1
|
Lim J, Hwang J, Min H, Wester M, Kim C, Valera E, Kong HJ, Bashir R. Dried Blood Matrix as a New Material for the Detection of DNA Viruses. Adv Healthc Mater 2024:e2402506. [PMID: 39075818 DOI: 10.1002/adhm.202402506] [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: 07/08/2024] [Revised: 07/16/2024] [Indexed: 07/31/2024]
Abstract
The gold standard for diagnosing viruses such as the Hepatitis B Virus has remained largely unchanged, relying on conventional methods involving extraction, purification, and polymerase chain reaction (PCR). This approach is hindered by limited availability, as it is time-consuming and requires highly trained personnel. Moreover, it suffers from low recovery rates of the nucleic acid molecules for samples with low copy numbers. To address the challenges of complex instrumentation and low recovery rate of DNA, a drying process coupled with thermal treatment of whole blood is employed, resulting in the creation of a dried blood matrix characterized by a porous structure with a high surface-to-volume ratio where it also inactivates the amplification inhibitors present in whole blood. Drawing on insights from Brunauer-Emmett-Teller (BET)- Barrett-Joyner-Halenda (BJH) analysis, scanning electron microscopy (SEM), and fluorescence recovery after photobleaching (FRAP), detection assay is devised for HBV, as a demonstration, from whole blood with high recovery of DNA and simplified instrumentation achieving a limit of detection (LOD) of 10 IU mL-1. This assay can be completed in <1.5 h using a simple heater, can be applied to other DNA viruses, and is expected to be suitable for point-of-care, especially in low-resource settings.
Collapse
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
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Joanne Hwang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hyegi Min
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew Wester
- 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
| | - Chansong Kim
- Department of Materials Science and Engineering, 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
| | - Hyun Joon Kong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Departments of Pathobiology, 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
- Carl R. Woese Institute for Genomic Biology, 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 Mechanical 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
- Chan Zuckerberg Biohub Chicago, Chicago, IL, 60642, USA
| |
Collapse
|
2
|
Heller C, Bachmann I, Spiegel M, Hufert FT, Dame G. Detection of Klebsiella pneumoniae Carbapenem Resistance Genes by qPCR: Choosing the Right Method for Total DNA Extraction. Microorganisms 2024; 12:1285. [PMID: 39065054 PMCID: PMC11278521 DOI: 10.3390/microorganisms12071285] [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: 05/16/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Rapid and accurate detection of Klebsiella pneumoniae carbapenem resistance is important for infection control and targeted antibiotic therapy. PCR-based assay performance heavily depends on the quality and quantity of template DNA. Challenges arise from the necessity to isolate chromosomal and large plasmid-encoded resistance genes simultaneously from a limited number of target cells and to remove PCR inhibitors. qPCRs for the detection of K. pneumoniae strains carrying blaOXA-48, blaNDM-1, blaKPC-2, and blaVIM-1 carbapenemase genes were developed. We compared the performance of template DNA extracted with silica column-based methods, reversed elution systems, and lysis-only methods either from diluted culture fluid or from a synthetic stool matrix which contained PCR inhibitors typically present in stool. The synthetic stool matrix was chosen to mimic K. pneumoniae containing rectal swabs or stool samples in a reproducible manner. For total DNA isolated from culture fluid, resistance gene detection by qPCR was always possible, independent of the extraction method. However, when total DNA was isolated from synthetic stool matrix spiked with K. pneumoniae, most methods were insufficient. The best performance of template DNA was obtained with reversed elution. This highlights the importance of choosing the right DNA extraction method for consistent carbapenem resistance detection by PCR.
Collapse
Affiliation(s)
- Cecilia Heller
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany; (C.H.); (I.B.); (M.S.); (F.T.H.)
| | - Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany; (C.H.); (I.B.); (M.S.); (F.T.H.)
| | - Martin Spiegel
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany; (C.H.); (I.B.); (M.S.); (F.T.H.)
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Frank T. Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany; (C.H.); (I.B.); (M.S.); (F.T.H.)
- Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Am Neuen Palais 10, House 9, 14469 Potsdam, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Universitätsplatz 1, 01968 Senftenberg, Germany; (C.H.); (I.B.); (M.S.); (F.T.H.)
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Am Neuen Palais 10, House 9, 14469 Potsdam, Germany
| |
Collapse
|
3
|
Goto A, Moriya Y, Nakayama M, Iwasaki S, Yamamoto S. DMPK perspective on quantitative model analysis for chimeric antigen receptor cell therapy: Advances and challenges. Drug Metab Pharmacokinet 2024; 56:101003. [PMID: 38843652 DOI: 10.1016/j.dmpk.2024.101003] [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: 11/01/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 06/24/2024]
Abstract
Chimeric antigen receptor (CAR) cells are genetically engineered immune cells that specifically target tumor-associated antigens and have revolutionized cancer treatment, particularly in hematological malignancies, with ongoing investigations into their potential applications in solid tumors. This review provides a comprehensive overview of the current status and challenges in drug metabolism and pharmacokinetics (DMPK) for CAR cell therapy, specifically emphasizing on quantitative modeling and simulation (M&S). Furthermore, the recent advances in quantitative model analysis have been reviewed, ranging from clinical data characterization to mechanism-based modeling that connects in vitro and in vivo nonclinical and clinical study data. Additionally, the future perspectives and areas for improvement in CAR cell therapy translation have been reviewed. This includes using formulation quality considerations, characterization of appropriate animal models, refinement of in vitro models for bottom-up approaches, and enhancement of quantitative bioanalytical methodology. Addressing these challenges within a DMPK framework is pivotal in facilitating the translation of CAR cell therapy, ultimately enhancing the patients' lives through efficient CAR cell therapies.
Collapse
Affiliation(s)
- Akihiko Goto
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Yuu Moriya
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Miyu Nakayama
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Shinji Iwasaki
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Syunsuke Yamamoto
- Center of Excellence for Drug Metabolism, Pharmacokinetics and Modeling, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan.
| |
Collapse
|
4
|
Schwaiger G, Matt M, Streich P, Bromann S, Clauß M, Elsner M, Seidel M. Standard addition method for rapid, cultivation-independent quantification of Legionella pneumophila cells by qPCR in biotrickling filters. Analyst 2024; 149:2978-2987. [PMID: 38602145 DOI: 10.1039/d3an02207b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Cultivation-independent molecular biological methods are essential to rapidly quantify pathogens like Legionella pneumophila (L. pneumophila) which is important to control aerosol-generating engineered water systems. A standard addition method was established to quantify L. pneumophila in the very complex matrix of process water and air of exhaust air purification systems in animal husbandry. Therefore, cryopreserved standards of viable L. pneumophila were spiked in air and water samples to calibrate the total bioanalytical process which includes cell lysis, DNA extraction, and qPCR. A standard addition algorithm was employed for qPCR to determine the initial concentration of L. pneumophila. In mineral water, the recovery rate of this approach (73%-134% within the concentration range of 100-5000 Legionella per mL) was in good agreement with numbers obtained from conventional genomic unit (GU) calibration with DNA standards. In air samples of biotrickling filters, in contrast, the conventional DNA standard approach resulted in a significant overestimation of up to 729%, whereas our standard addition gave a more realistic recovery of 131%. With this proof-of-principle study, we were able to show that the molecular biology-based standard addition approach is a suitable method to determine realistic concentrations of L. pneumophila in air and process water samples of biotrickling filter systems. Moreover, this quantification strategy is generally a promising method to quantify pathogens in challenging samples containing a complex microbiota and the classical GU approach used for qPCR leads to unreliable results.
Collapse
Affiliation(s)
- Gerhard Schwaiger
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Marco Matt
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Philipp Streich
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Sarah Bromann
- Thuenen-Institute for Agricultural Technology, Bundesallee 47, D-38116 Braunschweig, Germany
| | - Marcus Clauß
- Thuenen-Institute for Agricultural Technology, Bundesallee 47, D-38116 Braunschweig, Germany
| | - Martin Elsner
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Michael Seidel
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| |
Collapse
|
5
|
Song HH, Park H, Cho D, Bang HI, Oh HJ, Kim J. Optimization of a Protocol for Isolating Cell-free DNA From Cerebrospinal Fluid. Ann Lab Med 2024; 44:294-298. [PMID: 38151854 PMCID: PMC10813833 DOI: 10.3343/alm.2023.0267] [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: 07/10/2023] [Revised: 11/01/2023] [Accepted: 12/08/2023] [Indexed: 12/29/2023] Open
Abstract
A standardized protocol for the isolation of cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) is lacking. Therefore, we established a cfDNA isolation protocol optimized for clinical CSF specimens, integrating acceptable modifications and using artificial CSF generated from remnant CSF spiked with reference cell-free tumor DNA (ctDNA). We compared the isolation yields of in vitro diagnostic (IVD)-certified column-based (CB) and magnetic bead-based (MB) isolation. Furthermore, we modified both methods, including pre- and post-elution steps. To confirm ctDNA integrity and quantify the variant allele frequency after isolation, we performed droplet digital PCR (ddPCR) targeting IDH1 R132C in the reference ctDNA. MB isolation had a higher yield than CB isolation (P<0.0001), and post-isolation vacuum increased the final concentration in both methods, with little effect on cfDNA integrity. Our study provides a protocol to maximize CSF-ctDNA concentrations in IVD testing and future studies.
Collapse
Affiliation(s)
- Ho Hyun Song
- Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Asan, Korea
| | - Hyeran Park
- Department of Neurosurgery, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Doohwan Cho
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Hae In Bang
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Hyuk-Jin Oh
- Department of Neurosurgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Jieun Kim
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Seoul, Korea
| |
Collapse
|
6
|
Marius M, Fernandez C. Non-Microbiological Mycobacterial Detection Techniques for Quality Control of Biological Products: A Comprehensive Review. Microorganisms 2024; 12:788. [PMID: 38674732 PMCID: PMC11052345 DOI: 10.3390/microorganisms12040788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacteria can be one of the main contaminants of biological products, and their presence can have serious consequences on patients' health. For this reason, the European Pharmacopoeia mandates the specific testing of biological products for mycobacteria, a critical regulatory requirement aimed at ensuring the safety of these products before they are released to the market. The current pharmacopeial reference, i.e., microbial culture method, cannot ensure an exhaustive detection of mycobacteria due to their growth characteristics. Additionally, the method is time consuming and requires a continuous supply of culture media, posing logistical challenges. Thus, to overcome these issues, pharmaceutical industries need to consider alternative non-microbiological techniques to detect these fastidious, slow-growing contaminating agents. This review provides an overview of alternative methods, which could be applied within a quality control environment for biological products and underlines their advantages and limitations. Nucleic acid amplification techniques or direct measurement of mycobacteria stand out as the most suitable alternatives for mycobacterial testing in biological products.
Collapse
Affiliation(s)
- Marine Marius
- Sanofi, 1541 Ave. Marcel Mérieux, 69280 Marcy l’Etoile, France;
| | | |
Collapse
|
7
|
Sbruzzi RC, Feira MF, Cadore NA, Giudicelli GC, Kowalski TW, Gregianini TS, Chies JAB, Vianna FSL. An Efficient Extraction Method Allowing the Genetic Evaluation of Host DNA from Samples Collected for Virus Infection Diagnosis in Viral Transport Medium. Biopreserv Biobank 2024; 22:166-173. [PMID: 37579075 DOI: 10.1089/bio.2022.0188] [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: 08/16/2023] Open
Abstract
Introduction: During the COVID-19 pandemic, an extraordinary number of nasopharyngeal secretion samples inoculated in viral transport medium (VTM) were collected and analyzed to detect SARS-CoV-2 infection. In addition to viral detection, those samples can also be a source of host genomic material, providing excellent opportunities for biobanking and research. Objective: To describe a simple, in-house-developed DNA extraction method to obtain high yield and quality genomic DNA from VTM samples for host genetic analysis and assess its relative efficiency by comparing its yield and suitability to downstream applications to two different commercial DNA extraction kits. Methods: In this study, 13 VTM samples were processed by two commercial silica-based kits and compared with an in-House-developed protocol for host DNA extraction. An additional 452 samples were processed by the in-House method. The quantity and quality of the differentially extracted DNA samples were assessed by Qubit and spectrophotometric measurements. The suitability of extracted samples for downstream applications was tested by polymerase chain reaction (PCR) amplification followed by amplicon sequencing and allelic discrimination in real-time PCR. Results: The in-House method provided greater median DNA yield (0.81 μg), being significantly different from the PureLink® method (0.14 μg, p < 0.001), but not from the QIAamp® method (0.47 μg, p = 0.980). Overall satisfactory results in DNA concentrations and purity, in addition to cost, were observed using the in-House method, whose samples were able to produce clear amplification in PCR and sequencing reads, as well as effective allelic discrimination in real-time PCR TaqMan® assay. Conclusion: The described in-House method proved to be suitable and economically viable for genomic DNA extraction from VTM samples for biobanking purposes. These results are extremely valuable for the study of the COVID-19 pandemic and other emergent infectious diseases, allowing host genetic studies to be performed in samples initially collected for diagnosis.
Collapse
Affiliation(s)
- Renan C Sbruzzi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Mariléa F Feira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Nathan A Cadore
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Giovanna C Giudicelli
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
| | - Thayne W Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
- Núcleo de Bioinformática, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Tatiana S Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde, Secretaria Estadual de Saúde do estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, Brazil
| | - José A B Chies
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Xie M, Chen T, Cai Z, Lei B, Dong C. An All-in-One Platform for On-Site Multiplex Foodborne Pathogen Detection Based on Channel-Digital Hybrid Microfluidics. BIOSENSORS 2024; 14:50. [PMID: 38248427 PMCID: PMC10813315 DOI: 10.3390/bios14010050] [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: 11/14/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Recently, significant progress has been made in the development of microdevices for point-of-care infectious disease detection. However, most microdevices only allow limited steps, such as DNA amplification on the chip, while sample preparation, such as lysis and DNA extraction, is conducted off the chip using the traditional method. In this study, an all-in-one platform was developed, which incorporated all necessary procedures for nucleic acid detection. Our on-chip DNA extraction method utilized the magnetic bead-based technology on a hybrid channel-digital microfluidics (C-DMF) microdevice. It yielded high recovery rates, varying from 88.43% to 95.83%, with pathogen concentrations of 103-106 CFU/mL. In particular, the on-chip method exhibited significantly higher efficacy compared to the traditional off-chip manual method, for the DNA extraction of E. coli and S. aureus, representing Gram-negative and Gram-positive bacteria, respectively, at a sample concentration of 103 CFU/mL. To address the need for rapid and accessible diagnostics, colorimetric LAMP amplification was integrated into the proposed microdevice. The results were visually detectable with the naked eye, making it user-friendly for non-specialists. In addition, this platform demonstrated impressive sensitivity in simultaneously detecting common foodborne pathogens in spiked meat samples, achieving the LOD of 102-103 CFU/mL. The entire process, from sampling to result, was fully automated and only required approximately 60 min, offering promising applicability in resource-limited and on-site testing scenarios.
Collapse
Affiliation(s)
- Mei Xie
- Department of Life Sciences, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519000, China;
- Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | | | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Bo Lei
- Department of Life Sciences, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519000, China;
| | - Cheng Dong
- School of Intelligent Systems Science and Engineering, Jinan University, Zhuhai 519000, China
- Department of Biomedical Engineering, Jinan University, Guangzhou 510632, China
| |
Collapse
|
10
|
Zarouri A, Barnes AMT, Aboubakr H, Thekkudan Novi V, Dong Q, Nelson A, Goyal S, Abbas A. A high-performance polymer composite column for coronavirus nucleic acid purification. Sci Rep 2024; 14:1138. [PMID: 38212439 PMCID: PMC10784286 DOI: 10.1038/s41598-024-51671-x] [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: 08/14/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024] Open
Abstract
Here, we report the development of a novel polymer composite (PC) purification column and kit. The performance of the PC columns was compared to conventional silica gel (SG) columns for the purification of nucleic acids from coronaviruses, including SARS-CoV-2, in 82 clinical samples. The results shows that PC-based purification outperforms silica gel (SG)-based purification by enabling a higher sensitivity (94%), accuracy (97%), and by eliminating false positives (100% specificity). The high specificity is critical for efficient patient triage and resource management during pandemics. Furthermore, PC-based purification exhibits three times higher analytical precision than a commonly used SG-based nucleic acid purification thereby enabling a more accurate quantification of viral loads and higher reproducibility.
Collapse
Affiliation(s)
- Akli Zarouri
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
| | - Aaron M T Barnes
- Division of Molecular Pathology and Genomics, Department of Laboratory Medicine and Pathology, University of Minnesota Twin Cities, 420 Delaware Street SE, Minneapolis, MN, USA
- Department of Microbiology and Immunology, University of Minnesota Medical School, 689 23rd Ave SE, Minneapolis, MN, USA
| | - Hamada Aboubakr
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
- Department of Veterinary Population Medicine, University of Minnesota Twin Cities, 1333 Gortner Ave., Saint Paul, MN, USA
| | - Vinni Thekkudan Novi
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
| | - Qiuchen Dong
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
| | - Andrew Nelson
- Division of Molecular Pathology and Genomics, Department of Laboratory Medicine and Pathology, University of Minnesota Twin Cities, 420 Delaware Street SE, Minneapolis, MN, USA
| | - Sagar Goyal
- Department of Veterinary Population Medicine, University of Minnesota Twin Cities, 1333 Gortner Ave., Saint Paul, MN, USA
| | - Abdennour Abbas
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA.
| |
Collapse
|
11
|
Lin FX, Pan QL, Gu HY, Zeng FJ, Lu ZJ. The Role of Resveratrol on Spinal Cord Injury: from Bench to Bedside. Mol Neurobiol 2024; 61:104-119. [PMID: 37584822 DOI: 10.1007/s12035-023-03558-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/05/2023] [Indexed: 08/17/2023]
Abstract
Spinal cord injury (SCI) is a severe and disabling injury of the central nervous system, with complex pathological mechanisms leading to sensory and motor dysfunction. Pathological processes, such as oxidative stress, inflammatory response, apoptosis, and glial scarring are important factors that aggravate SCI. Therefore, the inhibition of these pathological processes may contribute to the treatment of SCI. Currently, the pathogenesis of SCI remains under investigation as SCI treatment has not progressed considerably. Resveratrol, a natural polyphenol with anti-inflammatory and antioxidant properties, is considered a potential therapeutic drug for various diseases and plays a beneficial role in nerve damage. Preclinical studies have confirmed that signaling pathways are closely related to the pathological processes in SCI, and resveratrol is believed to exert therapeutic effects in SCI by activating the related signaling pathways. Based on current research on the pathways of resveratrol and its role in SCI, resveratrol may be a potentially effective treatment for SCI. This review summarizes the role of resveratrol in promoting the recovery of nerve function by regulating oxidative stress, inflammation, apoptosis, and glial scar formation in SCI through various mechanisms and pathways, as well as the deficiency of resveratrol in SCI research and the current and anticipated research trends of resveratrol. In addition, this review provides a background for further studies on the molecular mechanisms of SCI and the development of potential therapeutic agents. This information could also help clinicians understand the known mechanisms of action of resveratrol and provide better treatment options for patients with SCI.
Collapse
Affiliation(s)
- Fei-Xiang Lin
- Department of Spine Surgery, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China.
- Department of Spine Surgery, The Affiliated Ganzhou Hospital of Nanchang University, (Ganzhou Hospital-Nanfang Hospital, Southern Medical University), 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China.
| | - Qi-Lin Pan
- Department of Spine Surgery, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China
- Department of Spine Surgery, The Affiliated Ganzhou Hospital of Nanchang University, (Ganzhou Hospital-Nanfang Hospital, Southern Medical University), 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China
| | - Hou-Yun Gu
- Department of Spine Surgery, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China
- Department of Spine Surgery, The Affiliated Ganzhou Hospital of Nanchang University, (Ganzhou Hospital-Nanfang Hospital, Southern Medical University), 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China
| | - Fang-Jun Zeng
- Department of Spine Surgery, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China
- Department of Spine Surgery, The Affiliated Ganzhou Hospital of Nanchang University, (Ganzhou Hospital-Nanfang Hospital, Southern Medical University), 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China
| | - Zhi-Jun Lu
- Department of Spine Surgery, Ganzhou People's Hospital, 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China
- Department of Spine Surgery, The Affiliated Ganzhou Hospital of Nanchang University, (Ganzhou Hospital-Nanfang Hospital, Southern Medical University), 16 Meiguan Avenue, Ganzhou, Jiangxi Province, 341000, People's Republic of China
| |
Collapse
|
12
|
Guthrie AM, Nevill P, Cooper CE, Bateman PW, van der Heyde M. On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces. BMC Res Notes 2023; 16:370. [PMID: 38111014 PMCID: PMC10726604 DOI: 10.1186/s13104-023-06669-5] [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: 10/27/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
OBJECTIVE Roller swabbing of surfaces is an effective way to obtain environmental DNA, but the current DNA extraction method for these samples is equipment heavy, time consuming, and increases potential contamination through multiple handling. Here, we used rollers to swab a dog kennel and compared three DNA extraction approaches (water filtration, roller trimming and direct buffer) using two different platforms (Qiacube, Kingfisher). DNA extraction methods were evaluated based on cost, effort, DNA concentration and PCR result. RESULTS The roller trim method emerged as the optimal method with the best PCR results, DNA concentration and cost efficiency, while the buffer-based methods were the least labour intensive but produced mediocre PCR results and DNA concentrations. Additionally, the Kingfisher magnetic bead extractions generally ranked higher in all categories over the Qiacube column-based DNA extractions. Ultimately, the ideal DNA extraction method for a particular study is influenced by logistical constraints in the field such as the size of the roller, the availability of cold storage, and time constraints on the project. Our results demonstrate the strengths and weaknesses of each approach, allowing for informed decision making by researchers.
Collapse
Affiliation(s)
- Austin M Guthrie
- MBioMe - Mine Site Biomonitoring Using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia.
| | - Paul Nevill
- MBioMe - Mine Site Biomonitoring Using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| | - Christine E Cooper
- School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| | - Philip W Bateman
- Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| | - Mieke van der Heyde
- MBioMe - Mine Site Biomonitoring Using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| |
Collapse
|
13
|
Thai DA, Park SK, Lee NY. A paper-embedded thermoplastic microdevice integrating additive-enhanced allele-specific amplification and silver nanoparticle-based colorimetric detection for point-of-care testing. LAB ON A CHIP 2023; 23:5081-5091. [PMID: 37929914 DOI: 10.1039/d3lc00739a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
This study introduces a thermoplastic microdevice integrated with additive-enhanced allele-specific amplification and hydrazine-induced silver nanoparticle-based detection of single nucleotide polymorphism (SNP) and opportunistic pathogens. For point-of-care testing of SNP, an allele-specific loop-mediated isothermal amplification reaction using nucleotide-mismatched primers and molecular additives was evaluated to discriminate single-nucleotide differences in the samples. The microdevice consists of purification and reaction units that enable DNA purification, amplification, and detection in a sequential manner. The purification unit enables the silica-based preparation of samples using an embedded glass fiber membrane. Hydrazine-induced silver nanoparticle formation was employed for endpoint colorimetric detection of amplicons within three min at room temperature. The versatile applicability of the microdevice was demonstrated by the successful identification of SNPs related to sickle cell anemia, genetically-induced hair loss, and Enterococcus faecium. The microdevice exhibited a detection limit of 103 copies per μL of SNP targets in serum and 102 CFU mL-1 of Enterococcus faecium in tap water within 70 min. The proposed microdevice is a promising and versatile platform for point-of-care nucleic acid testing of different samples in low-resource settings.
Collapse
Affiliation(s)
- Duc Anh Thai
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Korea.
| | - Seung Kyun Park
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Korea.
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Korea.
| |
Collapse
|
14
|
Zarouri A, Barnes AMT, Aboubakr H, Novi VT, Dong Q, Nelson A, Goyal S, Abbas A. A High-Performance Polymer Composite Column for Coronavirus Nucleic Acid Purification. RESEARCH SQUARE 2023:rs.3.rs-3261727. [PMID: 37674719 PMCID: PMC10479450 DOI: 10.21203/rs.3.rs-3261727/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Here, we report the development of a novel polymer composite (PC) purification column and kit. The performance of the PC columns was compared to conventional silica gel (SG) columns for the purification of nucleic acids from coronaviruses, including SARS-CoV-2, in 82 clinical samples. The results shows that PC-based purification outperforms silica gel (SG)-based purification by enabling a higher sensitivity (94%), accuracy (97%), and by eliminating false positives (100% selectivity). The high selectivity is critical for efficient patient triage and resource management during pandemics. Furthermore, PC-based purification exhibits three times higher analytical precision than a commonly used SG-based nucleic acid purification thereby enabling a more accurate quantification of viral loads and higher reproducibility.
Collapse
|
15
|
Ooi V, McMichael L, Hunter ME, Takoukam Kamla A, Lanyon JM. A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong. PLoS One 2023; 18:e0278792. [PMID: 37285349 DOI: 10.1371/journal.pone.0278792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new 'High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol' (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.
Collapse
Affiliation(s)
- Vicky Ooi
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Lee McMichael
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Sirenia Project, Gainesville, Florida, United States of America
| | - Aristide Takoukam Kamla
- Aquatic Animal Health Program, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- African Marine Mammal Conservation Organization, Dizangue, Littoral, Cameroon
| | - Janet M Lanyon
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| |
Collapse
|
16
|
Takahashi H, Yasui T, Hirano M, Shinjo K, Miyazaki Y, Shinoda W, Hasegawa T, Natsume A, Kitano Y, Ida M, Zhang M, Shimada T, Paisrisarn P, Zhu Z, Ohka F, Aoki K, Rahong S, Nagashima K, Yanagida T, Baba Y. Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy. Biosens Bioelectron 2023; 234:115318. [PMID: 37172361 DOI: 10.1016/j.bios.2023.115318] [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: 01/17/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 05/14/2023]
Abstract
Cell-free DNA (cfDNA) and extracellular vesicles (EVs) are molecular biomarkers in liquid biopsies that can be applied for cancer detection, which are known to carry information on the necessary conditions for oncogenesis and cancer cell-specific activities after oncogenesis, respectively. Analyses for both cfDNA and EVs from the same body fluid can provide insights into screening and identifying the molecular subtypes of cancer; however, a major bottleneck is the lack of efficient and standardized techniques for the isolation of cfDNA and EVs from clinical specimens. Here, we achieved catch-and-release isolation by hydrogen bond-mediated binding of cfDNA in urine to zinc oxide (ZnO) nanowires, which also capture EVs by surface charge, and subsequently we identified genetic mutations in urinary cfDNA. The binding strength of hydrogen bonds between single-crystal ZnO nanowires and DNA was found to be equal to or larger than that of conventional hydrophobic interactions, suggesting the possibility of isolating trace amounts of cfDNA. Our results demonstrated that nanowire-based cancer screening assay can screen cancer and can identify the molecular subtypes of cancer in urine from brain tumor patients through EV analysis and cfDNA mutation analysis. We anticipate our method to be a starting point for more sophisticated diagnostic models of cancer screening and identification.
Collapse
Affiliation(s)
- Hiromi Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Blk N3, Level 2, Room 86 (N3-02c-86), 639798, Singapore.
| | - Takao Yasui
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan; Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
| | - Masaki Hirano
- Division of Molecular Oncology, Aichi Cancer Center Research Institute, Kanokoden, Chikusa-ku, Nagoya, 464-0021, Japan
| | - Keiko Shinjo
- Division of Cancer Biology, Graduate School of Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yusuke Miyazaki
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Takeshi Hasegawa
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Atsushi Natsume
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yotaro Kitano
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Tsurumai-cho 65, Showa-ku, Nagoya, 466-8550, Japan
| | - Mikiko Ida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Min Zhang
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Taisuke Shimada
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Piyawan Paisrisarn
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Zetao Zhu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Tsurumai-cho 65, Showa-ku, Nagoya, 466-8550, Japan
| | - Kosuke Aoki
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Sakon Rahong
- College of Materials Innovation and Technology, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Rd., Ladkrabang, Bangkok, 10520, Thailand
| | - Kazuki Nagashima
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan; Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takeshi Yanagida
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka-cho, Ibaraki, Osaka, 567-0047, Japan; Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580, Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba, 263-8555, Japan.
| |
Collapse
|
17
|
Comparison of DNA extraction methods on CITES-listed timber species and application in species authentication of commercial products using DNA barcoding. Sci Rep 2023; 13:151. [PMID: 36599919 DOI: 10.1038/s41598-022-27195-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Quality and quantity of DNA extracted from wood is important for molecular identification of wood species, which can serve for conservation of wood species and law enforcement to combat illegal wood trading. Rosewood (Dalbergia and Pterocarpus) and agarwood (Aquilaria) are the most commonly found hardwood in timber seizure incidents. To monitor international trade of timber and commercial wood products and to protect these endangered wood species from further population decline, in this study, we have compared three extraction protocols for DNA extraction from 12 samples of rosewood and agarwood timber logs, and later applied the best DNA extraction protocol on 10 commercial wood products claimed to be rosewood and agarwood. We also demonstrated the applicability of DNA mini-barcoding with multi-loci combination with reference library for identifying the species of timber and commercial wood products. We found that a silica column-based method with guanidine thiocyanate-containing binding buffer served the best in DNA extraction from different parts of wood in all three genera with good quality and quantity. Single barcode region ITS2 or multi-loci combinations including ITS2 barcode region generally provide better discriminatory power for species identification for both rosewood and agarwood. All 10 products were identified to species-level using multi-loci combination. In terms of accuracy in labelling, 80% of them were labelled correctly. Our work has shown the feasibility of extracting good quality of DNA from authentic wood samples and processed wood products and identifying them to species level based on DNA barcoding technology.
Collapse
|
18
|
Jiang Q, Li Y, Huang L, Guo J, Wang A, Ma C, Shi C. Direct capture and amplification of nucleic acids using a universal, elution-free magnetic bead-based method for rapid pathogen detection in multiple types of biological samples. Anal Bioanal Chem 2023; 415:427-438. [PMID: 36385304 PMCID: PMC9668711 DOI: 10.1007/s00216-022-04422-8] [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: 09/13/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022]
Abstract
Nucleic acid amplification tests (NAATs) have become an attractive approach for pathogen detection, and obtaining high-quality nucleic acid extracts from biological samples plays a critical role in ensuring accurate NAATs. In this work, we established an elution-free magnetic bead (MB)-based method by introducing polyethylene-polypropylene glycol (PEPPG) F68 in lysis buffer and using NaOH solution instead of alcohols as the washing buffer for rapid nucleic acid extraction from multiple types of biological samples, including nasopharyngeal swabs, serum, milk, and pork, which bypassed the nucleic acid elution step and allowed the nucleic acid/MB composite to be directly used as the template for amplification reactions. The entire extraction process was able to be completed in approximately 7 min. Even though the nucleic acid/MB composite could not be used for quantitative real-time PCR (qPCR) assays, this elution-free MB-based method significantly improved the sensitivity of the loop-mediated isothermal amplification (LAMP) assay. The sensitivity of the quantitative real-time LAMP (qLAMP) assays combined with this elution-free MB-based method showed an improvement of one to three orders of magnitude compared with qLAMP or qPCR assays combined with the traditional MB-based method. In addition to manual operation, like the traditional MB-based method, this universal, rapid, and facile nucleic acid extraction method also has potential for integration into automated robotic processing, making it particularly suitable for the establishment of an analysis platform for ultrafast and sensitive pathogen detection in various biological samples both in centralized laboratories and at remote sites.
Collapse
Affiliation(s)
- Qianqian Jiang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Yang Li
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Lin Huang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Jinling Guo
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Ailin Wang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 People’s Republic of China
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| |
Collapse
|
19
|
Sofiev M, Sofieva S, Palamarchuk J, Šaulienė I, Kadantsev E, Atanasova N, Fatahi Y, Kouznetsov R, Kuula J, Noreikaite A, Peltonen M, Pihlajamäki T, Saarto A, Svirskaite J, Toiviainen L, Tyuryakov S, Šukienė L, Asmi E, Bamford D, Hyvärinen AP, Karppinen A. Bioaerosols in the atmosphere at two sites in Northern Europe in spring 2021: Outline of an experimental campaign. ENVIRONMENTAL RESEARCH 2022; 214:113798. [PMID: 35810819 DOI: 10.1016/j.envres.2022.113798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
A coordinated observational and modelling campaign targeting biogenic aerosols in the air was performed during spring 2021 at two locations in Northern Europe: Helsinki (Finland) and Siauliai (Lithuania), approximately 500 km from each other in north-south direction. The campaign started on March 1, 2021 in Siauliai (12 March in Helsinki) and continued till mid-May in Siauliai (end of May in Helsinki), thus recording the transition of the atmospheric biogenic aerosols profile from winter to summer. The observations included a variety of samplers working on different principles. The core of the program was based on 2- and 2.4--hourly sampling in Helsinki and Siauliai, respectively, with sticky slides (Hirst 24-h trap in Helsinki, Rapid-E slides in Siauliai). The slides were subsequently processed extracting the DNA from the collected aerosols, which was further sequenced using the 3-rd generation sequencing technology. The core sampling was accompanied with daily and daytime sampling using standard filter collectors. The hourly aerosol concentrations at the Helsinki monitoring site were obtained with a Poleno flow cytometer, which could recognize some of the aerosol types. The sampling campaign was supported by numerical modelling. For every sample, SILAM model was applied to calculate its footprint and to predict anthropogenic and natural aerosol concentrations, at both observation sites. The first results confirmed the feasibility of the DNA collection by the applied techniques: all but one delivered sufficient amount of DNA for the following analysis, in over 40% of the cases sufficient for direct DNA sequencing without the PCR step. A substantial variability of the DNA yield has been noticed, generally not following the diurnal variations of the total-aerosol concentrations, which themselves showed variability not related to daytime. An expected upward trend of the biological material amount towards summer was observed but the day-to-day variability was large. The campaign DNA analysis produced the first high-resolution dataset of bioaerosol composition in the North-European spring. It also highlighted the deficiency of generic DNA databases in applications to atmospheric biota: about 40% of samples were not identified with standard bioinformatic methods.
Collapse
Affiliation(s)
- Mikhail Sofiev
- Finnish Meteorological Institute, Helsinki, Finland; Vilnius University, Vilnius, Lithuania.
| | - Svetlana Sofieva
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | | | - Nina Atanasova
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | - Yalda Fatahi
- Finnish Meteorological Institute, Helsinki, Finland
| | | | - Joel Kuula
- Finnish Meteorological Institute, Helsinki, Finland
| | | | - Martina Peltonen
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | - Julija Svirskaite
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | | | - Eija Asmi
- Finnish Meteorological Institute, Helsinki, Finland
| | | | | | | |
Collapse
|
20
|
A culture-free biphasic approach for sensitive and rapid detection of pathogens in dried whole-blood matrix. Proc Natl Acad Sci U S A 2022; 119:e2209607119. [PMID: 36161889 DOI: 10.1073/pnas.2209607119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Blood stream infections (BSIs) cause high mortality, and their rapid detection remains a significant diagnostic challenge. Timely and informed administration of antibiotics can significantly improve patient outcomes. However, blood culture, which takes up to 5 d for a negative result, followed by PCR remains the gold standard in diagnosing BSI. Here, we introduce a new approach to blood-based diagnostics where large blood volumes can be rapidly dried, resulting in inactivation of the inhibitory components in blood. Further thermal treatments then generate a physical microscale and nanoscale fluidic network inside the dried matrix to allow access to target nucleic acid. The amplification enzymes and primers initiate the reaction within the dried blood matrix through these networks, precluding any need for conventional nucleic acid purification. High heme background is confined to the solid phase, while amplicons are enriched in the clear supernatant (liquid phase), giving fluorescence change comparable to purified DNA reactions. We demonstrate single-molecule sensitivity using a loop-mediated isothermal amplification reaction in our platform and detect a broad spectrum of pathogens, including gram-positive methicillin-resistant and methicillin-susceptible Staphylococcus aureus bacteria, gram-negative Escherichia coli bacteria, and Candida albicans (fungus) from whole blood with a limit of detection (LOD) of 1.2 colony-forming units (CFU)/mL from 0.8 to 1 mL of starting blood volume. We validated our assay using 63 clinical samples (100% sensitivity and specificity) and significantly reduced sample-to-result time from over 20 h to <2.5 h. The reduction in instrumentation complexity and costs compared to blood culture and alternate molecular diagnostic platforms can have broad applications in healthcare systems in developed world and resource-limited settings.
Collapse
|
21
|
Andreeva TV, Malyarchuk AB, Soshkina AD, Dudko NA, Plotnikova MY, Rogaev EI. Methodologies for Ancient DNA Extraction from Bones for Genomic Analysis: Approaches and Guidelines. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422090034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
22
|
MacLeod R, Chan FV, Yuan H, Ye X, Sin YJA, Vitelli TM, Cucu T, Leung A, Baljak I, Osinski S, Fu Y, Jung GID, Amar A, DeAngelis PL, Hellman U, Cowman MK. Selective isolation of hyaluronan by solid phase adsorption to silica. Anal Biochem 2022; 652:114769. [PMID: 35660507 PMCID: PMC9589902 DOI: 10.1016/j.ab.2022.114769] [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: 12/05/2021] [Revised: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 11/01/2022]
Abstract
A solid phase adsorption method for selective isolation of hyaluronan (HA) from biological samples is presented. Following enzymatic degradation of protein, HA can be separated from sulfated glycosaminoglycans, other unsulfated glycosaminoglycans, nucleic acids, and proteolytic fragments by adsorption to amorphous silica at specific salt concentrations. The adsorbed HA can be released from silica using neutral and basic aqueous solutions. HA ranging in size from ∼9 kDa to MDa polymers has been purified by this method from human serum and conditioned medium of cultured cells.
Collapse
Affiliation(s)
- Rebecca MacLeod
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, 433 First Avenue, 9thfloor, New York, NY, 10010, USA.
| | - Fok Vun Chan
- Echelon Biosciences Inc., 675 Arapeen Drive, Suite 302, Salt Lake City, UT, 84108, USA.
| | - Han Yuan
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, 6 Metrotech Center, Brooklyn, NY, 11201, USA.
| | - Xin Ye
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, 6 Metrotech Center, Brooklyn, NY, 11201, USA.
| | - Yun Jin Ashley Sin
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, 433 First Avenue, 9thfloor, New York, NY, 10010, USA.
| | - Teraesa M Vitelli
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, 433 First Avenue, 9thfloor, New York, NY, 10010, USA.
| | - Tudor Cucu
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, 6 Metrotech Center, Brooklyn, NY, 11201, USA.
| | - Annie Leung
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, 6 Metrotech Center, Brooklyn, NY, 11201, USA.
| | - Irene Baljak
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, 433 First Avenue, 9thfloor, New York, NY, 10010, USA.
| | - Samantha Osinski
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, 6 Metrotech Center, Brooklyn, NY, 11201, USA.
| | - Yuhong Fu
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, 6 Metrotech Center, Brooklyn, NY, 11201, USA.
| | - Gyu Ik Daniel Jung
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, 6 Metrotech Center, Brooklyn, NY, 11201, USA.
| | - Anant Amar
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, 6 Metrotech Center, Brooklyn, NY, 11201, USA.
| | - Paul L DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma, OK, 73104, USA.
| | - Urban Hellman
- Department of Public Health and Clinical Medicine, Umeå University, SE-901 87, Umeå, Sweden.
| | - Mary K Cowman
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, 433 First Avenue, 9thfloor, New York, NY, 10010, USA; Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, 6 Metrotech Center, Brooklyn, NY, 11201, USA.
| |
Collapse
|
23
|
Oligonucleotides Isolation and Separation—A Review on Adsorbent Selection. Int J Mol Sci 2022; 23:ijms23179546. [PMID: 36076941 PMCID: PMC9455468 DOI: 10.3390/ijms23179546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotides have many important applications, including as primers in polymerase chain reactions and probes for DNA sequencing. They are proposed as a diagnostic and prognostic tool for various diseases and therapeutics in antisense therapy. Accordingly, it is necessary to develop liquid chromatography and solid phase extraction methods to separate oligonucleotides and isolate them from biological samples. Many reviews have been written about the determination of these compounds using the separation technique or sample preparation for their isolation. However, presumably, there are no articles that critically review the adsorbents used in liquid chromatography or solid phase extraction. The present publication reviews the literature from the last twenty years related to supports (silica, polymers, magnetic nanoparticles) and their modifications. The discussed issues concern reversed phase (alkyl, aromatic, cholesterol, mixed ligands), ion-exchange (strong and weak ones), polar (silica, polyhydroxy, amide, zwitterionic), and oligonucleotide-based adsorbents.
Collapse
|
24
|
Xia Z, Patchin M, McKay CP, Drndić M. Deoxyribonucleic Acid Extraction from Mars Analog Soils and Their Characterization with Solid-State Nanopores. ASTROBIOLOGY 2022; 22:992-1008. [PMID: 35731031 DOI: 10.1089/ast.2021.0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for in situ biomarker detection that are compact, lightweight, and able to withstand operations in space. Solid-state nanopores are excellent candidates that allow fast single-molecule detection. They can withstand high temperatures and be sterilized to minimize planetary contamination. The instruments are portable with low-power requirements. We demonstrate a few key results in advancing the use of nanopores for in-space applications. First, we developed modified deoxyribonucleic acid (DNA) extraction protocols to extract DNA from Mars analog soils. Second, we used silicon nitride nanopores to demonstrate the detection of extracted DNA and corresponding current characteristics. The yields and properties of extracted DNA (e.g., estimated diameters) varied somewhat by soil types, extraction methods, and nanopores used. The yields varied from a minimum of 0.9 ng DNA/g soil for a magnesium carbonate sample from Lake Salda to a maximum of 210 ng DNA/g soil for a calcium carbonate sample from Trona Pinnacles. For a given soil type, yields from different methods varied by a factor of up to 50. These observations motivate future studies with a broader range of Mars-like soils and improved instruments to increase signal-to-noise-ratio at higher measurement bandwidths.
Collapse
Affiliation(s)
- Zehui Xia
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Margaret Patchin
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Marija Drndić
- David Rittenhouse Laboratory, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
25
|
Hapsianto BN, Kojima N, Kurita R, Yamagata H, Fujita H, Fujii T, Kim SH. Direct Capture and Amplification of Small Fragmented DNAs Using Nitrogen-Mustard-Coated Microbeads. Anal Chem 2022; 94:7594-7600. [PMID: 35578745 DOI: 10.1021/acs.analchem.2c00531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Circulating cell-free DNA (cfDNA) has been implicated as an important biomarker and has been intensively studied for "liquid biopsy" applications in cancer diagnostics. Owing to its small fragment size and its low concentration in circulation, cfDNA extraction and purification from serum samples are complicated, and the extraction yield affects the precision of subsequent molecular diagnostic tests. Here, we report a novel approach using nitrogen-mustard-coated DNA capture beads (NMD beads) that covalently capture DNA and allow direct subsequent polymerase chain reaction (PCR) amplification from the NMD bead without elusion. The complex DNA extraction and purification processes are not required. To illustrate the diagnostic use of the NMD beads, we detected short DNA fragments (142 bp) that were spiked into fetal bovine serum (as a model serum sample). The spiked DNAs were captured directly from serum samples and detected using real-time PCR at concentrations as low as 10 fg/mL. We anticipate that this DNA capture bead technique has the potential to simplify the preanalytical processes required for cfDNA detection, which could significantly expand the diagnostic applications of liquid biopsy.
Collapse
Affiliation(s)
- Benediktus N Hapsianto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan
| | - Naoshi Kojima
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Ryoji Kurita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB/DAICENTER, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Ibaraki, Japan
| | - Hitoshi Yamagata
- Advanced Research Laboratory (ARL), Canon Medical Systems Corporation, 1385 Shimoishigami, Otawara 324-8550, Tochigi, Japan
| | - Hiroyuki Fujita
- Advanced Research Laboratory (ARL), Canon Medical Systems Corporation, 1385 Shimoishigami, Otawara 324-8550, Tochigi, Japan
| | - Teruo Fujii
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Soo Hyeon Kim
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| |
Collapse
|
26
|
Nanfack CDV, Yang J, Yuan X, Sun J, Sun X, Ji J. 3, 4-Dihydroxy-l-phenylalanine Biopolymer Cellulose DNA Adhesive Card as an Enhanced Solid-Phase One-Step DNA Extraction Method from Foodborne Pathogens in Food Samples. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-021-02177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
27
|
Trick AY, Ngo HT, Nambiar AH, Morakis MM, Chen FE, Chen L, Hsieh K, Wang TH. Filtration-assisted magnetofluidic cartridge platform for HIV RNA detection from blood. LAB ON A CHIP 2022; 22:945-953. [PMID: 35088790 PMCID: PMC9035341 DOI: 10.1039/d1lc00820j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ability to detect and quantify HIV RNA in blood is essential to sensitive detection of infections and monitoring viremia throughout treatment. Current options for point-of-care HIV diagnosis (i.e. lateral flow rapid tests) lack sensitivity for early detection and are unable to quantify viral load. HIV RNA diagnostics typically require extensive pre-processing of blood to isolate plasma and extract nucleic acids, in addition to expensive equipment for conducting nucleic acid amplification and fluorescence detection. Therefore, molecular HIV diagnostics is still mainly limited to clinical laboratories and there is an unmet need for high sensitivity point-of-care screening and at-home HIV viral load quantification. In this work, we outline a streamlined workflow for extraction of plasma from whole blood coupled with HIV RNA extraction and quantitative polymerase chain reaction (qPCR) in a portable magnetofluidic cartridge platform for use at the point-of-care. Viral particles were isolated from blood using manual filtration through a 3D-printed filter module in seconds followed by automated nucleic acid capture, purification, and transfer to qPCR using magnetic beads. Both nucleic acid extraction and qPCR were integrated within cartridges using compact instrumentation consisting of a motorized magnet arm, miniaturized thermocycler, and image-based fluorescence detection. We demonstrated detection down to 1000 copies of HIV viral particles from whole blood in <30 minutes.
Collapse
Affiliation(s)
- Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Hoan Thanh Ngo
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Anju H Nambiar
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Marisa M Morakis
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
28
|
Turiello R, Dignan LM, Thompson B, Poulter M, Hickey J, Chapman J, Landers JP. Centrifugal Microfluidic Method for Enrichment and Enzymatic Extraction of Severe Acute Respiratory Syndrome Coronavirus 2 RNA. Anal Chem 2022; 94:3287-3295. [PMID: 35138818 PMCID: PMC8845438 DOI: 10.1021/acs.analchem.1c05215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/31/2022] [Indexed: 01/08/2023]
Abstract
The diversification of analytical tools for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is imperative for effective virus surveillance and transmission control worldwide. Development of robust methods for rapid, simple isolation of viral RNA permits more expedient pathogen detection by downstream real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR) to minimize stalled containment and enhance treatment efforts. Here, we describe an automatable rotationally driven microfluidic platform for enrichment and enzymatic extraction of SARS-CoV-2 RNA from multiple sample types. The multiplexed, enclosed microfluidic centrifugal device (μCD) is capable of preparing amplification-ready RNA from up to six samples in under 15 min, minimizing user intervention and limiting analyst exposure to pathogens. Sample enrichment leverages Nanotrap Magnetic Virus Particles to isolate intact SARS-CoV-2 virions from nasopharyngeal and/or saliva samples, enabling the removal of complex matrices that inhibit downstream RNA amplification and detection. Subsequently, viral capsids are lysed using an enzymatic lysis cocktail for release of pathogenic nucleic acids into a PCR-compatible buffer, obviating the need for downstream purification. Early in-tube assay characterization demonstrated comparable performance between our technique and a "gold-standard" commercial RNA extraction and purification kit. RNA obtained using the fully integrated μCDs permitted reliable SARS-CoV-2 detection by real-time RT-PCR. Notably, we successfully analyzed full-process controls, positive clinical nasopharyngeal swabs suspended in viral transport media, and spiked saliva samples, showcasing the method's broad applicability with multiple sample matrices commonly encountered in clinical diagnostics.
Collapse
Affiliation(s)
- Rachelle Turiello
- Department of Chemistry, Clinical Microbiology, Mechanical and Aerospace
Engineering, and Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Leah M. Dignan
- Department of Chemistry, Clinical Microbiology, Mechanical and Aerospace
Engineering, and Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Brayton Thompson
- Department of Chemistry, Clinical Microbiology, Mechanical and Aerospace
Engineering, and Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Melinda Poulter
- Department of Chemistry, Clinical Microbiology, Mechanical and Aerospace
Engineering, and Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Jeff Hickey
- MicroGEM
International, PLC, Charlottesville, Virginia 22903, United States
| | - Jeff Chapman
- MicroGEM
International, PLC, Charlottesville, Virginia 22903, United States
| | - James P. Landers
- Department of Chemistry, Clinical Microbiology, Mechanical and Aerospace
Engineering, and Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- MicroGEM
International, PLC, Charlottesville, Virginia 22903, United States
| |
Collapse
|
29
|
Liu H, Zou Q, Kim MG, Qiao Z, Nguyen DTT, Koo B, Lee HJ, Jang YO, Kim JK, Shin Y. Homobifunctional Imidoester Combined Black Phosphorus Nanosheets Used as Cofactors for Nucleic Acid Extraction. BIOCHIP JOURNAL 2022. [DOI: 10.1007/s13206-022-00046-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
30
|
Wang H, Liu C, Teng X, Liang Z, Zhu L, Xu G, Chen C, Ma K, Liu R, Zhou L, Yan B. A TbPO 4-based capturer for environmental extracellular antibiotic genes by interrogating lanthanide phosphates nanoneedles. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127139. [PMID: 34537653 DOI: 10.1016/j.jhazmat.2021.127139] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Accurate determination of antibiotic resistance genes (ARGs) in environmental DNA molecules (eDNA) is challenging owing to its low abundance in the aquatic environment. Here we report a facile and cost-efficient approach to extract trace amount of eDNAs in the aquatic environment using LnPO4 nanomaterials. Among the nanomaterials, less crystalline TbPO4 nanoneedles was identified as the most prominent candidate for long stranded DNA and short stranded DNA with adsorption efficiency above 97%. The adsorbed DNA was washed off from TbPO4 nanoneedles by optimized eluant (85% PBS, 15% EtOH, 4 g/L glycine, pH 10.0) with an optimal DNA recovery of 78.83%. Our approach showed a comparable or better eDNA extraction efficiency than a commercial extraction method for different environmental samples, but 89% less cost. The high purity of the extracted eDNA was demonstrated by a high A260/280 ratio. Using qPCR experiment, the occurrence of six common ARGs in the eDNA were detected with abundance ranging from 4.06 × 103 to 3.51 × 109 copies/L in river samples. This specific DNA capturer is valuable for the evaluation of spatial and temporal dynamic of ARGs pollution to provide insight into the potential risk with regard to the human health.
Collapse
Affiliation(s)
- Haiqing Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chao Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xuepeng Teng
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, China
| | - Zhenda Liang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Lishan Zhu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Gang Xu
- Nanzhou Waterworks of Guangzhou Water Supply Co. Ltd., Guangzhou 510000, China
| | - Chaoxiang Chen
- Nanzhou Waterworks of Guangzhou Water Supply Co. Ltd., Guangzhou 510000, China
| | - Kunyu Ma
- Nanzhou Waterworks of Guangzhou Water Supply Co. Ltd., Guangzhou 510000, China
| | - Rongrong Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Li Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Bing Yan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| |
Collapse
|
31
|
Cucchiara F, Scarpitta R, Crucitta S, Scatena C, Arici R, Naccarato AG, Fogli S, Danesi R, Del Re M. Diagnosis and treatment monitoring in breast cancer: how liquid biopsy can support patient management. Pharmacogenomics 2022; 23:119-134. [PMID: 35006002 DOI: 10.2217/pgs-2021-0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Imaging and tissue biopsies represent the current gold standard for breast cancer diagnosis and patient management. However, these practices are time-consuming, expensive and require invasive procedures. Moreover, tissue biopsies do not capture spatial and temporal tumor heterogeneity. Conversely, liquid biopsy, which includes circulating tumor cells, circulating free nucleic acids and extracellular vesicles, is minimally invasive, easy to perform and can be repeated during a patient's follow-up. Increasing evidence also suggests that liquid biopsy can be used to efficiently screen and diagnose tumors at an early stage, and to monitor changes in the tumor molecular profile. In the present review, clinical applications and prospects are discussed.
Collapse
Affiliation(s)
- Federico Cucchiara
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Rosa Scarpitta
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Stefania Crucitta
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Cristian Scatena
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Roberta Arici
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Antonio Giuseppe Naccarato
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Stefano Fogli
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| |
Collapse
|
32
|
Abouali H, Hosseini SA, Purcell E, Nagrath S, Poudineh M. Recent Advances in Device Engineering and Computational Analysis for Characterization of Cell-Released Cancer Biomarkers. Cancers (Basel) 2022; 14:288. [PMID: 35053452 PMCID: PMC8774172 DOI: 10.3390/cancers14020288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
During cancer progression, tumors shed different biomarkers into the bloodstream, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). The analysis of these biomarkers in the blood, known as 'liquid biopsy' (LB), is a promising approach for early cancer detection and treatment monitoring, and more recently, as a means for cancer therapy. Previous reviews have discussed the role of CTCs and ctDNA in cancer progression; however, ctDNA and EVs are rapidly evolving with technological advancements and computational analysis and are the subject of enormous recent studies in cancer biomarkers. In this review, first, we introduce these cell-released cancer biomarkers and briefly discuss their clinical significance in cancer diagnosis and treatment monitoring. Second, we present conventional and novel approaches for the isolation, profiling, and characterization of these markers. We then investigate the mathematical and in silico models that are developed to investigate the function of ctDNA and EVs in cancer progression. We convey our views on what is needed to pave the way to translate the emerging technologies and models into the clinic and make the case that optimized next-generation techniques and models are needed to precisely evaluate the clinical relevance of these LB markers.
Collapse
Affiliation(s)
- Hesam Abouali
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Seied Ali Hosseini
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Emma Purcell
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Mahla Poudineh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| |
Collapse
|
33
|
Choi G, Guan W. Sample-to-Answer Microfluidic Nucleic Acid Testing (NAT) on Lab-on-a-Disc for Malaria Detection at Point of Need. Methods Mol Biol 2022; 2393:297-313. [PMID: 34837186 PMCID: PMC9191616 DOI: 10.1007/978-1-0716-1803-5_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
One of the grand challenges for field-deployable NATs is related to the front end of the assays-nucleic acid extraction from raw samples. The ideal nucleic acid sample preparation should be simple, scalable, and easy-to-operate. In this chapter, we present a lab-on-a-disc NAT device for sample-to-answer malaria diagnosis. The parasite DNA sample preparation and subsequent real-time LAMP detection are seamlessly integrated on a disposable single microfluidic compact disc, driven by energy-efficient, non-centrifuge-based magnetic field interactions. Each disc contains four parallel testing units, which could be configured either as four identical tests or as four species-specific tests. When configured as species-specific tests, it could identify two of the most life-threatening malaria species (P. falciparum and P. vivax). The reagent disc with a 4-plex analyzer (discussed in Chapter 1 ) is capable of processing four samples simultaneously with 40 min turnaround time. It achieves a detection limit of ~0.5 parasites/μl for whole blood, sufficient for detecting asymptomatic parasite carriers. The assay is performed with an automated device described in Chapter 14 . The combination of sensitivity, specificity, cost, and scalable sample preparation suggests the real-time fluorescence LAMP device could be particularly useful for malaria screening in field settings.
Collapse
Affiliation(s)
- Gihoon Choi
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, USA.
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA.
| |
Collapse
|
34
|
Jiang X, Liu X, Yu Q, Shen W, Mei X, Tian H, Wu C. Functional resveratrol-biodegradable manganese doped silica nanoparticles for the spinal cord injury treatment. Mater Today Bio 2021; 13:100177. [PMID: 34938991 DOI: 10.1016/j.mtbio.2021.100177] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/25/2021] [Accepted: 12/01/2021] [Indexed: 11/20/2022] Open
Abstract
Spinal cord injury (SCI) causes secondary injury, accompanied by pathological changes such as oxidative stress, inflammation and neuronal apoptosis. This leads to permanent disabilities such as paralysis and loss of movement or sensation. Due to the ineffectiveness of drugs passing through the blood spinal cord barrier (BSCB), there is currently no effective treatment for SCI. The aim of this experiment was to design plasma complex component functionalized manganese-doped silica nanoparticles (PMMSN) with a redox response as a targeted drug carrier for resveratrol (RES), which effectively transports insoluble drugs to cross the BSCB. RES was adsorbed into PMMSN with a particle size of approximately 110 nm by the adsorption method, and the drug loading reached 32.61 ± 3.38%. The RES release results for the loaded sample (PMMSN-RES) showed that the PMMSN-RES exhibited a release slowly effect. In vitro and vivo experiments demonstrated that PMMSN-RES decreased reactive oxygen species (ROS) and malondialdehyde (MDA), increased superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities, reduced the expression of inflammatory (TNF-α, IL-1β and IL-6) and apoptotic cytokines (cleaved caspase-3) in spinal cord tissue after SCI. In summary, PMMSN-RES may be a potential pharmaceutical preparation for the treatment of SCI by reducing neuronal apoptosis and inhibiting inflammation caused by reducing oxidative stress to promote the recovery of mouse motor function.
Collapse
Key Words
- BSCB, blood spinal cord barrier
- GSH-Px, glutathione peroxidase
- H2O2, hydrogen peroxide
- MDA, malondialdehyde
- MMSN, manganese-doped mesoporous silica nanoparticles
- Manganese-doped silica nanoparticles
- MnO2, manganese dioxide
- Neuronal apoptosis
- Oxidative stress
- PMMSN, plasma complex component functionalized manganese-doped silica nanoparticles
- RES, resveratrol
- ROS, reactive oxygen species
- Redox response
- Resveratrol
- SCI, spinal cord injury
- SOD, increased superoxide dismutase
- Spinal cord injury
Collapse
Affiliation(s)
- Xue Jiang
- Pharmacy School, Jinzhou Medical University, Jinzhou, Liaoning, 121001, China
| | - Xiaoyao Liu
- Pharmacy School, Jinzhou Medical University, Jinzhou, Liaoning, 121001, China
| | - Qi Yu
- Pharmacy School, Jinzhou Medical University, Jinzhou, Liaoning, 121001, China
| | - Wenwen Shen
- Pharmacy School, Jinzhou Medical University, Jinzhou, Liaoning, 121001, China
| | - Xifan Mei
- Department of Orthopedics, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, 121001, China
| | - He Tian
- Department of Histology and Embryology, Jinzhou Medical University, Jinzhou, Liaoning, 121001, China
| | - Chao Wu
- Pharmacy School, Jinzhou Medical University, Jinzhou, Liaoning, 121001, China
| |
Collapse
|
35
|
Bag S, Konrad M, Schlöder T, Friederich P, Wenzel W. Fast Generation of Machine Learning-Based Force Fields for Adsorption Energies. J Chem Theory Comput 2021; 17:7195-7202. [PMID: 34623804 DOI: 10.1021/acs.jctc.1c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adsorption and desorption of molecules are key processes in extraction and purification of biomolecules, engineering of drug carriers, and designing of surface-specific coatings. To understand the adsorption process on the atomic scale, state-of-the-art quantum mechanical and classical simulation methodologies are widely used. However, studying adsorption using a full quantum mechanical treatment is limited to picoseconds simulation timescales, while classical molecular dynamics simulations are limited by the accuracy of the existing force fields. To overcome these challenges, we propose a systematic way to generate flexible, application-specific highly accurate force fields by training artificial neural networks. As a proof of concept, we study the adsorption of the amino acid alanine on graphene and gold (111) surfaces and demonstrate the force field generation methodology in detail. We find that a molecule-specific force field with Lennard-Jones type two-body terms incorporating the 3rd and 7th power of the inverse distances between the atoms of the adsorbent and the surfaces yields optimal results, which is surprisingly different from typical Lennard-Jones potentials used in traditional force fields. Furthermore, we present an efficient and easy-to-train machine learning model that incorporates system-specific three-body (or higher order) interactions that are required, for example, for gold surfaces. Our final machine learning-based force field yields a mean absolute error of less than 4.2 kJ/mol at a speed-up of ∼105 times compared to quantum mechanical calculation, which will have a significant impact on the study of adsorption in different research areas.
Collapse
Affiliation(s)
- Saientan Bag
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Manuel Konrad
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Tobias Schlöder
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Pascal Friederich
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen 76344, Germany.,Institute of Theoretical Informatics (ITI), Karlsruhe Institute of Technology (KIT), Am Fasanengarten 5, Karlsruhe 76131, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| |
Collapse
|
36
|
Abstract
Bacterial communities in water, soil, and humans play an essential role in environmental ecology and human health. PCR-based amplicon analysis, such as 16S rRNA sequencing, is a fundamental tool for quantifying and studying microbial composition, dynamics, and interactions. However, given the complexity of microbial communities, a substantial number of samples becomes necessary for analyses that parse the factors that determine microbial composition. A common bottleneck in performing these kinds of experiments is genomic DNA (gDNA) extraction, which is time-consuming, expensive, and often biased based on the types of species present. Direct PCR method is a potentially simpler and more accurate alternative to gDNA extraction methods that do not require the intervening purification step. In this study, we evaluated three variations of direct PCR methods using diverse heterogeneous bacterial cultures, including both Gram-positive and Gram-negative species, ZymoBIOMICS microbial community standards, and groundwater. By comparing direct PCR methods with DNeasy Blood and Tissue Kits for microbial isolates and DNeasy PowerSoil Kits for microbial communities, we found that a specific variant of the direct PCR method exhibits an overall efficiency comparable to that of the conventional DNeasy PowerSoil protocol in the circumstances we tested. We also found that the method showed higher efficiency for extracting gDNA from the Gram-negative strains compared to DNeasy Blood and Tissue protocol. This direct PCR method is 1,600 times less expensive ($0.34 for 96 samples) and 10 times simpler (15 min hands-on time for 96 samples) than the DNeasy PowerSoil protocol. The direct PCR method can also be fully automated and is compatible with small-volume samples, thereby permitting scaling of samples and replicates needed to support high-throughput large-scale bacterial community analysis. IMPORTANCE Understanding bacterial interactions and assembly in complex microbial communities using 16S rRNA sequencing normally requires a large experimental load. However, the current DNA extraction methods, including cell disruption and genomic DNA purification, are normally biased, costly, time-consuming, labor-intensive, and not amenable to miniaturization by droplets or 1,536-well plates due to the significant DNA loss during the purification step for tiny-volume and low-cell-density samples. A direct PCR method could potentially solve these problems. In this study, we developed a direct PCR method which exhibits similar efficiency as the widely used method, the DNeasy PowerSoil protocol, while being 1,600 times less expensive and 10 times faster to execute. This simple, cost-effective, and automation-friendly direct-PCR-based 16S rRNA sequencing method allows us to study the dynamics, microbial interaction, and assembly of various microbial communities in a high-throughput fashion.
Collapse
|
37
|
Point-of-care molecular diagnosis of Mycoplasma pneumoniae including macrolide sensitivity using quenching probe polymerase chain reaction. PLoS One 2021; 16:e0258694. [PMID: 34648603 PMCID: PMC8516298 DOI: 10.1371/journal.pone.0258694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/02/2021] [Indexed: 12/22/2022] Open
Abstract
Objectives Macrolides are generally considered to be the drugs of choice for treatment of patients with Mycoplasma pneumoniae infection. However, macrolide-resistant M. pneumoniae has been emerging since about 2000. The Smart Gene® system (MIZUHO MEDY Co., Ltd., Tosu, Japan) is a novel fully automated system for detection of pathogens using the method of quantitative polymerase chain reaction (qPCR) with QProbe (QProbe PCR). The entire procedure is completed within 50 min and the size of the instrument is small (15 x 34 x 30 cm). The purpose of this study was to evaluate the usefulness of the Smart Gene® system for detection of M. pneumoniae and detection of a point mutation at domain V of the 23S rRNA gene of M. pneumoniae. Materials Pharyngeal swab samples were collected from 154 patients who were suspected of having respiratory tract infections associated with M. pneumoniae. Results Compared with the results of qPCR, the sensitivity and specificity of the Smart Gene® system were 98.7% (78/79) and 100.0% (75/75), respectively. A point mutation at domain V of the 23S rRNA gene was detected from 7 (9.0%) of 78 M. pneumoniae-positive samples by the Smart Gene® system and these results were confirmed by direct sequencing. The minimum inhibitory concentrations of clarithromycin among the 5 isolates of M. pneumoniae with a point mutation at domain V of the 23S rRNA gene were >64 μg/ml and those among the 33 isolates without a mutation in the 23S rRNA gene were <0.0625 μg/ml. Conclusion The Smart Gene® system is a rapid and accurate assay for detection of the existence of M. pneumoniae and a point mutation at domain V of the 23S rRNA gene of M. pneumoniae at the same time. The Smart Gene® system is suitable for point-of-care testing in both hospital and outpatient settings.
Collapse
|
38
|
Tsuboi I, Iinuma K. Immunochromatography-Application Example and POCT Type Genetic Testing. Chem Pharm Bull (Tokyo) 2021; 69:984-988. [PMID: 34602580 DOI: 10.1248/cpb.c21-00164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Membrane-based rapid test reagents including immunochromatography are widely used in clinical practice. Recently, high-sensitive reagents based on the immunochromatography method, such as silver amplification method and time resolved fluorescence method for influenza testing, has been developed and early confirmation of infection can be achieved. Furthermore, genetic testing, automated all the steps from extraction till detection, is getting popular. Genetic testing of mycoplasma by Smart Gene Myco system and Coronavirus disease 2019 (COVID-19) test is a good example of membrane-based rapid test reagents. This system uses silica particle-containing membrane filter and enable to shorten the assay time by automates pre-treatment process for removing contamination substances in the sample which affect polymerase-chain-reaction amplification. We hope utilized genetic testing application will help quick confirmation of COVID-19 positive patient and prevent the collapse of medical system under COVID-19 development.
Collapse
Affiliation(s)
- Isami Tsuboi
- Pharmaceutical Affairs Department, BML Medical Works Inc
| | | |
Collapse
|
39
|
Song Y, Kim YT, Choi Y, Kim H, Yeom MH, Kim Y, Lee TJ, Lee KG, Im SG. All-in-One DNA Extraction Tube for Facilitated Real-Time Detection of Infectious Pathogens. Adv Healthc Mater 2021; 10:e2100430. [PMID: 34050626 DOI: 10.1002/adhm.202100430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/29/2021] [Indexed: 12/23/2022]
Abstract
An "all-in-one tube" platform is developed, where the genetic analysis involving DNA extraction, amplification, and detection can be performed in a single tube. The all-in-one tube consists of a polymerase chain reaction (PCR) tube in which the inner surface is conformally modified with a tertiary-amine-containing polymer to generate a strong electrostatic interaction with DNA. The all-in-one tube provides high DNA capture efficiency exceeding 80% from Escherichia coli O157: H7 pathogen at a wide range of DNA amount from 0.003 to 3 ng. Indeed, the use of the surface-functionalized PCR tube enables direct amplification and detection of the surface-captured DNA without the modification of standard real-time PCR instrument. Besides, this platform has sensitivity, selectivity, and reliability enough for accurate detection at the minimal infective dose of both gram-positive and negative pathogens. The all-in-one tube enables the direct molecular diagnosis, substantially reducing the labor-intensive pathogen detection steps while providing high compatibility with the currently established real-time PCR instruments, and illustrates its on-site applicability with convenience expandable to various genetic analyses including food safety testing, forensic analysis, and clinical diagnosis.
Collapse
Affiliation(s)
- Younseong Song
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Yong Tae Kim
- Department of Chemical Engineering & Biotechnology Korea Polytechnic University 237 Sangidaehak‐ro Siheung‐si 15073 Republic of Korea
| | - Yunho Choi
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Hogi Kim
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Min Hee Yeom
- Nanobio Application Team National NanoFab Center 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Yesol Kim
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Tae Jae Lee
- Nanobio Application Team National NanoFab Center 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Kyoung G. Lee
- Nanobio Application Team National NanoFab Center 291 Daehak‐ro Daejeon 34141 Republic of Korea
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
- KAIST Institute for NanoCentury Korea Advanced Institute of Science and Technology 291 Daehak‐ro Daejeon 34141 Republic of Korea
| |
Collapse
|
40
|
Gutierrez R, LaRue B, Houston R. Novel extraction chemistry and alternative amplification strategies for use with rootless hair shafts. J Forensic Sci 2021; 66:1929-1936. [PMID: 34057738 DOI: 10.1111/1556-4029.14763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/14/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Abstract
Rootless hair shafts are often considered unsuitable for STR genotyping due to the known high failure rate. The same samples can be reliably processed with mitochondrial sequencing. However, the minimal discriminatory power of widely implemented control region mitochondrial sequencing techniques limits its utility in some forensic casework. In this research, multiple variables were tested to provide information on rootless hair shaft sample genotyping success. Results showed external decontamination procedures decreased drop-in alleles but also greatly reduced profile recovery. The novel InnoXtract™ chemistry was comparable to automated EZ1 DNA Investigator extraction. With thoroughly decontaminated hairs, InnoTyper® 21 amplification generated random match probabilities higher than STR chemistry in 71.875% of samples and 18.75% of samples benefitted from the use of InnoTyper® 21 amplification compared with estimated mtDNA profile rarity. Compared with the capillary electrophoresis-based amplification chemistries tested, the ForenSeq™ DNA Signature Prep chemistry paired with massively parallel sequencing was the most discriminatory amplification strategy tested.
Collapse
Affiliation(s)
- Ryan Gutierrez
- Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA
| | | | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA
| |
Collapse
|
41
|
Refinement of 16S rRNA gene analysis for low biomass biospecimens. Sci Rep 2021; 11:10741. [PMID: 34031485 PMCID: PMC8144411 DOI: 10.1038/s41598-021-90226-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/05/2021] [Indexed: 02/04/2023] Open
Abstract
High-throughput phylogenetic 16S rRNA gene analysis has permitted to thoroughly delve into microbial community complexity and to understand host-microbiota interactions in health and disease. The analysis comprises sample collection and storage, genomic DNA extraction, 16S rRNA gene amplification, high-throughput amplicon sequencing and bioinformatic analysis. Low biomass microbiota samples (e.g. biopsies, tissue swabs and lavages) are receiving increasing attention, but optimal standardization for analysis of low biomass samples has yet to be developed. Here we tested the lower bacterial concentration required to perform 16S rRNA gene analysis using three different DNA extraction protocols, three different mechanical lysing series and two different PCR protocols. A mock microbiota community standard and low biomass samples (108, 107, 106, 105 and 104 microbes) from two healthy donor stools were employed to assess optimal sample processing for 16S rRNA gene analysis using paired-end Illumina MiSeq technology. Three DNA extraction protocols tested in our study performed similar with regards to representing microbiota composition, but extraction yield was better for silica columns compared to bead absorption and chemical precipitation. Furthermore, increasing mechanical lysing time and repetition did ameliorate the representation of bacterial composition. The most influential factor enabling appropriate representation of microbiota composition remains sample biomass. Indeed, bacterial densities below 106 cells resulted in loss of sample identity based on cluster analysis for all tested protocols. Finally, we excluded DNA extraction bias using a genomic DNA standard, which revealed that a semi-nested PCR protocol represented microbiota composition better than classical PCR. Based on our results, starting material concentration is an important limiting factor, highlighting the need to adapt protocols for dealing with low biomass samples. Our study suggests that the use of prolonged mechanical lysing, silica membrane DNA isolation and a semi-nested PCR protocol improve the analysis of low biomass samples. Using the improved protocol we report a lower limit of 106 bacteria per sample for robust and reproducible microbiota analysis.
Collapse
|
42
|
Methods for ensuring the highest DNA concentration and yield in future and retrospective trace DNA extracts. Sci Justice 2021; 61:193-197. [PMID: 33736853 DOI: 10.1016/j.scijus.2020.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/01/2020] [Indexed: 11/21/2022]
Abstract
In forensic laboratories, increased extraction efficiency of trace evidence is paramount because analytical success is intrinsically dependent on the quantity of DNA recovered. Moreover, highly concentrated nucleic acids are vital for effective downstream analysis and high quality results. This study investigated the efficiency of extraction with the Qiagen® QIAamp® DNA Investigator kit, and explored improvements to the methodology that would maximise the recovery of low concentration forensic samples. Controlled amounts of starting cellular material were used to mimic trace (or low level) DNA deposits prior to DNA extraction with the Investigator kit. Addition of the provided carrier RNA along with conducting two successive elutions of 50 µL improved the net recovery of DNA to 95%. Concentration with centrifugal filters post-extraction were able to concentrate DNA but a large net loss was observed. For the concentration of historic, retrospectively extracted DNA, centrifugal methods are able to concentrate DNA extracts previously too dilute for analysis. These concentrated volumes, however are small, allowing for minimal downstream analysis attempts before the sample is exhausted.
Collapse
|
43
|
Cheng X, Liu C, Yang Y, Liang L, Chen B, Yu H, Xia J, Liu S, Li Y. Advances in sulfur mustard-induced DNA adducts: Characterization and detection. Toxicol Lett 2021; 344:46-57. [PMID: 33705862 DOI: 10.1016/j.toxlet.2021.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
Sulfur mustard (SM) is a blister chemical warfare agent with severe cytotoxicity and genotoxicity. It can extensively alkylate important macromolecules in organisms, such as proteins, DNA, and lipids, and produce a series of metabolites, among which the characteristic ones can be used as biomarkers. The exact toxicological mechanisms of SM remain unclear but mainly involve the DNA lesions induced by alkylation and oxidative stress caused by glutathione depletion. Various methods have been used to analyze DNA damage caused by SM. Among these methods, liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology stands out and makes it possible to observe damage in view of biomarkers induced by SM. Sample preparation is critical for detection by LC-MS/MS and mainly includes DNA isolation, adduct hydrolysis, and adduct purification. Moreover, optimization of chromatographic conditions, selection of MS transitions, and quantitative strategies are also essential. SM-DNA adducts are generally considered to be N7-HETEG, O6-HETEG, N7-BisG, and N3-HETEA. This article proposes some other possibilities of SM-DNA adducts for the identification of SM genotoxicity.
Collapse
Affiliation(s)
- Xi Cheng
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, PR China; State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Changcai Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Yang Yang
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Longhui Liang
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Bo Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Huilan Yu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Junmei Xia
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China
| | - Shilei Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, PR China.
| | - Yihe Li
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, PR China.
| |
Collapse
|
44
|
Oreskovic A, Lutz BR. Ultrasensitive hybridization capture: Reliable detection of <1 copy/mL short cell-free DNA from large-volume urine samples. PLoS One 2021; 16:e0247851. [PMID: 33635932 PMCID: PMC7909704 DOI: 10.1371/journal.pone.0247851] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/12/2021] [Indexed: 12/19/2022] Open
Abstract
Urine cell-free DNA (cfDNA) is a valuable non-invasive biomarker with broad potential clinical applications, but there is no consensus on its optimal pre-analytical methodology, including the DNA extraction step. Due to its short length (majority of fragments <100 bp) and low concentration (ng/mL), urine cfDNA is not efficiently recovered by conventional silica-based extraction methods. To maximize sensitivity of urine cfDNA assays, we developed an ultrasensitive hybridization method that uses sequence-specific oligonucleotide capture probes immobilized on magnetic beads to improve extraction of short cfDNA from large-volume urine samples. Our hybridization method recovers near 100% (95% CI: 82.6-117.6%) of target-specific DNA from 10 mL urine, independent of fragment length (25-150 bp), and has a limit of detection of ≤5 copies of double-stranded DNA (0.5 copies/mL). Pairing hybridization with an ultrashort qPCR design, we can efficiently capture and amplify fragments as short as 25 bp. Our method enables amplification of cfDNA from 10 mL urine in a single qPCR well, tolerates variation in sample composition, and effectively removes non-target DNA. Our hybridization protocol improves upon both existing silica-based urine cfDNA extraction methods and previous hybridization-based sample preparation protocols. Two key innovations contribute to the strong performance of our method: a two-probe system enabling recovery of both strands of double-stranded DNA and dual biotinylated capture probes, which ensure consistent, high recovery by facilitating optimal probe density on the bead surface, improving thermostability of the probe-bead linkage, and eliminating interference by endogenous biotin. We originally designed the hybridization method for tuberculosis diagnosis from urine cfDNA, but expect that it will be versatile across urine cfDNA targets, and may be useful for other cfDNA sample types and applications beyond cfDNA. To make our hybridization method accessible to new users, we present a detailed protocol and straightforward guidelines for designing new capture probes.
Collapse
Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| |
Collapse
|
45
|
Nuckowski Ł, Kilanowska A, Studzińska S. Hydrophilic interaction in solid-phase extraction of antisense oligonucleotides. J Chromatogr Sci 2021; 58:383-387. [PMID: 32043121 DOI: 10.1093/chromsci/bmz114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 09/12/2019] [Accepted: 11/13/2019] [Indexed: 11/13/2022]
Abstract
The presented studies aimed to develop a new and simple extraction method based on hydrophilic interaction for antisense oligonucleotides with different modifications. For this purpose, solid-phase extraction cartridges with unmodified silica were used. All extraction steps were performed by utilizing water, acetonitrile, acetone or their mixtures. The results obtained show that a high content (95%) of organic solvent, used during sample loading, is critical to achieve a successful extraction, while elution with pure water allows effective oligonucleotides desorption. The recovery values were greater than 90% in the case of unmodified DNA, phosphorothioate, 2'-O-(2-methoxyethyl) and 2'-O-methyl oligonucleotides. For the mixture of phosphorothioate oligonucleotide and its two synthetic metabolites, the recovery values for the standard solutions were in the range of 70-75%, while for spiked human plasma, 45-50%. The developed method is simple, may be performed in a short time and requires simple solvents like water or acetonitrile/acetone, thus showing promise as an alternative to chaotropic salt-based or ion pair-based SPE methods.
Collapse
Affiliation(s)
- Łukasz Nuckowski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin St., PL-87-100 Toruń, Poland
| | - Anna Kilanowska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin St., PL-87-100 Toruń, Poland
| | - Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin St., PL-87-100 Toruń, Poland
| |
Collapse
|
46
|
Calderón-Franco D, van Loosdrecht MCM, Abeel T, Weissbrodt DG. Free-floating extracellular DNA: Systematic profiling of mobile genetic elements and antibiotic resistance from wastewater. WATER RESEARCH 2021; 189:116592. [PMID: 33171295 DOI: 10.1016/j.watres.2020.116592] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/08/2020] [Accepted: 11/01/2020] [Indexed: 05/11/2023]
Abstract
The free-floating extracellular DNA (exDNA) fraction of microbial ecosystems harbors antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Natural transformation of these xenogenetic elements can generate microbial cells resistant to one or more antibiotics. Isolating and obtaining a high yield of exDNA is challenging due to its low concentration in wastewater environments. Profiling exDNA is crucial to unravel the ecology of free-floating ARGs and MGEs and their contribution to horizontal genetransfer. We developed a method using chromatography to isolate and enrich exDNA without causing cell lysis from complex wastewater matrices like influent (9 µg exDNA out of 1 L), activated sludge (5.6 µg out of 1 L), and treated effluent (4.3 µg out of 1 L). ARGs and MGEs were metagenomically profiled for both the exDNA and intracellular DNA (iDNA) of activated sludge, and quantified by qPCR in effluent water. qPCR revealed that ARGs and MGEs are more abundant in the iDNA fraction while still significant on exDNA (100-1000 gene copies mL-1) in effluent water. The metagenome highlighted that exDNA is mainly composed of MGEs (65%). According to their relatively low abundance in the resistome of exDNA, ARGs uptake by natural transformation is likely not the main transfer mechanism. Although ARGs are not highly abundant in exDNA, the prevalence of MGEs in the exDNA fraction can indirectly promote antibiotic resistance development. The combination of this method with functional metagenomics can help to elucidate the transfer and development of resistances in microbial communities. A systematic profiling of the different DNA fractions will foster microbial risk assessments across water systems, supporting water authorities to delineate measures to safeguard environmental and public health.
Collapse
Affiliation(s)
| | | | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| |
Collapse
|
47
|
Sullivan BP, Bender AT, Ngyuen DN, Zhang JY, Posner JD. Nucleic acid sample preparation from whole blood in a paper microfluidic device using isotachophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1163:122494. [PMID: 33401049 DOI: 10.1016/j.jchromb.2020.122494] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023]
Abstract
Nucleic acid amplification tests (NAATs) are a crucial diagnostic and monitoring tool for infectious diseases. A key procedural step for NAATs is sample preparation: separating and purifying target nucleic acids from crude biological samples prior to nucleic acid amplification and detection. Traditionally, sample preparation has been performed with liquid- or solid-phase extraction, both of which require multiple trained user steps and significant laboratory equipment. The challenges associated with sample preparation have limited the dissemination of NAAT point-of-care diagnostics in low resource environments, including low- and middle-income countries. We report on a paper-based device for purification of nucleic acids from whole blood using isotachophoresis (ITP) for point-of-care NAATs. We show successful extraction and purification of target nucleic acids from large volumes (33 µL) of whole human blood samples with no moving parts and few user steps. Our device utilizes paper-based buffer reservoirs to fully contain the liquid ITP buffers and does not require complex filling procedures, instead relying on the natural wicking of integrated paper membranes. We perform on-device blood fractionation via filtration to remove leukocytes and erythrocytes from our sample, followed by integrated on-paper proteolytic digestion of endogenous plasma proteins to allow for successful isotachophoretic extraction. Paper-based isotachophoresis purifies and concentrates target nucleic acids that are added directly to recombinase polymerase amplification (RPA) reactions. We show consistent amplification of input copy concentrations of as low as 3 × 103 copies nucleic acid per mL input blood with extraction and purification taking only 30 min. By employing a paper architecture, we are able to incorporate these processes in a single, robust, low-cost design, enabling the direct processing of large volumes of blood, with the only intermediate user steps being the removal and addition of tape. Our device represents a step towards a simple, fully integrated sample preparation system for nucleic acid amplification tests at the point-of-care.
Collapse
Affiliation(s)
- Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Duy N Ngyuen
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jane Yuqian Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA; Department of Chemical Engineering, University of Washington, Seattle, WA, USA; Department of Family Medicine, University of Washington, Seattle, WA, USA.
| |
Collapse
|
48
|
Guo J, Liang Z, Huang Y, Kim K, Vandeventer P, Fan D. Acceleration of Biomolecule Enrichment and Detection with Rotationally Motorized Opto-Plasmonic Microsensors and the Working Mechanism. ACS NANO 2020; 14:15204-15215. [PMID: 33095572 DOI: 10.1021/acsnano.0c05429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Vigorous research efforts have advanced the state-of-the-art nanosensors with ultrahigh sensitivity for bioanalysis. However, a dilemmatic challenge remains: it is extremely difficult to obtain nanosensors that are both sensitive and high-speed for the detection of low-concentration molecules in aqueous samples. Herein, we report how the controlled mechanical rotation (or rotary motorization) of designed opto-plasmonic microsensors can substantially and robustly accelerate the enrichment and detection speed of deoxyribonucleic acid (DNA) with retained high sensitivity. At least 4-fold augmentation of the capture speed of DNA molecules is obtained from a microsensor rotating at 1200 rpm. Theoretical analysis and modeling shed light on the underlying working mechanism, governed by the molecule-motor-flow interaction as well as its application range and limitation. This work provides a device scheme that alleviates the dilemmatic challenge in biomolecule sensing and offers the understanding of the complex interactions of molecules and moving microobjects in suspension. The results may assist the rational design of efficient microrobotic systems for the capture, translocation, sensing, and release of biocargoes.
Collapse
Affiliation(s)
- Jianhe Guo
- Texas Materials Institute and Materials Science and Engineering Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zexi Liang
- Texas Materials Institute and Materials Science and Engineering Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yun Huang
- Texas Materials Institute and Materials Science and Engineering Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Kwanoh Kim
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Peter Vandeventer
- Defense Threat Reduction Agency, Fort Belvoir, Virginia 22060, United States
| | - Donglei Fan
- Texas Materials Institute and Materials Science and Engineering Program, The University of Texas at Austin, Austin, Texas 78712, United States
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
49
|
Tardani F, Casciardi S, Ruzicka B, Sennato S. Salt enhanced sedimentation of halloysite nanotubes for precise determination of DNA adsorption isotherm. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.125400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
50
|
Yamamoto S, Matsumoto SI, Goto A, Ugajin M, Nakayama M, Moriya Y, Hirabayashi H. Quantitative PCR methodology with a volume-based unit for the sophisticated cellular kinetic evaluation of chimeric antigen receptor T cells. Sci Rep 2020; 10:17884. [PMID: 33087808 PMCID: PMC7578827 DOI: 10.1038/s41598-020-74927-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/05/2020] [Indexed: 11/16/2022] Open
Abstract
Although the cellular kinetics of chimeric antigen receptor T (CAR T) cells are expressed in units of copies/μg gDNA, this notation carries the risk of misrepresentation owing to dramatic changes in blood gDNA levels after lymphocyte-depleting chemotherapy and rapid expansion of CAR T cells. Therefore, we aimed to establish a novel qPCR methodology incorporating a spike-in calibration curve that expresses cellular kinetics in units of copies/μL blood, as is the case for conventional pharmacokinetic studies of small molecules and other biologics. Dog gDNA was used as an external control gene. Our methodology enables more accurate evaluation of in vivo CAR T-cell expansion than the conventional approach; the unit “copies/μL blood” is therefore more appropriate for evaluating cellular kinetics than the unit “copies/μg gDNA.” The results of the present study provide new insights into the relationship between cellular kinetics and treatment efficacy, thereby greatly benefiting patients undergoing CAR T-cell therapy.
Collapse
Affiliation(s)
- Syunsuke Yamamoto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.
| | - Shin-Ichi Matsumoto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| | - Akihiko Goto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| | - Miyuki Ugajin
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| | - Miyu Nakayama
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| | - Yuu Moriya
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| | - Hideki Hirabayashi
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| |
Collapse
|