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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 523 Documents
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Computational modeling of AGO-mediated molecular inhibition of ARF6 by miR-145 Jeremias Ivan; Rizky Nurdiansyah; Arli Aditya Parikesit
Indonesian Journal of Biotechnology Vol 25, No 2 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.55631

Abstract

Inhibition of ADP-ribosylation factor 6 messenger RNA (ARF6 mRNA) by microRNA-145 (miR-145), mediated by Argonaute (AGO) protein, has been found to play essential roles in several types of cancer and cellular processes. This study aimed to model the molecular interaction between miR-145 and ARF6 mRNA with AGO protein. The sequences of miR-145 and the 3’ untranslated region (UTR) of ARF6 mRNA were retrieved from miRTarBase, followed by miRNA target-site and structure predictions were done using RNAhybrid, RNAfold, and simRNAweb, respectively. The interaction between the miRNA-mRNA duplex and AGO was further assessed via molecular docking, interaction analysis, and dynamics, using PatchDock Server, PLIP, and VMD/NAMD, respectively. The models between miR-145, predicted target site of ARF6 mRNA, and AGO protein returned stable thermodynamic variables with negative free energy. Specifically, the RNA duplex had an energy of -19.80 kcal/mol, while the docking had -84.58 atomic contact energy supported by 70 hydrogen bonds and 14 hydrophobic interactions. However, the stability of the RMSD plot was still unclear due to limited computational resources. Nevertheless, these results computationally confirm favorable interaction of the three molecules, which can be utilized for further transcriptomics-based drugs or treatments.
Optimization of solid‐state fermentation condition for crude protein enrichment of rice bran using Rhizopus oryzae in tray bioreactor Andhika Cahaya Titisan Sukma; Herawati Oktavianty; Siswo Sumardiono
Indonesian Journal of Biotechnology Vol 26, No 1 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.57561

Abstract

Enhancement of crude protein content in rice bran with the solid‐state fermentation method in tray bioreactor using Rhizopus oryzae FNCC 6011 has been investigated. This research aimed to optimize the fermentation condition using the response surface methodology (RSM). The central composite design (CCD) with three independent variables, including substrate thickness (1 to 3 cm), fermentation temperature (28 to 32 °C), and nutrient concentration of KH2PO4 (2 to 6 g/L) used to determine the crude protein enrichment. The quadratic model has successfully described the effect of variable interactions on responses very well as indicated by the F value and p‐value are 11.20 and 0.0041, respectively. The multiple correlation coefficients (R2) of 0.9438 indicated that 94.38% of the model data has approached the actual data with a deviation of 5.62%. The interaction between the variable substrate thickness and the fermentation temperature is the most influential variable on the crude protein enrichment of rice bran, indicated by the highest F value of 24.08 and the lowest p‐value of 0.0027. The highest protein increase of 62.51% was obtained at 2 cm substrate thickness, fermentation temperature of 30 °C, and KH2PO4 concentration of 4 g/L.
Characterization of recombinant Bacillus halodurans CM1 xylanase produced by Pichia pastoris KM71 and its potential application in bleaching process of bagasse pulp Haniyya Haniyya; Lina Mulyawati; Is Helianti; Phitsanu Pinmanee; Kanokarn Kocharin; Duriya Cantasingh; Thidarat Nimchua
Indonesian Journal of Biotechnology Vol 26, No 1 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.57701

Abstract

Thermoalkalophilic xylanases promise potential application in pulp biobleaching to reduce the use of toxic chlorinated chemical agents, which are harmful to the environment. In this study, a thermoalkalophilic endoxylanase gene (bhxyn3) originating from Indonesian indigenous Bacillus halodurans CM1 was cloned into yeast expression vector pPICZα A and expressed in Pichia pastoris KM71 under the control of AOX1 promoter. Recombinant P. pastoris expressed the highest final level of xylanase (146 U/mL) on BMGY medium after five days of cultivation. Optimization of xylanase production on a small scale was carried out by varying the methanol concentrations and the optimal xylanase production by the recombinant P. pastoris was observed in the culture with 2% (v/v) methanol after four days of the induction phase. The recombinant xylanase (BHxyn3E) was thermotolerant and alkalophilic, with an optimal temperature at around 55‐65 °C and under pH 8.0. The enzyme activity was slightly induced by K+, Fe2+, and MoO42‐. Enzymatic bleaching of bagasse pulp with no prior pH adjustment (pH 9) using BHxyn3E at 200 U/g oven dried pulp increased the lightness index (L*) and changed substantially the color a index (a*); however, the treatments did not change the whiteness index in a significant way. Therefore, further optimization and assessment such as adjustment of incubation temperature and pH in biobleaching were needed to reduce the use of harmful chemical agents in industrial applications.
Anammox biofilm process using sugarcane bagasse as an organic carrier Zulkarnaini Zulkarnaini; Puti Sri Komala; Arief Almi
Indonesian Journal of Biotechnology Vol 26, No 1 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.58554

Abstract

The anaerobic ammonium oxidation (anammox) biofilm process commonly uses various inorganic carriers to enhance nitrogen removal under anaerobic conditions. This study aims to analyze the performance of nitrogen removal in anammox process using sugarcane bagasse as an organic carrier. The experiment was carried out by using an up‐flow anaerobic sludge blanket (UASB) reactor for treating artificial wastewater at room temperature. The reactor was fed with ammonium and nitrite with the concentrations of 70‐150 mg–N/L and variations in the hydraulic retention time of 24 and 12 h. The granular anammox belongs to the genus Candidatus Brocadia sinica that was added as an inoculum of the reactor operation. The experimental stoichiometric of anammox for ΔNO2‐–N: ΔNH4+–N and ΔNO3‐: ΔNH4+ were 1.24 and 0.18, respectively, which is similar to anammox stoichiometry. The maximum Nitrogen Removal Rate (NRR) has achieved 0.29 kg–N/m3.d at Nitrogen Loading Rate (NLR) 0.6 kg–N/m3.d. The highest ammonium conversion efficiency (ACE) and nitrogen removal efficiency (NRE) were 88% and 85%, respectively. Based on this results, it indicated that sugarcane bagasse as organic carriers could increase the amount of total nitrogen removal by provided of denitrification process but inhibited the anammox process at a certain COD concentration.
Antiviral activities of curcumin and 6‐gingerol against infection of four dengue virus serotypes in A549 human cell line in vitro Jonathan Alvin Nugraha Halim; Stefanie Natalia Halim; Dionisius Denis; Sotianingsih Haryanto; Edi Dharmana; Rebriarina Hapsari; R. Tedjo Sasmono; Benediktus Yohan
Indonesian Journal of Biotechnology Vol 26, No 1 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.60174

Abstract

Dengue virus (DENV) is the most geographically widespread arbovirus causing dengue disease epidemics in tropical and subtropical regions. Nature provides abundant plants as a source for lead molecules against various diseases including DENV infection. We investigated the antiviral effect of curcumin and 6‐gingerol, the major active constituent of turmeric (Curcuma longa Linn.) and ginger (Zingiber officinale Roscoe), respectively, against all four serotypes of DENV infecting human lung epithelial carcinoma (A549) cell line in vitro. Both compounds generated cell cytotoxicity to A549 cells at CC50 values of 108 µM for curcumin and 210 µM for 6‐gingerol. The compound curcumin showed antiviral properties as described by IC50 of 20.60, 13.95, 25.54, and 12.35 µM, while 6‐gingerol of 14.70, 14.17, 78.76, and 112.84 µM for DENV‐1, ‐2, ‐3, and ‐4, respectively. Different levels of antiviral properties were observed between DENV serotypes. Our findings suggest that the antiviral assay of compounds against DENV should be performed to all four serotypes and not limited to a particular serotype. In conclusion, curcumin and 6‐gingerol exhibit antiviral properties against DENV infection and could provide a new therapeutic approach for dengue disease treatment strategies.
Obtaining of transgenic potato (Solanum tuberosum L.) cultivar IPB CP3 containing LYZ‐C gene resistant to bacterial wilt disease Pasmawati Pasmawati; Aris Tjahjoleksono; Suharsono Suharsono
Indonesian Journal of Biotechnology Vol 26, No 1 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.61682

Abstract

Bacterial wilt caused by Ralstonia solanacearum is one of the most important bacterial diseases in potato production. This study aimed to obtain the transgenic potato (Solanum tuberosum L.) cultivar IPB CP3, containing LYZ‐C gene encoding for lysozyme type C, resistant to bacterial disease caused by R. solanacearum. Genetic transformation using Agrobacterium tumefaciens LBA4404 to 124 internode explants resulted in the transformation efficiency of about 47.58% with a regeneration efficiency of approximately 30.51%. Gene integration analysis showed that 16 clones were confirmed as transgenic clones containing the LYZ‐C gene. Analysis of resistance to R. solanacearum of three transgenic clones showed that all three transgenic clones were more resistant than a non‐transgenic one. This result showed that the LYZ‐C gene integrated in the genome of transgenic potato increased the resistance of potato plants to R. solanacearum. We obtained two transgenic clones considered resistant to bacterial wilt disease.
Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions Mohammad Rizki Fadhil Pratama; Hadi Poerwono; Siswandono Siswodihardjo
Indonesian Journal of Biotechnology Vol 26, No 1 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.62194

Abstract

Observation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained between the test and the reference ligands as the graph’s x‐axis. Meanwhile, the y‐axis contains the similarity of ligand‐receptor interactions, obtained from the ratio of amino acid residues and the types of interactions between the test and reference ligands. Docking result analysis was more straightforward because two critical parameters were presented in one graph. This graph could be used to support the analysis of the docking results.
Identification of gene expression location of angiotensin‐converting enzyme‐2 SNPs as a receptor for SARS‐CoV‐2 in different populations by using various databases Dyah Aryani Perwitasari; Rita Maliza; Bayu Tri Murti; Haafizah Dania; Athika Darumas Putri
Indonesian Journal of Biotechnology Vol 26, No 2 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.63260

Abstract

The World Health Organization (WHO) has announced that Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) and Coronavirus disease (COVID‐19) is considered a worldwide pandemic. Rapidly rising numbers of patients have been reported in almost every country, along with the growing mortality rates. Uncontrolled growth in patient numbers may be due to reasons such as treatment options and vaccine availabilities and unidentified targets of SARS‐CoV‐2. Previous study has revealed that the molecular target of SARS‐CoV‐2 is analogous to SARS (2003), i.e. angiotensin‐converting enzyme‐2 (ACE‐2). Therefore, the determination of ACE‐2 may enrich existing information and facilitate development of drugs targeted toward SARS‐CoV‐2. This study aims to screen the expression of ACE‐2 genes and their relationship to the types of SNP variants in SARS‐CoV‐2. We explored a series of observations using powerful databases, e.g. GTEx portal, HaploReg, 1000 Genome and Ensembl, to identify the gene variant of ACE‐2. We showed that ACE‐2 is highly expressed in the testes and small intestine, while its lowest level is observed in lymphocytes. Subsequently, we observed 17 gene variants containing a missense mutation potentially damaging protein level. Among these genes, single nucleotide polymorphism (SNP) rs370187012 shows the highest damage‐level score, while the lowest effect is in SNP rs4646116. The highest frequency of the C allele was observed in European populations (1%). In addition to showing that ACE‐2 is expressed in several organs, we concluded that the ACE‐2 gene variation can be found in African, American, Southeast and East Asian, and European populations. The polymorphisms of ACE‐2 impact on the ACE2 protein structure and the binding capacity of the ACE‐2 receptor with the S‐Protein of SARS‐CoV‐2.
The potential of mesenchymal stem‐cell secretome for regeneration of intervertebral disc: A review article Romaniyanto Romaniyanto; Cita Rosita Sigit Prakoeswa; Damayanti Tinduh; Hari Basuki Notobroto; Fedik Abdul Rantam; Dwikora Novembri Utomo; Heri Suroto; Ferdiansyah Ferdiansyah
Indonesian Journal of Biotechnology Vol 26, No 2 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.63318

Abstract

Low back pain is a crucial public health problem that is commonly associated with intervertebral disc de‐ generation and has vast socio‐economic impact worldwide. Current treatments for disc degeneration are conservative, non‐surgical, or surgical interventions, and there is no current clinical therapy aimed at directly reversing the degeneration. Given the limited capacity of intervertebral disc (IVD) cells to self‐repair, treatment aiming to regenerate IVDs is a topic of interest and mesenchymal stem cells (MSCs) have been identified as having potential in this regeneration. Recent studies have revealed that the benefits of MSC therapy could result from the molecules the cells secrete and that play principal roles in regulating essential biologic processes, rather than from the implanted cells themselves. Therefore, the objective of this study is to review the potential use of the MSC secretome to regenerate IVDs. Current evidence shows that the secretome may regenerate IVDs by modulating the gene expressions of nucleus pulposus cells (upregulation of keratin 19 and downregulation of matrix metalloproteinase 12 and matrix Gla protein) and stimulating IVD progenitor cells to repair the degenerated disc.
Genetic diversity of local rice varieties (Oryza sativa L.) in Vietnam’s Mekong Delta based on SSR markers and morphological characteristics Tran Huu Phuc; Van Quoc Giang; Nguyen Van Manh; Huynh Ky
Indonesian Journal of Biotechnology Vol 26, No 2 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.63648

Abstract

Based on target traits, use of the genetic diversity of rice is beneficial for crop improvement. In this study, 41 rice varieties local to Vietnam’s Mekong Delta were evaluated on the basis of 11 quantitative morphological traits, along with the assessment of genetic diversity according to 50 SSR markers. The actual yield had a significance level of 0.05, while plant height and panicles per square meter had a high significance level of 0.001. Cluster analysis based on 11 quantitative traits also revealed that two were the optimal number of clusters used in this study. The highest polymorphic information content (PIC) value obtained was for RM286 (0.49), with a range of 0.00 to 0.49 and an average PIC of 0.14. Both structure and phylogenetic tree analyses as inferred from 50 SSR markers by the unweighted pair‐group method with arithmetic mean (UPGMA) also indicated that the 41 local rice varieties could be divided into two major groups. This study provides a useful information for Mot bui do cao CM, and Mot bui five varieties for improvements in the yield and intermediate amylose content of local rice‐breeding programs in future, especially for the Mekong Delta region.

Page 40 of 53 | Total Record : 523

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