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Angeli E, Buzio R, Firpo G, Magrassi R, Mussi V, Repetto L, Valbusa U. Nanotechnology Applications in Medicine. TUMORI JOURNAL 2018; 94:206-15. [DOI: 10.1177/030089160809400213] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In recent years there has been a rapid increase in nanotechnology applications to medicine in order to prevent and treat diseases in the human body. The established and future applications have the potential to dramatically change medical science. The present paper will give a few examples that could transform common medical procedures.
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Affiliation(s)
- Elena Angeli
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Renato Buzio
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Giuseppe Firpo
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Raffaella Magrassi
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Valentina Mussi
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Luca Repetto
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
| | - Ugo Valbusa
- NanoMed Labs, Centro di Biotecnologie Avanzate CBA and Dipartimento di Fisica dell'Università di Genova, Genoa, Italy
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Huang M, Tu J, Lu Z. Recent Advances in Experimental Whole Genome Haplotyping Methods. Int J Mol Sci 2017; 18:E1944. [PMID: 28891974 PMCID: PMC5618593 DOI: 10.3390/ijms18091944] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 01/06/2023] Open
Abstract
Haplotype plays a vital role in diverse fields; however, the sequencing technologies cannot resolve haplotype directly. Pioneers demonstrated several approaches to resolve haplotype in the early years, which was extensively reviewed. Since then, numerous methods have been developed recently that have significantly improved phasing performance. Here, we review experimental methods that have emerged mainly over the past five years, and categorize them into five classes according to their maximum scale of contiguity: (i) encapsulation, (ii) 3D structure capture and construction, (iii) compartmentalization, (iv) fluorography, (v) long-read sequencing. Several subsections of certain methods are attached to each class as instances. We also discuss the relative advantages and disadvantages of different classes and make comparisons among representative methods of each class.
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Affiliation(s)
- Mengting Huang
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Jing Tu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zuhong Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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Fan TW, Yu HLL, Hsing IM. Conditional Displacement Hybridization Assay for Multiple SNP Phasing. Anal Chem 2017; 89:9961-9966. [DOI: 10.1021/acs.analchem.7b02300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tsz Wing Fan
- Department
of Chemical and Biomolecular Engineering and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henson L. Lee Yu
- Department
of Chemical and Biomolecular Engineering and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - I-Ming Hsing
- Department
of Chemical and Biomolecular Engineering and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Lee J, Kim Y, Lee S, Jo K. Visualization of large elongated DNA molecules. Electrophoresis 2015; 36:2057-71. [PMID: 25994517 DOI: 10.1002/elps.201400479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/08/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022]
Abstract
Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Yongkyun Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
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Abstract
Human genomes are diploid and, for their complete description and interpretation, it is necessary not only to discover the variation they contain but also to arrange it onto chromosomal haplotypes. Although whole-genome sequencing is becoming increasingly routine, nearly all such individual genomes are mostly unresolved with respect to haplotype, particularly for rare alleles, which remain poorly resolved by inferential methods. Here, we review emerging technologies for experimentally resolving (that is, 'phasing') haplotypes across individual whole-genome sequences. We also discuss computational methods relevant to their implementation, metrics for assessing their accuracy and completeness, and the relevance of haplotype information to applications of genome sequencing in research and clinical medicine.
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Han R, Li Z, Fan Y, Jiang Y. Recent Advances in Super-Resolution Fluorescence Imaging and Its Applications in Biology. J Genet Genomics 2013; 40:583-95. [DOI: 10.1016/j.jgg.2013.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/11/2013] [Accepted: 11/11/2013] [Indexed: 11/16/2022]
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A dual-mode single-molecule fluorescence assay for the detection of expanded CGG repeats in Fragile X syndrome. Mol Biotechnol 2013; 53:19-28. [PMID: 22311273 DOI: 10.1007/s12033-012-9505-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fragile X syndrome is the leading cause of inherited mental impairment and is associated with expansions of CGG repeats within the FMR1 gene. To detect expanded CGG repeats, we developed a dual-mode single-molecule fluorescence assay that allows acquisition of two parallel, independent measures of repeat number based on (1) the number of Cy3-labeled probes bound to the repeat region and (2) the physical length of the electric field-linearized repeat region, obtained from the relative position of a single Cy5 dye near the end of the repeat region. Using target strands derived from cell-line DNA with defined numbers of CGG repeats, we show that this assay can rapidly and simultaneously measure the repeats of a collection of individual sample strands within a single field of view. With a low occurrence of false positives, the assay differentiated normal CGG repeat lengths (CGG( N ), N = 23) and expanded CGG repeat lengths (CGG( N ), N = 118), representing a premutation disease state. Further, mixtures of these DNAs gave results that correlated with their relative populations. This strategy may be useful for identifying heterozygosity or for screening collections of individuals, and it is readily adaptable for screening other repeat disorders.
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Baday M, Cravens A, Hastie A, Kim H, Kudeki DE, Kwok PY, Xiao M, Selvin PR. Multicolor super-resolution DNA imaging for genetic analysis. NANO LETTERS 2012; 12:3861-6. [PMID: 22698062 PMCID: PMC3880789 DOI: 10.1021/nl302069q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Many types of cancer and neurodegenerative diseases are caused by abnormalities and variations in the genome. We have designed a high-resolution imaging technique with high throughput and low cost for determining structural variations of genes related to genetic diseases. We initially mapped all seven nicking sites of Nb.BbvCI endonuclease enzyme on lambda DNA. Then we resolved densely labeled patterns of 107 nicking sites on human BAC DNA that is digested by Nb.BsmI and Nb.BbvCI endonuclease enzymes. This high density resulted in several dyes being closer together than the diffraction limit. Overall, detailed DNA nicking sites mapping with 100 bp resolution was achieved, which has the potential to reveal information about genetic variance and to facilitate medical diagnosis of several genetic diseases.
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Affiliation(s)
- Murat Baday
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aaron Cravens
- Physics Dept, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Alex Hastie
- Center for Physics of the Living Cell, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - HyeongJun Kim
- Physics Dept, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Deren E. Kudeki
- Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pui-Yan Kwok
- Institute of Human Genetics, University of California, San Francisco, San Francisco, California, United States
| | - Ming Xiao
- Center for Physics of the Living Cell, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Corresponding Author: (P.R.S.) Telephone: (217) 244-3371. Fax: (217) 244-7559. . (M.X) Telephone: (267)499-2021. Fax: (215) 966-6001.
| | - Paul R. Selvin
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Physics Dept, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- BioNano Genomics Inc., San Diego, California 92121, United States
- Corresponding Author: (P.R.S.) Telephone: (217) 244-3371. Fax: (217) 244-7559. . (M.X) Telephone: (267)499-2021. Fax: (215) 966-6001.
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Zohar H, Muller SJ. Labeling DNA for single-molecule experiments: methods of labeling internal specific sequences on double-stranded DNA. NANOSCALE 2011; 3:3027-39. [PMID: 21734993 PMCID: PMC3322637 DOI: 10.1039/c1nr10280j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review is a practical guide for experimentalists interested in specifically labeling internal sequences on double-stranded (ds) DNA molecules for single-molecule experiments. We describe six labeling approaches demonstrated in a single-molecule context and discuss the merits and drawbacks of each approach with particular attention to the amount of specialized training and reagents required. By evaluating each approach according to criteria relevant to single-molecule experiments, including labeling yield and compatibility with cofactors such as Mg(2+), we provide a simple reference for selecting a labeling method for given experimental constraints. Intended for non-specialists seeking accessible solutions to DNA labeling challenges, the approaches outlined emphasize simplicity, robustness, suitability for use by non-biologists, and utility in diverse single-molecule experiments.
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Affiliation(s)
- Hagar Zohar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
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Xu W, Muller SJ. Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping. LAB ON A CHIP 2011; 11:435-42. [PMID: 21072428 PMCID: PMC3322636 DOI: 10.1039/c0lc00176g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We demonstrate the feasibility of a single-molecule microfluidic approach to both sequence detection and obtaining kinetic information for restriction endonucleases on dsDNA. In this method, a microfluidic stagnation point flow is designed to trap, hold, and linearize double-stranded (ds) genomic DNA to which a restriction endonuclease has been pre-bound sequence-specifically. By introducing the cofactor magnesium, we determine the binding location of the enzyme by the cleavage process of dsDNA as in optical restriction mapping, however here the DNA need not be immobilized on a surface. We note that no special labeling of the enzyme is required, which makes it simpler than our previous scheme using stagnation point flows for sequence detection. Our accuracy in determining the location of the recognition site is comparable to or better than other single molecule techniques due to the fidelity with which we can control the linearization of the DNA molecules. In addition, since the cleavage process can be followed in real time, information about the cleavage kinetics, and subtle differences in binding and cleavage frequencies among the recognition sites, may also be obtained. Data for the five recognition sites for the type II restriction endonuclease EcoRI on λ-DNA are presented as a model system. While the roles of the varying fluid velocity and tension along the chain backbone on the measured kinetics remain to be determined, we believe this new method holds promise for a broad range of studies of DNA-protein interactions, including the kinetics of other DNA cleavage processes, the dissociation of a restriction enzyme from the cleaved substrate, and other macromolecular cleavage processes.
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Affiliation(s)
- Weilin Xu
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, CA 94720, U.S.A
| | - Susan J. Muller
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, CA 94720, U.S.A
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Zohar H, Hetherington CL, Bustamante C, Muller SJ. Peptide nucleic acids as tools for single-molecule sequence detection and manipulation. NANO LETTERS 2010; 10:4697-701. [PMID: 20923183 PMCID: PMC3322611 DOI: 10.1021/nl102986v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability to strongly and sequence-specifically attach modifications such as fluorophores and haptens to individual double-stranded (ds) DNA molecules is critical to a variety of single-molecule experiments. We propose using modified peptide nucleic acids (PNAs) for this purpose and implement them in two model single-molecule experiments where individual DNA molecules are manipulated via microfluidic flow and optical tweezers, respectively. We demonstrate that PNAs are versatile and robust sequence-specific tethers.
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Affiliation(s)
- Hagar Zohar
- Department of Chemical Engineering, California Institute for Quantitative Biosciences, and Howard Hughes Medical InstituteUniversity of California, Berkeley, California 94720, United States
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Dylla-Spears R, Townsend JE, Jen-Jacobson L, Sohn LL, Muller SJ. Single-molecule sequence detection via microfluidic planar extensional flow at a stagnation point. LAB ON A CHIP 2010; 10:1543-9. [PMID: 20358051 PMCID: PMC3322643 DOI: 10.1039/b926847b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We demonstrate the use of a microfluidic stagnation point flow to trap and extend single molecules of double-stranded (ds) genomic DNA for detection of target sequences along the DNA backbone. Mutant EcoRI-based fluorescent markers are bound sequence-specifically to fluorescently labeled ds lambda-DNA. The marker-DNA complexes are introduced into a microfluidic cross slot consisting of flow channels that intersect at ninety degrees. Buffered solution containing the marker-DNA complexes flows in one channel of the cross slot, pure buffer flows in the opposing channel at the same flow rate, and fluid exits the two channels at ninety degrees from the inlet channels. This creates a stagnation point at the center of a planar extensional flow, where marker-DNA complexes may be trapped and elongated along the outflow axis. The degree of elongation can be controlled using the flow strength (i.e., a non-dimensional flow rate) in the device. Both the DNA backbone and the markers bound along the stretched DNA are observed directly using fluorescence microscopy, and the location of the markers along the DNA backbone is measured. We find that our method permits detection of each of the five expected target site positions to within 1.5 kb with standard deviations of <1.5 kb. We compare the method's precision and accuracy at molecular extensions of 68% and 88% of the contour length to binding distributions from similar data obtained via molecular combing. We also provide evidence that increased mixing of the sample during binding of the marker to the DNA improves binding to internal target sequences of dsDNA, presumably by extending the DNA and making the internal binding sites more accessible.
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Abstract
Whole genome sequencing provides the most comprehensive collection of an individual's genetic variation. With the falling costs of sequencing technology, we envision paradigm shift from microarray-based genotyping studies to whole genome sequencing. We review methodologies for whole genome sequencing. There are two approaches for assembling short shotgun sequence reads into longer contiguous genomic sequences. In the de novo assembly approach, sequence reads are compared to each other, and then overlapped to build longer contiguous sequences. The reference-based assembly approach involves mapping each read to a reference genome sequence. We discuss methods for identifying genetic variation (single nucleotide polymorphisms, small indels, and copy number variants) and building haplotypes from genome assemblies, and discuss potential pitfalls. We expect methodologies to evolve rapidly as sequencing technologies improve and more human genomes are sequenced.
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Affiliation(s)
- Pauline C Ng
- The J. Craig Venter Institute, Rockville, MD, USA
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Abstract
DNA combing is a useful strategy for manipulating single DNA molecules and has a wide range of applications in genetics, single molecule studies, and nanobiotechnology. Visualization of combed DNA molecules is usually performed by using DNA binding organic dyes. Such dyes are not suitable in all circumstances, especially because of their photoreactivity. We have developed a method for the detection of combed DNA molecules by fluorescence microscopy that avoids the use of DNA-staining agents and does not perturb the structure of the DNA molecule. Biotin- and/or digoxigenin-modified DNA fragments are covalently linked at both ends of a DNA molecule via sequence-specific hybridization and subsequent ligation. After the modified DNA molecules have been combed on a polystyrene-coated surface, their ends are visualized by multicolor fluorescence microscopy using conjugated quantum dots.
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Xiao M, Wan E, Chu C, Hsueh WC, Cao Y, Kwok PY. Direct determination of haplotypes from single DNA molecules. Nat Methods 2009; 6:199-201. [PMID: 19198595 DOI: 10.1038/nmeth.1301] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 01/09/2009] [Indexed: 11/09/2022]
Abstract
Determining the long-range haplotypes in a diploid individual is a major technical challenge. Here we report a method of molecular haplotyping by directly imaging multiple polymorphic sites on individual human DNA molecules simultaneously. We demonstrate the utility of this technology by accurately determining the haplotypes consisting of up to 16 single-nucleotide polymorphisms in genomic regions up to 50 kilobases.
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Affiliation(s)
- Ming Xiao
- Cardiovascular Research Institute, University of California-San Francisco, 513 Parnassus Ave., San Francisco, CA 94143, USA.
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Four years of DNA barcoding: Current advances and prospects. INFECTION GENETICS AND EVOLUTION 2008; 8:727-36. [DOI: 10.1016/j.meegid.2008.05.005] [Citation(s) in RCA: 240] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 05/23/2008] [Accepted: 05/27/2008] [Indexed: 11/21/2022]
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Dapprich J, Ferriola D, Magira EE, Kunkel M, Monos D. SNP-specific extraction of haplotype-resolved targeted genomic regions. Nucleic Acids Res 2008; 36:e94. [PMID: 18611953 PMCID: PMC2528194 DOI: 10.1093/nar/gkn345] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The availability of genotyping platforms for comprehensive genetic analysis of complex traits has resulted in a plethora of studies reporting the association of specific single-nucleotide polymorphisms (SNPs) with common diseases or drug responses. However, detailed genetic analysis of these associated regions that would correlate particular polymorphisms to phenotypes has lagged. This is primarily due to the lack of technologies that provide additional sequence information about genomic regions surrounding specific SNPs, preferably in haploid form. Enrichment methods for resequencing should have the specificity to provide DNA linked to SNPs of interest with sufficient quality to be used in a cost-effective and high-throughput manner. We describe a simple, automated method of targeting specific sequences of genomic DNA that can directly be used in downstream applications. The method isolates haploid chromosomal regions flanking targeted SNPs by hybridizing and enzymatically elongating oligonucleotides with biotinylated nucleotides based on their selective binding to unique sequence elements that differentiate one allele from any other differing sequence. The targeted genomic region is captured by streptavidin-coated magnetic particles and analyzed by standard genotyping, sequencing or microarray analysis. We applied this technology to determine contiguous molecular haplotypes across a ∼150 kb genomic region of the major histocompatibility complex.
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Citations. Biotechniques 2007. [DOI: 10.2144/000112570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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