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Ivandini Tribidasari A.
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Makara Journal of Science
Published by Universitas Indonesia
ISSN : 23391995     EISSN : 23560851     DOI : https://doi.org/10.7454/mss
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Makara Journal of Science publishes original research or theoretical papers, notes, and minireviews on new knowledge and research or research applications on current issues in basic sciences, namely: Material Sciences (including: physics, biology, and chemistry); Biochemistry, Genetics, and Molecular Biology (including: microbiology, physiology, ecology, taxonomy and evolution); and Biotechnology.
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Articles 910 Documents
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Comparing the Effectiveness of Eggshell Spectra from Laser-Induced Break-down Spectroscopy and Near-Infrared Spectroscopy Using Principal Compo-nent Analysis to Determine the Authenticity of Organic Eggs Qusthalani, Ahmad; Mitaphonna, Rara; Ramli, Muliadi; Rajibussalim, Rajibussalim; Lahna, Kurnia; Zaini, Nasrullah; Idris, Nasrullah
Makara Journal of Science Vol. 29, No. 4
Publisher : UI Scholars Hub

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Abstract

This study aimed to explore the potential of modern spectroscopy in the authentication of organic and non-organic chicken eggs using near-infrared spectroscopy (NIRS) and laser-induced breakdown spectroscopy (LIBS) spectra. A total of 175 eggs were analyzed, which were grouped into seven categories based on the source of feed given: 100% organic, 100% non-organic, 75% organic, 75% non-organic, 50% organic, free-range chickens, and eggs obtained from the local traditional market. Each group consisted of 25 eggs. NIRS spectra were recorded in the wavelength range of 350–2500 nm, whereas LIBS spectra were recorded in the range of 200–900 nm. A total of 350 spectral data were normalized and processed using multiplicative scatter correction, Savitzky–Golay filter, and detrending before being analyzed with principal component analysis (PCA). Analysis based on the PCA score plot showed that NIRS successfully distinguished organic and non-organic eggs with a separation percentage of 100%, whereas LIBS achieved a separation percentage of 86%. These results indicate that NIRS has significant advantages over LIBS in the authentication of organic and non-organic eggs. In addition, eggs from the uncaged chicken category showed similar spectral patterns to eggs from chickens fed 100% organic feed. Eggs obtained from the local traditional market were evenly distributed in the organic and non-organic groups. This study provides an important contribution to the development of nondestructive methods for controlling the quality and authentication of eggs in the food industry.
Development of Shigella flexneri Detection Method by Real-Time Polymerase Chain Reaction Targeting the sfmD Gene Nurjayadi, Muktiningsih; Azizah, Puan Aqila; Setiawan, Agus; Sihombing, Ananda Indah Putri; Fitriyanti, Anisa; Grace, Grace; Putri, Gusti Angieta; Angelina, Helzi; Musie, Royna Rahma; Declan, Jefferson Lynford; Putri, Gladys Indira; Juliansyah, Dandy Akbar; Fatimah, Siti; Fahriza, Tiara; Kartika, Irma Ratna; Kurniadewi, Fera; Novitasari, Novitasari; Abomoelak, Bassam; El Enshasy, Hesham Ali; Chen, Shyi-Tien
Makara Journal of Science Vol. 29, No. 4
Publisher : UI Scholars Hub

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Shigella flexneri can cause shigellosis, which results in high fever, vomiting, diarrhea, or death. This study developed a detection method based on real-time polymerase chain reaction that targets the sfmD gene of S. flexneri given that the virulence factor encoded by this gene is thought to facilitate adhesion to a host surface. The proposed method involves primer design, DNA isolation, the optimization of primer annealing temperature, and confirmation, specificity, and sensitivity tests. A sfmD primer with an amplicon length of 155 bp was annealed to the target DNA at an optimized temperature of 60 ℃ (range 54 °C–62 °C). This primer pair amplified the target sequences at a cycle threshold (Ct) of 15.11 ± 0.38 and a melting temperature of 82.41 ± 0.01 ℃. The primer specificity test showed that the primer distinguished S. flexneri from nontarget bacteria. The findings also revealed that the primer detected S. flexneri down to a limit of 16 pg/μL at a Ct of 26.68, equivalent to 2.79×102 CFU. Overall, the sfmD primer can effectively amplify S. flexneri DNA. Future research can be directed toward the detection of S. flexneri in artificially contaminated food samples to validate the real-food applicability and strengthen its potential use in food safety monitoring and clinical diagnostics.
Microplastic Degradation using Laccase Enzyme from Trametes hirsuta: In the Silico Study Riyanto, Hanzhola Gusman; Sylvia, Diana
Makara Journal of Science Vol. 29, No. 4
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Microplastics are a serious global problem that arises worldwide because of their widespread use. Exposure to microplastics can negatively affect human and environmental health. In this study, we used molecular docking methods with MOE software (version 2014.0901) to investigate the interaction between the laccase enzyme and several microplastic compounds as a preliminary study of microplastic degradation using enzymes. The Quantitative Structure Analysis Relationship (QSAR) analysis revealed that all microplastic ligands had higher Pa values than Pi, indicating that the laccase enzyme may be biologically active. The findings of the present study show that polyamide (PA) has the lowest binding energy among microplastics, implying that the enzyme can interact well with both active sites. In contrast, polypropylene exhibited the highest binding energy, indicating a lack of strong residue interactions between the ligand and the active sites. The Phe463 active site work well when dealing with nonpolar aromatic polymers, including polycarbonate, poly (methyl methacrylate), polystyrene, and polyurethane, allowing for significant π–π stacking interactions. The Ile455 active sites are more effective when dealing with polar aromatic polymers, such as PET and polyamide, due to their better hydrogen bonding or dipole interactions. This finding can be used as an initial basis for microplastic enzymatic degradation
Effect of Niobium Addition on Corrosion Behavior, Mechanical Properties, and Microstructures of U6Zr Alloys in an Aerated Environment Masrukan, Masrukan; Handoko, Djati; Djuhana, Dede; Sigit, Rohmad; Al Hasa, M. Husna; Adi, Wisnu Ari; Mardiah, Siti
Makara Journal of Science Vol. 29, No. 4
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Abstract

The effect of Nb addition on the corrosion behavior of U–6Zr alloys within an aerated, demineralized water (DW) environment (pH 5.61) and its correlation of this addition with the mechanical and microstructural properties of the alloys were investigated. The U–6Zr–xNb alloys (x = 1, 4, and 7 wt.%) were synthesized by arc-melting U, Zr, and Nb. Additionally, the samples were mounted and polished, after which they were subjected to electrochemical corrosion analysis using a potentiostat. This evaluation was conducted in a DW medium (pH 5.6), representing an aerated atmosphere, at room temperature (27°C) and a potentiodynamic scan rate of 1 mV/cm2. The results demonstrate that Nb addition to the U–6Zr alloy, which yielded a U–6Zr–xNb (x = 1.4 and 7 wt.%) alloy, influenced the corrosion behavior in media, exhibiting a slightly acidic pH (5.61). Nb additions of up to 4 wt.% caused a continuous increase in the open-circuit potential, corrosion-current density, and corrosion rate (CR); however, these values decreased with the continuous increase in Nb concentrations to 7 wt.%. Furthermore, microstructural analysis via scanning electron microscopy and energy-dispersive X-ray spectroscopy revealed that the corrosion products across almost all U–6Zr–xNb test samples (x = 0, 1, 4, and 7 wt.%) were primarily stable uranium dioxide, which formed a protective layer, followed by oxynitride and zirconium(IV) oxide.Overall, the findings indicated that the varying Nb contents (1, 4, and 7 wt.%) dictated the CR, mechanical properties, and microstructure of the alloys. Ultimately, this study demonstrates the synthesis of U–6Zr–xNb alloys (x = 0, 1, 4, and 7 wt.%) with enhanced performance characteristics.
Quantitative Structure-Activity Relationship, Pharmacokinetics, Drug-likeness, Toxicity, and Molecular Docking Studies of 4-N-(Methyl)-4-Aminoquinoline Derivatives as Antimalarial Compounds Baari, Muhamad Jalil; Hardiyanti, Devi
Makara Journal of Science Vol. 29, No. 4
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Antimalarial drug resistance has encouraged various innovations to develop novel drug compounds that are effective, feasible, and safe, adhering to health standards. One way to do that is by observing and predicting the biological activity of drug compounds using quantitative structure–activity relationship (QSAR) analysis. In this study, QSAR analysis was conducted on the 4-N-(methyl)-4-aminoquinoline derivatives, which effectively inhibit the growth of Plasmodium falciparum as a source of malaria. The research stages involved molecular structure modeling, molecular geometry optimization using the AM1 semi-empirical method, and QSAR descriptor calculations, including electronic (atomic charges (q), HOMO and LUMO energies, polarizability (α), and dipole moment (DM)), hydrophobic (log P), and steric (molecular weight (MW) and molecular refractivity (MR)) parameters. Optimizations and calculations were performed using the Hyperchem software version 8.0. Multiple linear regression (MLR) analysis and external validation generated the best QSAR equation for Model 5: Log (1/IC50) = 11.132 + 42.074qC1 + 853.716qC7 + 444.151qC8 − 1380.73qC9 + 12.577qC16 + 1.155E HOMO − 1.0LogP − 1.365DM. The design of the novel derivatives was based on the QSAR equation’s influential parameters. Subsequently, the pharmacokinetic, drug-likeness, and toxicity aspects were investigated using the SwissADME and ProTox web servers. The results showed that several types of derivative compounds that have been synthesized and designed fulfill these three aspects. Derivatives 1D and 1E with higher antimalarial activities tended to have good pharmacokinetic profiles and drug-like properties but had higher toxicity levels than the other derivatives. Compounds 1B and 1C have relatively lower antimalarial activity but more favorable toxicity profiles. Compound 1A was considered the best potential drug candidate because of its high antimalarial efficacy and relatively low toxicity. The binding affinity of the 4-N-(methyl)-4-aminoquinoline derivatives (−7.5 to −8.3 kcal/mol) with the PfDHODH receptor was close to its native ligand (−10.9 kcal/mol). This is corroborated by the stability and flexibility of PfDHODH-1A obtained from the molecular dynamics (MD) simulations. Therefore, these designed compounds have potential as novel antimalarial drugs.
Morphological Characteristics of the Mediophyceae Diatom Lampriscus cf. shadboltianus var. crenulatus Collected from Gili Meno, Indonesia Rachman, Arief; Widiarti, Riani; Sukotjo, Setiarti; Wells, Mark
Makara Journal of Science Vol. 30, No. 1
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Diatoms are the most common and abundant microalgae group in seawater, with an estimated 200 genera and 200,000 species categorized into three distinct taxonomic classes: Mediophyceae, Bacillariophyceae, and Coscinodiscophyceae. This study describes the morphological characteristics of Lampriscus GM052022, a diatom belonging to the Mediophyceae family, which was collected from Gili Matra, Lombok, Indonesia. Analysis using light microscopy (LM) and electron microscopy (EM) showed that the morphological characteristics of the Lampriscus GM052022 specimen are similar to those of Lampriscus shadboltianus var. crenulatus due to the distinct crenulation lines on the frustule, which differentiate this variation from Lampriscus shadboltianus. However, the presence of distinct morphological features in this diatom specimen from Gili Meno suggests that it might not be L. shadboltianus var. crenulatus. The triangular spines (spinules) observed on the Lampriscus GM052022 valve surface have not been previously documented. However, whether the presence of spinules is a sign of different taxa or a result of polymorphism within the species or variation cannot be confirmed. Due to this characteristic, Lampriscus GM052022 is given the temporary name L. cf. shadboltianus var. crenulatus. The next step will be to conduct genetic analyses to confirm whether these morphological differences support the separation of this Gili Meno Lampriscus specimen into a new species (sp. nov.) or variation (var.).
Performance of Membrane Bioreactor in Nitrogen Removal using Anammox Bacteria Cultivated from Lake Koto Baru Zulkarnaini, Zulkarnaini; Amanda, Tiffany Azhra; Putra, Alqadri Asri; Komala, Puti Sri; Nilawati, Dewi; Widyarani, Widyarani; Sembiring, Tarzan; Mawarda, Panji Cahya; Septevani, Athanasia Amanda; Rustama, Mia Miranti; Andriyani, Rina
Makara Journal of Science Vol. 30, No. 1
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Anaerobic ammonium oxidation (anammox) is the biological conversion of ammonium to nitrogen gas (N2) using nitrite as an electron acceptor. This study evaluated the performance of a membrane bioreactor (MBR) in nitrogen removal at room temperature using Candidatus Brocadia fulgida, an anammox bacterium previously cultivated from Lake Koto Baru, Tanah Datar, Indonesia. The MBR was operated for 48 days with a hydraulic retention time of 24 h under a continuous supply of ammonium and nitrite, with both substrates provided at influent concentrations of 70, 150, and 250 mg-N/L. Samples were collected twice a week and analyzed via UV–Vis spectrophotometry. The stoichiometric ratios of ∆NO2−-N/∆NH4+-N and ∆NO3−-N/∆NH4+-N were 1.13 and 0.15, respectively, which were consistent with the anammox reaction. The maximum nitrogen removal performance, including nitrogen removal rate, ammonium conversion efficiency, and nitrogen removal efficiency (NRE), reached 0.515 kg-N/m³∙d, 92.76%, and 91.27%, respectively, at a nitrogen loading rate of 0.566 kg-N/m³∙d. Anammox bacteria from Koto Baru Lake showed high NRE at room temperature using MBR.
Identification of Xanthine Oxidase Inhibitors in Single-Clove Black Garlic using Metabolomics and Molecular Docking Approaches Setiawan, Abdul Aziz; Kumala, Shirly; Laksmitawati, Dian Ratih; Yuniarto, Ari; Yuliana, Nancy Dewi
Makara Journal of Science Vol. 30, No. 1
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Black garlic is produced through controlled fermentation under specific temperature and humidity conditions, during which the Maillard reaction enhances its sensory properties and bioactivity. The anti-hyperuricemic potential of single-clove black garlic (SBG) remains unexplored. This study combined Ultra High-Performance Liquid Chromatography–High Resolution Mass Spectrometry-based metabolomics and an in-silico approach to identify the potential xanthine oxidase inhibitors (XOI) in SBG. Methanolic extracts (10 ppm) exhibited xanthine oxidase inhibition ranging from 50.09% to 68.01%, which is comparable to allopurinol (78.74%) at the same concentration. Metabolomic profiling tentatively identified 45 compounds, and orthogonal partial least squares analysis revealed seven metabolites as strongly correlated with XOI activity, namely α-(1-deoxy-D-fructose-1-yl)-L-arginine, alliin, 2-amino-2-deoxy-D-glucose, S-allyl-L-cysteine, quercetin, and m-coumaric acid. Molecular docking showed that these compounds exhibited binding energies comparable to allopurinol, thus indicating favorable interactions within the xanthine oxidase active site. Molecular dynamics simulations confirmed the stability of ligand–enzyme complexes, with consistent hydrogen bond interactions, which support their stable binding conformations. ADMET analysis revealed that most compounds demonstrated acceptable pharmacokinetic profiles, high intestinal absorption, low blood–brain barrier permeability, and non-hepatotoxic and non-mutagenic properties. The integration of metabolomics, molecular docking, molecular dynamics, and ADMET prediction supports the potential of SBG-derived compounds as safe and effective XOIs, thereby highlighting SBG as a promising functional food candidate for the management of hyperuricemia
In Vitro and In Silico Analysis of the Antibacterial Activity of Bioactive Compounds Extracted from Pineapple Peel Sadik, Wafa Mohammad; Abdullah, Iman Tajer; Alnajar, Lana Abed
Makara Journal of Science Vol. 30, No. 1
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Antibiotic resistance is a critical global challenge that requires the discovery of alternative therapeutic agents. Plants -derived compounds, such as those found in Ananas comosus (pineapple)peel, offer promising antibacterial potential. This study aimed to evaluate the antibacterial activity of pineapple peel extract using both in vitro and in silico approaches. Ethanolic extracts of pineapple peel were fractionated using silica gel chromatography, and the resulting fractions were analyzed by GC-MS. Antibacterial activity was tested against Gram-positive and Gram-negative pathogens using the agar well diffusion method, and the inhibition zones were recorded. Molecular docking was performed to assess the interaction of identified compounds with the CoA-bound OdaA protein of Pseudomonas aeruginosa (PDB ID:7BOR). Fractions 3 and 4 exhibited the strongest antibacterial activity, producing inhibition zones up to 23 mm against P. aeruginosa at 50 mg/ml. GC-MS identified several bioactive compounds, among which 4-Methoxyphenylglyoxal hydrate showed the highest docking affinity (-5.56 Kcal/mole) and formed two hydrogen bonds with the bacterial target protein. These findings demonstrate that pineapple peel, often considered agricultural waste, is a valuable source of bioactive antibacterial agents. The strong in vitro activity combined with promising in silico binding results highlights its potential in developing novel treatments, particularly against Gram-negative pathogens
Design and In Silico Modeling of Heterocyclic-based Xanthone Derivatives as Potential Anticancer Agents Through Tyrosine Kinase Inhibition Kurniawan, Yehezkiel Steven; Yudha, Ervan; Fatmasari, Nela; Yogaswara, Radite; Pranowo, Harno Dwi; Sholikhah, Eti Nurwening; Jumina, Jumina
Makara Journal of Science Vol. 30, No. 1
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Cancer is one of the deadliest diseases nowadays, and tyrosine kinase receptors play crucial roles in cancer cell survival, differentiation, proliferation, and migration. This study designed and developed a new inhibitor from heterocyclic-based xanthone derivatives to target two tyrosine kinase receptors, epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor (PDGFR), through in silico screening. Eighteen heterocyclic-based xanthones were evaluated through molecular docking for both receptors. All heterocyclic-based xanthones gave the root mean square deviation (RMSD) value lower than 2.00 Å. Xanthone with isobenzothiazole substituent (iBzThio) was found as the most potent inhibitor with binding energies of -10.60 and -12.90 kcal/mol against EGFR and PDGFR, respectively. Further investigation has been performed through molecular dynamics (MD) simulation for 100 ns. From the results of MD simulations, i.e., RMSD, root mean square fluctuation, radius of gyration, solvent accessible surface area, hydrogen bonds, and binding energy parameters, as well as secondary structure fraction, dictionary of protein secondary structure, and Ramachandran plot, iBzThio demonstrated good stability to interact with the active site of both receptors. The binding energies of IBzThio against EGFR and PDGFR receptors were -12.58 and -12.61 kcal/mol after the MD simulations, indicating its potential application as an effective tyrosine kinase inhibitor.

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