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Abdul Rashid JI, Yusof NA, Abdullah J, Shomiad Shueb RH. Strategies for the preparation of non-amplified and amplified genomic dengue gene samples for electrochemical DNA biosensing applications. RSC Adv 2021; 12:1-10. [PMID: 35424522 PMCID: PMC8978653 DOI: 10.1039/d1ra06753b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/25/2021] [Indexed: 11/21/2022] Open
Abstract
The application of electrochemical DNA biosensors in real genomic sample detection is challenging due to the existence of complex structures and low genomic concentrations, resulting in inconsistent and low current signals. This work highlights strategies for the treatment of non-amplified and amplified genomic dengue virus gene samples based on real samples before they can be used directly in our DNA electrochemical sensing system, using methylene blue (MB) as a redox indicator. The main steps in this study for preparing non-amplified cDNA were cDNA conversion, heat denaturation, and sonication. To prepare amplified cDNA dengue virus genomic samples using an RT-PCR approach, we optimized a few parameters, such as the annealing temperature, sonication time, and reverse to forward (R/F) primer concentration ratio. We discovered that the generated methylene blue (MB) signals during the electrochemical sensing of non-amplified and amplified samples differ due to the different MB binding affinities based on the sequence length and base composition. The findings show that our developed electrochemical DNA biosensor successfully discriminates MB current signals in the presence and absence of the target genomic dengue virus, indicating that both samples were successfully treated. This work also provides interesting information about the critical factors in the preparation of genomic gene samples for developing miniaturized PCR-based electrochemical sensing applications in the future. We also discuss the limitations and provide suggestions related to using redox-indicator-based electrochemical biosensors to detect real genomic nucleic acid genes.
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Affiliation(s)
- Jahwarhar Izuan Abdul Rashid
- Department of Chemistry and Biology, Centre for Defence Foundation Studies, National Defence University of Malaysia Sungai Besi Camp 57000 Kuala Lumpur Malaysia
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Jaafar Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Rafidah Hanim Shomiad Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 16150 Kubang Kerian Kelantan Malaysia
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Genetic and comparative mapping of Lupinus luteus L. highlight syntenic regions with major orthologous genes controlling anthracnose resistance and flowering time. Sci Rep 2020; 10:19174. [PMID: 33154532 PMCID: PMC7645761 DOI: 10.1038/s41598-020-76197-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/23/2020] [Indexed: 01/12/2023] Open
Abstract
Anthracnose susceptibility and ill-adapted flowering time severely affect Lupinus luteus yield, which has high seed protein content, is excellent for sustainable agriculture, but requires genetic improvement to fulfil its potential. This study aimed to (1) develop a genetic map; (2) define collinearity and regions of synteny with Lupinus angustifolius; and (3) map QTLs/candidate genes for anthracnose resistant and flowering time. A few linkage groups/genomic regions tended to be associated with segregation distortion, but did not affect the map. The developed map showed collinearity, and syntenic regions with L. angustifolius. Major QTLs were mapped in syntenic regions. Alleles from the wild parent and cultivar, explained 75% of the phenotypic variance for anthracnose resistance and 83% for early flowering, respectively. Marker sequences flanking the QTLs showed high homology with the Lanr1 gene and Flowering-locus-T of L. angustifolius. This suggests orthologous genes for both traits in the L. luteus genome. The findings are remarkable, revealing the potential to combine early flowering/anthracnose resistant in fulfilling yield capacity in L. luteus, and can be a major strategy in the genetic improvement and usage of this species for sustainable protein production. Allele sequences and PCR-marker tagging of these genes are being applied in marker assisted selection.
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Grímsson F, Graham SA, Coiro M, Jacobs BF, Xafis A, Neumann FH, Scott L, Sakala J, Currano ED, Zetter R. Origin and divergence of Afro-Indian Picrodendraceae: linking pollen morphology, dispersal modes, fossil records, molecular dating and paleogeography. GRANA 2019; 58:227-275. [PMID: 31275086 PMCID: PMC6582451 DOI: 10.1080/00173134.2019.1594357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/19/2019] [Indexed: 05/31/2023]
Abstract
The pantropical Picrodendraceae produce mostly spheroidal to slightly oblate, echinate pollen grains equipped with narrow circular to elliptic pori that can be hard to identify to family level in both extant and fossil material using light microscopy only. Fossil pollen of the family have been described from the Paleogene of America, Antarctica, Australia, New Zealand, and Europe, but until now none have been reported from Afro-India. Extant pollen described here include representatives from all recent Picrodendraceae genera naturally occurring in Africa and/or Madagascar and south India and selected closely related tropical American taxa. Our analyses, using combined light microscopy and scanning electron microscopy, show that pollen of the Afro-Indian genera encompass three morphological types: Type 1, comprising only Hyaenanche; Type 2, including Aristogeitonia, Mischodon, Oldfieldia and Voatamalo; Type 3, comprising the remaining two genera, Androstachys and Stachyandra. Based on the pollen morphology presented here it is evident that some previous light microscopic accounts of spherical and echinate fossil pollen affiliated with Arecaceae, Asteraceae, Malvaceae, and Myristicaceae from the African continent could belong to Picrodendraceae. The pollen morphology of Picrodendraceae, fossil pollen records, a dated intra-familial phylogeny, seed dispersal modes, and the regional Late Cretaceous to early Cenozoic paleogeography, together suggest the family originated in the Americas and dispersed from southern America across Antarctica and into Australasia. A second dispersal route is believed to have occurred from the Americas into continental Africa via the North Atlantic Land Bridge and Europe.
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Affiliation(s)
- Friðgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Mario Coiro
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Bonnie F. Jacobs
- Roy M. Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX, USA
| | - Alexandros Xafis
- Department of Paleontology, University of Vienna, Vienna, Austria
| | - Frank H. Neumann
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Louis Scott
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Jakub Sakala
- Institute of Geology and Palaeontology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ellen D. Currano
- Departments of Botany and Geology & Geophysics, University of Wyoming, Laramie, WY, USA
| | - Reinhard Zetter
- Department of Paleontology, University of Vienna, Vienna, Austria
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Gening LV, Shevchenko OV, Kazachenko KY, Tarantul VZ. "Mirror" Method to Estimate Mutagenic Activity of DNA Lesions. Methods Protoc 2018; 1:mps1030032. [PMID: 31164573 PMCID: PMC6481070 DOI: 10.3390/mps1030032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/16/2018] [Accepted: 08/24/2018] [Indexed: 12/13/2022] Open
Abstract
We propose an improved method for detecting mutations that arise in DNA due to misincorporations of deoxyadenosine-5′-monophosphate (dAMP) opposite 7,8-dihydro-8-oxoguanine (8-oxoG). The method is based on the synthesis of complementary chains (“mirror” products) using a template containing 8-oxoG. The misincorporation of dAMP in the “mirror” product forms EcoRI sites. The restriction analysis of double-stranded DNAs obtained by PCR of “mirror” product allows quantification of the mutagenesis frequency. In addition, single-strand conformational polymorphism (SSCP) analysis of the single-stranded “mirror” products shows that different DNA polymerases only incorporate dA or dC opposite 8-oxoG. The proposed approach used in developing this technique can be applied in the study of other lesions as well, both single and clustered.
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Affiliation(s)
- Leonid V Gening
- Institute of Molecular Genetics, Kurchatov Sq. 2, Moscow 123182, Russia.
| | - Oleg V Shevchenko
- Institute of Molecular Genetics, Kurchatov Sq. 2, Moscow 123182, Russia.
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Cai D, Rodríguez F, Teng Y, Ané C, Bonierbale M, Mueller LA, Spooner DM. Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota). BMC Evol Biol 2012; 12:70. [PMID: 22624678 PMCID: PMC3416576 DOI: 10.1186/1471-2148-12-70] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/24/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Recent genomic studies have drastically altered our knowledge of polyploid evolution. Wild potatoes (Solanum section Petota) are a highly diverse and economically important group of about 100 species widely distributed throughout the Americas. Thirty-six percent of the species in section Petota are polyploid or with diploid and polyploid cytotypes. However, the group is poorly understood at the genomic level and the series is ideal to study polyploid evolution. Two separate studies using the nuclear orthologs GBSSI and nitrate reductase confirmed prior hypotheses of polyploid origins in potato and have shown new origins not proposed before. These studies have been limited, however, by the use of few accessions per polyploid species and by low taxonomic resolution, providing clade-specific, but not species-specific origins within clades. The purpose of the present study is to use six nuclear orthologs, within 54 accessions of 11 polyploid species, 34 accessions of 29 diploid species of section Petota representing their putative progenitors, and two outgroups, to see if phenomena typical of other polyploid groups occur within wild potatoes, to include multiple origins, loss of alleles, or gain of new alleles. RESULTS Our results increase resolution within clades, giving better ideas of diploid progenitors, and show unexpected complexity of allele sharing within clades. While some species have little diversity among accessions and concur with the GBSSI and nitrate reductase results, such as S. agrimonifolium, S. colombianum, S. hjertingii, and S. moscopanum, the results give much better resolution of species-specific progenitors. Seven other species, however, show variant patterns of allele distributions suggesting multiple origins and allele loss. Complex three-genome origins are supported for S. hougasii, and S. schenckii, and one of the ten accessions of S. stoloniferum. A very unexpected shared presence of alleles occurs within one clade of S. verrucosum from Central America, and S. berthaultii from South America in six polyploid species S. demissum, S. hjertingii, S. hougasii, S. iopetalum, S. schenckii, and S. stoloniferum. CONCLUSIONS Our results document considerable genomic complexity of some wild potato polyploids. These can be explained by multiple hybrid origins and allele losses that provide a clear biological explanation for the taxonomic complexity in wild potato polyploids. These results are of theoretical and practical benefit to potato breeders, and add to a growing body of evidence showing considerable complexity in polyploid plants in general.
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Affiliation(s)
- Danying Cai
- Department of Horticulture, the State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, 866 Yuhangtang Road, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Department of Horticulture, USDA, Agricultural Research Service, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706-1590, USA
| | - Flor Rodríguez
- Department of Horticulture, USDA, Agricultural Research Service, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706-1590, USA
- Centro Regional de Investigación Remehue, INIA, Xa Región de los Lagos, Km 8 Norte, Ruta 5 Sur, Casilla de Correos 24-O, Osorno, Chile
| | - Yuanwen Teng
- Department of Horticulture, the State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, 866 Yuhangtang Road, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Cécile Ané
- Departments of Botany and of Statistics, 1300 University Ave., University of Wisconsin-Madison, Madison, WI, 53706-1590, USA
| | | | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY, 14853, USA
| | - David M Spooner
- Department of Horticulture, USDA, Agricultural Research Service, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706-1590, USA
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