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Kou HS, Wang CC. Molecular inversion probes equipped with discontinuous rolling cycle amplification for targeting nucleotide variants: Determining SMN1 and SMN2 genes in diagnosis of spinal muscular atrophy. Anal Chim Acta 2017; 977:65-73. [PMID: 28577599 DOI: 10.1016/j.aca.2017.04.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 10/19/2022]
Abstract
The novel techniques of molecular inversion probes (MIPs) combined with discontinuous rolling cycle amplification (DRCA) was developed for determination of the multi-nucleotide variants at single base. The different-length MIPs, a padlock-probe based technology, are designed to simultaneously recognize the identical nucleotide variants. After ligation and DRCA, the different-length genetic products representing the certain genotypes could be simply determined by the short-end capillary electrophoresis (CE) method. By using MIPs-DRCA method, the various gene dosages of SMN1 and SMN2 genes in homologous or heterologous subjects were successfully quantified for diagnosis of spinal muscular atrophy (SMA). The length of the MIP for SMN1 gene was 106 bp, and for SMN2 gene was 86 bp. After method optimization, the MIP products of SMN1 and SMN2 were well separated with the resolution of 1.13 ± 0.17 (n = 3) within 10 min. There were total of 56 DNA blind samples analyzed by this strategy, including 38 wild types, 12 carriers and 6 SMA patients, and the data of gene dosages was corresponding to those analyzed by conformation sensitive CE and denatured high performance liquid chromatography (DHPLC) methods. This MIPs-DRCA method which could be applied to simultaneously genotype multi nucleotide variants at single base, such as K-ras gene, was very feasible for determination of genetic diseases in clinical.
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Affiliation(s)
- Hwang-Shang Kou
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.
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2
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Nie B, Yang M, Fu W, Liang Z. Surface invasive cleavage assay on a maskless light-directed diamond DNA microarray for genome-wide human SNP mapping. Analyst 2016; 140:4549-57. [PMID: 25996555 DOI: 10.1039/c5an00349k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The surface invasive cleavage assay, because of its innate accuracy and ability for self-signal amplification, provides a potential route for the mapping of hundreds of thousands of human SNP sites. However, its performance on a high density DNA array has not yet been established, due to the unusual "hairpin" probe design on the microarray and the lack of chemical stability of commercially available substrates. Here we present an applicable method to implement a nanocrystalline diamond thin film as an alternative substrate for fabricating an addressable DNA array using maskless light-directed photochemistry, producing the most chemically stable and biocompatible system for genetic analysis and enzymatic reactions. The surface invasive cleavage reaction, followed by degenerated primer ligation and post-rolling circle amplification is consecutively performed on the addressable diamond DNA array, accurately mapping SNP sites from PCR-amplified human genomic target DNA. Furthermore, a specially-designed DNA array containing dual probes in the same pixel is fabricated by following a reverse light-directed DNA synthesis protocol. This essentially enables us to decipher thousands of SNP alleles in a single-pot reaction by the simple addition of enzyme, target and reaction buffers.
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Affiliation(s)
- Bei Nie
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Shuitu Town, Beibei District, Chongqing, 400714, P. R. China.
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3
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Lockett MR, Smith LM. Carbon Substrates: A Stable Foundation for Biomolecular Arrays. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:263-285. [PMID: 26048550 PMCID: PMC6287745 DOI: 10.1146/annurev-anchem-071114-040146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Since their advent in the early 1990s, microarray technologies have developed into a powerful and ubiquitous platform for biomolecular analysis. Microarrays consist of three major elements: the substrate upon which they are constructed, the chemistry employed to attach biomolecules, and the biomolecules themselves. Although glass substrates and silane-based attachment chemistries are used for the vast majority of current microarray platforms, these materials suffer from severe limitations in stability, due to hydrolysis of both the substrate material itself and of the silyl ether linkages employed for attachment. These limitations in stability compromise assay performance and render impossible many potential microarray applications. We describe here a suite of alternative carbon-based substrates and associated attachment chemistries for microarray fabrication. The substrates themselves, as well as the carbon-carbon bond-based attachment chemistries, offer greatly increased chemical stability, enabling a myriad of novel applications.
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Affiliation(s)
- Matthew R Lockett
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599;
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4
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Wang D, Tang W, Wu X, Wang X, Chen G, Chen Q, Li N, Liu F. Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction. Anal Chem 2012; 84:7008-14. [PMID: 22830619 DOI: 10.1021/ac301064g] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Toehold-mediated strand displacement reaction (SDR) is first introduced to develop a simple quartz crystal microbalance (QCM) biosensor without an enzyme or label at normal temperature for highly selective and sensitive detection of single-nucleotide polymorphism (SNP) in the p53 tumor suppressor gene. A hairpin capture probe with an external toehold is designed and immobilized on the gold electrode surface of QCM. A successive SDR is initiated by the target sequence hybridization with the toehold domain and ends with the unfolding of the capture probe. Finally, the open-loop capture probe hybridizes with the streptavidin-coupled reporter probe as an efficient mass amplifier to enhance the QCM signal. The proposed biosensor displays remarkable specificity to target the p53 gene fragment against single-base mutant sequences (e.g., the largest discrimination factor is 63 to C-C mismatch) and high sensitivity with the detection limit of 0.3 nM at 20 °C. As the crucial component of the fabricated biosensor for providing the high discrimination capability, the design rationale of the capture probe is further verified by fluorescence sensing and atomic force microscopy imaging. Additionally, a recovery of 84.1% is obtained when detecting the target sequence in spiked HeLa cells lysate, demonstrating the feasibility of employing this biosensor in detecting SNPs in biological samples.
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Affiliation(s)
- Dingzhong Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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5
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Frisk ML, Tepp WH, Johnson EA, Beebe DJ. Self-assembled peptide monolayers as a toxin sensing mechanism within arrayed microchannels. Anal Chem 2009; 81:2760-7. [PMID: 19253949 PMCID: PMC2760437 DOI: 10.1021/ac802707u] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A sensor for the lethal bacterial enzyme, botulinum neurotoxin type A (BoNT/A), was developed using self-assembled monolayers (SAMs). SAMs consisting of an immobilized synthetic peptide that mimicked the toxin's in vivo SNAP-25 protein substrate were formed on Au and interfaced with arrayed microfluidic channels. Efforts to optimize SAM composition and assay conditions for greatest reaction efficiency and sensitivity are described in detail. Channel design provided facile fluid manipulation, sample incubation, analyte concentration, and fluorescence detection all within a single microfluidic channel, thus avoiding sample transfer and loss. Peptide SAMs were exposed to varying concentrations of BoNT/A or its catalytic light chain (ALC), resulting in enzymatic cleavage of the peptide substrate from the surface. Fluorescence detection was achieved down to 20 pg/mL ALC and 3 pg/mL BoNT/A in 3 h. Toxin sensing was also accomplished in vegetable soup, demonstrating practicality of the method. The modular design of this microfluidic SAM platform allows for extension to sensing other toxins that operate via enzymatic cleavage, such as the remaining BoNT serotypes B-G, anthrax, and tetanus toxin.
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Affiliation(s)
- Megan L. Frisk
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - William H. Tepp
- Department of Food Microbiology and Toxicology, Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
| | - Eric A. Johnson
- Department of Food Microbiology and Toxicology, Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
| | - David J. Beebe
- Department of Biomedical Engineering, University of Wisconsin, Madison, Wisconsin 53706
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6
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Vainrub A, Deluge N, Zhang X, Zhou X, Gao X. Predicting DNA duplex stability on oligonucleotide arrays. Methods Mol Biol 2008; 382:393-403. [PMID: 18220244 DOI: 10.1007/978-1-59745-304-2_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
DNA duplex stability on oligonucleotide microarray was calculated using recently developed electrostatic theory of on-array hybridization thermodynamics. In this method, the first step is to finding the enthalpy and entropy of duplex formation in solution. This standard calculation was done with nearest-neighbor scheme and on-line software. Next the defined parameters and the array's single characteristic, the surface density of probes, are used to predict on-array duplex melting behavior. Reasonable accords of calculated and experimental melting curves for in situ synthesized microfluidic array were observed. The proposed method could be useful in microarray design and hybridization optimization. However, lack of melting curve measurements for different microarray platforms makes more experiments desirable to determine the method's accuracy.
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Affiliation(s)
- Arnold Vainrub
- College of Veterinary Medicine, Auburn University, AL, USA
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Phillips MF, Lockett MR, Rodesch MJ, Shortreed MR, Cerrina F, Smith LM. In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication. Nucleic Acids Res 2007; 36:e7. [PMID: 18084027 PMCID: PMC2248760 DOI: 10.1093/nar/gkm1103] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Glass has become the standard substrate for the preparation of DNA arrays. Typically, glass is modified using silane chemistries to provide an appropriate functional group for nucleic acid synthesis or oligonucleotide immobilization. We have found substantial issues with the stability of these surfaces as manifested in the unwanted release of oligomers from the surface when incubated in aqueous buffers at moderate temperatures. To address this issue, we have explored the use of carbon-based substrates. Here, we demonstrate in situ synthesis of oligonucleotide probes on carbon-based substrates using light-directed photolithographic phosphoramidite chemistry and evaluate the stabilities of the resultant DNA arrays compared to those fabricated on silanized glass slides. DNA arrays on carbon-based substrates are substantially more stable than arrays prepared on glass. This superior stability enables the use of high-density DNA arrays for applications involving high temperatures, basic conditions, or where serial hybridization and dehybridization is desired.
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Affiliation(s)
- Margaret F Phillips
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave. Madison, Madison, WI 53706, USA
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Li N, Mei L, Xiang Y, Tong A, Nishizawa S, Teramae N. Fluorescence detection of single-nucleotide polymorphisms with two simple and low cost methods: A double-DNA-probe method and a bulge form method. Anal Chim Acta 2007; 597:97-102. [PMID: 17658318 DOI: 10.1016/j.aca.2007.06.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 06/08/2007] [Accepted: 06/14/2007] [Indexed: 11/16/2022]
Abstract
Two 10-mer DNA probes, or one 20-mer DNA probe, respectively, hybridize with a 21-mer target DNA to form a vacancy or bulge opposite the target nucleotide. The former double-DNA-probe method and the latter bulge form method are applicable to the detection of single-nucleotide polymorphisms (SNPs). A small fluorescent dye enters into the vacancy or bulge and binds with a target nucleotide via a hydrogen bonding interaction, which causes fluorescence quenching. The interaction between fluorescent dye and the target nucleotide is confirmed by measuring the melting temperature and fluorescence spectra. The fluorescent dye, ADMND (2-amino-5,7-dimethyl-1,8-naphthyridine), is found to selectively bind with C over A or G. The methods proposed here are economic, convenient, and effective for the fluorescence detection of SNPs. Finally, the double-DNA-probe method and bulge form method are successfully applied to the detection of C/G and C/A mutations in the estrogen receptor 2 gene and progesterone receptor gene using ADMND.
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Affiliation(s)
- Na Li
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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9
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Nie B, Shortreed MR, Smith LM. Quantitative detection of individual cleaved DNA molecules on surfaces using gold nanoparticles and scanning electron microscope imaging. Anal Chem 2007; 78:1528-34. [PMID: 16503604 PMCID: PMC2533858 DOI: 10.1021/ac052067g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are the most frequent type of human genetic variation. Recent work has shown that it is possible to directly analyze SNPs in unamplified human genomic DNA samples using the surface-invasive cleavage reaction followed by rolling circle amplification (RCA) labeling of the cleavage products. The individual RCA amplicon molecules were counted on the surface using fluorescence microscopy. Two principal limitations of such single-molecule counting are the variability in the amplicon size, which results in a large variation in fluorescence signal intensity from the dye-labeled DNA molecules, and a high level of background fluorescence. It is shown here that an excellent alternative to RCA labeling is tagging with gold nanoparticles followed by imaging with a scanning electron microscope. Gold nanoparticles have a uniform diameter (15 +/- 0.5 nm) and provide excellent contrast against the background of the silicon substrate employed. Individual gold nanoparticles are readily counted using publicly available software. The results demonstrate that the labeling efficiency is improved by as much as approximately 15-fold, and the signal-to-noise ratio is improved by approximately 4-fold. Detection of individual cleaved DNA molecules following surface-invasive cleavage was linear and quantitative over 3 orders of magnitude in amount of target DNA (10(-18)-10(-15) mol).
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Affiliation(s)
| | | | - Lloyd M. Smith
- To whom correspondence should be addressed. Phone: (608) 262-9207. Fax: (608) 265-6780. E-mail: . Internet: http://www.chem.wisc.edu/~smith
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Thoeni S, Kressierer C, Giese B. Selektiver DNA-Strangbruch an fester Phase – eine Methode zur Detektion von Basenfehlpaarungen. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Thoeni S, Kressierer CJ, Giese B. Site-Specific DNA Cleavage on a Solid Support: A Method for Mismatch Detection. Angew Chem Int Ed Engl 2007; 46:2112-4. [PMID: 17278170 DOI: 10.1002/anie.200603092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sandra Thoeni
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
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12
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Special-Purpose Modifications and Immobilized Functional Nucleic Acids for Biomolecular Interactions. Top Curr Chem (Cham) 2005. [DOI: 10.1007/b136673] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Abstract
The Invader assay uses a structure-specific flap endonuclease (FEN) to cleave a three-dimensional complex formed by hybridization of allele-specific overlapping oligonucleotides to target DNA containing a single nucleotide polymorphism (SNP) site. Annealing of the oligonucleotide complementary to the SNP allele in the target molecule triggers the cleavage of the oligonucleotide by cleavase, a thermostable FEN. Cleavage can be detected by several different approaches. Most commonly, the cleavage product triggers a secondary cleavage reaction on a fluorescence resonance energy transfer (FRET) cassette to release a fluorescent signal. Alternatively, the cleavage can be detected directly by use of fluorescence polarization (FP) probes, or by mass spectrometry. The invasive cleavage reaction is highly specific, has a low failure rate, and can detect zeptomol quantities of target DNA. While the assay traditionally has been used to interrogate one SNP in one sample per reaction, novel chip- or bead-based approaches have been tested to make this efficient and accurate assay adaptable to multiplexing and high-throughput SNP genotyping.
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Affiliation(s)
- Michael Olivier
- Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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Mishima K, Takarada T, Maeda M. Capillary electrophoretic discrimination of single nucleotide polymorphisms using an oligodeoxyribonucleotidepolyacrylamide conjugate as a pseudo-immobilized affinity ligand: optimum ligand length predicted by the melting temperature values. ANAL SCI 2005; 21:25-9. [PMID: 15675511 DOI: 10.2116/analsci.21.25] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We developed a weak-affinity separation system for single-nucleotide polymorphisms (SNPs) based on capillary electrophoresis. In this approach, single-stranded DNA (ssDNA)-polyacrylamide (polyAAm) conjugate was used as a pseudo-immobilized affinity ligand to separate the target DNA, cytochrome P450 2C9 (CYP2C9), and its point mutant. The ligand DNA was designed to be complementary to the normal DNA, and the target DNA was electrophoretically separated by the difference in the affinity with the pseudo-immobilized ligand in the capillary. We showed that the separation efficiency was closely associated with the Tm value of double-stranded DNA (dsDNA) consisting of the target and ligand DNA, which depends on the measurement conditions, such as the base number of the ligand DNA and the concentration of Mg2+ in the buffer solution.
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Affiliation(s)
- Keiko Mishima
- Bioengineering Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan
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15
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Gooding JJ, King GC. Nucleic acid biosensors based upon surface-assembled monolayers: exploiting and enhancing materials properties. ACTA ACUST UNITED AC 2005. [DOI: 10.1039/b506602f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Vainrub A, Pettitt BM. Theoretical aspects of genomic variation screening using DNA microarrays. Biopolymers 2004; 73:614-20. [PMID: 15048785 DOI: 10.1002/bip.20008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We present a theoretical model for typical microarray-based single nucleotide polymorphism (SNP) assay of small genomic DNA amount. We derived the adsorption isotherm expressing the on-array hybridization efficiency in terms of genomic target sequence and concentration, oligonucleotide probe sequence and surface density, hybridization buffer, and temperature. This isotherm correctly describes the surface probe density effects, the sensitivity peak, and the melting temperature depression, and is in accord with published experiments. We discuss optimization of parallel SNP genotyping. Our estimates show that SNP detection at a single temperature in aqueous hybridization buffer is restricted by DNA regions that differ by less than 20% in GC content. We predict that the variety of genotyped SNPs could be substantially extended using an assay design with high probe density and a large fraction of probes hybridized.
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Affiliation(s)
- Arnold Vainrub
- Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA
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Lu M, Knickerbocker T, Cai W, Yang W, Hamers RJ, Smith LM. Invasive cleavage reactions on DNA-modified diamond surfaces. Biopolymers 2004; 73:606-13. [PMID: 15048784 DOI: 10.1002/bip.20007] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recently developed DNA-modified diamond surfaces exhibit excellent chemical stability to high-temperature incubations in biological buffers. The stability of these surfaces is substantially greater than that of gold or silicon surfaces, using similar surface attachment chemistry. The DNA molecules attached to the diamond surfaces are accessible to enzymes and can be modified in surface enzymatic reactions. An important application of these surfaces is for surface invasive cleavage reactions, in which target DNA strands added to the solution may result in specific cleavage of surface-bound probe oligonucleotides, permitting analysis of single nucleotide polymorphisms (SNPs). Our previous work demonstrated the feasibility of performing such cleavage reactions on planar gold surfaces using PCR-amplified human genomic DNA as target. The sensitivity of detection in this earlier work was substantially limited by a lack of stability of the gold surface employed. In the present work, detection sensitivity is improved by a factor of approximately 100 (100 amole of DNA target compared with 10 fmole in the earlier work) by replacing the DNA-modified gold surface with a more stable DNA-modified diamond surface.
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Affiliation(s)
- Manchun Lu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1396, USA
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18
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Demidov VV. Invader assay goes on surface. Trends Biotechnol 2002. [DOI: 10.1016/s0167-7799(02)02067-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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