cover
Article Per Year (5 Year)
All
Home Page
OAI Link
Editorial Team
Contact
Reviewer
Google Scholar
Contact Name
-
Contact Email
-
Phone
-
Journal Mail Official
-
Editorial Address
-
Location
Kab. sleman,
Daerah istimewa yogyakarta
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
 47   48   49   50   51 
Expression profiles of XIK1 and OsSWEET14 genes in parental and back‐ crossing rice lines after Xanthomonas oryzae pv. oryzae infection Atirada Boondech; Kawee Sujipuli; Kumrop Ratanasut; Tepsuda Rungrat; Thanita Boonsangsrom; Niran Aeksiri; Wittaya Tawong; Pongsanat Pongcharoen
Indonesian Journal of Biotechnology Vol 29, No 2 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.89092

Abstract

Oryza sativa L. ssp. indica (RD47 cultivar) is a major commercial rice variety known for its highly stable yields. However, it is highly susceptible to bacterial blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo). While previous research has focused on improving rice cultivars through breeding programs, no reports involved the interaction between Xoo infection and gene expression. This study aimed to analyze the relationship between bacterial blight disease and gene expression, focusing on two resistance genes (Xa21 and XIK1) and one susceptible gene (OsSWEET14). Gene expression analysis revealed that the Xa21 gene conferred effective resistance against bacterial blight Xoo16PK002 infection, providing high and moderate resistance to bacterial blight symptoms in two rice varieties carrying the Xa21 gene, IRBB21 and the near–isogenic RD47–Xa21 BC4F4, respectively. Additionally, the Xa21 gene directly induced XIK1 expression in both resistance rice cultivars. Moreover, one susceptible gene, OsSWEET14, was consistently up–regulated in only the bacterial blight–susceptible indica rice cultivar RD47. Therefore, the up–regulation of resistance genes and the suppression of susceptible genes contributed to the improvement of bacterial blight disease in the RD47 cultivar. Xa21 emerged as a criti‐ cally important gene in directly inducing mechanisms against Xoo, thereby promoting the reduction of bacterial blight disease.
Specific PCR primers for rapid detection of five rat and mouse species in Java, Indonesia Pramana Yuda; Stephanie Rani Tiurma Siregar; Sena Adi Subrata
Indonesian Journal of Biotechnology Vol 29, No 2 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.89125

Abstract

Identifying rat and mouse species quickly, affordably, and accurately is crucial for effective population management, as well as for eradication or conservation purposes. However, the sheer diversity of these species poses a challenge. To address this, a molecular approach has been developed, involving the amplification of a short genetic marker from materials commonly left by the animal, such as hairs and feces. Recent available PCR primers were not suitable for the surveillance of large sample sizes. As a solution, this study designed and validated a PCR primer set capable of detecting five species of rats and mice (Mus musculus, Rattus tanezumi, Bandicota indica, Rattus tiomanicus, and Rattus argentiventer) commonly found in Java, Indonesia. The specific primers were derived from the cytochrome c oxidase subunit 1 (COI) gene, designed using the SP‐Designer V7.0 application, and validated using both in silico and in vitro methods. The validation results demonstrated that all five pairs of primers were highly specific, generated correct amplicons, and successfully detected the five distinct species present in a Javan mongoose feces sample. These findings are significantly important as they enable the effective detection of rat and mouse species and potentially provide valuable ecological insights from the field.
Identification of medium‐grain rice based on GS3, a gene linked to rice grain size Bui Phuo Tam; Pham Thi Be Tu; Nguyen Thi Pha
Indonesian Journal of Biotechnology Vol 29, No 2 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.89421

Abstract

Previous studies have used molecular markers associated with the GS3 gene to differentiate between short and long rice. However, there are three classifications of grain size: long, short, and medium. The identification of medium‐grain rice using these markers linked to the GS3 gene is yet to be confirmed. Hence, this study aimed to identify medium‐grain rice through phenotyping and genotyping. Grain characteristics including grain length (GL), grain width (GW), and the length‐to‐width ratio (GL/GW) were measured using SmartGrain software. The genotype was then amplified with the GS3 gene‐linked DRR‐GL (double round‐robin for grain length) molecular marker. The results revealed that medium‐grain rice, as identified by the DRR‐GL marker, exhibited DNA bands at the position of 150 bp. These bands differed from those observed in long‐grain rice, but they were consistent with those found in short‐grain rice. The genotypic results further indicated that PCR products obtained with the DRR‐GL marker in medium‐grain rice accounted for 86.8% of the phenotypic variation in grain size. This study provides fundamental genetic insights into the identification of medium‐grain rice and contributes to optimizing effects on rice breeding related to grain size.
Exploring the mechanism of Glycyrrhiza glabra and Curcuma domestica against skin photoaging based on network pharmacology Oktavia Rahayu Adianingsih; Fifi Farida Fajrin; Christopher Kuncoro Johan
Indonesian Journal of Biotechnology Vol 29, No 2 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.93332

Abstract

Excessive exposure to UV radiation results in skin photoaging, which may be prevented or treated using natural plant compounds. Herbal cosmetics and medicines have grown in popularity due to the abundance of relatively safe compounds. This research aims to explore the network pharmacology of Glycyrrhiza glabra (GG) and Curcuma domestica (CD) against skin photoaging. Active compounds from GG‐CD were sourced from databases including TCSMP, KnapSack, TCMID, and published literature, while disease targets were collected from GeneCards and OMIM databases. The STRING database was utilized to construct the protein‐protein interaction (PPI) network. Enrichment analyses for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed using Metascape. The herb‐compounds‐target‐pathway‐disease (H‐C‐T‐P‐D) network was visualized using Cytoscape software. A total of 529 compounds, 2,335 active compound targets, and 120 skin aging targets were obtained. GO enrichment revealed 1,635 biological processes, 67 cellular components, and 121 molecular functions. The study suggests that GG and CD have the potential to treat skin photoaging by targeting multiple targets, such as TP53, TNF, AKT1, IL6, and IL‐1B, as well as multiple pathways, such as those in cancer, apoptosis, TNF, IL‐17, and the AGE‐RAGE signaling pathway. Experiment validation is necessary to confirm the preliminary network pharmacology results.
Genes expression analysis of EgUnk1, EgZFP2, and EgIPK2b in oil palm using Ct value correction and two relative quantification approaches Rokhana Faizah; Riza Arief Putranto; Sudarsono Sudarsono; Sri Wening; Dewi Sukma; Asmini Budiani
Indonesian Journal of Biotechnology Vol 29, No 3 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.71816

Abstract

The determination of transcript accumulation values significantly affects gene expression in oil palm. Various genes are involved in pathogen infection, including probable 2‐oxoglutarate‐dependent dioxygenase At5g05600 (EgUnk3), zinc finger protein 2‐like (EgZFP2), and inositol polyphosphate multikinase beta‐like (EgIPK2b). Gene expression is typically measured using relative quantitative methods to calculate differences in quantitative values in the expression levels of targeted genes compared to a reference gene. However, the effectiveness of these methods in assessing the expression of EgUnk3, EgZFP2, and EgIPK2b, which are involved in Ganoderma boninense infection in oil palm seedlings, requires evaluation. This study aimed to establish an effective and straightforward method for analyzing the expression of EgUnk1, EgZFP2, and EgIPK2b genes in oil palm seedlings infected with G. boninense, utilizing Ct value correction through regression coefficients on the 2‐ΔΔCt and E‐ΔΔCt approaches. A correlation regression revealed values of 0.28, ‐0.32, and 0.29 for delta Ct of EgUnk1, EgZFP2, and EgIPK2b, respectively. However, a negative correlation in the Ct mean was corrected by linear regression for the targeted genes: ‐0.55, ‐0.81, and ‐0.29 for EgUnk1, EgZFP2, and EgIPK2b, respectively. The amplification factor (E) and efficiency value (R) using the EgActin gene were 1.95 and 94.92%, respectively. Normalization of log10 on the fold change value 2‐ΔΔCt and 1.95‐ΔΔCt approaches using the regression coefficient yielded consistent results for the EgUnk1, EgZFP2, and EgIPK2b genes. Overall, EgUnk3 and EgIPK2b genes exhibited downregulated expression in susceptible oil palm seedlings (‐0.60 for 2(‐ΔΔCt) and ‐0.58 for 1.95(‐ΔΔCt)), whereas EgIPK2b gene showed up‐regulated and the highest value in inoculated resistant seedlings (1.39 for 2(‐ΔΔCt) and 1.34 for 1.95(‐ΔΔCt)). Basal stem rot disease (BSR) in oil palm decreased EgUnk1 and EgIPK2b expression in susceptible seedlings but increased EgZFP2 gene expression in resistant ones. The results of this research provide valuable corrections to Ct values obtained directly from RT‐qPCR machines using simple linear regression. Consequently, the Ct values of target genes and reference genes exhibit smaller bias values, rendering gene expression levels more reliable.
Moringa oleifera leaf extract ameliorates collagen degradation via the inhibition of MMP‐3 expression in UVB‐induced rats Riska Rachmania; Titiek Sumarawati; Agung Putra; Nurul Hidayah; Iffan Alif; Sofian Azalia Husain; Ade Indra Mukti; Reynaldi Suryajaya; Salma Yasmine Azzahara
Indonesian Journal of Biotechnology Vol 29, No 3 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.77538

Abstract

Prolonged exposure to high‐intensity UVB induces the formation of reactive oxygen species (ROS) in skin tissue, triggering an increase in matrix metalloproteinase‐3 (MMP‐3) enzyme production and leading to collagen degradation. Moringa oleifera (MO) contains bioactive compounds known for ROS‐scavenging and anti‐inflammatory properties. However, the precise molecular mechanism of action remains unclear, requiring the inhibition of MMP‐3 activation and regulation of collagen deposition. This study aims to elucidate the potential effect of MO leaf extract‐based gel in restoring collagen deposition by reducing MMP‐3 activation in UVB irradiate‐induced collagen loss in rats. This study employed a completely randomized design, comprising four groups: a healthy group without UVB radiation, a negative control group subjected to UVB radiation and receiving a placebo, and two treatment groups exposed to UVB radiation with 5% or 10% moringa leaf extract‐based gel (MO‐5% or MO‐10%), respectively. Results showed that MO‐5% and MO‐10% significantly reduced MMP‐3 gene expression and increased collagen density compared to the negative control group (p < 0.05). Moringa oleifera leaf extract ameliorates collagen degradation by inhibiting MMP‐3 expression in UVB‐induced rats, suggesting its potential as a pharmacological and cosmetic agent for UVB‐induced skin damage.
Improving transient gene expression and agroinfiltration‐based transformation effectiveness in Indonesian orchid Phalaenopsis amabilis (L.) Blume Dionysia Heviarie Primasiwi; Yekti Asih Purwestri; Endang Semiarti
Indonesian Journal of Biotechnology Vol 29, No 3 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.80555

Abstract

Transient gene expression is an approach used to study transient genes across various species, with infiltration by Agrobacterium tumefaciens (agroinfiltration) being a commonly used method. Agroinfiltration offers a simple and effective means of delivering transgenes into the plant genome. An alternative method for enhancing the quality and productivity of orchids as ornamental plants is genetic modification through agroinfiltration. Although Agrobacterium‐mediated genetic transformation by immersion has been used on the Phalaenopsis amabilis (L.) Blume species of orchid, transformation efficiency using the immersion technique remains relatively low and the method itself is challenging due to its requirement for aseptic handling. The application of agroinfiltration in P. amabilis has not previously been reported. This study investigates the impact of the injection site, acetosyringone concentration, bacterial density (OD600), and injection volume to determine the optimum conditions for agroinfiltration on P. amabilis. The results demonstrated that injection site had a noticeably distinct impact on transformation effectiveness, with the abaxial position of the leaf being the optimal site for Agrobacterium culture suspension injection. While adjustments in acetosyringone concentration, bacterial density (OD600), and injection volume did not significantly affect transformation efficiency, they did influence the peak time of GFP fluorescence. Acetosyringone at a concentration of 200 µM, an OD600 of 1.0 for Agrobacterium culture, and an injection volume of 500 µL effectively accelerated GFP expression duration.
Development of a dimer‐based screening system that targets PhoR, a sensor kinase of the two‐component regulatory system, in Mycobacterium tuberculosis
Indonesian Journal of Biotechnology Vol 29, No 3 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.89602

Abstract

The PhoR‐PhoP two‐component regulatory system, which is responsible for regulating the virulence of Mycobacterium tuberculosis, presents a promising target for the development of novel tuberculosis drugs. Disrupting the interaction of PhoR‐PhoP proteins has the potential to decrease the virulence of the bacterium, rendering it more vulnerable to immune system clearance. A dimer‐based screening system was developed to screen for inhibitors of PhoR dimerization. The coding sequence for the cytoplasmic domain of PhoR (cytoPhoR) was combined with the DNA‐binding domain of the AraC repressor coding sequence. These sequences were positioned upstream of the emerald green fluorescent protein (EmGFP), which serves as a reporter gene. and controlled by the araC promoter. The in silico investigation examined the modeling of the fusion AraC_cytoPhoR and its binding to the promoter. The plasmid construct generated, namely pAraC_PhoRMTB, was synthesized and confirmed using DNA sequencing. The confirmed plasmid was then transformed into Escherichia coli BL21(DE3). Both SDS PAGE and fluorescence analysis indicated that the transformed culture expressed the AraC‐cytoPhoR fusion protein and displayed lower relative fluorescence in comparison to the transformed culture consisting solely of the AraC DNA‐binding domain coding sequence. This reduction in fluorescence suggests that the dimer‐based screening system effectively monitors the inhibition of dimerization of cytoPhoR. These analysis findings indicate that the system is now ready for use in the screening of PhoR dimerization inhibitors.
The diversity of fungal associates of Dendrobium ovatum (L.) Kraenzl., an endemic orchid of the Western Ghats of India
Indonesian Journal of Biotechnology Vol 29, No 3 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.92378

Abstract

Dendrobium ovatum is a tropical epiphytic orchid endemic to the Western Ghats of India and has been listed as a threatened species in recent research due to its declining populations and changes in flowering and fruit set patterns. This study aims to investigate the mycoflora associated with the roots, stems and leaves of D. ovatum. Both surface‐associated and endophytic fungal associates were isolated and identified using morphological and molecular methods. The study resulted in the isolation of 139 cultures, which were divided into 24 morphotypes, 99% of which belonged to Ascomycota. The most dominant members, Trichoderma harzianum and Colletotrichum gloeosporioides, were consistently observed across all the study sites. Tissue‐specific fungal diversity analysis revealed that each organ was dominated by a distinct fungal group, forming characteristic communities specific to each tissue. The roots of D. ovatum exhibited the highest species richness and diversity, compared to the stem and leaves. This research also represents the first documentation of fungal associates of the threatened orchid D. ovatum.
Detection and quantification of pork and rat DNA in processed meats using multiplex quantitative Real‐Time PCR (m‐qPCR)
Indonesian Journal of Biotechnology Vol 29, No 3 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.94212

Abstract

In addition to the issue of pork contamination, processed meats frequently contain traces of rat meat. Therefore, detection and quantification of the pork and rat DNA in cases of meat and processed meat adulteration are necessary. In the current study, two gene targets of the cytochrome b for pigs and the Mt‐atp6 of Rattus norvegicus for rats were used in the absolute multiplex quantitative real‐time PCR (m‐qPCR). The sample DNA was amplified with a standard as positive control in the various concentration of 1000 pg, 100 pg, 10 pg, 0.1 pg, 0.01 pg, and 0.001 pg. There were 25 processed meat samples and 5 fresh meat samples identified in this study. Among the total of 30 samples assessed, 6 samples were successfully detected and quantified their pork and rat DNA contamination. One sample was contaminated with pork DNA with a concentration of 2.451×10‐4 pg (“Meatball 3). Five samples were contaminated with rat DNA with a concentration of 3.603×10‐11 pg (“Sempol 3”), 2.196×10‐10pg (“Meatball 6”), 4.908×10‐11 pg (“Siomay 3”), 1.489×10‐10 pg (“Grinding 2”), and 3.564×10‐10 pg (“Grinding 4”). In this study, we have discovered that the contamination of pork and rat were detected in the samples. It suggested that this method is applicable for detecting the contaminant in processed meat samples

Page 49 of 52 | Total Record : 518

 47   48   49   50   51 

Filter by Year

2005 2025


Reset
Filter By Issues
All Issue Vol 30, No 3 (2025) Vol 30, No 2 (2025) Vol 30, No 1 (2025) Vol 29, No 4 (2024) Vol 29, No 3 (2024) Vol 29, No 2 (2024) Vol 29, No 1 (2024) Vol 28, No 4 (2023) Vol 28, No 3 (2023) Vol 28, No 2 (2023) Vol 28, No 1 (2023) Vol 27, No 4 (2022) Vol 27, No 3 (2022) Vol 27, No 2 (2022) Vol 27, No 1 (2022) Vol 26, No 4 (2021) Vol 26, No 3 (2021) Vol 26, No 2 (2021) Vol 26, No 1 (2021) Vol 25, No 2 (2020) Vol 25, No 1 (2020) Vol 24, No 2 (2019) Vol 24, No 1 (2019) Vol 23, No 2 (2018) Vol 23, No 1 (2018) Vol 22, No 2 (2017) Vol 22, No 1 (2017) Vol 21, No 2 (2016) Vol 21, No 1 (2016) Vol 20, No 2 (2015) Vol 20, No 1 (2015) Vol 19, No 2 (2014) Vol 19, No 1 (2014) Vol 19, No 1 (2014) Vol 18, No 2 (2013) Vol 18, No 2 (2013) Vol 18, No 1 (2013) Vol 18, No 1 (2013) Vol 17, No 2 (2012) Vol 17, No 2 (2012) Vol 17, No 1 (2012) Vol 17, No 1 (2012) Vol 16, No 2 (2011) Vol 16, No 2 (2011) Vol 16, No 1 (2011) Vol 16, No 1 (2011) Vol 15, No 2 (2010) Vol 15, No 2 (2010) Vol 15, No 1 (2010) Vol 15, No 1 (2010) Vol 14, No 2 (2009) Vol 14, No 2 (2009) Vol 14, No 1 (2009) Vol 14, No 1 (2009) Vol 13, No 2 (2008) Vol 13, No 2 (2008) Vol 13, No 1 (2008) Vol 13, No 1 (2008) Vol 12, No 2 (2007) Vol 12, No 2 (2007) Vol 12, No 1 (2007) Vol 12, No 1 (2007) Vol 11, No 2 (2006) Vol 11, No 2 (2006) Vol 11, No 1 (2006) Vol 11, No 1 (2006) Vol 10, No 2 (2005) Vol 10, No 2 (2005) Vol 10, No 1 (2005) Vol 10, No 1 (2005) More Issue