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INDONESIA
Indonesian Journal of Biotechnology
Published by Universitas Gadjah Mada
ISSN : 08538654     EISSN : 20892241     DOI : -
Core Subject : Science,
Biochemistry, Genetics & Molecular Biology Immunology & microbiology Materials Science & Nanotechnology
The Indonesian Journal of Biotechnology (IJBiotech) is an open access, peer-reviewed, multidisciplinary journal dedicated to the publication of novel research in all aspects of biotechnology, with particular attention paid to the exploration and development of natural products derived from tropical—and especially Indonesian—biodiversity. IJBiotech is published biannually and accepts original research articles featuring well-designed studies with clearly analyzed and logically interpreted results. A strong preference is given to research that has the potential to make significant contributions to both the field of biotechnology and society in general.
Arjuna Subject : -
Articles 518 Documents
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Morphological and molecular identification of an unknown fungal isolate from Al‐Dujail District: A new record of Tulostoma winterhoffii in Iraq Taghreed Khudhur Mohammed; Hanaa Naji Abdullah; Sinai Waleed Mohammed; Muntadher Fadhil Jassim
Indonesian Journal of Biotechnology Vol 30, No 2 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.102372

Abstract

The Tulostoma genus, known as stalkballs or stalked puffballs, belongs to the Agaricaceae family. This study was designed to identify an unknown fungal species collected from the Al‐Dujail district in Iraq based on morphological examination and molecular analysis of the internal transcribed spacer (ITS) region. Between April and July 2019, samples were collected from garden soil in the Al‐Dujail district, Salah Al‐Din Governorate, Iraq. Morphological characteristics were documented using light microscopy. Genomic DNA was extracted and purified, and the ITS region was amplified using conventional PCR with specific primers. The amplified products were sequenced, and phylogenetic analysis was conducted using MEGA11 software. Morphological analysis revealed smooth, yellow to brown, nearly circular basidiospores. The ITS region amplification yielded a 588 bp fragment. Basic Local Alignment Search Tool (BLAST) analysis showed 91% similarity between the sample (S1‐ITS‐Iraq) and Tulostoma winterhoffii (accession number KU518975.1). The isolate was assigned in GenBank under accession number PV249065, with phylogenetic analysis positioning S1‐ITS‐Iraq in a cluster with the Tulostoma species, with a bootstrap value of 97%, indicating a close relationship. The fungal sample from Iraq was identified as a new record within the genus Tulostoma, marking the first report of T. winterhoffii in the region.
Osteogenic induction of human Wharton’s jelly‐derived mesenchymal stem cells using a composite scaffold from poly(ɛ‐caprolactone) and biosilica sponge Xestospongia testudinaria Andika Ardiyansyah; Anggraini Barlian; Candrani Khoirinaya; Sony Heru Sumarsono
Indonesian Journal of Biotechnology Vol 30, No 2 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.103519

Abstract

Bone defects occur when bones cannot function properly due to trauma, such as accidents. In Indonesia, such defects are mainly treated by bone grafting, but the limited availability of transplants has led to the development of bone tissue engineering as an alternative. This study uses human Wharton’s jelly‐derived mesenchymal stem cells (hWJ‐MSCs) as these can differentiate into osteoblasts when stimulated by a composite scaffold containing biosilica from the sponge Xestospongia testudinaria. Four main steps were performed in this study, i.e. scaffold fabrication with varying biosilica concentrations, material characterization to see whether the scaffold resembled bone tissue, hWJ‐MSC isolation from the umbilical cord and cultured until passage 6, and scaffold testing to assess its compatibility and ability to support cell adhesion, proliferation, differentiation, and mineralization into bone cells. The results indicated that a scaffold with 50% biosilica has good properties for supporting hWJ‐MSC growth, proliferation, and differentiation. The scaffold exhibits strong mechanical strength and hydrophilic characteristics, enhances cell proliferation, and promotes osteogenic differentiation, as confirmed by collagen type I and osteopontin expression with a higher optical density value in the Alizarin Red assay. Therefore, the 50% biosilica composite scaffold is biocompatible and osteoconductive, making it a promising candidate for bone tissue engineering.
Mutations in RNA‐dependent RNA polymerase could be major cause of high pandemic potential of SARS‐CoV‐2: An in‐silico study Bhawna Sharma; Bennet Angel; Annette Angel; Vinod Joshi; Shareef Mohammed Buvvaji; Neha Singh; Khushbu Kumari; Aarya Chitransh; Poorna Khaneja; Devendra Kumar
Indonesian Journal of Biotechnology Vol 30, No 2 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.104453

Abstract

Human coronaviruses (HCoVs) are responsible for mild common cold to severe pneumonia‐like symptoms in infected individuals. The first HCoV was HCoV‐229E, discovered in 1962 in the US, which causes moderate symptoms. Since then, HCoVs have evolved, leading to epidemics or the recent SARS‐CoV‐2 pandemic. The main objective of this study was to understand the modifications occurred and what led to the transition from mild to pandemic form. Of the viral proteins, the RNA‐dependent RNA polymerase (RdRp) plays a crucial role in viral evolution, mutation, pathogenesis and transmission; this protein was therefore analyzed using in silico tools. We observed that RdRp has shown many mutations during its transition from mild to severe forms in HCoVs, which may have affected its enzymatic activity. The RdRp of HoV‐229E and HCoV‐NL63 showed 171 mutations, while SARS‐CoV‐2 showed the presence of 312. SARS‐CoV‐2 also showed a reduction in hydrophobic amino acid compared to the other HCoVs, consequently contributing to faster replication. Although mutations in the RdRp subdomains were found, yet five conserved regions was also presence among all the seven HCoVs; the finger and thumb subdomains had one conserved region, while the palm subdomains had three. Therefore, it can be inferred that on one hand the mutations reported in RdRp appeared to be the major cause of increased virulence leading to sporadic disease outbreaks, while on the other hand the presence of five conserved regions might prove to be potential targets for the development of new antiviral drugs.
In vitro evaluation, molecular docking, and molecular dynamics studies of resorcinol derivatives against yeast α‐glucosidase Danova, Ade; Hermawati, Elvira; Chavasiri, Warinthorn; Mujahidin, Didin; Musthapa, Iqbal; Kurniadewi, Fera
Indonesian Journal of Biotechnology Vol 30, No 3 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.106495

Abstract

Nine resorcinol derivatives were evaluated for their ability to inhibit yeast α‐glucosidase using the in vitro method. Three molecular docking programs (Autodock Vina, Autodock4 and DockThor) were employed to determine the binding energies. The results showed that two resorcinol derivatives possessing butanoyl (1) and butyl (9) groups demonstrated good inhibitory activity against α‐glucosidase, with IC50 values of 75.9 and 33.3 µM respectively, compared with other derivatives (2–8) and acarbose (IC50 = 832.8 µM). Furthermore, molecular docking indicated that compounds 1 and 9 had better binding affinities than acarbose and the native ligand. Both compounds showed similar interactions with Asp349 and Glu408, which were associated with acarbose and the native ligand. Moreover, molecular dynamics analysis indicated that compound 9 exhibited greater stability than compound 1 when complexed with α‐glucosidase. Therefore, compound 9 has the potential for further studies, both in vitro and in vivo, to evaluate its toxicity, side effects and efficacy.
Biodegradable plant pots made from dried banana pseudo‐stems enriched with a Bacillus sp.‐biochar composite as an eco‐friendly alternative to plastic pots Sangsuwan, Parisatcha; Detraksa, Janejira; Inchomrit, Pranitda
Indonesian Journal of Biotechnology Vol 30, No 3 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.107036

Abstract

Agricultural plastic waste is a major environmental pollutant due to its non‐biodegradable nature. This study discusses the production of biodegradable pots (bio‐pots) using a biochar composed of banana pseudo‐stems and Bacillus sp. The isolated Bacillus sp. produced indole‐3‐acetic acid (IAA), solubilized potassium and phosphate, and secreted siderophores immobilized in banana pseudo‐stem biochar. X‐ray diffraction analysis revealed CaCO3 and KCl as the major elements, aside from carbon, released to the soil. Bio‐pots were made from banana pseudo‐stem biochar mixed with a Bacillus sp.–biochar composite at various formulations: 0%, 1%, 3%, 5%, and 10%. Mechanical testing indicated that the porous structure of the biochar contributed to low pot density and tensile strength. Moreover, the air‐filled spaces within the biochar enhanced water absorption, correlating with the amount of biochar used. Marigolds were cultivated outdoors in the bio‐pots to assess growth and yield. Our findings showed that those grown in biopot‐4 (10%) displayed improved growth and yield compared to the control group (grown in the ground). After 10 weeks, the control plants became infected with fungi and aphids, whereas those grown in biopot‐4 remained unaffected. In summary, bio‐pots incorporating 10% Bacillus sp.–biochar are eco‐friendly, reducing the need for chemical fertilizers, fungicides, and insecticides, while contributing to environmental sustainability. Moreover, the combination of biochar and Bacillus sp. is more effective than an unmixed form, since Bacillus sp. can inhabit and propagate in biochar pores if the conditions are otherwise unsuitable for growth.
Network pharmacology‐based exploration of gut microbiota‐derived metabolites for type‐2 diabetes Widjaja, Nadia; Simatupang, Stefeny Theresia; Tan, Santi; Tjandrawinata, Raymond Rubianto
Indonesian Journal of Biotechnology Vol 30, No 3 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.107382

Abstract

Probiotics confer health benefits and have been investigated for their potential therapeutic properties in type‐2 diabetes (T2D) treatment. This study employs a network pharmacology approach to explore gut microbiota‐derived metabolites that potentially alleviate T2D. Several strains and species of gut microbiota were identified that may produce metabolites with therapeutic potential for T2D. Interestingly, quercetin produced by Bacteroides uniformis and daidzein produced by Bifidobacterium adolescentis and Bifidobacterium breve have been studied for their antidiabetic effects. Using a network pharmacology approach, it was found that quercetin may target AKT1 and EGFR, critical proteins involved in insulin signaling pathways related to T2D. Additionally, 10‐oxo‐11‐octadecenoic acid produced by Lactobacillus plantarum and 10‐keto‐12Z‐octadecenoic acid produced by Lactobacillus paracasei were found to target PPARG, a gene regulating insulin signaling. These findings were further validated by the molecular docking analysis, which showed suitable to satisfactory binding strengths.
Antibacterial activity of mycelial extract from a local fungus, Sclerotium rolfsii Zahra, Muhandinni; Aryantha, I Nyoman Pugeg; Sukrasno, Sukrasno; Suhardi, Veronica Sri Harjati
Indonesian Journal of Biotechnology Vol 30, No 3 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.108408

Abstract

Mycelium‐to‐sclerotium differentiation in fungi involves not only morphological but also biochemical changes throughout the process, which may contribute to their persistence and be a possible source of bioactive compounds. This study aims to evaluate the antibacterial activity and identify the bioactive compound in the local isolate Sclerotium rolfsii. Fungal culture was grown in media containing potato extract (20 g/L), dextrose (20 g/L), and peptone (5 g/L) for 27 days under static conditions at room temperature. Mycelium, sclerotium and filtrate were collected every three days and extracted with methanol, followed by evaporation and antibacterial screening. Significant activity was observed in day three of mycelial extract, which showed morphology of initial sclerotium formation (MIC 0.39 mg/mL) against B. subtilis and E. coli. An improved extraction method (sequential extraction) was employed for mycelial sample on the third day. N‐hexane and ethyl acetate extracts exhibited stronger activities (0.20 mg/mL). Ergosterol was identified after TLC‐bioautography, radial chromatography, and NMR elucidation analysis. S. rolfsii mycelium (third day‐sclerotial initiation) was found to contain ergosterol, demonstrating strong defense against bacteria, and possibly related to sclerotium‐differentiation metabolites. These findings may pave the way for more extensive studies of sclerotium differentiation as an interesting phenomenon of fungal development and bioactive compound origins.
Extracellular alpha‐amylase from halophilic bacteria Marinobacter sp. LES TG5: Isolation, optimization, and characterization Parwata, I Putu; Julyasih, Ketut Srie Marhaeni
Indonesian Journal of Biotechnology Vol 30, No 3 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.108853

Abstract

The growing demand for stable and effective enzymes requires the discovery of novel microbial producers. Alpha‐amylase is an enzyme in high demand by various industries; however, the discovery of novel and stable alpha‐amylase producers remains limited. This study aims to isolate, optimize, and characterize extracellular alpha‐amylase from halophilic bacteria Marinobacter sp. LES TG5. Bacteria were isolated from saltwater and soil samples collected from traditional salt ponds in Les Village, Bali, Indonesia. Initial screening on starch agar yielded several amylase‐producing colonies, and subsequent spectrophotometric assays identified one promising isolate (LES TG5), which demonstrated an initial activity of 0.63 U/mL. The production of amylase was significantly enhanced by a multi‐stage optimization process. This involved first identifying optimal carbon and nitrogen sources, followed by a one‐variable‐at‐a‐time approach to determine the ideal nutrient levels, salt concentration, and incubation time. This optimization led to an 11‐fold increase in activity, from 0.63 U/mL to 6.99 U/mL, achieved with a medium containing 2.4% (w/v) nutrient broth, 0.4% (w/v) maltose, and 3% (w/v) NaCl with an incubation time of 22 hours. Enzyme characterization revealed optimal amylase activity at pH 7, 55 °C, and 3% (w/v) NaCl. While Ca2+ and Mg2+ had no effect on amylase activity, Pb2+, Fe2+, Sn2+, and Al3+ significantly reduced it. Importantly, the amylase demonstrated outstanding stability in organic solvents such as methanol, ethanol, and n‐hexane, suggesting its potential as a biocatalyst for chemical synthesis in non‐aqueous systems. Furthermore, its notable stability against surfactants and detergents highlights its promise as an additive in cleaning product formulations.

Page 52 of 52 | Total Record : 518

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