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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 8 Documents
 1 
Search results for , issue "Vol 25, No 2 (2020)" : 8 Documents clear
Spatial analysis of toxoplasmosis through EcoHealth approaches using GRA-1 recombinant: case in Sleman, Yogyakarta Fihiruddin Fihiruddin; Wayan Tunas Artama; Barandi Sapta Widartono
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.50750

Abstract

Toxoplasmosis is an obligate intracellular zoonotic parasite caused by Toxoplasma gondii that can infect all warm-blooded animals including humans. Prevalence of toxoplasmosis varies depending on climate, geography, and the presence of cats in an area. This study aimed to identify the prevalence and distribution of toxoplasmosis in Sleman, Yogyakarta through EcoHealth approaches. A total of  385 blood samples were collected from residents in the district of Sleman. Seven people from 55 villages were selected for blood sampling using a cluster method. The collected serums were tested by ELISA using recombinant Granule 1 protein (GRA-1) as  coated antigen. Data on altitude and coordinates of sampling sites were collected using GPS.  instruments, soil surface temperature in Sleman was obtained by satellite imagery, and cat population in residential areas was determined by questionnaire. The prevalence of toxoplasmosis in Sleman was 58%, of which distributed around rivers and in cattle pens. Based on altitude and temperature, toxoplasmosis cases were found the highest at 0-150 m (66.3%) and at temperatures of 26-30°C (66.4%). Areas with large numbers of cats had toxoplasmosis prevalence of 75.8% while areas with moderate and few cats were 56.5% and 49.0%, respectively. Thus, differences in the prevalence of toxoplasmosis at settlement were found based on altitude, soil surface temperature, and cat populations.
Metagenomic analysis of intestinal microbiota in geese from different farming systems in Gunungpati, Semarang R Susanti; Ari Yuniastuti; Fitri Arum Sasi; Muchamad Dafip
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.53936

Abstract

The diversity of intestinal bacteria in geese correlates with environmental conditions, rearing methods, and consumed feeds. The intestinal bacteria composition is useful for the absorption of nutrition, improving the metabolism, and may be related to the immune system. This study was conducted to examine the intestinal bacteria composition and the diversity of maintained goose in aviaries and barns. This research was an observational exploratory. Five geese were taken purposively from local breeders in Gunungpati District, Semarang City. A total of 5 g of intestinal contents from each sample was used for microbial genome isolation. Then, the genome was amplified to collect 16S rRNA gene region V3-V4. The amplicons were then sequenced using the next generation sequencing (NGS) method (Illumina high-throughput sequencing; paired-end reads) and analyzed using QIIME2 to identify bacterial species. In addition, GC-MS was performed to identify and measure fatty acid contents in the intestinal. The results showed that both rearing and caged goose contained nine phyla of intestinal bacteria. The number of intestinal bacteria of barn geese (SU) reached 32,748 Operational Taxonomy Units (OTU); higher than aviary geese (SK), which was 11,646 OTU. The intestinal bacteria community in barn geese was approved by Phylum TM7 (Saccharibacteria candidate) (53.18%), followed by Firmicutes (32.51%) and Bacteriodetes (5.42%). Whereas on SK Firmicutes was compiled 49.3 4% of total OTU, TM7 (S. candidate) up to 21.17%, and Actinobacteria up to 15.99 %. The abundance of TM7 may contribute to high 9,12-octadecadienoic acid production, while Firmicutes was related to the high production of oleic acid. Based on these data, the reared geese had a more abundant diversity of bacteria than the caged one.
Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar Imam Bagus Nugroho; Fahrurrozi Fahrurrozi
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.53937

Abstract

Theobroma cacao L. is an important Indonesian estate crop, which suffers from biotic and abiotic stresses. TcOSM, which encodes osmotin as a response to pathogens and environmental stresses, is, therefore, a focus of interest in this research, aiming to characterize TcOSM in an Indonesian local cacao cultivar. Bioinformatics queries for putative TcOSM were performed against the reference genome of a Criollo-type cacao cultivar. Based on nucleotide sequence determination, our results revealed two genes, TcOSM1 and TcOSM2, which have the highest similarity (≥ 90\%) to the cacao reference genes. Heterozygosity was detected in the TcOSM1-encoding gene, which contained two overlapping peaks in Sanger-sequencing chromatograms. One of the alleles resulted from a single nucleotide change (G to A), leading to a same-sense mutation that did not substitute corresponding alanine residue. Homology modeling using Phyre2 and structural alignment (superimposition) was conducted to examine the influence of genetic variations in TcOSM sequences upon the global protein structures. The result showed no significant changes (RMSD ≤ 0.206 Å, TM-score > 0.5) in tertiary protein structures. Altogether, this research succeeded in characterizing TcOSM while providing a fundamental study for future cacao biotechnology endeavors. 
Enhanced astaxanthin production by oxidative stress using methyl viologen as a reactive oxygen species (ROS) reagent in green microalgae Coelastrum sp. Ameerah Tharek; Shaza Eva Mohamad; Koji Iwamoto; Iwane Suzuki; Hirofumi Hara; Rozzeta Dolah; Shinji Yoshizaki; Haryati Jamaluddin; Madihah Md Salleh; Adibah Yahya
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.54092

Abstract

Microalgae are known to be a potential resource of high-value metabolites that can be used in the growing field of biotechnology. These metabolites constitute valuable compounds with a wide range of applications that strongly enhance a bio-based economy. Among these metabolites, astaxanthin is considered the most important secondary metabolite, having superior antioxidant properties. For commercial feasibility, microalgae with enhanced astaxanthin production need to be developed. In this study, the tropical green microalgae strain, Coelastrum sp., isolated from the environment in Malaysia, was incubated with methyl viologen, a reactive oxygen species (ROS) reagent that generates superoxide anion radicals (O2-) as an enhancer to improve the accumulation of astaxanthin. The effect of different concentrations of methyl viologen on astaxanthin accumulation was investigated. The results suggested that the supplementation of methyl viologen at low concentration (0.001 mM) was successfully used as a ROS reagent in facilitating and thereby increasing the production of astaxanthin in Coelastrum sp. at a rate 1.3 times higher than in the control.
Genetic recombination of bovine viral diarrhea virus subgenotype -1a and -1c in persistently infected dairy cattle Sri Handayani Irianingsih; Bagoes Poermadjaja; Hastari Wuryastuti; Raden Wasito
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.54111

Abstract

The bovine viral diarrhea virus (BVDV) is a major viral pathogen in cattle worldwide. In Indonesia,  diversity in subgenotypes of BVDV-1 has been observed, with the highest proportion of subgenotype -1a, followed by -1c, -1b, and -1d. So far, phylogenetic analysis of BVDV-1 is based on nucleotide sequences of the 5′ UTR and partial NS5B regions. Accuracy in identifying the subgenotype and antigenic type is critical for vaccine development and effective vaccination. The aim of this study was to determine genetic recombination of BVDV through phylogenetic analysis of five different regions (5′ UTR, NPro, E2, NS3, and NS5B) of BVDV in persistently infected dairy cattle. Five isolates were sequenced using next-generation sequencing, and data were analyzed with the CLC Genomic Workbench 9.0 and MEGA-X programs. Phylogenetic analysis based on the 5′ UTR (275 nt), NPro (504 nt), E2 (1,122 nt), NS3 (2,049 nt), and NS5B (2,157 nt) regions indicated  that one BVDV isolate from Banyumas, Central Java, could be classified into different subgenotypes based on the E2 region (-1c), but the same subgenotype based on the other four regions (-1a), suggesting  the presence of genetic recombination of the BVDV subgenotypes -1a and -1c in persistently infected dairy cattle.
In vitro expression of the recombinant fusion protein of Newcastle disease virus from local Indonesian isolates by using a cell-free protein expression system Aris Haryanto; Hevi Wihadmadyatami; Nastiti Wijayanti
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.54703

Abstract

The aim of this work was the in vitro expression of the recombinant fusion (F) protein of Newcastle disease virus (NDV).  The pBT7-N-His-Fusion-NDV expression plasmid which carries the recombinant F protein encoding gene from local Indonesian isolates, was prepared and transformed into E. coli BL21 (DE3). To detect bacterial colonies carrying the recombinant plasmid, a restriction endonuclease analysis was performed using the EcoRI restriction endonuclease. These results showed that the pBT-N-His-Fusion-NDV plasmid was successfully isolated with a size of 4.601 bp, and three recombinant plasmids carrying the gene coding for the recombinant F protein of NDV were obtained. Selected recombinant plasmids were then in vitro by using a cell-free protein expression system followed by visualization of the recombinant F protein on a 12% SDS-PAGE gel both by Coomassie Brilliant Blue staining and Western blotting. Recombinant F protein was successfully in vitro expressed by using a cell-free protein expression system as indicated by a specific single protein band with a molecular mass of 25.6 kDa.
Expression and characterization of Trichoderma reesei endoglucanase II in Pichia pastoris under the regulation of the GAP promoter Kezia Abib Yerah Tjandra; Kartika Sari Dewi; Asrul Muhamad Fuad; Trisanti Anindyawati
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.55604

Abstract

Trichoderma reesei is known to be one of the organisms capable for producing various types of cellulase in high concentrations. Among these cellulases, the highest catalytic efficiency of endoglucanases II (EGII, EC 3.2.1.4) are considered important for industrial application. The characterization of the EGII is necessary since it is widely used in high-temperature reactions in the industries. In this study, the recombinant EGII protein was expressed in Pichia pastoris and it has a molecular mass of approximately 52 kDa. Recombinant EGII was purified using Ni-NTA affinity chromatography and characterized by SDS-PAGE and western blot analyses. The enzyme activity of recombinant EGII was measured using the Nelson Somogyi method to determine its optimum pH and temperature. The result showed that the maximum EGII expression was achieved after 72 h of culture incubation. The crude enzyme has optimum activity at pH 5.0, resulting in 16.3 U/mL and 14.6 U/mL activity at 40 °C and 50 °C, respectively. While the purified enzyme gave the specific activity of 115.7 U/mg under the optimum condition. Finally, our study demonstrated that recombinant EGII could retain the endoglucanase activity for 89% and 80% at 40 °C and 50 °C, respectively.
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.

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