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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 8 Documents
 1 
Search results for , issue "Vol 25, No 1 (2020)" : 8 Documents clear
Application of CRISPR/Cas9 genome editing system for molecular breeding of orchids Endang Semiarti; Sri Nopitasari; Yuli Setiawati; Muhammad Dylan Lawrie; Aziz Purwantoro; Jaka Widada; Yasushi Yoshioka; Shogo Matsumoto; Kana Ninomiya; Yuuki Asano
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.39485

Abstract

Orchid is an important ornamental plant in Indonesia due to their natural beauty of flowers. In the tropical forest, orchids are being acquired for trading and commercial market. Thus, the effort is required to proliferate orchid in large quantities for conservation and improve the floral variation for plant breeding. The purpose of this study is to develop a firmed methodology of molecular breeding of orchids using CRISPR/Cas9 KO system. The plant material used was Phalaenopsis amabilis protocorms growth on NP medium+pepton (2 g/L). Protocorm were submerged in the culture of Agrobacterium tumefaciens that Ti‐plasmid had been filled with a T‐DNA construct of a pRGEB32 vector harboring sgRNA with PDS3 sequence. Detection for transformants was confirmed by PCR using HPT primers (545 bp), Cas9 primers (402 bp), PDS primers (280 bp) and trnL‐F (1200 bp) as an internal control. The results showed that 0.96% PDS transformants were obtained from PDS3T2 lines. Several transformant showed pale leaf color compared to non‐transformant plants. This study suggests that the target gene has successfully edited by CRISPR/Cas9 system and could be applied for that functional gene editing in orchids.
Differentiation ability of rat‐mesenchymal stem cells from bone marrow and adipose tissue to neurons and glial cells Ariyani Noviantari; Ratih Rinendyaputri; Ibnu Ariyanto
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.42511

Abstract

Mesenchymal stem cells (MSCs) are multipotent cells and can differentiate into neurons and glial cells. In vitro differentiation would be done by the addition of various factors. There remains no comparison for the differentiation of MSCs from rat bone marrow (rBMMSCs) and adipose tissue (rATMSCS) into neurons and glial cells with basic fibroblast growth factor (bFGF), epidermal growth factor (EGF), and brain‐derived neurotrophic factor (BDNF). The aims of this study were to investigate the effect of bFGF, EGF, and BDNF supplementation on the differentiation ability of rBMMSCs and rATMSCs into neurons and glial cells. MSCs were cultured with bFGF and EGF for 4 days and then BDNF was added until day 8. Characterization of MSCs before and after induction was carried out by observing the cell morphology and several cell markers. Flowcytometry analysis was performed for MSCs markers (CD90, CD29) and neurons and glial cell markers (A2B5, Beta‐III‐tubulin, PSAN‐CAM); while MAP‐2, a neuron marker, was analyzed by immunocytochemistry. Induction of both types of MSCs showed MAP‐2‐positive cells, decreased MSCs markers, and in rBMMSCs showed increased neuron markers. The number of neuron marker positive cells in rBMMSCS was higher than rATMSCs. This study showed that the addition of bFGF, EGF, and BDNF to the medium induced rBMMSCs into neurons and glial cells, but the conditions were not optimal for rATMSC as judged by the expression of neural markers (A2B5, Beta‐III‐tubulin, PSAN‐CAM, and MAP‐2).
Phylogenetic analysis of 23 accessions of Indonesian banana cultivars based on Internal Transcribed Spacer 2 (ITS2) region Karlia Meitha; Intan Fatmawati; Fenny Martha Dwivany; Agus Sutanto; Sigit Nur Pratama; Husna Nugrahapraja; Ketut Wikantika
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.49506

Abstract

Pisang Kepok (Musa spp. [ABB ’Saba’ subgroup]) has several unique characteristics, such as tolerance to drought and Fusarium Foc (TR4) disease. Currently, the genetic diversity of Pisang Kepok in Indonesia is not well identified, although it is widely cultivated. Information on genetic diversity is essential for developing breeding strategies to achieve efficient cultivar improvement in the future. Aims of this research were to analyze the genetic variation of Pisang Kepok from some islands in Indonesia and to determine the genetic relationship between Pisang Kepok and other accessions banana cultivars based on ITS2 region, as a basis for future research in improving banana quality through molecular breeding. We have conducted the multiple sequence alignment and built the phylogenetic tree analysis using the Bayesian Inference Phylogeny method of one million generations (ngen = 1,000,000). The ITS2 region showed two clade ingroups: first clade consists of banana with B genome (balbisiana), while the second clade consists of banana with only A genome (acuminata). In general, all accessions of Pisang Kepok cultivars were clustered in the B genome of bananas cultivars. In addition, the ITS2 sequences and secondary structures among Pisang Kepok from various regions are identical, suggesting that there was no genetic variation in the ITS2 region of Pisang Kepok from multiple areas in Indonesia.
Physiological, biochemical and HSP70 and HSP90 gene expression profiles of tropical abalone Haliotis squamata in response to Vibrio alginolyticus infection Ngurah S. Yasa; Murwantoko Murwantoko; Niken S. N. Handayani; Gemi Triastutik; Lutfi Anshory
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.51322

Abstract

Vibrio spp. have been known responsible for fish diseases in marine and brackish‐water systems in the tropics regions. Heat shock proteins are a highly conserved protein group that is known for its rapid response to environmental stresses, including infection. This study aimed to investigate physiological and biochemical responses of tropical abalone Haliotis squamata to Vibrio alginolyticus infection. Abalones were infected with V. alginolyticus by intramuscular injection at a dose of 105,106,107 cfu/abalone. The expression of HSP70 and HSP90 genes, the activity of superoxide dismutase, phenol oxidase and catalase enzymes, histology, falling and mortality were observed at 12, 24, 48, 72, and 96 hours post‐infection (hpi). The different expression of HSPs was found in this study. While the expression of HSP70 was downregulated after infection, the expression of HSP90 was upregulated at 12 hpi and followed by downregulated after 24 hpi for 106 cfu infection, but expressed at a normal level for 105 infection treatment. The expression ofsuperoxide dismutase and catalase increased within 12 hpi, and the expression of phenol oxidase increased after 24 hpi. V. alginolyticus is virulent with LD50 of less than 105 cfu on H. squamata with an average weight of 5.13 g, and caused enlargement of hemolymph sinus and development intraepithelial and intramuscular abscesses.
The potency of Pentagamavunone‐0 (PGV‐0) as chemopreventive agent for the formation and growth of breast cancer as revealed in 3D model Wulandari Wulandari; Muthi’ Ikawati; Edy Meiyanto
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.51759

Abstract

Pentagamavunone‐0 (PGV‐0) or 2,5‐bis(4’‐hydroxy‐3‐methoxybenzylidine)‐cyclopentanone is a curcumin analogue that exhibits anticancer activity in breast cancer cells. However, most of previous reports are limited to the use of two‐dimensional (2D) cell culture. The use of three‐dimensional (3D) cell culture model in cancer research can represent the real condition of cancer growth in patients better than the 2D culture. The purpose of this study was to determine the anticancer activity of PGV‐0 on a 3D model of HCC 1954 breast cancer cells. HCC 1954 cells were grown in the 3D culture in the presence of PGV‐0, and the spheroid formation and growth of formed spheroids were observed using microscope at 24 and 96 h, respectively. The cytotoxic effects were measured by MTT assay. PGV‐0 inhibited the formation and growth of spheroids at the concentration as low as 60 µM. The cytotoxic effect of PGV‐0 appeared in a dose‐dependent manner with the IC50 value of 70.9 µM. The results of this study indicate that PGV‐0 has an anticancer activity on a 3D model of HCC 1954 breast cancer cell line. Therefore, the result supported the potency of PGV‐0 as cancer chemopreventive agent.
Enhancement of transient erythropoietin protein expression by valproic acid in CHO‐K1 suspension adapted cells Yana Rubiyana; Retno Damajanti Soejoedono; Adi Santoso
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.52621

Abstract

Erythropoietin (EPO) is a therapeutic protein that is widely used to increase red blood cell production in chronic kidney failure. EPO protein can be produced quickly with a transient gene expression system (TGE). However, the titer produced using TGE is usually lower than the stable gene expression system (SGE). It has been known that TGE can be improved by histone deacetylase inhibitors (iHDACs) such as valproic acid (VPA). This study was conducted to examine the VPA effect on EPO protein expression in CHO‐K1 suspension adapted cells and to find the optimum concentration of VPA on transient EPO protein production. EPO proteins was quantified using the enzyme‐linked immunosorbent assay (ELISA) method. The optimization of VPA concentrations showed that VPA increased the EPO protein yield by up to 2‐fold in transient EPO production, and the optimum concentration of VPA was 4 mM. VPA optimization was very helpful to obtain the maximum increase in the transiently expressed protein. Furthermore, this study can be used as a model to produce EPO proteins or other recombinant proteins rapidly with TGE of CHO‐K1 suspension adapted cells.
The structural insight of class III of polyhydroxyalkanoate synthase from Bacillus sp. PSA10 as revealed by in silico analysis Listia Pradani; Muhammad Saifur Rohman; Sebastian Margino
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.53717

Abstract

PhaC synthase is an enzyme responsible for PHA polymerization. In this work, the catalytic mechanism class III of PhaC synthase from Bacillus sp. PSA10 (BacPhaCSynt) was reported through in silico modelling approach based on the primary sequence of the PhaC synthase. The open reading frame BacPhaCSynt has been successfully isolated, cloned and overexpressed the recombinant protein in Escherichia coli BL21(DE3). To know the global architecture and catalytic mechanism, the structural prediction of BacPhaCSynt has been carried out by using MODELLER. The recombinant BacPhaCSynt exhibited monomeric molecular weight (MW) of 43.6 kDa, when it was analyzed on 12% SDS‐PAGE gel. Based on the structural prediction, BacPhaCSynt exhibited global architecture of α/β hydrolase fold, with the root mean square deviation (r.m.s.d) value of 0.94Å. The catalytic residues composition of BacPhaCSynt consists of C151, D307, and H336, but the H336 and D307 residues of the model have been distorted 62.8o and 175.2o from the corresponding residues of the template. Since the D307 is quite a distance from the H336, it might act as a general base for the activation of ‐OH group of the substrate. The results strongly suggested that the mode of action of BacPhaCSynt obeyed the covalent catalysis mechanism.
Chitosan suppresses the expression level of WRKY17 on red chili (Capsicum annuum) plant under drought stress Muhammad Abdul Aziz; Rizkita Rachmi Esyanti; Karlia Meitha; Fenny Martha Dwivany; Hany Husnul Chotimah
Indonesian Journal of Biotechnology Vol 25, No 1 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.55016

Abstract

Chili pepper plays a significant role in the global market. However, the production is often impeded by drought stress involving WRKY genes as the defense regulator. Chitosan is considered as a promising alternative fertilizer and defense elicitor. Hence, this study aimed to determine the role of chitosan in improving plant growth and survival of red chili pepper against drought stress. At the onset of the generative phase, chili plants were subjected to 1 mg mL‐1 chitosan, 50 percent drought, or chitosan‐drought treatment. Observations were made on several growth parameters, opened stomata, and WRKY gene expression. The results showed that chitosan‐drought treatment decreased plant growth and yielded significantly. The percentage of opened stomata was recorded at 0.56‐fold lower than control. It was followed by the decrease of the relative expression of WRKY17 and WRKY53 genes up to 0.56 and 0.72‐fold lower than control, respectively. Therefore, we suggested that the double treatment of chitosan‐drought might decrease plant growth performance but increase the defense system by suppressing the expression level of the WRKY17 gene. Interestingly, the drought treatment significantly increased WRKY17 expression level up to 7‐fold higher than control. Hence, it was suggested that WRKY17 has a specific role in response to drought stress.

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