Papers by Ima Mulyama Zainuddin
Fruit ripening and chitosan coating impacts on the expression profile of Banana Lectin (BanLec) genes
Scientia horticulturae, Sep 1, 2024
Genetic diversity analysis of F2 red chili (Capsicum annum L.) population of laris x SSP cross breeding based on SSR markers
AIP Conference Proceedings, Dec 31, 2022
Journal of Genetic Engineering and Biotechnology, Nov 27, 2023
Background The ongoing concern surrounding coronavirus disease 2019 (COVID-19) primarily stems fr... more Background The ongoing concern surrounding coronavirus disease 2019 (COVID-19) primarily stems from continuous mutations in the genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), leading to the emergence of numerous variants. The receptor-binding domain (RBD) in the S1 subunit of the S protein of the virus plays a crucial role in recognizing the host's angiotensin-converting enzyme 2 (hACE2) receptor and facilitating cell membrane fusion processes, making it a potential target for preventing viral entrance into cells. This research aimed to determine the potential of banana lectin (BanLec) proteins to inhibit SARS-CoV-2 attachment to host cells by interacting with RBD through computational modeling. The BanLecs were selected through a sequence analysis process. Subsequently, the genes encoding BanLec proteins were retrieved from the Banana Genome Hub database. The FGENESH online tool was then employed to predict protein sequences, while web-based tools were utilized to assess the physicochemical properties, allergenicity, and toxicity of BanLecs. The RBDs of SARS-CoV-2 were modeled using the SWISS-MODEL in the following step. Molecular docking procedures were conducted with the aid of ClusPro 2.0 and HDOCK web servers. The three-dimensional structures of the docked complexes were visualized using PyMOL. Finally, molecular dynamics simulations were performed to investigate and validate the interactions of the complexes exhibiting the highest interactions, facilitating the simulation of their dynamic properties. The BanLec proteins were successfully modeled based on the RNA sequences from two species of banana (Musa sp.). Moreover, an amino acid modification in the BanLec protein was made to reduce its mitogenicity. Theoretical allergenicity and toxicity predictions were conducted on the BanLecs, which suggested they were likely nonallergenic and contained no discernible toxic domains. Molecular docking analysis demonstrated that both altered and wild-type BanLecs exhibited strong affinity with the RBD of different SARS-CoV-2 variants. Further analysis of the molecular docking results showed that the BanLec proteins interacted with the active site of RBD, particularly the key amino acids residues responsible for RBD's binding to hACE2. Molecular dynamics simulation indicated a stable interaction between the Omicron RBD and BanLec, maintaining a root-mean-square deviation (RMSD) of approximately
Annales Bogorienses, Jun 9, 2007
Hepatitis B is a seriuus infectious disease In the third world countries including Indonesia . Va... more Hepatitis B is a seriuus infectious disease In the third world countries including Indonesia . Vaccination i the mo t effective way to prevent the spread of the disease; therefore the demand for I (BY vaccine is high. In order to produce more vaccine at lower cost, transgenic plant can be chosen to express the vaccine wi th the above criteria. Several researches were successfully producing lransgenic plants expressing HBsAg lbat formed virus-like particles and induced immune response in human. However. HB Ag expression in transgenic plant needs to be improved e pecially on gene xpression control system . Here, we describe lbe construction of HBsAg . tructural gene under the control of wound inducible promoter, MeEFl promoter from lv/anihol escu/enla Crantz. The HB.I'Ag gene wa anlplified using P R[rom IfBV genome isolated from an Indon ian patient. The gene was subsequently fused willi V PaS s ignal peptide, which targeted the reticulum endoplasm of plant cell . The construct was cloned into binary expression veclor for Agrobac;lenum plant lransfonnation in near future.
Plant Methods, Jul 11, 2012
Recent progress in cassava transformation has allowed the robust production of transgenic cassava... more Recent progress in cassava transformation has allowed the robust production of transgenic cassava even under suboptimal plant tissue culture conditions. The transformation protocol has so far been used mostly for the cassava model cultivar 60444 because of its good regeneration capacity of embryogenic tissues. However, for deployment and adoption of transgenic cassava in the field it is important to develop robust transformation methods for farmer-and industry-preferred landraces and cultivars. Because dynamics of multiplication and regeneration of embryogenic tissues differ between cassava genotypes, it was necessary to adapt the efficient cv. 60444 transformation protocol to genotypes that are more recalcitrant to transformation. Here we demonstrate that an improved cassava transformation protocol for cv. 60444 could be successfully modified for production of transgenic farmer-preferred cassava landraces. The modified transformation method reports on procedures for optimization and is likely transferable to other cassava genotypes reportedly recalcitrant to transformation provided production of high quality FEC. Because the three farmer-preferred cassava landraces selected in this study have been identified as resistant or tolerant to cassava mosaic disease (CMD), the adapted protocol will be essential to mobilize improved traits into cassava genotypes suitable for regions where CMD limits production.
PLOS ONE, Sep 25, 2012
Cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) are currently two major vira... more Cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) are currently two major viral diseases that severely reduce cassava production in large areas of Sub-Saharan Africa. Natural resistance has so far only been reported for CMD in cassava. CBSD is caused by two virus species, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). A sequence of the CBSV coat protein (CP) highly conserved between the two virus species was used to demonstrate that a CBSV-CP hairpin construct sufficed to generate immunity against both viral species in the cassava model cultivar (cv. 60444). Most of the transgenic lines showed high levels of resistance under increasing viral loads using a stringent top-grafting method of inoculation. No viral replication was observed in the resistant transgenic lines and they remained free of typical CBSD root symptoms 7 month post-infection. To generate transgenic cassava lines combining resistance to both CBSD and CMD the hairpin construct was transferred to a CMD-resistant farmer-preferred Nigerian landrace TME 7 (Oko-Iyawo). An adapted protocol allowed the efficient Agrobacterium-based transformation of TME 7 and the regeneration of transgenic lines with high levels of CBSV-CP hairpin-derived small RNAs. All transgenic TME 7 lines were immune to both CBSV and UCBSV infections. Further evaluation of the transgenic TME 7 lines revealed that CBSD resistance was maintained when plants were co-inoculated with East African cassava mosaic virus (EACMV), a geminivirus causing CMD. The innovative combination of natural and engineered virus resistance in farmer-preferred landraces will be particularly important to reducing the increasing impact of cassava viral diseases in Africa.
Current Research on Biosciences and Biotechnology, Feb 28, 2023
Cat's whiskers plant (Orthosiphon aristatus B. Miq) is a medicinal plant containing various metab... more Cat's whiskers plant (Orthosiphon aristatus B. Miq) is a medicinal plant containing various metabolites that act as antioxidants and anti-inflammatory, including rosmarinic acid. The domestic market demand for dry leaves was 20-40 tons and abroad it was 141-180 tons in the 1990-2005 period, while production from 2013 to 2017 decreased from 116 tons to 56 tons. Therefore, it is necessary to increase the cat's whiskers biomass production, one of which can be done through the engineering of growing media using organic fertilizers, including goat manure and microbes, e.g., Plant Growth Promoting Microorganisms (PGPM). This study aims to determine the optimal combination of PGPM -Goat Manure for biomass and the rosmarinic acid content in O. aristatus. The study was conducted using a 2-factor randomized block design (RBD) with 12 treatment combinations and 3 repetitions on cultivated land in the Tanjungsari area and analysis of the results was carried out in the SITH laboratory from October 2020 to March 2021. The rosmarinic acid content in the leaves ranged from 144.43 -206.31 mg/g or 14.
Investigation of Natural Tolerance to Post-Harvest Physiological Deterioration and Development of Methods to Prolong Shelf-Life of Cassava Storage Roots
Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement
Journal of Proteomics, Nov 1, 2013
In the last decade proteomics studies have gained increasing importance in plant research. The de... more In the last decade proteomics studies have gained increasing importance in plant research. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins have been particularly instrumental to characterize proteomes and their modulation during plant development, biotic and abiotic stresses. Despite important advances, plant proteome analysis, including those of model plant species, remain constrained by limitations inherent to proteomics techniques and data interpretation. Here we review the approaches and achievements of proteomics with model plant and crop species (i.e. Arabidopsis and rice) and discuss the current limitations of crop proteomics. We anticipate future directions that could advance the contribution of plant proteomics to crop improvement.
In silico Comparative Analysis of Gene and Protein of Plant Lectins
Pertanika Journal of Tropical Agricultural Science
Lectins are a family of proteins that can recognize and bind specific carbohydrates. Plant lectin... more Lectins are a family of proteins that can recognize and bind specific carbohydrates. Plant lectins play various roles in plant defense and can be utilized as insecticidal, antibacterial, antifungal, and antiviral agents. This study compares genes, proteins, and carbohydrate-binding motifs between 15 plant lectins using in silico methods. The lectin genes of Artocarpus hypargyreus Hance, Hordeum vulgare var. Betzes, Triticum aestivum L. cv. Marshall, Galanthus nivalis L., Allium sativum L., Phaseolus vulgaris, Lens culinaris subsp. tomentosus, Robinia pseudoacacia, Glycine max, Cicer arietinum, Pisum sativum, Canavalia ensiformis, Amaranthus caudatus, Amaranthus hypochondriacus, and Musa acuminata subsp. malaccensis were obtained from National Center for Biotechnology Information and Banana Genome Hub. The gene comparison results revealed different characteristics of the 15 plant lectin genes, with A. hypargyreus having the shortest lectin gene and G. max having the longest. Overall,...
Current Research on Biosciences and Biotechnology
Cat’s whiskers plant (Orthosiphon aristatus B. Miq) is a medicinal plant containing various metab... more Cat’s whiskers plant (Orthosiphon aristatus B. Miq) is a medicinal plant containing various metabolites that act as antioxidants and anti-inflammatory, including rosmarinic acid. The domestic market demand for dry leaves was 20-40 tons and abroad it was 141-180 tons in the 1990-2005 period, while production from 2013 to 2017 decreased from 116 tons to 56 tons. Therefore, it is necessary to increase the cat's whiskers biomass production, one of which can be done through the engineering of growing media using organic fertilizers, including goat manure and microbes, e.g., Plant Growth Promoting Microorganisms (PGPM). This study aims to determine the optimal combination of PGPM – Goat Manure for biomass and the rosmarinic acid content in O. aristatus. The study was conducted using a 2-factor randomized block design (RBD) with 12 treatment combinations and 3 repetitions on cultivated land in the Tanjungsari area and analysis of the results was carried out in the SITH laboratory from ...
Plant Methods, Jan 18, 2023
Cassava is the most cultivated and consumed root crop in the world. One of the major constraints ... more Cassava is the most cultivated and consumed root crop in the world. One of the major constraints to the cassava value chain is the short shelf life of cassava storage roots which is primarily due to the so-called post-harvest physiological deterioration (PPD). The identification of natural sources of PPD tolerance represents a key approach to mitigating PPD losses by generating farmer-and industry-preferred cassava cultivars with prolonged shelf life. In the present study, a PPD assessment method was developed to screen for PPD tolerance in the cassava germplasm. The proposed PPD assessment method displayed a reduced rate of microbial infection and allowed a rapid and homogenous development of typical PPD symptoms in the cassava storage roots. We successfully used the PPD assessment method in combination with an image-based PPD scoring method to identify and characterize PPD tolerance in 28 cassava cultivars from the Indonesian cassava germplasm. Our analysis showed a significant and positive correlation between PPD score and dry matter content (r = 0.589-0.664, p-value < 0.001). Analysis of additional root parameters showed a significant and positive correlation between PPD scores at 2 days post-harvest (dph) and root length (r = 0.388, p-value < 0.05). Our analysis identified at least 4 cultivars displaying a significantly delayed onset of PPD symptoms as compared to the other selected cultivars. The availability of cassava cultivars contrasting for tolerance to PPD will be particularly instrumental to understanding the molecular mechanisms associated with delayed PPD in cassava roots.
International Journal of Entrepreneurship and Management Practices, 2021
Coffee is one of Indonesia's leading export commodities. One of the coffee-producing areas in... more Coffee is one of Indonesia's leading export commodities. One of the coffee-producing areas in Indonesia is Sukawangi Village, Sumedang Regency, West Java Province. As the sole actor in running a business, the business actor never calculates the production costs that arise into the cost element. One of the problems of SMEs is the lack of knowledge of SME entrepreneurs about good business management. The next problem faced by SME entrepreneurs is increasing their business competitiveness. Another problem of SMEs that often escapes the attention of UKM entrepreneurs is branding. The last mistake that many UKM players make is that many are not aware that manual bookkeeping is a serious problem for SMEs. In this study, the authors performed a literature synthesis to understand the underlying reasons for issues faced by SMEs about good business management. From the analysis, it can be concluded that consumer behaviour/ preferences/ shops; value chain/ geographical; sustainability/ env...
3BIO: Journal of Biological Science, Technology and Management, 2021
The promoter is a part of the gene that functions in carrying out the gene expression, and its wo... more The promoter is a part of the gene that functions in carrying out the gene expression, and its work activity becomes a matter of concern to ensure that expression works effectively. MeEF1A6 (Manihot esculenta Elongation Factor 1 Alfa - 6) is a promoter derived from cassava plants (Manihot esculenta). In previous studies, the MeEF1A6 promoter was successfully isolated, introduced, and characterized into the pBI121 plasmid, replacing the CaMV35S promoter. This study aims to analyze the activity of MeEF1A6 promoters in-vivo and in-vitro by using transient and transgenic techniques in tobacco plants. The pBI121 plasmid containing the MeEF1A6 promoter was introduced into Agrobacterium tumefaciens strain AGL1 and LBA4404. The promoter's work was then analyzed by the result of introducing it into the tobacco plant using the transient and stable transformation. The whole part of explants was used for transient study and tested in a minimum of two biological replicates. Sixty sheets of e...
Jurnal Ilmu Sosial Politik dan Humaniora, 2019
In this paper, the authors propose solutions to increase the added value of coffee in the form of... more In this paper, the authors propose solutions to increase the added value of coffee in the form of the process of making the process of making coffee using appropriate technology adoption. This paper uses qualitative methods of locational survey and literature study. Survey activities are conducted in the form of interviews and observations. The team conducted interviews with coffee farming communities in the area and observed the conditions of coffee farming. The literature study was conducted by synthesizing literature reviews and continued by formulating the theory and principles of appropriate technology in the context of local agriculture in Sukawangi Village, Sumedang Regency, West Java. In this paper, the authors describe the solution proposals related to the problems of coffee farmers in Sukawangi, Sumedang. Two suggestions for increasing the value added of coffee beans are by using appropriate technology adoption. With both of these solutions, it is expected that the quality...
Plant Methods, 2018
Aim: We report the construction of a Virus-Induced Gene Silencing (VIGS) vector and an agroinocul... more Aim: We report the construction of a Virus-Induced Gene Silencing (VIGS) vector and an agroinoculation protocol for gene silencing in cassava (Manihot esculenta Crantz) leaves and roots. The African cassava mosaic virus isolate from Nigeria (ACMV-[NOg]), which was initially cloned in a binary vector for agroinoculation assays, was modified for application as VIGS vector. The functionality of the VIGS vector was validated in Nicotiana benthamiana and subsequently applied in wild-type and transgenic cassava plants expressing the uidA gene under the control of the CaMV 35S promoter in order to facilitate the visualization of gene silencing in root tissues. VIGS vectors were targeted to the Mg2+-chelatase gene in wild type plants and both the coding and promoter sequences of the 35S::uidA transgene in transgenic plants to induce silencing. We established an efficient agro-inoculation method with the hyper-virulent Agrobacterium tumefaciens strain AGL1, which allows high virus infection rates. The method can be used as a low-cost and rapid high-throughput evaluation of gene function in cassava leaves, fibrous roots and storage roots. Background: VIGS is a powerful tool to trigger transient sequence-specific gene silencing in planta. Gene silencing in different organs of cassava plants, including leaves, fibrous and storage roots, is useful for the analysis of gene function. We developed an African cassava mosaic virus-based VIGS vector as well as a rapid and efficient agroinoculation protocol to inoculate cassava plants. The VIGS vector was validated by targeting endogenous genes from Nicotiana benthamiana and cassava as well as the uidA marker gene in transgenic cassava for visualization of gene silencing in cassava leaves and roots. The African cassava mosaic virus-based VIGS vector allows efficient and cost-effective inoculation of cassava for high-throughput analysis of gene function in cassava leaves and roots.
Plant molecular biology, 2017
Cassava (Manihot esculenta Crantz) is a major world crop, whose storage roots provide food for ov... more Cassava (Manihot esculenta Crantz) is a major world crop, whose storage roots provide food for over 800 million throughout the humid tropics. Despite many advantages as a crop, the development of cassava is seriously constrained by the rapid post-harvest physiological deterioration (PPD) of its roots that occurs within 24-72 h of harvest, rendering the roots unpalatable and unmarketable. PPD limits cassava's marketing possibilities in countries that are undergoing increased development and urbanisation due to growing distances between farms and consumers. The inevitable wounding of the roots caused by harvesting triggers an oxidative burst that spreads throughout the cassava root, together with the accumulation of secondary metabolites including phenolic compounds, of which the coumarin scopoletin (7-hydroxy-6-methoxy-2H-1-benzopyran-2-one) is the most abundant. Scopoletin oxidation yields a blue-black colour, which suggests its involvement in the discoloration observed during P...
Cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) are currently two major vira... more Cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) are currently two major viral diseases that severely reduce cassava production in large areas of Sub-Saharan Africa. Natural resistance has so far only been reported for CMD in cassava. CBSD is caused by two virus species, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). A sequence of the CBSV coat protein (CP) highly conserved between the two virus species was used to demonstrate that a CBSV-CP hairpin construct sufficed to generate immunity against both viral species in the cassava model cultivar (cv. 60444). Most of the transgenic lines showed high levels of resistance under increasing viral loads using a stringent top-grafting method of inoculation. No viral replication was observed in the resistant transgenic lines and they remained free of typical CBSD root symptoms 7 month post-infection. To generate transgenic cassava lines combining resistance to both CBSD and CMD the hairpin construct was transferred to a CMD-resistant farmer-preferred Nigerian landrace TME 7 (Oko-Iyawo). An adapted protocol allowed the efficient Agrobacterium-based transformation of TME 7 and the regeneration of transgenic lines with high levels of CBSV-CP hairpin-derived small RNAs. All transgenic TME 7 lines were immune to both CBSV and UCBSV infections. Further evaluation of the transgenic TME 7 lines revealed that CBSD resistance was maintained when plants were co-inoculated with East African cassava mosaic virus (EACMV), a geminivirus causing CMD. The innovative combination of natural and engineered virus resistance in farmer-preferred landraces will be particularly important to reducing the increasing impact of cassava viral diseases in Africa.
Plant Methods, 2012
Recent progress in cassava transformation has allowed the robust production of transgenic cassava... more Recent progress in cassava transformation has allowed the robust production of transgenic cassava even under suboptimal plant tissue culture conditions. The transformation protocol has so far been used mostly for the cassava model cultivar 60444 because of its good regeneration capacity of embryogenic tissues. However, for deployment and adoption of transgenic cassava in the field it is important to develop robust transformation methods for farmer- and industry-preferred landraces and cultivars. Because dynamics of multiplication and regeneration of embryogenic tissues differ between cassava genotypes, it was necessary to adapt the efficient cv. 60444 transformation protocol to genotypes that are more recalcitrant to transformation. Here we demonstrate that an improved cassava transformation protocol for cv. 60444 could be successfully modified for production of transgenic farmer-preferred cassava landraces. The modified transformation method reports on procedures for optimization a...
Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement
Journal of Proteomics, 2013
In the last decade proteomics studies have gained increasing importance in plant research. The de... more In the last decade proteomics studies have gained increasing importance in plant research. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins have been particularly instrumental to characterize proteomes and their modulation during plant development, biotic and abiotic stresses. Despite important advances, plant proteome analysis, including those of model plant species, remain constrained by limitations inherent to proteomics techniques and data interpretation. Here we review the approaches and achievements of proteomics with model plant and crop species (i.e. Arabidopsis and rice) and discuss the current limitations of crop proteomics. We anticipate future directions that could advance the contribution of plant proteomics to crop improvement.
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Papers by Ima Mulyama Zainuddin