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The correlation of structural and binding affinity of insulin analog to the onset of action for diabetic therapy Galuh Wening Permatasari; Didik Huswo Utomo; Dian Laila Purwaningroom; Djoko Soeatmadji
Health Science Journal of Indonesia Vol 12 No 1 (2021)
Publisher : Sekretariat Badan Penelitian dan Pengembangan Kesehatan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22435/hsji.v12i1.4783

Abstract

Background: These days, insulin analog production has been improved and becoming popular. The advantages of insulin analog have been extensively reviewed in terms of effectiveness compared to human insulin. Each of the insulin analog industries has claimed their safety and efficacy based on in vivo and in vitro to overcome type 2 diabetes. Hereby, we report on the identification of highly effective analog-based insulin on structure and binding affinity computationally, to confirm its potential and give a broader point of view to insulin analog users. Methods: Five types of insulin analogs, Aspart, Glargine, Detemir, Lispro and Degludec, were analyzed. We grouped and clustered the sequence by alignment to identify the closeness and sequence similarity between samples, continued by superimposing analysis and undertaking binding affinity identification utilizing of a docking analysis approach. Results: Lispro had the least sequence similarity to other types, close to Aspart (96%) and Glargine (90.5%), while Detemir and Degludec showed 100% similarity we decide to only use Degludec for the next analysis. Furthermore, Lispro, Aspart, and Glargine exhibited structural similarity strengthened by the lack of significant difference in the RMSD data. Importantly, Aspart had the highest binding affinity score (-66.1 +/- 7.1 Kcal/mol) in the docking analysis to the insulin receptor (INSR) and similar binding site areas to human insulin. Conclusion: Our finding revealed that the strength of insulin analogs towards insulin receptors is identic with its rapid mechanism in the human body. Keywords: computation, docking, insulin analog, sequence similarity, structure Abstrak Latar belakang: Saat ini, produksi analog insulin meningkat dan menjadi popular. Keuntungan analog insulin telah ditinjau secara ekstensif dalam hal efektivitas dibandingkan dengan insulin manusia. Masing-masing industri analog insulin mengklaim keamanan dan kemanjurannya berdasarkan in vivo dan in vitro untuk mengatasi diabetes tipe 2. Kami melaporkan identifikasi insulin analog yang efektif berdasarkan struktur dan afinitas pengikatan secara komputasi, untuk mengonfirmasi potensi serta memberikan sudut pandang yang lebih luas kepada pengguna insulin analog. Metode: Lima jenis analog insulin, Aspart, Glargine, Detemir, Lispro, dan Degludec, dianalisis. Kami membandingkan dan mengelompokkan urutan tersebut dengan penyelarasan untuk mengidentifikasi kedekatan dan kesamaan urutan antar sampel dilanjutkan dengan superimposing analysis dan melakukan identifikasi binding affinity menggunakan pendekatan analisis docking. Hasil: Lispro memiliki kemiripan sekuen paling rendah dengan jenis lainnya, mendekati Aspart (96%) dan glargine (90,5%), sedangkan Determir dan Degludec menunjukkan kemiripan 100% sehingga kami menggunakan Degludec untuk analisis selanjutnya. Selain itu, Lispro, Aspart, dan Glargine menunjukkan kesamaan struktural yang diperkuat oleh rendahnya nilai signifikansi pada data RMSD. Perlu digarisbawahi bahwa Aspart memiliki skor afinitas pengikatan tertinggi (-66.1 +/- 7.1 kkal / mol) dalam analisis docking ke reseptor insulin (INSR) dan memiliki area pengikatan yang serupa dengan insulin manusia. Kesimpulan: Penemuan kami mengungkapkan bahwa kekuatan insulin analog sejalan dengan laju mekanismenya di dalam tubuh manusia Kata kunci: komputasi, docking, insulin analog, kemiripan sekuen, struktur
Application of organic fungicide in controlling basal stem rot disease for mature oil palm Happy WIDIASTUTI; Hayati MINARSIH; Djoko SANTOSO; Deden Dewantara ERIS; Galuh Wening PERMATASARI
E-Journal Menara Perkebunan Vol 88, No 1 (2020): April, 2020
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (200.537 KB) | DOI: 10.22302/iribb.jur.mp.v88i1.368

Abstract

Ganoderma is a major pathogen in oil palm crops. Some efforts related to control the growth of Ganoderma have been conducted but still have not found an effective method. This study aims to develop an organic fungicide that has been tested in vitro, which effective in controlling the growth of Ganoderma. The optimization carried out includes the determination of the dose and time interval for application in 13-year-old mature oil palm. This organic fungicide application was the continuation of application during the previous year especially for the two best treatment which is application organic fungicide every week (1w) and every two weeks (2w). In this study, the treatments tested were three levels dose of organic fungicide (0, 1x and 2x) and two types of frequency application, i.e. every week (1w) and every other week (2w). The results showed that the best application of organic fungicides was every week application with twice doses (1w.2x), based on the parameters of the inhibition of Ganoderma’s fruiting body formation, primary and secondary root formation, the opening of spear leaves, and harvesting parameters. The application of organic fungicide able to recover the oil palm infected Ganoderma sp., with increasing the fresh fruit bunch and its weight around 70% and 78%, respectively.
Trenching Construction in Peat Soil and the DGGE Analyses of nif Gene and Activity of Dehydrogenase HAPPY WIDIASTUTI; DARMONO TANIWIRYONO; IMAN RUSMANA; GALUH WENING PERMATASARI
Microbiology Indonesia Vol. 14 No. 4 (2020): December 2020
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (2068.239 KB) | DOI: 10.5454/mi.14.4.2

Abstract

Basal stem rot (BSR) is a major disease in oil palm crops which also possible happen on peat soils. Ganoderma boninense is the pathogen that causes this disease infects the plants through the root. Maintaining root health expects to reduce the intensity of the occurrence of BSR disease and its spread. In this research, trenching construction and maintenance is carried out which aims to break the spread and activity of Ganoderma. Trenching maintenance is carried out by giving empty bunches oil palm inoculated with decomposer, Azotobacter inoculants and humic acid. Four treatments tested were trenched (T1) and untrenched (T0) in combination with two level of Ganoderma attack, which are moderate (Mo) and severe (Se). The soil sample were retrieved from different point, which are in the trenching area (TR), harvest path zone (H), and frond stack zone (M). The soil characteristic including microbe abundance, dehydrogenase activity, and PCR-DGGE of microbe community in each treatment were analyzed to reveal the effect of trenching construction. The results showed that trenching implementation reveals major results related to the abundance of microbes and fungi population, supported by the enhancement of dehydrogenase activity at the block with moderate Ganoderma attack. In addition, the DGGE study effectively separates the microbial population of four separate treatment into two clusters, splitting the grouping depending on the Ganoderma level attack. This study shows enhancement of soil characteristics biologically and nutrients status of oil palm leaves especially P, as the results of trenching construction in peatland. Keywords: peatland; oil palm; trenching, DGGE; microbes
Application of organic fungicide in controlling basal stem rot disease for mature oil palm Happy WIDIASTUTI; Hayati MINARSIH; Djoko SANTOSO; Deden Dewantara ERIS; Galuh Wening PERMATASARI
Menara Perkebunan Vol. 88 No. 1 (2020): 88 (1), 2020
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v88i1.368

Abstract

Ganoderma is a major pathogen in oil palm crops. Some efforts related to control the growth of Ganoderma have been conducted but still have not found an effective method. This study aims to develop an organic fungicide that has been tested in vitro, which effective in controlling the growth of Ganoderma. The optimization carried out includes the determination of the dose and time interval for application in 13-year-old mature oil palm. This organic fungicide application was the continuation of application during the previous year especially for the two best treatment which is application organic fungicide every week (1w) and every two weeks (2w). In this study, the treatments tested were three levels dose of organic fungicide (0, 1x and 2x) and two types of frequency application, i.e. every week (1w) and every other week (2w). The results showed that the best application of organic fungicides was every week application with twice doses (1w.2x), based on the parameters of the inhibition of Ganoderma’s fruiting body formation, primary and secondary root formation, the opening of spear leaves, and harvesting parameters. The application of organic fungicide able to recover the oil palm infected Ganoderma sp., with increasing the fresh fruit bunch and its weight around 70% and 78%, respectively.