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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 7 Documents
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Search results for , issue "Vol 30, No 2 (2025)" : 7 Documents clear
Identification and genetic study of lactic acid bacteria from intestine of domestic chickens (Gallus gallus domesticus) Ixora Sartika Mercuriani; Heru Nurcahyo; Bernadetta Octavia; Astuti Astuti; Adinda Yuslia Rukmanandita; Fita Nilasari
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.85963

Abstract

The gastrointestinal tract is one of the habitats of lactic acid bacteria (LAB). This research aims to identify the LAB isolated from the intestines of domestic chickens (Gallus gallus domesticus) based on phenotypic and genotypic characteristics. The LAB was cultivated on enrichment media MRSA + CaCO3 1% and a selection of isolates based on the halo zone. The phenotypic character identification using morphological, physiological and biochemical tests was analyzed by similarity simple matching (SSM) and a dendrogram (MVSP 3.1). Genotypic identification was made by 16S rRNA gene sequences with PCR methods, sequencing and analysis using BLAST at www.ncbi.nlm.nih.gov. The results show that 87 isolates were isolated based on the halo zone. Phenotypic tests were performed on eight isolates (J6, J15, J18, J28, B11, B24, B25 and B26). The results show that four isolates have similarities with the genus Bacillus, two isolates with the genus Lactobacillus, and two with the genus Streptococcus. The identification based on the 16S rRNA gene of four selected isolates (J15, J28, B24 and B26) showed that J15 was identified as Bacillus cereus (98.56% similarity); J28 as Lactobacillus johnsonii (99.67%); B24 as Bacillus cereus (98.30%), and B26 as Streptococcus pluranimalium (96.68%).
Integrated omics for increasing plant production and health‐related nutrition under extreme conditions: The Indonesia perspective Enny Sudarmonowati; Alfia Aini Annur Azizi; Aviv Andriani; Sri Koerniati; Eny Ida Riyanti; Edy Listanto; Carla Frieda Pantouw; Bernadetta Rina Hastilestari; Decintya Jaya Maysha
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.99156

Abstract

Despite Indonesia being a megadiverse country that provides germplasm for breeding to produce improved future varieties, significant threats are faced related to biodiversity extinction. Such threats, for example habitat degradation and climate change, which lead to extreme conditions, must be addressed as they have contributed to stresses at the molecular level and affect plant production and health‐related nutrition. Integrated omics approaches have been applied to address the problems, as well as to produce varieties with superior traits, which are critical factors in achieving improved plant production and better naturally derived human nutrition. The paper discusses the omics research agenda in Indonesia; Indonesian biodiversity of nutraceutical plants and how omics can increase its production. Besides, current progress of omics application in Indonesia, policies and regulations to enhance integrated omics research are elucidated. By applying these approaches in Indonesia, breeding for better traits to support human needs and improve health quality will be greatly accelerated in the future.
Optimization of methanol‐induced expression and His‐tag purification of Saccharomycopsis fibuligera R64 mutant α‐amylase in Pichia pastoris Clara Claudia; Elsa Destiana; Rista Awalia; Mia Tria Novianti; Taufik Ramdani Tohari; Dewi Astriany; Shinta Kusumawardani; Muhammad Yusuf; Umi Baroroh
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.100845

Abstract

The Sfamy R64 α‐amylase mutant from Saccharomycopsis fibuligera was expressed in Pichia pastoris to explore its industrial potential. The gene encoding the mutant enzyme was cloned into the pPICZαA vector and transformed into P. pastoris SMD1168. Optimal expression was achieved at 1.5% methanol concentration, with the highest enzyme activity observed at 48 h, reaching 24.06 U/mL. The recombinant protein was purified using Ni‐Sepharose affinity chromatography in native and denaturing conditions. The native conditions retained higher protein integrity and activity, while the denaturing process resulted in partial degradation. Molecular dynamics (MD) simulations conducted to assess the structural stability of the His‐tagged Sfamy R64 α‐amylase mutant and its interaction with the maltose substrate. The simulation confirmed the stable binding of maltose in the active site and the solvent accessibility of the His‐tag, supporting its effectiveness in affinity chromatography. The RMSD, RMSF, and time‐evolution snapshots demonstrated that the protein remained structurally stable over 100 ns at an optimum temperature of 50 °C. The findings suggest that the Sfamy R64 mutant α‐amylase is a promising candidate for industrial applications, combining high expression yields, efficient purification, and stable enzyme‐substrate interactions. The results offer a strong basis for further optimization and large‐scale enzyme production.
Agrobacterium‐mediated transformation of yeast using a vir binary vector system Kiao Huio Yap; Shu Ting Chang; Wai Keat Toh; Pek Chin Loh; Boon Hoe Lim; Khomaizon Abdul Kadir Pahirulzaman; Chai-Ling Ho; Hann Ling Wong
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.100929

Abstract

Agrobacterium‐mediated transformation (AMT) is a widely used genetic engineering tool for generating transgenic plants for crop improvement and functional genomics. Beyond plants, AMT has been successfully applied to non‐plant organisms, further expanding its utility. Given their broad applications, enhancing AMT systems to improve their usability, simplicity, and efficiency is highly desirable. In this study, we developed a novel AMT system, the vir binary vector system, comprising the following core components: the binary vector pG103‐GDE‐1 and the miniaturized helper tumor‐inducing (Ti) plasmid pRIDE101, together with the auxiliary replication helper plasmid pSoup. Yeast was used as a model organism to evaluate its functionality in stable transformation, with the neomycin phosphotransferase II (NptII) gene serving as a selectable marker. The system’s functionality was assessed by comparing its transformation frequency to that of the widely used pGWB1 binary vector system. The results demonstrate that the vir binary vector system achieved a trans‐ formation frequency of 0.76 × 10‐6, approximately 75 percent of that of pGWB1 (1.01 × 10‐6). Polymerase chain reaction (PCR) analyses confirmed the presence of the transgene in yeast transformants. These findings validate the functionality of the vir binary vector system and highlight the need for further optimization to enhance its efficiency for broader app
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.

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