7 results on '"Vermando M. Aquino"'
Search Results
2. Multiplex reverse transcription-polymerase chain reaction for simultaneous detection of banana bract mosaic virus (BBrMV) and sugarcane mosaic virus (SCMV) in abaca
- Author
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Rhosener Bhea L. Koh, Vermando M. Aquino, L. C. Galvez, and C. F. C. Barbosa
- Subjects
0106 biological sciences ,food and beverages ,Plant Science ,Biology ,biology.organism_classification ,01 natural sciences ,Sugarcane mosaic virus SCMV ,Crop ,Reverse transcription polymerase chain reaction ,Horticulture ,Banana bract mosaic virus ,Musa textilis ,Multiplex ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
The abaca (Musa textilis Nee) is an important fibre crop in the Philippines. Its fibre yield and quality is severely impacted by two potyviruses, namely, banana bract mosaic virus (BBrMV) and sugar...
- Published
- 2020
3. Immunodiagnosis of bunchy top viruses in abaca with polyclonal antibodies against their recombinant coat proteins
- Author
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Leny C. Galvez, Cris Francis C. Barbosa, Vermando M. Aquino, Fides Angeli D. L. C. Zaulda, and Rhosener Bhea L. Koh
- Subjects
0106 biological sciences ,biology ,viruses ,biology.organism_classification ,01 natural sciences ,Virology ,Banana bunchy top virus ,law.invention ,010602 entomology ,law ,Polyclonal antibodies ,Musa textilis ,Recombinant DNA ,biology.protein ,Coat Proteins ,Abaca bunchy top virus ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Polyclonal antibodies against abaca bunchy top virus (ABTV) and banana bunchy top virus (BBTV) proteins are necessary for immuno-based detection of these two viruses in abaca (Musa textilis Nee). In this study, recombinant bunchy top viral coat proteins fused with a 6xHis tag at the N-terminus were expressed in E. coli BL21StarTM(DE3)pLysS strain and purified under denaturing conditions. Purified recombinant ABTV and BBTV coat proteins were used as antigens for the production of rabbit polyclonal antibodies. IgG was purified and evaluated by Direct Antigen Coating (DAC)-ELISA and further optimized by testing primary to secondary antibody dilution combinations. Analysis of ABTV and BBTV-infected abaca samples using the optimized DAC-ELISA assay showed that the anti-ABTV CP IgG can react to BBTV and that anti-BBTV CP IgG can react to ABTV, hence, a cross-reaction. The study demonstrates the advantage of using recombinant DNA technology for mass production of antigens for antibody production. Although specificity of the polyclonal antibodies may have been compromised when renatured recombinant proteins were used as immunogens, the ability of the purified IgGs to detect positive abaca samples reveals that the DAC-ELISA can be routinely used for screening disease-free abaca planting materials.
- Published
- 2020
4. Agro-morphological Characteristics of Local Upland Rice in Arakan Valley, Cotabato, Philippines
- Author
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Juliet P. Candog â€' Bangi, Vermando M. Aquino, and Mary Ann Robelle L. Polido
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Grain weight ,Horticulture ,biology ,Sowing ,Cultivar ,Upland rice ,biology.organism_classification ,Aroma ,Caryopsis ,Panicle - Abstract
Agronomic and morphological characteristics of fourteen (14) local upland rice cultivars of Arakan Valley, Cotabato, Philippines were evaluated to determine desirable traits in improving upland rice production and for future breeding purposes. Traditional upland rice seeds differ in shape, size, colour and aroma. Azucena and Kapalawan have longer grains of 9-12 mm and the smallest grain was from Mal-os of 5.5 - 8 mm.  Bungulan, Ulipapa, and Magalitok cultivars have medium size grain of about 8-11 mm. Azucena and Bungulan have translucent caryopsis and aromatic. Mubpon had medium grain size and semi-aromatic and Dinorado had aromatic pinkish to purplish caryopsis and medium size grain. Hinumay and Azucena have the tallest height among rice cultivars with 126.5 and 127 cm, respectively.  Malundiang got the shortest height of 91 cm. Kawilan got the highest number of tillers with 6.5 and 5 panicles per plant. Malundiang cultivar flowered early at 65-70 days while Azucena and Kawilan have late flowering of more than 90 days after planting. Magalitok  had the longest panicle with 31.06 cm and the shortest panicle was measured from Malundiang with 16.63 cm. Ulipapa had the highest 1,000-grain weight of 28.54 g while Manisi got the lowest grain weight of 15.33 g only.  The result of the study showed variation in the agro-morphological characteristics of the indigenous upland rice. Bungulan, Ulipapa, Malundiang, Mubpon, Sinulid and Kawilan have potential agronomic characteristics in improving upland rice production in the IP community. Dinorado, Hinumay, and Azucena have been planted by the local farmers for its desirable grain characteristics and aroma. https://doi.org/10.26803/ijhss.11.2.2
- Published
- 2019
5. Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome
- Author
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Dapeng Zhang, Vermando M. Aquino, Robert Gomez Atienza, Jayson Calundre Asunto, Leny C. Galvez, Cris Francis C. Barbosa, Jose Leonido Catalla, Rhosener Bhea L. Koh, and Kennedy Trinidad Costales
- Subjects
0106 biological sciences ,0301 basic medicine ,Manila hemp ,Musa textilis Née ,Sequence assembly ,QH426-470 ,de novo assembly ,Biology ,01 natural sciences ,Genome ,Article ,Crop ,03 medical and health sciences ,Genetics ,Gene ,Genome size ,Genetics (clinical) ,fiber crop ,Whole genome sequencing ,whole genome sequencing ,Musa spp ,Genetic diversity ,Musa ,biology.organism_classification ,Plant Breeding ,030104 developmental biology ,NGS ,Musa textilis ,Abuab ,Genome, Plant ,010606 plant biology & botany - Abstract
Abaca (Musa textilis Née), an indigenous crop to the Philippines, is known to be the source of the strongest natural fiber. Despite its huge economic contributions, research on crop improvement is limited due to the lack of genomic data. In this study, the whole genome of the abaca var. Abuab was sequenced using Illumina Novaseq 6000 and Pacific Biosciences Single-Molecule Real-Time Sequel. The genome size of Abuab was estimated to be 616 Mbp based on total k-mer number and volume peak. Its genome was assembled at 65× depth, mapping 95.28% of the estimated genome size. BUSCO analysis recovered 78.2% complete BUSCO genes. A total of 33,277 gene structures were predicted which is comparable to the number of predicted genes from recently assembled Musa spp. genomes. A total of 330 Mbp repetitive elements were also mined, accounting to 53.6% of the genome length. Here we report the sequencing and genome assembly of the abaca var. Abuab that will facilitate gene discovery for crop improvement and an indispensable source for genetic diversity studies in Musa.
- Published
- 2021
6. Extraction of high molecular weight DNA suitable for next-generation sequencing from the fiber crop abaca
- Author
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Cris Francis C. Barbosa, Rhosener Bhea L. Koh, Leny C. Galvez, and Vermando M. Aquino
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0106 biological sciences ,Chromatography ,biology ,010405 organic chemistry ,Chemistry ,biology.organism_classification ,01 natural sciences ,DNA extraction ,DNA sequencing ,0104 chemical sciences ,chemistry.chemical_compound ,Polyphenol ,Musa textilis ,Homogenizer ,Cellulose ,Sodium dodecyl sulfate ,Agronomy and Crop Science ,DNA ,010606 plant biology & botany - Abstract
Deoxyribonucleic acid (DNA) extraction in abaca (Musa textilis Nee), the source of the strongest natural fiber (Manila hemp), is difficult due to its fibrous nature, high cellulose content, and polyphenol compounds. Thus an optimized DNA extraction method is required for extracting high quality abaca DNA for next-generation sequencing applications. This study, hence, aimed to test and compare five different methods for the extraction of high molecular weight DNA from abaca leaves. The methods are the traditional cetyl trimethylammonium bromide (CTAB) method (Protocol 1), the CTAB with polyvinylpyrrolidone (PVP) method (Protocol 2), the CTAB with 0.3 % β-mercaptoethanol method (Protocol 3), sodium dodecyl sulfate method (Protocol 4), and CTAB with Triton X-100 and PVP method (Protocol 5). The use of a high throughput homogenizer (TissueLyserII) was also tested in tandem with select extraction protocols for applications in high-throughput DNA extraction. DNA from two abaca varieties were extracted via Protocol 3 and were sent for sequencing based on the Illumina Novaseq platform. After passing the quality control parameters for library preparation, Protocol 3 was found to be the simplest and most consistent method for extracting average yield DNA with high quality for next-generation sequencing applications, while Protocol 4 was determined to have the shortest processing time. Together with TissueLyserII-facilitated homogenization, Protocol 4 is the most appropriate combination for high-throughput extraction of abaca samples which will be useful for genotyping-by-sequencing (GBS) strategies as a molecular tool for plant breeding.
- Published
- 2021
7. Loop-mediated isothermal amplification (LAMP) assays for the detection of abaca bunchy top virus and banana bunchy top virus in abaca
- Author
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Rhosener Bhea L. Koh, Vermando M. Aquino, Cris Francis C. Barbosa, and Leny C. Galvez
- Subjects
0106 biological sciences ,010602 entomology ,biology ,Loop-mediated isothermal amplification ,Abaca bunchy top virus ,Primer (molecular biology) ,biology.organism_classification ,01 natural sciences ,Agronomy and Crop Science ,Virology ,Virus ,010606 plant biology & botany ,Banana bunchy top virus - Abstract
Abaca bunchy top virus (ABTV) and banana bunchy top virus (BBTV) are pathogens that infect abaca in the Philippines causing significant reduction in abaca fiber yield and quality. In this study, a sensitive loop-mediated isothermal amplification (LAMP) assay was developed for detecting ABTV and BBTV in abaca, Musa textilis Nee. Five primer sets were designed and tested to detect ABTV while three primer sets were designed and tested to detect BBTV. Out of which only one primer set for each virus was specific to their respective targets that is DNA-N for ABTV and DNA-S for BBTV for successful LAMP based detection applications. The concentrations of Bst DNA polymerase, dNTPs, incubation time and temperature were optimized for both viruses using either GelRed™ or SYBR™ Green I as detection dyes. The ABTV and BBTV LAMP assays were more sensitive than conventional PCR and were able to detect ABTV or BBTV in asymptomatic abaca samples. The developed LAMP protocols provide a simple, fast and accurate detection method that will be indispensable for the production of ABTV- and BBTV-free abaca tissue cultured plantlets. This is the first report of a LAMP-based assay for detection of ABTV and BBTV in abaca.
- Published
- 2020
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