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Articles by D.S. Diningrat
Total Records ( 3 ) for D.S. Diningrat
  D.S. Diningrat , S.M. Widiyanto , A. Pancoro , Iriawati , D. Shim , B. Panchangam , N. Zembower and J.E. Carlson
  Teak is one of the highly famous woody plant species for its premier quality of wood. Teak has problem on productivity because of long reproductive cycle. The problem is basically related to mechanism of flower development. The aim of this study was preliminary development of expressed gene database to characterize the floral transcriptome in teak. Two subtracted cDNA libraries were constructed from vegetative and generative bud tissues. Libraries were sequenced using Illumina MiSeq technology which generated paired-end read sequences 3,778,316 for vegetative and 3,701,878 for generative. The sequences assembled de novo into 87,365 transcript contigs consisting of 42,435,728 bases with N50 of 498 bp using CLC-Genomics Workbench. 76,169 (87.18%) of the 87,365 assembled contigs exhibited significant similarity BLASTN to Solanum lycopersicum database ( The assembled contigs were annotated through high stringency BLASTX analysis to proteome of S. lycopersicum. Distribution of contigs abundance between vegetative and generative stages analyzed using the DEGseq approach. The numbers of contigs distribution are 24,730 in vegetative, 28,912 in generative and 33,723 in both stages. The functionally protein datasets characterized by Gene Ontology (GO) annotation and KEGG metabolic pathways assignments for the result of DEG analysis. These contigs, 18,756 (75.84%) from vegetative, 22,089 (76.40%) from generative and 22,917 (67.96%) from both stages were assigned to GO classes. A total of 1455 (13.77%) were mapped to 30 pathways from vegetative, 1,638 (13.70%) were mapped to 27 pathways from generative and 1,652 (12.20%) were mapped to 30 pathways from both by BLAST comparison against the KEGG database. The biological processes of flowering developments were identified in the biological process dataset and the numbers of contigs were discovered different between stages. This transcriptome dataset information will act as a valuable resource for further molecular genetic studies teak, as well as for isolation and characterization of functional genes involved in flowering development pathways.
  Kusdianti , D.S. Diningrat , Iriawati and S.N. Widiyanto
  Background and Objective: Banana (Musa acuminata spp.) is a fruit as a source of staple food of Asia. Musa acuminata cv Barangan is a type of banana that live in low-lying areas and most widely consumed by an Indonesian people. Bananas are thought to have resistance to salinity stress by knowing the defense mechanisms against stress is expected banana can be used as an alternative crop for marginal land. Banana (Musa spp.) is mesophytic plant that intolerant to high salinity. The presence of proline and Heat Shock Protein (HSP) compounds are an indicator that the plant is under stress conditions. The purpose of this study was to evaluate the banana plant defense mechanisms against the state of high salinity. Methodology: In this study will be observed accumulation of proline produced by the activity of banana planlets after being treated in the form of salinity stress condition. In this study was observed as well, Heat Shock Protein 81-2 (HSP 81-2) and delta-1-pyrroline-5-carboxylate synthase (P5CS1) gene expression profiles of plantlets were treated by salinity stress condition. To achieve the study objectives, Musa acuminata Barangan cultivar culturing in vitro carried out. Banana shoots were cultured in MS medium with BAP with additional 25, 50, 75 and 100 mM NaCl. Proline analyzed with ninhydrin methods. The RNA was isolated from control (K) and treated plantlets. The cDNA made from isolated RNA to be used for qRT-PCR analysis. Transcript levels determination was validated and confirmed using quantitative real-time PCR (qRT-PCR). Results: The results of this study are as follows, proline accumulated by plantlets treated with NaCl, HSP 81-2 and P5CS1 genes expressed by all plantlets with different levels. The HSP 81-2 highest expressed by shoots and roots of plants with 75 mM NaCl treatment. Likewise, the highest proline accumulation occurred in this treatment. On the whole of the roots and shoots treated by NaCl, HSP 81-2 gene expression is higher than the P5CS1 gene expression. Results from this study may answer the purpose of the study itself. Conclusion: Musa acuminata cv Barangan plant has defense mechanisms against the state of high salinity. The expected contribution of this study is that Musa acuminata cv Barangan can be used as plant resistant to soil with high salt content conditions to resolve the problem of exploitation of critical marginal land.
  D.S. Diningrat , S.M. Widiyanto , A. Pancoro , Iriawati , D. Shim , B. Panchangam , N. Zembower and J.E. Carlson
  Teak is woody plants; a member of the Lamiaceae family. Teak is a plant that has a very high quality timber. Teak has constraints due to low reproductive rates and slow growth of the wood after entering the reproductive phase. Teak genetic engineering efforts by delaying flowering time was facing difficulties due to the lack of information about the role of genes regulating flowering identity in teak. Teak has indeterminate inflorescence same as the model plant Arabidopsis. In Arabidopsis, the role of Terminal Flowering 1 (TFL1) gene as a member of the Floral Meristem Identity (FMI) in regulating the vegetative to generative transition is by down regulation, so that, the downstream of the FMI genes up-regulation which resulted in the development towards the formation of flowers. In teak, this mechanism is not well known. The development of NGS technology-transcriptome analysis has allowed us to identify specific interest genes from non-model plant rapidly and cheaply relative. To determine the activity of the interest genes in silico can be undertaken with RNA-seq and QRT-PCR analysis approaches. In this study, it is identified that, TFL1 genes in teak with NGS transcriptome analysis approach that is annotated with S. lycopersicum. The TFL1 genes obtained from EST teak derived from vegetative and generative shoots buds RNA. The TFL1 genes activities on the tissues are done with RNA-seq analysis approach in order to obtain Digitally Gene Expression (DGE) of TFL1. The TFL1 gene activity was then validated in silico by QRT-PCR analysis. The results of the analysis showed that the TFL1-14 gene activity equivalent to the TFL1 gene activity in the model plant.
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