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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 15 Documents
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Search results for , issue "Vol. 29, No. 1" : 15 Documents clear
Roles of the Survivin BIR Domain in Cellular Apoptosis and Proliferation: An In Silico Study Nihayah, Silviatun; Wanandi, Septelia Inawati; Erlina, Linda; Syahrani, Resda Akhra
Makara Journal of Science Vol. 29, No. 1
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Survivin is an antiapoptotic protein that is highly expressed in cancer cells. We investigated the dual roles of the Bacu-lovirus IAP Repeats (BIR) domain within survivin, encompassing both apoptosis and proliferation, through an in silico study. The protein-protein interaction (PPI) network of survivin was analyzed using Cytoscape software. Functional enrichment (FE) analysis and data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify the implicated signaling pathways. The binding affinity of the BIR domain with the targeted proteins was visualized via molecular docking analysis. Drawing insights from the PPI network and FE analysis, we identified two key proteins in-volved in apoptosis such as X-linked Inhibitor of Apoptosis Proteins (XIAP) and caspase-9, and proliferation such as Cyclin-dependent Kinase 1 (CDK1) and Inner Centromere Protein (INCENP) for further analysis of their binding with the survivin BIR domain. These proteins were found to bind to the BIR domain at the Thr34, Thr48, and Ser20 resi-dues that have critical roles to regulate the apoptosis and proliferation. This study provides future insights into how the BIR domain of survivin could emerge as a potential target for cancer treatment, such as determining knockout targets for the development of genome editing technology
Morphological, Molecular, and Morphometric Analysis of Aphelenchoides besseyi on Organic Rice (Oryza sativa) Seeds in the Beringin District, Deli Serdang Regency, Indonesia Suswati, Suswati; Azwana, Azwana; Candra, Ifan Aulia; Kuniawati, Fitrianingrum; Siregar, Khofifah Muhaimini; Hasanah, Asmaul; Nasution, Aldy Elvanandar
Makara Journal of Science Vol. 29, No. 1
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Aphelenchoides besseyi, a nematode, can infect rice resulting in the white shoot disease, which decreases the germina-tion rate and even causes seedling death. A. besseyi has recently been reported to mainly attack the organic rice varie-ties especially Pandanwangi and Ciherang in the Pasar Kawat, Beringin District, Deli Serdang, Indonesia. This research investigated A. besseyi via morphological, molecular, and morphometric approaches. The nematodes were observed in an area of 2000 m2, divided into five sample plots each with an area of 400 m2 on which Pandan Wangi and Ciherang rice were cultivated. Nematode morphology was observed using a stereo microscope at a 10–100x magnification. Mo-lecular identification employed PCR, followed by sequencing and phylogenetic analysis. This nematode possessed typ-ical morphological characteristics namely a longer female body (457.07–738.86 µm) than males (385.23–505.29 µm), and cured spicules, 17 to 21 µm long. The tail was ribbon-shaped with a tapered tip that had a mucrone with 2–4 points. Sequencing and phylogenetic analysis revealed that A. besseyi isolated from Indonesia (Deli Serdang/North Sumatra) was closely related to those from China, India, Russia, Taiwan, and Portugal with a 98% homology level.
Effect of Niobium Dopant on ZnO Thin Films Prepared via the Sol–gel Spin Coating Method Eswar, Kevin Alvin; Rostan, Nur Fairuz; Mohamad, Maryam; Md Akhir, Rabiatuladawiyah; Rasmidi, Rosfayanti; Guliling, Muliyadi; Azhar, Najwa Ezira; Buniyamin, Irmaizatussyehdany; Malek, Mohd Firdaus; Mahmood, Mohamad Rusop; Suhaimi, Husairi Fadzilah; Abdullah, Saifollah
Makara Journal of Science Vol. 29, No. 1
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Thin films of zinc oxide (ZnO) and niobium (Nb)-doped ZnO were deposited on a glass substrate using the sol–gel spin coating method. Diethanolamine, isopropyl alcohol, and zinc acetate served as the stabilizers, solvent, and starting ma-terial, respectively. Niobium pentachloride was employed as the dopant source. Energy-dispersive X-ray analysis con-firmed Nb incorporation. Field emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), and ultravio-let–visible spectroscopy (UV–Vis) analyses characterized the morphology, structure, and optics of the films, respective-ly. Both films, comprising nanoparticles, were visible in FESEM. Nb doping reduced the particle size from 44.2 nm to 35.8 nm. The XRD peaks at 31.23°, 33.48°, and 35.7° indicate the (100), (002), and (101) orientations, respectively. Nb-doped ZnO exhibited enhanced visible-range transmission in UV–Vis analysis. However, UV spectrum transmission significantly decreased. Nb doping reduced the optical bandgap of ZnO from 3.30 eV to 3.27 eV.
Chitosan Extraction from Anabas testudineus Scales for Enhancing the Properties of Edible Corn Starch-Based Films: Characterization and Performance Evaluation Ristianingsih, Yuli; Hernadin, Ivan Aldino; Timotius, Daniel
Makara Journal of Science Vol. 29, No. 1
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The papuyu fish (Anabas testudineus) is a freshwater species found in South and Southeast Asia. It is known for its ability to survive in extreme conditions, such as low oxygen levels and poor water quality, making it a potential candi-date for climate-resilient aquaculture. In this study, chitosan was extracted from the scales of papuyu fish through de-mineralization using 1 N HCl solution, deproteination using 5% NaOH solution, and deacetylation using 70% NaOH solution, resulting in an overall yield of 5.11%. The extracted chitosan was added to edible film made from corn starch, and the properties of the prepared films were characterized via Fourier transform infrared spectroscopy, scanning elec-tron microscopy, water solubility test, and water vapor permeability test. Fourier transform infrared spectroscopy re-vealed the presence of characteristic peaks of chitosan, such as amide I (C=O) and amide II (C–N), at around 1647.26 cm−1. Scanning electron microscopy revealed the presence of pores in the edible films. Furthermore, the water solubility of the prepared films decreased with increasing chitosan content. However, the addition of chitosan did not significant-ly affect the permeability
Screening for Penicillin G Acylase (PGA)-Producing Bacteria and Gene Cloning Using Degenerate Oligonucleotide Primed-PCR Masdalifah, Masdalifah; Wulandari, Sri Rezeki; Sabbathini, Gabriela Christy; Ulfah, Maria; Achnafani, Dini; Wibisana, Ahmad; Sriherfyna, Feronika Heppy; Helianti, Is; Nurhayati, Niknik
Makara Journal of Science Vol. 29, No. 1
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The growing concern over antibiotic resistance has driven global efforts to explore innovative solutions, including the use of Penicillin G acylase (PGA) to produce semisynthetic β-lactam antibiotics. This study screened four potential in-tracellular PGA-producing bacteria: Alcaligenes faecalis InaCC B444 (AfPGA), Kluyvera cryocrescens InaCC B850 (KcPGA), Providencia rettgeri InaCC B25 (Pr25PGA), and P. rettgeri InaCC B466 (Pr466PGA). Penicillin G Acylase encoding genes (pgas) were isolated from them using a Degenerate Oligonucleotide Primed-PCR (DOP-PCR) approach and sequenced. Microbiological assays confirmed all tested crude extracts to exhibit inhibitory effects. Penicillin G was used for evaluating hydrolytic activity and 6-Amino Penicillanic Acid (6-APA) coupled with D-p-Hydroxyl-phenylglycine methyl ester hydrochloride (DHPGME) for the synthetic activity. Pr466PGA and Pr25PGA showed the highest synthetic and hydrolytic activities, respectively. DOP-PCR successfully amplified a 2,517 bp pga-encoding Pr25PGA. The deduced amino acid sequence shared 95.1% identity with the known PGA from P. rettgeri PX04. Sec-ondary structure analysis of Pr25PGA revealed 35% α-helices, 16% β-sheets, and 49% coils, suggesting that the enzyme may be flexible and dynamic, with structural stability primarily provided by the α-helices and β-sheets. These findings offer valuable insights for the future design and application of Pr25PGA, particularly in the production of semisynthetic β-lactam antibiotics.
Molecular Interaction of Purple Rice Ferulic Acid and Skin Aging-Related Enzymes Wijayanti, Ernanin Dyah; Fatchiyah, Fatchiyah; Safitri, Anna; Siswanto, Dian
Makara Journal of Science Vol. 29, No. 1
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Purple rice is rich in ferulic acid, a phenolic acid abundant in rice. Ferulic acid (FA) has long been recognized for its anti-oxidant properties, which are linked to its skin anti-aging activity owing to its ability to scavenge free radicals and pro-tect cells from damage. Skin anti-aging activity could be assessed by inhibiting skin aging enzymes. However, there was limited information on the mechanism of FA inhibition of these enzymes. This study focused on the molecular interac-tion between purple rice FA and collagenase or tyrosinase, both with and without their substrates. The interaction be-tween FA (CID 445858), collagenase (2Y6I), tyrosinase (5M8M), collagenase substrate (CID 5486160), and tyrosinase substrate (CID 6057) was docked using Hex 8.0.0 Cuda with the default settings. Discovery Studio 2020 and LigPlot software were used to visualize the docking results. Ascorbic acid (CID 54670067) and kojic acid (CID 3840) were used as positive controls for collagenase and tyrosinase, respectively. Molecular docking revealed that FA formed electro-static, hydrogen, and hydrophobic bonds with all aging enzymes, substrates, and enzyme–substrate complexes. FA could bind to both free enzymes and free substrates, consequently attenuating enzyme–substrate bonding, and preventing the substrate from binding appropriately in its normal position. Molecular dynamics simulations demonstrated that FA formed a stable bond with tyrosinase, similar to kojic acid, although the bond with collagenase was less stable. However, the pattern of each parameter during the simulation was comparable with that of ascorbic acid. The current study indicated that the FA from purple rice had the potential to act as an inhibitor of skin aging en-zymes and could be developed as a skin anti-aging candidate
Development of a Multi-Epitope Peptide Vaccine Against Monkeypox Virus: Immunoinformatics Analysis for South East Asian HLA Alleles Chandra, Nelson; Herdiansyah, Mochammad Aqilah; Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Parikesit, Arli Aditya
Makara Journal of Science Vol. 29, No. 1
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The monkeypox virus (MPXV), a DNA virus causing zoonotic disease, poses major global public health challenges, with mortality rates between 3%–6%. Although smallpox vaccines provide partial cross-protection, there is a critical need for a dedicated, effective monkeypox (mpox) vaccine. This study aimed to design a multi-epitope peptide-based vaccine specifically adapted to the HLA allele profiles common in Southeast Asian populations, where MPXV cases are rising. Using immunoinformatics, we screened for and detected B and T cell epitopes from the MPXV cell surface antigen and IFN-alpha/beta receptor proteins. The vaccine design was validated through a rigorous evaluation of its antigenicity, immunogenicity, allergenicity, and toxicity to ensure both safety and efficacy. Key epitopes were mapped to HLA alleles including HLA-A*11:01, HLA-A*24:02, and HLA-B*15:02, which are highly prevalent in Southeast Asia populations. Molecular docking analyses demonstrated stable interactions between the vaccine construct and TLR3/TLR4 immune receptors, suggesting a robust immune response activation. Additionally, molecular dynamics simulations confirmed the structural stability of the vaccine-receptor complex. This immunoinformatics-driven multi-epitope vaccine design offers a promising candidate for combating MPXV, with high projected coverage and immuno-genic potential for Southeast Asian populations. Validation in laboratory and clinical settings is recommended to con-firm these findings.
Cloning and Expression of SCAMP3 in Escherichia coli BL21(DE3) with In Silico Sequence-Based Cancer Epitopes Prediction Rajagukguk, Selly Setiati; Pambudi, Sabar; Dwiranti, Astari; Utomo, Doddy Irawan Setyo; Bowolaksono, Anom
Makara Journal of Science Vol. 29, No. 1
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Secretory carrier membrane protein 3 (SCAMP3) is a crucial membrane protein involved in intracellular vesicle traffick-ing and exocytosis. The SCAMP3 expression has been observed in diverse cancer types, such as melanoma, glioma, hepatocellular and breast cancer. Increased SCAMP3 expression has been reported in certain cancer cells relative to that in normal cells, suggesting the potential role of SCAMP3 in cancer development or progression. In this study, we successfully cloned and expressed SCAMP3 in Escherichia coli strain BL21(DE3). SCAMP3 was amplified and insert-ed directionally into the prokaryotic expression vector pET21d(+). The transformation of recombinant plasmid into E. coli BL21(DE3) cells were performed for the protein expression. SDS–PAGE and Western blotting were performed to detect the expression product induced by IPTG, which confirmed the presence of a recombinant pET21d(+)-SCAMP3 at 38-kDa protein weight. Bioinformatics analyses helped discover several possible epitopes distributed throughout the SCAMP3 protein sequence. These findings together serve as a basis for future biochemical and functional studies on this important membrane protein alongside immunotherapy research related to SCAMP3 as a cancer biomarker.
Assessment of Fish Biodiversity of the Cimandiri Watershed, West Java, Indonesia Gustiano, Rudhy; Haryono, Haryono; Wahyudewantoro, Gema; Krismono, Krismono; Rusdianto, Rusdianto; Nur, Firman M.
Makara Journal of Science Vol. 29, No. 1
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Information on the fish biodiversity of the Cimandiri Watershed is incomplete, and human activities and anthropogen-ic impacts pose a significant threat to this biodiversity. The purpose of this study was to assess the biodiversity of fish in the Cimandiri Watershed. The results indicated that fish biodiversity in the area included 104 species belonging to 49 families. There were 26 species in the upstream area, 47 species in the middle area, and 61 species in the downstream area. Forty-three species were native to Indonesia, and 7 of the native fish were endemic to the area. There were 11 introduced species belonging to 6 families. Analysis of biodiversity status shows that 4 species were threatened, 2 spe-cies were near-threatened, 76 species were less considered, and 18 species have not yet been evaluated. Among the economically important species present, the eel is the most common in the Cimandiri Watershed. This study has re-vealed the profile of the Cimandiri Watershed, the characteristics of its ecosystem, fish biodiversity, economically im-portant fish species, the conservation status of fish species, and the threats to the fish biodiversity within it.
Effect of Temperature on Physicochemical Properties of Plasticized Hydroxypropyl Methylcellulose K100–Carbopol 934 Films Containing Propylene Glycol as Plasticizer Panda, Braja Bihari; Sahoo, Rudra Narayan; Nayak, Amit Kumar
Makara Journal of Science Vol. 29, No. 1
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This paper studies the effect of different temperatures on different important physicochemical characteristics of plasti-cized hydroxypropyl methylcellulose (HPMC) K100-Carbopol 934 films containing propylene glycol (as a plasticizer), such as the rheology, thickness, folding endurance, tensile strength, elongation, and in vitro swelling with diffusion ki-netics. Rheology of HPMC K100-Carbopol 934 blend dispersions containing propylene glycol (before film casting) demonstrates that the flow is shear thinning and pseudoplastic. In the study of in vitro swelling, the relaxation-controlled transport is the predominant process of solvent diffusion into these plasticized HPMC K100–Carbopol 934 blend films under study. The results suggest that the solvent transport process followed second-order kinetics, and the diffusion mechanism is non-Fickian diffusion. Regular measurements of mass variation, as well as the isothermal ki-netic curves, are plotted. The plasticized HPMC K100–Carbopol 934 blend films are characterized by differential scanning calorimetry and scanning electron microscopy.

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