increasing the information content of the result. This review covers advances in forensic DNA quantification methods and recent developments in RNA quantification.
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Affiliation(s)
- Steven B Lee
- Department of Justice Studies, San Jose State University, San Jose, CA, USA
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48
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Thompson RE, Duncan G, McCord BR. An Investigation of PCR Inhibition Using Plexor®-Based Quantitative PCR and Short Tandem Repeat Amplification. J Forensic Sci 2014; 59:1517-29. [DOI: 10.1111/1556-4029.12556] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 09/08/2013] [Accepted: 10/18/2013] [Indexed: 01/09/2023]
Affiliation(s)
- Robyn E. Thompson
- Department of Chemistry and Biochemistry; Florida International University; 11200 SW 8th Street Miami FL 33199
| | - George Duncan
- Department of Chemistry and Biochemistry; Florida International University; 11200 SW 8th Street Miami FL 33199
| | - Bruce R. McCord
- Department of Chemistry and Biochemistry; Florida International University; 11200 SW 8th Street Miami FL 33199
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49
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Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One 2013; 8:e74787. [PMID: 24040342 PMCID: PMC3770609 DOI: 10.1371/journal.pone.0074787] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 08/06/2013] [Indexed: 01/25/2023] Open
Abstract
Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.
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Thomas JT, Berlin RM, Barker JM, Dawson Cruz T. Qiagen's Investigator™ Quantiplex Kit as a predictor of STR amplification success from low-yield DNA samples. J Forensic Sci 2013; 58:1306-1309. [PMID: 23786239 DOI: 10.1111/1556-4029.12171] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/25/2012] [Accepted: 07/14/2012] [Indexed: 11/29/2022]
Abstract
Qiagen's Investigator™ Quantiplex kit, a total human DNA quantitation kit, has a 200-base pair internal control, fast cycling time, and scorpion molecules containing a covalently linked primer, probe, fluorophore, and quencher. The Investigator™ Quantiplex kit was evaluated to investigate a value under which complete short tandem repeat (STR) failure was consistently obtained. Buccal swabs were extracted using the Qiagen QIAamp(®) DNA Blood Mini Kit, quantified with the Investigator™ Quantiplex kit using a tested half-volume reaction, amplified with the ABI AmpFlSTR(®) Identifiler kit, separated on the 3100Avant Genetic Analyzer, and data analyzed with GeneMapper(®) ID v.3.2. While undetected samples were unlikely to produce sufficient data for statistical calculations or CODIS upload (2.00 alleles and 0.82 complete loci on average), data may be useful for exclusionary purposes. Thus, the Investigator™ Quantiplex kit may be useful for predicting STR success. These findings are comparable with previously reported data from the Quantifiler™ Human kit.
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Affiliation(s)
- Jacqueline T Thomas
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Ave., Box 843079, Richmond, VA 23284
| | - Rebecca M Berlin
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Ave., Box 843079, Richmond, VA 23284
| | - Jessica M Barker
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Ave., Box 843079, Richmond, VA 23284
| | - Tracey Dawson Cruz
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Ave., Box 843079, Richmond, VA 23284
- Department of Biology, Virginia Commonwealth University, P.O. Box 843079, 1020 W. Main Street, Room 2015, Richmond, VA 23284
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