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Dass MA, Sherman CDH, van Oorschot RAH, Tuohey K, Hartman D, Carter G, Durdle A. Assessing eDNA capture method from aquatic environment to optimise recovery of human mt-eDNA. Forensic Sci Int 2024; 361:112085. [PMID: 38850619 DOI: 10.1016/j.forsciint.2024.112085] [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: 02/20/2024] [Revised: 05/05/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Previous studies have shown that environmental DNA (eDNA) from human sources can be recovered from natural bodies of water, and the generation of DNA profiles from such environmental samples may assist in forensic investigations. However, fundamental knowledge gaps exist around the factors influencing the probability of detecting human eDNA and the design of optimal sampling protocols. One of these is understanding the particle sizes eDNA signals are most strongly associated with and the most appropriate filter size needed for efficiently capturing eDNA particles. This study assessed the amount of mitochondrial eDNA associated with different particle sizes from human blood and skin cells recovered from freshwater samples. Samples (300 mL) were taken from experimental 10 L tanks of freshwater spiked with 50 µL of human blood or skin cells deposited by vigorously rubbing hands together for two minutes in freshwater. Subsamples were collected by passing 250 mL of experimental water sample through six different filter pore sizes (from 0.1 to 8 µm). This process was repeated at four time intervals after spiking over 72 hours to assess if the particle size of the amount of eDNA recovered changes as the eDNA degrades. Using a human-specific quantitative polymerase chain reaction (qPCR) assay targeting the HV1 mitochondrial gene region, the total amount of mitochondrial eDNA associated with different particle size fractions was determined. In the case of human blood, at 0 h, the 0.45 µm filter pore size captured the greatest amount of mitochondrial eDNA, capturing 42 % of the eDNA detected. The pattern then changed after 48 h, with the 5 µm filter pore size capturing the greatest amount of eDNA (67 %), and 81 % of eDNA at 72 h. Notably, a ten-fold dilution proved to be a valuable strategy for enhancing eDNA recovery from the 8 µm filter at all time points, primarily due to the PCR inhibition observed in hemoglobin. For human skin cells, the greatest amounts of eDNA were recovered from the 8 µm filter pore size and were consistent through time (capturing 37 %, 56 %, and 88 % of eDNA at 0 hours, 48 hours, and 72 hours respectively). There is a clear variation in the amount of eDNA recovered between different cell types, and in some forensic scenarios, there is likely to be a mix of cell types present. These results suggest it would be best to use a 5 µm filter pore size to capture human blood and an 8 µm filter pore size to capture human skin cells to maximize DNA recovery from freshwater samples. Depending on the cell type contributing to the eDNA, a combination of different filter pore sizes may be employed to optimize the recovery of human DNA from water samples. This study provides the groundwork for optimizing a strategy for the efficient recovery of human eDNA from aquatic environments, paving the way for its broader application in forensic and environmental sciences.
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Affiliation(s)
- Marie Antony Dass
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia.
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, VIC 3085, Australia; School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
| | - Kate Tuohey
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia
| | - Dadna Hartman
- Victorian Institute of Forensic Medicine, Southbank, VIC 3006, Australia; Department of Forensic Medicine, Monash University, Southbank, VIC 3006, Australia
| | - Gemma Carter
- Victorian Institute of Forensic Medicine, Southbank, VIC 3006, Australia
| | - Annalisa Durdle
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, VIC 3085, Australia
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2
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Schmitt SE, das Neves GB, Withoeft JA, Costa LS, Biezus G, Pagani RS, Miletti LC, Costa UM, Casagrande RA. PARROT BORNAVIRUSES IN PSITTACINES KEPT IN CAPTIVITY IN THE STATE OF SANTA CATARINA, BRAZIL. J Zoo Wildl Med 2024; 55:341-354. [PMID: 38875191 DOI: 10.1638/2023-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2024] [Indexed: 06/16/2024] Open
Abstract
Parrot bornaviruses are responsible for proventricular dilatation disease (PDD) in psittacines. This study aimed to determine the occurrence and factors associated with Parrot bornaviruses infection in psittacines kept in captivity in a state in the southern region of Brazil. A cross-sectional study was carried out with 192 birds from two facilities (A and B) in 2019, using choanal, esophageal, and cloacal swabs and feathers, totaling 768 samples subjected to reverse-transcription polymerase chain reaction (RT-PCR), for the matrix (M) protein gene with a final product of 350 base pairs (bp). Genetic sequencing of three positive samples was performed by the Sanger method. In the study, the overall virus occurrence was 35.9% (69/192), with 40.4% (42/104) in Facility A and 30.7% (27/88) in Facility B. Sequencing analysis of the samples revealed the presence of Parrot bornavirus 2 (PaBV-2) in both facilities. Swab samples from the choanal (40/69), esophageal (30/69), cloacal (35/69), and feather (15/69) tested positive, facilitating the molecular diagnosis of Parrot bornaviruses. The results indicated that there is no single ideal sample type for antemortem molecular diagnosis of this virus. Simultaneously testing all four samples at the same time point yielded more diagnoses than testing any single sample among the four. Most of the 29 sampled psittacine species were native, and 46.9% of the birds (90/192) consisted of endangered species. Among the psittacines that tested positive, 88.4% (61/69) were clinically healthy, and 8.7% (6/69) exhibited clinical or behavioral signs, including behavioral changes, alterations in feathering, and changes in body score at the time of collection. This study showcases the application of minimally invasive sampling for diagnosing Parrot bornaviruses, enabling sample collection when the birds are restrained for clinical evaluation. This approach facilitates a prompt and effective antemortem diagnosis, thereby serving as an efficient screening method for parrots kept in captivity.
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Affiliation(s)
- Sara E Schmitt
- Department of Veterinary Medicine, Universidade do Estado de Santa Catarina (UDESC), Avenida Luís de Camões, Santa Catarina 88520-000, Brazil
| | - Gabriela B das Neves
- Department of Veterinary Medicine, Universidade do Estado de Santa Catarina (UDESC), Avenida Luís de Camões, Santa Catarina 88520-000, Brazil
| | - Jéssica A Withoeft
- Department of Veterinary Medicine, Universidade do Estado de Santa Catarina (UDESC), Avenida Luís de Camões, Santa Catarina 88520-000, Brazil
| | - Leonardo S Costa
- Department of Veterinary Medicine, Universidade do Estado de Santa Catarina (UDESC), Avenida Luís de Camões, Santa Catarina 88520-000, Brazil
| | - Giovana Biezus
- Department of Veterinary Medicine, Universidade do Estado de Santa Catarina (UDESC), Avenida Luís de Camões, Santa Catarina 88520-000, Brazil
| | - Rafael S Pagani
- Department of Veterinary Medicine, Universidade do Estado de Santa Catarina (UDESC), Avenida Luís de Camões, Santa Catarina 88520-000, Brazil
| | - Luiz C Miletti
- Department of Veterinary Medicine, Universidade do Estado de Santa Catarina (UDESC), Avenida Luís de Camões, Santa Catarina 88520-000, Brazil
| | - Ubirajara M Costa
- Department of Veterinary Medicine, Universidade do Estado de Santa Catarina (UDESC), Avenida Luís de Camões, Santa Catarina 88520-000, Brazil
| | - Renata A Casagrande
- Department of Veterinary Medicine, Universidade do Estado de Santa Catarina (UDESC), Avenida Luís de Camões, Santa Catarina 88520-000, Brazil,
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3
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Stabile HD, McCandless K, Donlan RA, Gaston JR, Humphreys TL. Transmission of viable Haemophilus ducreyi by Musca domestica. PLoS Negl Trop Dis 2024; 18:e0012194. [PMID: 38814945 PMCID: PMC11139276 DOI: 10.1371/journal.pntd.0012194] [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: 12/12/2023] [Accepted: 05/06/2024] [Indexed: 06/01/2024] Open
Abstract
Haemophilus ducreyi was historically known as the causative agent of chancroid, a sexually-transmitted disease causing painful genital ulcers endemic in many low/middle-income nations. In recent years the species has been implicated as the causative agent of nongenital cutaneous ulcers affecting children of the South Pacific Islands and West African countries. Much is still unknown about the mechanism of H. ducreyi transmission in these areas, and recent studies have identified local insect species, namely flies, as potential transmission vectors. H. ducreyi DNA has been detected on the surface and in homogenates of fly species sampled from Lihir Island, Papua New Guinea. The current study develops a model system using Musca domestica, the common house fly, as a model organism to demonstrate proof of concept that flies are a potential vector for the transmission of viable H. ducreyi. Utilizing a green fluorescent protein (GFP)-tagged strain of H. ducreyi and three separate exposure methods, we detected the transmission of viable H. ducreyi by 86.11% ± 22.53% of flies sampled. Additionally, the duration of H. ducreyi viability was found to be directly related to the bacterial concentration, and transmission of H. ducreyi was largely undetectable within one hour of initial exposure. Push testing, Gram staining, and PCR were used to confirm the identity and presence of GFP colonies as H. ducreyi. This study confirms that flies are capable of mechanically transmitting viable H. ducreyi, illuminating the importance of investigating insects as vectors of cutaneous ulcerative diseases.
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Affiliation(s)
- Haley D. Stabile
- Department of Biology, Allegheny College, Meadville, Pennsylvania, United States of America
- Lake Erie College of Osteopathic Medicine, Erie, Pennsylvania, United States of America
| | - Kayla McCandless
- Department of Biology, Allegheny College, Meadville, Pennsylvania, United States of America
- Krystal Biotech, Inc., Pittsburgh, Pennsylvania, United States of America
| | - Rachel A. Donlan
- Department of Biology, Allegheny College, Meadville, Pennsylvania, United States of America
- University of Pittsburgh Medical Center, Department of Microbiology and Molecular Genetics, Pittsburgh, Pennsylvania, United States of America
| | - Jordan R. Gaston
- Department of Biology, Allegheny College, Meadville, Pennsylvania, United States of America
- University of Pittsburgh Medical Center, St. Margaret Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Tricia L. Humphreys
- Department of Biology, Allegheny College, Meadville, Pennsylvania, United States of America
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Lee K, Tripathi A. Insight into Increased Recovery and Simplification of Genomic DNA Extraction Methods from Dried Blood Spots. Biopreserv Biobank 2024; 22:130-138. [PMID: 37410524 DOI: 10.1089/bio.2022.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
There is no consensus on how to perform the manual extraction of nucleic acids from dried blood spots (DBSs). Current methods typically involve agitation of the DBSs in a solution for varying amounts of time with or without heat, and then purification of the eluted nucleic acids with a purification protocol. We explored several characteristics of genomic DNA (gDNA) DBS extraction such as extraction efficiency, the role of red blood cells (RBCs) in extraction and critical kinetic factors to understand if these protocols can be simplified while maintaining sufficient gDNA recovery. We found that agitation in a RBC lysis buffer before performing a DBS gDNA extraction protocol increases yield 1.5 to 5-fold, depending upon the anticoagulant used. The use of an alkaline lysing agent along with either heat or agitation was sufficient to elute quantitative polymerase chain reaction (qPCR) amplifiable gDNA in 5 minutes. This work adds insight into the extraction of gDNA from DBSs with the intention of informing a simple, standardized manual protocol for extraction.
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Affiliation(s)
- Kiara Lee
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
- Brown University School of Public Health, Providence, Rhode Island, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
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Mullins N, Alashraf AR, McDermott K, Brown RS, Payne SJ. Polyethylenimine mediated recovery of SARS-CoV-2 and total viral RNA: Impact of aqueous conditions on behaviour and recovery. WATER RESEARCH 2024; 253:121207. [PMID: 38401469 DOI: 10.1016/j.watres.2024.121207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/28/2023] [Accepted: 01/26/2024] [Indexed: 02/26/2024]
Abstract
Wastewater-based epidemiology (WBE) is an emerging, practical surveillance tool for monitoring community levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, SC2). However, a paucity of data exists regarding SARS-CoV-2 and viral biomarker behaviour in aqueous and wastewater environments. Therefore, there is a pressing need to develop efficient and robust methods that both improve method sensitivity and reduce time and cost. We present a novel method for SARS-CoV-2, Human Coronavirus 229E (229E), and Pepper Mild Mottle Virus (PMMoV) recovery utilizing surface charge-based attraction via the branched cationic polymer, polyethylenimine (PEI). Initially, dose-optimization experiments demonstrated that low concentrations of PEI (0.001% w/v) proved most effective at flocculating suspended viruses and viral material, including additional unbound SC2 viral fragments and/or RNA from raw wastewater. A design-of-experiments (DOE) approach was used to optimize virus and/or viral material aggregation behaviour and recovery across varying aqueous conditions, revealing pH as a major influence on recoverability in this system, combinatorially due to both a reduction in viral material surface charge and increased protonation of PEI-bound amine groups. Overall, this method has shown great promise in significantly improving quantitative viral recovery, providing a straightforward and effective augmentation to standard centrifugation techniques.
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Affiliation(s)
- Nathan Mullins
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; McMaster University, Department of Chemical Engineering, Hamilton, Ontario, L8S 4L7, Canada
| | - Abdul Rahman Alashraf
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada
| | | | - R Stephen Brown
- Queen's University, Department of Chemistry and School of Environmental Studies, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
| | - Sarah Jane Payne
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
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6
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McDonald C, Taylor D, Linacre A. PCR in Forensic Science: A Critical Review. Genes (Basel) 2024; 15:438. [PMID: 38674373 PMCID: PMC11049589 DOI: 10.3390/genes15040438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
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Affiliation(s)
- Caitlin McDonald
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
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7
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Li Z, Wang Y, Wang X, Niu S, Su Z, Wang F, Ni J, Gong Y, Rao B. A Fusion of Taq DNA Polymerase with the CL7 Protein from Escherichia coli Remarkably Improves DNA Amplification. Molecules 2024; 29:1145. [PMID: 38474657 DOI: 10.3390/molecules29051145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/11/2024] [Accepted: 01/26/2024] [Indexed: 03/14/2024] Open
Abstract
DNA polymerases are important enzymes that synthesize DNA molecules and therefore are critical to various scientific fields as essential components of in vitro DNA synthesis reactions, including PCR. Modern diagnostics, molecular biology, and genetic engineering require DNA polymerases with improved performance. This study aimed to obtain and characterize a new CL7-Taq fusion DNA polymerase, in which the DNA coding sequence of Taq DNA polymerase was fused with that of CL7, a variant of CE7 (Colicin E7 DNase) from Escherichia coli. The resulting novel recombinant open reading frame was cloned and expressed in E. coli. The recombinant CL7-Taq protein exhibited excellent thermostability, extension rate, sensitivity, and resistance to PCR inhibitors. Our results showed that the sensitivity of CL7-Taq DNA polymerase was 100-fold higher than that of wild-type Taq, which required a template concentration of at least 1.8 × 105 nM. Moreover, the extension rate of CL7-Taq was 4 kb/min, which remarkably exceeded the rate of Taq DNA polymerase (2 kb/min). Furthermore, the CL7 fusion protein showed increased resistance to inhibitors of DNA amplification, including lactoferrin, heparin, and blood. Single-cope human genomic targets were readily available from whole blood, and pretreatment to purify the template DNA was not required. Thus, this is a novel enzyme that improved the properties of Taq DNA polymerase, and thus may have wide application in molecular biology and diagnostics.
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Affiliation(s)
- Zhongchen Li
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Yaping Wang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Xiangyi Wang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Shuhui Niu
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Zhenlong Su
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Jing Ni
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Yan Gong
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
- Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, China
| | - Ben Rao
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
- Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, China
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Lim J, Zhou S, Baek J, Kim AY, Valera E, Sweedler J, Bashir R. A Blood Drying Process for DNA Amplification. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307959. [PMID: 37888793 DOI: 10.1002/smll.202307959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Indexed: 10/28/2023]
Abstract
The presence of numerous inhibitors in blood makes their use in nucleic acid amplification techniques difficult. Current methods for extracting and purifying pathogenic DNA from blood involve removal of inhibitors, resulting in low and inconsistent DNA recovery rates. To address this issue, a biphasic method is developed that simultaneously achieves inhibitor inactivation and DNA amplification without the need for a purification step. Inhibitors are physically trapped in the solid-phase dried blood matrix by blood drying, while amplification reagents can move into the solid nano-porous dried blood and initiate the amplification. It is demonstrated that the biphasic method has significant improvement in detection limits for bacteria such as Escherichia coli, Methicillin-resistant Staphylococcus aureus, Methicillin-Sensitive Staphylococcus aureus using loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA). Several factors, such as drying time, sample volume, and material properties are characterized to increase sensitivity and expand the application of the biphasic assay to blood diagnostics. With further automation, this biphasic technique has the potential to be used as a diagnostic platform for the detection of pathogens eliminating lengthy culture steps.
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Affiliation(s)
- Jongwon Lim
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shuaizhen Zhou
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Janice Baek
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alicia Yeaeun Kim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Enrique Valera
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jonathan Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Rashid Bashir
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biomedical and Translational Science, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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9
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Abafogi AT, Lee J, Kim J, Lee SW, Jang S, Park S. Automated sepsis detection with vancomycin- and allantoin-polydopamine magnetic nanoparticles. Sci Rep 2024; 14:3693. [PMID: 38355732 PMCID: PMC10867076 DOI: 10.1038/s41598-024-54236-0] [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: 10/29/2023] [Accepted: 02/10/2024] [Indexed: 02/16/2024] Open
Abstract
Rapid and accurate identification of the bacteria responsible for sepsis is paramount for effective patient care. Molecular diagnostic methods, such as polymerase chain reaction (PCR), encounter challenges in sepsis due to inhibitory compounds in the blood, necessitating their removal for precise analysis. In this study we present an innovative approach that utilizes vancomycin (Van) and allantoin (Al)-conjugated polydopamine (PDA)-coated magnetic nanoparticles (MNPs) for the rapid and automated enrichment of bacteria and their DNA extraction from blood without inducing clumping and aggregation of blood. Al/Van-PDA-MNPs, facilitated by IMS, eliminate the need for preliminary sample treatments, providing a swift and efficient method for bacterial concentration and DNA extraction within an hour. Employing Al/Van-PDA-MNPs within an automated framework has markedly improved our ability to pre-concentrate various Gram-negative and Gram-positive bacteria directly from blood samples. This advancement has effectively reduced the detection threshold to 102 colony-forming unit/mL by both PCR and quantitative PCR. The method's expedited processing time, combined with its precision, positions it as a feasible diagnostic tool for diverse healthcare settings, ranging from small clinics to large hospitals. Furthermore, the innovative application of nanoparticles for DNA extraction holds promising potential for advancing sepsis diagnostics, enabling earlier interventions and improving patient outcomes.
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Affiliation(s)
| | - Jinyeop Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
- KingoBio Inc., Seoul, 08390, Korea
| | - Joochan Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Sei Won Lee
- Department of Pulmonology and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Seongsoo Jang
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Sungsu Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea.
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10
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Edgar RH, Samson AP, Viator JA. The Application of Bacteriophage and Photoacoustic Flow Cytometry in Bacterial Identification. Methods Mol Biol 2024; 2738:347-355. [PMID: 37966609 DOI: 10.1007/978-1-0716-3549-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Infection with resistant bacteria has become an ever-increasing problem in modern medical practice. Bacteremia is a serious and potentially lethal condition that can lead to sepsis without early intervention. Currently, broad-spectrum antibiotics are prescribed until bacteria can be identified through blood cultures, a process that can take 2-3 days and is unable to provide quantitative information. Staphylococcus aureus (S. aureus) is a leading cause of bacteremia, and methicillin-resistant S. aureus (MRSA) accounts for more than a third of the cases. Other bacteria such as Clostridium difficile, Acinetobacter baumannii, and Carbapenem-resistant Enterobacteriaceae are becoming more prevalent and antibiotic-resistant. Rapid diagnostics for each of these superbugs has been a priority for health organizations around the world. Bacteriophages have evolved for millions of years to develop exquisite specificity in target binding using their host attachment proteins. Bacteriophages are viruses that infect bacteria. Bacteriophages use tail spikes, specialized attachment proteins, to bind specifically to their target bacterial cell surface proteins. We use bacteriophages and parts of bacteriophages as specific tags coupled with photoacoustic flow cytometry for the detection and quantification of bacteria. In photoacoustic flow cytometry, laser light is absorbed by particles under flow, and the ultrasound waves generated on the release of the energy are detected. Photoacoustics involves the detection of ultrasound waves resulting from laser irradiation. In photoacoustic flow cytometry, pulsed laser light is delivered to a sample flowing past a focused transducer, and particles that absorb laser light create a photoacoustic response. Bacteria can be tagged with dyed bacteriophage and processed through a photoacoustic flow cytometer where they are detected by the acoustic response. In this chapter, we describe the procedure and methods used to accomplish this. Often the limiting factor for the treatment of patients is the time spent waiting for results. It is our hope that the work presented in this chapter can be a foundation for future work and provide an ability to detect bacterial pathogens in blood cultures. Bacterial plate cultures and Gram staining are nineteenth-century technologies that have been the gold standards for decades, but current trends in resistant bacteria have necessitated a move toward more rapid and quantifiable diagnostic tools.
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Affiliation(s)
- Robert H Edgar
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anie-Pier Samson
- Department of Engineering, Duquesne University, Pittsburgh, PA, USA
| | - John A Viator
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Engineering, Duquesne University, Pittsburgh, PA, USA.
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11
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Mhamadi M, Mencattelli G, Gaye A, Ndiaye EH, Sow AA, Faye M, Ndione MHD, Diagne MM, Mhamadi M, Faye O, Weidmann M, Faye O, Diallo M, Diagne CT. Rapid On-Site Detection of Arboviruses by a Direct RT-qPCR Assay. BIOSENSORS 2023; 13:1035. [PMID: 38131795 PMCID: PMC10741549 DOI: 10.3390/bios13121035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023]
Abstract
Arthropod-borne diseases currently constitute a source of major health concerns worldwide. They account for about 50% of global infectious diseases and cause nearly 700,000 deaths every year. Their rapid increase and spread constitute a huge challenge for public health, highlighting the need for early detection during epidemics, to curtail the virus spread, and to enhance outbreak management. Here, we compared a standard quantitative polymerase chain reaction (RT-qPCR) and a direct RT-qPCR assay for the detection of Zika (ZIKV), Chikungunya (CHIKV), and Rift Valley Fever (RVFV) viruses from experimentally infected-mosquitoes. The direct RT-qPCR could be completed within 1.5 h and required 1 µL of viral supernatant from homogenized mosquito body pools. Results showed that the direct RT-qPCR can detect 85.71%, 89%, and 100% of CHIKV, RVFV, and ZIKV samples by direct amplifications compared to the standard method. The use of 1:10 diluted supernatant is suggested for CHIKV and RVFV direct RT-qPCR. Despite a slight drop in sensitivity for direct PCR, our technique is more affordable, less time-consuming, and provides a better option for qualitative field diagnosis during outbreak management. It represents an alternative when extraction and purification steps are not possible because of insufficient sample volume or biosecurity issues.
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Affiliation(s)
- Moufid Mhamadi
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Giulia Mencattelli
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Alioune Gaye
- Department of Medical Zoology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (A.G.); (E.H.N.)
| | - El Hadji Ndiaye
- Department of Medical Zoology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (A.G.); (E.H.N.)
| | - Aïssatou Aïcha Sow
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Martin Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Marie Henriette Dior Ndione
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Moussa Moïse Diagne
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Moundhir Mhamadi
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
| | - Ousmane Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 01968 Senftenberg, Germany;
| | - Oumar Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Mawlouth Diallo
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
| | - Cheikh Tidiane Diagne
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
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12
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Bouike Y, Sakima M, Taninishi Y, Matsutani T, Noguchi Y, Bo R, Awano H, Nishio H. Real-Time PCR-Based Screening for Homozygous SMN2 Deletion Using Residual Dried Blood Spots. Genes (Basel) 2023; 14:2159. [PMID: 38136980 PMCID: PMC10742981 DOI: 10.3390/genes14122159] [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: 11/09/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The survival motor neuron 2 (SMN2) gene is a recognized modifier gene of spinal muscular atrophy (SMA). However, our knowledge about the role of SMN2-other than its modification of SMA phenotypes-is very limited. Discussions regarding the relationship between homozygous SMN2 deletion and motor neuron diseases, including amyotrophic lateral sclerosis, have been mainly based on retrospective epidemiological studies of the diseases, and the precise relationship remains inconclusive. In the present study, we first estimated that the frequency of homozygous SMN2 deletion was ~1 in 20 in Japan. We then established a real-time polymerase chain reaction (PCR)-based screening method using residual dried blood spots to identify infants with homozygous SMN2 deletion. This method can be applied to a future prospective cohort study to clarify the relationship between homozygous SMN2 deletion and motor neuron diseases. In our real-time PCR experiment, both PCR (low annealing temperatures) and blood (high hematocrit values and low white blood cell counts) conditions were associated with incorrect results (i.e., false negatives and positives). Together, our findings not only help to elucidate the role of SMN2, but also aid in our understanding of the pitfalls of current SMA newborn screening programs for detecting homozygous SMN1 deletions.
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Affiliation(s)
- Yoshihiro Bouike
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan; (Y.B.); (M.S.); (Y.T.)
| | - Makoto Sakima
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan; (Y.B.); (M.S.); (Y.T.)
| | - Yuya Taninishi
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan; (Y.B.); (M.S.); (Y.T.)
| | - Takanori Matsutani
- Division of Physiology, Shinko Hospital, 1-4-47 Wakinohama-cho, Chuo-ku, Kobe 651-0072, Japan;
| | - Yoriko Noguchi
- Department of Clinical Laboratory, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan;
| | - Ryosuke Bo
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan;
| | - Hiroyuki Awano
- Organization for Research Initiative and Promotion, Research Initiative Center, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan;
| | - Hisahide Nishio
- Department of Occupational Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan
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13
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Alex-Sanders N, Woodhall N, Farkas K, Scott G, Jones DL, Walker DI. Development and validation of a duplex RT-qPCR assay for norovirus quantification in wastewater samples. J Virol Methods 2023; 321:114804. [PMID: 37643662 DOI: 10.1016/j.jviromet.2023.114804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 08/31/2023]
Abstract
Norovirus (NoV) is a highly contagious enteric virus that causes widespread outbreaks and a substantial number of deaths across communities. As clinical surveillance is often insufficient, wastewater-based epidemiology (WBE) may provide novel pathways of tracking outbreaks. To utilise WBE, it is important to use accurate and sensitive methods for viral quantification. In this study, we developed a one-step duplex RT-qPCR assay to simultaneously test the two main human pathogenic NoV genogroups, GI and GII, in wastewater samples. The assay had low limits of detection (LOD), namely 0.52 genome copies (gc)/µl for NoVGI and 1.37 gc/µl for NoVGII. No significant concentration-dependent interactions were noted for both NoVGI and for NoVGII when the two targets were mixed at different concentrations in the samples. When tested on wastewater-derived RNA eluents, no significant difference between duplex and singleplex concentrations were found for either target. Low levels of inhibition (up to 32 %) were noted due to organic matter present in the wastewater extracts. From these results we argue that the duplex RT-qPCR assay developed enables the sensitive detection of both NoVGI and NoVGII in wastewater-derived RNA eluents, in a time and cost-effective way and may be used for surveillance to monitor public and environmental health.
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Affiliation(s)
| | - Nick Woodhall
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - George Scott
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
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14
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Li J, Li Y, Li Y, Ma Y, Xu W, Wang J. An enhanced activity and thermostability of chimeric Bst DNA polymerase for isothermal amplification applications. Appl Microbiol Biotechnol 2023; 107:6527-6540. [PMID: 37672070 DOI: 10.1007/s00253-023-12751-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/31/2023] [Accepted: 08/28/2023] [Indexed: 09/07/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a widely used method for clinical diagnosis, customs quarantine, and disease prevention. However, the low catalytic activity of Bst DNA polymerase has made it challenging to develop rapid and reliable point-of-care testing. Herein, we developed a series of Bst DNA polymerase mutants with enhanced activity by predicting and analyzing the activity sites. Among these mutants, single mutants K431D and K431E showed a 1.93- and 2.03-fold increase in catalytic efficiency, respectively. We also created a chimeric protein by fusing the DNA-binding domain of DNA ligase from Pyrococcus abyssi (DBD), namely DBD-K431E, which enabled real-time LAMP at high temperatures up to 73 ℃ and remained active after heating at 70 ℃ for 8 h. The chimeric DBD-K431E remained active in the presence of 50 U/mL heparin, 10% ethanol, and up to 100 mM NaCl, and showed higher activity in 110 mM (NH4)2SO4, 110 mM KCl, and 12 mM MgSO4. Notably, it generated a fluorescence signal during the detection of Salmonella typhimurium at 2 × 102 ag/μL of genomic DNA and 1.24 CFU/mL of bacterial colony, outperforming the wild type and the commercial counterpart Bst 2.0. Our results suggest that the DBD-K431E variant could be a promising tool for general molecular biology research and clinical diagnostics. KEY POINTS: • Residue K431 is probably a key site of Bst DNA polymerase activity • The chimeric DBD-K431E is more inhibitor tolerant and thermostable than Bst-LF • The DBD-K431E variant can detect Salmonella typhimurium at 102 ag/μL or 100 CFU/mL.
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Affiliation(s)
- Jiaxuan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yanmei Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Wei Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China.
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15
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Sajeer Paramabth M, Varma M. Demystifying PCR tests, challenges, alternatives, and future: A quick review focusing on COVID and fungal infections. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:719-728. [PMID: 37485773 DOI: 10.1002/bmb.21771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
The polymerase chain reaction (PCR) technique is one of the most potent tools in molecular biology. It is extensively used for various applications ranging from medical diagnostics to forensic science and food quality testing. This technique has facilitated to survive COVID-19 pandemic by identifying the virus-infected individuals effortlessly and effectively. This review explores the principles, recent advancements, challenges, and alternatives of PCR technique in the context of COVID-19 and fungal infections. The introduction of PCR technique for anyone new to this field is the primary aim of this review and thereby equips them to understand the science of COVID-19 and related fungal infections in a simplistic manner.
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Affiliation(s)
| | - Manoj Varma
- Center for Nano Science and Engineering (CeNSE), Indian Institute of Science, Bangalore, India
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16
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Li X, Chen B, Chen W, Pu Z, Qi X, Yang L, Wu J, Yu H. Customized multiple sequence alignment as an effective strategy to improve performance of Taq DNA polymerase. Appl Microbiol Biotechnol 2023; 107:6507-6525. [PMID: 37658164 DOI: 10.1007/s00253-023-12744-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/06/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Engineering Taq DNA polymerase (TaqPol) for improved activity, stability and sensitivity was critical for its wide applications. Multiple sequence alignment (MSA) has been widely used in engineering enzymes for improved properties. Here, we first designed TaqPol mutations based on MSA of 2756 sequences from both thermophilic and non-thermophilic organisms. Two double mutations were generated including a variant H676F/R677G showing a decrease in both activity and stability, and a variant Y686R/E687K showing an improved activity, but a decreased stability. Mutations targeted on coevolutionary residues of Arg677 and Tyr686 were then applied to rescue stability or activity loss of the double mutants, which achieved a partial success. Sequence analysis revealed that the two mutations are abundant in non-thermophilic sequences but not in thermophilic homologues. Then, a small-scale MSA containing sequences from only thermophilic organisms was applied to predict 13 single variants and two of them, E507Q and E734N showed a simultaneous increase in both stability and activity, even in sensitivity. A customized MSA was hence more effective in engineering a thermophilic enzyme and could be used in engineering other enzymes. Molecular dynamics simulations revealed the impact of mutations on the protein dynamics and interactions between TaqPol and substrates. KEY POINTS: • The pool of sequence for alignment is critical to engineering Taq DNA polymerase. • The variants with low properties can be rescued by mutations in coevolving network. • Improving binding with DNA can improve DNA polymerase stability and activity.
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Affiliation(s)
- Xinjia Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Binbin Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Wanyi Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Xin Qi
- Building No.4, Zhongguancun Dongsheng International Science Park, No. 1 North Yongtaizhuang Road, Haidian District, Beijing, 100192, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China.
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17
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Song W, Zhang C, Lin H, Zhang T, Liu H, Huang X. Portable rotary PCR system for real-time detection of Pseudomonas aeruginosa in milk. LAB ON A CHIP 2023; 23:4592-4599. [PMID: 37772426 DOI: 10.1039/d3lc00401e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
The rapid quantitative detection of Pseudomonas aeruginosa in milk is of great significance to food safety. Quantitative real-time polymerase chain reaction (qPCR) technology is a good choice to meet this requirement. A good qPCR system should show the advantages of being low cost, having low-power consumption, having potential for miniaturization and be portable. However, most of the time-domain-based qPCR systems reported to date do not meet these requirements. In this study, we propose a novel real-time rotary PCR reaction system (RRP) that meets all the abovementioned specifications, and contains four modules: a heating control module, a disposable PCR capillary tube, a mechanical control module, and a photoelectric detection module. The volume of our homemade-PCR capillary tube is only 3 μL. The total manufacturing cost is cheaper than $200, and the capillary tube is about 1.4 cents. The size parameter of the RRP is less than 300 mm × 150 mm × 150 mm, using low mobile power sources to operate. All the features mean that the RRP meets the advantages of low sample volumes, enhanced thermal conductivity and being portable. Through conducting the experimental quantitative detection of Pseudomonas aeruginosa in milk and theoretical simulations by COMSOL, we prove the feasibility of this rotary PCR real-time detection system, which has broad application prospects in the rapid detection of bacteria and food safety.
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Affiliation(s)
- Weidu Song
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Chuanhao Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Huichao Lin
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Taiyi Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Haixia Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
| | - Xiaowen Huang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China.
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18
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Saito K, Ito R, Sekiya C, Akiyama H. Identification of animal species by nucleic acid chromatography of hair samples and investigation of its applicability to human biological samples. Forensic Sci Int 2023; 351:111811. [PMID: 37660638 DOI: 10.1016/j.forsciint.2023.111811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023]
Abstract
GeneFields®-Hair is a simple analysis kit that uses nucleic acid chromatography and polymerase chain reaction (PCR) to identify animal species of hair-like food contaminants. In this study, we evaluated GeneFields®-Hair as a simple and rapid method for identifying animal species from hair-like materials collected in forensic science, such as at crime scenes. The use of this kit with other human biological materials (whole blood, head dandruff, nails, saliva, oral mucosa, sebum, and urine) was also investigated. Animal body hair samples were pretreated by grinding in a buffer solution, centrifuged, and the supernatant was used for PCR. Nucleic acid chromatography of the PCR products allowed the identification of the animal species by the presence or absence of coloration on the decision line. For human biological materials, nucleic acid chromatography was performed after the appropriate pretreatment like body hair material. The determination of some animal species was difficult, even if they had a dedicated DNA Strip determination line. Furthermore, animals from the same family but different genera were sometimes detected on the same determination line. All the human biological samples were correctly identified. Smartphone photographs of the coloration of the judgment line were processed using the ImageJ software for quantitative determination.
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Affiliation(s)
- Koichi Saito
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Hoshi University, 2-4-41, Ebara, Shinagawa-ku, Tokyo 142-8501, Japan.
| | - Rie Ito
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Hoshi University, 2-4-41, Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Chiharu Sekiya
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Hoshi University, 2-4-41, Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Hiroshi Akiyama
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Hoshi University, 2-4-41, Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
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19
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Song J, Kim S, Kwak E, Park Y. Routine breast milk monitoring using automated molecular assay system reduced postnatal CMV infection in preterm infants. Front Microbiol 2023; 14:1257124. [PMID: 37795306 PMCID: PMC10546183 DOI: 10.3389/fmicb.2023.1257124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/05/2023] [Indexed: 10/06/2023] Open
Abstract
Human cytomegalovirus (CMV) transmitted through breast milk poses fatal risks to preterm infants. However, current molecular assay systems often do not accommodate breast milk samples. In this study, we evaluated the analytical and clinical performance of the measurement procedure of CMV load in breast milk utilizing the Cobas CMV test on the Cobas 6,800 system. This was enabled by incorporating a simple independent sample preparation procedure before the application of samples on the automated assay system. Clinical data from electronic medical records were retrospectively analyzed. Breast milk samples from mothers of preterm infants born before 33 weeks of gestation were screened for CMV using the automated assay system. CMV positivity rates in breast milk and neonatal samples and the CMV transmission rate were calculated. Furthermore, to validate the analytical accuracy of the overall measurement procedure with newly obtained residual breast milk samples, the linearity of the measurement procedure was assessed, and a simplified sample preparation method was validated against a conventional method. The CMV positivity rates in maternal breast milk and neonatal samples were 57.8 and 5.2%, respectively. The CMV transmission rate through breast milk was 7.7%. No significant differences in gestational age or birth weight were found between the CMV-negative and CMV-positive neonates. The linearity of the procedure was observed within a range of 1.87-4.73 log IU/mL. The simplified sample preparation method had an equivalent or even improved CMV detection sensitivity than the conventional method. Incorporating a simple independent sample preparation procedure effectively resolved any potential issues regarding the application of breast milk on the automated assay system. Our approach contributed to reduced vertical transmission of CMV by providing a convenient and reliable method for the monitoring of breast milk CMV positivity for clinicians.
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Affiliation(s)
| | | | | | - Younhee Park
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
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d'Otreppe S, Lefèvre P, Meex C, Devey A, Sacheli R, Gerard M, Melin P. Multicenter Performance Evaluation of the Revogene ® GBS DS Real-Time PCR Assay for Group B Streptococcus Detection During Labor. Mol Diagn Ther 2023; 27:611-620. [PMID: 37470972 DOI: 10.1007/s40291-023-00660-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2023] [Indexed: 07/21/2023]
Abstract
PURPOSE This study aimed to evaluate the performance and ease of use of the Revogene® GBS DS PCR assay for the intrapartum detection of Group B Streptococcus (GBS) colonization, as compared with intrapartum culture and antenatal culture-based screening. METHODS Between April and August 2019, 398 women who gave birth in one of the three maternities participating in this study agreed to the collection of a vaginal swab when they arrived in the labor ward. The samples were immediately sent to the adjacent laboratory where they were discharged into the buffer provided with the Revogene® GBS DS assay. Part of the buffer was used to perform the Revogene® GBS DS test, and part of the same buffer was used for GBS culture. RESULTS The Revogene® GBS DS assay provided a valid result in less than 70 min for 356 (89%) women. The sensitivity of the test was 85.7% (66.4-95.3%). The specificity of the test was 99.1% (97.3-99.8%). The positive predictive value was 88.9% (69.7-97.1%). The negative predictive value was 98.9% (96.9-99.6%). CONCLUSION The easy-to-use Revogene® GBS DS assay provides a valuable tool for the detection of GBS colonization at the beginning of labor. The sensitivity and turn-around time are adequate. The high number of invalid results needs to be addressed before the Revogene® GBS DS test can be expected to replace the current screening-based approach.
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Affiliation(s)
- Stéphanie d'Otreppe
- Department of Clinical Biology, Hôpital de Marche, Vivalia, Marche-en-Famenne, Belgium. stephanie.d'
| | - Philippe Lefèvre
- Department of Clinical Biology, Hôpital de Marche, Vivalia, Marche-en-Famenne, Belgium
| | - Cécile Meex
- Department of Clinical Microbiology, University Hospital of Liege, Liege, Belgium
- National Reference Center Streptococcus agalactiae, Department of Clinical Microbiology, University Hospital Center of Liege, Liege, Belgium
| | - Anaïs Devey
- Department of Clinical Biology, Hôpital de Libramont, Vivalia, Libramont-Chevigny, Belgium
| | - Rosalie Sacheli
- National Reference Center Streptococcus agalactiae, Department of Clinical Microbiology, University Hospital Center of Liege, Liege, Belgium
| | - Martin Gerard
- Department of Obstetrics and Gynecology, Hôpital de Marche, Vivalia, Marche-en-Famenne, Belgium
| | - Pierrette Melin
- Department of Clinical Microbiology, University Hospital of Liege, Liege, Belgium
- National Reference Center Streptococcus agalactiae, Department of Clinical Microbiology, University Hospital Center of Liege, Liege, Belgium
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21
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Kreitlow A, Ningrum SG, Lämmler C, Erhard M, Hoffmann C, Plötz M, Abdulmawjood A. Identification of the novel potential pathogen Trueperella pecoris with interspecies significance by LAMP diagnostics. Sci Rep 2023; 13:14005. [PMID: 37635174 PMCID: PMC10460790 DOI: 10.1038/s41598-023-40787-1] [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: 06/02/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023] Open
Abstract
Trueperella pecoris was described as a new species of the genus Trueperella in 2021 and might be pathogenic to various animal species. However, the lack of a suitable diagnostic test system stands in the way of epidemiological surveys to clarify possible causalities. In this study, a Loop-mediated Isothermal Amplification (LAMP) assay was developed and validated that was highly specific for T. pecoris. The assay provided an analytical sensitivity of 0.5 pg/25 µL and showed 100% inclusivity and exclusivity for 11 target and 33 non-target strains, respectively. Three different DNA extraction methods were evaluated to select the most LAMP-compatible method for cell disruption in pure and complex samples. Using an on-site applicable single-buffer DNA extraction with additional heating, the cell-based detection limit was 2.3 CFU/reaction. Finally, the LAMP assay was validated by means of artificially contaminated porcine lung tissue samples in which minimal microbial loads between 6.54 and 8.37 × 103 CFU per swab sample were detectable. The LAMP assay established in this study represents a suitable diagnostic procedure for identifying T. pecoris in clinical specimens and will help to collect epidemiological data on the pathogenicity of this species.
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Affiliation(s)
- Antonia Kreitlow
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Siti Gusti Ningrum
- Faculty of Veterinary Medicine, Universitas Wijaya Kusuma Surabaya, Jl. Dukuh Kupang XXV No.54, Dukuh Kupang, Surabaya, 60225, Indonesia
| | - Christoph Lämmler
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Frankfurter Str. 87-89, 35392, Giessen, Germany
| | - Marcel Erhard
- RIPAC-LABOR GmbH, Am Mühlenberg 11, 14476, Potsdam, Germany
| | - Christiane Hoffmann
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Frankfurter Str. 87-89, 35392, Giessen, Germany
| | - Madeleine Plötz
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173, Hannover, Germany.
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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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23
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McIlwraith EK, He W, Belsham DD. Promise and Perils of MicroRNA Discovery Research: Working Toward Quality Over Quantity. Endocrinology 2023; 164:bqad111. [PMID: 37453100 DOI: 10.1210/endocr/bqad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Since the first microRNA (miRNA) was described in 1993 in the humble worm Caenorhabditis elegans, the miRNA field has boomed, with more than 100 000 related patents filed and miRNAs now in ongoing clinical trials. Despite an advanced understanding of the biogenesis and action of miRNAs, applied miRNA research faces challenges and irreproducibility due to a lack of standardization. This review provides guidelines regarding miRNA investigation, while focusing on the pitfalls and considerations that are often overlooked in prevailing applied miRNA research. These include miRNA annotation and quantification, to modulation, target prediction, validation, and the study of circulating miRNAs.
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Affiliation(s)
- Emma K McIlwraith
- Department of Physiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Wenyuan He
- Department of Physiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Denise D Belsham
- Department of Physiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
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24
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Schröder HM, Niebergall-Roth E, Norrick A, Esterlechner J, Ganss C, Frank MH, Kluth MA. Drug Regulatory-Compliant Validation of a qPCR Assay for Bioanalysis Studies of a Cell Therapy Product with a Special Focus on Matrix Interferences in a Wide Range of Organ Tissues. Cells 2023; 12:1788. [PMID: 37443822 PMCID: PMC10340683 DOI: 10.3390/cells12131788] [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: 05/25/2023] [Revised: 06/23/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Quantitative polymerase chain reaction (qPCR) has emerged as an important bioanalytical method for assessing the pharmacokinetics of human-cell-based medicinal products after xenotransplantation into immunodeficient mice. A particular challenge in bioanalytical qPCR studies is that the different tissues of the host organism can affect amplification efficiency and amplicon detection to varying degrees, and ignoring these matrix effects can easily cause a significant underestimation of the true number of target cells in a sample. Here, we describe the development and drug regulatory-compliant validation of a TaqMan® qPCR assay for the quantification of mesenchymal stromal cells in the range of 125 to 20,000 cells/200 µL lysate via the amplification of a human-specific, highly repetitive α-satellite DNA sequence of the chromosome 17 centromere region HSSATA17. An assessment of matrix effects in 14 different mouse tissues and blood revealed a wide range of spike recovery rates across the different tissue types, from 11 to 174%. Based on these observations, we propose performing systematic spike-and-recovery experiments during assay validation and correcting for the effects of the different tissue matrices on cell quantification in subsequent bioanalytical studies by multiplying the back-calculated cell number by tissue-specific factors derived from the inverse of the validated percent recovery rate.
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Affiliation(s)
| | | | | | | | | | - Markus H. Frank
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
- Transplant Research Program, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia
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25
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Ratzlaff FR, Osmari V, da Silva D, de Paula Vasconcellos JS, Pötter L, Fernandes FD, de Mello Filho JA, de Avila Botton S, Vogel FSF, Sangioni LA. Identification of infection by Leishmania spp. in wild and domestic animals in Brazil: a systematic review with meta-analysis (2001-2021). Parasitol Res 2023; 122:1605-1619. [PMID: 37154922 DOI: 10.1007/s00436-023-07862-y] [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: 12/11/2022] [Accepted: 04/28/2023] [Indexed: 05/10/2023]
Abstract
Leishmaniasis is a zoonosis caused by protozoan species of the genus Leishmania. It generates different clinical manifestations in humans and animals, and it infects multiple hosts. Leishmania parasites are transmitted by sandfly vectors. The main objective of this systematic review was to identify the host, or reservoir animal species, of Leishmania spp., with the exception of domestic dogs, that were recorded in Brazil. This review included identification of diagnostic methods, and the species of protozoan circulating in the country. For this purpose, a literature search was conducted across index journals. This study covered the period from 2001 to 2021, and 124 studies were selected. Eleven orders possible hosts were identified, including 229 mammalian species. Perissodactyla had the highest number of infected individuals (30.69%, 925/3014), with the highest occurrence in horses. In Brazil, the most commonly infected species were found to be: horses, domestic cats, rodents, and marsupials. Bats, that were infected by one or more protozoan species, were identified as potential reservoirs of Leishmania spp. Molecular tests were the most commonly used diagnostic methods (94 studies). Many studies have detected Leishmania spp. (n = 1422): Leishmania (Leishmania) infantum (n = 705), Leishmania (Viannia) braziliensis (n = 319), and Leishmania (Leishmania) amazonensis (n = 141). Recognizing the species of animals involved in the epidemiology and biological cycle of the protozoan is important, as this allows for the identification of environmental biomarkers, knowledge of Leishmania species can improve the control zoonotic leishmaniasis.
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Affiliation(s)
- Fabiana Raquel Ratzlaff
- Laboratório de Doenças Parasitárias (LADOPAR), Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, N°1000, Prédio 63D, Bairro Camobi, Santa Maria, RS, CEP 97105900, Brazil
| | - Vanessa Osmari
- Laboratório de Doenças Parasitárias (LADOPAR), Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, N°1000, Prédio 63D, Bairro Camobi, Santa Maria, RS, CEP 97105900, Brazil
| | - Daniele da Silva
- Laboratório de Doenças Parasitárias (LADOPAR), Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, N°1000, Prédio 63D, Bairro Camobi, Santa Maria, RS, CEP 97105900, Brazil
| | - Jaíne Soares de Paula Vasconcellos
- Laboratório de Doenças Parasitárias (LADOPAR), Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, N°1000, Prédio 63D, Bairro Camobi, Santa Maria, RS, CEP 97105900, Brazil
| | - Luciana Pötter
- Laboratório de Pastos e Suplementos, Departamento de Zootecnia, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, N°1000, Bairro Camobi, Santa Maria, RS, CEP 97105900, Brazil
| | - Fagner D'ambroso Fernandes
- Laboratório de Doenças Parasitárias (LADOPAR), Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, N°1000, Prédio 63D, Bairro Camobi, Santa Maria, RS, CEP 97105900, Brazil.
- Centro Universitário Ritter Dos Reis (UniRitter), Campus FAPA, Av. Manoel Elias, 2001 - Passo das Pedras, Porto Alegre, 91240-261, Brazil.
| | - José Américo de Mello Filho
- Laboratório de Análises Ambientais por Geoprocessamento (LAGEO), Departamento de Engenharia Rural, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, N°1000, Prédio 44 J, Bairro Camobi, Santa Maria, RS, CEP 97105-900, Brazil
| | - Sônia de Avila Botton
- Laboratório de Saúde Única (LASUS), Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, nº 1000, Prédio 44, Bairro Camobi, Santa Maria, Rio Grande do Sul, CEP 97105-900, Brazil
| | - Fernanda Silveira Flores Vogel
- Laboratório de Doenças Parasitárias (LADOPAR), Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, N°1000, Prédio 63D, Bairro Camobi, Santa Maria, RS, CEP 97105900, Brazil
| | - Luís Antônio Sangioni
- Laboratório de Doenças Parasitárias (LADOPAR), Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais (CCR), Universidade Federal de Santa Maria (UFSM), Av. Roraima, N°1000, Prédio 63D, Bairro Camobi, Santa Maria, RS, CEP 97105900, Brazil
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Kumari S, Singh K, Singh N, Khan S, Kumar A. Phage display and human disease detection. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:151-172. [PMID: 37770169 DOI: 10.1016/bs.pmbts.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Phage display is a significant and active molecular method and has continued crucial for investigative sector meanwhile its unearthing in 1985. This practice has numerous benefits: the association among physiology and genome, the massive variety of variant proteins showed in sole collection and the elasticity of collection that can be achieved. It suggests a diversity of stages for manipulating antigen attachment; yet, variety and steadiness of exhibited library are an alarm. Additional improvements, like accumulation of non-canonical amino acids, resulting in extension of ligands that can be recognized through collection, will support in expansion of the probable uses and possibilities of technology. Epidemic of COVID-19 had taken countless lives, and while indicative prescriptions were provided to diseased individuals, still no prevention was observed for the contamination. Phage demonstration has presented an in-depth understanding into protein connections included in pathogenesis. Phage display knowledge is developing as an influential, inexpensive, quick, and effectual method to grow novel mediators for the molecular imaging and analysis of cancer.
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Affiliation(s)
- Sonu Kumari
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India
| | - Krati Singh
- Department of Biotechnology, Banasthali University, Newai, Rajasthan, India
| | - Neha Singh
- Department of Biotechnology, Banasthali University, Newai, Rajasthan, India
| | - Suphiya Khan
- Department of Biotechnology, Banasthali University, Newai, Rajasthan, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Kanpur, Uttar Pradesh, India.
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Wei ZH, Xie L, Wang YJ, Zhuang JX, Niu JJ, Liu LL. Red Blood Cell Lysis Pretreatment Can Significantly Improve the Yield of Treponema pallidum DNA from Blood. Microbiol Spectr 2023; 11:e0519822. [PMID: 37222624 PMCID: PMC10269841 DOI: 10.1128/spectrum.05198-22] [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] [Received: 12/21/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023] Open
Abstract
PCR can be a supplement to Treponema serological testing. However, its sensitivity is not satisfactory for blood sample testing. The aim of this study was to investigate whether pretreatment with red blood cell (RBC) lysis could enhance the yield of Treponema pallidum subsp. pallidum DNA extraction from blood. We developed and verified the efficacy of a quantitative PCR (qPCR) assay that utilizes TaqMan technology to specifically detect T. pallidum DNA by targeting the polA gene. Simulation media with 106 to 100 treponemes/mL were prepared in normal saline (NS), whole blood, plasma, and serum, and RBC lysis pretreatment was performed on a portion of whole blood. Then, blood samples drawn from 50 syphilitic rabbits were divided in parallel into five groups, labeled whole blood, whole blood/lysed RBCs, plasma, serum, and blood cells/lysed RBCs. DNA extraction and qPCR detection were performed. The detection rate and copy number were compared among different groups. The polA assay showed good linearity and an excellent amplification efficiency of 102%. In the simulated blood samples, the detection limit of the polA assay reached 1 × 102 treponemes/mL in whole blood/lysed RBCs, plasma, and serum. However, the detection limit was only 1 × 104 treponemes/mL in NS and whole blood. Among the blood samples from syphilitic rabbits, whole blood/lysed RBCs showed the best detection rate (82.0%), while the detection rate for whole blood was only 6%. The copy number of whole blood/lysed RBCs was higher than that of whole blood. RBC lysis pretreatment can significantly improve the yield of T. pallidum DNA from whole blood, and the yield is better than that from whole blood, plasma, serum, and blood cells/lysed RBCs. IMPORTANCE Syphilis is a sexually transmitted disease caused by T. pallidum that can spread into the blood. T. pallidum DNA can be detected in blood by PCR but with low sensitivity. Few studies have applied RBC lysis pretreatment to blood T. pallidum DNA extraction. This study shows that the detection limit, detection rate, and copy number of whole blood/lysed RBCs were better than those of whole blood, plasma, and serum. After RBC lysis pretreatment, the yield of low concentrations of T. pallidum DNA was improved, and the low sensitivity of blood-based T. pallidum PCR was improved. Therefore, whole blood/lysed RBCs are the ideal sample for acquiring blood T. pallidum DNA.
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Affiliation(s)
- Zi-Han Wei
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Lin Xie
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yong-Jing Wang
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jiang-Xing Zhuang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Jian-Jun Niu
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Li-Li Liu
- Center of Clinical Laboratory, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Clinical Laboratory Quality Control Center, Xiamen, China
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Scaglione S, Gotta F, Vay D, Leli C, Roveta A, Maconi A, Rocchetti A. Rapid RT-PCR identification of SARS-CoV-2 in screening donors of fecal microbiota transplantation. Heliyon 2023; 9:e17438. [PMID: 37366528 PMCID: PMC10277158 DOI: 10.1016/j.heliyon.2023.e17438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/22/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Since its first appearance in late 2019 in Wuhan, China, severe acute respiratory syndrome caused by Coronavirus 2 (SARS-CoV-2) has had a major impact on healthcare facilities around the world. Although in the past year, mass vaccination and the development of monoclonal antibody treatments have reduced the number of deaths and severe cases, the circulation of SARS-CoV-2 remains high. Over the past two years, diagnostics have played a crucial role in virus containment both in health care facilities and at the community level. For SARS-CoV-2 detection, the commonly used specimen type is the nasopharyngeal swab, although the virus can be identified in other matrices such as feces. Since fecal microbiota transplantation (FMT) assumes significant importance in the treatment of chronic gut infections and that feces may be a potential vehicle for transmission of SARS-CoV-2, in this study we have evaluated the performance of the rapid cartridge-based RT-PCR test STANDARD™ M10 SARS-CoV-2 (SD Biosensor Inc., Suwon, South Korea) using fecal samples. The results obtained indicates that STANDARD™ M10 SARS-CoV-2 can detect SARS-CoV-2 in stool samples even at low concentration. For this reason, STANDARD™ M10 SARS-CoV-2 could be used as reliable methods for the detection of SARS-CoV-2 in fecal samples and for the screening of FMT donors.
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Affiliation(s)
- Sara Scaglione
- Microbiology Laboratory, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy, EU
| | - Franca Gotta
- Microbiology Laboratory, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy, EU
| | - Daria Vay
- Microbiology Laboratory, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy, EU
| | - Christian Leli
- Microbiology Laboratory, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy, EU
| | - Annalisa Roveta
- Research Training Innovation Infrastructure, Research and Innovation Department (DAIRI), Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, 15121, Alessandria, Italy
| | - Antonio Maconi
- Research Training Innovation Infrastructure, Research and Innovation Department (DAIRI), Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, 15121, Alessandria, Italy
| | - Andrea Rocchetti
- Microbiology Laboratory, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy, EU
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Wang K, Seol H, Cheng A, McKeague N, Carlson M, Degraff W, Huang S, Kim S. Simple Bioparticle Filtration Device Based on an Ultralow-Fouling Zwitterionic Polyurethane Membrane for Rapid Large-Volume Separation of Plasma and Viruses from Whole Blood. MEMBRANES 2023; 13:membranes13050524. [PMID: 37233584 DOI: 10.3390/membranes13050524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Plasma separation from whole blood is oftent required as an essential first step when performing blood tests with a viral assay. However, developing a point-of-care plasma extraction device with a large output and high virus recovery remains a significant obstacle to the success of on-site viral load tests. Here, we report a portable, easy-to-use, cost-efficient, membrane-filtration-based plasma separation device that enables rapid large-volume plasma extraction from whole blood, designed for point-of-care virus assays. The plasma separation is realized by a low-fouling zwitterionic polyurethane-modified cellulose acetate (PCBU-CA) membrane. The zwitterionic coating on the cellulose acetate membrane can decrease surface protein adsorption by 60% and increase plasma permeation by 46% compared with a pristine membrane. The PCBU-CA membrane, with its ultralow-fouling properties, enables rapid plasma separation. The device can yield a total of 1.33 mL plasma from 10 mL whole blood in 10 min. The extracted plasma is cell-free and exhibits a low hemoglobin level. In addition, our device demonstrated a 57.8% T7 phage recovery in the separated plasma. The results of real-time polymerase chain reaction analysis confirmed that the nucleic acid amplification curve of the plasma extracted by our device is comparable to that obtained by centrifugation. With its high plasma yield and good phage recovery, our plasma separation device provides an excellent replacement for traditional plasma separation protocols for point-of-care virus assays and a broad spectrum of clinical tests.
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Affiliation(s)
- Kun Wang
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hyang Seol
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alex Cheng
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
- New Trier High School, New Trier, IL 60093, USA
| | - Nash McKeague
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
- University of Chicago Laboratory Schools, Chicago, IL 60637, USA
| | - Megan Carlson
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Wade Degraff
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Sijia Huang
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sangil Kim
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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Martins NDS, Rodrigues APS, Bicalho JM, Albuquerque JJ, Reis LL, Alves LL, de Oliveira RM, Santos LSD, de Carvalho Neta AV, de Oliveira RA, Carvalho RC, Melo FA, Dos Reis JKP, Abreu-Silva AL. Molecular characterization of Brazilian FeLV strains in São Luis, Maranhão Brazil. Virus Genes 2023:10.1007/s11262-023-01997-x. [PMID: 37195404 DOI: 10.1007/s11262-023-01997-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 04/11/2023] [Indexed: 05/18/2023]
Abstract
The feline leukemia virus (FeLV) belongs to the Retroviridae family and Gammaretrovirus genus, and causes a variety of neoplastic and non-neoplastic diseases in domestic cats (Felis catus), such as thymic and multicentric lymphomas, myelodysplastic syndromes, acute myeloid leukemia, aplastic anemia, and immunodeficiency. The aim of the present study was to carry out the molecular characterization of FeLV-positive samples and determine the circulating viral subtype in the city of São Luís, Maranhão, Brazil, as well as identify its phylogenetic relationship and genetic diversity. The FIV Ac/FeLV Ag Test Kit (Alere™) and the commercial immunoenzymatic assay kit (Alere™) were used to detect the positive samples, which were subsequently confirmed by ELISA (ELISA - SNAP® Combo FeLV/FIV). To confirm the presence of proviral DNA, a polymerase chain reaction (PCR) was performed to amplify the target fragments of 450, 235, and 166 bp of the FeLV gag gene. For the detection of FeLV subtypes, nested PCR was performed for FeLV-A, B, and C, with amplification of 2350-, 1072-, 866-, and 1755-bp fragments for the FeLV env gene. The results obtained by nested PCR showed that the four positive samples amplified the A and B subtypes. The C subtype was not amplified. There was an AB combination but no ABC combination. Phylogenetic analysis revealed similarities (78% bootstrap) between the subtype circulating in Brazil and FeLV-AB and with the subtypes of Eastern Asia (Japan) and Southeast Asia (Malaysia), demonstrating that this subtype possesses high genetic variability and a differentiated genotype.
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Affiliation(s)
- Nathálya Dos Santos Martins
- Departament of Pathology, State University of Maranhão, University City Paulo VI, Cx. Postal 9, Tirirical, São Luís, MA, 65055-970, Brazil
| | - Ana Paula Sousa Rodrigues
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, UFMG 30 123-970, Belo Horizonte, MG, Brazil
| | - Juliana Marques Bicalho
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, UFMG 30 123-970, Belo Horizonte, MG, Brazil
| | - Joanna Jéssica Albuquerque
- Departament of Pathology, State University of Maranhão, University City Paulo VI, Cx. Postal 9, Tirirical, São Luís, MA, 65055-970, Brazil
| | - Luana Luz Reis
- Laboratory of Genetics and Molecular Biology, Department of Chemistry and Biology, State University of Maranhão (UEMA), Praça Duque de Caxias, s/n, Morro do Alecrim, Caxias, MA, 65604-380, Brazil
| | - Luciana Luz Alves
- Laboratory of Genetics and Molecular Biology, Department of Chemistry and Biology, State University of Maranhão (UEMA), Praça Duque de Caxias, s/n, Morro do Alecrim, Caxias, MA, 65604-380, Brazil
| | - Renata Mondego de Oliveira
- Departament of Pathology, State University of Maranhão, University City Paulo VI, Cx. Postal 9, Tirirical, São Luís, MA, 65055-970, Brazil
| | - Larissa Sarmento Dos Santos
- Departament of Pathology, State University of Maranhão, University City Paulo VI, Cx. Postal 9, Tirirical, São Luís, MA, 65055-970, Brazil
| | - Alcina Vieira de Carvalho Neta
- Departament of Pathology, State University of Maranhão, University City Paulo VI, Cx. Postal 9, Tirirical, São Luís, MA, 65055-970, Brazil
| | - Rudson Almeida de Oliveira
- Department of Veterinary Clinics, State University of Maranhão, University City Paulo VI, Cx. Postal 9, Tirirical, São Luís, MA, 65055-970, Brazil
| | - Rafael Cardoso Carvalho
- Center for Biological and Health Sciences, Federal University of Maranhão, UFMA, Rodovia BR 222, Km 04, s/n, Boa Vista, Chapadinha, MA, 65500-000, Brazil
| | - Ferdinan Almeida Melo
- Departament of Pathology, State University of Maranhão, University City Paulo VI, Cx. Postal 9, Tirirical, São Luís, MA, 65055-970, Brazil
| | - Jenner Karlisson Pimenta Dos Reis
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, UFMG 30 123-970, Belo Horizonte, MG, Brazil
| | - Ana Lucia Abreu-Silva
- Departament of Pathology, State University of Maranhão, University City Paulo VI, Cx. Postal 9, Tirirical, São Luís, MA, 65055-970, Brazil.
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Guillen‐Otero T, Lee S, Chen C, Szoevenyi P, Kessler M. A metabarcoding protocol targeting two DNA regions to analyze root-associated fungal communities in ferns and lycophytes. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11523. [PMID: 37342167 PMCID: PMC10278937 DOI: 10.1002/aps3.11523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 06/22/2023]
Abstract
Premise Detailed studies of the fungi associated with lycophytes and ferns provide crucial insights into the early evolution of land plants. However, most investigations to date have assessed fern-fungus interactions based only on visual root inspection. In the present research, we establish and evaluate a metabarcoding protocol to analyze the fungal communities associated with fern and lycophyte roots. Methods We used two primer pairs focused on the ITS rRNA region to screen the general fungal communities, and the 18S rRNA to target Glomeromycota fungi (i.e., arbuscular mycorrhizal fungi). To test these approaches, we collected and processed roots from 12 phylogenetically distant fern and lycophyte species. Results We found marked compositional differences between the ITS and 18S data sets. While the ITS data set demonstrated the dominance of orders Glomerales (phylum Glomeromycota), Pleosporales, and Helotiales (both in phylum Ascomycota), the 18S data set revealed the greatest diversity of Glomeromycota. Non-metric multidimensional scaling (NMDS) ordination suggested an important geographical effect in sample similarities. Discussion The ITS-based approach is a reliable and effective method to analyze the fungal communities associated with fern and lycophyte roots. The 18S approach is more appropriate for studies focused on the detailed screening of arbuscular mycorrhizal fungi.
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Affiliation(s)
- Thais Guillen‐Otero
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Soon‐Jae Lee
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Cheng‐Wei Chen
- Biodiversity Program, Taiwan International Graduate ProgramAcademia Sinica and National Taiwan Normal UniversityTaipei115Taiwan
| | - Peter Szoevenyi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
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Conrad S, Gant Kanegusuku A, Conklin SE. Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics. Clin Biochem 2023; 115:22-32. [PMID: 36495954 PMCID: PMC9729171 DOI: 10.1016/j.clinbiochem.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Recent studies evaluating the preanalytical factors that impact the outcome of nucleic-acid based methods for the confirmation of SARS-CoV-2 have illuminated the importance of identifying variables that promoted accurate testing, while using scarce resources efficiently. The majority of laboratory errors occur in the preanalytical phase. While there are many resources identifying and describing mechanisms for main laboratory testing on automated platforms, there are fewer comprehensive resources for understanding important preanalytical and environmental factors that affect accurate molecular diagnostic testing of infectious diseases. This review identifies evidence-based factors that have been documented to impact the outcome of nucleic acid-based molecular techniques for the diagnosis of infectious diseases.
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Affiliation(s)
- Stephanie Conrad
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | | | - Steven E Conklin
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA; Department of Anatomic & Clinical Pathology, Tufts University School of Medicine, Boston, MA, USA.
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Qian J, Zhang Q, Lu M. Integration of on-chip lysis and paper-based sensor for rapid detection of viral and exosomal RNAs. Biosens Bioelectron 2023; 226:115114. [PMID: 36753990 DOI: 10.1016/j.bios.2023.115114] [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: 11/03/2022] [Revised: 01/15/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
In recent years, paper-based nucleic acid sensors have been demonstrated for the ability to detect DNA and RNA molecules extracted from viruses and bacteria. In clinical samples, these nucleic acids are mostly encapsulated in lipid membranes and need to be released before being analyzed using paper-based sensors. For the nucleic acid amplification tests (NAATs), it is also desirable to remove the interfering molecules that can inhibit the nucleic acid amplification. To achieve a field deployable NAAT, we report a portable sensor system that combines the thermolysis and paper-based NAATs to detect target RNA molecules carried by viral and exosomal nanoparticles. The sensor cartridge includes a lysis chamber with a pressure-controlled diaphragm valve, paper flow channels, and three paper-based NAAT reaction chambers to extract, transport, and detect nucleic acids respectively. A compact instrument was prototyped to automate the assay, collect fluorescence images of the nucleic acid amplification, and generate amplification curves for NAATs. The pump-free and paper-based sensor achieved quantitative analysis of influenza A virus (IAV) RNA and exosome microRNA within 1 h, with the lowest detect concentration of 104 TCID50/mL and 106 EV/mL for IAV and exosome, respectively. Owing to the advantages of easy storage, simple operation, and low cost, such as system has great potential to be used as a point-of-care test for in-field diagnosis of viral and bacterial infections.
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Affiliation(s)
- Jingjing Qian
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
| | - Qinming Zhang
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
| | - Meng Lu
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA; Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA.
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34
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Rey Gomez LM, Hirani R, Care A, Inglis DW, Wang Y. Emerging Microfluidic Devices for Sample Preparation of Undiluted Whole Blood to Enable the Detection of Biomarkers. ACS Sens 2023; 8:1404-1421. [PMID: 37011238 DOI: 10.1021/acssensors.2c02696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Blood testing allows for diagnosis and monitoring of numerous conditions and illnesses; it forms an essential pillar of the health industry that continues to grow in market value. Due to the complex physical and biological nature of blood, samples must be carefully collected and prepared to obtain accurate and reliable analysis results with minimal background signal. Examples of common sample preparation steps include dilutions, plasma separation, cell lysis, and nucleic acid extraction and isolation, which are time-consuming and can introduce risks of sample cross-contamination or pathogen exposure to laboratory staff. Moreover, the reagents and equipment needed can be costly and difficult to obtain in point-of-care or resource-limited settings. Microfluidic devices can perform sample preparation steps in a simpler, faster, and more affordable manner. Devices can be carried to areas that are difficult to access or that do not have the resources necessary. Although many microfluidic devices have been developed in the last 5 years, few were designed for the use of undiluted whole blood as a starting point, which eliminates the need for blood dilution and minimizes blood sample preparation. This review will first provide a short summary on blood properties and blood samples typically used for analysis, before delving into innovative advances in microfluidic devices over the last 5 years that address the hurdles of blood sample preparation. The devices will be categorized by application and the type of blood sample used. The final section focuses on devices for the detection of intracellular nucleic acids, because these require more extensive sample preparation steps, and the challenges involved in adapting this technology and potential improvements are discussed.
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Affiliation(s)
| | - Rena Hirani
- Australian Red Cross Lifeblood, Sydney, New South Wales 2015, Australia
| | - Andrew Care
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - David W Inglis
- School of Engineering, Faculty of Science and Engineering and △School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
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35
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Schurig S, Kobialka R, Wende A, Ashfaq Khan MA, Lübcke P, Eger E, Schaufler K, Daugschies A, Truyen U, Abd El Wahed A. Rapid Reverse Purification DNA Extraction Approaches to Identify Microbial Pathogens in Wastewater. Microorganisms 2023; 11:microorganisms11030813. [PMID: 36985386 PMCID: PMC10056086 DOI: 10.3390/microorganisms11030813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/06/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Wastewater monitoring became a promising solution in the early detection of outbreaks. Despite the achievements in the identification of pathogens in wastewater using real-time PCR, there is still a lack of reliable rapid nucleic acid extraction protocols. Therefore, in this study, samples were subjected to alkali, proteinase K and/or bead-beating followed by reverse purification magnetic beads-based separation. Wastewater samples spiked with S. aureus, E. coli and C. parvum were used as examples for Gram-positive and -negative bacteria and protozoa, respectively. All results were compared with a spin column technology as a reference method. Proteinase K with bead beating (vortexing with 0.1 mm glass beads for three minutes) was particularly successful for bacterial DNA extraction (three- to five-fold increase). The most useful extraction protocol for protozoa was pre-treatment with proteinase K (eight-fold increase). The selected methods were sensitive as far as detecting one bacterial cell per reaction for S. aureus, ten bacterial cells for E. coli and two oocysts for C. parvum. The extraction reagents are cold chain independent and no centrifuge or other large laboratory equipment is required to perform DNA extraction. A controlled validation trial is needed to test the effectiveness at field levels.
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Affiliation(s)
- Sarah Schurig
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
- Xpedite Diagnostics GmbH, 80687 Munich, Germany
| | - Rea Kobialka
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
| | - Andy Wende
- Xpedite Diagnostics GmbH, 80687 Munich, Germany
| | - Md Anik Ashfaq Khan
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
| | - Phillip Lübcke
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Elias Eger
- Institute of Infection Medicine, Christian-Albrecht University Kiel, 24105 Kiel, Germany
- University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Katharina Schaufler
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University Kiel, 24105 Kiel, Germany
- University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Arwid Daugschies
- Institute of Parasitology, Centre for Infectious Disease, Leipzig University, 04103 Leipzig, Germany
| | - Uwe Truyen
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
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36
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Edgar RH, Samson AP, Kocsis T, Viator JA. Photoacoustic Flow Cytometry Using Functionalized Microspheres for Selective Detection of Bacteria. MICROMACHINES 2023; 14:573. [PMID: 36984980 PMCID: PMC10057399 DOI: 10.3390/mi14030573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Photoacoustic flow cytometry is a method to detect rare analytes in fluids. We developed photoacoustic flow cytometry to detect pathological cells in body fluids, such as circulating tumor cells or bacteria in blood. In order to induce specific optical absorption in bacteria, we use modified bacteriophage that precisely target bacterial species or subspecies for rapid identification. In order to reduce detection variability and to halt the lytic lifescycle that results in lysis of the bacteria, we attached dyed latex microspheres to the tail fibers of bacteriophage that retained the bacterial recognition binding sites. We tested these microsphere complexes using Salmonella enterica (Salmonella) and Escherichia coli (E. coli) bacteria and found robust and specific detection of targeted bacteria. In our work we used LT2, a strain of Salmonella, against K12, a strain of E. coli. Using Det7, a bacteriophage that binds to LT2 and not to K12, we detected an average of 109.3±9.0 of LT2 versus 2.0±1.7 of K12 using red microspheres and 86.7±13.2 of LT2 versus 0.3±0.6 of K12 using blue microspheres. These results confirmed our ability to selectively detect bacterial species using photoacoustic flow cytometry.
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Affiliation(s)
- Robert H. Edgar
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Anie-Pier Samson
- Department of Engineering, Duquesne University, Pittsburgh, PA 15282, USA
| | - Tori Kocsis
- Department of Engineering, Duquesne University, Pittsburgh, PA 15282, USA
| | - John A. Viator
- Department of Engineering, Duquesne University, Pittsburgh, PA 15282, USA
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37
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Kim EJ, Lee J, Yoon Y, Lee D, Baek Y, Takano C, Sakai J, Iijima T, Kanamori D, Gardner H, McLaughlin RE, Kilgore PE, Nakamura A, Ogihara T, Hayakawa S, Hoshino T, Kim DW, Seki M. Development of a novel loop-mediated isothermal amplification assay for ß-lactamase gene identification using clinical isolates of Gram-negative bacteria. Front Cell Infect Microbiol 2023; 12:1000445. [PMID: 36710975 PMCID: PMC9877619 DOI: 10.3389/fcimb.2022.1000445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/12/2022] [Indexed: 01/13/2023] Open
Abstract
Rapid evaluation of antimicrobial susceptibility is important in the treatment of nosocomial infections by Gram-negative bacteria, which increasingly carry carbapenemases and metallo-β-lactamases. We developed loop-mediated isothermal amplification (LAMP)-based assays for four β-lactamase genes (bla KPC, bla NDM-1, bla IMP-1 group, and bla VIM). The assays were evaluated using eight reference bacterial strains (Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter bereziniae) harboring six β-lactamase genes. A total of 55 Gram-negative bacterial strains, including 47 clinical P. aeruginosa isolates, fully characterized by next-generation sequencing (NGS), were used to evaluate the LAMP assays. The results were compared to those of conventional PCR. The LAMP assays were able to detect as few as 10 to 100 copies of a gene, compared to 10 to 104 copies for conventional PCR. The LAMP assay detected four β-lactamase genes with a sensitivity similar to that using purified DNA as the template in DNA-spiked urine, sputum, and blood specimens. By contrast, the sensitivity of PCR was 1- to 100-fold lower with DNA-spiked clinical specimens. Therefore, the LAMP assays were proved to be an appropriate tool for the detection of four β-lactamases.
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Affiliation(s)
- Eun Jin Kim
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan,Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Jiwon Lee
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan,Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Youngbae Yoon
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan,Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Donghyun Lee
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan,Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Yeongjun Baek
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan,Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Chika Takano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
| | - Takahiro Iijima
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
| | - Dai Kanamori
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
| | | | | | - Paul E. Kilgore
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, United States
| | - Akihiro Nakamura
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
| | - Takashi Ogihara
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tomonori Hoshino
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea,*Correspondence: Mitsuko Seki, ; Dong Wook Kim,
| | - Mitsuko Seki
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan,Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan,*Correspondence: Mitsuko Seki, ; Dong Wook Kim,
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Hudson BC, Connon CC. DNA Purification from Bloodstains and Buccal Cells/Saliva on FTA ® Cards. Methods Mol Biol 2023; 2685:119-126. [PMID: 37439979 DOI: 10.1007/978-1-0716-3295-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
FTA® cards enable efficient, long-term storage of blood and buccal cells/saliva samples for future forensic DNA analysis; these are typically collected as known reference samples, as opposed to evidentiary, crime scene samples. Upon contact with the FTA® card, cells are lysed and the DNA is immobilized. Different FTA® cards are available and have been specially formulated based on sample type: bloodstains are added to the traditional FTA® Card, while colorless sources (e.g., buccal cells/saliva) are added to the FTA® Indicating Card. The main difference between these cards is the presence of a pink dye embedded in the indicating cards that becomes white when exposed to colorless fluids, like saliva; this aids in location confirmation of the stain for future sampling. Although DNA can be eluted/extracted from FTA® punches using various methods or, alternatively, direct STR amplification from unpurified punches can be performed, the protocol herein describes a simple purification method for bloodstained punches from FTA® Cards as well as buccal/saliva-stained punches from FTA® Indicating Cards. Following this purification, STR amplification can be performed via the "punch-in" method.
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Affiliation(s)
- Brittany C Hudson
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA.
- Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, USA.
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Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution. Microbiol Spectr 2022; 10:e0225522. [PMID: 36377933 PMCID: PMC9769501 DOI: 10.1128/spectrum.02255-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The major aquatic interface between host and environment in teleost finfish species is the gill. The diversity of this infraclass, high complexity of the organ, and its direct exposure to the surrounding environment make it an ideal candidate for furthering our understanding of the intertwined relationships between host and microbiome. Capturing the structure and diversity of bacterial communities from this low-biomass, inhibitor-rich tissue can, however, prove challenging. Lessons learned in doing so are directly applicable to similar sample types in other areas of microbiology. Through the development of a quantitative PCR assay for both host material and 16S rRNA genes, we tested and developed a robust method for low-biomass sample collection which minimized host DNA contamination. Quantification of 16S rRNA facilitated not only the screening of samples prior to costly library construction and sequencing but also the production of equicopy libraries based on 16S rRNA gene copies. A significant increase in diversity of bacteria captured was achieved, providing greater information on the true structure of the microbial community. Such findings offer important information for determining functional processes. Results were confirmed across fresh, brackish, and marine environs with four different fish species, with results showing broad homology between samples, demonstrating the robustness of the approach. Evidence presented is widely applicable to samples similar in composition, such as sputum or mucus, or those that are challenging due to the inherent inclusion of inhibitors. IMPORTANCE The interaction between the fish gill and surrounding bacteria-rich water provides an intriguing model for examining the interaction between the fish, free-floating bacteria, and the bacterial microbiome on the gill surface. Samples that are inherently low in bacteria, or that have components that inhibit the ability to produce libraries that identify the components of microbial communities, present significant challenges. Gill samples present both of these types of challenges. We developed methods for quantifying both the bacterial and host DNA material and established a sampling method which both reduced inhibitor content and maximized bacterial diversity. By quantifying and normalizing bacteria prior to library construction, we showed significant improvements with regards to the fidelity of the final data. Our results support wide-ranging applications for analyzing samples of similar composition, such as mucus and sputum, in other microbiological spheres.
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Wang G, Du Y, Ma X, Ye F, Qin Y, Wang Y, Xiang Y, Tao R, Chen T. Thermophilic Nucleic Acid Polymerases and Their Application in Xenobiology. Int J Mol Sci 2022; 23:ijms232314969. [PMID: 36499296 PMCID: PMC9738464 DOI: 10.3390/ijms232314969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Thermophilic nucleic acid polymerases, isolated from organisms that thrive in extremely hot environments, possess great DNA/RNA synthesis activities under high temperatures. These enzymes play indispensable roles in central life activities involved in DNA replication and repair, as well as RNA transcription, and have already been widely used in bioengineering, biotechnology, and biomedicine. Xeno nucleic acids (XNAs), which are analogs of DNA/RNA with unnatural moieties, have been developed as new carriers of genetic information in the past decades, which contributed to the fast development of a field called xenobiology. The broad application of these XNA molecules in the production of novel drugs, materials, and catalysts greatly relies on the capability of enzymatic synthesis, reverse transcription, and amplification of them, which have been partially achieved with natural or artificially tailored thermophilic nucleic acid polymerases. In this review, we first systematically summarize representative thermophilic and hyperthermophilic polymerases that have been extensively studied and utilized, followed by the introduction of methods and approaches in the engineering of these polymerases for the efficient synthesis, reverse transcription, and amplification of XNAs. The application of XNAs facilitated by these polymerases and their mutants is then discussed. In the end, a perspective for the future direction of further development and application of unnatural nucleic acid polymerases is provided.
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Agarkar T, Tripathy S, Chawla V, Sengupta M, Ghosh S, Kumar A. A batch processed titanium-vanadium oxide nanocomposite based solid-state electrochemical sensor for zeptomolar nucleic acid detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4495-4513. [PMID: 36326012 DOI: 10.1039/d2ay01141g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Approaching a nucleic acid amplification test (NAAT) based diagnosis of a pathogen from an electrochemistry pathway is a relatively economical, decentralized, and yet highly sensitive route. This work aimed to construct an electrochemical biosensor with a 2-electrode geometry using a transition metal oxide (TMO) based sensing layer. A series of batch-processed TiO2-V2O5 (TVO) nanocomposite-based electrodes were fabricated to probe their electrochemical performance and attain a highly sensitive dual-electrode electrochemical sensor (DEES) compared to pristine V2O5. The XRD analysis of the electrodes confirmed the formation of a nanocomposite, while the XPS analysis correlated the formation of oxygen vacancies with improved electrical conduction measured via EIS and I-V characterization. Furthermore, the work demonstrated the application of the optimized electrode in electrochemical detection of end-point loop-mediated isothermal amplification (LAMP) readout for 101-104 copies (0.1 zeptomoles to 0.1 attomoles) of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) plasmid DNA and in vitro transcribed RNA in an aqueous solution. The device achieved a limit of detection as low as 2.5 and 0.25 copies per μL for plasmid DNA and in vitro transcribed RNA, respectively. The DEES was able to successfully detect in situ LAMP performed on magneto-extracted SARS-CoV-2 plasmid and RNA from (a) an aqueous solution, (b) a sample spiked with excess human genomic DNA, and (c) a serum-spiked sample. The DEES results were then compared with those of real-time fluorescence and commercially available screen-printed electrodes (SPEs).
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Affiliation(s)
- Tanvi Agarkar
- Department of Physics, Bennett University, India
- Center of Excellence for Nanosensors and Nanomedicine, Bennett University, India
- Pristine Diamonds Pvt. Ltd., India
| | - Sayantan Tripathy
- Department of Chemistry, Bennett University, India
- Department of Biotechnology, Bennett University, India
- Center of Excellence for Nanosensors and Nanomedicine, Bennett University, India
| | - Vipin Chawla
- Institute Instrumentation Centre, Indian Institute of Technology Roorkee, India
| | - Mrittika Sengupta
- Department of Biotechnology, Bennett University, India
- Center of Excellence for Nanosensors and Nanomedicine, Bennett University, India
| | - Souradyuti Ghosh
- Department of Chemistry, Bennett University, India
- Department of Biotechnology, Bennett University, India
- Center of Excellence for Nanosensors and Nanomedicine, Bennett University, India
- Division of Radiation and Stress Biology, UGC-DAE CSR, Kolkata Center, India
| | - Ashvani Kumar
- Department of Physics, Bennett University, India
- Pristine Diamonds Pvt. Ltd., India
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Zhang J, Yang F, Sun Z, Fang Y, Zhu H, Zhang D, Zeng X, Liu W, Liu T, Liu Y, Chi W, Wang S, Ding L, Wu Y, Zhang Y, Zhao H. Rapid and precise identification of bloodstream infections using a pre-treatment protocol combined with high-throughput multiplex genetic detection system. BMC Infect Dis 2022; 22:823. [DOI: 10.1186/s12879-022-07793-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
Bloodstream infection (BSI) is a life-threatening condition with high morbidity and mortality rates worldwide. Early diagnosis of BSI is critical to avoid the unnecessary application of antimicrobial agents and for proper treatment. However, the current standard methods based on blood culture are time-consuming, thus failing to provide a timely etiological diagnosis of BSI, and common PCR-based detection might be inhibited by matrix components.
Methods
The current study explored an integrated pre-analytical treatment protocol for whole blood samples, wherein pathogens are enriched and purified by incubation and concentration, and inhibitors are inactivated and removed. Further, this study developed and evaluated a novel high-throughput multiplex genetic detection system (HMGS) to detect 24 of the most clinically prevalent BSI pathogens in blood culture samples and pre-treated whole blood samples. The specificity and sensitivity were evaluated using related reference strains and quantified bacterial/fungal suspensions. The clinical utility of BSI-HMGS combined with the pre-analytical treatment protocol was verified using blood cultures and whole blood samples.
Results
The combined pre-treatment protocol and BSI-HMGS was highly specific for target pathogens and possessed a low detection limit for clinical whole blood samples. The pre-treatment protocol could deplete the PCR inhibitors effectively. For blood culture samples, the current method showed 100.0% negative percent agreements and > 87.5% positive percent agreements compared to the reference results based on blood culture findings. For whole blood samples, the current method showed 100.0% negative percent agreements and > 80.0% positive percent agreements compared to the reference results for most pathogens. The turnaround time was ≤ 8 h, and all the procedures could be conducted in a general clinical laboratory.
Conclusion
The BSI-HMGS combined with the pre-treatment protocol was a practical and promising method for early and precise detection of BSIs, especially for areas without access to advanced medical facilities.
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Sarathkumara YD, Browne DJ, Kelly AM, Pattinson DJ, Rush CM, Warner J, Proietti C, Doolan DL. The Effect of Tropical Temperatures on the Quality of RNA Extracted from Stabilized Whole-Blood Samples. Int J Mol Sci 2022; 23:ijms231810609. [PMID: 36142559 PMCID: PMC9503649 DOI: 10.3390/ijms231810609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022] Open
Abstract
Whole-blood-derived transcriptional profiling is widely used in biomarker discovery, immunological research, and therapeutic development. Traditional molecular and high-throughput transcriptomic platforms, including molecular assays with quantitative PCR (qPCR) and RNA-sequencing (RNA-seq), are dependent upon high-quality and intact RNA. However, collecting high-quality RNA from field studies in remote tropical locations can be challenging due to resource restrictions and logistics of post-collection processing. The current study tested the relative performance of the two most widely used whole-blood RNA collection systems, PAXgene® and Tempus™, in optimal laboratory conditions as well as suboptimal conditions in tropical field sites, including the effects of extended storage times and high storage temperatures. We found that Tempus™ tubes maintained a slightly higher RNA quantity and integrity relative to PAXgene® tubes at suboptimal tropical conditions. Both PAXgene® and Tempus™ tubes gave similar RNA purity (A260/A280). Additionally, Tempus™ tubes preferentially maintained the stability of mRNA transcripts for two reference genes tested, Succinate dehydrogenase complex, subunit A (SDHA) and TATA-box-binding protein (TBP), even when RNA quality decreased with storage length and temperature. Both tube types preserved the rRNA transcript 18S ribosomal RNA (18S) equally. Our results suggest that Tempus™ blood RNA collection tubes are preferable to PAXgene® for whole-blood collection in suboptimal tropical conditions for RNA-based studies in resource-limited settings.
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Affiliation(s)
- Yomani D. Sarathkumara
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Daniel J. Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Ashton M. Kelly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - David J. Pattinson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Catherine M. Rush
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Jeffrey Warner
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Carla Proietti
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Denise L. Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- Correspondence:
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Vancomycin-conjugated polydopamine-coated magnetic nanoparticles for molecular diagnostics of Gram-positive bacteria in whole blood. J Nanobiotechnology 2022; 20:400. [PMID: 36064405 PMCID: PMC9446563 DOI: 10.1186/s12951-022-01606-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/28/2022] [Indexed: 11/22/2022] Open
Abstract
Background Sepsis is caused mainly by infection in the blood with a broad range of bacterial species. It can be diagnosed by molecular diagnostics once compounds in the blood that interfere with molecular diagnostics are removed. However, this removal relies on ultracentrifugation. Immunomagnetic separation (IMS), which typically uses antibody-conjugated silica-coated magnetic nanoparticles (Ab-SiO2-MNPs), has been widely applied to isolate specific pathogens in various types of samples, such as food and environmental samples. However, its direct use in blood samples containing bacteria is limited due to the aggregation of SiO2-MNPs in the blood and inability to isolate multiple species of bacteria causing sepsis. Results In this study, we report the synthesis of vancomycin-conjugated polydopamine-coated (van-PDA-MNPs) enabling preconcentration of multiple bacterial species from blood without aggregation. The presence of PDA and van on MNPs was verified using transmission electron microscopy, X-ray photoelectron spectroscopy, and energy disruptive spectroscopy. Unlike van-SiO2-MNPs, van-PDA-MNPs did not aggregate in the blood. Van-PDA-MNPs were able to preconcentrate several species of Gram-positive bacteria in the blood, lowering the limit of detection (LOD) to 10 colony forming units/mL by polymerase chain reaction (PCR) and quantitative PCR (qPCR). This is 10 times more sensitive than the LOD obtained by PCR and qPCR using van-SiO2-MNPs. Conclusion These results suggest that PDA-MNPs can avoid aggregation in blood and be conjugated with receptors, thereby improving the sensitivity of molecular diagnostics of bacteria in blood samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12951-022-01606-3.
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Nagatake Y, Sato M, Mouri Y, Tomita N. Fully automated microRNA quantification technique based on bioluminescent enzyme immunoassay. Anal Biochem 2022; 656:114880. [PMID: 36063916 DOI: 10.1016/j.ab.2022.114880] [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: 05/06/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022]
Abstract
MicroRNAs (miRNAs) are potential clinical biomarkers for the detection of various diseases. However, their quantification has not been implemented in clinical practice given the inconsistencies in their variable recovery rate and accuracy of the results. Thus, we utilized a technique based on bioluminescent enzyme immunoassay (BLEIA) to perform fully automated miRNA quantification using magnetic particles conjugated with antibodies targeting DNA-RNA hybrids, biotinylated DNA probes specific to miRNAs, and firefly luciferase-labeled streptavidin. This method enabled direct use of diluted serum and automation of all processes within 1 h. The results revealed a wide linear range between 10 fmol/L and 1 nmol/L, high sensitivity with a detection limit of 6.3 fmol/L or below, high specificity with a false positive rate under 2.4%, and high reproducibility in intra- and inter-experimental observations (under CV 10% and r = 0.9965, respectively). Furthermore, a significant correlation was revealed between quantitative reverse transcription-polymerase chain reaction and BLEIA assay for the quantification of synthetic miRNA (r = 0.9993) and endogenous miRNA in healthy serums (r = 0.8203), respectively. Overall, we developed a fully automated miRNA quantification method based on BLEIA, which can be adopted in a clinical setting. However, further studies are needed to assess its clinical performance.
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Affiliation(s)
- Yuka Nagatake
- Department-I, Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimoishigami, Tochigi, Japan
| | - Masaki Sato
- Department-I, Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimoishigami, Tochigi, Japan.
| | - Yuta Mouri
- Department-I, Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimoishigami, Tochigi, Japan
| | - Norihiro Tomita
- Department-I, Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimoishigami, Tochigi, Japan
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Chavez‐Pineda OG, Rodriguez‐Moncayo R, Cedillo‐Alcantar DF, Guevara‐Pantoja PE, Amador‐Hernandez JU, Garcia‐Cordero JL. Microfluidic systems for the analysis of blood‐derived molecular biomarkers. Electrophoresis 2022; 43:1667-1700. [DOI: 10.1002/elps.202200067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Oriana G. Chavez‐Pineda
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Roberto Rodriguez‐Moncayo
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Diana F. Cedillo‐Alcantar
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Pablo E. Guevara‐Pantoja
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Josue U. Amador‐Hernandez
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
| | - Jose L. Garcia‐Cordero
- Laboratory of Microtechnologies Applied to Biomedicine (LMAB) Centro de Investigación y de Estudios Avanzados (Cinvestav) Monterrey Nuevo León Mexico
- Roche Institute for Translational Bioengineering (ITB) Roche Pharma Research and Early Development, Roche Innovation Center Basel Basel Switzerland
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Lee K, Murphy J, Tripathi A. Electro-DBS: A Simple Method to Rapidly Extract Genomic DNA from Dried Blood Spots. Anal Chem 2022; 94:13404-13412. [DOI: 10.1021/acs.analchem.2c02021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kiara Lee
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912 United States
- Brown University School of Public Health, Providence, Rhode Island 02912, United States
| | - John Murphy
- Brown BioMed Machine Shop, Division of Biology and Medicine, Brown University, Providence, Rhode Island 02912, United States
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912 United States
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Kanapathy S, Obande GA, Chuah C, Shueb RH, Yean CY, Banga Singh KK. Sequence-Specific Electrochemical Genosensor for Rapid Detection of blaOXA-51-like Gene in Acinetobacter baumannii. Microorganisms 2022; 10:1413. [PMID: 35889132 PMCID: PMC9322073 DOI: 10.3390/microorganisms10071413] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/26/2022] Open
Abstract
Acinetobacter baumannii (A. baumannii) are phenotypically indistinguishable from the Acinetobacter calcoaceticus−A. baumannii (ACB) complex members using routine laboratory methods. Early diagnosis plays an important role in controlling A. baumannii infections and this could be assisted by the development of a rapid, yet sensitive diagnostic test. In this study, we developed an enzyme-based electrochemical genosensor for asymmetric PCR (aPCR) amplicon detection of the blaOXA-51-like gene in A. baumannii. A. baumanniiblaOXA-51-like gene PCR primers were designed, having the reverse primer modified at the 5′ end with FAM. A blaOXA-51-like gene sequence-specific biotin labelled capture probe was designed and immobilized using a synthetic oligomer (FAM-labelled) deposited on the working electrode of a streptavidin-modified, screen-printed carbon electrode (SPCE). The zot gene was used as an internal control with biotin and FAM labelled as forward and reverse primers, respectively. The blaOXA-51-like gene was amplified using asymmetric PCR (aPCR) to generate single-stranded amplicons that were detected using the designed SPCE. The amperometric current response was detected with a peroxidase-conjugated, anti-fluorescein antibody. The assay was tested using reference and clinical A. baumannii strains and other nosocomial bacteria. The analytical sensitivity of the assay at the genomic level and bacterial cell level was 0.5 pg/mL (1.443 µA) and 103 CFU/mL, respectively. The assay was 100% specific and sensitive for A. baumannii. Based on accelerated stability performance, the developed genosensor was stable for 1.6 years when stored at 4 °C and up to 28 days at >25 °C. The developed electrochemical genosensor is specific and sensitive and could be useful for rapid, accurate diagnosis of A. baumannii infections even in temperate regions.
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Affiliation(s)
- Swarnaletchumi Kanapathy
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
| | - Godwin Attah Obande
- Department of Microbiology, Faculty of Science, Federal University of Lafia, Lafia 950101, Nasarawa State, Nigeria;
| | - Candy Chuah
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
- Faculty of Health Sciences, Universiti Teknologi MARA, Kampus Bertam, Kepala Batas 13200, Penang, Malaysia
| | - Rafidah Hanim Shueb
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
| | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
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Burke D, Pinheiro L, Glover ES, Moon F, Deans Z, Corner A. Between Laboratory Reproducibility of DNA Extraction from Human Blood and Fresh Frozen Tissue. J Mol Diagn 2022; 24:1041-1049. [PMID: 35835375 DOI: 10.1016/j.jmoldx.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/29/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022] Open
Abstract
Standardization of molecular diagnostics is fundamental for effective application of genetic analyses in personalized medicine. The amount of DNA extracted from a specimen can have a significant impact on diagnostic accuracy, especially in cases where the diagnostic variant has a low concentration such as cancer. Blood and tissue samples were supplied to genetic laboratories to assess the reproducibility of extraction methodologies; DNA was extracted using participants' routine procedures and returned to the external quality assessment provider. The amount of DNA was measured by two independent analytical techniques, fluorescence intensity of intercalating dye and digital PCR; DNA quality was evaluated by DNA integrity number scores. The amount of DNA extracted varied widely between and within participants and for different blood volumes, indicating that consistent diagnostic quality is challenging even within a single test center. The median digital PCR-measured amount of DNA was on average six times higher than the intercalating dye measurements obtained in this study, indicating the possibility that the latter quantitative method may significantly underestimate the amount of DNA, thus making it not fit for purpose. Standardization of genetic diagnostic tests will require a significant improvement in the reproducibility of DNA extraction; this could be achieved if suppliers and users of DNA extraction kits validate their extraction methodology using reliable quantitative measurements or reference materials.
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Affiliation(s)
- Daniel Burke
- National Measurement Institute, Australia (NMIA), Lindfield, New South Wales, Australia.
| | - Leonardo Pinheiro
- National Measurement Institute, Australia (NMIA), Lindfield, New South Wales, Australia
| | | | - Fiona Moon
- Genomics Quality Assessment, the Department of Laboratory Medicine, The Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Zandra Deans
- Genomics Quality Assessment, the Department of Laboratory Medicine, The Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Adam Corner
- Bio-Rad Laboratories Ltd., Digital Biology Group, Pleasanton, California
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Reifenberger GC, Thomas BA, Rhodes DVL. Comparison of DNA Extraction and Amplification Techniques for Use with Engorged Hard-Bodied Ticks. Microorganisms 2022; 10:microorganisms10061254. [PMID: 35744772 PMCID: PMC9228219 DOI: 10.3390/microorganisms10061254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/30/2022] [Accepted: 06/16/2022] [Indexed: 02/04/2023] Open
Abstract
Tick-borne infections are a serious threat to humans, livestock, and companion animals in many parts of the world, often leading to high morbidity and mortality rates, along with decreased production values and/or costly treatments. The prevalence of the microbes responsible for these infections is typically assessed by the molecular identification of pathogens within the tick vectors. Ticks sampled from animals are often engorged with animal blood, presenting difficulties in the amplification of nucleic acids due to the inhibitory effects of mammalian blood on the enzymes used in polymerase chain reactions (PCRs). This study tested two tick preparation methods, three methods of DNA extraction, and four commercially available DNA polymerases to determine the most reliable method of extracting and amplifying DNA from engorged ticks. Our study found that the phenol–chloroform extraction method yielded the highest concentration of DNA, yet DNA extracted by this method was amplified the least successfully. Thermo Scientific’s Phusion Plus PCR Master Mix was the best at amplifying the tick 16s rRNA gene, regardless of extraction method. Finally, our study identified that using the Qiagen DNeasy Blood & Tissues kit for DNA extraction coupled with either Phusion Plus PCR Master Mix or GoTaq DNA polymerase Master Mix is the best combination for the optimized amplification of DNA extracted from engorged ticks.
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