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Anak Agung Istri Ratnadewi
Department Of Chemistry, Faculty Of Mathematics And Natural Sciences, Universitas Jember. Center For Development Of Advanced Sciences And Technology, Universitas Jember
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Optimum pH Buffer of Phosphate and Carbonate on The Crude Extraction of Uricase Enzyme from Goat Liver: Uricase Wuryanti Handayani; Leyla Novita Brigiyanti; Sudarko; Istri Ratnadewi, Anak Agung
Indonesian Chimica Letters Vol. 2 No. 1 (2023)
Publisher : Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/icl.v2i1.365

Abstract

Uricase enzyme (urate oxidase) is an enzyme that catalyze the oxidation of uric acid in the presence of oxygen to produce allantoin, carbon dioxide (CO2) and hydrogen peroxide (H2O2). Human and primates do not have this enzyme while other mammals have it in the liver therefore the uricase enzymes are extracted from goat liver use a buffer that is compatible with the human buffer system. The type of buffer selected adjusted at the appropriate pH. The optimum uricase pH ranged from 7.5 to 9.5. The selection of buffer type is adjusted to the human buffer system. The purpose of the study was to determine the effect of the type and pH of the extraction buffer on the total activity, protein total and specific activity of crude uricase. The types of buffer selected are phosphate buffer and carbonate buffer, while the selected pH is 7.5; 8.5; and 9.5. The method used is enzyme extraction, then determination of enzyme activity and protein content to determine the specific activity of the enzyme. The results obtained the highest total enzyme activity at pH 8.5 both in carbonate buffer (0.0481 U/mL) and phosphate buffer (0.0383 U/mL). The highest protein total in carbonate buffer was at pH 9.5 (4.55 mg/mL) while the highest value was in phosphate buffer pH 8.5 (4.1 mg/mL). The specific activity of uricase pH 8.5 was carbonate buffer (0.0114 U/mg) and phosphate buffer (0.0094 U/mg). The highest uricase specific activity value was at pH 8.5 for both carbonate and phosphate buffer types and in the long term it is used as a gout therapy.
Development of Dihydrofolate Reductase Inhibitor Based on QSAR and Molecular Docking Sudarko, Sudarko; Kristiyono, Rimba Candra; Ratnadewi, Anak Agung Istri; Handayani, Wuryanti
Indonesian Chimica Letters Vol. 3 No. 1 (2024)
Publisher : Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/icl.v3i1.940

Abstract

QSAR modeling allows for predicting activity through quantitative relationships between molecular structure and activity. This research uses DEEPScreen, which is a development of QSAR for searching new drugs. This research leverages DEEPScreen-QSAR modeling to optimize the predictive power of machine learning algorithms on a dataset of 645 molecules from previous research. The optimized model achieves an accuracy of 0.7461 and precision of 0.8169, demonstrating its effectiveness in the virtual screening stage. The optimized DEEPscreen-QSAR model is used to screen approximately 1.9 million small molecules in the ChEMBL database, resulting in binary classification predictions of active (1) molecules as 781,213 and inactive (0) molecules as 1,133,325 (molecules with IC50 activity ≤10,000 nM are considered active). The active (1) molecules obtained are screened again to find molecules that can be absorbed by the body (orally) using Lipinski’s RO5 with 0 deviations, resulting in 557,428 active molecules that can be absorbed by the body. These screening results are validated using molecular docking methods by linking protein and ligand to determine Gibbs free energy (∆G) and interactions using PyRx, PyMOL, and Biovia Discovery Studio programs. Based on the results of this research, candidate DHFR inhibitors with codes CHEMBL3302655, CHEMBL1384989, and CHEMBL1729486 are recommended.
Purification of Xylooligosaccharide From Casavva Pulp by Ultrafiltration Method Ratnadewi, Anak Agung Istri; Fauziyah, Kamelia Rizqi; Indarti, Dwi
BERKALA SAINSTEK Vol 9 No 2 (2021)
Publisher : Universitas Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/bst.v9i2.23388

Abstract

Xylan is the main component of hemicellulose. Xylan can be extracted from agricultural waste, such as cassava pulp. Xylan is used as an endo-β-1,4-D-xylanase substrate to produce impure xylooligosaccharides (XOS)This study aims to purify XOS from cassava pulp using the ultrafiltration method. The components of XOS obtained from the enzymatic hydrolysis were analyzed using thin layer chromatography (TLC) and densitometry methods. In addition, the XOS was purified by the ultrafiltration method using a cellulose membrane with a Molecular Weight Cut Off (MWCO) of 12 kDa. The permeate obtained from the purification results was also analyzed using TLC and densitometry. The results of this study indicated that the components in XOS cassava pulp before and after purification by the TLC method were X5 and X6, while the XOS components before and after purification by the densitometric method were X3, X4 and X5.
EXPLORATION OF BROTH CHICKEN GUT AS GROWTH MEDIA OF Escherichia coli BL21 pET-Endo FOR ENDO-Β-1,4-D-XYLANASE PRODUCTION Anak Agung Istri Ratnadewi; Moch. Yoris Alidion; Agung Budi Santoso; Ika Oktavianawatia
ALCHEMY Jurnal Penelitian Kimia Vol 13, No 2 (2017): September
Publisher : UNIVERSITAS SEBELAS MARET (UNS)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/alchemy.13.2.4356.191-204

Abstract

Endo-β-1,4-D-xylanase is a hydrolytic enzyme that breakdown the 1.4 chain of xylan polysaccharide. We have succes to transform the plasmid pET-Endo gene encoding endo-1,4-β-D-xylanase from Bacillus sp. originally from termites abdominal to E. coli BL21. The clone was ready for large scale of enzyme production. To reduce production cost, we look for subtitute media for the expensive Luria Berthani broth. Chicken guts broth is good alternative while rich of protein and very cheap. The content of N dissolved chicken guts broth reaches 87 % of LB broth. Growth of E. Coli BL21 in Chicken guts broth and LB broth (as control) was observed by Optical Density (OD) using spectrofotometer. Concentration of glucose added in broth and incubation temperature was varied. The result showed that optimal growth was in addition of 1.5 % glucose and incubated at  37 oC for 16 h. This optimal condition was used to grow E. coli BL21 pET-Endo for xylanase production. Enzyme purification was done by Ni-NTA affinity chromatography. Highest protein yield was 0.076 mg/mL obtained in 100 mM imidazole elucidation. The activity and specific activity of xylanase were estimated as 0.042 U/mL and 0.556 U/µg, respectively. The purification factor was 3.16 time and the molecular weight of enzyme was ± 30, 000 Dalton
The Effect of Substrate Concentration and Incubation Time on The Activity of The Uricase Enzyme From Goat Liver Handayani, Wuryanti; Febriani, Nurul Afifah; Ratnadewi, Anak Agung Istri; Sudarko; Pertiwi, Andriana Kusuma
Indonesian Chimica Letters Vol. 3 No. 2 (2024)
Publisher : Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/icl.v3i2.4255

Abstract

Uricase is an oxidoreductase enzyme that catalyzes the degradation of uric acid into allantoin, hydrogen peroxide, and carbon dioxide. Allantoin, the primary product of uric acid degradation, exhibits 5-10 times greater solubility in water compared to uric acid. This property underscores the importance of uricase in managing hyperuricemia, a condition characterized by elevated uric acid levels in the blood. Hyperuricemia is associated with diseases such as gout, kidney dysfunction, and hypertension. While humans and primates lack the uricase enzyme, it is naturally present in the liver of non-primate mammals, including goats. This study investigated the activity of uricase extracted from goat liver, focusing on the optimum concentration of uric acid as the substrate and incubation time necessary for achieving maximum enzymatic activity. Goat liver samples were processed using borate buffer (pH 8.5) ammonium sulfate fractionation and dialysis to isolate uricase. The enzymatic activity was evaluated at uric acid concentrations of 1.0, 1.5, 2.0, 2.5, and 3.0 mM and incubation times of 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, and 6.0 hours. The results revealed that the optimum substrate concentration for uricase was 2 mM, yielding total enzyme activity of 0.6704 U/mL and specific activity of 0.0443 U/mg. Additionally, the optimum incubation time was determined to be 5 hours, resulting in total enzyme activity of 0.8421 U/mL and specific activity of 0.0556 U/mg. These findings provide valuable insights into enhancing uricase activity and optimizing its application in therapeutic strategies for hyperuricemia management. Further research is recommended to explore the potential of uricase in clinical and pharmaceutical contexts.
Isolation and Characterization of Uricase Produced from Chicken Liver Wuryanti Handayani; Nasrul Amaliyatun Naja; Muhamad Kiki Afindia Joenata; Ratnadewi, Anak Agung Istri
Journal of Bio-Molecule Research and Engineering Vol 1 No 1 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i1.35859

Abstract

Uricase is an enzyme that degrades uric acid into allantoin. One of the uricase sources is obtained from chicken species (Gallus gallus domesticus) liver which are broiler and native chicken. This study aims to determine the maximum uricase activity in broiler and native chicken liver. The uricase activity was obtained by measuring the uric acid concentration as uricase substrate using spectrophotometric method and wavelength at 291 nm. Uricase isolation was carried out into extraction process, ammonium sulfate fractionation (0-60% saturation of ammonium sulfate), and dialysis. During isolation process, centrifugation speed was also optimized to obtain the maximum uricase crude extract and uricase activity. The molecular weight of uricase was also determined by SDS PAGE. The result showed that the highest uricase activity remained using centrifugation speed of 15,000 rpm. The optimum uricase fraction for broiler chicken liver was obtained at 20-40% saturation of ammonium sulfate with uricase activity was 1.854 x 10-2 U/mg, and the uricase fraction for native chicken liver was obtained at 40-60% saturation of ammonium sulfate with uricase activity was 2.496 x 10-2 U/mg. The optimum fraction for uricase production and isolation is carried out to the dialysis process. The optimum uricase activity of broiler chicken liver crude extract was 4.921 x 10-4 U/mg, the uricase fraction was 3.989 x 10-3 U/mg, and the dialysate was 5.120 x 10-3 U/mg. While the native chicken liver crude extract was 2.980 x 10-4 U/mg, the uricase fraction was1.415 x 10-2 U/mg, and the dialysate was 1.753 x 10-2 U/mg. The molecular weight of the uricase was around 35 kDA according to the SDS PAGE result.
Hybrid DFT-ML-MD Approach for Derivation of Lennard-Jones Interatomic Potential Parameters of Al Arkundato, Artoto; Widiasih; Ratnadewi, Anak Agung Istri Ratnadewi; Syah, Khalif Ardian; Yulianti, Yanti
Journal of Energy, Material, and Instrumentation Technology Vol 6 No 2 (2025): Journal of Energy, Material, and Instrumentation Technology
Publisher : Departement of Physics, Faculty of Mathematics and Natural Sciences, University of Lampung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23960/jemit.v6i2.306

Abstract

Atomistic simulation based on computational physics of methods is used to develop accurate interatomic potentials based on DFT (density functional theory) data. The accuracy of predicting the physical properties of a material is highly dependent on the quality of the interatomic potential used. The purpose of this study is to determine the Lennard-Jones potential parameters of Al metal (epsilon and sigma) from fitting the DFT simulation output data. The use of a “robust” fitting method to reduce the influence of outliers on the potential results is very important and therefore a machine learning method is used to help find the right potential parameters. The method used is a hybrid method using DFT to generate training data, using ML (machine learning) to fit DFT data to the Lennard-Jones (LJ) potential model, and using the MD (molecular dynamics) method to validate the LJ potential parameters. Python-based programming is applied to facilitate how the three methods can be connected. The results of this study are that Al metal has an epsilon value = 0.5000 eV and sigma Al = 3.2072 Å, with a regression coefficient R2 = 0.9441 so that it can be concluded that this study can be said to be quite good and the hybrid method can be further developed to obtain the LJ potential parameter values of various other materials, especially metals.
Immobilization of Endo-Β-1,4-D-Xylanase using Alginate/Nanocellulose for Xylooligosaccharide Production Ratnadewi, Anak Agung Istri; Aprilia, Selvina Rizky; Piluharto, Bambang; Yulvia, Ana
Indonesian Chimica Letters Vol. 2 No. 2 (2023)
Publisher : Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/icl.v2i2.5607

Abstract

Free endo-β-1,4-D-xylanase cannot be used more than once, so it needs to be modified by immobilizing the enzyme. Endo-β-1,4-D-xylanase was obtained from termite abdomen sources by isolation, ammonium sulfate purification, and dialysis methods. Endo-β-1,4-D-xylanase was immobilized with an alginate/nanocellulose matrix. This study aims to determine the activity, protein content, and repeated use of immobilized Endo-β-1,4-D-xylanase. This study used variations of Alginate/nanocellulose (0; 2.5; 5; 7.5; 10) %. Protein levels of Endo-β-1,4-D-xylanase were tested using the Bradford method and activity using the Miller method. The total protein bound to the immobilized Endo-β-1,4-D-xylanase was stated with the immobilized yield data. The immobilized yield with the composition of Alginate Nanocellulose (ANC) (0%) was 45.33% greater than the other compositions. Immobilized Endo-β-1,4-D-xylanase activity is efficient. ANC 5% produces an efficiency of 62.384% at the 12th hour, which is greater than the other ANC compositions.
Strategic Optimization of Fractionation and Dialysis Buffer pH to Enhance Goat Liver-Uricase Activity Zain, Romzi Al Amiri; Handayani, Wuryanti; Sjaifullah, Achmad; Pertiwi, Andriana Kusuma; Ratnadewi, Anak Agung Istri; Sudarko, Sudarko
Indonesian Chimica Letters Vol. 5 No. 1 (2026)
Publisher : Department of Chemistry, FMIPA, UNEJ

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/icl.v5i1.60008

Abstract

Uricase is an important enzyme that catalyzes the oxidation of uric acid to allantoin and has potential applications in clinical diagnostics and biotechnology. However, its activity and stability are greatly influenced by purification conditions. This study aimed to optimize ammonium sulfate fractionation and the pH of the dialysis solution to enhance the activity of uricase isolated from goat liver. The enzyme was extracted and subjected to stepwise ammonium sulfate precipitation at different saturation levels, followed by dialysis using buffers with varying pH values. Enzyme activity and protein concentration were determined to calculate specific activity, and SDS–PAGE analysis was performed to evaluate the purification profile. The results showed that the optimal ammonium sulfate fraction for uricase precipitation was 0–20% saturation, yielding the highest specific activity of 0.0034 ± 0.001 U/mg. Further dialysis optimization indicated that a pH of 8.5 was the most favorable condition, yielding the highest enzyme activity of 0.0038 ± 0.001 U/mg. SDS–PAGE analysis showed reduced contaminant protein bands after purification, indicating improved enzyme purity. These findings suggest that precise control of salt concentration and buffer pH is crucial for maintaining uricase stability and enhancing its catalytic performance. Overall, the combination of optimized ammonium sulfate fractionation and dialysis conditions effectively improved the purity and activity of uricase, providing a useful basis for further development and application of this enzyme in biochemical and industrial processes.
The Scientific Aspects of the Balinese Wariga Calendar I Made Tirta; I Wayan Windu Sara; Anak Agung Istri Ratnadewi
Jurnal Inovasi Sains dan Teknologi Untuk Masyarakat Vol. 4 No. 1 (2026): Mei
Publisher : Faculty of Mathematics and Natural Sciences, University of Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/instem.v4i1.60005

Abstract

The Balinese Calendar, known as the Wariga Calendar, played a significant role in the religious and cultural life of Hindus, particularly in Bali. It was commonly found in Balinese Hindu households and remained an important reference for Balinese Hindus living outside the island. The Wariga Calendar represented a unique integration of Hindu philosophical values with scientific and mathematical calculations. One of its primary functions was determining the cycles of Hindu holy days and major festivals, including Saraswati, Pagerwesi, Galungan, and Kuningan. The introduction of the Wariga Calendar, especially its scientific and mathematical aspects, was considered important for Hindu Religious Education teachers throughout Indonesia. First, the holy days calculated using the Wariga Calendar had been celebrated by Hindu communities across the Indonesian archipelago, not only by the Balinese ethnic community. Second, only a limited number of Hindu Religious Education teachers outside Bali understood the mathematical principles underlying the calendar system. An introduction to the Wariga Calendar was delivered during a National Technical Guidance Program (Bimbingan Teknis) for Hindu Religious Education teachers held in a hybrid format on 2–3 August 2025. The program involved participants from various regions of Indonesia. The results showed that most participants considered the knowledge valuable for improving their understanding of the cyclical nature of Hindu holy days. Furthermore, many participants recognized that several elements of the Wariga Calendar exhibited mathematical patterns that were closely aligned with the philosophical messages embedded in the calendar, particularly those associated with the Galungan festival.
Co-Authors Achmad Sjaifullah Agung Budi Santoso Agung Budi Santoso Andika Ade Kurniawan Andika Ade Kurniawan, Andika Ade Andriana Kusuma Pertiwi Aprilia, Selvina Rizky Arianti, Fefpi Nur Afnifitri Wias Artoto Arkundato Asnawati Asnawati Bambang Piluharto Dwi Indarti Eka Yuni Kurniawati Eka Yuni Kurniawati, Eka Yuni Fauziyah, Kamelia Rizqi Febriani, Nurul Afifah Firda Marta Safitri Hefinda Erfiandika I Made Tirta I Wayan Windu Sara Ika Oktavianawatia Indras Dwi Anggita Jayus, Jay Kristiyono, Rimba Candra Leyla Novita Brigiyanti Linda Faiqotul Himmah Moch. Yoris Alidion Muhamad Kiki Afindia Joenata Nasrul Amaliyatun Naja Nasution, Annio Indah Lestari NG. Krishnabudi Nurhayati Nurhayati Nyoman Gede Krishnabudi Rosa Safitri S. Sudarko Selvi Marcellia Siti Nur Avida Sudarko Sudarko Sudarko Syah, Khalif Ardian Tri Mulyono Widiasih Wuryanti Handayani Yanti Yulianti Yulvia, Ana Zain, Romzi Al Amiri