Papers by rahmaniar mulyani
Journal of Proteomics & Bioinformatics, 2021
Diabetic mellitus and cataracts are common mitochondrial diseases in Indonesia, occurring as a re... more Diabetic mellitus and cataracts are common mitochondrial diseases in Indonesia, occurring as a result of a lack of ATP, which is produced in mitochondria via oxidative phosphorylation (OXPHOS). The OXPHOS chain is composed of five complex proteins encoded by genes from nuclear DNA and mitochondrial DNA. One such gene is the CYB gene, with its locus in mitochondrial DNA. The CYB gene encodes part of the complex III subunit, cytochrome b, an electron transfer agent. A novel mutation has been identified at T15458C in type 2 diabetes mellitus patients and T15663C in cataract patients, both of which are in the CYB gene, leading to amino acid alterations S238P and I306T. This study investigated the relationship between T15458C and T15663C mutations in the CYB gene of mitochondrial DNA to the OXPHOS process via an in silico method. Wild type and mutant CYB were modelled via homology modelling using Modeller 9.19 with a 5XTE template, then evaluated using the Ramachandran plot, packaging quality score, and the DOPE profile. The results of the S238P mutant structure analysis showed that proline acts as a helix-breaker due to the loss of a hydrogen bond, while I306T causes a hydrophobic interaction as the helix stabiliser is lost in the mutant. It is assumed the threonine was phosphorylation mutations also destabilises the complex, as proven by the ΔΔG < 0. In conclusion, S238P and I306T mutations affect the function of complex III as an electron transfer agent in the respiratory process.
HAYATI Journal of Biosciences
The association of type-2 diabetes mellitus (T2DM) and cataract with mtDNA mutation has been repo... more The association of type-2 diabetes mellitus (T2DM) and cataract with mtDNA mutation has been reported before. Despite the high prevalence of DM and cataract in Indonesia, a study of the mtDNA variants in Indonesia in correlation with the two diseases is still limited. MT.3243A>G is one of the hotspots mutations for mitochondrial diseases, but the explanation for its occurrence in patients with pure cataract is still elusive. Therefore, the objective of this study was to analyze the mitochondrial genome variants from T2DM and cataract patients in Indonesia using the direct sequencing method. The homology analysis of the genome to the Cambridge reference sequence resulted in 86 variants, including 20 variants that cause amino acid substitutions. Based on the Mitomap data, 17 of the 20 variants were novel. Upon comparison with the 12 normal variant genomes, 11 of 17 variants were suggested to be associated with T2DM and cataract diseases since they code the protein in complex-I (ND4...
IOP Conference Series: Earth and Environmental Science, 2020
Inulin fructotransferase is an enzyme which converts inulin into difructose anhydride III (DFA II... more Inulin fructotransferase is an enzyme which converts inulin into difructose anhydride III (DFA III). Inulin fructrotransferase was produced by fermentation in medium containing various concentrations of inulin (10 g/L, 20 g/L) as carbon source, yeast extract (1 g/L, 2g/L) as organic nitrogen source and (NH4)2SO4 (2g/L, 5g/L) as inorganic nitrogen source using Nonomuraea sp. ID06-A0189. The aim of the study was to optimize the medium composition using various concentrations of carbon and nitrogen sources for inulin fructotransferase production by Nonomuraea sp. ID06-A0189, through shake flask system. Fermentation was conducted at 30 °C, pH 7.0 and agitated in 130 rpm for three days. The result showed that comparable with those found in another condition the highest enzyme activity was produced in medium using inulin as carbon source with concentration of 10 g/L, yeast extract as organic nitrogen source with concentration of 5 g/L and ammonium sulfate as inorganic nitrogen source with...
Design and Optimization of PCR-RFLP Assay for Detection of G9053A and T15663C Mutation in Mitochondrial DNA
Research Journal of Chemistry and Environment
Mutation of mitochondrial DNA (mtDNA) such as G9053A and T1566C is involved in type 2 diabetes me... more Mutation of mitochondrial DNA (mtDNA) such as G9053A and T1566C is involved in type 2 diabetes mellitus. The G9053A mutation in the ATP6 gen and the T15663C in the CYB gene has been reported to cause structure changes and interfering the respiration process in mitochondria. However, diagnosis method of type 2 diabetes mellitus by measuring blood sugar level is unable to detect point mutations in mtDNA. PCR has been extensively used for amplification of DNA sequences. Genetic analysis by restriction fragment length polymorphism (RFLP) is one of the most common methods used to examine nucleic acids for the presence of point mutation. In this study, PCR-RFLPs were designed and optimized in order to diagnose type 2 diabetes mellitus by detecting G9053A and T15663C mutation. The PCR primers forward and reverse were designed to amplify target gene by the PCR reaction. The DNA template was isolated from urinary epithelial cells of type 2 DM patients and then amplified through the PCR proce...
Indonesian Journal of Chemistry, Sep 28, 2022
Electrochemical biosensors are used to detect adenosine triphosphate (ATP) levels, which are invo... more Electrochemical biosensors are used to detect adenosine triphosphate (ATP) levels, which are involved in a variety of biological processes, such as regulating cellular metabolism and biochemical pathways. Therefore, this research aims to develop an aptamer-based electrochemical biosensor with Screen Printed Carbon Electrode/gold nanoparticles (SPCE/AuNP) and collect data as well as information related to ATP detection. The modification of SPCE with AuNP increased the analyte's binding sensitivity and biocompatibility. The aptamer was selected based on its excellent bioreceptor characteristics. Furthermore, aptamer-SH (F1) and aptamer-NH 2 (F2) were immobilized on the SPCE/AuNP surface, which had been characterized using SEM, EIS, and DPV. Also, the ATP-binding aptamers were electrochemically characterized using the K 3 [Fe(CN) 6 ] redox system and Differential Pulse Voltammetry (DPV). According to the optimization results using the Box-Behnken experimental design, the ideal conditions obtained from the factors influencing the experiment were the F1 concentration and incubation time of 4 μM and 24 h, respectively, as well as F1/F2/ATP incubation time of 7.5 min. Meanwhile, for the range of 0.1 to 100 μM, the detection (LoD) and quantification (LoQ) limits were 7.43 and 24.78 μM, respectively. Therefore, this aptasensor method can be used to measure ATP levels in real samples.
Indonesian Journal of Chemistry
Mitochondrial DNA mutations, such as A3243G, can affect changes in the structure of biomolecules,... more Mitochondrial DNA mutations, such as A3243G, can affect changes in the structure of biomolecules, resulting in changes in the structure of Leucine transfer Ribose Nucleic Acid to form a dimer. Dimer structure modeling is needed to determine the properties of the structure. However, the lack of a structure template for the transfer of Ribose Nucleic Acid (tRNA) is challenging for the modeling of mutant structures of tRNA, especially mitochondrial tRNA that are susceptible to mutation. Therefore, this study predicted the structure of mitochondrial leucine tRNA and its stability through a knowledge-based method and molecular dynamics. Structural modeling and initial assessment were performed using RNAComposer and MolProbity, HNADOCK, and Discovery studios to form the dimer structure. Molecular dynamics simulations for stability analysis were performed using Amber and AmberTools20 software, showing that the conformational energy of the mutant leucine tRNA dimer structure was lower than ...
Potensi Antibakteri Staphylococcus aureus dan Escherichia coli dari Ekstrak Biji Serta Daun Bengkuang (Pachyrhizus erosus (L) Urban)
LPPM - Unjani, 2017
sj-docx-1-bbi-10.1177_1177932220978672 – Supplemental material for Molecular Dynamics Simulation of T10609C and C10676G Mutations of Mitochondrial ND4L Gene Associated With Proton Translocation in Type 2 Diabetes Mellitus and Cataract Patients
Supplemental material, sj-docx-1-bbi-10.1177_1177932220978672 for Molecular Dynamics Simulation o... more Supplemental material, sj-docx-1-bbi-10.1177_1177932220978672 for Molecular Dynamics Simulation of T10609C and C10676G Mutations of Mitochondrial ND4L Gene Associated With Proton Translocation in Type 2 Diabetes Mellitus and Cataract Patients by Wanda Destiarani, Rahmaniar Mulyani, Muhammad Yusuf and Iman Permana Maksum in Bioinformatics and Biology Insights
Bioinformatics and Biology Insights, 2020
The mutation rate of mitochondrial DNA (mtDNA) is 17 times higher than nuclear DNA, and these mut... more The mutation rate of mitochondrial DNA (mtDNA) is 17 times higher than nuclear DNA, and these mutations can cause mitochondrial disease in 1 of 10.000 people. The T10609C mutation was identified in type 2 diabetes mellitus (T2DM) patients and the C10676G mutation in cataract patients, with both mutations occurring in the ND4L gene of mtDNA that encodes ND4L protein. ND4L protein, a subunit of complex I in the respiratory complex, has been shown to play a role in the proton translocation process. The purpose of this study was to investigate the effect of both mutations on the proton translocation mechanism. Mutation mapping showed changes in amino acids M47T (T10609C) and C69W (C10676G). The 100 ns molecular dynamics (MD) simulations performed on native and mutants of ND4L-ND6 subunits. It is revealed that the native model had a similar proton translocation pathway to that of complex I from other organisms. Interestingly, the mutant M47T and C69W showed the interruption of the transl...
Jurnal Abdimas Kartika Wijayakusuma, 2021
learning media. The approach is carried out through webinars on chemical science literacy and onl... more learning media. The approach is carried out through webinars on chemical science literacy and online workshops on computational chemistry. The results of the activity, to increase people's understanding of the using of technology and the development of interactive learning media, an activity like webinar is needed that is useful for them and explains how to develop and make learning media that are easy and acceptable to students, whereas to improve skills workshop/training are needed in order to improve the making of attractive learning media.
Jurnal Kartika Kimia, 2020
Diabetes mellitus tipe 2 (DMT2) adalah penyakit yang disebabkan oleh penurunan jumlan insulin ole... more Diabetes mellitus tipe 2 (DMT2) adalah penyakit yang disebabkan oleh penurunan jumlan insulin oleh sel beta pankreas atau kerja insulin yang tidak efektif. Penyakit ini terakumulasi dari gaya hidup tidak sehat atau karena keturunan. Penyebab DMT2 dapat dikaitkan dengan disfungsi DNA mitokondria (mtDNA) yang disebabkan oleh penumpukkan mutasi. Daerah D-loop merupakan bagian dari mtDNA yang memiliki dua daerah yaitu HV1 dan HV2 dengan laju mutasi paling tinggi. Maka, dilakukan penelitian untuk mengidentifikasi mutasi d-loop daerah HV1 dan HV2 untuk mencari mutasi baru yang berkaitan dengan DMT2. Tahapan yang dilakukan meliputi isolasi mtDNA, amplifikasi fragmen HV1 dan HV2 dengan teknik Polymerase Chain Reaction (PCR), visualisasi hasil PCR dengan elektroforesis gel agarosa, penentuan urutan nukleotida daerah HV1 dan HV2 mtDNA, dan analisis hasil sekuensing. Berdasarkan hasil analisis dari perbandingan antara urutan nukleotida sampel dengan revised Cambridge Reference Sequence (rCRS), ditemukan mutasi 16189T>C pada sampel DM02; DM03, dan mutasi 16223C>T pada sampel DM02; DM03; DM04 daerah HV1 D-loop mtDNA, juga mutasi 73A>G pada sampel DM02; DM03; DM04 daerah HV2 D-loop mtDNA. Hasil analisis pada MITOMAP menunjukkan bahwa mutasi 16189T>C tercatat sebagai mutasi yang terdapat pada diabetes, mutasi 16223C>T tidak terkait dengan penyakit apapun, dan mutasi 73A>G terdapat pada penuaan sel otak.
Indonesian Journal of Cancer Chemoprevention, 2019
Fragaria x ananassa (strawberry) is a subtropical plant that can adapt well in tropical highlands... more Fragaria x ananassa (strawberry) is a subtropical plant that can adapt well in tropical highlands. Fragaria x ananassa have been widely used to cope with health problems. The active compound component of secondary metabolites contained in Fragaria x ananassa has the potential as an antioxidant. This research is done to isolate secondary metabolites from extract of Fragaria x ananassa fruits. Extract Fragaria x ananassa was produced by maceration using ethanol as the solvent. Separation and isolation compound were carried out using Vacuum Liquid Chromatography (VLC) and Gravity Column Chromatography (GCC) guided by Thin Layer Chromatography (TLC) using hexane: ethyl acetate (3:7) as the eluent. The flavonoid compound was determined by the total content of phenolic and flavonoid in extract of Fragaria x ananassa fruits. The results of total phenolic content and total flavonoid content were 0.1130 mg/g and 0.0112 mg/g, respectively. The alkaloid compound was determined by Dragendorff t...
JURNAL SELULOSA, 2019
Industri kertas menghasilkan air limbah dari kegiatan produksi dan proses flue gas desulphurizati... more Industri kertas menghasilkan air limbah dari kegiatan produksi dan proses flue gas desulphurization (air limbah wet scrubber). Senyawa nutrisi (senyawa karbon, nitrogen, dan fosfat) yang masih terdapat dalam air limbah terolah dan air limbah wet scrubber belum dimanfaatkan secara optimal dan berpotensi sebagai media pertumbuhan Spirulina platensis. Penelitian dengan variasi komposisi air limbah dan fotoperiode (24 jam terang dan 12 jam terang/12 jam gelap) telah dilakukan dalam skala laboratorium selama 9 hari. Pengukuran pH media, pertumbuhan S. platensis (konsentrasi biomassa, laju pertumbuhan spesifik, dan waktu penggandaan), dan kandungan fikosianin dilakukan setiap hari untuk melihat pengaruh komposisi media dan perlakuan fotoperiode terhadap pertumbuhan S. platensis. Hasil menunjukkan bahwa S. platensis dapat tumbuh dengan baik pada semua komposisi air limbah terolah dan air limbah wet scrubber yang diujicobakan. Konsentrasi biomassa tertinggi sebesar 831 mg/L dan laju pertumb...
JURNAL SELULOSA, 2018
Proses flue gas desulohurization (FGD) dengan wet scrubber adalah suatu proses untuk menurunkan k... more Proses flue gas desulohurization (FGD) dengan wet scrubber adalah suatu proses untuk menurunkan konsentrasi SOx gas buang hasil pembakaran. Proses inidapat mengatasi polusi udara dengan cara menurunkan emisi gas dan partikel debu sehingga menghasilkan gas buangan yang lebih bersih. Air limbah wet scrubber bersifat asam. Salah satu alternatif pemanfaatan air limbah wet scrubber adalah untuk budidaya mikroalga. Spirulina platensis merupakan mikroalga yang berwarna hijau kebiruan yang mempunyai nilai gizi tinggi. Penelitian ini bertujuan untuk mengetahui potensi air limbah wet scrubber sebagai medium pertumbuhan S. platensis dan untuk mengetahui konsentrasi air limbah yang optimum bagi pertumbuhan S. platensis. Metode yang digunakan adalah Rancangan Acak Lengkap (RAL) dengan 5 perlakuan dan 5 ulangan. Air limbah wet srubber dengan konsentrasi 0%, 25%, 50%, 75%, dan 100% digunakan sebagai medium pertumbuhan S. platensis. Selama kultivasi, dilakukan pengamatan pH, produksi biomassa, dan ...
Identification of ATPase6 gene mutation from cimahi clinical isolates
Journal of Physics: Conference Series, 2020
Diabetes mellitus is a mitochondrial disease, caused by ATP deficiency. ATP was produced by the O... more Diabetes mellitus is a mitochondrial disease, caused by ATP deficiency. ATP was produced by the OXPHOS system in the mitochondria. Mitochondrial ATPase6 was one of important enzyme in oxidative phosphorylation process of ATP synthesis. The aim of this research was to provide information of ATP6 gene mutation that correlated to DMT2. A pair of primers was designed by in silico study. Blood samples were taken from DMT2 patients. Blood cells were lysed to obtain DNA template. Amplification of ATP6 gene was done by Polymerase Chain Reaction (PCR) technique. The amplicon was analyzed by 1% agarose gel electrophoresis. The gel showed 0,7 kb band of amplicon. The nucleotide sequencing showed that the amplicon was 681 base pairs. Analysis of phylogenetic showed that the sequence was 94,08% identical to homo sapiens ATP6 gene. Homology analysis between ATP6 gene from genbank and ATP6 gene fragments showed that there was a mutation 8860A>G. Amino acid analysis showed that 8860A>G change...
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Papers by rahmaniar mulyani