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Xiao B, Zhou T, Wang N, Zhang J, Sun X, Chen J, Huang F, Wang J, Li N, Chen A. Toothpick DNA extraction combined with handheld LAMP microfluidic platform for simple and rapid meat authentication. Food Chem 2024; 460:140659. [PMID: 39111039 DOI: 10.1016/j.foodchem.2024.140659] [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: 01/08/2024] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 09/06/2024]
Abstract
Adulteration of meat is a global issue, necessitating rapid, inexpensive, and simple on-site testing methods. Therefore, the present study aimed to develop a one-minute toothpick-based DNA extraction method, a handheld microfluidic chip, and a smartphone-controlled portable analyzer for detecting multiple meat adulterations. A toothpick was inserted into the meat to promote DNA release and adsorption. Furthermore, a handheld microfluidic chip was designed for DNA elution on toothpicks and fluid distribution. Finally, a smartphone-actuated portable analyzer was developed to function as a heater, signal detector, and result reader. The portable device comprises a microcontroller, a fluorescence detection module, a step scanning unit, and a heating module. The proposed device is portable, and the app is user-friendly. This simple design, easy operation, and fast-response system could rapidly detect as little as 1% of simulated adulterated samples (following UK standards) within 40 min at a cost of less than USD 1 per test.
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Affiliation(s)
- Bin Xiao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tianping Zhou
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Wang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Juan Zhang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyun Sun
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiaci Chen
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fengchun Huang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junbo Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China.
| | - Ailiang Chen
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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2
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Liu G, Shi G, Liu H, Xu N, Fan L, Wang L. A three-minute solid phase-based plant RNA extraction method. MOLECULAR HORTICULTURE 2024; 4:7. [PMID: 38424604 PMCID: PMC10905925 DOI: 10.1186/s43897-024-00084-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024]
Affiliation(s)
- Guiling Liu
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China
| | - Gongfa Shi
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China
| | - Huijun Liu
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China
| | - Nuo Xu
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China
| | - Lijuan Fan
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China
| | - Ling Wang
- College of Landscape Architecture, Northeast Forestry University, Harbin, 150040, China.
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3
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Gaines D, Brodsky E, Kaur H, Nestorova GG. RNA capture pin technology: investigating long-term stability and mRNA purification specificity of oligonucleotide immobilization on gold and streptavidin surfaces. Anal Bioanal Chem 2023; 415:6077-6089. [PMID: 37516691 DOI: 10.1007/s00216-023-04882-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
Advancing biomedical studies necessitates the development of cutting-edge technologies for the rapid extraction of nucleic acid. We characterized an RNA capture pin (RCP) tool that is non-destructive to the sample and enables rapid purification and enrichment of mRNA for subsequent genetic analysis. At the core of this technology is a pin (200 µm × 3 cm) functionalized with dT15 capture sequences that hybridize to mRNA within 2 min of insertion in the specimen. Two methods for immobilizing the oligos on the surface of the RCPs were investigated: gold-thiol and biotin-streptavidin. The RNA capture efficiency of the RCPs was assessed using a radish plant. The average reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle amplification values were 19.93 and 24.84 for gold- and streptavidin-coated pins, respectively. The amount of RNA present on the surface of the probes was measured using the Agilent 2100 Bioanalyzer. RNA sequencing was performed to determine the mRNA selectivity of the RNA capture pin. Gene read count analysis confirmed that the RNA purified via the gold-plated RCPs contained 70% messenger RNA, 10% ribosomal RNA, and 20% non-coding RNA. The long-term stability of the bond between the dT15 oligos and the surface of the RCPs was assessed over 4 months. A significant decrease in the dT15 surface coverage of the streptavidin-coated RCPs was observed after 2 weeks of storage at 4 °C. The gold-thiol RNA capture pins exhibited a retention rate of 40% of the oligos after 4 months of storage.
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Affiliation(s)
- Deriesha Gaines
- Molecular Sciences and Nanotechnology, Louisiana Tech University, Ruston, LA, USA
| | | | | | - Gergana G Nestorova
- School of Biological Sciences, Louisiana Tech University, 1 Adams Blvd., Ruston, LA, 71272, USA.
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Hasenstein KH, John SP, Vandenbrink JP. Assessing Radish Health during Space Cultivation by Gene Transcription. PLANTS (BASEL, SWITZERLAND) 2023; 12:3458. [PMID: 37836197 PMCID: PMC10574649 DOI: 10.3390/plants12193458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
During the Advanced Plant Habitat experiment 2, radish plants were grown in two successive grow-outs on the International Space Station (ISS) for 27 days each. On days 10, 18, and 24, leaf punch (LP) samples were collected and frozen. At harvest, bulb tissue was sampled with oligo-dT functionalized Solid Phase Gene Extraction (SPGE) probes. The space samples were compared with samples from ground controls (GC) grown at the Kennedy Space Center (KSC) under the same conditions as on the ISS, with notably elevated CO2 (about 2500 ppm), and from lab plants grown under atmospheric CO2 but with light and temperature conditions similar to the KSC control. Genes corresponding to peroxidase (RPP), glucosinolate biosynthesis (GIS), protein binding (CBP), myrosinase (RMA), napin (RSN), and ubiquitin (UBQ) were measured by qPCR. LP from day 24 and bulb samples collected at harvest were compared with RNA-seq data from material that was harvested, frozen, and analyzed after return to Earth. The results showed stable transcription in LP samples in GC but decreasing values in ISS samples during both grow-outs, possibly indicative of stress. SPGE results were similar between GC and ISS samples. However, the RNA-seq analyses showed different transcription profiles than SPGE or LP results, possibly related to localized sampling. RNA-seq of leaf samples showed greater variety than LP data, possibly because of different sampling times. RSN and RPP showed the lowest transcription regardless of method. Temporal analyses showed relatively small changes during plant development in space and in ground controls. This is the first study that compares developmental changes in space-grown plants with ground controls based on a comparison between RNA-seq and qPCR analyses.
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Affiliation(s)
- Karl H. Hasenstein
- Biology Department, University of Louisiana Lafayette, Lafayette, LA 70504, USA;
| | - Susan P. John
- Biology Department, University of Louisiana Lafayette, Lafayette, LA 70504, USA;
| | - Joshua P. Vandenbrink
- Department of Biological Sciences, Louisiana Tech University, Ruston, LA 71272, USA;
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Chakraborty S, Luchena C, Elton JJ, Schilling MP, Reischl M, Roux M, Levkin PA, Popova AA. "Cells-to-cDNA on Chip": Phenotypic Assessment and Gene Expression Analysis from Live Cells in Nanoliter Volumes Using Droplet Microarrays. Adv Healthc Mater 2022; 11:e2102493. [PMID: 35285171 PMCID: PMC11469226 DOI: 10.1002/adhm.202102493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/08/2022] [Indexed: 11/11/2022]
Abstract
In vitro cell-based experiments are particularly important in fundamental biological research. Microscopy-based readouts to identify cellular changes in response to various stimuli are a popular choice, but gene expression analysis is essential to delineate the underlying molecular dynamics in cells. However, cell-based experiments often suffer from interexperimental variation, especially while using different readout methods. Therefore, establishment of platforms that allow for cell screening, along with parallel investigations of morphological features, as well as gene expression levels, is crucial. The droplet microarray (DMA) platform enables cell screening in hundreds of nanoliter droplets. In this study, a "Cells-to-cDNA on Chip" method is developed enabling on-chip mRNA isolation from live cells and conversion to cDNA in individual droplets of 200 nL. This novel method works efficiently to obtain cDNA from different cell numbers, down to single cell per droplet. This is the first established miniaturized on-chip strategy that enables the entire course of cell screening, phenotypic microscopy-based assessments along with mRNA isolation and its conversion to cDNA for gene expression analysis by real-time PCR on an open DMA platform. The principle demonstrated in this study sets a beginning for myriad of possible applications to obtain detailed information about the molecular dynamics in cultured cells.
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Affiliation(s)
- Shraddha Chakraborty
- Institute of Biological and Chemical Systems‐Functional Molecular SystemsKarlsruhe Institute of TechnologyHermann‐von‐Helmholtz‐Platz 1Eggenstein‐Leopoldshafen76344Germany
| | - Charlotte Luchena
- Institute of Biological and Chemical Systems‐Functional Molecular SystemsKarlsruhe Institute of TechnologyHermann‐von‐Helmholtz‐Platz 1Eggenstein‐Leopoldshafen76344Germany
| | - Jonathan J. Elton
- Institute of Biological and Chemical Systems‐Functional Molecular SystemsKarlsruhe Institute of TechnologyHermann‐von‐Helmholtz‐Platz 1Eggenstein‐Leopoldshafen76344Germany
| | - Marcel P. Schilling
- Institute for Automation and Applied InformaticsKarlsruhe Institute of TechnologyHermann‐von‐Helmholtz‐Platz 1Eggenstein‐Leopoldshafen76344Germany
| | - Markus Reischl
- Institute for Automation and Applied InformaticsKarlsruhe Institute of TechnologyHermann‐von‐Helmholtz‐Platz 1Eggenstein‐Leopoldshafen76344Germany
| | - Margaux Roux
- Cellenion SASUBioserra 2, 60 avenue RockefellerLyon69008France
| | - Pavel A. Levkin
- Institute of Biological and Chemical Systems‐Functional Molecular SystemsKarlsruhe Institute of TechnologyHermann‐von‐Helmholtz‐Platz 1Eggenstein‐Leopoldshafen76344Germany
- Institute of Organic ChemistryKarlsruhe Institute of TechnologyFritz‐Haber Weg 6Karlsruhe76131Germany
| | - Anna A. Popova
- Institute of Biological and Chemical Systems‐Functional Molecular SystemsKarlsruhe Institute of TechnologyHermann‐von‐Helmholtz‐Platz 1Eggenstein‐Leopoldshafen76344Germany
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6
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Advances in improvement strategies of digital nucleic acid amplification for pathogen detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116568] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Cunha ML, da Silva SS, Stracke MC, Zanette DL, Aoki MN, Blanes L. Sample Preparation for Lab-on-a-Chip Systems in Molecular Diagnosis: A Review. Anal Chem 2021; 94:41-58. [PMID: 34870427 DOI: 10.1021/acs.analchem.1c04460] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rapid and low-cost molecular analysis is especially required for early and specific diagnostics, quick decision-making, and sparing patients from unnecessary tests and hospitals from extra costs. One way to achieve this objective is through automated molecular diagnostic devices. Thus, sample-to-answer microfluidic devices are emerging with the promise of delivering a complete molecular diagnosis system that includes nucleic acid extraction, amplification, and detection steps in a single device. The biggest issue in such equipment is the extraction process, which is normally laborious and time-consuming but extremely important for sensitive and specific detection. Therefore, this Review focuses on automated or semiautomated extraction methodologies used in lab-on-a-chip devices. More than 15 different extraction methods developed over the past 10 years have been analyzed in terms of their advantages and disadvantages to improve extraction procedures in future studies. Herein, we are able to explain the high applicability of the extraction methodologies due to the large variety of samples in which different techniques were employed, showing that their applications are not limited to medical diagnosis. Moreover, we are able to conclude that further research in the field would be beneficial because the methodologies presented can be affordable, portable, time efficient, and easily manipulated, all of which are strong qualities for point-of-care technologies.
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Affiliation(s)
- Mylena Lemes Cunha
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Stella Schuster da Silva
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Mateus Cassaboni Stracke
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010.,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Dalila Luciola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Lucas Blanes
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010.,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
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8
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Alidoust M, Baharfar M, Manouchehri M, Yamini Y, Tajik M, Seidi S. Emergence of microfluidic devices in sample extraction; an overview of diverse methodologies, principals, and recent advancements. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Nucleic acid extraction: Fundamentals of sample preparation methodologies, current advancements, and future endeavors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115985] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Arabi M, Ostovan A, Bagheri AR, Guo X, Wang L, Li J, Wang X, Li B, Chen L. Strategies of molecular imprinting-based solid-phase extraction prior to chromatographic analysis. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115923] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Yin J, Hu J, Sun J, Wang B, Mu Y. A fast nucleic acid extraction system for point-of-care and integration of digital PCR. Analyst 2019; 144:7032-7040. [DOI: 10.1039/c9an01067j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This work showcases a PTFE-based nucleic acid extraction system for point-of-care and integration of digital PCR.
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Affiliation(s)
- Juxin Yin
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
| | - Jiumei Hu
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
| | - Jingjing Sun
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
| | - Ben Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention
- National Ministry of Education)
- The Second Affiliated Hospital
- Zhejiang University School of Medicine
- Hangzhou
| | - Ying Mu
- Research Centre for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou
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Nacham O, Clark KD, Varona M, Anderson JL. Selective and Efficient RNA Analysis by Solid-Phase Microextraction. Anal Chem 2017; 89:10661-10666. [DOI: 10.1021/acs.analchem.7b02733] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Omprakash Nacham
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Kevin D. Clark
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Marcelino Varona
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L. Anderson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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