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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 6 Documents
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Search results for , issue "Vol 27, No 1 (2022)" : 6 Documents clear
Increased serial levels of platelet‐derived growth factor using hypoxic mesenchymal stem cell‐conditioned medium to promote closure acceler‐ ation in a full‐thickness wound Pangesti Drawina; Agung Putra; Taufiqurrachman Nasihun; Yan Wisnu Prajoko; Bayu Tirta Dirja; Nur Dina Amalina
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.64021

Abstract

The healing process of a full‐thickness wound involves a complex cascade of cellular responses to reverse skin integrity formation. These processes require growth factors, particularly platelet‐derived growth factor (PDGF). Conversely, hypoxic mesenchymal stem‐cell‐conditioned medium (HMSC‐CM)‐contained growth factors notably contribute to acceleration of wound healing. This study aims to investigate the role of HMSC‐CM in controlling the serial levels of PDGF associated with accelerated wound closure in full‐thickness wounds. Twenty male Wistar rats with full‐thickness wounds were developed as animal models. The animals were randomly assigned to four groups, comprising two treatment groups (treated using HMSC‐CM at a high dose as P1 and at a low dose as P2), a control group (administration of base gel), and sham group (healthy group). PDGF levels were examined using an enzyme‐linked immunosorbent assay. Using ImageJ software, wound closure percentages were determined photographically. The study showed that there was a significant increase in PDGF levels on days 3 and 6 after HMSC‐CM treatment, followed by a decrease in PDGF levels on day 9. In line with these findings, wound closure percentage also increased significantly on days 6 and 9. In the rat model, HMSC‐CM administration may promote acceleration of wound closure by increasing serial PDGF levels in the full‐thickness wound.
Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 Anggi Laksmita Dewi; Dewi Kartikawati Paramita; Jajah Fachiroh
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.64933

Abstract

Rs1948 A>G is a single nucleotide variation (SNV) in the 3’‐UTR of CHRNB4. Genotyping the synonymous CHRNB4 rs1948 may be useful in identifying a lung cancer susceptibility gene. The study aimed to develop a simple and easy tetra‐primer amplification refractory mutation system (ARMS PCR) for CHRNB4 rs1948. The following steps were taken to optimize tetra‐primer ARMS PCR: 1) determining the gene sequence and position of a single mutation; 2) developing outer and inner primers; 3) amplification of target gene fragments via PCR using an outer primer; 4) genotyping PCR product using Sanger sequencing; 5) determining the optimal annealing temperature and PCR cycle; 6) determining optimal outer and inner primer ratio; and 7) testing the reproducibility of the PCR program and final validation with Sanger sequencing. Genotype (PCR result) was visualized with 3% agarose gel electrophoresis. Optimum condition was determined as annealing temperature of 64.8 ºC and 35 cycles, outer and inner primer ratio of 1:6, and DNA volume of 3 µL. Sanger sequencing confirmed the results of the tetra‐primer ARMS PCR and it was shown that ARMS PCR was able to identify three different variants of CHRNB4 rs1948.
The relationship between morpho‐physiological changes and expression of transcription factors in NTT local rice cultivars as a response to drought stress Yustina Carolina Febrianti Salsinha; Alfino Sebastian; Ekris Sutiyanti; Yekti Asih Purwestri; Didik Indradewa; Diah Rachmawati
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.65728

Abstract

Response by plants to drought occurs through a series of mechanisms that involve transcription regulation. This research was conducted to study transcription factors (TF) and physiological changes in the drought response of local rice cultivars from East Nusa Tenggara (Nusa Tenggara Timur, NTT) during drought stress. Using three NTT local rice cultivars (Boawae Seratus Malam (BSM), Gogo Jak (GJ), and Kisol Manggarai (KM)) and the fraction of transpirable soil water (FTSW) method with two treatment levels, FTSW 1 (control) and FTSW 0.2 (severe stress), we analyzed the TF expression of OsDREB1A, OsDREB2A, OsWRKY45, and OsNAC6. Based on the result, the highest level of TF expression occurred in the BSM, followed by the GJ and KM cultivars. Analysis of physiological characteristics showed an association between TF expression levels and physiological response, with the BSM cultivar showing high pigment levels, high proline content, and lower H2O2 levels. A linkage was also found in relation to water conservation, as indicated by the higher relative water content and cell membrane stability index in the BSM cultivar in contrast to lower electronic leakage and malondialdehyde percentage when exposed to drought. Based on the results, it can be concluded that the BSM cultivar can be considered as a drought‐tolerant local cultivar according to morpho‐physiological analysis. In this study, all NTT local rice cultivars showed a subtle upregulation of stress‐responsive transcription factors OsDREB1A, OsDREB2A, OsWRKY45, and OsNAC6 as responses to drought stress.
The design of Indonesian SARS‐CoV‐2 primers based on phylogenomic analysis of the SARS‐CoV‐2 clades Tsania Taskia Nabila; Ata Rofita Wasiati; Afif Pranaya Jati; Annisa Khumaira
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.66854

Abstract

Molecular detection needs to be augmented for COVID‐19 detection in Indonesia using the PCR method with primer‐based gene analysis. This is necessary because the RNA of the SARS‐CoV‐2 virus, the causative infectious agent of the pandemic, has been mutated. Therefore, this study aimed to develop a primer design for determining SARS‐CoV‐2 clades in Indonesia using phylogenomic analysis. Data were obtained from 38 GISAID (Global Initiative on Sharing All Influenza Data) viruses and the relationships were analyzed using maximum likelihood (ML) phylogenomic analysis with a substitution model of generalized time‐reversible (GTR) to construct the tree topology. The results showed that the five types of SARS‐CoVs‐2 clades in Indonesia were L, G, GH, GR, and O. It also indicated that the GH region had the highest rate of clade at 50%, with the S clade affecting its formation. Furthermore, the genome sequences of the GH type used to design its primer were based on three genes, namely RdRp, S, and N. The RdRp and N genes were found to be conserved and hardy mutants, while the S gene occurred repeatedly. Several previous studies have stated that the designed primers produced missense mutations compared to another in silico. Therefore, three sets of primers were achieved from the GC contents and clamps, Tm range, and structural secondary indicator standards.
The prevalence of KRAS and BRAF mutation in colorectal cancer patients in Bali Ayu Dewi Ni Nyoman; Ni Made Pramita Widya Suksmarini; Anak Agung Ngurah Satya Pranata; Andreliano Yosua Rompis; I Wayan Juli Sumadi
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.67506

Abstract

Mutations in the KRAS (Kirsten rat sarcoma viral oncogene homolog gene) and BRAF (v‐Raf murine sarcoma viral oncogene homolog B1) gene play a significant role in primary resistance to colorectal cancer therapy. Around 85‐90% of KRAS mutations in colorectal cancer occur in exon 2 (codon 12 and 13), whereas approximately 96% of BRAF mutations occur in exon 15 codon 600 (V600E). This study aimed to determine the prevalence and mutation characteristics of the KRAS and BRAF genes in colorectal cancer patients in Bali. The DNA was isolated from 44 formalin‐fixed paraffin‐embedded colorectal cancer samples which were stored in the Department of Pathology, Sanglah General Hospital in 2017. Detection of mutation was carried out by polymerase chain reaction (PCR) and direct sequencing. Out of 44 samples, only 27 were successfully amplified and sequenced. Our findings showed six samples (22.2%) with mutated KRAS at codons 12 and 13 (including two samples with G12D, one sample with G12V, and three samples with G13D). Interestingly, we found three samples (11.1%) of BRAF mutation, including two samples with V600E mutation and one with V600L mutation. Taken together, our results showed that KRAS and BRAF mutations were identified and occurred exclusively. Further studies are essential to identify the correlation of these mutations with colorectal cancer prognosis and response to chemotherapy
Increased activity of sugarcane sucrose‐phosphate synthase in transgenic tomato in response to N‐terminal truncation Siti Nurul Afidah; Inyana Dwi Agustien; Parawita Dewanti; Bambang Sugiharto
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.69337

Abstract

Sucrose‐phosphate synthase (SPS) is a key enzyme catalyzing the formation of sucrose‐6‐phosphate through the transfer of uridine‐diphosphate glucose (UDP‐G) as a donor to fructose‐6‐phosphate (F6P) as an acceptor. Plant SPS consists of three main domains: N‐terminal, glycosyltransferase, and C‐terminal domains. Among these, the N‐terminal domain is involved in regulating the allosteric activator glucose‐6‐phosphate (G6P). This study was directed toward determining the regulation and characterization of N‐terminal truncated SPS in transgenic tomato. In this study, the N‐terminal truncated mutant of sugarcane SPS (ΔN‐SoSPS1) and full‐length sugarcane SPS (FL‐SoSPS1) were expressed into tomato plants to verify the functional role and importance of the N‐terminal domain in plant SPS. Overexpression of ΔN‐SoSPS1 led to an up to 3‐fold increase in the specific activity of SPS compared to non‐transformant plants (WT), while the specific activity of ΔN‐SoSPS1 was higher than FL‐SoSPS1 in transgenic tomato plants. Unlike WT and FL‐SoSPS1, the ΔN‐SoSPS1 mutant was not allosterically regulated by G6P. These results indicated that deletion of the N‐terminal domain promotes the loss of allosteric activation by G6P and increases binding affinity between enzyme and substrate.

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