1
|
Hou Y, Chen R, Wang Z, Lu R, Wang Y, Ren S, Li S, Wang Y, Han T, Yang S, Zhou H, Gao Z. Bio-barcode assay: A useful technology for ultrasensitive and logic-controlled specific detection in food safety: A review. Anal Chim Acta 2023; 1267:341351. [PMID: 37257972 DOI: 10.1016/j.aca.2023.341351] [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: 10/14/2022] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
Food safety is one of the greatest public health challenges. Developing ultrasensitive detection methods for analytes at ultra-trace levels is, therefore, essential. In recent years, the bio-barcode assay (BCA) has emerged as an effective ultrasensitive detection strategy that is based on the indirect amplification of various DNA probes. This review systematically summarizes the progress of fluorescence, PCR, and colorimetry-based BCA methods for the detection of various contaminants, including pathogenic bacteria, toxins, pesticides, antibiotics, and other chemical substances in food in over 120 research papers. Current challenges, including long experimental times and strict storage conditions, and the prospects for the application of BCA in biomedicine and environmental analyses, have also been discussed herein.
Collapse
Affiliation(s)
- Yue Hou
- The Education Ministry Key Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Normal University, Shanghai, 200234, People's Republic of China; Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Ruipeng Chen
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Zhiguang Wang
- The Education Ministry Key Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Normal University, Shanghai, 200234, People's Republic of China; Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Ran Lu
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Yonghui Wang
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Shuyue Ren
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Shuang Li
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Yu Wang
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Tie Han
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China
| | - Shiping Yang
- The Education Ministry Key Lab of Resource Chemistry and Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Normal University, Shanghai, 200234, People's Republic of China.
| | - Huanying Zhou
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China.
| | - Zhixian Gao
- Institute of Environmental and Operational Medicine, Academy of Military Medical Sciences, Academy of Military Sciences, Tianjin, 300050, People's Republic of China.
| |
Collapse
|
2
|
Cytochrome c in cancer therapy and prognosis. Biosci Rep 2022; 42:232225. [PMID: 36479932 PMCID: PMC9780037 DOI: 10.1042/bsr20222171] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022] Open
Abstract
Cytochrome c (cyt c) is an electron transporter of the mitochondrial respiratory chain. Upon permeabilization of the mitochondrial outer membrane, cyt c is released into the cytoplasm, where it triggers the intrinsic pathway of apoptosis. Cytoplasmic cyt c can further reach the bloodstream. Apoptosis inhibition is one of the hallmarks of cancer and its induction in tumors is a widely used therapeutic approach. Apoptosis inhibition and induction correlate with decreased and increased serum levels of cyt c, respectively. The quantification of cyt c in the serum is useful in the monitoring of patient response to chemotherapy, with potential prognosis value. Several highly sensitive biosensors have been developed for the quantification of cyt c levels in human serum. Moreover, the delivery of exogenous cyt c to the cytoplasm of cancer cells is an effective approach for inducing their apoptosis. Similarly, several protein-based and nanoparticle-based systems have been developed for the therapeutic delivery of cyt c to cancer cells. As such, cyt c is a human protein with promising value in cancer prognosis and therapy. In addition, its thermal stability can be extended through PEGylation and ionic liquid storage. These processes could contribute to enhancing its therapeutic exploitation in clinical facilities with limited refrigeration conditions. Here, I discuss these research lines and how their timely conjunction can advance cancer therapy and prognosis.
Collapse
|
3
|
Xu Y, Wang Y, Hu J, Bao Z, Wang M. Development and Visualization Improvement for the Rapid Detection of Decapod Iridescent Virus 1 (DIV1) in Penaeus vannamei Based on an Isothermal Recombinase Polymerase Amplification Assay. Viruses 2022; 14:v14122752. [PMID: 36560756 PMCID: PMC9783574 DOI: 10.3390/v14122752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/27/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Viral diseases have seriously restricted the healthy development of aquaculture, and decapod iridescent virus 1 (DIV1) has led to heavy losses in the global shrimp aquaculture industry. Due to the lack of effective treatment, early detection and regular monitoring are the most effective ways to avoid infection with DIV1. In this study, a novel real-time quantitative recombinase polymerase amplification (qRPA) assay and its instrument-free visualization improvement were described for the rapid detection of DIV1. Optimum primer pairs, suitable reaction temperatures, and probe concentrations of a DIV1-qRPA assay were screened to determine optimal reaction conditions. Then, its ability to detect DIV1 was evaluated and compared with real-time quantitative polymerase chain reactions (qPCRs). The sensitivity tests demonstrated that the limit of detection (LOD) of the DIV1-qRPA assay was 1.0 copies μL-1. Additionally, the presentation of the detection results was improved with SYBR Green I, and the LOD of the DIV1-RPA-SYBR Green I assay was 1.0 × 103 copies μL-1. Both the DIV1-qRPA and DIV1-RPA-SYBR Green I assays could be performed at 42 °C within 20 min and without cross-reactivity with the following: white spot syndrome virus (WSSV), Vibrio parahaemolyticus associated with acute hepatopancreatic necrosis disease (VpAHPND), Enterocytozoon hepatopenaei (EHP), and infectious hypodermal and hematopoietic necrosis virus (IHHNV). In conclusion, this approach yields rapid, straightforward, and simple DIV1 diagnoses, making it potentially valuable as a reliable tool for the detection and prevention of DIV1, especially where there is a paucity of laboratory equipment.
Collapse
Affiliation(s)
- Yajin Xu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
| | - Yan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
- Correspondence: (Y.W.); (M.W.)
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Center for Marine Molecular Biotechnology, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Center for Marine Molecular Biotechnology, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Mengqiang Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Center for Marine Molecular Biotechnology, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
- Correspondence: (Y.W.); (M.W.)
| |
Collapse
|
4
|
Yadav S, Sawarni N, Kumari P, Sharma M. Advancement in analytical techniques fabricated for the quantitation of cytochrome c. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
5
|
Ma X, Xu J, Zhou F, Ye J, Yang D, Wang H, Wang P, Li M. Recent advances in PCR-free nucleic acid detection for SARS-COV-2. Front Bioeng Biotechnol 2022; 10:999358. [PMID: 36277389 PMCID: PMC9585218 DOI: 10.3389/fbioe.2022.999358] [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: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
As the outbreak of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory disease coronavirus 2 (SARS-COV-2), fast, accurate, and economic detection of viral infection has become crucial for stopping the spread. Polymerase chain reaction (PCR) of viral nucleic acids has been the gold standard method for SARS-COV-2 detection, which, however, generally requires sophisticated facilities and laboratory space, and is time consuming. This review presents recent advances in PCR-free nucleic acid detection methods for SARS-CoV-2, including emerging methods of isothermal amplification, nucleic acid enzymes, electrochemistry and CRISPR.
Collapse
Affiliation(s)
| | | | | | | | | | - Hua Wang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pengfei Wang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Min Li
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
6
|
Fabrication of a label-free electrochemical aptasensor to detect cytochrome c in the early stage of cell apoptosis. Mikrochim Acta 2022; 189:279. [PMID: 35829926 DOI: 10.1007/s00604-022-05373-8] [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] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 10/17/2022]
Abstract
A label-free direct electrochemical aptasensor is presented for the identification of cytochrome c (Cyt c) at the nM concentration level. Carbon nanofibers (CNF), as a highly conductive material, were used to modify a glassy carbon electrode (GCE) and thus increase its conductivity. Moreover, to enhance the immobilization of aptamers (Apt) on the electrode surface, graphene oxide functionalized with aspartic acid (GOAsp) was added to the surface. Aspartic acid with countless carboxyl groups (-COOH) on its surface caused more aptamers to be immobilized on the electrode surface. Electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), and differential pulse voltammetry (DPV) were used to monitor the step-by-step fabrication of the label-free direct electrochemical aptasensor. The label-free quantification of Cyt c was also done by the direct electron transfer between the Fe(III)/Fe(II)-heme redox-active sites which were selectively bound to the aptamers on the GCE and the surface of the electrode. Under optimum conditions, the peak currents of differential pulse voltammograms at 0.26 V (vs. Ag/AgCl) were used for calibration. The proposed aptasensor performs in a wide dynamic range from 10 nM to 100 µM with a low detection limit of 0.74 nM for cytochrome c. It also has high selectivity as well as acceptable stability. These advantages make the biosensor capable of detecting early-stage apoptotic cells that contribute to early cancer diagnosis.
Collapse
|
7
|
Mota DS, Guimarães JM, Gandarilla AMD, Filho JCBS, Brito WR, Mariúba LAM. Recombinase polymerase amplification in the molecular diagnosis of microbiological targets and its applications. Can J Microbiol 2022; 68:383-402. [PMID: 35394399 DOI: 10.1139/cjm-2021-0329] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the introduction of the polymerase chain reaction (PCR) technique in 1983, nucleic acid amplification has permeated all fields of biological science, particularly clinical research. Despite its importance, PCR has been restricted to specialized centers and its use in laboratories with few resources is limited. In recent decades, there has been a notable increase in the development of new isothermal technologies for molecular diagnosis with the hope of overcoming the traditional limitations of the laboratory. Among these technologies, recombinase polymerase amplification (RPA) has a wide application potential because it does not require thermocyclers and has high sensitivity, specificity, simplicity, and detection speed. This technique has been used for DNA and RNA amplification in various pathogenic organisms such as viruses, bacteria, and parasites. In addition, RPA has been successfully implemented in different detection strategies, making it a promising alternative for performing diagnoses in environments with scarce resources and a high burden of infectious diseases. In this study, we present a review of the use of RPA in clinical settings and its implementation in various research areas.
Collapse
Affiliation(s)
- D S Mota
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J M Guimarães
- Centro Multiusuário para Análises de Fenômenos Biomédicos, Universidade do Estado do Amazonas (UEA), Manaus, AM, 69065-00, Brazil
| | - A M D Gandarilla
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J C B S Filho
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - W R Brito
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - L A M Mariúba
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| |
Collapse
|
8
|
Redox state changes of mitochondrial cytochromes in brain and breast cancers by Raman spectroscopy and imaging. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132134] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
9
|
Mushtaq I, Bashir Z, Sarwar M, Arshad M, Ishtiaq A, Khan W, Khan U, Tabassum S, Ali T, Fatima T, Valadi H, Nawaz M, Murtaza I. N-Acetyl Cysteine, Selenium, and Ascorbic Acid Rescue Diabetic Cardiac Hypertrophy via Mitochondrial-Associated Redox Regulators. Molecules 2021; 26:7285. [PMID: 34885867 PMCID: PMC8659237 DOI: 10.3390/molecules26237285] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Metabolic disorders often lead to cardiac complications. Metabolic deregulations during diabetic conditions are linked to mitochondrial dysfunctions, which are the key contributing factors in cardiac hypertrophy. However, the underlying mechanisms involved in diabetes-induced cardiac hypertrophy are poorly understood. In the current study, we initially established a diabetic rat model by alloxan-administration, which was validated by peripheral glucose measurement. Diabetic rats displayed myocardial stiffness and fibrosis, changes in heart weight/body weight, heart weight/tibia length ratios, and enhanced size of myocytes, which altogether demonstrated the establishment of diabetic cardiac hypertrophy (DCH). Furthermore, we examined the expression of genes associated with mitochondrial signaling impairment. Our data show that the expression of PGC-1α, cytochrome c, MFN-2, and Drp-1 was deregulated. Mitochondrial-signaling impairment was further validated by redox-system dysregulation, which showed a significant increase in ROS and thiobarbituric acid reactive substances, both in serum and heart tissue, whereas the superoxide dismutase, catalase, and glutathione levels were decreased. Additionally, the expression levels of pro-apoptotic gene PUMA and stress marker GATA-4 genes were elevated, whereas ARC, PPARα, and Bcl-2 expression levels were decreased in the heart tissues of diabetic rats. Importantly, these alloxan-induced impairments were rescued by N-acetyl cysteine, ascorbic acid, and selenium treatment. This was demonstrated by the amelioration of myocardial stiffness, fibrosis, mitochondrial gene expression, lipid profile, restoration of myocyte size, reduced oxidative stress, and the activation of enzymes associated with antioxidant activities. Altogether, these data indicate that the improvement of mitochondrial dysfunction by protective agents such as N-acetyl cysteine, selenium, and ascorbic acid could rescue diabetes-associated cardiac complications, including DCH.
Collapse
Affiliation(s)
- Iram Mushtaq
- Signal Transduction Laboratory, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (I.M.); (Z.B.); (M.S.); (M.A.); (A.I.); (T.A.)
| | - Zainab Bashir
- Signal Transduction Laboratory, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (I.M.); (Z.B.); (M.S.); (M.A.); (A.I.); (T.A.)
| | - Mehvish Sarwar
- Signal Transduction Laboratory, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (I.M.); (Z.B.); (M.S.); (M.A.); (A.I.); (T.A.)
| | - Maria Arshad
- Signal Transduction Laboratory, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (I.M.); (Z.B.); (M.S.); (M.A.); (A.I.); (T.A.)
| | - Ayesha Ishtiaq
- Signal Transduction Laboratory, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (I.M.); (Z.B.); (M.S.); (M.A.); (A.I.); (T.A.)
| | - Wajiha Khan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbotabad 22060, Pakistan;
| | - Uzma Khan
- Faculty of Biological Sciences, Hazara University, Mansehra 21040, Pakistan;
| | - Sobia Tabassum
- Department of Bioinformatics and Biotechnology, Islamic International University Islamabad (IIUI), Islamabad 44000, Pakistan;
| | - Tahir Ali
- Signal Transduction Laboratory, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (I.M.); (Z.B.); (M.S.); (M.A.); (A.I.); (T.A.)
| | - Tahzeeb Fatima
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden; (T.F.); (H.V.)
| | - Hadi Valadi
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden; (T.F.); (H.V.)
| | - Muhammad Nawaz
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden; (T.F.); (H.V.)
| | - Iram Murtaza
- Signal Transduction Laboratory, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (I.M.); (Z.B.); (M.S.); (M.A.); (A.I.); (T.A.)
| |
Collapse
|
10
|
Live-cell visualization of cytochrome c: a tool to explore apoptosis. Biochem Soc Trans 2021; 49:2903-2915. [PMID: 34747968 DOI: 10.1042/bst20211028] [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] [Received: 07/29/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Apoptosis dysfunction is associated with several malignancies, including cancer and autoimmune diseases. Apoptosis restoration could be an attractive therapeutic approach to those diseases. Mitochondrial outer membrane permeabilization is regarded as the point of no return in the 'classical' apoptosis triggering pathway. Cytoplasmic release of cytochrome c (cyt c), a mitochondrial electron transporter, is a prominent indicator of such critical step. Therefore, visualizing cyt c efflux in living cells is a convenient approach to address apoptosis triggering and monitor performance of apoptosis restoration strategies. Recent years have been prolific in the development of biosensors to visualize cyt c mitochondrial efflux in living cells, by fluorescence microscopy. These biosensors specifically detect endogenous, untagged cyt c, while showing efficient cellular uptake and reduced cell toxicity. A common aspect is their fluorescence quenching in the absence or presence of bound cyt c, resulting in two main biosensor types: 'turn ON' and 'turn OFF'. In some of these systems, fluorescence intensity of fluorophore-bound aptamers is enhanced upon cyt c binding. In others, cyt c binding to quantum dots quenches their fluorescence. In the present minireview, I describe these biosensors and briefly introduce some hypotheses that could be addressed using these novel tools.
Collapse
|
11
|
Fu J, Li J, Chen J, Li Y, Liu J, Su X, Shi S. Ultra-specific nucleic acid testing by target-activated nucleases. Crit Rev Biotechnol 2021; 42:1061-1078. [PMID: 34706599 DOI: 10.1080/07388551.2021.1983757] [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] [Indexed: 12/24/2022]
Abstract
Specific and sensitive detection of nucleic acids is essential to clinical diagnostics and biotechnological applications. Currently, amplification steps are necessary for most detection methods due to the low concentration of nucleic acid targets in real samples. Although amplification renders high sensitivity, poor specificity is prevalent because of the lack of highly accurate precise strategies, resulting in significant false positives and false negatives. Nucleases exhibit high catalytic activity for nucleic acid cleavage which is regulated in a programmable manner. This review focuses on the latest progress in nucleic acid testing methods based on the target-activated nucleases. It summarizes the property of enzymes such as CRISPR/Cas, Argonautes, and some gene-editing irrelevant nucleases, which have been leveraged to create highly specific and sensitive nucleic acid testing tools. We elaborate on recent advances in the field of nuclease-mediated DNA recognition techniques for nucleic acid detection, and discuss its future applications and challenges in molecular diagnostics.
Collapse
Affiliation(s)
- Jinyu Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yabei Li
- Department of Neurosurgery, People's Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jiajia Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| |
Collapse
|
12
|
Chen K, Sun Z. Estrogen inhibits renal Na-Pi Co-transporters and improves klotho deficiency-induced acute heart failure. Redox Biol 2021; 47:102173. [PMID: 34678656 PMCID: PMC8577443 DOI: 10.1016/j.redox.2021.102173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 01/06/2023] Open
Abstract
Objective and hypothesis Klotho is an aging-suppressor gene. Mutation of Klotho gene causes hyperphosphatemia and acute heart failure. However, the relationship of hyperphosphatemia and acute heart failure is unclear. We hypothesize that hyperphosphatemia mediates Klotho deficiency-induced acute heart failure and further that therapeutic reduction of hyperphosphatemia prevents acute heart failure in Klotho mutant (KL(−/−)) mice. Methods and results A significant elevation of serum phosphorus levels and a large reduction of heart function were found in KL(−/−) mice by six weeks of age. Normalization of serum phosphorus levels by low phosphate diet (LPD) rescued Klotho deficiency-induced heart failure and extended lifespan in male mice. Klotho deficiency impaired cardiac mitochondrial respiratory enzyme function and increased superoxide production, oxidative stress, and cardiac cell apoptosis in male KL(−/−) mice which can be eliminated by LPD. LPD, however, did not rescue hyperphosphatemia or heart failure in female KL(−/−) mice. LPD did not affect estrogen depletion in female KL(−/−) mice. Normalization of serum estrogen levels by treatment with 17β-estradiol prevented hyperphosphatemia and heart failure in female KL(−/−) mice. Mechanistically, treatment with 17β-estradiol rescued hyperphosphatemia via inhibiting renal Na-Pi co-transporter expression. Normalization of serum phosphorus levels by treatment with 17β-estradiol also abolished cardiac mitochondrial respiratory enzyme dysfunction, ROS overproduction, oxidative stress and cardiac cell apoptosis in female KL(−/−) mice. Conclusion Klotho deficiency causes acute heart failure via hyperphosphatemia in male mice which can be prevented by LPD. 17β-estradiol prevents Klotho deficiency-induced hyperphosphatemia and heart failure by eliminating upregulation of renal Na-Pi co-transporter expression in female mice.
Collapse
Affiliation(s)
- Kai Chen
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Zhongjie Sun
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| |
Collapse
|
13
|
Du Y, Liu D, Wang M, Guo F, Lin JS. Preparation of DNA aptamer and development of lateral flow aptasensor combining recombinase polymerase amplification for detection of erythromycin. Biosens Bioelectron 2021; 181:113157. [PMID: 33756378 DOI: 10.1016/j.bios.2021.113157] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023]
Abstract
Erythromycin has polluted our aquatic environment for decades, leading to the risk of bacterial resistance and harmful effects on human beings, wildlife and ecosystem. There is an urgent demand of developing a portable tool capable of detecting erythromycin on site. In this study, ten aptamer candidates against erythromycin were prepared through Capture-SELEX (systematic evolution of ligands by exponential enrichment) process in 20 rounds. Aptamer candidate Ery_06 with the highest enrichment was chosen for further study, whose affinity was characterized by gold nanoparticles colorimetric assay, quartz crystal microbalance with dissipation and agarose chasing diffusion assay. It was determined by SYBR Green I fluorimetric assay that the characterized aptamer binds to erythromycin with high affinity (Kd: 20 ± 9 nM). Its specificity was also characterized by distinguishing erythromycin from different antibiotics tested. A novel lateral flow aptasensor was constructed by using the newly identified aptamer combined with recombinase polymerase amplification (RPA) and lateral flow strip (LFS). Aptamer acted as a sensing element anchoring on the surface of solid phase could be eluted by erythromycin. RPA functioned to amplify and convert the signal to be visible on LFS. The lateral flow was completed in 15 min, achieving a detection limit of 3 pM. The application feasibility of the aptasensor was proved by the detection of tap water samples spiked with erythromycin.
Collapse
Affiliation(s)
- Yepeng Du
- School of Clinical Medicine, Huaqiao University, Quanzhou Campus, 363021, Fujian, China
| | - Dan Liu
- School of Clinical Medicine, Huaqiao University, Xiamen Campus, 361021, Fujian, China
| | - Min Wang
- University Hospital, Huaqiao University, Quanzhou Campus, 363021, Fujian, China
| | - Fangke Guo
- School of Clinical Medicine, Huaqiao University, Quanzhou Campus, 363021, Fujian, China
| | - Jun Sheng Lin
- School of Clinical Medicine, Huaqiao University, Quanzhou Campus, 363021, Fujian, China.
| |
Collapse
|
14
|
Kang J, Jang H, Yeom G, Kim MG. Ultrasensitive Detection Platform of Disease Biomarkers Based on Recombinase Polymerase Amplification with H-Sandwich Aptamers. Anal Chem 2020; 93:992-1000. [PMID: 33296598 DOI: 10.1021/acs.analchem.0c03822] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The detection of trace protein biomarkers is essential in the diagnostic field. Protein detection systems ranging from widely used enzyme-linked immunosorbent assays to simple, inexpensive approaches, such as lateral flow immunoassays, play critical roles in medical and drug research. Despite continuous progress, current systems are insufficient for the diagnosis of diseases that require high sensitivity. In this study, we developed a heterogeneous sandwich-type sensing platform based on recombinase polymerase amplification using DNA aptamers specific to the target biomarker. Only the DNA bound to the target in the form of a heterogeneous sandwich was selectively amplified, and the fluorescence signal of an intercalating dye added before the amplification reaction was detected, thereby enabling high specificity and sensitivity. We applied this method for the detection of protein biomarkers for various infectious diseases including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and observed attomolar-level detection of biomarkers and low cross-reactivity between different viruses. We also confirmed detection efficiency of the proposed method using clinical samples. These results demonstrate that the proposed sensing platform can be used to diagnose various diseases requiring high sensitivity, specificity, and accuracy.
Collapse
Affiliation(s)
- Juyoung Kang
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Hyungjun Jang
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Gyuho Yeom
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Min-Gon Kim
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| |
Collapse
|
15
|
Establishment of Recombinase Polymerase Amplification assay for rapid and sensitive detection of Orientia tsutsugamushi in Southeast Asia. Acta Trop 2020; 210:105541. [PMID: 32492397 DOI: 10.1016/j.actatropica.2020.105541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 11/20/2022]
Abstract
Scrub typhus, caused by Orientia tsutsugamushi, is a common fever in parts of Southern and Southeast Asia. As delayed diagnosis of scrub typhus leads to inappropriate treatment and high mortality rates, of up to 70%, sensitive and rapid detection of O. tsutsugamushi is required for timely and appropriate treatment. Molecular assays, such as PCR and real-time PCR, have been shown to be more sensitive than conventional immunoassay, however, they are only available in centralized laboratories. In contrast to PCR assays, Recombinase Polymerase Amplification (RPA) is conducted under a constant temperature ranging from 24°C to 45°C. Therefore, this technology is very promising for nucleic acid testing in the field, and in resource-limited areas. An RPA assay for the detection of O. tsutsugamushi based on the target gene encoding for the 47 kDa outer membrane protein has been reported, but the primer and probe sequences of this assay are suboptimal for detection of the majority of recently published sequences of O. tsutsugamushi isolates from Southeast Asia. We have established a real-time RPA assay with primer and probe sequences that are optimized for most Southeast Asia's isolates of O. tsutsugamushi. As a result, the new RPA assay showed better performance than the previous assay in detecting O. tsutsugamushi in clinical samples of scrub typhus cases found in Vietnam. The specificity of RPA assay was also evaluated using genomic DNA from microorganisms commonly encountered in the differential diagnosis of scrub typhus, and blood samples from healthy controls and O. tsutsugamushi negative confirmed cases.
Collapse
|
16
|
Single universal primer recombinase polymerase amplification-based lateral flow biosensor (SUP-RPA-LFB) for multiplex detection of genetically modified maize. Anal Chim Acta 2020; 1127:217-224. [PMID: 32800127 DOI: 10.1016/j.aca.2020.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 04/26/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022]
Abstract
In this study, an isothermal paper biosensor, combining single universal primer recombinase polymerase amplification (SUP-RPA) and the lateral flow technique was developed for the multiplex detection of genetically modified maize (GMM). In pre-amplification stage, the event-specific primers contain a universal sequence at the 5' end, with a biotin-labeled deoxycytidine triphosphate (dCTP) deoxynucleotide providing additional amplification, which improves their amplification ability and ensures consistent multiplex amplification efficiency. In the signal recognition strategy, the SUP-RPA products are identified visually using the lateral flow biosensor (LFB) through dual hybridization. The accumulation of gold nanoparticles (AuNPs) produces a characteristic red band. Through this biosensor, a limit of detection of at least 50 copies was achieved, which is sensitive enough to detect MON810, MON863 and MON89034 simultaneously. The entire process of analysis was completed within 30 min and without any large-scale instrumentation. This biosensor, therefore, provides a novel rapid and portable multiple detection method for point-of-care applications, especially genetically modified organism (GMO) event-specific detection.
Collapse
|
17
|
Multi-cycle signal-amplified colorimetric detection of tobramycin based on dual-strand displacement and three-way DNA junction. Microchem J 2020. [DOI: 10.1016/j.microc.2020.104823] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
18
|
Wang Y, Jin M, Chen G, Cui X, Zhang Y, Li M, Liao Y, Zhang X, Qin G, Yan F, Abd El-Aty A, Wang J. Bio-barcode detection technology and its research applications: A review. J Adv Res 2019; 20:23-32. [PMID: 31193255 PMCID: PMC6522771 DOI: 10.1016/j.jare.2019.04.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/11/2022] Open
Abstract
With the rapid development of nanotechnology, the bio-barcode assay (BCA), as a new diagnostic tool, has been gradually applied to the detection of protein and nucleic acid targets and small-molecule compounds. BCA has the advantages of high sensitivity, short detection time, simple operation, low cost, good repeatability and good linear relationship between detection results. However, bio-barcode technology is not yet fully formed as a complete detection system, and the detection process in all aspects and stages is unstable. Therefore, studying the optimal reaction conditions, optimizing the experimental steps, exploring the multi-residue detection of small-molecule substances, and preparing immuno-bio-barcode kits are important research directions for the standardization and commercialization of BCA. The main theme of this review was to describe the principle of BCA, provide a comparison of its application, and introduce the single-residue and multi-residue detection of macromolecules and single-residue detection of small molecules. We also compared it with other detection methods, summarized its feasibility and limitations, expecting that with further improvement and development, the technique can be more widely used in the field of stable small-molecule and multi-residue detection.
Collapse
Affiliation(s)
- Yuanshang Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Maojun Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Ge Chen
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Xueyan Cui
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Yudan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Mingjie Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Yun Liao
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Xiuyuan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| | - Guoxin Qin
- Agro-products Quality Safety and Testing Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, PR China
| | - Feiyan Yan
- Agro-products Quality Safety and Testing Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, PR China
| | - A.M. Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, 25240 Erzurum, Turkey
| | - Jing Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-Product Quality and Safety, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing 100081, PR China
| |
Collapse
|
19
|
Chen Z, Huang J, Zhang F, Zhou Y, Huang H. Detection of shrimp hemocyte iridescent virus by recombinase polymerase amplification assay. Mol Cell Probes 2019; 49:101475. [PMID: 31655105 DOI: 10.1016/j.mcp.2019.101475] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/27/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Shrimp hemocyte iridescent virus (SHIV), which was first identified in white leg shrimp (Litopenaeus vannamei) in China in 2014, can cause extensive shrimp mortality and major economic losses in the shrimp farming industry in China. In this study, a novel real-time isothermal recombinase polymerase amplification (RPA) assay was developed using a TwistAmp exo kit for SHIV detection. First, five primers and a probe were designed for the major capsid protein gene (GenBank: KY681039.1) according to the TwistDx manual; next, the optimal primers were selected by a comparison experiment. The primers and probe were specific for SHIV and did not react with shrimp white spot syndrome virus (WSSV), shrimp infectious hypodermal and hematopoietic necrosis virus (IHHNV), shrimp enterocytozoon hepatopenaei (EHP), and macrobrachium rosenbergii nodavirus (MrNV) samples, as well as pathogens of acute hepatopancreatic necrosis disease (AHPND). The RPA assay reached a detection limit of 11 copies per reaction according to probit regression analysis. In addition, RPA assay detected the positive plasmid samples at concentration of 1000 copies/μL within 16.04 ± 0.72 min at a single low operation temperature (39 °C). The results proved that the proposed RPA method was an accurate, sensitive, affordable, and rapid detection tool that can be suitably applied for the diagnosis of SHIV in field conditions and in resource-poor settings.
Collapse
Affiliation(s)
- Zhengwei Chen
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China; Center of Engineering Training, Zhejiang University of Science and Technology, Hangzhou, P.R. China.
| | - Jun Huang
- College of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Fang Zhang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China.
| | - Yang Zhou
- College of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Huijie Huang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China.
| |
Collapse
|
20
|
Cytochrome c: An extreme multifunctional protein with a key role in cell fate. Int J Biol Macromol 2019; 136:1237-1246. [DOI: 10.1016/j.ijbiomac.2019.06.180] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/25/2023]
|
21
|
Screening DNA-targeted anticancer drug in vitro based on cancer cells DNA-templated silver nanoclusters. Sci Rep 2019; 9:8911. [PMID: 31222176 PMCID: PMC6586784 DOI: 10.1038/s41598-019-45523-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/03/2019] [Indexed: 01/10/2023] Open
Abstract
A reliable and sensitive cancer cells DNA-templated silver nanoclusters probe has been proposed for screening DNA-targeted anticancer drugs in vitro. In this paper, the DNA-templated silver nanoclusters was used to investigate the binding between anthracycline antibiotics and DNA. The template of DNA-templated silver nanoclusters was extracted from human liver carcinoma cells directly, which can express the drug activities against cancer cells more direct than the normal cells DNA. The anti-tumor activities of the four drugs were validated by MTT and apoptotic assay as Mitoxantrone > Epirubicin > Daunorubicin > Adriamycin.
Collapse
|
22
|
Cong H, Loo J, Chen J, Wang Y, Kong SK, Ho HP. Target trapping and in situ single-cell genetic marker detection with a focused optical beam. Biosens Bioelectron 2019; 133:236-242. [PMID: 30953882 DOI: 10.1016/j.bios.2019.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 01/01/2023]
Abstract
Optical trapping of single particles or cells with the capability of in situ bio-sensing or genetic profiling opens the possibility of rapid screening of biological specimens. However, common optical tweezers suffer from the lack of long-range forces. Consequently, their application areas are predominantly limited to target manipulation instead of biological diagnostics. To solve this problem, we herein report an all-in-one approach by combining optical forces and convective drag forces generated through localized optothermal effect for long-range target manipulation. The device consists of a 2D array of gold coated polydimethylsiloxane (PDMS) micro-wells, which are immersed by colloidal particles or cell solution. Upon excitation of a 785-nm laser, the hydrodynamic convective force and optical forces will drag the targets of interest into their designated micro-wells. Moreover, the plasmonic thermal dissipation provides a constant temperature environment for following cell analysis procedures of cell isolation, lysis and isothermal nucleic acid amplification for the detection of genetic markers. With the merits of fabrication simplicity, short sample-to-answer cycle time and the compatibility with optical microscopes, the reported technique offers an attractive and highly versatile approach for on-site single cell analysis systems.
Collapse
Affiliation(s)
- Hengji Cong
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Jacky Loo
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China; Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Jiajie Chen
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
| | - Yuye Wang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Siu-Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
23
|
Chung Y, Lee J, Jung S, Lee Y, Cho JW, Oh YJ. Dysregulated autophagy contributes to caspase-dependent neuronal apoptosis. Cell Death Dis 2018; 9:1189. [PMID: 30538224 PMCID: PMC6289995 DOI: 10.1038/s41419-018-1229-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/29/2018] [Accepted: 11/20/2018] [Indexed: 02/08/2023]
Abstract
Autophagy is a regulated, intracellular degradation process that delivers unnecessary or dysfunctional cargo to the lysosome. Autophagy has been viewed as an adaptive survival response to various stresses, whereas in other cases, it promotes cell death. Therefore, both deficient and excessive autophagy may lead to cell death. In this study, we specifically attempted to explore whether and how dysregulated autophagy contributes to caspase-dependent neuronal cell death induced by the neurotoxin 6-hydroxydopamine (6-OHDA). Ultrastructural and biochemical analyses indicated that MN9D neuronal cells and primary cultures of cortical neurons challenged with 6-OHDA displayed typical features of autophagy. Cotreatment with chloroquine and monitoring autophagic flux by a tandem mRFP-EGFP-tagged LC3 probe indicated that the autophagic phenomena were primarily caused by dysregulated autophagic flux. Consequently, cotreatment with an antioxidant but not with a pan-caspase inhibitor significantly blocked 6-OHDA-stimulated dysregulated autophagy. These results indicated that 6-OHDA-induced generation of reactive oxygen species (ROS) played a critical role in triggering neuronal death by causing dysregulated autophagy and subsequent caspase-dependent apoptosis. The results of the MTT reduction, caspase-3 activation, and TUNEL assays indicated that pharmacological inhibition of autophagy using 3-methyladenine or deletion of the autophagy-related gene Atg5 significantly inhibited 6-OHDA-induced cell death. Taken together, our results suggest that abnormal induction of autophagic flux promotes apoptotic neuronal cell death, and that the treatments limiting dysregulated autophagy may have a strong neuroprotective potential.
Collapse
Affiliation(s)
- Yuhyun Chung
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul, 120-749, South Korea
| | - Juhyung Lee
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul, 120-749, South Korea
| | - Shinae Jung
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul, 120-749, South Korea
| | - Yangsin Lee
- Glycosylation Network Research Center, Yonsei University, Seoul, 120-749, South Korea
| | - Jin Won Cho
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul, 120-749, South Korea.,Glycosylation Network Research Center, Yonsei University, Seoul, 120-749, South Korea.,Interdisciplinary Program of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, 120-749, South Korea
| | - Young J Oh
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul, 120-749, South Korea.
| |
Collapse
|
24
|
Duan Y, Yuan T, Xu Y, Zhao M, Guo B, Cheng W, Ding S. Detection of BCR/ABL Fusion Gene Based on MNAzyme-mediated Target-cycling and ssDNA-assisted Cascade Hybridization Reaction. ELECTROANAL 2018. [DOI: 10.1002/elan.201800254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yu Duan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education); College of Laboratory Medicine, Chongqing Medical University; Chongqing 400016 China
| | - Taixian Yuan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education); College of Laboratory Medicine, Chongqing Medical University; Chongqing 400016 China
| | - Yongjie Xu
- Department of Laboratory Medicine; Guizhou Provincial People's Hospital; Guiyang 550002 China
| | - Min Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education); College of Laboratory Medicine, Chongqing Medical University; Chongqing 400016 China
| | - Bin Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education); College of Laboratory Medicine, Chongqing Medical University; Chongqing 400016 China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection; The First Affiliated Hospital of Chongqing Medical University; Chongqing 400016 China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education); College of Laboratory Medicine, Chongqing Medical University; Chongqing 400016 China
| |
Collapse
|
25
|
Goux HJ, Chavan D, Crum M, Kourentzi K, Willson RC. Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay. Front Cell Infect Microbiol 2018; 8:237. [PMID: 30050871 PMCID: PMC6052657 DOI: 10.3389/fcimb.2018.00237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/20/2018] [Indexed: 01/03/2023] Open
Abstract
Changes in the population levels of specific bacterial species within the gut microbiome have been linked to a variety of illnesses. Most assays that determine the relative abundance of specific taxa are based on amplification and sequencing of stable phylogenetic gene regions. Such lab-based analysis requires pre-analytical sample preservation and storage that have been shown to introduce biases in the characterization of microbial profiles. Recombinase polymerase amplification (RPA) is an isothermal nucleic acid amplification method that employs commercially available, easy-to-use freeze-dried enzyme pellets that can be used to analyze specimens rapidly in the field or clinic, using a portable fluorometer. Immediate analysis of diverse bacterial communities can lead to a more accurate quantification of relative bacterial abundance. In this study, we discovered that universal bacterial 16S ribosomal DNA primers give false-positive signals in RPA analysis because manufacturing host Escherichia coli DNA is present in the RPA reagents. The manufacturer of RPA reagents advises against developing an RPA assay that detects the presence of E. coli due to the presence of contaminating E. coli DNA in the reaction buffer (www.twistdx.co.uk/). We, therefore, explored four strategies to deplete or fragment extraneous DNA in RPA reagents while preserving enzyme activity: metal-chelate affinity chromatography, sonication, DNA cleavage using methylation-dependent restriction endonucleases, and DNA depletion using anti-DNA antibodies. Removing DNA with anti-DNA antibodies enabled the development of a quantitative RPA microbiome assay capable of determining the relative abundance of the physiologically-important bacterium Akkermansia muciniphila in human feces.
Collapse
Affiliation(s)
- Heather J Goux
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Dimple Chavan
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Mary Crum
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Richard C Willson
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States.,Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States.,Tecnológico de Monterrey-ITESM Campus Monterrey, Monterrey, Mexico
| |
Collapse
|
26
|
Liu Y, Wang XY, Wei XM, Gao ZT, Han JP. Rapid Authentication of Ginkgo biloba Herbal Products Using the Recombinase Polymerase Amplification Assay. Sci Rep 2018; 8:8002. [PMID: 29789688 PMCID: PMC5964079 DOI: 10.1038/s41598-018-26402-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/14/2018] [Indexed: 12/27/2022] Open
Abstract
Species adulteration in herbal products (HPs) exposes consumers to health risks. Chemical and morphological methods have their own deficiencies when dealing with the detection of species containing the same active compounds in HPs. In this study, we developed a rapid identification method using the recombinase polymerase amplification (RPA) assay to detect two species, Ginkgo biloba and Sophora japonica (as adulteration), in Ginkgo biloba HPs. Among 36 Ginkgo biloba HP samples, 34 were found to have Ginkgo biloba sequences, and 9 were found to have Sophora japonica sequences. During the authentication process, the RPA-LFS assay showed a higher specificity, sensitivity and efficiency than PCR-based methods. We initially applied the RPA-LSF technique to detect plant species in HPs, demonstrating that this assay can be developed into an efficient tool for the rapid on-site authentication of plant species in Ginkgo biloba HPs.
Collapse
Affiliation(s)
- Yang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiao-Yue Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xue-Min Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Zi-Tong Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jian-Ping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| |
Collapse
|
27
|
Automated real-time detection of drug-resistant Mycobacterium tuberculosis on a lab-on-a-disc by Recombinase Polymerase Amplification. Anal Biochem 2018; 544:98-107. [DOI: 10.1016/j.ab.2017.12.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/26/2017] [Accepted: 12/29/2017] [Indexed: 12/12/2022]
|
28
|
Shahin K, Gustavo Ramirez-Paredes J, Harold G, Lopez-Jimena B, Adams A, Weidmann M. Development of a recombinase polymerase amplification assay for rapid detection of Francisella noatunensis subsp. orientalis. PLoS One 2018; 13:e0192979. [PMID: 29444148 PMCID: PMC5812721 DOI: 10.1371/journal.pone.0192979] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/01/2018] [Indexed: 11/18/2022] Open
Abstract
Francisella noatunensis subsp. orientalis (Fno) is the causative agent of piscine francisellosis in warm water fish including tilapia. The disease induces chronic granulomatous inflammation with high morbidity and can result in high mortality. Early and accurate detection of Fno is crucial to set appropriate outbreak control measures in tilapia farms. Laboratory detection of Fno mainly depends on bacterial culture and molecular techniques. Recombinase polymerase amplification (RPA) is a novel isothermal technology that has been widely used for the molecular diagnosis of various infectious diseases. In this study, a recombinase polymerase amplification (RPA) assay for rapid detection of Fno was developed and validated. The RPA reaction was performed at a constant temperature of 42°C for 20 min. The RPA assay was performed using a quantitative plasmid standard containing a unique Fno gene sequence. Validation of the assay was performed not only by using DNA from Fno, closely related Francisella species and other common bacterial pathogens in tilapia farms, but also by screening 78 Nile tilapia and 5 water samples. All results were compared with those obtained by previously established real-time qPCR. The developed RPA showed high specificity in detection of Fno with no cross-detection of either the closely related Francisella spp. or the other tested bacteria. The Fno-RPA performance was highly comparable to the published qPCR with detection limits at 15 and 11 DNA molecules detected, respectively. The RPA gave quicker results in approximately 6 min in contrast to the qPCR that needed about 90 min to reach the same detection limit, taking only 2.7–3 min to determine Fno in clinical samples. Moreover, RPA was more tolerant to reaction inhibitors than qPCR when tested with field samples. The fast reaction, simplicity, cost-effectiveness, sensitivity and specificity make the RPA an attractive diagnostic tool that will contribute to controlling the infection through prompt on-site detection of Fno.
Collapse
Affiliation(s)
- Khalid Shahin
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
- Aquatic Animal Diseases Lab, Division of Aquaculture, National Institute of Oceanography and Fisheries, Suez, Egypt
- * E-mail:
| | - Jose Gustavo Ramirez-Paredes
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Graham Harold
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Benjamin Lopez-Jimena
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Alexandra Adams
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Manfred Weidmann
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| |
Collapse
|
29
|
Mayboroda O, Katakis I, O'Sullivan CK. Multiplexed isothermal nucleic acid amplification. Anal Biochem 2018; 545:20-30. [PMID: 29353064 DOI: 10.1016/j.ab.2018.01.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/14/2022]
Abstract
Multiplexed isothermal amplification and detection of nucleic acid sequences and biomarkers is of increasing importance in diverse areas including advanced diagnostics, food quality control and environmental monitoring. Whilst there are several very elegant isothermal amplification approaches, multiplexed amplification remains a challenge, requiring careful experimental design and optimisation, from judicious primer design in order to avoid the formation of primer dimers and non-specific amplification, applied temperature as well as the ratio and concentration of primers. In this review, we describe the various approaches that have been reported to date for multiplexed isothermal amplification, for both "one-pot" multiplexing as well as parallelised multiplexing using loop-mediated isothermal amplification, strand-displacement amplification, helicase-dependent amplification, rolling circle amplification, nucleic acid sequence-based amplification, with a particular focus on recombinase polymerase amplification.
Collapse
Affiliation(s)
- Olena Mayboroda
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ioanis Katakis
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain.
| | - Ciara K O'Sullivan
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain.
| |
Collapse
|
30
|
Dao TNT, Lee EY, Koo B, Jin CE, Lee TY, Shin Y. A microfluidic enrichment platform with a recombinase polymerase amplification sensor for pathogen diagnosis. Anal Biochem 2017; 544:87-92. [PMID: 29289485 DOI: 10.1016/j.ab.2017.12.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 02/06/2023]
Abstract
Rapid and sensitive detection of low amounts of pathogen in large samples is needed for early diagnosis and treatment of patients and surveillance of pathogen. In this study, we report a microfluidic platform for detection of low pathogen levels in a large sample volume that couples an Magainin 1 based microfluidic platform for pathogen enrichment and a recombinase polymerase amplification (RPA) sensor for simultaneous pathogenic DNA amplification and detection in a label-free and real-time manner. Magainin 1 is used as a pathogen enrichment agent with a herringbone microfluidic chip. Using this enrichment platform, the detection limit was found to be 20 times more sensitive in 10 ml urine with Salmonella and 10 times more sensitive in 10 ml urine with Brucella than that of real-time PCR without the enrichment process. Furthermore, the combination system of the enrichment platform and an RPA sensor that based on an isothermal DNA amplification method with rapidity and sensitivity for detection can detect a pathogen at down to 50 CFU in 10 ml urine for Salmonella and 102 CFU in 10 ml urine for Brucella within 60 min. This system will be useful as it has the potential for better diagnosis of pathogens by increasing the capture efficiency of the pathogen in large samples, subsequently enhancing the detection limit of pathogenic DNA.
Collapse
Affiliation(s)
- Thuy Nguyen Thi Dao
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Tae Yoon Lee
- Department of Technology Education and Department of Biomedical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea.
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul 05505, Republic of Korea.
| |
Collapse
|
31
|
Hou P, Zhao G, Wang H, He C, Huan Y, He H. Development of a recombinase polymerase amplification combined with lateral-flow dipstick assay for detection of bovine ephemeral fever virus. Mol Cell Probes 2017; 38:31-37. [PMID: 29288049 PMCID: PMC7126596 DOI: 10.1016/j.mcp.2017.12.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/07/2017] [Accepted: 12/19/2017] [Indexed: 11/18/2022]
Abstract
Bovine ephemeral fever virus (BEFV), identified as the causative pathogen of bovine ephemeral fever (BEF), is responsible for increasing numbers of epidemics/outbreaks and has a significant harmful effect on the livestock industry. Therefore, a rapid detection assay is imperative for BEFV diagnosis. In this study, we described the development of lateral-flow dipstick isothermal recombinase polymerase amplification (LFD-RPA) assays for detection of BEFV. RPA primers and LF probes were designed by targeting the specific G gene, and the amplification product can be visualized on a simple lateral flow dipstick with the naked eyes. The amplification reaction was performed at 38 °C for 20 min and LFD incubation time within 5 min. The detection limit of this assay was 8 copies per reaction, and there was no cross-reactivity with other bovine infectious viruses such as bovine viral diarrhea virus, infectious bovine rhinotracheitis virus, bovine respiratory syncytial virus, bovine coronavirus, bovine parainfluenza virus type 3, bovine vesicular stomatitis virus. In addition, the assay was performed with total 128 clinical specimens and the diagnostic results were compared with conventional RT-PCR, real-time quantative(q) PCR. The result showed that the coincidence rate of BEFV LFD-RPA and real-time qPCR was 96.09% (123/128), which was higher than conventional RT-PCR. The RPA combined with LFD assay probably provides a rapid and sensitive alternative for diagnosis of BEFV infections outbreak. RPA combined with LFD assay was developed first time to detect BEFV. The detection from cDNA could be completed within 30 min and be easily visualized with the naked eyes. The RPA combined with LFD assay probably provides a alternative for diagnosis of BEFV.
Collapse
Affiliation(s)
- Peili Hou
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
| | - Guimin Zhao
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
| | - Hongmei Wang
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
| | - Chengqiang He
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
| | - Yanjun Huan
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.
| | - Hongbin He
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China.
| |
Collapse
|
32
|
An Assay Using Localized Surface Plasmon Resonance and Gold Nanorods Functionalized with Aptamers to Sense the Cytochrome-c Released from Apoptotic Cancer Cells for Anti-Cancer Drug Effect Determination. MICROMACHINES 2017; 8:mi8110338. [PMID: 30400530 PMCID: PMC6190337 DOI: 10.3390/mi8110338] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/31/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022]
Abstract
To determine the degree of cancer cell killing after treatment with chemotherapeutic drugs, we have developed a sensitive platform using localized surface plasmon resonance (LSPR) and aptamers to detect the extracellular cytochrome-c (cyto-c), a mitochondrial protein released from cancer cells for the induction of apoptosis after treatment, to evaluate the effectiveness of cancer therapy. In this assay, a short single-stranded 76-mer DNA aptamer with a unique DNA sequence, which binds towards the cyto-c like an antibody with a high binding affinity and specificity, was conjugated to gold nanorods (AuNR) for LSPR sensing. Practically, cyto-c was first grabbed by a capturing antibody functionalized on the surface of micro-magnetic particles (MMPs). Subsequently, the AuNR-conjugated aptamer was added to form a complex sandwich structure with cyto-c (i.e., (MMP-Ab)-(cyto-c)-(AuNR-aptamer)) after washing away the non-target impurities, such as serum residues and intracellular contents, in a microfluidic chip. The sandwich complex led to formation of AuNR aggregates, which changed the LSPR signals in relation to the amount of cyto-c. With the LSPR signal enhancement effects from the AuNRs, the detection limit of cyto-c, sparked in human serum or culture medium, was found to be 0.1 ng/mL in our platform and the whole sensing process could be completed within two hours. Moreover, we have applied this assay to monitor the apoptosis in leukemia cancer cells induced by a potential anti-cancer agent phenylarsine oxide.
Collapse
|
33
|
Abstract
Recombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37-42°C, with minimal sample preparation and capable of amplifying as low as 1-10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.
Collapse
Affiliation(s)
- Ivan Magriñá Lobato
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain
| | - Ciara K O'Sullivan
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
| |
Collapse
|
34
|
Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| |
Collapse
|
35
|
Loo J, Yang C, Tsang HL, Lau PM, Yong KT, Ho HP, Kong SK. An Aptamer Bio-barCode (ABC) assay using SPR, RNase H, and probes with RNA and gold-nanorods for anti-cancer drug screening. Analyst 2017; 142:3579-3587. [PMID: 28852760 DOI: 10.1039/c7an01026e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With modifications to an ultra-sensitive bio-barcode (BBC) assay, we have developed a next generation aptamer-based bio-barcode (ABC) assay to detect cytochrome-c (Cyto-c), a cell death marker released from cancer cells, for anti-cancer drug screening. An aptamer is a short single-stranded DNA selected from a synthetic DNA library that is capable of binding to its target with high affinity and specificity based on its unique DNA sequence and 3D structure after folding. Similar to the BBC assay, Cyto-c is captured by a micro-magnetic particle (MMP) coated with capturing antibodies (Ab) and an aptamer specifically against Cyto-c to form sandwich structures ([MMP-Ab]-[Cyto-c]-[Aptamer]). After washing and melting, our aptamers, acting as a DNA bio-barcode, are released from the sandwiches and hybridized with the probes specially designed for RNase H for surface plasmon resonance (SPR) sensing. In an aptamer-probe duplex, RNase H digests the RNA in the probe and releases the intact aptamer for another round of hybridization and digestion. With signal enhancement effects from gold-nanorods (Au-NRs) on probes for SPR sensing, the detection limit was found to be 1 nM for the aptamer and 80 pM for Cyto-c. Without the time-consuming DNA amplification steps by PCR, the detection process of this new ABC assay can be completed within three hours. As a proof-of-concept, phenylarsine oxide was found to be a potent agent to kill liver cancer cells with multi-drug resistance at the nano-molar level. This approach thus provides a fast, sensitive and robust tool for anti-cancer drug screening.
Collapse
Affiliation(s)
- Jacky Loo
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Chengbin Yang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore
| | - Hing Lun Tsang
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
| | - Pui Man Lau
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
| | - Ken-Tye Yong
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore
| | - Ho Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Siu Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
| |
Collapse
|
36
|
Giuffrida MC, Spoto G. Integration of isothermal amplification methods in microfluidic devices: Recent advances. Biosens Bioelectron 2017; 90:174-186. [DOI: 10.1016/j.bios.2016.11.045] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 01/02/2023]
|
37
|
Manickam P, Kaushik A, Karunakaran C, Bhansali S. Recent advances in cytochrome c biosensing technologies. Biosens Bioelectron 2016; 87:654-668. [PMID: 27619529 DOI: 10.1016/j.bios.2016.09.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 11/27/2022]
Abstract
This review is an attempt, for the first time, to describe advancements in sensing technology for cytochrome c (cyt c) detection, at point-of-care (POC) application. Cyt c, a heme containing metalloprotein is located in the intermembrane space of mitochondria and released into bloodstream during pathological conditions. The release of cyt c from mitochondria is a key initiative step in the activation of cell death pathways. Circulating cyt c levels represents a novel in-vivo marker of mitochondrial injury after resuscitation from heart failure and chemotherapy. Thus, cyt c detection is not only serving as an apoptosis biomarker, but also is of great importance to understand certain diseases at cellular level. Various existing techniques such as enzyme-linked immunosorbent assays (ELISA), Western blot, high performance liquid chromatography (HPLC), spectrophotometry and flow cytometry have been used to estimate cyt c. However, the implementation of these techniques at POC application is limited due to longer analysis time, expensive instruments and expertise needed for operation. To overcome these challenges, significant efforts are being made to develop electrochemical biosensing technologies for fast, accurate, selective, and sensitive detection of cyt c. Presented review describes the cutting edge technologies available in the laboratories to detect cyt c. The recent advancements in designing and development of electrochemical cyt c biosensors for the quantification of cyt c are also discussed. This review also highlights the POC cyt c biosensors developed recently, that would prove of interest to biologist and therapist to get real time informatics needed to evaluate death process, diseases progression, therapeutics and processes related with mitochondrial injury.
Collapse
Affiliation(s)
- Pandiaraj Manickam
- Bio-MEMS and Microsystems Laboratory, Department of Electrical and Computer Engineering, Florida International University, Miami, FL, USA.
| | - Ajeet Kaushik
- Center for Personalized Nanomedicine, Institute of Neuro immune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Chandran Karunakaran
- Biomedical Research Laboratory, Department of Chemistry, VHNSN College (Autonomous), Virudhunagar, Tamil Nadu, India
| | - Shekhar Bhansali
- Bio-MEMS and Microsystems Laboratory, Department of Electrical and Computer Engineering, Florida International University, Miami, FL, USA
| |
Collapse
|
38
|
Bin N, Li W, Yin X, Huang X, Cai Q. Electrochemiluminescence aptasensor of TiO2/CdS:Mn hybrids for ultrasensitive detection of cytochrome c. Talanta 2016; 160:570-576. [PMID: 27591652 DOI: 10.1016/j.talanta.2016.07.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/25/2022]
Abstract
A novel electrochemiluminescence (ECL) aptasensor was proposed for ultrasensitive detection of cytochrome c (cyt c) using CdS:Mn quantum dot-modified TiO2 nanowires (NWs) as electrode. The Mn-doped CdS was deposited on the TiO2 NWs by successive ion layer adsorption and reaction (SILAR) as ECL emitter, on which thiol-modified aptamer of cyt c was attached via Cd-S bond. Due to the high photo-electrical transfer efficiency, the as-prepared aptasensor shows high selectivity and sensitivity towards cyt c with a detection limit of 9.5fM and a linear range from 50fM to 125pM.
Collapse
Affiliation(s)
- Na Bin
- State Key Lab of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Weili Li
- State Key Lab of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Xuehua Yin
- State Key Lab of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Xiaohua Huang
- State Key Lab of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Qingyun Cai
- State Key Lab of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China.
| |
Collapse
|
39
|
Electrochemical detection of Piscirickettsia salmonis genomic DNA from salmon samples using solid-phase recombinase polymerase amplification. Anal Bioanal Chem 2016; 408:8611-8620. [PMID: 27220649 DOI: 10.1007/s00216-016-9639-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
Abstract
Electrochemical detection of solid-phase isothermal recombinase polymerase amplification (RPA) of Piscirickettsia salmonis in salmon genomic DNA is reported. The electrochemical biosensor was constructed by surface functionalization of gold electrodes with a thiolated forward primer specific to the genomic region of interest. Solid-phase RPA and primer elongation were achieved in the presence of the specific target sequence and biotinylated reverse primers. The formation of the subsequent surface-tethered duplex amplicons was electrochemically monitored via addition of streptavidin-linked HRP upon completion of solid-phase RPA. Successful quantitative amplification and detection were achieved in less than 1 h at 37 °C, calibrating with PCR-amplified genomic DNA standards and achieving a limit of detection of 5 · 10-8 μg ml-1 (3 · 103 copies in 10 μl). The presented system was applied to the analysis of eight real salmon samples, and the method was also compared to qPCR analysis, observing an excellent degree of correlation. Graphical abstract Schematic of use of electrochemical RPA for detection of Psiricketessia salmonis in salmon liver.
Collapse
|
40
|
Daher RK, Stewart G, Boissinot M, Bergeron MG. Recombinase Polymerase Amplification for Diagnostic Applications. Clin Chem 2016; 62:947-58. [PMID: 27160000 PMCID: PMC7108464 DOI: 10.1373/clinchem.2015.245829] [Citation(s) in RCA: 390] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/15/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND First introduced in 2006, recombinase polymerase amplification (RPA) has stirred great interest, as evidenced by 75 publications as of October 2015, with 56 of them just in the last 2 years. The widespread adoption of this isothermal molecular tool in many diagnostic fields represents an affordable (approximately 4.3 USD per test), simple (few and easy hands-on steps), fast (results within 5–20 min), and sensitive (single target copy number detected) method for the identification of pathogens and the detection of single nucleotide polymorphisms in human cancers and genetically modified organisms. CONTENT This review summarizes the current knowledge on RPA. The molecular diagnostics of various RNA/DNA pathogens is discussed while highlighting recent applications in clinical settings with focus on point-of-care (POC) bioassays and on automated fluidic platforms. The strengths and limitations of this isothermal method are also addressed. SUMMARY RPA is becoming a molecular tool of choice for the rapid, specific, and cost-effective identification of pathogens. Owing to minimal sample-preparation requirements, low operation temperature (25–42 °C), and commercial availability of freeze-dried reagents, this method has been applied outside laboratory settings, in remote areas, and interestingly, onboard automated sample-to-answer microfluidic devices. RPA is undoubtedly a promising isothermal molecular technique for clinical microbiology laboratories and emergence response in clinical settings.
Collapse
Affiliation(s)
- Rana K Daher
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City (Québec), Canada
| | - Gale Stewart
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada
| | - Maurice Boissinot
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada
| | - Michel G Bergeron
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City (Québec), Canada.
| |
Collapse
|
41
|
Spengler M, Adler M, Niemeyer CM. Highly sensitive ligand-binding assays in pre-clinical and clinical applications: immuno-PCR and other emerging techniques. Analyst 2016. [PMID: 26196036 DOI: 10.1039/c5an00822k] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recombinant DNA technology and corresponding innovations in molecular biology, chemistry and medicine have led to novel therapeutic biomacromolecules as lead candidates in the pharmaceutical drug development pipelines. While monoclonal antibodies and other proteins provide therapeutic potential beyond the possibilities of small molecule drugs, the concomitant demand for supportive bioanalytical sample testing creates multiple novel challenges. For example, intact macromolecules can usually not be quantified by mass-spectrometry without enzymatic digestion and isotopically labeled internal standards are costly and/or difficult to prepare. Classical ELISA-type immunoassays, on the other hand, often lack the sensitivity required to obtain pharmacokinetics of low dosed drugs or pharmacodynamics of suitable biomarkers. Here we summarize emerging state-of-the-art ligand-binding assay technologies for pharmaceutical sample testing, which reveal enhanced analytical sensitivity over classical ELISA formats. We focus on immuno-PCR, which combines antibody specificity with the extremely sensitive detection of a tethered DNA marker by quantitative PCR, and alternative nucleic acid-based technologies as well as methods based on electrochemiluminescence or single-molecule counting. Using case studies, we discuss advantages and drawbacks of these methods for preclinical and clinical sample testing.
Collapse
Affiliation(s)
- Mark Spengler
- Chimera Biotec GmbH, Emil-Figge-Str. 76 A, D-44227 Dortmund, Germany.
| | | | | |
Collapse
|
42
|
Shamsipur M, Molaabasi F, Hosseinkhani S, Rahmati F. Detection of Early Stage Apoptotic Cells Based on Label-Free Cytochrome c Assay Using Bioconjugated Metal Nanoclusters as Fluorescent Probes. Anal Chem 2016; 88:2188-97. [DOI: 10.1021/acs.analchem.5b03824] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mojtaba Shamsipur
- Department of Chemistry, Razi University, 67149-67346, Kermanshah, Iran
| | - Fatemeh Molaabasi
- Department of Chemistry, Tarbiat Modares University, 14115-111, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biology, Tarbiat Modares University, 14115-111, Tehran, Iran
| | - Fereshteh Rahmati
- Department of Biology, Tarbiat Modares University, 14115-111, Tehran, Iran
| |
Collapse
|
43
|
A novel graphene nanodots inlaid porous gold electrode for electrochemically controlled drug release. Talanta 2016; 147:184-92. [DOI: 10.1016/j.talanta.2015.09.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/05/2015] [Accepted: 09/07/2015] [Indexed: 11/23/2022]
|
44
|
Aptamers as Synthetic Receptors for Food Quality and Safety Control. BIOSENSORS FOR SUSTAINABLE FOOD - NEW OPPORTUNITIES AND TECHNICAL CHALLENGES 2016. [DOI: 10.1016/bs.coac.2016.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
45
|
James A, Macdonald J. Recombinase polymerase amplification: Emergence as a critical molecular technology for rapid, low-resource diagnostics. Expert Rev Mol Diagn 2015; 15:1475-89. [PMID: 26517245 DOI: 10.1586/14737159.2015.1090877] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Isothermal molecular diagnostics are bridging the technology gap between traditional diagnostics and polymerase chain reaction-based methods. These new techniques enable timely and accurate testing, especially in settings where there is a lack of infrastructure to support polymerase chain reaction facilities. Despite this, there is a significant lack of uptake of these technologies in developing countries where they are highly needed. Among these novel isothermal technologies, recombinase polymerase amplification (RPA) holds particular potential for use in developing countries. This rapid nucleic acid amplification approach is fast, highly sensitive and specific, and amenable to countries with a high burden of infectious diseases. Implementation of RPA technology in developing countries is critically required to assess limitations and potentials of the diagnosis of infectious disease, and may help identify impediments that prevent adoption of new molecular technologies in low resource- and low skill settings. This review focuses on approaching diagnosis of infectious disease with RPA.
Collapse
Affiliation(s)
- Ameh James
- a 1 Genecology Research Centre, Inflammation and Healing Research Cluster, School of Science and Engineering, University of the Sunshine Coast , Queensland, Australia.,b 2 Keystone Laboratories International, Kuje, FCT , Abuja, Nigeria
| | - Joanne Macdonald
- a 1 Genecology Research Centre, Inflammation and Healing Research Cluster, School of Science and Engineering, University of the Sunshine Coast , Queensland, Australia.,c 3 Division of Experimental Therapeutics, Department of Medicine, Columbia University , NY, USA
| |
Collapse
|
46
|
Clancy E, Higgins O, Forrest MS, Boo TW, Cormican M, Barry T, Piepenburg O, Smith TJ. Development of a rapid recombinase polymerase amplification assay for the detection of Streptococcus pneumoniae in whole blood. BMC Infect Dis 2015; 15:481. [PMID: 26515409 PMCID: PMC4625855 DOI: 10.1186/s12879-015-1212-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/13/2015] [Indexed: 01/02/2023] Open
Abstract
Background Streptococcus pneumoniae is an important cause of microbial disease in humans. The introduction of multivalent vaccines has coincided with a dramatic decrease in the number of pneumococcal-related deaths. In spite of this, at a global level, pneumococcal infection remains an important cause of death among children under 5 years of age and in adults 65 years of age or older. In order to properly manage patients and control the spread of infection, a rapid and highly sensitive diagnostic method is needed for routine implementation, especially in resource-limited regions where pneumococcal disease is most prevalent. Methods Using the gene encoding leader peptidase A as a molecular diagnostics target, a real-time RPA assay was designed and optimised for the detection of S. pneumoniae in whole blood. The performance of the assay was compared to real-time PCR in terms of its analytical limit of detection and specificity. The inhibitory effect of human genomic DNA on amplification was investigated. The potential clinical utility of the assay was investigated using a small number of clinical samples. Results The RPA assay has a limit of detection equivalent to PCR (4.0 and 5.1 genome equivalents per reaction, respectively) and was capable of detecting the equivalent of <1 colony forming unit of S. pneumoniae when spiked into human whole blood. The RPA assay was 100 % inclusive (38/38 laboratory reference strains and 19/19 invasive clinical isolates) and 100 % exclusive; differentiating strains of S. pneumoniae species from other viridans group streptococci, including S. pseudopneumoniae. When applied to the analysis of a small number (n = 11) of clinical samples (blood culture positive for S. pneumoniae), the RPA assay was demonstrated to be both rapid and sensitive. Conclusions The RPA assay developed in this work is shown to be as sensitive and as specific as PCR. In terms of reaction kinetics, the RPA assay is shown to exceed those of the PCR, with the RPA running to completion in 20 minutes and capable generating a positive signal in as little as 6 minutes. This work represents a potentially suitable assay for application in point-of-care settings.
Collapse
Affiliation(s)
- Eoin Clancy
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland. .,Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| | - Owen Higgins
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland. .,Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| | | | - Teck Wee Boo
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland. .,School of Medicine, National University of Ireland , Galway, Ireland.
| | - Martin Cormican
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland. .,School of Medicine, National University of Ireland , Galway, Ireland.
| | - Thomas Barry
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland. .,Nucleic Acids Diagnostics Research Laboratory, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.
| | | | - Terry J Smith
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland. .,Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| |
Collapse
|
47
|
Crannell ZA, Rohrman B, Richards-Kortum R. Development of a quantitative recombinase polymerase amplification assay with an internal positive control. J Vis Exp 2015:52620. [PMID: 25867513 PMCID: PMC4401391 DOI: 10.3791/52620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to quantify DNA sample concentration using a standard curve. In this manuscript, a detailed protocol for developing and implementing a real-time quantitative recombinase polymerase amplification assay (qRPA assay) is provided. Using HIV-1 DNA quantification as an example, the assembly of real-time RPA reactions, the design of an internal positive control (IPC) sequence, and co-amplification of the IPC and target of interest are all described. Instructions and data processing scripts for the construction of a standard curve using data from multiple experiments are provided, which may be used to predict the concentration of unknown samples or assess the performance of the assay. Finally, an alternative method for collecting real-time fluorescence data with a microscope and a stage heater as a step towards developing a point-of-care qRPA assay is described. The protocol and scripts provided may be used for the development of a qRPA assay for any DNA target of interest.
Collapse
|
48
|
Yin X, Cai J, Feng H, Wu Z, Zou J, Cai Q. A novel VS2nanosheet-based biosensor for rapid fluorescence detection of cytochrome c. NEW J CHEM 2015. [DOI: 10.1039/c4nj01971g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A VS2/aptamer-based cytochromecsensor was successfully constructed by first applying the DNA-adsorbing ability/fluorescence-quenching properties of VS2in bioanalysis.
Collapse
Affiliation(s)
- Xuehua Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Jin Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Hongyan Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Zeming Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Jianmei Zou
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| | - Qingyun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha 410082
- China
| |
Collapse
|
49
|
Sharma N, Hoshika S, Hutter D, Bradley KM, Benner SA. Recombinase-based isothermal amplification of nucleic acids with self-avoiding molecular recognition systems (SAMRS). Chembiochem 2014; 15:2268-74. [PMID: 25209570 PMCID: PMC7162014 DOI: 10.1002/cbic.201402250] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Indexed: 12/27/2022]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal method to amplify nucleic acid sequences without the temperature cycling that classical PCR uses. Instead of using heat to denature the DNA duplex, RPA uses recombination enzymes to swap single-stranded primers into the duplex DNA product; these are then extended using a strand-displacing polymerase to complete the cycle. Because RPA runs at low temperatures, it never forces the system to recreate base-pairs following Watson-Crick rules, and therefore it produces undesired products that impede the amplification of the desired product, complicating downstream analysis. Herein, we show that most of these undesired side products can be avoided if the primers contain components of a self-avoiding molecular recognition system (SAMRS). Given the precision that is necessary in the recombination systems for them to function biologically, it is surprising that they accept SAMRS. SAMRS-RPA is expected to be a powerful tool within the range of amplification techniques available to scientists.
Collapse
Affiliation(s)
- Nidhi Sharma
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville FL 32604 (USA)
| | | | | | | | | |
Collapse
|
50
|
Daher RK, Stewart G, Boissinot M, Bergeron MG. Isothermal Recombinase Polymerase Amplification Assay Applied to the Detection of Group B Streptococci in Vaginal/Anal Samples. Clin Chem 2014; 60:660-6. [DOI: 10.1373/clinchem.2013.213504] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Group B streptococcal infections are the leading cause of sepsis and meningitis in newborns. A rapid and reliable method for the detection of this pathogen at the time of delivery is needed for the early treatment of neonates. Isothermal amplification techniques such as recombinase polymerase amplification have advantages relative to PCR in terms of the speed of reaction and simplicity.
METHODS
We studied the clinical performance of recombinase polymerase amplification for the screening of group B streptococci in vaginal/anal samples from 50 pregnant women. We also compared the limit of detection and the analytical specificity of this isothermal assay to real-time PCR (RT-PCR).
RESULTS
Compared to RT-PCR, the recombinase polymerase amplification assay showed a clinical sensitivity of 96% and a clinical specificity of 100%. The limit of detection was 98 genome copies and the analytical specificity was 100% for a panel of 15 bacterial and/or fungal strains naturally found in the vaginal/anal flora. Time-to-result for the recombinase polymerase amplification assay was <20 min compared to 45 min for the RT-PCR assay; a positive sample could be detected as early as 8 min.
CONCLUSIONS
We demonstrate the potential of isothermal recombinase polymerase amplification assay as a clinically useful molecular diagnostic tool that is simple and faster than PCR/RT-PCR. Recombinase polymerase amplification offers great potential for nucleic acid–based diagnostics at the point of care.
Collapse
Affiliation(s)
- Rana K Daher
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), Quebec, Canada
- Département de microbiologie-immunologie, faculté de médecine, Université Laval, Quebec, Canada
| | - Gale Stewart
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), Quebec, Canada
| | - Maurice Boissinot
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), Quebec, Canada
| | - Michel G Bergeron
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), Quebec, Canada
| |
Collapse
|